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Sample records for protein sp-b strongly

  1. A Function of Lung Surfactant Protein SP-B

    NASA Astrophysics Data System (ADS)

    Longo, M. L.; Bisagno, A. M.; Zasadzinski, J. A. N.; Bruni, R.; Waring, A. J.

    1993-07-01

    The primary function of lung surfactant is to form monolayers at the alveolar interface capable of lowering the normal surface tension to near zero. To accomplish this process, the surfactant must be capable of maintaining a coherent, tightly packed monolayer that avoids collapse during expiration. The positively charged amino-terminal peptide SP-B1-25 of lung surfactant-specific protein SP-B increases the collapse pressure of an important component of lung surfactant, palmitic acid (PA), to nearly 70 millinewtons per meter. This alteration of the PA isotherms removes the driving force for "squeeze-out" of the fatty acids from the primarily dipalmitoylphosphatidylcholine monolayers of lung surfactant. An uncharged mutant of SP-B1-25 induced little change in the isotherms, suggesting that a specific charge interaction between the cationic peptide and the anionic lipid is responsible for the stabilization. The effect of SP-B1-25 on fatty acid isotherms is remarkably similar to that of simple poly-cations, suggesting that such polymers might be useful as components of replacement surfactants for the treatment of respiratory distress syndrome.

  2. Environmental Pollutant Ozone Causes Damage to Lung Surfactant Protein B (SP-B).

    PubMed

    Hemming, Joanna M; Hughes, Brian R; Rennie, Adrian R; Tomas, Salvador; Campbell, Richard A; Hughes, Arwel V; Arnold, Thomas; Botchway, Stanley W; Thompson, Katherine C

    2015-08-25

    Lung surfactant protein B (SP-B) is an essential protein found in the surfactant fluid at the air-water interface of the lung. Exposure to the air pollutant ozone could potentially damage SP-B and lead to respiratory distress. We have studied two peptides, one consisting of the N-terminus of SP-B [SP-B(1-25)] and the other a construct of the N- and C-termini of SP-B [SP-B(1-25,63-78)], called SMB. Exposure to dilute levels of ozone (~2 ppm) of monolayers of each peptide at the air-water interface leads to a rapid reaction, which is evident from an increase in the surface tension. Fluorescence experiments revealed that this increase in surface tension is accompanied by a loss of fluorescence from the tryptophan residue at the interface. Neutron and X-ray reflectivity experiments show that, in contrast to suggestions in the literature, the peptides are not solubilized upon oxidation but rather remain at the interface with little change in their hydration. Analysis of the product material reveals that no cleavage of the peptides occurs, but a more hydrophobic product is slowly formed together with an increased level of oligomerization. We attributed this to partial unfolding of the peptides. Experiments conducted in the presence of phospholipids reveal that the presence of the lipids does not prevent oxidation of the peptides. Our results strongly suggest that exposure to low levels of ozone gas will damage SP-B, leading to a change in its structure. The implication is that the oxidized protein will be impaired in its ability to interact at the air-water interface with negatively charged phosphoglycerol lipids, thus compromising what is thought to be its main biological function. PMID:26270023

  3. Environmental Pollutant Ozone Causes Damage to Lung Surfactant Protein B (SP-B)

    PubMed Central

    2015-01-01

    Lung surfactant protein B (SP-B) is an essential protein found in the surfactant fluid at the air–water interface of the lung. Exposure to the air pollutant ozone could potentially damage SP-B and lead to respiratory distress. We have studied two peptides, one consisting of the N-terminus of SP-B [SP-B(1–25)] and the other a construct of the N- and C-termini of SP-B [SP-B(1–25,63–78)], called SMB. Exposure to dilute levels of ozone (∼2 ppm) of monolayers of each peptide at the air–water interface leads to a rapid reaction, which is evident from an increase in the surface tension. Fluorescence experiments revealed that this increase in surface tension is accompanied by a loss of fluorescence from the tryptophan residue at the interface. Neutron and X-ray reflectivity experiments show that, in contrast to suggestions in the literature, the peptides are not solubilized upon oxidation but rather remain at the interface with little change in their hydration. Analysis of the product material reveals that no cleavage of the peptides occurs, but a more hydrophobic product is slowly formed together with an increased level of oligomerization. We attributed this to partial unfolding of the peptides. Experiments conducted in the presence of phospholipids reveal that the presence of the lipids does not prevent oxidation of the peptides. Our results strongly suggest that exposure to low levels of ozone gas will damage SP-B, leading to a change in its structure. The implication is that the oxidized protein will be impaired in its ability to interact at the air–water interface with negatively charged phosphoglycerol lipids, thus compromising what is thought to be its main biological function. PMID:26270023

  4. Different modes of interaction of pulmonary surfactant protein SP-B in phosphatidylcholine bilayers.

    PubMed Central

    Cruz, A; Casals, C; Keough, K M; Pérez-Gil, J

    1997-01-01

    Pulmonary surfactant-associated protein B (SP-B) has been incorporated into vesicles of dipalmitoyl phosphatidylcholine (DPPC) or egg yolk phosphatidylcholine (PC) by two different procedures to characterize the dependence of lipid-protein interactions on the method of reconstitution. In method A the protein was dissolved in a small volume of either methanol or 60% (v/v) acetonitrile and injected into an aqueous phase containing phospholipid vesicles. In method B the vesicles were prepared by injection of a mixture of phospholipid and SP-B dissolved in methanol or aqueous acetonitrile. Both methods of reconstitution led to the extensive interaction of SP-B with PC bilayers as demonstrated by co-migration during centrifugation, marked protection against proteolysis, change in the fluorescence emission intensity of SP-B, and protection of SP-B tryptophan fluorescence from quenching by acrylamide. SP-B promoted the rapid adsorption of DPPC on an air/liquid interface irrespective of the method of protein reconstitution. However, the interfacial adsorption activity of SP-B reconstituted by method B remained stable for hours, but that of SP-B prepared by method A decreased with time. Electron microscopy showed that the injection of SP-B into an aqueous phase containing PC or DPPC vesicles (method A) induced a rapid aggregation of vesicles. By contrast, a much longer time was required for detecting vesicle aggregation when the protein was reconstituted by co-injection of SP-B and phospholipids (method B). The presence of 5% (w/w) SP-B in DPPC bilayers prepared by method B broadened the differential scanning calorimetry thermogram and decreased the enthalpy of the transition. In contrast, the injection of SP-B into preformed DPPC vesicles (method A) did not influence the gel-to-liquid phase transition of DPPC bilayers. Taken together, these results indicate that the mode and extent of interaction of SP-B with surfactant phospholipids depends on the conditions of

  5. Role of the N-Terminal Seven Residues of Surfactant Protein B (SP-B)

    PubMed Central

    Sharifahmadian, Mahzad; Sarker, Muzaddid; Palleboina, Dharamaraju; Waring, Alan J.; Walther, Frans J.; Morrow, Michael R.; Booth, Valerie

    2013-01-01

    Breathing is enabled by lung surfactant, a mixture of proteins and lipids that forms a surface-active layer and reduces surface tension at the air-water interface in lungs. Surfactant protein B (SP-B) is an essential component of lung surfactant. In this study we probe the mechanism underlying the important functional contributions made by the N-terminal 7 residues of SP-B, a region sometimes called the “insertion sequence”. These studies employed a construct of SP-B, SP-B (1–25,63–78), also called Super Mini-B, which is a 41-residue peptide with internal disulfide bonds comprising the N-terminal 7-residue insertion sequence and the N- and C-terminal helices of SP-B. Circular dichroism, solution NMR, and solid state 2H NMR were used to study the structure of SP-B (1–25,63–78) and its interactions with phospholipid bilayers. Comparison of results for SP-B (8–25,63–78) and SP-B (1–25,63–78) demonstrates that the presence of the 7-residue insertion sequence induces substantial disorder near the centre of the lipid bilayer, but without a major disruption of the overall mechanical orientation of the bilayers. This observation suggests the insertion sequence is unlikely to penetrate deeply into the bilayer. The 7-residue insertion sequence substantially increases the solution NMR linewidths, most likely due to an increase in global dynamics. PMID:24023779

  6. Infant formula alters surfactant protein A (SP-A) and SP-B expression in pulmonary epithelial cells.

    PubMed

    Chen, Maurice G; Atkins, Constance L; Bruce, Shirley R; Khan, Amir M; Liu, Yuying; Alcorn, Joseph L

    2011-09-01

    Surfactant proteins A (SP-A) and SP-B are critical in the ability of pulmonary surfactant to reduce alveolar surface tension and provide innate immunity. Aspiration of infant milk formula can lead to lung dysfunction, but direct effects of aspirated formula on surfactant protein expression in pulmonary cells have not been described. The hypothesis that infant formula alters surfactant protein homeostasis was tested in vitro by assessing surfactant protein gene expression in cultured pulmonary epithelial cell lines expressing SP-A and SP-B that were transiently exposed (6 hr) to infant formula. Steady-state levels of SP-A protein and mRNA and SP-B mRNA in human bronchiolar (NCI-H441) and mouse alveolar (MLE15) epithelial cells were reduced in a dose-dependent manner 18 hr after exposure to infant formula. SP-A mRNA levels remained reduced 42 hr after exposure, but SP-B mRNA levels increased 10-fold. Neither soy formula nor non-fat dry milk affected steady-state SP-A and SP-B mRNA levels; suggesting a role of a component of infant formula derived from cow milk. These results indicate that infant formula has a direct, dose-dependent effect to reduce surfactant protein gene expression. Ultimately, milk aspiration may potentially result in a reduced capacity of the lung to defend against environmental insults. PMID:21520433

  7. Glucocorticoid regulation of human pulmonary surfactant protein-B (SP-B) mRNA stability is independent of activated glucocorticoid receptor.

    PubMed

    Tillis, Ceá C; Huang, Helen W; Bi, Weizhen; Pan, Su; Bruce, Shirley R; Alcorn, Joseph L

    2011-06-01

    Adequate expression of surfactant protein-B (SP-B) is critical in the function of pulmonary surfactant to reduce alveolar surface tension. Expression of SP-B mRNA is restricted to specific lung-airway epithelial cells, and human SP-B mRNA stability is increased in the presence of the synthetic glucocorticoid dexamethasone (DEX). Although the mechanism of SP-B mRNA stabilization by DEX is unknown, studies suggest involvement of the glucocorticoid receptor (GR). We developed a dual-cistronic plasmid-based expression assay in which steady-state levels of SP-B mRNA, determined by Northern analysis, reproducibly reflect changes in SP-B mRNA stability. Using this assay, we found that steady-state levels of SP-B mRNA increased greater than twofold in transfected human-airway epithelial cells (A549) incubated with DEX (10(-7) M). DEX-mediated changes in SP-B mRNA levels required the presence of the SP-B mRNA 3'-untranslated region but did not require ongoing protein synthesis. The effect of DEX on SP-B mRNA levels was dose dependent, with maximal effect at 10(-7) M. DEX increased levels of SP-B mRNA in cells lacking GR, and the presence of the GR antagonist RU486 did not interfere with the effect of DEX. Surprisingly, other steroid hormones (progesterone, estradiol, and vitamin D; 10(-7) M) significantly increased SP-B mRNA levels, suggesting a common pathway of steroid hormone action on SP-B mRNA stability. These results indicate that the effect of DEX to increase SP-B mRNA stability is independent of activated GR and suggests that the mechanism is mediated by posttranscriptional or nongenomic effects of glucocorticoids. PMID:21398497

  8. Proteasome dysfunction inhibits surfactant protein gene expression in lung epithelial cells: mechanism of inhibition of SP-B gene expression.

    PubMed

    Das, Aparajita; Boggaram, Vijayakumar

    2007-01-01

    Surfactant proteins maintain lung function through their actions to reduce alveolar surface tension and control of innate immune responses in the lung. The ubiquitin proteasome pathway is responsible for the degradation of majority of intracellular proteins in eukaryotic cells, and proteasome dysfunction has been linked to the development of neurodegenerative, cardiac, and other diseases. Proteasome function is impaired in interstitial lung diseases associated with surfactant protein C (SP-C) mutation mapping to the BRICHOS domain located in the proSP-C protein. In this study we determined the effects of proteasome inhibition on surfactant protein expression in H441 and MLE-12 lung epithelial cells to understand the relationship between proteasome dysfunction and surfactant protein gene expression. Proteasome inhibitors lactacystin and MG132 reduced the levels of SP-A, SP-B, and SP-C mRNAs in a concentration-dependent manner in H441 and MLE-12 cells. In H441 cells, lactacystin and MG132 inhibition of SP-B mRNA was associated with similar decreases in SP-B protein, and the inhibition was due to inhibition of gene transcription. Proteasome inhibitors decreased thyroid transcription factor-1 (TTF-1)/Nkx2.1 DNA binding activity, and the reduced TTF-1 DNA binding activity was due to reduced expression levels of TTF-1 protein. These data indicated that the ubiquitin proteasome pathway is essential for the maintenance of surfactant protein gene expression and that disruption of this pathway inhibits surfactant protein gene expression via reduced expression of TTF-1 protein. PMID:16905641

  9. Conformational Stability of the NH2-Terminal Propeptide of the Precursor of Pulmonary Surfactant Protein SP-B

    PubMed Central

    Bañares-Hidalgo, Ángeles; Estrada, Pilar

    2016-01-01

    Assembly of pulmonary surfactant lipid-protein complexes depends on conformational changes coupled with proteolytic maturation of proSP-B, the precursor of pulmonary surfactant protein B (SP-B), along the surfactant biogenesis pathway in pneumocytes. Conformational destabilization of the N-terminal propeptide of proSP-B (SP-BN) triggers exposure of the mature SP-B domain for insertion into surfactant lipids. We have studied the conformational stability during GdmCl- or urea-promoted unfolding of SP-BN with trp fluorescence and circular dichroism spectroscopies. Binding of the intermediate states to bis-ANS suggests their molten globule-like character. ΔG0H2O was ~ 12.7 kJ·mol-1 either with urea or GdmCl. None of the thermal transitions of SP-BN detected by CD correspond to protein unfolding. Differential scanning calorimetry of SP-BN evidenced two endothermic peaks involved in oligomer dissociation as confirmed with 2 M urea. Ionic strength was relevant since at 150 mM NaCl, the process originating the endotherm at the highest temperature was irreversible (Tm2 = 108.5°C) with an activation energy of 703.8 kJ·mol-1. At 500 mM NaCl the process became reversible (Tm2 = 114.4°C) and data were fitted to the Non-two States model with two subpeaks. No free thiols in the propeptide could be titrated by DTNB with or without 5.7 M GdmCl, indicating disulfide bonds establishment. PMID:27380171

  10. Combined and Independent Action of Proteins SP-B and SP-C in the Surface Behavior and Mechanical Stability of Pulmonary Surfactant Films

    PubMed Central

    Schürch, David; Ospina, Olga L.; Cruz, Antonio; Pérez-Gil, Jesús

    2010-01-01

    The hydrophobic proteins SP-B and SP-C are essential for pulmonary surfactant function, even though they are a relatively minor component (<2% of surfactant dry mass). Despite countless studies, their specific differential action and their possible concerted role to optimize the surface properties of surfactant films have not been completely elucidated. Under conditions kept as physiologically relevant as possible, we tested the surface activity and mechanical stability of several surfactant films of varying protein composition in vitro using a captive bubble surfactometer and a novel (to our knowledge) stability test. We found that in the naturally derived surfactant lipid mixtures, surfactant protein SP-B promoted film formation and reextension to lower surface tensions than SP-C, and in particular played a vital role in sustaining film stability at the most compressed states, whereas SP-C produced no stabilization. Preparations containing both proteins together revealed a slight combined effect in enhancing film formation. These results provide a qualitative and quantitative framework for the development of future synthetic therapeutic surfactants, and illustrate the crucial need to include SP-B or an efficient SP-B analog for optimal function. PMID:21081077

  11. Experimental Study on How Human Lung Surfactant Protein SP-B1-25 is Oxidized by Ozone in the Presence of Fe(II) and Ascorbic Acid

    NASA Astrophysics Data System (ADS)

    Colussi, A. J.; Enami, S.; Hoffmann, M. R.

    2014-12-01

    We will report the results of experiments on the chemical fate of the human lung surfactant protein SP-B1-25 upon exposure to gaseous ozone in realistic aqueous media simulating the conditions prevalent in epithelial lining fluids in polluted ambient air. Our experiments consist of exposing aqueous microjets containing SP-B1-25, the natural antioxidant ascorbic acid, and the Fe2+ carried by most atmospheric fine particulates, under mild acidic conditions, such as those created by the innate lung host defense response. Reactants and the products of such interactions are detected via online electrospray ionization mass spectrometry. We will show that ascorbic acid largely inhibits the ozonation of SP-B1-25 in the absence of Fe2+, leading to the formation of an ascorbic acid ozonide (Enami et al., PNAS 2008). In the presence of Fe2+, however, the ozonide decomposes into reactive intermediates that result in the partial oxidation of SP-B1-25, presumable affecting its function as surfactant. We infer that these experimental results establish a plausible causal link for the observed synergic adverse health effects of ambient ozone and fine particulates

  12. Effect of a bovine lung surfactant protein isolate (SP-B/C) on egg phosphatidylglycerol acyl chain order in a lipid mixture with dipalmitoylphosphatidylcholine and palmitic acid.

    PubMed

    Krill, S L; Gupta, S L

    1994-04-01

    Dynamic surface tension measurements of films of a d62 1,2-dipalmitoyl-sn-glycero-3-phosphatidylcholine:L-alpha-phosphatidyl-DL - glycerol:d31 palmitic acid (d62-DPPC:EggPG:d31-PA) lipid matrix in the presence of a bovine pulmonary surfactant protein isolate (SP-B/C) demonstrate the improved surface activity over that of the lipids alone. Thus, significant interaction of the proteins with the lipid matrix is demonstrated. The effect of SP-B/C on the acyl chain order of the negatively charged EggPG within a d62-DPPC:EggPG:d31-PA lipid matrix in D2O saline was investigated in thermal perturbation Fourier transform IR spectroscopic studies. The EggPG thermotropic phase behavior was determined independently of the other lipid components with perdeuterated lipids and D2O. The data demonstrate the high degree of EggPG acyl chain disorder in the absence of the protein isolate. A broad transition occurs between 30 and 40 degrees C. The addition of the protein isolate did not alter the acyl chain order at 0.281 and 1.46 mg/mL of protein. However, alterations in the lipid carbonyl vibrational mode were observed. PMID:8046609

  13. A small key unlocks a heavy door: The essential function of the small hydrophobic proteins SP-B and SP-C to trigger adsorption of pulmonary surfactant lamellar bodies.

    PubMed

    Hobi, Nina; Giolai, Michael; Olmeda, Bárbara; Miklavc, Pika; Felder, Edward; Walther, Paul; Dietl, Paul; Frick, Manfred; Pérez-Gil, Jesus; Haller, Thomas

    2016-08-01

    The molecular basis involving adsorption of pulmonary surfactant at the respiratory air-liquid interface and the specific roles of the surfactant proteins SP-B and SP-C in this process have not been completely resolved. The reasons might be found in the largely unknown structural assembly in which surfactant lipids and proteins are released from alveolar type II cells, and the difficulties to sample, manipulate and visualize the adsorption of these micron-sized particles at an air-liquid interface under appropriate physiological conditions. Here, we introduce several approaches to overcome these problems. First, by immunofluorescence we could demonstrate the presence of SP-B and SP-C on the surface of exocytosed surfactant particles. Second, by sampling the released particles and probing their adsorptive capacity we could demonstrate a remarkably high rate of interfacial adsorption, whose rate and extent was dramatically affected by treatment with antibodies against SP-B and SP-C. The effect of both antibodies was additive and specific. Third, direct microscopy of an inverted air-liquid interface revealed that the blocking effect is due to a stabilization of the released particles when contacting the air-liquid interface, precluding their transformation and the formation of surface films. We conclude that SP-B and SP-C are acting as essential, preformed molecular keys in the initial stages of surfactant unpacking and surface film formation. We further propose that surfactant activation might be transduced by a conformational change of the surfactant proteins upon contact with surface forces acting on the air-liquid interface. PMID:27155084

  14. 3'-untranslated region of SP-B mRNA mediates inhibitory effects of TPA and TNF-alpha on SP-B expression.

    PubMed

    Pryhuber, G S; Church, S L; Kroft, T; Panchal, A; Whitsett, J A

    1994-07-01

    Surfactant protein-B (SP-B) is a small hydrophobic polypeptide that enhances spreading and stability of surfactant phospholipids in the alveolus of the lung. Decreased expression of SP-B is associated with respiratory failure in premature infants and in adult patients with acute respiratory distress syndrome (ARDS). Tumor necrosis factor-alpha (TNF-alpha) and 12-O-tetradecanoylphorbol-13 acetate (TPA) cause ARDS-like lung injury in vivo. Inhibitory effects of TPA and TNF-alpha on SP-B mRNA expression in vitro were mediated by decreased SP-B mRNA stability rather than by decreased rate of SP-B gene transcription. In the present study, a human pulmonary adenocarcinoma cell line, NCI H441-4, was stably transfected with expression vectors consisting of the thymidine kinase (TK) promotor and human growth hormone (hGH) gene, in which the hGH 3'-untranslated region (3'-UTR) was replaced by the 2.0-kb human SP-B cDNA [pTKGH(SP-B2.0)] or the 837-bp human SP-B 3'-UTR [pTKGH(SP-B.837)]. The mRNAs and cellular growth hormone protein generated from the chimeric TKGH(SP-B2.0) and TKGH(SP-B.837) genes were each inhibited by approximately 50% by TPA and TNF-alpha. Dexamethasone decreased the inhibitory effects of TPA and TNF-alpha. The inhibition of steady-state hGH-SP-B mRNA by TPA and TNF-alpha was mediated by a cis-active element located in the 3-UTR region of SP-B mRNA. PMID:8048538

  15. Palmitoylation of Pulmonary Surfactant Protein SP-C Is Critical for Its Functional Cooperation with SP-B to Sustain Compression/Expansion Dynamics in Cholesterol-Containing Surfactant Films

    PubMed Central

    Baumgart, Florian; Ospina, Olga L.; Mingarro, Ismael; Rodríguez-Crespo, Ignacio; Pérez-Gil, Jesús

    2010-01-01

    Recent data suggest that a functional cooperation between surfactant proteins SP-B and SP-C may be required to sustain a proper compression-expansion dynamics in the presence of physiological proportions of cholesterol. SP-C is a dually palmitoylated polypeptide of 4.2 kDa, but the role of acylation in SP-C activity is not completely understood. In this work we have compared the behavior of native palmitoylated SP-C and recombinant nonpalmitoylated versions of SP-C produced in bacteria to get a detailed insight into the importance of the palmitic chains to optimize interfacial performance of cholesterol-containing surfactant films. We found that palmitoylation of SP-C is not essential for the protein to promote rapid interfacial adsorption of phospholipids to equilibrium surface tensions (∼22 mN/m), in the presence or absence of cholesterol. However, palmitoylation of SP-C is critical for cholesterol-containing films to reach surface tensions ≤1 mN/m at the highest compression rates assessed in a captive bubble surfactometer, in the presence of SP-B. Interestingly, the ability of SP-C to facilitate reinsertion of phospholipids during expansion was not impaired to the same extent in the absence of palmitoylation, suggesting the existence of palmitoylation-dependent and -independent functions of the protein. We conclude that palmitoylation is key for the functional cooperation of SP-C with SP-B that enables cholesterol-containing surfactant films to reach very low tensions under compression, which could be particularly important in the design of clinical surfactants destined to replacement therapies in pathologies such as acute respiratory distress syndrome. PMID:21081071

  16. The Effect of a C-Terminal Peptide of Surfactant Protein B (SP-B) on Oriented Lipid Bilayers, Characterized by Solid-State 2H- and 31P-NMR

    PubMed Central

    Yang, Tran-Chin; McDonald, Mark; Morrow, Michael R.; Booth, Valerie

    2009-01-01

    SP-BCTERM, a cationic, helical peptide based on the essential lung surfactant protein B (SP-B), retains a significant fraction of the function of the full-length protein. Solid-state 2H- and 31P-NMR were used to examine the effects of SP-BCTERM on mechanically oriented lipid bilayer samples. SP-BCTERM modified the multilayer structure of bilayers composed of POPC, POPG, POPC/POPG, or bovine lipid extract surfactant (BLES), even at relatively low peptide concentrations. The 31P spectra of BLES, which contains ∼1% SP-B, and POPC/POPG with 1% SP-BCTERM, look very similar, supporting a similarity in lipid interactions of SP-BCTERM and its parent protein, full-length SP-B. In the model systems, although the peptide interacted with both the oriented and unoriented fractions of the lipids, it interacted differently with the two fractions, as demonstrated by differences in lipid headgroup structure induced by the peptide. On the other hand, although SP-BCTERM induced similar disruptions in overall bilayer orientation in BLES, there was no evidence of lipid headgroup conformational changes in either the oriented or the unoriented fractions of the BLES samples. Notably, in the model lipid systems the peptide did not induce the formation of small, rapidly tumbling lipid structures, such as micelles, or of hexagonal phases, the observation of which would have provided support for functional mechanisms involving peptide-induced lipid flip-flop or stabilization of curved lipid structures, respectively. PMID:19413982

  17. Lipid polymorphism induced by surfactant peptide SP-B(1-25).

    PubMed

    Farver, R Suzanne; Mills, Frank D; Antharam, Vijay C; Chebukati, Janetricks N; Fanucci, Gail E; Long, Joanna R

    2010-09-22

    Pulmonary surfactant protein B (SP-B) is an essential protein for lowering surface tension in the alveoli. SP-B(1-25), a peptide comprised of the N-terminal 25 amino-acid residues of SP-B, is known to retain much of the biological activity of SP-B. Circular dichroism has shown that when SP-B(1-25) interacts with negatively charged lipid vesicles, it contains significant helical structure for the lipid compositions and peptide/lipid ratios studied here. The effect of SP-B(1-25) on lipid organization and polymorphisms was investigated via DSC, dynamic light scattering, transmission electron microscopy, and solid-state NMR spectroscopy. At 1-3 mol% peptide and physiologic temperature, SP-B(1-25) partitions at the interface of negatively charged PC/PG lipid bilayers. In lipid mixtures containing 1-5 mol% peptide, the structure of SP-B(1-25) remains constant, but (2)H and (31)P NMR spectra show the presence of an isotropic lipid phase in exchange with the lamellar phase below the T(m) of the lipids. This behavior is observed for both DPPC/POPG and POPC/POPG lipid mixtures as well as for both the PC and PG components of the mixtures. For 1-3 mol% SP-B(1-25), a return to a single lamellar phase above the lipid mixture T(m) is observed, but for 5 mol% SP-B(1-25) a significant isotropic component is observed at physiologic temperatures for DPPC and exchange broadening is observed in (2)H and (31)P NMR spectra of the other lipid components in the two mixtures. DLS and TEM rule out the formation of micellar structures and suggest that SP-B(1-25) promotes the formation of a fluid isotropic phase. The ability of SP-B(1-25) to fuse lipid lamellae via this mechanism, particularly those enriched in DPPC, suggests a specific role for the highly conserved N-terminus of SP-B in the packing of lipid lamellae into surfactant lamellar bodies or in stabilizing multilayer structures at the air-liquid interface. Importantly, this behavior has not been seen for the other SP-B fragments of

  18. Lipid Polymorphism Induced by Surfactant Peptide SP-B1-25

    PubMed Central

    Farver, R. Suzanne; Mills, Frank D.; Antharam, Vijay C.; Chebukati, Janetricks N.; Fanucci, Gail E.; Long, Joanna R.

    2010-01-01

    Pulmonary surfactant protein B (SP-B) is an essential protein for lowering surface tension in the alveoli. SP-B1-25, a peptide comprised of the N-terminal 25 amino-acid residues of SP-B, is known to retain much of the biological activity of SP-B. Circular dichroism has shown that when SP-B1-25 interacts with negatively charged lipid vesicles, it contains significant helical structure for the lipid compositions and peptide/lipid ratios studied here. The effect of SP-B1-25 on lipid organization and polymorphisms was investigated via DSC, dynamic light scattering, transmission electron microscopy, and solid-state NMR spectroscopy. At 1-3 mol% peptide and physiologic temperature, SP-B1-25 partitions at the interface of negatively charged PC/PG lipid bilayers. In lipid mixtures containing 1-5 mol% peptide, the structure of SP-B1-25 remains constant, but 2H and 31P NMR spectra show the presence of an isotropic lipid phase in exchange with the lamellar phase below the Tm of the lipids. This behavior is observed for both DPPC/POPG and POPC/POPG lipid mixtures as well as for both the PC and PG components of the mixtures. For 1-3 mol% SP-B1-25, a return to a single lamellar phase above the lipid mixture Tm is observed, but for 5 mol% SP-B1-25 a significant isotropic component is observed at physiologic temperatures for DPPC and exchange broadening is observed in 2H and 31P NMR spectra of the other lipid components in the two mixtures. DLS and TEM rule out the formation of micellar structures and suggest that SP-B1-25 promotes the formation of a fluid isotropic phase. The ability of SP-B1-25 to fuse lipid lamellae via this mechanism, particularly those enriched in DPPC, suggests a specific role for the highly conserved N-terminus of SP-B in the packing of lipid lamellae into surfactant lamellar bodies or in stabilizing multilayer structures at the air-liquid interface. Importantly, this behavior has not been seen for the other SP-B fragments of SP-B8-25 and SP-B59

  19. Hydrophobic surfactant proteins strongly induce negative curvature.

    PubMed

    Chavarha, Mariya; Loney, Ryan W; Rananavare, Shankar B; Hall, Stephen B

    2015-07-01

    The hydrophobic surfactant proteins SP-B and SP-C greatly accelerate the adsorption of vesicles containing the surfactant lipids to form a film that lowers the surface tension of the air/water interface in the lungs. Pulmonary surfactant enters the interface by a process analogous to the fusion of two vesicles. As with fusion, several factors affect adsorption according to how they alter the curvature of lipid leaflets, suggesting that adsorption proceeds via a rate-limiting structure with negative curvature, in which the hydrophilic face of the phospholipid leaflets is concave. In the studies reported here, we tested whether the surfactant proteins might promote adsorption by inducing lipids to adopt a more negative curvature, closer to the configuration of the hypothetical intermediate. Our experiments used x-ray diffraction to determine how the proteins in their physiological ratio affect the radius of cylindrical monolayers in the negatively curved, inverse hexagonal phase. With binary mixtures of dioleoylphosphatidylethanolamine (DOPE) and dioleoylphosphatidylcholine (DOPC), the proteins produced a dose-related effect on curvature that depended on the phospholipid composition. With DOPE alone, the proteins produced no change. With an increasing mol fraction of DOPC, the response to the proteins increased, reaching a maximum 50% reduction in cylindrical radius at 5% (w/w) protein. This change represented a doubling of curvature at the outer cylindrical surface. The change in spontaneous curvature, defined at approximately the level of the glycerol group, would be greater. Analysis of the results in terms of a Langmuir model for binding to a surface suggests that the effect of the lipids is consistent with a change in the maximum binding capacity. Our findings show that surfactant proteins can promote negative curvature, and support the possibility that they facilitate adsorption by that mechanism. PMID:26153706

  20. Kraft lignin biodegradation by Novosphingobium sp. B-7 and analysis of the degradation process.

    PubMed

    Chen, Yuehui; Chai, Liyuan; Tang, Chongjian; Yang, Zhihui; Zheng, Yu; Shi, Yan; Zhang, Huan

    2012-11-01

    This study focused on the biodegradation of kraft lignin (KL) by Novosphingobium sp. B-7 using KL as sole carbon source. Results revealed that Novosphingobium sp. B-7 reduced the chemical oxygen demand (COD) by 34.7% in KL mineral salt medium after 7days of incubation. Additionally, the maximum activities of manganese peroxidase (MnP) of 3229.8Ul(-1) and laccase (Lac) of 1275Ul(-1) were observed at 4th and 5th day, respectively. GC-MS analysis indicated that after incubated with Novosphingobium sp. B-7, low molecular weight alcohols and lignin-related monomer compounds such as ethanediol, p-hydroxy benzoic acid and vanillic acid were formed in the system, which strongly confirmed the degradation of KL by Novosphingobium sp. B-7. PMID:22921251

  1. Transcriptional regulation of SP-B gene expression by nitric oxide in H441 lung epithelial cells.

    PubMed

    Boggaram, Vijay; Chandru, Hemakumar; Gottipati, Koteswara Rao; Thakur, Vijayander; Das, Aparajita; Berhane, Kiflu

    2010-08-01

    Surfactant protein B (SP-B) is essential for the surface tension-lowering function of pulmonary surfactant. Surfactant dysfunction and reduced SP-B levels are associated with elevated nitric oxide (NO) in inflammatory lung diseases, such as acute respiratory distress syndrome. We previously found that NO donors decreased SP-B expression in H441 and MLE-12 lung epithelial cells by reducing SP-B promoter activity. In this study, we determined the roles of DNA elements and interacting transcription factors necessary for NO inhibition of SP-B promoter activity in H441 cells. We found that the NO donor diethylenetriamine-nitric oxide adduct (DETA-NO) decreased SP-B promoter thyroid transcription factor 1 (TTF-1), hepatocyte nuclear factor 3 (HNF-3), and Sp1 binding activities but increased activator protein 1 (AP-1) binding activity. DETA-NO decreased TTF-1, but not Sp1, levels, suggesting that reduced TTF-1 expression contributes to reduced TTF-1 binding activity. Lack of effect on Sp1 levels suggested that DETA-NO inhibits Sp1 binding activity per se. Overexpression of Sp1, but not TTF-1, blocked DETA-NO inhibition of SP-B promoter activity. DETA-NO inhibited SP-B promoter induction by exogenous TTF-1 without altering TTF-1 levels. DETA-NO decreased TTF-1 mRNA levels and gene transcription rate, indicating that DETA-NO inhibits TTF-1 expression at the transcriptional level. We conclude that NO inhibits SP-B promoter by decreasing TTF-1, Sp1, and HNF-3 binding activities and increasing AP-1 binding activity. NO inhibits TTF-1 levels and activity to decrease SP-B expression. NO inhibition of SP-B expression could be a mechanism by which surfactant dysfunction occurs in inflammatory lung diseases. PMID:20418387

  2. DIFFERENTIAL SUSCEPTIBILITY OF HUMAN SP-B GENETIC VARIANTS ON LUNG INJURY CAUSED BY BACTERIAL PNEUMONIA AND THE EFFECT OF A CHEMICALLY MODIFIED CURCUMIN.

    PubMed

    Xu, Yongan; Ge, Lin; Abdel-Razek, Osama; Jain, Sumeet; Liu, Zhiyong; Hong, Yucai; Nieman, Gary; Johnson, Francis; Golub, Lorne M; Cooney, Robert N; Wang, Guirong

    2016-04-01

    Staphylococcus aureus is a common cause of nosocomial pneumonia frequently resulting in acute respiratory distress syndrome (ARDS). Surfactant protein B (SP-B) gene expresses two proteins involved in lowering surface tension and host defense. Genotyping studies demonstrate a significant association between human SP-B genetic variants and ARDS. Curcumins have been shown to attenuate host inflammation in many sepsis models. Our hypothesis is that functional differences of SP-B variants and treatment with curcumin (CMC2.24) modulate lung injury in bacterial pneumonia. Humanized transgenic mice, expressing either SP-B T or C allele without mouse SP-B gene, were used. Bioluminescent labeled S. aureus Xen 36 (50 μL) was injected intratracheally to cause pneumonia. Infected mice received daily CMC2.24 (40 mg/kg) or vehicle alone by oral gavage. Dynamic changes of bacteria were monitored using in vivo imaging system. Histological, cellular, and molecular indices of lung injury were studied in infected mice 48 h after infection. In vivo imaging analysis revealed total flux (bacterial number) was higher in the lung of infected SP-B-C mice compared with infected SP-B-T mice (P < 0.05). Infected SP-B-C mice demonstrated increased mortality, lung injury, apoptosis, and NF-κB expression compared with infected SP-B-T mice. Compared with controls, CMC2.24 treatment significantly reduced the following: mortality, total bacterial flux and lung tissue apoptosis, inflammatory cells, NF-κB expression (P < 0.05), and MMPs-2, -9, -12 activities (P < 0.05). We conclude that mice with SP-B-C allele are more susceptible to S. aureus pneumonia than mice with SP-B-T allele, and that CMC2.24 attenuates lung injury thus reducing mortality. PMID:26863117

  3. Membrane-Mediated Interaction between Strongly Anisotropic Protein Scaffolds

    PubMed Central

    Schweitzer, Yonatan; Kozlov, Michael M.

    2015-01-01

    Specialized proteins serve as scaffolds sculpting strongly curved membranes of intracellular organelles. Effective membrane shaping requires segregation of these proteins into domains and is, therefore, critically dependent on the protein-protein interaction. Interactions mediated by membrane elastic deformations have been extensively analyzed within approximations of large inter-protein distances, small extents of the protein-mediated membrane bending and small deviations of the protein shapes from isotropic spherical segments. At the same time, important classes of the realistic membrane-shaping proteins have strongly elongated shapes with large and highly anisotropic curvature. Here we investigated, computationally, the membrane mediated interaction between proteins or protein oligomers representing membrane scaffolds with strongly anisotropic curvature, and addressed, quantitatively, a specific case of the scaffold geometrical parameters characterizing BAR domains, which are crucial for membrane shaping in endocytosis. In addition to the previously analyzed contributions to the interaction, we considered a repulsive force stemming from the entropy of the scaffold orientation. We computed this interaction to be of the same order of magnitude as the well-known attractive force related to the entropy of membrane undulations. We demonstrated the scaffold shape anisotropy to cause a mutual aligning of the scaffolds and to generate a strong attractive interaction bringing the scaffolds close to each other to equilibrium distances much smaller than the scaffold size. We computed the energy of interaction between scaffolds of a realistic geometry to constitute tens of kBT, which guarantees a robust segregation of the scaffolds into domains. PMID:25710602

  4. Strong Keratin-like Nanofibers Made of Globular Protein

    NASA Astrophysics Data System (ADS)

    Dror, Yael; Makarov, Vadim; Admon, Arie; Zussman, Eyal

    2008-03-01

    Protein fibers as elementary structural and functional elements in nature inspire the engineering of protein-based products for versatile bio-medical applications. We have recently used the electrospinning process to fabricate strong sub-micron fibers made solely of serum albumin (SA). This raises the challenges of turning a globular non-viscous protein solution into a polymer--like spinnable solution and producing keratin-like fibers enriched in inter S-S bridges. A stable spinning process was achieved by using SA solution in a rich trifluoroethanol-water mixture with β-mercaptoethanol. The breakage of the intra disulfide bridges, as identified by mass spectrometry, together with the denaturing alcohol, enabled a pronounced expansion of the protein. This in turn, affects the rheological properties of the solution. X-ray diffraction pattern of the fibers revealed equatorial orientation, indicating the alignment of structures along the fiber axis. The mechanical properties reached remarkable average values (Young's modulus of 1.6GPa, and max stress of 36MPa) as compared to other fibrous protein nanofibers. These significant results are attributed to both the alignment and inter disulfide bonds (cross linking) that were formed by spontaneous post-spinning oxidation.

  5. Depolymerization and decolorization of kraft lignin by bacterium Comamonas sp. B-9.

    PubMed

    Chai, Li-yuan; Chen, Yue-hui; Tang, Chong-jian; Yang, Zhi-hui; Zheng, Yu; Shi, Yan

    2014-02-01

    There is no commercial or industrial-scale process for the remediation of black liquor using microorganisms to date. One of the most important causes is that most microorganisms are not able to use lignin as their principal metabolic carbon or energy source. The bacterial strain Comamonas sp. B-9 has shown remarkable ability to degrade kraft lignin and decolorize black liquor using lignin as its principal metabolic carbon and energy source. This report looks at the depolymerization and decolorization of kraft lignin by Comamonas sp. B-9. The degradation, decolorization, and total carbon removal reached 45, 54, and 47.3%, respectively, after 7 days treatment. Comamonas sp. B-9 was capable of depolymerizing kraft lignin effectively as analyzed by gel permeation chromatography and decolorization via degrading benzene ring structures as shown using Fourier transform infrared spectroscopy analysis. PMID:23948726

  6. [Clinical, biological and genetic heterogeneity of the inborn errors of pulmonary surfactant metabolism: SP-B deficiency and alveolar proteinosis].

    PubMed

    Tredano, M; Blic, J D; Griese, M; Fournet, J C; Elion, J; Bahuau, M

    2001-01-01

    Pulmonary surfactant is a multimolecular complex located at the air-water interface within the alveolus and to which a bulk of functions has been assigned, physical (surface-active properties) as well as immune or depurant. This complex consists of a surface active lipid layer (mainly phospholipids), and of an aqueous subphase. From discrete surfactant sub-fractions, one can isolate very hydrophobic proteins SP-B and SP-C as well as the collectins SP-A and SP-D, which were shown to have structural, metabolic, or defensive properties. Inborn or acquired abnormalities of surfactant, qualitative or quantitative in nature, account for a number human diseases. Beside hyaline membrane disease of the preterm neonate, a cluster of hereditary or acquired lung diseases have been characterized by the storage of periodic acid Schiff-positive material filling the alveoli. From this heterogeneous nosologic bulk, at least two discrete entities presently seem to emerge: 1) SP-B deficiency, in which an essentially proteinaceous material is stored within the alveoli, and which is a bona fide autosomal recessive Mendelian entity linked to the SFTPB gene (MIM 1786640), generally entailing neonatal respiratory distress with rapid fatal outcome, although partial or transient deficiencies have also been observed; 2) alveolar proteinosis, characterized by the storage of a mixed, protein and lipid material, and which constitutes a relatively heterogeneous clinical biological syndrome, with regards to age at onset (from the neonate through to adulthood) as well as the severity of associated signs. Murine models with a targeted mutation of the gene encoding GM-CSF (Csfgm) or the beta subunit of its receptor (Il3rbl) support the hypothesis of an abnormality of surfactant turnover in which the alveolar macrophage would be a key player. Beside SP-B deficiency, in which a near-consensus diagnostic chart can be designed, the ascertainment of other abnormalities of surfactant metabolism is not

  7. Environmentally safe treatment of black liquor with Comamonas sp. B-9 under high-alkaline conditions.

    PubMed

    Zheng, Yu; Chai, Liyuan; Yang, Zhihui; Chen, Yuehui; Shi, Yan; Wang, Yangyang

    2014-02-01

    The strain Comamonas sp. B-9 was isolated from steeping fluid of erosive bamboo slips derived from Kingdom Wu during the Three-Kingdoms Dynasty of ancient China (A.D. 220-280). It could be used to treat black liquor (BL) with high-alkaline pH and with an initial chemical oxygen demand (COD) of 18,000-25,000 mg L(-1) , without the addition of other carbon and nitrogen sources. The results revealed that Comamonas sp. B-9 was capable of reducing the COD, color, and lignin content of BL by up to 56.8, 35.3, and 43.5%, respectively. High levels of laccase, manganese peroxidase, cellulase, and xylanase enzymatic activities were also observed, and these enzymes could play an important role in the biotreatment of BL. Further, GC-MS analysis showed that most of the compounds detected in BL after biotreatment with Comamonas sp. B-9 were diminished, while 4-methyl benzaldehyde, 3,4,5-trihydroxybenzoic acid ethyl ester, and 4-hydroxy-3,5-dimethoxy benzaldehyde were produced as metabolites. The presented results indicate that Comamonas sp. B-9 has potential application for the treatment of wastewaters from pulp and paper processing with high COD load under high-alkaline conditions. PMID:23553551

  8. Metabolic networks and bioenergetics of Aurantiochytrium sp. B-072 during storage lipid formation

    PubMed Central

    Chaisawang, Montri; Verduyn, Cornelis; Chauvatcharin, Somchai; Suphantharika, Manop

    2012-01-01

    Baffled shake flask cultivation of Aurantiochytrium sp. B-072 was carried out at in a glucose-monosodium glutamate mineral medium at different C/N-ratios (30–165) with glucose fixed at 90 g/L. With increasing C/N-ratio, a modest increase in lipid content (60 to 73 % w/w) was observed whereas fat-free biomass decreased but overall biomass showed little variation. FA-profiles were not affected to a large extent by C/N-ratio and absolute docosahexaenoic (DHA)-levels fell in narrow range (5–6 g/L). However at C/N > 64 a rapid decrease in lipid synthetic rate and/or incomplete glucose utilization occurred. Glucose and FA-fluxes based on fat-free biomass peaked at a C/N ratio of 56. This condition was chosen for calculation of the redox balance (NAD(P)H) and energy (ATP) requirement and to estimate the in vivo P/O ratio during the main period of fatty acid biosynthesis. Several models with different routes for NADPH, acetyl-CoA formation and re-oxidation of OAA formed via ATP-citrate lyase were considered as these influence the redox- and energy balance. As an example, using a commonly shown scheme whereby NADPH is supplied by a cytosolic “transhydrogenase cycle” (pyruvate-OAA-malate-pyruvate) and OAA formed by ATP-citrate lyase is recycled via import into the mitochondria as malate, the calculated NADPH-requirement amounted to 5.5 with an ATP-demand of 10.5 mmol/(g fat-free biomass x h) and an in vivo P/O-ratio (not including non-growth associated maintenance) of 1.6. The lowest ATP requirement is found when acetyl-CoA would be transported directly from the mitochondria to the cytosol by carnitine acetyltransferase. Assay of some enzymes critical for NADPH supply indicates that activity of glucose-6-phosphate dehydrogenase, the first enzyme in the HMP pathway, is far insufficient for the required NADPH-flux and malic enzyme must be a major source. Activity of the latter (ca. 300 mU/mg protein) far exceeds that in oleaginous fungi and yeast. PMID:24031944

  9. Synthetic surfactant containing SP-B and SP-C mimics is superior to single-peptide formulations in rabbits with chemical acute lung injury

    PubMed Central

    Hernández-Juviel, José M.; Gordon, Larry M.; Waring, Alan J.

