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Sample records for additional proteins including

  1. Photoactive devices including porphyrinoids with coordinating additives

    DOEpatents

    Forrest, Stephen R; Zimmerman, Jeramy; Yu, Eric K; Thompson, Mark E; Trinh, Cong; Whited, Matthew; Diev, Vlacheslav

    2015-05-12

    Coordinating additives are included in porphyrinoid-based materials to promote intermolecular organization and improve one or more photoelectric characteristics of the materials. The coordinating additives are selected from fullerene compounds and organic compounds having free electron pairs. Combinations of different coordinating additives can be used to tailor the characteristic properties of such porphyrinoid-based materials, including porphyrin oligomers. Bidentate ligands are one type of coordinating additive that can form coordination bonds with a central metal ion of two different porphyrinoid compounds to promote porphyrinoid alignment and/or pi-stacking. The coordinating additives can shift the absorption spectrum of a photoactive material toward higher wavelengths, increase the external quantum efficiency of the material, or both.

  2. Constant-Pressure Combustion Charts Including Effects of Diluent Addition

    NASA Technical Reports Server (NTRS)

    Turner, L Richard; Bogart, Donald

    1949-01-01

    Charts are presented for the calculation of (a) the final temperatures and the temperature changes involved in constant-pressure combustion processes of air and in products of combustion of air and hydrocarbon fuels, and (b) the quantity of hydrocarbon fuels required in order to attain a specified combustion temperature when water, alcohol, water-alcohol mixtures, liquid ammonia, liquid carbon dioxide, liquid nitrogen, liquid oxygen, or their mixtures are added to air as diluents or refrigerants. The ideal combustion process and combustion with incomplete heat release from the primary fuel and from combustible diluents are considered. The effect of preheating the mixture of air and diluents and the effect of an initial water-vapor content in the combustion air on the required fuel quantity are also included. The charts are applicable only to processes in which the final mixture is leaner than stoichiometric and at temperatures where dissociation is unimportant. A chart is also included to permit the calculation of the stoichiometric ratio of hydrocarbon fuel to air with diluent addition. The use of the charts is illustrated by numerical examples.

  3. Simple model of membrane proteins including solvent.

    PubMed

    Pagan, D L; Shiryayev, A; Connor, T P; Gunton, J D

    2006-05-14

    We report a numerical simulation for the phase diagram of a simple two-dimensional model, similar to the one proposed by Noro and Frenkel [J. Chem. Phys. 114, 2477 (2001)] for membrane proteins, but one that includes the role of the solvent. We first use Gibbs ensemble Monte Carlo simulations to determine the phase behavior of particles interacting via a square-well potential in two dimensions for various values of the interaction range. A phenomenological model for the solute-solvent interactions is then studied to understand how the fluid-fluid coexistence curve is modified by solute-solvent interactions. It is shown that such a model can yield systems with liquid-liquid phase separation curves that have both upper and lower critical points, as well as closed loop phase diagrams, as is the case with the corresponding three-dimensional model.

  4. Using a biomimetic membrane surface experiment to investigate the activity of the magnetite biomineralisation protein Mms6† †Electronic supplementary information (ESI) available: Including Mms6 protein and peptide sequences, additional QCM-D and SEM data and protein modelling. See DOI: 10.1039/c5ra16469a Click here for additional data file.

    PubMed Central

    Bird, Scott M.; Rawlings, Andrea E.; Galloway, Johanna M.

    2016-01-01

    Magnetotactic bacteria are able to synthesise precise nanoparticles of the iron oxide magnetite within their cells. These particles are formed in dedicated organelles termed magnetosomes. These lipid membrane compartments use a range of biomineralisation proteins to nucleate and regulate the magnetite crystallisation process. A key component is the membrane protein Mms6, which binds to iron ions and helps to control the formation of the inorganic core. We have previously used Mms6 on gold surfaces patterned with a self-assembled monolayer to successfully produce arrays of magnetic nanoparticles. Here we use this surface system as a mimic of the interior face of the magnetosome membrane to study differences between intact Mms6 and the acid-rich C-terminal peptide subregion of the Mms6 protein. When immobilised on surfaces, the peptide is unable to reproduce the particle size or homogeneity control exhibited by the full Mms6 protein in our experimental setup. Moreover, the peptide is unable to support anchoring of a dense array of nanoparticles to the surface. This system also allows us to deconvolute particle binding from particle nucleation, and shows that Mms6 particle binding is less efficient when supplied with preformed magnetite nanoparticles when compared to particles precipitated from solution in the presence of the surface immobilised Mms6. This suggests that Mms6 binds to iron ions rather than to magnetite surfaces in our system, and is perhaps a nucleating agent rather than a controller of magnetite crystal growth. The comparison between the peptide and the protein under identical experimental conditions indicates that the full length sequence is required to support the full function of Mms6 on surfaces. PMID:27019707

  5. Use of Vitelline Protein B as a Microencapsulating Additive

    NASA Technical Reports Server (NTRS)

    Ficht, Allison R. (Inventor); Carson, Ken (Inventor); Sheffield, Cynthia (Inventor); Waite, John Herbert (Inventor)

    2017-01-01

    The present invention includes compositions and methods for the use of an encapsulation additive having between about 0.1 to about 30 percent isolated and purified vitelline protein B to provide for mixed and extended release formulations.

  6. 25 CFR 1000.83 - Can additional provisions be included in an AFA?

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... 25 Indians 2 2010-04-01 2010-04-01 false Can additional provisions be included in an AFA? 1000.83... Scope of Annual Funding Agreements § 1000.83 Can additional provisions be included in an AFA? Yes, any provision that the parties mutually agreed upon may be included in an AFA....

  7. 25 CFR 1000.83 - Can additional provisions be included in an AFA?

    Code of Federal Regulations, 2012 CFR

    2012-04-01

    ... 25 Indians 2 2012-04-01 2012-04-01 false Can additional provisions be included in an AFA? 1000.83... Scope of Annual Funding Agreements § 1000.83 Can additional provisions be included in an AFA? Yes, any provision that the parties mutually agreed upon may be included in an AFA....

  8. 25 CFR 1000.83 - Can additional provisions be included in an AFA?

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 25 Indians 2 2011-04-01 2011-04-01 false Can additional provisions be included in an AFA? 1000.83... Scope of Annual Funding Agreements § 1000.83 Can additional provisions be included in an AFA? Yes, any provision that the parties mutually agreed upon may be included in an AFA....

  9. 25 CFR 1000.83 - Can additional provisions be included in an AFA?

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 25 Indians 2 2014-04-01 2014-04-01 false Can additional provisions be included in an AFA? 1000.83... Scope of Annual Funding Agreements § 1000.83 Can additional provisions be included in an AFA? Yes, any provision that the parties mutually agreed upon may be included in an AFA....

  10. 25 CFR 1000.83 - Can additional provisions be included in an AFA?

    Code of Federal Regulations, 2013 CFR

    2013-04-01

    ... 25 Indians 2 2013-04-01 2013-04-01 false Can additional provisions be included in an AFA? 1000.83... Scope of Annual Funding Agreements § 1000.83 Can additional provisions be included in an AFA? Yes, any provision that the parties mutually agreed upon may be included in an AFA....

  11. Synergistic effect of additives including multifunctional acrylates in wood plastic composites

    NASA Astrophysics Data System (ADS)

    Khan, Mubarak A.; Idriss Ali, K. M.; Garnett, John L.

    1993-07-01

    Wood Plastic Composite (WPC) was prepared with simul (soft wood, density = 0.4g/cc) and butylmethacrylate (BMA) monomer using 10% methanol as the swelling agent. Effect of additives including (i) multifunctional acrylates such as tripropylene glycol diacrylate (TPGDA), trimethylol propane triacrylate (TMPTA) (ii) oligomer acrylates like the urethane (UA), epoxy (EA) and polyester (PEA) acrylates and (iii) N-vinyl pyrrolidone (NVP) was investigated using 1 to 3 Mrad dose at 0.8 Mrad/h. Synergistic increases in polymer loading yields was achieved in presence of the additives, particularly with the trifunctional acrylate (TMPTA). In addition, acid as well as urea were also used as co-additives and synergistic enhancement in yields of polymer loading were obtained. The synergistic polymer loading by acid addition causes substantial decrease in tensile strength of the composite; but other additives and co-additives increase both the polymer loading and the tensile strength in these systems.

  12. Systems and Methods for Fabricating Objects Including Amorphous Metal Using Techniques Akin to Additive Manufacturing

    NASA Technical Reports Server (NTRS)

    Hofmann, Douglas (Inventor)

    2017-01-01

    Systems and methods in accordance with embodiments of the invention fabricate objects including amorphous metals using techniques akin to additive manufacturing. In one embodiment, a method of fabricating an object that includes an amorphous metal includes: applying a first layer of molten metallic alloy to a surface; cooling the first layer of molten metallic alloy such that it solidifies and thereby forms a first layer including amorphous metal; subsequently applying at least one layer of molten metallic alloy onto a layer including amorphous metal; cooling each subsequently applied layer of molten metallic alloy such that it solidifies and thereby forms a layer including amorphous metal prior to the application of any adjacent layer of molten metallic alloy; where the aggregate of the solidified layers including amorphous metal forms a desired shape in the object to be fabricated; and removing at least the first layer including amorphous metal from the surface.

  13. Combinatorial Synthesis of Linearly Condensed Polycyclic Compounds, Including Anthracyclinones, Through Tandem Diels-Alder Additions

    NASA Astrophysics Data System (ADS)

    Vogel, Pierre

    Double exocyclic 1,3-dienes such as 2,3,5,6-tetramethylidene-7-oxabicyclo[2.2.1]heptane and its 1-substituted derivatives undergo two successive Diels-Alder additions with large reactivity difference between the addition of the first equivalent (k 1) and the second equivalent (k 2) of dienophile. This allows one to prepare, through parallel synthesis, a large number of linearly condensed polycyclic systems containing three annulated six-membered rings, including naphthacenyl systems and anthracyclinones. The large k 1/k 2 rate constant ratio is a consequence of the Dimroth principle, the first cycloaddition being significantly more exothermic then the second one. Control of regio- and stereoselectivity of the two successive cycloadditions is possible by 1-substitution of the 2,3,5,6-tetramethylidene-7-oxabicyclo[2.2.1]heptane, for instance by a 1-(dimethoxymethyl) group, or by stereoselective disubstitution of the double diene by arenesulfenyl substituents. Enantiomerically pure anthracyclinones and analogues are obtained using enantiomerically pure dienophiles such as 3-oxo-but-2-en-2-yl esters. The chemistry so-developed has allowed the preparation of enantiomerically pure 6-((aminoalkoxy)oxy)methyl-6,7-dideoxyidarubicinones that are DNA intercalators and inhibitors of topoisomerase II-induced DNA strained religation.

  14. Additives

    NASA Technical Reports Server (NTRS)

    Smalheer, C. V.

    1973-01-01

    The chemistry of lubricant additives is discussed to show what the additives are chemically and what functions they perform in the lubrication of various kinds of equipment. Current theories regarding the mode of action of lubricant additives are presented. The additive groups discussed include the following: (1) detergents and dispersants, (2) corrosion inhibitors, (3) antioxidants, (4) viscosity index improvers, (5) pour point depressants, and (6) antifouling agents.

  15. Quantitative analysis of EGR proteins binding to DNA: assessing additivity in both the binding site and the protein

    PubMed Central

    Liu, Jiajian; Stormo, Gary D

    2005-01-01

    Background Recognition codes for protein-DNA interactions typically assume that the interacting positions contribute additively to the binding energy. While this is known to not be precisely true, an additive model over the DNA positions can be a good approximation, at least for some proteins. Much less information is available about whether the protein positions contribute additively to the interaction. Results Using EGR zinc finger proteins, we measure the binding affinity of six different variants of the protein to each of six different variants of the consensus binding site. Both the protein and binding site variants include single and double mutations that allow us to assess how well additive models can account for the data. For each protein and DNA alone we find that additive models are good approximations, but over the combined set of data there are context effects that limit their accuracy. However, a small modification to the purely additive model, with only three additional parameters, improves the fit significantly. Conclusion The additive model holds very well for every DNA site and every protein included in this study, but clear context dependence in the interactions was detected. A simple modification to the independent model provides a better fit to the complete data. PMID:16014175

  16. Identification of an additional protein involved in mannan biosynthesis

    PubMed Central

    Wang, Yan; Mortimer, Jennifer C; Davis, Jonathan; Dupree, Paul; Keegstra, Kenneth

    2013-01-01

    Galactomannans comprise a β-1,4-mannan backbone substituted with α-1,6-galactosyl residues. Genes encoding the enzymes that are primarily responsible for backbone synthesis and side-chain addition of galactomannans were previously identified and characterized. To identify additional genes involved in galactomannan biosynthesis, we previously performed deep EST profiling of fenugreek (Trigonella foenum-graecum L.) seed endosperm, which accumulates large quantities of galactomannans as a reserve carbohydrate during seed development. One of the candidate genes encodes a protein that is likely to be a glycosyltransferase. Because this protein is involved in mannan biosynthesis, we named it ‘mannan synthesis-related’ (MSR). Here, we report the characterization of a fenugreek MSR gene (TfMSR) and its two Arabidopsis homologs, AtMSR1 and AtMSR2. TfMSR was highly and specifically expressed in the endosperm. TfMSR, AtMSR1 and AtMSR2 proteins were all determined to be localized to the Golgi by fluorescence confocal microscopy. The level of mannosyl residues in stem glucomannans decreased by approximately 40% for Arabidopsis msr1 single T-DNA insertion mutants and by more than 50% for msr1 msr2 double mutants, but remained unchanged for msr2 single mutants. In addition, in vitro mannan synthase activity from the stems of msr1 single and msr1 msr2 double mutants also decreased. Expression of AtMSR1 or AtMSR2 in the msr1 msr2 double mutant completely or partially restored mannosyl levels. From these results, we conclude that the MSR protein is important for mannan biosynthesis, and offer some ideas about its role. PMID:22966747

  17. Influence of urea additives on micellar morphology/protein conformation.

    PubMed

    Gull, Nuzhat; Kumar, Sanjeev; Ahmad, Basir; Khan, Rizwan Hassan; Kabir-ud-Din

    2006-08-01

    The present study highlights the fact that the effect of additives (urea, monomethylurea, thiourea) on the supramolecular assemblies and proteins is strikingly similar. To investigate the effect, a viscometeric study on sphere-to-rod transition (s-->r) was undertaken in a system (3.5% tetradecyltrimethylammonium bromide+0.05 M NaBr + 1-pentanol [P.M. Lindemuth, G.L. Bertand, J. Phys. Chem. 97 (1993) 7769]) in the presence and absence of the said additives. [1-pentanol] needed for s-->r (i.e. [1-pentanol]s-->r) was determined from the relative viscosity versus [1-pentanol] profiles. It was observed that the additives preponed as well as postponed s-->r depending upon their nature and concentrations. These effects are explained in terms of increased polarity of the medium and the adsorption ability of urea/monomethylurea on the charged surfactant monomers of the micelle. In case of thiourea, postponement of s-->r was observed throughout which is attributed to its structure. To derive an analogy between micelles and proteins the additive-induced conformational changes of the protein, bovine serum albumin (BSA) was taken to monitor secondary structural changes and tryptophanyl fluorescence. A marked increase in secondary structure (far-UVCD) and increased tryptophanyl fluorescence with a marked blue shift in lambdamax was observed in presence of low concentrations of urea or alkylurea. This indicates that a more compact environment is created in presence of these additives, if added judiciously. Addition of thiourea to BSA caused a marked quenching without any significant change in lambdamax. The large decrease in tryptophanyl emission in presence of low thiourea concentrations seems to be specific and related to thiourea structure as no corresponding changes were observed in urea/alkylurea. All these effects pertaining to protein behavior fall in line with that of morphological observations on the present as well as surfactant systems studied earlier [S. Kumar, N

  18. 78 FR 67369 - National Vaccine Injury Compensation Program: Addition to the Vaccine Injury Table to Include All...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-11-12

    ... HUMAN SERVICES Health Resources and Services Administration National Vaccine Injury Compensation Program: Addition to the Vaccine Injury Table to Include All Vaccines Against Seasonal Influenza AGENCY: Health... vaccines against seasonal influenza are covered under the National Vaccine Injury Compensation...

  19. Study of Anti-Fatigue Effect in Rats of Ferrous Chelates Including Hairtail Protein Hydrolysates

    PubMed Central

    Huang, Saibo; Lin, Huimin; Deng, Shang-gui

    2015-01-01

    The ability of ferrous chelates including hairtail protein hydrolysates to prevent and reduce fatigue was studied in rats. After hydrolysis of hairtail surimi with papain, the hairtail protein hydrolysates (HPH) were separated into three groups by range of relative molecular weight using ultrafiltration membrane separation. Hairtail proteins were then chelated with ferrous ions, and the antioxidant activity, the amino acid composition and chelation rate of the three kinds of ferrous chelates including hairtail protein hydrolysates (Fe-HPH) were determined. Among the three groups, the Fe-HPH chelate showing the best conditions was selected for the anti-fatigue animal experiment. For it, experimental rats were randomly divided into seven groups. Group A was designated as the negative control group given distilled water. Group B, the positive control group, was given glutathione. Groups C, D and E were designated as the Fe-HPH chelate treatment groups and given low, medium, and high doses, respectively. Group F was designated as HPH hydrolysate treatment group, and Group G was designated as FeCl2 treatment group. The different diets were orally administered to rats for 20 days. After that time, rats were subjected to forced swimming training after 1 h of gavage. Rats given Fe-FPH chelate had higher haemoglobin regeneration efficiency (HRE), longer exhaustive swimming time and higher SOD activity. Additionally, Fe-FPH chelate was found to significantly decrease the malondialdehyde content, visibly enhance the GSH-Px activity in liver and reduce blood lactic acid of rats. Fe-HPH chelate revealed an anti-fatigue effect, similar to or better than the positive control substance and superior to HPH or Fe when provided alone. PMID:26633476

  20. Biophysical Insights into How Surfaces, Including Lipid Membranes, Modulate Protein Aggregation Related to Neurodegeneration

    PubMed Central

    Burke, Kathleen A.; Yates, Elizabeth A.; Legleiter, Justin

    2013-01-01

    There are a vast number of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD), associated with the rearrangement of specific proteins to non-native conformations that promotes aggregation and deposition within tissues and/or cellular compartments. These diseases are commonly classified as protein-misfolding or amyloid diseases. The interaction of these proteins with liquid/surface interfaces is a fundamental phenomenon with potential implications for protein-misfolding diseases. Kinetic and thermodynamic studies indicate that significant conformational changes can be induced in proteins encountering surfaces, which can play a critical role in nucleating aggregate formation or stabilizing specific aggregation states. Surfaces of particular interest in neurodegenerative diseases are cellular and subcellular membranes that are predominately comprised of lipid components. The two-dimensional liquid environments provided by lipid bilayers can profoundly alter protein structure and dynamics by both specific and non-specific interactions. Importantly for misfolding diseases, these bilayer properties can not only modulate protein conformation, but also exert influence on aggregation state. A detailed understanding of the influence of (sub)cellular surfaces in driving protein aggregation and/or stabilizing specific aggregate forms could provide new insights into toxic mechanisms associated with these diseases. Here, we review the influence of surfaces in driving and stabilizing protein aggregation with a specific emphasis on lipid membranes. PMID:23459674

  1. The Cellulosome System of Acetivibrio cellulolyticus Includes a Novel Type of Adaptor Protein and a Cell Surface Anchoring Protein

    PubMed Central

    Xu, Qi; Gao, Wenchen; Ding, Shi-You; Kenig, Rina; Shoham, Yuval; Bayer, Edward A.; Lamed, Raphael

    2003-01-01

    A scaffoldin gene cluster was identified in the mesophilic cellulolytic anaerobe Acetivibrio cellulolyticus. The previously described scaffoldin gene, cipV, encodes an N-terminal family 9 glycoside hydrolase, a family 3b cellulose-binding domain, seven cohesin domains, and a C-terminal dockerin. The gene immediately downstream of cipV was sequenced and designated scaB. The protein encoded by this gene has 942 amino acid residues and a calculated molecular weight of 100,358 and includes an N-terminal signal peptide, four type II cohesions, and a C-terminal dockerin. ScaB cohesins 1 and 2 are very closely linked. Similar, but not identical, 39-residue Thr-rich linker segments separate cohesin 2 from cohesin 3 and cohesin 3 from cohesin 4, and an 84-residue Thr-rich linker connects the fourth cohesin to a C-terminal dockerin. The scaC gene downstream of scaB codes for a 1,237-residue polypeptide that includes a signal peptide, three cohesins, and a C-terminal S-layer homology (SLH) module. A long, ca. 550-residue linker separates the third cohesin and the SLH module of ScaC and is characterized by an 18-residue Pro-Thr-Ala-Ser-rich segment that is repeated 27 times. The calculated molecular weight of the mature ScaC polypeptide (excluding the signal peptide) is 124,162. The presence of the cohesins and the conserved SLH module implies that ScaC acts as an anchoring protein. The ScaC cohesins are on a separate branch of the phylogenetic tree that is close to, but distinct from, the type I cohesins. Affinity blotting with representative recombinant probes revealed the following specific intermodular interactions: (i) an expressed CipV cohesin binds selectively to an enzyme-borne dockerin, (ii) a representative ScaB cohesin binds to the CipV band of the cell-free supernatant fraction, and (iii) a ScaC cohesin binds to the ScaB dockerin. The experimental evidence thus indicates that CipV acts as a primary (enzyme-recognizing) scaffoldin, and the protein was also

  2. Use of Composite Protein Database including Search Result Sequences for Mass Spectrometric Analysis of Cell Secretome

    PubMed Central

    Shin, Jihye; Kim, Gamin; Kabir, Mohammad Humayun; Park, Seong Jun; Lee, Seoung Taek; Lee, Cheolju

    2015-01-01

    Mass spectrometric (MS) data of human cell secretomes are usually run through the conventional human database for identification. However, the search may result in false identifications due to contamination of the secretome with fetal bovine serum (FBS) proteins. To overcome this challenge, here we provide a composite protein database including human as well as 199 FBS protein sequences for MS data search of human cell secretomes. Searching against the human-FBS database returned more reliable results with fewer false-positive and false-negative identifications compared to using either a human only database or a human-bovine database. Furthermore, the improved results validated our strategy without complex experiments like SILAC. We expect our strategy to improve the accuracy of human secreted protein identification and to also add value for general use. PMID:25822838

  3. Apology in the criminal justice setting: evidence for including apology as an additional component in the legal system.

    PubMed

    Petrucci, Carrie J

    2002-01-01

    The criminal justice system has reached unprecedented scope in the United States, with over 6.4 million people under some type of supervision. Remedies that have the potential to reduce this number are continually being sought. This article analyzes an innovative strategy currently being reconsidered in criminal justice: the apology. Despite a legal system that only sporadically acknowledges it, evidence for the use of apology is supported by social science research, current criminal justice theories, case law, and empirical studies. Social psychological, sociological and socio-legal studies pinpoint the elements and function of apology, what makes apologies effective, and concerns about apology if it were implemented in the criminal justice system. Theoretical evidence is examined (including restorative justice, therapeutic jurisprudence, crime, shame, and reintegration) to explore the process of apology in the criminal justice context. Attribution theory and social conduct theory are used to explain the apology process specifically for victims and offenders. A brief examination of case law reveals that though apology has no formal place in criminal law, it has surfaced recently under the federal sentencing guidelines. Finally, empirical evidence in criminal justice settings reveals that offenders want to apologize and victims desire an apology. Moreover, by directly addressing the harmful act, apology may be the link to reduced recidivism for offenders, as well as empowerment for victims. This evidence combined suggests that apology is worthy of further study as a potentially valuable addition to the criminal justice process.

  4. An atomic view of additive mutational effects in a protein structure

    SciTech Connect

    Skinner, M.M.; Terwilliger, T.C.

    1996-04-01

    Substitution of a single amino acid in a protein will often lead to substantial changes in properties. If these properties could be altered in a rational way then proteins could be readily generated with functions tailored to specific uses. When amino acid substitutions are made at well-separated locations in a single protein, their effects are generally additive. Additivity of effects of amino acid substitutions is very useful because the properties of proteins with any combination of substitutions can be inferred directly from those of the proteins with single changes. It would therefore be of considerable interest to have a means of knowing whether substitutions at a particular pair of sites in a protein are likely to lead to additive effects. The structural basis for additivity of effects of mutations on protein function was examined by determining crystal structures of single and double mutants in the hydrophobic core of gene V protein. Structural effects of mutations were found to be cumulative when two mutations were made in a single protein. Additivity occurs in this case because the regions structurally affected by mutations at the two sites do not overlap even though the sites are separated by only 9 {angstrom}. Structural distortions induced by mutations in gene V protein decrease rapidly, but not isotropically, with distance from the site of mutation. It is anticipated that cases where structural and functional effects of mutations will be additive could be identified simply by examining whether the regions structurally affected by each component mutation overlap.

  5. Rational Design of Solution Additives for the Prevention of Protein Aggregation

    PubMed Central

    Baynes, Brian M.; Trout, Bernhardt L.

    2004-01-01

    We have developed a statistical-mechanical model of the effect of solution additives on protein association reactions. This model incorporates solvent radial distribution functions obtained from all-atom molecular dynamics simulations of particular proteins into simple models of protein interactions. In this way, the effects of additives can be computed along the entire association/dissociation reaction coordinate. We used the model to test our hypothesis that a class of large solution additives, which we term “neutral crowders,” can slow protein association and dissociation by being preferentially excluded from protein-protein encounter complexes, in a manner analogous to osmotic stress. The magnitude of this proposed “gap effect” was probed for two simple model systems: the association of two spheres and the association of two planes. Our results suggest that for a protein of 20 Å radius, an 8 Å additive can increase the free energy barrier for association and dissociation by as much as 3–6 kcal/mol. Because the proposed gap effect is present only for reactions involving multiple molecules, it can be exploited to develop novel additives that affect protein association reactions although having little or no effect on unimolecular reactions such as protein folding. This idea has many potential applications in areas such as the stabilization of proteins against aggregation during folding and in pharmaceutical formulations. PMID:15345542

  6. Rational design of solution additives for the prevention of protein aggregation.

    PubMed

    Baynes, Brian M; Trout, Bernhardt L

    2004-09-01

    We have developed a statistical-mechanical model of the effect of solution additives on protein association reactions. This model incorporates solvent radial distribution functions obtained from all-atom molecular dynamics simulations of particular proteins into simple models of protein interactions. In this way, the effects of additives can be computed along the entire association/dissociation reaction coordinate. We used the model to test our hypothesis that a class of large solution additives, which we term "neutral crowders," can slow protein association and dissociation by being preferentially excluded from protein-protein encounter complexes, in a manner analogous to osmotic stress. The magnitude of this proposed "gap effect" was probed for two simple model systems: the association of two spheres and the association of two planes. Our results suggest that for a protein of 20 A radius, an 8 A additive can increase the free energy barrier for association and dissociation by as much as 3-6 kcal/mol. Because the proposed gap effect is present only for reactions involving multiple molecules, it can be exploited to develop novel additives that affect protein association reactions although having little or no effect on unimolecular reactions such as protein folding. This idea has many potential applications in areas such as the stabilization of proteins against aggregation during folding and in pharmaceutical formulations.

  7. Structural changes in gluten protein structure after addition of emulsifier. A Raman spectroscopy study

    NASA Astrophysics Data System (ADS)

    Ferrer, Evelina G.; Gómez, Analía V.; Añón, María C.; Puppo, María C.

    2011-06-01

    Food protein product, gluten protein, was chemically modified by varying levels of sodium stearoyl lactylate (SSL); and the extent of modifications (secondary and tertiary structures) of this protein was analyzed by using Raman spectroscopy. Analysis of the Amide I band showed an increase in its intensity mainly after the addition of the 0.25% of SSL to wheat flour to produced modified gluten protein, pointing the formation of a more ordered structure. Side chain vibrations also confirmed the observed changes.

  8. Major histocompatibility complex harbors widespread genotypic variability of non-additive risk of rheumatoid arthritis including epistasis

    PubMed Central

    Wei, Wen-Hua; Bowes, John; Plant, Darren; Viatte, Sebastien; Yarwood, Annie; Massey, Jonathan; Worthington, Jane; Eyre, Stephen

    2016-01-01

    Genotypic variability based genome-wide association studies (vGWASs) can identify potentially interacting loci without prior knowledge of the interacting factors. We report a two-stage approach to make vGWAS applicable to diseases: firstly using a mixed model approach to partition dichotomous phenotypes into additive risk and non-additive environmental residuals on the liability scale and secondly using the Levene’s (Brown-Forsythe) test to assess equality of the residual variances across genotype groups per marker. We found widespread significant (P < 2.5e-05) vGWAS signals within the major histocompatibility complex (MHC) across all three study cohorts of rheumatoid arthritis. We further identified 10 epistatic interactions between the vGWAS signals independent of the MHC additive effects, each with a weak effect but jointly explained 1.9% of phenotypic variance. PTPN22 was also identified in the discovery cohort but replicated in only one independent cohort. Combining the three cohorts boosted power of vGWAS and additionally identified TYK2 and ANKRD55. Both PTPN22 and TYK2 had evidence of interactions reported elsewhere. We conclude that vGWAS can help discover interacting loci for complex diseases but require large samples to find additional signals. PMID:27109064

  9. Determination of processed animal proteins, including meat and bone meal, in animal feed.

    PubMed

    Gizzi, Giséile; von Holst, Christoph; Baeten, Vincent; Berben, Gilbert; van Raamsdonk, Leo

    2004-01-01

    An intercomparison study was conducted to determine the presence of processed animal proteins (PAPs), including meat and bone meal (MBM) from various species, in animal feed. The performances of different methods, such as microscopy, polymerase chain reaction (PCR), immunoassays, and a protocol based on iquid chromatography (LC), were compared. Laboratories were asked to analyze for PAPs from all terrestrial animals and fish (total PAPs); mammalian PAPs; ruminant PAPs; and porcine PAPs. They were free to use their method of choice. In addition, laboratories using microscopy were asked to determine the presence of PAPs from terrestrial animals, which is applicable only to microscopy. For total PAPs microscopy, LC and some immunoassays showed sufficient results at a concentration as low as 0.1% MBM in the feed. In contrast, PCR was not fit for purpose. In differentiating between MBM from terrestrial animals and fishmeal, microscopy detected 0.5% of terrestrial MBM in feed in the presence of 5% fishmeal, but was less successful when the concentration of MBM from terrestrial animals was 0.1%. The animal-specific determination of MBM from mammals or, more specifically from either ruminants or pigs, by PCR showed poor results, as indicated by a high number of false-positive and false-negative results. The only PCR method that scored quite well was applied by a member of the organizer team of the study. Immunoassays scored much better than PCR, showing sufficient sensitivity but some deficiency in terms of specificity. The results also demonstrated that the reliable determination of MBM from ruminants has not been resolved, especially for low concentrations of MBM (0.1%) in feed. Comparison of the results for mammalian MBM from all methods indicated that, for control purposes, the immunoassay method, especially when applied as dipsticks, could be used as a rapid screening method combined with microscopy to confirm the positive samples. However, implementation of such a

  10. The green tea polyphenol (-)-epigallocatechin gallate precipitates salivary proteins including alpha-amylase: biochemical implications for oral health.

    PubMed

    Hara, Kumiko; Ohara, Masaru; Hayashi, Ikue; Hino, Takamune; Nishimura, Rumi; Iwasaki, Yoriko; Ogawa, Tetsuji; Ohyama, Yoshihiko; Sugiyama, Masaru; Amano, Hideaki

    2012-04-01

    Green tea is a popular drink throughout the world, and it contains various components, including the green tea polyphenol (-)-epigallocatechin gallate (EGCG). Tea interacts with saliva upon entering the mouth, so the interaction between saliva and EGCG interested us, especially with respect to EGCG-protein binding. SDS-PAGE revealed that several salivary proteins were precipitated after adding EGCG to saliva. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) peptide mass fingerprinting indicated that the major proteins precipitated by EGCG were alpha-amylase, S100, and cystatins. Surface plasmon resonance revealed that EGCG bound to alpha-amylase at dissociation constant (K(d)) = 2.74 × 10(-6) M, suggesting that EGCG interacts with salivary proteins with a relatively strong affinity. In addition, EGCG inhibited the activity of alpha-amylase by non-competitive inhibition, indicating that EGCG is effective at inhibiting the formation of fermentable carbohydrates involved in caries formation. Interestingly, alpha-amylase reduced the antimicrobial activity of EGCG against the periodontal bacterium Aggregatibacter actinomycetemcomitans. Therefore, we considered that EGCG-salivary protein interactions might have both protective and detrimental effects with respect to oral health.

  11. Addition of carrageenan at different stages of winemaking for white wine protein stabilization.

    PubMed

    Marangon, Matteo; Stockdale, Vanessa J; Munro, Peter; Trethewey, Timra; Schulkin, Alex; Holt, Helen E; Smith, Paul A

    2013-07-03

    Carrageenan added at different stages of winemaking was assessed for its protein removal and impact on wine heat stability and on the chemical and sensorial profile of the wines. Carrageenan was added to a Semillon during fermentation and after fermentation and to finished wines, and the effect of each addition was compared to that of bentonite fining at the same time point. Data on protein concentration, heat stability, and bentonite requirement indicate that when added at the correct dosage carrageenan was very effective in stabilizing wines at dosages at least three times lower than those of bentonite. In addition, carrageenan treatment did not cause an increase in lees volume relative to bentonite and resulted in very similar chemical parameters to the unfined and bentonite-treated wine. Sensorially, although carrageenan-treated wine was significantly different from the unfined wine, the magnitude of difference did not vary significantly when compared to bentonite treatment. The feasibility of carrageenan use in a winery production setting will need to be determined by individual wineries, as technical issues including frothing, slower filterability, and risk of overfining will need to be considered relative to the benefits, particularly when carrageenan is used before or during fermentation.

  12. 36 CFR 1290.4 - Types of materials included in scope of assassination record and additional records and information.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 36 Parks, Forests, and Public Property 3 2010-07-01 2010-07-01 false Types of materials included..., Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION JFK ASSASSINATION RECORDS... documentary material; (b) Photographs; (c) Motion pictures; (d) Sound and video recordings; (e)...

  13. 36 CFR 1290.4 - Types of materials included in scope of assassination record and additional records and information.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 36 Parks, Forests, and Public Property 3 2014-07-01 2014-07-01 false Types of materials included..., Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION JFK ASSASSINATION RECORDS... documentary material; (b) Photographs; (c) Motion pictures; (d) Sound and video recordings; (e)...

  14. 36 CFR 1290.4 - Types of materials included in scope of assassination record and additional records and information.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 36 Parks, Forests, and Public Property 3 2012-07-01 2012-07-01 false Types of materials included..., Forests, and Public Property NATIONAL ARCHIVES AND RECORDS ADMINISTRATION JFK ASSASSINATION RECORDS... documentary material; (b) Photographs; (c) Motion pictures; (d) Sound and video recordings; (e)...

  15. 7 CFR 984.437 - Methods for proposing names of additional candidates to be included on walnut growers' nomination...

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... to be included on walnut growers' nomination ballots. 984.437 Section 984.437 Agriculture Regulations... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Administrative... walnut growers' nomination ballots. (a) With regard to Board grower member positions specified in §...

  16. 7 CFR 984.437 - Methods for proposing names of additional candidates to be included on walnut growers' nomination...

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... to be included on walnut growers' nomination ballots. 984.437 Section 984.437 Agriculture Regulations... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Administrative... walnut growers' nomination ballots. (a) With regard to Board grower member positions specified in §...

  17. 7 CFR 984.437 - Methods for proposing names of additional candidates to be included on walnut growers' nomination...

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... to be included on walnut growers' nomination ballots. 984.437 Section 984.437 Agriculture Regulations... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Administrative... walnut growers' nomination ballots. (a) With regard to Board grower member positions specified in §...

  18. 7 CFR 984.437 - Methods for proposing names of additional candidates to be included on walnut growers' nomination...

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... to be included on walnut growers' nomination ballots. 984.437 Section 984.437 Agriculture Regulations... ORDERS; FRUITS, VEGETABLES, NUTS), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Administrative... walnut growers' nomination ballots. (a) With regard to Board grower member positions specified in §...

  19. 7 CFR 984.437 - Methods for proposing names of additional candidates to be included on walnut growers' nomination...

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... to be included on walnut growers' nomination ballots. 984.437 Section 984.437 Agriculture Regulations... Orders; Fruits, Vegetables, Nuts), DEPARTMENT OF AGRICULTURE WALNUTS GROWN IN CALIFORNIA Administrative... walnut growers' nomination ballots. (a) With regard to Board grower member positions specified in §...

  20. Benchmarking spliced alignment programs including Spaln2, an extended version of Spaln that incorporates additional species-specific features

    PubMed Central

    Iwata, Hiroaki; Gotoh, Osamu

    2012-01-01

    Spliced alignment plays a central role in the precise identification of eukaryotic gene structures. Even though many spliced alignment programs have been developed, recent rapid progress in DNA sequencing technologies demands further improvements in software tools. Benchmarking algorithms under various conditions is an indispensable task for the development of better software; however, there is a dire lack of appropriate datasets usable for benchmarking spliced alignment programs. In this study, we have constructed two types of datasets: simulated sequence datasets and actual cross-species datasets. The datasets are designed to correspond to various real situations, i.e. divergent eukaryotic species, different types of reference sequences, and the wide divergence between query and target sequences. In addition, we have developed an extended version of our program Spaln, which incorporates two additional features to the scoring scheme of the original version, and examined this extended version, Spaln2, together with the original Spaln and other representative aligners based on our benchmark datasets. Although the effects of the modifications are not individually striking, Spaln2 is consistently most accurate and reasonably fast in most practical cases, especially for plants and fungi and for increasingly divergent pairs of target and query sequences. PMID:22848105

  1. Titration of the bacteriorhodopsin Schiff base involves titration of an additional protein residue.

    PubMed

    Zadok, Uri; Asato, Alfred E; Sheves, Mordechai

    2005-06-14

    The retinal protein protonated Schiff base linkage plays a key role in the function of bacteriorhodopsin (bR) as a light-driven proton pump. In the unphotolyzed pigment, the Schiff base (SB) is titrated with a pK(a) of approximately 13, but following light absorption, it experiences a decrease in the pK(a) and undergoes several alterations, including a deprotonation process. We have studied the SB titration using retinal analogues which have intrinsically lower pK(a)'s which allow for SB titrations over a much lower pH range. We found that above pH 9 the channel for the SB titration is perturbed, and the titration rate is considerably reduced. On the basis of studies with several mutants, it is suggested that the protonation state of residue Glu204 is responsible for the channel perturbation. We suggest that above pH 12 a channel for the SB titration is restored probably due to titration of an additional protein residue. The observations may imply that during the bR photocycle and M photointermediate formation the rate of Schiff base protonation from the bulk is decreased. This rate decrease may be due to the deprotonation process of the "proton-releasing complex" which includes Glu204. In contrast, during the lifetime of the O intermediate, the protonated SB is exposed to the bulk. Possible implications for the switch mechanism, and the directionality of the proton movement, are discussed.

  2. Functional Investigation of Iron-Responsive Microsomal Proteins, including MirC, in Aspergillus fumigatus

    PubMed Central

    Mulvihill, Eoin D.; Moloney, Nicola M.; Owens, Rebecca A.; Dolan, Stephen K.; Russell, Lauren; Doyle, Sean

    2017-01-01

    The functionality of many microsome-associated proteins which exhibit altered abundance in response to iron limitation in Aspergillus fumigatus is unknown. Here, we generate and characterize eight gene deletion strains, and of most significance reveal that MirC (AFUA_2G05730) contributes to the maintenance of intracellular siderophore [ferricrocin (FC)] levels, augments conidiation, confers protection against oxidative stress, exhibits an intracellular localization and contributes to fungal virulence in the Galleria mellonella animal model system. FC levels were unaffected following deletion of all other genes encoding microsome-associated proteins. MirC does not appear to play a role in either siderophore export from, or uptake into, A. fumigatus. Label-free quantitative proteomic analysis unexpectedly revealed increased abundance of siderophore biosynthetic enzymes. In addition, increased expression of hapX (7.2 and 13.8-fold at 48 and 72 h, respectively; p < 0.001) was observed in ΔmirC compared to wild-type under iron-replete conditions by qRT-PCR. This was complemented by significantly elevated extracellular triacetylfusarinine C (TAFC; p < 0.01) and fusarinine C (FSC; p < 0.05) siderophore secretion. We conclude that MirC plays an important role in FC biosynthesis and contributes to the maintenance of iron homeostasis in A. fumigatus. PMID:28367141

  3. Uranium hydrogeochemical and stream sediment reconnaissance of the Newcastle NTMS quadrangle, Wyoming, including concentrations of forty-two additional elements

    SciTech Connect

    Goff, S.J.; Sandoval, W.F.; Gallimore, D.L.; Talcott, C.L.; Martinez, R.G.; Minor, M.E.; Mills, C.F.

    1980-06-01

    During the summer and fall of 1977, 533 water and 1226 sediment samples were collected from 1740 locations within the 18,000 km/sup 2/ area of the Newcastle quadrangle, Wyoming. Water samples were collected from wells and springs; sediment samples were collected from stream channels and from springs. Each water sample was analyzed for uranium, and each sediment sample was analyzed for 43 elements, including uranium and thorium. Uranium concentrations in water samples range from below the detection limit of 0.02 ppB to 702.26 ppB and have a median of 1.73 ppB and a mean of 11.76 ppB. Water samples containing high uranium concentrations (>20 ppB) generally are associated with known uranium mining activity or units known to be uranium bearing. About one-third of the water samples containing high uranium concentrations were collected from locations within the Pumpkin Buttes and Turnercrest-Ross Districts. Nearly half of the water samples containing high uranium concentrations were collected from locations just west of the Monument Hill and Highland Flats-Box Creek Districts. Similar anomalous uranium concentrations in this region have been reported updip from Exxon's Highland uranium deposits. High uranium concentrations were also found associated with the Lance Creek-Old Woman Anticline District.

  4. Performance of portland limestone cements: Cements designed to be more sustainable that include up to 15% limestone addition

    NASA Astrophysics Data System (ADS)

    Barrett, Timothy J.

    In 2009, ASTM and AASHTO permitted the use of up to 5% interground limestone in ordinary portland cement (OPC) as a part of a change to ASTM C150/AASHTO M85. When this work was initiated a new proposal was being discussed that would enable up to 15% interground limestone cement to be considered in ASTM C595/AASHTO M234. This work served to provide rapid feedback to the state department of transportation and concrete industry for use in discussions regarding these specifications. Since the time this work was initiated, ASTM C595/AASHTO M234 was passed (2012c) and PLCs are now able to be specified, however they are still not widely used. The proposal for increasing the volume of limestone that would be permitted to be interground in cement is designed to enable more sustainable construction, which may significantly reduce the CO2 that is embodied in the built infrastructure while also extending the life of cement quarries. Research regarding the performance of cements with interground limestone has been conducted by the cement industry since these cements became widely used in Europe over three decades ago, however this work focuses on North American Portland Limestone Cements (PLCs) which are specifically designed to achieve similar performance as the OPCs they replace.This thesis presents a two-phase study in which the potential for application of cements containing limestone was assessed. The first phase of this study utilized a fundamental approach to determine whether cement with up to 15% of interground or blended limestone can be used as a direct substitute to ordinary portland cement. The second phase of the study assessed the concern of early age shrinkage and cracking potential when using PLCs, as these cements are typically ground finer than their OPC counterparts. For the first phase of the study, three commercially produced PLCs were obtained and compared to three commercially produced OPCs made from the same clinker. An additional cement was tested

  5. Uranium hydrogeochemical and stream sediment reconnaissance of the Newcastle NTMS Quadrangle, Wyoming, including concentrations of forty-two additional elements

    SciTech Connect

    Goff, S.J.; Sandoval, W.F.; Gallimore, D.L.; Talcott, C.L.; Martinez, R.G.; Minor, M.E.; Mills, C.F.

    1980-06-01

    Water and sediment samples were collected and each water sample was analyzed for U, and each sediment sample was analyzed for 43 elements, including U and Th. Uranium concentrations in water samples range from below the detection limit of 0.02 ppB to 702.26 ppB and have a median of 1.73 ppB and a mean of 11.76 ppB. Water samples containing high uranium concentrations generally are associated with known uranium mining activity or units known to be uranium bearing. About one-third of the water samples containing high uranium concentrations were collected from locations within the Pumpkin Buttes and Turnercrest-Ross Districts. Nearly half of the water samples containing high uranium concentrations were collected from locations just west of the Monument Hill and Highland Flats-Box Creek Districts. Similar anomalous uranium concentrations in this region have been reported updip from Exxon's Highland uranium deposits. High uranium concentrations were also found associated with the Lance Creek-Old Woman Anticline District. Uranium concentrations in sediment samples range from 1.14 to 220.70 ppM and have a median of 3.37 ppM and a mean of 4.03 ppM. Throughout the major uranium mining districts of the Powder River Basin, sediment samples with high uranium concentrations were collected from dry streams located near wells producing water samples with high uranium concentrations. High uranium concentrations were also found associated with the Lance Creek oil field where uranium mineralization is known in the White River formation. High uranium concentrations were also found in sediment samples in areas where uranium mineralization is not known. These samples are from dry streams in areas underlain by the White River formation, the Niobrara formation, and the Pierre, Carlisle, Belle Fourche, and Mowry shales.

  6. Ammonium Bicarbonate Addition Improves the Detection of Proteins by Desorption Electrospray Ionization Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Honarvar, Elahe; Venter, Andre R.

    2017-03-01

    The analysis of protein by desorption electrospray ionization mass spectrometry (DESI-MS) is considered impractical due to a mass-dependent loss in sensitivity with increase in protein molecular weights. With the addition of ammonium bicarbonate to the DESI-MS analysis the sensitivity towards proteins by DESI was improved. The signal to noise ratio (S/N) improvement for a variety of proteins increased between 2- to 3-fold relative to solvent systems containing formic acid and more than seven times relative to aqueous methanol spray solvents. Three methods for ammonium bicarbonate addition during DESI-MS were investigated. The additive delivered improvements in S/N whether it was mixed with the analyte prior to sample deposition, applied over pre-prepared samples, or simply added to the desorption spray solvent. The improvement correlated well with protein pI but not with protein size. Other ammonium or bicarbonate salts did not produce similar improvements in S/N, nor was this improvement in S/N observed for ESI of the same samples. As was previously described for ESI, DESI also caused extensive protein unfolding upon the addition of ammonium bicarbonate.

  7. Bacillus licheniformis Contains Two More PerR-Like Proteins in Addition to PerR, Fur, and Zur Orthologues.

    PubMed

    Kim, Jung-Hoon; Ji, Chang-Jun; Ju, Shin-Yeong; Yang, Yoon-Mo; Ryu, Su-Hyun; Kwon, Yumi; Won, Young-Bin; Lee, Yeh-Eun; Youn, Hwan; Lee, Jin-Won

    2016-01-01

    The ferric uptake regulator (Fur) family proteins include sensors of Fe (Fur), Zn (Zur), and peroxide (PerR). Among Fur family proteins, Fur and Zur are ubiquitous in most prokaryotic organisms, whereas PerR exists mainly in Gram positive bacteria as a functional homologue of OxyR. Gram positive bacteria such as Bacillus subtilis, Listeria monocytogenes and Staphylococcus aureus encode three Fur family proteins: Fur, Zur, and PerR. In this study, we identified five Fur family proteins from B. licheniformis: two novel PerR-like proteins (BL00690 and BL00950) in addition to Fur (BL05249), Zur (BL03703), and PerR (BL00075) homologues. Our data indicate that all of the five B. licheniformis Fur homologues contain a structural Zn2+ site composed of four cysteine residues like many other Fur family proteins. Furthermore, we provide evidence that the PerR-like proteins (BL00690 and BL00950) as well as PerRBL (BL00075), but not FurBL (BL05249) and ZurBL (BL03703), can sense H2O2 by histidine oxidation with different sensitivity. We also show that PerR2 (BL00690) has a PerR-like repressor activity for PerR-regulated genes in vivo. Taken together, our results suggest that B. licheniformis contains three PerR subfamily proteins which can sense H2O2 by histidine oxidation not by cysteine oxidation, in addition to Fur and Zur.

  8. Bacillus licheniformis Contains Two More PerR-Like Proteins in Addition to PerR, Fur, and Zur Orthologues

    PubMed Central

    Ju, Shin-Yeong; Yang, Yoon-Mo; Ryu, Su-Hyun; Kwon, Yumi; Won, Young-Bin; Lee, Yeh-Eun; Youn, Hwan; Lee, Jin-Won

    2016-01-01

    The ferric uptake regulator (Fur) family proteins include sensors of Fe (Fur), Zn (Zur), and peroxide (PerR). Among Fur family proteins, Fur and Zur are ubiquitous in most prokaryotic organisms, whereas PerR exists mainly in Gram positive bacteria as a functional homologue of OxyR. Gram positive bacteria such as Bacillus subtilis, Listeria monocytogenes and Staphylococcus aureus encode three Fur family proteins: Fur, Zur, and PerR. In this study, we identified five Fur family proteins from B. licheniformis: two novel PerR-like proteins (BL00690 and BL00950) in addition to Fur (BL05249), Zur (BL03703), and PerR (BL00075) homologues. Our data indicate that all of the five B. licheniformis Fur homologues contain a structural Zn2+ site composed of four cysteine residues like many other Fur family proteins. Furthermore, we provide evidence that the PerR-like proteins (BL00690 and BL00950) as well as PerRBL (BL00075), but not FurBL (BL05249) and ZurBL (BL03703), can sense H2O2 by histidine oxidation with different sensitivity. We also show that PerR2 (BL00690) has a PerR-like repressor activity for PerR-regulated genes in vivo. Taken together, our results suggest that B. licheniformis contains three PerR subfamily proteins which can sense H2O2 by histidine oxidation not by cysteine oxidation, in addition to Fur and Zur. PMID:27176811

  9. Effects of protein and peptide addition on lipid oxidation in powder model system.

    PubMed

    Park, Eun Young; Murakami, Hiroshi; Mori, Tomohiko; Matsumura, Yasuki

    2005-01-12

    The effect of protein and peptide addition on the oxidation of eicosapentaenoic acid ethyl ester (EPE) encapsulated by maltodextrin (MD) was investigated. The encapsulated lipid (powder lipid) was prepared in two steps, i.e., mixing of EPE with MD solutions (+/- protein and peptides) to produce emulsions and freeze-drying of the resultant emulsions. EPE oxidation in MD powder progressed more rapidly in the humid state [relative humidity (RH) = 70%] than in the dry state (RH = 10%). The addition of soy protein, soy peptide, and gelatin peptides improved the oxidation stability of EPE encapsulated by MD, and the inhibition of lipid oxidation by the protein and the peptides was more dramatic in the humid state. Especially, the oxidation of EPE was almost perfectly suppressed when the lipid was encapsulated with MD + soy peptide during storage in the humid state for 7 days. Several physical properties such as the lipid particle size of the emulsions, the fraction of nonencapsulated lipids, scanning electron microscopy images of powder lipids, and the mobility of the MD matrix were investigated to find the modification of encapsulation behavior by the addition of the protein and peptides, but no significant change was observed. On the other hand, the protein and peptides exhibited a strong radical scavenging activity in the powder systems as well as in the solution systems. These results suggest that a chemical mechanism such as radical scavenging ability plays an important role in the suppression of EPE oxidation in MD powder by soy proteins, soy peptides, and gelatin peptides.

  10. Poly(A) RNAs including coding proteins RNAs occur in plant Cajal bodies.

    PubMed

    Niedojadło, Janusz; Kubicka, Ewa; Kalich, Beata; Smoliński, Dariusz J

    2014-01-01

    The localisation of poly(A) RNA in plant cells containing either reticular (Allium cepa) or chromocentric (Lupinus luteus, Arabidopsis thaliana) nuclei was studied through in situ hybridisation. In both types of nuclei, the amount of poly(A) RNA was much greater in the nucleus than in the cytoplasm. In the nuclei, poly(A) RNA was present in structures resembling nuclear bodies. The molecular composition as well as the characteristic ultrastructure of the bodies containing poly(A) RNA demonstrated that they were Cajal bodies. We showed that some poly(A) RNAs in Cajal bodies code for proteins. However, examination of the localisation of active RNA polymerase II and in situ run-on transcription assays both demonstrated that CBs are not sites of transcription and that BrU-containing RNA accumulates in these structures long after synthesis. In addition, it was demonstrated that accumulation of poly(A) RNA occurs in the nuclei and CBs of hypoxia-treated cells. Our findings indicated that CBs may be involved in the later stages of poly(A) RNA metabolism, playing a role storage or retention.

  11. Effect of the addition of CMC on the aggregation behaviour of proteins

    NASA Astrophysics Data System (ADS)

    Yu, H.; Sabato, S. F.; D'Aprano, G.; Lacroix, M.

    2004-09-01

    The effect of carboxymethylcellulose (CMC) on the aggregation of formulation based on calcium caseinate, commercial whey protein (WPC), and a 1:1 mixture of soy protein isolate (SPI) and whey protein isolate (WPI) was investigated. Protein aggregation could be observed upon addition of CMC, as demonstrated by size-exclusion chromatography. This aggregation behaviour was enhanced by means of physical treatments, such as heating at 90°C for 30 min or gamma-irradiation at 32 kGy. A synergy resulted from the combination of CMC to gamma-irradiation in Caseinate/CMC and SPI/WPI/CMC formulations. Furthermore, CMC prevented precipitation in irradiated protein solutions for a period of more than 3 months at 4°C.

  12. Effect of additives on the tensile performance and protein solubility of industrial oilseed residual based plastics.

    PubMed

    Newson, William R; Kuktaite, Ramune; Hedenqvist, Mikael S; Gällstedt, Mikael; Johansson, Eva

    2014-07-16

    Ten chemical additives were selected from the literature for their proposed modifying activity in protein-protein interactions. These consisted of acids, bases, reducing agents, and denaturants and were added to residual deoiled meals of Crambe abyssinica (crambe) and Brassica carinata (carinata) to modify the properties of plastics produced through hot compression molding at 130 °C. The films produced were examined for tensile properties, protein solubility, molecular weight distribution, and water absorption. Of the additives tested, NaOH had the greatest positive effect on tensile properties, with increases of 105% in maximum stress and 200% in strain at maximum stress for crambe and a 70% increase in strain at maximum stress for carinata. Stiffness was not increased by any of the applied additives. Changes in tensile strength and elongation for crambe and elongation for carinata were related to changes in protein solubility. Increased pH was the most successful in improving the protein aggregation and mechanical properties within the complex chemistry of residual oilseed meals.

  13. Phospha-Michael Addition as a New Click Reaction for Protein Functionalization.

    PubMed

    Lee, Yan-Jiun; Kurra, Yadagiri; Liu, Wenshe R

    2016-03-15

    A new type of click reaction between an alkyl phosphine and acrylamide was developed and applied for site-specific protein labeling in vitro and in live cells. Acrylamide is a small electrophilic olefin that readily undergoes phospha-Michael addition with an alkyl phosphine. Our kinetic study indicated a second-order rate constant of 0.07 m(-1)  s(-1) for the reaction between tris(2-carboxyethyl)phosphine and acrylamide at pH 7.4. To demonstrate its application in protein functionalization, we used a dansyl-phosphine conjugate to successfully label proteins that were site-specifically installed with N(ɛ) -acryloyl-l-lysine and employed a biotin-phosphine conjugate to selectively probe human proteins that were metabolically labeled with N-acryloyl-galactosamine.

  14. An approach to including protein quality when assessing the net contribution of livestock to human food supply.

    PubMed

    Ertl, P; Knaus, W; Zollitsch, W

    2016-11-01

    The production of protein from animal sources is often criticized because of the low efficiency of converting plant protein from feeds into protein in the animal products. However, this critique does not consider the fact that large portions of the plant-based proteins fed to animals may be human-inedible and that the quality of animal proteins is usually superior as compared with plant proteins. The aim of the present study was therefore to assess changes in protein quality in the course of the transformation of potentially human-edible plant proteins into animal products via livestock production; data from 30 Austrian dairy farms were used as a case study. A second aim was to develop an approach for combining these changes with quantitative aspects (e.g. with the human-edible feed conversion efficiency (heFCE), defined as kilogram protein in the animal product divided by kilogram potentially human-edible protein in the feeds). Protein quality of potentially human-edible inputs and outputs was assessed using the protein digestibility-corrected amino acid score and the digestible indispensable amino acid score, two methods proposed by the Food and Agriculture Organization of the United Nations to describe the nutritional value of proteins for humans. Depending on the method used, protein scores were between 1.40 and 1.87 times higher for the animal products than for the potentially human-edible plant protein input on a barn-gate level (=protein quality ratio (PQR)). Combining the PQR of 1.87 with the heFCE for the same farms resulted in heFCE×PQR of 2.15. Thus, considering both quantity and quality, the value of the proteins in the animal products for human consumption (in this case in milk and beef) is 2.15 times higher than that of proteins in the potentially human-edible plant protein inputs. The results of this study emphasize the necessity of including protein quality changes resulting from the transformation of plant proteins to animal proteins when

  15. Protein

    MedlinePlus

    ... Go lean with protein. • Choose lean meats and poultry. Lean beef cuts include round steaks (top loin, ... main dishes. • Use nuts to replace meat or poultry, not in addition to meat or poultry (i. ...

  16. Water-in-carbon dioxide microemulsions: An environment for hydrophiles including proteins

    SciTech Connect

    Johnston, K.P.; Harrison, K.L.; Clarke, M.J.

    1996-02-02

    Carbon dioxide in the liquid and supercritical fluid states is useful as a replacement for toxic organic solvents. However, nonvolatile hydrophilic substances such as proteins, ions, and most catalysts are insoluble. This limitation was overcome by the formation of aqueous microemulsion droplets in a carbon dioxide-continuous phase with a nontoxic ammonium carboxylate perfluoropolyether surfactant. Several spectroscopic techniques consistently indicated that the properties of the droplets approach those of bulk water. The protein bovine serum albumin (BSA) with a molecular weight of 67,000 is soluble in this microemulsion and experiences an environment similar to that of native BSA in buffer. 23 refs., 4 figs.

  17. Temperature, pressure, and electrochemical constraints on protein speciation: Group additivity calculation of the standard molal thermodynamic properties of ionized unfolded proteins

    NASA Astrophysics Data System (ADS)

    Dick, J. M.; Larowe, D. E.; Helgeson, H. C.

    2006-07-01

    Thermodynamic calculations can be used to quantify environmental constraints on the speciation of proteins, such as the pH and temperature dependence of ionization state, and the relative chemical stabilities of proteins in different biogeochemical settings. These calculations depend in part on values of the standard molal Gibbs energies of proteins and their ionization reactions as a function of temperature and pressure. Because these values are not generally available, we calculated values of the standard molal thermodynamic properties at 25°C and 1 bar as well as the revised Helgeson-Kirkham-Flowers equations of state parameters of neutral and charged zwitterionic reference model compounds including aqueous amino acids, polypeptides, and unfolded proteins. The experimental calorimetric and volumetric data for these species taken from the literature were combined with group additivity algorithms to calculate the properties and parameters of neutral and ionized sidechain and backbone groups in unfolded proteins. The resulting set of group contributions enables the calculation of the standard molal Gibbs energy, enthalpy, entropy, isobaric heat capacity, volume, and isothermal compressibility of unfolded proteins in a range of proton ionization states to temperatures and pressures exceeding 100°C and 1000 bar. This approach provides a useful frame of reference for thermodynamic studies of protein folding and complexation reactions. It can also be used to assign provisional values of the net charge and Gibbs energy of ionized proteins as a function of temperature and pH. Using these values, an Eh-pH diagram for a reaction representing the speciation of extracellular proteins from Pyrococcus furiosus and Bacillus subtilis was generated. The predicted predominance limits of these proteins correspond with the different electrochemical conditions of hydrothermal vents and soils. More comprehensive calculations of this kind may reveal pervasive chemical potential

  18. The Arabidopsis thaliana vernalization response requires a polycomb-like protein complex that also includes VERNALIZATION INSENSITIVE 3.

    PubMed

    Wood, Craig C; Robertson, Masumi; Tanner, Greg; Peacock, W James; Dennis, Elizabeth S; Helliwell, Chris A

    2006-09-26

    In Arabidopsis thaliana, the promotion of flowering by cold temperatures, vernalization, is regulated via a floral-repressive MADS box transcription factor, FLOWERING LOCUS C (FLC). Vernalization leads to the epigenetic repression of FLC expression, a process that requires the polycomb group (PcG) protein VERNALIZATION 2 (VRN2) and the plant homeodomain protein VERNALIZATION INSENSITIVE 3 (VIN3). We demonstrate that the repression of FLC by vernalization requires homologues of other Polycomb Repressive Complex 2 proteins and VRN2. We show in planta that VRN2 and VIN3 are part of a large protein complex that can include the PcG proteins FERTILIZATION INDEPENDENT ENDOSPERM, CURLY LEAF, and SWINGER. These findings suggest a single protein complex is responsible for histone deacetylation at FLC and histone methylation at FLC in vernalized plants. The abundance of the complex increases during vernalization and declines after plants are returned to higher temperatures, consistent with the complex having a role in establishing FLC repression.

  19. 41 CFR 302-7.21 - If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e...

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 41 Public Contracts and Property Management 4 2014-07-01 2014-07-01 false If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e.g., boat, trailer... is assessed by the HHG carrier (e.g., boat, trailer, ultralight vehicle), am I responsible...

  20. 41 CFR 302-7.21 - If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e...

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 41 Public Contracts and Property Management 4 2013-07-01 2012-07-01 true If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e.g., boat, trailer... the HHG carrier (e.g., boat, trailer, ultralight vehicle), am I responsible for payment? (a) No,...

  1. 41 CFR 302-7.21 - If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e...

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 41 Public Contracts and Property Management 4 2012-07-01 2012-07-01 false If my HHG shipment includes an item for which a weight additive is assessed by the HHG carrier (e.g., boat, trailer... Management Federal Travel Regulation System RELOCATION ALLOWANCES TRANSPORTATION AND STORAGE OF PROPERTY...

  2. Traveling-wave Ion Mobility-Mass Spectrometry Reveals Additional Mechanistic Details in the Stabilization of Protein Complex Ions through Tuned Salt Additives

    PubMed Central

    Han, Linjie; Ruotolo, Brandon T.

    2013-01-01

    Ion mobility–mass spectrometry is often applied to the structural elucidation of multiprotein assemblies in cases where X-ray crystallography or NMR experiments have proved challenging. Such applications are growing steadily as we continue to probe regions of the proteome that are less-accessible to such high-resolution structural biology tools. Since ion mobility measures protein structure in the absence of bulk solvent, strategies designed to more-broadly stabilize native-like protein structures in the gas-phase would greatly enable the application of such measurements to challenging structural targets. Recently, we have begun investigating the ability of salt-based solution additives that remain bound to protein ions in the gas-phase to stabilize native-like protein structures. These experiments, which utilize collision induced unfolding and collision induced dissociation in a tandem mass spectrometry mode to measure protein stability, seek to develop a rank-order similar to the Hofmeister series that categorizes the general ability of different anions and cations to stabilize gas-phase protein structure. Here, we study magnesium chloride as a potential stabilizing additive for protein structures in vacuo, and find that the addition of this salt to solutions prior to nano-electrospray ionization dramatically enhances multiprotein complex structural stability in the gas-phase. Based on these experiments, we also refine the physical mechanism of cation-based protein complex ion stabilization by tracking the unfolding transitions experienced by cation-bound complexes. Upon comparison with unbound proteins, we find strong evidence that stabilizing cations act to tether protein complex structure. We conclude by putting the results reported here in context, and by projecting the future applications of this method. PMID:23539363

  3. Darwin at the molecular scale: selection and variance in electron tunnelling proteins including cytochrome c oxidase

    PubMed Central

    Moser, Christopher C; Page, Christopher C; Dutton, P. Leslie

    2006-01-01

    Biological electron transfer is designed to connect catalytic clusters by chains of redox cofactors. A review of the characterized natural redox proteins with a critical eye for molecular scale measurement of variation and selection related to physiological function shows no statistically significant differences in the protein medium lying between cofactors engaged in physiologically beneficial or detrimental electron transfer. Instead, control of electron tunnelling over long distances relies overwhelmingly on less than 14 Å spacing between the cofactors in a chain. Near catalytic clusters, shorter distances (commonly less than 7 Å) appear to be selected to generate tunnelling frequencies sufficiently high to scale the barriers of multi-electron, bond-forming/-breaking catalysis at physiological rates. We illustrate this behaviour in a tunnelling network analysis of cytochrome c oxidase. In order to surmount the large, thermally activated, adiabatic barriers in the 5–10 kcal mol−1 range expected for H+ motion and O2 reduction at the binuclear centre of oxidase on the 103–105 s−1 time-scale of respiration, electron access with a tunnelling frequency of 109 or 1010 s−1 is required. This is provided by selecting closely placed redox centres, such as haem a (6.9 Å) or tyrosine (4.9 Å). A corollary is that more distantly placed redox centres, such as CuA, cannot rapidly scale the catalytic site barrier, but must send their electrons through more closely placed centres, avoiding direct short circuits that might circumvent proton pumping coupled to haems a to a3 electron transfer. The selection of distances and energetic barriers directs electron transfer from CuA to haem a rather than a3, without any need for delicate engineering of the protein medium to ‘hard wire’ electron transfer. Indeed, an examination of a large number of oxidoreductases provides no evidence of such naturally selected wiring of electron tunnelling pathways

  4. A method for including protein flexibility in protein-ligand docking: improving tools for database mining and virtual screening.

    PubMed

    Broughton, H B

    2000-06-01

    Second-generation methods for docking ligands into their biological receptors, such as FLOG, provide for flexibility of the ligand but not of the receptor. Molecular dynamics based methods, such as free energy perturbation, account for flexibility, solvent effects, etc., but are very time consuming. We combined the use of statistical analysis of conformational samples from short-run protein molecular dynamics with grid-based docking protocols and demonstrated improved performance in two test cases. Our statistical analysis explores the importance of the average strength of a potential interaction with the biological target and optionally applies a weighting depending on the variability in the strength of the interaction seen during dynamics simulation. Using these methods, we improved the num-top-ranked 10% of a database of drug-like molecules, in searches based on the three-dimensional structure of the protein. These methods are able to match the ability of manual docking to assess likely inactivity on steric grounds and indeed to rank order ligands from a homologous series of cyclooxygenase-2 inhibitors with good correlation to their true activity. Furthermore, these methods reduce the need for human intervention in setting up molecular docking experiments.

  5. Wave propagation in protein microtubules modeled as orthotropic elastic shells including transverse shear deformations.

    PubMed

    Daneshmand, Farhang; Ghavanloo, Esmaeal; Amabili, Marco

    2011-07-07

    Wave propagation along the microtubules is one of the issues of major concern in various microtubule cellular functions. In this study, the general wave propagation behavior in protein microtubules is investigated based on a first-order shear deformation shell theory for orthotropic materials, with particular emphasis on the role of strongly anisotropic elastic properties of microtubules. According to experimental observation, the first-order shear deformation theory is used for the modeling of microtubule walls. A general displacement representation is introduced and a type of coupled polynomial eigenvalue problem is developed. Numerical examples describe the effects of shear deformation and rotary inertia on wave velocities in orthotropic microtubules. Finally, the influences of the microtubule shear modulus, axial external force, effective thickness and material temperature dependency on wave velocities along the microtubule protofilaments, helical pathway and radial directions are elucidated. Most results presented in the present investigation have been absent from the literature for the wave propagation in microtubules.

  6. Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna

    PubMed Central

    DeMilio, Erica; Lawton, Colin; Marley, Nigel J.

    2016-01-01

    Abstract The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909–1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare. PMID:27667947

  7. Tardigrada of Ireland: a review of records and an updated checklist of species including a new addition to the Irish fauna.

    PubMed

    DeMilio, Erica; Lawton, Colin; Marley, Nigel J

    2016-01-01

    The phylum Tardigrada was not recorded in Ireland until the Clare Island Survey of 1909-1911, with only rare subsequent reports on Irish tardigrade species. In recent decades, significant taxonomic revision has occurred within Tardigrada. This has resulted in the need for a review of all known historical records from Ireland and Northern Ireland in order to produce an updated checklist of valid taxa. The new checklist includes fifty-one tardigrade species and subspecies including a new addition to the Irish fauna reported herein, Echiniscus quadrispinosus quadrispinosus Richters, 1902 from Newtown, Ballyvaughan, Co. Clare.

  8. Human Cornea Proteome: Identification and Quantitation of the Proteins of the Three Main Layers Including Epithelium, Stroma, and Endothelium

    PubMed Central

    2012-01-01

    Diseases of the cornea are common and refer to conditions like infections, injuries and genetic defects. Morphologically, many corneal diseases affect only certain layers of the cornea and separate analysis of the individual layers is therefore of interest to explore the basic molecular mechanisms involved in corneal health and disease. In this study, the three main layers including, the epithelium, stroma and endothelium of healthy human corneas were isolated. Prior to analysis by LC–MS/MS the proteins from the different layers were either (i) separated by SDS-PAGE followed by in-gel trypsinization, (ii) in-solution digested without prior protein separation or, (iii) in-solution digested followed by cation exchange chromatography. A total of 3250 unique Swiss-Prot annotated proteins were identified in human corneas, 2737 in the epithelium, 1679 in the stroma, and 880 in the endothelial layer. Of these, 1787 proteins have not previously been identified in the human cornea by mass spectrometry. In total, 771 proteins were quantified, 157 based on in-solution digestion and 770 based on SDS-PAGE separation followed by in-gel digestion of excised gel pieces. Protein analysis showed that many of the identified proteins are plasma proteins involved in defense responses. PMID:22698189

  9. Nitrogen balancing and xylose addition enhances growth capacity and protein content in Chlorella minutissima cultures.