    2014-01-01

    Background. Chemical spills are on the rise and inhalation of toxic chemicals may induce chemical acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Although the pathophysiology of ALI/ARDS is well understood, the absence of specific antidotes has limited the effectiveness of therapeutic interventions. Objectives. Surfactant inactivation and formation of free radicals are important pathways in (chemical) ALI. We tested the potential of lipid mixtures with advanced surfactant protein B and C (SP-B and C) mimics to improve oxygenation and lung compliance in rabbits with lavage- and chemical-induced ALI/ARDS. Methods. Ventilated young adult rabbits underwent repeated saline lung lavages or underwent intratracheal instillation of hydrochloric acid to induce ALI/ARDS. After establishment of respiratory failure rabbits were treated with a single intratracheal dose of 100 mg/kg of synthetic surfactant composed of 3% Super Mini-B (S-MB), a SP-B mimic, and/or SP-C33 UCLA, a SP-C mimic, in a lipid mixture (DPPC:POPC:POPG 5:3:2 by weight), the clinical surfactant Infasurf®, a bovine lung lavage extract with SP-B and C, or synthetic lipids alone. End-points consisted of arterial oxygenation, dynamic lung compliance, and protein and lipid content in bronchoalveolar lavage fluid. Potential mechanism of surfactant action for S-MB and SP-C33 UCLA were investigated with captive bubble surfactometry (CBS) assays. Results. All three surfactant peptide/lipid mixtures and Infasurf equally lowered the minimum surface tension on CBS, and also improved oxygenation and lung compliance. In both animal models, the two-peptide synthetic surfactant with S-MB and SP-C33 UCLA led to better arterial oxygenation and lung compliance than single peptide synthetic surfactants and Infasurf. Synthetic surfactants and Infasurf improved lung function further in lavage- than in chemical-induced respiratory failure, with the difference probably due to greater capillary-alveolar protein

  10. Chitin and L(+)-lactic acid production from crab (Callinectes bellicosus) wastes by fermentation of Lactobacillus sp. B2 using sugar cane molasses as carbon source.

    PubMed

    Flores-Albino, Belem; Arias, Ladislao; Gómez, Jorge; Castillo, Alberto; Gimeno, Miquel; Shirai, Keiko

    2012-09-01

    Crab wastes are employed for simultaneous production of chitin and L(+)-lactic acid by submerged fermentation of Lactobacillus sp. B2 using sugar cane molasses as carbon source. Response surface methodology was applied to design the culture media considering demineralization. Fermentations in stirred tank reactor (2L) using selected conditions produced 88% demineralization and 56% deproteinization with 34% yield of chitin and 19.5 gL(-1) of lactic acid (77% yield). The chitin purified from fermentation displayed 95% degree of acetylation and 0.81 and 1 ± 0.125% of residual ash and protein contents, respectively. PMID:22367529

  11. Synthetic surfactant containing SP-B and SP-C mimics is superior to single-peptide formulations in rabbits with chemical acute lung injury.

    PubMed

    Walther, Frans J; Hernández-Juviel, José M; Gordon, Larry M; Waring, Alan J

    2014-01-01

    Background. Chemical spills are on the rise and inhalation of toxic chemicals may induce chemical acute lung injury (ALI)/acute respiratory distress syndrome (ARDS). Although the pathophysiology of ALI/ARDS is well understood, the absence of specific antidotes has limited the effectiveness of therapeutic interventions. Objectives. Surfactant inactivation and formation of free radicals are important pathways in (chemical) ALI. We tested the potential of lipid mixtures with advanced surfactant protein B and C (SP-B and C) mimics to improve oxygenation and lung compliance in rabbits with lavage- and chemical-induced ALI/ARDS. Methods. Ventilated young adult rabbits underwent repeated saline lung lavages or underwent intratracheal instillation of hydrochloric acid to induce ALI/ARDS. After establishment of respiratory failure rabbits were treated with a single intratracheal dose of 100 mg/kg of synthetic surfactant composed of 3% Super Mini-B (S-MB), a SP-B mimic, and/or SP-C33 UCLA, a SP-C mimic, in a lipid mixture (DPPC:POPC:POPG 5:3:2 by weight), the clinical surfactant Infasurf(®), a bovine lung lavage extract with SP-B and C, or synthetic lipids alone. End-points consisted of arterial oxygenation, dynamic lung compliance, and protein and lipid content in bronchoalveolar lavage fluid. Potential mechanism of surfactant action for S-MB and SP-C33 UCLA were investigated with captive bubble surfactometry (CBS) assays. Results. All three surfactant peptide/lipid mixtures and Infasurf equally lowered the minimum surface tension on CBS, and also improved oxygenation and lung compliance. In both animal models, the two-peptide synthetic surfactant with S-MB and SP-C33 UCLA led to better arterial oxygenation and lung compliance than single peptide synthetic surfactants and Infasurf. Synthetic surfactants and Infasurf improved lung function further in lavage- than in chemical-induced respiratory failure, with the difference probably due to greater capillary-alveolar protein

  12. Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein.

    PubMed

    Gupta, Aditi; Adami, Christoph

    2016-03-01

    Epistatic interactions between residues determine a protein's adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1) using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient) condition that detects epistasis in most cases. We analyze the "fossils" of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing environment. PMID

  13. Quantitative determination of proteins based on strong fluorescence enhancement in curcumin-chitosan-proteins system.

    PubMed

    Wang, Feng; Huang, Wei; Jiang, Lingyan; Tang, Bo

    2012-03-01

    We found that the fluorescence intensity of curcumin (CU) can be highly enhanced by protein bovine serum albumin (BSA) and human serum albumin (HSA) in the presence of chitosan (CTS). Based on this finding, a new fluorimetric method to determine the concentration of protein was developed. Under optimized conditions, the enhanced intensities of fluorescence are quantitatively in proportion to the concentrations of protein in range of 0.007-100 μg·mL(-1) for BSA and 0.004-100 μg·mL(-1) for HSA at 426 nm excitation, and 0.007-100 μg·mL(-1) for BSA and 0.01-100 μg·mL(-1)for HSA at 280 nm excitation, while corresponding qualitative detection limits (S/N = 3) can lower to 3.96, 2.46, 4.56, 9.20 ng·mL(-1), respectively. The method has been successfully used for the determination of HSA in real samples. Based on resonance light scattering and UV-visible absorption spectroscopic analysis, mechanism studies suggested that the highly enhanced fluorescence of CU was resulted from synergic effects of favorable hydrophobic microenvironment provided by BSA and CTS and efficient intermolecular energy transfer between BSA and CU. Protein BSA may bind to CTS through hydrogen bonds, which causes the protein conformation to convert from β-fold to α-helix. CU can combine with the BSA-CTS complex through its center carbonyl carbon, and CTS plays a key role in promoting the energy transfer process by shortening the distance between BSA and CU. PMID:22271351

  14. Strong Selection Significantly Increases Epistatic Interactions in the Long-Term Evolution of a Protein

    PubMed Central

    Gupta, Aditi; Adami, Christoph

    2016-01-01

    Epistatic interactions between residues determine a protein’s adaptability and shape its evolutionary trajectory. When a protein experiences a changed environment, it is under strong selection to find a peak in the new fitness landscape. It has been shown that strong selection increases epistatic interactions as well as the ruggedness of the fitness landscape, but little is known about how the epistatic interactions change under selection in the long-term evolution of a protein. Here we analyze the evolution of epistasis in the protease of the human immunodeficiency virus type 1 (HIV-1) using protease sequences collected for almost a decade from both treated and untreated patients, to understand how epistasis changes and how those changes impact the long-term evolvability of a protein. We use an information-theoretic proxy for epistasis that quantifies the co-variation between sites, and show that positive information is a necessary (but not sufficient) condition that detects epistasis in most cases. We analyze the “fossils” of the evolutionary trajectories of the protein contained in the sequence data, and show that epistasis continues to enrich under strong selection, but not for proteins whose environment is unchanged. The increase in epistasis compensates for the information loss due to sequence variability brought about by treatment, and facilitates adaptation in the increasingly rugged fitness landscape of treatment. While epistasis is thought to enhance evolvability via valley-crossing early-on in adaptation, it can hinder adaptation later when the landscape has turned rugged. However, we find no evidence that the HIV-1 protease has reached its potential for evolution after 9 years of adapting to a drug environment that itself is constantly changing. We suggest that the mechanism of encoding new information into pairwise interactions is central to protein evolution not just in HIV-1 protease, but for any protein adapting to a changing environment. PMID

  15. Differential susceptibility of transgenic mice expressing human surfactant protein B genetic variants to Pseudomonas aeruginosa induced pneumonia.

    PubMed

    Ge, Lin; Liu, Xinyu; Chen, Rimei; Xu, Yongan; Zuo, Yi Y; Cooney, Robert N; Wang, Guirong

    2016-01-01

    Surfactant protein B (SP-B) is essential for lung function. Previous studies have indicated that a SP-B 1580C/T polymorphism (SNP rs1130866) was associated with lung diseases including pneumonia. The SNP causes an altered N-linked glycosylation modification at Asn129 of proSP-B, e.g. the C allele with this glycosylation site but not in the T allele. This study aimed to generate humanized SP-B transgenic mice carrying either SP-B C or T allele without a mouse SP-B background and then examine functional susceptibility to bacterial pneumonia in vivo. A total of 18 transgenic mouse founders were generated by the DNA microinjection method. These founders were back-crossed with SP-B KO mice to eliminate mouse SP-B background. Four founder lines expressing similar SP-B levels to human lung were chosen for further investigation. After intratracheal infection with 50 μl of Pseudomonas aeruginosa solution (1 × 10(6) CFU/mouse) or saline in SP-B-C, SP-B-T mice the mice were sacrificed 24 h post-infection and tissues were harvested. Analysis of surfactant activity revealed differential susceptibility between SP-B-C and SP-B-T mice to bacterial infection, e.g. higher minimum surface tension in infected SP-B-C versus infected SP-B-T mice. These results demonstrate for the first time that human SP-B C allele is more susceptible to bacterial pneumonia than SP-B T allele in vivo. PMID:26620227

  16. Effect of pH on protein adsorption capacity of strong cation exchangers with grafted layer.

    PubMed

    Wrzosek, Katarzyna; Polakovič, Milan

    2011-09-28

    The effect of pH on the static adsorption capacity of immunoglobulin G, human serum albumin, and equine myoglobin was investigated for a set of five strong cation exchangers with the grafted tentacle layer having a different ligand density. A sharp maximum of adsorption capacity with pH was observed for adsorbents with a high ligand density. The results were elucidated using the protein structure and calculations of pK(a) of ionizable groups of surface basic residues. Inverse size-exclusion experiments were carried out to understand the relation between the adsorption capacity and pore accessibility of the investigated proteins. PMID:21855072

  17. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design

    PubMed Central

    Xie, Neng-Zhong; Du, Qi-Shi; Li, Jian-Xiu; Huang, Ri-Bo

    2015-01-01

    Objectives Three strong interactions between amino acid side chains (salt bridge, cation-π, and amide bridge) are studied that are stronger than (or comparable to) the common hydrogen bond interactions, and play important roles in protein-protein interactions. Methods Quantum chemical methods MP2 and CCSD(T) are used in calculations of interaction energies and structural optimizations. Results The energies of three types of amino acid side chain interactions in gaseous phase and in aqueous solutions are calculated using high level quantum chemical methods and basis sets. Typical examples of amino acid salt bridge, cation-π, and amide bridge interactions are analyzed, including the inhibitor design targeting neuraminidase (NA) enzyme of influenza A virus, and the ligand binding interactions in the HCV p7 ion channel. The inhibition mechanism of the M2 proton channel in the influenza A virus is analyzed based on strong amino acid interactions. Conclusion (1) The salt bridge interactions between acidic amino acids (Glu- and Asp-) and alkaline amino acids (Arg+, Lys+ and His+) are the strongest residue-residue interactions. However, this type of interaction may be weakened by solvation effects and broken by lower pH conditions. (2) The cation- interactions between protonated amino acids (Arg+, Lys+ and His+) and aromatic amino acids (Phe, Tyr, Trp and His) are 2.5 to 5-fold stronger than common hydrogen bond interactions and are less affected by the solvation environment. (3) The amide bridge interactions between the two amide-containing amino acids (Asn and Gln) are three times stronger than hydrogen bond interactions, which are less influenced by the pH of the solution. (4) Ten of the twenty natural amino acids are involved in salt bridge, or cation-, or amide bridge interactions that often play important roles in protein-protein, protein-peptide, protein-ligand, and protein-DNA interactions. PMID:26339784

  18. Embedded proteins and sacrificial bonds provide the strong adhesive properties of gastroliths

    NASA Astrophysics Data System (ADS)

    Thormann, Esben; MizunoPresent Address: Nihon L'Oreal, Research; Innovation Center, 3-2-1 Sakado, Takatsu, Kawasaki, Kanagawa, Japan., Hiroyasu; Jansson, Kjell; Hedin, Niklas; Fernández, M. Soledad; Arias, José Luis; Rutland, Mark W.; PaiPresent Address: CenterFunctional Nanomaterials, Brookhaven National Laboratory, 735 Brookhaven Avenue, Upton, New York 11973., Ranjith Krishna; Bergström, Lennart

    2012-06-01

    The adhesive properties of gastroliths from a freshwater crayfish (Cherax quadricarinatus) were quantified by colloidal probe atomic force microscopy (AFM) between heavily demineralized gastrolith microparticles and gastrolith substrates of different composition. Combined AFM and transmission electron microscopy studies demonstrated that the sequential detachment and large adhesion energies that characterise the adhesive behaviour of a native gastrolith substrate are dominated by sacrificial bonds between chitin fibres and between chitin fibres and CaCO3. The sacrificial bonds were shown to be strongly related to the gastrolith proteins and when the majority of these proteins were removed by ethylenediaminetetraacetic acid (EDTA), the sequential detachment disappeared and the adhesive energy was reduced by more than two orders of magnitude.The adhesive properties of gastroliths from a freshwater crayfish (Cherax quadricarinatus) were quantified by colloidal probe atomic force microscopy (AFM) between heavily demineralized gastrolith microparticles and gastrolith substrates of different composition. Combined AFM and transmission electron microscopy studies demonstrated that the sequential detachment and large adhesion energies that characterise the adhesive behaviour of a native gastrolith substrate are dominated by sacrificial bonds between chitin fibres and between chitin fibres and CaCO3. The sacrificial bonds were shown to be strongly related to the gastrolith proteins and when the majority of these proteins were removed by ethylenediaminetetraacetic acid (EDTA), the sequential detachment disappeared and the adhesive energy was reduced by more than two orders of magnitude. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30536d

  19. Discovery of a super-strong promoter enables efficient production of heterologous proteins in cyanobacteria.

    PubMed

    Zhou, Jie; Zhang, Haifeng; Meng, Hengkai; Zhu, Yan; Bao, Guanhui; Zhang, Yanping; Li, Yin; Ma, Yanhe

    2014-01-01

    Cyanobacteria are oxygenic photosynthetic prokaryotes that play important roles in the global carbon cycle. Recently, engineered cyanobacteria capable of producing various small molecules from CO2 have been developed. However, cyanobacteria are seldom considered as factories for producing proteins, mainly because of the lack of efficient strong promoters. Here, we report the discovery and verification of a super-strong promoter P(cpc560), which contains two predicted promoters and 14 predicted transcription factor binding sites (TFBSs). Using P(cpc560), functional proteins were produced at a level of up to 15% of total soluble protein in the cyanobacterium Synechocystis sp. 6803, a level comparable to that produced in Escherichia coli. We demonstrated that the presence of multiple TFBSs in P(cpc560) is crucial for its promoter strength. Genetically transformable cyanobacteria neither have endotoxins nor form inclusion bodies; therefore, P(cpc560) opens the possibility to use cyanobacteria as alternative hosts for producing heterogeneous proteins from CO2 and inorganic nutrients. PMID:24675756

  20. General Strategy for the Bioorthogonal Incorporation of Strongly Absorbing, Solvation-Sensitive Infrared Probes into Proteins

    PubMed Central

    2015-01-01

    A high-sensitivity metal-carbonyl-based IR probe is described that can be incorporated into proteins or other biomolecules in very high yield via Click chemistry. A two-step strategy is demonstrated. First, a methionine auxotroph is used to incorporate the unnatural amino acid azidohomoalanine at high levels. Second, a tricarbonyl (η5-cyclopentadienyl) rhenium(I) probe modified with an alkynyl linkage is coupled via the Click reaction. We demonstrate these steps using the C-terminal domain of the ribosomal protein L9 as a model system. An overall incorporation level of 92% was obtained at residue 109, which is a surface-exposed residue. Incorporation of the probe into a surface site is shown not to perturb the stability or structure of the target protein. Metal carbonyls are known to be sensitive to solvation and protein electrostatics through vibrational lifetimes and frequency shifts. We report that the frequencies and lifetimes of this probe also depend on the isotopic composition of the solvent. Comparison of the lifetimes measured in H2O versus D2O provides a probe of solvent accessibility. The metal carbonyl probe reported here provides an easy and robust method to label very large proteins with an amino-acid-specific tag that is both environmentally sensitive and a very strong absorber. PMID:24749542

  1. Immunohistochemical characteristics of surfactant proteins a, B, C and d in inflammatory and tumorigenic lung lesions of f344 rats.

    PubMed

    Yokohira, Masanao; Yamakawa, Keiko; Nakano, Yuko; Numano, Takamasa; Furukawa, Fumio; Kishi, Sosuke; Ninomiya, Fumiko; Kanie, Shohei; Hitotsumachi, Hiroko; Saoo, Kousuke; Imaida, Katsumi

    2014-10-01

    Surfactant proteins (SPs), originally known as human lung surfactants, are essential to respiratory structure and function. There are 4 subtypes, SP-A, SP-B, SP-C and SP-D, with SP-A and SP-D having immunological functions, and SP-B and SP-C having physicochemical properties that reduce the surface tension at biological interfaces. In this experiment, the expressions of SP-A, SP-B, SP-C and SP-D in lung neoplastic lesions induced by N-bis (2-hydroxypropyl) nitrosamine (DHPN) and inflammatory lesions due to quartz instillation were examined and compared immunohistochemically. Formalin fixed paraffin embedded (FFPE) lung samples featuring inflammation were obtained with a rat quartz instillation model, and neoplastic lesions, hyperplasias and adenomas, were obtained with the rat DHPN-induced lung carcinogenesis model. In the rat quartz instillation model, male 10-week old F344 rats were exposed by intratracheal instillation (IT) to quartz at a dose of 2 mg/rat suspended in saline (0.2 ml) on day 0, and sacrificed on day 28. Lung tumorigenesis in F344 male rats was initiated by DHPN in drinking water for 2 weeks, and the animals were then sacrificed in week 30. Lung proliferative lesions, hyperplasias and adenomas, were observed with DHPN, and inflammation was observed with quartz. The expressions of SP-A, SP-B, SP-C and SP-D were examined immunohistochemically. SP-B and SP-C showed strong expression in lung hyperplasias and adenomas, while SP-A and SP-D were observed in mucus or exudates in inflammatory alveoli. These results suggest the possibility that SP-B and SP-C are related to lung tumorigenesis. PMID:25378802

  2. Study of Fluid Flow Control In Protein Crystallization Using Strong Magnetic Fields

    NASA Technical Reports Server (NTRS)

    Ramachandran, N.; Leslie, F.; Ciszak, E.; Curreri, Peter A. (Technical Monitor)

    2002-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in 'microgravity', researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  3. Strong underwater adhesives made by self-assembling multi-protein nanofibres

    NASA Astrophysics Data System (ADS)

    Zhong, Chao; Gurry, Thomas; Cheng, Allen A.; Downey, Jordan; Deng, Zhengtao; Stultz, Collin M.; Lu, Timothy K.

    2014-10-01

    Many natural underwater adhesives harness hierarchically assembled amyloid nanostructures to achieve strong and robust interfacial adhesion under dynamic and turbulent environments. Despite recent advances, our understanding of the molecular design, self-assembly and structure-function relationships of these natural amyloid fibres remains limited. Thus, designing biomimetic amyloid-based adhesives remains challenging. Here, we report strong and multi-functional underwater adhesives obtained from fusing mussel foot proteins (Mfps) of Mytilus galloprovincialis with CsgA proteins, the major subunit of Escherichia coli amyloid curli fibres. These hybrid molecular materials hierarchically self-assemble into higher-order structures, in which, according to molecular dynamics simulations, disordered adhesive Mfp domains are exposed on the exterior of amyloid cores formed by CsgA. Our fibres have an underwater adhesion energy approaching 20.9 mJ m-2, which is 1.5 times greater than the maximum of bio-inspired and bio-derived protein-based underwater adhesives reported thus far. Moreover, they outperform Mfps or curli fibres taken on their own and exhibit better tolerance to auto-oxidation than Mfps at pH ≥ 7.0.

  4. Embedded proteins and sacrificial bonds provide the strong adhesive properties of gastroliths.

    PubMed

    Thormann, Esben; Mizuno, Hiroyasu; Jansson, Kjell; Hedin, Niklas; Fernández, M Soledad; Arias, José Luis; Rutland, Mark W; Pai, Ranjith Krishna; Bergström, Lennart

    2012-07-01

    The adhesive properties of gastroliths from a freshwater crayfish (Cherax quadricarinatus) were quantified by colloidal probe atomic force microscopy (AFM) between heavily demineralized gastrolith microparticles and gastrolith substrates of different composition. Combined AFM and transmission electron microscopy studies demonstrated that the sequential detachment and large adhesion energies that characterise the adhesive behaviour of a native gastrolith substrate are dominated by sacrificial bonds between chitin fibres and between chitin fibres and CaCO(3). The sacrificial bonds were shown to be strongly related to the gastrolith proteins and when the majority of these proteins were removed by ethylenediaminetetraacetic acid (EDTA), the sequential detachment disappeared and the adhesive energy was reduced by more than two orders of magnitude. PMID:22653376

  5. Global analysis of TDP-43 interacting proteins reveals strong association with RNA splicing and translation machinery

    PubMed Central

    Freibaum, Brian D.; Chitta, Raghu; High, Anthony A.; Taylor, J. Paul

    2010-01-01

    TDP-43 is a highly conserved and ubiquitously expressed member of the heterogeneous nuclear ribonucleoprotein (hnRNP) family of proteins. Recently, TDP-43 was shown to be a major disease protein in the ubiquitinated inclusions characteristic of most cases of amyotrophic lateral sclerosis (ALS), tau-negative frontotemporal lobar degeneration (FTLD), and inclusion body myopathy. In these diseases, TDP-43 is redistributed from its predominantly nuclear location to ubiquitin-positive, cytoplasmic foci. The extent to which TDP-43 drives pathophysiology is unknown, but the identification of mutations in TDP-43 in familial forms of ALS and FTLD-U suggests an important role for this protein in pathogenesis. Little is known about TDP-43 function and only a few TDP-43 interacting proteins have been previously identified, which makes further insight into both the normal and pathological functions of TDP-43 difficult. Here we show, via a global proteomic approach, that TDP-43 has extensive interaction with proteins that regulate RNA metabolism. Some interactions with TDP-43 were found to be dependent on RNA-binding, whereas other interactions are RNA-independent. Disease-causing mutations in TDP-43 (A315T and M337V) do not alter its interaction profile. TDP-43 interacting proteins largely cluster into two distinct interaction networks, a nuclear/splicing cluster and a cytoplasmic/translation cluster, strongly suggesting that TDP-43 has multiple roles in RNA metabolism and functions in both the nucleus and the cytoplasm. Finally, we found numerous TDP-43 interactors that are known components of stress granules and, indeed, we find that TDP-43 is also recruited to stress granules. PMID:20020773

  6. L233P mutation of the Tax protein strongly correlated with leukemogenicity of bovine leukemia virus.

    PubMed

    Inoue, Emi; Matsumura, Keiko; Soma, Norihiko; Hirasawa, Shintaro; Wakimoto, Mayuko; Arakaki, Yoshihiro; Yoshida, Takashi; Osawa, Yoshiaki; Okazaki, Katsunori

    2013-12-27

    The bovine leukemia virus (BLV) Tax protein is believed to play a crucial role in leukemogenesis by the virus. BLV usually causes asymptomatic infections in cattle, but only one-third develop persistent lymphocytosis that rarely progress after a long incubation period to lymphoid tumors, namely enzootic bovine leucosis (EBL). In the present study, we demonstrated that the BLV tax genes could be divided into two alleles and developed multiplex PCR detecting an L233P mutation of the Tax protein. Then, in order to define the relationship between the Tax protein and leukemogenicity, we examined 360 tumor samples randomly collected from dairy or breeding cattle in Japan, of which Tax proteins were categorized, for age at the time of diagnosis of EBL. The ages of 288 animals (80.0%) associated with L233-Tax and those of 70 animals (19.4%) with P233-Tax individually followed log-normal distributions. Only the two earliest cases (0.6%) with L233-Tax disobeyed the log-normal distribution. These findings suggest that the animals affected by EBL were infected with the virus at a particular point in life, probably less than a few months after birth. Median age of those with P233-Tax was 22 months older than that with L233-Tax and geometric means exhibited a significant difference (P<0.01). It is also quite unlikely that viruses carrying the particular Tax protein infect older cattle. Here, we conclude that BLV could be divided into two categories on the basis of amino acid at position 233 of the Tax protein, which strongly correlated with leukemogenicity. PMID:24139177

  7. The General Phosphotransferase System Proteins Localize to Sites of Strong Negative Curvature in Bacterial Cells

    PubMed Central

    Govindarajan, Sutharsan; Elisha, Yair; Nevo-Dinur, Keren; Amster-Choder, Orna

    2013-01-01

    ABSTRACT The bacterial cell poles are emerging as subdomains where many cellular activities take place, but the mechanisms for polar localization are just beginning to unravel. The general phosphotransferase system (PTS) proteins, enzyme I (EI) and HPr, which control preferential use of carbon sources in bacteria, were recently shown to localize near the Escherichia coli cell poles. Here, we show that EI localization does not depend on known polar constituents, such as anionic lipids or the chemotaxis receptors, and on the cell division machinery, nor can it be explained by nucleoid occlusion or localized translation. Detection of the general PTS proteins at the budding sites of endocytotic-like membrane invaginations in spherical cells and their colocalization with the negative curvature sensor protein DivIVA suggest that geometric cues underlie localization of the PTS system. Notably, the kinetics of glucose uptake by spherical and rod-shaped E. coli cells are comparable, implying that negatively curved “pole-like” sites support not only the localization but also the proper functioning of the PTS system in cells with different shapes. Consistent with the curvature-mediated localization model, we observed the EI protein from Bacillus subtilis at strongly curved sites in both B. subtilis and E. coli. Taken together, we propose that changes in cell architecture correlate with dynamic survival strategies that localize central metabolic systems like the PTS to subcellular domains where they remain active, thus maintaining cell viability and metabolic alertness. PMID:24129255

  8. Analysis of heat kernel highlights the strongly modular and heat-preserving structure of proteins

    NASA Astrophysics Data System (ADS)

    Livi, Lorenzo; Maiorino, Enrico; Pinna, Andrea; Sadeghian, Alireza; Rizzi, Antonello; Giuliani, Alessandro

    2016-01-01

    In this paper, we study the structure and dynamical properties of protein contact networks with respect to other biological networks, together with simulated archetypal models acting as probes. We consider both classical topological descriptors, such as modularity and statistics of the shortest paths, and different interpretations in terms of diffusion provided by the discrete heat kernel, which is elaborated from the normalized graph Laplacians. A principal component analysis shows high discrimination among the network types, by considering both the topological and heat kernel based vector characterizations. Furthermore, a canonical correlation analysis demonstrates the strong agreement among those two characterizations, providing thus an important justification in terms of interpretability for the heat kernel. Finally, and most importantly, the focused analysis of the heat kernel provides a way to yield insights on the fact that proteins have to satisfy specific structural design constraints that the other considered networks do not need to obey. Notably, the heat trace decay of an ensemble of varying-size proteins denotes subdiffusion, a peculiar property of proteins.

  9. Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

    NASA Technical Reports Server (NTRS)

    Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

    2002-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  10. Utilization of modified surfactant-associated protein B for delivery of DNA to airway cells in culture.

    PubMed Central

    Baatz, J E; Bruno, M D; Ciraolo, P J; Glasser, S W; Stripp, B R; Smyth, K L; Korfhagen, T R

    1994-01-01

    Pulmonary surfactant lines the airway epithelium and creates a potential barrier to successful transfection of the epithelium in vivo. Based on the functional properties of pulmonary surfactant protein B (SP-B) and the fact that this protein is neither toxic nor immunogenic in the airway, we hypothesized that SP-B could be modified to deliver DNA to airway cells. We have modified native bovine SP-B by the covalent linkage of poly(lysine) (average molecular mass of 3.3 or 10 kDa) to the N terminus of SP-B and formed complexes between a test plasmid and the modified SP-B. Transfection efficiency was determined by transfection of pulmonary adenocarcinoma cells (H441) in culture with the test plasmid pCPA-RSV followed by measurement of activity of the reporter gene encoding chloramphenicol acetyltransferase (CAT). Transfections were performed with DNA.protein complexes using poly(lysine)10kDa-SP-B ([Lys]10kDa-SP-B) or poly(lysine)3.3kDa-SP-B ([Lys]3.3kDa-SP-B), and results were compared with transfections using unmodified poly(lysine).DNA, unmodified SP-B.DNA, or DNA only. For [Lys]10kDa-SP-B.pCPA-RSV preparations, CAT activity was readily detectable above the background of [Lys]3.3kDa-SP-B or unmodified SP-B. The SP-B-poly(lysine) conjugates were effective over a broad range of protein-to-DNA molar ratios, although they were optimal at approximately 500:1-1000:1. Transfection efficiency varied with the tested cell line but was not specific to airway cells. Addition of replication-defective adenovirus to the [Lys]10kDa-SP-B.pCPA-RSV complex enhanced CAT activity about 30-fold with respect to that produced by the [Lys]10kDa-SP-B.pCPA-RSV complex alone. This increase suggests routing of the adenoviral.[Lys]10kDa-SP-B.pCPA-RSV complex through an endosomal pathway. Effects of covalent modification on the secondary structure of SP-B were examined by Fourier transform infrared spectrometry (FTIR). Results of FTIR indicated that the conformation of [Lys]10kDa-SP-B was

  11. Two Novel Antioxidant Nonapeptides from Protein Hydrolysate of Skate (Raja porosa) Muscle

    PubMed Central

    Hu, Fa-Yuan; Chi, Chang-Feng; Wang, Bin; Deng, Shang-Gui

    2015-01-01

    In the current study, the preparation conditions of neutrase hydrolysate (SMH) from skate (Raja porosa) muscle protein were optimized using orthogonal L9(3)4 tests, and R values indicated that pH was the most important factor affecting HO· scavenging activity of SMH. Under the optimum conditions of pH 7.0, enzymolysis temperature 60 °C, enzyme/substrate ratio (E/S) 2%, and enzymolysis time 5 h, EC50 of SMH on HO· was 2.14 ± 0.17 mg/mL. Using ultrafiltration, gel filtration chromatography, and RP-HPLC, two novel antioxidant nonapeptides (SP-A and SP-B) were isolated from SMH and their amino acid sequences were found to be APPTAYAQS (SP-A) and NWDMEKIWD (SP-B) with calculated molecular masses of 904.98 Da and 1236.38 Da, respectively. Both showed strong antioxidant activities. SP-A and SP-B exhibited good scavenging activities on HO· (EC50 0.390 and 0.176 mg/mL), DPPH· (EC50 0.614 and 0.289 mg/mL), and O2−· (EC50 0.215 and 0.132 mg/mL) in a dose-dependent manner. SP-B was also effective against lipid peroxidation in the model system. The aromatic (2Trp), acidic (2Asp and Glu), and basic (Lys) amino acid residues within the sequences of SP-B might account for its pronounced antioxidant activity. The results of this study suggested that protein hydrolysate and peptides from skate muscle might be effective as food additives for retarding lipid peroxidation occurring in foodstuffs. PMID:25854645

  12. Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

    NASA Technical Reports Server (NTRS)

    Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

    2002-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  13. Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

    NASA Astrophysics Data System (ADS)

    Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

    2002-11-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately

  14. Biochemical investigation of kraft lignin degradation by Pandoraea sp. B-6 isolated from bamboo slips.

    PubMed

    Shi, Yan; Chai, Liyuan; Tang, Chongjian; Yang, Zhihui; Zheng, Yu; Chen, Yuehui; Jing, Qingxiu

    2013-12-01

    Kraft lignin (KL) is the major pollutant in black liquor. The bacterial strain Pandoraea sp. B-6 was able to degrade KL without any co-substrate under high alkaline conditions. At least 38.2 % of chemical oxygen demand and 41.6 % of color were removed in 7 days at concentrations from 1 to 6 g L(-1). The optimum pH for KL degradation was 10 and the optimum temperature was 30 °C. The greatest activities of 2,249.2 U L(-1) for manganese peroxidase and 1,120.6 U L(-1) for laccase were detected on the third and fifth day at pH 10, respectively. Many small molecules, such as cinnamic acid, ferulic acid, 2-hydroxy benzyl alcohol, and vanillyl methyl ketone, were formed during the period of KL degradation based on GC-MS analysis. These results indicate that this strain has great potential for biotreatment of black liquor. PMID:23877715

  15. [Preparation of highly hydrophilic strong cation exchangers and their applications in protein analysis].

    PubMed

    Liu, Jizhong; Huang, Yanyan; Yang, Bo; Chang, Jianhua; Liu, Guoquan; Zhao, Rui

    2013-04-01

    Based on the needs of new packing materials for rapid and efficient separation, purification and analysis of biomacromolecules, a novel sulfonic acid-type strong cation exchange resin (SP-G-PGMA SCX resin) was prepared. The porous poly(glycidyl methacrylate) microspheres (PGMA) were selected as the matrix and glucose was used as the hydrophilic modifier to block the hydrophobic domains of PGMA beads. Glucose modification on PGMA beads improved the biocompatibility and reduced the non-specific adsorption so as to increase the recoveries of protein. The PGMA beads possess the porous structure and the relatively high specific surface area, which make the PGMA-based resins good permeability and high loading capacity. The application of such SP-G-PGMA SCX resin for the chromatographic separation of biomacromolecules was explored. Four basic proteins were baseline separated within 6 min with the column size of 100 mm x 4.6 mm. The adsorption capacity of lysozyme on SP-G-PGMA SCX resin was determined as 39.5 g/L. The results make the material promising for the separation and purification of biomacromolecules. PMID:23898627

  16. Association of Strong Immune Responses to PPE Protein Rv1168c with Active Tuberculosis ▿

    PubMed Central

    Khan, Nooruddin; Alam, Kaiser; Nair, Shiny; Valluri, Vijaya Lakshmi; Murthy, Kolluri J. R.; Mukhopadhyay, Sangita

    2008-01-01

    Accurate diagnosis of tuberculosis (TB) infection is critical for the treatment, prevention, and control of TB. Conventional diagnostic tests based on purified protein derivative (PPD) do not achieve the required diagnostic sensitivity. Therefore, in this study, we have evaluated the immunogenic properties of Rv1168c, a member of the PPE family, in comparison with PPD, which is routinely used in the tuberculin test, and Hsp60 and ESAT-6, well-known immunodominant antigens of Mycobacterium tuberculosis. In a conventional enzyme immunoassay, the recombinant Rv1168c protein displayed stronger immunoreactivity against the sera obtained from patients with clinically active TB than did PPD, Hsp60, or ESAT-6 and could distinguish TB patients from Mycobacterium bovis BCG-vaccinated controls. Interestingly, Rv1168c antigen permits diagnosis of smear-negative pulmonary TB as well as extrapulmonary TB cases, which are often difficult to diagnose by conventional tests. The immunodominant nature of Rv1168c makes it a promising candidate to use in serodiagnosis of TB. In addition, our studies also show that Rv1168c is a potent T-cell antigen which elicits a strong gamma interferon response in sensitized peripheral blood mononuclear cells obtained from TB patients. PMID:18400969

  17. Short strong hydrogen bonds in proteins: a case study of rhamnogalacturonan acetylesterase

    PubMed Central

    Langkilde, Annette; Kristensen, Søren M.; Lo Leggio, Leila; Mølgaard, Anne; Jensen, Jan H.; Houk, Andrew R.; Navarro Poulsen, Jens-Christian; Kauppinen, Sakari; Larsen, Sine

    2008-01-01

    An extremely low-field signal (at approximately 18 p.p.m.) in the 1H NMR spectrum of rhamnogalacturonan acetylesterase (RGAE) shows the presence of a short strong hydrogen bond in the structure. This signal was also present in the mutant RGAE D192N, in which Asp192, which is part of the catalytic triad, has been replaced with Asn. A careful analysis of wild-type RGAE and RGAE D192N was conducted with the purpose of identifying possible candidates for the short hydrogen bond with the 18 p.p.m. deshielded proton. Theor­etical calculations of chemical shift values were used in the interpretation of the experimental 1H NMR spectra. The crystal structure of RGAE D192N was determined to 1.33 Å resolution and refined to an R value of 11.6% for all data. The structure is virtually identical to the high-resolution (1.12 Å) structure of the wild-type enzyme except for the interactions involving the mutation and a disordered loop. Searches of the Cambridge Structural Database were conducted to obtain information on the donor–acceptor distances of different types of hydrogen bonds. The short hydrogen-bond inter­actions found in RGAE have equivalents in small-molecule structures. An examination of the short hydrogen bonds in RGAE, the calculated pK a values and solvent-accessibilities identified a buried carboxylic acid carboxylate hydrogen bond between Asp75 and Asp87 as the likely origin of the 18 p.p.m. signal. Similar hydrogen-bond interactions between two Asp or Glu carboxy groups were found in 16% of a homology-reduced set of high-quality structures extracted from the PDB. The shortest hydrogen bonds in RGAE are all located close to the active site and short interactions between Ser and Thr side-chain OH groups and backbone carbonyl O atoms seem to play an important role in the stability of the protein structure. These results illustrate the significance of short strong hydrogen bonds in proteins. PMID:18645234

  18. Glucocorticoid regulation of human pulmonary surfactant protein-B mRNA stability involves the 3'-untranslated region.

    PubMed

    Huang, Helen W; Bi, Weizhen; Jenkins, Gaye N; Alcorn, Joseph L

    2008-04-01

    Expression of pulmonary surfactant, a complex mixture of lipids and proteins that acts to reduce alveolar surface tension, is developmentally regulated and restricted to lung alveolar type II cells. The hydrophobic protein surfactant protein-B (SP-B) is essential in surfactant function, and insufficient levels of SP-B result in severe respiratory dysfunction. Glucocorticoids accelerate fetal lung maturity and surfactant synthesis both experimentally and clinically. Glucocorticoids act transcriptionally and post-transcriptionally to increase steady-state levels of human SP-B mRNA; however, the mechanism(s) by which glucocorticoids act post-transcriptionally is unknown. We hypothesized that glucocorticoids act post-transcriptionally to increase SP-B mRNA stability via sequence-specific mRNA-protein interactions. We found that glucocorticoids increase SP-B mRNA stability in isolated human type II cells and in nonpulmonary cells, but do not alter mouse SP-B mRNA stability in a mouse type II cell line. Deletion analysis of an artificially-expressed SP-B mRNA indicates that the SP-B mRNA 3'-untranslated region (UTR) is necessary for stabilization, and the region involved can be restricted to a 126-nucleotide-long region near the SP-B coding sequence. RNA electrophoretic mobility shift assays indicate that cytosolic proteins bind to this region in the absence or presence of glucocorticoids. The formation of mRNA:protein complexes is not seen in other regions of the SP-B mRNA 3'-UTR. These results indicate that a specific 126-nucleotide region of human SP-B 3'-UTR is necessary for increased SP-B mRNA stability by glucocorticoids by a mechanism that is not lung cell specific and may involve mRNA-protein interactions. PMID:18006875

  19. Surfactant protein B deficiency: insights into surfactant function through clinical surfactant protein deficiency.

    PubMed

    Thompson, M W

    2001-01-01

    Surfactant protein B (SP-B) deficiency is a disorder of surfactant function with complete or transient absence of SP-B in term neonates. SP-B, 1 of 4 described surfactant-associated proteins, plays a key role in surfactant metabolism, particularly in intracellular packaging of surfactant components, formation of tubular myelin, and the presentation of the surfactant phospholipid monolayer to the air-fluid interface within the alveolus. Neonates with clinical SP-B deficiency best demonstrate the key role of SP-B in surfactant function. "Classic" deficiency results in severe respiratory failure in term infants and death unless lung transplantation is performed. Because the initial description of complete deficiency secondary to a homozygous frameshift mutation in codon 121 of the SP-B cDNA, partial deficiencies with differing genetic backgrounds and less severe clinical courses have been reported. These partial deficiency states may provide a clearer picture of genotype/phenotype relationships in SP-B function and surfactant metabolism. SP-B deficiency or dysfunction may be more common than once thought and may play a significant role in neonatal lung disease. PMID:11202476

  20. Metabolic effects of milk protein intake strongly depend on pre-existing metabolic and exercise status.

    PubMed

    Melnik, Bodo C; Schmitz, Gerd; John, Swen; Carrera-Bastos, Pedro; Lindeberg, Staffan; Cordain, Loren

    2013-01-01

    Milk protein intake has recently been suggested to improve metabolic health. This Perspective provides evidence that metabolic effects of milk protein intake have to be regarded in the context of the individual's pre-existing metabolic and exercise status. Milk proteins provide abundant branched-chain amino acids (BCAAs) and glutamine. Plasma BCAAs and glutamine are increased in obesity and insulin resistance, but decrease after gastric bypass surgery resulting in weight loss and improved insulin sensitivity. Milk protein consumption results in postprandial hyperinsulinemia in obese subjects, increases body weight of overweight adolescents and may thus deteriorate pre-existing metabolic disturbances of obese, insulin resistant individuals. PMID:24225036

  1. Metabolic effects of milk protein intake strongly depend on pre-existing metabolic and exercise status

    PubMed Central

    2013-01-01

    Milk protein intake has recently been suggested to improve metabolic health. This Perspective provides evidence that metabolic effects of milk protein intake have to be regarded in the context of the individual’s pre-existing metabolic and exercise status. Milk proteins provide abundant branched-chain amino acids (BCAAs) and glutamine. Plasma BCAAs and glutamine are increased in obesity and insulin resistance, but decrease after gastric bypass surgery resulting in weight loss and improved insulin sensitivity. Milk protein consumption results in postprandial hyperinsulinemia in obese subjects, increases body weight of overweight adolescents and may thus deteriorate pre-existing metabolic disturbances of obese, insulin resistant individuals. PMID:24225036

  2. Mapping Protein Conformational Landscapes under Strongly Native Conditions with Hydrogen Exchange Mass Spectrometry.

    PubMed

    Witten, Jacob; Ruschak, Amy; Poterba, Timothy; Jaramillo, Alexis; Miranker, Andrew D; Jaswal, Sheila S

    2015-08-01

    The thermodynamic stability and kinetic barriers separating protein conformations under native conditions are critical for proper protein function and for understanding dysfunction in diseases of protein conformation. Traditional methods to probe protein unfolding and folding employ denaturants and highly non-native conditions, which may destabilize intermediate species or cause irreversible aggregation, especially at the high protein concentrations typically required. Hydrogen exchange (HX) is ideal for detecting conformational behavior under native conditions without the need for denaturants, but detection by NMR is limited to small highly soluble proteins. Mass spectrometry (MS) can, in principle, greatly extend the applicability of native-state HX to larger proteins and lower concentrations. However, quantitative analysis of HXMS profiles is currently limited by experimental and theoretical challenges. Here we address both limitations, by proposing an approach based on using standards to eliminate the systematic experimental artifacts in HXMS profiles, and developing the theoretical framework to describe HX behavior across all regimes based on the Linderstrøm-Lang formalism. We demonstrate proof of principle by a practical application to native-state HX of a globular protein. The framework and the practical tools developed advance the ability of HXMS to extract thermodynamic and kinetic conformational parameters of proteins under native conditions. PMID:26146955

  3. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    NASA Astrophysics Data System (ADS)

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-06-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed `clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length.

  4. Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites.

    PubMed

    Marsh, Lorraine

    2015-01-01

    Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where "nonspecific" interactions contribute to biological function. PMID:26064949

  5. Coarsening of protein clusters on subcellular drops exhibits strong and sudden size selectivity

    NASA Astrophysics Data System (ADS)

    Brown, Aidan; Rutenberg, Andrew

    2015-03-01

    Autophagy is an important process for the degradation of cellular components, with receptor proteins targeting substrates to downstream autophagy machinery. An important question is how receptor protein interactions lead to their selective accumulation on autophagy substrates. Receptor proteins have recently been observed in clusters, raising the possibility that clustering could affect autophagy selectivity. We investigate the clustering dynamics of the autophagy receptor protein NBR1. In addition to standard receptor protein domains, NBR1 has a ``J'' domain that anchors it to membranes, and a coiled-coil domain that enhances self-interaction. We model coarsening clusters of NBR1 on the surfaces of a polydisperse collection of drops, representing organelles. Despite the disconnected nature of the drop surfaces, we recover dynamical scaling of cluster sizes. Significantly, we find that at a well-defined time after coarsening begins, clusters evaporate from smaller drops and grow on larger drops. Thus, coarsening-driven size selection will localize protein clusters to larger substrates, leaving smaller substrates without clusters. This provides a possible physical mechanism for autophagy selectivity, and can explain reports of size selection during peroxisome degradation.