    PubMed

    Freitas, B C B; Esquível, M G; Matos, R G; Arraiano, C M; Morais, M G; Costa, J A V

    2016-10-01

    This study aimed to examine the metabolic changes in Chlorella minutissima cells grown under nitrogen-deficient conditions and with the addition of xylose. The cell density, maximum photochemical efficiency, and chlorophyll and lipid levels were measured. The expression of two photosynthetic proteins, ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) and the beta subunit (AtpB) of adenosine triphosphate synthase, were measured. Comparison of cells grown in medium with a 50% reduction in the nitrogen concentration versus the traditional medium solution revealed that the cells grown under nitrogen-deficient conditions exhibited an increased growth rate, higher maximum cell density (12.7×10(6)cellsmL(-1)), optimal PSII efficiency (0.69) and decreased lipid level (25.08%). This study has taken the first steps toward protein detection in Chlorella minutissima, and the results can be used to optimize the culturing of other microalgae.

  10. Hepatitis C Virus E1 and E2 Proteins Used as Separate Immunogens Induce Neutralizing Antibodies with Additive Properties

    PubMed Central

    Beaumont, Elodie; Roch, Emmanuelle; Chopin, Lucie; Roingeard, Philippe

    2016-01-01

    Various strategies involving the use of hepatitis C virus (HCV) E1 and E2 envelope glycoproteins as immunogens have been developed for prophylactic vaccination against HCV. However, the ideal mode of processing and presenting these immunogens for effective vaccination has yet to be determined. We used our recently described vaccine candidate based on full-length HCV E1 or E2 glycoproteins fused to the heterologous hepatitis B virus S envelope protein to compare the use of the E1 and E2 proteins as separate immunogens with their use as the E1E2 heterodimer, in terms of immunogenetic potential and the capacity to induce neutralizing antibodies. The specific anti-E1 and anti-E2 antibody responses induced in animals immunized with vaccine particles harboring the heterodimer were profoundly impaired with respect to those in animals immunized with particles harboring E1 and E2 separately. Moreover, the anti-E1 and anti-E2 antibodies had additive neutralizing properties that increase the cross-neutralization of heterologous strains of various HCV genotypes, highlighting the importance of including both E1 and E2 in the vaccine for an effective vaccination strategy. Our study has important implications for the optimization of HCV vaccination strategies based on HCV envelope proteins, regardless of the platform used to present these proteins to the immune system. PMID:26966906

  11. An extended gene protein/products boolean network model including post-transcriptional regulation

    PubMed Central

    2014-01-01

    Background Networks Biology allows the study of complex interactions between biological systems using formal, well structured, and computationally friendly models. Several different network models can be created, depending on the type of interactions that need to be investigated. Gene Regulatory Networks (GRN) are an effective model commonly used to study the complex regulatory mechanisms of a cell. Unfortunately, given their intrinsic complexity and non discrete nature, the computational study of realistic-sized complex GRNs requires some abstractions. Boolean Networks (BNs), for example, are a reliable model that can be used to represent networks where the possible state of a node is a boolean value (0 or 1). Despite this strong simplification, BNs have been used to study both structural and dynamic properties of real as well as randomly generated GRNs. Results In this paper we show how it is possible to include the post-transcriptional regulation mechanism (a key process mediated by small non-coding RNA molecules like the miRNAs) into the BN model of a GRN. The enhanced BN model is implemented in a software toolkit (EBNT) that allows to analyze boolean GRNs from both a structural and a dynamic point of view. The open-source toolkit is compatible with available visualization tools like Cytoscape and allows to run detailed analysis of the network topology as well as of its attractors, trajectories, and state-space. In the paper, a small GRN built around the mTOR gene is used to demonstrate the main capabilities of the toolkit. Conclusions The extended model proposed in this paper opens new opportunities in the study of gene regulation. Several of the successful researches done with the support of BN to understand high-level characteristics of regulatory networks, can now be improved to better understand the role of post-transcriptional regulation for example as a network-wide noise-reduction or stabilization mechanisms. PMID:25080304

  12. Automatic identification of highly conserved family regions and relationships in genome wide datasets including remote protein sequences.

    PubMed

    Doğan, Tunca; Karaçalı, Bilge

    2013-01-01

    Identifying shared sequence segments along amino acid sequences generally requires a collection of closely related proteins, most often curated manually from the sequence datasets to suit the purpose at hand. Currently developed statistical methods are strained, however, when the collection contains remote sequences with poor alignment to the rest, or sequences containing multiple domains. In this paper, we propose a completely unsupervised and automated method to identify the shared sequence segments observed in a diverse collection of protein sequences including those present in a smaller fraction of the sequences in the collection, using a combination of sequence alignment, residue conservation scoring and graph-theoretical approaches. Since shared sequence fragments often imply conserved functional or structural attributes, the method produces a table of associations between the sequences and the identified conserved regions that can reveal previously unknown protein families as well as new members to existing ones. We evaluated the biological relevance of the method by clustering the proteins in gold standard datasets and assessing the clustering performance in comparison with previous methods from the literature. We have then applied the proposed method to a genome wide dataset of 17793 human proteins and generated a global association map to each of the 4753 identified conserved regions. Investigations on the major conserved regions revealed that they corresponded strongly to annotated structural domains. This suggests that the method can be useful in predicting novel domains on protein sequences.

  13. Multiple factors including subgenomic RNAs and reduced viral protein expression are associated with a persistent infection by porcine rubulavirus (LPMV).

    PubMed

    Hjertner, B; Wiman, A C; Svenda, M; Berg, M; Moreno-López, J; Linné, T

    1998-01-01

    The synthesis of virus specific RNA and the expression of viral proteins in PK-15 cells persistently infected with the porcine rubulavirus LPMV have been studied at two different cell-passages following establishment of persistency (passages 25 and 65). Protein analysis of persistently infected cells and the virus particles released from these failed to demonstrate the presence of the polymerase (L) protein. A decrease in the amount of the phospho- (P) protein was also noted. The genome and mRNAs, both mono- and bicistronic, could readily be identified in the persistently infected cells with the exception of the L mRNA. By analysis of transcription gradients generated using the NIH Image analysis software, as well as analysis of the editing frequency, it was concluded that the changes in viral protein levels in persistently infected cells could be associated with a reduction in the amount of L mRNA and a shift in editing of the P gene. In addition, several large subgenomic RNAs of both the internally deleted and copy-back type were found in the persistently infected cells. The relevance of these findings to the persistent state is discussed.

  14. Computation of binding energies including their enthalpy and entropy components for protein-ligand complexes using support vector machines.

    PubMed

    Koppisetty, Chaitanya A K; Frank, Martin; Kemp, Graham J L; Nyholm, Per-Georg

    2013-10-28

    Computing binding energies of protein-ligand complexes including their enthalpy and entropy terms by means of computational methods is an appealing approach for selecting initial hits and for further optimization in early stages of drug discovery. Despite the importance, computational predictions of thermodynamic components have evaded attention and reasonable solutions. In this study, support vector machines are used for developing scoring functions to compute binding energies and their enthalpy and entropy components of protein-ligand complexes. The binding energies computed from our newly derived scoring functions have better Pearson's correlation coefficients with experimental data than previously reported scoring functions in benchmarks for protein-ligand complexes from the PDBBind database. The protein-ligand complexes with binding energies dominated by enthalpy or entropy term could be qualitatively classified by the newly derived scoring functions with high accuracy. Furthermore, it is found that the inclusion of comprehensive descriptors based on ligand properties in the scoring functions improved the accuracy of classification as well as the prediction of binding energies including their thermodynamic components. The prediction of binding energies including the enthalpy and entropy components using the support vector machine based scoring functions should be of value in the drug discovery process.

  15. Extracellular matrix protein in calcified endoskeleton: a potential additive for crystal growth and design

    NASA Astrophysics Data System (ADS)

    Azizur Rahman, M.; Fujimura, Hiroyuki; Shinjo, Ryuichi; Oomori, Tamotsu

    2011-06-01

    In this study, we demonstrate a key function of extracellular matrix proteins (ECMPs) on seed crystals, which are isolated from calcified endoskeletons of soft coral and contain only CaCO 3 without any living cells. This is the first report that an ECMP protein extracted from a marine organism could potentially influence in modifying the surface of a substrate for designing materials via crystallization. We previously studied with the ECMPs from a different type of soft coral ( Sinularia polydactyla) without introducing any seed crystals in the process , which showed different results. Thus, crystallization on the seed in the presence of ECMPs of present species is an important first step toward linking function to individual proteins from soft coral. For understanding this interesting phenomenon, in vitro crystallization was initiated in a supersaturated solution on seed particles of calcite (1 0 4) with and without ECMPs. No change in the crystal growth shape occurred without ECMPs present during the crystallization process. However, with ECMPs, the morphology and phase of the crystals in the crystallization process changed dramatically. Upon completion of crystallization with ECMPs, an attractive crystal morphology was found. Scanning electron microscopy (SEM) was utilized to observe the crystal morphologies on the seeds surface. The mineral phases of crystals nucleated by ECMPs on the seeds surface were examined by Raman spectroscopy. Although 50 mM Mg 2+ is influential in making aragonite in the crystallization process, the ECMPs significantly made calcite crystals even when 50 mM Mg 2+ was present in the process. Crystallization with the ECMP additive seems to be a technically attractive strategy to generate assembled micro crystals that could be used in crystals growth and design in the Pharmaceutical and biotechnology industries.

  16. Genetic evidence for an additional function of phage T4 gene 32 protein: interaction with ligase.

    PubMed

    Mosig, G; Breschkin, A M

    1975-04-01

    Gene 32 of bacteriophage T4 is essential for DNA replication, recombination, and repair. In an attempt to clarify the role of the corresponding gene product, we have looked for mutations that specifically inactivate one but not all of its functions and for compensating suppressor mutations in other genes. Here we describe a gene 32 ts mutant that does not produce progeny, but in contrast to an am mutant investigated by others, is capable of some primary and secondary DNA replication and of forming "joint" recombinational intermediates after infection of Escherichia coli B at the restrictive temperature. However, parental and progeny DNA strands are not ligated to covalently linked "recombinant" molecules, and single strands of vegetative DNA do not exceed unit length. Progeny production as well as capacity for covalent linkage in this gene 32 ts mutant are partially restored by additional rII mutations. Suppression by rII depends on functioning host ligase [EC 6.5.1.2; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming, NMN-forming)]. This gene 32 ts mutation (unlike some others) in turn suppresses the characteristic plaque morphology of rII mutants. We conclude that gene 32 protein, in addition to its role in DNA replication and in the formation of "joint" recombinational intermediates, interacts with T4 ligase [EC 6.5.1.1; poly(deoxyribonucleotide):poly(deoxyribonucleotide) ligase (AMP-forming)] when recombining DNA strands are covalently linked. The protein of the mutant that we describe here is mainly defective in this interaction, thus inactivating T4 ligase in recombination. Suppressing rII mutations facilitate substitution of host ligase. There is suggestive evidence that these interactions occur at the membrane.

  17. Soybean protein as a cost-effective lignin-blocking additive for the saccharification of sugarcane bagasse.

    PubMed

    Florencio, Camila; Badino, Alberto C; Farinas, Cristiane S

    2016-12-01

    Addition of surfactants, polymers, and non-catalytic proteins can improve the enzymatic hydrolysis of lignocellulosic materials by blocking the exposed lignin surfaces, but involves extra expense. Here, soybean protein, one of the cheapest proteins available, was evaluated as an alternative additive for the enzymatic hydrolysis of pretreated sugarcane bagasse. The effect of the enzyme source was investigated using enzymatic cocktails from A. niger and T. reesei cultivated under solid-state, submerged, and sequential fermentation. The use of soybean protein led to approximately 2-fold increases in hydrolysis, relative to the control, for both A. niger and T. reesei enzymatic cocktails from solid-state fermentation. The effect was comparable to that of BSA. Moreover, the use of soybean protein and a 1:1 combination of A. niger and T. reesei enzymatic cocktails resulted in 54% higher glucose release, compared to the control. Soybean protein is a potential cost-effective additive for use in the biomass conversion process.

  18. Heteromeric complexes of heat shock protein 70 (HSP70) family members, including Hsp70B′, in differentiated human neuronal cells

    PubMed Central

    Chow, Ari M.; Mok, Philip; Xiao, Dawn; Khalouei, Sam

    2010-01-01

    Human neurodegenerative disorders such as Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis have been termed “protein misfolding disorders.” Upregulation of heat shock proteins that target misfolded aggregation-prone proteins has been proposed as a potential therapeutic strategy to counter neurodegenerative disorders. The heat shock protein 70 (HSP70) family is well characterized for its cytoprotective effects against cell death and has been implicated in neuroprotection by overexpression studies. HSP70 family members exhibit sequence and structural conservation. The significance of the multiplicity of HSP70 proteins is unknown. In this study, coimmunoprecipitation was employed to determine if association of HSP70 family members occurs, including Hsp70B′ which is present in the human genome but not in mouse and rat. Heteromeric complexes of Hsp70B′, Hsp70, and Hsc70 were detected in differentiated human SH-SY5Y neuronal cells. Hsp70B′ also formed complexes with Hsp40 suggesting a common co-chaperone for HSP70 family members. PMID:20084477

  19. Characterization of the Soluble NSF Attachment Protein gene family identifies two members involved in additive resistance to a plant pathogen

    PubMed Central

    Lakhssassi, Naoufal; Liu, Shiming; Bekal, Sadia; Zhou, Zhou; Colantonio, Vincent; Lambert, Kris; Barakat, Abdelali; Meksem, Khalid

    2017-01-01

    Proteins with Tetratricopeptide-repeat (TPR) domains are encoded by large gene families and distributed in all plant lineages. In this study, the Soluble NSF-Attachment Protein (SNAP) subfamily of TPR containing proteins is characterized. In soybean, five members constitute the SNAP gene family: GmSNAP18, GmSNAP11, GmSNAP14, GmSNAP02, and GmSNAP09. Recently, GmSNAP18 has been reported to mediate resistance to soybean cyst nematode (SCN). Using a population of recombinant inbred lines from resistant and susceptible parents, the divergence of the SNAP gene family is analysed over time. Phylogenetic analysis of SNAP genes from 22 diverse plant species showed that SNAPs were distributed in six monophyletic clades corresponding to the major plant lineages. Conservation of the four TPR motifs in all species, including ancestral lineages, supports the hypothesis that SNAPs were duplicated and derived from a common ancestor and unique gene still present in chlorophytic algae. Syntenic analysis of regions harbouring GmSNAP genes in soybean reveals that this family expanded from segmental and tandem duplications following a tetraploidization event. qRT-PCR analysis of GmSNAPs indicates a co-regulation following SCN infection. Finally, genetic analysis demonstrates that GmSNAP11 contributes to an additive resistance to SCN. Thus, GmSNAP11 is identified as a novel minor gene conferring resistance to SCN. PMID:28338077

  20. Infection with Chlamydia trachomatis alters the tyrosine phosphorylation and/or localization of several host cell proteins including cortactin.

    PubMed Central

    Fawaz, F S; van Ooij, C; Homola, E; Mutka, S C; Engel, J N

    1997-01-01

    Infection of epithelial cells by two biovars of Chlamydia trachomatis results in the tyrosine phosphorylation of several host proteins. The most prominent change in host protein tyrosine phosphorylation involves a complex of proteins with molecular masses of 75 to 85 kDa (pp75/85) and 100 kDa (pp100). The C. trachomatis-induced tyrosine phosphorylation of pp75/85 and pp100 is observed in several cell lines, including epithelial cells, fibroblasts, and macrophages. Subcellular fractionation and detergent solubility properties of pp75/85 are consistent with its association with the cytoskeleton. Phosphoamino acid analysis demonstrates that the pp75/85 complex is phosphorylated on both tyrosine and serine residues. Immunofluorescence studies of chlamydia-infected cells by using fluorescein isothiocyanate-phalloidin and antibodies to phosphotyrosine and cortactin demonstrate that tyrosine-phosphorylated proteins, as well as cortactin, are localized to the chlamydial vacuole and that this process is facilitated by actin. PMID:9393830

  1. The sphingoid long chain base phytosphingosine activates AGC-type protein kinases in Saccharomyces cerevisiae including Ypk1, Ypk2, and Sch9.

    PubMed

    Liu, Ke; Zhang, Xiping; Lester, Robert L; Dickson, Robert C

    2005-06-17

    The Pkh1 protein kinase of Saccharomyces cerevisiae, a homolog of the mammalian 3-phosphoinositide-dependent kinase (PDK1), regulates downstream AGC-type protein kinases including Ypk1/2 and Pkc1, which control cell wall integrity, growth, and other processes. Phytosphingosine (PHS), a sphingoid long chain base, is hypothesized to be a lipid activator of Pkh1 and thereby controls the activity of Ypk1/2. Here we present biochemical evidence supporting this hypothesis, and in addition we demonstrate that PHS also stimulates autophosphorylation and activation of Ypk1/2. Greatest stimulation of Ypk1/2 phosphorylation and activity are achieved by inclusion of both PHS and Pkh1 in an in vitro kinase reaction. We also demonstrate for the first time that Pkh1 phosphorylates the Sch9 protein kinase in vitro and that such phosphorylation is stimulated by PHS. This is the first biochemical demonstration of Sch9 activators, and the results further support roles for long chain bases in heat stress resistance in addition to implying roles in chronological aging and cell size determination, since Sch9 functions in these processes. Thus, our data support a model in which PHS, rather than simply being an upstream activator of Pkh1, also activates kinases that are downstream targets of Pkh1 including Ypk1/2 and Sch9.

  2. Soy Protein Isolate As Fluid Loss Additive in Bentonite-Water-Based Drilling Fluids.

    PubMed

    Li, Mei-Chun; Wu, Qinglin; Song, Kunlin; Lee, Sunyoung; Jin, Chunde; Ren, Suxia; Lei, Tingzhou

    2015-11-11

    Wellbore instability and formation collapse caused by lost circulation are vital issues during well excavation in the oil industry. This study reports the novel utilization of soy protein isolate (SPI) as fluid loss additive in bentonite-water based drilling fluids (BT-WDFs) and describes how its particle size and concentration influence on the filtration property of SPI/BT-WDFs. It was found that high pressure homogenization (HPH)-treated SPI had superior filtration property over that of native SPI due to the improved ability for the plugging pore throat. HPH treatment also caused a significant change in the surface characteristic of SPI, leading to a considerable surface interaction with BT in aqueous solution. The concentration of SPI had a significant impact on the dispersion state of SPI/BT mixtures in aquesous solution. At low SPI concentrations, strong aggregations were created, resulting in the formation of thick, loose, high-porosity and high-permeability filter cakes and high fluid loss. At high SPI concentrations, intercatlated/exfoliated structures were generated, resulting in the formation of thin, compact, low-porosity and low-permeability filter cakes and low fluid loss. The SPI/BT-WDFs exhibited superior filtration property than pure BT-WDFs at the same solid concentraion, demonstrating the potential utilization of SPI as an effective, renewable, and biodegradable fluid loss reducer in well excavation applications.

  3. Use of additives to enhance the properties of cottonseed protein as wood adhesives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soy protein is currently being used commercially as a “green” wood adhesive. Previous work in this laboratory has shown that cottonseed protein isolate, tested on maple wood veneer, produced higher adhesive strength and hot water resistance relative to soy protein. In the present study, cottonseed...

  4. Sensory aroma characteristics of alcalase hydrolyzed rice bran protein concentrate as affected by spray drying and sugar addition.

    PubMed

    Arsa, Supeeraya; Theerakulkait, Chockchai

    2015-08-01

    The sensory aroma characteristics of alcalase hydrolyzed rice bran protein concentrate as affected by spray drying and sugar addition were investigated. Rice bran protein concentrate (RBPC) was hydrolyzed by alcalase. Sucrose, glucose or fructose was added to the liquid rice bran protein hydrolysate (LRBPH) and subsequently spray dried. The sensory aroma intensities of the hydrolysates were evaluated. Results showed that after spray drying, the rice bran protein concentrate powder (RBPC-P) had higher sweet and cocoa-like aroma intensities than RBPC (p ≤ 0.05) and hydrolyzed rice bran protein powder (HRBPP) had higher milk powder-like aroma intensities than LRBPH (p ≤ 0.05). The sweet, cocoa-like and milk powder-like aroma intensities in hydrolyzed rice bran protein powder with fructose addition (HRBPP-F) were significantly higher (p ≤ 0.05) than those of hydrolyzed rice bran protein powder with sucrose or glucose addition (HRBPP-S or HRBPP-G). HRBPP-F had the highest overall aroma liking score. These results also indicate that spray drying and sugar addition could improve the sensory aroma characteristics of alcalase hydrolyzed RBPC.

  5. Ectoine-induced proteins in Sinorhizobium meliloti include an Ectoine ABC-type transporter involved in osmoprotection and ectoine catabolism.

    PubMed

    Jebbar, Mohamed; Sohn-Bösser, Linda; Bremer, Erhard; Bernard, Théophile; Blanco, Carlos

    2005-02-01

    To understand the mechanisms of ectoine-induced osmoprotection in Sinorhizobium meliloti, a proteomic examination of S. meliloti cells grown in minimal medium supplemented with ectoine was undertaken. This revealed the induction of 10 proteins. The protein products of eight genes were identified by using matrix-assisted laser desorption ionization-time-of-flight mass spectrometry. Five of these genes, with four other genes whose products were not detected on two-dimensional gels, belong to the same gene cluster, which is localized on the pSymB megaplasmid. Four of the nine genes encode the characteristic components of an ATP-binding cassette transporter that was named ehu, for ectoine/hydroxyectoine uptake. This transporter was encoded by four genes (ehuA, ehuB, ehuC, and ehuD) that formed an operon with another gene cluster that contains five genes, named eutABCDE for ectoine utilization. On the basis of sequence homologies, eutABCDE encode enzymes with putative and hypothetical functions in ectoine catabolism. Analysis of the properties of ehuA and eutA mutants suggests that S. meliloti possesses at least one additional ectoine catabolic pathway as well as a lower-affinity transport system for ectoine and hydroxyectoine. The expression of ehuB, as determined by measurements of UidA activity, was shown to be induced by ectoine and hydroxyectoine but not by glycine betaine or by high osmolality.

  6. Effect of the addition of conventional additives and whey proteins concentrates on technological parameters, physicochemical properties, microstructure and sensory attributes of sous vide cooked beef muscles.

    PubMed

    Szerman, N; Gonzalez, C B; Sancho, A M; Grigioni, G; Carduza, F; Vaudagna, S R

    2012-03-01

    Beef muscles submitted to four enhancement treatments (1.88% whey protein concentrate (WPC)+1.25% sodium chloride (NaCl); 1.88% modified whey protein concentrate (MWPC)+1.25%NaCl; 0.25% sodium tripolyphosphate (STPP)+1.25%NaCl; 1.25%NaCl) and a control treatment (non-injected muscles) were sous vide cooked. Muscles with STPP+NaCl presented a significantly higher total yield (106.5%) in comparison to those with WPC/MWPC+NaCl (94.7% and 92.9%, respectively), NaCl alone (84.8%) or controls (72.1%). Muscles with STPP+NaCl presented significantly lower shear force values than control ones; also, WPC/MWPC+NaCl added muscles presented similar values than those from the other treatments. After cooking, muscles with STPP+NaCl or WPC/MWPC+NaCl depicted compacted and uniform microstructures. Muscles with STPP+NaCl showed a pink colour, meanwhile other treatment muscles presented colours between pinkish-grey and grey-brown. STPP+NaCl added samples presented the highest values of global tenderness and juiciness. The addition of STPP+NaCl had a better performance than WPC/MWPC+NaCl. However, the addition of WPC/MWPC+NaCl improved total yield in comparison to NaCl added or control ones.

  7. Rapid detection of the addition of soybean proteins to cheese and other dairy products by reversed-phase perfusion chromatography.

    PubMed

    García, M C; Marina, M L

    2006-04-01

    The undeclared addition of soybean proteins to milk products is forbidden and a method is needed for food control and enforcement. This paper reports the development of a chromatographic method for routine analysis enabling the detection of the addition of soybean proteins to dairy products. A perfusion chromatography column and a linear binary gradient of acetonitrile-water-0.1% (v/v) trifluoroacetic acid at a temperature of 60 degrees C were used. A very simple sample treatment consisting of mixing the sample with a suitable solvent (Milli-Q water or bicarbonate buffer (pH=11)) and centrifuging was used. The method enabled the separation of soybean proteins from milk proteins in less than 4 min (at a flow-rate of 3 ml/min). The method has been successfully applied to the detection of soybean proteins in milk, cheese, yogurt, and enteral formula. The correct quantitation of these vegetable proteins has also been possible in milk adulterated at origin with known sources of soybean proteins. The application of the method to samples adulterated at origin also leads to interesting conclusions as to the effect of the processing conditions used for the preparation of each dairy product on the determination of soybean proteins.

  8. Kinetics of nitric oxide dissociation from five- and six-coordinate nitrosyl hemes and heme proteins, including soluble guanylate cyclase.

    PubMed

    Kharitonov, V G; Sharma, V S; Magde, D; Koesling, D

    1997-06-03

    Kinetics of NO dissociation were characterized for three five-coordinate systems, heme-NO, HSA-heme-NO (human serum albumin), GC-NO (soluble guanylate cyclase), and for the six-coordinate system, Im-heme-NO. Nitrosyl myoglobin was redetermined for comparison. Previously known, six-coordinate R and T state nitrosyl hemoglobins are also included in the comparison. The data indicate that NO dissociates more than 1000 times faster from five-coordinate model heme than it does from the six-coordinate analog. Such a negative trans-effect between NO and a proximal base is in sharp contrast to carboxy heme derivatives, in which ligand dissociation rates are greatly slowed in when a trans base is present. As a result of opposite trans-effects, six-coordinate carboxy and nitrosyl derivatives have comparable dissociation rates, even though the five-coordinate species are very different. In proteins, five- and six-coordinate forms do not show a large difference in dissociation rates. Part of the reason may be due to different probabilities for geminate recombination in the different proteins, but this cannot explain all the facts. There must also be influences of the protein structure on bond-breaking rate constants themselves. With the exception of hemoglobin in the T state, nitrosyl guanylate cyclase shows the highest NO dissociation rate constant, k(obs) = 6 x 10(-4) s(-1). This would yield a half-life of about 2 min at 37 degrees C for dissociation of NO from GC-NO, a number that has implications for the mechanism of regulation of the activity of this key heme enzyme.

  9. Measurement of [Formula: see text] production with additional jet activity, including [Formula: see text] quark jets, in the dilepton decay channel using pp collisions at [Formula: see text].

    PubMed

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Ralph, D; Roland, C; Roland, G; Salfeld-Nebgen, J; Stephans, G S F; Sumorok, K; Varma, M; Velicanu, D; Veverka, J; Wang, J; Wang, T W; Wyslouch, B; Yang, M; Zhukova, V; Dahmes, B; Evans, A; Finkel, A; Gude, A; Hansen, P; Kalafut, S; Kao, S C; Klapoetke, K; Kubota, Y; Lesko, Z; Mans, J; Nourbakhsh, S; Ruckstuhl, N; Rusack, R; Tambe, N; Turkewitz, J; Acosta, J G; Oliveros, S; Avdeeva, E; Bloom, K; Bose, S; Claes, D R; Dominguez, A; Fangmeier, C; Gonzalez Suarez, R; Kamalieddin, R; Keller, J; Knowlton, D; Kravchenko, I; Meier, F; Monroy, J; Ratnikov, F; Siado, J E; Snow, G R; Alyari, M; Dolen, J; George, J; Godshalk, A; Harrington, C; Iashvili, I; Kaisen, J; Kharchilava, A; Kumar, A; Rappoccio, S; Roozbahani, B; Alverson, G; Barberis, E; Baumgartel, D; Chasco, M; Hortiangtham, A; Massironi, A; Morse, D M; Nash, D; Orimoto, T; Teixeira De Lima, R; Trocino, D; Wang, R-J; Wood, D; Zhang, J; Hahn, K A; Kubik, A; Mucia, N; Odell, N; Pollack, B; Pozdnyakov, A; Schmitt, M; Stoynev, S; Sung, K; Trovato, M; Velasco, M; Brinkerhoff, A; Dev, N; Hildreth, M; Jessop, C; Karmgard, D J; Kellams, N; Lannon, K; Lynch, S; Marinelli, N; Meng, F; Mueller, C; Musienko, Y; Pearson, T; Planer, M; Reinsvold, A; Ruchti, R; Smith, G; Taroni, S; Valls, N; Wayne, M; Wolf, M; Woodard, A; Antonelli, L; Brinson, J; Bylsma, B; Durkin, L S; Flowers, S; Hart, A; Hill, C; Hughes, R; Ji, W; Kotov, K; Ling, T Y; Liu, B; Luo, W; Puigh, D; Rodenburg, M; Winer, B L; Wulsin, H W; Driga, O; Elmer, P; Hardenbrook, J; Hebda, P; Koay, S A; Lujan, P; Marlow, D; Medvedeva, T; Mooney, M; Olsen, J; Palmer, C; Piroué, P; Saka, H; Stickland, D; Tully, C; Zuranski, A; Malik, S; Barnes, V E; Benedetti, D; Bortoletto, D; Gutay, L; Jha, M K; Jones, M; Jung, K; Miller, D H; Neumeister, N; Primavera, F; Radburn-Smith, B C; Shi, X; Shipsey, I; Silvers, D; Sun, J; Svyatkovskiy, A; Wang, F; Xie, W; Xu, L; Parashar, N; Stupak, J; Adair, A; Akgun, B; Chen, Z; Ecklund, K M; Geurts, F J M; Guilbaud, M; Li, W; Michlin, B; Northup, M; Padley, B P; Redjimi, R; Roberts, J; Rorie, J; Tu, Z; Zabel, J; Betchart, B; Bodek, A; de Barbaro, P; Demina, R; Eshaq, Y; Ferbel, T; Galanti, M; Galanti, M; Garcia-Bellido, A; Han, J; Harel, A; Hindrichs, O; Hindrichs, O; Khukhunaishvili, A; Petrillo, G; Tan, P; Verzetti, M; Arora, S; Barker, A; Chou, J P; Contreras-Campana, C; Contreras-Campana, E; Duggan, D; Ferencek, D; Gershtein, Y; Gray, R; Halkiadakis, E; Hidas, D; Hughes, E; Kaplan, S; Kunnawalkam Elayavalli, R; Lath, A; Nash, K; Panwalkar, S; Park, M; Salur, S; Schnetzer, S; Sheffield, D; Somalwar, S; Stone, R; Thomas, S; Thomassen, P; Walker, M; Foerster, M; Riley, G; Rose, K; Spanier, S; York, A; Bouhali, O; Castaneda Hernandez, A; Dalchenko, M; De Mattia, M; Delgado, A; Dildick, S; Dildick, S; Eusebi, R; Gilmore, J; Kamon, T; Krutelyov, V; Krutelyov, V; Mueller, R; Osipenkov, I; Pakhotin, Y; Patel, R; Patel, R; Perloff, A; Rose, A; Safonov, A; Tatarinov, A; Ulmer, K A; Akchurin, N; Cowden, C; Damgov, J; Dragoiu, C; Dudero, P R; Faulkner, J; Kunori, S; Lamichhane, K; Lee, S W; Libeiro, T; Undleeb, S; Volobouev, I; Appelt, E; Delannoy, A G; Greene, S; Gurrola, A; Janjam, R; Johns, W; Maguire, C; Mao, Y; Melo, A; Ni, H; Sheldon, P; Snook, B; Tuo, S; Velkovska, J; Xu, Q; Arenton, M W; Cox, B; Francis, B; Goodell, J; Hirosky, R; Ledovskoy, A; Li, H; Lin, C; Neu, C; Sinthuprasith, T; Sun, X; Wang, Y; Wolfe, E; Wood, J; Xia, F; Clarke, C; Harr, R; Karchin, P E; Kottachchi Kankanamge Don, C; Lamichhane, P; Sturdy, J; Belknap, D A; Carlsmith, D; Cepeda, M; Dasu, S; Dodd, L; Duric, S; Gomber, B; Grothe, M; Hall-Wilton, R; Herndon, M; Hervé, A; Klabbers, P; Lanaro, A; Levine, A; Long, K; Loveless, R; Mohapatra, A; Ojalvo, I; Perry, T; Pierro, G A; Polese, G; Ruggles, T; Sarangi, T; Savin, A; Sharma, A; Smith, N; Smith, W H; Taylor, D; Woods, N; Collaboration, Authorinst The Cms

    2016-01-01

    Jet multiplicity distributions in top quark pair ([Formula: see text]) events are measured in pp collisions at a centre-of-mass energy of 8 TeV with the CMS detector at the LHC using a data set corresponding to an integrated luminosity of 19.7[Formula: see text]. The measurement is performed in the dilepton decay channels ([Formula: see text], [Formula: see text], and [Formula: see text]). The absolute and normalized differential cross sections for [Formula: see text] production are measured as a function of the jet multiplicity in the event for different jet transverse momentum thresholds and the kinematic properties of the leading additional jets. The differential [Formula: see text] and [Formula: see text] cross sections are presented for the first time as a function of the kinematic properties of the leading additional [Formula: see text] jets. Furthermore, the fraction of events without additional jets above a threshold is measured as a function of the transverse momenta of the leading additional jets and the scalar sum of the transverse momenta of all additional jets. The data are compared and found to be consistent with predictions from several perturbative quantum chromodynamics event generators and a next-to-leading order calculation.

  10. ProFold: Protein Fold Classification with Additional Structural Features and a Novel Ensemble Classifier

    PubMed Central

    2016-01-01

    Protein fold classification plays an important role in both protein functional analysis and drug design. The number of proteins in PDB is very large, but only a very small part is categorized and stored in the SCOPe database. Therefore, it is necessary to develop an efficient method for protein fold classification. In recent years, a variety of classification methods have been used in many protein fold classification studies. In this study, we propose a novel classification method called proFold. We import protein tertiary structure in the period of feature extraction and employ a novel ensemble strategy in the period of classifier training. Compared with existing similar ensemble classifiers using the same widely used dataset (DD-dataset), proFold achieves 76.2% overall accuracy. Another two commonly used datasets, EDD-dataset and TG-dataset, are also tested, of which the accuracies are 93.2% and 94.3%, higher than the existing methods. ProFold is available to the public as a web-server. PMID:27660761

  11. Rapid addition of unlabeled silent solubility tags to proteins using a new substrate-fused sortase reagent.

    PubMed

    Amer, Brendan R; Macdonald, Ramsay; Jacobitz, Alex W; Liauw, Brandon; Clubb, Robert T

    2016-03-01

    Many proteins can't be studied using solution NMR methods because they have limited solubility. To overcome this problem, recalcitrant proteins can be fused to a more soluble protein that functions as a solubility tag. However, signals arising from the solubility tag hinder data analysis because they increase spectral complexity. We report a new method to rapidly and efficiently add a non-isotopically labeled Small Ubiquitin-like Modifier protein (SUMO) solubility tag to an isotopically labeled protein. The method makes use of a newly developed SUMO-Sortase tagging reagent in which SUMO and the Sortase A (SrtA) enzyme are present within the same polypeptide. The SUMO-Sortase reagent rapidly attaches SUMO to any protein that contains the sequence LPXTG at its C-terminus. It modifies proteins at least 15-times faster than previously described approaches, and does not require active dialysis or centrifugation during the reaction to increase product yields. In addition, silently tagged proteins are readily purified using the well-established SUMO expression and purification system. The utility of the SUMO-Sortase tagging reagent is demonstrated using PhoP and green fluorescent proteins, which are ~90% modified with SUMO at room temperature within four hours. SrtA is widely used as a tool to construct bioconjugates. Significant rate enhancements in these procedures may also be achieved by fusing the sortase enzyme to its nucleophile substrate.

  12. Rapid Addition of Unlabeled Silent Solubility Tags to Proteins Using a New Substrate-Fused Sortase Reagent

    PubMed Central

    Amer, Brendan R.; Macdonald, Ramsay; Jacobitz, Alex W.; Liauw, Brandon; Clubb, Robert T.

    2016-01-01

    Many proteins can’t be studied using solution NMR methods because they have limited solubility. To overcome this problem, recalcitrant proteins can be fused to a more soluble protein that functions as a solubility tag. However, signals arising from the solubility tag hinder data analysis because they increase spectral complexity. We report a new method to rapidly and efficiently add a non-isotopically labeled Small Ubiquitin-like Modifier protein (SUMO) solubility tag to an isotopically labeled protein. The method makes use of a newly developed SUMO-Sortase tagging reagent in which SUMO and the Sortase A (SrtA) enzyme are present within the same polypeptide. The SUMO-Sortase reagent rapidly attaches SUMO to any protein that contains the sequence LPXTG at its C-terminus. It modifies proteins at least 15-times faster than previously described approaches, and does not require active dialysis or centrifugation during the reaction to increase product yields. In addition, silently tagged proteins are readily purified using the well-established SUMO expression and purification system. The utility of the SUMO-Sortase tagging reagent is demonstrated using PhoP and green fluorescent proteins, which are ~90% modified with SUMO at room temperature within four hours. SrtA is widely used as a tool to construct bioconjugates. Significant rate enhancements in these procedures may also be achieved by fusing the sortase enzyme to its nucleophile substrate. PMID:26852413

  13. Including xpc® feed additive in the diet of inoculated broilers during grow-out helps control salmonella associated with their carcasses after processing

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The objective of this study was to test XPC® feed additive for control of Salmonella in poultry meat products. Day of hatch broiler chicks were gavaged with 106 cells of a nalidixic acid resistant marker strain of Salmonella Typhimurium and placed on clean pine shavings in 9 separate floor pens (25 ...

  14. Multi-faceted proteomic characterization of host protein complement of Rift Valley fever virus virions and identification of specific heat shock proteins, including HSP90, as important viral host factors.

    PubMed

    Nuss, Jonathan E; Kehn-Hall, Kylene; Benedict, Ashwini; Costantino, Julie; Ward, Michael; Peyser, Brian D; Retterer, Cary J; Tressler, Lyal E; Wanner, Laura M; McGovern, Hugh F; Zaidi, Anum; Anthony, Scott M; Kota, Krishna P; Bavari, Sina; Hakami, Ramin M

    2014-01-01

    Rift Valley fever is a potentially fatal disease of humans and domestic animals caused by Rift Valley fever virus (RVFV). Infection with RVFV in ruminants can cause near 100% abortion rates and recent outbreaks in naïve human populations have suggested case fatality rates of greater than thirty percent. To elucidate the roles that host proteins play during RVFV infection, proteomic analysis of RVFV virions was conducted using complementary analytical approaches, followed by functional validation studies of select identified host factors. Coupling the more traditional Gel LC/MS/MS approach (SDS PAGE followed by liquid chromatography tandem mass spectrometry) with an alternative technique that preserves protein complexes allowed the protein complement of these viral particles to be thoroughly examined. In addition to viral proteins present within the virions and virion-associated host proteins, multiple macromolecular complexes were identified. Bioinformatic analysis showed that host chaperones were among over-represented protein families associated with virions, and functional experiments using siRNA gene silencing and small molecule inhibitors identified several of these heat shock proteins, including heat shock protein 90 (HSP90), as important viral host factors. Further analysis indicated that HSP inhibition effects occur during the replication/transcription phase of the virus life cycle, leading to significant lowering of viral titers without compromising the functional capacity of released virions. Overall, these studies provide much needed further insight into interactions between RVFV and host cells, increasing our understanding of the infection process and suggesting novel strategies for anti-viral development. In particular, considering that several HSP90 inhibitors have been advancing through clinical trials for cancer treatment, these results also highlight the exciting potential of repurposing HSP90 inhibitors to treat RVF.

  15. The addition of a protein-rich breakfast and its effects on acute appetite control and food intake in ‘breakfast-skipping’ adolescents

    PubMed Central

    Leidy, HJ; Racki, EM

    2014-01-01

    Background Breakfast skipping (BS) is closely associated with overeating (in the evening), weight gain and obesity. It is unclear whether the addition of breakfast, with emphasis on dietary protein, leads to better appetite and energy intake regulation in adolescents. Objective The purpose of the study was to examine the impact of addition of a normal-protein (PN) breakfast vs protein-rich (PR) breakfast on appetite and food intake in ‘breakfast-skipping’ adolescents. Subjects and Design A total of 13 adolescents (age 14.3 ± 0.3 years; body mass index percentile 79 ± 4 percentile; skipped breakfast 5 ± 1× per week) randomly completed 3 testing days that included a PN (18 ± 1 g protein), PR (48 ± 2 g protein) or BS. Breakfast was 24% of estimated daily energy needs. Appetite, satiety and hormonal responses were collected over 5 h followed by an ad libitum lunch and 24-h food intake assessments. Results Perceived appetite was not different following PN vs BS; PR led to greater reductions vs BS (P<0.01) and PN (P< 0.001). Fullness was greater following both breakfast meals vs BS (P<0.01) but was not different between meals. Ghrelin was not different among treatments. Greater PYY concentrations were observed following both breakfast meals vs BS (P<0.01) but was not different between meals. Lunch energy intake was not different following PN vs BS; PR led to fewer kcal consumed vs BS (P<0.01) and PN (P<0.005). Daily food intake was not different among treatments. Conclusions Breakfast led to increased satiety through increased fullness and PYY concentrations in ‘breakfast skipping’ adolescents. A breakfast rich in dietary protein provides additional benefits through reductions in appetite and energy intake. These findings suggest that the addition of a protein-rich breakfast might be an effective strategy to improve appetite control in young people. PMID:20125103

  16. Dose response of whey protein isolate in addition to a typical mixed meal on blood amino acids and hormonal concentrations.

    PubMed

    Forbes, Scott C; McCargar, Linda; Jelen, Paul; Bell, Gordon J

    2014-04-01

    The purpose was to investigate the effects of a controlled typical 1-day diet supplemented with two different doses of whey protein isolate on blood amino acid profiles and hormonal concentrations following the final meal. Nine males (age: 29.6 ± 6.3 yrs) completed four conditions in random order: a control (C) condition of a typical mixed diet containing ~10% protein (0.8 g·kg1), 65% carbohydrate, and 25% fat; a placebo (P) condition calorically matched with carbohydrate to the whey protein conditions; a low-dose condition of 0.8 grams of whey protein isolate per kilogram body mass per day (g·kg1·d1; W1) in addition to the typical mixed diet; or a high-dose condition of 1.6 g·kg1·d1 (W2) of supplemental whey protein in addition to the typical mixed diet. Following the final meal, significant (p < .05) increases in total amino acids, essential amino acids (EAA), branch-chained amino acids (BCAA), and leucine were observed in plasma with whey protein supplementation while no changes were observed in the control and placebo conditions. There was no significant group difference for glucose, insulin, testosterone, cortisol, or growth hormone. In conclusion, supplementing a typical daily food intake consisting of 0.8 g of protein·kg1·d1 with a whey protein isolate (an additional 0.8 or 1.6 g·kg1·d1) significantly elevated total amino acids, EAA, BCAA, and leucine but had no effect on glucose, insulin, testosterone, cortisol, or growth hormone following the final meal. Future acute and chronic supplementation research examining the physiological and health outcomes associated with elevated amino acid profiles is warranted.

  17. Quantum ring-polymer contraction method: Including nuclear quantum effects at no additional computational cost in comparison to ab initio molecular dynamics

    NASA Astrophysics Data System (ADS)

    John, Christopher; Spura, Thomas; Habershon, Scott; Kühne, Thomas D.

    2016-04-01

    We present a simple and accurate computational method which facilitates ab initio path-integral molecular dynamics simulations, where the quantum-mechanical nature of the nuclei is explicitly taken into account, at essentially no additional computational cost in comparison to the corresponding calculation using classical nuclei. The predictive power of the proposed quantum ring-polymer contraction method is demonstrated by computing various static and dynamic properties of liquid water at ambient conditions using density functional theory. This development will enable routine inclusion of nuclear quantum effects in ab initio molecular dynamics simulations of condensed-phase systems.

  18. Study Modules for Calculus-Based General Physics. [Includes Modules 1 and 2: Dimensions and Vector Addition; Rectilinear Motion; plus a Trigonometry and Calculus Review].

    ERIC Educational Resources Information Center

    Fuller, Robert G., Ed.; And Others

    This is part of a series of 42 Calculus Based Physics (CBP) modules totaling about 1,000 pages. The modules include study guides, practice tests, and mastery tests for a full-year individualized course in calculus-based physics based on the Personalized System of Instruction (PSI). The units are not intended to be used without outside materials;…

  19. Towards the synthesis of hydroxyapatite/protein scaffolds with controlled porosities: bulk and interfacial shear rheology of a hydroxyapatite suspension with protein additives.

    PubMed

    Maas, Michael; Bodnar, Pedro Marcus; Hess, Ulrike; Treccani, Laura; Rezwan, Kurosch

    2013-10-01

    The synthesis of porous hydroxyapatite scaffolds is essential for biomedical applications such as bone tissue engineering and replacement. One way to induce macroporosity, which is needed to support bone in-growth, is to use protein additives as foaming agents. Another reason to use protein additives is the potential to introduce a specific biofunctionality to the synthesized scaffolds. In this work, we study the rheological properties of a hydroxyapatite suspension system with additions of the proteins bovine serum albumin (BSA), lysozyme (LSZ) and fibrinogen (FIB). Both the rheology of the bulk phase as well as the interfacial shear rheology are studied. The bulk rheological data provides important information on the setting behavior of the thixotropic suspension, which we find to be faster with the addition of FIB and LSZ and much slower with BSA. Foam bubble stabilization mechanisms can be rationalized via interfacial shear rheology and we show that it depends on the growth of interfacial films at the suspension/air interface. These interfacial films support the stabilization of bubbles within the ceramic matrix and thereby introduce macropores. Due to the weak interaction of the protein molecules with the hydroxyapatite particles of the suspension, we find that BSA forms the most stable interfacial films, followed by FIB. LSZ strongly interacts with the hydroxyapatite particles and thus only forms thin films with very low elastic moduli. In summary, our study provides fundamental rheological insights which are essential for tailoring hydroxyapatite/protein suspensions in order to synthesize scaffolds with controlled porosities.

  20. Localization of eight additional genes in the human major histocompatibility complex, including the gene encoding the casein kinase II {beta} subunit (CSNK2B)

    SciTech Connect

    Albertella, M.R.; Jones, H.; Thomson, W.

    1996-09-01

    A wide range of autoimmune and other diseases are known to be associated with the major histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility complex. Many of these diseases are linked to the genes encoding the polymorphic histocompatibility antigens in the class I and class II regions, but some appear to be more strongly associated with genes in the central 1100-kb class III region, making it important to characterize this region fully for the presence of novel genes. An {approximately}220-kb segment of DNA in the class III region separating the Hsp70 (HSPA1L) and BAT1 (D6S8IE) genes, which was previously known to contain 14 genes. Genomic DNA fragments spanning the gaps between the known genes were used as probes to isolate cDNAs corresponding to five new genes within this region. Evidence from Northern blot analysis and exon trapping experiments that suggested the presence of at least two more new genes was also obtained. Partial cDNA and complete exonic genomic sequencing of one of the new genes has identified it as the casein kinase II{beta} subunit (CSNK2B). Two of the other novel genes lie within a region syntenic to that implicated in susceptibility to experimental allergic orchitis in the mouse, an autoimmune disease of the testis, and represent additional candidates for the Orch-1 locus associated with this disease. In addition, characterization of the 13-kb intergenic gap separating the RD (D6545) and G11 (D6S60E) genes has revealed the presence of a gene encoding a 1246-amino-acid polypeptide that shows significant sequence similarity to the yeast anti-viral Ski2p gene product. 49 refs., 8 figs.

  1. The Phosphoproteome of a Chlamydomonas reinhardtii Eyespot Fraction Includes Key Proteins of the Light Signaling Pathway1[W

    PubMed Central

    Wagner, Volker; Ullmann, Katharina; Mollwo, Anne; Kaminski, Marc; Mittag, Maria; Kreimer, Georg

    2008-01-01

    Flagellate green algae have developed a visual system, the eyespot apparatus, which allows the cell to phototax. In a recent proteomic approach, we identified 202 proteins from a fraction enriched in eyespot apparatuses of Chlamydomonas reinhardtii. Among these proteins, five protein kinases and two protein phosphatases were present, indicating that reversible protein phosphorylation occurs in the eyespot. About 20 major phosphoprotein bands were detected in immunoblots of eyespot proteins with an anti-phosphothreonine antibody. Toward the profiling of the targets of protein kinases in the eyespot fraction, we analyzed its phosphoproteome. The solubilized proteins of the eyespot fraction were treated with the endopeptidases LysC and trypsin prior to enrichment of phosphopeptides with immobilized metal-ion affinity chromatography. Phosphopeptides were analyzed by nano-liquid chromatography-electrospray ionization-mass spectrometry (MS) with MS/MS as well as neutral-loss-triggered MS/MS/MS spectra. We were able to identify 68 different phosphopeptides along with 52 precise in vivo phosphorylation sites corresponding to 32 known proteins of the eyespot fraction. Among the identified phosphoproteins are enzymes of carotenoid and fatty acid metabolism, putative signaling components, such as a SOUL heme-binding protein, a Ca2+-binding protein, and an unusual protein kinase, but also several proteins with unknown function. Notably, two unique photoreceptors, channelrhodopsin-1 and channelrhodopsin-2, contain three and one phosphorylation sites, respectively. Phosphorylation of both photoreceptors occurs in the cytoplasmatic loop next to their seven transmembrane regions in a similar distance to that observed in vertebrate rhodopsins, implying functional importance for regulation of these directly light-gated ion channels relevant for the photoresponses of C. reinhardtii. PMID:18065559

  2. Mutation of the gene encoding a major outer-membrane protein in Xanthomonas campestris pv. campestris causes pleiotropic effects, including loss of pathogenicity.

    PubMed

    Chen, Yih-Yuan; Wu, Chieh-Hao; Lin, Juey-Wen; Weng, Shu-Fen; Tseng, Yi-Hsiung

    2010-09-01

    Xanthomonas campestris pv. campestris (Xcc) is the phytopathogen that causes black rot in crucifers. The xanthan polysaccharide and extracellular enzymes produced by this organism are virulence factors, the expression of which is upregulated by Clp (CRP-like protein) and DSF (diffusible signal factor), which is synthesized by RpfF. It is also known that biofilm formation/dispersal, regulated by the effect of controlled synthesis of DSF on cell-cell signalling, is required for virulence. Furthermore, a deficiency in DSF causes cell aggregation with concomitant production of a gum-like substance that can be dispersed by addition of DSF or digested by exogenous endo-beta-1,4-mannanase expressed by Xcc. In this study, Western blotting of proteins from a mopB mutant (XcMopB) showed Xcc MopB to be the major outer-membrane protein (OMP); Xcc MopB shared over 97 % identity with homologues from other members of Xanthomonas. Similarly to the rpfF mutant, XcMopB formed aggregates with simultaneous production of a gummy substance, but these aggregates could not be dispersed by DSF or endo-beta-1,4-mannanase, indicating that different mechanisms were involved in aggregation. In addition, XcMopB showed surface deformation, altered OMP composition, impaired xanthan production, increased sensitivity to stressful conditions including SDS, elevated temperature and changes in pH, reduced adhesion and motility and defects in pathogenesis. The finding that the major OMP is required for pathogenicity is unprecedented in phytopathogenic bacteria.

  3. Revisiting automated G-protein coupled receptor modeling: the benefit of additional template structures for a neurokinin-1 receptor model.

    PubMed

    Kneissl, Benny; Leonhardt, Bettina; Hildebrandt, Andreas; Tautermann, Christofer S

    2009-05-28

    The feasibility of automated procedures for the modeling of G-protein coupled receptors (GPCR) is investigated on the example of the human neurokinin-1 (NK1) receptor. We use a combined method of homology modeling and molecular docking and analyze the information content of the resulting docking complexes regarding the binding mode for further refinements. Moreover, we explore the impact of different template structures, the bovine rhodopsin structure, the human beta(2) adrenergic receptor, and in particular a combination of both templates to include backbone flexibility in the target conformational space. Our results for NK1 modeling demonstrate that model selection from a set of decoys can in general not solely rely on docking experiments but still requires additional mutagenesis data. However, an enrichment factor of 2.6 in a nearly fully automated approach indicates that reasonable models can be created automatically if both available templates are used for model construction. Thus, the recently resolved GPCR structures open new ways to improve the model building fundamentally.

  4. Effect of low molecular weight additives on immobilization strength, activity, and conformation of protein immobilized on PVC and UHMWPE.

    PubMed

    Kondyurin, Alexey; Nosworthy, Neil J; Bilek, Marcela M M

    2011-05-17

    Horseradish peroxidase (HRP) was immobilized onto both plasticized and unplasticized polyvinylchloride (PVC) and ultrahigh molecular weight polyethylene (UHMWPE). Plasma immersion ion implantation (PIII) in a nitrogen plasma with 20 kV bias was used to facilitate covalent immobilization and to improve the wettability of the surfaces. The surfaces and immobilized protein were studied using attenuated total reflection infrared (ATR-IR) spectroscopy and water contact angle measurements. Protein elution on exposure to repeated sodium dodecyl sulfate (SDS) washing was used to assess the strength of HRP immobilization. The presence of low molecular weight components (plasticizer, additives in solvent, unreacted monomers, adsorbed molecules on surface) was found to have a major influence on the strength of immobilization and the conformation of the protein on the samples not exposed to the PIII treatment. A phenomenological model considering interactions between the low molecular weight components, the protein molecule, and the surface is developed to explain these observations.

  5. Petrographic and Geochemical Characterization of Ore-Bearing Intrusions of the Noril'sk type, Siberia; With Discussion of Their Origin, Including Additional Datasets and Core Logs

    USGS Publications Warehouse

    Czamanske, Gerald K.

    2002-01-01

    The Noril'sk I, Talnakh, and Kharaelakh intrusions of the Noril'sk district host one of the outstanding metal concentrations in the world; contained Cu-Ni resources are comparable to the deposits at Sudbury, Ontario and the platinum group element (PGE) resource is second only to that of the Bushveld Complex. Our opportunity to cooperatively sample and study this district in Siberian Russia arose in 1990 through a memorandum of understanding between the U.S. Geological Survey and the former Ministry of Geology of the U.S.S.R. The world-class significance of these deposits and the possibility that understanding their geologic context, including construction of a credible 'ore-deposit model,' will lead to discovery of similar deposits elsewhere, inspired extensive studies of the ores, the mafic-intrusions which host them, and associated flood basalts.

  6. Addition of Amino Acids to Further Stabilize Lyophilized Sucrose-Based Protein Formulations: I. Screening of 15 Amino Acids in Two Model Proteins.

    PubMed

    Forney-Stevens, Kelly M; Bogner, Robin H; Pikal, Michael J

    2016-02-01

    In small amounts, the low molecular weight excipients-sorbitol and glycerol-have been shown to stabilize lyophilized sucrose-based protein formulations. The purpose of this study was to explore the use of amino acids as low molecular weight excipients to similarly enhance stability. Model proteins, recombinant human serum albumin and α-chymotrypsin, were formulated with sucrose in combination with one of 15 amino acid additives. Each formulation was lyophilized at 1:1:0.3 (w/w) protein-sucrose-amino acid. Percent total soluble aggregate was measured by size-exclusion chromatography before and after storage at 50 °C for 2 months. Classical thought might suggest that the addition of the amino acids to the sucrose-protein formulations would be destabilizing because of a decrease in the system's glass transition temperature. However, significant improvement in storage stability was observed for almost all formulations at the ratio of amino acid used. Weak correlations were found between the extent of stabilization and both amino acid molar volume and side-chain charge. The addition of amino acids at a modest level generally improves storage stability, often by more than a 50% increase, for lyophilized sucrose-based protein formulations.

  7. Uranium hydrogeochemical and stream sediment reconnaissance of the Dalhart NTMS quadrangle, New Mexico/Texas/Oklahoma, including concentrations of forty-two additional elements

    SciTech Connect

    Morgan, T.L.

    1980-08-01

    Totals of 1583 water samples and 503 sediment samples were collected from 2028 locations within the 20 000-km/sup 2/ area of the quadrangle at an average density of one location per 9.86 km/sup 2/. Water samples were collected from wells, springs, and streams and were analyzed for uranium. Sediment samples were collected from streams and springs and were analyzed for uranium, thorium, and 41 additional elements. All field and analytical data are listed in the appendixes of this report. Discussion is limited to anomalous samples, which are considered to be those containing over 20 ppB uranium for waters and over 5 ppM uranium for sediments. Uranium concentrations in water samples range from below the detection limit of 0.2 ppB to 1457.65 ppB and average 7.41 ppB. Most of the seventy anomalous water samples (4.4% of all water samples) are grouped spatially into five clusters or areas of interest. Samples in three of the clusters were collected along the north edge of the quadrangle where Mesozoic strata are exposed. The other two clusters are from the central and southern portions where the Quaternary Ogallala formation is exposed. Sediment samples from the quadrangle have uranium concentrations that range from 0.90 ppM to 27.20 ppM and average 3.27 ppM. Fourteen samples (2.8% of all sediment samples) contain over 5 ppM uranium and are considered anomalous. The five samples with the highest concentrations occur where downcutting streams expose Cretaceous units beneath the Quaternary surficial deposits. The remaining anomalous sediment samples were collected from scattered locations and do not indicate any single formation or unit as a potential source for the anomalous concentrations.

  8. Uranium hydrogeochemical and stream sediment reconnaissance data release for the Elk City NTMS Quadrangle, Idaho/Montana, including concentrations of forty-five additional elements

    SciTech Connect

    Broxton, D.E.; Beyth, M.

    1980-07-01

    Totals of 1580 water and 1720 sediment samples were collected from 1754 locations in the quadrangle. Elemental concentration, field measurement, weather, geologic, and geographic data for each sample location are listed for waters in Appendix I-A and for sediments in Appendix I-B. Uranium/thorium ratios for sediment samples are also included in Appendix I-B. All elemental analyses were performed at the LASL. Water samples were initially analyzed for uranium by fluorometry. All water samples containing more than 40 parts per billion (ppB) uranium were reanalyzed by delayed-neutron counting (DNC). A supplemental report containing the multielement analyses of water samples will be open filed in the near future. Sediments were analyzed for uranium and thorium as well as aluminum, antimony, arsenic, barium, beryllium, bismuth, cadmium, calcium, cerium, cesium, chlorine, chromium, cobalt, copper, dysprosium, europium, gold, hafnium, iron, lanthanum, lead, lithium, lutetium, magnesium, manganese, nickel, niobium, potassium, rubidium, samarium, selenium, scandium, silver, sodium, strontium, tantalum, terbium, tin, titanium, tungsten, vanadium, ytterbium, zinc, and zirconium. Basic statistics for 40 of these elements are presented. All sediments were analyzed for uranium by delayed-neutron counting. Other elemental concentrations in sediments were determined by neutron-activation analysis for 30 elements, by x-ray fluorescence for 12 elements, and by arc-source emission spectrography for 2 elements. Analytical results for sediments are reported as parts per million.

  9. Effective covalent immobilization of quinone and aptamer onto a gold electrode via thiol addition for sensitive and selective protein biosensing.

    PubMed

    Su, Zhaohong; Xu, Haitao; Xu, Xiaolin; Zhang, Yi; Ma, Yan; Li, Chaorong; Xie, Qingji

    2017-03-01

    Effective covalent immobilization of quinone and aptamer onto a gold electrode via thiol addition (a Michael addition) for sensitive and selective protein (with thrombin as the model) biosensing is reported, with a detection limit down to 20 fM for thrombin. Briefly, the thiol addition reaction of a gold electrode-supported 1,6-hexanedithiol (HDT) with p-benzoquinone (BQ) yielded BQ-HDT/Au, and the similar reaction of thiolated thrombin aptamer (TTA) with activated BQ-HDT/Au under 0.3V led to formation of a gold electrode-supported novel electrochemical probe TTA-BQ-HDT/Au. The thus-prepared TTA-BQ-HDT/Au exhibits a pair of well-defined redox peaks of quinone moiety, and the TTA-thrombin interaction can sensitively decrease the electrochemical signal. Herein the thiol addition acts as an effective and convenient binding protocols for aptasensing, and a new method (electrochemical conversion of Michael addition complex for signal generation) for the fabrication of biosensor is presented. The cyclic voltammetry (CV) was used to characterize the film properties. In addition, the proposed amperometric aptasensor exhibits good sensitivity, selectivity, and reproducibility. The aptasensor also has acceptable recovery for detection in complex protein sample.

  10. Uranium hydrogeochemical and stream sediment reconnaissance data release for the Lewistown NTMS Quadrangle, Montana, including concentrations of forty-two additional elements

    SciTech Connect

    Shannon, S.S. Jr.

    1980-08-01

    Totals of 758 water and 1170 sediment samples were collected from 1649 locations in the Levistown quadrangle. Water samples were collected at streams, springs, wells, ponds, and marshes; sediment samples were obtained from streams, springs, and ponds. Histograms and statistical data for uranium concentrations in water and sediment samples and thorium concentrations in sediment samples are given. All samples were collected at the nominal reconnaissance density of one sample location per 10 km/sup 2/. Elemental concentration, field measurement, weather, geologic, and geographic data for each sample location are listed for waters and for sediments. Uranium to thorium (U/Th) ratios for sediment samples are included. Water samples were initially analyzed for uranium by fluorometry. All water samples containing more than 40 ppB U were reanalyzed by delayed-neutron counting. Sediments were analyzed for U and Th as well as Al, Sb, Ba, Be, Bi, Cd, Ca, Ce, Cs, Cl, Cr, Co, Cu, Dy, Eu, Au, Hf, Fe, La, Pb, Li, Lu, Mg, Mn, Ni, Nb, K, Rb, Sa, Sc, Ag, Na, Sr, Ta, Tb, Sn, Ti, W, V, Yb, and Zn. All sediments were analyzed for U by delayed neutron counting. Other elemental concentrations in sediments were determined by neutron activation analysis for 31 elements, by x-ray fluorescence for 9 elements, and by arc-source emission spectrography for 2 elements. Analytical results are reported as parts per million. Descriptions of procedures used for analysis of water and sediments samples as well as analytical precisions and detection limits are given.

  11. [Effect of the addition of soy flour and whey protein concentrate on bread quality and mineral dialyzability].

    PubMed

    Visentín, Alexis N; Drago, Silvina R; Osella, Carlos A; de la Torre, María A; Sánchez, Hugo D; González, Rolando J

    2009-09-01

    The effects of the addition of soy flour and whey protein concentrate (WPC) on dough properties and mold bread quality were studied. Farinograph and alveograph were used to evaluate dough properties. Mold bread quality was evaluated by assessing sensory attributes using a trained panel and analyzing some nutritional characteristics, such as: protein chemical score, available lysine, and potential availability of fortified iron and also of the intrinsic calcium and zinc. Addition of soy flour and WPC caused significant changes on dough properties. Chemical score of bread was increased from 40.2 to 41.4 when 6% WPC was used, from 40.2 to 52.2 when 6% soy flour was added and up to 60.0 when substitution was made with 6% WPC plus 6% soy flour. This last improvement was obtained without impairing sensory attributes. The highest value of available lysine loss during baking, corresponded to the blend containing WPC, but it was reduced when WPC was used together with soy flour. WPC addition increased calcium content but reduced potential availability of iron and zinc. This negative effect on iron availability was overcome by adding mineral absorption promoters, being EDTA the most effective. On the other hand addition of 6% soy flour improved protein value without affecting mineral availability.

  12. Identification of drug-binding sites on human serum albumin using affinity capillary electrophoresis and chemically modified proteins as buffer additives.

    PubMed

    Kim, Hee Seung; Austin, John; Hage, David S

    2002-03-01

    A technique based on affinity capillary electrophoresis (ACE) and chemically modified proteins was used to screen the binding sites of various drugs on human serum albumin (HSA). This involved using HSA as a buffer additive, following the site-selective modification of this protein at two residues (tryptophan 214 or tyrosine 411) located in its major binding regions. The migration times of four compounds (warfarin, ibuprofen, suprofen and flurbiprofen) were measured in the presence of normal or modified HSA. These times were then compared and the mobility shifts observed with the modified proteins were used to identify the binding regions of each injected solute on HSA. Items considered in optimizing this assay included the concentration of protein placed into the running buffer, the reagents used to modify HSA, and the use of dextran as a secondary additive to adjust protein mobility. The results of this method showed good agreement with those of previous reports. The advantages and disadvantages of this approach are examined, as well as its possible extension to other solutes.

  13. Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production

    PubMed Central

    Tufail, Soban; Ismat, Fouzia; Imran, Muhammad; Iqbal, Mazhar; Mirza, Osman; Rhaman, Moazur

    2016-01-01

    Proteases are widely used to remove affinity and solubility tags from recombinant proteins to avoid potential interference of these tags with the structure and function of the fusion partner. In recent years, great interest has been seen in use of the human rhinovirus 3C protease owing to its stringent sequence specificity and enhanced activity. Like other proteases, activity of the human rhinovirus 3C protease can be affected in part by the buffer components and additives that are generally employed for purification and stabilization of proteins, hence, necessitate their removal by tedious and time-consuming procedures before proteolysis can occur. To address this issue, we examined the effect of elution buffers used for common affinity based purifications, salt ions, stability/solubility and reducing agents, and detergents on the activity of the human rhinovirus 3C protease using three different fusion proteins at 4°C, a temperature of choice for purification of many proteins. The results show that the human rhinovirus 3C protease performs better at 4°C than the frequently used tobacco etch virus protease and its activity was insensitive to most of the experimental conditions tested. Though number of fusion proteins tested is limited, we expect that these finding will facilitate the use of the human rhinovirus 3C protease in recombinant protein production for pharmaceutical and biotechnological applications. PMID:27093053

  14. Activity of the Human Rhinovirus 3C Protease Studied in Various Buffers, Additives and Detergents Solutions for Recombinant Protein Production.

    PubMed

    Ullah, Raheem; Shah, Majid Ali; Tufail, Soban; Ismat, Fouzia; Imran, Muhammad; Iqbal, Mazhar; Mirza, Osman; Rhaman, Moazur

    2016-01-01

    Proteases are widely used to remove affinity and solubility tags from recombinant proteins to avoid potential interference of these tags with the structure and function of the fusion partner. In recent years, great interest has been seen in use of the human rhinovirus 3C protease owing to its stringent sequence specificity and enhanced activity. Like other proteases, activity of the human rhinovirus 3C protease can be affected in part by the buffer components and additives that are generally employed for purification and stabilization of proteins, hence, necessitate their removal by tedious and time-consuming procedures before proteolysis can occur. To address this issue, we examined the effect of elution buffers used for common affinity based purifications, salt ions, stability/solubility and reducing agents, and detergents on the activity of the human rhinovirus 3C protease using three different fusion proteins at 4°C, a temperature of choice for purification of many proteins. The results show that the human rhinovirus 3C protease performs better at 4°C than the frequently used tobacco etch virus protease and its activity was insensitive to most of the experimental conditions tested. Though number of fusion proteins tested is limited, we expect that these finding will facilitate the use of the human rhinovirus 3C protease in recombinant protein production for pharmaceutical and biotechnological applications.

  15. Robotic large-scale application of wheat cell-free translation to structural studies including membrane proteins

    PubMed Central

    Beebe, Emily T.; Makino, Shin-ichi; Nozawa, Akira; Matsubara, Yuko; Frederick, Ronnie O.; Primm, John G.; Goren, Michael A.; Fox, Brian G.

    2010-01-01

    The use of the Protemist XE, an automated discontinuous-batch protein synthesis robot, in cell-free translation is reported. The soluble Galdieria sulphuraria protein DCN1 was obtained in greater than 2 mg total synthesis yield per mL of reaction mixture from the Protemist XE, and the structure was subsequently solved by X-ray crystallography using material from one 10 mL synthesis (PDB ID: 3KEV). The Protemist XE was also capable of membrane protein translation. Thus human sigma-1 receptor was translated in the presence of unilamellar liposomes and bacteriorhodopsin was translated directly into detergent micelles in the presence of all-trans-retinal. The versatility, ease of use, and compact size of the Protemist XE robot demonstrate its suitability for large-scale synthesis of many classes of proteins. PMID:20637905

  16. Do we see what we should see? Describing non-covalent interactions in protein structures including precision

    PubMed Central

    Gurusaran, Manickam; Shankar, Mani; Nagarajan, Raju; Helliwell, John R.; Sekar, Kanagaraj

    2014-01-01

    The power of X-ray crystal structure analysis as a technique is to ‘see where the atoms are’. The results are extensively used by a wide variety of research communities. However, this ‘seeing where the atoms are’ can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software. PMID:25075321

  17. Do we see what we should see? Describing non-covalent interactions in protein structures including precision.

    PubMed

    Gurusaran, Manickam; Shankar, Mani; Nagarajan, Raju; Helliwell, John R; Sekar, Kanagaraj

    2014-01-01

    The power of X-ray crystal structure analysis as a technique is to 'see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this 'seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and α-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

  18. Impact of bentonite additions during vinification on protein stability and volatile compounds of Albariño wines.

    PubMed

    Lira, Eugenio; Rodríguez-Bencomo, Juan José; Salazar, Fernando N; Orriols, Ignacio; Fornos, Daniel; López, Francisco

    2015-03-25

    Today, bentonite continues to be one of the most used products to remove proteins in white wines in order to avoid their precipitation in bottles. However, excessive use of bentonite has negative effects on the aroma of final wine, so the optimization of the dose and the time of its application are important for winemakers. This paper analyzes how applying an equal dose of bentonite at different stages (must clarification; beginning, middle, and end of fermentation) affects the macromolecular profile, protein stability, physical-chemical characteristics and aromatic profile of the wine obtained. The results showed the addition during fermentation (especially in the middle and at the end) reduced the total dose required for protein stabilization of Albariño wines and maintained the sensory characteristics of this variety.

  19. Functional characterization of Escherichia coli GlpG and additional rhomboid proteins using an aarA mutant of Providencia stuartii.