  6. Strong Ligand-Protein Interactions Derived from Diffuse Ligand Interactions with Loose Binding Sites

    PubMed Central

    2015-01-01

    Many systems in biology rely on binding of ligands to target proteins in a single high-affinity conformation with a favorable ΔG. Alternatively, interactions of ligands with protein regions that allow diffuse binding, distributed over multiple sites and conformations, can exhibit favorable ΔG because of their higher entropy. Diffuse binding may be biologically important for multidrug transporters and carrier proteins. A fine-grained computational method for numerical integration of total binding ΔG arising from diffuse regional interaction of a ligand in multiple conformations using a Markov Chain Monte Carlo (MCMC) approach is presented. This method yields a metric that quantifies the influence on overall ligand affinity of ligand binding to multiple, distinct sites within a protein binding region. This metric is essentially a measure of dispersion in equilibrium ligand binding and depends on both the number of potential sites of interaction and the distribution of their individual predicted affinities. Analysis of test cases indicates that, for some ligand/protein pairs involving transporters and carrier proteins, diffuse binding contributes greatly to total affinity, whereas in other cases the influence is modest. This approach may be useful for studying situations where “nonspecific” interactions contribute to biological function. PMID:26064949

  7. Efficacy of Acinetobacter sp. B9 for simultaneous removal of phenol and hexavalent chromium from co-contaminated system.

    PubMed

    Bhattacharya, Amrik; Gupta, Anshu; Kaur, Amarjeet; Malik, Darshan

    2014-12-01

    The present study shows the feasibility of a newly isolated strain Acinetobacter sp. B9 for concurrent removal of phenol and Cr (VI) from wastewater. The experiments were conducted in a batch reactor under aerobic conditions. Initially, when mineral salt solution was used as the culture medium, the strain was found to utilize phenol as sole carbon and energy source while no Cr (VI) removal was observed. However, the addition of glucose as co-carbon source resulted in the removal of both toxicants. This co-removal efficiency of the strain was further improved with nutrient-rich media (NB). Optimum co-removal was determined at 188 mg L(-1) of phenol and 3.5 mg L(-1) of Cr (VI) concentrations at pH 7.0. Strain B9 followed the orthometabolic pathway for phenol degradation. Transmission electron microscopy (TEM) and Fourier transform infrared spectroscopy (FT-IR) studies showed sorption of chromium as one of the major mechanisms for Cr (VI) removal by B9 cells. Acinetobacter sp. B9 was later on checked for bioremediation of real tannery wastewater. After 96 h of batch treatment of tannery effluent containing an initial 47 mg L(-1) phenol and 16 mg L(-1) Cr (VI), complete removal of phenol and 87 % reduction of Cr (VI) were attained, showing high efficiency of the bacterial strain for potential application in industrial pollution control. PMID:25062955

  8. Native-sized recombinant spider silk protein produced in metabolically engineered Escherichia coli results in a strong fiber.

    PubMed

    Xia, Xiao-Xia; Qian, Zhi-Gang; Ki, Chang Seok; Park, Young Hwan; Kaplan, David L; Lee, Sang Yup

    2010-08-10

    Spider dragline silk is a remarkably strong fiber that makes it attractive for numerous applications. Much has thus been done to make similar fibers by biomimic spinning of recombinant dragline silk proteins. However, success is limited in part due to the inability to successfully express native-sized recombinant silk proteins (250-320 kDa). Here we show that a 284.9 kDa recombinant protein of the spider Nephila clavipes is produced and spun into a fiber displaying mechanical properties comparable to those of the native silk. The native-sized protein, predominantly rich in glycine (44.9%), was favorably expressed in metabolically engineered Escherichia coli within which the glycyl-tRNA pool was elevated. We also found that the recombinant proteins of lower molecular weight versions yielded inferior fiber properties. The results provide insight into evolution of silk protein size related to mechanical performance, and also clarify why spinning lower molecular weight proteins does not recapitulate the properties of native fibers. Furthermore, the silk expression, purification, and spinning platform established here should be useful for sustainable production of natural quality dragline silk, potentially enabling broader applications. PMID:20660779

  9. Structure and dynamics of an imidazoline nitroxide side chain with strongly hindered internal motion in proteins

    NASA Astrophysics Data System (ADS)

    Toledo Warshaviak, Dora; Khramtsov, Valery V.; Cascio, Duilio; Altenbach, Christian; Hubbell, Wayne L.

    2013-07-01

    A disulfide-linked imidazoline nitroxide side chain (V1) has a similar and highly constrained internal motion at diverse topological sites in a protein, unlike that for the disulfide-linked pyrroline nitroxide side chain (R1) widely used in site directed spin labeling EPR. Crystal structures of V1 at two positions in a helix of T4 Lysozyme and quantum mechanical calculations suggest the source of the constraints as intra-side chain interactions of the disulfide sulfur atoms with both the protein backbone and the 3-nitrogen in the imidazoline ring. These interactions apparently limit the conformation of the side chain to one of only three possible rotamers, two of which are observed in the crystal structure. An inter-spin distance measurement in frozen solution using double electron-electron resonance (DEER) gives a value essentially identical to that determined from the crystal structure of the protein containing two copies of V1, indicating that lattice forces do not dictate the rotamers observed. Collectively, the results suggest the possibility of predetermining a unique rotamer of V1 in helical structures. In general, the reduced rotameric space of V1 compared to R1 should simplify interpretation of inter-spin distance information in terms of protein structure, while the highly constrained internal motion is expected to extend the dynamic range for characterizing large amplitude nanosecond backbone fluctuations.

  10. Strong Ionic Hydrogen Bonding Causes a Spectral Isotope Effect in Photoactive Yellow Protein

    PubMed Central

    Kaledhonkar, Sandip; Hara, Miwa; Stalcup, T. Page; Xie, Aihua; Hoff, Wouter D.

    2013-01-01

    Standard hydrogen bonds are of great importance for protein structure and function. Ionic hydrogen bonds often are significantly stronger than standard hydrogen bonds and exhibit unique properties, but their role in proteins is not well understood. We report that hydrogen/deuterium exchange causes a redshift in the visible absorbance spectrum of photoactive yellow protein (PYP). We expand the range of interpretable isotope effects by assigning this spectral isotope effect (SIE) to a functionally important hydrogen bond at the active site of PYP. The inverted sign and extent of this SIE is explained by the ionic nature and strength of this hydrogen bond. These results show the relevance of ionic hydrogen bonding for protein active sites, and reveal that the inverted SIE is a novel, to our knowledge, tool to probe ionic hydrogen bonds. Our results support a classification of hydrogen bonds that distinguishes the properties of ionic hydrogen bonds from those of both standard and low barrier hydrogen bonds, and show how this classification helps resolve a recent debate regarding active site hydrogen bonding in PYP. PMID:24314088

  11. Cooperative folding of intrinsically disordered domains drives assembly of a strong elongated protein

    PubMed Central

    Gruszka, Dominika T.; Whelan, Fiona; Farrance, Oliver E.; Fung, Herman K. H.; Paci, Emanuele; Jeffries, Cy M.; Svergun, Dmitri I.; Baldock, Clair; Baumann, Christoph G.; Brockwell, David J.; Potts, Jennifer R.; Clarke, Jane

    2015-01-01

    Bacteria exploit surface proteins to adhere to other bacteria, surfaces and host cells. Such proteins need to project away from the bacterial surface and resist significant mechanical forces. SasG is a protein that forms extended fibrils on the surface of Staphylococcus aureus and promotes host adherence and biofilm formation. Here we show that although monomeric and lacking covalent cross-links, SasG maintains a highly extended conformation in solution. This extension is mediated through obligate folding cooperativity of the intrinsically disordered E domains that couple non-adjacent G5 domains thermodynamically, forming interfaces that are more stable than the domains themselves. Thus, counterintuitively, the elongation of the protein appears to be dependent on the inherent instability of its domains. The remarkable mechanical strength of SasG arises from tandemly arrayed ‘clamp' motifs within the folded domains. Our findings reveal an elegant minimal solution for the assembly of monomeric mechano-resistant tethers of variable length. PMID:26027519

  12. Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction.

    PubMed

    Müller, Jochen P; Mielke, Salomé; Löf, Achim; Obser, Tobias; Beer, Christof; Bruetzel, Linda K; Pippig, Diana A; Vanderlinden, Willem; Lipfert, Jan; Schneppenheim, Reinhard; Benoit, Martin

    2016-02-01

    The large plasma glycoprotein von Willebrand factor (VWF) senses hydrodynamic forces in the bloodstream and responds to elevated forces with abrupt elongation, thereby increasing its adhesiveness to platelets and collagen. Remarkably, forces on VWF are elevated at sites of vascular injury, where VWF's hemostatic potential is important to mediate platelet aggregation and to recruit platelets to the subendothelial layer. Adversely, elevated forces in stenosed vessels lead to an increased risk of VWF-mediated thrombosis. To dissect the remarkable force-sensing ability of VWF, we have performed atomic force microscopy (AFM)-based single-molecule force measurements on dimers, the smallest repeating subunits of VWF multimers. We have identified a strong intermonomer interaction that involves the D4 domain and critically depends on the presence of divalent ions, consistent with results from small-angle X-ray scattering (SAXS). Dissociation of this strong interaction occurred at forces above [Formula: see text]50 pN and provided [Formula: see text]80 nm of additional length to the elongation of dimers. Corroborated by the static conformation of VWF, visualized by AFM imaging, we estimate that in VWF multimers approximately one-half of the constituent dimers are firmly closed via the strong intermonomer interaction. As firmly closed dimers markedly shorten VWF's effective length contributing to force sensing, they can be expected to tune VWF's sensitivity to hydrodynamic flow in the blood and to thereby significantly affect VWF's function in hemostasis and thrombosis. PMID:26787887

  13. Force sensing by the vascular protein von Willebrand factor is tuned by a strong intermonomer interaction

    PubMed Central

    Müller, Jochen P.; Mielke, Salomé; Löf, Achim; Obser, Tobias; Beer, Christof; Bruetzel, Linda K.; Pippig, Diana A.; Vanderlinden, Willem; Lipfert, Jan; Schneppenheim, Reinhard; Benoit, Martin

    2016-01-01

    The large plasma glycoprotein von Willebrand factor (VWF) senses hydrodynamic forces in the bloodstream and responds to elevated forces with abrupt elongation, thereby increasing its adhesiveness to platelets and collagen. Remarkably, forces on VWF are elevated at sites of vascular injury, where VWF’s hemostatic potential is important to mediate platelet aggregation and to recruit platelets to the subendothelial layer. Adversely, elevated forces in stenosed vessels lead to an increased risk of VWF-mediated thrombosis. To dissect the remarkable force-sensing ability of VWF, we have performed atomic force microscopy (AFM)-based single-molecule force measurements on dimers, the smallest repeating subunits of VWF multimers. We have identified a strong intermonomer interaction that involves the D4 domain and critically depends on the presence of divalent ions, consistent with results from small-angle X-ray scattering (SAXS). Dissociation of this strong interaction occurred at forces above ∼50 pN and provided ∼80 nm of additional length to the elongation of dimers. Corroborated by the static conformation of VWF, visualized by AFM imaging, we estimate that in VWF multimers approximately one-half of the constituent dimers are firmly closed via the strong intermonomer interaction. As firmly closed dimers markedly shorten VWF’s effective length contributing to force sensing, they can be expected to tune VWF’s sensitivity to hydrodynamic flow in the blood and to thereby significantly affect VWF’s function in hemostasis and thrombosis. PMID:26787887

  14. Blood proteins strongly reduce the mobility of artificial self-propelled micromotors.

    PubMed

    Wang, Hong; Zhao, Guanjia; Pumera, Martin

    2013-12-01

    Autonomous self-propelled catalytic microjets are envisaged as an important technology in biomedical applications, including drug delivery, micro/nanosurgery, and active dynamic bioassays. The direct in vivo application of these microjets, specifically in blood, is however impeded by insufficient knowledge on the in vivo viability of the technique. This study highlights the effect of blood proteins on the viability of the microjets. The presence of blood proteins, including serum albumin and γ-globulins at physiological concentrations, has been found to dramatically reduce the viability of the microjets. The reduction of viability has been measured in terms of a lower number of active microjets and a decrease in the velocity of propulsion. It is clear from this study that in order for microjets to function in biomedical applications, different modes of propulsion besides platinum-catalyzed oxygen bubble ejection must be employed. These findings have serious implications for the biomedical applications of catalytic microjets. PMID:24166769

  15. Strong seed-specific protein expression from the Vigna radiata storage protein 8SGα promoter in transgenic Arabidopsis seeds.

    PubMed

    Chen, Mo-Xian; Zheng, Shu-Xiao; Yang, Yue-Ning; Xu, Chao; Liu, Jie-Sheng; Yang, Wei-Dong; Chye, Mee-Len; Li, Hong-Ye

    2014-03-20

    Vigna radiata (mung bean) is an important crop plant and is a major protein source in developing countries. Mung bean 8S globulins constitute nearly 90% of total seed storage protein and consist of three subunits designated as 8SGα, 8SGα' and 8SGβ. The 5'-flanking sequences of 8SGα' has been reported to confer high expression in transgenic Arabidopsis seeds. In this study, a 472-bp 5'-flanking sequence of 8SGα was identified by genome walking. Computational analysis subsequently revealed the presence of numerous putative seed-specific cis-elements within. The 8SGα promoter was then fused to the gene encoding β-glucuronidase (GUS) to create a reporter construct for Arabidopsis thaliana transformation. The spatial and temporal expression of 8SGα∷GUS, as investigated using GUS histochemical assays, showed GUS expression exclusively in transgenic Arabidopsis seeds. Quantitative GUS assays revealed that the 8SGα promoter showed 2- to 4-fold higher activity than the Cauliflower Mosaic Virus (CaMV) 35S promoter. This study has identified a seed-specific promoter of high promoter strength, which is potentially useful for directing foreign protein expression in seed bioreactors. PMID:24503210

  16. Individual protein balance strongly influences δ15N and δ13C values in Nile tilapia, Oreochromis niloticus

    NASA Astrophysics Data System (ADS)

    Gaye-Siessegger, Julia; Focken, Ulfert; Abel, Hansjörg; Becker, Klaus

    Although stable isotope ratios in animals have often been used as indicators of the trophic level and for the back-calculation of diets, few experiments have been done under standardized laboratory conditions to investigate factors influencing δ15N and δ13C values. An experiment using Nile tilapia [Oreochromis niloticus (L.)] was therefore carried out to test the effect of different dietary protein contents (35.4, 42.3, and 50.9%) on δ15N and δ13C values of the whole tilapia. The fish were fed the isoenergetic and isolipidic semi-synthetic diets at a relatively low level. δ15N and δ13C values of the lipid-free body did not differ between the fish fed the diets with different protein contents, but the trophic shift for N and C isotopes decreased with increasing protein accretion in the individual fish, for N from 6.5‰ to 4‰ and for C in the lipid-free body from 4‰ to 2.5‰. This is the first study showing the strong influence of the individual protein balance to the degree to which the isotopic signature of dietary protein was modified in tissue protein of fish. The extrapolation of the trophic level or the reconstruction of the diet of an animal from stable isotope ratios without knowledge of the individual physiological condition and the feeding rate may lead to erroneous results.

  17. Pluripotency transcription factor Sox2 is strongly adsorbed by heparin but requires a protein transduction domain for cell internalization

    SciTech Connect

    Albayrak, Cem; Yang, William C.; Swartz, James R.

    2013-02-15

    Highlights: ► Both R9Sox2 and Sox2 bind heparin with comparable affinity. ► Both R9Sox2 and Sox2 bind to fibroblasts, but only R9Sox2 is internalized. ► Internalization efficiency of R9Sox2 is 0.3% of the administered protein. ► Heparan sulfate adsorption may be part of a mechanism for managing cell death. -- Abstract: The binding of protein transduction domain (PTD)-conjugated proteins to heparan sulfate is an important step in cellular internalization of macromolecules. Here, we studied the pluripotency transcription factor Sox2, with or without the nonaarginine (R9) PTD. Unexpectedly, we observed that Sox2 is strongly adsorbed by heparin and by the fibroblasts without the R9 PTD. However, only the R9Sox2 fusion protein is internalized by the cells. These results collectively show that binding to heparan sulfate is not sufficient for cellular uptake, thereby supporting a recent hypothesis that other proteins play a role in cell internalization of PTD-conjugated proteins.

  18. Bone morphogenetic protein-4 strongly potentiates growth factor-induced proliferation of mammary epithelial cells

    SciTech Connect

    Montesano, Roberto Sarkoezi, Rita; Schramek, Herbert

    2008-09-12

    Bone morphogenetic proteins (BMPs) are multifunctional cytokines that elicit pleiotropic effects on biological processes such as cell proliferation, cell differentiation and tissue morphogenesis. With respect to cell proliferation, BMPs can exert either mitogenic or anti-mitogenic activities, depending on the target cells and their context. Here, we report that in low-density cultures of immortalized mammary epithelial cells, BMP-4 did not stimulate cell proliferation by itself. However, when added in combination with suboptimal concentrations of fibroblast growth factor (FGF)-2, FGF-7, FGF-10, epidermal growth factor (EGF) or hepatocyte growth factor (HGF), BMP-4 potently enhanced growth factor-induced cell proliferation. These results reveal a hitherto unsuspected interplay between BMP-4 and growth factors in the regulation of mammary epithelial cell proliferation. We suggest that the ability of BMP-4 to potentiate the mitogenic activity of multiple growth factors may contribute to mammary gland ductal morphogenesis as well as to breast cancer progression.

  19. Strong morphological defects in conditional Arabidopsis abp1 knock-down mutants generated in absence of functional ABP1 protein

    PubMed Central

    Perrot-Rechenmann, Catherine; Friml, Jiří

    2016-01-01

    The Auxin Binding Protein 1 (ABP1) is one of the most studied proteins in plants. Since decades ago, it has been the prime receptor candidate for the plant hormone auxin with a plethora of described functions in auxin signaling and development. The developmental importance of ABP1 has recently been questioned by identification of Arabidopsis thaliana abp1 knock-out alleles that show no obvious phenotypes under normal growth conditions. In this study, we examined the contradiction between the normal growth and development of the abp1 knock-outs and the strong morphological defects observed in three different ethanol-inducible abp1 knock-down mutants ( abp1-AS, SS12K, SS12S). By analyzing segregating populations of abp1 knock-out vs. abp1 knock-down crosses we show that the strong morphological defects that were believed to be the result of conditional down-regulation of ABP1 can be reproduced also in the absence of the functional ABP1 protein. This data suggests that the phenotypes in  abp1 knock-down lines are due to the off-target effects and asks for further reflections on the biological function of ABP1 or alternative explanations for the missing phenotypic defects in the abp1 loss-of-function alleles. PMID:26925228

  20. Structural Ensembles of Intrinsically Disordered Proteins Depend Strongly on Force Field: A Comparison to Experiment.

    PubMed

    Rauscher, Sarah; Gapsys, Vytautas; Gajda, Michal J; Zweckstetter, Markus; de Groot, Bert L; Grubmüller, Helmut

    2015-11-10

    Intrinsically disordered proteins (IDPs) are notoriously challenging to study both experimentally and computationally. The structure of IDPs cannot be described by a single conformation but must instead be described as an ensemble of interconverting conformations. Atomistic simulations are increasingly used to obtain such IDP conformational ensembles. Here, we have compared the IDP ensembles generated by eight all-atom empirical force fields against primary small-angle X-ray scattering (SAXS) and NMR data. Ensembles obtained with different force fields exhibit marked differences in chain dimensions, hydrogen bonding, and secondary structure content. These differences are unexpectedly large: changing the force field is found to have a stronger effect on secondary structure content than changing the entire peptide sequence. The CHARMM 22* ensemble performs best in this force field comparison: it has the lowest error in chemical shifts and J-couplings and agrees well with the SAXS data. A high population of left-handed α-helix is present in the CHARMM 36 ensemble, which is inconsistent with measured scalar couplings. To eliminate inadequate sampling as a reason for differences between force fields, extensive simulations were carried out (0.964 ms in total); the remaining small sampling uncertainty is shown to be much smaller than the observed differences. Our findings highlight how IDPs, with their rugged energy landscapes, are highly sensitive test systems that are capable of revealing force field deficiencies and, therefore, contributing to force field development. PMID:26574339

  1. Mycobacterium tuberculosis PPE protein Rv0256c induces strong B cell response in tuberculosis patients.

    PubMed

    Abraham, Philip Raj; Latha, Gaddam Suman; Valluri, Vijaya Lakshmi; Mukhopadhyay, Sangita

    2014-03-01

    Tuberculosis (TB) is one of the most important diseases of humans and major public health problem worldwide. Early and accurate diagnosis of TB is necessary for the treatment, prevention, and control of TB. Therefore, it is important to identify suitable antigens that can differentiate active tuberculosis patients from BCG-vaccinated individuals. In the present study, we have used Rv0256c (PPE2) protein of Mycobacterium tuberculosis to screen the sera of infected patients belonging to different clinical TB presentations, and BCG-vaccinated clinically healthy individuals by enzyme immunoassay. Our results demonstrated that Rv0256c displayed stronger and specific immunoreactivity against the sera obtained from clinically active tuberculosis patients compared to PPD and ESAT-6 and could differentiate the TB-patients from the BCG-vaccinated controls. Importantly, Rv0256c was also found to detect even the extrapulmonary and smear-negative pulmonary cases which often are tedious and difficult to detect using conventional diagnostic methods. This study suggests that Rv0256c can be used as a potential marker for the serodiagnosis of tuberculosis patients. PMID:23827809

  2. Functional importance of the NH2-terminal insertion sequence of lung surfactant protein B

    PubMed Central

    Frey, Shelli L.; Pocivavsek, Luka; Waring, Alan J.; Walther, Frans J.; Hernandez-Juviel, Jose M.; Ruchala, Piotr

    2010-01-01

    Lung surfactant protein B (SP-B) is required for proper surface activity of pulmonary surfactant. In model lung surfactant lipid systems composed of saturated and unsaturated lipids, the unsaturated lipids are removed from the film at high compression. It is thought that SP-B helps anchor these lipids closely to the monolayer in three-dimensional cylindrical structures termed “nanosilos” seen by atomic force microscopy imaging of deposited monolayers at high surface pressures. Here we explore the role of the SP-B NH2 terminus in the formation and stability of these cylindrical structures, specifically the distribution of lipid stack height, width, and density with four SP-B truncation peptides: SP-B 1–25, SP-B 9–25, SP-B 11–25, and SP-B 1–25Nflex (prolines 2 and 4 substituted with alanine). The first nine amino acids, termed the insertion sequence and the interface seeking tryptophan residue 9, are shown to stabilize the formation of nanosilos while an increase in the insertion sequence flexibility (SP-B 1–25Nflex) may improve peptide functionality. This provides a functional understanding of the insertion sequence beyond anchoring the protein to the two-dimensional membrane lining the lung, as it also stabilizes formation of nanosilos, creating reversible repositories for fluid lipids at high compression. In lavaged, surfactant-deficient rats, instillation of a mixture of SP-B 1–25 (as a monomer or dimer) and synthetic lung lavage lipids quickly improved oxygenation and dynamic compliance, whereas SP-B 11–25 surfactants showed oxygenation and dynamic compliance values similar to that of lipids alone, demonstrating a positive correlation between formation of stable, but reversible, nanosilos and in vivo efficacy. PMID:20023175

  3. Achieving efficient protein expression in Trichoderma reesei by using strong constitutive promoters

    PubMed Central

    2012-01-01

    Backgrounds The fungus Trichoderma reesei is an important workhorse for expression of homologous or heterologous genes, and the inducible cbh1 promoter is generally used. However, constitutive expression is more preferable in some cases than inducible expression that leads to production of unwanted cellulase components. In this work, constitutive promoters of T. reesei were screened and successfully used for high level homologous expression of xylanase II. Results The transcriptional profiles of 13 key genes that participate in glucose metabolism in T. reesei were analyzed by quantitative real-time reverse-transcription polymerase chain reaction (RT-qPCR). The results indicated that the mRNA levels of pdc (encoding pyruvate decarboxylase) and eno (encoding enolase) genes were much higher than other genes under high glucose conditions. Recombinant T. reesei strains that homologously expressed xylanase II were constructed by using the promoters of the pdc and eno genes, and they respectively produced 9266 IU/ml and 8866 IU/ml of xylanase activities in the cultivation supernatant in a medium with high glucose concentration. The productivities of xylanase II were 1.61 g/L (with the pdc promoter) and 1.52 g/L (with the eno promoter), approximately accounted for 83% and 82% of the total protein secreted by T. reesei, respectively. Conclusions This work demonstrates the screening of constitutive promoters by using RT-qPCR in T. reesei, and has obtained the highest expression of recombinant xylanase II to date by using these promoters. PMID:22709462

  4. Dengue E Protein Domain III-Based DNA Immunisation Induces Strong Antibody Responses to All Four Viral Serotypes

    PubMed Central

    Chan, Kuan Rong; Tan, Hwee Cheng; Bestagno, Marco; Ooi, Eng Eong; Burrone, Oscar R.

    2015-01-01

    Dengue virus (DENV) infection is a major emerging disease widely distributed throughout the tropical and subtropical regions of the world affecting several millions of people. Despite constants efforts, no specific treatment or effective vaccine is yet available. Here we show a novel design of a DNA immunisation strategy that resulted in the induction of strong antibody responses with high neutralisation titres in mice against all four viral serotypes. The immunogenic molecule is an engineered version of the domain III (DIII) of the virus E protein fused to the dimerising CH3 domain of the IgG immunoglobulin H chain. The DIII sequences were also codon-optimised for expression in mammalian cells. While DIII alone is very poorly secreted, the codon-optimised fusion protein is rightly expressed, folded and secreted at high levels, thus inducing strong antibody responses. Mice were immunised using gene-gun technology, an efficient way of intradermal delivery of the plasmid DNA, and the vaccine was able to induce neutralising titres against all serotypes. Additionally, all sera showed reactivity to a recombinant DIII version and the recombinant E protein produced and secreted from mammalian cells in a mono-biotinylated form when tested in a conformational ELISA. Sera were also highly reactive to infective viral particles in a virus-capture ELISA and specific for each serotype as revealed by the low cross-reactive and cross-neutralising activities. The serotype specific sera did not induce antibody dependent enhancement of infection (ADE) in non-homologous virus serotypes. A tetravalent immunisation protocol in mice showed induction of neutralising antibodies against all four dengue serotypes as well. PMID:26218926

  5. Sand fly salivary proteins induce strong cellular immunity in a natural reservoir of visceral leishmaniasis with adverse consequences for Leishmania.

    PubMed

    Collin, Nicolas; Gomes, Regis; Teixeira, Clarissa; Cheng, Lily; Laughinghouse, Andre; Ward, Jerrold M; Elnaiem, Dia-Eldin; Fischer, Laurent; Valenzuela, Jesus G; Kamhawi, Shaden

    2009-05-01

    Immunity to a sand fly salivary protein protects against visceral leishmaniasis (VL) in hamsters. This protection was associated with the development of cellular immunity in the form of a delayed-type hypersensitivity response and the presence of IFN-gamma at the site of sand fly bites. To date, there are no data available regarding the cellular immune response to sand fly saliva in dogs, the main reservoirs of VL in Latin America, and its role in protection from this fatal disease. Two of 35 salivary proteins from the vector sand fly Lutzomyia longipalpis, identified using a novel approach termed reverse antigen screening, elicited strong cellular immunity in dogs. Immunization with either molecule induced high IgG(2) antibody levels and significant IFN-gamma production following in vitro stimulation of PBMC with salivary gland homogenate (SGH). Upon challenge with uninfected or infected flies, immunized dogs developed a cellular response at the bite site characterized by lymphocytic infiltration and IFN-gamma and IL-12 expression. Additionally, SGH-stimulated lymphocytes from immunized dogs efficiently killed Leishmania infantum chagasi within autologous macrophages. Certain sand fly salivary proteins are potent immunogens obligatorily co-deposited with Leishmania parasites during transmission. Their inclusion in an anti-Leishmania vaccine would exploit anti-saliva immunity following an infective sand fly bite and set the stage for a protective anti-Leishmania immune response. PMID:19461875

  6. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific.

    PubMed

    Wang, Tong; Cui, Yizhi; Jin, Jingjie; Guo, Jiahui; Wang, Guibin; Yin, Xingfeng; He, Qing-Yu; Zhang, Gong

    2013-05-01

    As a well-known phenomenon, total mRNAs poorly correlate to proteins in their abundances as reported. Recent findings calculated with bivariate models suggested even poorer such correlation, whereas focusing on the translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) subset. In this study, we analysed the relative abundances of mRNAs, RNC-mRNAs and proteins on genome-wide scale, comparing human lung cancer A549 and H1299 cells with normal human bronchial epithelial (HBE) cells, respectively. As discovered, a strong correlation between RNC-mRNAs and proteins in their relative abundances could be established through a multivariate linear model by integrating the mRNA length as a key factor. The R(2) reached 0.94 and 0.97 in A549 versus HBE and H1299 versus HBE comparisons, respectively. This correlation highlighted that the mRNA length significantly contributes to the translational modulation, especially to the translational initiation, favoured by its correlation with the mRNA translation ratio (TR) as observed. We found TR is highly phenotype specific, which was substantiated by both pathway analysis and biased TRs of the splice variants of BDP1 gene, which is a key transcription factor of transfer RNAs. These findings revealed, for the first time, the intrinsic and genome-wide translation modulations at translatomic level in human cells at steady-state, which are tightly correlated to the protein abundance and functionally relevant to cellular phenotypes. PMID:23519614

  7. Translating mRNAs strongly correlate to proteins in a multivariate manner and their translation ratios are phenotype specific

    PubMed Central

    Wang, Tong; Cui, Yizhi; Jin, Jingjie; Guo, Jiahui; Wang, Guibin; Yin, Xingfeng; He, Qing-Yu; Zhang, Gong

    2013-01-01

    As a well-known phenomenon, total mRNAs poorly correlate to proteins in their abundances as reported. Recent findings calculated with bivariate models suggested even poorer such correlation, whereas focusing on the translating mRNAs (ribosome nascent-chain complex-bound mRNAs, RNC-mRNAs) subset. In this study, we analysed the relative abundances of mRNAs, RNC-mRNAs and proteins on genome-wide scale, comparing human lung cancer A549 and H1299 cells with normal human bronchial epithelial (HBE) cells, respectively. As discovered, a strong correlation between RNC-mRNAs and proteins in their relative abundances could be established through a multivariate linear model by integrating the mRNA length as a key factor. The R2 reached 0.94 and 0.97 in A549 versus HBE and H1299 versus HBE comparisons, respectively. This correlation highlighted that the mRNA length significantly contributes to the translational modulation, especially to the translational initiation, favoured by its correlation with the mRNA translation ratio (TR) as observed. We found TR is highly phenotype specific, which was substantiated by both pathway analysis and biased TRs of the splice variants of BDP1 gene, which is a key transcription factor of transfer RNAs. These findings revealed, for the first time, the intrinsic and genome-wide translation modulations at translatomic level in human cells at steady-state, which are tightly correlated to the protein abundance and functionally relevant to cellular phenotypes. PMID:23519614

  8. Prion protein gene (PRNP) variants and evidence for strong purifying selection in functionally important regions of bovine exon 3

    PubMed Central

    Seabury, Christopher M.; Honeycutt, Rodney L.; Rooney, Alejandro P.; Halbert, Natalie D.; Derr, James N.

    2004-01-01

    Amino acid replacements encoded by the prion protein gene (PRNP) have been associated with transmissible and hereditary spongiform encephalopathies in mammalian species. However, an association between bovine spongiform encephalopathy (BSE) and bovine PRNP exon 3 has not been detected. Moreover, little is currently known regarding the mechanisms of evolution influencing the bovine PRNP gene. Therefore, in this study we evaluated the patterns of nucleotide variation associated with PRNP exon 3 for 36 breeds of domestic cattle and representative samples for 10 additional species of Bovinae. The results of our study indicate that strong purifying selection has intensely constrained PRNP over the long-term evolutionary history of the subfamily Bovinae, especially in regions considered to be of functional, structural, and pathogenic importance in humans as well as other mammals. The driving force behind this intense level of purifying selection remains to be explained. PMID:15477588

  9. Sulfonamide inhibition studies of the β-carbonic anhydrase from the newly discovered bacterium Enterobacter sp. B13.

    PubMed

    Eminoğlu, Ayşenur; Vullo, Daniela; Aşık, Aycan; Çolak, Dilşat Nigar; Çanakçı, Sabriye; Beldüz, Ali Osman; Supuran, Claudiu T

    2016-04-01

    The genome of the newly identified bacterium Enterobacter sp. B13 encodes for a β-class carbonic anhydrases (CAs, EC 4.2.1.1), EspCA. This enzyme was recently cloned, and characterized kinetically by this group (J. Enzyme Inhib. Med. Chem. 2016, 31). Here we report an inhibition study with sulfonamides and sulfamates of this enzyme. The best EspCA inhibitors were some sulfanylated sulfonamides with elongated molecules, metanilamide, 4-aminoalkyl-benzenesulfonamides, acetazolamide, and deacetylated methazolamide (KIs in the range of 58.7-96.5nM). Clinically used agents such as methazolamide, ethoxzolamide, dorzolamide, brinzolamide, benzolamide, zonisamide, sulthiame, sulpiride, topiramate and valdecoxib were slightly less effective inhibitors (KIs in the range of 103-138nM). Saccharin, celecoxib, dichlorophenamide and many simple benzenesulfonamides were even less effective as EspCA inhibitors, with KIs in the range of 384-938nM. Identification of effective inhibitors of this bacterial enzyme may lead to pharmacological tools useful for understanding the physiological role(s) of the β-class CAs in bacterial pathogenicity/virulence. PMID:26920803

  10. Elongation Factor Tu and Heat Shock Protein 70 Are Membrane-Associated Proteins from Mycoplasma ovipneumoniae Capable of Inducing Strong Immune Response in Mice.

    PubMed

    Jiang, Fei; He, Jinyan; Navarro-Alvarez, Nalu; Xu, Jian; Li, Xia; Li, Peng; Wu, Wenxue

    2016-01-01

    Chronic non-progressive pneumonia, a disease that has become a worldwide epidemic has caused considerable loss to sheep industry. Mycoplasma ovipneumoniae (M. ovipneumoniae) is the causative agent of interstitial pneumonia in sheep, goat and bighorn. We here have identified by immunogold and immunoblotting that elongation factor Tu (EF-Tu) and heat shock protein 70 (HSP 70) are membrane-associated proteins on M. ovipneumonaiea. We have evaluated the humoral and cellular immune responses in vivo by immunizing BALB/c mice with both purified recombinant proteins rEF-Tu and rHSP70. The sera of both rEF-Tu and rHSP70 treated BALB/c mice demonstrated increased levels of IgG, IFN-γ, TNF-α, IL-12(p70), IL-4, IL-5 and IL-6. In addition, ELISPOT assay showed significant increase in IFN-γ+ secreting lymphocytes in the rHSP70 group when compared to other groups. Collectively our study reveals that rHSP70 induces a significantly better cellular immune response in mice, and may act as a Th1 cytokine-like adjuvant in immune response induction. Finally, growth inhibition test (GIT) of M. ovipneumoniae strain Y98 showed that sera from rHSP70 or rEF-Tu-immunized mice inhibited in vitro growth of M. ovipneumoniae. Our data strongly suggest that EF-Tu and HSP70 of M. ovipneumoniae are membrane-associated proteins capable of inducing antibody production, and cytokine secretion. Therefore, these two proteins may be potential candidates for vaccine development against M. ovipneumoniae infection in sheep. PMID:27537186

  11. Elongation Factor Tu and Heat Shock Protein 70 Are Membrane-Associated Proteins from Mycoplasma ovipneumoniae Capable of Inducing Strong Immune Response in Mice

    PubMed Central

    Jiang, Fei; He, Jinyan; Navarro-Alvarez, Nalu; Xu, Jian; Li, Xia; Li, Peng; Wu, Wenxue

    2016-01-01

    Chronic non-progressive pneumonia, a disease that has become a worldwide epidemic has caused considerable loss to sheep industry. Mycoplasma ovipneumoniae (M. ovipneumoniae) is the causative agent of interstitial pneumonia in sheep, goat and bighorn. We here have identified by immunogold and immunoblotting that elongation factor Tu (EF-Tu) and heat shock protein 70 (HSP 70) are membrane-associated proteins on M. ovipneumonaiea. We have evaluated the humoral and cellular immune responses in vivo by immunizing BALB/c mice with both purified recombinant proteins rEF-Tu and rHSP70. The sera of both rEF-Tu and rHSP70 treated BALB/c mice demonstrated increased levels of IgG, IFN-γ, TNF-α, IL-12(p70), IL-4, IL-5 and IL-6. In addition, ELISPOT assay showed significant increase in IFN-γ+ secreting lymphocytes in the rHSP70 group when compared to other groups. Collectively our study reveals that rHSP70 induces a significantly better cellular immune response in mice, and may act as a Th1 cytokine-like adjuvant in immune response induction. Finally, growth inhibition test (GIT) of M. ovipneumoniae strain Y98 showed that sera from rHSP70 or rEF-Tu-immunized mice inhibited in vitro growth of M. ovipneumoniae. Our data strongly suggest that EF-Tu and HSP70 of M. ovipneumoniae are membrane-associated proteins capable of inducing antibody production, and cytokine secretion. Therefore, these two proteins may be potential candidates for vaccine development against M. ovipneumoniae infection in sheep. PMID:27537186

  12. Lipid oxidation in trout muscle is strongly inhibited by a protein that specifically binds hemin released from hemoglobin

    PubMed Central

    Cai, He; Grunwald, Eric W; Park, Sungyong; Lei, Benfang; Richards, Mark P.

    2013-01-01

    The recombinant Streptococcal protein apoShp can be used as a probe for hemoglobin (Hb) reactivity in fish muscle due to its specific affinity for hemin that is released from Hb at post mortem pH values. Hemin affinity measurements indicated that apoShp binds hemin released from Hb but not myoglobin (Mb). Hemin affinity of holoShp was higher at pH 5.7 compared to pH 8.0. This may be attributed to enhanced electrostatic interaction of His58 with the heme-7-propionate at lower pH. ApoShp readily acquired hemin that was released from trout IV metHb in the presence of washed cod muscle during 2°C storage at pH 6.3. This was based on increases in redness in the washed cod matrix which occurs when apoShp binds hemin that is released from metHb. ApoShp prevented Hb-mediated lipid oxidation in washed cod muscle during 2°C storage. The prevention of Hb-mediated lipid oxidation by apoShp was likely due to bis-methionyl coordination of hemin that dissociated from metHb. This hexa-coordination of hemin appears to prevent peroxide-mediated redox reactions and there is no component in the matrix capable of dissociating hemin from Shp. ApoShp was also added to minced muscle from Rainbow trout (Oncorhynchus mykiss) to examine the degree to which Hb contributes to lipid oxidation in trout muscle. Addition of apoShp inhibited approximately 90% of the lipid oxidation that occurred in minced trout muscle during 9 days of 2°C storage based on lipid peroxide, hexanal, and thiobarituric acid reactive substances (TBARS) values. These results strongly suggest that Hb is the primary promoter of lipid oxidation in trout muscle. PMID:23570608

  13. A specific blend of intact protein rich in aspartate has strong postprandial glucose attenuating properties in rats.

    PubMed

    Hageman, Robert; Severijnen, Chantal; van de Heijning, Bert J M; Bouritius, Hetty; van Wijk, Nick; van Laere, Katrien; van der Beek, Eline M

    2008-09-01

    Three studies were carried out to help define an optimal protein blend for use in a nutritional product for diabetic patients. To this end, we tested the effects of coinfusions of combinations of different types of carbohydrates and proteins on the postprandial glycemic plasma response in healthy rats. Expt. 1 compared the effects of administering different forms of soy protein (intact protein, its hydrolysate, or an equivalent amount of the same amino acids), all in combination with a fixed amount of glucose (Glu), on postprandial Glu and insulin plasma concentrations. Intact soy protein (SI) had stronger insulinogenic properties compared with its hydrolysate but was equally potent in reducing the postprandial Glu response. In Expt. 2, we compared the effect of replacing 50% of the SI with the whey-derived protein alpha-lactalbumin when coingested with maltodextrin as the carbohydrate source. Only the specific aspartate-rich blend of SI and alpha-lactalbumin significantly improved the postprandial Glu response. In Expt. 3, we studied the effect of using the blend of SI and alpha-lactalbumin combined with a slowly digestible carbohydrate. The protein blend was still capable of significantly decreasing the postprandial Glu response even when a slow-release carbohydrate source was included. Combining this aspartate-rich protein blend with a slow-release carbohydrate might therefore lead to a low-glycemic nutritional product beneficial for dietary management in diabetic patients. PMID:18716162

  14. Strong improvement of interfacial properties can result from slight structural modifications of proteins: the case of native and dry-heated lysozyme.

    PubMed

    Desfougères, Yann; Saint-Jalmes, Arnaud; Salonen, Anniina; Vié, Véronique; Beaufils, Sylvie; Pezennec, Stéphane; Desbat, Bernard; Lechevalier, Valérie; Nau, Françoise

    2011-12-20

    Identification of the key physicochemical parameters of proteins that determine their interfacial properties is still incomplete and represents a real stake challenge, especially for food proteins. Many studies have thus consisted in comparing the interfacial behavior of different proteins, but it is difficult to draw clear conclusions when the molecules are completely different on several levels. Here the adsorption process of a model protein, the hen egg-white lysozyme, and the same protein that underwent a thermal treatment in the dry state, was characterized. The consequences of this treatment have been previously studied: net charge and hydrophobicity increase and lesser protein stability, but no secondary and tertiary structure modification (Desfougères, Y.; Jardin, J.; Lechevalier, V.; Pezennec, S.; Nau, F. Biomacromolecules 2011, 12, 156-166). The present study shows that these slight modifications dramatically increase the interfacial properties of the protein, since the adsorption to the air-water interface is much faster and more efficient (higher surface pressure). Moreover, a thick and strongly viscoelastic multilayer film is created, while native lysozyme adsorbs in a fragile monolayer film. Another striking result is that completely different behaviors were observed between two molecular species, i.e., native and native-like lysozyme, even though these species could not be distinguished by usual spectroscopic methods. This suggests that the air-water interface could be considered as a useful tool to reveal very subtle differences between protein molecules. PMID:22040020

  15. Novel Halomonas sp. B15 isolated from Larnaca Salt Lake in Cyprus that generates vanillin and vanillic acid from ferulic acid.

    PubMed

    Vyrides, Ioannis; Agathangelou, Maria; Dimitriou, Rodothea; Souroullas, Konstantinos; Salamex, Anastasia; Ioannou, Aristostodimos; Koutinas, Michalis

    2015-08-01

    Vanillin is a high value added product with many applications in the food, fragrance and pharmaceutical industries. A natural and low-cost method to produce vanillin is by microbial bioconversions through ferulic acid. Until now, limited microorganisms have been found capable of bioconverting ferulic acid to vanillin at high yield. This study aimed to screen halotolerant strains of bacteria from Larnaca Salt Lake which generate vanillin and vanillic acid from ferulic acid. From a total of 50 halotolenant/halophilic strains 8 grew in 1 g/L ferulic acid and only 1 Halomonas sp. B15 and 3 Halomonas elognata strains were capable of bioconverting ferulic acid to vanillic acid at 100 g NaCl/L. The highest vanillic acid (365 mg/L) at these conditions generated by Halomonas sp. B15 which corresponds to ferulic acid bioconversion yield of 36.5%. Using the resting cell technique with an initial ferulic acid concentration of 0.5 g/L at low salinity, the highest production of vanillin (245 mg/L) took place after 48 h, corresponding to a bioconversion yield of 49%. This is the first reported Halomonas sp. with high yield of vanillin production from ferulic acid at low salinity. PMID:26026278

  16. Crystallization and preliminary X-ray analysis of the complex of NADH and 3α-hydroxysteroid dehydrogenase from Pseudomonas sp. B-0831

    SciTech Connect

    Kataoka, Sachiyo; Nakamura, Shota; Ohkubo, Tadayasu; Ueda, Shigeru; Uchiyama, Susumu; Kobayashi, Yuji; Oda, Masayuki

    2006-06-01

    The complex of NADH and 3α-HSD from Pseudomonas sp. B-0831 has been crystallized and X-ray diffraction data have been collected to 1.8 Å resolution. The NAD(P){sup +}-dependent enzyme 3α-hydroxysteroid dehydrogenase (3α-HSD) catalyzes the reversible interconversion of hydroxyl and oxo groups at position 3 of the steroid nucleus. The complex of NADH and 3α-HSD from Pseudomonas sp. B-0831 was crystallized by the hanging-drop vapour-diffusion method. Refinement of crystallization conditions with microseeding improved the quality of the X-ray diffraction data to a resolution of 1.8 Å. The crystals belonged to the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 62.46, b = 82.25, c = 86.57 Å, and contained two molecules, reflecting dimer formation of 3α-HSD, in the asymmetric unit.

  17. Lentiviral Protein Transfer Vectors Are an Efficient Vaccine Platform and Induce a Strong Antigen-Specific Cytotoxic T Cell Response

    PubMed Central

    Uhlig, Katharina M.; Schülke, Stefan; Scheuplein, Vivian A. M.; Malczyk, Anna H.; Reusch, Johannes; Kugelmann, Stefanie; Muth, Anke; Koch, Vivian; Hutzler, Stefan; Bodmer, Bianca S.; Schambach, Axel; Buchholz, Christian J.; Waibler, Zoe; Scheurer, Stephan

    2015-01-01

    ABSTRACT To induce and trigger innate and adaptive immune responses, antigen-presenting cells (APCs) take up and process antigens. Retroviral particles are capable of transferring not only genetic information but also foreign cargo proteins when they are genetically fused to viral structural proteins. Here, we demonstrate the capacity of lentiviral protein transfer vectors (PTVs) for targeted antigen transfer directly into APCs and thereby induction of cytotoxic T cell responses. Targeting of lentiviral PTVs to APCs can be achieved analogously to gene transfer vectors by pseudotyping the particles with truncated wild-type measles virus (MV) glycoproteins (GPs), which use human SLAM (signaling lymphocyte activation molecule) as a main entry receptor. SLAM is expressed on stimulated lymphocytes and APCs, including dendritic cells. SLAM-targeted PTVs transferred the reporter protein green fluorescent protein (GFP) or Cre recombinase with strict receptor specificity into SLAM-expressing CHO and B cell lines, in contrast to broadly transducing vesicular stomatitis virus G protein (VSV-G) pseudotyped PTVs. Primary myeloid dendritic cells (mDCs) incubated with targeted or nontargeted ovalbumin (Ova)-transferring PTVs stimulated Ova-specific T lymphocytes, especially CD8+ T cells. Administration of Ova-PTVs into SLAM-transgenic and control mice confirmed the observed predominant induction of antigen-specific CD8+ T cells and demonstrated the capacity of protein transfer vectors as suitable vaccines for the induction of antigen-specific immune responses. IMPORTANCE This study demonstrates the specificity and efficacy of antigen transfer by SLAM-targeted and nontargeted lentiviral protein transfer vectors into antigen-presenting cells to trigger antigen-specific immune responses in vitro and in vivo. The observed predominant activation of antigen-specific CD8+ T cells indicates the suitability of SLAM-targeted and also nontargeted PTVs as a vaccine for the induction of

  18. Structural Insights into the Unusually Strong ATPase Activity of the AAA Domain of the Caenorhabditis elegans Fidgetin-like 1 (FIGL-1) Protein*

    PubMed Central

    Peng, Wentao; Lin, Zhijie; Li, Weirong; Lu, Jing; Shen, Yuequan; Wang, Chunguang

    2013-01-01

    The FIGL-1 (fidgetin like-1) protein is a homolog of fidgetin, a protein whose mutation leads to multiple developmental defects. The FIGL-1 protein contains an AAA (ATPase associated with various activities) domain and belongs to the AAA superfamily. However, the biological functions and developmental implications of this protein remain unknown. Here, we show that the AAA domain of the Caenorhabditis elegans FIGL-1 protein (CeFIGL-1-AAA), in clear contrast to homologous AAA domains, has an unusually high ATPase activity and forms a hexamer in solution. By determining the crystal structure of CeFIGL-1-AAA, we found that the loop linking helices α9 and α10 folds into the short helix α9a, which has an acidic surface and interacts with a positively charged surface of the neighboring subunit. Disruption of this charge interaction by mutagenesis diminishes both the ATPase activity and oligomerization capacity of the protein. Interestingly, the acidic residues in helix α9a of CeFIGL-1-AAA are not conserved in other homologous AAA domains that have relatively low ATPase activities. These results demonstrate that the sequence of CeFIGL-1-AAA has adapted to establish an intersubunit charge interaction, which contributes to its strong oligomerization and ATPase activity. These unique properties of CeFIGL-1-AAA distinguish it from other homologous proteins, suggesting that CeFIGL-1 may have a distinct biological function. PMID:23979136

  19. Hypoxia Strongly Affects Mitochondrial Ribosomal Proteins and Translocases, as Shown by Quantitative Proteomics of HeLa Cells.

    PubMed

    Bousquet, Paula A; Sandvik, Joe Alexander; Arntzen, Magnus Ø; Jeppesen Edin, Nina F; Christoffersen, Stine; Krengel, Ute; Pettersen, Erik O; Thiede, Bernd

    2015-01-01

    Hypoxia is an important and common characteristic of many human tumors. It is a challenge clinically due to the correlation with poor prognosis and resistance to radiation and chemotherapy. Understanding the biochemical response to hypoxia would facilitate the development of novel therapeutics for cancer treatment. Here, we investigate alterations in gene expression in response to hypoxia by quantitative proteome analysis using stable isotope labeling with amino acids in cell culture (SILAC) in conjunction with LCMS/MS. Human HeLa cells were kept either in a hypoxic environment or under normoxic conditions. 125 proteins were found to be regulated, with maximum alteration of 18-fold. In particular, three clusters of differentially regulated proteins were identified, showing significant upregulation of glycolysis and downregulation of mitochondrial ribosomal proteins and translocases. This interaction is likely orchestrated by HIF-1. We also investigated the effect of hypoxia on the cell cycle, which shows accumulation in G1 and a prolonged S phase under these conditions. Implications. This work not only improves our understanding of the response to hypoxia, but also reveals proteins important for malignant progression, which may be targeted in future therapies. PMID:26421188

  20. A strong 13C chemical shift signature provides the coordination mode of histidines in zinc-binding proteins.

    PubMed

    Barraud, Pierre; Schubert, Mario; Allain, Frédéric H-T

    2012-06-01

    Zinc is the second most abundant metal ion incorporated in proteins, and is in many cases a crucial component of protein three-dimensional structures. Zinc ions are frequently coordinated by cysteine and histidine residues. Whereas cysteines bind to zinc via their unique S(γ) atom, histidines can coordinate zinc with two different coordination modes, either N(δ1) or N(ε2) is coordinating the zinc ion. The determination of this coordination mode is crucial for the accurate structure determination of a histidine-containing zinc-binding site by NMR. NMR chemical shifts contain a vast amount of information on local electronic and structural environments and surprisingly their utilization for the determination of the coordination mode of zinc-ligated histidines has been limited so far to (15)N nuclei. In the present report, we observed that the (13)C chemical shifts of aromatic carbons in zinc-ligated histidines represent a reliable signature of their coordination mode. Using a statistical analysis of (13)C chemical shifts, we show that (13)C(δ2) chemical shift is sensitive to the histidine coordination mode and that the chemical shift difference δ{(13)C(ε1)} - δ{(13)C(δ2)} provides a reference-independent marker of this coordination mode. The present approach allows the direct determination of the coordination mode of zinc-ligated histidines even with non-isotopically enriched protein samples and without any prior structural information. PMID:22528293

  1. Investigations of ultrafast ligand rebinding to heme and heme proteins using temperature and strong magnetic field perturbations

    NASA Astrophysics Data System (ADS)

    Zhang, Zhenyu

    This thesis is written to summarize investigations of the mechanisms that underlie the kinetics of diatomic ligand rebinding to the iron atom of the heme group, which is chelated inside heme proteins. The family of heme proteins is a major object of studies for several branches of scientific research activity. Understanding the ligand binding mechanisms and pathways is one of the major goals for biophysics. My interests mainly focus on the physics of this ligand binding process. Therefore, to investigate the problem, isolated from the influence of the protein matrix, Fe-protophorphyrin IX is chosen as the prototype system in my studies. Myoglobin, the most extensively and intensively studied protein, is another ideal system that allows coupling the protein polypeptide matrix into the investigation. A technique to synchro-lock two laser pulse trains electronically is applied to our pump-probe spectroscopic studies. Based on this technique, a two color, fs/ps pump-probe system is developed which extends the temporal window for our investigation to 13ns and fills a gap existing in previous pump-probe investigations. In order to apply this newly-developed pump-probe laser system to implement systematic studies on the kinetics of diatomic ligand (NO, CO, O2) rebinding to heme and heme proteins, several experimental setups are utilized. In Chapter 1, the essential background knowledge, which helps to understand the iron-ligand interaction, is briefly described. In Chapter 2, in addition to a description of the preparation protocols of protein samples and details of the method for data analysis, three home-made setups are described, which include: a picosecond laser regenerative amplifier, a pump-probe application along the bore (2-inch in diameter) of a superconducting magnet and a temperature-controllable cryostat for spinning sample cell. Chapter 3 presents high magnetic field studies of several heme-ligand or protein-ligand systems. Pump-probe spectroscopy is used to

  2. MEGF9: a novel transmembrane protein with a strong and developmentally regulated expression in the nervous system.

    PubMed

    Brandt-Bohne, Ulrike; Keene, Douglas R; White, Fletcher A; Koch, Manuel

    2007-01-15

    MEGF9 [multiple EGF (epidermal growth factor)-like-domains 9], a novel transmembrane protein with multiple EGF-like repeats, is predominantly expressed in the developing and adult CNS (central nervous system) and PNS (peripheral nervous system). The domain structure of MEGF9 consists of an N-terminal region with several potential O-glycosylation sites followed by five EGF-like domains, which are highly homologous with the short arms of laminins. Following one single pass transmembrane domain, a highly conserved short intracellular domain with potential phosphorylation sites is present. The protein was recombinantly expressed and characterized as a tissue component. To study the expression pattern further, immunohistochemistry was performed and staining was detected in Purkinje cells of the cerebellum and in glial cells of the PNS. Additional expression was observed in the epidermal layer of skin, papillae of the tongue and the epithelium of the gastrointestinal tract. By immunoelectron microscopy, MEGF9 was detected in glial cells of the sciatic nerve facing the basement membrane. MEGF9 represents a novel putative receptor, expressed in neuronal and non-neuronal tissues, that is regulated during development and could function as a guidance or signalling molecule. PMID:16981854

  3. An alternatively spliced surfactant protein B mRNA in normal human lung: disease implication.

    PubMed Central

    Lin, Z; Wang, G; Demello, D E; Floros, J

    1999-01-01

    We identified an alternatively-spliced surfactant protein B (SP-B) mRNA from normal human lung with a 12 nt deletion at the beginning of exon 8. This deletion causes a loss of four amino acids in the SP-B precursor protein. Sequence comparison of the 3' splice sites reveals only one difference in the frequency of U/C in the 11 predominantly-pyrimidine nucleotide tract, 73% for the normal and 45% for the alternatively-spliced SP-B mRNA (77-99% for the consensus sequence). Analysis of SP-B mRNA in lung indicates that the abundance of the alternatively-spliced form is very low and varies among individuals. Although the relative abundance of the deletion form of SP-B mRNA remains constant among normal lungs, it is found with relatively higher abundance in the lungs of some individuals with diseases such as congenital alveolar proteinosis, respiratory distress syndrome, bronchopulmonary dysplasia, alveolar capillary dysplasia and hypophosphatasia. This observation points to the possibility that the alternative splicing is a potential regulatory mechanism of SP-B and may play a role in the pathogenesis of disease under certain circumstances. PMID:10493923

  4. Molecular energy dissipation in nanoscale networks of Dentin Matrix Protein 1 is strongly dependent on ion valence

    PubMed Central

    Adams, J; Fantner, G E; Fisher, L W; Hansma, P K

    2008-01-01

    The fracture resistance of biomineralized tissues such as bone, dentin, and abalone is greatly enhanced through the nanoscale interactions of stiff inorganic mineral components with soft organic adhesive components. A proper understanding of the interactions that occur within the organic component, and between the organic and inorganic components, is therefore critical for a complete understanding of the mechanics of these tissues. In this paper, we use Atomic Force Microscope (AFM) force spectroscopy and dynamic force spectroscopy to explore the effect of ionic interactions within a nanoscale system consisting of networks of Dentin Matrix Protein 1 (DMP1) (a component of both bone and dentin organic matrix), a mica surface, and an AFM tip. We find that DMP1 is capable of dissipating large amounts of energy through an ion-mediated mechanism, and that the effectiveness increases with increasing ion valence. PMID:18843380

  5. Mercury (II) removal by resistant bacterial isolates and mercuric (II) reductase activity in a new strain of Pseudomonas sp. B50A.

    PubMed

    Giovanella, Patricia; Cabral, Lucélia; Bento, Fátima Menezes; Gianello, Clesio; Camargo, Flávio Anastácio Oliveira

    2016-01-25

    This study aimed to isolate mercury resistant bacteria, determine the minimum inhibitory concentration for Hg, estimate mercury removal by selected isolates, explore the mer genes, and detect and characterize the activity of the enzyme mercuric (II) reductase produced by a new strain of Pseudomonas sp. B50A. The Hg removal capacity of the isolates was determined by incubating the isolates in Luria Bertani broth and the remaining mercury quantified by atomic absorption spectrophotometry. A PCR reaction was carried out to detect the merA gene and the mercury (II) reductase activity was determined in a spectrophotometer at 340 nm. Eight Gram-negative bacterial isolates were resistant to high mercury concentrations and capable of removing mercury, and of these, five were positive for the gene merA. The isolate Pseudomonas sp. B50A removed 86% of the mercury present in the culture medium and was chosen for further analysis of its enzyme activity. Mercuric (II) reductase activity was detected in the crude extract of this strain. This enzyme showed optimal activity at pH 8 and at temperatures between 37 °C and 45 °C. The ions NH4(+), Ba(2+), Sn(2+), Ni(2+) and Cd(2+) neither inhibited nor stimulated the enzyme activity but it decreased in the presence of the ions Ca(2+), Cu(+) and K(+). The isolate and the enzyme detected were effective in reducing Hg(II) to Hg(0), showing the potential to develop bioremediation technologies and processes to clean-up the environment and waste contaminated with mercury. PMID:26051077

  6. Strong-light photoinhibition treatment accelerates the changes of protein secondary structures in triton-treated photosystem I and photosystem II complexes.

    PubMed

    Ruan, X; Xu, Q; Mao, H B; Li, G F; Wei, J; Gong, Y D; Kuang, T Y; Zhao, N M

    2001-04-01

    Changes in the protein secondary structure and electron transport activity of the Triton X-100-treated photosystem I (PSI) and photosystem II (PSII) complexes after strong illumination treatment were studied using Fourier transform-infrared (FT-IR) spectroscopy and an oxygen electrode. Short periods of photoinhibitory treatment led to obvious decreases in the rates of PSI-mediated electron transport activity and PSII-mediated oxygen evolution in the native or Triton-treated PSI and PSII complexes. In the native PSI and PSII complexes, the protein secondary structures had little changes after the photoinhibitory treatment. However, in both Triton-treated PSI and PSII complexes, short photoinhibition times caused significant loss of alpha-helical content and increase of beta-sheet structure, similar to the conformational changes in samples of Triton-treated PSI and PSII complexes after long periods of dark incubation. Our results demonstrate that strong-light treatment to the Triton-treated PSI and PSII complexes accelerates destruction of the transmembrane structure of proteins in the two photosynthetic membranes. PMID:11565905

  7. Strong protection against ricin challenge induced by a novel modified ricin A-chain protein in mouse model

    PubMed Central

    Zhang, Tao; Yang, Hao; Kang, Lin; Gao, Shan; Xin, Wenwen; Yao, Wenwu; Zhuang, Xiangjin; Ji, Bin; Wang, Jinglin

    2015-01-01

    Ricin toxin (RT) is an extremely potent toxin derived from the castor bean plant. As a possible bioterrorist weapon, it was categorized as a level B agent in international society. With the growing awareness and concerns of the “white powder incident” in recent years, it is indispensable to develop an effective countermeasure against RT intoxication. In this study we used site-directed mutagenesis and polymerase chain reaction (PCR) techniques to modify the gene of ricin A-chain (RTA). As a result, we have generated a mutated and truncated ricin A-chain (mtRTA) vaccine antigen by E.coli strain. The cytotoxicity assay was used to evaluate the safety of the as-prepared mtRTA antigen, and the results showed that there was no residual toxicity observed when compared to the recombinant RTA (rRTA) or native RT. Furthermore, BALB/c mice were subcutaneously (s.c.) vaccinated with mtRTA 3 times at an interval of 2 weeks, and then the survivals were evaluated after intraperitoneal (i.p.) or intratracheal challenge of RT. The vaccinated mice developed a strong protective immune response that was wholly protective against 40 × LD50 of RT i.p. injection or 20 × LD50 of RT intratracheal spraying. The mtRTA antigen has great potential to be a vaccine candidate for future application in humans. PMID:26038805

  8. CD163-L1 is an endocytic macrophage protein strongly regulated by mediators in the inflammatory response.

    PubMed

    Moeller, Jesper B; Nielsen, Marianne J; Reichhardt, Martin P; Schlosser, Anders; Sorensen, Grith L; Nielsen, Ole; Tornøe, Ida; Grønlund, Jørn; Nielsen, Maria E; Jørgensen, Jan S; Jensen, Ole N; Mollenhauer, Jan; Moestrup, Søren K; Holmskov, Uffe

    2012-03-01

    CD163-L1 belongs to the group B scavenger receptor cysteine-rich family of proteins, where the CD163-L1 gene arose by duplication of the gene encoding the hemoglobin scavenger receptor CD163 in late evolution. The current data demonstrate that CD163-L1 is highly expressed and colocalizes with CD163 on large subsets of macrophages, but in contrast to CD163 the expression is low or absent in monocytes and in alveolar macrophages, glia, and Kupffer cells. The expression of CD163-L1 increases when cultured monocytes are M-CSF stimulated to macrophages, and the expression is further increased by the acute-phase mediator IL-6 and the anti-inflammatory mediator IL-10 but is suppressed by the proinflammatory mediators IL-4, IL-13, TNF-α, and LPS/IFN-γ. Furthermore, we show that CD163-L1 is an endocytic receptor, which internalizes independently of cross-linking through a clathrin-mediated pathway. Two cytoplasmic splice variants of CD163-L1 are differentially expressed and have different subcellular distribution patterns. Despite its many similarities to CD163, CD163-L1 does not possess measurable affinity for CD163 ligands such as the haptoglobin-hemoglobin complex or various bacteria. In conclusion, CD163-L1 exhibits similarity to CD163 in terms of structure and regulated expression in cultured monocytes but shows clear differences compared with the known CD163 ligand preferences and expression pattern in the pool of tissue macrophages. We postulate that CD163-L1 functions as a scavenger receptor for one or several ligands that might have a role in resolution of inflammation. PMID:22279103

  9. Strong ligand-protein interactions revealed by ultrafast infrared spectroscopy of CO in the heme pocket of the oxygen sensor FixL.

    PubMed

    Nuernberger, Patrick; Lee, Kevin F; Bonvalet, Adeline; Bouzhir-Sima, Latifa; Lambry, Jean-Christophe; Liebl, Ursula; Joffre, Manuel; Vos, Marten H

    2011-11-01

    In heme-based sensor proteins, ligand binding to heme in a sensor domain induces conformational changes that eventually lead to changes in enzymatic activity of an associated catalytic domain. The bacterial oxygen sensor FixL is the best-studied example of these proteins and displays marked differences in dynamic behavior with respect to model globin proteins. We report a mid-IR study of the configuration and ultrafast dynamics of CO in the distal heme pocket site of the sensor PAS domain FixLH, employing a recently developed method that provides a unique combination of high spectral resolution and range and high sensitivity. Anisotropy measurements indicate that CO rotates toward the heme plane upon dissociation, as is the case in globins. Remarkably, CO bound to the heme iron is tilted by ~30° with respect to the heme normal, which contrasts to the situation in myoglobin and in present FixLH-CO X-ray crystal structure models. This implies protein-environment-induced strain on the ligand, which is possibly at the origin of a very rapid docking-site population in a single conformation. Our observations likely explain the unusually low affinity of FixL for CO that is at the origin of the weak ligand discrimination between CO and O(2). Moreover, we observe orders of magnitude faster vibrational relaxation of dissociated CO in FixL than in globins, implying strong interactions of the ligand with the distal heme pocket environment. Finally, in the R220H FixLH mutant protein, where CO is H-bonded to a distal histidine, we demonstrate that the H-bond is maintained during photolysis. Comparison with extensively studied globin proteins unveils a surprisingly rich variety in both structural and dynamic properties of the interaction of a diatomic ligand with the ubiquitous b-type heme-proximal histidine system in different distal pockets. PMID:21970443

  10. NMR study of the phosphoryl binding loop in purine nucleotide proteins: Evidence for strong hydrogen binding in human N-ras p21

    SciTech Connect

    Redfield, A.G.; Papastavros, M.Z. )

    1990-04-10

    The structure of the phosphoryl binding region of human N-ras p21 was probed by using heteronuclear proton-observed NMR methods. Normal protein and a Gly-12 {yields} Asp-12 mutant protein were prepared with two amino acids labeled with {sup 15}N at their amide positions: valine and glycine, aspartic acid and glycine, and lysine and glycine. The authors completed the identification of amide {sup 15}NH resonances from Gly-12 and Asp-12 to the end of the phosphoryl binding domain consensus sequence (Lys-16) in protein complexed with GDP and have made tentative amide identifications from Val-9 to Ser-17. The methods used, together with initial identifications of the Gly-12 and -13 amide resonances, were described previously. The amide resonances of both Gly-13 and Lys-16 are shifted downfield below 10.4 ppm in both the normal and mutant proteins. These downfield shifts are presumed to be due to strong hydrogen bonds with the {beta}-phosphate of GDP.

  11. New Surfactant with SP-B and C Analogs Gives Survival Benefit after Inactivation in Preterm Lambs

    PubMed Central

    Kuypers, Elke; Jellema, Reint K.; Ophelders, Daan R. M. G.; Ospina, Olga L.; Perez-Gil, J.; Bianco, Federico; Garzia, Raffaella; Razzetti, Roberta; Kramer, Boris W.

    2012-01-01

    Background Respiratory distress syndrome in preterm babies is caused by a pulmonary surfactant deficiency, but also by its inactivation due to various conditions, including plasma protein leakage. Surfactant replacement therapy is well established, but clinical observations and in vitro experiments suggested that its efficacy may be impaired by inactivation. A new synthetic surfactant (CHF 5633), containing synthetic surfactant protein B and C analogs, has shown comparable effects on oxygenation in ventilated preterm rabbits versus Poractant alfa, but superior resistance against inactivation in vitro. We hypothesized that CHF 5633 is also resistant to inactivation by serum albumin in vivo. Methodology/Principal Findings Nineteen preterm lambs of 127 days gestational age (term = 150 days) received CHF 5633 or Poractant alfa and were ventilated for 48 hours. Ninety minutes after birth, the animals received albumin with CHF 5633 or Poractant alfa. Animals received additional surfactant if PaO2 dropped below 100 mmHg. A pressure volume curve was done post mortem and markers of pulmonary inflammation, surfactant content and biophysiology, and lung histology were assessed. CHF 5633 treatment resulted in improved arterial pH, oxygenation and ventilation efficiency index. The survival rate was significantly higher after CHF 5633 treatment (5/7) than after Poractant alfa (1/8) after 48 hours of ventilation. Biophysical examination of the surfactant recovered from bronchoalveolar lavages revealed that films formed by CHF 5633-treated animals reached low surface tensions in a wider range of compression rates than films from Poractant alfa-treated animals. Conclusions For the first time a synthetic surfactant containing both surfactant protein B and C analogs showed significant benefit over animal derived surfactant in an in vivo model of surfactant inactivation in premature lambs. PMID:23091635

  12. Strong Interaction

    SciTech Connect

    Karsch, F.; Vogelsang, V.

    2009-09-29

    We will give here an overview of our theory of the strong interactions, Quantum Chromo Dynamics (QCD) and its properties. We will also briefly review the history of the study of the strong interactions, and the discoveries that ultimately led to the formulation of QCD. The strong force is one of the four known fundamental forces in nature, the others being the electromagnetic, the weak and the gravitational force. The strong force, usually referred to by scientists as the 'strong interaction', is relevant at the subatomic level, where it is responsible for the binding of protons and neutrons to atomic nuclei. To do this, it must overcome the electric repulsion between the protons in an atomic nucleus and be the most powerful force over distances of a few fm (1fm=1 femtometer=1 fermi=10{sup -15}m), the typical size of a nucleus. This property gave the strong force its name.

  13. Goose parvovirus structural proteins expressed by recombinant baculoviruses self-assemble into virus-like particles with strong immunogenicity in goose

    SciTech Connect

    Ju, Huanyu; Wei, Na; Wang, Qian; Wang, Chunyuan; Jing, Zhiqiang; Guo, Lu; Liu, Dapeng; Gao, Mingchun; Ma, Bo; Wang, Junwei

    2011-05-27

    Highlights: {yields} All three capsid proteins can be expressed in insect cells in baculovirus expression system. {yields} All three recombinant proteins were spontaneously self-assemble into virus-like particles whose size and appearance were similar to those of native purified GPV virions. {yields} The immunogenicity of GPV-VLPs was better than commercial inactivated vaccine and attenuated vaccine. -- Abstract: Goose parvovirus (GPV), a small non-enveloped ssDNA virus, can cause Derzsy's disease, and three capsid proteins of VP1, VP2, and VP3 are encoded by an overlapping nucleotide sequence. However, little is known on whether recombinant viral proteins (VPs) could spontaneously assemble into virus-like particles (VLPs) in insect cells and whether these VLPs could retain their immunoreactivity and immunogenicity in susceptible geese. To address these issues, genes for these GPV VPs were amplified by PCR, and the recombinant VPs proteins were expressed in insect cells using a baculovirus expression system for the characterization of their structures, immunoreactivity, and immunogenicity. The rVP1, rVP2, and rVP3 expressed in Sf9 cells were detected by anti-GPV sera, anti-VP3 sera, and anti-His antibodies, respectively. Electron microscopy revealed that these rVPs spontaneously assembled into VLPs in insect cells, similar to that of the purified wild-type GPV virions. In addition, vaccination with individual types of VLPs, particularly with the rVP2-VLPs, induced higher titers of antibodies and neutralized different strains of GPVs in primary goose and duck embryo fibroblast cells in vitro. These data indicated that these VLPs retained immunoreactivity and had strong immunogenicity in susceptible geese. Therefore, our findings may provide a framework for development of new vaccines for the prevention of Derzsy's disease and vehicles for the delivery of drugs.

  14. Interactions of the C-terminus of lung surfactant protein B with lipid bilayers are modulated by acyl chain saturation.

    PubMed

    Antharam, Vijay C; Farver, R Suzanne; Kuznetsova, Anna; Sippel, Katherine H; Mills, Frank D; Elliott, Douglas W; Sternin, Edward; Long, Joanna R

    2008-11-01

    Lung surfactant protein B (SP-B) is critical to minimizing surface tension in the alveoli. The C-terminus of SP-B, residues 59-80, has much of the surface activity of the full protein and serves as a template for the development of synthetic surfactant replacements. The molecular mechanisms responsible for its ability to restore lung compliance were investigated with circular dichroism, differential scanning calorimetry, and (31)P and (2)H solid-state NMR spectroscopy. SP-B(59-80) forms an amphipathic helix which alters lipid organization and acyl chain dynamics in fluid lamellar phase 4:1 DPPC:POPG and 3:1 POPC:POPG MLVs. At higher levels of SP-B(59-80) in the POPC:POPG lipid system a transition to a nonlamellar phase is observed while DPPC:POPG mixtures remain in a lamellar phase. Deuterium NMR shows an increase in acyl chain order in DPPC:POPG MLVs on addition of SP-B(59-80); in POPC:POPG MLVs, acyl chain order parameters decrease. Our results indicate SP-B(59-80) penetrates deeply into DPPC:POPG bilayers and binds more peripherally to POPC:POPG bilayers. Similar behavior has been observed for KL(4), a peptide mimetic of SP-B which was originally designed using SP-B(59-80) as a template and has been clinically demonstrated to be successful in treating respiratory distress syndrome. The ability of these helical peptides to differentially partition into lipid lamellae based on their degree of monounsaturation and subsequent changes in lipid dynamics suggest a mechanism for lipid organization and trafficking within the dynamic lung environment. PMID:18694722

  15. Hydrophobic surfactant proteins and their analogues.

    PubMed

    Walther, Frans J; Waring, Alan J; Sherman, Mark A; Zasadzinski, Joseph A; Gordon, Larry M

    2007-01-01

    Lung surfactant is a complex mixture of phospholipids and four surfactant-associated proteins (SP-A, SP-B, SP-C and SP-D). Its major function in the lung alveolus is to reduce surface tension at the air-water interface in the terminal airways by the formation of a surface-active film enriched in surfactant lipids, hence preventing cellular collapse during respiration. Surfactant therapy using bovine or porcine lung surfactant extracts, which contain only polar lipids and native SP-B and SP-C, has dramatically improved the therapeutic outcomes of preterm infants with respiratory distress syndrome (RDS). One important goal of surfactant researchers is to replace animal-derived therapies with fully synthetic preparations based on SP-B and SP-C, produced by recombinant technology or peptide synthesis, and reconstituted with selected synthetic lipids. Here, we review recent research developments with peptide analogues of SP-B and SP-C, designed using either the known primary sequence and three-dimensional (3D) structure of the native proteins or, alternatively, the known 3D structures of closely homologous proteins. Such SP-B and SP-C mimics offer the possibility of studying the mechanisms of action of the respective native proteins, and may allow the design of optimized surfactant formulations for specific pulmonary diseases (e.g., acute lung injury (ALI) or acute respiratory distress syndrome (ARDS)). These synthetic surfactant preparations may also be a cost-saving therapeutic approach, with better quality control than may be obtained with animal-based treatments. PMID:17575474

  16. A Strongly Absorbing Class of Non-Natural Labels for Probing Protein Electrostatics and Solvation with FTIR and 2D IR Spectroscopies

    PubMed Central

    Woys, Ann Marie; Mukherjee, Sudipta S.; Skoff, David R.; Moran, Sean D.; Zanni, Martin T.

    2013-01-01

    A series of non-natural infrared probes is reported that consist of a metal-tricarbonyl modified with a -(CH2)n- linker and cysteine-specific leaving group. They can be site-specifically attached to proteins using mutagenesis and similar protocols for EPR spin labels, which have the same leaving group. We characterize the label’s frequencies and lifetimes using 2D IR spectroscopy in solvents of varying dielectric. The frequency range spans 10 cm−1, and the variation in lifetimes ranges from 6 to 19 ps, indicating that these probes are very sensitive to their environments. Also, we attached probes with -(CH2)-, -(CH2)3-, -(CH2)4- linkers to ubiquitin at positions 6 and 63 and collected spectra in aqueous buffer. The frequencies and lifetimes were correlated for 3C and 4C linkers, as they were in the solvents, but did not correlate for the 1C linker. We concluded that lifetime measures solvation, whereas frequency reflects the electrostatics of the environment, which in the case of the 1C linker is a measure of the protein electrostatic field. We also labeled V71C α-synuclein in buffer and membrane-bound. Unlike most other infrared labels, this label has extremely-strong cross-sections and so can be measured with 2D IR spectroscopy at sub-millimolar concentrations. We expect that these labels will find use in studying the structure and dynamics of membrane-bound, aggregated, and kinetically-evolving proteins for which high signal-to-noise at low protein concentrations is imperative. PMID:23537223

  17. Glucocorticoids regulate surfactant protein synthesis in a pulmonary adenocarcinoma cell line

    SciTech Connect

    O'Reilly, M.A.; Gazdar, A.F.; Clark, J.C.; Pilot-Matias, T.J.; Wert, S.E.; Hull, W.M.; Whitsett, J.A. )

    1989-12-01

    Synthesis of pulmonary surfactant proteins SP-A, SP-B, and SP-C was demonstrated in a cell line derived from a human adenocarcinoma of the lung. The cells contained numerous lamellar inclusion bodies and formed organized groups of cells containing well-developed junctional complexes and apical microvillous membranes. Synthesis of SP-A was detected in the cells by enzyme-linked immunoabsorbent assay and by immunoprecipitation of (35S)methionine-labeled protein. SP-A was identified as an Mr 31,000-36,000 polypeptide containing asparagine-linked carbohydrate. Northern blot analysis detected SP-A mRNA of 2.2 kb. Dexamethasone (1-10 nM) enhanced the relative abundance of SP-A mRNA. Despite stimulation of SP-A mRNA, intracellular SP-A content was unaltered or inhibited by dexamethasone. SP-B and SP-C mRNAs and synthesis of the SP-B and SP-C precursors were markedly induced by dexamethasone. ProSP-B was synthesized and secreted primarily as an Mr 42,000-46,000 polypeptide. Proteolysis of the proSP-B resulted in the generation of endoglycosidase F-sensitive Mr = 19,000-21,000 and 25,000-27,000 peptides, which were detected both intra- and extracellularly. SP-C proprotein of Mr = 22,000 and smaller SP-C fragments were detected intracellularly but were not detected in the media. Mature forms of SP-B (Mr = 8,000) and SP-C (Mr = 4,000) were not detected. Glucocorticoids directly enhance the relative synthesis and mRNA of the surfactant proteins SP-A, SP-B, and SP-C. Discrepancies among SP-A mRNA, its de novo synthesis, and cell content suggest that glucocorticoid may alter both pre- and posttranslational factors modulating SP-A expression.

  18. Cysteine-Rich Secretory Protein-3 (CRISP3) Is Strongly Up-Regulated in Prostate Carcinomas with the TMPRSS2-ERG Fusion Gene

    PubMed Central

    Costa, Vera L.; Barros-Silva, João D.; Ramalho-Carvalho, João; Jerónimo, Carmen; Henrique, Rui; Lind, Guro E.; Skotheim, Rolf I.; Lothe, Ragnhild A.; Teixeira, Manuel R.

    2011-01-01

    A large percentage of prostate cancers harbor TMPRSS2-ERG gene fusions, leading to aberrant overexpression of the transcription factor ERG. The target genes deregulated by this rearrangement, however, remain mostly unknown. To address this subject we performed genome-wide mRNA expression analysis on 6 non-malignant prostate samples and 24 prostate carcinomas with (n = 16) and without (n = 8) TMPRSS2-ERG fusion as determined by FISH. The top-most differentially expressed genes and their associations with ERG over-expression were technically validated by quantitative real-time PCR and biologically validated in an independent series of 200 prostate carcinomas. Several genes encoding metabolic enzymes or extracellular/transmembrane proteins involved in cell adhesion, matrix remodeling and signal transduction pathways were found to be co-expressed with ERG. Within those significantly over-expressed in fusion-positive carcinomas, CRISP3 showed more than a 50-fold increase when compared to fusion-negative carcinomas, whose expression levels were in turn similar to that of non-malignant samples. In the independent validation series, ERG and CRISP3 mRNA levels were strongly correlated (rs = 0.65, p<0.001) and both were associated with pT3 disease staging. Furthermore, immunohistochemistry results showed CRISP3 protein overexpression in 63% of the carcinomas and chromatin immunoprecipitation with an anti-ERG antibody showed that CRISP3 is a direct target of the transcription factor ERG. We conclude that ERG rearrangement is associated with significant expression alterations in genes involved in critical cellular pathways that define a subset of locally advanced PCa. In particular, we show that CRISP3 is a direct target of ERG that is strongly overexpressed in PCa with the TMPRSS2-ERG fusion gene. PMID:21814574

  19. Receptor activating NF-κB ligand (RANKL) is a constitutive intracellular protein in resting human basophils and is strongly induced on their surface by interleukin 3.

    PubMed

    Poli, Caroline; Martin, Jérôme C; Braudeau, Cécile; Bériou, Gaelle; Hémont, Caroline; Charrier, Céline; Guérin, Sarah; Heslan, Michèle; Josien, Régis

    2015-05-01

    Receptor activating NF-κB ligand (RANKL) is a member of the TNF superfamily that plays a pivotal role in bone homeostasis as being the major osteoclastogenesis factor. RANKL also has pleiotropic effects in the immune system in which it is expressed by activated T and B cells and some innate lymphoid cells. RANKL-RANK interactions mediate lymph node organogenesis and immunoregulatory functions in autoimmune disease and carcinogenesis as well as cross talk between the immune system and bone. In this study, we show that basophils were the strongest RANKL mRNA-expressing cells amongst major leukocyte subsets in human blood. RANKL was preformed as an intracellular protein in resting basophils and was rapidly and strongly expressed on their surface upon stimulation with IL-3, but not other stimuli. This expression was stable for at least 6 days. Activated basophils could also release soluble RANKL in small quantities upon interaction with DCs or monocytes. In the blood, basophils were the sole cells to express membrane RANKL in response to IL-3. This study indicates that basophils should be considered as new players in the pleiotropic and complex RANKL-RANK interaction system and suggests a role for RANKL in the interaction between basophils and immune cells in inflammatory allergic tissues and secondary lymphoid organs. PMID:25433635

  20. A vaccine based on a mutant transferrin binding protein B of Haemophilus parasuis induces a strong T-helper 2 response and bacterial clearance after experimental infection.

    PubMed

    Martínez-Martínez, Sonia; Frandoloso, Rafael; Rodríguez-Ferri, Elías-Fernando; García-Iglesias, María-José; Pérez-Martínez, Claudia; Álvarez-Estrada, Álvaro; Gutiérrez-Martín, César-Bernardo

    2016-10-15

    This study aimed to characterize the type of immune response induced by an experimental vaccine based on a mutant Haemophilus parasuis transferrin binding protein (Tbp) B (Y167A) defective in its ability to bind porcine transferrin. Clinical and pathological signs, bacterial clearance, antibody response and the cytokine profile in alveolar macrophages and spleen after the vaccination and challenge of twenty-two colostrum-deprived pigs with 10(8) CFU of H. parasuis were analysed. Pigs vaccinated with Y167A were compared to those vaccinated with native TbpB (nTbpB), those treated with a commercial bacterin (CB) against Glässer's disease, those unvaccinated challenged (CH) and those unvaccinated unchallenged (UNCH) pigs. The rectal temperatures of Y167A pigs resembled those of UNCH pigs and were significantly lower than those of the nTbpB, CB and CH animals. A major reduction in pathological changes of the challenged pigs was observed in the Y167A group. H. parasuis was cleared from 88.9% of the samples from Y167A pigs versus 60.0% and 55.6% from those of the CB and nTbpB groups, respectively. The antibody response elicited by Y167A by ELISA was notably higher than that observed for nTbpB and CB pigs and was capable of preventing the expression and secretion of IL-8. The expression of IL-4 and IL-5, which were associated with the specific antibody levels, suggests that the main mechanism of protection conferred by Y167A vaccine is based on a strong T-helper 2 response. PMID:27590421

  1. Endogenous proteolytic cleavage of disease-associated prion protein to produce C2 fragments is strongly cell- and tissue-dependent.

    PubMed

    Dron, Michel; Moudjou, Mohammed; Chapuis, Jérôme; Salamat, Muhammad Khalid Farooq; Bernard, Julie; Cronier, Sabrina; Langevin, Christelle; Laude, Hubert

    2010-04-01

    The abnormally folded form of the prion protein (PrP(Sc)) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrP(Sc) N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrP(Sc) accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrP(Sc) proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrP(Sc) fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrP(Sc) and cell pathogenesis of prion infection. PMID:20154089

  2. A novel human BTB-kelch protein KLHL31, strongly expressed in muscle and heart, inhibits transcriptional activities of TRE and SRE.

    PubMed

    Yu, Weishi; Li, Yongqing; Zhou, Xijin; Deng, Yun; Wang, Zequn; Yuan, Wuzhou; Li, Dali; Zhu, Chuanbing; Zhao, Xueying; Mo, Xiaoyang; Huang, Wen; Luo, Na; Yan, Yan; Ocorr, Karen; Bodmer, Rolf; Wang, Yuequn; Wu, Xiushan

    2008-11-30

    The Bric-a-brac, Tramtrack, Broad-complex (BTB) domain is a protein-protein interaction domain that is found in many zinc finger transcription factors. BTB containing proteins play important roles in a variety of cellular functions including regulation of transcription, regulation of the cytoskeleton, protein ubiquitination, angiogenesis, and apoptosis. Here, we report the cloning and characterization of a novel human gene, KLHL31, from a human embryonic heart cDNA library. The cDNA of KLHL31 is 5743 bp long, encoding a protein product of 634 amino acids containing a BTB domain. The protein is highly conserved across different species. Western blot analysis indicates that the KLHL31 protein is abundantly expressed in both embryonic skeletal and heart tissue. In COS-7 cells, KLHL31 proteins are localized to both the nucleus and the cytoplasm. In primary cultures of nascent mouse cardiomyocytes, the majority of endogenous KLHL31 proteins are localized to the cytoplasm. KLHL31 acts as a transcription repressor when fused to GAL4 DNA-binding domain and deletion analysis indicates that the BTB domain is the main region responsible for this repression. Overexpression of KLHL31 in COS-7 cells inhibits the transcriptional activities of both the TPA-response element (TRE) and serum response element (SRE). KLHL31 also significantly reduces JNK activation leading to decreased phosphorylation and protein levels of the JNK target c-Jun in both COS-7 and Hela cells. These results suggest that KLHL31 protein may act as a new transcriptional repressor in MAPK/JNK signaling pathway to regulate cellular functions. PMID:18719355

  3. Hypoxia-induced mitogenic factor modulates surfactant protein B and C expression in mouse lung.

    PubMed

    Tong, Qiangsong; Zheng, Liduan; Dodd-o, Jeffrey; Langer, John; Wang, Danming; Li, Dechun

    2006-01-01

    Previous studies have demonstrated a robust pulmonary expression of hypoxia-induced mitogenic factor (HIMF) during the perinatal period, when surfactant protein (SP) synthesis begins. We hypothesized that HIMF modulates SP expression and participates in lung development and maturation. The temporal-spatial expression of HIMF, SP-B, and SP-C in developing mouse lungs was examined by immunohistochemical staining, Western blot, and RT-PCR. The expression and localization of SP-B and SP-C were investigated in mouse lungs after intratracheal instillation of HIMF in adult mice. The effects of HIMF on SP-B and SP-C transcription activity, and on mRNA degradation, were investigated in mouse lung epithelial (MLE)-12 and C10 cells using the promoter-luciferase reporter assay and actinomycin D incubation. The activation of Akt, extracellular signal-regulated kinase (ERK)1/2, and p38 mitogen-activated protein kinase was explored by Western blot. Intratracheal instillation of HIMF resulted in significant increases of SP-B and SP-C production, predominantly localized to alveolar type II cells. In MLE-12 and C10 cells, HIMF enhanced SP-B and SP-C mRNA levels in a dose-dependent manner. Meanwhile, HIMF increased transcription activity and prevented actinomycin D-facilitated SP-B and SP-C mRNA degradation in MLE-12 cells. Incubation of cells with LY294002, PD098059, or U0126 abolished HIMF-induced Akt and ERK1/2 phosphorylation and suppressed HIMF-induced SP-B and SP-C production, whereas SB203580 had no effect. These results indicate that HIMF induces SP-B and SP-C production in mouse lungs and alveolar type II-like cell lines via activations of phosphatidylinositol 3-kinase/Akt and ERK1/2 mitogen-activated protein kinase, suggesting that HIMF plays critical roles in lung development and maturation. PMID:16166744

  4. Burkholderia Hep_Hap autotransporter (BuHA) proteins elicit a strong antibody response during experimental glanders but not human melioidosis

    PubMed Central

    Tiyawisutsri, Rachaneeporn; Holden, Matthew TG; Tumapa, Sarinna; Rengpipat, Sirirat; Clarke, Simon R; Foster, Simon J; Nierman, William C; Day, Nicholas PJ; Peacock, Sharon J

    2007-01-01

    Background The bacterial biothreat agents Burkholderia mallei and Burkholderia pseudomallei are the cause of glanders and melioidosis, respectively. Genomic and epidemiological studies have shown that B. mallei is a recently emerged, host restricted clone of B. pseudomallei. Results Using bacteriophage-mediated immunoscreening we identified genes expressed in vivo during experimental equine glanders infection. A family of immunodominant antigens were identified that share protein domain architectures with hemagglutinins and invasins. These have been designated Burkholderia Hep_Hag autotransporter (BuHA) proteins. A total of 110/207 positive clones (53%) of a B. mallei expression library screened with sera from two infected horses belonged to this family. This contrasted with 6/189 positive clones (3%) of a B. pseudomallei expression library screened with serum from 21 patients with culture-proven melioidosis. Conclusion Members of the BuHA proteins are found in other Gram-negative bacteria and have been shown to have important roles related to virulence. Compared with other bacterial species, the genomes of both B. mallei and B. pseudomallei contain a relative abundance of this family of proteins. The domain structures of these proteins suggest that they function as multimeric surface proteins that modulate interactions of the cell with the host and environment. Their effect on the cellular immune response to B. mallei and their potential as diagnostics for glanders requires further study. PMID:17362501

  5. Sequences of a hairpin structure in the 3'-untranslated region mediate regulation of human pulmonary surfactant protein B mRNA stability.