    PubMed

    Clemmer, Katy M; Sturgill, Gwen M; Veenstra, Alexander; Rather, Philip N

    2006-05-01

    The Providencia stuartii AarA protein is a member of the rhomboid family of intramembrane serine proteases and required for the production of an extracellular signaling molecule that regulates cellular functions including peptidoglycan acetylation, methionine transport, and cysteine biosynthesis. Additional aarA-dependent phenotypes include (i) loss of an extracellular yellow pigment, (ii) inability to grow on MacConkey agar, and (iii) abnormal cell division. Since these phenotypes are easily assayed, the P. stuartii aarA mutant serves as a useful host system to investigate rhomboid function. The Escherichia coli GlpG protein was shown to be functionally similar to AarA and rescued the above aarA-dependent phenotypes in P. stuartii. GlpG proteins containing single alanine substitutions at the highly conserved catalytic triad of asparagine (N154A), serine (S201A), or histidine (H254A) residues were nonfunctional. The P. stuartii aarA mutant was also used as a biosensor to demonstrate that proteins from a variety of diverse sources exhibited rhomboid activity. In an effort to further investigate the role of a rhomboid protein in cell physiology, a glpG mutant of E. coli was constructed. In phenotype microarray experiments, the glpG mutant exhibited a slight increase in resistance to the beta-lactam antibiotic cefotaxime.

  20. Effect of antibiotic, Lacto-lase and probiotic addition in chicken feed on protein and fat content of chicken meat

    NASA Astrophysics Data System (ADS)

    Azhar, Noor Amiza; Abdullah, Aminah

    2015-09-01

    This research was conducted to investigate the effect of chicken feed additives (antibiotic, Lacto-lase® and probiotic) on protein and fat content of chicken meat. Chicken fed with control diet (corn-soy based diet) served as a control. The treated diets were added with zinc bacitracin (antibiotic), different amount of Lacto-lase® (a mixture of probiotic and enzyme) and probiotic. Chicken were slaughtered at the age of 43-48 days. Each chicken was divided into thigh, breast, drumstick, drumette and wing. Protein content in chicken meat was determined by using macro-Kjeldahl method meanwhile Soxhlet method was used to analyse fat content. The result of the study showed that the protein content of chicken breast was significantly higher (p≤0.05) while thigh had the lowest protein content (p≤0.05). Antibiotic fed chicken was found to have the highest protein content among the treated chickens but there was no significant different with 2g/kg Lacto-lase® fed chicken (p>0.05). All thighs were significantly higher (p≤0.05) in fat content except for drumette of control chicken while breast contained the lowest fat content compared to other chicken parts studied. The control chicken meat contained significantly higher (p≤0.05) amount of fat compared to the other treated chickens. Chicken fed with 2g/kg Lacto-lase® had the lowest (p≤0.05) fat content. The result of this study indicated that the addition of Lacto-lase® as a replacement of antibiotic in chicken feed will not affect the content of protein and fat of chicken meat.

  1. Protein interaction module-assisted function X (PIMAX) approach to producing challenging proteins including hyperphosphorylated tau and active CDK5/p25 kinase complex.

    PubMed

    Sui, Dexin; Xu, Xinjing; Ye, Xuemei; Liu, Mengyu; Mianecki, Maxwell; Rattanasinchai, Chotirat; Buehl, Christopher; Deng, Xiexiong; Kuo, Min-Hao

    2015-01-01

    Many biomedically critical proteins are underrepresented in proteomics and biochemical studies because of the difficulty of their production in Escherichia coli. These proteins might possess posttranslational modifications vital to their functions, tend to misfold and be partitioned into bacterial inclusion bodies, or act only in a stoichiometric dimeric complex. Successful production of these proteins requires efficient interaction between these proteins and a specific "facilitator," such as a protein-modifying enzyme, a molecular chaperone, or a natural physical partner within the dimeric complex. Here we report the design and application of a protein interaction module-assisted function X (PIMAX) system that effectively overcomes these hurdles. By fusing two proteins of interest to a pair of well-studied protein-protein interaction modules, we were able to potentiate the association of these two proteins, resulting in successful production of an enzymatically active cyclin-dependent kinase complex and hyperphosphorylated tau protein, which is intimately linked to Alzheimer disease. Furthermore, using tau isoforms quantitatively phosphorylated by GSK-3β and CDK5 kinases via PIMAX, we demonstrated the hyperphosphorylation-stimulated tau oligomerization in vitro, paving the way for new Alzheimer disease drug discoveries. Vectors for PIMAX can be easily modified to meet the needs of different applications. This approach thus provides a convenient and modular suite with broad implications for proteomics and biomedical research.

  2. Espin actin-cytoskeletal proteins are in rat type I spiral ganglion neurons and include splice-isoforms with a functional nuclear localization signal.

    PubMed

    Sekerková, Gabriella; Zheng, Lili; Mugnaini, Enrico; Bartles, James R

    2008-08-20

    The espins are Ca(2+)-resistant actin-bundling proteins that are enriched in hair cell stereocilia and sensory cell microvilli. Here, we report a novel localization of espins to a large proportion of rat type I spiral ganglion neurons (SGNs) and their projections to the cochlear nucleus (CN). Moreover, we show that a fraction of these espins is in the nucleus of SGNs owing to the presence of splice-isoforms that contain a functional nuclear localization signal (NLS). Espin antibody labeled approximately 83% of type I SGNs, and the labeling intensity increased dramatically during early postnatal development. Type II SGNs and vestibular ganglion neurons were unlabeled. In the CN, espin-positive auditory nerve fibers showed a projection pattern typical of type I SGNs, with intense labeling in the nerve root region and posteroventral CN (PVCN). The anteroventral CN (AVCN) showed moderate labeling, whereas the dorsal CN showed weak labeling that was restricted to the deep layer. Espin-positive synaptic terminals were enriched around nerve root neurons and octopus cells in the PVCN and were also found on globular bushy cells and multipolar neurons in the PVCN and AVCN. SGNs expressed multiple espin transcripts and proteins, including splice-isoforms that contain a nonapeptide, which is rich in positively charged amino acids and creates a bipartite NLS. The nonapeptide was necessary to target espin isoforms to the nucleus and was sufficient to target an unrelated protein to the nucleus when joined with the upstream di-arginine-containing octapeptide. The presence of cytoplasmic and nuclear espins in SGNs suggests additional roles for espins in auditory neuroscience.

  3. Yeast prion-protein, sup35, fibril formation proceeds by addition and substraction of oligomers.

    PubMed

    Narayanan, Saravanakumar; Walter, Stefan; Reif, Bernd

    2006-05-01

    In analogy to human prions, a domain of the translation-termination protein in Saccharomyces cerevisiae, Sup35, can switch its conformation from a soluble functional state, [psi-], to a conformation, [PSI+], that facilitates aggregation and impairs its native function. Overexpression of the molecular chaperone Hsp104 abolishes the [PSI+] phenotype and restores the normal function of Sup35. We have recently shown that Hsp104 interacts preferably with low oligomeric species of a Sup35 derived peptide, Sup35[5-26]; however, due to possible exchange between different oligomeric states, it was not possible to obtain information on the distribution and stability of the oligomeric state. We show here, that low-molecular-weight oligomers (Sup35[5-26])n (n approximately = 4-6) are indeed important for the fibril formation and disassembly process. We find that Hsp104 is able to disaggregate Sup35[5-26] fibrils by substraction of hexameric to decameric Sup35[5-26] oligomers. This disaggregation effect does not require assistance from other chaperones and is independent of ATP at high Hsp104 concentrations. Furthermore, we demonstrate that critical oligomers have a preference for alpha-helical conformations. The conformational reorganization into beta-sheet structures seems to occur only upon incorporation of these oligomers into fibrillar structures. The results are demonstrated by using an equilibrium dialysis experiment that employed different molecular-weight cut-off membranes. A combination of thioflavin-T (ThT) fluorescence and UV measurements allowed the quantification of fibril formation and the amount of peptide diffusing out of the dialysis bag. CD and NMR spectroscopy data were combined to obtain structural information.

  4. The heterogeneity of spermatogonia is revealed by their topology and expression of marker proteins including the germ cell-specific proteins Nanos2 and Nanos3.

    PubMed

    Suzuki, Hitomi; Sada, Aiko; Yoshida, Shosei; Saga, Yumiko

    2009-12-15

    Spermatogonial stem cells (SSCs) reside in undifferentiated type-A spermatogonia and contribute to continuous spermatogenesis by maintaining the balance between self-renewal and differentiation, thereby meeting the biological demand in the testis. Spermatogonia have to date been characterized principally through their morphology, but we herein report the detailed characterization of undifferentiated spermatogonia in mouse testes based on their gene expression profiles in combination with topological features. The detection of the germ cell-specific proteins Nanos2 and Nanos3 as markers of spermatogonia has enabled the clear dissection of complex populations of these cells as Nanos2 was recently shown to be involved in the maintenance of stem cells. Nanos2 is found to be almost exclusively expressed in A(s) to A(pr) cells, whereas Nanos3 is detectable in most undifferentiated spermatogonia (A(s) to A(al)) and differentiating A(1) spermatogonia. In our present study, we find that A(s) and A(pr) can be basically classified into three categories: (1) GFRalpha1(+)Nanos2(+)Nanos3(-)Ngn3(-), (2) GFRalpha1(+)Nanos2(+)Nanos3(+)Ngn3(-), and (3) GFRalpha1(-)Nanos2(+/-)Nanos3(+)Ngn3(+). We propose that the first of these groups is most likely to include the stem cell population and that Nanos3 may function in transit amplifying cells.

  5. Multiple phosphorylated forms of the Saccharomyces cerevisiae Mcm1 protein include an isoform induced in response to high salt concentrations.

    PubMed Central

    Kuo, M H; Nadeau, E T; Grayhack, E J

    1997-01-01

    The Saccharomyces cerevisiae Mcm1 protein is an essential multifunctional transcription factor which is highly homologous to human serum response factor. Mcm1 protein acts on a large number of distinctly regulated genes: haploid cell-type-specific genes, G2-cell-cycle-regulated genes, pheromone-induced genes, arginine metabolic genes, and genes important for cell wall and cell membrane function. We show here that Mcm1 protein is phosphorylated in vivo. Several (more than eight) isoforms of Mcm1 protein, resolved by isoelectric focusing, are present in vivo; two major phosphorylation sites lie in the N-terminal 17 amino acids immediately adjacent to the conserved MADS box DNA-binding domain. The implications of multiple species of Mcm1, particularly the notion that a unique Mcm1 isoform could be required for regulation of a specific set of Mcm1's target genes, are discussed. We also show here that Mcm1 plays an important role in the response to stress caused by NaCl. G. Yu, R. J. Deschenes, and J. S. Fassler (J. Biol. Chem. 270:8739-8743, 1995) showed that Mcm1 function is affected by mutations in the SLN1 gene, a signal transduction component implicated in the response to osmotic stress. We find that mcm1 mutations can confer either reduced or enhanced survival on high-salt medium; deletion of the N terminus or mutation in the primary phosphorylation site results in impaired growth on high-salt medium. Furthermore, Mcm1 protein is a target of a signal transduction system responsive to osmotic stress: a new isoform of Mcm1 is induced by NaCl or KCl; this result establishes that Mcm1 itself is regulated. PMID:9001236

  6. The impact of antioxidant addition on flavor of cheddar and mozzarella whey and cheddar whey protein concentrate.

    PubMed

    Liaw, I W; Eshpari, H; Tong, P S; Drake, M A

    2010-08-01

    Lipid oxidation products are primary contributors to whey ingredient off-flavors. The objectives of this study were to evaluate the impact of antioxidant addition in prevention of flavor deterioration of fluid whey and spray-dried whey protein. Cheddar and Mozzarella cheeses were manufactured in triplicate. Fresh whey was collected, pasteurized, and defatted by centrifugal separation. Subsequently, 0.05% (w/w) ascorbic acid or 0.5% (w/w) whey protein hydrolysate (WPH) were added to the pasteurized whey. A control with no antioxidant addition was also evaluated. Wheys were stored at 3 degrees C and evaluated after 0, 2, 4, 6, and 8 d. In a subsequent experiment, selected treatments were then incorporated into liquid Cheddar whey and processed into whey protein concentrate (WPC). Whey and WPC flavors were documented by descriptive sensory analysis, and volatile components were evaluated by solid phase micro-extraction with gas chromatography mass spectrometry. Cardboard flavors increased in fluid wheys with storage. Liquid wheys with ascorbic acid or WPH had lower cardboard flavor across storage compared to control whey. Lipid oxidation products, hexanal, heptanal, octanal, and nonanal increased in liquid whey during storage, but liquid whey with added ascorbic acid or WPH had lower concentrations of these products compared to untreated controls. Mozzarella liquid whey had lower flavor intensities than Cheddar whey initially and after refrigerated storage. WPC with added ascorbic acid or WPH had lower cardboard flavor and lower concentrations of pentanal, heptanal, and nonanal compared to control WPC. These results suggest that addition of an antioxidant to liquid whey prior to further processing may be beneficial to flavor of spray-dried whey protein. Practical Application: Lipid oxidation products are primary contributors to whey ingredient off-flavors. Flavor plays a critical and limiting role in widespread use of dried whey ingredients, and enhanced understanding

  7. Vitellogenin-RNAi and ovariectomy each increase lifespan, increase protein storage, and decrease feeding, but are not additive in grasshoppers.

    PubMed

    Tetlak, Alicia G; Burnett, Jacob B; Hahn, Daniel A; Hatle, John D

    2015-12-01

    Reduced reproduction has been shown to increase lifespan in many animals, yet the mechanisms behind this trade-off are unclear. We addressed this question by combining two distinct, direct means of life-extension via reduced reproduction, to test whether they were additive. In the lubber grasshopper, Romalea microptera, ovariectomized (OVX) individuals had a ~20% increase in lifespan and a doubling of storage relative to controls (Sham operated). Similarly, young female grasshoppers treated with RNAi against vitellogenin (the precursor to egg yolk protein) had increased fat body mass and halted ovarian growth. In this study, we compared VgRNAi to two control groups that do not reduce reproduction, namely buffer injection (Buffer) and injection with RNAi against a hexameric storage protein (Hex90RNAi). Each injection treatment was tested with and without ovariectomy. Hence, we tested feeding, storage, and lifespans in six groups: OVX and Buffer, OVX and Hex90RNAi, OVX and VgRNAi, Sham and Buffer, Sham and Hex90RNAi, and Sham and VgRNAi. Ovariectomized grasshoppers and VgRNAi grasshoppers each had similar reductions in feeding (~40%), increases in protein storage in the hemolymph (150-300%), and extensions in lifespan (13-21%). Ovariectomized grasshoppers had higher vitellogenin protein levels than did VgRNAi grasshoppers. Last but not least, when ovariectomy and VgRNAi were applied together, there was no greater effect on feeding, protein storage, or longevity. Hence, feeding regulation, and protein storage in insects, may be conserved components of life-extension via reduced reproduction.

  8. Addition of Surfactants and Non-Hydrolytic Proteins and Their Influence on Enzymatic Hydrolysis of Pretreated Sugarcane Bagasse.

    PubMed

    Méndez Arias, Johanna; de Oliveira Moraes, Anelize; Modesto, Luiz Felipe Amarante; de Castro, Aline Machado; Pereira, Nei

    2017-02-01

    Poly(ethylene glycol) (PEG 4000) and bovine serum albumin (BSA) were investigated with the purpose of evaluating their influence on enzymatic hydrolysis of sugarcane bagasse. Effects of these supplements were assayed for different enzymatic cocktails (Trichoderma harzianum and Penicillium funiculosum) that acted on lignocellulosic material submitted to different pretreatment methods with varying solid (25 and 100 g/L) and protein (7.5 and 20 mg/g cellulose) loadings. The highest levels of glucose release were achieved using partially delignified cellulignin as substrate, along with the T. harzianum cocktail: increases of 14 and 18 % for 25 g/L solid loadings and of 33 and 43 % for 100 g/L solid loadings were reached for BSA and PEG supplementation, respectively. Addition of these supplements could maintain hydrolysis yield even for higher solid loadings, but for higher enzymatic cocktail protein loadings, increases in glucose release were not observed. Results indicate that synergism might occur among these additives and cellulase and xylanases. The use of these supplements, besides depending on factors such as pretreatment method of sugarcane bagasse, enzymatic cocktails composition, and solid and protein loadings, may not always lead to positive effects on the hydrolysis of lignocellulosic material, making it necessary further statistical studies, according to process conditions.

  9. How cholesterol interacts with membrane proteins: an exploration of cholesterol-binding sites including CRAC, CARC, and tilted domains.

    PubMed

    Fantini, Jacques; Barrantes, Francisco J

    2013-01-01

    The plasma membrane of eukaryotic cells contains several types of lipids displaying high biochemical variability in both their apolar moiety (e.g., the acyl chain of glycerolipids) and their polar head (e.g., the sugar structure of glycosphingolipids). Among these lipids, cholesterol is unique because its biochemical variability is almost exclusively restricted to the oxidation of its polar -OH group. Although generally considered the most rigid membrane lipid, cholesterol can adopt a broad range of conformations due to the flexibility of its isooctyl chain linked to the polycyclic sterane backbone. Moreover, cholesterol is an asymmetric molecule displaying a planar α face and a rough β face. Overall, these structural features open up a number of possible interactions between cholesterol and membrane lipids and proteins, consistent with the prominent regulatory functions that this unique lipid exerts on membrane components. The aim of this review is to describe how cholesterol interacts with membrane lipids and proteins at the molecular/atomic scale, with special emphasis on transmembrane domains of proteins containing either the consensus cholesterol-binding motifs CRAC and CARC or a tilted peptide. Despite their broad structural diversity, all these domains bind cholesterol through common molecular mechanisms, leading to the identification of a subset of amino acid residues that are overrepresented in both linear and three-dimensional membrane cholesterol-binding sites.

  10. Lateral diffusion of peripheral membrane proteins on supported lipid bilayers is controlled by the additive frictional drags of (1) bound lipids and (2) protein domains penetrating into the bilayer hydrocarbon core.

    PubMed

    Ziemba, Brian P; Falke, Joseph J

    2013-01-01

    Peripheral membrane proteins bound to lipids on bilayer surfaces play central roles in a wide array of cellular processes, including many signaling pathways. These proteins diffuse in the plane of the bilayer and often undergo complex reactions involving the binding of regulatory and substrate lipids and proteins they encounter during their 2D diffusion. Some peripheral proteins, for example pleckstrin homology (PH) domains, dock to the bilayer in a relatively shallow position with little penetration into the bilayer. Other peripheral proteins exhibit more complex bilayer contacts, for example classical protein kinase C isoforms (PKCs) bind as many as six lipids in stepwise fashion, resulting in the penetration of three PKC domains (C1A, C1B, C2) into the bilayer headgroup and hydrocarbon regions. A molecular understanding of the molecular features that control the diffusion speeds of proteins bound to supported bilayers would enable key molecular information to be extracted from experimental diffusion constants, revealing protein-lipid and protein-bilayer interactions difficult to study by other methods. The present study investigates a range of 11 different peripheral protein constructs comprised by 1-3 distinct domains (PH, C1A, C1B, C2, anti-lipid antibody). By combining these constructs with various combinations of target lipids, the study measures 2D diffusion constants on supported bilayers for 17 different protein-lipid complexes. The resulting experimental diffusion constants, together with the known membrane interaction parameters of each complex, are used to analyze the molecular features correlated with diffusional slowing and bilayer friction. The findings show that both (1) individual bound lipids and (2) individual protein domains that penetrate into the hydrocarbon core make additive contributions to the friction against the bilayer, thereby defining the 2D diffusion constant. An empirical formula is developed that accurately estimates the diffusion

  11. The cellular proteins which can associate specifically with polyomavirus middle T antigen in human 293 cells include the major human 70-kilodalton heat shock proteins.

    PubMed

    Pallas, D C; Morgan, W; Roberts, T M

    1989-11-01

    We compared the proteins which associate with middle T antigen (MT) of polyomavirus in human cells infected with Ad5(pymT), a recombinant adenovirus which directs the overexpression of MT, with the MT-associated proteins (MTAPs) previously identified in murine fibroblasts expressing MT. MTAPs of 27, 29, 36, and 63 kilodaltons (kDa) appeared to be fairly well conserved between the two species, as judged by comigration on two-dimensional gels. Several 61-kDa MTAP species detected in MT immunoprecipitates from both cell sources also comigrated on these gels. However, no protein comigrating precisely with the murine 85-kDa MTAP could be detected in the human cells. Furthermore, two proteins of 72 and 74 kDa associated with wild-type MT in the infected human cells but not in murine fibroblasts expressing MT. It had been previously reported for murine cells that the 70-kDa heat shock protein associates with a particular mutant MT but not with wild-type MT (G. Walter, A. Carbone, and W.J. Welch, J. Virol. 61:405-410, 1987). By the criteria of comigration on two-dimensional gels, tryptic peptide mapping, and immunoblotting, we showed that the 72- and 74-kDa proteins that associate with wild-type MT in human cells are the major human 70-kDa heat shock proteins.

  12. The addition of whey protein to a carbohydrate-electrolyte drink does not influence post-exercise rehydration.

    PubMed

    Hobson, Ruth; James, Lewis

    2015-01-01

    The addition of whey protein to a carbohydrate-electrolyte drink has been shown to enhance post-exercise rehydration when a volume below that recommended for full fluid balance restoration is provided. We investigated if this held true when volumes sufficient to restore fluid balance were consumed and if differences might be explained by changes in plasma albumin content. Sixteen participants lost ~1.9% of their pre-exercise body mass by cycling in the heat and rehydrated with 150% of body mass lost with either a 60 g · L(-1) carbohydrate drink (CHO) or a 60 g · L(-1) carbohydrate, 20 g · L(-1) whey protein isolate drink (CHO-P). Urine and blood samples were collected pre-exercise, post-exercise, post-rehydration and every hour for 4 h post-rehydration. There was no difference between trials for total urine production (CHO 1057 ± 319 mL; CHO-P 970 ± 334 mL; P = 0.209), drink retention (CHO 51 ± 12%; CHO-P 55 ± 15%; P = 0.195) or net fluid balance (CHO -393 ± 272 mL; CHO-P -307 ± 331 mL; P = 0.284). Plasma albumin content relative to pre-exercise was increased from 2 to 4 h during CHO-P only. These results demonstrate that the addition of whey protein isolate to a carbohydrate-electrolyte drink neither enhances nor inhibits rehydration. Therefore, where post-exercise protein ingestion might benefit recovery, this can be consumed without effecting rehydration.

  13. Cholesteryl ester loading of mouse peritoneal macrophages is associated with changes in the expression or modification of specific cellular proteins, including increase in an alpha-enolase isoform.

    PubMed

    Bottalico, L A; Kendrick, N C; Keller, A; Li, Y; Tabas, I

    1993-02-01

    This report explores the hypothesis that massive cholesteryl ester (CE) accumulation in macrophages, such as that occurring in atheroma foam cells, results in changes in the expression or modification of specific cellular proteins. Two-dimensional (2-D) gel electrophoretic patterns of metabolically labeled cellular proteins from mouse peritoneal macrophages that were loaded with CE (through incubation with acetylated low density lipoprotein [acetyl-LDL] for 4 days) were compared with those of control macrophages. Densitometric analysis of 2-D gel autoradiograms from the cell lysates revealed statistically significant changes in seven cellular proteins (five decreases and two increases). The changes in protein expression (foam cell versus control) ranged from a 458 +/- 164% (p < 0.001) increase to a 35 +/- 34% (p < 0.001) decrease (n = 11). Incubation of macrophages with beta-very low density lipoprotein, which also increased the CE content of macrophages (albeit to a lesser extent than acetyl-LDL), resulted in changes in five of the seven proteins. In contrast, incubation of cells with LDL, fucoidan, or latex beads, none of which caused CE accumulation, did not lead to significant changes in four of these five proteins. One of these four proteins, which increased fourfold to fivefold in foam cells (M(r) = 49,000; isoelectric point of 6.8), was purified by preparative 2-D gel electrophoresis. Internal amino acid sequence of cyanogen bromide fragments of this protein as well as Western blot analysis identified this protein as an isoform of alpha-enolase. The increased expression of this alpha-enolase isoform, which was seen as early as day 2 of acetyl-LDL incubation of the macrophages, was diminished by including an inhibitor of cholesterol esterification during the acetyl-LDL incubation period. In conclusion, macrophage foam cell formation is associated with distinct changes in protein expression, including a marked increase in an isoform of alpha

  14. Influence of boron addition to Ti-13Zr-13Nb alloy on MG63 osteoblast cell viability and protein adsorption.

    PubMed

    Majumdar, P; Singh, S B; Dhara, S; Chakraborty, M

    2015-01-01

    Cell proliferation, cell morphology and protein adsorption on near β-type Ti-13Zr-13Nb (TZN) alloy and Ti-13Zr-13Nb-0.5B (TZNB) composite have been investigated and compared to evaluate the effect of boron addition which has been added to the Ti alloy to improve their poor tribological properties by forming in situ TiB precipitates. MG63 cell proliferation on substrates with different chemistry but the same topography was compared. The MTT assay test showed that the cell viability on the TZN alloy was higher than the boron containing TZNB composite after 36 h of incubation and the difference was pronounced after 7 days. However, both the materials showed substantially higher cell attachment than the control (polystyrene). For the same period of incubation in fetal bovine serum (FBS), the amount of protein adsorbed on the surface of boron free TZN samples was higher than that in the case of boron containing TZNB composite. The presence of boron in the TZN alloy influenced protein adsorption and cell response and they are lower in TZNB than in TZN as a result of the associated difference in chemical characteristics.

  15. Proteome profiles of HDL particles of patients with chronic heart failure are associated with immune response and also include bacteria proteins.

    PubMed

    Oberbach, Andreas; Adams, Volker; Schlichting, Nadine; Heinrich, Marco; Kullnick, Yvonne; Lehmann, Stefanie; Lehmann, Sven; Feder, Stefan; Correia, Joao Carlos; Mohr, Friedrich-Wilhelm; Völker, Uwe; Jehmlich, Nico

    2016-01-30

    Besides modulation of reverse cholesterol transport, high density lipoprotein (HDL) is able to modulate vascular function by stimulating endothelial nitric oxide synthase. Recently, it could be documented that this function of HDL was significantly impaired in patients with chronic heart failure (CHF). We investigated alterations in the HDL proteome in CHF patients. Therefore, HDL was isolated from 5 controls (HDLhealthy) and 5 CHF patients of NYHA-class IIIb (HDLCHF). Proteome analysis of HDL particles was performed by two-dimensional liquid chromatography-mass spectrometry (SCX/RP LC-MS/MS). In total, we identified 494 distinct proteins, of which 107 proteins were commonly found in both groups (HDLCHF and HDLhealthy) indicating a high inter-subject variability across HDL particles. Several important proteins (e.g. ITGA2, APBA1 or A2M) varied in level. Functional analysis revealed regulated pathways. A minor proportion of bacteria-derived proteins were also identified in the HDL-particles. The extension of the list of HDL-associated proteins allows besides their mere description new insights into alterations in HDL function in diseases. In addition, the detection of bacterial proteins bound to HDL will broaden our view of HDL not only as a cholesterol carrier but also as a carrier of proteins.

  16. Template-dependent nucleotide addition in the reverse (3′-5′) direction by Thg1-like protein

    PubMed Central

    Kimura, Shoko; Suzuki, Tateki; Chen, Meirong; Kato, Koji; Yu, Jian; Nakamura, Akiyoshi; Tanaka, Isao; Yao, Min

    2016-01-01

    Thg1-like protein (TLP) catalyzes the addition of a nucleotide to the 5′-end of truncated transfer RNA (tRNA) species in a Watson-Crick template–dependent manner. The reaction proceeds in two steps: the activation of the 5′-end by adenosine 5′-triphosphate (ATP)/guanosine 5′-triphosphate (GTP), followed by nucleotide addition. Structural analyses of the TLP and its reaction intermediates have revealed the atomic detail of the template-dependent elongation reaction in the 3′-5′ direction. The enzyme creates two substrate binding sites for the first- and second-step reactions in the vicinity of one reaction center consisting of two Mg2+ ions, and the two reactions are executed at the same reaction center in a stepwise fashion. When the incoming nucleotide is bound to the second binding site with Watson-Crick hydrogen bonds, the 3′-OH of the incoming nucleotide and the 5′-triphosphate of the tRNA are moved to the reaction center where the first reaction has occurred. That the 3′-5′ elongation enzyme performs this elaborate two-step reaction in one catalytic center suggests that these two reactions have been inseparable throughout the process of protein evolution. Although TLP and Thg1 have similar tetrameric organization, the tRNA binding mode of TLP is different from that of Thg1, a tRNAHis-specific G−1 addition enzyme. Each tRNAHis binds to three of the four Thg1 tetramer subunits, whereas in TLP, tRNA only binds to a dimer interface and the elongation reaction is terminated by measuring the accepter stem length through the flexible β-hairpin. Furthermore, mutational analyses show that tRNAHis is bound to TLP in a similar manner as Thg1, thus indicating that TLP has a dual binding mode. PMID:27051866

  17. The TAL effector PthA4 interacts with nuclear factors involved in RNA-dependent processes including a HMG protein that selectively binds poly(U) RNA.

    PubMed

    de Souza, Tiago Antonio; Soprano, Adriana Santos; de Lira, Nayara Patricia Vieira; Quaresma, Alexandre José Christino; Pauletti, Bianca Alves; Paes Leme, Adriana Franco; Benedetti, Celso Eduardo

    2012-01-01

    Plant pathogenic bacteria utilize an array of effector proteins to cause disease. Among them, transcriptional activator-like (TAL) effectors are unusual in the sense that they modulate transcription in the host. Although target genes and DNA specificity of TAL effectors have been elucidated, how TAL proteins control host transcription is poorly understood. Previously, we showed that the Xanthomonas citri TAL effectors, PthAs 2 and 3, preferentially targeted a citrus protein complex associated with transcription control and DNA repair. To extend our knowledge on the mode of action of PthAs, we have identified new protein targets of the PthA4 variant, required to elicit canker on citrus. Here we show that all the PthA4-interacting proteins are DNA and/or RNA-binding factors implicated in chromatin remodeling and repair, gene regulation and mRNA stabilization/modification. The majority of these proteins, including a structural maintenance of chromosomes protein (CsSMC), a translin-associated factor X (CsTRAX), a VirE2-interacting protein (CsVIP2), a high mobility group (CsHMG) and two poly(A)-binding proteins (CsPABP1 and 2), interacted with each other, suggesting that they assemble into a multiprotein complex. CsHMG was shown to bind DNA and to interact with the invariable leucine-rich repeat region of PthAs. Surprisingly, both CsHMG and PthA4 interacted with PABP1 and 2 and showed selective binding to poly(U) RNA, a property that is novel among HMGs and TAL effectors. Given that homologs of CsHMG, CsPABP1, CsPABP2, CsSMC and CsTRAX in other organisms assemble into protein complexes to regulate mRNA stability and translation, we suggest a novel role of TAL effectors in mRNA processing and translational control.

  18. A common set of conserved motifs in a vast variety of putative nucleic acid-dependent ATPases including MCM proteins involved in the initiation of eukaryotic DNA replication.

    PubMed Central

    Koonin, E V

    1993-01-01

    A new superfamily of (putative) DNA-dependent ATPases is described that includes the ATPase domains of prokaryotic NtrC-related transcription regulators, MCM proteins involved in the initiation of eukaryotic DNA replication, and a group of uncharacterized bacterial and chloroplast proteins. MCM proteins are shown to contain a modified form of the ATP-binding motif and are predicted to mediate ATP-dependent opening of double-stranded DNA in the replication origins. In a second line of investigation, it is demonstrated that the products of unidentified open reading frames from Marchantia mitochondria and from yeast, and a domain of a baculovirus protein involved in viral DNA replication are related to the superfamily III of DNA and RNA helicases that previously has been known to include only proteins of small viruses. Comparison of the multiple alignments showed that the proteins of the NtrC superfamily and the helicases of superfamily III share three related sequence motifs tightly packed in the ATPase domain that consists of 100-150 amino acid residues. A similar array of conserved motifs is found in the family of DnaA-related ATPases. It is hypothesized that the three large groups of nucleic acid-dependent ATPases have similar structure of the core ATPase domain and have evolved from a common ancestor. PMID:8332451

  19. Experimental Validation of Multi-Epitope Peptides Including Promising MHC Class I- and II-Restricted Epitopes of Four Known Leishmania infantum Proteins.

    PubMed

    Agallou, Maria; Athanasiou, Evita; Koutsoni, Olga; Dotsika, Eleni; Karagouni, Evdokia

    2014-01-01

    Leishmaniasis is a significant worldwide health problem for which no vaccine exists. Activation of CD4(+) and CD8(+) T cells is crucial for the generation of protective immunity against parasite. Recent trend in vaccine design has been shifted to epitope-based vaccines that are more specific, safe, and easy to produce. In the present study, four known antigenic Leishmania infantum proteins, cysteine peptidase A (CPA), histone H1, KMP-11, and Leishmania eukaryotic initiation factor (LeIF) were analyzed for the prediction of binding epitopes to H2(d) MHC class I and II molecules, using online available algorithms. Based on in silico analysis, eight peptides including highly scored MHC class I- and II-restricted epitopes were synthesized. Peptide immunogenicity was validated in MHC compatible BALB/c mice immunized with each synthetic peptide emulsified in complete Freund's adjuvant/incomplete Freund's adjuvant. CPA_p2, CPA_p3, H1_p1, and LeIF_p6 induced strong spleen cell proliferation upon in vitro peptide re-stimulation. In addition, the majority of the peptides, except of LeIF_p1 and KMP-11_p1, induced IFN-γ secretion, while KMP-11_p1 indicated a suppressive effect on IL-10 production. CPA_p2, CPA_p3, LeIF_p3, and LeIF_p6 induced IFN-γ-producing CD4(+) T cells indicating a TH1-type response. In addition, CPA_p2, CPA_p3, and H1_p1 induced also the induction of CD8(+) T cells. The induction of peptide-specific IgG in immunized mice designated also the existence of B cell epitopes in peptide sequences. Combining immunoinformatic tools and experimental validation, we demonstrated that CPA_p2, CPA_p3, H1_p1, H1_p3, CPA_p2, LeIF_p3, and LeIF_p6 are likely to include potential epitopes for the induction of protective cytotoxic and/or TH1-type immune responses supporting the feasibility of peptide-based vaccine development for leishmaniasis.

  20. Slx8 Removes Pli1-Dependent Protein-SUMO Conjugates Including SUMOylated Topoisomerase I to Promote Genome Stability

    PubMed Central

    Steinacher, Roland; Osman, Fekret; Lorenz, Alexander; Bryer, Claire; Whitby, Matthew C.

    2013-01-01

    The SUMO-dependent ubiquitin ligase Slx8 plays key roles in promoting genome stability, including the processing of trapped Topoisomerase I (Top1) cleavage complexes and removal of toxic SUMO conjugates. We show that it is the latter function that constitutes Slx8's primary role in fission yeast. The SUMO conjugates in question are formed by the SUMO ligase Pli1, which is necessary for limiting spontaneous homologous recombination when Top1 is present. Surprisingly there is no requirement for Pli1 to limit recombination in the vicinity of a replication fork blocked at the programmed barrier RTS1. Notably, once committed to Pli1-mediated SUMOylation Slx8 becomes essential for genotoxin resistance, limiting both spontaneous and RTS1 induced recombination, and promoting normal chromosome segregation. We show that Slx8 removes Pli1-dependent Top1-SUMO conjugates and in doing so helps to constrain recombination at RTS1. Overall our data highlight how SUMOylation and SUMO-dependent ubiquitylation by the Pli1-Slx8 axis contribute in different ways to maintain genome stability. PMID:23936535

  1. Nucleotide sequence of Marchantia polymorpha chloroplast DNA: a region possibly encoding three tRNAs and three proteins including a homologue of E. coli ribosomal protein S14.

    PubMed Central

    Umesono, K; Inokuchi, H; Ohyama, K; Ozeki, H

    1984-01-01

    The nucleotide sequence of a region of Marchantia polymorpha chloroplast DNA was determined. On this DNA sequence (3.38kb), three open reading frames (ORFs) and three putative tRNA genes were detected in the following order: -ORF701-tRNASer(UGA)-ORF702-tRNAGly(GCC)-initiator tRNAMet(CAU)-ORF703-. The ORF703 is composed of 100 codons in which those for lysine (15%) and arginine (11%) are abundant, and could be accounted for as a counterpart of E. coli ribosomal protein S14 since they share 45% homology in the amino acid sequences. The ORF701 appears to code for a membrane protein, showing a periodic appearance of seven clusters of hydrophobic amino acids. Although the mechanisms remain unknown, the ORF701 causes a streptomycin-sensitive phenotype in resistant mutants of E. coli. The ORFs and tRNA genes are separated from each other by extremely AT-rich spacers containing sequences of dyad symmetry. The third letter positions of the codons in the ORFs are also rich in A and T residues. PMID:6393057

  2. Anti-Fatigue Effect by Peptide Fraction from Protein Hydrolysate of Croceine Croaker (Pseudosciaena crocea) Swim Bladder through Inhibiting the Oxidative Reactions including DNA Damage

    PubMed Central

    Zhao, Yu-Qin; Zeng, Li; Yang, Zui-Su; Huang, Fang-Fang; Ding, Guo-Fang; Wang, Bin

    2016-01-01

    The swim bladder of the croceine croaker (Pseudosciaena crocea) was believed to have good curative effects in various diseases, including amnesia, insomnia, dizziness, anepithymia, and weakness after giving birth, in traditional Chinese medicine. However, there is no research focusing on the antioxidant and anti-fatigue peptides from croceine croaker swim bladders at present. Therefore, the purpose of this study was to investigate the bioactivities of peptide fractions from the protein hydrolysate of croceine croaker related to antioxidant and anti-fatigue effects. In the study, swim bladder peptide fraction (SBP-III-3) was isolated from the protein hydrolysate of the croceine croaker, and its antioxidant and anti-fatigue activities were measured using in vitro and in vivo methods. The results indicated that SBP-III-3 exhibited good scavenging activities on hydroxyl radicals (HO•) (EC50 (the concentration where a sample caused a 50% decrease of the initial concentration of HO•) = 0.867 mg/mL), 2,2-diphenyl-1-picrylhydrazyl radicals (DPPH•) (EC50 = 0.895 mg/mL), superoxide anion radical (O2−•) (EC50 = 0.871 mg/mL), and 2,2′-azino-bis-3-ethylbenzothiazoline-6-sulfonic acid radical (ABTS+•) (EC50 = 0.346 mg/mL). SBP-III-3 also showed protective effects on DNA damage in a concentration-effect manner and prolonged the swimming time to exhaustion of Institute of Cancer Research (ICR) mice by 57.9%–107.5% greater than that of the control. SBP-III-3 could increase the levels of muscle glucose (9.4%–115.2% increase) and liver glycogen (35.7%–157.3%), and decrease the levels of blood urea nitrogen (BUN), lactic acid (LA), and malondialdehyde (MDA) by 16.4%–22.4%, 13.9%–20.1%, and 28.0%–53.6%, respectively. SBP-III-3 also enhanced the activity of lactic dehydrogenase to scavenge excessive LA for slowing the development of fatigue. In addition, SBP-III-3 increased the activities superoxide dismutase, catalase, and glutathione peroxidase to reduce the

  3. Additional copies of the proteolipid protein gene causing Pelizaeus-Merzbacher disease arise by separate integration into the X chromosome.

    PubMed

    Hodes, M E; Woodward, K; Spinner, N B; Emanuel, B S; Enrico-Simon, A; Kamholz, J; Stambolian, D; Zackai, E H; Pratt, V M; Thomas, I T; Crandall, K; Dlouhy, S R; Malcolm, S

    2000-07-01

    The proteolipid protein gene (PLP) is normally present at chromosome Xq22. Mutations and duplications of this gene are associated with Pelizaeus-Merzbacher disease (PMD). Here we describe two new families in which males affected with PMD were found to have a copy of PLP on the short arm of the X chromosome, in addition to a normal copy on Xq22. In the first family, the extra copy was first detected by the presence of heterozygosity of the AhaII dimorphism within the PLP gene. The results of FISH analysis showed an additional copy of PLP in Xp22.1, although no chromosomal rearrangements could be detected by standard karyotype analysis. Another three affected males from the family had similar findings. In a second unrelated family with signs of PMD, cytogenetic analysis showed a pericentric inversion of the X chromosome. In the inv(X) carried by several affected family members, FISH showed PLP signals at Xp11.4 and Xq22. A third family has previously been reported, in which affected members had an extra copy of the PLP gene detected at Xq26 in a chromosome with an otherwise normal banding pattern. The identification of three separate families in which PLP is duplicated at a noncontiguous site suggests that such duplications could be a relatively common but previously undetected cause of genetic disorders.

  4. A comprehensive proteomics and genomics analysis reveals novel transmembrane proteins in human platelets and mouse megakaryocytes including G6b-B, a novel immunoreceptor tyrosine-based inhibitory motif protein.

    PubMed

    Senis, Yotis A; Tomlinson, Michael G; García, Angel; Dumon, Stephanie; Heath, Victoria L; Herbert, John; Cobbold, Stephen P; Spalton, Jennifer C; Ayman, Sinem; Antrobus, Robin; Zitzmann, Nicole; Bicknell, Roy; Frampton, Jon; Authi, Kalwant S; Martin, Ashley; Wakelam, Michael J O; Watson, Stephen P

    2007-03-01

    The platelet surface is poorly characterized due to the low abundance of many membrane proteins and the lack of specialist tools for their investigation. In this study we identified novel human platelet and mouse megakaryocyte membrane proteins using specialist proteomics and genomics approaches. Three separate methods were used to enrich platelet surface proteins prior to identification by liquid chromatography and tandem mass spectrometry: lectin affinity chromatography, biotin/NeutrAvidin affinity chromatography, and free flow electrophoresis. Many known, abundant platelet surface transmembrane proteins and several novel proteins were identified using each receptor enrichment strategy. In total, two or more unique peptides were identified for 46, 68, and 22 surface membrane, intracellular membrane, and membrane proteins of unknown subcellular localization, respectively. The majority of these were single transmembrane proteins. To complement the proteomics studies, we analyzed the transcriptome of a highly purified preparation of mature primary mouse megakaryocytes using serial analysis of gene expression in view of the increasing importance of mutant mouse models in establishing protein function in platelets. This approach identified all of the major classes of platelet transmembrane receptors, including multitransmembrane proteins. Strikingly 17 of the 25 most megakaryocyte-specific genes (relative to 30 other serial analysis of gene expression libraries) were transmembrane proteins, illustrating the unique nature of the megakaryocyte/platelet surface. The list of novel plasma membrane proteins identified using proteomics includes the immunoglobulin superfamily member G6b, which undergoes extensive alternate splicing. Specific antibodies were used to demonstrate expression of the G6b-B isoform, which contains an immunoreceptor tyrosine-based inhibition motif. G6b-B undergoes tyrosine phosphorylation and association with the SH2 domain-containing phosphatase

  5. Effect of protein source and protease addition on performance, blood metabolites and nutrient digestibility of turkeys fed on low-protein diets from 28 to 55 d post hatch.

    PubMed

    Shahir, M H; Rahimi, R; Taheri, H R; Heidariniya, A; Baradaran, N; Asadi Kermani, Z

    2016-06-01

    The objective of this study was to investigate the effect of a monocomponent protease and dietary inclusion of canola meal (CM) and poultry by-product meal (PBM) on growth performance, carcass characteristics and blood metabolites of turkeys fed on low crude protein (CP) diets from 28 to 55 d post hatch. Experimental treatments included control, maize-soybean meal diet including 258.3 g/kg CP; negative control 1 (NC1), maize-soybean meal diet with reduced CP (232.4 g/kg); NC2, control diet (CP, 258.3 g/kg) including CM (80 g/kg) and PBM (80 g/kg); NC3, maize-soybean meal diet with reduced CP (232.4 g/kg) including CM (80 g/kg) and PBM (80 g/kg). Also, the NC1 + P and NC3 + P diets were created by addition of protease enzyme (30 000 units/kg of diet) to the NC1 and NC3 diets, respectively. The NC3 group had lower body weight gain (BWG) compared to those fed on the control diet, and no improvement with enzyme addition (NC3 + P) was achieved. The protease addition to the NC1 diet (NC1 + P) improved BWG to the level of the control diet. The NC1 group had higher feed conversion ratio (FCR) compared to the control and NC3 + P, but protease addition to the NC1 diet improved FCR. Protease addition to the low CP diets resulted in higher nitrogen (N) retention than in the control and NC2 groups. Also, the NC1 + P and NC3 + P diets increased apparent ileal digestibility (AID) of CP compared to the control group. It was concluded that addition of CM (up to 80 g/kg) and PBM (up to 80 g/kg) to turkey diets had no negative effect on growth performance from 28 to 55 d of age. The NC1 + P group achieved the BWG of the control group which was partially due to increases in N retention and AID of CP, but the NC3 + P group failed to recover the growth losses. This difference implies that the efficacy of the protease may depend upon the protein source in the ration.

  6. Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination

    PubMed Central

    Song, In-Kang; Lee, Jae-Jin; Cho, Jin-Hwan; Jeong, Jihye; Shin, Dong-Hae; Lee, Kong-Joo

    2016-01-01

    Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1. PMID:27703196

  7. Degradation of Redox-Sensitive Proteins including Peroxiredoxins and DJ-1 is Promoted by Oxidation-induced Conformational Changes and Ubiquitination

    NASA Astrophysics Data System (ADS)

    Song, In-Kang; Lee, Jae-Jin; Cho, Jin-Hwan; Jeong, Jihye; Shin, Dong-Hae; Lee, Kong-Joo

    2016-10-01

    Reactive oxygen species (ROS) are key molecules regulating various cellular processes. However, what the cellular targets of ROS are and how their functions are regulated is unclear. This study explored the cellular proteomic changes in response to oxidative stress using H2O2 in dose- and recovery time-dependent ways. We found discernible changes in 76 proteins appearing as 103 spots on 2D-PAGE. Of these, Prxs, DJ-1, UCH-L3 and Rla0 are readily oxidized in response to mild H2O2 stress, and then degraded and active proteins are newly synthesized during recovery. In studies designed to understand the degradation process, multiple cellular modifications of redox-sensitive proteins were identified by peptide sequencing with nanoUPLC-ESI-q-TOF tandem mass spectrometry and the oxidative structural changes of Prx2 explored employing hydrogen/deuterium exchange-mass spectrometry (HDX-MS). We found that hydrogen/deuterium exchange rate increased in C-terminal region of oxidized Prx2, suggesting the exposure of this region to solvent under oxidation. We also found that Lys191 residue in this exposed C-terminal region of oxidized Prx2 is polyubiquitinated and the ubiquitinated Prx2 is readily degraded in proteasome and autophagy. These findings suggest that oxidation-induced ubiquitination and degradation can be a quality control mechanism of oxidized redox-sensitive proteins including Prxs and DJ-1.

  8. The Escherichia coli O157:H7 cattle immunoproteome includes outer membrane protein A (OmpA), a modulator of adherence to bovine rectoanal junction squamous epithelial (RSE) cells.

    PubMed

    Kudva, Indira T; Krastins, Bryan; Torres, Alfredo G; Griffin, Robert W; Sheng, Haiqing; Sarracino, David A; Hovde, Carolyn J; Calderwood, Stephen B; John, Manohar

    2015-06-01

    Building on previous studies, we defined the repertoire of proteins comprising the immunoproteome (IP) of Escherichia coli O157:H7 (O157) cultured in DMEM supplemented with norepinephrine (O157 IP), a β-adrenergic hormone that regulates E. coli O157 gene expression in the gastrointestinal tract, using a variation of a novel proteomics-based platform proteome mining tool for antigen discovery, called "proteomics-based expression library screening" (PELS; Kudva et al., 2006). The E. coli O157 IP (O157-IP) comprised 91 proteins, and included those identified previously using proteomics-based expression library screening, and also proteins comprising DMEM and bovine rumen fluid proteomes. Outer membrane protein A (OmpA), a common component of the above proteomes, and reportedly a contributor to E. coli O157 adherence to cultured HEp-2 epithelial cells, was interestingly found to be a modulator rather than a contributor to E. coli O157 adherence to bovine rectoanal junction squamous epithelial cells. Our results point to a role for yet to be identified members of the O157-IP in E. coli O157 adherence to rectoanal junction squamous epithelial cells, and additionally implicate a possible role for the outer membrane protein A regulator, TdcA, in the expression of such adhesins. Our observations have implications for the development of efficacious vaccines for preventing E. coli O157 colonization of the bovine gastrointestinal tract.

  9. Thiazolidinedione addition reduces the serum retinol-binding protein 4 in type 2 diabetic patients treated with metformin and sulfonylurea.

    PubMed

    Lin, Kun-Der; Chang, Yu-Hung; Wang, Chiao-Ling; Yang, Yi-Hsin; Hsiao, Pi-Jung; Li, Tzu-Hui; Shin, Shyi-Jang

    2008-06-01

    Retinol-binding protein 4 (RBP4) has been found to induce insulin resistance and to be increased in type 2 diabetes. Thiazolidinediones (TZDs) can improve insulin sensitivity through the activation of peroxisome proliferators-activated receptor-gamma (PPAR-gamma) and have been suggested as an adjunct to metformin (MF) and sulfonylurea (SU) in type 2 diabetes in a consensus statement from the ADA and EASD. Therefore, we investigated whether TZD could affect serum RBP4 level in type 2 diabetes already treated with MF and/or SU. Eighty-one type 2 diabetic patients were divided into 2 groups: (1) TZD group (n = 55): Pioglitazone 30 mg/day was given as an add-on medication; (2) SU group (n = 26): Gliclazide MR 30-120 mg or glimepiride 2-8 mg/day was prescribed. The average period of study was 97.1 days. Serum RBP4 and adiponectin were measured by enzyme-linked immunosorbent assay and radioimmunoassay, respectively. The addition of pioglitazone (TZD group) markedly decreased homeostasis model assessment of insulin resistance (HOMA-IR) (P = 0.021) compared with the SU group (P = 0.688). The change of RBP4 in the TZD group (-3.87 +/- 11.27 microg/mL) significantly differed from that in the SU group (2.52 +/- 8.24 microg/mL, P < 0.012). The increase of adiponectin in the TZD group (11.49 +/- 7.85 microg/mL) was apparently higher than that in the SU group (1.54 +/- 5.62 microg/mL, P < 0.001). Despite the change of glycosylated hemoglobin (HbA1c) did not differ (-0.77 +/- 1.3 vs -0.50 +/- 1.7, P = 0.446), the addition of pioglitazone could significantly lower serum RBP4 and HOMA-IR values, whereas an increased dosage of sulfonylurea agents did not alter HOMA-IR, RBP4, or adiponectin in type 2 diabetic patients who had been treated with metformin and/or sulfonylurea.

  10. The Brd4 Extraterminal Domain Confers Transcription Activation Independent of pTEFb by Recruiting Multiple Proteins, Including NSD3 ▿ †

    PubMed Central

    Rahman, Shaila; Sowa, Mathew E.; Ottinger, Matthias; Smith, Jennifer A.; Shi, Yang; Harper, J. Wade; Howley, Peter M.

    2011-01-01

    Bromodomain protein 4 (Brd4) plays critical roles in development, cancer progression, and virus-host pathogenesis. To gain mechanistic insight into the various biological functions of Brd4, we performed a proteomic analysis to identify and characterize Brd4-associated cellular proteins. We found that the extraterminal (ET) domain, whose function has to date not been determined, interacts with NSD3, JMJD6, CHD4, GLTSCR1, and ATAD5. These ET-domain interactions were also conserved for Brd2 and Brd3, the other human BET proteins tested. We demonstrated that GLTSCR1, NSD3, and JMJD6 impart a pTEFb-independent transcriptional activation function on Brd4. NSD3 as well as JMJD6 is recruited to regulated genes in a Brd4-dependent manner. Moreover, we found that depletion of Brd4 or NSD3 reduces H3K36 methylation, demonstrating that the Brd4/NSD3 complex regulates this specific histone modification. Our results indicate that the Brd4 ET domain through the recruitment of the specific effectors regulates transcriptional activity. In particular, we show that one of these effectors, NSD3, regulates transcription by modifying the chromatin microenvironment at Brd4 target genes. Our study thus identifies the ET domain as a second important transcriptional regulatory domain for Brd4 in addition to the carboxyl-terminal domain (CTD) that interacts with pTEFb. PMID:21555454

  11. Interaction of Photobacterium leiognathi and Vibrio fischeri Y1 luciferases with fluorescent (antenna) proteins: bioluminescence effects of the aliphatic additive.

    PubMed

    Petushkov, V N; Ketelaars, M; Gibson, B G; Lee, J

    1996-09-17

    The kinetics of the bacterial bioluminescence reaction is altered in the presence of the fluorescent (antenna) proteins, lumazine protein (LumP) from Photobacterium or the yellow fluorescence proteins (YFP) having FMN or Rf bound, from Vibrio fischeri strain Y1. Depending on reaction conditions, the bioluminescence intensity and its decay rate may be either enhanced or strongly quenched in the presence of the fluorescent proteins. These effects can be simply explained on the basis of the same protein-protein complex model that accounts for the bioluminescence spectral shifts induced by these fluorescent proteins. In such a complex, where the fluorophore evidently is in proximity to the luciferase active site, it is expected that the on-off rate of certain aliphatic components of the reaction should be altered with a consequent shift in the equilibria among the luciferase intermediates, as recently elaborated in a kinetic scheme. These aliphatic components are the bioluminescence reaction substrate, tetradecanal or other long-chain aldehyde, its carboxylic acid product, or dodecanol used as a stabilizer of the luciferase peroxyflavin. No evidence can be found for the protein-protein interaction in the absence of the aliphatic component.

  12. Identification of 17 HrpX-regulated proteins including two novel type III effectors, XOC_3956 and XOC_1550, in Xanthomonas oryzae pv. oryzicola.

    PubMed

    Xue, Xiao-bo; Zou, Li-fang; Ma, Wen-xiu; Liu, Zhi-yang; Chen, Gong-you

    2014-01-01

    The function of some hypothetical proteins, possibly regulated by key hrp regulators, in the pathogenicity of phytopathogenic bacteria remains largely unknown. In the present study, in silicon microarray data demonstrated that the expression of 17 HrpX-regulated protein (Xrp) genes of X. oryzae pv. oryzicola (Xoc), which causes bacterial leaf streak in rice, were either positively or negatively regulated by HrpX or/and HrpG. Bioinformatics analysis demonstrated that five Xrps possess a putative type III secretion (T3S) signal in the first 50 N-terminal amino acids, six xrp genes contain a PIP-box-like sequence (TTCGB-NX-TTCGB, 9 ≤ X ≤ 25) in the promoter regions, and two Xrps have both motifs. Twelve Xrps are widely conserved in Xanthomonas spp., whereas four are specific for X. oryzae (Xrp6) or Xoc (Xrp8, Xrp14 and Xrp17). In addition to the regulation by HrpG/HrpX, some of the 17 genes were also modulated by another hrp regulator HrpD6. Mutagenesis of these 17 genes indicated that five Xrps (Xrp1, Xrp2, Xrp5, Xrp8 and Xrp14) were required for full virulence and bacterial growth in planta. Immunoblotting assays and fusion with N-terminally truncated AvrXa10 indicated that Xrp3 and Xrp5 were secreted and translocated into rice cells through the type-III secretion system (T3S), suggesting they are novel T3S effectors. Our results suggest that Xoc exploits an orchestra of proteins that are regulated by HrpG, HrpX and HrpD6, and these proteins facilitate both infection and metabolism.

  13. High confidence proteomic analysis of yeast LDs identifies additional droplet proteins and reveals connections to dolichol synthesis and sterol acetylation[S

    PubMed Central

    Currie, Erin; Guo, Xiuling; Christiano, Romain; Chitraju, Chandramohan; Kory, Nora; Harrison, Kenneth; Haas, Joel; Walther, Tobias C.; Farese, Robert V.

    2014-01-01

    Accurate protein inventories are essential for understanding an organelle’s functions. The lipid droplet (LD) is a ubiquitous intracellular organelle with major functions in lipid storage and metabolism. LDs differ from other organelles because they are bounded by a surface monolayer, presenting unique features for protein targeting to LDs. Many proteins of varied functions have been found in purified LD fractions by proteomics. While these studies have become increasingly sensitive, it is often unclear which of the identified proteins are specific to LDs. Here we used protein correlation profiling to identify 35 proteins that specifically enrich with LD fractions of Saccharomyces cerevisiae. Of these candidates, 30 fluorophore-tagged proteins localize to LDs by microscopy, including six proteins, several with human orthologs linked to diseases, which we newly identify as LD proteins (Cab5, Rer2, Say1, Tsc10, YKL047W, and YPR147C). Two of these proteins, Say1, a sterol deacetylase, and Rer2, a cis-isoprenyl transferase, are enzymes involved in sterol and polyprenol metabolism, respectively, and we show their activities are present in LD fractions. Our results provide a highly specific list of yeast LD proteins and reveal that the vast majority of these proteins are involved in lipid metabolism. PMID:24868093

  14. Food additives

    MedlinePlus

    ... or natural. Natural food additives include: Herbs or spices to add flavor to foods Vinegar for pickling ... Certain colors improve the appearance of foods. Many spices, as well as natural and man-made flavors, ...

  15. Effect of annatto addition and bleaching treatments on ultrafiltration flux during production of 80% whey protein concentrate and 80% serum protein concentrate.

    PubMed

    Adams, Michael C; Zulewska, Justyna; Barbano, David M

    2013-04-01

    The goals of this study were to determine if adding annatto color to milk or applying a bleaching process to whey or microfiltration (MF) permeate influenced ultrafiltration (UF) flux, diafiltration (DF) flux, or membrane fouling during production of 80% whey protein concentrate (WPC80) or 80% serum protein concentrate (SPC80). Separated Cheddar cheese whey (18 vats using 900 kg of whole milk each) and MF permeate of skim milk (18 processing runs using 800 kg of skim milk each) were produced to make WPC80 and SPC80, respectively. The 6 treatments, replicated 3 times each, that constituted the 18 processing runs within either whey or MF permeate UF were as follows: (1) no annatto; (2) no annatto+benzoyl peroxide (BPO); (3) no annatto+hydrogen peroxide (H2O2); (4) annatto; (5) annatto+BPO; and (6) annatto+H2O2. Approximately 700 kg of whey or 530 kg of MF permeate from each treatment were heated to 50°C and processed in 2 stages (UF and DF) with the UF system in batch recirculation mode using a polyethersulfone spiral-wound UF membrane with a molecular weight cutoff of 10,000 Da. Addition of annatto color had no effect on UF or DF flux. The processes of bleaching whey or MF permeate with or without added color improved flux during processing. Bleaching with H2O2 usually produced higher flux than bleaching with BPO. Bleaching with BPO increased WPC80 flux to a greater extent than it did SPC80 flux. Though no differences in mean flux were observed for a common bleaching treatment between the WPC80 and SPC80 production processes during the UF stage, mean flux during WPC80 DF was higher than mean flux during SPC80 DF for each bleaching treatment. Water flux values before and after processing were used to calculate a fouling coefficient that demonstrated differences in fouling which were consistent with flux differences among treatments. In both processes, bleaching with H2O2 led to the largest reduction in fouling. No effect of annatto on fouling was observed. The

  16. [Evaluation of ten fish species to be included as part of renal diet, due to their protein, phosphorus and fatty acids content].

    PubMed

    Castro-González, Maria Isabel; Maafs-Rodríguez, Ana Gabriela; Pérez-Gil Romo, Fernando

    2012-06-01

    Because renal disease is highly complex, its nutritional treatment is complicated and many foods are restricted, including fish because its phosphorus content. The aim of the present study was to analyze ten fillet fish species, commonly consumed in Mexico (Cyprinus carpio carpio, Ophichthus rex, Symphurus elongatus, Eucinostomus entomelas, Chirostoma patzcuaro, Bairdiella chrysoura, Salmo salar Oreochromis urolepis hornorum, Sphyraena guachancho, Istiophorus albicans), to determine their phosphorus (P), protein (Pr), cholesterol, sodium, potassium, vitamins D3 and E, and n-3 PUFA (EPA+DHA) according to the AOAC techniques, in order to identify which species could be included in renal diet; particularly because of their risk:benefit relations (calculated with those results). Protein values ranged from 16.5 to 33.5g/100 g of fillet; the specie with the highest phosphorus contest was Salmo salar, and with the lowest, Symphurus elongatus. EPA+DHA quantity ranged from 79.64 mg/100 g to 1,381.53 mg/100 g. Considering de P/Pr relation recommended to renal patients, all analyzed species (except Salmo salar, Ophichthus rex and Istiophorus albicans) could be included in their diet. As for the P/EPA+DHA relation, the species most recommended to renal patients are Symphurus elongatus, Bairdiella chrysoura and Sphyraena guachancho.

  17. Effect of the addition of flavan-3-ols on the HPLC-DAD salivary-protein profile.

    PubMed

    Quijada-Morín, Natalia; Crespo-Expósito, Carlos; Rivas-Gonzalo, Julián C; García-Estévez, Ignacio; Escribano-Bailón, María Teresa

    2016-09-15

    The interaction between monomeric flavan-3-ols and salivary proteins has been studied using HPLC-DAD. A chromatographic method has been described and seven protein fractions were collected. The peptides and proteins present in each fraction have been identified using nLC-MS-MS analysis. The interaction between saliva and catechin, epicatechin and gallocatechin has been studied. These compounds interact in a discriminated way with salivary proteins: catechin causes a decrease of some fractions, epicatechin causes the decrease or increase of fractions while gallocatechin seems to cause an increase of two fractions. This variable behavior is explained, for the decrease in the chromatographic area, by the precipitation of salivary proteins and, for the increase of the area, by the formation of soluble complexes and/or for the formation of new peaks.

  18. The epidermis of scales in gecko lizards contains multiple forms of beta-keratins including basic glycine-proline-serine-rich proteins.

    PubMed

    Toni, M; Dalla Valle, L; Alibardi, L

    2007-05-01

    The epidermis of scales of gecko lizards comprises alpha- and beta-keratins. Using bidimensional electrophoresis and immunoblotting, we have characterized keratins of corneous layers of scales in geckos, especially beta-keratins in digit pad lamellae. In the latter, the formation of thin bristles (setae) allow for the adhesion and climbing vertical or inverted surfaces. alpha-Keratins of 55-66 kDa remain in the acidic and neutral range of pI, while beta-keratins of 13-18 kDa show a broader variation of pI (4-10). Some protein spots for beta-keratins correspond to previously sequenced, basic glycine-proline-serine-rich beta-keratins of 169-191 amino acids. The predicted secondary structure shows that a large part of the molecule has a random-coiled conformation, small alpha helix regions, and a central region with 2-3 strands (beta-folding). The latter, termed core-box, shows homology with feather-scale-claw keratins of birds and is involved in the formation of beta-keratin filaments. Immunolocalization of beta-keratins indicates that these proteins are mainly present in the beta-layer and oberhautchen layer, including setae. The sequenced proteins of setae form bundles of keratins that determine their elongation. This process resembles that of feather-keratin on the elongation of barbule cells in feathers. It is suggested that small proteins rich in glycine, serine, and proline evolved in reptiles and birds to reinforce the mechanical resistance of the cytokeratin cytoskeleton initially present in the epidermis of scales and feathers.

  19. Addition of capsaicin and exchange of carbohydrate with protein counteract energy intake restriction effects on fullness and energy expenditure.

    PubMed

    Smeets, Astrid J; Janssens, Pilou L H R; Westerterp-Plantenga, Margriet S

    2013-04-01

    Energy intake restriction causes a yo-yo effect by decreasing energy expenditure (EE) and decreasing fullness. We investigated the 24-h effect of protein and capsaicin, singly or combined, on fullness and EE during 20% energy intake restriction. The 24 participants (12 male, 12 female; BMI, 25.2 ± 0.4 kg/m(2); age, 27 ± 4 y; body fat, 25.6 ± 5.7%; 3-factor eating questionnaire, F1: 6 ± 2, F2: 4 ± 2, F3: 3 ± 2) underwent eight 36-h sessions in a respiration chamber. The study had a randomized crossover design with 8 randomly sequenced conditions. The participants were fed 100 or 80% of their daily energy requirements. There were 2 control (C) conditions: 100%C and 80%C; 2 conditions with capsaicin (Caps): 100%Caps and 80%Caps; 2 conditions with elevated protein (P): 100%P and 80%P; and 2 conditions with a mixture of protein and capsaicin (PCaps): 100%PCaps and 80%PCaps. Appetite profile, EE, and substrate oxidation were monitored. Compared with 100%C, the 80%C group had expected negative energy-balance effects with respect to total EE, diet-induced thermogenesis, and fullness, whereas the 80%Caps diet counteracted these effects, and the 80%P and 80%PCaps diets exceeded these effects (P < 0.01). In energy balance and negative energy balance, fat balance was more negative in the 80%Caps, P, and PCaps groups than in the 80%C group (P < 0.05) and respiratory quotient values were lower. A negative protein balance was prevented with the 80%P and 80%PCaps diets compared with the 80%C diet. Our results suggest that protein and capsaicin, consumed singly or mixed, counteracted the energy intake restriction effects on fullness and EE. During energy restriction, protein and capsaicin promoted a negative fat balance and protein treatments also prevented a negative protein balance.

  20. TMEFF2 Is a PDGF-AA Binding Protein with Methylation-Associated Gene Silencing in Multiple Cancer Types Including Glioma

    PubMed Central

    Lin, Kui; Taylor, James R.; Wu, Thomas D.; Gutierrez, Johnny; Elliott, J. Michael; Vernes, Jean-Michel; Koeppen, Hartmut; Phillips, Heidi S.; de Sauvage, Frederic J.; Meng, Y. Gloria

    2011-01-01

    Background TMEFF2 is a protein containing a single EGF-like domain and two follistatin-like modules. The biological function of TMEFF2 remains unclear with conflicting reports suggesting both a positive and a negative association between TMEFF2 expression and human cancers. Methodology/Principal Findings Here we report that the extracellular domain of TMEFF2 interacts with PDGF-AA. This interaction requires the amino terminal region of the extracellular domain containing the follistatin modules and cannot be mediated by the EGF-like domain alone. Furthermore, the extracellular domain of TMEFF2 interferes with PDGF-AA–stimulated fibroblast proliferation in a dose–dependent manner. TMEFF2 expression is downregulated in human brain cancers and is negatively correlated with PDGF-AA expression. Suppressed expression of TMEFF2 is associated with its hypermethylation in several human tumor types, including glioblastoma and cancers of ovarian, rectal, colon and lung origins. Analysis of glioma subtypes indicates that TMEFF2 hypermethylation and decreased expression are associated with a subset of non-Proneural gliomas that do not display CpG island methylator phentoype. Conclusions/Significance These data provide the first evidence that TMEFF2 can function to regulate PDGF signaling and that it is hypermethylated and downregulated in glioma and several other cancers, thereby suggesting an important role for this protein in the etiology of human cancers. PMID:21559523

  1. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller's organ, of the cattle tick, Rhipicephalus australis.

    PubMed

    Munoz, Sergio; Guerrero, Felix D; Kellogg, Anastasia; Heekin, Andrew M; Leung, Ming-Ying

    2017-01-01

    The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller's organ, located in the tick's forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs) from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor.

  2. Bioinformatic prediction of G protein-coupled receptor encoding sequences from the transcriptome of the foreleg, including the Haller’s organ, of the cattle tick, Rhipicephalus australis

    PubMed Central

    Munoz, Sergio; Guerrero, Felix D.; Kellogg, Anastasia; Heekin, Andrew M.

    2017-01-01

    The cattle tick of Australia, Rhipicephalus australis, is a vector for microbial parasites that cause serious bovine diseases. The Haller’s organ, located in the tick’s forelegs, is crucial for host detection and mating. To facilitate the development of new technologies for better control of this agricultural pest, we aimed to sequence and annotate the transcriptome of the R. australis forelegs and associated tissues, including the Haller's organ. As G protein-coupled receptors (GPCRs) are an important family of eukaryotic proteins studied as pharmaceutical targets in humans, we prioritized the identification and classification of the GPCRs expressed in the foreleg tissues. The two forelegs from adult R. australis were excised, RNA extracted, and pyrosequenced with 454 technology. Reads were assembled into unigenes and annotated by sequence similarity. Python scripts were written to find open reading frames (ORFs) from each unigene. These ORFs were analyzed by different GPCR prediction approaches based on sequence alignments, support vector machines, hidden Markov models, and principal component analysis. GPCRs consistently predicted by multiple methods were further studied by phylogenetic analysis and 3D homology modeling. From 4,782 assembled unigenes, 40,907 possible ORFs were predicted. Using Blastp, Pfam, GPCRpred, TMHMM, and PCA-GPCR, a basic set of 46 GPCR candidates were compiled and a phylogenetic tree was constructed. With further screening of tertiary structures predicted by RaptorX, 6 likely GPCRs emerged and the strongest candidate was classified by PCA-GPCR to be a GABAB receptor. PMID:28231302

  3. Fish meal replacement by plant protein substitution and guar gum addition in trout feed. Part II: Effects on faeces stability and rheology.

    PubMed

    Brinker, Alexander; Friedrich, Christian

    2012-01-01

    In the explosively growing aquaculture industry, the challenge of sustainability includes a requirement to produce more fish than are consumed by stock. A promising avenue of research is the substitution of the fish meal in feeds with plant protein. However, there are inherent risks in the development of such feeds, and serious consideration should be given not only to nutritional content, but also to the mechanical quality of resulting faecal wastes. The present study uses a plate on plate rheometer running in different flow modes (creep, oscillation) to assess the rheological properties of wastes resulting from different diets.All faeces were shown to be thixotropic in nature, independent of diet composition. Details of dietary composition influence the consistency and the characteristic stresses at which faecal structure changes from a viscoelastic solid into a viscoelastic liquid. Furthermore, in linking active food components with mechanical properties of chyme faeces, rheological studies may be used to understand and counteract some problematic properties. Substituting 100% of fish meal with plant proteins leads to faeces that rapidly disintegrate into very fine solids which threaten the viability of aquacultural operations. Adding just 0.3% of the rapidly hydrating non-starch polysaccharide, guar gum (GG), significantly increased the viscosity and elastic modulus of the faeces. These mechanical improvements increase the size of the resulting particles and the effectiveness with which they can be removed, thereby leading to optimized water quality. GG addition was sufficiently effective to counter the stability and particle size effects of a 50% substitution of fish meal, but could not mitigate those of a 100% substitution, wherein dissolution effects of an unknown emulsifier are suspected.