    PubMed

    Huang, Helen W; Payne, David E; Bi, Weizhen; Pan, Su; Bruce, Shirley R; Alcorn, Joseph L

    2012-05-15

    The ability of pulmonary surfactant to reduce alveolar surface tension requires adequate expression of surfactant protein B (SP-B). Dexamethasone (DEX, 10(-7) M) increases human SP-B mRNA stability by a mechanism that requires a 126-nt-long segment (the 7.6S region) of the 3'-untranslated region (3'-UTR). The objective of this study was to identify sequences in the 7.6S region that mediate regulation of SP-B mRNA stability. The 7.6S region was found to be sufficient for DEX-mediated stabilization of mRNA. Sequential substitution mutagenesis of the 7.6S region indicates that a 90-nt region is required for DEX-mediated stabilization and maintenance of intrinsic stability. In this region, one 30-nt-long element (002), predicted to form a stem-loop structure, is sufficient for DEX-mediated stabilization of mRNA and intrinsic mRNA stability. Cytosolic proteins specifically bind element 002, and binding activity is unaffected whether proteins are isolated from cells incubated in the absence or presence of DEX. While loop sequences of element 002 have no role in regulation of SP-B mRNA stability, the proximal stem sequences are required for DEX-mediated stabilization and specific binding of proteins. Mutation of the sequences that comprise the proximal or distal arm of the stem negates the destabilizing activity of element 002 on intrinsic SP-B mRNA stability. These results indicate that cytosolic proteins bind a single hairpin structure that mediates intrinsic and hormonal regulation of SP-B mRNA stability via mechanisms that involve sequences of the stems of the hairpin structure. PMID:22367784

  6. Motifs within the CA-repeat-rich region of Surfactant Protein B (SFTPB) intron 4 differentially affect mRNA splicing

    PubMed Central

    Yang, Wenjun; Ni, Lan; Silveyra, Patricia; Wang, Guirong; Noutsios, Georgios T; Singh, Anamika; DiAngelo, Susan L; Sanusi, Olabisi; Raval, Manmeet; Floros, Joanna

    2013-01-01

    The first half of the surfactant protein B (SP-B) gene intron 4 is a CA-repeat-rich region that contains 11 motifs. To study the role of this region on SP-B mRNA splicing, minigenes were generated by systematic removal of motifs from either the 5′ or 3′ end. These were transfected in CHO cells to study their splicing efficiency. The latter was determined as the ratio of completely to incompletely spliced SP-B RNA. Our results indicate that SP-B intron 4 motifs differentially affect splicing. Motifs 8 and 9 significantly enhanced and reduced splicing of intron 4, respectively. RNA mobility shift assays performed with a Motif 8 sequence that contains a CAUC cis-element and cell extracts resulted in a RNA:protein shift that was lost upon mutation of the element. Furthermore, in silico analysis of mRNA secondary structure stability for minigenes with and without motif 8 indicated a correlation between mRNA stability and splicing ratio. We conclude that differential loss of specific intron 4 motifs results in one or more of the following: a) altered splicing, b) differences in RNA stability and c) changes in secondary structure. These, in turn, may affect SP-B content in lung health or disease. PMID:23687636

  7. Functional and evolutionary analyses of Helicobacter pylori HP0231 (DsbK) protein with strong oxidative and chaperone activity characterized by a highly diverged dimerization domain

    PubMed Central

    Bocian-Ostrzycka, Katarzyna M.; Łasica, Anna M.; Dunin-Horkawicz, Stanisław; Grzeszczuk, Magdalena J.; Drabik, Karolina; Dobosz, Aneta M.; Godlewska, Renata; Nowak, Elżbieta; Collet, Jean-Francois; Jagusztyn-Krynicka, Elżbieta K.

    2015-01-01

    Helicobacter pylori does not encode the classical DsbA/DsbB oxidoreductases that are crucial for oxidative folding of extracytoplasmic proteins. Instead, this microorganism encodes an untypical two proteins playing a role in disulfide bond formation – periplasmic HP0231, which structure resembles that of EcDsbC/DsbG, and its redox partner, a membrane protein HpDsbI (HP0595) with a β-propeller structure. The aim of presented work was to assess relations between HP0231 structure and function. We showed that HP0231 is most closely related evolutionarily to the catalytic domain of DsbG, even though it possesses a catalytic motif typical for canonical DsbA proteins. Similarly, the highly diverged N-terminal dimerization domain is homologous to the dimerization domain of DsbG. To better understand the functioning of this atypical oxidoreductase, we examined its activity using in vivo and in vitro experiments. We found that HP0231 exhibits oxidizing and chaperone activities but no isomerizing activity, even though H. pylori does not contain a classical DsbC. We also show that HP0231 is not involved in the introduction of disulfide bonds into HcpC (Helicobacter cysteine-rich protein C), a protein involved in the modulation of the H. pylori interaction with its host. Additionally, we also constructed a truncated version of HP0231 lacking the dimerization domain, denoted HP0231m, and showed that it acts in Escherichia coli cells in a DsbB-dependent manner. In contrast, HP0231m and classical monomeric EcDsbA (E. coli DsbA protein) were both unable to complement the lack of HP0231 in H. pylori cells, though they exist in oxidized forms. HP0231m is inactive in the insulin reduction assay and possesses high chaperone activity, in contrast to EcDsbA. In conclusion, HP0231 combines oxidative functions characteristic of DsbA proteins and chaperone activity characteristic of DsbC/DsbG, and it lacks isomerization activity. PMID:26500620

  8. Lipid Specificity of Surfactant Protein B Studied by Time-of-Flight Secondary Ion Mass Spectrometry

    PubMed Central

    Breitenstein, D.; Batenburg, J. J.; Hagenhoff, B.; Galla, H.-J.

    2006-01-01

    One of the key functions of mammalian pulmonary surfactant is the reduction of surface tension to minimal values. To fulfill this function it is expected to become enriched in dipalmitoylphosphatidylcholine either on its way from the alveolar type II pneumocytes to the air/water interface of the lung or within the surface film during compression and expansion of the alveoli during the breathing cycle. One protein that may play a major role in this enrichment process is the surfactant protein B. The aim of this study was to identify the lipidic interaction partner of this protein. Time-of-flight secondary ion mass spectrometry was used to analyze the lateral distribution of the components in two SP-B-containing model systems. Either native or partly isotopically labeled lipids were analyzed. The results of both setups give strong indications that, at least under the specific conditions of the chosen model systems (e.g., concerning pH and lipid composition), the lipid interacting with surfactant protein B is not phosphatidylglycerol as generally accepted, but dipalmitoylphosphatidylcholine instead. PMID:16632503

  9. Development of high-productivity, strong cation-exchange adsorbers for protein capture by graft polymerization from membranes with different pore sizes

    PubMed Central

    Chenette, Heather C.S.; Robinson, Julie R.; Hobley, Eboni; Husson, Scott M.

    2012-01-01

    This paper describes the surface modification of macroporous membranes using ATRP (atom transfer radical polymerization) to create cation-exchange adsorbers with high protein binding capacity at high product throughput. The work is motivated by the need for a more economical and rapid capture step in downstream processing of protein therapeutics. Membranes with three reported nominal pore sizes (0.2, 0.45, 1.0 μm) were modified with poly(3-sulfopropyl methacrylate, potassium salt) tentacles, to create a high density of protein binding sites. A special formulation was used in which the monomer was protected by a crown ether to enable surface-initiated ATRP of this cationic polyelectrolyte. Success with modification was supported by chemical analysis using Fourier-transform infrared spectroscopy and indirectly by measurement of pure water flux as a function of polymerization time. Uniformity of modification within the membranes was visualized with confocal laser scanning microscopy. Static and dynamic binding capacities were measured using lysozyme protein to allow comparisons with reported performance data for commercial cation-exchange materials. Dynamic binding capacities were measured for flow rates ranging from 13 to 109 column volumes (CV)/min. Results show that this unique ATRP formulation can be used to fabricate cation-exchange membrane adsorbers with dynamic binding capacities as high as 70 mg/mL at a throughput of 100 CV/min and unprecedented productivity of 300 mg/mL/min. PMID:23175597

  10. In Vivo-Expressed Proteins of Virulent Leptospira interrogans Serovar Autumnalis N2 Elicit Strong IgM Responses of Value in Conclusive Diagnosis.

    PubMed

    Raja, Veerapandian; Shanmughapriya, Santhanam; Kanagavel, Murugesan; Artiushin, Sergey C; Velineni, Sridhar; Timoney, John F; Natarajaseenivasan, Kalimuthusamy

    2016-01-01

    Leptospirosis is a serious zoonosis that is underdiagnosed because of limited access to laboratory facilities in Southeast Asia, Central and South America, and Oceania. Timely diagnosis of locally distributed serovars of high virulence is crucial for successful care and outbreak management. Using pooled patient sera, an expression gene library of a virulent Leptospira interrogans serovar Autumnalis strain N2 isolated in South India was screened. The identified genes were characterized, and the purified recombinant proteins were used as antigens in IgM enzyme-linked immunosorbent assay (ELISA) either singly or in combination. Sera (n = 118) from cases of acute leptospirosis along with sera (n = 58) from healthy subjects were tested for reactivity with the identified proteins in an ELISA designed to detect specific IgM responses. We have identified nine immunoreactive proteins, ArgC, RecA, GlpF, FliD, TrmD, RplS, RnhB, Lp28.6, and Lrr44.9, which were found to be highly conserved among pathogenic leptospires. Apparently, the proteins ArgC, RecA, GlpF, FliD, TrmD, and Lrr44.9 are expressed during natural infection of the host and undetectable in in vitro cultures. Among all the recombinant proteins used as antigens in IgM ELISA, ArgC had the highest sensitivity and specificity, 89.8% and 95.5%, respectively, for the conclusive diagnosis of leptospirosis. The use of ArgC and RecA in combination for IgM ELISA increased the sensitivity and specificity to 95.7% and 94.9%, respectively. ArgC and RecA thus elicited specific IgM responses and were therefore effective in laboratory confirmation of Leptospira infection. PMID:26607308

  11. In Vivo-Expressed Proteins of Virulent Leptospira interrogans Serovar Autumnalis N2 Elicit Strong IgM Responses of Value in Conclusive Diagnosis

    PubMed Central

    Raja, Veerapandian; Shanmughapriya, Santhanam; Kanagavel, Murugesan; Artiushin, Sergey C.; Velineni, Sridhar; Timoney, John F.

    2015-01-01

    Leptospirosis is a serious zoonosis that is underdiagnosed because of limited access to laboratory facilities in Southeast Asia, Central and South America, and Oceania. Timely diagnosis of locally distributed serovars of high virulence is crucial for successful care and outbreak management. Using pooled patient sera, an expression gene library of a virulent Leptospira interrogans serovar Autumnalis strain N2 isolated in South India was screened. The identified genes were characterized, and the purified recombinant proteins were used as antigens in IgM enzyme-linked immunosorbent assay (ELISA) either singly or in combination. Sera (n = 118) from cases of acute leptospirosis along with sera (n = 58) from healthy subjects were tested for reactivity with the identified proteins in an ELISA designed to detect specific IgM responses. We have identified nine immunoreactive proteins, ArgC, RecA, GlpF, FliD, TrmD, RplS, RnhB, Lp28.6, and Lrr44.9, which were found to be highly conserved among pathogenic leptospires. Apparently, the proteins ArgC, RecA, GlpF, FliD, TrmD, and Lrr44.9 are expressed during natural infection of the host and undetectable in in vitro cultures. Among all the recombinant proteins used as antigens in IgM ELISA, ArgC had the highest sensitivity and specificity, 89.8% and 95.5%, respectively, for the conclusive diagnosis of leptospirosis. The use of ArgC and RecA in combination for IgM ELISA increased the sensitivity and specificity to 95.7% and 94.9%, respectively. ArgC and RecA thus elicited specific IgM responses and were therefore effective in laboratory confirmation of Leptospira infection. PMID:26607308

  12. Cell-specific modulation of surfactant proteins by ambroxol treatment.

    PubMed

    Seifart, Carola; Clostermann, Ursula; Seifart, Ulf; Müller, Bernd; Vogelmeier, Claus; von Wichert, Peter; Fehrenbach, Heinz

    2005-02-15

    Ambroxol [trans-4-(2-amino-3,5-dibromobenzylamino)-cyclohexanole hydrochloride], a mucolytic agent, was postulated to provide surfactant stimulatory properties and was previously used to prevent surfactant deficiency. Currently, the underlying mechanisms are not exactly clear. Because surfactant homeostasis is regulated by surfactant-specific proteins (SP), we analyzed protein amount and mRNA expression in whole lung tissue, isolated type II pneumocytes and bronchoalveolar lavage of Sprague-Dawley rats treated with ambroxol i.p. (75 mg/kg body weight, twice a day [every 12 h]). The methods used included competitive polymerase chain reaction (RT-PCR), Northern blotting, Western immunoblotting, and immunohistochemistry. In isolated type II pneumocytes of ambroxol-treated animals, SP-C protein and mRNA content were increased, whereas SP-A, -B and -D protein, mRNA, and immunoreactivity remained unaffected. However, ambroxol treatment resulted in a significant increase of SP-B and in a decrease of SP-D in whole lung tissue with enhanced immunostaining for SP-B in Clara Cells. SP-A and SP-D were significantly decreased in BAL fluid of ambroxol-treated animals. The data suggest that surfactant protein expression is modulated in a cell-specific manner by ambroxol, as type II pneumocytes exhibited an increase in SP-C, whereas Clara cells exhibited an increase in the immunoreactivity for SP-B accounting for the increased SP-B content of whole lung tissue. The results indicate that ambroxol may exert its positive effects, observed in the treatment of diseases related to surfactant deficiency, via modulation of surfactant protein expression. PMID:15694461

  13. Cell-specific modulation of surfactant proteins by ambroxol treatment

    SciTech Connect

    Seifart, Carola . E-mail: zwiebel@mailer.uni-marburg.de; Clostermann, Ursula; Seifart, Ulf

    2005-02-15

    Ambroxol [trans-4-(2-amino-3,5-dibromobenzylamino)-cyclohexanole hydrochloride], a mucolytic agent, was postulated to provide surfactant stimulatory properties and was previously used to prevent surfactant deficiency. Currently, the underlying mechanisms are not exactly clear. Because surfactant homeostasis is regulated by surfactant-specific proteins (SP), we analyzed protein amount and mRNA expression in whole lung tissue, isolated type II pneumocytes and bronchoalveolar lavage of Sprague-Dawley rats treated with ambroxol i.p. (75 mg/kg body weight, twice a day [every 12 h]). The methods used included competitive polymerase chain reaction (RT-PCR), Northern blotting, Western immunoblotting, and immunohistochemistry. In isolated type II pneumocytes of ambroxol-treated animals, SP-C protein and mRNA content were increased, whereas SP-A, -B and -D protein, mRNA, and immunoreactivity remained unaffected. However, ambroxol treatment resulted in a significant increase of SP-B and in a decrease of SP-D in whole lung tissue with enhanced immunostaining for SP-B in Clara Cells. SP-A and SP-D were significantly decreased in BAL fluid of ambroxol-treated animals. The data suggest that surfactant protein expression is modulated in a cell-specific manner by ambroxol, as type II pneumocytes exhibited an increase in SP-C, whereas Clara cells exhibited an increase in the immunoreactivity for SP-B accounting for the increased SP-B content of whole lung tissue. The results indicate that ambroxol may exert its positive effects, observed in the treatment of diseases related to surfactant deficiency, via modulation of surfactant protein expression.

  14. Effects of the lung surfactant protein B construct Mini-B on lipid bilayer order and topography

    PubMed Central

    Palleboina, Dharamaraju; Waring, Alan J.; Notter, Robert H.; Booth, Valerie

    2013-01-01

    The hydrophobic lung surfactant protein, SP-B, is essential for survival. Cycling of lung volume during respiration requires a surface-active lipid–protein layer at the alveolar air–water interface. SP-B may contribute to surfactant layer maintenance and renewal by facilitating contact and transfer between the surface layer and bilayer reservoirs of surfactant material. However, only small effects of SP-B on phospholipid orientational order in model systems have been reported. In this study, N-terminal (SP-B8–25) and C-terminal (SP-B63–78) helices of SP-B, either linked as Mini-B or unlinked but present in equal amounts, were incorporated into either model phospholipid mixtures or into bovine lipid extract surfactant in the form of vesicle dispersions or mechanically oriented bilayer samples. Deuterium and phosphorus nuclear magnetic resonance (NMR) were used to characterize effects of these peptides on phospholipid chain orientational order, headgroup orientation, and the response of lipid–peptide mixtures to mechanical orientation by mica plates. Only small effects on chain orientational order or headgroup orientation, in either vesicle or mechanically oriented samples, were seen. In mechanically constrained samples, however, Mini-B and its component helices did have specific effects on the propensity of lipid–peptide mixtures to form unoriented bilayer populations which do not exchange with the oriented fraction on the timescale of the NMR experiment. Modification of local bilayer orientation, even in the presence of mechanical constraint, may be relevant to the transfer of material from bilayer reservoirs to a flat surface-active layer, a process that likely requires contact facilitated by the formation of highly curved protrusions. PMID:22903196

  15. The bovine viral diarrhea virus E2 protein formulated with a novel adjuvant induces strong, balanced immune responses and provides protection from viral challenge in cattle.

    PubMed

    Snider, Marlene; Garg, Ravendra; Brownlie, Robert; van den Hurk, Jan V; van Drunen Littel-van den Hurk, Sylvia

    2014-11-28

    Bovine viral diarrhea virus (BVDV) is still one of the most serious pathogens in cattle, meriting the development of improved vaccines. Recently, we developed a new adjuvant consisting of poly[di(sodium carboxylatoethylphenoxy)]-phosphazene (PCEP), either CpG ODN or poly(I:C), and an immune defense regulator (IDR) peptide. As this adjuvant has been shown to mediate the induction of robust, balanced immune responses, it was evaluated in an E2 subunit vaccine against BVDV in lambs and calves. The BVDV type 2 E2 protein was produced at high levels in a mammalian expression system and purified. When formulated with either CpG ODN or poly(I:C), together with IDR and PCEP, the E2 protein elicited high antibody titers and production of IFN-γ secreting cells in lambs. As the immune responses were stronger when poly(I:C) was used, the E2 protein with poly(I:C), IDR and PCEP was subsequently tested in cattle. Robust virus neutralizing antibodies as well as cell-mediated immune responses, including CD8(+) cytotoxic T cell (CTL) responses, were induced. The fact that CTL responses were demonstrated in calves vaccinated with an E2 protein subunit vaccine indicates that this adjuvant formulation promotes cross-presentation. Furthermore, upon challenge with a high dose of virulent BVDV-2, the vaccinated calves showed almost no temperature response, weight loss, leukopenia or virus replication, in contrast to the control animals, which had severe clinical disease. These data suggest that this E2 subunit formulation induces significant protection from BVDV-2 challenge, and thus is a promising BVDV vaccine candidate; in addition, the adjuvant platform has applications in bovine vaccines in general. PMID:25454860

  16. Aggressive behaviour and physiological responses to pheromones are strongly impaired in mice deficient for the olfactory G-protein -subunit G8.

    PubMed

    Montani, Giorgia; Tonelli, Simone; Sanghez, Valentina; Ferrari, Pier Francesco; Palanza, Paola; Zimmer, Andreas; Tirindelli, Roberto

    2013-08-15

    Heterotrimeric G-proteins are critical players in the transduction mechanisms underlying odorant and pheromonal signalling. In the vomeronasal organ (VNO) of the adult mouse, two different G-protein complexes have been identified. Gαoβ2γ8 is preferentially expressed in the basal neurons and coexpresses with type-2 vomeronasal pheromone receptors (V2Rs) whereas Gαi2β2γ2 is found in the apical neurons and coexpresses with type-1 vomeronasal pheromone receptors (V1Rs). V2R-expressing neurons project to the posterior accessory olfactory bulb (AOB) whereas neurons expressing V1Rs send their axon to the anterior AOB. Gγ8 is also expressed in developing olfactory neurons where this protein is probably associated with Go. Here, we generated mice with a targeted deletion of the Gγ8 gene and investigated the behavioural effects and the physiological consequences of this mutation. Gγ8(-/-) mice show a normal development of the main olfactory epithelium; moreover, they do not display major deficits in odour perception. In contrast, the VNO undergoes a slow but remarkable loss of basal neurons starting from the fourth postnatal week, with a 40% reduction of cells at 2 months and 70% at 1 year. This loss is associated with a reduced early-gene expression in the posterior AOB of mice stimulated with pheromones. More interestingly, the Gγ8 deletion specifically leads to a reduced pheromone-mediated aggressiveness in both males and females, all other socio-sexual behaviours remaining unaltered. This study defines a specific role for Gγ8 in maintenance of the neuronal population of the VNO and in the mechanisms of pheromonal signalling that involve the aggressive behaviour towards conspecifics. PMID:23836683

  17. Multivalent Pneumococcal Protein Vaccines Comprising Pneumolysoid with Epitopes/Fragments of CbpA and/or PspA Elicit Strong and Broad Protection.

    PubMed

    Chen, Austen; Mann, Beth; Gao, Geli; Heath, Richard; King, Janice; Maissoneuve, Jeff; Alderson, Mark; Tate, Andrea; Hollingshead, Susan K; Tweten, Rodney K; Briles, David E; Tuomanen, Elaine I; Paton, James C

    2015-10-01

    Immunization with the pneumococcal proteins pneumolysin (Ply), choline binding protein A (CbpA), or pneumococcal surface protein A (PspA) elicits protective responses against invasive pneumococcal disease in animal models. In this study, we used different mouse models to test the efficacy of a variety of multivalent protein-based vaccines that comprised various combinations of full-length or peptide regions of the immunogens Ply, CbpA, or PspA: Ply toxoid with the L460D substitution (referred to herein as L460D); L460D fused with protective peptide epitopes from CbpA (YPT-L460D-NEEK [YLN]); L460D fused with the CD2 peptide containing the proline-rich region (PRR) of PspA (CD2-L460D); a combination of L460D and H70 (L460D+H70), a slightly larger PspA-derived peptide containing the PRR and the SM1 region; H70+YLN; and other combinations. Each mouse was immunized either intraperitoneally (i.p.) or subcutaneously (s.c.) with three doses (at 2-week intervals) of the various antigen combinations in alum adjuvant and then challenged in mouse models featuring different infection routes with multiple Streptococcus pneumoniae strains. In the i.p. infection sepsis model, H70+YLN consistently provided significant protection against three different challenge strains (serotypes 1, 2, and 6A); the CD2+YLN and H70+L460D combinations also elicited significant protection. Protection against intravenous (i.v.) sepsis (type 3 and 6A challenge strains) was largely dependent on PspA-derived antigen components, and the most protection was elicited by H70 with or without L460D or YLN. In a type 4 intratracheal (i.t.) challenge model that results in progression to meningitis, antigen combinations that contained YLN elicited the strongest protection. Thus, the trivalent antigen combination of H70+YLN elicited the strongest and broadest protection in diverse pneumococcal challenge models. PMID:26245351

  18. Accessory Interaction Motifs in the Atg19 Cargo Receptor Enable Strong Binding to the Clustered Ubiquitin-related Atg8 Protein*

    PubMed Central

    Abert, Christine; Kontaxis, Georg

    2016-01-01

    Selective autophagy contributes to cellular homeostasis by delivering harmful material into the lysosomal system for degradation via vesicular intermediates referred to as autophagosomes. The cytoplasm-to-vacuole targeting pathway is a variant of selective autophagy in Saccharomyces cerevisiae during which hydrolases such as prApe1 are transported into the vacuole. In general, selectivity is achieved by autophagic cargo receptors that link the cargo to autophagosomal membranes because of their ability to simultaneously interact with the cargo and Atg8 proteins that coat the membrane. The Atg19 receptor contains multiple Atg8 interaction sites in its C terminus in addition to a canonical Atg8-interacting LC3-interacting region (LIR, with LC3 being a homolog of Atg8) motif, but their mode of interaction with Atg8 is unclear. Here we show, using a combination of NMR, microscopy-based interaction assays, and prApe1 processing experiments, that two additional sites interact with Atg8 in a LIR-like and thus mutually exclusive manner. We term these motifs accessory LIR motifs because their affinities are lower than that of the canonical LIR motif. Thus, one Atg19 molecule has the ability to interact with multiple Atg8 proteins simultaneously, resulting in a high-avidity interaction that may confer specific binding to the Atg8-coated autophagosomal membrane on which Atg8 is concentrated. PMID:27402840

  19. Structure of the DNA distal to the gene for ribosomal protein S20 in Escherichia coli K12: presence of a strong terminator and an IS1 element.

    PubMed Central

    Mackie, G A

    1986-01-01

    The sequence of nucleotides extending over 2.3 kb distal to the gene for ribosomal protein S20 of E. coli has been determined. Included in the sequence is an efficient rho-independent terminator 50 b.p. distal to the coding sequence for S20, a complete copy of IS1 which lacks, however, flanking direct repeats, and finally, an open reading frame capable of encoding a 28 kDa polypeptide of unknown function. Several lines of evidence suggest that the IS1 sequence described here must represent one of the copies resident in the bacterial chromosome rather than a newly transposed copy. Northern blotting experiments show that the gene for S20 is functionally monocistronic under all conditions tested in several genetic backgrounds. Thus it seems unlikely that the distal copy of IS1 plays any role in the termination or stability of mRNA transcribed from the gene for S20. Images PMID:2429258

  20. The serodominant secreted effector protein of Salmonella, SseB, is a strong CD4 antigen containing an immunodominant epitope presented by diverse HLA class II alleles

    PubMed Central

    Reynolds, Catherine J; Jones, Claire; Blohmke, Christoph J; Darton, Thomas C; Goudet, Amelie; Sergeant, Ruhena; Maillere, Bernard; Pollard, Andrew J; Altmann, Daniel M; Boyton, Rosemary J

    2014-01-01

    Detailed characterization of the protective T-cell response in salmonellosis is a pressing unmet need in light of the global burden of human Salmonella infections and the likely contribution of CD4 T cells to immunity against this intracellular infection. In previous studies screening patient sera against antigen arrays, SseB was noteworthy as a serodominant target of adaptive immunity, inducing significantly raised antibody responses in HIV-seronegative compared with seropositive patients. SseB is a secreted protein, part of the Espa superfamily, localized to the bacterial surface and forming part of the translocon of the type III secretion system (T3SS) encoded by Salmonella pathogenicity island 2. We demonstrate here that SseB is also a target of CD4 T-cell immunity, generating a substantial response after experimental infection in human volunteers, with around 0·1% of the peripheral repertoire responding to it. HLA-DR/peptide binding studies indicate that this protein encompasses a number of peptides with ability to bind to several different HLA-DR alleles. Of these, peptide 11 (p11) was shown in priming of both HLA-DR1 and HLA-DR4 transgenic mice to contain an immunodominant CD4 epitope. Analysis of responses in human donors showed immunity focused on p11 and another epitope in peptide 2. The high frequency of SseB-reactive CD4 T cells and the broad applicability to diverse HLA genotypes coupled with previous observations of serodominance and protective vaccination in mouse challenge experiments, make SseB a plausible candidate for next-generation Salmonella vaccines. PMID:24891088

  1. Strong conservation of rhoptry-associated-protein-1 (RAP-1) locus organization and sequence among Babesia isolates infecting sheep from China (Babesia motasi-like phylogenetic group).

    PubMed

    Niu, Qingli; Valentin, Charlotte; Bonsergent, Claire; Malandrin, Laurence

    2014-12-01

    Rhoptry-associated-protein 1 (RAP-1) is considered as a potential vaccine candidate due to its involvement in red blood cell invasion by parasites in the genus Babesia. We examined its value as a vaccine candidate by studying RAP-1 conservation in isolates of Babesia sp. BQ1 Ningxian, Babesia sp. Tianzhu and Babesia sp. Hebei, responsible for ovine babesiosis in different regions of China. The rap-1 locus in these isolates has very similar features to those described for Babesia sp. BQ1 Lintan, another Chinese isolate also in the B. motasi-like phylogenetic group, namely the presence of three types of rap-1 genes (rap-1a, rap-1b and rap-1c), multiple conserved rap-1b copies (5) interspaced with more or less variable rap-1a copies (6), and the 3' localization of one rap-1c. The isolates Babesia sp. Tianzhu, Babesia sp. BQ1 Lintan and Ningxian were almost identical (average nucleotide identity of 99.9%) over a putative locus of about 31 Kb, including the intergenic regions. Babesia sp. Hebei showed a similar locus organization but differed in the rap-1 locus sequence, for each gene and intergenic region, with an average nucleotide identity of 78%. Our results are in agreement with 18S rDNA phylogenetic studies performed on these isolates. However, in extremely closely related isolates the rap-1 locus seems more conserved (99.9%) than the 18S rDNA (98.7%), whereas in still closely related isolates the identities are much lower (78%) compared with the 18S rDNA (97.7%). The particularities of the rap-1 locus in terms of evolution, phylogeny, diagnosis and vaccine development are discussed. PMID:25200723

  2. Nearly 1000 Protein Identifications from 50 ng of Xenopus laevis Zygote Homogenate Using Online Sample Preparation on a Strong Cation Exchange Monolith Based Microreactor Coupled with Capillary Zone Electrophoresis.

    PubMed

    Zhang, Zhenbin; Sun, Liangliang; Zhu, Guijie; Cox, Olivia F; Huber, Paul W; Dovichi, Norman J

    2016-01-01

    A sulfonate-silica hybrid strong cation exchange monolith microreactor was synthesized and coupled to a linear polyacrylamide coated capillary for online sample preparation and capillary zone electrophoresis-tandem mass spectrometry (CZE-MS/MS) bottom-up proteomic analysis. The protein sample was loaded onto the microreactor in an acidic buffer. After online reduction, alkylation, and digestion with trypsin, the digests were eluted with 200 mM ammonium bicarbonate at pH 8.2 for CZE-MS/MS analysis using 1 M acetic acid as the background electrolyte. This combination of basic elution and acidic background electrolytes results in both sample stacking and formation of a dynamic pH junction. 369 protein groups and 1274 peptides were identified from 50 ng of Xenopus laevis zygote homogenate, which is comparable with an offline sample preparation method, but the time required for sample preparation was decreased from over 24 h to less than 40 min. Dramatically improved performance was produced by coupling the reactor to a longer separation capillary (∼100 cm) and a Q Exactive HF mass spectrometer. 975 protein groups and 3749 peptides were identified from 50 ng of Xenopus protein using the online sample preparation method. PMID:26670623

  3. A Truncated Receptor-Binding Domain of MERS-CoV Spike Protein Potently Inhibits MERS-CoV Infection and Induces Strong Neutralizing Antibody Responses: Implication for Developing Therapeutics and Vaccines

    PubMed Central

    Ma, Cuiqing; Tao, Xinrong; Wang, Lili; Zhao, Guangyu; Chen, Yaoqing; Yu, Fei; Tseng, Chien-Te K.; Zhou, Yusen; Jiang, Shibo

    2013-01-01

    An emerging respiratory infectious disease with high mortality, Middle East respiratory syndrome (MERS), is caused by a novel coronavirus (MERS-CoV). It was first reported in 2012 in Saudi Arabia and has now spread to eight countries. Development of effective therapeutics and vaccines is crucial to save lives and halt the spread of MERS-CoV. Here, we show that a recombinant protein containing a 212-amino acid fragment (residues 377-588) in the truncated receptor-binding domain (RBD: residues 367–606) of MERS-CoV spike (S) protein fused with human IgG Fc fragment (S377-588-Fc) is highly expressed in the culture supernatant of transfected 293T cells. The purified S377-588-Fc protein efficiently binds to dipeptidyl peptidase 4 (DPP4), the receptor of MERS-CoV, and potently inhibited MERS-CoV infection, suggesting its potential to be further developed as a therapeutic modality for treating MERS-CoV infection and saving the patients’ lives. The recombinant S377-588-Fc is able to induce in the vaccinated mice strong MERS-CoV S-specific antibodies, which blocks the binding of RBD to DPP4 receptor and effectively neutralizes MERS-CoV infection. These findings indicate that this truncated RBD protein shows promise for further development as an effective and safe vaccine for the prevention of MERS-CoV infection. PMID:24324708

  4. Serum Levels of High-sensitivity C-Reactive Protein at Admission Are More Strongly Associated with Poststroke Depression in Acute Ischemic Stroke than Homocysteine Levels.

    PubMed

    Tang, Chao-Zhi; Zhang, Yu-Ling; Wang, Wen-Sheng; Li, Wei-Guo; Shi, Ji-Peng

    2016-05-01

    Inflammatory processes have fundamental roles in depression. The primary purpose of this study was to assess the serum levels of high-sensitivity C-reactive protein (Hs-CRP) and homocysteine (HCY) at admission to the presence of poststroke depression (PSD). From December 2012 to December 2013, first-ever acute ischemic stroke patients who were admitted to the hospital within the first 24 h after stroke onset were consecutively recruited and followed up for 6 months. Serum levels of Hs-CRP and HCY were tested at admission. Based on the symptoms, diagnoses of depression were made in accordance with DSM-IV criteria for depression at 6 months after stroke. Ninety-five patients (42.0 %) showed depression (major + minor) at 6 months after admission, and in 69 patients (30.5 %), this depression was classified as major. In the 69 patients with major depression, our results showed significantly higher Hs-CRP and HCY levels at admission than patients without major depression. After adjusting all other possible covariates, Hs-CRP and HCY still were independent predicators of PSD with adjusted OR of 1.332 (95 % CI, 1.230-1.452; P < 0.001) and 1.138 (95 % CI, 1.072-1.274; P < 0.001), respectively. The area under the receiver operating characteristic curve values of Hs-CRP and HCY were 0.765 (95 % CI, 0.701-0.9825) and 0.684 (95 % CI, 0.610-0.757) for PSD, respectively. The prognostic accuracy of combined model (HCY and Hs-CRP) was higher compared to those biomarkers alone and other markers. Elevated serum levels of Hs-CRP and HCY at admission were found to be associated with depression 6 months after stroke, suggesting that these alterations might participate in the pathophysiology of depression symptoms in stroke patients. PMID:25941076

  5. Protein

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Proteins are the major structural and functional components of all cells in the body. They are macromolecules that comprise 1 or more chains of amino acids that vary in their sequence and length and are folded into specific 3-dimensional structures. The sizes and conformations of proteins, therefor...

  6. 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)

  7. Critical Structural and Functional Roles for the N-Terminal Insertion Sequence in Surfactant Protein B Analogs

    PubMed Central

    Walther, Frans J.; Waring, Alan J.; Hernandez-Juviel, Jose M.; Gordon, Larry M.; Wang, Zhengdong; Jung, Chun-Ling; Ruchala, Piotr; Clark, Andrew P.; Smith, Wesley M.; Sharma, Shantanu; Notter, Robert H.

    2010-01-01

    Background Surfactant protein B (SP-B; 79 residues) belongs to the saposin protein superfamily, and plays functional roles in lung surfactant. The disulfide cross-linked, N- and C-terminal domains of SP-B have been theoretically predicted to fold as charged, amphipathic helices, suggesting their participation in surfactant activities. Earlier structural studies with Mini-B, a disulfide-linked construct based on the N- and C-terminal regions of SP-B (i.e., ∼residues 8–25 and 63–78), confirmed that these neighboring domains are helical; moreover, Mini-B retains critical in vitro and in vivo surfactant functions of the native protein. Here, we perform similar analyses on a Super Mini-B construct that has native SP-B residues (1–7) attached to the N-terminus of Mini-B, to test whether the N-terminal sequence is also involved in surfactant activity. Methodology/Results FTIR spectra of Mini-B and Super Mini-B in either lipids or lipid-mimics indicated that these peptides share similar conformations, with primary α-helix and secondary β-sheet and loop-turns. Gel electrophoresis demonstrated that Super Mini-B was dimeric in SDS detergent-polyacrylamide, while Mini-B was monomeric. Surface plasmon resonance (SPR), predictive aggregation algorithms, and molecular dynamics (MD) and docking simulations further suggested a preliminary model for dimeric Super Mini-B, in which monomers self-associate to form a dimer peptide with a “saposin-like” fold. Similar to native SP-B, both Mini-B and Super Mini-B exhibit in vitro activity with spread films showing near-zero minimum surface tension during cycling using captive bubble surfactometry. In vivo, Super Mini-B demonstrates oxygenation and dynamic compliance that are greater than Mini-B and compare favorably to full-length SP-B. Conclusion Super Mini-B shows enhanced surfactant activity, probably due to the self-assembly of monomer peptide into dimer Super Mini-B that mimics the functions and putative structure of

  8. A sugar beet chlorophyll a/b binding protein promoter void of G-box like elements confers strong and leaf specific reporter gene expression in transgenic sugar beet

    PubMed Central

    Stahl, Dietmar J; Kloos, Dorothee U; Hehl, Reinhard

    2004-01-01

    Background Modification of leaf traits in sugar beet requires a strong leaf specific promoter. With such a promoter, expression in taproots can be avoided which may otherwise take away available energy resources for sugar accumulation. Results Suppression Subtractive Hybridization (SSH) was utilized to generate an enriched and equalized cDNA library for leaf expressed genes from sugar beet. Fourteen cDNA fragments corresponding to thirteen different genes were isolated. Northern blot analysis indicates the desired tissue specificity of these genes. The promoters for two chlorophyll a/b binding protein genes (Bvcab11 and Bvcab12) were isolated, linked to reporter genes, and transformed into sugar beet using promoter reporter gene fusions. Transient and transgenic analysis indicate that both promoters direct leaf specific gene expression. A bioinformatic analysis revealed that the Bvcab11 promoter is void of G-box like regulatory elements with a palindromic ACGT core sequence. The data indicate that the presence of a G-box element is not a prerequisite for leaf specific and light induced gene expression in sugar beet. Conclusions This work shows that SSH can be successfully employed for the identification and subsequent isolation of tissue specific sugar beet promoters. These promoters are shown to drive strong leaf specific gene expression in transgenic sugar beet. The application of these promoters for expressing resistance improving genes against foliar diseases is discussed. PMID:15579211

  9. Expression profile of heat shock proteins in acute myeloid leukaemia patients reveals a distinct signature strongly associated with FLT3 mutation status--consequences and potentials for pharmacological intervention.

    PubMed

    Reikvam, Håkon; Hatfield, Kimberley J; Ersvaer, Elisabeth; Hovland, Randi; Skavland, Jørn; Gjertsen, Bjørn T; Petersen, Kjell; Bruserud, Oystein

    2012-02-01

    Heat shock proteins (HSPs) are molecular chaperones that assist proteins in their folding to native structures. HSPs are regarded as possible therapeutic targets in acute myeloid leukaemia (AML). We used bioinformatical approaches to characterize the HSP profile in AML cells from 75 consecutive patients, in addition to the effect of the HSP90 inhibitor 17-DMAG. Patients harbouring a FLT3-internal tandem duplication (FLT3-ITD) were extensively overrepresented in the cluster with high HSP levels, indicating a strong dependence of HSPs in stabilizing FLT3-ITD encoded oncoproteins. FLT3 ligation further increased the levels of HSP90 and its co-chaperone HSP70. HSP90 inhibition had a stronger pro-apoptotic effect for AML cells with FLT3-ITD than for cells with wild-type FLT3, whereas the anti-proliferative effect of HSP90 inhibition was similar for the two patient subsets. HSP90 inhibition altered the constitutive cytokine release profile in an anti-angiogenic direction independent of FLT3 mutational status: (i) pro-angiogenic CXCL8, MMP-2 and MMP-9 showed a stronger decrease than anti-angiogenic CXCL9-11, (ii) the Tie-2 agonist Ang-1 showed a stronger decrease than the potentially antagonistic Ang-2, and (iii) VEGF and HGF levels were decreased. Finally, HSP90 inhibition counteracted the leukaemia-stimulating effect of endothelial cells. Our studies demonstrate that HSP90 inhibition mediates anti-leukaemic effects through both direct and indirect activity. PMID:22150087

  10. Vaccination of koalas (Phascolarctos cinereus) with a recombinant chlamydial major outer membrane protein adjuvanted with poly I:C, a host defense peptide and polyphosphazine, elicits strong and long lasting cellular and humoral immune responses.

    PubMed

    Khan, Shahneaz Ali; Waugh, Courtney; Rawlinson, Galit; Brumm, Jacqui; Nilsson, Karen; Gerdts, Volker; Potter, Andrew; Polkinghorne, Adam; Beagley, Kenneth; Timms, Peter

    2014-10-01

    Chlamydial infections are wide spread in koalas across their range and a solution to this debilitating disease has been sought for over a decade. Antibiotics are the currently accepted therapeutic measure, but are not an effective treatment due to the asymptomatic nature of some infections and a low efficacy rate. Thus, a vaccine would be an ideal way to address this infectious disease threat in the wild. Previous vaccine trials have used a three-dose regimen; however this is very difficult to apply in the field as it would require multiple capture events, which are stressful and invasive processes for the koala. In addition, it requires skilled koala handlers and a significant monetary investment. To overcome these challenges, in this study we utilized a polyphosphazine based poly I:C and a host defense peptide adjuvant combined with recombinant chlamydial major outer membrane protein (rMOMP) antigen to induce long lasting (54 weeks) cellular and humoral immunity in female koalas with a novel single immunizing dose. Immunized koalas produced a strong IgG response in plasma, as well as at mucosal sites. Moreover, they showed high levels of C. pecorum specific neutralizing antibodies in the plasma as well as vaginal and conjunctival secretions. Lastly, Chlamydia-specific lymphocyte proliferation responses were produced against both whole chlamydial elementary bodies and rMOMP protein, over the 12-month period. The results of this study suggest that a single dose rMOMP vaccine incorporating a poly I:C, host defense peptide and polyphosphazine adjuvant is able to stimulate both arms of the immune system in koalas, thereby providing an alternative to antibiotic treatment and/or a three-dose vaccine regime. PMID:25196393

  11. Novel influenza virus vectors expressing Brucella L7/L12 or Omp16 proteins in cattle induced a strong T-cell immune response, as well as high protectiveness against B. abortus infection.

    PubMed

    Tabynov, Kaissar; Kydyrbayev, Zhailaubay; Ryskeldinova, Sholpan; Yespembetov, Bolat; Zinina, Nadezhda; Assanzhanova, Nurika; Kozhamkulov, Yerken; Inkarbekov, Dulat; Gotskina, Tatyana; Sansyzbay, Abylai

    2014-04-11

    This paper presents the results of a study of the immunogenicity and protectiveness of new candidate vector vaccine against Brucella abortus - a bivalent vaccine formulation consisting of a mixture of recombinant influenza A subtype H5N1 or H1N1 (viral constructs vaccine formulation) viruses expressing Brucella ribosomal protein L7/L12 and Omp16, in cattle. To increase the effectiveness of the candidate vaccine, adjuvants such as Montanide Gel01 or chitosan were included in its composition. Immunization of cattle (heifers aged 1-1.5 years, 5 animals per group) with the viral constructs vaccine formulation only, or its combination with adjuvants Montanide Gel01 or chitosan, was conducted via the conjunctival method using cross prime (influenza virus subtype H5N1) and booster (influenza virus subtype H1N1) vaccination schedules at an interval of 28 days. Vaccine candidates were evaluated in comparison with the positive (B. abortus S19) and negative (PBS) controls. The viral constructs vaccine formulations, particularly in combination with Montanide Gel01 adjuvant promoted formation of IgG antibodies (with a predominance of antibodies of isotype IgG2a) against Brucella L7/L12 and Omp16 proteins in ELISA. Moreover, these vaccines in cattle induced a strong antigen-specific T-cell immune response, as indicated by a high number of CD4(+) and CD8(+) cells, as well as the concentration of IFN-γ, and most importantly provided a high level of protectiveness comparable to the commercial B. abortus S19 vaccine and superior to the B. abortus S19 vaccine in combination with Montanide Gel01 adjuvant. Based on these findings, we recommended the bivalent vaccine formulation containing the adjuvant Montanide Gel01 for practical use in cattle. PMID:24598723

  12. DNA-Protein Immunization Using Leishmania Peroxidoxin-1 Induces a Strong CD4+ T Cell Response and Partially Protects Mice from Cutaneous Leishmaniasis: Role of Fusion Murine Granulocyte-Macrophage Colony-Stimulating Factor DNA Adjuvant

    PubMed Central

    Bayih, Abebe Genetu; Daifalla, Nada S.; Gedamu, Lashitew

    2014-01-01

    Background To date, no universally effective and safe vaccine has been developed for general human use. Leishmania donovani Peroxidoxin-1 (LdPxn-1) is a member of the antioxidant family of proteins and is predominantly expressed in the amastigote stage of the parasite. The aim of this study was to evaluate the immunogenicity and protective efficacy of LdPxn-1 in BALB/c mice in heterologous DNA-Protein immunization regimen in the presence of fusion murine granulocyte-macrophage colony-stimulating factor (mGMCSF) DNA adjuvant. Methodology and Principal Findings A fusion DNA of LdPxn1 and mGMCSF was cloned into a modified pcDNA vector. To confirm the expression in mammalian system, Chinese hamster ovary cells were transfected with the plasmid vector containing LdPxn1 gene. BALB/c mice were immunized twice with pcDNA-mGMCSF-LdPxn-1 or pcDNA-LdPxn1 DNA and boosted once with recombinant LdPxn-1 protein. Three weeks after the last immunization, mice were infected with Leishmania major promastigotes. The result showed that immunization with pcDNA-mGMCSF-LdPxn1 elicited a mixed Th-1/Th-2 immune response with significantly higher production of IFN-γ than controls. Intracellular cytokine staining of antigen-stimulated spleen cells showed that immunization with this antigen elicited significantly higher proportion of CD4+ T cells that express IFN-γ, TNF-α, or IL-2. The antigen also induced significantly higher proportion of multipotent CD4+ cells that simultaneously express the three Th-1 cytokines. Moreover, a significant reduction in the footpad swelling was seen in mice immunized with pcDNA-mGMCSF-LdPxn1 antigen. Expression study in CHO cells demonstrated that pcDNA-mGMCSF-LdPxn-1 was expressed in mammalian system. Conclusion The result demonstrates that immunization of BALB/c mice with a plasmid expressing LdPxn1 in the presence of mGMCSF adjuvant elicits a strong specific immune response with high level induction of multipotent CD4+ cells that mediate protection of the

  13. What Is Strong Correlation?

    ERIC Educational Resources Information Center

    Kozak, Marcin

    2009-01-01

    Interpretation of correlation is often based on rules of thumb in which some boundary values are given to help decide whether correlation is non-important, weak, strong or very strong. This article shows that such rules of thumb may do more harm than good, and instead of supporting interpretation of correlation--which is their aim--they teach a…

  14. Strong Navajo Marriages

    ERIC Educational Resources Information Center

    Skogrand, Linda; Mueller, Mary Lou; Arrington, Rachel; LeBlanc, Heidi; Spotted Elk, Davina; Dayzie, Irene; Rosenbrand, Reva

    2008-01-01

    The purpose of this qualitative study, conducted in two Navajo Nation chapters, was to learn what makes Navajo marriages strong because no research has been done on this topic. Twenty-one Navajo couples (42 individuals) who felt they had strong marriages volunteered to participate in the study. Couples identified the following marital strengths:…

  15. Quantification of HDL Proteins, Cardiac Events, and Mortality in Patients with Type 2 Diabetes on Hemodialysis

    PubMed Central

    Kopecky, Chantal; Genser, Bernd; Drechsler, Christiane; Krane, Vera; Kaltenecker, Christopher C.; Hengstschläger, Markus; März, Winfried; Wanner, Christoph; Säemann, Marcus D.