  4. Effect of addition of thermally modified cowpea protein on sensory acceptability and textural properties of wheat bread and sponge cake.

    PubMed

    Campbell, Lydia; Euston, Stephen R; Ahmed, Mohamed A

    2016-03-01

    This paper investigates the sensory acceptability and textural properties of leavened wheat bread and sponge cake fortified with cow protein isolates that had been denatured and glycated by thermal treatment. Defatted cowpea flour was prepared from cow pea beans and the protein isolate was prepared (CPI) and thermally denatured (DCPI). To prepare glycated cowpea protein isolate (GCPI) the cowpea flour slurry was heat treated before isolation of the protein. CPI was more susceptible to thermal denaturation than GCPI as determined by turbidity and sulphydryl groups resulting in greater loss of solubility. This is attributed to the higher glycation degree and higher carbohydrate content of GCPI as demonstrated by glycoprotein staining of SDS PAGE gels. Water absorption of bread dough was significantly enhanced by DCPI and to a larger extent GCPI compared to the control, resulting in softer texture. CPI resulted in significantly increased crumb hardness in baked bread than the control whereas DCPI or GCPI resulted in significantly softer crumb. Bread fortified with 4% DCPI or GCPI was similar to control as regards sensory and textural properties whereas 4% CPI was significantly different, limiting its inclusion level to 2%. There was a trend for higher sensory acceptability scores for GCPI containing bread compared DCPI. Whole egg was replaced by 20% by GCPI (3.5%) in sponge cake without affecting the sensory acceptability, whereas CPI and DCPI supplemented cakes were significantly different than the control.

  5. Conversion of canola meal into a high-protein feed additive via solid-state fungal incubation process

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The study goal was to determine the optimal fungal culture to reduce glucosinolates (GLS), fiber, and residual sugars while increasing the protein content and nutritional value of canola meal. Solid-state incubation conditions were used to enhance filamentous growth of the fungi. Flask trials were p...

  6. Effect of milk protein addition to a carbohydrate-electrolyte rehydration solution ingested after exercise in the heat.

    PubMed

    James, Lewis J; Clayton, David; Evans, Gethin H

    2011-02-01

    The present study examined the effects of milk protein on rehydration after exercise in the heat, via the comparison of energy- and electrolyte content-matched carbohydrate and carbohydrate-milk protein solutions. Eight male subjects lost 1·9 (SD 0·2) % of their body mass by intermittent exercise in the heat and rehydrated with 150% of their body mass loss with either a 65 g/l carbohydrate solution (trial C) or a 40 g/l carbohydrate, 25 g/l milk protein solution (trial CP). Urine samples were collected before and after exercise and for 4 h after rehydration. Total cumulative urine output after rehydration was greater for trial C (1212 (SD 310) ml) than for trial CP (931 (SD 254) ml) (P < 0·05), and total fluid retention over the study was greater after ingestion of drink CP (55 (SD 12) %) than that after ingestion of drink C (43 (SD 15) %) (P < 0·05). At the end of the study period, whole body net fluid balance (P < 0·05) was less negative for trial CP (-0·26 (SD 0·27) litres) than for trial C (-0·52 (SD 0·30) litres), and although net negative for both the trials, it was only significantly negative after ingestion of drink C (P < 0·05). The results of the present study suggest that when matched for energy density and fat content, as well as for Na and K concentration, and when ingested after exercise-induced dehydration, a carbohydrate-milk protein solution is better retained than a carbohydrate solution. These results suggest that gram-for-gram, milk protein is more effective at augmenting fluid retention than carbohydrate.

  7. The NsrR Regulon of Escherichia coli K-12 Includes Genes Encoding the Hybrid Cluster Protein and the Periplasmic, Respiratory Nitrite Reductase▿

    PubMed Central

    Filenko, Nina; Spiro, Stephen; Browning, Douglas F.; Squire, Derrick; Overton, Tim W.; Cole, Jeff; Constantinidou, Chrystala

    2007-01-01

    Successful pathogens must be able to protect themselves against reactive nitrogen species generated either as part of host defense mechanisms or as products of their own metabolism. The regulatory protein NsrR (a member of the Rrf2 family of transcription factors) plays key roles in this stress response. Microarray analysis revealed that NsrR represses nine operons encoding 20 genes in Escherichia coli MG1655, including the hmpA, ytfE, and ygbA genes that were previously shown to be regulated by NsrR. Novel NsrR targets revealed by this study include hcp-hcr (which were predicted in a recent bioinformatic study to be NsrR regulated) and the well-studied nrfA promoter that directs the expression of the periplasmic respiratory nitrite reductase. Conversely, transcription from the ydbC promoter is strongly activated by NsrR. Regulation of the nrf operon by NsrR is consistent with the ability of the periplasmic nitrite reductase to reduce nitric oxide and hence protect against reactive nitrogen species. Gel retardation assays were used to show that both FNR and NarL bind to the hcp promoter. The expression of hcp and the contiguous gene hcr is not induced by hydroxylamine. As hmpA and ytfE encode a nitric oxide reductase and a mechanism to repair iron-sulfur centers damaged by nitric oxide, the demonstration that hcp-hcr, hmpA, and ytfE are the three transcripts most tightly regulated by NsrR highlights the possibility that the hybrid cluster protein, HCP, might also be part of a defense mechanism against reactive nitrogen stress. PMID:17449618

  8. In Planta Expression Screens of Phytophthora infestans RXLR Effectors Reveal Diverse Phenotypes, Including Activation of the Solanum bulbocastanum Disease Resistance Protein Rpi-blb2[W

    PubMed Central

    Oh, Sang-Keun; Young, Carolyn; Lee, Minkyoung; Oliva, Ricardo; Bozkurt, Tolga O.; Cano, Liliana M.; Win, Joe; Bos, Jorunn I.B.; Liu, Hsin-Yin; van Damme, Mireille; Morgan, William; Choi, Doil; Van der Vossen, Edwin A.G.; Vleeshouwers, Vivianne G.A.A.; Kamoun, Sophien

    2009-01-01

    The Irish potato famine pathogen Phytophthora infestans is predicted to secrete hundreds of effector proteins. To address the challenge of assigning biological functions to computationally predicted effector genes, we combined allele mining with high-throughput in planta expression. We developed a library of 62 infection-ready P. infestans RXLR effector clones, obtained using primer pairs corresponding to 32 genes and assigned activities to several of these genes. This approach revealed that 16 of the 62 examined effectors cause phenotypes when expressed inside plant cells. Besides the well-studied AVR3a effector, two additional effectors, PexRD8 and PexRD3645-1, suppressed the hypersensitive cell death triggered by the elicitin INF1, another secreted protein of P. infestans. One effector, PexRD2, promoted cell death in Nicotiana benthamiana and other solanaceous plants. Finally, two families of effectors induced hypersensitive cell death specifically in the presence of the Solanum bulbocastanum late blight resistance genes Rpi-blb1 and Rpi-blb2, thereby exhibiting the activities expected for Avrblb1 and Avrblb2. The AVRblb2 family was then studied in more detail and found to be highly variable and under diversifying selection in P. infestans. Structure-function experiments indicated that a 34–amino acid region in the C-terminal half of AVRblb2 is sufficient for triggering Rpi-blb2 hypersensitivity and that a single positively selected AVRblb2 residue is critical for recognition by Rpi-blb2. PMID:19794118

  9. Lateral Diffusion of Proteins on Supported Lipid Bilayers: Additive Friction of Synaptotagmin 7 C2A–C2B Tandem Domains

    PubMed Central

    2015-01-01

    The synaptotagmin (Syt) family of proteins contains tandem C2 domains, C2A and C2B, which bind membranes in the presence of Ca2+ to trigger vesicle fusion during exocytosis. Despite recent progress, the role and extent of interdomain interactions between C2A and C2B in membrane binding remain unclear. To test whether the two domains interact on a planar lipid bilayer (i.e., experience thermodynamic interdomain contacts), diffusion of fluorescent-tagged C2A, C2B, and C2AB domains from human Syt7 was measured using total internal reflection fluorescence microscopy with single-particle tracking. The C2AB tandem exhibits a lateral diffusion constant approximately half the value of the isolated single domains and does not change when additional residues are engineered into the C2A–C2B linker. This is the expected result if C2A and C2B are separated when membrane-bound; theory predicts that C2AB diffusion would be faster if the two domains were close enough together to have interdomain contact. Stopped-flow measurements of membrane dissociation kinetics further support an absence of interdomain interactions, as dissociation kinetics of the C2AB tandem remain unchanged when rigid or flexible linker extensions are included. Together, the results suggest that the two C2 domains of Syt7 bind independently to planar membranes, in contrast to reported interdomain cooperativity in Syt1. PMID:25437758

  10. Protein recovery from rainbow trout (Oncorhynchus mykiss) processing byproducts via isoelectric solubilization/precipitation and its gelation properties as affected by functional additives.

    PubMed

    Chen, Yi-Chen; Jaczynski, Jacek

    2007-10-31

    Solubility of rainbow trout proteins was determined between pH 1.5 and 13.0 and various ionic strengths (IS). Minimum solubility occurred at pH 5.5; however, when IS = 0.2, the minimum solubility shifted toward more acidic pH. Isoelectric solubilization/precipitation was applied to trout processing byproducts (fish meat left over on bones, head, skin, etc.), resulting in protein recovery yields (Kjeldahl, dry basis) between 77.7% and 89.0%, depending of the pH used for solubilization and precipitation. The recovered protein contained 1.4-2.1% ash (dry basis), while the trout processing byproducts (i.e., starting material) 13.9%. Typical boneless and skinless trout fillets contain 5.5% ash, and therefore, the isoelectric solubilization/precipitation effectively removed impurities such as bones, scales, skin, etc., from the trout processing byproducts. The recovered proteins retained gel-forming ability as assessed with dynamic rheology, torsion test, and texture profile analysis (TPA). However, the recovered proteins failed to gel unless beef plasma protein (BPP) was added. Even with BPP, the recovered protein showed some proteolysis between 40 and 55 degrees C. Addition of potato starch, transglutaminase, and phosphate to the recovered proteins resulted in good texture of trout gels as confirmed by torsion test and TPA. Higher ( P < 0.05) shear stress and strain were measured for gels developed from basic pH treatments than the acidic counterparts. However, proteins recovered from acidic treatments had higher ( P < 0.05) lipid content than the basic treatments. This is probably why the gels from acidic treatments were whiter ( L* - 3 b*) ( P < 0.05) than those from the basic ones. Our study demonstrates that functional proteins can be efficiently recovered from low-value fish processing byproducts using isoelectric solubilization/precipitation and subsequently be used in value-added human foods.

  11. New variants including ARG1 polymorphisms associated with C-reactive protein levels identified by genome-wide association and pathway analysis.

    PubMed

    Vinayagamoorthy, Nadimuthu; Hu, Hae-Jin; Yim, Seon-Hee; Jung, Seung-Hyun; Jo, Jaeseong; Jee, Sun Ha; Chung, Yeun-Jun

    2014-01-01

    C-reactive protein (CRP) is a general marker of systemic inflammation and cardiovascular disease (CVD). The genetic contribution to differences in CRP levels remains to be explained, especially in non-European populations. Thus, the aim of this study was to identify genetic loci associated with CRP levels in Korean population. We performed genome-wide association studies (GWAS) using SNPs from 8,529 Korean individuals (7,626 for stage 1 and 903 for stage 2). We also performed pathway analysis. We identified a new genetic locus associated with CRP levels upstream of ARG1 gene (top significant SNP: rs9375813, Pmeta = 2.85×10(-8)), which encodes a key enzyme of the urea cycle counteract the effects of nitric oxide, in addition to known CRP (rs7553007, Pmeta = 1.72×10(-16)) and HNF1A loci (rs2259816, Pmeta = 2.90×10(-10)). When we evaluated the associations between the CRP-related SNPs with cardiovascular disease phenotypes, rs9375813 (ARG1) showed a marginal association with hypertension (P = 0.0440). To identify more variants and pathways, we performed pathway analysis and identified six candidate pathways comprised of genes related to inflammatory processes and CVDs (CRP, HNF1A, PCSK6, CD36, and ABCA1). In addition to the previously reported loci (CRP, HNF1A, and IL6) in diverse ethnic groups, we identified novel variants in the ARG1 locus associated with CRP levels in Korean population and a number of interesting genes related to inflammatory processes and CVD through pathway analysis.

  12. New Variants Including ARG1 Polymorphisms Associated with C-Reactive Protein Levels Identified by Genome-Wide Association and Pathway Analysis

    PubMed Central

    Yim, Seon-Hee; Jung, Seung-Hyun; Jo, Jaeseong; Jee, Sun Ha; Chung, Yeun-Jun

    2014-01-01

    C-reactive protein (CRP) is a general marker of systemic inflammation and cardiovascular disease (CVD). The genetic contribution to differences in CRP levels remains to be explained, especially in non-European populations. Thus, the aim of this study was to identify genetic loci associated with CRP levels in Korean population. We performed genome-wide association studies (GWAS) using SNPs from 8,529 Korean individuals (7,626 for stage 1 and 903 for stage 2). We also performed pathway analysis. We identified a new genetic locus associated with CRP levels upstream of ARG1 gene (top significant SNP: rs9375813, Pmeta = 2.85×10−8), which encodes a key enzyme of the urea cycle counteract the effects of nitric oxide, in addition to known CRP (rs7553007, Pmeta = 1.72×10−16) and HNF1A loci (rs2259816, Pmeta = 2.90×10−10). When we evaluated the associations between the CRP-related SNPs with cardiovascular disease phenotypes, rs9375813 (ARG1) showed a marginal association with hypertension (P = 0.0440). To identify more variants and pathways, we performed pathway analysis and identified six candidate pathways comprised of genes related to inflammatory processes and CVDs (CRP, HNF1A, PCSK6, CD36, and ABCA1). In addition to the previously reported loci (CRP, HNF1A, and IL6) in diverse ethnic groups, we identified novel variants in the ARG1 locus associated with CRP levels in Korean population and a number of interesting genes related to inflammatory processes and CVD through pathway analysis. PMID:24763700

  13. Absorption-enhancing effects of gemini surfactant on the intestinal absorption of poorly absorbed hydrophilic drugs including peptide and protein drugs in rats.

    PubMed

    Alama, Tammam; Kusamori, Kosuke; Katsumi, Hidemasa; Sakane, Toshiyasu; Yamamoto, Akira

    2016-02-29

    In general, the intestinal absorption of small hydrophilic molecules and macromolecules like peptides, after oral administration is very poor. Absorption enhancers are considered to be one of the most promising agents to enhance the intestinal absorption of drugs. In this research, we focused on a gemini surfactant, a new type of absorption enhancer. The intestinal absorption of drugs, with or without sodium dilauramidoglutamide lysine (SLG-30), a gemini surfactant, was examined by an in situ closed-loop method in rats. The intestinal absorption of 5(6)-carboxyfluorescein (CF) and fluorescein isothiocyanate-dextrans (FDs) was significantly enhanced in the presence of SLG-30, such effect being reversible. Furthermore, the calcium levels in the plasma significantly decreased when calcitonin was co-administered with SLG-30, suggestive of the increased intestinal absorption of calcitonin. In addition, no significant increase in the of lactate dehydrogenase (LDH) activity or in protein release from the intestinal epithelium was observed in the presence of SLG-30, suggestive of the safety of this compound. These findings indicate that SLG-30 is an effective absorption-enhancer for improving the intestinal absorption of poorly absorbed drugs, without causing serious damage to the intestinal epithelium.

  14. Structure–function analysis of Plasmodium RNA triphosphatase and description of a triphosphate tunnel metalloenzyme superfamily that includes Cet1-like RNA triphosphatases and CYTH proteins

    PubMed Central

    Gong, Chunling; Smith, Paul; Shuman, Stewart

    2006-01-01

    RNA triphosphatase catalyzes the first step in mRNA capping. The RNA triphosphatases of fungi and protozoa are structurally and mechanistically unrelated to the analogous mammalian enzyme, a situation that recommends RNA triphosphatase as an anti-infective target. Fungal and protozoan RNA triphosphatases belong to a family of metal-dependent phosphohydrolases exemplified by yeast Cet1. The Cet1 active site is unusually complex and located within a topologically closed hydrophilic β-barrel (the triphosphate tunnel). Here we probe the active site of Plasmodium falciparum RNA triphosphatase by targeted mutagenesis and thereby identify eight residues essential for catalysis. The functional data engender an improved structural alignment in which the Plasmodium counterparts of the Cet1 tunnel strands and active-site functional groups are located with confidence. We gain insight into the evolution of the Cet1-like triphosphatase family by noting that the heretofore unique tertiary structure and active site of Cet1 are recapitulated in recently deposited structures of proteins from Pyrococcus (PBD 1YEM) and Vibrio (PDB 2ACA). The latter proteins exemplify a CYTH domain found in CyaB-like adenylate cyclases and mammalian thiamine triphosphatase. We conclude that the tunnel fold first described for Cet1 is the prototype of a larger enzyme superfamily that includes the CYTH branch. This superfamily, which we name “triphosphate tunnel metalloenzyme,” is distributed widely among bacterial, archaeal, and eukaryal taxa. It is now clear that Cet1-like RNA triphosphatases did not arise de novo in unicellular eukarya in tandem with the emergence of caps as the defining feature of eukaryotic mRNA. They likely evolved by incremental changes in an ancestral tunnel enzyme that conferred specificity for RNA 5′-end processing. PMID:16809816

  15. Expansion for the Brachylophosaurus canadensis Collagen I Sequence and Additional Evidence of the Preservation of Cretaceous Protein.

    PubMed

    Schroeter, Elena R; DeHart, Caroline J; Cleland, Timothy P; Zheng, Wenxia; Thomas, Paul M; Kelleher, Neil L; Bern, Marshall; Schweitzer, Mary H

    2017-02-03

    Sequence data from biomolecules such as DNA and proteins, which provide critical information for evolutionary studies, have been assumed to be forever outside the reach of dinosaur paleontology. Proteins, which are predicted to have greater longevity than DNA, have been recovered from two nonavian dinosaurs, but these results remain controversial. For proteomic data derived from extinct Mesozoic organisms to reach their greatest potential for investigating questions of phylogeny and paleobiology, it must be shown that peptide sequences can be reliably and reproducibly obtained from fossils and that fragmentary sequences for ancient proteins can be increasingly expanded. To test the hypothesis that peptides can be repeatedly detected and validated from fossil tissues many millions of years old, we applied updated extraction methodology, high-resolution mass spectrometry, and bioinformatics analyses on a Brachylophosaurus canadensis specimen (MOR 2598) from which collagen I peptides were recovered in 2009. We recovered eight peptide sequences of collagen I: two identical to peptides recovered in 2009 and six new peptides. Phylogenetic analyses place the recovered sequences within basal archosauria. When only the new sequences are considered, B. canadensis is grouped more closely to crocodylians, but when all sequences (current and those reported in 2009) are analyzed, B. canadensis is placed more closely to basal birds. The data robustly support the hypothesis of an endogenous origin for these peptides, confirm the idea that peptides can survive in specimens tens of millions of years old, and bolster the validity of the 2009 study. Furthermore, the new data expand the coverage of B. canadensis collagen I (a 33.6% increase in collagen I alpha 1 and 116.7% in alpha 2). Finally, this study demonstrates the importance of reexamining previously studied specimens with updated methods and instrumentation, as we obtained roughly the same amount of sequence data as the

  16. Modification of water absorption capacity of a plastic based on bean protein using gamma irradiated starches as additives

    NASA Astrophysics Data System (ADS)

    Köber, E.; Gonzalez, M. E.; Gavioli, N.; Salmoral, E. M.

    2007-01-01

    Some properties of a bean protein-starch plastic were modified by irradiation of the starch. Two kinds of starch from bean and cassava were irradiated with doses until 50 kGy before their inclusion in the composite. Water absorption of the resultant product was reduced by 36% and 60% in materials containing bean and cassava starch, respectively. A large decline in the elongation is observed till 10 kGy in both materials, while tensile strength diminished by 11% in the cassava composite.

  17. Bioinformatics annotation of the hypothetical proteins found by omics techniques can help to disclose additional virulence factors.

    PubMed

    Hernández, Sergio; Gómez, Antonio; Cedano, Juan; Querol, Enrique

    2009-10-01

    The advent of genomics should have facilitated the identification of microbial virulence factors, a key objective for vaccine design. When the bacterial pathogen infects the host it expresses a set of genes, a number of them being virulence factors. Among the genes identified by techniques as microarrays, in vivo expression technology, signature-tagged mutagenesis and differential fluorescence induction there are many related to cellular stress, basal metabolism, etc., which cannot be directly involved in virulence, or at least cannot be considered useful candidates to be deleted for designing a live attenuated vaccine. Among the genes disclosed by these methodologies there are a number of hypothetical or unknown proteins. As they can hide some true virulence factors, we have reannotated all of these hypothetical proteins from several respiratory pathogens by a careful and in-depth analysis of each one. Although some of the re-annotations match with functions that can be related to microbial virulence, the identification of virulence factors remains difficult.

  18. Affinity and Specificity of Protein U1A-RNA Complex Formation Based on an Additive Component Free Energy Model

    PubMed Central

    Kormos, Bethany L.; Benitex, Yulia; Baranger, Anne M.; Beveridge, David L.

    2007-01-01

    Summary A MM-GBSA computational protocol was used successfully to account for wild type U1A-RNA and F56 U1A mutant experimental binding free energies. The trend in mutant binding free energies compared to wild type is well-reproduced. Following application of a linear-response-like equation to scale the various energy components, the binding free energies agree quantitatively with observed experimental values. Conformational adaptation contributes to the binding free energy for both the protein and the RNA in these systems. Small differences in ΔGs are the result of different and sometimes quite large relative contributions from various energetic components. Residual free energy decomposition indicates differences not only at the site of mutation, but throughout the entire protein. MM-GBSA and ab initio calculations performed on model systems suggest that stacking interactions may nearly, but not completely, account for observed differences in mutant binding affinities. This study indicates that there may be different underlying causes of ostensibly similar experimentally observed binding affinities of different mutants, and thus recommends caution in the interpretation of binding affinities and specificities purely by inspection. PMID:17603075

  19. Azasugar inhibitors as pharmacological chaperones for Krabbe disease† †Electronic supplementary information (ESI) available: Details of IGF, AGF, IGL and DIL syntheses including NMR spectra. Table containing X-ray data collection and refinement statistics. Dose dependence of thermal stabilization of GALC. Controls for DSF assays. IGF- and AGF-mediated stabilization of GALC is buffer and pH dependent. See DOI: 10.1039/c5sc00754b Click here for additional data file. ‡ ‡Data deposition: the atomic coordinates and structure factors have been deposited in the Protein Data Bank, http://www.pdb.org [PDB ID codes 4UFH (IGF), 4UFI (AGF), 4UFJ (IGL), 4UFK (DIL), 4UFL (DGN) and 4UFM (DGJ)].

    PubMed Central

    Hill, Chris H.; Viuff, Agnete H.; Spratley, Samantha J.; Salamone, Stéphane; Christensen, Stig H.; Read, Randy J.; Moriarty, Nigel W.

    2015-01-01

    Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe a new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease. PMID:26029356

  20. Interferon-induced guanylate-binding proteins lack an N(T)KXD consensus motif and bind GMP in addition to GDP and GTP.

    PubMed

    Cheng, Y S; Patterson, C E; Staeheli, P

    1991-09-01

    The primary structures of interferon (IFN)-induced guanylate-binding proteins (GBPs) were deduced from cloned human and murine cDNAs. These proteins contained only two of the three sequence motifs typically found in GTP/GDP-binding proteins. The N(T)KXD motif, which is believed to confer guanine specificity in other nucleotide-binding proteins, was absent. Nevertheless, the IFN-induced GBPs exhibited a high degree of selectivity for binding to agarose-immobilized guanine nucleotides. An interesting feature of IFN-induced GBPs is that they strongly bound to GMP agarose in addition to GDP and GTP agaroses but failed to bind to ATP agarose and all other nucleotide agaroses tested. Both GTP and GMP, but not ATP, competed for binding of murine GBP-1 to agarose-immobilized GMP. The IFN-induced GBPs thus define a distinct novel family of proteins with GTP-binding activity. We further demonstrate that human and murine cells contain at least two genes encoding IFN-induced GBPs. The cloned murine cDNA codes for GBP-1, an IFN-induced protein previously shown to be absent from mice of Gbp-1b genotype.

  1. Surface protein imprinted core-shell particles for high selective lysozyme recognition prepared by reversible addition-fragmentation chain transfer strategy.

    PubMed

    Li, Qinran; Yang, Kaiguang; Liang, Yu; Jiang, Bo; Liu, Jianxi; Zhang, Lihua; Liang, Zhen; Zhang, Yukui

    2014-12-24

    A novel kind of lysozyme (Lys) surface imprinted core-shell particles was synthesized by reversible addition-fragmentation chain transfer (RAFT) strategy. With controllable polymer shell chain length, such particles showed obviously improved selectivity for protein recognition. After the RAFT initial agent and template protein was absorbed on silica particles, the prepolymerization solution, with methacrylic acid and 2-hydroxyethyl methacrylate as the monomers, and N,N'-methylenebis(acrylamide) as the cross-linker, was mixed with the silica particles, and the polymerization was performed at 40 °C in aqueous phase through the oxidation-reduction initiation. Ater polymerization, with the template protein removal and destroying dithioester groups with hexylamine, the surface Lyz imprinted particles were obtained with controllable polymer chain length. The binding capacity of the Lys imprinted particles could reach 5.6 mg protein/g material, with the imprinting factor (IF) as 3.7, whereas the IF of the control material prepared without RAFT strategy was only 1.6. The absorption equilibrium could be achieved within 60 min. Moreover, Lys could be selectively recognized by the imprinted particles from both a four-proteins mixture and egg white sample. All these results demonstrated that these particles prepared by RAFT strategy are promising to achieve the protein recognition with high selectivity.

  2. Group additivity calculation of the standard molal thermodynamic properties of aqueous amino acids, polypeptides and unfolded proteins as a function of temperature, pressure and ionization state

    NASA Astrophysics Data System (ADS)

    Dick, J. M.; Larowe, D. E.; Helgeson, H. C.

    2005-10-01

    Thermodynamic calculation of the chemical speciation of proteins and the limits of protein metastability affords a quantitative understanding of the biogeochemical constraints on the distribution of proteins within and among different organisms and chemical environments. These calculations depend on accurate determination of the ionization states and standard molal Gibbs free energies of proteins as a function of temperature and pressure, which are not generally available. Hence, to aid predictions of the standard molal thermodynamic properties of ionized proteins as a function of temperature and pressure, calculated values are given below of the standard molal thermodynamic properties at 25°C and 1 bar and the revised Helgeson-Kirkham-Flowers equations of state parameters of the structural groups comprising amino acids, polypeptides and unfolded proteins. Group additivity and correlation algorithms were used to calculate contributions by ionized and neutral sidechain and backbone groups to the standard molal Gibbs free energy (Δ G°), enthalpy (Δ H°), entropy (S°), isobaric heat capacity (C°P), volume (V°) and isothermal compressibility (κ°T) of multiple reference model compounds. Experimental values of C°P, V° and κ°T at high temperature were taken from the recent literature, which ensures an internally consistent revision of the thermodynamic properties and equations of state parameters of the sidechain and backbone groups of proteins, as well as organic groups. As a result, Δ G°, Δ H°, S° C°P, V° and κ°T of unfolded proteins in any ionization state can be calculated up to T~-300°C and P~-5000 bars. In addition, the ionization states of unfolded proteins as a function of not only pH, but also temperature and pressure can be calculated by taking account of the degree of ionization of the sidechain and backbone groups present in the sequence. Calculations of this kind represent a first step in the prediction of chemical affinities of many

  3. Two additional human serum proteins structurally related to complement factor H: Evidence for a family of factor H-related genes

    SciTech Connect

    Skerka, C.; Timmann, C.; Horstmann, R.D. ); Zipfel, P.F.

    1992-05-15

    The authors identify and characterize two human serum proteins with an apparent molecular mass of 24 and 29 kDa, which are antigenically related to complement factor H. These proteins represent differently glycosylated forms and are encoded by the same mRNA. The corresponding cDNA clone is 1051 bp in size and hybridized to a 1.4-kb mRNA derived from human liver. The predicted translation product represents a protein of 270 amino acids, which displays a hydrophobic leader sequence, indicative of a secreted protein. The secreted part is organized in four short consensus repeats (SCR) and has a single putative N-linked glycosylation site. The predicted sequence is closely related to that of the previously described factor H-related proteins h37 and h42, which are also derived from a 1.4-kb mRNA. Amino acid comparison of these factor H-related proteins showed identical leader sequences, an exchange of three amino acids in SCR1, identical sequences of SCR2, and a lower degree of homology between SCR3-4 (h24 and h29) and SCR4-5 (h37 and h42). In addition, SCR3-4 of h24 and h29 display homology to SCR19-20 of human complement factor H. The relatedness of structural elements of the factor H-related proteins h24, h29, h37, and h42 and of factor H, suggests a function common to these proteins and indicates the existence of a gene family consisting of factor H and at least two factor H-related genes. 28 refs., 7 figs., 1 tab.

  4. Simultaneous quantification of five proteins and seven additives in dairy products with a heart-cutting two-dimensional liquid chromatography method.

    PubMed

    Hou, Xiaofang; Sun, Meng; He, Xiaoshuang; Chen, Liang; Zhang, Ping; He, Langchong

    2015-09-01

    A heart-cutting two-dimensional high-performance liquid chromatography method was developed to simultaneously quantify five major proteins and seven food additives (maltol, ethyl maltol, vanillin, ethyl vanillin, benzoic acid, sorbic acid, and saccharin sodium) in milk and milk powders. In this two-dimensional system, a Venusil XBP-C4 column was selected in the first dimension for protein separation, and a Hypersil ODS-2 C18 column was employed in the second dimension for additive separation; a two-position, six-port switching valve was used to transfer the targets (additives) from the first dimension to the second dimension. Method validation consisted of selectivity, response function, linearity, precision, sensitivity, and recovery. In addition, a conventional one-dimensional high-performance liquid chromatography method was also tested for comparison. The two-dimensional method resulted in significantly improved recovery of the food additives compared to the conventional method (90.6-105.4% and 65.5-86.5%, respectively). Furthermore, this novel method has a simple one-step sample preparation procedure, which shortens the analysis time, resulting in more efficient analysis and less solvent usage.

  5. Solvation free energy of the peptide group: its model dependence and implications for the additive-transfer free-energy model of protein stability.

    PubMed

    Tomar, Dheeraj S; Asthagiri, D; Weber, Valéry

    2013-09-17

    The group-additive decomposition of the unfolding free energy of a protein in an osmolyte solution relative to that in water poses a fundamental paradox: whereas the decomposition describes the experimental results rather well, theory suggests that a group-additive decomposition of free energies is, in general, not valid. In a step toward resolving this paradox, here we study the peptide-group transfer free energy. We calculate the vacuum-to-solvent (solvation) free energies of (Gly)n and cyclic diglycine (cGG) and analyze the data according to experimental protocol. The solvation free energies of (Gly)n are linear in n, suggesting group additivity. However, the slope interpreted as the free energy of a peptide unit differs from that for cGG scaled by a factor of half, emphasizing the context dependence of solvation. However, the water-to-osmolyte transfer free energies of the peptide unit are relatively independent of the peptide model, as observed experimentally. To understand these observations, a way to assess the contribution to the solvation free energy of solvent-mediated correlation between distinct groups is developed. We show that linearity of solvation free energy with n is a consequence of uniformity of the correlation contributions, with apparent group-additive behavior in the water-to-osmolyte transfer arising due to their cancellation. Implications for inferring molecular mechanisms of solvent effects on protein stability on the basis of the group-additive transfer model are suggested.

  6. Quantitative mass spectrometric analysis of dipeptides in protein hydrolysate by a TNBS derivatization-aided standard addition method.

    PubMed

    Hanh, Vu Thi; Kobayashi, Yutaro; Maebuchi, Motohiro; Nakamori, Toshihiro; Tanaka, Mitsuru; Matsui, Toshiro

    2016-01-01

    The aim of this study was to establish, through a standard addition method, a convenient quantification assay for dipeptides (GY, YG, SY, YS, and IY) in soybean hydrolysate using 2,4,6-trinitrobenzene sulfonate (TNBS) derivatization-aided LC-TOF-MS. Soybean hydrolysate samples (25.0 mg mL(-1)) spiked with target standards were subjected to TNBS derivatization. Under the optimal LC-MS conditions, five target dipeptides derivatized with TNBS were successfully detected. Examination of the standard addition curves, with a correlation coefficient of r(2) > 0.979, provided a reliable quantification of the target dipeptides, GY, YG, SY, YS, and IY, in soybean hydrolysate to be 424 ± 20, 184 ± 9, 2188 ± 199, 327 ± 16, and 2211 ± 133 μg g(-1) of hydrolysate, respectively. The proposed LC-MS assay is a reliable and convenient assay method, with no interference from matrix effects in hydrolysate, and with no requirement for the use of an isotope labeled internal standard.

  7. Enzymes as feed additive to aid in responses against Eimeria species in coccidia-vaccinated broilers fed corn-soybean meal diets with different protein levels.

    PubMed

    Parker, J; Oviedo-Rondón, E O; Clack, B A; Clemente-Hernández, S; Osborne, J; Remus, J C; Kettunen, H; Mäkivuokko, H; Pierson, E M

    2007-04-01

    This research aimed to evaluate the effects of adding a combination of exogenous enzymes to starter diets varying in protein content and fed to broilers vaccinated at day of hatch with live oocysts and then challenged with mixed Eimeria spp. Five hundred four 1-d-old male Cobb-500 chickens were distributed in 72 cages. The design consisted of 12 treatments. Three anticoccidial control programs [ionophore (IO), coccidian vaccine (COV), and coccidia-vaccine + enzymes (COV + EC)] were evaluated under 3 CP levels (19, 21, and 23%), and 3 unmedicated-uninfected (UU) negative controls were included for each one of the protein levels. All chickens except those in unmedicated-uninfected negative controls were infected at 17 d of age with a mixed oral inoculum of Eimeria acervulina, Eimeria maxima, and Eimeria tenella. Live performance, lesion scores, oocyst counts, and samples for gut microflora profiles were evaluated 7 d postinfection. Ileal digestibility of amino acids (IDAA) was determined 8 d postinfection. Microbial communities (MC) were analyzed by G + C%, microbial numbers were counted by flow cytometry, and IgA concentrations were measured by ELISA. The lowest CP diets had poorer (P < or = 0.001) BW gain and feed conversion ratio in the preinfection period. Coccidia-vaccinated broilers had lower performance than the ones fed ionophore diets during pre- and postchallenge periods. Intestinal lesion scores were affected (P < or = 0.05) by anticoccidial control programs, but responses changed according to gut section. Feed additives or vaccination had no effect (P > or = 0.05) on IDAA, and diets with 23% CP had the lowest (P < or = 0.001) IDAA. Coccidial infection had no effect on MC numbers in the ileum but reduced MC numbers in ceca and suppressed ileal IgA production. The COV + EC treatment modulated MC during mixed coccidiosis infection but did not significantly improve chicken performance. Results indicated that feed enzymes may be used to modulate the gut

  8. Gabapentin Inhibits Protein Kinase C Epsilon Translocation in Cultured Sensory Neurons with Additive Effects When Coapplied with Paracetamol (Acetaminophen)

    PubMed Central

    2017-01-01

    Gabapentin is a well-established anticonvulsant drug which is also effective for the treatment of neuropathic pain. Although the exact mechanism leading to relief of allodynia and hyperalgesia caused by neuropathy is not known, the blocking effect of gabapentin on voltage-dependent calcium channels has been proposed to be involved. In order to further evaluate its analgesic mechanisms, we tested the efficacy of gabapentin on protein kinase C epsilon (PKCε) translocation in cultured peripheral neurons isolated from rat dorsal root ganglia (DRGs). We found that gabapentin significantly reduced PKCε translocation induced by the pronociceptive peptides bradykinin and prokineticin 2, involved in both inflammatory and chronic pain. We recently showed that paracetamol (acetaminophen), a very commonly used analgesic drug, also produces inhibition of PKCε. We tested the effect of the combined use of paracetamol and gabapentin, and we found that the inhibition of translocation adds up. Our study provides a novel mechanism of action for gabapentin in sensory neurons and suggests a mechanism of action for the combined use of paracetamol and gabapentin, which has recently been shown to be effective, with a cumulative behavior, in the control of postoperative pain in human patients. PMID:28299349

  9. Gabapentin Inhibits Protein Kinase C Epsilon Translocation in Cultured Sensory Neurons with Additive Effects When Coapplied with Paracetamol (Acetaminophen).

    PubMed

    Vellani, Vittorio; Giacomoni, Chiara

    2017-01-01

    Gabapentin is a well-established anticonvulsant drug which is also effective for the treatment of neuropathic pain. Although the exact mechanism leading to relief of allodynia and hyperalgesia caused by neuropathy is not known, the blocking effect of gabapentin on voltage-dependent calcium channels has been proposed to be involved. In order to further evaluate its analgesic mechanisms, we tested the efficacy of gabapentin on protein kinase C epsilon (PKCε) translocation in cultured peripheral neurons isolated from rat dorsal root ganglia (DRGs). We found that gabapentin significantly reduced PKCε translocation induced by the pronociceptive peptides bradykinin and prokineticin 2, involved in both inflammatory and chronic pain. We recently showed that paracetamol (acetaminophen), a very commonly used analgesic drug, also produces inhibition of PKCε. We tested the effect of the combined use of paracetamol and gabapentin, and we found that the inhibition of translocation adds up. Our study provides a novel mechanism of action for gabapentin in sensory neurons and suggests a mechanism of action for the combined use of paracetamol and gabapentin, which has recently been shown to be effective, with a cumulative behavior, in the control of postoperative pain in human patients.

  10. Pairwise additivity of energy components in protein-ligand binding: The HIV II protease-Indinavir case

    NASA Astrophysics Data System (ADS)

    Ucisik, Melek N.; Dashti, Danial S.; Faver, John C.; Merz, Kenneth M.

    2011-08-01

    An energy expansion (binding energy decomposition into n-body interaction terms for n ≥ 2) to express the receptor-ligand binding energy for the fragmented HIV II protease-Indinavir system is described to address the role of cooperativity in ligand binding. The outcome of this energy expansion is compared to the total receptor-ligand binding energy at the Hartree-Fock, density functional theory, and semiempirical levels of theory. We find that the sum of the pairwise interaction energies approximates the total binding energy to ˜82% for HF and to >95% for both the M06-L density functional and PM6-DH2 semiempirical method. The contribution of the three-body interactions amounts to 18.7%, 3.8%, and 1.4% for HF, M06-L, and PM6-DH2, respectively. We find that the expansion can be safely truncated after n = 3. That is, the contribution of the interactions involving more than three parties to the total binding energy of Indinavir to the HIV II protease receptor is negligible. Overall, we find that the two-body terms represent a good approximation to the total binding energy of the system, which points to pairwise additivity in the present case. This basic principle of pairwise additivity is utilized in fragment-based drug design approaches and our results support its continued use. The present results can also aid in the validation of non-bonded terms contained within common force fields and in the correction of systematic errors in physics-based score functions.

  11. The human myelin basic protein gene is included within a 179-kilobase transcription unit: Expression in the immune and central nervous systems

    SciTech Connect

    Pribyl, T.M.; Campagnoni, C.W.; Kampf, K.; Kashima, T.; Handley, V.W.; Campagnoni, A.T. ); McMahon, J. )

    1993-11-15

    Two human Golli (for gene expressed in the oligodendrocyte lineage)-MBP (for myelin basic protein) cDNAs have been isolated from a human oligodendroglioma cell line. Analysis of these cDNAs has enabled the authors to determine the entire structure of the human Golli-MBP gene. The Golli-MBP gene, which encompasses the MBP transcription unit, is [approx] 179 kb in length and consists of 10 exons, seven of which constitute the MBP gene. The human Golli-MBP gene contains two transcription start sites, each of which gives rise to a family of alternatively spliced transcipts. At least two Golli-MBP transcripts, containing the first three exons of the gene and one or more MBP exons, are produced from the first transcription start site. The second family of transcripts contains only MBP exons and produces the well-known MBPs. In humans, RNA blot analysis revealed that Golli-MBP transcripts were expressed in fetal thymus, spleen, and human B-cell and macrophage cell lines, as well as in fetal spinal cord. These findings clearly link the expression of exons encoding the autoimmunogen/encephalitogen MBP in the central nervous system to cells and tissues of the immune system through normal expression of the Golli-MBP gene. They also establish that this genetic locus, which includes the MBP gene, is conserved among species, providing further evidence that the MBP transcription unit is an integral part of the Golli transcription unit and suggest that this structural arrangement is important for the genetic function and/or regulation of these genes.

  12. Bioinformatic analyses of the publicly accessible crustacean expressed sequence tags (ESTs) reveal numerous novel neuropeptide-encoding precursor proteins, including ones from members of several little studied taxa.

    PubMed

    Christie, Andrew E; Durkin, Christopher S; Hartline, Niko; Ohno, Paul; Lenz, Petra H

    2010-05-15

    ESTs have been generated for many crustacean species, providing an invaluable resource for peptide discovery in members of this arthropod subphylum. Here, these data were mined for novel peptide-encoding transcripts, with the mature peptides encoded by them predicted using a combination of online peptide prediction programs and homology to known arthropod sequences. In total, 70 mature full-length/partial peptides representing members of 16 families/subfamilies were predicted, the vast majority being novel; the species from which the peptides were identified included members of the Branchiopoda (Daphnia carinata and Triops cancriformis), Maxillopoda (Caligus clemensi, Caligus rogercresseyi, Lepeophtheirus salmonis and Lernaeocera branchialis) and Malacostraca (Euphausia superba, Marsupenaeus japonicus, Penaeus monodon, Homarus americanus, Petrolisthes cinctipes, Callinectes sapidus and Portunus trituberculatus). Of particular note were the identifications of an intermediate between the insect adipokinetic hormones and crustacean red pigment concentrating hormone and a modified crustacean cardioactive peptide from the daphnid D. carinata; Arg(7)-corazonin was also deduced from this species, the first identification of a corazonin from a non-decapod crustacean. Our data also include the first reports of members of the calcitonin-like diuretic hormone, FMRFamide-related peptide (neuropeptide F subfamily) and orcokinin families from members of the Copepoda. Moreover, the prediction of a bursicon alpha from the euphausid E. superba represents the first peptide identified from any member of the basal eucaridean order Euphausiacea. In addition, large collections of insect eclosion hormone- and neuroparsin-like peptides were identified from a variety of species, greatly expanding the number of known members of these families in crustaceans.

  13. Improvement of texture and sensory properties of cakes by addition of potato peel powder with high level of dietary fiber and protein.

    PubMed

    Ben Jeddou, Khawla; Bouaziz, Fatma; Zouari-Ellouzi, Soumaya; Chaari, Fatma; Ellouz-Chaabouni, Semia; Ellouz-Ghorbel, Raoudha; Nouri-Ellouz, Oumèma

    2017-02-15

    Demand for health oriented products such as low calories and high fiber product is increasing. The aim of the present work was to determine the effect of the addition of potato peel powders as protein and dietary fiber source on the quality of the dough and the cake. Powders obtained from the two types of peel flour showed interesting water binding capacity and fat absorption capacity. Potato peel flours were incorporated in wheat flours at different concentration. The results showed that peel powders additionally considerably improved the Alveograph profile of dough and the texture of the prepared cakes. In addition color measurements showed a significant difference between the control dough and the dough containing potato peels. The replacement of wheat flour with the potato powders reduced the cake hardness significantly and the L(*) and b(*) dough color values. The increased consumption of cake enriched with potato peel fiber is proposed for health reasons. The study demonstrated that protein/fiber-enriched cake with good sensory quality could be produced by the substitution of wheat flour by 5% of potato peel powder. In addition and technological point of view, the incorporation of potato peel powder at 5% increase the dough strength and elasticity-to-extensibility ratio (P/L).

  14. Measurement of $\\mathrm{ t \\bar{t} } $ production with additional jet activity, including b quark jets, in the dilepton decay channel using pp collisions at $\\sqrt{s} =$ 8 TeV

    SciTech Connect

    Khachatryan, Vardan

    2016-07-07

    Jet multiplicity distributions in top quark pair (tt-bar) events are measured in pp collisions at a centre-of-mass energy of 8 TeV with the CMS detector at the LHC using a data set corresponding to an integrated luminosity of 19.7 fb-1. The measurement is performed in the dilepton decay channels (e+e-+μ- and e±μ). Furthermore, the absolute and normalized differential cross sections for tt-bar production are measured as a function of the jet multiplicity in the event for different jet transverse momentum thresholds and the kinematic properties of the leading additional jets. The differential tt-barb and tt-barbb-bar cross sections are presented for the first time as a function of the kinematic properties of the leading additional b jets. Furthermore, the fraction of events without additional jets above a threshold is measured as a function of the transverse momenta of the leading additional jets and the scalar sum of the transverse momenta of all additional jets. Finally, the data are compared and found to be consistent with predictions from several perturbative quantum chromodynamics event generators and a next-to-leading ordercalculation.

  15. Measurement of $$\\mathrm{ t \\bar{t} } $$ production with additional jet activity, including b quark jets, in the dilepton decay channel using pp collisions at $$\\sqrt{s} =$$ 8 TeV

    DOE PAGES

    Khachatryan, Vardan

    2016-07-07

    Jet multiplicity distributions in top quark pair (tt-bar) events are measured in pp collisions at a centre-of-mass energy of 8 TeV with the CMS detector at the LHC using a data set corresponding to an integrated luminosity of 19.7 fb-1. The measurement is performed in the dilepton decay channels (e+e-,μ+μ- and e±μ∓). Furthermore, the absolute and normalized differential cross sections for tt-bar production are measured as a function of the jet multiplicity in the event for different jet transverse momentum thresholds and the kinematic properties of the leading additional jets. The differential tt-barb and tt-barbb-bar cross sections are presented formore » the first time as a function of the kinematic properties of the leading additional b jets. Furthermore, the fraction of events without additional jets above a threshold is measured as a function of the transverse momenta of the leading additional jets and the scalar sum of the transverse momenta of all additional jets. Finally, the data are compared and found to be consistent with predictions from several perturbative quantum chromodynamics event generators and a next-to-leading ordercalculation.« less

  16. Measurement of toverline{t} production with additional jet activity, including b quark jets, in the dilepton decay channel using pp collisions at √{s} = 8 {TeV}

    NASA Astrophysics Data System (ADS)

    Khachatryan, V.; Sirunyan, A. M.; Tumasyan, A.; Adam, W.; Asilar, E.; Bergauer, T.; Brandstetter, J.; Brondolin, E.; Dragicevic, M.; Erö, J.; Friedl, M.; Frühwirth, R.; Ghete, V. M.; Hartl, C.; Hörmann, N.; Hrubec, J.; Jeitler, M.; Knünz, V.; König, A.; Krammer, M.; Krätschmer, I.; Liko, D.; Matsushita, T.; Mikulec, I.; Rabady, D.; Rahbaran, B.; Rohringer, H.; Schieck, J.; Schöfbeck, R.; Strauss, J.; Treberer-Treberspurg, W.; Waltenberger, W.; Wulz, C.-E.; Mossolov, V.; Shumeiko, N.; Suarez Gonzalez, J.; Alderweireldt, S.; Cornelis, T.; de Wolf, E. A.; Janssen, X.; Knutsson, A.; Lauwers, J.; Luyckx, S.; van de Klundert, M.; van Haevermaet, H.; van Mechelen, P.; van Remortel, N.; van Spilbeeck, A.; Abu Zeid, S.; Blekman, F.; D'Hondt, J.; Daci, N.; de Bruyn, I.; Deroover, K.; Heracleous, N.; Keaveney, J.; Lowette, S.; Moreels, L.; Olbrechts, A.; Python, Q.; Strom, D.; Tavernier, S.; van Doninck, W.; van Mulders, P.; van Onsem, G. P.; van Parijs, I.; Barria, P.; Brun, H.; Caillol, C.; Clerbaux, B.; de Lentdecker, G.; Fasanella, G.; Favart, L.; Grebenyuk, A.; Karapostoli, G.; Lenzi, T.; Léonard, A.; Maerschalk, T.; Marinov, A.; Perniè, L.; Randle-Conde, A.; Reis, T.; Seva, T.; Vander Velde, C.; Yonamine, R.; Vanlaer, P.; Yonamine, R.; Zenoni, F.; Zhang, F.; Adler, V.; Beernaert, K.; Benucci, L.; Cimmino, A.; Crucy, S.; Dobur, D.; Fagot, A.; Garcia, G.; Gul, M.; McCartin, J.; Ocampo Rios, A. A.; Poyraz, D.; Ryckbosch, D.; Salva, S.; Sigamani, M.; Strobbe, N.; Tytgat, M.; van Driessche, W.; Yazgan, E.; Zaganidis, N.; Basegmez, S.; Beluffi, C.; Bondu, O.; Brochet, S.; Bruno, G.; Caudron, A.; Ceard, L.; da Silveira, G. G.; Delaere, C.; Favart, D.; Forthomme, L.; Giammanco, A.; Hollar, J.; Jafari, A.; Jez, P.; Komm, M.; Lemaitre, V.; Mertens, A.; Musich, M.; Nuttens, C.; Perrini, L.; Pin, A.; Piotrzkowski, K.; Popov, A.; Quertenmont, L.; Selvaggi, M.; Vidal Marono, M.; Beliy, N.; Hammad, G. H.; Júnior, W. L. Aldá; Alves, F. L.; Alves, G. A.; Brito, L.; Correa Martins Junior, M.; Hamer, M.; Hensel, C.; Mora Herrera, C.; Moraes, A.; Pol, M. E.; Rebello Teles, P.; Belchior Batista Das Chagas, E.; Carvalho, W.; Chinellato, J.; Custódio, A.; da Costa, E. M.; de Jesus Damiao, D.; de Oliveira Martins, C.; Fonseca de Souza, S.; Huertas Guativa, L. M.; Malbouisson, H.; Matos Figueiredo, D.; Mundim, L.; Nogima, H.; Prado da Silva, W. L.; Santoro, A.; Sznajder, A.; Tonelli Manganote, E. J.; Vilela Pereira, A.; Ahuja, S.; Bernardes, C. A.; de Souza Santos, A.; Dogra, S.; Fernandez Perez Tomei, T. R.; Gregores, E. M.; Mercadante, P. G.; Moon, C. S.; Novaes, S. F.; Padula, Sandra S.; Romero Abad, D.; Ruiz Vargas, J. C.; Aleksandrov, A.; Hadjiiska, R.; Iaydjiev, P.; Rodozov, M.; Stoykova, S.; Sultanov, G.; Vutova, M.; Dimitrov, A.; Glushkov, I.; Litov, L.; Pavlov, B.; Petkov, P.; Ahmad, M.; Bian, J. G.; Chen, G. M.; Chen, H. S.; Chen, M.; Cheng, T.; Du, R.; Jiang, C. H.; Plestina, R.; Romeo, F.; Shaheen, S. M.; Spiezia, A.; Tao, J.; Wang, C.; Wang, Z.; Zhang, H.; Asawatangtrakuldee, C.; Ban, Y.; Li, Q.; Liu, S.; Mao, Y.; Qian, S. J.; Wang, D.; Xu, Z.; Avila, C.; Cabrera, A.; Chaparro Sierra, L. F.; Florez, C.; Gomez, J. P.; Gomez Moreno, B.; Sanabria, J. C.; Godinovic, N.; Lelas, D.; Puljak, I.; Ribeiro Cipriano, P. M.; Antunovic, Z.; Kovac, M.; Brigljevic, V.; Kadija, K.; Luetic, J.; Micanovic, S.; Sudic, L.; Attikis, A.; Mavromanolakis, G.; Mousa, J.; Nicolaou, C.; Ptochos, F.; Razis, P. A.; Rykaczewski, H.; Bodlak, M.; Finger, M.; Finger, M.; El Sawy, M.; El-Khateeb, E.; Elkafrawy, T.; Mohamed, A.; Salama, E.; Calpas, B.; Kadastik, M.; Murumaa, M.; Raidal, M.; Tiko, A.; Veelken, C.; Eerola, P.; Pekkanen, J.; Voutilainen, M.; Härkönen, J.; Karimäki, V.; Kinnunen, R.; Lampén, T.; Lassila-Perini, K.; Lehti, S.; Lindén, T.; Luukka, P.; Mäenpää, T.; Peltola, T.; Tuominen, E.; Tuominiemi, J.; Tuovinen, E.; Wendland, L.; Talvitie, J.; Tuuva, T.; Besancon, M.; Couderc, F.; Dejardin, M.; Denegri, D.; Fabbro, B.; Faure, J. L.; Favaro, C.; Ferri, F.; Ganjour, S.; Givernaud, A.; Gras, P.; Hamel de Monchenault, G.; Jarry, P.; Locci, E.; Machet, M.; Malcles, J.; Rander, J.; Rosowsky, A.; Titov, M.; Zghiche, A.; Antropov, I.; Baffioni, S.; Beaudette, F.; Busson, P.; Cadamuro, L.; Chapon, E.; Charlot, C.; Dahms, T.; Davignon, O.; Filipovic, N.; Florent, A.; Granier de Cassagnac, R.; Lisniak, S.; Mastrolorenzo, L.; Miné, P.; Naranjo, I. N.; Nguyen, M.; Ochando, C.; Ortona, G.; Paganini, P.; Pigard, P.; Regnard, S.; Salerno, R.; Sauvan, J. B.; Sirois, Y.; Strebler, T.; Yilmaz, Y.; Zabi, A.; Agram, J.-L.; Andrea, J.; Aubin, A.; Bloch, D.; Brom, J.-M.; Buttignol, M.; Chabert, E. C.; Chanon, N.; Collard, C.; Conte, E.; Coubez, X.; Fontaine, J.-C.; Gelé, D.; Goerlach, U.; Goetzmann, C.

    2016-07-01

    Jet multiplicity distributions in top quark pair ({t}{overline{t}}) events are measured in pp collisions at a centre-of-mass energy of 8 TeV with the CMS detector at the LHC using a data set corresponding to an integrated luminosity of 19.7 {fb}^ {-1}. The measurement is performed in the dilepton decay channels (e^+e^-, μ^+ μ^-, and e^{±} μ^{∓}). The absolute and normalized differential cross sections for {t}overline{t} production are measured as a function of the jet multiplicity in the event for different jet transverse momentum thresholds and the kinematic properties of the leading additional jets. The differential {t overline{t} b} and {t overline{t} b overline{b}} cross sections are presented for the first time as a function of the kinematic properties of the leading additional b jets. Furthermore, the fraction of events without additional jets above a threshold is measured as a function of the transverse momenta of the leading additional jets and the scalar sum of the transverse momenta of all additional jets. The data are compared and found to be consistent with predictions from several perturbative quantum chromodynamics event generators and a next-to-leading order calculation.

  17. Dietary soya protein intake and exercise training have an additive effect on skeletal muscle fatty acid oxidation enzyme activities and mRNA levels in rats.

    PubMed

    Morifuji, Masashi; Sanbongi, Chiaki; Sugiura, Katsumi

    2006-09-01

    Exercise training and regular physical activity increase oxidation of fat. Enhanced oxidation of fat is important for preventing lifestyle diseases such as hypertension and obesity. The aim of the present study in rats was to determine whether intake of dietary soya protein and exercise training have an additive effect on the activity and mRNA expression of enzymes involved in skeletal muscle fatty acid oxidation. Male Sprague-Dawley rats (n 32) were assigned randomly into four groups (eight rats per group) and then divided further into sedentary or exercise-trained groups fed either casein or soya protein diets. Rats in the exercise groups were trained for 2 weeks by swimming for 120 min/d, 6 d/week. Exercise training decreased hepatic triacylglycerol levels and retroperitoneal adipose tissue weight and increased skeletal muscle carnitine palmitoyltransferase 1 (CPT1) activity and mRNA expression of CPT1, beta-hydroxyacyl-CoA dehydrogenase (HAD), acyl-CoA oxidase, PPARgamma coactivator 1alpha (PGC1alpha) and PPARalpha. Soya protein significantly decreased hepatic triacylglycerol levels and epididymal adipose tissue weight and increased skeletal muscle CPT1 activity and CPT1, HAD, acyl-CoA oxidase, medium-chain acyl-CoA dehydrogenase, PGC1alpha and PPARalpha mRNA levels. Furthermore, skeletal muscle HAD activity was the highest in exercise-trained rats fed soya protein. We conclude that exercise training and soya protein intake have an important additive role on induction of PPAR pathways, leading to increased activity and mRNA expression of enzymes involved in fatty acid oxidation in skeletal muscle and reduced accumulation of body fat.

  18. Tandem Mass Spectrometry identifies many mouse brain O-GlcNAcylated proteins including EGF domain-specific O-GlcNAc transferase targets

    SciTech Connect

    Alfaro, Joshua F.; Gong, Cheng-Xin; Monroe, Matthew E.; Aldrich, Joshua T.; Clauss, Therese RW; Purvine, Samuel O.; Wang, Zihao; Camp, David G.; Shabanowitz, Jeffrey; Stanley, Pamela; Hart, Gerald W.; Hunt, Donald F.; Yang, Feng; Smith, Richard D.

    2012-05-08

    O-Linked N-Acetylglucosamine (O-GlcNAc) is a reversible post-translational modification of Ser and Thr residues on cytosolic and nuclear proteins found in all higher eukaryotes. Aberrant O-GlcNAc modification of brain proteins has been linked to Alzheimer's disease (AD). However, understanding specific functions of O-GlcNAcylation in AD has been impeded by the difficulty in characterization of O-GlcNAc sites on proteins. In this study, we modified a chemical/enzymatic photochemical cleavage approach for enriching O-GlcNAcylated peptides in samples containing {approx}100 {micro}g of tryptic peptides from mouse cerebrocortical brain tissue. A total of 274 O-GlcNAcylated proteins were identified. Of these 168 were not previously known to be modified by O-GlcNAc. Overall, 458 O-GlcNAc sites on Ser and Thr residues in 195 proteins were identified. Many of the modified residues are either known phosphorylation sites or located in close proximity to known phosphorylation sites. These findings support the proposed regulatory crosstalk between O-GlcNAcylation and phosphorylation. This study produced the most comprehensive O-GlcNAc proteome of mammalian brain tissue with both protein identification and O-GlcNAc site assignment. Interestingly, we observed O-{beta}-GlcNAc on EGF-like repeats in the extracellular domains of five membrane proteins, thus representing the first evidence for extracellular O-GlcNAcylation in mammalian systems by the ER-resident O-GlcNAc transferase (EOGT). We also report a GlcNAc-{beta}-1,3-Fuc-{alpha}-1-O-Thr modification on the EGF-like repeat of the Versican core protein, a novel substrate of Fringe {beta}1,3-N-acetylglucosaminyltransferases.

  19. The Saccharomyces cerevisiae poly(A)-binding protein is subject to multiple post-translational modifications, including the methylation of glutamic acid.

    PubMed

    Low, Jason K K; Hart-Smith, Gene; Erce, Melissa A; Wilkins, Marc R

    2014-01-10

    Poly(A)-binding protein in mouse and man was recently found to be highly post-translationally modified. Here we analysed an ortholog of this protein, Pab1 from Saccharomyces cerevisiae, to assess the conservation and thus likely importance of these modifications. Pab1 showed the presence of six sites of methylated glutamate, five sites of lysine acetylation, and one phosphorylation of serine. Many modifications on Pab1 showed either complete conservation with those on human or mouse PABPC1, were present on nearby residues and/or were present in the same domain(s). The conservation of methylated glutamate, an unusual modification, was of particular note and suggests a conserved function. Comparison of methylated glutamate sites in human, mouse and yeast poly(A)-binding protein, along with methylation sites catalysed by CheR L-glutamyl protein methyltransferase from Salmonella typhimurium, revealed that the methylation of glutamate preferentially occurs in EE and DE motifs or other small regions of acidic amino acids. The conservation of methylated glutamate in the same protein between mouse, man and yeast suggests the presence of a eukaryotic l-glutamyl protein methyltransferase and that the modification is of functional significance.

  20. The E1 replication protein of bovine papillomavirus type 1 contains an extended nuclear localization signal that includes a p34cdc2 phosphorylation site.

    PubMed Central

    Lentz, M R; Pak, D; Mohr, I; Botchan, M R

    1993-01-01

    Bovine papillomavirus (BPV) DNA replication occurs in the nucleus of infected cells. Most enzymatic activities are carried out by host cell proteins, with the viral E1 and E2 proteins required for the assembly of an initiation complex at the replication origin. In latently infected cells, viral DNA replication occurs in synchrony with the host cell chromosomes, maintaining a constant average copy number of BPV genomes per infected cell. By analyzing a series of mutants of the amino-terminal region of the E1 protein, we have identified the signal for transport of this protein to the cell nucleus. The E1 nuclear transport motif is highly conserved in the animal and human papillomaviruses and is encoded in a similar region in the related E1 genes. The signal is extended relative to the simple nuclear localization signals and contains two short amino acid sequences which contribute to nuclear transport, located between amino acids 85 and 108 of the BPV-1 E1 protein. Mutations in either basic region reduce nuclear transport of E1 protein and interfere with viral DNA replication. Mutations in both sequences simultaneously prevent any observable accumulation of the protein and reduce replication in transient assays to barely detectable levels. Surprisingly, these mutations had no effect on the ability of viral genomes to morphologically transform cells, although the plasmid DNA in the transformed cells was maintained at a very low copy number. Between these two basic amino acid blocks in the nuclear transport signal, at threonine 102, is a putative site for phosphorylation by the cell cycle regulated kinase p34cdc2. Utilizing an E1 protein purified from either a baculovirus vector system or Escherichia coli, we have shown that the E1 protein is a substrate for this kinase. An E1 gene mutant at threonine 102 encodes for a protein which is no longer a substrate for the p34cdc2 kinase. Mutation of this threonine to isoleucine had no observable effect on either nuclear

  1. A factor that regulates the class II major histocompatibility complex gene DPA is a member of a subfamily of zinc finger proteins that includes a Drosophila developmental control protein.

    PubMed Central

    Sugawara, M; Scholl, T; Ponath, P D; Strominger, J L

    1994-01-01

    A novel DNA sequence element termed the J element involved in the regulated expression of class II major histocompatibility complex genes was recently described. To study this element and its role in class II gene regulation further, a cDNA library was screened with oligonucleotide probes containing both the S element and the nearby J element of the human DPA gene. Several DNA clones were obtained by this procedure, one of which, clone 18, is reported and characterized here. It encodes a protein predicted to contain 688 amino acid residues, including 11 zinc finger motifs of the C2H2 type in the C-terminal region, that are Krüppel-like in the conservation of the H/C link sequence connecting them. The 160 N-terminal amino acids in the nonfinger region of clone 18 are highly homologous with similar regions of several other human, mouse, and Drosophila sequences, defining a subfamily of Krüppel-like zinc finger proteins termed TAB (tramtrack [ttk]-associated box) here. One of the Drosophila sequences, ttk, is a developmental control gene, while a second does not contain a zinc finger region but encodes a structure important in oocyte development. An acidic activation domain is located between the N-terminal conserved region of clone 18 and its zinc fingers. This protein appears to require both the S and J elements, which are separated by 10 bp for optimal binding. Antisense cDNA to clone 18 inhibited the expression of a reporter construct containing the DPA promoter, indicating its functional importance in the expression of this class II gene. Images PMID:7969177

  2. Soldier use of dietary supplements, including protein and body building supplements, in a combat zone is different than use in garrison.

    PubMed

    Austin, Krista G; McLellan, Tom M; Farina, Emily K; McGraw, Susan M; Lieberman, Harris R

    2016-01-01

    United States Army personnel in garrison who are not deployed to combat theater report using dietary supplements (DSs) to promote health, increase physical and mental strength, and improve energy levels. Given the substantial physical and cognitive demands of combat, DS use may increase during deployment. This study compared DS use by garrison soldiers with DS use by personnel deployed to a combat theater in Afghanistan. Prevalence and patterns of DS use, demographic factors, and health behaviors were assessed by survey (deployed n = 221; garrison n = 1001). Eighty-two percent of deployed and 74% of garrison soldiers used DSs ≥ 1 time·week(-1). Logistic regression analyses, adjusted for significant demographic and health predictors of DS use, showed deployed personnel were more likely than garrison soldiers to use protein, amino acids, and combination products. Deployed females were more likely to use protein supplements and deployed males were more likely to use multivitamins, combination products, protein, and body building supplements than garrison respondents. Significantly more deployed (17%) than garrison (10%) personnel spent more than $50∙month(-1) on DSs. Higher protein supplement use among deployed personnel was associated with higher frequency of strength training and lower amounts of aerobic exercise for males but similar amounts of strength training and aerobic exercise for females. Protein supplements and combination products are used more frequently by deployed than garrison soldiers with the intent of enhancing strength and energy.

  3. Ligand binding characteristics and aggregation behavior of purified cow's milk folate binding protein depends on the presence of amphiphatic substances including cholesterol, phospholipids, and synthetic detergents.

    PubMed

    Holm, Jan; Hansen, Steen Ingemann

    2002-01-01

    Folate binding protein was purified from cow's milk by a combination of cation exchange chromatography and methotrexate-AH-sepharose affinity chromatography. Dilution of the preparation to concentrations of protein less than 10 nM resulted in drastic changes of radioligand (folate) binding characteristics, i.e., a decrease in binding affinity with a change from upward to downward convex Scatchard plots and increased ligand dissociation combined with appearance of weak-affinity aggregated forms of the binding protein on gel filtration. These findings, consistent with a model predicting dimerization between unliganded and liganded monomers, were reversed in the presence of material eluted from the affinity column after adsorption of the protein(cofactor) or cholesterol, phospholipids, and synthetic detergents. The latter amphiphatic substances form micelles and lipid bilayers which could separate hydrophobic unliganded monomers from hydrophilic liganded monomers in the surrounding aqueous medium and thereby prevent association between these monomeric forms prevailing at low concentrations of the protein. Our data have some bearings on studies which show that cholesterol and phospholipids are necessary for the clustering of folate receptors in the cell membrane; a process required for optimum receptor function and internalization of folate.

  4. Effects of a Dissostichus mawsoni-CaM recombinant proteins feed additive on the juvenile orange-spotted grouper (Epinephelus coioides) under the acute low temperature challenge.

    PubMed

    Luo, Sheng-Wei; Wang, Wei-Na; Cai, Luo; Qi, Zeng-Hua; Wang, Cong; Liu, Yuan; Peng, Chang-Lian; Chen, Liang-Biao

    2015-10-01

    The effects of Dissostichus mawsoni-Calmodulin (Dm-CaM) on growth performance, enzyme activities, respiratory burst, MDA level and immune-related gene expressions of the orange-spotted grouper (Epinephelus coioides) exposed to the acute low temperature stress were evaluated. The commercial diet supplemented with Dm-CaM protein was fed to the groupers for 6 weeks. No significant difference was observed in the specific growth rates, weight gains and survivals. After the feeding trial, the groupers were exposed to acute low temperature challenge. The groupers fed with Dm-CaM additive diet showed a significant decrease in the respiratory burst activity, while the blood cell number increased significantly at 25 °C by comparing with the control and additive control group. The enzymatic activity of SOD, ACP and ALP increased significantly in Dm-CaM additive group, while MDA level maintained stable with the lowest value. qRT-PCR analysis indicated that the up-regulated transcript expressions of CaM, C3, SOD2, LysC and HSPA4 were observed in Dm-CaM additive group. These results indicated that Dm-CaM additive diet may regulate the grouper immune response to the acute low temperature challenge.

  5. The use of additive and subtractive approaches to examine the nuclear localization sequence of the polyomavirus major capsid protein VP1

    NASA Technical Reports Server (NTRS)

    Chang, D.; Haynes, J. I. 2nd; Brady, J. N.; Consigli, R. A.; Spooner, B. S. (Principal Investigator)

    1992-01-01

    A nuclear localization signal (NLS) has been identified in the N-terminal (Ala1-Pro-Lys-Arg-Lys-Ser-Gly-Val-Ser-Lys-Cys11) amino acid sequence of the polyomavirus major capsid protein VP1. The importance of this amino acid sequence for nuclear transport of VP1 protein was demonstrated by a genetic "subtractive" study using the constructs pSG5VP1 (full-length VP1) and pSG5 delta 5'VP1 (truncated VP1, lacking amino acids Ala1-Cys11). These constructs were used to transfect COS-7 cells, and expression and intracellular localization of the VP1 protein was visualized by indirect immunofluorescence. These studies revealed that the full-length VP1 was expressed and localized in the nucleus, while the truncated VP1 protein was localized in the cytoplasm and not transported to the nucleus. These findings were substantiated by an "additive" approach using FITC-labeled conjugates of synthetic peptides homologous to the NLS of VP1 cross-linked to bovine serum albumin or immunoglobulin G. Both conjugates localized in the nucleus after microinjection into the cytoplasm of 3T6 cells. The importance of individual amino acids found in the basic sequence (Lys3-Arg-Lys5) of the NLS was also investigated. This was accomplished by synthesizing three additional peptides in which lysine-3 was substituted with threonine, arginine-4 was substituted with threonine, or lysine-5 was substituted with threonine. It was found that lysine-3 was crucial for nuclear transport, since substitution of this amino acid with threonine prevented nuclear localization of the microinjected, FITC-labeled conjugate.

  6. In vivo footprinting of the mouse inducible nitric oxide synthase gene: inducible protein occupation of numerous sites including Oct and NF-IL6.

    PubMed Central

    Goldring, C E; Reveneau, S; Algarté, M; Jeannin, J F

    1996-01-01

    A wide variety of cells usefully but sometimes destructively produce nitric oxide via inducible nitric oxide synthase (iNOS). Data obtained by gel shift analysis and reporter assays have linked murine iNOS gene induction by cytokines and bacterial products with the binding of a number of proteins to a proximal promoter, as well as to a distal enhancer of the iNOS gene. Nevertheless, these techniques do not necessarily reflect protein occupation of sites in vivo. To address this, we have used dimethyl sulphate in vivo footprinting to determine binding events in the two murine iNOS transcription control regions, using a classical lipopolysaccharide induction of RAW 264.7 macrophages. Protein-DNA interactions are absent before activation. Exposure to lipopolysaccharide induces protection at a NF-kappaB site and hypersensitivity at a shared gamma-activated site/interferon-stimulated response element within the enhancer. Protections are seen at a NF-IL6, and an Oct site within the promoter. We also observe modulations in guanine methylation at two regions which do not correspond to any known putative binding elements. Furthermore, we confirm the probable involvement of interferon regulatory factor-1 (binding to its -901 to -913 site) and the binding of NF-kappaB to its proximal site. Our data demonstrate an abundance of hitherto-unrecognised protein-DNA binding events upon simple lipopolysaccharide activation of the iNOS gene and suggests a role for protein-protein interactions in its transcriptional induction. PMID:8649986

  7. Photostationary state compositions of retinal and related compounds included in beta-lactoglobulin. Effects of protein host on isomer distribution of polyene substrates.

    PubMed

    Li, X Y; Liu, R S

    1995-08-01

    The UV-visible absorption spectra and photostationary state compositions of retinal (or the related C-18 ketone, 3-dehydroretinal and the C-22 aldehyde) imbedded in the binding cavity of beta-lactoglobulin (BLG) are consistent with the view that the carbonyl group of these polyenes are hydrogen-bonded with the protein host, most likely with the lone protonated lysine residue in the binding pocket. Patterns of variation in photochemical behavior of the imbedded chromophore versus that in solution are discussed in terms of possible specific protein-substrate interactions. The results are also compared with that of the methyl ether of retinol where similar hydrogen bonding is not possible.

  8. Prediction of individual milk proteins including free amino acids in bovine milk using mid-infrared spectroscopy and their correlations with milk processing characteristics.

    PubMed

    McDermott, A; Visentin, G; De Marchi, M; Berry, D P; Fenelon, M A; O'Connor, P M; Kenny, O A; McParland, S

    2016-04-01

    The aim of this study was to evaluate the effectiveness of mid-infrared spectroscopy in predicting milk protein and free amino acid (FAA) composition in bovine milk. Milk samples were collected from 7 Irish research herds and represented cows from a range of breeds, parities, and stages of lactation. Mid-infrared spectral data in the range of 900 to 5,000 cm(-1) were available for 730 milk samples; gold standard methods were used to quantify individual protein fractions and FAA of these samples with a view to predicting these gold standard protein fractions and FAA levels with available mid-infrared spectroscopy data. Separate prediction equations were developed for each trait using partial least squares regression; accuracy of prediction was assessed using both cross validation on a calibration data set (n=400 to 591 samples) and external validation on an independent data set (n=143 to 294 samples). The accuracy of prediction in external validation was the same irrespective of whether undertaken on the entire external validation data set or just within the Holstein-Friesian breed. The strongest coefficient of correlation obtained for protein fractions in external validation was 0.74, 0.69, and 0.67 for total casein, total β-lactoglobulin, and β-casein, respectively. Total proteins (i.e., total casein, total whey, and total lactoglobulin) were predicted with greater accuracy then their respective component traits; prediction accuracy using the infrared spectrum was superior to prediction using just milk protein concentration. Weak to moderate prediction accuracies were observed for FAA. The greatest coefficient of correlation in both cross validation and external validation was for Gly (0.75), indicating a moderate accuracy of prediction. Overall, the FAA prediction models overpredicted the gold standard values. Near-unity correlations existed between total casein and β-casein irrespective of whether the traits were based on the gold standard (0.92) or mid

  9. Increase in the carbohydrate content of the microalgae Spirulina in culture by nutrient starvation and the addition of residues of whey protein concentrate.

    PubMed

    Vieira Salla, Ana Cláudia; Margarites, Ana Cláudia; Seibel, Fábio Ivan; Holz, Luiz Carlos; Brião, Vandré Barbosa; Bertolin, Telma Elita; Colla, Luciane Maria; Costa, Jorge Alberto Vieira

    2016-06-01

    Non-renewable sources that will end with time are the largest part of world energy consumption, which emphasizes the necessity to develop renewable sources of energy. This necessity has created opportunities for the use of microalgae as a biofuel. The use of microalgae as a feedstock source for bioethanol production requires high yields of both biomass and carbohydrates. With mixotrophic cultures, wastewater can be used to culture algae. The aim of the study was to increase the carbohydrate content in the microalgae Spirulina with the additions of residues from the ultra and nanofiltration of whey protein. The nutrient deficit in the Zarrouk medium diluted to 20% and the addition of 2.5% of both residue types led to high carbohydrate productivity (60 mg L(-1) d(-1)). With these culture conditions, the increase in carbohydrate production in Spirulina indicated that the conditions were appropriate for use with microalgae as a feedstock in the production of bioethanol.

  10. Lithium dodecyl sulfate/polyacrylamide gel electrophoresis of thylakoid membranes at 4 degrees C: Characterizations of two additional chlorophyll a-protein complexes.

    PubMed

    Delepelaire, P; Chua, N H

    1979-01-01

    Lithium dodecyl sulfate/polyacrylamide gel electrophoresis of Chlamydomonas reinhardtii thylakoid membranes at room temperature gave two chlorophyll-protein complexes, CP I and CP II, as had been reported previously. However, when the electrophoresis was performed at 4 degrees C, there was an increase in the amount of chlorophyll associated with CP I and CP II, and in addition, three other chlorophyll-protein complexes appeared. Two of these complexes, designated CP III and CP IV, were characterized and found to be similar in their compositions. Each complex contains four to five molecules of chlorophyll a, one molecule of beta-carotene, and one polypeptide chain. The apoprotein of CP III is polypeptide 5 (M(r) 50,000) and that of CP IV is polypeptide 6 (M(r) 47,000); the two polypeptides are structurally unrelated. Chlorophyll-protein complexes similar to C. reinhardtii CP III and CP IV were also detected in higher plants (e.g., Pisum sativum). The apoproteins of the higher plant complexes are immunochemically related to those of the C. reinhardtii complexes, as shown by crossed immunoelectrophoresis. Absorption spectra of CP III and CP IV at -196 degrees C revealed a component at 682 nm. This observation, together with the previous results on photosystem II mutants [Chua, N.-H. & Bennoun, P. (1975) Proc. Natl. Acad. Sci. USA 72, 2175-2179], provides indirect evidence that CP III and CP IV may be involved in the primary photochemistry of photosystem II.

  11. Diacylglycerol kinase is phosphorylated in vivo upon stimulation of the epidermal growth factor receptor and serine/threonine kinases, including protein kinase C-epsilon.

    PubMed Central

    Schaap, D; van der Wal, J; van Blitterswijk, W J; van der Bend, R L; Ploegh, H L

    1993-01-01

    In signal transduction, diacylglycerol (DG) kinase attenuates levels of the second messenger DG by converting it to phosphatidic acid. A previously cloned full-length human 86 kDa DG kinase cDNA was expressed as fusion protein in Escherichia coli, to aid in the generation of DG-kinase-specific monoclonal antibodies suitable for immunoprecipitation experiments. To investigate whether phosphorylation of DG kinase is a possible mechanism for its regulation, COS-7 cells were transiently transfected with the DG kinase cDNA and phosphorylation of the expressed DG kinase was induced by various stimuli. Activation of both cyclic AMP-dependent protein kinase and protein kinase C (PKC) resulted in phosphorylation of DG kinase on serine residues in vivo, and both kinases induced this phosphorylation within the same tryptic phosphopeptide, suggesting that they may exert similar control over DG kinase. No phosphorylation was observed upon ionomycin treatment, intended to activate Ca2+/calmodulin-dependent kinases. Co-transfections of DG kinase with either PKC-alpha or PKC-epsilon cDNA revealed that both protein kinases, when stimulated, are able to phosphorylate DG kinase. For PKC-epsilon, DG kinase is the first in vivo substrate identified. Stimulation with epidermal growth factor (EGF) of COS-7 cells transfected with both DG kinase and EGF-receptor cDNA results mainly in phosphorylation of DG kinase on tyrosine. Since the EGF receptor has an intrinsic tyrosine kinase activity, this finding implies that DG kinase may be a direct substrate for the activated EGF receptor. Images Figure 2 Figure 3 Figure 4 PMID:7679574

  12. Proteome analysis reveals differential expression of proteins involved in triacylglycerol accumulation by Rhodococcus jostii RHA1 after addition of methyl viologen.

    PubMed

    Dávila Costa, José Sebastián; Silva, Roxana A; Leichert, Lars; Alvarez, Héctor M

    2017-03-01

    Rhodococcus jostii RHA1 is able to degrade toxic compounds and accumulate high amounts of triacylglycerols (TAG) upon nitrogen starvation. These NADPH-dependent processes are essential for the adaptation of rhodococci to fluctuating environmental conditions. In this study, we used an MS-based, label-free and quantitative proteomic approach to better understand the integral response of R. jostii RHA1 to the presence of methyl viologen (MV) in relation to the synthesis and accumulation of TAG. The addition of MV promoted a decrease of TAG accumulation in comparison to cells cultivated under nitrogen-limiting conditions in the absence of this pro-oxidant. Proteomic analyses revealed that the abundance of key proteins of fatty acid biosynthesis, the Kennedy pathway, glyceroneogenesis and methylmalonyl-CoA pathway, among others, decreased in the presence of MV. In contrast, some proteins involved in lipolysis and β-oxidation of fatty acids were upregulated. Some metabolic pathways linked to the synthesis of NADPH remained activated during oxidative stress as well as under nitrogen starvation conditions. Additionally, exposure to MV resulted in the activation of complete antioxidant machinery comprising superoxide dismutases, catalases, mycothiol biosynthesis, mycothione reductase and alkyl hydroperoxide reductases, among others. Our study suggests that oxidative stress response affects TAG accumulation under nitrogen-limiting conditions through programmed molecular mechanisms when both stresses occur simultaneously.

  13. Additive method for the prediction of protein-peptide binding affinity. Application to the MHC class I molecule HLA-A*0201.

    PubMed

    Doytchinova, Irini A; Blythe, Martin J; Flower, Darren R

    2002-01-01

    A method has been developed for prediction of binding affinities between proteins and peptides. We exemplify the method through its application to binding predictions of peptides with affinity to major histocompatibility complex class I molecule HLA-A*0201. The method is named "additive" because it is based on the assumption that the binding affinity of a peptide could be presented as a sum of the contributions of the amino acids at each position and the interactions between them. The amino acid contributions and the contributions of the interactions between adjacent side chains and every second side chain were derived using a partial least squares (PLS) statistical methodology using a training set of 420 experimental IC50 values. The predictive power of the method was assessed using rigorous cross-validation and using an independent test set of 89 peptides. The mean value of the residuals between the experimental and predicted pIC50 values was 0.508 for this test set. The additive method was implemented in a program for rapid T-cell epitope search. It is universal and can be applied to any peptide-protein interaction where binding data is known.

  14. Static and turnover kinetic measurement of protein biomarkers involved in triglyceride metabolism including apoB48 and apoA5 by LC/MS/MS[S

    PubMed Central

    Pan, Yi; Zhou, Haihong; Mahsut, Ablatt; Rohm, Rory J.; Berejnaia, Olga; Price, Olga; Chen, Ying; Castro-Perez, Jose; Lassman, Michael E.; McLaren, David; Conway, James; Jensen, Kristian K.; Thomas, Tiffany; Reyes-Soffer, Gissette; Ginsberg, Henry N.; Gutstein, David E.; Cleary, Michele; Previs, Stephen F.; Roddy, Thomas P.

    2014-01-01

    LC/MS quantification of multiple plasma proteins that differ by several orders of magnitude in concentration from a single sample is challenging. We present a strategy that allows the simultaneous determination of the concentration and turnover kinetics of higher and lower abundant proteins from a single digestion mixture. Our attention was directed at a cluster of proteins that interact to affect the absorption and interorgan lipid trafficking. We demonstrate that apos involved in TG metabolism such as apoC2, C3, E, and A4 (micromolar concentration), and apoB48 and apoA5 (single-digit nanomolar concentration) can be quantified from a single digestion mixture. A high degree of correlation between LC/MS and immunobased measurements for apoC2, C3, E, and B48 was observed. Moreover, apoA5 fractional synthesis rate was measured in humans for the first time. Finally, the method can be directly applied to studies involving nonhuman primates because peptide sequences used in the method are conserved between humans and nonhuman primates. PMID:24694356

  15. Addition of CpG ODN to recombinant Pseudomonas aeruginosa ExoProtein A conjugates of AMA1 and Pfs25 greatly increases the number of responders.

    PubMed

    Qian, Feng; Rausch, Kelly M; Muratova, Olga; Zhou, Hong; Song, Guanhong; Diouf, Ababacar; Lambert, Lynn; Narum, David L; Wu, Yimin; Saul, Allan; Miller, Louis H; Long, Carole A; Mullen, Gregory E D

    2008-05-12

    Both the blood-stage protein apical membrane antigen 1 (AMA1) and the 25-kDa sexual-stage protein (Pfs25) of Plasmodium falciparum are two leading candidates in malarial vaccine development. We have previously demonstrated that conjugation of these malarial antigens to recombinant Pseudomonas aeruginosa ExoProtein A (rEPA) significantly increased the mean-specific functional antibody responses in mice; however, some mice responded poorly and were unable to demonstrate a functional response. We hypothesized that the immunogenicities of these two malarial antigens could be further enhanced by the inclusion of a CpG oligodeoxynucleotide in the formulation. Mice were immunized with either rEPA-conjugated or unconjugated AMA1 and Pfs25 formulated on Alhydrogel with or without the addition of CPG 7909. Mice received the formulations on days 0 and 28, and mouse sera were collected on day 42. ELISA analyses on these sera showed that the addition of CPG 7909 to AMA1-rEPA and Pfs25-rEPA formulated on Alhydrogel induced significantly higher mean antibody titers than the formulations without CPG 7909, and led to a mixed Th1/Th2 response as demonstrated by the production of mouse IgG1 and IgG2a subclasses. The presence of CPG 7909 in the formulations of both conjugated antigens greatly increased the proportion of responders with antibody titers sufficient to inhibit blood-stage parasite growth in vitro or block transmission of sexual-stage parasites to mosquitoes. The results obtained in this study indicate the potential use of a combination strategy to increase the number of responders to malarial antigens in humans.

  16. Effects of salt or cosolvent addition on solubility of a hydrophobic solute in water: Relevance to those on thermal stability of a protein

    NASA Astrophysics Data System (ADS)

    Murakami, Shota; Hayashi, Tomohiko; Kinoshita, Masahiro

    2017-02-01

    The solubility of a nonpolar solute in water is changed upon addition of a salt or cosolvent. Hereafter, "solvent" is formed by water molecules for pure water, by water molecules, cations, and anions for water-salt solution, and by water and cosolvent molecules for water-cosolvent solution. Decrease and increase in the solubility, respectively, are ascribed to enhancement and reduction of the hydrophobic effect. Plenty of experimental data are available for the change in solubility of argon or methane arising from the addition. We show that the integral equation theory combined with a rigid-body model, in which the solute and solvent particles are modeled as hard spheres with different diameters, can reproduce the data for the following items: salting out by an alkali halide and salting in by tetramethylammonium bromide, increase in solubility by a monohydric alcohol, and decrease in solubility by sucrose or urea. The orders of cation or anion species in terms of the power of decreasing the solubility can also be reproduced for alkali halides. With the rigid-body model, the analyses are focused on the roles of entropy originating from the translational displacement of solvent particles. It is argued by decomposing the solvation entropy of a nonpolar solute into physically insightful constituents that the solvent crowding in the bulk is a pivotal factor of the hydrophobic effect: When the solvent crowding in the bulk becomes more serious, the effect is strengthened, and when it becomes less serious, the effect is weakened. It is experimentally known that the thermal stability of a protein is also influenced by the salt or cosolvent addition. The additions which decrease and increase the solubility of a nonpolar solute, respectively, usually enhance and lower the thermal stability. This suggests that the enhanced or reduced hydrophobic effect is also a principal factor governing the stability change. However, urea decreases the solubility but lowers the stability

  17. Efficacy of humidity retention bags for the reduced adsorption and improved cleaning of tissue proteins including prion-associated amyloid to surgical stainless steel surfaces.

    PubMed

    Secker, T J; Pinchin, H E; Hervé, R C; Keevil, C W

    2015-01-01

    Increasing drying time adversely affects attachment of tissue proteins and prion-associated amyloid to surgical stainless steel, and reduces the efficacy of commercial cleaning chemistries. This study tested the efficacy of commercial humidity retention bags to reduce biofouling on surgical stainless steel and to improve subsequent cleaning. Surgical stainless steel surfaces were contaminated with ME7-infected brain homogenates and left to dry for 15 to 1,440 min either in air, in dry polythene bags or within humidity retention bags. Residual contamination pre/post cleaning was analysed using Thioflavin T/SYPRO Ruby dual staining and microscope analysis. An increase in biofouling was observed with increased drying time in air or in sealed dry bags. Humidity retention bags kept both protein and prion-associated amyloid minimal across the drying times both pre- and post-cleaning. Therefore, humidity bags demonstrate a cheap, easy to implement solution to improve surgical instrument reprocessing and to potentially reduce associated hospital acquired infections.

  18. The effect of membrane fluidization on protein kinase C: Inhibition by ethanol and higher alcohols and stimulation by increased lipid unsaturation or addition non-esterified fatty acids

    SciTech Connect

    Cox, K.J.A.; Rubin, E.; Stubbs, C.D. )

    1992-01-01

    Protein kinase C (PKC) is a membrane bound enzyme that is dependent on calcium, anionic phospholipids, and sn-1,2-diacylglycerol (DAG) to be fully active. The relationship between membrane fluidity and PKC activity was investigated using model vesicle systems composed of phosphatidylserine alone or in combination with phosphatidylcholine. Effects on membrane fluidity were assessed using the fluorescence anisotropy of diphenylhexatriene. When membrane fluidity was increased by the addition of short chain n-alkanols, PKC activity was inhibited. There was a linear relationship for a given level of inhibition and the membrane-buffer partition coefficient. By contrast, when the degree of unsaturation in the phosphatidylcholine was increased, although the bilayer was again fluidized, PKC activity was enhanced. The addition of non-esterified fatty acid also activated PKC, either when directly added to the vesicles or when generated by the addition of exogenous phospholipase A[sub 2], and again the bilayer was fluidized. It is proposed that a more fluid membrane lipid bilayer, induced by increased unsaturation or non-esterified fatty acids, facilitated optimal interaction at the DAG site since the effect could be demonstrated in a lipid free system using protamine sulfate.

  19. {sup 13}C chemical shift anisotropies for carbonate ions in cement minerals and the use of {sup 13}C, {sup 27}Al and {sup 29}Si MAS NMR in studies of Portland cement including limestone additions

    SciTech Connect

    Sevelsted, Tine F.; Herfort, Duncan

    2013-10-15

    {sup 13}C isotropic chemical shifts and chemical shift anisotropy parameters have been determined for a number of inorganic carbonates relevant in cement chemistry from slow-speed {sup 13}C MAS or {sup 13}C({sup 1}H) CP/MAS NMR spectra (9.4 T or 14.1 T) for {sup 13}C in natural abundance. The variation in the {sup 13}C chemical shift parameters is relatively small, raising some doubts that different carbonate species in Portland cement-based materials may not be sufficiently resolved in {sup 13}C MAS NMR spectra. However, it is shown that by combining {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR carbonate anions in anhydrous and hydrated phases can be distinguished, thereby providing valuable information about the reactivity of limestone in cement blends. This is illustrated for three cement pastes prepared from an ordinary Portland cement, including 0, 16, and 25 wt.% limestone, and following the hydration for up to one year. For these blends {sup 29}Si MAS NMR reveals that the limestone filler accelerates the hydration for alite and also results in a smaller fraction of tetrahedrally coordinated Al incorporated in the C-S-H phase. The latter result is more clearly observed in {sup 27}Al MAS NMR spectra of the cement–limestone blends and suggests that dissolved aluminate species in the cement–limestone blends readily react with carbonate ions from the limestone filler, forming calcium monocarboaluminate hydrate. -- Highlights: •{sup 13}C chemical shift anisotropies for inorganic carbonates from {sup 13}C MAS NMR. •Narrow {sup 13}C NMR chemical shift range (163–171 ppm) for inorganic carbonates. •Anhydrous and hydrated carbonate species by {sup 13}C MAS and {sup 13}C({sup 1}H) CP/MAS NMR. •Limestone accelerates the hydration for alite in Portland – limestone cements. •Limestone reduces the amount of aluminium incorporated in the C-S-H phase.

  20. The semidominant Mi(b) mutation identifies a role for the HLH domain in DNA binding in addition to its role in protein dimerization.

    PubMed Central

    Steingrímsson, E; Nii, A; Fisher, D E; Ferré-D'Amaré, A R; McCormick, R J; Russell, L B; Burley, S K; Ward, J M; Jenkins, N A; Copeland, N G

    1996-01-01

    The mouse microphthalmia (mi) locus encodes a basic helix-loop-helix-leucine zipper (bHLH-Zip) transcription factor called MITF (microphthalmia transcription factor). Mutations at mi affect the development of several different cell types, including melanocytes, mast cells, osteoclasts and pigmented epithelial cells of the eye. Here we describe the phenotypic and molecular characterization of the semidominant Microphthalmia(brwnish) (Mi(b)) mutation. We show that this mutation primarily affects melanocytes and produces retinal degeneration. The mutation is a G to A transition leading to a Gly244Glu substitution in helix 2 of the HLH dimerization domain. This location is surprising since other semidominant mi mutations characterized to date have been shown to affect DNA binding or transcriptional activation domains of MITF and act as dominant negatives, while mutations that affect MITF dimerization are inherited recessively. Gel retardation assays showed that while the mutant MITF(Mi-b) protein retains its dimerization potential, it is defective in its ability to bind DNA. Computer modeling suggested that the Gly244Glu mutation might disrupt DNA binding by interfering with productive docking of the protein dimer onto DNA. The Mi(b) mutation therefore appears to dissociate a DNA recognition function of the HLH domain from its role in protein dimerization. Images PMID:8947051

  1. Protein thiol modification by 15-deoxy-Delta12,14-prostaglandin J2 addition in mesangial cells: role in the inhibition of pro-inflammatory genes.

    PubMed

    Sánchez-Gómez, Francisco J; Cernuda-Morollón, Eva; Stamatakis, Konstantinos; Pérez-Sala, Dolores

    2004-11-01

    The cyclopentenone prostaglandin and PPARgamma agonist 15-deoxy-Delta(12,14)-prostaglandin J(2) (15d-PGJ(2)) displays anti-inflammatory effects in several experimental models. Direct modification of protein thiols is arising as an important mechanism of cyclopentenone prostaglandin action. However, little is known about the extent or specificity of this process. Mesangial cells (MC) play a key role in glomerulonephritis. In this work, we have studied the selectivity of protein modification by 15d-PGJ(2) in MC, and the correlation with the modulation of several proinflammatory genes. MC incubation with biotinylated 15d-PGJ(2) results in the labeling of a distinct set of proteins as evidenced by two-dimensional electrophoresis. 15d-PGJ(2) binds to nuclear and cytosolic targets as detected by fluorescence microscopy and subcellular fractionation. The pattern of biotinylated 15d-PGJ(2)-modified polypeptides is readily distinguishable from that of total protein staining or labeling with biotinylated iodoacetamide. 15d-PGJ(2) addition requires the double bond in the cyclopentane ring. 9,10-Dihydro-15d-PGJ(2), a 15d-PGJ(2) analog that shows the same potency as peroxisome proliferator-activated receptor (PPAR) agonist in MC but lacks the cyclopentenone moiety, displays reduced ability to modify proteins and to block 15d-PGJ(2) binding. Micromolar concentrations of 15d-PGJ(2) inhibit cytokine-elicited levels of inducible nitricoxide synthase, cyclooxygenase-2, and intercellular adhesion molecule-1 in MC. In contrast, 9,10-dihydro-15d-PGJ(2) does not reproduce this inhibition. 15d-PGJ(2) effect is not blocked by the PPARgamma antagonist 2-chloro-5-nitro-N-phenylbenzamide (GW9662). Moreover, compounds possessing an alpha,beta-unsaturated carbonyl group, like 2-cyclopenten-1-one and 2-cyclohexen-1-one, reduce pro-inflammatory gene expression. These observations indicate that covalent modification of cellular thiols by 15d-PGJ(2) is a selective process that plays an important

  2. Computer modelling integrated with micro-CT and material testing provides additional insight to evaluate bone treatments: Application to a beta-glycan derived whey protein mice model.

    PubMed

    Sreenivasan, D; Tu, P T; Dickinson, M; Watson, M; Blais, A; Das, R; Cornish, J; Fernandez, J

    2016-01-01

    The primary aim of this study was to evaluate the influence of a whey protein diet on computationally predicted mechanical strength of murine bones in both trabecular and cortical regions of the femur. There was no significant influence on mechanical strength in cortical bone observed with increasing whey protein treatment, consistent with cortical tissue mineral density (TMD) and bone volume changes observed. Trabecular bone showed a significant decline in strength with increasing whey protein treatment when nanoindentation derived Young׳s moduli were used in the model. When microindentation, micro-CT phantom density or normalised Young׳s moduli were included in the model a non-significant decline in strength was exhibited. These results for trabecular bone were consistent with both trabecular bone mineral density (BMD) and micro-CT indices obtained independently. The secondary aim of this study was to characterise the influence of different sources of Young׳s moduli on computational prediction. This study aimed to quantify the predicted mechanical strength in 3D from these sources and evaluate if trends and conclusions remained consistent. For cortical bone, predicted mechanical strength behaviour was consistent across all sources of Young׳s moduli. There was no difference in treatment trend observed when Young׳s moduli were normalised. In contrast, trabecular strength due to whey protein treatment significantly reduced when material properties from nanoindentation were introduced. Other material property sources were not significant but emphasised the strength trend over normalised material properties. This shows strength at the trabecular level was attributed to both changes in bone architecture and material properties.

  3. A dietary pattern including nopal, chia seed, soy protein, and oat reduces serum triglycerides and glucose intolerance in patients with metabolic syndrome.

    PubMed

    Guevara-Cruz, Martha; Tovar, Armando R; Aguilar-Salinas, Carlos A; Medina-Vera, Isabel; Gil-Zenteno, Lidia; Hernández-Viveros, Isaac; López-Romero, Patricia; Ordaz-Nava, Guillermo; Canizales-Quinteros, Samuel; Guillen Pineda, Luz E; Torres, Nimbe

    2012-01-01

    Metabolic syndrome (MetS) is a health problem throughout the world and is associated with cardiovascular disease and diabetes. Thus, the purpose of the present work was to evaluate the effects of a dietary pattern (DP; soy protein, nopal, chia seed, and oat) on the biochemical variables of MetS, the AUC for glucose and insulin, glucose intolerance (GI), the relationship of the presence of certain polymorphisms related to MetS, and the response to the DP. In this randomized trial, the participants consumed their habitual diet but reduced by 500 kcal for 2 wk. They were then assigned to the placebo (P; n = 35) or DP (n = 32) group and consumed the reduced energy diet plus the P or DP beverage (235 kcal) minus the energy provided by these for 2 mo. All participants had decreases in body weight (BW), BMI, and waist circumference during the 2-mo treatment (P < 0.0001); however, only the DP group had decreases in serum TG, C-reactive protein (CRP), and AUC for insulin and GI after a glucose tolerance test. Interestingly, participants in the DP group with MetS and the ABCA1 R230C variant had a greater decrease in BW and an increase in serum adiponectin concentration after 2 mo of dietary treatment than those with the ABCA1 R230R variant. The results from this study suggest that lifestyle interventions involving specific DP for the treatment of MetS could be more effective if local foods and genetic variations of the population are considered.

  4. Purification to homogeneity and partial amino acid sequence of a fragment which includes the methyl acceptor site of the human DNA repair protein for O6-methylguanine.

    PubMed

    Major, G N; Gardner, E J; Carne, A F; Lawley, P D

    1990-03-25

    DNA repair by O6-methylguanine-DNA methyltransferase (O6-MT) is accomplished by removal by the enzyme of the methyl group from premutagenic O6-methylguanine-DNA, thereby restoring native guanine in DNA. The methyl group is transferred to an acceptor site cysteine thiol group in the enzyme, which causes the irreversible inactivation of O6-MT. We detected a variety of different forms of the methylated, inactivated enzyme in crude extracts of human spleen of molecular weights higher and lower than the usually observed 21-24kDa for the human O6-MT. Several apparent fragments of the methylated form of the protein were purified to homogeneity following reaction of partially-purified extract enzyme with O6-[3H-CH3]methylguanine-DNA substrate. One of these fragments yielded amino acid sequence information spanning fifteen residues, which was identified as probably belonging to human methyltransferase by virtue of both its significant sequence homology to three procaryote forms of O6-MT encoded by the ada, ogt (both from E. coli) and dat (B. subtilis) genes, and sequence position of the radiolabelled methyl group which matched the position of the conserved procaryote methyl acceptor site cysteine residue. Statistical prediction of secondary structure indicated good homologies between the human fragment and corresponding regions of the constitutive form of O6-MT in procaryotes (ogt and dat gene products), but not with the inducible ada protein, indicating the possibility that we had obtained partial amino acid sequence for a non-inducible form of the human enzyme. The identity of the fragment sequence as belonging to human methyltransferase was more recently confirmed by comparison with cDNA-derived amino acid sequence from the cloned human O6-MT gene from HeLa cells (1). The two sequences compared well, with only three out of fifteen amino acids being different (and two of them by only one nucleotide in each codon).

  5. Determination of additivity of apparent and standardized ileal digestibility of amino acids in diets containing multiple protein sources fed to growing pigs.

    PubMed

    Xue, P C; Ragland, D; Adeola, O

    2014-09-01

    An experiment was conducted in growing pigs to investigate the additivity of apparent ileal digestibility (AID) or standardized ileal digestibility (SID) of CP and AA in mixed diets containing multiple protein sources. Using the determined AID or SID for CP and AA in corn, soybean meal (SBM), corn distillers' dried grains with solubles (DDGS), or canola meal (CM), the AID or SID for 4 mixed diets based on corn-SBM, corn-SBM-DDGS, corn-SBM-CM, or corn-SBM-DDGS-CM were predicted and compared with determined AID or SID, respectively. Eighteen growing pigs (initial BW = 61.3 ± 5.5 kg) were surgically fitted with T-cannulas and assigned to a duplicated 9 × 4 incomplete Latin square design with 9 diets and 4 periods. The 9 experimental diets consisted of a nitrogen-free diet (NFD) to estimate basal ileal endogenous loss (BEL) of AA, 4 semipurified diets to determine the AID and SID of CP and AA in the 4 ingredients, and 4 mixed diets to test the additivity of AID and SID. Chromic oxide was added as an indigestible marker. Pigs were fed 1 of the 9 diets during each 7-d period, and ileal digesta were collected on d 6 and 7, from 0800 to 1800 h. The analyzed AA levels for the mixed diets were close to the calculated values based on the AA composition of each ingredient. The results revealed that the predicted SID were consistent with determined values, except for Leu, Thr, Asp, Cys, Pro, and Ser in the corn-SBM diet and Met and Cys in the corn-SBM-DDGS diet. The determined AID for total AA and Arg, His, Trp, Gly, and Pro in the corn-SBM diet were greater (P < 0.05) than predicted. For the corn-SBM-DDGS diet, the determined AID were greater (P < 0.05) than predicted AID for CP, total AA, and all AA except for Arg, Leu, and Pro. In the corn-SBM-CM diet, the determined AID were greater (P < 0.05) than predicted AID for Arg, Cys, and Gly. When compared with determined values, predicted AID in the corn-SBM-DDGS-CM diet were lower (P < 0.05) for total AA and Arg, Met, Cys, and

  6. Early decrease in dietary protein:energy ratio by fat addition and ontogenetic changes in muscle growth mechanisms of rainbow trout: short- and long-term effects.

    PubMed

    Alami-Durante, Hélène; Cluzeaud, Marianne; Duval, Carine; Maunas, Patrick; Girod-David, Virginia; Médale, Françoise

    2014-09-14

    As the understanding of the nutritional regulation of muscle growth mechanisms in fish is fragmentary, the present study aimed to (1) characterise ontogenetic changes in muscle growth-related genes in parallel to changes in muscle cellularity; (2) determine whether an early decrease in dietary protein:energy ratio by fat addition affects the muscle growth mechanisms of rainbow trout (Oncorhynchus mykiss) alevins; and (3) determine whether this early feeding of a high-fat (HF) diet to alevins had a long-term effect on muscle growth processes in juveniles fed a commercial diet. Developmental regulation of hyperplasia and hypertrophy was evidenced at the molecular (expression of myogenic regulatory factors, proliferating cell nuclear antigen and myosin heavy chains (MHC)) and cellular (number and diameter of white muscle fibres) levels. An early decrease in dietary protein:energy ratio by fat addition stimulated the body growth of alevins but led to a fatty phenotype, with accumulation of lipids in the anterior part, and less caudal muscle when compared at similar body weights, due to a decrease in both the white muscle hyperplasia and maximum hypertrophy of white muscle fibres. These HF diet-induced cellular changes were preceded by a very rapid down-regulation of the expression of fast-MHC. The present study also demonstrated that early dietary composition had a long-term effect on the subsequent muscle growth processes of juveniles fed a commercial diet for 3 months. When compared at similar body weights, initially HF diet-fed juveniles indeed had a lower mean diameter of white muscle fibres, a smaller number of large white muscle fibres, and lower expression levels of MyoD1 and myogenin. These findings demonstrated the strong effect of early feed composition on the muscle growth mechanisms of trout alevins and juveniles.

  7. Additive Promotion of Viral Internal Ribosome Entry Site-Mediated Translation by Far Upstream Element-Binding Protein 1 and an Enterovirus 71-Induced Cleavage Product

    PubMed Central

    Hung, Chuan-Tien; Kung, Yu-An; Li, Mei-Ling; Lee, Kuo-Ming; Liu, Shih-Tung; Shih, Shin-Ru

    2016-01-01

    The 5' untranslated region (5' UTR) of the enterovirus 71 (EV71) RNA genome contains an internal ribosome entry site (IRES) that is indispensable for viral protein translation. Due to the limited coding capacity of their RNA genomes, EV71 and other picornaviruses typically recruit host factors, known as IRES trans-acting factors (ITAFs), to mediate IRES-dependent translation. Here, we show that EV71 viral proteinase 2A is capable of cleaving far upstream element-binding protein 1 (FBP1), a positive ITAF that directly binds to the EV71 5' UTR linker region to promote viral IRES-driven translation. The cleavage occurs at the Gly-371 residue of FBP1 during the EV71 infection process, and this generates a functional cleavage product, FBP11-371. Interestingly, the cleavage product acts to promote viral IRES activity. Footprinting analysis and gel mobility shift assay results showed that FBP11-371 similarly binds to the EV71 5' UTR linker region, but at a different site from full-length FBP1; moreover, FBP1 and FBP11-371 were found to act additively to promote IRES-mediated translation and virus yield. Our findings expand the current understanding of virus-host interactions with regard to viral recruitment and modulation of ITAFs, and provide new insights into translational control during viral infection. PMID:27780225

  8. Lipid and protein stability and sensory evaluation of ostrich (Struthio camelus) droëwors with the addition of rooibos tea extract (Aspalathus linearis) as a natural antioxidant.

    PubMed

    Hoffman, Louwrens C; Jones, Maxine; Muller, Nina; Joubert, Elizabeth; Sadie, Annalene

    2014-03-01

    The effect of rooibos tea extract (RBTE 0%, 0.25%, 0.50%, 1.00%) as a natural antioxidant on the lipid and protein stability of ostrich droëwors (traditional South African dried sausage) after a 15 day drying period was investigated. The lipid stability of the droëwors increased with 0.25% RBTE having lower TBARS. The protein stability of the droëwors did not differ (P≥0.05) between treatments. The heme-iron content did not differ (P≥0.05) between the treatments and increased from day 0 to day 15. Drying resulted in a decrease in the total moisture content by 45% and a corresponding increase in all other components. There were no differences between the moisture, fat and ash contents between treatments within a specific day. The droëwors had high concentrations of oleic acid, palmitic acid and linoleic acid. The addition of RBTE also improved the sensory attributes and can thus be added and marketed as a natural flavourant from 'out of Africa' for a traditional South African meat product.

  9. Planar optical waveguide based sandwich assay sensors and processes for the detection of biological targets including protein markers, pathogens and cellular debris

    DOEpatents

    Martinez, Jennifer S.; Swanson, Basil I.; Grace, Karen M.; Grace, Wynne K.; Shreve, Andrew P.

    2009-06-02

    An assay element is described including recognition ligands bound to a film on a single mode planar optical waveguide, the film from the group of a membrane, a polymerized bilayer membrane, and a self-assembled monolayer containing polyethylene glycol or polypropylene glycol groups therein and an assay process for detecting the presence of a biological target is described including injecting a biological target-containing sample into a sensor cell including the assay element, with the recognition ligands adapted for binding to selected biological targets, maintaining the sample within the sensor cell for time sufficient for binding to occur between selected biological targets within the sample and the recognition ligands, injecting a solution including a reporter ligand into the sensor cell; and, interrogating the sample within the sensor cell with excitation light from the waveguide, the excitation light provided by an evanescent field of the single mode penetrating into the biological target-containing sample to a distance of less than about 200 nanometers from the waveguide thereby exciting the fluorescent-label in any bound reporter ligand within a distance of less than about 200 nanometers from the waveguide and resulting in a detectable signal.

  10. New recA mutations that dissociate the various RecA protein activities in Escherichia coli provide evidence for an additional role for RecA protein in UV mutagenesis.

    PubMed Central

    Dutreix, M; Moreau, P L; Bailone, A; Galibert, F; Battista, J R; Walker, G C; Devoret, R

    1989-01-01

    To isolate strains with new recA mutations that differentially affect RecA protein functions, we mutagenized in vitro the recA gene carried by plasmid mini-F and then introduced the mini-F-recA plasmid into a delta recA host that was lysogenic for prophage phi 80 and carried a lac duplication. By scoring prophage induction and recombination of the lac duplication, we isolated new recA mutations. A strain carrying mutation recA1734 (Arg-243 changed to Leu) was found to be deficient in phi 80 induction but proficient in recombination. The mutation rendered the host not mutable by UV, even in a lexA(Def) background. Yet, the recA1734 host became mutable upon introduction of a plasmid encoding UmuD*, the active carboxyl-terminal fragment of UmuD. Although the recA1734 mutation permits cleavage of lambda and LexA repressors, it renders the host deficient in the cleavage of phi 80 repressor and UmuD protein. Another strain carrying mutation recA1730 (Ser-117 changed to Phe) was found to be proficient in phi 80 induction but deficient in recombination. The recombination defect conferred by the mutation was partly alleviated in a cell devoid of LexA repressor, suggesting that, when amplified, RecA1730 protein is active in recombination. Since LexA protein was poorly cleaved in the recA1730 strain while phage lambda was induced, we conclude that RecA1730 protein cannot specifically mediate LexA protein cleavage. Our results show that the recA1734 and recA1730 mutations differentially affect cleavage of various substrates. The recA1730 mutation prevented UV mutagenesis, even upon introduction into the host of a plasmid encoding UmuD* and was dominant over recA+. With respect to other RecA functions, recA1730 was recessive to recA+. This demonstrates that RecA protein has an additional role in mutagenesis beside mediating the cleavage of LexA and UmuD proteins. Images PMID:2651400

  11. The Neurospora crassa cyt-20 gene encodes cytosolic and mitochondrial valyl-tRNA synthetases and may have a second function in addition to protein synthesis.

    PubMed Central

    Kubelik, A R; Turcq, B; Lambowitz, A M

    1991-01-01

    The cyt-20-1 mutant of Neurospora crassa is a temperature-sensitive, cytochrome b- and aa3-deficient strain that is severely deficient in both mitochondrial and cytosolic protein synthesis (R.A. Collins, H. Bertrand, R.J. LaPolla, and A.M. Lambowitz, Mol. Gen. Genet. 177:73-84, 1979). We cloned the cyt-20+ gene by complementation of the cyt-20-1 mutation and found that it contains a 1,093-amino-acid open reading frame (ORF) that encodes both the cytosolic and mitochondrial valyl-tRNA synthetases (vaIRSs). A second mutation, un-3, which is allelic with cyt-20-1, also results in temperature-sensitive growth, but not in gross deficiencies in cytochromes b and aa3 or protein synthesis. The un-3 mutant had also been reported to have pleiotropic defects in cellular transport process, resulting in resistance to amino acid analogs (M.S. Kappy and R.L. Metzenberg, J. Bacteriol. 94:1629-1637, 1967), but this resistance phenotype is separable from the temperature sensitivity in crosses and may result from a mutation in a different gene. The 1,093-amino-acid ORF encoding vaIRSs is the site of missense mutations resulting in temperature sensitivity in both cyt-20-1 and un-3 and is required for the transformation of both mutants. The opposite strand of the cyt-20 gene encodes an overlapping ORF of 532 amino acids, which may also be functional but is not required for transformation of either mutant. The cyt-20-1 mutation in the vaIRS ORF results in severe deficiencies of both mitochondrial and cytosolic vaIRS activities, whereas the un-3 mutation does not appear to result in a deficiency of these activities or of mitochondrial or cytosolic protein synthesis sufficient to account for its temperature-sensitive growth. The phenotype of the un-3 mutant raises the possibility that the vaIRS ORF has a second function in addition to protein synthesis. PMID:1830127

  12. Characterization and regulation of an additional actin-filament-binding site in large isoforms of the stereocilia actin-bundling protein espin.

    PubMed

    Zheng, Lili; Beeler, Dina M; Bartles, James R

    2014-03-15

    The espin actin-bundling proteins, which are produced as isoforms of different sizes from a single gene, are required for the growth of hair cell stereocilia. We have characterized an additional actin-filament-binding site present in the extended amino-termini of large espin isoforms. Constitutively active in espin 2, the site increased the size of actin bundles formed in vitro and inhibited actin fluorescence recovery in microvilli. In espin 1, which has an N-terminal ankyrin repeat domain, the site was autoinhibited by binding between the ankyrin repeat domain and a peptide near the actin-binding site. Deletion of this peptide from espin 1 activated its actin-binding site. The peptide resembled tail homology domain I of myosin III, a ligand of the ankyrin repeat domain localized with espin 1 at the tip of stereocilia. A myosin III tail homology domain I peptide, but not scrambled control peptides, inhibited internal binding of the ankyrin repeat domain and released the espin 1 actin-binding site from autoinhibition. Thus, this regulation could result in local activation of the additional actin-binding site of espin 1 by myosin III in stereocilia.

  13. A higher-order mathematical modeling for dynamic behavior of protein microtubule shell structures including shear deformation and small-scale effects.

    PubMed

    Daneshmand, Farhang; Farokhi, Hamed; Amabili, Marco

    2014-06-01

    Microtubules in mammalian cells are cylindrical protein polymers which structurally and dynamically organize functional activities in living cells. They are important for maintaining cell structures, providing platforms for intracellular transport, and forming the spindle during mitosis, as well as other cellular processes. Various in vitro studies have shown that microtubules react to applied mechanical loading and physical environment. To investigate the mechanisms underlying such phenomena, a mathematical model based on the orthotropic higher-order shear deformation shell formulation and Hamilton's principle is presented in this paper for dynamic behavior of microtubules. The numerical results obtained by the proposed shell model are verified by the experimental data from the literature, showing great consistency. The nonlocal elasticity theory is also utilized to describe the nano-scale effects of the microtubule structure. The wave propagation and vibration characteristics of the microtubule are examined in the presence and absence of the cytosol employing proposed formulations. The effects of different system parameters such as length, small scale parameter, and cytosol viscosity on vibrational behavior of a microtubule are elucidated. The definitions of critical length and critical viscosity are introduced and the results obtained using the higher order shell model are compared with those obtained employing a first-order shear deformation theory. This comparison shows that the small scale effects become important for higher values of the wave vector and the proposed model gives more accurate results for both small and large values of wave vectors. Moreover, it is shown that for higher circumferential wave number, the torsional wave velocity obtained by the higher-order shell model tend to be higher than the one predicted by the first-order shell model.

  14. Food additives

    PubMed Central

    Spencer, Michael

    1974-01-01

    Food additives are discussed from the food technology point of view. The reasons for their use are summarized: (1) to protect food from chemical and microbiological attack; (2) to even out seasonal supplies; (3) to improve their eating quality; (4) to improve their nutritional value. The various types of food additives are considered, e.g. colours, flavours, emulsifiers, bread and flour additives, preservatives, and nutritional additives. The paper concludes with consideration of those circumstances in which the use of additives is (a) justified and (b) unjustified. PMID:4467857

  15. Effects of feeding corn silage inoculated with microbial additives on the ruminal fermentation, microbial protein yield, and growth performance of lambs.

    PubMed

    Basso, F C; Adesogan, A T; Lara, E C; Rabelo, C H S; Berchielli, T T; Teixeira, I A M A; Siqueira, G R; Reis, R A

    2014-12-01

    This study aimed to examine the effects of feeding corn silage inoculated without or with either Lactobacillus buchneri (LB) alone or a combination of LB and Lactobacillus plantarum (LBLP) on the apparent digestibility, ruminal fermentation, microbial protein synthesis, and growth performance of lambs. Thirty Santa Inês×Dorper crossbred intact males lambs weighing 20.4±3.8 kg were blocked by weight into 10 groups. Lambs in each group were randomly assigned to 1 of the following 3 dietary treatments: untreated (Control), LB, and LBLP silage. Lambs were fed experimental diets for 61 d. The apparent digestibility was indirectly estimated from indigestible NDF measured on d 57 to 59. Spot urine samples were collected from all animals on d 59 to estimate microbial protein synthesis. Lambs were slaughtered for carcass evaluation on d 61 when they weighed 32.4±5.2 kg. Six additional ruminally cannulated Santa Inês×Dorper crossbred wethers weighing 40.5±1.8 kg were used to examine dietary effects on ruminal fermentation. Average daily gain was increased when lambs were fed LBLP silage (P<0.05) but not LB silage. The LBLP silage had the highest (P<0.05) lactic acid concentration and both inoculated silages had greater acetic acid concentrations than the Control silage (P<0.05). Inoculation of corn silage increased intakes of DM, OM, CP, NDF, total carbohydrate (CHO), and GE by the lambs but decreased digestibility of DM, OM, CP, total and nonstructural carbohydrates, and concentration of GE and ME. (P<0.05). Nevertheless, lambs fed inoculated silages had greater microbial N supply than those on the Control treatment (P<0.05). The acetate to propionate ratio was lower in ruminal fluid of wethers in LBLP treatment than LB and Control treatment (P<0.05) and ruminal pH tended to be greater in LB lambs than in LBLP and Control wethers (P<0.10). Finally, the inoculation with both bacteria combined enhanced the silage fermentation. The intakes of DM, OM, CP, NDF, and GE

  16. Nutritional therapies (including fosteum).

    PubMed

    Nieves, Jeri W

    2009-03-01

    Nutrition is important in promoting bone health and in managing an individual with low bone mass or osteoporosis. In adult women and men, known losses of bone mass and microarchitecture occur, and nutrition can help minimize these losses. In every patient, a healthy diet with adequate protein, fruits, vegetables, calcium, and vitamin D is required to maintain bone health. Recent reports on nutritional remedies for osteoporosis have highlighted the importance of calcium in youth and continued importance in conjunction with vitamin D as the population ages. It is likely that a calcium intake of 1200 mg/d is ideal, and there are some concerns about excessive calcium intakes. However, vitamin D intake needs to be increased in most populations. The ability of soy products, particularly genistein aglycone, to provide skeletal benefit has been recently studied, including some data that support a new medical food marketed as Fosteum (Primus Pharmaceuticals, Scottsdale, AZ).

  17. C-Reactive Protein in Stable Cystic Fibrosis: An Additional Indicator of Clinical Disease Activity and Risk of Future Pulmonary Exacerbations

    PubMed Central

    Matouk, Elias; Nguyen, Dao; Benedetti, Andrea; Bernier, Joanie; Gruber, James; Landry, Jennifer; Rousseau, Simon; Ahlgren, Heather G; Lands, Larry C; Wojewodka, Gabriella; Radzioch, Danuta

    2016-01-01

    Introduction In stable adult cystic fibrosis (CF) patients, we assessed the role of baseline high sensitivity C-reactive protein (hs-CRP) on CF clinical variables and frequency of intravenous (IV) treated pulmonary exacerbations (PExs) 1-year post-baseline. Methods We recruited 51 clinically stable CF patients from our Adult CF Center. We incorporated collected parameters into Matouk CF clinical score and CF questionnaire-revised quality of life score (QOL). We used the clinical minus complications subscores as a clinical disease activity score (CDAS). We dichotomized our patients according to the cohort median baseline hs-CRP of 5.2 mg/L. Results Patients in the high hs-CRP group (≥ 5.2 mg/L) demonstrated worse CDAS (r=0.67, p=0.0001) and QOL scores (r=0.57, p=0.0017) at a given FEV1% predicted. In both hs-CRP groups, prior-year IV-treated PExs and baseline CDASs were significant predictors of future IV-treated PExs. Interestingly, the association between baseline CDAS and future PExs frequency was more robust in the high compared to the low hs-CRP group (r=−0.88, p<0.0001, r=−0.48, p=0.017, respectively) with a steeper regression slope (p=0.001). In addition, a significant interaction was demonstrated between elevated baseline hs-CRP levels and CDASs for the prediction of increased risk of future PExs (p=0.02). This interaction provided an additional indicator of clinical disease activity and added another dimension to the prior year PExs frequency phenotype to identify patients at increased risk for future PExs. Conclusion Stable CF patients with elevated baseline hs-CRP (≥ 5.2 mg/L) demonstrated worse clinical disease activity and QOL scores at a given level of disease severity (FEV1% predicted). Elevated baseline hs-CRP values combined with clinical disease activity scores are associated with increased risk for future IV-treated PExs even in those with mild clinical disease activity scores. PMID:28066689

  18. Water makes the difference: rearrangement of water solvation layer triggers non-additivity of functional group contributions in protein-ligand binding.

    PubMed

    Biela, Adam; Betz, Michael; Heine, Andreas; Klebe, Gerhard

    2012-08-01

    The binding of four congeneric peptide-like thermolysin inhibitors has been studied by high-resolution crystal structure analysis and isothermal titration calorimetry. The ligands differ only by a terminal carboxylate and/or methyl group. A surprising non-additivity of functional group contributions for the carboxylate and/or methyl groups is detected. Adding the methyl first and then the carboxylate group results in a small Gibbs free energy increase and minor enthalpy/entropy partitioning for the first modification, whereas the second involves a strong affinity increase combined with large enthalpy/entropy changes. However, first adding the carboxylate and then the methyl group yields reverse effects: the acidic group attachment now causes minor effects, whereas the added methyl group provokes large changes. As all crystal structures show virtually identical binding modes, affinity changes are related to rearrangements of the first solvation layer next to the S(2)' pocket. About 20-25 water molecules are visible next to the studied complexes. The added COO(-) groups perturb the local water network in both carboxylated complexes, and the attached methyl groups provide favorable interaction sites for water molecules. Apart from one example, a contiguously connected water network between protein and ligand functional groups is observed in all complexes. In the complex with the carboxylated ligand, which still lacks the terminal methyl group, the water network is unfavorably ruptured. This results in a surprising thermodynamic signature showing only a minor affinity increase upon COO(-) group attachment. Because the further added methyl group provides a favorable interaction site for water, the network can be reestablished, and a strong affinity increase with a large enthalpy/entropy signature is then detected.

  19. Potlining Additives

    SciTech Connect

    Rudolf Keller

    2004-08-10

    In this project, a concept to improve the performance of aluminum production cells by introducing potlining additives was examined and tested. Boron oxide was added to cathode blocks, and titanium was dissolved in the metal pool; this resulted in the formation of titanium diboride and caused the molten aluminum to wet the carbonaceous cathode surface. Such wetting reportedly leads to operational improvements and extended cell life. In addition, boron oxide suppresses cyanide formation. This final report presents and discusses the results of this project. Substantial economic benefits for the practical implementation of the technology are projected, especially for modern cells with graphitized blocks. For example, with an energy savings of about 5% and an increase in pot life from 1500 to 2500 days, a cost savings of $ 0.023 per pound of aluminum produced is projected for a 200 kA pot.

  20. Phosphazene additives

    DOEpatents

    Harrup, Mason K; Rollins, Harry W

    2013-11-26

    An additive comprising a phosphazene compound that has at least two reactive functional groups and at least one capping functional group bonded to phosphorus atoms of the phosphazene compound. One of the at least two reactive functional groups is configured to react with cellulose and the other of the at least two reactive functional groups is configured to react with a resin, such as an amine resin of a polycarboxylic acid resin. The at least one capping functional group is selected from the group consisting of a short chain ether group, an alkoxy group, or an aryloxy group. Also disclosed are an additive-resin admixture, a method of treating a wood product, and a wood product.

  1. Addition of TAT protein transduction domain and GrpE to human p53 provides soluble fusion proteins that can be transduced into dendritic cells and elicit p53-specific T-cell responses in HLA-A*0201 transgenic mice

    PubMed Central

    Justesen, S; Buus, S; Claesson, M H; Pedersen, A E

    2007-01-01

    The protein p53 has been shown to be an efficient tumour antigen in both murine and human cancer vaccine studies and cancer vaccines targeting p53 based on major histocompatibility complex (MHC) class I binding p53-derived peptides that induce cytotoxic T lymphocytes (CTLs) without p53-specific CD4+ T-cell help have been tested by several research groups including ours. To obtain such CD4+ T-cell help and cover a broader repertoire of MHC haplotypes we have previously attempted to produce recombinant human p53 for vaccination purposes. However, attempts to refold a hexahis-tagged p53 protein in our laboratory were unsuccessful. Here, we show that fusion of an 11-amino-acid region of the human immunodeficiency virus TAT protein transduction domain (PTD) to human p53 increases the solubility of the otherwise insoluble p53 protein and this rTAT-p53 protein can be transduced into human monocyte-derived dendritic cells (DCs). The induction of a p53-specific HLA-A*0201 immune response was tested in HLA-A*0201/Kb transgenic mice after immunization with rTAT-p53-transduced bone-marrow-derived DCs. In these mice, p53-specific CD4+ and CD8+ T-cell proliferation was observed and immunization resulted in the induction of HLA-A*0201-restricted CTLs specific for two human p53-derived HLA-A*0201-binding peptides, p5365−73 and p53149−157. Addition of GrpE to generate rTAT-GrpE-p53 led to a further increase in protein solubility and to a small increase in DC maturation but did not increase the observed p53-specific T-cell responses. The use of rTAT-p53 in ongoing clinical protocols should be applicable and offers advantages to current strategies omitting the use of HLA-typed patients. PMID:17610503

  2. Destabilized bioluminescent proteins

    DOEpatents

    Allen, Michael S.; Rakesh, Gupta; Gary, Sayler S.

    2007-07-31

    Purified nucleic acids, vectors and cells containing a gene cassette encoding at least one modified bioluminescent protein, wherein the modification includes the addition of a peptide sequence. The duration of bioluminescence emitted by the modified bioluminescent protein is shorter than the duration of bioluminescence emitted by an unmodified form of the bioluminescent protein.

  3. Characterisation and quantification of changes in odorants from litter headspace of meat chickens fed diets varying in protein levels and additives.

    PubMed

    Sharma, Nishchal K; Choct, Mingan; Dunlop, Mark W; Wu, Shu-Biao; Castada, Hardy Z; Swick, Robert A

    2016-09-23

    The effect of dietary crude protein (CP) and additives on odor flux from meat chicken litter was investigated using 180 day-old Ross 308 male chicks randomly allocated to five dietary treatments with three replicates of 12 birds each. A 5 × 3 factorial arrangement of treatments was employed. Factors were: diet (low CP, high CP, high CP+antibiotic, high CP+probiotic, high CP+saponin) and age (15, 29, 35 days). The antibiotic used was Zn bacitracin, the probiotic was a blend of three Bacillus subtilis strains and the saponin came from a blend of Yucca and Quillaja. Odorants were collected from litter headspace with a flux hood and measured using selective ion flow tube mass spectrometry (SIFT-MS). Litter moisture, water activity (Aw), and litter headspace odorant concentrations were correlated. The results showed that low CP group produced lower flux of dimethyl amine, trimethyl amine, H2S, NH3, and phenol in litter compared to high CP group (P < 0.05). Similarly, high CP+probiotic group produced lower flux of H2S (P < 0.05) and high CP+saponin group produced lower flux of trimethylamine and phenol in litter compared to high CP group (P < 0.05). The dietary treatments tended (P = 0.065) to have higher flux of methanethiol in high CP group compared to others. There was a diet × age interaction for litter flux of diacetyl, 3-hydroxy-2-butanone (acetoin), 3-methyl-1-butanol, 3-methylbutanal, ethanethiol, propionic acid, and hexane (P < 0.05). Concentrations of diacetyl, acetoin, propionic acid, and hexane in litter were higher from low CP group compared to all other treatments on d 35 (P < 0.05) but not on d 15 and 29. A high litter moisture increased water activity (P < 0.01) and favored the emissions of methyl mercaptan, hydrogen sulfide, dimethyl sulfide, ammonia, trimethyl amine, phenol, indole, and 3-methylindole over others. Thus, the low CP diet, Bacillus subtilis based probiotic and the blend of Yucca/Quillaja saponin were effective in reducing the emissions

  4. Proteins.

    ERIC Educational Resources Information Center

    Doolittle, Russell F.

    1985-01-01

    Examines proteins which give rise to structure and, by virtue of selective binding to other molecules, make genes. Binding sites, amino acids, protein evolution, and molecular paleontology are discussed. Work with encoding segments of deoxyribonucleic acid (exons) and noncoding stretches (introns) provides new information for hypotheses. (DH)

  5. Protein

    MedlinePlus

    ... Search for: Harvard T.H. Chan School of Public Health Email People Departments Calendar Careers Give my.harvard ... Nutrition Source Harvard T.H. Chan School of Public Health > The Nutrition Source > What Should I Eat? > Protein ...

  6. Enhanced mRNA-protein fusion efficiency of a single-domain antibody by selection of mRNA display with additional random sequences in the terminal translated regions

    PubMed Central

    Takahashi, Kazuki; Sunohara, Masato; Terai, Takuya; Kumachi, Shigefumi; Nemoto, Naoto

    2017-01-01

    In vitro display technologies such as mRNA and cDNA display are powerful tools to create and select functional peptides. However, in some cases, efficiency of mRNA-protein fusion is very low, which results in decreased library size and lower chance of successful selection. In this study, to improve mRNA-protein fusion efficiency, we prepared an mRNA display library of a protein with random N- and C-terminal coding regions consisting of 12 nucleotides (i.e. four amino acids), and performed an electrophoresis mobility shift assay (EMSA)-based selection of successfully formed mRNA display molecules. A single-domain antibody (Nanobody, or VHH) was used as a model protein, and as a result, a pair of sequences was identified that increased mRNA-protein fusion efficiency of this protein by approximately 20%. Interestingly, enhancement of the fusion efficiency induced by the identified sequences was protein-specific, and different results were obtained for other proteins including VHHs with different CDRs. The results suggested that conformation of mRNA as a whole, rather than the amino acid sequence of the translated peptide, is an important factor to determine mRNA-protein fusion efficiency. PMID:28275529

  7. Enhanced mRNA-protein fusion efficiency of a single-domain antibody by selection of mRNA display with additional random sequences in the terminal translated regions.

    PubMed

    Takahashi, Kazuki; Sunohara, Masato; Terai, Takuya; Kumachi, Shigefumi; Nemoto, Naoto

    2017-01-01

    In vitro display technologies such as mRNA and cDNA display are powerful tools to create and select functional peptides. However, in some cases, efficiency of mRNA-protein fusion is very low, which results in decreased library size and lower chance of successful selection. In this study, to improve mRNA-protein fusion efficiency, we prepared an mRNA display library of a protein with random N- and C-terminal coding regions consisting of 12 nucleotides (i.e. four amino acids), and performed an electrophoresis mobility shift assay (EMSA)-based selection of successfully formed mRNA display molecules. A single-domain antibody (Nanobody, or VHH) was used as a model protein, and as a result, a pair of sequences was identified that increased mRNA-protein fusion efficiency of this protein by approximately 20%. Interestingly, enhancement of the fusion efficiency induced by the identified sequences was protein-specific, and different results were obtained for other proteins including VHHs with different CDRs. The results suggested that conformation of mRNA as a whole, rather than the amino acid sequence of the translated peptide, is an important factor to determine mRNA-protein fusion efficiency.

  8. A novel zinc-finger HIT protein with an additional PAPA-1-like region from Suaeda liaotungensis K. enhanced transgenic Arabidopsis drought and salt stresses tolerance.

    PubMed

    Li, Xiao-Lan; Hu, Yu-Xin; Yang, Xing; Yu, Xiao-Dong; Li, Qiu-Li

    2014-12-01

    Zinc-finger HIT belongs to the cross-brace zinc finger protein family and is involved in the regulation of plant defense and stress responses. In this study, we cloned a full-length zinc-finger HIT gene (1,377 bp) named SlPAPA1 using polymerase chain reaction from Suaeda liaotungensis K. and investigated its function by overexpression in transgenic Arabidopsis. SlPAPA1 contains a zinc-finger HIT domain and a Pim-1-associated protein-1 (PAP-1)-associated protein-1-like (PAPA-1-like) conserved region. Its expression in S. liaotungensis was induced by drought, high-salt, and cold (4 °C) stresses and by abscisic acid (ABA). Subcellular localization experiments in onion epidermal cells indicated that SlPAPA1 is localized in the nucleus. Yeast-one hybrid assays showed that SlPAPA1 functions as a transcriptional activator. SlPAPA1 transgenic Arabidopsis displayed a higher survival ratio and lower rate of water loss under drought stress; a higher germination ratio, higher survival ratio, and lower root inhibition rate under salt stress; and a lower germination ratio and root inhibition rate under ABA treatment, compared with wild-type Arabidopsis. These results suggested that SlPAPA1 functions as a stress-responsive zinc-finger HIT protein involved in the ABA-dependent signaling pathway and may have potential applications in transgenic breeding to enhance crops abiotic stress tolerances.

  9. Purification and characterisation of epithiospecifier protein from Brassica napus: enzymic intramolecular sulphur addition within alkenyl thiohydroximates derived from alkenyl glucosinolate hydrolysis.

    PubMed

    Foo, H L; Gronning, L M; Goodenough, L; Bones, A M; Danielsen, B; Whiting, D A; Rossiter, J T

    2000-02-25

    Epithiospecifier protein (ESP), a ferrous ion dependent protein, has a potential role in regulating the release of elemental sulphur, nitriles, isothiocyanates and cyanoepithioalkanes from glucosinolates. Two classes of ESP polypeptides were purified with molecular masses of 39 and 35 kDa, and we show that the previously reported instability was conditionally dependent. The 39 kDa polypeptide was made up of two distinct isozymes (5.00, 5.14) whilst several were present for the 35 kDa form of ESP (5.40-5.66). An anti-ESP antibody reacted with both the 39 and 35 kDa ESP forms in Brassica napus and strongly with a polypeptide corresponding to the 35 kDa ESP form in Crambe abyssinica, but did not detect any ESP in Sinapis alba or Raphanus sativus. A cytochrome P-450 mediated iron dependent epoxidation type mechanism is suggested for ESP.

  10. Interaction of toxic azo dyes with heme protein: biophysical insights into the binding aspect of the food additive amaranth with human hemoglobin.

    PubMed

    Basu, Anirban; Kumar, Gopinatha Suresh

    2015-05-30

    A biophysical study on the interaction of the food colorant amaranth with hemoglobin was undertaken. Spectrophotometric and spectrofluorimetric studies proposed for an intimate binding interaction between the dye and the protein. The dye quenched the fluorescence of the protein remarkably and the mechanism of quenching was found to be static in nature. Synchronous fluorescence studies suggested that the polarity around the tryptophan residues was altered in the presence of amaranth whereas the polarity around tyrosine residues remained largely unaltered. 3D fluorescence, FTIR and circular dichroism results suggested that the binding reaction caused conformational changes in hemoglobin. The negative far-UV CD bands exhibited a significantly large decrease in magnitude in the presence of amaranth. From calorimetry studies it was established that the binding was driven by a large positive entropic contribution and a small but favorable enthalpy change.

  11. An energy-reduced dietary pattern, including moderate protein and increased nonfat dairy intake combined with walking promotes beneficial body composition and metabolic changes in women with excess adiposity: a randomized comparative trial

    PubMed Central

    Shlisky, Julie D; Durward, Carrie M; Zack, Melissa K; Gugger, Carolyn K; Campbell, Jessica K; Nickols-Richardson, Sharon M

    2015-01-01

    Moderate protein and nonfat dairy intake within an energy-reduced diet (ERD) may contribute to health benefits achieved with body weight (BW) loss. The current study examined the effectiveness of a weight-loss/weight-loss maintenance intervention using an ERD with moderate dietary protein (30% of kcals) and increased nonfat dairy intake (4–5 svg/d), including yogurt (INT group) and daily walking compared to an ERD with standard protein (16–17% of kcals) and standard nonfat dairy intake (3 svg/d) (COM group) with daily walking. A randomized comparative trial with 104 healthy premenopausal women with overweight/obesity was conducted in a university setting. Women were randomized to INT group or COM group. Anthropometric measurements, as well as dietary intake, selected vital signs, resting energy expenditure, blood lipids, glucose, insulin, and selected adipose-derived hormones were measured at baseline, and weeks 2, 12, and 24. Targets for dietary protein and nonfat dairy intake, while initially achieved, were not sustained in the INT group. There were no significant effects of diet group on anthropometric measurements. Women in the INT group and COM group, respectively, reduced BW (−4.9 ± 3.2 and −4.3 ± 3.3 kg, P < 0.001) and fat mass (−3.0 ± 2.2 and −2.3 ± 2.3 kg, P < 0.001) during the 12-week weight-loss phase and maintained these losses at 24 weeks. Both groups experienced significant decreases in body mass index, fat-free soft tissue mass, body fat percentage, waist and hip circumferences and serum triglycerides, total cholesterol, and leptin (all P < 0.001). Healthy premenopausal women with excess adiposity effectively lost BW and fat mass and improved some metabolic risk factors following an ERD with approximately 20% protein and 3 svg/d of nonfat dairy intake. PMID:26405524

  12. An energy-reduced dietary pattern, including moderate protein and increased nonfat dairy intake combined with walking promotes beneficial body composition and metabolic changes in women with excess adiposity: a randomized comparative trial.

    PubMed

    Shlisky, Julie D; Durward, Carrie M; Zack, Melissa K; Gugger, Carolyn K; Campbell, Jessica K; Nickols-Richardson, Sharon M

    2015-09-01

    Moderate protein and nonfat dairy intake within an energy-reduced diet (ERD) may contribute to health benefits achieved with body weight (BW) loss. The current study examined the effectiveness of a weight-loss/weight-loss maintenance intervention using an ERD with moderate dietary protein (30% of kcals) and increased nonfat dairy intake (4-5 svg/d), including yogurt (INT group) and daily walking compared to an ERD with standard protein (16-17% of kcals) and standard nonfat dairy intake (3 svg/d) (COM group) with daily walking. A randomized comparative trial with 104 healthy premenopausal women with overweight/obesity was conducted in a university setting. Women were randomized to INT group or COM group. Anthropometric measurements, as well as dietary intake, selected vital signs, resting energy expenditure, blood lipids, glucose, insulin, and selected adipose-derived hormones were measured at baseline, and weeks 2, 12, and 24. Targets for dietary protein and nonfat dairy intake, while initially achieved, were not sustained in the INT group. There were no significant effects of diet group on anthropometric measurements. Women in the INT group and COM group, respectively, reduced BW (-4.9 ± 3.2 and -4.3 ± 3.3 kg, P < 0.001) and fat mass (-3.0 ± 2.2 and -2.3 ± 2.3 kg, P < 0.001) during the 12-week weight-loss phase and maintained these losses at 24 weeks. Both groups experienced significant decreases in body mass index, fat-free soft tissue mass, body fat percentage, waist and hip circumferences and serum triglycerides, total cholesterol, and leptin (all P < 0.001). Healthy premenopausal women with excess adiposity effectively lost BW and fat mass and improved some metabolic risk factors following an ERD with approximately 20% protein and 3 svg/d of nonfat dairy intake.