    2015-01-01

    Background and objectives Impairment of HDL function has been associated with cardiovascular events in patients with kidney failure. The protein composition of HDLs is altered in these patients, presumably compromising the cardioprotective effects of HDLs. This post hoc study assessed the relation of distinct HDL-bound proteins with cardiovascular outcomes in a dialysis population. Design, setting, participants, & measurements The concentrations of HDL-associated serum amyloid A (SAA) and surfactant protein B (SP-B) were measured in 1152 patients with type 2 diabetes mellitus on hemodialysis participating in The German Diabetes Dialysis Study who were randomly assigned to double-blind treatment of 20 mg atorvastatin daily or matching placebo. The association of SAA(HDL) and SP-B(HDL) with cardiovascular outcomes was assessed in multivariate regression models adjusted for known clinical risk factors. Results High concentrations of SAA(HDL) were significantly and positively associated with the risk of cardiac events (hazard ratio per 1 SD higher, 1.09; 95% confidence interval, 1.01 to 1.19). High concentrations of SP-B(HDL) were significantly associated with all-cause mortality (hazard ratio per 1 SD higher, 1.10; 95% confidence interval, 1.02 to 1.19). Adjustment for HDL cholesterol did not affect these associations. Conclusions In patients with diabetes on hemodialysis, SAA(HDL) and SP-B(HDL) were related to cardiac events and all-cause mortality, respectively, and they were independent of HDL cholesterol. These findings indicate that a remodeling of the HDL proteome was associated with a higher risk for cardiovascular events and mortality in patients with ESRD. PMID:25424990

  16. Living Bones, Strong Bones

    NASA Video Gallery

    In this classroom activity, engineering, nutrition, and physical activity collide when students design and build a healthy bone model of a space explorer which is strong enough to withstand increas...

  17. Thyroid transcription factor-1, hepatocyte nuclear factor-3β and surfactant protein A and B in the developing chick lung

    PubMed Central

    ZENG, XIN; YUTZEY, KATHERINE E.; WHITSETT, JEFFREY A.

    1998-01-01

    Expression of surfactant proteins SP-A, SP-B and the transcription factors TTF-1 and HNF-3β was identified by immunohistochemistry in the developing chicken. SP-B, a small hydrophobic peptide critical for lung function and surfactant homeostasis in mammals, was detected in the epithelial cells of parabronchi in embryonic chicken lung from the 15th day of incubation, prior to the onset of the breathing movements and was expressed at high levels in the posthatching chicken lung. SP-A, an abundant surfactant protein involved in innate defence of the mammalian lung, was detected in the chick embryo in subsets of epithelial cells in the mesobronchus, starting from d 15 and was detected in the posthatching chicken lung. The transcription factors hepatocyte nuclear factor 3β (HNF-3β) and thyroid transcription factor-1 (TTF-1), both regulators epithelial cell differentiation and gene expression in mammalian species, were detected at the onset of lung bud formation (d 4 of incubation) and throughout lung development. Abundant nuclear expression was detected in nuclei of respiratory epithelial cells of developing bronchial tubules for both transcription factors. In contrast to the surfactant proteins, expression of both TTF-1 and HNF-3β decreased markedly in posthatching chicken lung. The expression of SP-A and SP-B in chick lung demonstrates the conservation of surfactant proteins in vertebrates. The temporospatial pattern of TTF-1 and HNF-3β overlaps with that of SP-A and SP-B, supporting their potential roles in chick lung development and demonstrating the conservation of regulatory mechanisms contributing to gene expression in respiratory epithelial cells in vertebrates. PMID:9877295

  18. On Strong Anticipation

    PubMed Central

    Stepp, N.; Turvey, M. T.

    2009-01-01

    We examine Dubois's (2003) distinction between weak anticipation and strong anticipation. Anticipation is weak if it arises from a model of the system via internal simulations. Anticipation is strong if it arises from the system itself via lawful regularities embedded in the system's ordinary mode of functioning. The assumption of weak anticipation dominates cognitive science and neuroscience and in particular the study of perception and action. The assumption of strong anticipation, however, seems to be required by anticipation's ubiquity. It is, for example, characteristic of homeostatic processes at the level of the organism, organs, and cells. We develop the formal distinction between strong and weak anticipation by elaboration of anticipating synchronization, a phenomenon arising from time delays in appropriately coupled dynamical systems. The elaboration is conducted in respect to (a) strictly physical systems, (b) the defining features of circadian rhythms, often viewed as paradigmatic of biological behavior based in internal models, (c) Pavlovian learning, and (d) forward models in motor control. We identify the common thread of strongly anticipatory systems and argue for its significance in furthering understanding of notions such as “internal”, “model” and “prediction”. PMID:20191086

  19. Strong acoustic wave action

    NASA Astrophysics Data System (ADS)

    Gokhberg, M. B.

    1983-07-01

    Experiments devoted to acoustic action on the atmosphere-magnetosphere-ionosphere system using ground based strong explosions are reviewed. The propagation of acoustic waves was observed by ground observations over 2000 km in horizontal direction and to an altitude of 200 km. Magnetic variations up to 100 nT were detected by ARIEL-3 satellite near the epicenter of the explosion connected with the formation of strong field aligned currents in the magnetosphere. The enhancement of VLF emission at 800 km altitude is observed.

  20. Strong Little Magnets

    ERIC Educational Resources Information Center

    Moloney, Michael J.

    2007-01-01

    Did you know that some strong little cylindrical magnets available in local hardware stores can have an effective circumferential current of 2500 A? This intriguing information can be obtained by hanging a pair of magnets at the center of a coil, as shown in Fig. 1, and measuring the oscillation frequency as a function of coil current.

  1. A strong comeback

    SciTech Connect

    Marier, D.

    1992-03-01

    This article presents the results of a financial rankings survey which show a strong economic activity in the independent energy industry. The topics of the article include advisor turnover, overseas banks, and the increase in public offerings. The article identifies the top project finance investors for new projects and restructurings and rankings for lenders.

  2. Strong subadditivity and holography

    NASA Astrophysics Data System (ADS)

    Prudenziati, Andrea

    2016-05-01

    We study in detail the relationship between strong subadditivity for a boundary field theory and energy conditions for its bulk dual in 2 +1 dimensions. We provide a discussion of known facts and new results organized from the simplest case of a static system with collinear intervals to a time-dependent one in a generic configuration, with particular focus on the holographic geometric description.

  3. Plasmons in strong superconductors

    SciTech Connect

    Baldo, M.; Ducoin, C.

    2011-10-15

    We present a study of the possible plasmon excitations that can occur in systems where strong superconductivity is present. In these systems the plasmon energy is comparable to or smaller than the pairing gap. As a prototype of these systems we consider the proton component of Neutron Star matter just below the crust when electron screening is not taken into account. For the realistic case we consider in detail the different aspects of the elementary excitations when the proton, electron components are considered within the Random-Phase Approximation generalized to the superfluid case, while the influence of the neutron component is considered only at qualitative level. Electron screening plays a major role in modifying the proton spectrum and spectral function. At the same time the electron plasmon is strongly modified and damped by the indirect coupling with the superfluid proton component, even at moderately low values of the gap. The excitation spectrum shows the interplay of the different components and their relevance for each excitation modes. The results are relevant for neutrino physics and thermodynamical processes in neutron stars. If electron screening is neglected, the spectral properties of the proton component show some resemblance with the physical situation in high-T{sub c} superconductors, and we briefly discuss similarities and differences in this connection. In a general prospect, the results of the study emphasize the role of Coulomb interaction in strong superconductors.

  4. Establishment of LC-MS methods for the analysis of palmitoylated surfactant proteins.

    PubMed

    Harayama, Takeshi; Shindou, Hideo; Kita, Yoshihiro; Otsubo, Eiji; Ikeda, Kazushige; Chida, Shoichi; Weaver, Timothy E; Shimizu, Takao

    2015-07-01

    The surfactant proteins (SPs), SP-B and SP-C, are important components of pulmonary surfactant involved in the reduction of alveolar surface tension. Quantification of SP-B and SP-C in surfactant drugs is informative for their quality control and the evaluation of their biological activity. Western blot analysis enabled the quantification of SP-B, but not SP-C, in surfactant drugs. Here, we report a new procedure involving chemical treatments and LC-MS to analyze SP-C peptides. The procedure enabled qualitative analysis of SP-C from different species with discrimination of the palmitoylation status and the artificial modifications that occur during handling and/or storage. In addition, the method can be used to estimate the total amount of SP-C in pulmonary surfactant drugs. The strategy described here might serve as a prototype to establish analytical methods for peptides that are extremely hydrophobic and behave like lipids. The new method provides an easy measurement of SP-C from various biological samples, which will help the characterization of various experimental animal models and the quality control of surfactant drugs, as well as diagnostics of human samples. PMID:26022805

  5. Strong Poison Revisited

    SciTech Connect

    Prince, R.C.; Gailer, J.; Gunson, D.E.; Turner, R.J.; George, G.N.; Pickering, I.J.

    2009-06-04

    Selenium in the form of selenocysteine plays an essential role in a number of proteins, but its role in non-enzymatic biochemistry is also important. In this short review we discuss the interactions between inorganic selenium, arsenic and mercury under physiological conditions, especially in the presence of glutathione. This chemistry is obviously important in making the arsenic and mercury unavailable for more toxic interactions, but in the process it suggests that a side-effect of chronic arsenic and/or mercury exposure is likely to be functional selenium deficiency.

  6. Interdependent TTF1 - ErbB4 interactions are critical for surfactant protein-B homeostasis in primary mouse lung alveolar type II cells.

    PubMed

    Marten, Elger; Nielsen, Heber C; Dammann, Christiane E L

    2015-09-01

    ErbB4 receptor and thyroid transcription factor (TTF)-1 are important modulators of fetal alveolar type II (ATII) cell development and injury. ErbB4 is an upstream regulator of TTF-1, promoting its expression in MLE-12 cells, an ATII cell line. Both proteins are known to promote surfactant protein-B gene (SftpB) and protein (SP-B) expression, but their feedback interactions on each other are not known. We hypothesized that TTF-1 expression has a feedback effect on ErbB4 expression in an in-vitro model of isolated mouse ATII cells. We tested this hypothesis by analyzing the effects of overexpressing HER4 and Nkx2.1, the genes of ErbB4 and TTF-1 on TTF-1 and ErbB4 protein expression, respectively, as well as SP-B protein expression in primary fetal mouse lung ATII cells. Transient ErbB4 protein overexpression upregulated TTF-1 protein expression in primary fetal ATII cells, similarly to results previously shown in MLE-12 cells. Transient TTF-1 protein overexpression down regulated ErbB4 protein expression in both cell types. TTF-1 protein was upregulated in primary transgenic ErbB4-depleted adult ATII cells, however SP-B protein expression in these adult transgenic ATII cells was not affected by the absence of ErbB4. The observation that TTF-1 is upregulated in fetal ATII cells by ErbB4 overexpression and also in ErbB4-deleted adult ATII cells suggests additional factors interact with ErbB4 to regulate TTF-1 levels. We conclude that the interdependency of TTF-1 and ErbB4 is important for surfactant protein levels. The interactive regulation of ErbB4 and TTF-1 needs further elucidation. PMID:26198867

  7. Strongly correlated electronic materials

    SciTech Connect

    Bedell, K.; Albers, R.; Balatsky, A.; Bishop, A.; Bonca, J.; Gubernatis, J.; Gulasci, M.; Silver, R.; Trugman, S.

    1996-04-01

    This is the final report of a 3-year project. Novel electronic materials characterized by strong electronic correlations display a number of unexpected, often extraordinary, properties. These are likely to play a major role in purpose-specific high-technology electronic materials of the future developed for electronic, magnetic, and optical applications. This project sought to develop predictive control of the novel properties by formulating, solving and applying many-body models for the underlying microscopic physics. This predictive control required the development of new analytical and numerical many-body techniques and strategies for materials of varying strengths of interactions, dimensionality and geometry. Results are compared with experiment on classes of novel materials, and the robust techniques are used to predict additional properties and motivate key additional experiments.

  8. Strongly-correlated heterostructures

    SciTech Connect

    Okamoto, Satoshi

    2012-01-01

    Electronic phase behavior in correlated-electron systems is a fundamental problem of condensed matter physics. The change in the phase behavior near surfaces and interfaces, i.e., {\\em electronic reconstruction}, is therefore the fundamental issue of the correlated-electron surface or interface science. In addition to basic science, understanding of such a phase behavior is of crucial importance for potential devices exploiting the novel properties of the correlated systems. In this article, we present a general overview of the field, and then discuss the recent theoretical progress mainly focusing on the correlation effects. We illustrate the general concept of {\\em electronic reconstruction} by studying model heterostructures consisting of strongly-correlated systems. Future directions for research are also discussed.

  9. Strong, Lightweight, Porous Materials

    NASA Technical Reports Server (NTRS)

    Leventis, Nicholas; Meador, Mary Ann B.; Johnston, James C.; Fabrizio, Eve F.; Ilhan, Ulvi

    2007-01-01

    A new class of strong, lightweight, porous materials has been invented as an outgrowth of an effort to develop reinforced silica aerogels. The new material, called X-Aerogel is less hygroscopic, but no less porous and of similar density to the corresponding unmodified aerogels. However, the property that sets X-Aerogels apart is their mechanical strength, which can be as much as two and a half orders of magnitude stronger that the unmodified aerogels. X-Aerogels are envisioned to be useful for making extremely lightweight, thermally insulating, structural components, but they may also have applications as electrical insulators, components of laminates, catalyst supports, templates for electrode materials, fuel-cell components, and filter membranes.

  10. Strongly correlated surface states

    NASA Astrophysics Data System (ADS)

    Alexandrov, Victor A.

    Everything has an edge. However trivial, this phrase has dominated theoretical condensed matter in the past half a decade. Prior to that, questions involving the edge considered to be more of an engineering problem rather than a one of fundamental science: it seemed self-evident that every edge is different. However, recent advances proved that many surface properties enjoy a certain universality, and moreover, are 'topologically' protected. In this thesis I discuss a selected range of problems that bring together topological properties of surface states and strong interactions. Strong interactions alone can lead to a wide spectrum of emergent phenomena: from high temperature superconductivity to unconventional magnetic ordering; interactions can change the properties of particles, from heavy electrons to fractional charges. It is a unique challenge to bring these two topics together. The thesis begins by describing a family of methods and models with interactions so high that electrons effectively disappear as particles and new bound states arise. By invoking the AdS/CFT correspondence we can mimic the physical systems of interest as living on the surface of a higher dimensional universe with a black hole. In a specific example we investigate the properties of the surface states and find helical spin structure of emerged particles. The thesis proceeds from helical particles on the surface of black hole to a surface of samarium hexaboride: an f-electron material with localized magnetic moments at every site. Interactions between electrons in the bulk lead to insulating behavior, but the surfaces found to be conducting. This observation motivated an extensive research: weather the origin of conduction is of a topological nature. Among our main results, we confirm theoretically the topological properties of SmB6; introduce a new framework to address similar questions for this type of insulators, called Kondo insulators. Most notably we introduce the idea of Kondo

  11. Kinematics of Strong Discontinuities

    NASA Technical Reports Server (NTRS)

    Peterson, K.; Nguyen, G.; Sulsky, D.

    2006-01-01

    Synthetic Aperture Radar (SAR) provides a detailed view of the Arctic ice cover. When processed with the RADARSAT Geophysical Processor System (RGPS), it provides estimates of sea ice motion and deformation over large regions of the Arctic for extended periods of time. The deformation is dominated by the appearance of linear kinematic features that have been associated with the presence of leads. The RGPS deformation products are based on the assumption that the displacement and velocity are smooth functions of the spatial coordinates. However, if the dominant deformation of multiyear ice results from the opening, closing and shearing of leads, then the displacement and velocity can be discontinuous. This presentation discusses the kinematics associated with strong discontinuities that describe possible jumps in displacement or velocity. Ice motion from SAR data are analyzed using this framework. It is assumed that RGPS cells deform due to the presence of a lead. The lead orientation is calculated to optimally account for the observed deformation. It is shown that almost all observed deformation can be represented by lead opening and shearing. The procedure used to reprocess motion data to account for leads will be described and applied to regions of the Beaufort Sea. The procedure not only provides a new view of ice deformation, it can be used to obtain information about the presence of leads for initialization and/or validation of numerical simulations.

  12. Strong-interaction nonuniversality

    SciTech Connect

    Volkas, R. R.; Foot, R.; He, X.; Joshi, G. C.

    1989-07-01

    The universal QCD color theory is extended to an SU(3)/sub 1//direct product/SU(3)/sub 2//direct product/SU(3)/sub 3/ gauge theory, where quarks of the /ital i/th generation transform as triplets under SU(3)/sub /ital i// and singlets under the other two factors. The usual color group is then identified with the diagonal subgroup, which remains exact after symmetry breaking. The gauge bosons associated with the 16 broken generators then form two massive octets under ordinary color. The interactions between quarks and these heavy gluonlike particles are explicitly nonuniversal and thus an exploration of their physical implications allows us to shed light on the fundamental issue of strong-interaction universality. Nonuniversality and weak flavor mixing are shown to generate heavy-gluon-induced flavor-changing neutral currents. The phenomenology of these processes is studied, as they provide the major experimental constraint on the extended theory. Three symmetry-breaking scenarios are presented. The first has color breaking occurring at the weak scale, while the second and third divorce the two scales. The third model has the interesting feature of radiatively induced off-diagonal Kobayashi-Maskawa matrix elements.

  13. Foreshocks of strong earthquakes

    NASA Astrophysics Data System (ADS)

    Guglielmi, A. V.; Sobisevich, L. E.; Sobisevich, A. L.; Lavrov, I. P.

    2014-07-01

    The specific enhancement of ultra-low-frequency (ULF) electromagnetic oscillations a few hours prior to the strong earthquakes, which was previously mentioned in the literature, motivated us to search for the distinctive features of the mechanical (foreshock) activity of the Earth's crust in the epicentral zones of the future earthquakes. Activation of the foreshocks three hours before the main shock is revealed, which is roughly similar to the enhancement of the specific electromagnetic ULF emission. It is hypothesized that the round-the-world seismic echo signals from the earthquakes, which form the peak of energy release 2 h 50 min before the main events, act as the triggers of the main shocks due to the cumulative action of the surface waves converging to the epicenter. It is established that the frequency of the fluctuations in the foreshock activity decreases at the final stages of the preparation of the main shocks, which probably testifies to the so-called mode softening at the approach of the failure point according to the catastrophe theory.

  14. A strong antibody response to the periplasmic C-terminal domain of the OmpA protein of Escherichia coli is produced by immunization with purified OmpA or with whole E. coli or Salmonella typhimurium bacteria.

    PubMed Central

    Puohiniemi, R; Karvonen, M; Vuopio-Varkila, J; Muotiala, A; Helander, I M; Sarvas, M

    1990-01-01

    We produced in Bacillus subtilis the complete, as well as the N-terminal two-thirds, OmpA protein of Escherichia coli (called here Bac-OmpA and Bac-OmpA-dN, respectively). These Bac-OmpA proteins were used to examine the immunological properties of different parts of OmpA, free of lipopolysaccharide and other components of the outer membrane. The full-length Bac-OmpA was indistinguishable from the authentic protein isolated from E. coli (Coli-OmpA) both as immunogen and as antigen in enzyme immunoassay (EIA). The N-terminal Bac-OmpA-dN was a poor immunogen which gave rise to significantly lower titers of anti-OmpA antibody than did the full-length OmpA preparations. When used as an antigen in EIA, the Bac-OmpA-dN detected anti-OmpA antibody in serum samples from animals immunized with the full-length OmpA much less efficiently than did either Bac-OmpA or Coli-OmpA. The periplasmic C-terminal domain therefore appears to be an immunodominant epitope of the purified OmpA protein. Also, when rabbits and mice were immunized with intact, live or dead E. coli, the antibody response detected by EIA with the full-length protein, Bac-OmpA, was much stronger than that detected with the N-terminal two-thirds, Bac-OmpA-dN. Similar results were obtained with the OmpA of Salmonella typhimurium. Because the ompA gene of enterobacteria is highly conserved, the Bac-OmpA might be useful as a group-specific EIA antigen to diagnose diseases caused by members of the family Enterobacteriaceae. Images PMID:2111285

  15. Glutamine May Repress the Weak LPS and Enhance the Strong Heat Shock Induction of Monocyte and Lymphocyte HSP72 Proteins but May Not Modulate the HSP72 mRNA in Patients with Sepsis or Trauma

    PubMed Central

    Briassouli, Efrossini; Tzanoudaki, Marianna; Goukos, Dimitris; Routsi, Christina; Nanas, Serafim; Vardas, Kostas; Apostolou, Kleovoulos; Kanariou, Maria; Daikos, George; Briassoulis, George

    2015-01-01

    Objective. We assessed the lipopolysaccharide (LPS) or heat shock (HS) induction of heat shock protein-72 (HSP72) in peripheral blood mononuclear cells (PBMCs) of patients with severe sepsis (SS) or trauma-related systemic inflammatory response syndrome (SIRS), compared to healthy individuals (H); we also investigated any pre- or posttreatment modulating glutamine (Gln) effect. Methods. SS (11), SIRS (10), and H (19) PBMCs were incubated with 1 μg/mL LPS or 43°HS. Gln 10 mM was either added 1 h before or 1 h after induction or was not added at all. We measured monocyte (m), lymphocyte (l), mRNA HSP72, HSP72 polymorphisms, interleukins (ILs), monocyte chemoattractant protein-1 (MCP-1), and cortisol levels. Results. Baseline lHSP72 was higher in SS (p < 0.03), and mHSP72 in SIRS (p < 0.02), compared to H. Only HS induced l/mHSP72/mRNA HSP72; LPS induced IL-6, IL-8, IL-10, and MCP-1. Induced mRNA was related to l/mHSP72, and was related negatively to cytokines. Intracellular l/mHSP72/HSP72 mRNA was related to serum ILs, not being influenced by cortisol, illness severity, and HSP72 polymorphisms. Gln did not induce mRNA in any group but modified l/mHSP72 after LPS/HS induction unpredictably. Conclusions. HSP72 mRNA and l/mHSP72 are higher among critically ill patients, further induced by HS, not by LPS. HSP72 proteins and HSP72 mRNA are related to serum ILs and are negatively related to supernatant cytokines, not being influenced by HSP72 polymorphisms, cortisol, or illness severity. Gln may depress l/mHSP72 after LPS exposure and enhance them after HS induction, but it may not affect early induced HSP72 mRNA. PMID:26550577

  16. Expression and Localization of Lung Surfactant Proteins in Human Testis

    PubMed Central

    Wagner, Walter; Matthies, Cord; Ruf, Christian; Hartmann, Arndt; Garreis, Fabian; Paulsen, Friedrich

    2015-01-01

    Background Surfactant proteins (SPs) have been described in various tissues and fluids including tissues of the nasolacrimal apparatus, airways and digestive tract. Human testis have a glandular function as a part of the reproductive and the endocrine system, but no data are available on SPs in human testis and prostate under healthy and pathologic conditions. Objective The aim of the study was the detection and characterization of the surfactant proteins A, B, C and D (SP-A, SP-B, SP-C, SP-D) in human testis. Additionally tissue samples affected by testicular cancer were investigated. Results Surfactant proteins A, B, C and D were detected using RT-PCR in healthy testis. By means of Western blot analysis, these SPs were detected at the protein level in normal testis, seminoma and seminal fluid, but not in spermatozoa. Expression of SPs was weaker in seminoma compared to normal testicular tissue. SPs were localized in combination with vimentin immunohistochemically in cells of Sertoli and Leydig. Conclusion Surfactant proteins seem to be inherent part of the human testis. By means of physicochemical properties the proteins appear to play a role during immunological and rheological process of the testicular tissue. The presence of SP-B and SP-C in cells of Sertoli correlates with their function of fluid secretion and may support transportation of spermatozoa. In seminoma the expression of all SP's was generally weaker compared to normal germ cells. This could lead to a reduction of immunomodulatory and rheology processes in the germ cell tumor. PMID:26599233

  17. Pulmonary surfactant proteins and polymer combinations reduce surfactant inhibition by serum.

    PubMed

    Lu, Karen W; Pérez-Gil, Jesús; Echaide, Mercedes; Taeusch, H William

    2011-10-01

    Acute respiratory distress syndrome (ARDS) is an inflammatory condition that can be associated with capillary leak of serum into alveoli causing inactivation of surfactant. Resistance to inactivation is affected by types and concentrations of surfactant proteins, lipids, and polymers. Our aim was to investigate the effects of different combinations of these three components. A simple lipid mixture (DPPC/POPG) or a more complex lipid mixture (DPPC/POPC/POPG/cholesterol) was used. Native surfactant proteins SP-B and SP-C obtained from pig lung lavage were added either singly or combined at two concentrations. Also, non-ionic polymers polyethylene glycol and dextran and the anionic polymer hyaluronan were added either singly or in pairs with hyaluronan included. Non-ionic polymers work by different mechanisms than anionic polymers, thus the purpose of placing them together in the same surfactant mixture was to evaluate if the combination would show enhanced beneficial effects. The resulting surfactant mixtures were studied in the presence or absence of serum. A modified bubble surfactometer was used to evaluate surface activities. Mixtures that included both SP-B and SP-C plus hyaluronan and either dextran or polyethylene glycol were found to be the most resistant to inhibition by serum. These mixtures, as well as some with either SP-B or SP-C with combined polymers were as or more resistant to inactivation than native surfactant. These results suggest that improved formulations of lung surfactants are possible and may be useful in reducing some types of surfactant inactivation in treating lung injuries. PMID:21741354

  18. Strong-back safety latch

    SciTech Connect

    DeSantis, G.N.

    1995-03-06

    The calculation decides the integrity of the safety latch that will hold the strong-back to the pump during lifting. The safety latch will be welded to the strong-back and will latch to a 1.5-in. dia cantilever rod welded to the pump baseplate. The static and dynamic analysis shows that the safety latch will hold the strong-back to the pump if the friction clamps fail and the pump become free from the strong-back. Thus, the safety latch will meet the requirements of the Lifting and Rigging Manual for under the hook lifting for static loading; it can withstand shock loads from the strong-back falling 0.25 inch.

  19. Recent advances of strong-strong beam-beam simulation

    SciTech Connect

    Qiang, Ji; Furman, Miguel A.; Ryne, Robert D.; Fischer, Wolfram; Ohmi,Kazuhito

    2004-09-15

    In this paper, we report on recent advances in strong-strong beam-beam simulation. Numerical methods used in the calculation of the beam-beam forces are reviewed. A new computational method to solve the Poisson equation on nonuniform grid is presented. This method reduces the computational cost by a half compared with the standard FFT based method on uniform grid. It is also more accurate than the standard method for a colliding beam with low transverse aspect ratio. In applications, we present the study of coherent modes with multi-bunch, multi-collision beam-beam interactions at RHIC. We also present the strong-strong simulation of the luminosity evolution at KEKB with and without finite crossing angle.

  20. Titanium: light, strong, and white

    USGS Publications Warehouse

    Woodruff, Laurel; Bedinger, George

    2013-01-01

    Titanium (Ti) is a strong silver-gray metal that is highly resistant to corrosion and is chemically inert. It is as strong as steel but 45 percent lighter, and it is twice as strong as aluminum but only 60 percent heavier. Titanium dioxide (TiO2) has a very high refractive index, which means that it has high light-scattering ability. As a result, TiO2 imparts whiteness, opacity, and brightness to many products. ...Because of the unique physical properties of titanium metal and the whiteness provided by TiO2, titanium is now used widely in modern industrial societies.

  1. Simulating strongly correlated electrons with a strongly interacting Fermi gas

    SciTech Connect

    Thomas, John E.

    2013-05-28

    The quantum many-body physics of strongly-correlated fermions is studied in a degenerate, strongly- interacting atomic Fermi gas, first realized by our group with DOE support in 2002. This system, which exhibits strong spin pairing, is now widely studied and provides an important paradigm for testing predictions based on state-of-the-art many-body theory in fields ranging from nuclear matter to high temperature superfluidity and superconductivity. As the system is strongly interacting, both the superfluid and the normal fluid are nontrivial and of great interest. A central part of our program on Fermi gases is the connection between the study of thermodynamics, supported by DOE and the study of hydrodynamic transport, supported by NSF. This connection is especially interesting in view of a recent conjecture from the string theory community on the concept of nearly perfect normal fluids, which exhibit a minimum ratio of shear viscosity to entropy density in strongly-interacting, scale-invariant systems.

  2. Serum Levels of Surfactant Proteins in Patients with Combined Pulmonary Fibrosis and Emphysema (CPFE)

    PubMed Central

    Papaioannou, Andriana I.; Kostikas, Konstantinos; Manali, Effrosyni D.; Papadaki, Georgia; Roussou, Aneza; Spathis, Aris; Mazioti, Argyro; Tomos, Ioannis; Papanikolaou, Ilias; Loukides, Stelios; Chainis, Kyriakos; Karakitsos, Petros; Griese, Matthias; Papiris, Spyros

    2016-01-01

    Introduction Emphysema and idiopathic pulmonary fibrosis (IPF) present either per se or coexist in combined pulmonary fibrosis and emphysema (CPFE). Serum surfactant proteins (SPs) A, B, C and D levels may reflect lung damage. We evaluated serum SP levels in healthy controls, emphysema, IPF, and CPFE patients and their associations to disease severity and survival. Methods 122 consecutive patients (31 emphysema, 62 IPF, and 29 CPFE) and 25 healthy controls underwent PFTs, ABG-measurements, 6MWT and chest HRCT. Serum levels of SPs were measured. Patients were followed-up for 1-year. Results SP-A and SP-D levels differed between groups (p = 0.006 and p<0.001 respectively). In post-hoc analysis, SP-A levels differed only between controls and CPFE (p<0.05) and CPFE and emphysema (p<0.05). SP-D differed between controls and IPF or CPFE (p<0.001 for both comparisons). In IPF SP-B correlated to pulmonary function while SP-A, correlated to the Composite Physiological Index (CPI). Controls current smokers had higher SP-A and SP-D levels compared to non-smokers (p = 0.026 and p = 0.023 respectively). SP-D levels were higher in CPFE patients with extended emphysema (p = 0.042). In patients with IPF, SP-B levels at the upper quartile of its range (≥26 ng/mL) presented a weak association with reduced survival (p = 0.05). Conclusion In conclusion, serum SP-A and SP-D levels were higher where fibrosis exists or coexists and related to disease severity, suggesting that serum SPs relate to alveolar damage in fibrotic lungs and may reflect either local overproduction or overleakage. The weak association between high levels of SP-B and survival needs further validation in clinical trials. PMID:27337142

  3. Strongly Secure Linear Network Coding

    NASA Astrophysics Data System (ADS)

    Harada, Kunihiko; Yamamoto, Hirosuke

    In a network with capacity h for multicast, information Xh=(X1, X2, …, Xh) can be transmitted from a source node to sink nodes without error by a linear network code. Furthermore, secret information Sr=(S1, S2, …, Sr) can be transmitted securely against wiretappers by k-secure network coding for k≤h-r. In this case, no information of the secret leaks out even if an adversary wiretaps k edges, i. e. channels. However, if an adversary wiretaps k+1 edges, some Si may leak out explicitly. In this paper, we propose strongly k-secure network coding based on strongly secure ramp secret sharing schemes. In this coding, no information leaks out for every (Si1, Si2, …,Sir-j) even if an adversary wiretaps k+j channels. We also give an algorithm to construct a strongly k-secure network code directly and a transform to convert a nonsecure network code to a strongly k-secure network code. Furthermore, some sufficient conditions of alphabet size to realize the strongly k-secure network coding are derived for the case of k

  4. Strong Bragg backscattering in reflectometry

    NASA Astrophysics Data System (ADS)

    Gusakov, E. Z.; Heuraux, S.; Popov, A. Yu

    2009-06-01

    The reflection of the probing microwave occurring in the vicinity of the backscattering Bragg resonance point (far from the cut-off) at a high enough density fluctuation level and leading to a large jump of the reflected wave phase and a corresponding time delay is described analytically using a 1D model. Explicit expressions for the reflection and transmission coefficients are derived and compared against results of numerical modelling. The criteria for transition to the nonlinear regime of strong Bragg backscattering (BBS) is obtained for both O-mode and X-mode reflectometry. It is shown that a strong nonlinear regime of BBS may occur in ITER at the 0.5-2% relative density perturbation level both for the ordinary and extraordinary mode probing. The possibility of probing wave trapping leading to strong enhancement of the electric field and associated high phase variation of the reflected wave due to BBS is demonstrated.

  5. Strongly interacting ultracold polar molecules

    NASA Astrophysics Data System (ADS)

    Gadway, Bryce; Yan, Bo

    2016-08-01

    This paper reviews recent advances in the study of strongly interacting systems of dipolar molecules. Heteronuclear molecules feature large and tunable electric dipole moments, which give rise to long-range and anisotropic dipole–dipole interactions. Ultracold samples of dipolar molecules with long-range interactions offer a unique platform for quantum simulations and the study of correlated many-body physics. We provide an introduction to the physics of dipolar quantum gases, both electric and magnetic, and summarize the multipronged efforts to bring dipolar molecules into the quantum regime. We discuss in detail the recent experimental progress in realizing and studying strongly interacting systems of polar molecules trapped in optical lattices, with particular emphasis on the study of interacting spin systems and non-equilibrium quantum magnetism. Finally, we conclude with a brief discussion of the future prospects for studies of strongly interacting dipolar molecules.

  6. The SNAP Strong Lens Survey

    SciTech Connect

    Marshall, P.

    2005-01-03

    Basic considerations of lens detection and identification indicate that a wide field survey of the types planned for weak lensing and Type Ia SNe with SNAP are close to optimal for the optical detection of strong lenses. Such a ''piggy-back'' survey might be expected even pessimistically to provide a catalogue of a few thousand new strong lenses, with the numbers dominated by systems of faint blue galaxies lensed by foreground ellipticals. After sketching out our strategy for detecting and measuring these galaxy lenses using the SNAP images, we discuss some of the scientific applications of such a large sample of gravitational lenses: in particular we comment on the partition of information between lens structure, the source population properties and cosmology. Understanding this partitioning is key to assessing strong lens cosmography's value as a cosmological probe.

  7. Strong Photoassociation in Ultracold Fermions

    NASA Astrophysics Data System (ADS)

    Jing, Li; Jamison, Alan; Rvachov, Timur; Ebadi, Sepher; Son, Hyungmok; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2016-05-01

    Despite many studies there are still open questions about strong photoassociation in ultracold gases. Photoassociation occurs only at short range and thus can be used as a tool to probe and control the two-body correlation function in an interacting many-body system and to engineer Hamiltonians using dissipation. We propose the possibility to slow down decoherence by photoassociation through the quantum Zeno effect. This can realized by shining strong photoassociation light on the superposition of the lowest two hyperfine states of Lithium 6. NSF, ARO-MURI, Samsung, NSERC.

  8. Interfacial Protein-Protein Associations

    PubMed Central

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

    2014-01-01

    While traditional models of protein adsorption focus primarily on direct protein-surface interactions, recent findings suggest that protein-protein interactions may play a central role. Using high-throughput intermolecular resonance energy transfer (RET) tracking, we directly observed dynamic, protein-protein associations of bovine serum albumin on poly(ethylene glycol) modified surfaces. The associations were heterogeneous and reversible, and associating molecules resided on the surface for longer times. The appearance of three distinct RET states suggested a spatially heterogeneous surface – with areas of high protein density (i.e. strongly-interacting clusters) coexisting with mobile monomers. Distinct association states exhibited characteristic behavior, i.e. partial-RET (monomer-monomer) associations were shorter-lived than complete-RET (protein-cluster) associations. While the fractional surface area covered by regions with high protein density (i.e. clusters) increased with increasing concentration, the distribution of contact times between monomers and clusters was independent of solution concentration, suggesting that associations were a local phenomenon, and independent of the global surface coverage. PMID:24274729

  9. PREFACE: Strongly Coupled Coulomb Systems Strongly Coupled Coulomb Systems

    NASA Astrophysics Data System (ADS)

    Neilson, David; Senatore, Gaetano

    2009-05-01

    This special issue contains papers presented at the International Conference on Strongly Coupled Coulomb Systems (SCCS), held from 29 July-2 August 2008 at the University of Camerino. Camerino is an ancient hill-top town located in the Apennine mountains of Italy, 200 kilometres northeast of Rome, with a university dating back to 1336. The Camerino conference was the 11th in a series which started in 1977: 1977: Orleans-la-Source, France, as a NATO Advanced Study Institute on Strongly Coupled Plasmas (hosted by Marc Feix and Gabor J Kalman) 1982: Les Houches, France (hosted by Marc Baus and Jean-Pierre Hansen) 1986: Santa Cruz, California, USA (hosted by Forrest J Rogers and Hugh E DeWitt) 1989: Tokyo, Japan (hosted by Setsuo Ichimaru) 1992: Rochester, New York, USA (hosted by Hugh M Van Horn and Setsuo Ichimaru) 1995: Binz, Germany (hosted by Wolf Dietrich Kraeft and Manfred Schlanges) 1997: Boston, Massachusetts, USA (hosted by Gabor J Kalman) 1999: St Malo, France (hosted by Claude Deutsch and Bernard Jancovici) 2002: Santa Fe, New Mexico, USA (hosted by John F Benage and Michael S Murillo) 2005: Moscow, Russia (hosted by Vladimir E Fortov and Vladimir Vorob'ev). The name of the series was changed in 1996 from Strongly Coupled Plasmas to Strongly Coupled Coulomb Systems to reflect a wider range of topics. 'Strongly Coupled Coulomb Systems' encompasses diverse many-body systems and physical conditions. The purpose of the conferences is to provide a regular international forum for the presentation and discussion of research achievements and ideas relating to a variety of plasma, liquid and condensed matter systems that are dominated by strong Coulomb interactions between their constituents. Each meeting has seen an evolution of topics and emphases that have followed new discoveries and new techniques. The field has continued to see new experimental tools and access to new strongly coupled conditions, most recently in the areas of warm matter, dusty plasmas

  10. Strong coupling electroweak symmetry breaking

    SciTech Connect

    Barklow, T.L.; Burdman, G.; Chivukula, R.S.

    1997-04-01

    The authors review models of electroweak symmetry breaking due to new strong interactions at the TeV energy scale and discuss the prospects for their experimental tests. They emphasize the direct observation of the new interactions through high-energy scattering of vector bosons. They also discuss indirect probes of the new interactions and exotic particles predicted by specific theoretical models.

  11. A strongly coupled anyon material

    NASA Astrophysics Data System (ADS)

    Brattan, Daniel K.

    2015-11-01

    We use alternative quantisation of the D3-D5 system to explore properties of a strongly coupled anyon material at finite density and temperature. We study the transport properties of the material and find both diffusion and massive holographic zero sound modes. By studying the anyon number conductivity we also find evidence for the anyonic analogue of the metal-insulator transition.

  12. STRONG HEART STUDY DATA BOOK

    EPA Science Inventory

    Epidemiologic study of cardiovascular disease in American Indians. Examination on the prevalence of major risk factors of CVD in American Indian men and women ages 45-74 in the American Indian communities from the three centers that participate in the Strong Heart Study.

  13. Quality control by <strong>HyperS>pectral <strong>I>maging (HSI) in solid waste recycling: logics, algorithms and procedures

    NASA Astrophysics Data System (ADS)

    Bonifazi, Giuseppe; Serranti, Silvia

    2014-03-01

    In secondary raw materials and recycling sectors, the products quality represents, more and more, the key issue to pursuit in order to be competitive in a more and more demanding market, where quality standards and products certification play a preheminent role. These goals assume particular importance when recycling actions are applied. Recovered products, resulting from waste materials, and/or dismissed products processing, are, in fact, always seen with a certain suspect. An adequate response of the industry to the market can only be given through the utilization of equipment and procedures ensuring pure, high-quality production, and efficient work and cost. All these goals can be reached adopting not only more efficient equipment and layouts, but also introducing new processing logics able to realize a full control of the handled material flow streams fulfilling, at the same time, i) an easy management of the procedures, ii) an efficient use of the energy, iii) the definition and set up of reliable and robust procedures, iv) the possibility to implement network connectivity capabilities finalized to a remote monitoring and control of the processes and v) a full data storage, analysis and retrieving. Furthermore the ongoing legislation and regulation require the implementation of recycling infrastructure characterised by high resources efficiency and low environmental impacts, both aspects being strongly linked to the waste materials and/or dismissed products original characteristics. For these reasons an optimal recycling infrastructure design primarily requires a full knowledge of the characteristics of the input waste. What previously outlined requires the introduction of a new important concept to apply in solid waste recycling, the recycling-oriented characterization, that is the set of actions addressed to strategically determine selected attributes, in order to get goaloriented data on waste for the development, implementation or improvement of recycling

  14. PREFACE: Strongly correlated electron systems Strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Saxena, Siddharth S.; Littlewood, P. B.

    2012-07-01

    This special section is dedicated to the Strongly Correlated Electron Systems Conference (SCES) 2011, which was held from 29 August-3 September 2011, in Cambridge, UK. SCES'2011 is dedicated to 100 years of superconductivity and covers a range of topics in the area of strongly correlated systems. The correlated electronic and magnetic materials featured include f-electron based heavy fermion intermetallics and d-electron based transition metal compounds. The selected papers derived from invited presentations seek to deepen our understanding of the rich physical phenomena that arise from correlation effects. The focus is on quantum phase transitions, non-Fermi liquid phenomena, quantum magnetism, unconventional superconductivity and metal-insulator transitions. Both experimental and theoretical work is presented. Based on fundamental advances in the understanding of electronic materials, much of 20th century materials physics was driven by miniaturisation and integration in the electronics industry to the current generation of nanometre scale devices. The achievements of this industry have brought unprecedented advances to society and well-being, and no doubt there is much further to go—note that this progress is founded on investments and studies in the fundamentals of condensed matter physics from more than 50 years ago. Nevertheless, the defining challenges for the 21st century will lie in the discovery in science, and deployment through engineering, of technologies that can deliver the scale needed to have an impact on the sustainability agenda. Thus the big developments in nanotechnology may lie not in the pursuit of yet smaller transistors, but in the design of new structures that can revolutionise the performance of solar cells, batteries, fuel cells, light-weight structural materials, refrigeration, water purification, etc. The science presented in the papers of this special section also highlights the underlying interest in energy-dense materials, which

  15. EDITORIAL: Strongly correlated electron systems Strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Ronning, Filip; Batista, Cristian

    2011-03-01

    Strongly correlated electrons is an exciting and diverse field in condensed matter physics. This special issue aims to capture some of that excitement and recent developments in the field. Given that this issue was inspired by the 2010 International Conference on Strongly Correlated Electron Systems (SCES 2010), we briefly give some history in order to place this issue in context. The 2010 International Conference on Strongly Correlated Electron Systems was held in Santa Fe, New Mexico, a reunion of sorts from the 1989 International Conference on the Physics of Highly Correlated Electron Systems that also convened in Santa Fe. SCES 2010—co-chaired by John Sarrao and Joe Thompson—followed the tradition of earlier conferences, in this century, hosted by Buzios (2008), Houston (2007), Vienna (2005), Karlsruhe (2004), Krakow (2002) and Ann Arbor (2001). Every three years since 1997, SCES has joined the International Conference on Magnetism (ICM), held in Recife (2000), Rome (2003), Kyoto (2006) and Karlsruhe (2009). Like its predecessors, SCES 2010 topics included strongly correlated f- and d-electron systems, heavy-fermion behaviors, quantum-phase transitions, non-Fermi liquid phenomena, unconventional superconductivity, and emergent states that arise from electronic correlations. Recent developments from studies of quantum magnetism and cold atoms complemented the traditional subjects and were included in SCES 2010. 2010 celebrated the 400th anniversary of Santa Fe as well as the birth of astronomy. So what's the connection to SCES? The Dutch invention of the first practical telescope and its use by Galileo in 1610 and subsequent years overturned dogma that the sun revolved about the earth. This revolutionary, and at the time heretical, conclusion required innovative combinations of new instrumentation, observation and mathematics. These same combinations are just as important 400 years later and are the foundation of scientific discoveries that were discussed

  16. Composite strongly interacting dark matter

    NASA Astrophysics Data System (ADS)

    Cline, James M.; Liu, Zuowei; Moore, Guy D.; Xue, Wei

    2014-07-01

    It has been suggested that cold dark matter (CDM) has difficulties in explaining tentative evidence for noncuspy halo profiles in small galaxies, and the low velocity dispersions observed in the largest Milky Way satellites ("too-big-to-fail" problem). Strongly self-interacting dark matter has been noted as a robust solution to these problems. The elastic cross sections required are much larger than predicted by generic CDM models, but could naturally be of the right size if dark matter is composite. We explore in a general way the constraints on models where strongly interacting CDM is in the form of dark "atoms" or "molecules," or bound states of a confining gauge interaction ("hadrons"). These constraints include considerations of relic density, direct detection, big bang nucleosynthesis, the cosmic microwave background, and LHC data.

  17. Strongly interacting parton matter equilibration

    SciTech Connect

    Ozvenchuk, V.; Linnyk, O.; Bratkovskaya, E.; Gorenstein, M.; Cassing, W.