  13. Refraction, including prisms.

    PubMed

    Hiatt, R L

    1991-02-01

    The literature in the past year on refraction is replete with several isolated but very important topics that have been of interest to strabismologists and refractionists for many decades. The refractive changes in scleral buckling procedures include an increase in axial length as well as an increase in myopia, as would be expected. Tinted lenses in dyslexia show little positive effect in the nonasthmatic patients in one study. The use of spectacles or bifocals as a way to control increase in myopia is refuted in another report. It has been shown that in accommodative esotropia not all patients will be able to escape the use of bifocals in the teenage years, even though surgery might be performed. The hope that disposable contact lenses would cut down on the instance of giant papillary conjunctivitis and keratitis has been given some credence, and the conventional theory that sclerosis alone is the cause of presbyopia is attacked. Also, gas permeable bifocal contact lenses are reviewed and the difficulties of correcting presbyopia by this method outlined. The practice of giving an aphakic less bifocal addition instead of a nonaphakic, based on the presumption of increased effective power, is challenged. In the review of prisms, the majority of articles concern prism adaption. The most significant report is that of the Prism Adaptation Study Research Group (Arch Ophthalmol 1990, 108:1248-1256), showing that acquired esotropia in particular has an increased incidence of stable and full corrections surgically in the prism adaptation group versus the control group.(ABSTRACT TRUNCATED AT 250 WORDS)

  14. Guanosine 5'-triphosphate binding protein (G/sub i/) and two additional pertussis toxin substrates associated with muscarinic receptors in rat heart myocytes: characterization and age dependency

    SciTech Connect

    Moscona-Amir, E.; Henis, Y.I.; Sokolovsky, M.

    1988-07-12

    The coupling of muscarinic receptors with G-proteins was investigated in cultured myocytes prepared from the hearts of newborn rats. The coupling was investigated in both young (5 days after plating) and aged (14 days after plating) cultures, in view of the completely different effects of 5'-guanylyl imidodiphosphate (Gpp(NH)p) on muscarinic agonist binding to homogenates from young vs aged cultures. Pretreatment of cultures from both ages by Bordetella pertussis toxin (IAP) was found to eliminate any Gpp(NH)p effect on carbamylcholine binding. IAP by itself induced a rightward shift in the carbamylcholine competition curve in homogenates from aged cultures, but no such effect was observed in homogenates from young cultures. IAP-catalyzed (/sup 32/P)ADP-ribosylation of membrane preparations from young and aged cultures revealed major differences between them. Young cultures exhibited a major IAP substrate at 40 kDa, which was also recognized by anti-..cap alpha../sub i/ antibodies, and two novel IAP substrates at 28 and 42 kDa, which were weakly ADP-ribosylated by the toxin and were not recognized with either anti-..cap alpha../sub i/ or anti-..cap alpha../sub 0/ antibodies. In aged cultures, only the 40-kDa band (ribosylated to a lower degree) was detected. The parallel age-dependent changes in the three IAP substrates (28, 40, and 42 kDa) and in the interactions of the G-protein(s) with the muscarinic receptors strongly suggest close association between the two phenomena. All of these age-dependent changes in the G-protein related parameters were prevented by phosphatidylcholine-liposome treatment of the aged cultures. The role of the membrane lipid composition in these phenomena is discussed.

  15. Additive Manufactured Product Integrity

    NASA Technical Reports Server (NTRS)

    Waller, Jess; Wells, Doug; James, Steve; Nichols, Charles

    2017-01-01

    NASA is providing key leadership in an international effort linking NASA and non-NASA resources to speed adoption of additive manufacturing (AM) to meet NASA's mission goals. Participants include industry, NASA's space partners, other government agencies, standards organizations and academia. Nondestructive Evaluation (NDE) is identified as a universal need for all aspects of additive manufacturing.

  16. The diverse roles of the Nup93/Nic96 complex proteins - structural scaffolds of the nuclear pore complex with additional cellular functions.

    PubMed

    Vollmer, Benjamin; Antonin, Wolfram

    2014-05-01

    Nuclear pore complexes mediate the transport between the cell nucleoplasm and cytoplasm. These 125 MDa structures are among the largest assemblies found in eukaryotes, built from proteins organized in distinct subcomplexes that act as building blocks during nuclear pore complex biogenesis. In this review, we focus on one of these subcomplexes, the Nup93 complex in metazoa and its yeast counterpart, the Nic96 complex. We discuss its essential function in nuclear pore complex assembly as a linker between the nuclear membrane and the central part of the pore and its various roles in nuclear transport processes and beyond.

  17. The 2.1 A structure of an elicitin-ergosterol complex: a recent addition to the Sterol Carrier Protein family.

    PubMed Central

    Boissy, G.; O'Donohue, M.; Gaudemer, O.; Perez, V.; Pernollet, J. C.; Brunie, S.

    1999-01-01

    Elicitins, produced by most of the phytopathogenic fungi of the genus Phytophthora, provoke in tobacco both remote leaf necrosis and the induction of a resistance against subsequent attack by various microorganisms. Despite the recent description of the three-dimensional crystal structure of cryptogein (CRY), the molecular basis of the interactions between Phytophthora and plants largely remains unknown. The X-ray crystal structure, refined at 2.1 A, of a ligand complexed, mutated CRY, K13H, is reported. Analysis of this structure reveals that CRY is able to encapsulate a ligand that induces only a minor conformational change in the protein structure. The ligand has been identified as an ergosterol by gas chromatographic analysis coupled with mass spectrometry analysis. This result is consistent with biochemical data that have shown that elicitins are a distinct class of Sterol Carrier Proteins (SCP). Data presented here provide the first structural description of the pertinent features of the elicitin sterol interaction and permit a reassessment of the importance of both the key residue 13 and the mobility of the omega loop for the accessibility of the sterol to the cavity. The biological implications thereof are discussed. This paper reports the first structure of a SCP/sterol complex. PMID:10386869

  18. Inhibition and Promotion of Heat-Induced Gelation of Whey Proteins in the Presence of Calcium by Addition of Sodium Caseinate.

    PubMed

    Nguyen, Bach T; Balakrishnan, Gireeshkumar; Jacquette, Boris; Nicolai, Taco; Chassenieux, Christophe; Schmitt, Christophe; Bovetto, Lionel

    2016-11-14

    Heat-induced aggregation and gelation of aqueous solutions of whey protein isolate (WPI) in the presence of sodium caseinate (SC) and CaCl2 was studied at pH 6.6. The effect of adding SC (0-100 g/L) on the structure of the aggregates and the gels was investigated by light scattering and confocal laser scanning microscopy at different CaCl2 concentration ([CaCl2] = 0-30 mM). The gelation process was studied by oscillatory shear rheology. At the whey protein concentrations studied here (34 and 60 g/L), no gels were formed in the absence of CaCl2 and SC. However, WPI solutions gelled above a critical CaCl2 concentration that increased with increasing SC concentration. In the absence of CaCl2, WPI gels were formed only above a critical SC concentration. The critical SC concentration needed to induce WPI gelation decreased weakly when CaCl2 was added. In an intermediate range of CaCl2 concentrations, gels were formed both at low and high SC concentrations, but not at intermediate SC concentrations. Finally, at high CaCl2 concentrations gels were formed at all SC concentrations. The gelation rate and the gel structure of the gels formed at low and high casein concentrations were very different. The effect of SC on the thermal gelation of WPI was interpreted by competition for Ca(2+), a chaperon effect, and microphase separation.

  19. Salmon testes meal as a functional feed additive in fish meal and plant-protein based diets for rainbow trout(Oncorhynchus mykiss walbaum)and nile tilapia(Oreochromis niloticus L.) fry

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We report that salmon testes meal (TM) produced from Alaskan seafood processing byproducts is a potential protein source for aquafeed formulations. A series of feeding trials was conducted using three different fish species; including Nile tilapia, rainbow trout, and white sturgeon at their early gr...

  20. Pump apparatus including deconsolidator

    DOEpatents

    Sonwane, Chandrashekhar; Saunders, Timothy; Fitzsimmons, Mark Andrew

    2014-10-07

    A pump apparatus includes a particulate pump that defines a passage that extends from an inlet to an outlet. A duct is in flow communication with the outlet. The duct includes a deconsolidator configured to fragment particle agglomerates received from the passage.

  1. Optical modulator including grapene

    DOEpatents

    Liu, Ming; Yin, Xiaobo; Zhang, Xiang

    2016-06-07

    The present invention provides for a one or more layer graphene optical modulator. In a first exemplary embodiment the optical modulator includes an optical waveguide, a nanoscale oxide spacer adjacent to a working region of the waveguide, and a monolayer graphene sheet adjacent to the spacer. In a second exemplary embodiment, the optical modulator includes at least one pair of active media, where the pair includes an oxide spacer, a first monolayer graphene sheet adjacent to a first side of the spacer, and a second monolayer graphene sheet adjacent to a second side of the spacer, and at least one optical waveguide adjacent to the pair.

  2. Design of phosphonium-type zwitterion as an additive to improve saturated water content of phase-separated ionic liquid from aqueous phase toward reversible extraction of proteins.

    PubMed

    Ito, Yoritsugu; Kohno, Yuki; Nakamura, Nobuhumi; Ohno, Hiroyuki

    2013-09-05

    We designed phosphonium-type zwitterion (ZI) to control the saturated water content of separated ionic liquid (IL) phase in the hydrophobic IL/water biphasic systems. The saturated water content of separated IL phase, 1-butyl-3-methyimidazolium bis(trifluoromethanesulfonyl)imide, was considerably improved from 0.4 wt% to 62.8 wt% by adding N,N,N-tripentyl-4-sulfonyl-1-butanephosphonium-type ZI (P555C4S). In addition, the maximum water content decreased from 62.8 wt% to 34.1 wt% by increasing KH2PO4/K2HPO4 salt content in upper aqueous phosphate buffer phase. Horse heart cytochrome c (cyt.c) was dissolved selectively in IL phase by improving the water content of IL phase, and spectroscopic analysis revealed that the dissolved cyt.c retained its higher ordered structure. Furthermore, cyt. c dissolved in IL phase was re-extracted again from IL phase to aqueous phase by increasing the concentration of inorganic salts of the buffer solution.

  3. Including Jews in Multiculturalism.

    ERIC Educational Resources Information Center

    Langman, Peter F.

    1995-01-01

    Discusses reasons for the lack of attention to Jews as an ethnic minority within multiculturalism both by Jews and non-Jews; why Jews and Jewish issues need to be included; and addresses some of the issues involved in the ethical treatment of Jewish clients. (Author)

  4. The Escherichia coli O157:H7 cattle immunoproteome includes outer membrane protein A (OmpA), a modulator of adherence to bovine rectoanal junction squamous epithelial (RSE) cells

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Building on previous studies, we defined the repertoire of proteins comprising the antigenome of Escherichia coli (E. coli) O157 cultured in Dulbecco's Modified Eagles Medium (DMEM) supplemented with norepinephrine (NE; O157 protein-antigenome), a beta-adrenergic hormone that regulates E. coli O157 ...

  5. Co-electroosmotic capillary electrophoresis of basic proteins with 1-alkyl-3-methylimidazolium tetrafluoroborate ionic liquids as non-covalent coating agents of the fused-silica capillary and additives of the electrolyte solution.

    PubMed

    Corradini, Danilo; Nicoletti, Isabella; Bonn, Günther K

    2009-06-01

    The paper reports the results of a study carried out to evaluate the use of three 1-alkyl-3-methylimidazolium-based ionic liquids as non-covalent coating agents for bare fused-silica capillaries and additives of the electrolyte solutions (BGE) for CE of basic proteins in the co-EOF separation mode. The three ionic liquids are differentiated from each other by the length of the alkyl group on the imidazolium cation, consisting of either an ethyl, butyl or octyl substituent, whereas tetrafluoroborate is the common anionic component of the ionic liquids. Coating the capillary with the ionic liquid resulted in improved peak shape and protein separation, while the EOF was maintained cathodic. This indicates that each ionic liquid is effective at masking the protein interaction sites on the inner surface of the capillary, also when its adsorption onto the capillary wall has not completely neutralized all the negative charges arising from the ionization of the silanol groups and the ionic liquid is not incorporated into the BGE employed for separation. Using the coated capillaries with BGE containing the ionic liquid employed for the coating, at concentration low enough to maintaining the EOF cathodic, both peak shape and protein separation varied to different extents, based on the particular ionic liquid used and its concentration. Fast and efficient separation of the model basic protein mixture in co-electroosmotic CE is obtained with the 1-butyl-3-methylimidazolium tetrafluoroborate coated capillary and 100 mM acetate buffer (pH 4.0) containing 4.4 mM 1-butyl-3-methylimidazolium tetrafluoroborate as the BGE.

  6. Anatomy of the pectoral and forelimb muscles of wildtype and green fluorescent protein-transgenic axolotls and comparison with other tetrapods including humans: a basis for regenerative, evolutionary and developmental studies

    PubMed Central

    Diogo, R; Tanaka, E M

    2012-01-01

    The axolotl Ambystoma mexicanum is one of the most used model organisms in evolutionary, developmental and regenerative studies, particularly because it can reconstitute a fully functional and complete forelimb/hindlimb. Surprisingly, there is no publication that describes all the pectoral and forelimb muscles of this species or provides a comparative framework between these muscles and those of other model organisms and of modern humans. In the present paper we describe and illustrate all these muscles in A. mexicanum and provide the first report about the myology of adults of a model organism that is based on analyses and dissections of both wildtype animals and transgenic animals that express green fluorescent protein (GFP) in muscle fibers. On the one hand, the inclusion of GFP-transgenic animals allows us to show the muscles as more commonly seen, and thus easier to understand, by current developmental and regenerative biologists. On the other hand, by including wildtype and GFP-transgenic animals and by visualizing these latter animals with and without a simultaneous transmission laser light, we were able to obtain a more complete and clearer understanding of the exact limit of the fleshy and tendinous parts of the muscles and their specific connections with the skeletal elements. This in turn allowed us to settle some controversies in previous anatomical and comparative studies. As most developmental, regenerative and evolutionary biologists are interested in comparing their observations of A. mexicanum with observations in other model organisms, and ultimately in using this information to increase the understanding of human evolution and medicine, we also provide tables showing the homologies between the pectoral and forelimb muscles of axolotls, of model organisms such as mice, frogs and chicken, and of Homo sapiens. An example illustrating the outcomes of using our methodology and of our observations is that they revealed that, contrary to what is often

  7. Loci Related to Metabolic-Syndrome Pathways Including LEPR,HNF1A, IL6R, and GCKR Associate with Plasma C-Reactive Protein: The Women's Genome Health Study

    PubMed Central

    Ridker, Paul M.; Pare, Guillaume; Parker, Alex; Zee, Robert Y.L.; Danik, Jacqueline S.; Buring, Julie E.; Kwiatkowski, David; Cook, Nancy R.; Miletich, Joseph P.; Chasman, Daniel I.

    2008-01-01

    Although elevated levels of C-reactive protein (CRP) independently predict increased risk of development of metabolic syndrome, diabetes, myocardial infarction, and stroke, comprehensive analysis of the influence of genetic variation on CRP is not available. To address this issue, we performed a genome-wide association study among 6345 apparently healthy women in which we evaluated 336,108 SNPs as potential determinants of plasma CRP concentration. Overall, seven loci that associate with plasma CRP at levels achieving genome-wide statistical significance were found (range of p values for lead SNPs within the seven loci: 1.9 × 10−8 to 6.2 × 10−28). Two of these loci (GCKR and HNF1A) are suspected or known to be associated with maturity-onset diabetes of the young, one is a gene-desert region on 12q23.2, and the remaining four loci are in or near the leptin receptor protein gene, the apolipoprotein E gene, the interleukin-6 receptor protein gene, or the CRP gene itself. The protein products of six of these seven loci are directly involved in metabolic syndrome, insulin resistance, beta cell function, weight homeostasis, and/or premature atherothrombosis. Thus, common variation in several genes involved in metabolic and inflammatory regulation have significant effects on CRP levels, consistent with CRP's identification as a useful biomarker of risk for incident vascular disease and diabetes. PMID:18439548

  8. Including whey protein and whey permeate in ready-to-use supplementary food improves recovery rates in children with moderate acute malnutrition: A randomized, double-blind clinical trial

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The utility of dairy ingredients in the supplementary foods used in the treatment of childhood moderate acute malnutrition (MAM) remains unsettled. We evaluated the effectiveness of a peanut-based ready-to-use supplementary food (RUSF) with soy protein compared with a novel RUSF containing dairy in...

  9. The F-Box Protein OsFBK12 Targets OsSAMS1 for Degradation and Affects Pleiotropic Phenotypes, Including Leaf Senescence, in Rice1[W][OPEN

    PubMed Central

    Chen, Yuan; Xu, Yunyuan; Luo, Wei; Li, Wenxuan; Chen, Na; Zhang, Dajian; Chong, Kang

    2013-01-01

    Leaf senescence is related to the grain-filling rate and grain weight in cereals. Many components involved in senescence regulation at either the genetic or physiological level are known. However, less is known about molecular regulation mechanisms. Here, we report that OsFBK12 (an F-box protein containing a Kelch repeat motif) interacts with S-ADENOSYL-l-METHIONINE SYNTHETASE1 (SAMS1) to regulate leaf senescence and seed size as well as grain number in rice (Oryza sativa). Yeast two-hybrid, pull-down, and bimolecular fluorescence complementation assays indicate that OsFBK12 interacts with Oryza sativa S-PHASE KINASE-ASSOCIATED PROTEIN1-LIKE PROTEIN and with OsSAMS1. Biochemical and physiological data showed that OsFBK12 targets OsSAMS1 for degradation. OsFBK12-RNA interference lines and OsSAMS1 overexpression lines showed increased ethylene levels, while OsFBK12-OX lines and OsSAMS1-RNA interference plants exhibited decreased ethylene. Phenotypically, overexpression of OsFBK12 led to a delay in leaf senescence and germination and increased seed size, whereas knockdown lines of either OsFBK12 or OsSAMS1 promoted the senescence program. Our results suggest that OsFBK12 is involved in the 26S proteasome pathway by interacting with Oryza sativa S-PHASE KINASE-ASSOCIATED PROTEIN1-LIKE PROTEIN and that it targets the substrate OsSAMS1 for degradation, triggering changes in ethylene levels for the regulation of leaf senescence and grain size. These data have potential applications in the molecular breeding of rice. PMID:24144792

  10. Prediction of binding modes between protein L-isoaspartyl (D-aspartyl) O-methyltransferase and peptide substrates including isomerized aspartic acid residues using in silico analytic methods for the substrate screening.

    PubMed

    Oda, Akifumi; Noji, Ikuhiko; Fukuyoshi, Shuichi; Takahashi, Ohgi

    2015-12-10

    Because the aspartic acid (Asp) residues in proteins are occasionally isomerized in the human body, not only l-α-Asp but also l-β-Asp, D-α-Asp and D-β-Asp are found in human proteins. In these isomerized aspartic acids, the proportion of D-β-Asp is the largest and the proportions of l-β-Asp and D-α-Asp found in human proteins are comparatively small. To explain the proportions of aspartic acid isomers, the possibility of an enzyme able to repair l-β-Asp and D-α-Asp is frequently considered. The protein L-isoaspartyl (D-aspartyl) O-methyltransferase (PIMT) is considered one of the possible repair enzymes for l-β-Asp and D-α-Asp. Human PIMT is an enzyme that recognizes both l-β-Asp and D-α-Asp, and catalyzes the methylation of their side chains. In this study, the binding modes between PIMT and peptide substrates containing l-β-Asp or D-α-Asp residues were investigated using computational protein-ligand docking and molecular dynamics simulations. The results indicate that carboxyl groups of both l-β-Asp and D-α-Asp were recognized in similar modes by PIMT and that the C-terminal regions of substrate peptides were located in similar positions on PIMT for both the l-β-Asp and D-α-Asp peptides. In contrast, for peptides containing l-α-Asp or D-β-Asp residues, which are not substrates of PIMT, the computationally constructed binding modes between PIMT and peptides greatly differed from those between PIMT and substrates. In the nonsubstrate peptides, not inter- but intra-molecular hydrogen bonds were observed, and the conformations of peptides were more rigid than those of substrates. Thus, the in silico analytical methods were able to distinguish substrates from nonsubstrates and the computational methods are expected to complement experimental analytical methods.

  11. [Information about phosphorus additives and nutritional counseling].

    PubMed

    Kido, Shinsuke; Nomura, Kengo; Sasaki, Shohei; Shiozaki, Yuji; Segawa, Hiroko; Tatsumi, Sawako

    2012-10-01

    Hyperphosphatemia is a common disorder in patients with chronic kidney disease (CKD) , and may result in hyperparathyroidism and renal osteodystrophy. Hyperphosphatemia also may contribute to deterioration vascular calcification and increase mortality. Hence, correction and prevention of hyperphosphatemia is a main component of the management of CKD. This goal is usually approached both by administering phosphorus binders and by restricting dietary phosphorus (P) intake. Dietary intake of phosphorus (P) is derived largely from foods with high protein content or food additives and is an important determinant of P balance in patient with CKD. Food additives (PO4) can dramatically increase the amount of P consumed in the daily diet, especially because P is more readily absorbed in its inorganic form. In addition, information about the P content and type in prepared foods is often unavailable or misleading. Therefore, during dietary counseling of patients with CKD, we recommended that they consider both the absolute dietary P content and the P-to-protein ratio of foods and meals including food additives.

  12. Screening somatic cell nuclear transfer parameters for generation of transgenic cloned cattle with intragenomic integration of additional gene copies that encode bovine adipocyte-type fatty acid-binding protein (A-FABP).

    PubMed

    Guo, Yong; Li, Hejuan; Wang, Ying; Yan, Xingrong; Sheng, Xihui; Chang, Di; Qi, Xiaolong; Wang, Xiangguo; Liu, Yunhai; Li, Junya; Ni, Hemin

    2017-02-01

    Somatic cell nuclear transfer (SCNT) is frequently used to produce transgenic cloned livestock, but it is still associated with low success rates. To our knowledge, we are the first to report successful production of transgenic cattle that overexpress bovine adipocyte-type fatty acid binding proteins (A-FABPs) with the aid of SCNT. Intragenomic integration of additional A-FABP gene copies has been found to be positively correlated with the intramuscular fat content in different farm livestock species. First, we optimized the cloning parameters to produce bovine embryos integrated with A-FABP by SCNT, such as applied voltage field strength and pulse duration for electrofusion, morphology and size of donor cells, and number of donor cells passages. Then, bovine fibroblast cells from Qinchuan cattle were transfected with A-FABP and used as donor cells for SCNT. Hybrids of Simmental and Luxi local cattle were selected as the recipient females for A-FABP transgenic SCNT-derived embryos. The results showed that a field strength of 2.5 kV/cm with two 10-μs duration electrical pulses was ideal for electrofusion, and 4-6th generation circular smooth type donor cells with diameters of 15-25 μm were optimal for producing transgenic bovine embryos by SCNT, and resulted in higher fusion (80%), cleavage (73%), and blastocyst (27%) rates. In addition, we obtained two transgenic cloned calves that expressed additional bovine A-FABP gene copies, as detected by PCR-amplified cDNA sequencing. We proposed a set of optimal protocols to produce transgenic SCNT-derived cattle with intragenomic integration of ectopic A-FABP-inherited exon sequences.

  13. Perspectives on Additive Manufacturing

    NASA Astrophysics Data System (ADS)

    Bourell, David L.

    2016-07-01

    Additive manufacturing (AM) has skyrocketed in visibility commercially and in the public sector. This article describes the development of this field from early layered manufacturing approaches of photosculpture, topography, and material deposition. Certain precursors to modern AM processes are also briefly described. The growth of the field over the last 30 years is presented. Included is the standard delineation of AM technologies into seven broad categories. The economics of AM part generation is considered, and the impacts of the economics on application sectors are described. On the basis of current trends, the future outlook will include a convergence of AM fabricators, mass-produced AM fabricators, enabling of topology optimization designs, and specialization in the AM legal arena. Long-term developments with huge impact are organ printing and volume-based printing.

  14. Overview of Protein Microarrays

    PubMed Central

    Reymond Sutandy, FX; Qian, Jiang; Chen, Chien-Sheng; Zhu, Heng

    2013-01-01

    Protein microarray is an emerging technology that provides a versatile platform for characterization of hundreds of thousands of proteins in a highly parallel and high-throughput way. Two major classes of protein microarrays are defined to describe their applications: analytical and functional protein microarrays. In addition, tissue or cell lysates can also be fractionated and spotted on a slide to form a reverse-phase protein microarray. While the fabrication technology is maturing, applications of protein microarrays, especially functional protein microarrays, have flourished during the past decade. Here, we will first review recent advances in the protein microarray technologies, and then present a series of examples to illustrate the applications of analytical and functional protein microarrays in both basic and clinical research. The research areas will include detection of various binding properties of proteins, study of protein posttranslational modifications, analysis of host-microbe interactions, profiling antibody specificity, and identification of biomarkers in autoimmune diseases. As a powerful technology platform, it would not be surprising if protein microarrays will become one of the leading technologies in proteomic and diagnostic fields in the next decade. PMID:23546620

  15. Phenolic promiscuity in the cell nucleus--epigallocatechingallate (EGCG) and theaflavin-3,3'-digallate from green and black tea bind to model cell nuclear structures including histone proteins, double stranded DNA and telomeric quadruplex DNA.

    PubMed

    Mikutis, Gediminas; Karaköse, Hande; Jaiswal, Rakesh; LeGresley, Adam; Islam, Tuhidul; Fernandez-Lahore, Marcelo; Kuhnert, Nikolai

    2013-02-01

    Flavanols from tea have been reported to accumulate in the cell nucleus in considerable concentrations. The nature of this phenomenon, which could provide novel approaches in understanding the well-known beneficial health effects of tea phenols, is investigated in this contribution. The interaction between epigallocatechin gallate (EGCG) from green tea and a selection of theaflavins from black tea with selected cell nuclear structures such as model histone proteins, double stranded DNA and quadruplex DNA was investigated using mass spectrometry, Circular Dichroism spectroscopy and fluorescent assays. The selected polyphenols were shown to display affinity to all of the selected cell nuclear structures, thereby demonstrating a degree of unexpected molecular promiscuity. Most interestingly theaflavin-digallate was shown to display the highest affinity to quadruplex DNA reported for any naturally occurring molecule reported so far. This finding has immediate implications in rationalising the chemopreventive effect of the tea beverage against cancer and possibly the role of tea phenolics as "life span essentials".

  16. Distribution of the AQP4 water channel in normal human tissues: protein and tissue microarrays reveal expression in several new anatomical locations, including the prostate gland and seminal vesicles.

    PubMed

    Mobasheri, Ali; Marples, David; Young, Iain S; Floyd, Rachel V; Moskaluk, Christopher A; Frigeri, Antonio

    2007-01-01

    Aquaporins facilitate osmotically driven water movement across cell membranes. Aquaporin 4 (AQP4) is a major water channel in the central nervous system where it participates in cerebral water balance. AQP4 is also present in basolateral membranes of lower respiratory tract airway and renal collecting duct epithelial cells, gastric parietal cells and skeletal muscle cells. However, the distribution of AQP4 in many other tissues is still unknown. The aim of this study was to determine the expression and relative abundance of AQP4 in human Tissue MicroArrays (TMAs) and human protein microarrays by immunohistochemistry and chemiluminescence. In the central nervous system AQP4 was abundantly expressed in the cerebral cortex, cerebellar cortex (purkinje/granular layer), ependymal cell layer, hippocampus and spinal cord. Lower levels were detected in choroid plexus, white matter and meninges. In the musculoskeletal system AQP4 was highly expressed in the sarcolemma of skeletal muscle from the chest and neck. In the male genital system AQP4 was moderately expressed in seminiferous tubules, seminal vesicles, prostate and epidiymis. In the respiratory system AQP4 was moderately expressed in lung and bronchus. AQP expression was abundant in the kidney. In the gastrointestinal system AQP4 was moderately present in basolateral membranes of parietal cells at the base of gastric glands. AQP4 was also detected in salivary glands, adrenals, anterior pituitary, prostate and seminal vesicles. Human protein microarrays verified the TMA data. Our findings suggest that AQP4 is expressed more widely than previously thought in human organs and may be involved in prostatic and seminal fluid formation.

  17. An Integrated Biochemistry Laboratory, Including Molecular Modeling

    NASA Astrophysics Data System (ADS)

    Hall, Adele J. Wolfson Mona L.; Branham, Thomas R.

    1996-11-01

    ), time of incubation, wavelength of measurement, addition of salts, and addition of detergent. In these independent projects, students sometimes discover ways to improve the methodology for the assays, and these improvements are incorporated into the suggested procedures for the rest of the semester. The results of this project are written up as a short paper in a style appropriate for a rapid communication in a scientific journal. The papers go through a round of peer review and revision. Ion-Exchange Chromatography Once each group has decided on a project and discussed the details with the instructor, they prepare their own buffers and equilibrate the resins. DEAE-Sephacel and CM-Sepharose, both from Pharmacia/LKB (Piscataway, NJ) are supplied, about 20 mL of packed resin for each egg-white preparation. (These resins can be regenerated and reused many times.) Each group uses one egg white for the entire purification project. The egg white is filtered through one layer of cheesecloth and diluted 5-fold with the starting buffer. The first step is done batchwise because of the viscosity of the sample. The diluted egg white is mixed with the resin for approximately 15 min, then centrifuged at 1500 μ g for 15 min. The supernatant, containing those proteins not adsorbed to the resin, is decanted. Subsequent washing and elution can then be carried out batchwise or by transferring to a column [1.5 - 20 cm Econocolumns (BioRad)]. The options for recovery of the enzyme from the CM resin include a batch or column method, elution by change in pH or ionic strength, and gradient or stepwise elution. Those carrying out elutions from a column use an automatic fraction collector; gradient formers are available for those who choose to elute with a linear salt gradient. When elution is carried out by a change in pH, it should be noted that lysozyme may precipitate near its isoelectric point, especially at low ionic strength. SDS - polyacrylamide gel electrophoresis is used to monitor

  18. Recombinant protein production technology

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  19. The t(11;14)(p15;q11) in a T-cell acute lymphoblastic leukemia cell line activates multiple transcripts, including Ttg-1, a gene encoding a potential zinc finger protein.

    PubMed Central

    McGuire, E A; Hockett, R D; Pollock, K M; Bartholdi, M F; O'Brien, S J; Korsmeyer, S J

    1989-01-01

    Interchromosomal translocations within lymphoid neoplasms frequently involve the antigen receptor genes. We cloned the breakpoints of the t(11;14)(p15;q11) in a CD3-negative T-cell acute lymphoblastic leukemia cell line (RPMI 8402) in order to identify new genes potentially involved in T-cell neoplasia. An extensive comparison of both breakpoints and their germ line counterparts indicated that an inadvertant recombinase-mediated break at chromosome segment 11p15 recombined with the delta T-cell receptor at 14q11. The derivative 11 breakpoint resembles a coding joint in which 11p15 rather than a variable region was introduced 5' to a D delta 1 D delta 2 J delta 1 intermediate rearrangement. Conversely, the derivative 14 breakpoint corresponds to a signal joint between the 5' heptamer-spacer-nonamer recombinational signal of D delta 1 and an isolated heptamer at 11p15. Multiple, apparently distinct transcripts were found flanking both breakpoints of 8402. RNAs of 3.5, 4.4, 1.4, and 8.0 kilobases originating from either side of the derivative 14 breakpoint were highly expressed in 8402 compared with other cells. This suggests that this translocation deregulated multiple genes and provides the opportunity to assess any multifactorial contribution they may have to malignancy. We cloned and sequenced several cDNAs representing the 1.4-kilobase transcript (termed Ttg-1 [T-cell translocation gene 1]) from an 8402 library. The predicted protein of 156 amino acids contained two internal repeats which could potentially form zinc fingers. Images PMID:2501659

  20. An evaluation of in vitro protein-protein interaction techniques: assessing contaminating background proteins.

    PubMed

    Howell, Jenika M; Winstone, Tara L; Coorssen, Jens R; Turner, Raymond J

    2006-04-01

    Determination of protein-protein interactions is an important component in assigning function and discerning the biological relevance of proteins within a broader cellular context. In vitro protein-protein interaction methodologies, including affinity chromatography, coimmunoprecipitation, and newer approaches such as protein chip arrays, hold much promise in the detection of protein interactions, particularly in well-characterized organisms with sequenced genomes. However, each of these approaches attracts certain background proteins that can thwart detection and identification of true interactors. In addition, recombinant proteins expressed in Escherichia coli are also extensively used to assess protein-protein interactions, and background proteins in these isolates can thus contaminate interaction studies. Rigorous validation of a true interaction thus requires not only that an interaction be found by alternate techniques, but more importantly that researchers be aware of and control for matrix/support dependence. Here, we evaluate these methods for proteins interacting with DmsD (an E. coli redox enzyme maturation protein chaperone), in vitro, using E. coli subcellular fractions as prey sources. We compare and contrast the various in vitro interaction methods to identify some of the background proteins and protein profiles that are inherent to each of the methods in an E. coli system.

  1. Employment, Training, and Literacy Enhancement Act of 1997. Report of the Committee on Education and the Workforce, House of Representatives, on H.R. 1385 Together with Additional and Dissenting Views [Including Cost Estimate of the Congressional Budget Office], 105th Congress, 1st Session.

    ERIC Educational Resources Information Center

    Congress of the U.S., Washington, DC. House Committee on Education and the Workforce.

    This document contains the text of the Employment, Training, and Literacy Enhancement Act of 1997, as amended by committee, including the titles that cover the following: general provisions; employment and training programs for disadvantaged youth; federally administered programs; adult education programs; miscellaneous provisions; the State Human…

  2. Atoms-in-molecules study of the genetically encoded amino acids. III. Bond and atomic properties and their correlations with experiment including mutation-induced changes in protein stability and genetic coding.

    PubMed

    Matta, Chérif F; Bader, Richard F W

    2003-08-15

    volume contributions) yielding linear regressions with r2 values of 0.78 and 0.89, respectively. These results are a prelude to the single-site mutation-induced changes in the stabilities of two typical proteins: ubiquitin and staphylococcal nuclease. Strong quadratic correlations (r2 approximately 0.9) were obtained between DeltaCSI upon mutation and each of the two terms DeltaDeltaH and TDeltaDeltaS taken from recent and accurate differential scanning calorimetry experiments on ubiquitin. When the two terms are summed to yield DeltaDeltaG, the quadratic terms nearly cancel, and the result is a simple linear fit between DeltaDeltaG and DeltaCSI with r2 = 0.88. As another example, the change in the stability of staphylococcal nuclease upon mutation has been fitted linearly (r2 = 0.83) to the sum of a DeltaCSI term and a term representing the change in the van der Waals volume of the side chains upon mutation. The suggested correlation of the polarity of the side chain with the second letter of the AA triplet genetic codon is given concrete expression in a classification of the side chains in terms of their CSI values and their group dipole moments. For example, all amino acids with a pyrimidine base as their second letter in mRNA possess side-chain CSI < or = 2.8 (with the exception of Cys), whereas all those with CSI > 2.8 possess an purine base. The article concludes with two proposals for measuring and predicting molecular complementarity: van der Waals complementarity expressed in terms of the van der Waals isodensity surface and Lewis complementarity expressed in terms of the local charge concentrations and depletions defined by the topology of the Laplacian of the electron density. A display of the experimentally accessible Laplacian distribution for a folded protein would offer a clear picture of the operation of the "stereochemical code" proposed as the determinant in the folding process.

  3. Identification of polymer surface adsorbed proteins implicated in pluripotent human embryonic stem cell expansion† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6bm00214e Click here for additional data file.

    PubMed Central

    Hammad, Moamen; Rao, Wei; Smith, James G. W.; Anderson, Daniel G.; Langer, Robert; Young, Lorraine E.; Barrett, David A.; Davies, Martyn C.; Denning, Chris

    2016-01-01

    Improved biomaterials are required for application in regenerative medicine, biosensing, and as medical devices. The response of cells to the chemistry of polymers cultured in media is generally regarded as being dominated by proteins adsorbed to the surface. Here we use mass spectrometry to identify proteins adsorbed from a complex mouse embryonic fibroblast (MEF) conditioned medium found to support pluripotent human embryonic stem cell (hESC) expansion on a plasma etched tissue culture polystyrene surface. A total of 71 proteins were identified, of which 14 uniquely correlated with the surface on which pluripotent stem cell expansion was achieved. We have developed a microarray combinatorial protein spotting approach to test the potential of these 14 proteins to support expansion of a hESC cell line (HUES-7) and a human induced pluripotent stem cell line (ReBl-PAT) on a novel polymer (N-(4-Hydroxyphenyl) methacrylamide). These proteins were spotted to form a primary array yielding several protein mixture ‘hits’ that enhanced cell attachment to the polymer. A second array was generated to test the function of a refined set of protein mixtures. We found that a combination of heat shock protein 90 and heat shock protein-1 encourage elevated adherence of pluripotent stem cells at a level comparable to fibronectin pre-treatment. PMID:27466628

  4. Proteomic analysis of salt tolerance in sugar beet monosomic addition line M14.

    PubMed

    Yang, Le; Zhang, Yanjun; Zhu, Ning; Koh, Jin; Ma, Chunquan; Pan, Yu; Yu, Bing; Chen, Sixue; Li, Haiying

    2013-11-01

    Understanding the mechanisms of plant salinity tolerance can facilitate plant engineering for enhanced salt stress tolerance. Sugar beet monosomic addition line M14 obtained from the intercross between Beta vulgaris L. and Beta corolliflora Zoss exhibits tolerance to salt stress. Here we report the salt-responsive characteristics of the M14 plants under 0, 200, and 400 mM NaCl conditions using quantitative proteomics approaches. Proteins from control and the salt treated M14 plants were separated using 2D-DIGE. Eighty-six protein spots representing 67 unique proteins in leaves and 22 protein spots representing 22 unique proteins in roots were identified. In addition, iTRAQ LC-MS/MS was employed to identify and quantify differentially expressed proteins under salt stress. Seventy-five differentially expressed proteins in leaves and 43 differentially expressed proteins in roots were identified. The proteins were mainly involved in photosynthesis, energy, metabolism, protein folding and degradation, and stress and defense. Moreover, gene transcription data obtained from the same samples were compared to the corresponding protein data. Thirteen proteins in leaves and 12 in roots showed significant correlation in gene expression and protein levels. These results suggest the important processes for the M14 tolerance to salt stress include enhancement of photosynthesis and energy metabolism, accumulation of osmolyte and antioxidant enzymes, and regulation of methionine metabolism and ion uptake/exclusion.

  5. Protein Solubilization: A Novel Approach

    PubMed Central

    Johnson, David H.; Wilson, W. William; DeLucas, Lawrence J.

    2014-01-01

    Formulation development presents significant challenges with respect to protein therapeutics. One component of these challenges is to attain high protein solubility (> 50 mg/ml for immunoglobulins) with minimal aggregation. Protein-protein interactions contribute to aggregation and the integral sum of these interactions can be quantified by a thermodynamic parameter known as the osmotic second virial coefficient (B-value). The method presented here utilizes high-throughput measurement of B-values to identify the influence of additives on protein-protein interactions. The experiment design uses three tiers of screens to arrive at final solution conditions that improve protein solubility. The first screen identifies individual additives that reduce protein interactions. A second set of B-values are then measured for different combinations of these additives via an incomplete factorial screen. Results from the incomplete factorial screen are used to train an artificial neural network (ANN). The “trained” ANN enables predictions of B-values for more than 4,000 formulations that include additive combinations not previously experimentally measured. Validation steps are incorporated throughout the screening process to ensure that 1) the protein’s thermal and aggregation stability characteristics are not reduced and 2) the artificial neural network predictive model is accurate. The ability of this approach to reduce aggregation and increase solubility is demonstrated using an IgG protein supplied by Minerva Biotechnologies, Inc. PMID:25270058

  6. Additive Similarity Trees

    ERIC Educational Resources Information Center

    Sattath, Shmuel; Tversky, Amos

    1977-01-01

    Tree representations of similarity data are investigated. Hierarchical clustering is critically examined, and a more general procedure, called the additive tree, is presented. The additive tree representation is then compared to multidimensional scaling. (Author/JKS)

  7. Additive lattice kirigami.

    PubMed

    Castle, Toen; Sussman, Daniel M; Tanis, Michael; Kamien, Randall D

    2016-09-01

    Kirigami uses bending, folding, cutting, and pasting to create complex three-dimensional (3D) structures from a flat sheet. In the case of lattice kirigami, this cutting and rejoining introduces defects into an underlying 2D lattice in the form of points of nonzero Gaussian curvature. A set of simple rules was previously used to generate a wide variety of stepped structures; we now pare back these rules to their minimum. This allows us to describe a set of techniques that unify a wide variety of cut-and-paste actions under the rubric of lattice kirigami, including adding new material and rejoining material across arbitrary cuts in the sheet. We also explore the use of more complex lattices and the different structures that consequently arise. Regardless of the choice of lattice, creating complex structures may require multiple overlapping kirigami cuts, where subsequent cuts are not performed on a locally flat lattice. Our additive kirigami method describes such cuts, providing a simple methodology and a set of techniques to build a huge variety of complex 3D shapes.

  8. Additive lattice kirigami

    PubMed Central

    Castle, Toen; Sussman, Daniel M.; Tanis, Michael; Kamien, Randall D.

    2016-01-01

    Kirigami uses bending, folding, cutting, and pasting to create complex three-dimensional (3D) structures from a flat sheet. In the case of lattice kirigami, this cutting and rejoining introduces defects into an underlying 2D lattice in the form of points of nonzero Gaussian curvature. A set of simple rules was previously used to generate a wide variety of stepped structures; we now pare back these rules to their minimum. This allows us to describe a set of techniques that unify a wide variety of cut-and-paste actions under the rubric of lattice kirigami, including adding new material and rejoining material across arbitrary cuts in the sheet. We also explore the use of more complex lattices and the different structures that consequently arise. Regardless of the choice of lattice, creating complex structures may require multiple overlapping kirigami cuts, where subsequent cuts are not performed on a locally flat lattice. Our additive kirigami method describes such cuts, providing a simple methodology and a set of techniques to build a huge variety of complex 3D shapes. PMID:27679822

  9. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Pratt, J. R.; St. Clair, T. L.; Burks, H. D.; Stoakley, D. M.

    1987-01-01

    A method has been found for enhancing the melt flow of thermoplastic polyimides during processing. A high molecular weight 422 copoly(amic acid) or copolyimide was fused with approximately 0.05 to 5 pct by weight of a low molecular weight amic acid or imide additive, and this melt was studied by capillary rheometry. Excellent flow and improved composite properties on graphite resulted from the addition of a PMDA-aniline additive to LARC-TPI. Solution viscosity studies imply that amic acid additives temporarily lower molecular weight and, hence, enlarge the processing window. Thus, compositions containing the additive have a lower melt viscosity for a longer time than those unmodified.

  10. [Food additives and healthiness].

    PubMed

    Heinonen, Marina

    2014-01-01

    Additives are used for improving food structure or preventing its spoilage, for example. Many substances used as additives are also naturally present in food. The safety of additives is evaluated according to commonly agreed principles. If high concentrations of an additive cause adverse health effects for humans, a limit of acceptable daily intake (ADI) is set for it. An additive is a risk only when ADI is exceeded. The healthiness of food is measured on the basis of nutrient density and scientifically proven effects.

  11. Mastitomics, the integrated omics of bovine milk in an experimental model of Streptococcus uberis mastitis: 1. High abundance proteins, acute phase proteins and peptidomics† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6mb00239k Click here for additional data file.

    PubMed Central

    Thomas, Funmilola Clara; Mullen, William; Tassi, Riccardo; Ramírez-Torres, Adela; Mudaliar, Manikhandan; McNeilly, Tom N.; Zadoks, Ruth N.; Burchmore, Richard

    2016-01-01

    A peptidomic investigation of milk from an experimental model of Streptococcus uberis mastitis in dairy cows has incorporated a study of milk high abundance and acute phase (APP) proteins as well as analysis of low molecular weight peptide biomarkers. Intramammary infection (IMI) with S. uberis caused a shift in abundance from caseins, β-lactoglobulin and α-lactalbumin to albumin, lactoferrin and IgG with the increase in lactoferrin occurring last. The APP response of haptoglobin, mammary associated serum amyloid A3 and C-reactive protein occurred between 30–48 hours post challenge with peak concentrations of APPs at 72–96 hours post challenge and declined thereafter at a rate resembling the fall in bacterial count rather than the somatic cell count. A peptide biomarker panel for IMI based on capillary electrophoresis and mass spectrometry was developed. It comprised 77 identified peptides (IMI77) composed mainly of casein derived peptides but also including peptides of glycosylation dependent cell adhesion molecule and serum amyloid A. The panel had a biomarker classification score that increased from 36 hour to 81 hour post challenge, significantly differentiating infected from non-infected milk, thus suggesting potential as a peptide biomarker panel of bovine mastitis and specifically that of S. uberis origin. The use of omic technology has shown a multifactorial cross system reaction in high and low abundance proteins and their peptide derivatives with changes of over a thousand fold in analyte levels in response to S. uberis infection. PMID:27412456

  12. Fermentation and addition of enzymes to a diet based on high-moisture corn, rapeseed cake, and peas improve digestibility of nonstarch polysaccharides, crude protein, and phosphorus in pigs.

    PubMed

    Jakobsen, G V; Jensen, B B; Bach Knudsen, K E; Canibe, N

    2015-05-01

    Fluctuating prices of cereals have led to an interest in alternative ingredients for feed. The aim of this study was to evaluate the effect of fermentation and the addition of nonstarch polysaccharide (NSP)-degrading enzymes on the ileal and total tract digestibility of nutrients of a diet based on locally grown crops. Four diets were fed including a nonfermented liquid standard grower diet (Control) and 3 experimental diets based on high-moisture corn, rapeseed cake, and peas fed as nonfermented liquid feed (nFLF), fermented liquid feed (FLF), or FLF supplemented with an enzyme mixture of β-glucanase + xylanase + pectinase (FLF+Enz). The FLF was prepared by mixing feed and water (1:2.5, wt/wt) and, once daily, replacing 50% of the mixture with an equal amount of fresh feed and water. The diets were fed to 8 ileal cannulated barrows in a double Latin square design. Ileal digesta and feces were collected after an adaption period of 10 d. Results showed microbiologically good-quality fermented diets. The levels of Enterobacteriaceae were 5.1 to 5.4 log cfu/g in FLF and FLF+Enz vs. 6.3 log cfu/g in nFLF in the ileum and 5.1 to 5.2 log cfu/g in FLF and FLF+Enz vs. 6.3 log cfu/g in nFLF in the feces. Apparent total tract digestibility (ATTD) of CP was increased by fermentation (73.2% in FLF vs. 69.0% in nFLF; P = 0.033), and digestibility of P showed a tendency (P = 0.073) toward an increase. Addition of the enzyme mixture resulted in a pronounced reduction of dietary NSP compared with FLF (12.8% total NSP in FLF+Enz vs. 15.9% total NSP in FLF; P< 0.001), which also led to increased apparent ileal digestibility (AID) of total and insoluble NSP (total NSP, 31.1% in FLF+Enz vs. 13.6% in FLF; P = 0.002). The Control did not, in general, show higher digestibility values than the experimental diet. However, in the cases were it did, fermentation and enzyme addition brought the digestibility to the level of the Control. In conclusion, fermentation increased the ATTD of CP

  13. Acanthamoeba castellanii STAT Protein

    PubMed Central

    Kicinska, Anna; Leluk, Jacek; Jarmuszkiewicz, Wieslawa

    2014-01-01

    STAT (signal transducers and activators of transcription) proteins are one of the important mediators of phosphotyrosine-regulated signaling in metazoan cells. We described the presence of STAT protein in a unicellular, free-living amoebae with a simple life cycle, Acanthamoeba castellanii. A. castellanii is the only, studied to date, Amoebozoan that does not belong to Mycetozoa but possesses STATs. A sequence of the A. castellanii STAT protein includes domains similar to those of the Dictyostelium STAT proteins: a coiled coil (characteristic for Dictyostelium STAT coiled coil), a STAT DNA-binding domain and a Src-homology domain. The search for protein sequences homologous to A. castellanii STAT revealed 17 additional sequences from lower eukaryotes. Interestingly, all of these sequences come from Amoebozoa organisms that belong to either Mycetozoa (slime molds) or Centramoebida. We showed that there are four separated clades within the slime mold STAT proteins. The A. castellanii STAT protein branches next to a group of STATc proteins from Mycetozoa. We also demonstrate that Amoebozoa form a distinct monophyletic lineage within the STAT protein world that is well separated from the other groups. PMID:25338074

  14. Solid-state nuclear magnetic resonance (NMR) spectroscopy of human immunodeficiency virus gp41 protein that includes the fusion peptide: NMR detection of recombinant Fgp41 in inclusion bodies in whole bacterial cells and structural characterization of purified and membrane-associated Fgp41.

    PubMed

    Vogel, Erica P; Curtis-Fisk, Jaime; Young, Kaitlin M; Weliky, David P

    2011-11-22

    Human immunodeficiency virus (HIV) infection of a host cell begins with fusion of the HIV and host cell membranes and is mediated by the gp41 protein, a single-pass integral membrane protein of HIV. The 175 N-terminal residues make up the ectodomain that lies outside the virus. This work describes the production and characterization of an ectodomain construct containing the 154 N-terminal gp41 residues, including the fusion peptide (FP) that binds to target cell membranes. The Fgp41 sequence was derived from one of the African clade A strains of HIV-1 that have been less studied than European/North American clade B strains. Fgp41 expression at a level of ~100 mg/L of culture was evidenced by an approach that included amino acid type (13)CO and (15)N labeling of recombinant protein and solid-state NMR (SSNMR) spectroscopy of lyophilized whole cells. The approach did not require any protein solubilization or purification and may be a general approach for detection of recombinant protein. The purified Fgp41 yield was ~5 mg/L of culture. SSNMR spectra of membrane-associated Fgp41 showed high helicity for the residues C-terminal of the FP. This was consistent with a "six-helix bundle" (SHB) structure that is the final gp41 state during membrane fusion. This observation and negligible Fgp41-induced vesicle fusion supported a function for SHB gp41 of membrane stabilization and fusion arrest. SSNMR spectra of residues in the membrane-associated FP provided evidence of a mixture of molecular populations with either helical or β-sheet FP conformation. These and earlier SSNMR data strongly support the existence of these populations in the SHB state of membrane-associated gp41.

  15. Food Additives and Hyperkinesis: A Controlled Double-Blind Experiment. (Includes NIE Staff Critique).

    ERIC Educational Resources Information Center

    Conners, C. Keith; And Others

    Fifteen hyperkinetic children (6-12 years old) were involved in a pilot study to test B. Feingold's hypothesis that hyperkinesis may be caused by artificial flavors and colors in food. Prior to treatment, parents and teachers completed bi-weekly questionnaires regarding each Ss' behavior both on medication (pretreatment period) and when medication…

  16. Additions to the knowledge of the land snails of Sabah (Malaysia, Borneo), including 48 new species

    PubMed Central

    Vermeulen, Jaap J.; Liew, Thor-Seng; Schilthuizen, Menno

    2015-01-01

    Abstract We present reviews of the Sabah (Malaysia, on the island of Borneo) species of the following problematical genera of land snails (Mollusca, Gastropoda): Acmella and Anaglyphula (Caenogastropoda: Assimineidae); Ditropopsis (Caenogastropoda: Cyclophoridae); Microcystina (Pulmonata: Ariophantidae); Philalanka and Thysanota (Pulmonata: Endodontidae); Kaliella, Rahula, (Pulmonata: Euconulidae); Trochomorpha and Geotrochus (Pulmonata: Trochomorphidae). Next to this, we describe new species in previously revised genera, such as Diplommatina (Diplommatinidae); Georissa (Hydrocenidae); as well as some new species of genera not revised previously, such as Japonia (Cyclophoridae); Durgella and Dyakia (Ariophantidae); Amphidromus, and Trachia (Camaenidae); Paralaoma (Punctidae); Curvella (Subulinidae). All descriptions are based on the morphology of the shells. We distinguish the following 48 new species: Acmella cyrtoglyphe, Acmella umbilicata, Acmella ovoidea, Acmella nana, Acmella subcancellata, Acmella striata, and Anaglyphula sauroderma (Assimineidae); Ditropopsis davisoni, Ditropopsis trachychilus, Ditropopsis constricta, Ditropopsis tyloacron, Ditropopsis cincta, and Japonia anceps (Cyclophoridae); Diplommatina bidentata and Diplommatina tylocheilos (Diplommatinidae); Georissa leucococca and Georissa nephrostoma (Hydrocenidae); Durgella densestriata, Dyakia chlorosoma, Microcystina microrhynchus, Microcystina callifera, Microcystina striatula, Microcystina planiuscula, and Microcystina physotrochus (Ariophantidae); Amphidromus psephos and Trachia serpentinitica (Camaenidae); Philalanka tambunanensis, Philalanka obscura, Philalanka anomphala, Philalanka rugulosa, and Philalanka malimgunung (Endodontidae); Kaliella eurytrochus, Kaliella sublaxa, Kaliella phacomorpha, Kaliella punctata, Kaliella microsoma, Rahula delopleura, (Euconulidae); Paralaoma angusta (Punctidae); Curvella hadrotes (Subulinidae); Trochomorpha trachus, Trochomorpha haptoderma, Trochomorpha thelecoryphe, Geotrochus oedobasis, Geotrochus spilokeiria, Geotrochus scolops, Geotrochus kitteli, Geotrochus subscalaris, and Geotrochus meristorhachis (Trochomorphidae). PMID:26692803

  17. Collaborative Assessment: Working with Students Who Are Blind or Visually Impaired, Including Those with Additional Disabilities.

    ERIC Educational Resources Information Center

    Goodman, Stephen A., Ed.; Wittenstein, Stuart H., Ed.

    This book offers a comprehensive text on the assessment of students with blindness or visual impairment with a focus on approaches used at the California School for the Blind. An introductory chapter is by Frances K. Liefert and Marsha A. Silver. Eleven chapters have the following titles and authors: (1) "Introduction to Visual Impairment"…

  18. Polylactides in additive biomanufacturing.

    PubMed

    Poh, Patrina S P; Chhaya, Mohit P; Wunner, Felix M; De-Juan-Pardo, Elena M; Schilling, Arndt F; Schantz, Jan-Thorsten; van Griensven, Martijn; Hutmacher, Dietmar W

    2016-12-15

    New advanced manufacturing technologies under the alias of additive biomanufacturing allow the design and fabrication of a range of products from pre-operative models, cutting guides and medical devices to scaffolds. The process of printing in 3 dimensions of cells, extracellular matrix (ECM) and biomaterials (bioinks, powders, etc.) to generate in vitro and/or in vivo tissue analogue structures has been termed bioprinting. To further advance in additive biomanufacturing, there are many aspects that we can learn from the wider additive manufacturing (AM) industry, which have progressed tremendously since its introduction into the manufacturing sector. First, this review gives an overview of additive manufacturing and both industry and academia efforts in addressing specific challenges in the AM technologies to drive toward AM-enabled industrial revolution. After which, considerations of poly(lactides) as a biomaterial in additive biomanufacturing are discussed. Challenges in wider additive biomanufacturing field are discussed in terms of (a) biomaterials; (b) computer-aided design, engineering and manufacturing; (c) AM and additive biomanufacturing printers hardware; and (d) system integration. Finally, the outlook for additive biomanufacturing was discussed.

  19. In vitro refolding with simultaneous purification of recombinant human parathyroid hormone (rhPTH 1-34) from Escherichia coli directed by protein folding size exclusion chromatography (PF-SEC): implication of solution additives and their role on aggregates and renaturation.

    PubMed

    Vemula, Sandeep; Vemula, Sushma; Dedaniya, Akshay; Ronda, Srinivasa Reddy

    2016-01-01

    Recombinant proteins are frequently hampered by aggregation during the refolding and purification process. A simple and rapid method for in vitro refolding and purification of recombinant human parathyroid hormone (rhPTH 1-34) expressed in Escherichia coli with protein folding size exclusion chromatography (PF-SEC) was developed in the present work. Discrete effects of potential solution additives such as urea, polypolyethylene glycol, proline, and maltose on the refolding with simultaneous purification of rhPTH were investigated. The results of individual additives indicated that both maltose and proline had remarkable influences on the efficiency of refolding with a recovery yield of 65 and 66% respectively. Further, the synergistic effect of these additives on refolding was also explored. These results demonstrate that the additive combinations are more effective for inhibiting protein aggregation during purification of rhPTH in terms of recovery yield, purity, and specific activity. The maltose and proline combination system achieved the highest renatured rhPTH having a recovery yield of 78%, a purity of ≥99%, and a specific activity of 3.31 × 10(3) cAMP pM/cell respectively, when compared to the classical dilution method yield (41%) and purity (97%). In addition, the role of maltose and proline in a combined system on protein aggregation and refolding has been explained. The molecular docking (in silico) scores of maltose (-10.91) and proline (-9.0) support the in vitro results.

  20. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Fletcher, James C. (Inventor); Pratt, J. Richard (Inventor); St.clair, Terry L. (Inventor); Stoakley, Diane M. (Inventor); Burks, Harold D. (Inventor)

    1992-01-01

    A process for preparing polyimides having enhanced melt flow properties is described. The process consists of heating a mixture of a high molecular weight poly-(amic acid) or polyimide with a low molecular weight amic acid or imide additive in the range of 0.05 to 15 percent by weight of additive. The polyimide powders so obtained show improved processability, as evidenced by lower melt viscosity by capillary rheometry. Likewise, films prepared from mixtures of polymers with additives show improved processability with earlier onset of stretching by TMA.

  1. Polyimide processing additives

    NASA Technical Reports Server (NTRS)

    Pratt, J. Richard (Inventor); St.clair, Terry L. (Inventor); Stoakley, Diane M. (Inventor); Burks, Harold D. (Inventor)

    1993-01-01

    A process for preparing polyimides having enhanced melt flow properties is described. The process consists of heating a mixture of a high molecular weight poly-(amic acid) or polyimide with a low molecular weight amic acid or imide additive in the range of 0.05 to 15 percent by weight of the additive. The polyimide powders so obtained show improved processability, as evidenced by lower melt viscosity by capillary rheometry. Likewise, films prepared from mixtures of polymers with additives show improved processability with earlier onset of stretching by TMA.

  2. Adverse reactions to drug additives.

    PubMed

    Simon, R A

    1984-10-01

    There is a long list of additives used by the pharmaceutical industry. Most of the agents used have not been implicated in hypersensitivity reactions. Among those that have, only reactions to parabens and sulfites have been well established. Parabens have been shown to be responsible for rare immunoglobulin E-mediated reactions that occur after the use of local anesthetics. Sulfites, which are present in many drugs, including agents commonly used to treat asthma, have been shown to provoke severe asthmatic attacks in sensitive individuals. Recent studies indicate that additives do not play a significant role in "hyperactivity." The role of additives in urticaria is not well established and therefore the incidence of adverse reactions in this patient population is simply not known. In double-blind, placebo-controlled studies, reactions to tartrazine or additives other than sulfites, if they occur at all, are indeed quite rare for the asthmatic population, even for the aspirin-sensitive subpopulation.

  3. Food Additives and Hyperkinesis

    ERIC Educational Resources Information Center

    Wender, Ester H.

    1977-01-01

    The hypothesis that food additives are causally associated with hyperkinesis and learning disabilities in children is reviewed, and available data are summarized. Available from: American Medical Association 535 North Dearborn Street Chicago, Illinois 60610. (JG)

  4. Smog control fuel additives

    SciTech Connect

    Lundby, W.

    1993-06-29

    A method is described of controlling, reducing or eliminating, ozone and related smog resulting from photochemical reactions between ozone and automotive or industrial gases comprising the addition of iodine or compounds of iodine to hydrocarbon-base fuels prior to or during combustion in an amount of about 1 part iodine per 240 to 10,000,000 parts fuel, by weight, to be accomplished by: (a) the addition of these inhibitors during or after the refining or manufacturing process of liquid fuels; (b) the production of these inhibitors for addition into fuel tanks, such as automotive or industrial tanks; or (c) the addition of these inhibitors into combustion chambers of equipment utilizing solid fuels for the purpose of reducing ozone.

  5. Optimization of protein buffer cocktails using Thermofluor.

    PubMed

    Reinhard, Linda; Mayerhofer, Hubert; Geerlof, Arie; Mueller-Dieckmann, Jochen; Weiss, Manfred S

    2013-02-01

    The stability and homogeneity of a protein sample is strongly influenced by the composition of the buffer that the protein is in. A quick and easy approach to identify a buffer composition which increases the stability and possibly the conformational homogeneity of a protein sample is the fluorescence-based thermal-shift assay (Thermofluor). Here, a novel 96-condition screen for Thermofluor experiments is presented which consists of buffer and additive parts. The buffer screen comprises 23 different buffers and the additive screen includes small-molecule additives such as salts and nucleotide analogues. The utilization of small-molecule components which increase the thermal stability of a protein sample frequently results in a protein preparation of higher quality and quantity and ultimately also increases the chances of the protein crystallizing.

  6. Regulation of highly homologous major urinary proteins in house mice quantified with label-free proteomic methods† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c6mb00278a Click here for additional data file.

    PubMed Central

    Enk, Viktoria M.; Baumann, Christian; Thoß, Michaela; Luzynski, Kenneth C.; Razzazi-Fazeli, Ebrahim

    2016-01-01

    Major urinary proteins (MUPs) are highly homologous proteoforms that function in binding, transporting and releasing pheromones in house mice. The main analytical challenge for studying variation in MUPs, even for state-of-the-art proteomics techniques, is their high degree of amino acid sequence homology. In this study we used unique peptides for proteoform-specific identification. We applied different search engines (ProteinPilot™ vs. PEAKS®) and protein databases (MUP database vs. SwissProt + unreviewed MUPs), and found that proteoform identification is influenced by addressing background proteins (unregulated urinary proteins, non-MUPs) during the database search. High resolution Q-TOF mass spectrometry was used to identify and precisely quantify the regulation of MUP proteoforms in male mice that were reared in standard housing and then transferred to semi-natural enclosures (within-subject design). By using a designated MUP database we were able to distinguish 19 MUP proteoforms, with A2CEK6 (a Mup11 gene product) being the most abundant based on spectral intensities. We compared three different quantification strategies based on MS1- (from IDA and SWATH™ spectra) and MS2 (SWATH™) data, and the results of these methods were correlated. Furthermore, three data normalization methods were compared and we found that increased statistical significance of fold-changes can be achieved by normalization based on urinary protein concentrations. We show that male mice living in semi-natural enclosures significantly up-regulated some but not all MUPs (differential regulation), e.g., A2ANT6, a Mup6 gene product, was upregulated between 9-fold (MS1) and 13-fold (MS2) using the designated MUP database. Finally, we show that 85 ± 7% of total MS intensity can be attributed to MUP-derived peptides, which supports the assumption that MUPs are the primary proteins in mouse urine. Our results provide new tools for assessing qualitative and quantitative variation of MUPs

  7. Role of protein-protein interactions in cytochrome P450-mediated drug metabolism and toxicity.

    PubMed

    Kandel, Sylvie E; Lampe, Jed N

    2014-09-15

    Through their unique oxidative chemistry, cytochrome P450 monooxygenases (CYPs) catalyze the elimination of most drugs and toxins from the human body. Protein-protein interactions play a critical role in this process. Historically, the study of CYP-protein interactions has focused on their electron transfer partners and allosteric mediators, cytochrome P450 reductase and cytochrome b5. However, CYPs can bind other proteins that also affect CYP function. Some examples include the progesterone receptor membrane component 1, damage resistance protein 1, human and bovine serum albumin, and intestinal fatty acid binding protein, in addition to other CYP isoforms. Furthermore, disruption of these interactions can lead to altered paths of metabolism and the production of toxic metabolites. In this review, we summarize the available evidence for CYP protein-protein interactions from the literature and offer a discussion of the potential impact of future studies aimed at characterizing noncanonical protein-protein interactions with CYP enzymes.

  8. Identification of cDNA encoding an additional. alpha. subunit of a human GTP-binding protein: Expression of three. alpha. sub i subtypes in human tissues and cell lines

    SciTech Connect

    Kim, S.; Ang, S.L.; Bloch, D.B.; Bloch, K.D.; Kawahara, Y.; Tolman, C.; Lee, R.; Seidman, J.G.; Neer, E.J. )

    1988-06-01

    The guanine nucleotide-binding proteins (G proteins), which mediate hormonal regulation of many membrane functions, are composed of {alpha}, {beta}, and {gamma} subunits. The authors have cloned and characterized cDNA from a human T-cell library encoding a form of {alpha}{sub i} that is different from the human {alpha}{sub i} subtypes previously reported. {alpha}{sub i} is the {alpha} subunit of a class of G proteins that inhibits adenylate cyclase and regulates other enzymes and ion channels. This cDNA encodes a polypeptide of 354 amino acids and is assigned to encode the {alpha}{sub i-3} subtype of G proteins on the basis of its similarity to other {alpha}{sub i}-like cDNAs and the presence of a predicted site for ADP ribosylation by pertussis toxin. They have determined the expression of mRNA for this and two other subtypes of human {alpha}{sub i} ({alpha}{sub i-1} and {alpha}{sub i-2}) in a variety of human fetal tissues and in human cell lines. All three {alpha}{sub i} subtypes were present in the tissues tested. However, analysis of individual cell types reveals specificity of {alpha}{sub i-1} expression. mRNA for {alpha}{i-1} is absent in T cells, B cells, and monocytes but is present in other cell lines. The finding of differential expression of {alpha}{sub i-1} genes may permit characterization of distinct physiological roles for this {alpha}{sub i} subunit. mRNA for {alpha}{sub i-2} and {alpha}{sub i-3} was found in all the primary and transformed cell lines tested. Thus, some cells contain all three {alpha}{sub i} subtypes. This observation raises the question of how cells prevent cross talk among receptors that are coupled to effectors through such similar {alpha} proteins.

  9. Addition of Cryoprotectant Significantly Alters the Epididymal Sperm Proteome

    PubMed Central

    Yoon, Sung-Jae; Rahman, Md Saidur; Kwon, Woo-Sung; Park, Yoo-Jin; Pang, Myung-Geol

    2016-01-01

    Although cryopreservation has been developed and optimized over the past decades, it causes various stresses, including cold shock, osmotic stress, and ice crystal formation, thereby reducing fertility. During cryopreservation, addition of cryoprotective agent (CPA) is crucial for protecting spermatozoa from freezing damage. However, the intrinsic toxicity and osmotic stress induced by CPA cause damage to spermatozoa. To identify the effects of CPA addition during cryopreservation, we assessed the motility (%), motion kinematics, capacitation status, and viability of epididymal spermatozoa using computer-assisted sperm analysis and Hoechst 33258/chlortetracycline fluorescence staining. Moreover, the effects of CPA addition were also demonstrated at the proteome level using two-dimensional electrophoresis. Our results demonstrated that CPA addition significantly reduced sperm motility (%), curvilinear velocity, viability (%), and non-capacitated spermatozoa, whereas straightness and acrosome-reacted spermatozoa increased significantly (p < 0.05). Ten proteins were differentially expressed (two decreased and eight increased) (>3 fold, p < 0.05) after CPA, whereas NADH dehydrogenase flavoprotein 2, f-actin-capping protein subunit beta, superoxide dismutase 2, and outer dense fiber protein 2 were associated with several important signaling pathways (p < 0.05). The present study provides a mechanistic basis for specific cryostresses and potential markers of CPA-induced stress. Therefore, these might provide information about the development of safe biomaterials for cryopreservation and basic ground for sperm cryopreservation. PMID:27031703

  10. Evaluation of certain food additives.

    PubMed

    2015-01-01

    This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, and to prepare specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of and assessment of dietary exposure to food additives, including flavouring agents. A summary follows of the Committee's evaluations of technical, toxicological and dietary exposure data for eight food additives (Benzoe tonkinensis; carrageenan; citric and fatty acid esters of glycerol; gardenia yellow; lutein esters from Tagetes erecta; octenyl succinic acid-modified gum arabic; octenyl succinic acid-modified starch; paprika extract; and pectin) and eight groups of flavouring agents (aliphatic and alicyclic hydrocarbons; aliphatic and aromatic ethers; ionones and structurally related substances; miscellaneous nitrogen-containing substances; monocyclic and bicyclic secondary alcohols, ketones and related esters; phenol and phenol derivatives; phenyl-substituted aliphatic alcohols and related aldehydes and esters; and sulfur-containing heterocyclic compounds). Specifications for the following food additives were revised: citric acid; gellan gum; polyoxyethylene (20) sorbitan monostearate; potassium aluminium silicate; and Quillaia extract (Type 2). Annexed to the report are tables summarizing the Committee's recommendations for dietary exposures to and toxicological evaluations of all of the food additives and flavouring agents considered at this meeting.

  11. Group Sparse Additive Models

    PubMed Central

    Yin, Junming; Chen, Xi; Xing, Eric P.

    2016-01-01

    We consider the problem of sparse variable selection in nonparametric additive models, with the prior knowledge of the structure among the covariates to encourage those variables within a group to be selected jointly. Previous works either study the group sparsity in the parametric setting (e.g., group lasso), or address the problem in the nonparametric setting without exploiting the structural information (e.g., sparse additive models). In this paper, we present a new method, called group sparse additive models (GroupSpAM), which can handle group sparsity in additive models. We generalize the ℓ1/ℓ2 norm to Hilbert spaces as the sparsity-inducing penalty in GroupSpAM. Moreover, we derive a novel thresholding condition for identifying the functional sparsity at the group level, and propose an efficient block coordinate descent algorithm for constructing the estimate. We demonstrate by simulation that GroupSpAM substantially outperforms the competing methods in terms of support recovery and prediction accuracy in additive models, and also conduct a comparative experiment on a real breast cancer dataset.

  12. Additive Manufacturing Infrared Inspection

    NASA Technical Reports Server (NTRS)

    Gaddy, Darrell

    2014-01-01

    Additive manufacturing is a rapid prototyping technology that allows parts to be built in a series of thin layers from plastic, ceramics, and metallics. Metallic additive manufacturing is an emerging form of rapid prototyping that allows complex structures to be built using various metallic powders. Significant time and cost savings have also been observed using the metallic additive manufacturing compared with traditional techniques. Development of the metallic additive manufacturing technology has advanced significantly over the last decade, although many of the techniques to inspect parts made from these processes have not advanced significantly or have limitations. Several external geometry inspection techniques exist such as Coordinate Measurement Machines (CMM), Laser Scanners, Structured Light Scanning Systems, or even traditional calipers and gages. All of the aforementioned techniques are limited to external geometry and contours or must use a contact probe to inspect limited internal dimensions. This presentation will document the development of a process for real-time dimensional inspection technique and digital quality record of the additive manufacturing process using Infrared camera imaging and processing techniques.