    2012-07-15

    We study the kinetic and chemical equilibration in 'infinite' parton matter within the Parton-Hadron-String Dynamics transport approach. The 'infinite' matter is simulated within a cubic box with periodic boundary conditions initialized at different energy densities. Particle abundances, kinetic energy distributions, and the detailed balance of the off-shell quarks and gluons in the strongly-interacting quarkgluon plasma are addressed and discussed.

  18. Strong CP and SUZ2

    NASA Astrophysics Data System (ADS)

    Albaid, Abdelhamid; Dine, Michael; Draper, Patrick

    2015-12-01

    Solutions to the strong CP problem typically introduce new scales associated with the spontaneous breaking of symmetries. Absent any anthropic argument for small overline{θ} , these scales require stabilization against ultraviolet corrections. Supersymmetry offers a tempting stabilization mechanism, since it can solve the "big" electroweak hierarchy problem at the same time. One family of solutions to strong CP, including generalized parity models, heavy axion models, and heavy η' models, introduces {Z}_2 copies of (part of) the Standard Model and an associated scale of {Z}_2 -breaking. We review why, without additional structure such as supersymmetry, the {Z}_2 -breaking scale is unacceptably tuned. We then study "SUZ2" models, supersymmetric theories with {Z}_2 copies of the MSSM. We find that the addition of SUSY typically destroys the {Z}_2 protection of overline{θ}=0 , even at tree level, once SUSY and {Z}_2 are broken. In theories like supersymmetric completions of the twin Higgs, where {Z}_2 addresses the little hierarchy problem but not strong CP, two axions can be used to relax overline{θ}.

  19. Strong interactive massive particles from a strong coupled theory

    SciTech Connect

    Khlopov, Maxim Yu.; Kouvaris, Chris

    2008-03-15

    Minimal walking technicolor models can provide a nontrivial solution for cosmological dark matter, if the lightest technibaryon is doubly charged. Technibaryon asymmetry generated in the early Universe is related to baryon asymmetry, and it is possible to create an excess of techniparticles with charge (-2). These excessive techniparticles are all captured by {sup 4}He, creating techni-O-helium tOHe atoms, as soon as {sup 4}He is formed in big bang nucleosynthesis. The interaction of techni-O-helium with nuclei opens new paths to the creation of heavy nuclei in big bang nucleosynthesis. Because of the large mass of technibaryons, the tOHe ''atomic'' gas decouples from the baryonic matter and plays the role of dark matter in large scale structure formation, while structures in small scales are suppressed. Nuclear interactions with matter slow down cosmic techni-O-helium in the Earth below the threshold of underground dark matter detectors, thus escaping severe cryogenic dark matter search constraints. On the other hand, these nuclear interactions are not sufficiently strong to exclude this form of strongly interactive massive particles by constraints from the XQC experiment. Experimental tests of this hypothesis are possible in the search for tOHe in balloon-borne experiments (or on the ground) and for its charged techniparticle constituents in cosmic rays and accelerators. The tOHe atoms can cause cold nuclear transformations in matter and might form anomalous isotopes, offering possible ways to exclude (or prove?) their existence.

  20. PREFACE: Strongly correlated electron systems Strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Saxena, Siddharth S.; Littlewood, P. B.

    2012-07-01

    This special section is dedicated to the Strongly Correlated Electron Systems Conference (SCES) 2011, which was held from 29 August-3 September 2011, in Cambridge, UK. SCES'2011 is dedicated to 100 years of superconductivity and covers a range of topics in the area of strongly correlated systems. The correlated electronic and magnetic materials featured include f-electron based heavy fermion intermetallics and d-electron based transition metal compounds. The selected papers derived from invited presentations seek to deepen our understanding of the rich physical phenomena that arise from correlation effects. The focus is on quantum phase transitions, non-Fermi liquid phenomena, quantum magnetism, unconventional superconductivity and metal-insulator transitions. Both experimental and theoretical work is presented. Based on fundamental advances in the understanding of electronic materials, much of 20th century materials physics was driven by miniaturisation and integration in the electronics industry to the current generation of nanometre scale devices. The achievements of this industry have brought unprecedented advances to society and well-being, and no doubt there is much further to go—note that this progress is founded on investments and studies in the fundamentals of condensed matter physics from more than 50 years ago. Nevertheless, the defining challenges for the 21st century will lie in the discovery in science, and deployment through engineering, of technologies that can deliver the scale needed to have an impact on the sustainability agenda. Thus the big developments in nanotechnology may lie not in the pursuit of yet smaller transistors, but in the design of new structures that can revolutionise the performance of solar cells, batteries, fuel cells, light-weight structural materials, refrigeration, water purification, etc. The science presented in the papers of this special section also highlights the underlying interest in energy-dense materials, which

  1. PREFACE: Strongly Coupled Coulomb Systems

    NASA Astrophysics Data System (ADS)

    Fortov, Vladimir E.; Golden, Kenneth I.; Norman, Genri E.

    2006-04-01

    This special issue contains papers presented at the International Conference on Strongly Coupled Coulomb Systems (SCCS) which was held during the week of 20 24 June 2005 in Moscow, Russia. The Moscow conference was the tenth in a series of conferences. The previous conferences were organized as follows. 1977: Orleans-la-Source, France, as a NATO Advanced Study Institute on Strongly Coupled Plasmas (organized by Marc Feix and Gabor J Kalman) 1982: Les Houches, France (organized by Marc Baus and Jean-Pierre Hansen) 1986: Santa Cruz, California, USA (hosted by Forrest J Rogers and Hugh E DeWitt) 1989: Tokyo, Japan (hosted by Setsuo Ichimaru) 1992: Rochester, NY, USA (hosted by Hugh M Van Horn and Setsuo Ichimaru) 1995: Binz, Germany (hosted by Wolf Dietrich Kraeft and Manfred Schlanges) 1997: Boston, Massachusetts, USA (hosted by Gabor J Kalman) 1999: St Malo, France (hosted by Claude Deutsch and Bernard Jancovici) 2002: Santa Fe, New Mexico, USA (hosted by John F Benage and Michael S Murillo) After 1995 the name of the series was changed from `Strongly Coupled Plasmas' to the present name in order to extend the topics of the conferences. The planned frequency for the future is once every three years. The purpose of these conferences is to provide an international forum for the presentation and discussion of research accomplishments and ideas relating to a variety of plasma liquid and condensed matter systems, dominated by strong Coulomb interactions between their constituents. Strongly coupled Coulomb systems encompass diverse many-body systems and physical conditions. Each meeting has seen an evolution of topics and emphasis as new discoveries and new methods appear. This year, sessions were organized for invited presentations and posters on dense plasmas and warm matter, astrophysics and dense hydrogen, non-neutral and ultracold plasmas, dusty plasmas, condensed matter 2D and layered charged-particle systems, Coulomb liquids, and statistical theory of SCCS. Within

  2. Strong turbulence of plasma waves

    NASA Technical Reports Server (NTRS)

    Goldman, M. V.

    1984-01-01

    This paper reviews recent work related to modulational instability and wave envelope self-focusing in dynamical and statistical systems. After introductory remarks pertinent to nonlinear optics realizations of these effects, the author summarizes the status of the subject in plasma physics, where it has come to be called 'strong Langmuir turbulence'. The paper treats the historical development of pertinent concepts, analytical theory, numerical simulations, laboratory experiments, and spacecraft observations. The role of self-similar self-focusing Langmuir envelope wave packets is emphasized, both in the Zakharov equation model for the wave dynamics and in a statistical theory based on this dynamical model.

  3. [DNA knots and strong triviality].

    PubMed

    Torisu, Ichiro

    2009-06-01

    A circle embedded in 3-space without self-intersection is called a knot. A knot is a mathematical object according to topology. Knot theory studies how complicated a given knot is, or whether it is trivial. Any knot can be represented by a diagram with above and below information at the crossings. Then a knot obtained by replacing the information at one crossing is generally another knot. This operation is called a crossing change. A crossing change is an important notion in knot theory. In this article, we survey the strong triviality of knots, which is one of the multi-crossing changes. PMID:19530562

  4. A metafluid exhibiting strong optical magnetism.

    PubMed

    Sheikholeslami, Sassan N; Alaeian, Hadiseh; Koh, Ai Leen; Dionne, Jennifer A

    2013-09-11

    Advances in the field of metamaterials have enabled unprecedented control of light-matter interactions. Metamaterial constituents support high-frequency electric and magnetic dipoles, which can be used as building blocks for new materials capable of negative refraction, electromagnetic cloaking, strong visible-frequency circular dichroism, and enhancing magnetic or chiral transitions in ions and molecules. While all metamaterials to date have existed in the solid-state, considerable interest has emerged in designing a colloidal metamaterial or "metafluid". Such metafluids would combine the advantages of solution-based processing with facile integration into conventional optical components. Here we demonstrate the colloidal synthesis of an isotropic metafluid that exhibits a strong magnetic response at visible frequencies. Protein-antibody interactions are used to direct the solution-phase self-assembly of discrete metamolecules comprised of silver nanoparticles tightly packed around a single dielectric core. The electric and magnetic response of individual metamolecules and the bulk metamaterial solution are directly probed with optical scattering and spectroscopy. Effective medium calculations indicate that the bulk metamaterial exhibits a negative effective permeability and a negative refractive index at modest fill factors. This metafluid can be synthesized in large-quantity and high-quality and may accelerate development of advanced nanophotonic and metamaterial devices. PMID:23919764

  5. EDITORIAL: Strongly correlated electron systems Strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Ronning, Filip; Batista, Cristian

    2011-03-01

    Strongly correlated electrons is an exciting and diverse field in condensed matter physics. This special issue aims to capture some of that excitement and recent developments in the field. Given that this issue was inspired by the 2010 International Conference on Strongly Correlated Electron Systems (SCES 2010), we briefly give some history in order to place this issue in context. The 2010 International Conference on Strongly Correlated Electron Systems was held in Santa Fe, New Mexico, a reunion of sorts from the 1989 International Conference on the Physics of Highly Correlated Electron Systems that also convened in Santa Fe. SCES 2010—co-chaired by John Sarrao and Joe Thompson—followed the tradition of earlier conferences, in this century, hosted by Buzios (2008), Houston (2007), Vienna (2005), Karlsruhe (2004), Krakow (2002) and Ann Arbor (2001). Every three years since 1997, SCES has joined the International Conference on Magnetism (ICM), held in Recife (2000), Rome (2003), Kyoto (2006) and Karlsruhe (2009). Like its predecessors, SCES 2010 topics included strongly correlated f- and d-electron systems, heavy-fermion behaviors, quantum-phase transitions, non-Fermi liquid phenomena, unconventional superconductivity, and emergent states that arise from electronic correlations. Recent developments from studies of quantum magnetism and cold atoms complemented the traditional subjects and were included in SCES 2010. 2010 celebrated the 400th anniversary of Santa Fe as well as the birth of astronomy. So what's the connection to SCES? The Dutch invention of the first practical telescope and its use by Galileo in 1610 and subsequent years overturned dogma that the sun revolved about the earth. This revolutionary, and at the time heretical, conclusion required innovative combinations of new instrumentation, observation and mathematics. These same combinations are just as important 400 years later and are the foundation of scientific discoveries that were discussed

  6. Hydrophobic Surfactant Proteins Induce a Phosphatidylethanolamine to Form Cubic Phases

    PubMed Central

    Chavarha, Mariya; Khoojinian, Hamed; Schulwitz, Leonard E.; Biswas, Samares C.; Rananavare, Shankar B.; Hall, Stephen B.

    2010-01-01

    Abstract The hydrophobic surfactant proteins SP-B and SP-C promote rapid adsorption of pulmonary surfactant to an air/water interface. Previous evidence suggests that they achieve this effect by facilitating the formation of a rate-limiting negatively curved stalk between the vesicular bilayer and the interface. To determine whether the proteins can alter the curvature of lipid leaflets, we used x-ray diffraction to investigate how the physiological mixture of these proteins affects structures formed by 1-palmitoyl-2-oleoyl phosphatidylethanolamine, which by itself undergoes the lamellar-to-inverse hexagonal phase transition at 71°C. In amounts as low as 0.03% (w:w) and at temperatures as low as 57°C, the proteins induce formation of bicontinuous inverse cubic phases. The proteins produce a dose-related shift of diffracted intensity to the cubic phases, with minimal evidence of other structures above 0.1% and 62°C, but no change in the lattice-constants of the lamellar or cubic phases. The induction of the bicontinuous cubic phases, in which the individual lipid leaflets have the same saddle-shaped curvature as the hypothetical stalk-intermediate, supports the proposed model of how the surfactant proteins promote adsorption. PMID:20409474

  7. Surfactant proteins, SP-A and SP-D, in respiratory fungal infections: their role in the inflammatory response.

    PubMed

    Carreto-Binaghi, Laura Elena; Aliouat, El Moukhtar; Taylor, Maria Lucia

    2016-01-01

    Pulmonary surfactant is a complex fluid that comprises phospholipids and four proteins (SP-A, SP-B, SP-C, and SP-D) with different biological functions. SP-B, SP-C, and SP-D are essential for the lungs' surface tension function and for the organization, stability and metabolism of lung parenchyma. SP-A and SP-D, which are also known as pulmonary collectins, have an important function in the host's lung immune response; they act as opsonins for different pathogens via a C-terminal carbohydrate recognition domain and enhance the attachment to phagocytic cells or show their own microbicidal activity by increasing the cellular membrane permeability. Interactions between the pulmonary collectins and bacteria or viruses have been extensively studied, but this is not the same for fungal pathogens. SP-A and SP-D bind glucan and mannose residues from fungal cell wall, but there is still a lack of information on their binding to other fungal carbohydrate residues. In addition, both their relation with immune cells for the clearance of these pathogens and the role of surfactant proteins' regulation during respiratory fungal infections remain unknown. Here we highlight the relevant findings associated with SP-A and SP-D in those respiratory mycoses where the fungal infective propagules reach the lungs by the airways. PMID:27250970

  8. Probability densities in strong turbulence

    NASA Astrophysics Data System (ADS)

    Yakhot, Victor

    2006-03-01

    In this work we, using Mellin’s transform combined with the Gaussian large-scale boundary condition, calculate probability densities (PDFs) of velocity increments P(δu,r), velocity derivatives P(u,r) and the PDF of the fluctuating dissipation scales Q(η,Re), where Re is the large-scale Reynolds number. The resulting expressions strongly deviate from the Log-normal PDF P(δu,r) often quoted in the literature. It is shown that the probability density of the small-scale velocity fluctuations includes information about the large (integral) scale dynamics which is responsible for the deviation of P(δu,r) from P(δu,r). An expression for the function D(h) of the multifractal theory, free from spurious logarithms recently discussed in [U. Frisch, M. Martins Afonso, A. Mazzino, V. Yakhot, J. Fluid Mech. 542 (2005) 97] is also obtained.

  9. Strongly Interacting Homogeneous Fermi Gases

    NASA Astrophysics Data System (ADS)

    Mukherjee, Biswaroop; Patel, Parth; Yan, Zhenjie; Struck, Julian; Zwierlein, Martin

    2016-05-01

    We present a homogeneous box potential for strongly interacting Fermi gases. The local density approximation (LDA) allows measurements on traditional inhomogeneous traps to observe a continuous distribution of Fermi gases in a single shot, but also suffer from a broadened response due to line-of-sight averaging over varying densities. We trap ultracold Fermionic (6 Li) in an optical homogeneous potential and characterize its flatness through in-situ tomography. A hybrid approach combining a cylindrical optical potential with a harmonic magnetic trap allows us to exploit the LDA and measure local RF spectra without requiring significant image reconstruction. We extract various quantities from the RF spectra such as the Tan's contact, and discuss further measurements of homogeneous Fermi systems under spin imbalance and finite temperature.

  10. Electrophoresis in strong electric fields.

    PubMed

    Barany, Sandor

    2009-01-01

    Two kinds of non-linear electrophoresis (ef) that can be detected in strong electric fields (several hundred V/cm) are considered. The first ("classical" non-linear ef) is due to the interaction of the outer field with field-induced ionic charges in the electric double layer (EDL) under conditions, when field-induced variations of electrolyte concentration remain to be small comparatively to its equilibrium value. According to the Shilov theory, the non-linear component of the electrophoretic velocity for dielectric particles is proportional to the cubic power of the applied field strength (cubic electrophoresis) and to the second power of the particles radius; it is independent of the zeta-potential but is determined by the surface conductivity of particles. The second one, the so-called "superfast electrophoresis" is connected with the interaction of a strong outer field with a secondary diffuse layer of counterions (space charge) that is induced outside the primary (classical) diffuse EDL by the external field itself because of concentration polarization. The Dukhin-Mishchuk theory of "superfast electrophoresis" predicts quadratic dependence of the electrophoretic velocity of unipolar (ionically or electronically) conducting particles on the external field gradient and linear dependence on the particle's size in strong electric fields. These are in sharp contrast to the laws of classical electrophoresis (no dependence of V(ef) on the particle's size and linear dependence on the electric field gradient). A new method to measure the ef velocity of particles in strong electric fields is developed that is based on separation of the effects of sedimentation and electrophoresis using videoimaging and a new flowcell and use of short electric pulses. To test the "classical" non-linear electrophoresis, we have measured the ef velocity of non-conducting polystyrene, aluminium-oxide and (semiconductor) graphite particles as well as Saccharomice cerevisiae yeast cells as a

  11. Strong shock implosion, approximate solution

    NASA Astrophysics Data System (ADS)

    Fujimoto, Y.; Mishkin, E. A.; Alejaldre, C.

    1983-01-01

    The self-similar, center-bound motion of a strong spherical, or cylindrical, shock wave moving through an ideal gas with a constant, γ= cp/ cv, is considered and a linearized, approximate solution is derived. An X, Y phase plane of the self-similar solution is defined and the representative curved of the system behind the shock front is replaced by a straight line connecting the mappings of the shock front with that of its tail. The reduced pressure P(ξ), density R(ξ) and velocity U1(ξ) are found in closed, quite accurate, form. Comparison with numerically obtained results, for γ= {5}/{3} and γ= {7}/{5}, is shown.

  12. New, non-quinone fluorogeldanamycin derivatives strongly inhibit Hsp90.

    PubMed

    Hermane, Jekaterina; Bułyszko, Ilona; Eichner, Simone; Sasse, Florenz; Collisi, Wera; Poso, Antti; Schax, Emilia; Walter, Johanna-Gabriela; Scheper, Thomas; Kock, Klaus; Herrmann, Christian; Aliuos, Pooyan; Reuter, Günter; Zeilinger, Carsten; Kirschning, Andreas

    2015-01-19

    Streptomyces hygroscopicus is a natural producer of geldanamycin. Mutasynthetic supplementation of an AHBA-blocked mutant with all possible monofluoro 3-aminobenzoic acids provided new fluorogeldanamycins. These showed strong antiproliferative activity and inhibitory effects on human heat shock protein Hsp90. Binding to Hsp90 in the low nanomolar range was determined from molecular modelling, AFM analysis and by calorimetric studies. PMID:25572106

  13. Eikonal Scattering at Strong Coupling

    NASA Astrophysics Data System (ADS)

    Irizarry-Gelpi, Melvin Eloy

    The scattering of subatomic particles is a source of important physical phenomena. Decades of work have yielded many techniques for the computation of scattering amplitudes. Most of these techniques involve perturbative quantum field theory and thus apply only at weak coupling. Complementary to scattering is the formation of bound states, which are intrinsically nonperturbative. Regge theory arose in the late 1950s as an attempt to describe, with a single framework, both scattering and the formation of bound states. In Regge theory one obtains an amplitude with bound state poles after analytic continuation of a nonperturbative scattering amplitude, corresponding to a sum of an infinite number of Feynman diagrams at large energy and fixed momentum transfer (but with crossed kinematics). Thus, in order to obtain bound states at fixed energy, one computes an amplitude at large momentum transfer. In this dissertation we calculate amplitudes with bound states in the regime of fixed energy and small momentum transfer. We formulate the elastic scattering problem in terms of many-body path integrals, familiar from quantum mechanics. Then we invoke the semiclassical JWKB approximation, where the path integral is dominated by classical paths. The dynamics in the semiclassical regime are strongly coupled, as found by Halpern and Siegel. When the momentum transfer is small, the classical paths are simple straight lines and the resulting semiclassical amplitudes display a spectrum of bound states that agrees with the spectrum found by solving wave equations with potentials. In this work we study the bound states of matter particles with various types of interactions, including electromagnetic and gravitational interactions. Our work has many analogies with the work started by Alday and Maldacena, who computed scattering amplitudes of gluons at strong coupling with semiclassical quantum mechanics of strings in anti de-Sitter spacetime. We hope that in the future we can apply our

  14. Strong Winds over the Keel

    NASA Astrophysics Data System (ADS)

    2009-02-01

    The latest ESO image reveals amazing detail in the intricate structures of one of the largest and brightest nebulae in the sky, the Carina Nebula (NGC 3372), where strong winds and powerful radiation from an armada of massive stars are creating havoc in the large cloud of dust and gas from which the stars were born. ESO PR Photo 05a/09 The Carina Nebula ESO PR Video 05a/09 Pan over the Carina Nebula ESO PR Video 05b/09 Carina Nebula Zoom-in The large and beautiful image displays the full variety of this impressive skyscape, spattered with clusters of young stars, large nebulae of dust and gas, dust pillars, globules, and adorned by one of the Universe's most impressive binary stars. It was produced by combining exposures through six different filters from the Wide Field Imager (WFI), attached to the 2.2 m ESO/MPG telescope at ESO's La Silla Observatory, in Chile. The Carina Nebula is located about 7500 light-years away in the constellation of the same name (Carina; the Keel). Spanning about 100 light-years, it is four times larger than the famous Orion Nebula and far brighter. It is an intensive star-forming region with dark lanes of cool dust splitting up the glowing nebula gas that surrounds its many clusters of stars. The glow of the Carina Nebula comes mainly from hot hydrogen basking in the strong radiation of monster baby stars. The interaction between the hydrogen and the ultraviolet light results in its characteristic red and purple colour. The immense nebula contains over a dozen stars with at least 50 to 100 times the mass of our Sun. Such stars have a very short lifespan, a few million years at most, the blink of an eye compared with the Sun's expected lifetime of ten billion years. One of the Universe's most impressive stars, Eta Carinae, is found in the nebula. It is one of the most massive stars in our Milky Way, over 100 times the mass of the Sun and about four million times brighter, making it the most luminous star known. Eta Carinae is highly

  15. Strongly correlated perovskite fuel cells.

    PubMed

    Zhou, You; Guan, Xiaofei; Zhou, Hua; Ramadoss, Koushik; Adam, Suhare; Liu, Huajun; Lee, Sungsik; Shi, Jian; Tsuchiya, Masaru; Fong, Dillon D; Ramanathan, Shriram

    2016-06-01

    Fuel cells convert chemical energy directly into electrical energy with high efficiencies and environmental benefits, as compared with traditional heat engines. Yttria-stabilized zirconia is perhaps the material with the most potential as an electrolyte in solid oxide fuel cells (SOFCs), owing to its stability and near-unity ionic transference number. Although there exist materials with superior ionic conductivity, they are often limited by their ability to suppress electronic leakage when exposed to the reducing environment at the fuel interface. Such electronic leakage reduces fuel cell power output and the associated chemo-mechanical stresses can also lead to catastrophic fracture of electrolyte membranes. Here we depart from traditional electrolyte design that relies on cation substitution to sustain ionic conduction. Instead, we use a perovskite nickelate as an electrolyte with high initial ionic and electronic conductivity. Since many such oxides are also correlated electron systems, we can suppress the electronic conduction through a filling-controlled Mott transition induced by spontaneous hydrogen incorporation. Using such a nickelate as the electrolyte in free-standing membrane geometry, we demonstrate a low-temperature micro-fabricated SOFC with high performance. The ionic conductivity of the nickelate perovskite is comparable to the best-performing solid electrolytes in the same temperature range, with a very low activation energy. The results present a design strategy for high-performance materials exhibiting emergent properties arising from strong electron correlations. PMID:27279218

  16. Strongly correlated perovskite fuel cells

    NASA Astrophysics Data System (ADS)

    Zhou, You; Guan, Xiaofei; Zhou, Hua; Ramadoss, Koushik; Adam, Suhare; Liu, Huajun; Lee, Sungsik; Shi, Jian; Tsuchiya, Masaru; Fong, Dillon D.; Ramanathan, Shriram

    2016-06-01

    Fuel cells convert chemical energy directly into electrical energy with high efficiencies and environmental benefits, as compared with traditional heat engines. Yttria-stabilized zirconia is perhaps the material with the most potential as an electrolyte in solid oxide fuel cells (SOFCs), owing to its stability and near-unity ionic transference number. Although there exist materials with superior ionic conductivity, they are often limited by their ability to suppress electronic leakage when exposed to the reducing environment at the fuel interface. Such electronic leakage reduces fuel cell power output and the associated chemo-mechanical stresses can also lead to catastrophic fracture of electrolyte membranes. Here we depart from traditional electrolyte design that relies on cation substitution to sustain ionic conduction. Instead, we use a perovskite nickelate as an electrolyte with high initial ionic and electronic conductivity. Since many such oxides are also correlated electron systems, we can suppress the electronic conduction through a filling-controlled Mott transition induced by spontaneous hydrogen incorporation. Using such a nickelate as the electrolyte in free-standing membrane geometry, we demonstrate a low-temperature micro-fabricated SOFC with high performance. The ionic conductivity of the nickelate perovskite is comparable to the best-performing solid electrolytes in the same temperature range, with a very low activation energy. The results present a design strategy for high-performance materials exhibiting emergent properties arising from strong electron correlations.

  17. Surfactant Proteins in Smoking-Related Lung Disease.

    PubMed

    Papaioannou, Andriana I; Papiris, Spyridon; Papadaki, Georgia; Manali, Effrosyni D; Roussou, Aneza; Spathis, Aris; Karakitsos, Petros; Kostikas, Konstantinos

    2016-01-01

    Pulmonary surfactant is a highly surface-active mixture of proteins and lipids that is synthesized and secreted in the alveoli by type II epithelial cells and is found in the fluid lining the alveolar surface. The protein part of surfactant constitutes two hydrophilic proteins (SP-A and SP-D) that regulate surfactant metabolism and have immunologic functions, and two hydrophobic proteins (SP-B and SP-C), which play a direct role in the organization of the surfactant structure in the interphase and in the stabilization of the lipid layers during the respiratory cycle. Several studies have shown that cigarette smoke seems to affect, in several ways, both surfactant homeostasis and function. The alterations in surfactants' biophysical properties caused by cigarette smoking, contribute to the development of several smoking related lung diseases. In this review we provide information on biochemical and physiological aspects of the pulmonary surfactant and on its possible association with the development of two major chronic diseases of the lung known to be related to smoking, i.e. chronic obstructive pulmonary disease (COPD) and idiopathic pulmonary fibrosis (IPF). Additional information on the possible role of surfactant protein alterations and/or dysfunction in the combination of these two conditions, recently described as combined pulmonary fibrosis and emphysema (CPFE) are also provided. PMID:26420367

  18. Promoting Strong Written Communication Skills

    NASA Astrophysics Data System (ADS)

    Narayanan, M.

    2015-12-01

    The reason that an improvement in the quality of technical writing is still needed in the classroom is due to the fact that universities are facing challenging problems not only on the technological front but also on the socio-economic front. The universities are actively responding to the changes that are taking place in the global consumer marketplace. Obviously, there are numerous benefits of promoting strong written communication skills. They can be summarized into the following six categories. First, and perhaps the most important: The University achieves learner satisfaction. The learner has documented verbally, that the necessary knowledge has been successfully acquired. This results in learner loyalty that in turn will attract more qualified learners.Second, quality communication lowers the cost per pupil, consequently resulting in increased productivity backed by a stronger economic structure and forecast. Third, quality communications help to improve the cash flow and cash reserves of the university. Fourth, having high quality communication enables the university to justify the need for high costs of tuition and fees. Fifth, better quality in written communication skills result in attracting top-quality learners. This will lead to happier and satisfied learners, not to mention greater prosperity for the university as a whole. Sixth, quality written communication skills result in reduced complaints, thus meaning fewer hours spent on answering or correcting the situation. The University faculty and staff are thus able to devote more time on scholarly activities, meaningful research and productive community service. References Boyer, Ernest L. (1990). Scholarship reconsidered: Priorities of the Professorate.Princeton, NJ: Carnegie Foundation for the Advancement of Teaching. Hawkins, P., & Winter, J. (1997). Mastering change: Learning the lessons of the enterprise.London: Department for Education and Employment. Buzzel, Robert D., and Bradley T. Gale. (1987

  19. Strong and Selective Adsorption of Lysozyme on Graphene Oxide

    PubMed Central

    2015-01-01

    Biosensing methods and devices using graphene oxide (GO) have recently been explored for detection and quantification of specific biomolecules from body fluid samples, such as saliva, milk, urine, and serum. For a practical diagnostics application, any sensing system must show an absence of nonselective detection of abundant proteins in the fluid matrix. Because lysozyme is an abundant protein in these body fluids (e.g., around 21.4 and 7 μg/mL of lysozyme is found in human milk and saliva from healthy individuals, and more than 15 or even 100 μg/mL in patients suffering from leukemia, renal disease, and sarcoidosis), it may interfere with detections and quantification if it has strong interaction with GO. Therefore, one fundamental question that needs to be addressed before any development of GO based diagnostics method is how GO interacts with lysozyme. In this study, GO has demonstrated a strong interaction with lysozyme. This interaction is so strong that we are able to subsequently eliminate and separate lysozyme from aqueous solution onto the surface of GO. Furthermore, the strong electrostatic interaction also renders the selective adsorption of lysozyme on GO from a mixture of binary and ternary proteins. This selectivity is confirmed by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), fluorescence spectroscopy, and UV–vis absorption spectroscopy. PMID:24684375

  20. Biomimicry of surfactant protein C.

    PubMed

    Brown, Nathan J; Johansson, Jan; Barron, Annelise E

    2008-10-01

    Since the widespread use of exogenous lung surfactant to treat neonatal respiratory distress syndrome, premature infant survival and respiratory morbidity have dramatically improved. Despite the effectiveness of the animal-derived surfactant preparations, there still remain some concerns and difficulties associated with their use. This has prompted investigation into the creation of synthetic surfactant preparations. However, to date, no clinically used synthetic formulation is as effective as the natural material. This is largely because the previous synthetic formulations lacked analogues of the hydrophobic proteins of the lung surfactant system, SP-B and SP-C, which are critical functional constituents. As a result, recent investigation has turned toward the development of a new generation of synthetic, biomimetic surfactants that contain synthetic phospholipids along with a mimic of the hydrophobic protein portion of lung surfactant. In this Account, we detail our efforts in creating accurate mimics of SP-C for use in a synthetic surfactant replacement therapy. Despite SP-C's seemingly simple structure, the predominantly helical protein is extraordinarily challenging to work with given its extreme hydrophobicity and structural instability, which greatly complicates the creation of an effective SP-C analogue. Drawing inspiration from Nature, two promising biomimetic approaches have led to the creation of rationally designed biopolymers that recapitulate many of SP-C's molecular features. The first approach utilizes detailed SP-C structure-activity relationships and amino acid folding propensities to create a peptide-based analogue, SP-C33. In SP-C33, the problematic and metastable polyvaline helix is replaced with a structurally stable polyleucine helix and includes a well-placed positive charge to prevent aggregation. SP-C33 is structurally stable and eliminates the association propensity of the native protein. The second approach follows the same design

  1. Modifications to surfactant protein B structure and lipid interactions under respiratory distress conditions: consequences of tryptophan oxidation.

    PubMed

    Sarker, Muzaddid; Rose, Jarratt; McDonald, Mark; Morrow, Michael R; Booth, Valerie

    2011-01-11

    These studies detail the altered structure-function relationships caused by oxidation of surfactant protein B (SP-B), a mode of damage thought to be important in acute respiratory distress syndrome (ARDS), a common and frequently fatal condition. An 18-residue fragment comprising the N-terminal helix of SP-B was investigated in oxidized and unmodified forms by solution and solid-state nuclear magnetic resonance (NMR), circular dichroism (CD), and molecular dynamics (MD) simulation. Taken together, the results indicate that tryptophan oxidation causes substantial disruptions in helical structure and lipid interactions. The structural modifications induced by tryptophan oxidation were severe, with a reduction in helical extent from approximately three helical turns to, at most, one turn, and were observed in a variety of solvent environments, including sodium dodecyl sulfate (SDS) micelles, dodecyl phosphocholine (DPC) micelles, and a 40% hexafluoro-2-propanol (HFIP) aqueous solution. The unmodified peptide takes on an orientation within lipid bilayers that is tilted approximately 30° away from an in-plane position. Tryptophan oxidation causes significant modifications to the peptide-lipid interactions, and the peptide likely shifts to a more in-plane orientation within the lipids. Interestingly, the character of the disruptions to peptide-lipid interactions caused by tryptophan oxidation was highly dependent on the charge of the lipid headgroup. PMID:21128671

  2. Quantum dynamics in strong fluctuating fields

    NASA Astrophysics Data System (ADS)

    Goychuk, Igor; Hänggi, Peter

    A large number of multifaceted quantum transport processes in molecular systems and physical nanosystems, such as e.g. nonadiabatic electron transfer in proteins, can be treated in terms of quantum relaxation processes which couple to one or several fluctuating environments. A thermal equilibrium environment can conveniently be modelled by a thermal bath of harmonic oscillators. An archetype situation provides a two-state dissipative quantum dynamics, commonly known under the label of a spin-boson dynamics. An interesting and nontrivial physical situation emerges, however, when the quantum dynamics evolves far away from thermal equilibrium. This occurs, for example, when a charge transferring medium possesses nonequilibrium degrees of freedom, or when a strong time-dependent control field is applied externally. Accordingly, certain parameters of underlying quantum subsystem acquire stochastic character. This may occur, for example, for the tunnelling coupling between the donor and acceptor states of the transferring electron, or for the corresponding energy difference between electronic states which assume via the coupling to the fluctuating environment an explicit stochastic or deterministic time-dependence. Here, we review the general theoretical framework which is based on the method of projector operators, yielding the quantum master equations for systems that are exposed to strong external fields. This allows one to investigate on a common basis, the influence of nonequilibrium fluctuations and periodic electrical fields on those already mentioned dynamics and related quantum transport processes. Most importantly, such strong fluctuating fields induce a whole variety of nonlinear and nonequilibrium phenomena. A characteristic feature of such dynamics is the absence of thermal (quantum) detailed balance.ContentsPAGE1. Introduction5262. Quantum dynamics in stochastic fields531 2.1. Stochastic Liouville equation531 2.2. Non-Markovian vs. Markovian discrete

  3. Surface Mediated Protein Disaggregation

    NASA Astrophysics Data System (ADS)

    Radhakrishna, Mithun; Kumar, Sanat K.

    2014-03-01

    Preventing protein aggregation is of both biological and industrial importance. Biologically these aggregates are known to cause amyloid type diseases like Alzheimer's and Parkinson's disease. Protein aggregation leads to reduced activity of the enzymes in industrial applications. Inter-protein interactions between the hydrophobic residues of the protein are known to be the major driving force for protein aggregation. In the current paper we show how surface chemistry and curvature can be tuned to mitigate these inter-protein interactions. Our results calculated in the framework of the Hydrophobic-Polar (HP) lattice model show that, inter-protein interactions can be drastically reduced by increasing the surface hydrophobicity to a critical value corresponding to the adsorption transition of the protein. At this value of surface hydrophobicity, proteins lose inter-protein contacts to gain surface contacts and thus the surface helps in reducing the inter-protein interactions. Further, we show that the adsorption of the proteins inside hydrophobic pores of optimal sizes are most efficient both in reducing inter-protein contacts and simultaneously retaining most of the native-contacts due to strong protein-surface interactions coupled with stabilization due to the confinement. Department of Energy (Grant No DE-FG02-11ER46811).

  4. Pigment-protein complexes

    SciTech Connect

    Siegelman, H W

    1980-01-01

    The photosynthetically-active pigment protein complexes of procaryotes and eucaryotes include chlorophyll proteins, carotenochlorophyll proteins, and biliproteins. They are either integral components or attached to photosynthetic membranes. Detergents are frequently required to solubilize the pigment-protein complexes. The membrane localization and detergent solubilization strongly suggest that the pigment-protein complexes are bound to the membranes by hydrophobic interactions. Hydrophobic interactions of proteins are characterized by an increase in entropy. Their bonding energy is directly related to temperature and ionic strength. Hydrophobic-interaction chromatography, a relatively new separation procedure, can furnish an important method for the purification of pigment-protein complexes. Phycobilisome purification and properties provide an example of the need to maintain hydrophobic interactions to preserve structure and function.

  5. Antenna factorization in strongly ordered limits

    SciTech Connect

    Kosower, David A.

    2005-02-15

    When energies or angles of gluons emitted in a gauge-theory process are small and strongly ordered, the emission factorizes in a simple way to all orders in perturbation theory. I show how to unify the various strongly ordered soft, mixed soft-collinear, and collinear limits using antenna factorization amplitudes, which are generalizations of the Catani-Seymour dipole factorization function.

  6. Keeping Marriages Strong in Challenging Times

    ERIC Educational Resources Information Center

    Ober, Marci Wolff

    2009-01-01

    What makes a strong marriage anyway...? There are definite qualities that exist in healthy marriages, that is, a marriage that is defined by both partners to be "mostly" or "usually" very satisfying. This article explores these qualities and looks at what really works to make and keep marriages strong, healthy, and satisfying for a lifetime. It…

  7. 78 FR 15710 - Strong Sensitizer Guidance

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-12

    ...The U.S. Consumer Product Safety Commission (CPSC or Commission) is announcing the availability of a document prepared by CPSC staff titled, ``Strong Sensitizer Guidance.'' This guidance document is intended to clarify the ``strong sensitizer'' definition, assist manufacturers in understanding how CPSC staff would assess whether a substance and/or product containing that substance should be......

  8. LHC Phenomenology and Lattice Strong Dynamics

    NASA Astrophysics Data System (ADS)

    Fleming, G. T.

    2013-03-01

    While the LHC experimentalists work to find evidence of physics beyond the standard model, lattice gauge theorists are working as well to characterize the range of possible phenomena in strongly-coupled models of electroweak symmetry breaking. I will summarize the current progress of the Lattice Strong Dynamics (LSD) collaboration on the flavor dependence of SU(3) gauge theories.

  9. Strong Adhesive Tape for Cold Environments

    NASA Technical Reports Server (NTRS)

    Woods, T. G.

    1986-01-01

    Strong tape remains sticky over wide temperature range. Strong tape for low temperatures consists of two layers of polyimide tape with layer of reinforcing mesh. Improved tape devised for repairs in space also finds use on Earth in polar regions and in superconducting applications. Tape retains adherence and strength at extreme temperatures, where conventional tapes fail.

  10. On the Strong Direct Summand Conjecture

    ERIC Educational Resources Information Center

    McCullough, Jason

    2009-01-01

    In this thesis, our aim is the study the Vanishing of Maps of Tor Conjecture of Hochster and Huneke. We mainly focus on an equivalent characterization called the Strong Direct Summand Conjecture, due to N. Ranganathan. Our results are separated into three chapters. In Chapter 3, we prove special cases of the Strong Direct Summand Conjecture in…

  11. Strongly correlated quantum spin liquid in herbertsmithite

    SciTech Connect

    Shaginyan, V. R.; Popov, K. G.; Khodel, V. A.

    2013-05-15

    Strongly correlated Fermi systems are among the most intriguing and fundamental systems in physics. We show that the herbertsmithite ZnCu{sub 3}(OH){sub 6}Cl{sub 2} can be regarded as a new type of strongly correlated electrical insulator that possesses properties of heavy-fermion metals with one exception: it resists the flow of electric charge. We demonstrate that herbertsmithite's low-temperature properties are defined by a strongly correlated quantum spin liquid made with hypothetic particles such as fermionic spinons that carry spin 1/2 and no charge. Our calculations of its thermodynamic and relaxation properties are in good agreement with recent experimental facts and allow us to reveal their scaling behavior, which strongly resembles that observed in heavy-fermion metals. Analysis of the dynamic magnetic susceptibility of strongly correlated Fermi systems suggests that there exist at least two types of its scaling.

  12. Seismic switch for strong motion measurement

    DOEpatents

    Harben, P.E.; Rodgers, P.W.; Ewert, D.W.

    1995-05-30

    A seismic switching device is described that has an input signal from an existing microseismic station seismometer and a signal from a strong motion measuring instrument. The seismic switch monitors the signal level of the strong motion instrument and passes the seismometer signal to the station data telemetry and recording systems. When the strong motion instrument signal level exceeds a user set threshold level, the seismometer signal is switched out and the strong motion signal is passed to the telemetry system. The amount of time the strong motion signal is passed before switching back to the seismometer signal is user controlled between 1 and 15 seconds. If the threshold level is exceeded during a switch time period, the length of time is extended from that instant by one user set time period. 11 figs.

  13. Seismic switch for strong motion measurement

    DOEpatents

    Harben, Philip E.; Rodgers, Peter W.; Ewert, Daniel W.

    1995-01-01

    A seismic switching device that has an input signal from an existing microseismic station seismometer and a signal from a strong motion measuring instrument. The seismic switch monitors the signal level of the strong motion instrument and passes the seismometer signal to the station data telemetry and recording systems. When the strong motion instrument signal level exceeds a user set threshold level, the seismometer signal is switched out and the strong motion signal is passed to the telemetry system. The amount of time the strong motion signal is passed before switching back to the seismometer signal is user controlled between 1 and 15 seconds. If the threshold level is exceeded during a switch time period, the length of time is extended from that instant by one user set time period.

  14. Puerto Rico Strong Motion Seismic Network

    NASA Astrophysics Data System (ADS)

    Huerta-Lopez, C. I.; Martínez-Cruzado, J. A.; Martínez-Pagan, J.; Santana-Torres, E. X.; Torres-O, D. M.

    2014-12-01

    The Puerto Rico Strong Motion Seismic Network is currently in charge of the operation of: (i) free-field (ff) strong motion stations, (ii) instrumented structures (STR) (Dams, Bridges, Buildings), and (iii) the data acquisition/monitoring and analysis of earthquakes considered strong from the point of view of their intensity and magnitude. All these instruments are deployed in the Puerto Rico Island (PRI), US-, and British-Virgin Islands (BVI), and Dominican Republic (DR). The Puerto Rico Island and the Caribbean region have high potential to be affected by earthquakes that could be catastrophic for the area. The Puerto Rico Strong Motion Seismic Network (actually Puerto Rico Strong Motion Program, PRSMP) has grown since 1970's from 7 ff strong motion stations and one instrumented building with analog accelerographs to 111 ff strong motion stations and 16 instrumented buildings with digital accelerographs: PRI: 88 ff, 16 STR., DR: 13 ff, BVI: 5 ff, 2 STR collecting data via IP (internet), DU (telephone), and stand alone stations The current stage of the PRSMP seismic network, the analysis of moderate earthquakes that were recorded and/or occurred on the island, results of the intensity distribution of selected earthquakes, as well as results of dynamic parameter identification of some of the instrumented structures are here presented.

  15. Strong photoassociation in a degenerate fermi gas

    NASA Astrophysics Data System (ADS)

    Rvachov, Timur; Jamison, Alan; Jing, Li; Son, Hyungmok; Ebadi, Sepehr; Jiang, Yijun; Zwierlein, Martin; Ketterle, Wolfgang

    2016-05-01

    Despite many studies there remain open questions about strong photoassociation in ultracold gases. We study the effects of strong photoassociation in ultracold fermions. Photoassociation occurs only at short range and thus can be used as a tool to probe and control the two-body correlation function in an interacting many-body system. We study the effects of strong photoassociation in 6 Li, the onset of saturation, and its effects on spin polarized and interacting spin-mixtures. This work was funded by the NSF, ARO-MURI, SAMSUNG, and NSERC.

  16. Strong correlation in Kohn-Sham DFT

    NASA Astrophysics Data System (ADS)

    Malet Giralt, Francesc; Mirtschink, André; Cremon, Jonas; Mendl, Christian; Giesbertz, Klaas; Reimann, Stephanie; Gori-Giorgi, Paola; Mathematical Physics, Lund University Collaboration; Mathematics Department, Technische Universität München Collaboration

    2014-03-01

    The knowledge on the strong-interacting limit of density functional theory can be used to construct exchange- correlation functionals able to address strongly-correlated systems without introducing any symmetry breaking. We report calculations on semiconductor nanostructures and one-dimensional models for chemical systems, showing that this approach yields quantitatively good results in both the weakly- and the strongly-correlated regimes, with a numerical cost much lower than the traditional wavefunction methods. This work has been supported by a VIDI grant of the NWO and a Marie Curie grant within the FP7 programme.

  17. Forces Stabilizing Proteins

    PubMed Central

    Pace, C. Nick; Scholtz, J. Martin; Grimsley, Gerald R.

    2014-01-01

    The goal of this article is to summarize what has been learned about the major forces stabilizing proteins since the late 1980s when site-directed mutagenesis became possible. The following conclusions are derived from experimental studies of hydrophobic and hydrogen bonding variants. 1. Based on studies of 138 hydrophobic interaction variants in 11 proteins, burying a –CH2– group on folding contributes 1.1 ± 0.5 kcal/mol to protein stability. 2. The burial of nonpolar side chains contributes to protein stability in two ways: first, a term that depends on the removal of the side chains from water and, more importantly, the enhanced London dispersion forces that result from the tight packing in the protein interior. 3. Based on studies of 151 hydrogen bonding variants in 15 proteins, forming a hydrogen bond on folding contributes 1.1 ± 0.8 kcal/mol to protein stability. 4. The contribution of hydrogen bonds to protein stability is strongly context dependent. 5. Hydrogen bonds by side chains and peptide groups make similar contributions to protein stability. 6. Polar group burial can make a favorable contribution to protein stability even if the polar group is not hydrogen bonded. 7. Hydrophobic interactions and hydrogen bonds both make large contributions to protein stability. PMID:24846139

  18. Determination of Lipid-Protein Interactions in Lung Surfactants Using Computer Simulations and Structural Bioinformatics.