  13. Additive Manufacturing of Aerospace Propulsion Components

    NASA Technical Reports Server (NTRS)

    Misra, Ajay K.; Grady, Joseph E.; Carter, Robert

    2015-01-01

    The presentation will provide an overview of ongoing activities on additive manufacturing of aerospace propulsion components, which included rocket propulsion and gas turbine engines. Future opportunities on additive manufacturing of hybrid electric propulsion components will be discussed.

  14. Phenylethynyl Containing Reactive Additives

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor)

    2002-01-01

    Phenylethynyl containing reactive additives were prepared from aromatic diamine, containing phenylethvnvl groups and various ratios of phthalic anhydride and 4-phenylethynviphthalic anhydride in glacial acetic acid to form the imide in one step or in N-methyl-2-pvrrolidinone to form the amide acid intermediate. The reactive additives were mixed in various amounts (10% to 90%) with oligomers containing either terminal or pendent phenylethynyl groups (or both) to reduce the melt viscosity and thereby enhance processability. Upon thermal cure, the additives react and become chemically incorporated into the matrix and effect an increase in crosslink density relative to that of the host resin. This resultant increase in crosslink density has advantageous consequences on the cured resin properties such as higher glass transition temperature and higher modulus as compared to that of the host resin.

  15. Fused Lasso Additive Model

    PubMed Central

    Petersen, Ashley; Witten, Daniela; Simon, Noah

    2016-01-01

    We consider the problem of predicting an outcome variable using p covariates that are measured on n independent observations, in a setting in which additive, flexible, and interpretable fits are desired. We propose the fused lasso additive model (FLAM), in which each additive function is estimated to be piecewise constant with a small number of adaptively-chosen knots. FLAM is the solution to a convex optimization problem, for which a simple algorithm with guaranteed convergence to a global optimum is provided. FLAM is shown to be consistent in high dimensions, and an unbiased estimator of its degrees of freedom is proposed. We evaluate the performance of FLAM in a simulation study and on two data sets. Supplemental materials are available online, and the R package flam is available on CRAN. PMID:28239246

  16. Phenylethynyl Containing Reactive Additives

    NASA Technical Reports Server (NTRS)

    Connell, John W. (Inventor); Smith, Joseph G., Jr. (Inventor); Hergenrother, Paul M. (Inventor)

    2002-01-01

    Phenylethynyl containing reactive additives were prepared from aromatic diamines containing phenylethynyl groups and various ratios of phthalic anhydride and 4-phenylethynylphthalic anhydride in glacial acetic acid to form the imide in one step or in N-methyl-2-pyrrolidi none to form the amide acid intermediate. The reactive additives were mixed in various amounts (10% to 90%) with oligomers containing either terminal or pendent phenylethynyl groups (or both) to reduce the melt viscosity and thereby enhance processability. Upon thermal cure, the additives react and become chemically incorporated into the matrix and effect an increase in crosslink density relative to that of the host resin. This resultant increase in crosslink density has advantageous consequences on the cured resin properties such as higher glass transition temperature and higher modulus as compared to that of the host resin.

  17. Additives in plastics.

    PubMed Central

    Deanin, R D

    1975-01-01

    The polymers used in plastics are generally harmless. However, they are rarely used in pure form. In almost all commercial plastics, they are "compounded" with monomeric ingredients to improve their processing and end-use performance. In order of total volume used, these monomeric additives may be classified as follows: reinforcing fibers, fillers, and coupling agents; plasticizers; colorants; stabilizers (halogen stabilizers, antioxidants, ultraviolet absorbers, and biological preservatives); processing aids (lubricants, others, and flow controls); flame retardants, peroxides; and antistats. Some information is already available, and much more is needed, on potential toxicity and safe handling of these additives during processing and manufacture of plastics products. PMID:1175566

  18. Additives in plastics.

    PubMed

    Deanin, R D

    1975-06-01

    The polymers used in plastics are generally harmless. However, they are rarely used in pure form. In almost all commercial plastics, they are "compounded" with monomeric ingredients to improve their processing and end-use performance. In order of total volume used, these monomeric additives may be classified as follows: reinforcing fibers, fillers, and coupling agents; plasticizers; colorants; stabilizers (halogen stabilizers, antioxidants, ultraviolet absorbers, and biological preservatives); processing aids (lubricants, others, and flow controls); flame retardants, peroxides; and antistats. Some information is already available, and much more is needed, on potential toxicity and safe handling of these additives during processing and manufacture of plastics products.

  19. Rational, yet simple, design and synthesis of an antifreeze-protein inspired polymer for cellular cryopreservation† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c5cc04647e Click here for additional data file.

    PubMed Central

    Mitchell, Daniel E.; Cameron, Neil R.

    2015-01-01

    Antifreeze (glyco) proteins AF(G)Ps are potent ice recrystallization inhibitors, which is a desirable property to enhance cryopreservation of donor tissue/cells. Here we present the rational synthesis of a new, biomimetic, ice-recrystallization inhibiting polymer derived from a cheap commodity polymer, based on an ampholyte structure. The polymer is used to enhance the cryopreservation of red blood cells, demonstrating a macromolecular solution to tissue storage. PMID:26176027

  20. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) method extension to quantify simultaneously melamine and cyanuric acid in egg powder and soy protein in addition to milk products.

    PubMed

    Rodriguez Mondal, Ana Mary; Desmarchelier, Aurélien; Konings, Erik; Acheson-Shalom, Ruth; Delatour, Thierry

    2010-11-24

    As a consequence of the adulteration of infant formulas and milk powders with melamine (MEL) in China in 2008, much attention has been devoted to the analysis of MEL [and cyanuric acid (CA)] in dairy products. Several methods based on high-performance liquid chromatography (HPLC), liquid chromatography-tandem mass spectrometry (LC-MS/MS), nuclear magnetic resonance (NMR), or Raman spectroscopy have been described in the literature. However, no method is available for the simultaneous determination of MEL and CA in other raw materials, which are considered as high-risk materials for economically motivated adulteration. The present paper reports the results of an interlaboratory-based performance evaluation conducted with seven laboratories worldwide. The purpose was to demonstrate the ability of a cleanup-free LC-MS/MS method, originally developed for cow's milk and milk-powdered infant formula, to quantify MEL and CA in egg powder and soy protein. Limit of detection (LOD) and limit of quantification (LOQ) were 0.02 and 0.05 mg/kg for MEL in egg powder and soy protein, respectively. For CA, LOD and LOQ were 0.05 and 0.10 mg/kg in egg powder and 1.0 and 1.50 mg/kg in soy protein, respectively. Recoveries ranged within a 97-113% range for both MEL and CA in egg powder and soy protein. Reproducibility values (RSD(R)) from seven laboratories were within a 5.4-11.7% range for both analytes in the considered matrices. Horwitz ratio (HorRat) values between 0.4 and 0.7 indicate acceptable among-laboratory precision for the method described.

  1. Biobased lubricant additives

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fully biobased lubricants are those formulated using all biobased ingredients, i.e. biobased base oils and biobased additives. Such formulations provide the maximum environmental, safety, and economic benefits expected from a biobased product. Currently, there are a number of biobased base oils that...

  2. More Than Additional Space...

    ERIC Educational Resources Information Center

    CEFP Journal, 1973

    1973-01-01

    A much needed addition to the Jamestown Elementary School turned out to be more than an expansion of walls for more space. A new educational program, a limited budget, and a short time line were tackled on a team approach basis and were successfully resolved. (Author)

  3. Protein Microarray Technology

    PubMed Central

    Hall, David A.; Ptacek, Jason

    2007-01-01

    Protein chips have emerged as a promising approach for a wide variety of applications including the identification of protein-protein interactions, protein-phospholipid interactions, small molecule targets, and substrates of proteins kinases. They can also be used for clinical diagnostics and monitoring disease states. This article reviews current methods in the generation and applications of protein microarrays. PMID:17126887

  4. Therapeutic proteins.

    PubMed

    Dimitrov, Dimiter S

    2012-01-01

    Protein-based therapeutics are highly successful in clinic and currently enjoy unprecedented recognition of their potential. More than 100 genuine and similar number of modified therapeutic proteins are approved for clinical use in the European Union and the USA with 2010 sales of US$108 bln; monoclonal antibodies (mAbs) accounted for almost half (48%) of the sales. Based on their pharmacological activity, they can be divided into five groups: (a) replacing a protein that is deficient or abnormal; (b) augmenting an existing pathway; (c) providing a novel function or activity; (d) interfering with a molecule or organism; and (e) delivering other compounds or proteins, such as a radionuclide, cytotoxic drug, or effector proteins. Therapeutic proteins can also be grouped based on their molecular types that include antibody-based drugs, Fc fusion proteins, anticoagulants, blood factors, bone morphogenetic proteins, engineered protein scaffolds, enzymes, growth factors, hormones, interferons, interleukins, and thrombolytics. They can also be classified based on their molecular mechanism of activity as (a) binding non-covalently to target, e.g., mAbs; (b) affecting covalent bonds, e.g., enzymes; and (c) exerting activity without specific interactions, e.g., serum albumin. Most protein therapeutics currently on the market are recombinant and hundreds of them are in clinical trials for therapy of cancers, immune disorders, infections, and other diseases. New engineered proteins, including bispecific mAbs and multispecific fusion proteins, mAbs conjugated with small molecule drugs, and proteins with optimized pharmacokinetics, are currently under development. However, in the last several decades, there are no conceptually new methodological developments comparable, e.g., to genetic engineering leading to the development of recombinant therapeutic proteins. It appears that a paradigm change in methodologies and understanding of mechanisms is needed to overcome major

  5. Molecular modelling of protein-protein/protein-solvent interactions

    NASA Astrophysics Data System (ADS)

    Luchko, Tyler

    The inner workings of individual cells are based on intricate networks of protein-protein interactions. However, each of these individual protein interactions requires a complex physical interaction between proteins and their aqueous environment at the atomic scale. In this thesis, molecular dynamics simulations are used in three theoretical studies to gain insight at the atomic scale about protein hydration, protein structure and tubulin-tubulin (protein-protein) interactions, as found in microtubules. Also presented, in a fourth project, is a molecular model of solvation coupled with the Amber molecular modelling package, to facilitate further studies without the need of explicitly modelled water. Basic properties of a minimally solvated protein were calculated through an extended study of myoglobin hydration with explicit solvent, directly investigating water and protein polarization. Results indicate a close correlation between polarization of both water and protein and the onset of protein function. The methodology of explicit solvent molecular dynamics was further used to study tubulin and microtubules. Extensive conformational sampling of the carboxy-terminal tails of 8-tubulin was performed via replica exchange molecular dynamics, allowing the characterisation of the flexibility, secondary structure and binding domains of the C-terminal tails through statistical analysis methods. Mechanical properties of tubulin and microtubules were calculated with adaptive biasing force molecular dynamics. The function of the M-loop in microtubule stability was demonstrated in these simulations. The flexibility of this loop allowed constant contacts between the protofilaments to be maintained during simulations while the smooth deformation provided a spring-like restoring force. Additionally, calculating the free energy profile between the straight and bent tubulin configurations was used to test the proposed conformational change in tubulin, thought to cause microtubule

  6. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T Ashton; Chin, Jason W; Anderson, J Christopher; Schultz, Peter G

    2011-02-15

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  7. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, Ashton T; Chin, Jason W; Anderson, Christopher J; Schultz, Peter G

    2013-05-21

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  8. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2011-08-09

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNAsyn-thetases, pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  9. Unnatural reactive amino acid genetic code additions

    SciTech Connect

    Deiters, Alexander; Cropp, T. Ashton; Chin, Jason W.; Anderson, J. Christopher; Schultz, Peter G.

    2014-08-26

    This invention provides compositions and methods for producing translational components that expand the number of genetically encoded amino acids in eukaryotic cells. The components include orthogonal tRNAs, orthogonal aminoacyl-tRNA synthetases, orthogonal pairs of tRNAs/synthetases and unnatural amino acids. Proteins and methods of producing proteins with unnatural amino acids in eukaryotic cells are also provided.

  10. EMC Recent Additions

    EPA Pesticide Factsheets

    This page has information about recent changes to promulgated and proposed test methods, perfomance specifications, and quality assurance procedures. It also includes updates and changes to all other approved and proposed test methods.

  11. Vinyl capped addition polyimides

    NASA Technical Reports Server (NTRS)

    Vannucci, Raymond D. (Inventor); Malarik, Diane C. (Inventor); Delvigs, Peter (Inventor)

    1991-01-01

    Polyimide resins (PMR) are generally useful where high strength and temperature capabilities are required (at temperatures up to about 700 F). Polyimide resins are particularly useful in applications such as jet engine compressor components, for example, blades, vanes, air seals, air splitters, and engine casing parts. Aromatic vinyl capped addition polyimides are obtained by reacting a diamine, an ester of tetracarboxylic acid, and an aromatic vinyl compound. Low void materials with improved oxidative stability when exposed to 700 F air may be fabricated as fiber reinforced high molecular weight capped polyimide composites. The aromatic vinyl capped polyimides are provided with a more aromatic nature and are more thermally stable than highly aliphatic, norbornenyl-type end-capped polyimides employed in PMR resins. The substitution of aromatic vinyl end-caps for norbornenyl end-caps in addition polyimides results in polymers with improved oxidative stability.

  12. Electrophilic addition of astatine

    SciTech Connect

    Norseev, Yu.V.; Vasaros, L.; Nhan, D.D.; Huan, N.K.

    1988-03-01

    It has been shown for the first time that astatine is capable of undergoing addition reactions to unsaturated hydrocarbons. A new compound of astatine, viz., ethylene astatohydrin, has been obtained, and its retention numbers of squalane, Apiezon, and tricresyl phosphate have been found. The influence of various factors on the formation of ethylene astatohydrin has been studied. It has been concluded on the basis of the results obtained that the univalent cations of astatine in an acidic medium is protonated hypoastatous acid.

  13. Functional Generalized Additive Models.

    PubMed

    McLean, Mathew W; Hooker, Giles; Staicu, Ana-Maria; Scheipl, Fabian; Ruppert, David

    2014-01-01

    We introduce the functional generalized additive model (FGAM), a novel regression model for association studies between a scalar response and a functional predictor. We model the link-transformed mean response as the integral with respect to t of F{X(t), t} where F(·,·) is an unknown regression function and X(t) is a functional covariate. Rather than having an additive model in a finite number of principal components as in Müller and Yao (2008), our model incorporates the functional predictor directly and thus our model can be viewed as the natural functional extension of generalized additive models. We estimate F(·,·) using tensor-product B-splines with roughness penalties. A pointwise quantile transformation of the functional predictor is also considered to ensure each tensor-product B-spline has observed data on its support. The methods are evaluated using simulated data and their predictive performance is compared with other competing scalar-on-function regression alternatives. We illustrate the usefulness of our approach through an application to brain tractography, where X(t) is a signal from diffusion tensor imaging at position, t, along a tract in the brain. In one example, the response is disease-status (case or control) and in a second example, it is the score on a cognitive test. R code for performing the simulations and fitting the FGAM can be found in supplemental materials available online.

  14. Siloxane containing addition polyimides

    NASA Technical Reports Server (NTRS)

    Maudgal, S.; St. Clair, T. L.

    1984-01-01

    Addition polyimide oligomers have been synthesized from bis(gamma-aminopropyl) tetramethyldisiloxane and 3, 3', 4, 4'-benzophenonetetracarboxylic dianhydride using a variety of latent crosslinking groups as endcappers. The prepolymers were isolated and characterized for solubility (in amide, chlorinated and ether solvents), melt flow and cure properties. The most promising systems, maleimide and acetylene terminated prepolymers, were selected for detailed study. Graphite cloth reinforced composites were prepared and properties compared with those of graphite/Kerimid 601, a commercially available bismaleimide. Mixtures of the maleimide terminated system with Kerimid 601, in varying proportions, were also studied.

  15. Evaluation of certain food additives.

    PubMed

    2012-01-01

    This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, with a view to concluding as to safety concerns and to preparing specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of and assessment of dietary exposure to food additives, including flavouring agents. A summary follows of the Committee's evaluations of technical, toxicological and dietary exposure data for five food additives (magnesium dihydrogen diphosphate; mineral oil (medium and low viscosity) classes II and III; 3-phytase from Aspergillus niger expressed in Aspergillus niger; serine protease (chymotrypsin) from Nocardiopsis prasina expressed in Bacillus licheniformis; and serine protease (trypsin) from Fusarium oxysporum expressed in Fusarium venenatum) and 16 groups of flavouring agents (aliphatic and aromatic amines and amides; aliphatic and aromatic ethers; aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers containing furan substitution; aliphatic linear alpha,beta-unsaturated aldehydes, acids and related alcohols, acetals and esters; amino acids and related substances; epoxides; furfuryl alcohol and related substances; linear and branched-chain aliphatic, unsaturated, unconjugated alcohols, aldehydes, acids and related esters; miscellaneous nitrogen-containing substances; phenol and phenol derivatives; pyrazine derivatives; pyridine, pyrrole and quinoline derivatives; saturated aliphatic acyclic branched-chain primary alcohols, aldehydes and acids; simple aliphatic and aromatic sulfides and thiols; sulfur-containing heterocyclic compounds; and sulfur-substituted furan derivatives). Specifications for the following food additives were revised: ethyl cellulose, mineral oil (medium viscosity), modified starches and titanium

  16. Platelet additive solution - electrolytes.

    PubMed

    Azuma, Hiroshi; Hirayama, Junichi; Akino, Mitsuaki; Ikeda, Hisami

    2011-06-01

    Recent attention to solutions that replace most or all plasma in platelet concentrates, while maintaining satisfactory platelet function, is motivated by the potential of plasma reduction or depletion to mitigate various transfusion-related adverse events. This report considers the electrolytic composition of previously described platelet additive solutions, in order to draw general conclusions about what is required for platelet function and longevity. The optimal concentrations of Na(+) and Cl(-) are 69-115 mM. The presence of both K(+) and Mg(2+) in platelet suspension at nearly physiological concentrations (3-5mM and 1.5-3mM, respectively) is indispensable for good preservation capacity because both electrolytes are required to prevent platelet activation. In contrast to K(+) and Mg(2+), Ca(2+) may not be important because no free Ca(2+) is available in M-sol, which showed excellent platelet preservation capacity at less than 5% plasma concentration. The importance of bicarbonate (approximately 40 mM) can be recognized when the platelets are suspended in additive solution under less than 5% residual plasma concentration.

  17. Advances in Additive Manufacturing

    DTIC Science & Technology

    2016-07-14

    casting molds for traditional casting processes on the battlefield, and 3) the use of recycled polymeric materials as feedstock for 3-D printers ...nondestructive characterization technique allows for 3D imaging that readily captures defects and voids on the conditions that the attenuation, which is...of 3D -printed structures. Analysis examples will include quantification of tolerance differences between the designed and manufactured parts, void

  18. Additive composition, for gasoline

    SciTech Connect

    Vataru, M.

    1989-01-10

    An admixture is described that comprises Diesel fuel and an additive composition added thereto which is between about 0.05 to about 2.0 percent by weight of the fuel, the composition comprising: (a) between about 0.05 and 25% relative weight parts of an organic peroxide, and (b) between about 0.1 and 25% relative weight parts of detergent selected from the component group that consists of: (i) fatty amines; (ii) ethoxylated and propoxylated derivatives of fatty amines; (iii) fatty diamines; (iv) fatty imidazlines; (v) polymeric amines and derivatives thereof; (vi) combination of one or more of the (i) through (v) components with carboxylic acid or acids having from three to forth carbon atoms, (c) from about 99.0 to about 50% by weight of a hydrocarbon solvent.

  19. Teardrop bladder: additional considerations

    SciTech Connect

    Wechsler, R.J.; Brennan, R.E.

    1982-07-01

    Nine cases of teardrop bladder (TDB) seen at excretory urography are presented. In some of these patients, the iliopsoas muscles were at the upper limit of normal in size, and additional evaluation of the perivesical structures with computed tomography (CT) was necessary. CT demonstrated only hypertrophied muscles with or without perivesical fat. The psoas muscles and pelvic width were measured in 8 patients and compared with the measurements of a control group of males without TDB. Patients with TDB had large iliopsoas muscles and narrow pelves compared with the control group. The psoas muscle width/pelvic width ratio was significantly greater (p < 0.0005) in patients with TDB than in the control group, with values of 1.04 + 0.05 and 0.82 + 0.09, respectively. It is concluded that TDB is not an uncommon normal variant in black males. Both iliopsoas muscle hypertrophy and a narrow pelvis are factors that predispose a patient to TDB.

  20. New addition curing polyimides

    NASA Technical Reports Server (NTRS)

    Frimer, Aryeh A.; Cavano, Paul

    1991-01-01

    In an attempt to improve the thermal-oxidative stability (TOS) of PMR-type polymers, the use of 1,4-phenylenebis (phenylmaleic anhydride) PPMA, was evaluated. Two series of nadic end-capped addition curing polyimides were prepared by imidizing PPMA with either 4,4'-methylene dianiline or p-phenylenediamine. The first resulted in improved solubility and increased resin flow while the latter yielded a compression molded neat resin sample with a T(sub g) of 408 C, close to 70 C higher than PME-15. The performance of these materials in long term weight loss studies was below that of PMR-15, independent of post-cure conditions. These results can be rationalized in terms of the thermal lability of the pendant phenyl groups and the incomplete imidization of the sterically congested PPMA. The preparation of model compounds as well as future research directions are discussed.

  1. Sewage sludge additive

    NASA Technical Reports Server (NTRS)

    Kalvinskas, J. J.; Mueller, W. A.; Ingham, J. D. (Inventor)

    1980-01-01

    The additive is for a raw sewage treatment process of the type where settling tanks are used for the purpose of permitting the suspended matter in the raw sewage to be settled as well as to permit adsorption of the dissolved contaminants in the water of the sewage. The sludge, which settles down to the bottom of the settling tank is extracted, pyrolyzed and activated to form activated carbon and ash which is mixed with the sewage prior to its introduction into the settling tank. The sludge does not provide all of the activated carbon and ash required for adequate treatment of the raw sewage. It is necessary to add carbon to the process and instead of expensive commercial carbon, coal is used to provide the carbon supplement.

  2. A method for investigating protein-protein interactions related to Salmonella typhimurium pathogenesis

    SciTech Connect

    Chowdhury, Saiful M.; Shi, Liang; Yoon, Hyunjin; Ansong, Charles; Rommereim, Leah M.; Norbeck, Angela D.; Auberry, Kenneth J.; Moore, R. J.; Adkins, Joshua N.; Heffron, Fred; Smith, Richard D.

    2009-02-10

    We successfully modified an existing method to investigate protein-protein interactions in the pathogenic bacterium Salmonella typhimurium (STM). This method includes i) addition of a histidine-biotin-histidine tag to the bait proteins via recombinant DNA techniques; ii) in vivo cross-linking with formaldehyde; iii) tandem affinity purification of bait proteins under fully denaturing conditions; and iv) identification of the proteins cross-linked to the bait proteins by liquid-chromatography in conjunction with tandem mass-spectrometry. In vivo cross-linking stabilized protein interactions permitted the subsequent two-step purification step conducted under denaturing conditions. The two-step purification greatly reduced nonspecific binding of non-cross-linked proteins to bait proteins. Two different negative controls were employed to reduce false-positive identification. In an initial demonstration of this approach, we tagged three selected STM proteins- HimD, PduB and PhoP- with known binding partners that ranged from stable (e.g., HimD) to transient (i.e., PhoP). Distinct sets of interacting proteins were identified with each bait protein, including the known binding partners such as HimA for HimD, as well as anticipated and unexpected binding partners. Our results suggest that novel protein-protein interactions may be critical to pathogenesis by Salmonella typhimurium. .

  3. Ionic liquids, electrolyte solutions including the ionic liquids, and energy storage devices including the ionic liquids

    SciTech Connect

    Gering, Kevin L.; Harrup, Mason K.; Rollins, Harry W.

    2015-12-08

    An ionic liquid including a phosphazene compound that has a plurality of phosphorus-nitrogen units and at least one pendant group bonded to each phosphorus atom of the plurality of phosphorus-nitrogen units. One pendant group of the at least one pendant group comprises a positively charged pendant group. Additional embodiments of ionic liquids are disclosed, as are electrolyte solutions and energy storage devices including the embodiments of the ionic liquid.

  4. Additive-driven assembly of block copolymers

    NASA Astrophysics Data System (ADS)

    Lin, Ying; Daga, Vikram; Anderson, Eric; Watkins, James

    2011-03-01

    One challenge to the formation of well ordered hybrid materials is the incorporation of nanoscale additives including metal, semiconductor and dielectric nanoparticles at high loadings while maintaining strong segregation. Here we describe the molecular and functional design of small molecule and nanoparticle additives that enhance phase segregation in their block copolymer host and enable high additive loadings. Our approach includes the use of hydrogen bond interactions between the functional groups on the additive or particle that serve as hydrogen bond donors and one segment of the block copolymer containing hydrogen bond acceptors. Further, the additives show strong selectively towards the targeted domains, leading to enhancements in contrast between properties of the phases. In addition to structural changes, we explore how large changes in the thermal and mechanical properties occur upon incorporation of the additives. Generalization of this additive-induced ordering strategy to various block copolymers will be discussed.

  5. Decontamination formulation with sorbent additive

    DOEpatents

    Tucker; Mark D. , Comstock; Robert H.

    2007-10-16

    A decontamination formulation and method of making that neutralizes the adverse health effects of both chemical and biological compounds, especially chemical warfare (CW) and biological warfare (BW) agents, and toxic industrial chemicals. The formulation provides solubilizing compounds that serve to effectively render the chemical and biological compounds, particularly CW and BW compounds, susceptible to attack, and at least one reactive compound that serves to attack (and detoxify or kill) the compound. The formulation includes at least one solubilizing agent, a reactive compound, a bleaching activator, a sorbent additive, and water. The highly adsorbent, water-soluble sorbent additive (e.g., sorbitol or mannitol) is used to "dry out" one or more liquid ingredients, such as the liquid bleaching activator (e.g., propylene glycol diacetate or glycerol diacetate) and convert the activator into a dry, free-flowing powder that has an extended shelf life, and is more convenient to handle and mix in the field.

  6. PMD: A Resource for Archiving and Analyzing Protein Microarray data

    PubMed Central

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-ce

    2016-01-01

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn. PMID:26813635

  7. PMD: A Resource for Archiving and Analyzing Protein Microarray data.

    PubMed

    Xu, Zhaowei; Huang, Likun; Zhang, Hainan; Li, Yang; Guo, Shujuan; Wang, Nan; Wang, Shi-Hua; Chen, Ziqing; Wang, Jingfang; Tao, Sheng-Ce

    2016-01-27

    Protein microarray is a powerful technology for both basic research and clinical study. However, because there is no database specifically tailored for protein microarray, the majority of the valuable original protein microarray data is still not publically accessible. To address this issue, we constructed Protein Microarray Database (PMD), which is specifically designed for archiving and analyzing protein microarray data. In PMD, users can easily browse and search the entire database by experimental name, protein microarray type, and sample information. Additionally, PMD integrates several data analysis tools and provides an automated data analysis pipeline for users. With just one click, users can obtain a comprehensive analysis report for their protein microarray data. The report includes preliminary data analysis, such as data normalization, candidate identification, and an in-depth bioinformatics analysis of the candidates, which include functional annotation, pathway analysis, and protein-protein interaction network analysis. PMD is now freely available at www.proteinmicroarray.cn.

  8. Deoxynivalenol impairs hepatic and intestinal gene expression of selected oxidative stress, tight junction and inflammation proteins in broiler chickens, but addition of an adsorbing agent shifts the effects to the distal parts of the small intestine.

    PubMed

    Osselaere, Ann; Santos, Regiane; Hautekiet, Veerle; De Backer, Patrick; Chiers, Koen; Ducatelle, Richard; Croubels, Siska

    2013-01-01

    Broiler chickens are rather resistant to deoxynivalenol and thus, clinical signs are rarely seen. However, effects of subclinical concentrations of deoxynivalenol on both the intestine and the liver are less frequently studied at the molecular level. During our study, we investigated the effects of three weeks of feeding deoxynivalenol on the gut wall morphology, intestinal barrier function and inflammation in broiler chickens. In addition, oxidative stress was evaluated in both the liver and intestine. Besides, the effect of a clay-based mycotoxin adsorbing agent on these different aspects was also studied. Our results show that feeding deoxynivalenol affects the gut wall morphology both in duodenum and jejenum of broiler chickens. A qRT-PCR analysis revealed that deoxynivalenol acts in a very specific way on the intestinal barrier, since only an up-regulation in mRNA expression of claudin 5 in jejunum was observed, while no effects were seen on claudin 1, zona occludens 1 and 2. Addition of an adsorbing agent resulted in an up-regulation of all the investigated genes coding for the intestinal barrier in the ileum. Up-regulation of Toll-like receptor 4 and two markers of oxidative stress (heme-oxigenase or HMOX and xanthine oxidoreductase or XOR) were mainly seen in the jejunum and to a lesser extent in the ileum in response to deoxynivalenol, while in combination with an adsorbing agent main effect was seen in the ileum. These results suggest that an adsorbing agent may lead to higher concentrations of deoxynivalenol in the more distal parts of the small intestine. In the liver, XOR was up-regulated due to DON exposure. HMOX and HIF-1α (hypoxia-inducible factor 1α) were down-regulated due to feeding DON but also due to feeding the adsorbing agent alone or in combination with DON.

  9. Ceramics with Different Additives

    NASA Astrophysics Data System (ADS)

    Wang, Juanjuan; Feng, Lajun; Lei, Ali; Zhao, Kang; Yan, Aijun

    2014-09-01

    Li2CO3, MgCO3, BaCO3, and Bi2O3 dopants were introduced into CaCu3Ti4O12 (CCTO) ceramics in order to improve the dielectric properties. The CCTO ceramics were prepared by conventional solid-state reaction method. The phase structure, microstructure, and dielectric behavior were carefully investigated. The pure structure without any impurity phases can be confirmed by the x-ray diffraction patterns. Scanning Electron Microscopy (SEM) analysis illuminated that the grains of Ca0.90Li0.20Cu3Ti4O12 ceramics were greater than that of pure CCTO. It was important for the properties of the CCTO ceramics to study the additives in complex impedance spectroscopy. It was found that the Ca0.90Li0.20Cu3Ti4O12 ceramics had the higher permittivity (>45000), the lower dielectric loss (<0.025) than those of CCTO at 1 kHz at room temperature and good temperature stability from -30 to 75 °C.

  10. Protein phosphorylation and photorespiration.

    PubMed

    Hodges, M; Jossier, M; Boex-Fontvieille, E; Tcherkez, G

    2013-07-01

    Photorespiration allows the recycling of carbon atoms of 2-phosphoglycolate produced by ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) oxygenase activity, as well as the removal of potentially toxic metabolites. The photorespiratory pathway takes place in the light, encompasses four cellular compartments and interacts with several other metabolic pathways and functions. Therefore, the regulation of this cycle is probably of paramount importance to plant metabolism, however, our current knowledge is poor. To rapidly respond to changing conditions, proteins undergo a number of different post-translational modifications that include acetylation, methylation and ubiquitylation, but protein phosphorylation is probably the most common. The reversible covalent addition of a phosphate group to a specific amino acid residue allows the modulation of protein function, such as activity, subcellular localisation, capacity to interact with other proteins and stability. Recent data indicate that many photorespiratory enzymes can be phosphorylated, and thus it seems that the photorespiratory cycle is, in part, regulated by protein phosphorylation. In this review, the known phosphorylation sites of each Arabidopsis thaliana photorespiratory enzyme and several photorespiratory-associated proteins are described and discussed. A brief account of phosphoproteomic protocols is also given since the published data compiled in this review are the fruit of this approach.

  11. Fire-Retardant Polymeric Additives

    NASA Technical Reports Server (NTRS)

    Williams, Martha K.; Smith, Trent M.

    2011-01-01

    Polyhydroxyamide (PHA) and polymethoxyamide (PMeOA) are fire-retardant (FR) thermoplastic polymers and have been found to be useful as an additive for imparting fire retardant properties to other compatible, thermoplastic polymers (including some elastomers). Examples of compatible flammable polymers include nylons, polyesters, and acrylics. Unlike most prior additives, PHA and PMeOA do not appreciably degrade the mechanical properties of the matrix polymer; indeed, in some cases, mechanical properties are enhanced. Also, unlike some prior additives, PHA and PMeOA do not decompose into large amounts of corrosive or toxic compounds during combustion and can be processed at elevated temperatures. PMeOA derivative formulations were synthesized and used as an FR additive in the fabrication of polyamide (PA) and polystyrene (PS) composites with notable reduction (>30 percent for PS) in peak heat release rates compared to the neat polymer as measured by a Cone Calorimeter (ASTM E1354). Synergistic effects were noted with nanosilica composites. These nanosilica composites had more than 50-percent reduction in peak heat release rates. In a typical application, a flammable thermoplastic, thermoplastic blend, or elastomer that one seeks to render flame-retardant is first dry-mixed with PHA or PMeOA or derivative thereof. The proportion of PHA or PMeOA or derivative in the mixture is typically chosen to lie between 1 and 20 weight percent. The dry blend can then be melt-extruded. The extruded polymer blend can further be extruded and/or molded into fibers, pipes, or any other of a variety of objects that may be required to be fire-retardant. The physical and chemical mechanisms which impart flame retardancy of the additive include inhibiting free-radical oxidation in the vapor phase, preventing vaporization of fuel (the polymer), and cooling through the formation of chemical bonds in either the vapor or the condensed phase. Under thermal stress, the cyclic hydroxyl/ methoxy

  12. Comparative proteomic analysis of drug sodium iron chlorophyllin addition to Hep 3B cell line.

    PubMed

    Zhang, Jun; Wang, Wenhai; Yang, Fengying; Zhou, Xinwen; Jin, Hong; Yang, Peng-yuan

    2012-09-21

    The human hepatoma 3B cell line was chosen as an experimental model for in vitro test of drug screening. The drugs included chlorophyllin and its derivatives such as fluo-chlorophyllin, sodium copper chlorophyllin, and sodium iron chlorophyllin. The 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrazolium bromide (MTT) method was used in this study to obtain the primary screening results. The results showed that sodium iron chlorophyllin had the best LC(50) value. Proteomic analysis was then performed for further investigation of the effect of sodium iron chlorophyllin addition to the Hep 3B cell line. The proteins identified from a total protein extract of Hep 3B before and after the drug addition were compared by two-dimensional-gel-electrophoresis. Then 32 three-fold differentially expressed proteins were successfully identified by MALDI-TOF-TOF-MS. There are 29 unique proteins among those identified proteins. These proteins include proliferating cell nuclear antigen (PCNA), T-complex protein, heterogeneous nuclear protein, nucleophosmin, heat shock protein A5 (HspA5) and peroxiredoxin. HspA5 is one of the proteins which are involved in protecting cancer cells against stress-induced apoptosis in cultured cells, protecting them against apoptosis through various mechanisms. Peroxiredoxin has anti-oxidant function and is related to cell proliferation, and signal transduction. It can protect the oxidation of other proteins. Peroxiredoxin has a close relationship with cancer and can eventually become a disease biomarker. This might help to develop a novel treatment method for carcinoma cancer.

  13. Should Relational Aggression Be Included in DSM-V?

    ERIC Educational Resources Information Center

    Keenan, Kate; Coyne, Claire; Lahey, Benjamin B.

    2008-01-01

    The study examines whether relational aggression should be included in DSM-V disruptive behavior disorders. The results conclude that some additional information is gathered from assessing relational aggression but not enough to be included in DSM-V.

  14. Protein Crystal Based Nanomaterials

    NASA Technical Reports Server (NTRS)

    Bell, Jeffrey A.; VanRoey, Patrick

    2001-01-01

    This is the final report on a NASA Grant. It concerns a description of work done, which includes: (1) Protein crystals cross-linked to form fibers; (2) Engineering of protein to favor crystallization; (3) Better knowledge-based potentials for protein-protein contacts; (4) Simulation of protein crystallization.

  15. Should family planning include STD services?

    PubMed

    Finger, W R

    1994-05-01

    Recent reviews suggest that the addition of programs aimed at preventing and controlling sexually transmitted diseases (STDs), specifically human immunodeficiency virus (HIV), to existing family planning programs does not necessarily dilute overall program effectiveness. In Colombia, Mexico, and Jamaica, where condom distribution and/or information to prevent HIV transmission was integrated into the activities of family planning field workers, no negative effect on the image of condoms as a pregnancy prevention method was observed and there was a great demand on the part of family planning clients for information about acquired immunodeficiency syndrome (AIDS). In Brazil, family planning staff are receiving training in HIV risk assessment and the counseling of women in partner negotiation skills. However, steps must be taken to reach men since it is their high-risk behavior that puts most women at risk of HIV. Both separate STD clinics for men and condom social marketing projects have yielded promising results. Obstacles to the addition of STD services to family planning programs include the need to treat male partners as well as female clients, a shortage of diagnostic tools and antibiotics for treatment, and the fact that the majority of women with STDs are asymptomatic. Indicative of the increased attention being given this approach, however, is the recent release of guidelines by the US Agency for International Development Office of Population on how family planning programs should approach integration. Suggested activities include condom promotion, behavior change, counseling, information, contraceptive development, and selected efforts at STD treatment.

  16. PSAIA – Protein Structure and Interaction Analyzer

    PubMed Central

    Mihel, Josip; Šikić, Mile; Tomić, Sanja; Jeren, Branko; Vlahoviček, Kristian

    2008-01-01

    Background PSAIA (Protein Structure and Interaction Analyzer) was developed to compute geometric parameters for large sets of protein structures in order to predict and investigate protein-protein interaction sites. Results In addition to most relevant established algorithms, PSAIA offers a new method PIADA (Protein Interaction Atom Distance Algorithm) for the determination of residue interaction pairs. We found that PIADA produced more satisfactory results than comparable algorithms implemented in PSAIA. Particular advantages of PSAIA include its capacity to combine different methods to detect the locations and types of interactions between residues and its ability, without any further automation steps, to handle large numbers of protein structures and complexes. Generally, the integration of a variety of methods enables PSAIA to offer easier automation of analysis and greater reliability of results. PSAIA can be used either via a graphical user interface or from the command-line. Results are generated in either tabular or XML format. Conclusion In a straightforward fashion and for large sets of protein structures, PSAIA enables the calculation of protein geometric parameters and the determination of location and type for protein-protein interaction sites. XML formatted output enables easy conversion of results to various formats suitable for statistic analysis. Results from smaller data sets demonstrated the influence of geometry on protein interaction sites. Comprehensive analysis of properties of large data sets lead to new information useful in the prediction of protein-protein interaction sites. PMID:18400099

  17. Heat Shock Proteins: Mediators of Atherosclerotic Development.

    PubMed

    Deniset, Justin F; Pierce, Grant N

    2015-01-01

    Heat shock proteins play important housekeeping roles in a variety of cells within the body during normal control conditions. The many different functions for heat shock proteins in the cell depend upon the specific heat shock protein involved. Each protein is nominally differentiated based upon its molecular size. However, in addition to their role in normal cell function, heat shock proteins may play an even more important role as pro-survival proteins conserved through evolution to protect the cell from a variety of stresses. The ability of a cell to withstand these environmental stresses is critical to its capacity to adapt and remain viable. Loss of this ability may lead to pathological states. Abnormal localization, structure or function of the heat shock proteins has been associated with many pathologies, including those involving heart disease. Heat shock proteins like HSP60 and HSP70 in particular have been identified as playing important roles in inflammation and immune reactions. Inflammation has been identified recently as an important pathological risk factor for heart disease. It is perhaps not surprising therefore, that heat shock protein family has been increasingly identified as an important intracellular pathway associated with inflammatory-mediated heart conditions including atherosclerosis. This paper reviews the evidence in support of a role for heat shock proteins in cardiovascular disease and the potential to target these proteins to alter the progression of atherosclerotic disease.

  18. Fermentation Quality and Additives: A Case of Rice Straw Silage

    PubMed Central

    Oladosu, Yusuff; Magaji, Usman; Hussin, Ghazali; Ramli, Asfaliza; Miah, Gous

    2016-01-01

    Rice cultivation generates large amount of crop residues of which only 20% are utilized for industrial and domestic purposes. In most developing countries especially southeast Asia, rice straw is used as part of feeding ingredients for the ruminants. However, due to its low protein content and high level of lignin and silica, there is limitation to its digestibility and nutritional value. To utilize this crop residue judiciously, there is a need for improvement of its nutritive value to promote its utilization through ensiling. Understanding the fundamental principle of ensiling is a prerequisite for successful silage product. Prominent factors influencing quality of silage product include water soluble carbohydrates, natural microbial population, and harvesting conditions of the forage. Additives are used to control the fermentation processes to enhance nutrient recovery and improve silage stability. This review emphasizes some practical aspects of silage processing and the use of additives for improvement of fermentation quality of rice straw. PMID:27429981

  19. Evaluation of certain food additives.

    PubMed

    2009-01-01

    This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, including flavouring agents, with a view to recommending acceptable daily intakes (ADIs) and to preparing specifications for identity and purity. The first part of the report contains a general discussion of the principles governing the toxicological evaluation and assessment of intake of food additives (in particular, flavouring agents). A summary follows of the Committee's evaluations of technical, toxicological and intake data for certain food additives (asparaginase from Aspergillus niger expressed in A. niger, calcium lignosulfonate (40-65), ethyl lauroyl arginate, paprika extract, phospholipase C expressed in Pichia pastoris, phytosterols, phytostanols and their esters, polydimethylsiloxane, steviol glycosides and sulfites [assessment of dietary exposure]) and 10 groups of related flavouring agents (aliphatic branched-chain saturated and unsaturated alcohols, aldehydes, acids and related esters; aliphatic linear alpha,beta-unsaturated aldehydes, acids and related alcohols, acetals and esters; aliphatic secondary alcohols, ketones and related esters; alkoxy-substituted allylbenzenes present in foods and essential oils and used as flavouring agents; esters of aliphatic acyclic primary alcohols with aliphatic linear saturated carboxylic acids; furan-substituted aliphatic hydrocarbons, alcohols, aldehydes, ketones, carboxylic acids and related esters, sulfides, disulfides and ethers; miscellaneous nitrogen-containing substances; monocyclic and bicyclic secondary alcohols, ketones and related esters; hydroxy- and alkoxy-substituted benzyl derivatives; and substances structurally related to menthol). Specifications for the following food additives were revised: canthaxanthin; carob bean gum and carob bean gum (clarified); chlorophyllin copper complexes, sodium and potassium salts; Fast Green FCF; guar gum and guar gum (clarified

  20. Topology and cellular localization of the small hydrophobic protein of avian metapneumovirus

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The small hydrophobic protein (SH) is a type II integral membrane protein that is packaged into virions and is only present in certain paramyxoviruses including metapneumovirus. In addition to a highly divergent primary sequence, SH proteins vary significantly in size among the different viruses. Hu...

  1. BAYESIAN PROTEIN STRUCTURE ALIGNMENT1

    PubMed Central

    RODRIGUEZ, ABEL; SCHMIDLER, SCOTT C.

    2015-01-01

    The analysis of the three-dimensional structure of proteins is an important topic in molecular biochemistry. Structure plays a critical role in defining the function of proteins and is more strongly conserved than amino acid sequence over evolutionary timescales. A key challenge is the identification and evaluation of structural similarity between proteins; such analysis can aid in understanding the role of newly discovered proteins and help elucidate evolutionary relationships between organisms. Computational biologists have developed many clever algorithmic techniques for comparing protein structures, however, all are based on heuristic optimization criteria, making statistical interpretation somewhat difficult. Here we present a fully probabilistic framework for pairwise structural alignment of proteins. Our approach has several advantages, including the ability to capture alignment uncertainty and to estimate key “gap” parameters which critically affect the quality of the alignment. We show that several existing alignment methods arise as maximum a posteriori estimates under specific choices of prior distributions and error models. Our probabilistic framework is also easily extended to incorporate additional information, which we demonstrate by including primary sequence information to generate simultaneous sequence–structure alignments that can resolve ambiguities obtained using structure alone. This combined model also provides a natural approach for the difficult task of estimating evolutionary distance based on structural alignments. The model is illustrated by comparison with well-established methods on several challenging protein alignment examples. PMID:26925188

  2. 19 CFR 134.2 - Additional duties.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... COUNTRY OF ORIGIN MARKING General Provisions § 134.2 Additional duties. Articles not marked as required by... container) to indicate the English name of the country of origin of the article or to include words...

  3. 19 CFR 134.2 - Additional duties.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... COUNTRY OF ORIGIN MARKING General Provisions § 134.2 Additional duties. Articles not marked as required by... container) to indicate the English name of the country of origin of the article or to include words...

  4. 16 CFR 1102.16 - Additional information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... PUBLICLY AVAILABLE CONSUMER PRODUCT SAFETY INFORMATION DATABASE (Eff. Jan. 10, 2011) Content Requirements... notices, the CPSC shall include in the Database any additional information it determines to be in...

  5. DEVELOPMENT OF WATER CIRCULATION MODEL INCLUDING IRRIGATION

    NASA Astrophysics Data System (ADS)

    Kotsuki, Shunji; Tanaka, Kenji; Kojiri, Toshiharu; Hamaguchi, Toshio

    It is well known that since agricultural water withdrawal has much affect on water circulation system, accurate analysis of river discharge or water balance are difficult with less regard for it. In this study, water circulation model composed of land surface model and distributed runoff model is proposed at 10km 10km resolution. In this model, irrigation water, which is estimated with land surface model, is introduced to river discharge analysis. The model is applied to the Chao Phraya River in Thailand, and reproduced seasonal water balance. Additionally, the discharge on dry season simulated with the model is improved as a result of including irrigation. Since the model, which is basically developed from global data sets, simulated seasonal change of river discharge, it can be suggested that our model has university to other river basins.

  6. Asthma and anaphylactoid reactions to food additives.

    PubMed Central

    Tarlo, S. M.; Sussman, G. L.

    1993-01-01

    Presumed allergic reactions to hidden food additives are both controversial and important. Clinical manifestations include asthma, urticaria, angioedema, and anaphylactic-anaphylactoid events. Most adverse reactions are caused by just a few additives, such as sulfites and monosodium glutamate. Diagnosis is suspected from the history and confirmed by specific challenge. The treatment is specific avoidance. PMID:8499792

  7. 78 FR 22209 - Additional Synthetic Drug Testing

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-15

    ... COMMISSION 10 CFR Part 26 Additional Synthetic Drug Testing AGENCY: Nuclear Regulatory Commission. ACTION... NRC amend its Fitness for Duty program regulations to amend drug testing requirements to test for additional synthetic drugs currently not included in the regulations. The NRC determined that the...

  8. 32 CFR 2001.24 - Additional requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 32 National Defense 6 2013-07-01 2013-07-01 false Additional requirements. 2001.24 Section 2001.24... Markings § 2001.24 Additional requirements. (a) Marking prohibitions. Markings other than “Top Secret... list for NSI portions.” The source list, as described in § 2001.22(c)(1)(ii), shall include...

  9. 32 CFR 2001.24 - Additional requirements.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 32 National Defense 6 2014-07-01 2014-07-01 false Additional requirements. 2001.24 Section 2001.24... Markings § 2001.24 Additional requirements. (a) Marking prohibitions. Markings other than “Top Secret... list for NSI portions.” The source list, as described in § 2001.22(c)(1)(ii), shall include...

  10. 32 CFR 2001.24 - Additional requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 32 National Defense 6 2012-07-01 2012-07-01 false Additional requirements. 2001.24 Section 2001.24... Markings § 2001.24 Additional requirements. (a) Marking prohibitions. Markings other than “Top Secret... list for NSI portions.” The source list, as described in § 2001.22(c)(1)(ii), shall include...

  11. 32 CFR 2001.24 - Additional requirements.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 32 National Defense 6 2010-07-01 2010-07-01 false Additional requirements. 2001.24 Section 2001.24... Markings § 2001.24 Additional requirements. (a) Marking prohibitions. Markings other than “Top Secret... list for NSI portions.” The source list, as described in § 2001.22(c)(1)(ii), shall include...

  12. Mid-infrared spectroscopy for protein analysis: potential and challenges.

    PubMed

    López-Lorente, Ángela I; Mizaikoff, Boris

    2016-04-01

    Mid-infrared (MIR) spectroscopy investigates the interaction of MIR photons with both organic and inorganic molecules via the excitation of vibrational and rotational modes, providing inherent molecular selectivity. In general, infrared (IR) spectroscopy is particularly sensitive to protein structure and structural changes via vibrational resonances originating from the polypeptide backbone or side chains; hence information on the secondary structure of proteins can be obtained in a label-free fashion. In this review, the challenges for IR spectroscopy for protein analysis are discussed as are the potential and limitations of different IR spectroscopic techniques enabling protein analysis. In particular, the amide I spectral range has been widely used to study protein secondary structure, conformational changes, protein aggregation, protein adsorption, and the formation of amyloid fibrils. In addition to representative examples of the potential of IR spectroscopy in various fields related to protein analysis, the potential of protein analysis taking advantage of miniaturized MIR systems, including waveguide-enhanced MIR sensors, is detailed.

  13. Additives in fibers and fabrics.

    PubMed Central

    Barker, R H

    1975-01-01

    The additives and contaminants which occur in textile fibers vary widely, depending on the type of fiber and the pretreatment which it has received. Synthetic fibers such as nylon and polyester contain trace amounts of contaminants such as catalysts and catalyst deactivators which remain after the synthesis of the basic polymers. In addition, there are frequently a number of materials which are added to perform specific functions in almost all man-made fibers. Examples of these would include traces of metals or metal salts used as tracers for identification of specific lots of fiber, TiO2 or similar materials added as delustrants, and a host of organic species added for such special purposes as antistatic agents or flame retardants. There may also be considerable quantities of residual monomer or small oligomers dissolved in the polymer matrix. The situation becomes even more complex after the fibers are converted into fabric form. Numerous materials are applied at various stages of fabric preparation to act as lubricants, sizing agents, antistats, bleaches, and wetting agents to facilitate the processing, but these are normally removed before the fabric reaches the cutters of the ultimate consumers and therefore usually do not constitute potential hazards. However, there are many other chemical agents which are frequently added during the later stages of fabric preparation and which are not designed to be removed. Aside from dyes and printing pigments, the most common additive for apparel fabrics is a durable press treatment. This generally involves the use of materials capable of crosslinking cellulosics by reacting through such functions as N-methylolated amides or related compounds such as ureas and carbamates. These materials pose some potential hazards due to both the nitrogenous bases and the formaldehyde which they usually release. There is usually also some residual catalyst in fabrics which have received such treatments. Other types of chemical treatments

  14. The protein interaction landscape of the human CMGC kinase group.

    PubMed

    Varjosalo, Markku; Keskitalo, Salla; Van Drogen, Audrey; Nurkkala, Helka; Vichalkovski, Anton; Aebersold, Ruedi; Gstaiger, Matthias

    2013-04-25

    Cellular information processing via reversible protein phosphorylation requires tight control of the localization, activity, and substrate specificity of protein kinases, which to a large extent is accomplished by complex formation with other proteins. Despite their critical role in cellular regulation and pathogenesis, protein interaction information is available for only a subset of the 518 human protein kinases. Here we present a global proteomic analysis of complexes of the human CMGC kinase group. In addition to subgroup-specific functional enrichment and modularity, the identified 652 high-confidence kinase-protein interactions provide a specific biochemical context for many poorly studied CMGC kinases. Furthermore, the analysis revealed a kinase-kinase subnetwork and candidate substrates for CMGC kinases. Finally, the presented interaction proteome uncovered a large set of interactions with proteins genetically linked to a range of human diseases, including cancer, suggesting additional routes for analyzing the role of CMGC kinases in controlling human disease pathways.

  15. Interferon-Lambda: A New Addition to an Old Family

    PubMed Central

    2010-01-01

    The discovery and initial description of the interferon-λ (IFN-λ) family in early 2003 opened an exciting new chapter in the field of IFN research. There are 3 IFN-λ genes that encode 3 distinct but highly related proteins denoted IFN-λ1, -λ2, and -λ3. These proteins are also known as interleukin-29 (IL-29), IL-28A, and IL-28B, respectively. Collectively, these 3 cytokines comprise the type III subset of IFNs. They are distinct from both type I and type II IFNs for a number of reasons, including the fact that they signal through a heterodimeric receptor complex that is different from the receptors used by type I or type II IFNs. Although type I IFNs (IFN-α/β) and type III IFNs (IFN-λ) signal via distinct receptor complexes, they activate the same intracellular signaling pathway and many of the same biological activities, including antiviral activity, in a wide variety of target cells. Consistent with their antiviral activity, expression of the IFN-λ genes and their corresponding proteins is inducible by infection with many types of viruses. Therefore, expression of the type III IFNs (IFN-λs) and their primary biological activity are very similar to the type I IFNs. However, unlike IFN-α receptors which are broadly expressed on most cell types, including leukocytes, IFN-λ receptors are largely restricted to cells of epithelial origin. The potential clinical importance of IFN-λ as a novel antiviral therapeutic agent is already apparent. In addition, preclinical studies by several groups indicate that IFN-λ may also be useful as a potential therapeutic agent for other clinical indications, including certain types of cancer. PMID:20712453

  16. Current Status of Protein Force Fields for Molecular Dynamics

    PubMed Central

    Lopes, Pedro E.M.; Guvench, Olgun

    2015-01-01

    Summary The current status of classical force fields for proteins is reviewed. These include additive force fields as well as the latest developments in the Drude and AMOEBA polarizable force fields. Parametrization strategies developed specifically for the Drude force field are described and compared with the additive CHARMM36 force field. Results from molecular simulations of proteins and small peptides are summarized to illustrate the performance of the Drude and AMOEBA force fields. PMID:25330958

  17. Immunoprecipitation of Plasma Membrane Receptor-Like Kinases for Identification of Phosphorylation Sites and Associated Proteins.

    PubMed

    Kadota, Yasuhiro; Macho, Alberto P; Zipfel, Cyril

    2016-01-01

    Membrane proteins are difficult to study for numerous reasons. The surface of membrane proteins is relatively hydrophobic and sometimes very unstable, additionally requiring detergents for their extraction from the membrane. This leads to challenges at all levels, including expression, solubilization, purification, identification of associated proteins, and the identification of post-translational modifications. However, recent advances in immunoprecipitation technology allow to isolate membrane proteins efficiently, facilitating the study of protein-protein interactions, the identification of novel associated proteins, and to identify post-translational modifications, such as phosphorylation. Here, we describe an optimized immunoprecipitation protocol for plant plasma membrane receptor-like kinases.

  18. Analysis of Smart Composite Structures Including Debonding

    NASA Technical Reports Server (NTRS)

    Chattopadhyay, Aditi; Seeley, Charles E.

    1997-01-01

    Smart composite structures with distributed sensors and actuators have the capability to actively respond to a changing environment while offering significant weight savings and additional passive controllability through ply tailoring. Piezoelectric sensing and actuation of composite laminates is the most promising concept due to the static and dynamic control capabilities. Essential to the implementation of these smart composites are the development of accurate and efficient modeling techniques and experimental validation. This research addresses each of these important topics. A refined higher order theory is developed to model composite structures with surface bonded or embedded piezoelectric transducers. These transducers are used as both sensors and actuators for closed loop control. The theory accurately captures the transverse shear deformation through the thickness of the smart composite laminate while satisfying stress free boundary conditions on the free surfaces. The theory is extended to include the effect of debonding at the actuator-laminate interface. The developed analytical model is implemented using the finite element method utilizing an induced strain approach for computational efficiency. This allows general laminate geometries and boundary conditions to be analyzed. The state space control equations are developed to allow flexibility in the design of the control system. Circuit concepts are also discussed. Static and dynamic results of smart composite structures, obtained using the higher order theory, are correlated with available analytical data. Comparisons, including debonded laminates, are also made with a general purpose finite element code and available experimental data. Overall, very good agreement is observed. Convergence of the finite element implementation of the higher order theory is shown with exact solutions. Additional results demonstrate the utility of the developed theory to study piezoelectric actuation of composite

  19. The Physiology of Protein S-acylation

    PubMed Central

    Chamberlain, Luke H.; Shipston, Michael J.

    2015-01-01

    Protein S-acylation, the only fully reversible posttranslational lipid modification of proteins, is emerging as a ubiquitous mechanism to control the properties and function of a diverse array of proteins and consequently physiological processes. S-acylation results from the enzymatic addition of long-chain lipids, most typically palmitate, onto intracellular cysteine residues of soluble and transmembrane proteins via a labile thioester linkage. Addition of lipid results in increases in protein hydrophobicity that can impact on protein structure, assembly, maturation, trafficking, and function. The recent explosion in global S-acylation (palmitoyl) proteomic profiling as a result of improved biochemical tools to assay S-acylation, in conjunction with the recent identification of enzymes that control protein S-acylation and de-acylation, has opened a new vista into the physiological function of S-acylation. This review introduces key features of S-acylation and tools to interrogate this process, and highlights the eclectic array of proteins regulated including membrane receptors, ion channels and transporters, enzymes and kinases, signaling adapters and chaperones, cell adhesion, and structural proteins. We highlight recent findings correlating disruption of S-acylation to pathophysiology and disease and discuss some of the major challenges and opportunities in this rapidly expanding field. PMID:25834228

  20. The tandem endocytic receptors megalin and cubilin are important proteins in renal pathology.

    PubMed

    Verroust, Pierre J; Birn, Henrik; Nielsen, Rikke; Kozyraki, Renata; Christensen, Erik Ilsø

    2002-09-01

    The molecular mechanisms controlling proximal tubule reabsorption of proteins have been much elucidated in recent years. Megalin and cubilin constitute two important endocytic receptor proteins involved in this process. Although structurally very different the two receptor proteins interact to mediate the reabsorption of a large number of filtered proteins, including carrier proteins important for transport and cellular uptake of several vitamins, lipids and other nutrients. Dysfunction of either protein results in tubular proteinuria and is associated with specific changes in vitamin metabolism due to the defective proximal tubular reabsorption of carrier proteins. Additional focus on the two receptors is attracted by the possible pathogenic role of excessive tubular protein uptake during conditions of increased filtration of proteins, and by recent findings implicating members of the low density lipoprotein-receptor family, which includes megalin, in the transduction of signals by association with cytoplasmic proteins.

  1. The Geobiochemistry of Methanogen Proteins

    NASA Astrophysics Data System (ADS)

    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

  2. How Safe Are Color Additives?

    MedlinePlus

    ... Home For Consumers Consumer Updates How Safe are Color Additives? Share Tweet Linkedin Pin it More sharing ... Consumer Updates RSS Feed Download PDF (380 K) Color additives give the red tint to your fruit ...

  3. Succination of proteins in diabetes.

    PubMed

    Frizzell, Norma; Lima, Maria; Baynes, John W

    2011-01-01

    Cysteine is arguably the most reactive amino acid in protein. A wide range of cysteine derivatives is formed in vivo, resulting from oxidation, nitrosation, alkylation and acylation reactions. This review describes succination of proteins, an irreversible chemical modification of cysteine by the Krebs cycle intermediate, fumarate, yielding S-(2-succinyl)cysteine (2SC). Intracellular fumarate concentration and succination of proteins are increased by hyperpolarization of the inner mitochondrial membrane and develop in concert with mitochondrial and oxidative stress in diabetes. Increased succination of glyceraldehyde-3-phosphate dehydrogenase explains the loss in specific activity of this enzyme in muscle of streptozotocin-diabetic rats and increased succination of adiponectin may explain the decreased secretion of adiponectin from adipose tissue in type 2 diabetes. In addition to GAPDH and adiponectin, other succinated proteins identified in adipocytes include cytoskeletal proteins (tubulin, actin) and chaperone proteins in the endoplasmic reticulum. Succination of adipocyte protein in vitro is inhibited by uncouplers of oxidative phosphorylation and by inhibitors of ER stress. 2SC serves as a biomarker of mitochondrial stress and recent studies suggest that succination is the mechanistic link between mitochondrial and ER stress in diabetes.

  4. Reconsidering remineralization strategies to include nanoparticle hydroxyapatite.

    PubMed

    Kutsch, V Kim; Chaiyabutr, Yada; Milicich, Graeme

    2013-03-01

    Dental caries is a transmissible biofilm-mediated disease of the teeth that is defined by prolonged periods of low pH resulting in net mineral loss from the teeth. Hydroxyapatite, fluorapatite, and the carbonated forms of calcium phosphate form the main mineral content of dental hard tissues: enamel, dentin, and cementum. Active dental caries results when the biofilm pH on the tooth surface drops below the dissolution threshold for hydroxyapatite and fluorapatite. The clinical evidence of this net mineral loss is porosity, whitespot lesions, caries lesions, and/or cavitation. The potential to reverse this mineral loss through remineralization has been well documented, although previous remineralization strategies for dental hard tissues have focused on the use of fluorides and forms of calcium phosphate. This in-vitro study documented the deposition of nanoparticle hydroxyapatite on demineralized enamel surfaces after treatment with an experimental remineralization gel. This finding supports consideration of an additional approach to remineralization that includes pH neutralization strategies and nanoparticle hydroxyapatite crystals.

  5. Detergent Additive for Lubricating Oils,

    DTIC Science & Technology

    The Russian patent pertains to a method of producing additives for lubricating oils . A method is known for producing an antiwear additive for... lubricating oils by processing phenols with phosphorus oxychloride, phosphoric acid esters are obtained. In order to give the additive detergent properties

  6. Additive Transforms Paint into Insulation

    NASA Technical Reports Server (NTRS)

    2007-01-01

    Tech Traders Inc. sought assistance developing low-cost, highly effective coatings and paints that created useful thermal reflectance and were safe and non-toxic. In cooperation with a group of engineers at Kennedy Space Center., Tech Traders created Insuladd, a powder additive made up of microscopic, inert gas-filled, ceramic microspheres that can be mixed into ordinary interior or exterior paint, allowing the paint to act like a layer of insulation. When the paint dries, this forms a radiant heat barrier, turning the ordinary house paint into heat-reflecting thermal paint. According to Tech Traders, the product works with all types of paints and coatings and will not change the coverage rate, application, or adhesion of the paint. Other useful applications include feed storage silos to help prevent feed spoilage, poultry hatcheries to reduce the summer heat and winter cold effects, and on military vehicles and ships. Tech Traders has continued its connection to the aerospace community by recently providing Lockheed Martin Corporation with one of its thermal products for use on the F-22 Raptor.

  7. Bacteria repelling poly(methylmethacrylate-co-dimethylacrylamide) coatings for biomedical devices† †Electronic supplementary information (ESI) available: Polymer microarray screening, including analysis of bacterial adhesion by fluorescence microscopy and SEM, and chemical composition of bacteria repelling polymers identified in the screen; polymer synthesis and characterisation; preparation of catheter pieces and solvent studies, and details for confocal imaging/analysis. See DOI: 10.1039/c4tb01129e Click here for additional data file.

    PubMed Central

    Venkateswaran, Seshasailam; Wu, Mei; Gwynne, Peter J.; Hardman, Ailsa; Lilienkampf, Annamaria; Pernagallo, Salvatore; Blakely, Garry; Swann, David G.

    2014-01-01

    Nosocomial infections due to bacteria have serious implications on the health and recovery of patients in a variety of medical scenarios. Since bacterial contamination on medical devices contributes to the majority of nosocomical infections, there is a need for redesigning the surfaces of medical devices, such as catheters and tracheal tubes, to resist the binding of bacteria. In this work, polyurethanes and polyacrylates/acrylamides, which resist binding by the major bacterial pathogens underpinning implant-associated infections, were identified using high-throughput polymer microarrays. Subsequently, two ‘hit’ polymers, PA13 (poly(methylmethacrylate-co-dimethylacrylamide)) and PA515 (poly(methoxyethylmethacrylate-co-diethylaminoethylacrylate-co-methylmethacrylate)), were used to coat catheters and substantially shown to decrease binding of a variety of bacteria (including isolates from infected endotracheal tubes and heart valves from intensive care unit patients). Catheters coated with polymer PA13 showed up to 96% reduction in bacteria binding in comparison to uncoated catheters. PMID:25580245

  8. Protein surface-distribution and protein-protein interactions in the binding of peripheral proteins to charged lipid membranes.

    PubMed Central

    Heimburg, T; Marsh, D

    1995-01-01

    The binding of native cytochrome c to negatively charged lipid dispersions of dioleoyl phosphatidylglycerol has been studied over a wide range of ionic strengths. Not only is the strength of protein binding found to decrease rapidly with increasing ionic strength, but also the binding curves reach an apparent saturation level that decreases rapidly with increasing ionic strength. Analysis of the binding isotherms with a general statistical thermodynamic model that takes into account not only the free energy of the electrostatic double layer, but also the free energy of the surface distribution of the protein, demonstrates that the apparent saturation effects could arise from a competition between the out-of-plane binding reaction and the lateral in-plane interactions between proteins at the surface. It is found that association with nonlocalized sites results in binding isotherms that display the apparent saturation effect to a much more pronounced extent than does the Langmuir adsorption isotherm for binding to localized sites. With the model for nonlocalized sites, the binding isotherms of native cytochrome c can be described adequately by taking into account only the entropy of the surface distribution of the protein, without appreciable enthalpic interactions between the bound proteins. The binding of cytochrome c to dioleoyl phosphatidylglycerol dispersions at a temperature at which the bound protein is denatured on the lipid surface, but is nondenatured when free in solution, has also been studied. The binding curves for the surface-denatured protein differ from those for the native protein in that the apparent saturation at high ionic strength is less pronounced. This indicates the tendency of the denatured protein to aggregate on the lipid surface, and can be described by the binding isotherms for nonlocalized sites only if attractive interactions between the surface-bound proteins are included in addition to the distributional entropic terms. Additionally

  9. Incorporation of additives into polymers

    DOEpatents

    McCleskey, T. Mark; Yates, Matthew Z.

    2003-07-29

    There has been invented a method for incorporating additives into polymers comprising: (a) forming an aqueous or alcohol-based colloidal system of the polymer; (b) emulsifying the colloidal system with a compressed fluid; and (c) contacting the colloidal polymer with the additive in the presence of the compressed fluid. The colloidal polymer can be contacted with the additive by having the additive in the compressed fluid used for emulsification or by adding the additive to the colloidal system before or after emulsification with the compressed fluid. The invention process can be carried out either as a batch process or as a continuous on-line process.

  10. Dynamic organization of the mitochondrial protein import machinery.

    PubMed

    Straub, Sebastian P; Stiller, Sebastian B; Wiedemann, Nils; Pfanner, Nikolaus

    2016-11-01

    Mitochondria contain elaborate machineries for the import of precursor proteins from the cytosol. The translocase of the outer mitochondrial membrane (TOM) performs the initial import of precursor proteins and transfers the precursors to downstream translocases, including the presequence translocase and the carrier translocase of the inner membrane, the mitochondrial import and assembly machinery of the intermembrane space, and the sorting and assembly machinery of the outer membrane. Although the protein translocases can function as separate entities in vitro, recent studies revealed a close and dynamic cooperation of the protein import machineries to facilitate efficient transfer of precursor proteins in vivo. In addition, protein translocases were found to transiently interact with distinct machineries that function in the respiratory chain or in the maintenance of mitochondrial membrane architecture. Mitochondrial protein import is embedded in a regulatory network that ensures protein biogenesis, membrane dynamics, bioenergetic activity and quality control.

  11. Therapeutic intervention based on protein prenylation and associated modifications

    PubMed Central

    Gelb, Michael H; Brunsveld, Lucas; Hrycyna, Christine A; Michaelis, Susan; Tamanoi, Fuyuhiko; Van Voorhis, Wesley C; Waldmann, Herbert

    2010-01-01

    In eukaryotic cells, a specific set of proteins are modified by C-terminal attachment of 15-carbon farnesyl groups or 20-carbon geranylgeranyl groups that function both as anchors for fixing proteins to membranes and as molecular handles for facilitating binding of these lipidated proteins to other proteins. Additional modification of these prenylated proteins includes C-terminal proteolysis and methylation, and attachment of a 16-carbon palmitoyl group; these modifications augment membrane anchoring and alter the dynamics of movement of proteins between different cellular membrane compartments. The enzymes in the protein prenylation pathway have been isolated and characterized. Blocking protein prenylation is proving to be therapeutically useful for the treatment of certain cancers, infection by protozoan parasites and the rare genetic disease Hutchinson-Gilford progeria syndrome. PMID:16983387

  12. Additive manufacturing of optical components

    NASA Astrophysics Data System (ADS)

    Heinrich, Andreas; Rank, Manuel; Maillard, Philippe; Suckow, Anne; Bauckhage, Yannick; Rößler, Patrick; Lang, Johannes; Shariff, Fatin; Pekrul, Sven

    2016-08-01

    The development of additive manufacturing methods has enlarged rapidly in recent years. Thereby, the work mainly focuses on the realization of mechanical components, but the additive manufacturing technology offers a high potential in the field of optics as well. Owing to new design possibilities, completely new solutions are possible. This article briefly reviews and compares the most important additive manufacturing methods for polymer optics. Additionally, it points out the characteristics of additive manufactured polymer optics. Thereby, surface quality is of crucial importance. In order to improve it, appropriate post-processing steps are necessary (e.g. robot polishing or coating), which will be discussed. An essential part of this paper deals with various additive manufactured optical components and their use, especially in optical systems for shape metrology (e.g. borehole sensor, tilt sensor, freeform surface sensor, fisheye lens). The examples should demonstrate the potentials and limitations of optical components produced by additive manufacturing.

  13. Environmental Sustainability - Including Land and Water Use

    EPA Science Inventory

    Assessments of environmental sustainability can be conducted in many ways with one of the most quantitative methods including Life Cycle Impact Assessment (LCIA). While historically LCIA has included a comprehensive list of impact categories including: ozone depletion, global c...

  14. Benchtop Detection of Proteins

    NASA Technical Reports Server (NTRS)

    Scardelletti, Maximilian C.; Varaljay, Vanessa

    2007-01-01

    A process, and a benchtop-scale apparatus for implementing the process, have been developed to detect proteins associated with specific microbes in water. The process and apparatus may also be useful for detection of proteins in other, more complex liquids. There may be numerous potential applications, including monitoring lakes and streams for contamination, testing of blood and other bodily fluids in medical laboratories, and testing for microbial contamination of liquids in restaurants and industrial food-processing facilities. A sample can be prepared and analyzed by use of this process and apparatus within minutes, whereas an equivalent analysis performed by use of other processes and equipment can often take hours to days. The process begins with the conjugation of near-infrared-fluorescent dyes to antibodies that are specific to a particular protein. Initially, the research has focused on using near-infrared dyes to detect antigens or associated proteins in solution, which has proven successful vs. microbial cells, and streamlining the technique in use for surface protein detection on microbes would theoretically render similar results. However, it is noted that additional work is needed to transition protein-based techniques to microbial cell detection. Consequently, multiple such dye/antibody pairs could be prepared to enable detection of multiple selected microbial species, using a different dye for each species. When excited by near-infrared light of a suitable wavelength, each dye fluoresces at a unique longer wavelength that differs from those of the other dyes, enabling discrimination among the various species. In initial tests, the dye/antibody pairs are mixed into a solution suspected of containing the selected proteins, causing the binding of the dye/antibody pairs to such suspect proteins that may be present. The solution is then run through a microcentrifuge that includes a membrane that acts as a filter in that it retains the dye/antibody/protein

  15. Protein-Protein Docking Benchmark Version 3.0

    PubMed Central

    Hwang, Howook; Pierce, Brian; Mintseris, Julian; Janin, Joël; Weng, Zhiping

    2009-01-01

    We present version 3.0 of our publicly available protein-protein docking benchmark. This update includes 40 new test cases, representing a 48% increase from Benchmark 2.0. For all of the new cases, the crystal structures of both binding partners are available. As with Benchmark 2.0, SCOP1 (Structural Classification of Proteins) was used to remove redundant test cases. The 124 unbound-unbound test cases in Benchmark 3.0 are classified into 88 rigid-body cases, 19 medium difficulty cases, and 17 difficult cases, based on the degree of conformational change at the interface upon complex formation. In addition to providing the community with more test cases for evaluating docking methods, the expansion of Benchmark 3.0 will facilitate the development of new algorithms that require a large number of training examples. Benchmark 3.0 is available to the public at http://zlab.bu.edu/benchmark. PMID:18491384

  16. Effusion plate using additive manufacturing methods

    DOEpatents

    Johnson, Thomas Edward; Keener, Christopher Paul; Ostebee, Heath Michael; Wegerif, Daniel Gerritt

    2016-04-12

    Additive manufacturing techniques may be utilized to construct effusion plates. Such additive manufacturing techniques may include defining a configuration for an effusion plate having one or more internal cooling channels. The manufacturing techniques may further include depositing a powder into a chamber, applying an energy source to the deposited powder, and consolidating the powder into a cross-sectional shape corresponding to the defined configuration. Such methods may be implemented to construct an effusion plate having one or more channels with a curved cross-sectional geometry.

  17. Enantioselective Michael addition of water.

    PubMed

    Chen, Bi-Shuang; Resch, Verena; Otten, Linda G; Hanefeld, Ulf

    2015-02-09

    The enantioselective Michael addition using water as both nucleophile and solvent has to date proved beyond the ability of synthetic chemists. Herein, the direct, enantioselective Michael addition of water in water to prepare important β-hydroxy carbonyl compounds using whole cells of Rhodococcus strains is described. Good yields and excellent enantioselectivities were achieved with this method. Deuterium labeling studies demonstrate that a Michael hydratase catalyzes the water addition exclusively with anti-stereochemistry.

  18. Enantioselective Michael Addition of Water

    PubMed Central

    Chen, Bi-Shuang; Resch, Verena; Otten, Linda G; Hanefeld, Ulf

    2015-01-01

    The enantioselective Michael addition using water as both nucleophile and solvent has to date proved beyond the ability of synthetic chemists. Herein, the direct, enantioselective Michael addition of water in water to prepare important β-hydroxy carbonyl compounds using whole cells of Rhodococcus strains is described. Good yields and excellent enantioselectivities were achieved with this method. Deuterium labeling studies demonstrate that a Michael hydratase catalyzes the water addition exclusively with anti-stereochemistry. PMID:25529526

  19. Antagonists of IAP proteins as cancer therapeutics.

    PubMed

    Dynek, Jasmin N; Vucic, Domagoj

    2013-05-28

    Inhibitor of apoptosis (IAP) proteins play pivotal roles in cellular survival by blocking apoptosis, modulating signal transduction, and affecting cellular proliferation. Through their interactions with inducers and effectors of apoptosis IAP proteins can effectively suppress apoptosis triggered by diverse stimuli including death receptor signaling, irradiation, chemotherapeutic agents, or growth factor withdrawal. Evasion of apoptosis, in part due to the action of IAP proteins, enhances resistance of cancer cells to treatment with chemotherapeutic agents and contributes to tumor progression. Additionally, IAP genes are known to be subject to amplification, mutation, and chromosomal translocation in human malignancies and autoimmune diseases. In this review we will discuss the role of IAP proteins in cancer and the development of antagonists targeting IAP proteins for cancer treatment.

  20. Color Addition and Subtraction Apps

    ERIC Educational Resources Information Center

    Ruiz, Frances; Ruiz, Michael J.

    2015-01-01

    Color addition and subtraction apps in HTML5 have been developed for students as an online hands-on experience so that they can more easily master principles introduced through traditional classroom demonstrations. The evolution of the additive RGB color model is traced through the early IBM color adapters so that students can proceed step by step…

  1. Additive Effects on Asymmetric Catalysis.

    PubMed

    Hong, Liang; Sun, Wangsheng; Yang, Dongxu; Li, Guofeng; Wang, Rui

    2016-03-23

    This review highlights a number of additives that can be used to make asymmetric reactions perfect. Without changing other reaction conditions, simply adding additives can lead to improved asymmetric catalysis, such as reduced reaction time, improved yield, or/and increased selectivity.

  2. Including nonadditive genetic effects in mating programs to maximize dairy farm profitability.

    PubMed

    Aliloo, H; Pryce, J E; González-Recio, O; Cocks, B G; Goddard, M E; Hayes, B J

    2017-02-01

    We compared the outcome of mating programs based on different evaluation models that included nonadditive genetic effects (dominance and heterozygosity) in addition to additive effects. The additive and dominance marker effects and the values of regression on average heterozygosity were estimated using 632,003 single nucleotide polymorphisms from 7,902 and 7,510 Holstein cows with calving interval and production (milk, fat, and protein yields) records, respectively. Expected progeny values were computed based on the estimated genetic effects and genotype probabilities of hypothetical progeny from matings between the available genotyped cows and the top 50 young genomic bulls. An index combining the traits based on their economic values was developed and used to evaluate the performance of different mating scenarios in terms of dollar profit. We observed that mating programs with nonadditive genetic effects performed better than a model with only additive effects. Mating programs with dominance and heterozygosity effects increased milk, fat, and protein yields by up to 38, 1.57, and 1.21 kg, respectively. The inclusion of dominance and heterozygosity effects decreased calving interval by up to 0.70 d compared with random mating. The average reduction in progeny inbreeding by the inclusion of nonadditive genetic effects in matings compared with random mating was between 0.25 to 1.57 and 0.64 to 1.57 percentage points for calving interval and production traits, respectively. The reduction in inbreeding was accompanied by an average of A$8.42 (Australian dollars) more profit per mating for a model with additive, dominance, and heterozygosity effects compared with random mating. Mate allocations that benefit from nonadditive genetic effects can improve progeny performance only in the generation where it is being implemented, and the gain from specific combining abilities cannot be accumulated over generations. Continuous updating of genomic predictions and mate

  3. Protein carriers of conjugate vaccines

    PubMed Central

    Pichichero, Michael E

    2013-01-01

    The immunogenicity of polysaccharides as human vaccines was enhanced by coupling to protein carriers. Conjugation transformed the T cell-independent polysaccharide vaccines of the past to T cell-dependent antigenic vaccines that were much more immunogenic and launched a renaissance in vaccinology. This review discusses the conjugate vaccines for prevention of infections caused by Hemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis. Specifically, the characteristics of the proteins used in the construction of the vaccines including CRM, tetanus toxoid, diphtheria toxoid, Neisseria meningitidis outer membrane complex, and Hemophilus influenzae protein D are discussed. The studies that established differences among and key features of conjugate vaccines including immunologic memory induction, reduction of nasopharyngeal colonization and herd immunity, and antibody avidity and avidity maturation are presented. Studies of dose, schedule, response to boosters, of single protein carriers with single and multiple polysaccharides, of multiple protein carriers with multiple polysaccharides and conjugate vaccines administered concurrently with other vaccines are discussed along with undesirable consequences of conjugate vaccines. The clear benefits of conjugate vaccines in improving the protective responses of the immature immune systems of young infants and the senescent immune systems of the elderly have been made clear and opened the way to development of additional vaccines using this technology for future vaccine products. PMID:23955057

  4. Enhancing recombinant protein production in human cell lines with a constitutive transport element and mRNA export proteins.

    PubMed

    Aihara, Yuki; Fujiwara, Naoko; Yamazaki, Tomohiro; Kambe, Taiho; Nagao, Masaya; Hirose, Yutaka; Masuda, Seiji

    2011-05-20

    Recent research into mRNA maturation processes in the nucleus has identified a number of proteins involved in mRNA transcription, capping, splicing, end processing and export. Among them, the Tap-p15 heterodimer acts as an mRNA export receptor. Tap-p15 is recruited onto fully processed mRNA in the nucleus, which is ready for export to the cytoplasm, through associating with Aly or SR proteins on mRNA, or by directly associating with a constitutive transport element (CTE), an RNA element derived from type D retroviruses. mRNA containing a CTE is exported to the cytoplasm by directly associating with Tap-p15, even in the absence of Tap-recruiting proteins such as Aly or SR proteins on the mRNA. Here, we showed that the use of a CTE enhanced the expression of recombinant protein in human cell lines. The co-expression of reporter proteins and Tap-p15 also enhanced recombinant protein expression. Moreover, the use of a CTE and Tap-p15 synergistically further enhanced the recombinant protein expression. In addition to Tap-p15, several Tap-p15-recruiting proteins, including Aly and SR proteins, enhanced recombinant protein expression, albeit independently of the CTE. The incorporation of a CTE and Tap-p15-recruiting proteins into protein expression system is useful to increase recombinant protein yield in human cells.

  5. 36 CFR 1290.7 - Additional guidance.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    .... Kennedy. (b) The inclusion of artifacts in the scope of the term assassination record is understood to... regulation. (c) Whenever artifacts are included in the JFK Assassination Records Collection, it shall be... materials depicting the artifacts. Additional display of or examination by the public of artifacts in...

  6. 36 CFR 1290.7 - Additional guidance.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    .... Kennedy. (b) The inclusion of artifacts in the scope of the term assassination record is understood to... regulation. (c) Whenever artifacts are included in the JFK Assassination Records Collection, it shall be... materials depicting the artifacts. Additional display of or examination by the public of artifacts in...

  7. 36 CFR 1290.7 - Additional guidance.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .... Kennedy. (b) The inclusion of artifacts in the scope of the term assassination record is understood to... regulation. (c) Whenever artifacts are included in the JFK Assassination Records Collection, it shall be... materials depicting the artifacts. Additional display of or examination by the public of artifacts in...

  8. 36 CFR 1290.7 - Additional guidance.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .... Kennedy. (b) The inclusion of artifacts in the scope of the term assassination record is understood to... regulation. (c) Whenever artifacts are included in the JFK Assassination Records Collection, it shall be... materials depicting the artifacts. Additional display of or examination by the public of artifacts in...

  9. 36 CFR 1290.7 - Additional guidance.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .... Kennedy. (b) The inclusion of artifacts in the scope of the term assassination record is understood to... regulation. (c) Whenever artifacts are included in the JFK Assassination Records Collection, it shall be... materials depicting the artifacts. Additional display of or examination by the public of artifacts in...

  10. 33 CFR 203.83 - Additional requirements.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    .../Cooperation Agreements § 203.83 Additional requirements. (a) Maintenance deficiencies. Rehabilitation... or deficient maintenance. Such correction must be accomplished by, or at the expense of, local.... Separable areas with minor damage will be included in the maintenance program of local interests. (c)...

  11. 33 CFR 203.83 - Additional requirements.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    .../Cooperation Agreements § 203.83 Additional requirements. (a) Maintenance deficiencies. Rehabilitation... or deficient maintenance. Such correction must be accomplished by, or at the expense of, local.... Separable areas with minor damage will be included in the maintenance program of local interests. (c)...

  12. 33 CFR 203.83 - Additional requirements.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    .../Cooperation Agreements § 203.83 Additional requirements. (a) Maintenance deficiencies. Rehabilitation... or deficient maintenance. Such correction must be accomplished by, or at the expense of, local.... Separable areas with minor damage will be included in the maintenance program of local interests. (c)...

  13. College of Architecture Addition, Burchard Hall.

    ERIC Educational Resources Information Center

    Design Cost Data, 2001

    2001-01-01

    Describes the architectural design, costs, general description, and square footage data for the College of Architecture Addition, Burchard Hall in Blacksburg, Virginia. A floor plan and photos are included along with a list of manufacturers and suppliers used for the project. (GR)

  14. Purine inhibitors of protein kinases, G proteins and polymerases

    DOEpatents

    Gray, Nathanael S.; Schultz, Peter; Kim, Sung-Hou; Meijer, Laurent

    2001-07-03

    The present invention relates to purine analogs that inhibit, inter alia, protein kinases, G-proteins and polymerases. In addition, the present invention relates to methods of using such purine analogs to inhibit protein kinases, G-proteins, polymerases and other cellular processes and to treat cellular proliferative diseases.

  15. p53 and rapamycin are additive

    PubMed Central

    Campisi, Judith; Huang, Jing; Jones, Diane; Dodds, Sherry G.; Williams, Charnae; Hubbard, Gene; Livi, Carolina B.; Gao, Xiaoli; Weintraub, Susan; Curiel, Tyler; Sharp, Z. Dave; Hasty, Paul

    2015-01-01

    Mechanistic target of rapamycin (mTOR) is a kinase found in a complex (mTORC1) that enables macromolecular synthesis and cell growth and is implicated in cancer etiology. The rapamycin-FK506 binding protein 12 (FKBP12) complex allosterically inhibits mTORC1. In response to stress, p53 inhibits mTORC1 through a separate pathway involving cell signaling and amino acid sensing. Thus, these different mechanisms could be additive. Here we show that p53 improved the ability of rapamycin to: 1) extend mouse life span, 2) suppress ionizing radiation (IR)-induced senescence-associated secretory phenotype (SASP) and 3) increase the levels of amino acids and citric acid in mouse embryonic stem (ES) cells. This additive effect could have implications for cancer treatment since rapamycin and p53 are anti-oncogenic. PMID:26158292

  16. Color Addition and Subtraction Apps

    NASA Astrophysics Data System (ADS)

    Ruiz, Frances; Ruiz, Michael J.

    2015-10-01

    Color addition and subtraction apps in HTML5 have been developed for students as an online hands-on experience so that they can more easily master principles introduced through traditional classroom demonstrations. The evolution of the additive RGB color model is traced through the early IBM color adapters so that students can proceed step by step in understanding mathematical representations of RGB color. Finally, color addition and subtraction are presented for the X11 colors from web design to illustrate yet another real-life application of color mixing.

  17. Haemophilus influenzae Disease (Including Hib) Symptoms

    MedlinePlus

    ... Search The CDC Cancel Submit Search The CDC Haemophilus influenzae Disease (Including Hib) Note: Javascript is disabled or ... and Symptoms Recommend on Facebook Tweet Share Compartir Haemophilus influenzae , including Hib, disease causes different symptoms depending on ...

  18. Additivity in protein–DNA interactions: how good an approximation is it?

    PubMed Central

    Benos, Panayiotis V.; Bulyk, Martha L.; Stormo, Gary D.

    2002-01-01

    Man and Stormo and Bulyk et al. recently presented their results on the study of the DNA binding affinity of proteins. In both of these studies the main conclusion is that the additivity assumption, usually applied in methods to search for binding sites, is not true. In the first study, the analysis of binding affinity data from the Mnt repressor protein bound to all possible DNA (sub)targets at positions 16 and 17 of the binding site, showed that those positions are not independent. In the second study, the authors analysed DNA binding affinity data of the wild-type mouse EGR1 protein and four variants differing on the middle finger. The binding affinity of these proteins was measured to all 64 possible trinucleotide (sub)targets of the middle finger using microarray technology. The analysis of the measurements also showed interdependence among the positions in the DNA target. In the present report, we review the data of both studies and we re- analyse them using various statistical methods, including a comparison with a multiple regression approach. We conclude that despite the fact that the additivity assumption does not fit the data perfectly, in most cases it provides a very good approximation of the true nature of the specific protein–DNA interactions. Therefore, additive models can be very useful for the discovery and prediction of binding sites in genomic DNA. PMID:12384591

  19. [Effect of a complex treatment, including glutargin and erbisol on the blood plasma content of protein P53, apoptotic markers of type II, activity of caspases and the level of sCD 117 in patients with autonomic-vascular dystonia].

    PubMed

    Krychun, I I

    2008-01-01

    It has been established that the blood content of protein P53 diminishes by 27%, the blood level of sTRAIL increases by 22%, sCD 117 increases by 44% in patients with vegeto-vascular dystonia of the hypertonic type that is accompanied by an increase of the activity of caspases-1 however the activity of caspases-3 and - 8 as well as the blood content of TNF-alpha do not change. Multimodality therapy using glutargin does not influence on the level of the blood plasma TNF-alpha and the activity of caspases-1,-3,-8, normalizes the blood content of sTRAIL and sCD 117, however does not change the plasma concentration of protein P53 which remains lower by 35% than the control indices. In patients with vegeto-vascular dystonia of the hypotonic type the concentration of blood plasma protein P53, TNF-alpha and sTRAIL and the activity of caspases-1,-3,-8 correspond to the control values against a background of an almost twofold increase of the plasma sCD 117 level. The use of erbisol in a complex of therapeutic agents does not change the activity of caspases-l,-3,-8 and does not influence on the blood content of protein p53, TNF-alpha and sTRAIL and diminishes the plasma level of sCD 117 up to control values. A considerable elevation of the blood content of type II apoptotic factors is characteristic of the mixed type of vegeto-vascular dystonia: the level of protein p53 increases 2,4 times, TNF-alpha - 1,9 times, sTRAIL - 2,3 times that is accompanied by an increased activity of caspase-1 - 4,1 times, caspase-3 - 3,3 times, caspase-8 - 3,8 times and an increase of the plasma concentration of sCD 117 - 3,5 times. The use of erbisol and glutargin in multimodality therapy normalizes the plasma concentration of TNF-alpha and diminishes the blood content of protein P53 by 33% and sTRAIL - by 42% which, nevertheless remains higher than the control value by 58% and 36% respectively. The combined effects of glutargin and erbisol in patients of this group are characterized by a

  20. Article Including Environmental Barrier Coating System

    NASA Technical Reports Server (NTRS)

    Lee, Kang N. (Inventor)

    2015-01-01

    An enhanced environmental barrier coating for a silicon containing substrate. The enhanced barrier coating may include a bond coat doped with at least one of an alkali metal oxide and an alkali earth metal oxide. The enhanced barrier coating may include a composite mullite bond coat including BSAS and another distinct second phase oxide applied over said surface.

  1. Protein Crosslinking by Genetically Encoded Noncanonical Amino Acids with Reactive Aryl Carbamate Side Chains.

    PubMed

    Xuan, Weimin; Shao, Sida; Schultz, Peter G

    2017-04-03

    The use of genetically encoded noncanonical amino acids (ncAAs) to construct crosslinks within or between proteins has emerged as a useful method to enhance protein stability, investigate protein-protein interactions, and improve the pharmacological properties of proteins. We report ncAAs with aryl carbamate side chains (PheK and FPheK) that can react with proximal nucleophilic residues to form intra- or intermolecular protein crosslinks. We evolved a pyrrolysyl-tRNA synthetase that incorporates site-specifically PheK and FPheK into proteins in both E. coli and mammalian cells. PheK and FPheK when incorporated into proteins showed good stability during protein expression and purification. FPheK reacted with adjacent Lys, Cys, and Tyr residues in thioredoxin in high yields. In addition, crosslinks could be formed between FPheK and Lys residue of two interacting proteins, including the heavy chain and light chain of an antibody Fab.

  2. Radiation Therapy: Additional Treatment Options

    MedlinePlus

    ... SNIPEND SNIPSTART Find A Radiation Oncologist SNIPEND Additional Treatment Options SNIPSTART A A SNIPEND Chemotherapy Medicines prescribed ... such as antibodies, to fight cancer. Novel Targeted Therapies Cancer doctors now know much more about how ...

  3. Calculators and Computers: Graphical Addition.

    ERIC Educational Resources Information Center

    Spero, Samuel W.

    1978-01-01

    A computer program is presented that generates problem sets involving sketching graphs of trigonometric functions using graphical addition. The students use calculators to sketch the graphs and a computer solution is used to check it. (MP)

  4. 78 FR 77666 - Notice and Request for Public Comment on State Requests To Include Additional Proof-of...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-12-24

    ...-Dyson, Director, Office of Research, Policy, and Programs, at (301) 563-3919 or 1-866- 747-1471 (toll... responsibilities of implementing and interpreting EAC regulations and policy, answering questions from stakeholders... Regulations and policies. State Requests to Modify State-Specific Instructions: The chief election official...

  5. 78 FR 56695 - Proposed Listing of Additional Waters To Be Included on Indiana's 2010 List of Impaired Waters...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-09-13

    ... EPA's proposed decision identifying water quality limited segments and associated pollutants in Indiana to be listed pursuant to the Clean Water Act Section 303(d)(2), and requests public comment. For... Under the Clean Water Act AGENCY: Environmental Protection Agency (EPA). ACTION: Reopening of...

  6. 78 FR 35929 - Proposed Listing of Additional Waters To Be Included on Indiana's 2010 List of Impaired Waters...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-06-14

    ... decision identifying water quality limited segments and associated pollutants in Indiana to be listed... pollution controls are not stringent enough to attain or maintain state water quality standards and for... certain water quality limited segments and associated pollutants (Table 1 in Appendix A1 of EPA's...

  7. 40 CFR 260.23 - Petitions to amend 40 CFR part 273 to include additional hazardous wastes.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... PROTECTION AGENCY (CONTINUED) SOLID WASTES (CONTINUED) HAZARDOUS WASTE MANAGEMENT SYSTEM: GENERAL Rulemaking... appropriate for the waste or category of waste; will improve management practices for the waste or category of... waste or category of waste, will improve management practices for the waste or category of......

  8. Uranium hydrogeochemical and stream sediment reconnasissance of the Trinidad NTMS Quadrangle, Colorado, including concentrations of forty-two additional elements

    SciTech Connect

    Shannon, S.S. Jr.

    1980-05-01

    Uranium and other elemental data resulting from the Hydrogeochemical and Stream Sediment Reconnaissance (HSSR) of the Trinidad National Topographic Map Series (NTMS) quadrangle, Colorado, by the Los Alamos Scientific Laboratory (LASL) are reported herein. This study was conducted as part of the United States Department of Energy's National Uranium Resource Evaluation (NURE), which is designed to provide improved estimates of the availability and economics of nuclear fuel resources and to make available to industry information for use in exploration and development of uranium resources. The HSSR data will ultimately be integrated with other NURE data (e.g., airborne radiometric surveys and geological investigations) to complete the entire NURE program. This report is a supplement to the HSSR uranium evaluation report for the Trinidad quadrange (Morris et al, 1978), which presented the field and uranium data for the 1060 water and 1240 sediment samples collected from 1768 locations in the quadrangle. The earlier report contains an evaluation of the uranium concentrations of the samples as well as descriptions of the geology, hydrology, climate, and uranium occurrences of the quadrange. This supplement presents the sediment field and uranium data again and the analyses of 42 other elements in the sediments. All uranium samples were redetermined by delayed-neutron counting (DNC) when the sediment samples were analyzed for 31 elements by neutron activation. For 99.6% of the sediment samples analyzed, the differences between the uranium contents first determined (Morris et al, 1978) and the analyses reported herein are less than 10%.

  9. 77 FR 1073 - Privacy Act of 1974; Report of an Altered System of Records, Including Addition of Routine Uses...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-01-09

    ... authorities; foreign governments/ Agencies; international organizations; and non-governmental regulatory... marketing permit for an FDA-regulated product. Records contain name, education, professional qualifications... governments/Agencies; international organizations; and non-governmental regulatory bodies of a foreign...

  10. Modification to the Joint Platform Allocation Tool (JPAT) to Include Additional Warfighting Functions. Aerial R&S Future

    DTIC Science & Technology

    2013-07-01

    initially in theater. [items] BLg ,c Identifies which groups g are available in a configuration c. [binary] UNCLASSIFIED 8 UNCLASSIFIED SATi,g...10 3.3.8. Objective and Constraints . . . . . . . . . . . . . . . . . . . . . . . . 10 3.4. Group ...13 3.4.4. New Group Generation Model formulation . . . . . . . . . . . . . . 13 UNCLASSIFIED iv UNCLASSIFIED

  11. Active mineral additives of sapropel ashes

    NASA Astrophysics Data System (ADS)

    Khomich, V. A.; Danilina, E. V.; Krivonos, O. I.; Plaksin, G. V.

    2015-01-01

    The goal of the presented research is to establish a scientific rational for the possibility of sapropel ashes usage as an active mineral additive. The research included the study of producing active mineral additives from sapropels by their thermal treatment at 850900 °C and afterpowdering, the investigation of the properties of paste matrix with an ash additive, and the study of the ash influence on the cement bonding agent. Thermogravimetric analysis and X-ray investigations allowed us to establish that while burning, organic substances are removed, clay minerals are dehydrated and their structure is broken. Sapropel ashes chemical composition was determined. An amorphous ash constituent is mainly formed from silica of the mineral sapropel part and alumosilicagels resulted from clay minerals decomposition. Properties of PC 400 and PC 500A0 sparopel ash additives were studied. Adding ashes containing Glenium plasticizer to the cement increases paste matrix strength and considerably reduces its water absorption. X-ray phase analysis data shows changes in the phase composition of the paste matrix with an ash additive. Ash additives produce a pozzolanic effect on the cement bonding agent. Besides, an ash additive due to the alumosilicagels content causes transformation from unstable calcium aluminate forms to the stable ones.

  12. Food additives and preschool children.

    PubMed

    Martyn, Danika M; McNulty, Breige A; Nugent, Anne P; Gibney, Michael J

    2013-02-01

    Food additives have been used throughout history to perform specific functions in foods. A comprehensive framework of legislation is in place within Europe to control the use of additives in the food supply and ensure they pose no risk to human health. Further to this, exposure assessments are regularly carried out to monitor population intakes and verify that intakes are not above acceptable levels (acceptable daily intakes). Young children may have a higher dietary exposure to chemicals than adults due to a combination of rapid growth rates and distinct food intake patterns. For this reason, exposure assessments are particularly important in this age group. The paper will review the use of additives and exposure assessment methods and examine factors that affect dietary exposure by young children. One of the most widely investigated unfavourable health effects associated with food additive intake in preschool-aged children are suggested adverse behavioural effects. Research that has examined this relationship has reported a variety of responses, with many noting an increase in hyperactivity as reported by parents but not when assessed using objective examiners. This review has examined the experimental approaches used in such studies and suggests that efforts are needed to standardise objective methods of measuring behaviour in preschool children. Further to this, a more holistic approach to examining food additive intakes by preschool children is advisable, where overall exposure is considered rather than focusing solely on behavioural effects and possibly examining intakes of food additives other than food colours.

  13. Pharmacokinetic and pharmacodynamic considerations for the next generation protein therapeutics

    PubMed Central

    Shah, Dhaval K.

    2015-01-01

    Increasingly sophisticated protein engineering efforts have been undertaken lately to generate protein therapeutics with desired properties. This has resulted in the discovery of the next generation of protein therapeutics, which include: engineered antibodies, immunoconjugates, bi/multi-specific proteins, antibody mimetic novel scaffolds, and engineered ligands/receptors. These novel protein therapeutics possess unique physicochemical properties and act via a unique mechanism-of-action, which collectively makes their pharmacokinetics (PK) and pharmacodynamics (PD) different than other established biological molecules. Consequently, in order to support the discovery and development of these next generation molecules, it becomes important to understand the determinants controlling their PK/PD. This review discusses the determinants that a PK/PD scientist should consider during the design and development of next generation protein therapeutics. In addition, the role of systems PK/PD models in enabling rational development of the next generation protein therapeutics is emphasized. PMID:26373957

  14. Pharmacokinetic and pharmacodynamic considerations for the next generation protein therapeutics.

    PubMed

    Shah, Dhaval K

    2015-10-01

    Increasingly sophisticated protein engineering efforts have been undertaken lately to generate protein therapeutics with desired properties. This has resulted in the discovery of the next generation of protein therapeutics, which include: engineered antibodies, immunoconjugates, bi/multi-specific proteins, antibody mimetic novel scaffolds, and engineered ligands/receptors. These novel protein therapeutics possess unique physicochemical properties and act via a unique mechanism-of-action, which collectively makes their pharmacokinetics (PK) and pharmacodynamics (PD) different than other established biological molecules. Consequently, in order to support the discovery and development of these next generation molecules, it becomes important to understand the determinants controlling their PK/PD. This review discusses the determinants that a PK/PD scientist should consider during the design and development of next generation protein therapeutics. In addition, the role of systems PK/PD models in enabling rational development of the next generation protein therapeutics is emphasized.

  15. Proteins of human milk. I. Identification of major components

    SciTech Connect

    Anderson, N.G.; Powers, M.T.; Tollaksen, S.L.

    1982-04-01

    Traditionally, human milk proteins are identified largely by reference to bovine milk. Hence, to identify the major proteins in human milk, we subjected human and bovine milk, in parallel, to high-resolution two-dimensional electrophoresis. Isoelectric precipitation at pH 4.6 was our criterion for distinguishing whey proteins from those of the casein complex. The ..cap alpha..- and..beta..-caseins were identified on the basis of relative abundance, relative molecular mass, and relative isoelectric points. No protein disappeared from ISO-DALT patterns of human milk after rennin treatment, and no new protein comparable to bovine para K-casein appeared in the BASO-DALT patterns; this suggests that K-casein is absent from human milk. The proteins identified in human milk patterns include the ..cap alpha.. and ..beta.. casein families, lactalbumin, albumin, transferrin, IgA, and lactoferrin. Numerous additional proteins seen in patterns for human milk remain to be identified.

  16. Analysis of secreted proteins.

    PubMed

    Severino, Valeria; Farina, Annarita; Chambery, Angela

    2013-01-01

    Most biological processes including growth, proliferation, differentiation, and apoptosis are coordinated by tightly regulated signaling pathways, which also involve secreted proteins acting in an autocrine and/or paracrine manner. In addition, extracellular signaling molecules affect local niche biology and influence the cross-talking with the surrounding tissues. The understanding of this molecular language may provide an integrated and broader view of cellular regulatory networks under physiological and pathological conditions. In this context, the profiling at a global level of cell secretomes (i.e., the subpopulations of a proteome secreted from the cell) has become an active area of research. The current interest in secretome research also deals with its high potential for the biomarker discovery and the identification of new targets for therapeutic strategies. Several proteomic and mass spectrometry platforms and methodologies have been applied to secretome profiling of conditioned media of cultured cell lines and primary cells. Nevertheless, the analysis of secreted proteins is still a very challenging task, because of the technical difficulties that may hamper the subsequent mass spectrometry analysis. This chapter describes a typical workflow for the analysis of proteins secreted by cultured cells. Crucial issues related to cell culture conditions for the collection of conditioned media, secretome preparation, and mass spectrometry analysis are discussed. Furthermore, an overview of quantitative LC-MS-based approaches, computational tools for data analysis, and strategies for validation of potential secretome biomarkers is also presented.

  17. Chemical methods for producing disulfide bonds in peptides and proteins to study folding regulation.

    PubMed

    Okumura, Masaki; Shimamoto, Shigeru; Hidaka, Yuji

    2014-04-01

    Disulfide bonds play a critical role in the folding of secretory and membrane proteins. Oxidative folding reactions of disulfide bond-containing proteins typically require several hours or days, and numerous misbridged disulfide isomers are often observed as intermediates. The rate-determining step in refolding is thought to be the disulfide-exchange reaction from nonnative to native disulfide bonds in folding intermediates, which often precipitate during the refolding process because of their hydrophobic properties. To overcome this, chemical additives or a disulfide catalyst, protein disulfide isomerase (PDI), are generally used in refolding experiments to regulate disulfide-coupled peptide and protein folding. This unit describes such methods in the context of the thermodynamic and kinetic control of peptide and protein folding, including (1) regulation of disulfide-coupled peptides and protein folding assisted by chemical additives, (2) reductive unfolding of disulfide-containing peptides and proteins, and (3) regulation of disulfide-coupled peptide and protein folding using PDI.

  18. Radial spoke proteins of Chlamydomonas flagella

    PubMed Central

    Yang, Pinfen; Diener, Dennis R.; Yang, Chun; Kohno, Takahiro; Pazour, Gregory J.; Dienes, Jennifer M.; Agrin, Nathan S.; King, Stephen M.; Sale, Winfield S.; Kamiya, Ritsu; Rosenbaum, Joel L.; Witman, George B.

    2007-01-01

    Summary The radial spoke is a ubiquitous component of ‘9+2’ cilia and flagella, and plays an essential role in the control of dynein arm activity by relaying signals from the central pair of microtubules to the arms. The Chlamydomonas reinhardtii radial spoke contains at least 23 proteins, only 8 of which have been characterized at the molecular level. Here, we use mass spectrometry to identify 10 additional radial spoke proteins. Many of the newly identified proteins in the spoke stalk are predicted to contain domains associated with signal transduction, including Ca2+-, AKAP- and nucleotide-binding domains. This suggests that the spoke stalk is both a scaffold for signaling molecules and itself a transducer of signals. Moreover, in addition to the recently described HSP40 family member, a second spoke stalk protein is predicted to be a molecular chaperone, implying that there is a sophisticated mechanism for the assembly of this large complex. Among the 18 spoke proteins identified to date, at least 12 have apparent homologs in humans, indicating that the radial spoke has been conserved throughout evolution. The human genes encoding these proteins are candidates for causing primary ciliary dyskinesia, a severe inherited disease involving missing or defective axonemal structures, including the radial spokes. PMID:16507594

  19. Mutations in RIT1 cause Noonan syndrome – additional functional evidence and expanding the clinical phenotype

    PubMed Central

    Koenighofer, Martin; Hung, Christina Y.; McCauley, Jacob L.; Dallman, Julia; Back, Emma J.; Mihalek, Ivana; Gripp, Karen W.; Sol-Church, Katia; Rusconi, Paolo; Zhang, Zhaiyi; Shi, Geng-Xian; Andres, Douglas A.; Bodamer, Olaf A.

    2015-01-01

    RASopathies are a clinically heterogeneous group of conditions caused by mutations in one of sixteen proteins in the RAS-MAPK pathway. Recently, mutations in RIT1 were identified as a novel cause for Noonan syndrome. Here we provide additional functional evidence for a causal role of RIT1 mutations and expand the associated phenotypic spectrum. We identified two de novo missense variants p.Met90Ile and, p.Ala57Gly. Both variants resulted in increased MEK-ERK signaling compared to wild-type, underscoring gain-of-function as the primary functional mechanism. Introduction of p.Met90Ile and p.Ala57Gly into zebrafish embryos reproduced not only aspects of the human phenotype but also revealed abnormalities of eye development, emphasizing the importance of RIT1 for spatial and temporal organization of the growing organism. In addition, we observed severe lymphedema of the lower extremity and genitalia in one patient. We provide additional evidence for a causal relationship between pathogenic mutations in RIT1, increased RAS-MAPK/MEK-ERK signaling and the clinical phenotype. The mutant RIT1 protein may possess reduced GTPase activity or a diminished ability to interact with cellular GTPase activating proteins, however the precise mechanism remains unknown. The phenotypic spectrum is likely to expand and includes lymphedema of the lower extremities in addition to nuchal hygroma. PMID:25959749

  20. Effect of additives on the purification of urease

    NASA Astrophysics Data System (ADS)

    Yu, X.; Wang, J.; Ulrich, J.

    2015-12-01

    The effect of additives on the purification of proteins was investigated. The target protein studied here is the enzyme urease. Studies on the purification of urease from jack bean meal were carried out. 32% (v/v) acetone was utilized to extract urease from the jack bean meal. Further purification by crystallization with the addition of 2-mercaptoethanol and EDTA disodium salt dehydrate was carried out. It was found out that the presence of additives can affect the selectivity of the crystallization. Increases in both purity and yield of the urease after crystallization were observed in the presence of additives, which were proven using both SDS-PAGE and activity. Urease crystals with a yield of 69.9% and a purity of 85.1% were obtained in one crystallization step in the presence of additives. Furthermore, the effect of additives on the thermodynamics and kinetics of urease crystallization was studied.

  1. [INVITED] Lasers in additive manufacturing

    NASA Astrophysics Data System (ADS)

    Pinkerton, Andrew J.

    2016-04-01

    Additive manufacturing is a topic of considerable ongoing interest, with forecasts predicting it to have major impact on industry in the future. This paper focusses on the current status and potential future development of the technology, with particular reference to the role of lasers within it. It begins by making clear the types and roles of lasers in the different categories of additive manufacturing. This is followed by concise reviews of the economic benefits and disadvantages of the technology, current state of the market and use of additive manufacturing in different industries. Details of these fields are referenced rather than expanded in detail. The paper continues, focusing on current indicators to the future of additive manufacturing. Barriers to its development, trends and opportunities in major industrial sectors, and wider opportunities for its development are covered. Evidence indicates that additive manufacturing may not become the dominant manufacturing technology in all industries, but represents an excellent opportunity for lasers to increase their influence in manufacturing as a whole.

  2. Composite Pressure Vessel Including Crack Arresting Barrier

    NASA Technical Reports Server (NTRS)

    DeLay, Thomas K. (Inventor)

    2013-01-01

    A pressure vessel includes a ported fitting having an annular flange formed on an end thereof and a tank that envelopes the annular flange. A crack arresting barrier is bonded to and forming a lining of the tank within the outer surface thereof. The crack arresting barrier includes a cured resin having a post-curing ductility rating of at least approximately 60% through the cured resin, and further includes randomly-oriented fibers positioned in and throughout the cured resin.

  3. Leptospira Protein Expression During Infection

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We are characterizing protein expression in vivo during experimental leptospirosis using immunofluorescence microscopy. Coding regions for several proteins were identified through analysis of Leptospira interrogans serovar Copenhageni and L. borgpetersenii serovar Hardjo genomes. In addition, codi...

  4. Additive manufacturing of hybrid circuits

    SciTech Connect

    Bell, Nelson S.; Sarobol, Pylin; Cook, Adam; Clem, Paul G.; Keicher, David M.; Hirschfeld, Deidre; Hall, Aaron Christopher

    2016-03-26

    There is a rising interest in developing functional electronics using additively manufactured components. Considerations in materials selection and pathways to forming hybrid circuits and devices must demonstrate useful electronic function; must enable integration; and must complement the complex shape, low cost, high volume, and high functionality of structural but generally electronically passive additively manufactured components. This article reviews several emerging technologies being used in industry and research/development to provide integration advantages of fabricating multilayer hybrid circuits or devices. First, we review a maskless, noncontact, direct write (DW) technology that excels in the deposition of metallic colloid inks for electrical interconnects. Second, we review a complementary technology, aerosol deposition (AD), which excels in the deposition of metallic and ceramic powder as consolidated, thick conformal coatings and is additionally patternable through masking. As a result, we show examples of hybrid circuits/devices integrated beyond 2-D planes, using combinations of DW or AD processes and conventional, established processes.

  5. Site-specific, covalent incorporation of Tus, a DNA-binding protein, on ionic-complementary self-assembling peptide hydrogels using transpeptidase Sortase A as a conjugation tool†Dedicated to the memory of Joachim H. G. Steinke.‡Electronic supplementary information (ESI) available: Further experimental data. See DOI: 10.1039/c3sm00131hClick here for additional data file.

    PubMed

    Piluso, Susanna; Cassell, Heather C; Gibbons, Jonathan L; Waller, Thomas E; Plant, Nick J; Miller, Aline F; Cavalli, Gabriel

    2013-08-07

    The site-specific conjugation of DNA-binding protein (Tus) to self-assembling peptide FEFEFKFKK was demonstrated. Rheology studies and TEM of the corresponding hydrogels (including PNIPAAm-containing systems) showed no significant variation in properties and hydrogel morphology compared to FEFEFKFKK. Critically, we demonstrate that Tus is accessible within the gel network displaying DNA-binding properties.

  6. Tougher Addition Polyimides Containing Siloxane

    NASA Technical Reports Server (NTRS)

    St. Clair, T. L.; Maudgal, S.

    1986-01-01

    Laminates show increased impact resistances and other desirable mechanical properties. Bismaleamic acid extended by reaction of diaminosiloxane with maleic anhydride in 1:1 molar ratio, followed by reaction with half this molar ratio of aromatic dianhydride. Bismaleamic acid also extended by reaction of diaminosiloxane with maleic anhydride in 1:2 molar ratio, followed by reaction with half this molar ratio of aromatic diamine (Michael-addition reaction). Impact resistances improved over those of unmodified bismaleimide, showing significant increase in toughness. Aromatic addition polyimides developed as both matrix and adhesive resins for applications on future aircraft and spacecraft.

  7. Evaluation of certain food additives and contaminants.

    PubMed

    2004-01-01

    This report represents the conclusions of a Joint FAO/WHO Expert Committee convened to evaluate the safety of various food additives, with a view to recommending acceptable daily intakes (ADIs) and to prepare specifications for the identity and purity of food additives. The first part of the report contains a general discussion of the principles governing the toxicological evaluation of food additives (including flavouring agents) and contaminants, assessments of intake, and the establishment and revision of specifications for food additives. A summary follows of the Committee's evaluations of toxicological and intake data on various specific food additives (alpha-amylase from Bacillus lichenformis containing a genetically engineered alpha-amylase gene from B. licheniformis, annatto extracts, curcumin, diacetyl and fatty acid esters of glycerol, D-tagatose, laccase from Myceliophthora thermophila expressed in Aspergillus oryzae, mixed xylanase, beta-glucanase enzyme preparation produced by a strain of Humicola insolens, neotame, polyvinyl alcohol, quillaia extracts and xylanase from Thermomyces lanuginosus expressed in Fusarium venenatum), flavouring agents, a nutritional source of iron (ferrous glycinate, processed with citric acid), a disinfectant for drinking-water (sodium dichloroisocyanurate) and contaminants (cadmium and methylmercury). Annexed to the report are tables summarizing the Committee's recommendations for ADIs of the food additives, recommendations on the flavouring agents considered, and tolerable intakes of the contaminants considered, changes in the status of specifications and further information requested or desired.

  8. 47 CFR 1.9005 - Included services.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... 47 Telecommunication 1 2010-10-01 2010-10-01 false Included services. 1.9005 Section 1.9005 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Spectrum Leasing Scope and Authority § 1.9005 Included services. The spectrum leasing policies and rules of this subpart apply to...

  9. 47 CFR 1.9005 - Included services.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... 47 Telecommunication 1 2013-10-01 2013-10-01 false Included services. 1.9005 Section 1.9005 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Spectrum Leasing Scope and Authority § 1.9005 Included services. The spectrum leasing policies and rules...

  10. 47 CFR 1.9005 - Included services.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... 47 Telecommunication 1 2012-10-01 2012-10-01 false Included services. 1.9005 Section 1.9005 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Grants by Random Selection Spectrum Leasing Scope and Authority § 1.9005 Included services. The spectrum leasing policies and rules...

  11. 47 CFR 1.9005 - Included services.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... 47 Telecommunication 1 2011-10-01 2011-10-01 false Included services. 1.9005 Section 1.9005 Telecommunication FEDERAL COMMUNICATIONS COMMISSION GENERAL PRACTICE AND PROCEDURE Spectrum Leasing Scope and Authority § 1.9005 Included services. The spectrum leasing policies and rules of this subpart apply to...

  12. 28 CFR 20.32 - Includable offenses.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL JUSTICE INFORMATION SYSTEMS Federal Systems and Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record information maintained in the III System and the FIRS shall include serious and/or significant adult...

  13. 28 CFR 20.32 - Includable offenses.

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL JUSTICE INFORMATION SYSTEMS Federal Systems and Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record information maintained in the III System and the FIRS shall include serious and/or significant adult...

  14. 28 CFR 20.32 - Includable offenses.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL JUSTICE INFORMATION SYSTEMS Federal Systems and Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record information maintained in the III System and the FIRS shall include serious and/or significant adult...

  15. 28 CFR 20.32 - Includable offenses.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL JUSTICE INFORMATION SYSTEMS Federal Systems and Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record information maintained in the III System and the FIRS shall include serious and/or significant adult...

  16. 28 CFR 20.32 - Includable offenses.

    Code of Federal Regulations, 2011 CFR

    2011-07-01

    ... Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL JUSTICE INFORMATION SYSTEMS Federal Systems and Exchange of Criminal History Record Information § 20.32 Includable offenses. (a) Criminal history record information maintained in the III System and the FIRS shall include serious and/or significant adult...

  17. Server-Side Includes Made Simple.

    ERIC Educational Resources Information Center

    Fagan, Jody Condit

    2002-01-01

    Describes server-side include (SSI) codes which allow Webmasters to insert content into Web pages without programming knowledge. Explains how to enable the codes on a Web server, provides a step-by-step process for implementing them, discusses tags and syntax errors, and includes examples of their use on the Web site for Southern Illinois…

  18. The grays of medical device color additives.

    PubMed

    Seidman, Brenda

    2014-01-01

    The United States' medical device color additive regulations are unknown to some, and confusing to many. This article reviews statutory language on color additives in the Federal Food, Drug, and Cosmetic Act (FFDCA), as amended, including the Delaney Clause on carcinogenicity; color additive regulatory language as it relates to medical devices in Title 21 of the Code of Federal Regulations (C.F.R.), Parts 70-82; reports on the Food and Drug Administration's (FDA's) likely current and historical practices in dealing with color additives in medical devices; and speculates on what may have given rise to decades of seemingly ad hoc color additives practices, which may now be difficult to reconstruct and satisfactorily modify. Also addressed is the Center for Devices and Radiological Health's (CDRH's) recent publicly-vetted approach to color additives in Section 7 of its April 2013 draft guidance, Use of International Standard ISO-10993, "Biological Evaluation of Medical Devices Part 1: Evaluation and Testing," which the author concludes is a change in the right direction, but which, at least in its current draft form, is not a fix to the CDRH's color additives dilemma. Lastly, the article suggests what the CDRH might consider in further developing a new approach to color additives. Such an approach would treat color additives as if they were any other potentially toxic group of chemicals, and could be fashioned in such a way that the CDRH could still satisfy the broad aspects of Congressional color additives mandates, and.yet be consistent with ISO 10993. In doing this, the CDRH would need to recommend a more directed use of its Quality System Regulation, 21 C.F.R. Part 820, for material and vendor qualification and validation in general; approach Congress for needed statutory changes; or make administrative changes. In order for any approach to be successful, whether it is a new twist on past practices, or an entirely new path forward, the FDA must, to the best of its

  19. New technology recipes include horseradish, vinegar, mushrooms

    SciTech Connect

    Bishop, J.

    1995-08-01

    Technology development for more effective environmental management continues to abound. This article contains some recent innovations in the following areas: wastewater treatment; site remediation; and air pollution control. In addition several emerging technologies address solid and hazardous waste management with techniques designed to reduce waste volume, recycle valuable materials and create new energy sources.

  20. Including School Libraries in National Bibliographic Systems.

    ERIC Educational Resources Information Center

    Dyer, Esther R.

    1979-01-01

    Considers the incorporation of school libraries and media centers into a national bibliographic system, and discusses questions pertaining to the contributions, advantages, points of access, obstacles, and international implications of such a program. A bibliography of additional readings is provided. (FM)

  1. Go! Including Movement during Routines and Transitions

    ERIC Educational Resources Information Center

    Orlowski, Marietta A.; Hart, Aaron

    2010-01-01

    Good schools for children ages 5 to 8 provide multiple opportunities for physical activity throughout the school day. Ideally, physical education, recess, extracurricular activities, and classroom activities together help ensure that children meet the recommended 60 minutes a day of structured activity and 60 of unstructured. Additionally, brief…

  2. The evolution of the protein synthesis system. I - A model of a primitive protein synthesis system

    NASA Technical Reports Server (NTRS)

    Mizutani, H.; Ponnamperuma, C.

    1977-01-01

    A model is developed to describe the evolution of the protein synthesis system. The model is comprised of two independent autocatalytic systems, one including one gene (A-gene) and two activated amino acid polymerases (O and A-polymerases), and the other including the addition of another gene (N-gene) and a nucleotide polymerase. Simulation results have suggested that even a small enzymic activity and polymerase specificity could lead the system to the most accurate protein synthesis, as far as permitted by transitions to systems with higher accuracy.

  3. The Additive Property of Energy.

    ERIC Educational Resources Information Center

    Tsaoussis, Dimitris S.

    1995-01-01

    Presents exercises that analyze the additive property of energy. Concludes that if a body has more than one component of energy depending on the same physical quantity, the body's total energy will be the algebraic sum of the components if a linear relationship exists between the energy components and that physical quantity. (JRH)

  4. Tetrasulfide extreme pressure lubricant additives

    SciTech Connect

    Gast, L.E.; Kenney, H.E.; Schwab, A.W.

    1980-08-19

    A novel class of compounds has been prepared comprising the tetrasulfides of /sup 18/C hydrocarbons, /sup 18/C fatty acids, and /sup 18/C fatty and alkyl and triglyceride esters. These tetrasulfides are useful as extreme pressure lubricant additives and show potential as replacements for sulfurized sperm whale oil.

  5. Out of bounds additive manufacturing

    SciTech Connect

    Holshouser, Chris; Newell, Clint; Palas, Sid; Love, Lonnie J.; Kunc, Vlastimil; Lind, Randall F.; Lloyd, Peter D.; Rowe, John C.; Blue, Craig A.; Duty, Chad E.; Peter, William H.; Dehoff, Ryan R.

    2013-03-01

    Lockheed Martin and Oak Ridge National Laboratory are working on an additive manufacturing system capable of manufacturing components measured not in terms of inches or feet, but multiple yards in all dimensions with the potential to manufacture parts that are completely unbounded in size.

  6. Addition of a single E2 binding site to the human papillomavirus (HPV) type 16 long control region enhances killing of HPV positive cells via HPV E2 protein-regulated herpes simplex virus type 1 thymidine kinase-mediated suicide gene therapy.

    PubMed

    Sharma, Rachna; Palefsky, Joel M

    2010-07-01

    Human papillomavirus type 16 (HPV16) is associated with the development of anogenital cancers and their precursor lesions, intraepithelial neoplasia. Treatment strategies against HPV-induced intraepithelial neoplasia are not HPV specific and mostly consist of physical removal or ablation of lesions. We had previously designed an HPV-specific approach to kill HPV-infected cells by the herpes simplex virus type 1 thymidine kinase (TK) gene driven by HPV E2 binding to E2-binding sites (E2BS) in the native HPV16 long control region. E2-induced TK expression renders the cells sensitive to the prodrug ganciclovir. To optimize this therapeutic approach, we modified the native long control region by adding variable numbers of E2BS adjacent to E2BS4, resulting in greatly increased cell death in HPV-positive cell lines with variable levels of E2 protein expression and no reduction in HPV specificity. Our results showed maximum increase in TK expression and cell killing when one additional E2BS was added adjacent to E2BS. As HPV-infected patients also exhibit variable E2 expression across lesions and within a lesion, this approach may potentiate the clinical utility of the herpes simplex virus type 1 TK/ganciclovir therapeutic approach.

  7. PCoM-DB Update: A Protein Co-Migration Database for Photosynthetic Organisms.

    PubMed

    Takabayashi, Atsushi; Takabayashi, Saeka; Takahashi, Kaori; Watanabe, Mai; Uchida, Hiroko; Murakami, Akio; Fujita, Tomomichi; Ikeuchi, Masahiko; Tanaka, Ayumi

    2016-12-22

    The identification of protein complexes is important for the understanding of protein structure and function and the regulation of cellular processes. We used blue-native PAGE and tandem mass spectrometry to identify protein complexes systematically, and built a web database, the protein co-migration database (PCoM-DB, http://pcomdb.lowtem.hokudai.ac.jp/proteins/top), to provide prediction tools for protein complexes. PCoM-DB provides migration profiles for any given protein of interest, and allows users to compare them with migration profiles of other proteins, showing the oligomeric states of proteins and thus identifying potential interaction partners. The initial version of PCoM-DB (launched in January 2013) included protein complex data for Synechocystis whole cells and Arabidopsis thaliana thylakoid membranes. Here we report PCoM-DB version 2.0, which includes new data sets and analytical tools. Additional data are included from whole cells of the pelagic marine picocyanobacterium Prochlorococcus marinus, the thermophilic cyanobacterium Thermosynechococcus elongatus, the unicellular green alga Chlamydomonas reinhardtii and the bryophyte Physcomitrella patens. The Arabidopsis protein data now include data for intact mitochondria, intact chloroplasts, chloroplast stroma and chloroplast envelopes. The new tools comprise a multiple-protein search form and a heat map viewer for protein migration profiles. Users can compare migration profiles of a protein of interest among different organelles or compare migration profiles among different proteins within the same sample. For Arabidopsis proteins, users can compare migration profiles of a protein of interest with putative homologous proteins from non-Arabidopsis organisms. The updated PCoM-DB will help researchers find novel protein complexes and estimate their evolutionary changes in the green lineage.

  8. Food additives and contaminants. An update.

    PubMed

    Newberne, P M; Conner, M W

    1986-10-15

    Food additives continue to be a source of benefits to the consuming public but there are also perceived risks. Concern for the latter in the last decade has produced a society afflicted with cancer phobia. The intentional additives including sugars, salt, corn syrup, and dextrose make up 90% of the direct additives. These, along with a limited number of familiar items make up a large proportion of the remainder of the additives. Such common ingredients as nitrates and nitrites, solanine, cyanogenetic compounds, arsenic, etc., are unavoidably consumed in the diet and with little if any evidence for public health consequences. Major concern on the part of the public in recent years has been focused on man-made chemicals which are intentionally added to foods to enhance flavors and acceptability, nutrient value, shelf life and increased availability. These include food colors, nonnutritive and low-nutrient sweeteners, (saccharin, cyclamate, aspartame); antioxidants; and nitrites. Contaminants, sometimes incorrectly included in lists of food additives, present the greatest potential threat to public health. Such contaminants as mycotoxins, nitrosamines, polychlorinated biphenyls (PCBs), pesticides, among others, provide a continuing challenge to our regulatory agencies and to public health authorities. Evidence to date indicate that these responsible for food safety are doing an admirable job, and as a society, our food supply has never been better, or safer, and, as a population, we have never been healthier. Aside from contaminants, major concerns relate to an excess of good food and to obesity. These comments should not be taken to infer that we should relax our concern and surveillance; instead more concern and surveillance should be exerted toward those uncontrolled substances such as natural plant products and alleged natural nutrients, roots, herbs, etc., which are given much credit for positive health effects, without meeting the high standards of our

  9. 47 CFR 1.9005 - Included services.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... Spectrum Leasing Scope and Authority § 1.9005 Included services. Link to an amendment published at 79 FR 48533, August 15, 2014. The spectrum leasing policies and rules of this subpart apply to the...

  10. 42 CFR 410.100 - Included services.

    Code of Federal Regulations, 2014 CFR

    2014-10-01

    ... function or dysfunction of the neuromuscular, musculoskeletal, cardiovascular and respiratory systems; and... create difficulties in communication. (e) Respiratory therapy services. (1) Respiratory therapy services... cardiopulmonary function. (2) Respiratory therapy services include the following: (i) Application of...

  11. 42 CFR 410.100 - Included services.

    Code of Federal Regulations, 2011 CFR

    2011-10-01

    ... function or dysfunction of the neuromuscular, musculoskeletal, cardiovascular and respiratory systems; and... create difficulties in communication. (e) Respiratory therapy services. (1) Respiratory therapy services... cardiopulmonary function. (2) Respiratory therapy services include the following: (i) Application of...

  12. 42 CFR 410.100 - Included services.

    Code of Federal Regulations, 2013 CFR

    2013-10-01

    ... function or dysfunction of the neuromuscular, musculoskeletal, cardiovascular and respiratory systems; and... create difficulties in communication. (e) Respiratory therapy services. (1) Respiratory therapy services... cardiopulmonary function. (2) Respiratory therapy services include the following: (i) Application of...

  13. 42 CFR 410.100 - Included services.

    Code of Federal Regulations, 2012 CFR

    2012-10-01

    ... function or dysfunction of the neuromuscular, musculoskeletal, cardiovascular and respiratory systems; and... create difficulties in communication. (e) Respiratory therapy services. (1) Respiratory therapy services... cardiopulmonary function. (2) Respiratory therapy services include the following: (i) Application of...

  14. 42 CFR 410.100 - Included services.

    Code of Federal Regulations, 2010 CFR

    2010-10-01

    ... function or dysfunction of the neuromuscular, musculoskeletal, cardiovascular and respiratory systems; and... create difficulties in communication. (e) Respiratory therapy services. (1) Respiratory therapy services... cardiopulmonary function. (2) Respiratory therapy services include the following: (i) Application of...

  15. Include Passive Solar in Your Renovations.

    ERIC Educational Resources Information Center

    Bender, Gerald F.; Probasco, Jack F.

    1981-01-01

    A checklist covers potential energy saving modifications in a building scheduled for renovation, and includes suggestions for room utilization, landscaping, and building envelope, solar control, and active system modifications. (Author)

  16. Lung Disease Including Asthma and Adult Vaccination

    MedlinePlus

    ... Healthcare Professionals Lung Disease including Asthma and Adult Vaccination Language: English Español (Spanish) Recommend on Facebook Tweet ... more about health insurance options. Learn about adult vaccination and other health conditions Asplenia Diabetes Heart Disease, ...

  17. Plant Protein and Animal Proteins: Do They Differentially Affect Cardiovascular Disease Risk?12

    PubMed Central

    Richter, Chesney K; Skulas-Ray, Ann C; Champagne, Catherine M; Kris-Etherton, Penny M

    2015-01-01

    Proteins from plant-based compared with animal-based food sources may have different effects on cardiovascular disease (CVD) risk factors. Numerous epidemiologic and intervention studies have evaluated their respective health benefits; however, it is difficult to isolate the role of plant or animal protein on CVD risk. This review evaluates the current evidence from observational and intervention studies, focusing on the specific protein-providing foods and populations studied. Dietary protein is derived from many food sources, and each provides a different composite of nonprotein compounds that can also affect CVD risk factors. Increasing the consumption of protein-rich foods also typically results in lower intakes of other nutrients, which may simultaneously influence outcomes. Given these complexities, blanket statements about plant or animal protein may be too general, and greater consideration of the specific protein food sources and the background diet is required. The potential mechanisms responsible for any specific effects of plant and animal protein are similarly multifaceted and include the amino acid content of particular foods, contributions from other nonprotein compounds provided concomitantly by the whole food, and interactions with the gut microbiome. Evidence to date is inconclusive, and additional studies are needed to further advance our understanding of the complexity of plant protein vs. animal protein comparisons. Nonetheless, current evidence supports the idea that CVD risk can be reduced by a dietary pattern that provides more plant sources of protein compared with the typical American diet and also includes animal-based protein foods that are unprocessed and low in saturated fat. PMID:26567196

  18. Plant protein and animal proteins: do they differentially affect cardiovascular disease risk?

    PubMed

    Richter, Chesney K; Skulas-Ray, Ann C; Champagne, Catherine M; Kris-Etherton, Penny M

    2015-11-01

    Proteins from plant-based compared with animal-based food sources may have different effects on cardiovascular disease (CVD) risk factors. Numerous epidemiologic and intervention studies have evaluated their respective health benefits; however, it is difficult to isolate the role of plant or animal protein on CVD risk. This review evaluates the current evidence from observational and intervention studies, focusing on the specific protein-providing foods and populations studied. Dietary protein is derived from many food sources, and each provides a different composite of nonprotein compounds that can also affect CVD risk factors. Increasing the consumption of protein-rich foods also typically results in lower intakes of other nutrients, which may simultaneously influence outcomes. Given these complexities, blanket statements about plant or animal protein may be too general, and greater consideration of the specific protein food sources and the background diet is required. The potential mechanisms responsible for any specific effects of plant and animal protein are similarly multifaceted and include the amino acid content of particular foods, contributions from other nonprotein compounds provided concomitantly by the whole food, and interactions with the gut microbiome. Evidence to date is inconclusive, and additional studies are needed to further advance our understanding of the complexity of plant protein vs. animal protein comparisons. Nonetheless, current evidence supports the idea that CVD risk can be reduced by a dietary pattern that provides more plant sources of protein compared with the typical American diet and also includes animal-based protein foods that are unprocessed and low in saturated fat.

  19. High performance, durable polymers including poly(phenylene)

    DOEpatents

    Fujimoto, Cy; Pratt, Harry; Anderson, Travis Mark

    2017-02-28

    The present invention relates to functionalized polymers including a poly(phenylene) structure. In some embodiments, the polymers and copolymers of the invention include a highly localized concentration of acidic moieties, which facilitate proton transport and conduction through networks formed from these polymers. In addition, the polymers can include functional moieties, such as electron-withdrawing moieties, to protect the polymeric backbone, thereby extending its durability. Such enhanced proton transport and durability can be beneficial for any high performance platform that employs proton exchange polymeric membranes, such as in fuel cells or flow batteries.

  20. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1,018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 11 figures.

  1. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli. 12 figs.

  2. CDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1995-03-21

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  3. cDNA encoding a polypeptide including a hevein sequence

    DOEpatents

    Raikhel, Natasha V.; Broekaert, Willem F.; Chua, Nam-Hai; Kush, Anil

    1999-05-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74-79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  4. cDNA encoding a polypeptide including a hevein sequence

    SciTech Connect

    Raikhel, N.V.; Broekaert, W.F.; Chua, N.H.; Kush, A.

    2000-07-04

    A cDNA clone (HEV1) encoding hevein was isolated via polymerase chain reaction (PCR) using mixed oligonucleotides corresponding to two regions of hevein as primers and a Hevea brasiliensis latex cDNA library as a template. HEV1 is 1018 nucleotides long and includes an open reading frame of 204 amino acids. The deduced amino acid sequence contains a putative signal sequence of 17 amino acid residues followed by a 187 amino acid polypeptide. The amino-terminal region (43 amino acids) is identical to hevein and shows homology to several chitin-binding proteins and to the amino-termini of wound-induced genes in potato and poplar. The carboxyl-terminal portion of the polypeptide (144 amino acids) is 74--79% homologous to the carboxyl-terminal region of wound-inducible genes of potato. Wounding, as well as application of the plant hormones abscisic acid and ethylene, resulted in accumulation of hevein transcripts in leaves, stems and latex, but not in roots, as shown by using the cDNA as a probe. A fusion protein was produced in E. coli from the protein of the present invention and maltose binding protein produced by the E. coli.

  5. Communications circuit including a linear quadratic estimator

    DOEpatents

    Ferguson, Dennis D.

    2015-07-07

    A circuit includes a linear quadratic estimator (LQE) configured to receive a plurality of measurements a signal. The LQE is configured to weight the measurements based on their respective uncertainties to produce weighted averages. The circuit further includes a controller coupled to the LQE and configured to selectively adjust at least one data link parameter associated with a communication channel in response to receiving the weighted averages.

  6. Gas storage materials, including hydrogen storage materials

    DOEpatents

    Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

    2014-11-25

    A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material, such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

  7. Gas storage materials, including hydrogen storage materials

    DOEpatents

    Mohtadi, Rana F; Wicks, George G; Heung, Leung K; Nakamura, Kenji

    2013-02-19

    A material for the storage and release of gases comprises a plurality of hollow elements, each hollow element comprising a porous wall enclosing an interior cavity, the interior cavity including structures of a solid-state storage material. In particular examples, the storage material is a hydrogen storage material such as a solid state hydride. An improved method for forming such materials includes the solution diffusion of a storage material solution through a porous wall of a hollow element into an interior cavity.

  8. Eddy Resolving Global Ocean Prediction including Tides

    DTIC Science & Technology

    2013-09-30

    tensor scheme reduced at supercritical slopes, and their scalar sisters, a Nycander scalar limited in shallow water , and the Jayne and St. Laurent [2001...NAVOCEANO) starting in FY14. The model will include shallow water and provide boundary conditions to finer resolution coastal models that may use HYCOM or a...latter out to 30 days in many deep water regions, including regions of high Navy interest such as the Western Pacific and the Arabian Sea/Gulf of

  9. Strategies for vascular disease prevention: the role of lipids and related markers including apolipoproteins, low-density lipoproteins (LDL)-particle size, high sensitivity C-reactive protein (hs-CRP), lipoprotein-associated phospholipase A2 (Lp-PLA₂) and lipoprotein(a) (Lp(a)).

    PubMed

    Dallmeier, Dhayana; Koenig, Wolfgang

    2014-06-01

    Considerable progress has been achieved in the treatment of dyslipidemias. However, half of cardiovascular events occur in individuals with average or low cholesterol levels and there is still a considerable residual risk with 70% of patients having an event despite statin treatment. In the era of personalized medicine there is increased interest in the incorporation of individual biomarkers in risk score algorithms in order to improve cardiovascular risk stratification followed by the prompt initiation of preventive measures. Since the 2001 third report of the National Cholesterol Education Program Expert Panel on Detection, Evaluation and Treatment on High Blood Cholesterol in Adults (ATP III) several studies have evaluated the prognostic value of lipid related biomarkers such as non-HDL-cholesterol, apolipoprotein B, apolipoprotein B/apolipoprotein A1 ratio, lipoprotein(a), lipoprotein-associated phospholipase A2, and C-reactive protein. This article tries to summarize the most recent results in this area.

  10. Additional Drive Circuitry for Piezoelectric Screw Motors

    NASA Technical Reports Server (NTRS)

    Smythe, Robert; Palmer, Dean; Gursel, Yekta; Reder, Leonard; Savedra, Raymond

    2004-01-01

    Modules of additional drive circuitry have been developed to enhance the functionality of a family of commercially available positioning motors (Picomotor . or equivalent) that provide linear motion controllable, in principle, to within increments .30 nm. A motor of this type includes a piezoelectric actuator that turns a screw. Unlike traditional piezoelectrically actuated mechanisms, a motor of this type does not rely on the piezoelectric transducer to hold position: the screw does not turn except when the drive signal is applied to the actuator.

  11. Regulation of protein turnover by heat shock proteins.

    PubMed

    Bozaykut, Perinur; Ozer, Nesrin Kartal; Karademir, Betul

    2014-12-01

    Protein turnover reflects the balance between synthesis and degradation of proteins, and it is a crucial process for the maintenance of the cellular protein pool. The folding of proteins, refolding of misfolded proteins, and also degradation of misfolded and damaged proteins are involved in the protein quality control (PQC) system. Correct protein folding and degradation are controlled by many different factors, one of the most important of which is the heat shock protein family. Heat shock proteins (HSPs) are in the class of molecular chaperones, which may prevent the inappropriate interaction of proteins and induce correct folding. On the other hand, these proteins play significant roles in the degradation pathways, including endoplasmic reticulum-associated degradation (ERAD), the ubiquitin-proteasome system, and autophagy. This review focuses on the emerging role of HSPs in the regulation of protein turnover; the effects of HSPs on the degradation machineries ERAD, autophagy, and proteasome; as well as the role of posttranslational modifications in the PQC system.

  12. The Frontiers of Additive Manufacturing

    SciTech Connect

    Grote, Christopher John

    2016-03-03

    Additive manufacturing, more commonly known as 3-D printing, has become a ubiquitous tool in science for its precise control over mechanical design. For additive manufacturing to work, a 3-D structure is split into thin 2D slices, and then different physical properties, such as photo-polymerization or melting, are used to grow the sequential layers. The level of control allows not only for devices to be made with a variety of materials: e.g. plastics, metals, and quantum dots, but to also have finely controlled structures leading to other novel properties. While 3-D printing is widely used by hobbyists for making models, it also has industrial applications in structural engineering, biological tissue scaffolding, customized electric circuitry, fuel cells, security, and more.

  13. PREFACE: Protein protein interactions: principles and predictions

    NASA Astrophysics Data System (ADS)

    Nussinov, Ruth; Tsai, Chung-Jung

    2005-06-01

    Proteins are the `workhorses' of the cell. Their roles span functions as diverse as being molecular machines and signalling. They carry out catalytic reactions, transport, form viral capsids, traverse membranes and form regulated channels, transmit information from DNA to RNA, making possible the synthesis of new proteins, and they are responsible for the degradation of unnecessary proteins and nucleic acids. They are the vehicles of the immune response and are responsible for viral entry into the cell. Given their importance, considerable effort has been centered on the prediction of protein function. A prime way to do this is through identification of binding partners. If the function of at least one of the components with which the protein interacts is known, that should let us assign its function(s) and the pathway(s) in which it plays a role. This holds since the vast majority of their chores in the living cell involve protein-protein interactions. Hence, through the intricate network of these interactions we can map cellular pathways, their interconnectivities and their dynamic regulation. Their identification is at the heart of fu