    NASA Astrophysics Data System (ADS)

    Kaznessis, Yiannis

    2001-06-01

    Proteins are the primary components of the networks that conduct the flows of mass, energy and information in living organisms. The discovery of the principles of protein structure and function allows the development of design rules for biological activities. The microscopic nature of the operating mechanisms of protein activity, and the vast complexity of the networks of interaction call for the employment of powerful computational methodologies that can decipher the physicochemical and evolutionary principles underlying protein structure and function. An example will be presented that reflects the strength of computational approaches. Atomistic molecular dynamics simulations and structural bioinformatics tools are employed to investigate the interactions between the first 25 N-terminal residues of surfactant protein B (SP-B 1-25) and the lipid components of the lung surfactant (LS). An understanding of the molecular level interactions between the LS components is essential for the establishment of design rules for the development of synthetic LS and the treatment of the neonatal respiratory distress syndrome, which results from deficiency or inactivation of LS.

  19. a New Feature of Strong Interactions

    NASA Astrophysics Data System (ADS)

    Arash, Firooz; Moravcsik, Michael J.; Goldstein, Gary R.

    Evidence is presented that in a broad energy and angular range, and for a variety of elementary particle reactions driven by strong interactions, the reaction amplitudes in the planar-transverse optimal system are relatively pure real or pure imaginary.

  20. Strongly magnetized accretion discs require poloidal flux

    NASA Astrophysics Data System (ADS)

    Salvesen, Greg; Armitage, Philip J.; Simon, Jacob B.; Begelman, Mitchell C.

    2016-08-01

    Motivated by indirect observational evidence for strongly magnetized accretion discs around black holes, and the novel theoretical properties of such solutions, we investigate how a strong magnetization state can develop and persist. To this end, we perform local simulations of accretion discs with an initially purely toroidal magnetic field of equipartition strength. We demonstrate that discs with zero net vertical magnetic flux and realistic boundary conditions cannot sustain a strong toroidal field. However, a magnetic pressure-dominated disc can form from an initial configuration with a sufficient amount of net vertical flux and realistic boundary conditions. Our results suggest that poloidal flux is a necessary prerequisite for the sustainability of strongly magnetized accretion discs.

  1. Norman Rostoker and strongly correlated plasmas

    NASA Astrophysics Data System (ADS)

    Ichimaru, Setsuo

    2016-03-01

    If Norman were alive and attended this symposium, he might have quipped: "Setsuo! What are you talking about! A plasma is, after all, a strongly correlated object, and there is nothing so special about it!" "Yes, Norman, you are so correct! A statistical system consisting of mutually non-interacting and thus uncorrelated particles may be an "ideal-gas" system from a physics teacher's pedagogical point of view, but real systems do consist of mutually interacting and thus strongly correlated particles; a plasma is definitely one of them.Here, in the memory of Professor Rostoker's outstanding contributions to strongly correlated plasmas for the past 60 years, we wish to survey on "Scattering of Electromagnetic Waves by a Strongly Correlated Plasma" and "Multi-particle Correlation, Equations of State, and Phase Diagrams" in what follows.

  2. Strongly magnetized accretion discs require poloidal flux

    NASA Astrophysics Data System (ADS)

    Salvesen, Greg; Armitage, Philip J.; Simon, Jacob B.; Begelman, Mitchell C.

    2016-05-01

    Motivated by indirect observational evidence for strongly magnetized accretion discs around black holes, and the novel theoretical properties of such solutions, we investigate how a strong magnetization state can develop and persist. To this end, we perform local simulations of accretion discs with an initially purely toroidal magnetic field of equipartition strength. We demonstrate that discs with zero net vertical magnetic flux and realistic boundary conditions cannot sustain a strong toroidal field. However, a magnetic pressure-dominated disc can form from an initial configuration with a sufficient amount of net vertical flux and realistic boundary conditions. Our results suggest that poloidal flux is a necessary prerequisite for the sustainability of strongly magnetized accretion discs.

  3. Cooking with Strong Lenses and Other Ingredients

    NASA Astrophysics Data System (ADS)

    Bolton, Adam; SLACS; BELLS; SDSS-III

    2013-07-01

    Strong lensing offers the most direct method for constraining the distribution of mass in galaxies at cosmological distances. The combination of strong lensing with other observables increases its power, but often in ways that are model-dependent and resistant to intuition. In this talk, I will unpack the information content of spectroscopic, photometric, kinematic, and strong-lensing observables as they translate into constraints on the macroscopic distribution of luminous and dark matter in massive elliptical galaxies. I will also highlight how the choice of priors and analysis methods affects the conclusions drawn from a given set of observations. Finally, in this context I will present the latest results from observational efforts to extend strong-lensing analyses to lower mass galaxies in the Sloan Lens ACS Survey (SLACS) and to earlier cosmic times in the BOSS Emission-Line Lens Survey (BELLS).

  4. Trident Pair Production in Strong Laser Pulses

    SciTech Connect

    Ilderton, Anton

    2011-01-14

    We calculate the trident pair production amplitude in a strong laser background. We allow for finite pulse durations, while still treating the laser fields nonperturbatively in strong-field QED. Our approach reveals explicitly the individual contributions of the one-step and two-step processes. We also expose the role gauge invariance plays in the amplitudes and discuss the relation between our results and the optical theorem.

  5. 77 FR 35711 - Strong Cities, Strong Communities National Resource Network Pilot Program Advance Notice and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-14

    ... URBAN DEVELOPMENT Strong Cities, Strong Communities National Resource Network Pilot Program Advance..., Strong Communities National Resource Network pilot program with its 19 federal agency and subagency... Resource Network, HUD and its partners will offer a central portal to connect America's most...

  6. The Italian Strong Motion Network (RAN)

    NASA Astrophysics Data System (ADS)

    Costa, Giovanni; Ammirati, Alfredo; de Nardis, Rita; Filippi, Luisa; Gallo, Antonella; Lavecchia, Giusy; Sirignano, Sebastiano; Zambonelli, Elisa; Nicoletti, Mario

    2014-05-01

    A network for the strong motion monitoring of the territory allows recording data that provide an excellent opportunity to study the source, path, and site effects on the ground motions, specifically in near source area, for updating seismic hazard map and consequently construction codes and earthquake resistant design. Strong motion data also help to increase the effective preparation and response to seismic emergencies and the ability of a community to quickly recover from the damages of an earthquake contributes to lower the seismic risk usually measured in term of casualties and economic losses. The Italian network for monitoring the strong movement of the national territory (RAN) is the result of a fruitful cooperation over the last 16 years between the Italian government, the regions and local authorities and now counts more than 500 stations. Over the years, as a priority the DPC has focused mainly on the expansion of the network in terms of the number of measurement points and technological improvement of instrumentation as well as the data transmission system. A data acquisition centre was implemented in which the Antelope software collects, processes and archives, automatically, the data of the RAN and of the external strong motion networks that contribute to the database of the RAN. Recently the DPC has dedicated specific resources to improve the response of the network, in particular, in case of emergency. The efficiency of the network on a daily basis is not less than 95% and temporary networks were installed in the epicentral area within 24 hours after the earthquake and connected to the data acquisition centre in Rome. A fast seismic data analysis is essential to provide useful information to Authorities which make decisions immediately after a strong earthquake occurrence. During a strong earthquake, the modern accelerometers are the only instruments which can provide near source high-quality data that are important both for scientific and for civil

  7. Strong Motion Recording in the United States

    NASA Astrophysics Data System (ADS)

    Archuleta, R. J.; Fletcher, J. B.; Shakal, A. F.

    2014-12-01

    The United States strong motion program began in 1932 when the Coast and Geodetic Survey (C&GS) installed eight strong motion accelerographs in California. During the March 1933 Long Beach earthquake, three of these produced the first strong motion records. With this success the C&GS expanded the number of accelerographs to 71 by 1964. With development of less expensive, mass-produced accelerographs the number of strong motion accelerographs expanded to ~575 by 1972. Responsibilities for operating the network and disseminating data were transferred to the National Oceanic and Atmospheric Administration in 1970 and then to the U.S. Geological Survey in 1973. In 1972 the California Legislature established the California Strong Motion Instrumentation Program (CSMIP). CSMIP operates accelerographs at 812 ground stations, with multi-channel accelerographs in 228 buildings, 125 lifelines and 37 geotechnical arrays, in California. The USGS and the ANSS effort operate accelerographs at 1584 ground stations, 96 buildings, 14 bridges, 70 dams, and 15 multi-channel geotechnical arrays. The USC Los Angeles array has 78 ground stations; UCSB operates 5 geotechnical arrays; other government and private institutions also operate accelerographs. Almost all accelerographs are now digital with a sampling rate of 200 Hz. Most of the strong motion data can be downloaded from the Center for Engineering Strong Motion Data (http://strongmotioncenter.org). As accelerographs have become more sophisticated, the concept of what constitutes strong motion has blurred because small earthquakes (M ~3) are well recorded on accelerometers as well as seismometers. However, when accelerations are over ~10%g and velocities over ~1 cm/s, the accelerometers remain on scale, providing the unclipped data necessary to analyze the ground motion and its consequences. Strong motion data are essential to the development of ground motion prediction equations, understanding structural response, performance

  8. Strong coupling theory for interacting lattice models

    NASA Astrophysics Data System (ADS)

    Stanescu, Tudor D.; Kotliar, Gabriel

    2004-11-01

    We develop a strong coupling approach for a general lattice problem. We argue that this strong coupling perspective represents the natural framework for a generalization of the dynamical mean field theory (DMFT). The main result of this analysis is twofold: (1) It provides the tools for a unified treatment of any nonlocal contribution to the Hamiltonian. Within our scheme, nonlocal terms such as hopping terms, spin-spin interactions, or nonlocal Coulomb interactions are treated on equal footing. (2) By performing a detailed strong-coupling analysis of a generalized lattice problem, we establish the basis for possible clean and systematic extensions beyond DMFT. To this end, we study the problem using three different perspectives. First, we develop a generalized expansion around the atomic limit in terms of the coupling constants for the nonlocal contributions to the Hamiltonian. By analyzing the diagrammatics associated with this expansion, we establish the equations for a generalized dynamical mean-field theory. Second, we formulate the theory in terms of a generalized strong coupling version of the Baym-Kadanoff functional. Third, following Pairault, Sénéchal, and Tremblay [Phys. Rev. Lett. 80, 5389 (1998)], we present our scheme in the language of a perturbation theory for canonical fermionic and bosonic fields and we establish the interpretation of various strong coupling quantities within a standard perturbative picture.

  9. The ontological basis of strong artificial life.

    PubMed

    Olson, E T

    1997-01-01

    This article concerns the claim that it is possible to create living organisms, not merely models that represent organisms, simply by programming computers ("virtual" strong alife). I ask what sort of things these computer-generated organisms are supposed to be (where are they, and what are they made of?). I consider four possible answers to this question: (a) The organisms are abstract complexes of pure information; (b) they are material objects made of bits of computer hardware; (c) they are physical processes going on inside the computer; and (d) they are denizens of an entire artificial world, different from our own, that the programmer creates. I argue that (a) could not be right, that (c) collapses into (b) and that (d) would make strong alife either absurd or uninteresting. Thus, "virtual" strong alife amounts to the claim that, by programming a computer, one can literally bring bits of its hardware to life. PMID:9090157

  10. Strong Coupling between Nanoscale Metamaterials and Phonons

    SciTech Connect

    Shelton, David J.; Brener, Igal; Ginn, James C.; Sinclair, Michael B.; Peters, David W.; Coffey, Kevin R.; Boreman, Glenn D.

    2011-05-11

    We use split ring resonators (SRRs) at optical frequencies to study strong coupling between planar metamaterials and phonon vibrations in nanometer-scale dielectric layers. A series of SRR metamaterials were fabricated on a semiconductor wafer with a thin intervening SiO{sub 2} dielectric layer. The dimensions of the SRRs were varied to tune the fundamental metamaterial resonance across the infrared (IR) active phonon band of SiO{sub 2} at 130 meV (31 THz). Strong anticrossing of these resonances was observed, indicative of strong coupling between metamaterial and phonon excitations. This coupling is very general and can occur with any electrically polarizable resonance including phonon vibrations in other thin film materials and semiconductor band-to-band transitions in the near to far IR. These effects may be exploited to reduce loss and to create unique spectral features that are not possible with metamaterials alone.

  11. Vacuum birefringence in strong inhomogeneous electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Karbstein, Felix; Gies, Holger; Reuter, Maria; Zepf, Matt

    2015-10-01

    Birefringence is one of the fascinating properties of the vacuum of quantum electrodynamics (QED) in strong electromagnetic fields. The scattering of linearly polarized incident probe photons into a perpendicularly polarized mode provides a distinct signature of the optical activity of the quantum vacuum and thus offers an excellent opportunity for a precision test of nonlinear QED. Precision tests require accurate predictions and thus a theoretical framework that is capable of taking the detailed experimental geometry into account. We derive analytical solutions for vacuum birefringence which include the spatio-temporal field structure of a strong optical pump laser field and an x-ray probe. We show that the angular distribution of the scattered photons depends strongly on the interaction geometry and find that scattering of the perpendicularly polarized scattered photons out of the cone of the incident probe x-ray beam is the key to making the phenomenon experimentally accessible with the current generation of FEL/high-field laser facilities.

  12. Strong field laser control of photochemistry.

    PubMed

    Solá, Ignacio R; González-Vázquez, Jesús; de Nalda, Rebeca; Bañares, Luis

    2015-05-28

    Strong ultrashort laser pulses have opened new avenues for the manipulation of photochemical processes like photoisomerization or photodissociation. The presence of light intense enough to reshape the potential energy surfaces may steer the dynamics of both electrons and nuclei in new directions. A controlled laser pulse, precisely defined in terms of spectrum, time and intensity, is the essential tool in this type of approach to control chemical dynamics at a microscopic level. In this Perspective we examine the current strategies developed to achieve control of chemical processes with strong laser fields, as well as recent experimental advances that demonstrate that properties like the molecular absorption spectrum, the state lifetimes, the quantum yields and the velocity distributions in photodissociation processes can be controlled by the introduction of carefully designed strong laser fields. PMID:25835746

  13. Coherency properties of strong Langmuir turbulence

    SciTech Connect

    Rose, H.A.; DuBois, D.F.; Russell, D. )

    1989-01-01

    Strongly correlated Langmuir wave collapse has been observed in two dimensional simulations of Zakharov's model in a regime characterized by strong ion sound wave damping and an external drive frequency, {omega}{sub 0}, close to but less than the plasma frequency, ({omega}{sub p} {minus} {omega}{sub 0})/{omega}{sub 0} > {epsilon} with {epsilon} {approx equal} 0.005. Caviton-caviton interactions induce temporal correlations between different collapse sites on a time scale the order of a collapse cycle, and on a longer time scale site locations migrate possibly leading to strong spatial correlations. Certain features of ionospheric incoherent scatter radar (ISR) spectra are consistent with such correlations. 6 refs.

  14. Strong diquark correlations inside the proton

    NASA Astrophysics Data System (ADS)

    Segovia, Jorge

    2016-03-01

    Quantum Chromodynamics is thought to be the relativistic quantum field theory that describes the strong interaction of the Standard Model. This interaction produces mesons but it is also able to generate quark-quark (diquark) correlations inside baryons. In this work, we employ a continuum approach to QCD based on Dyson-Schwinger equations to calculate the electromagnetic form factors of the proton and analyze in a deeper way the consequences of having strong diquark correlations. Comparison with the experimental data reveals that the presence of strong diquark correlations within the proton is sufficient to understand empirical extractions of the flavour-separated form factors. The explained reduction of the ratios F1d/F1u and F2d/F2u at high Q2 in the quark-diquark picture are responsible of the precocious scaling of the F2p/F1p observed experimentally.

  15. Enhanced betatron radiation in strongly magnetized plasma

    NASA Astrophysics Data System (ADS)

    Pan, K. Q.; Zheng, C. Y.; Cao, L. H.; Liu, Z. J.; He, X. T.

    2016-04-01

    Betatron radiation in strongly magnetized plasma is investigated by two dimensional (2D) particle-in-cell (PIC) simulations. The results show that the betatron radiation in magnetized plasmas is strongly enhanced and is more collimated compared to that in unmagnetized plasma. Single particle model analysis shows that the frequency and the amplitude of the electrons's betatron oscillation are strongly influenced by the axial external magnetic field and the axial self-generated magnetic field. And the 2D PIC simulation shows that the axial magnetic field is actually induced by the external magnetic field and tends to increase the betatron frequency. By disturbing the perturbation of the plasma density in the laser-produced channel, the hosing instability is also suppressed, which results in a better angular distribution and a better symmetry of the betatron radiation.

  16. Strongly coupled stress waves in heterogeneous plates.

    NASA Technical Reports Server (NTRS)

    Wang, A. S. D.; Chou, P. C.; Rose, J. L.

    1972-01-01

    Consideration of coupled stress waves generated by an impulsive load applied at one end of a semiinfinite plate. For the field equations governing the one-dimensional coupled waves a hyperbolic system of equations is obtained in which a strong coupling in the second derivatives exists. The method of characteristics described by Chou and Mortimer (1967) is extended to cover the case of strong coupling, and a study is made of the transient stress waves in a semiinfinite plate subjected to an initial step input. Coupled discontinuity fronts are found to propagate at different velocities. The normal plate stress and the bending moment at different time regimes are illustrated by graphs.

  17. Scintillation index in strong oceanic turbulence

    NASA Astrophysics Data System (ADS)

    Baykal, Yahya

    2016-09-01

    Scintillation index of spherical wave in strongly turbulent oceanic medium is evaluated. In the evaluation, modified Rytov solution and our recent formulation that expresses the oceanic turbulence parameters by the atmospheric turbulence structure constant, are employed. Variations of the scintillation index in strong oceanic turbulence are examined versus the oceanic turbulence parameters such as the rate of dissipation of kinetic energy per unit mass of fluid, the rate of dissipation of mean-squared temperature, viscosity, wavelength, the link length, and the ratio of temperature to salinity contributions to the refractive index spectrum.

  18. Weak side of strong topological insulators

    NASA Astrophysics Data System (ADS)

    Sbierski, Björn; Schneider, Martin; Brouwer, Piet W.

    2016-04-01

    Strong topological insulators may have nonzero weak indices. The nonzero weak indices allow for the existence of topologically protected helical states along line defects of the lattice. If the lattice admits line defects that connect opposite surfaces of a slab of such a "weak-and-strong" topological insulator, these states effectively connect the surface states at opposite surfaces. Depending on the phases accumulated along the dislocation lines, this connection results in a suppression of in-plane transport and the opening of a spectral gap or in an enhanced density of states and an increased conductivity.

  19. Strong-Field Resonant Dynamics in Semiconductors

    NASA Astrophysics Data System (ADS)

    Wismer, Michael S.; Kruchinin, Stanislav Yu.; Ciappina, Marcelo; Stockman, Mark I.; Yakovlev, Vladislav S.

    2016-05-01

    We predict that a direct band gap semiconductor (GaAs) resonantly excited by a strong ultrashort laser pulse exhibits a novel regime: kicked anharmonic Rabi oscillations. In this regime, Rabi oscillations are strongly coupled to intraband motion, and interband transitions mainly take place when electrons pass near the Brillouin zone center where electron populations undergo very rapid changes. The asymmetry of the residual population distribution induces an electric current controlled by the carrier-envelope phase of the driving pulse. The predicted effects are experimentally observable using photoemission and terahertz spectroscopies.

  20. Strong-Field Resonant Dynamics in Semiconductors.

    PubMed

    Wismer, Michael S; Kruchinin, Stanislav Yu; Ciappina, Marcelo; Stockman, Mark I; Yakovlev, Vladislav S

    2016-05-13

    We predict that a direct band gap semiconductor (GaAs) resonantly excited by a strong ultrashort laser pulse exhibits a novel regime: kicked anharmonic Rabi oscillations. In this regime, Rabi oscillations are strongly coupled to intraband motion, and interband transitions mainly take place when electrons pass near the Brillouin zone center where electron populations undergo very rapid changes. The asymmetry of the residual population distribution induces an electric current controlled by the carrier-envelope phase of the driving pulse. The predicted effects are experimentally observable using photoemission and terahertz spectroscopies. PMID:27232043

  1. Strong dynamics and inflation: A review

    NASA Astrophysics Data System (ADS)

    Channuie, Phongpichit

    2015-03-01

    In this article, we review how strong dynamics can be efficiently employed as a viable alternative to study the mechanism of cosmic inflation. We examine single-field inflation in which the inflaton emerges as a bound state stemming from various strongly interacting field theories. We constrain the number of e-foldings for composite models of inflation in order to obtain a successful inflation. We study a set of cosmological parameters, e.g., the primordial spectral index ns and tensor-to-scalar ratio r, and confront the predicted results with the joint Planck data, and with the recent BICEP2 data.

  2. Role of surfactant protein A in non-infectious lung diseases.

    PubMed

    Goto, Hisatsugu; Mitsuhashi, Atsushi; Nishioka, Yasuhiko

    2014-01-01

    Surfactant protein A (SP-A) is a large multimeric protein found in the airways and alveoli of the lungs. SP-A is a member of the collectin family of proteins, characterized by NH2-terminal collagen-like regions and COOH-terminal lectin domains. Although other surfactant proteins such as SP-B function to reduce surface tension in the lungs, SP-A as well as SP-D regulates the pulmonary immune response. To date, a number of studies have shown the immunoregulatory function of SP-A, mainly in the field of infectious diseases. By binding to a wide variety of pathogens, SP-A opsonizes and enhances pathogen uptake by phagocytes. In addition to the effect on pathogens, recent studies have shown that SP-A also modulates lung immune system in the area of non-infectious lung diseases. In this review, the potential role of SP-A in the multiple aspects of pulmonary host defense will be discussed, focusing mainly on non-infectious lung diseases such as acute and chronic pulmonary fibrosis and lung cancer. J. Med. Invest. 61: 1-6, February, 2014. PMID:24705741

  3. Using Strong Magnetic Fields to Control Solutal Convection

    NASA Technical Reports Server (NTRS)

    Ramachandran, N.; Leslie, F. W.

    2003-01-01

    An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity , we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility

  4. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2007-09-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  5. Protein Condensation

    NASA Astrophysics Data System (ADS)

    Gunton, James D.; Shiryayev, Andrey; Pagan, Daniel L.

    2014-07-01

    Preface; 1. Introduction; 2. Globular protein structure; 3. Experimental methods; 4. Thermodynamics and statistical mechanics; 5. Protein-protein interactions; 6. Theoretical studies of equilibrium; 7. Nucleation theory; 8. Experimental studies of nucleation; 9. Lysozyme; 10. Some other globular proteins; 11. Membrane proteins; 12. Crystallins and cataracts; 13. Sickle hemoglobin and sickle cell anemia; 14, Alzheimer's disease; Index.

  6. MRS photodiode in strong magnetic field

    SciTech Connect

    Beznosko, D.; Blazey, G.; Dyshkant, A.; Francis, K.; Kubik, D.; Rykalin, V.; Tartaglia, M.A.; Zutshi, v.; /Northern Illinois U.

    2004-12-01

    The experimental results on the performance of the MRS (Metal/Resistor/Semiconductor) photodiode in the strong magnetic field of 4.4T, and the possible impact of the quench of the magnet at 4.5T on sensor's operation are reported.

  7. Charm production in a strong magnetic field

    SciTech Connect

    Machado, C. S.; Navarra, F. S.; Noronha, J.; Oliveira, E. G. de; Strickland, M.

    2014-11-11

    We discuss the effects of a strong magnetic field on B and D mesons, focusing on the changes of the energy levels and the masses of the bound states. Using the Color Evaporation Model we discuss the possible changes in the production of J/ψ and Υ. We briefly comment the recent experimental data.

  8. CLASSSTRONG: Classical simulations of strong field processes

    NASA Astrophysics Data System (ADS)

    Ciappina, M. F.; Pérez-Hernández, J. A.; Lewenstein, M.

    2014-01-01

    A set of Mathematica functions is presented to model classically two of the most important processes in strong field physics, namely high-order harmonic generation (HHG) and above-threshold ionization (ATI). Our approach is based on the numerical solution of the Newton-Lorentz equation of an electron moving on an electric field and takes advantage of the symbolic languages features and graphical power of Mathematica. Like in the Strong Field Approximation (SFA), the effects of atomic potential on the motion of electron in the laser field are neglected. The SFA was proven to be an essential tool in strong field physics in the sense that it is able to predict with great precision the harmonic (in the HHG) and energy (in the ATI) limits. We have extended substantially the conventional classical simulations, where the electric field is only dependent on time, including spatial nonhomogeneous fields and spatial and temporal synthesized fields. Spatial nonhomogeneous fields appear when metal nanosystems interact with strong and short laser pulses and temporal synthesized fields are routinely generated in attosecond laboratories around the world. Temporal and spatial synthesized fields have received special attention nowadays because they would allow to exceed considerably the conventional harmonic and electron energy frontiers. Classical simulations are an invaluable tool to explore exhaustively the parameters domain at a cheap computational cost, before massive quantum mechanical calculations, absolutely indispensable for the detailed analysis, are performed.

  9. Semimetallization of dielectrics in strong optical fields

    DOE PAGESBeta

    Kwon, Ojoon; Paasch-Colberg, Tim; Apalkov, Vadym; Kim, Bum -Kyu; Kim, Ju -Jin; Stockman, Mark I.; Kim, D.

    2016-02-18

    At the heart of ever growing demands for faster signal processing is ultrafast charge transport and control by electromagnetic fields in semiconductors. Intense optical fields have opened fascinating avenues for new phenomena and applications in solids. Because the period of optical fields is on the order of a femtosecond, the current switching and its control by an optical field may pave a way to petahertz optoelectronic devices. Lately, a reversible semimetallization in fused silica on a femtosecond time scale by using a few-cycle strong field (~1 V/Å) is manifested. The strong Wannier-Stark localization and Zener-type tunneling were expected to drivemore » this ultrafast semimetallization. Wider spread of this technology demands better understanding of whether the strong field behavior is universally similar for different dielectrics. Here we employ a carrier-envelope-phase stabilized, few-cycle strong optical field to drive the semimetallization in sapphire, calcium fluoride and quartz and to compare this phenomenon and show its remarkable similarity between them. The similarity in response of these materials, despite the distinguishable differences in their physical properties, suggests the universality of the physical picture explained by the localization of Wannier-Stark states. Lastly, our results may blaze a trail to PHz-rate optoelectronics.« less

  10. Strong Student Governments...and Their Advisement.

    ERIC Educational Resources Information Center

    Boatman, Sara

    1988-01-01

    The ideal student government and the ideal student government adviser were discussed by advisers who met at the NACA National Student Government Workshop. Key issues in a strong student government are described including information, access, mutual respect, and institutional impact. (MLW)

  11. Three Strands Form Strong School Leadership

    ERIC Educational Resources Information Center

    Saphier, Jon; King, Matt; D'Auria, John

    2006-01-01

    In this article, the authors illustrate the three fundamental elements of school leadership: academic focus, shared beliefs and values, and productive professional relationships. These three elements purportedly produce strong organizational cultures, more teaching expertise, and better student achievement and more thoughtful and caring citizens.…

  12. Dynamo Activity in Strongly Magnetized Accretion Disks

    NASA Astrophysics Data System (ADS)

    Salvesen, Greg; Simon, Jacob B.; Armitage, Philip J.; Begelman, Mitchell C.

    2016-01-01

    Strongly magnetized accretion disks around black holes have many attractive features that may explain the enigmatic behavior observed from X-ray binaries. The physics and structure of these disks are governed by a dynamo-like mechanism, which channels the accretion power liberated by the magnetorotational instability into an ordered toroidal magnetic field. To study dynamo activity, we performed three-dimensional, stratified, isothermal, ideal magnetohydrodynamic shearing box simulations. In our simulations, the strength of this self-sustained toroidal magnetic field depends on the net vertical magnetic flux we impose, which allows us to study weak-to-strong magnetization regimes. We find that the entire disk develops into a magnetic pressure-dominated state for a sufficiently strong net vertical magnetic flux. Over the two orders of magnitude in net vertical magnetic flux that we consider, the effective α-viscosity parameter scales as a power-law. We quantify dynamo properties of toroidal magnetic flux production and its buoyant escape as a function of disk magnetization. Finally, we compare our simulations to an analytic model for the vertical structure of strongly magnetized disks applicable to the high/soft state of X-ray binaries.

  13. Semimetallization of dielectrics in strong optical fields

    PubMed Central

    Kwon, Ojoon; Paasch-Colberg, Tim; Apalkov, Vadym; Kim, Bum-Kyu; Kim, Ju-Jin; Stockman, Mark I.; Kim, D.

    2016-01-01

    At the heart of ever growing demands for faster signal processing is ultrafast charge transport and control by electromagnetic fields in semiconductors. Intense optical fields have opened fascinating avenues for new phenomena and applications in solids. Because the period of optical fields is on the order of a femtosecond, the current switching and its control by an optical field may pave a way to petahertz optoelectronic devices. Lately, a reversible semimetallization in fused silica on a femtosecond time scale by using a few-cycle strong field (~1 V/Å) is manifested. The strong Wannier-Stark localization and Zener-type tunneling were expected to drive this ultrafast semimetallization. Wider spread of this technology demands better understanding of whether the strong field behavior is universally similar for different dielectrics. Here we employ a carrier-envelope-phase stabilized, few-cycle strong optical field to drive the semimetallization in sapphire, calcium fluoride and quartz and to compare this phenomenon and show its remarkable similarity between them. The similarity in response of these materials, despite the distinguishable differences in their physical properties, suggests the universality of the physical picture explained by the localization of Wannier-Stark states. Our results may blaze a trail to PHz-rate optoelectronics. PMID:26888147

  14. Semimetallization of dielectrics in strong optical fields.

    PubMed

    Kwon, Ojoon; Paasch-Colberg, Tim; Apalkov, Vadym; Kim, Bum-Kyu; Kim, Ju-Jin; Stockman, Mark I; Kim, D

    2016-01-01

    At the heart of ever growing demands for faster signal processing is ultrafast charge transport and control by electromagnetic fields in semiconductors. Intense optical fields have opened fascinating avenues for new phenomena and applications in solids. Because the period of optical fields is on the order of a femtosecond, the current switching and its control by an optical field may pave a way to petahertz optoelectronic devices. Lately, a reversible semimetallization in fused silica on a femtosecond time scale by using a few-cycle strong field (~1 V/Å) is manifested. The strong Wannier-Stark localization and Zener-type tunneling were expected to drive this ultrafast semimetallization. Wider spread of this technology demands better understanding of whether the strong field behavior is universally similar for different dielectrics. Here we employ a carrier-envelope-phase stabilized, few-cycle strong optical field to drive the semimetallization in sapphire, calcium fluoride and quartz and to compare this phenomenon and show its remarkable similarity between them. The similarity in response of these materials, despite the distinguishable differences in their physical properties, suggests the universality of the physical picture explained by the localization of Wannier-Stark states. Our results may blaze a trail to PHz-rate optoelectronics. PMID:26888147

  15. Strong motion duration and earthquake magnitude relationships

    SciTech Connect

    Salmon, M.W.; Short, S.A.; Kennedy, R.P.

    1992-06-01

    Earthquake duration is the total time of ground shaking from the arrival of seismic waves until the return to ambient conditions. Much of this time is at relatively low shaking levels which have little effect on seismic structural response and on earthquake damage potential. As a result, a parameter termed ``strong motion duration`` has been defined by a number of investigators to be used for the purpose of evaluating seismic response and assessing the potential for structural damage due to earthquakes. This report presents methods for determining strong motion duration and a time history envelope function appropriate for various evaluation purposes, for earthquake magnitude and distance, and for site soil properties. There are numerous definitions of strong motion duration. For most of these definitions, empirical studies have been completed which relate duration to earthquake magnitude and distance and to site soil properties. Each of these definitions recognizes that only the portion of an earthquake record which has sufficiently high acceleration amplitude, energy content, or some other parameters significantly affects seismic response. Studies have been performed which indicate that the portion of an earthquake record in which the power (average rate of energy input) is maximum correlates most closely with potential damage to stiff nuclear power plant structures. Hence, this report will concentrate on energy based strong motion duration definitions.

  16. Strong Female Characters in Recent Children's Literature.

    ERIC Educational Resources Information Center

    Heine, Pat; Inkster, Christine; Kazemek, Frank; Williams, Sandra; Raschke, Sylvia; Stevens, Della

    1999-01-01

    Shares the authors' criteria for evaluating female characters as positive role models in children's literature. Explores the criteria by examining "The Ballad of Lucy Wipple" (Karen Cushman). Discusses other recently published picture books and novels which feature strong females in history, in contemporary times, and in fantasy. (SR)

  17. Semimetallization of dielectrics in strong optical fields

    NASA Astrophysics Data System (ADS)

    Kwon, Ojoon; Paasch-Colberg, Tim; Apalkov, Vadym; Kim, Bum-Kyu; Kim, Ju-Jin; Stockman, Mark I.; Kim, D.

    2016-02-01

    At the heart of ever growing demands for faster signal processing is ultrafast charge transport and control by electromagnetic fields in semiconductors. Intense optical fields have opened fascinating avenues for new phenomena and applications in solids. Because the period of optical fields is on the order of a femtosecond, the current switching and its control by an optical field may pave a way to petahertz optoelectronic devices. Lately, a reversible semimetallization in fused silica on a femtosecond time scale by using a few-cycle strong field (~1 V/Å) is manifested. The strong Wannier-Stark localization and Zener-type tunneling were expected to drive this ultrafast semimetallization. Wider spread of this technology demands better understanding of whether the strong field behavior is universally similar for different dielectrics. Here we employ a carrier-envelope-phase stabilized, few-cycle strong optical field to drive the semimetallization in sapphire, calcium fluoride and quartz and to compare this phenomenon and show its remarkable similarity between them. The similarity in response of these materials, despite the distinguishable differences in their physical properties, suggests the universality of the physical picture explained by the localization of Wannier-Stark states. Our results may blaze a trail to PHz-rate optoelectronics.

  18. Characteristics of strong motion duration in Taiwan

    NASA Astrophysics Data System (ADS)

    Lee, Y.; Wang, Y.; Ma, K.

    2012-12-01

    The duration of strong shaking plays an important role to affect the yield damage caused by an earthquake. In this study, we analyzed the acceleration seismograms of Taiwan Strong Motion Network to characterize the strong shacking duration with function of the earthquake magnitude. We defined the duration to be the time interval between the first and the last amplitude, which is equal to or greater than a level of 5gal. We estimated the duration for 70138 events with magnitude ranged from Mw=4.0 to 7.0 during 1994 to 2010. We, thus, obtained the empirical equation for the strong ground motion duration, magnitude and distance. Base on the two relations: the positive relation between duration and magnitude, and the negative relation between duration and distance. The empirical equation can be shown as: ME(τ) =2.45log(τ)+0.01225Δ+2.115, where Δ is distance (km), and τ is duration time (sec) The comparison between ME(τ) and Mw is satisfactory for the events Mw>5.5. For Mw 7.3 as 1999 Chi-Chi earthquake, the estimated duration according to the empirical equation at Δ=50km will be about 74 sec, which is comparable to the observations. The empirical equation would provide the characteristics of source during for large earthquakes.

  19. Strongly coupled fourth generation at the LHC

    SciTech Connect

    Burdman, G.; Da Rold, L.; Eboli, O. J. P.; Matheus, R. D.

    2009-04-01

    We study extensions of the standard model with a strongly coupled fourth generation. This occurs in models where electroweak symmetry breaking is triggered by the condensation of at least some of the fourth-generation fermions. With focus on the phenomenology at the LHC, we study the pair production of fourth-generation down quarks, D{sub 4}. We consider the typical masses that could be associated with a strongly coupled fermion sector, in the range (300-600) GeV. We show that the production and successive decay of these heavy quarks into final states with same-sign dileptons, trileptons, and four leptons can be easily seen above background with relatively low luminosity. On the other hand, in order to confirm the presence of a new strong interaction responsible for fourth-generation condensation, we study its contribution to D{sub 4} pair production, and the potential to separate it from standard QCD-induced heavy quark production. We show that this separation might require large amounts of data. This is true even if it is assumed that the new interaction is mediated by a massive colored vector boson, since its strong coupling to the fourth generation renders its width of the order of its mass. We conclude that, although this class of models can be falsified at early stages of the LHC running, its confirmation would require high integrated luminosities.

  20. PIC: Protein Interactions Calculator.

    PubMed

    Tina, K G; Bhadra, R; Srinivasan, N

    2007-07-01

    Interactions within a protein structure and interactions between proteins in an assembly are essential considerations in understanding molecular basis of stability and functions of proteins and their complexes. There are several weak and strong interactions that render stability to a protein structure or an assembly. Protein Interactions Calculator (PIC) is a server which, given the coordinate set of 3D structure of a protein or an assembly, computes various interactions such as disulphide bonds, interactions between hydrophobic residues, ionic interactions, hydrogen bonds, aromatic-aromatic interactions, aromatic-sulphur interactions and cation-pi interactions within a protein or between proteins in a complex. Interactions are calculated on the basis of standard, published criteria. The identified interactions between residues can be visualized using a RasMol and Jmol interface. The advantage with PIC server is the easy availability of inter-residue interaction calculations in a single site. It also determines the accessible surface area and residue-depth, which is the distance of a residue from the surface of the protein. User can also recognize specific kind of interactions, such as apolar-apolar residue interactions or ionic interactions, that are formed between buried or exposed residues or near the surface or deep inside. PMID:17584791

  1. Super-strong magneto-rheological fluids

    NASA Astrophysics Data System (ADS)

    Tao, R.

    2001-03-01

    A typical MR fluid is a suspension of magnetic particles of micrometer size in a liquid. Upon application of a strong magnetic field, the fluid turns into a solid. This process is reversible and the response time is of milliseconds. MR fluids presently have a yield shear stress around 80 kPa, which is adequate for applications in shock absorbers and vibration dampers, but is inadequate for automobile clutch etc. Efforts in searching for new materials in the past decades came with limited results. Thus we have developed a new approach to change the microstructure of MR fluids and make them super-strong. It is well known that under a strong magnetic field, the ideal structure of MR fluids is a body-centered tetragonal (bct) lattice. The mechanical strength of MR fluids strongly depends on the microstructure. A bct-lattice based thick column has a much higher yield stress than a single-chain structure. When a magnetic field is applied to a MR fluid, the particles first form chains. With time, the chains may aggregate into columns. However, the unassisted aggregation is not very useful, as it is slow and produces columns with a limited thickness. Our method is based on assisted aggregations. Immediately after a magnetic field is applied, we compress the MR fluid in the field direction before a shear force is applied. The compression pushes the induced chains together to form thick columns. This microstructure change greatly enhances the yield stress. The experiment on an iron-based MR fluid finds 800 kPa for the yield stress, ten times stronger than that without the compression. When the magnetic field is removed, the MR fluid still returns to the liquid state quickly. The upper limit of this structure-enhanced yield stress seems well above 800 kPa. The super-strong MR fluids are suitable for many industrial applications. *Supported by NSF Grant 0196022

  2. Total protein

    MedlinePlus

    The total protein test measures the total amount of two classes of proteins found in the fluid portion of your ... nutritional problems, kidney disease or liver disease . If total protein is abnormal, you will need to have more ...

  3. Storage Proteins

    PubMed Central

    Fujiwara, Toru; Nambara, Eiji; Yamagishi, Kazutoshi; Goto, Derek B.; Naito, Satoshi

    2002-01-01

    Plants accumulate storage substances such as starch, lipids and proteins in certain phases of development. Storage proteins accumulate in both vegetative and reproductive tissues and serve as a reservoir to be used in later stages of plant development. The accumulation of storage protein is thus beneficial for the survival of plants. Storage proteins are also an important source of dietary plant proteins. Here, we summarize the genome organization and regulation of gene expression of storage protein genes in Arabidopsis. PMID:22303197

  4. Proteins Take up Water Before Unfolding.

    PubMed

    Groot, Carien C M; Bakker, Huib J

    2016-05-19

    Proteins perform specific biological functions that strongly depend on their three-dimensional structure. This three-dimensional structure, i.e. the way the protein folds, is strongly determined by the interaction between the protein and the water solvent. We study the dynamics of water in aqueous solutions of several globular proteins at different degrees of urea-induced unfolding, using polarization-resolved femtosecond infrared spectroscopy. We observe that a fraction of the water molecules is strongly slowed down by their interaction with the protein surface. By monitoring the slow water fraction we can directly probe the amount of water-exposed protein surface. We find that at mild denaturing conditions, the water-exposed surface increases by almost 50%, while the secondary structure is still intact. This finding indicates that protein unfolding starts with the protein structure becoming less tight, thereby allowing water to enter. PMID:27120433

  5. Strong dynamics and lattice gauge theory

    NASA Astrophysics Data System (ADS)

    Schaich, David

    In this dissertation I use lattice gauge theory to study models of electroweak symmetry breaking that involve new strong dynamics. Electroweak symmetry breaking (EWSB) is the process by which elementary particles acquire mass. First proposed in the 1960s, this process has been clearly established by experiments, and can now be considered a law of nature. However, the physics underlying EWSB is still unknown, and understanding it remains a central challenge in particle physics today. A natural possibility is that EWSB is driven by the dynamics of some new, strongly-interacting force. Strong interactions invalidate the standard analytical approach of perturbation theory, making these models difficult to study. Lattice gauge theory is the premier method for obtaining quantitatively-reliable, nonperturbative predictions from strongly-interacting theories. In this approach, we replace spacetime by a regular, finite grid of discrete sites connected by links. The fields and interactions described by the theory are likewise discretized, and defined on the lattice so that we recover the original theory in continuous spacetime on an infinitely large lattice with sites infinitesimally close together. The finite number of degrees of freedom in the discretized system lets us simulate the lattice theory using high-performance computing. Lattice gauge theory has long been applied to quantum chromodynamics, the theory of strong nuclear interactions. Using lattice gauge theory to study dynamical EWSB, as I do in this dissertation, is a new and exciting application of these methods. Of particular interest is non-perturbative lattice calculation of the electroweak S parameter. Experimentally S ≈ -0.15(10), which tightly constrains dynamical EWSB. On the lattice, I extract S from the momentum-dependence of vector and axial-vector current correlators. I created and applied computer programs to calculate these correlators and analyze them to determine S. I also calculated the masses

  6. Model reduction of strong-weak neurons.

    PubMed

    Du, Bosen; Sorensen, Danny; Cox, Steven J

    2014-01-01

    We consider neurons with large dendritic trees that are weakly excitable in the sense that back propagating action potentials are severly attenuated as they travel from the small, strongly excitable, spike initiation zone. In previous work we have shown that the computational size of weakly excitable cell models may be reduced by two or more orders of magnitude, and that the size of strongly excitable models may be reduced by at least one order of magnitude, without sacrificing the spatio-temporal nature of its inputs (in the sense we reproduce the cell's precise mapping of inputs to outputs). We combine the best of these two strategies via a predictor-corrector decomposition scheme and achieve a drastically reduced highly accurate model of a caricature of the neuron responsible for collision detection in the locust. PMID:25566048

  7. Strong correlation induced charge localization in antiferromagnets

    PubMed Central

    Zhu, Zheng; Jiang, Hong-Chen; Qi, Yang; Tian, Chushun; Weng, Zheng-Yu

    2013-01-01

    The fate of a hole injected in an antiferromagnet is an outstanding issue of strongly correlated physics. It provides important insights into doped Mott insulators closely related to high-temperature superconductivity. Here, we report a systematic numerical study of t-J ladder systems based on the density matrix renormalization group. It reveals a surprising result for the single hole's motion in an otherwise well-understood undoped system. Specifically, we find that the common belief of quasiparticle picture is invalidated by the self-localization of the doped hole. In contrast to Anderson localization caused by disorders, the charge localization discovered here is an entirely new phenomenon purely of strong correlation origin. It results from destructive quantum interference of novel signs picked up by the hole, and since the same effect is of a generic feature of doped Mott physics, our findings unveil a new paradigm which may go beyond the single hole doped system. PMID:24002668

  8. New strong interactions above the electroweak scale

    SciTech Connect

    White, A.R.

    1994-08-09

    Theoretical arguments for a new higher-color quark sector, based on Pomeron physics in QCD, are briefly described. The electroweak symmetry-breaking, Strong CP conservation, and electroweak scale CP violation, that is naturally produced by this sector is also outlined. A further consequence is that above the electroweak scale there will be a radical change in the strong interaction. Electroweak states, in particular multiple W`s and Z`s, and new, semi-stable, very massive, baryons, will be commonly produced. The possible correlation of expected phenomena with a wide range of observed Cosmic Ray effects at and above the primary spectrum knee is described. Related phenomena that might be seen in the highest energy hard scattering events at the Fermilab Tevatron, some of which could be confused with top production, are also briefly discussed.

  9. Waves in strong centrifugal fields: dissipationless gas

    NASA Astrophysics Data System (ADS)

    Bogovalov, S. V.; Kislov, V. A.; Tronin, I. V.

    2015-04-01

    Linear waves are investigated in a rotating gas under the condition of strong centrifugal acceleration of the order 106 g realized in gas centrifuges for separation of uranium isotopes. Sound waves split into three families of the waves under these conditions. Dispersion equations are obtained. The characteristics of the waves strongly differ from the conventional sound waves on polarization, velocity of propagation and distribution of energy of the waves in space for two families having frequencies above and below the frequency of the conventional sound waves. The energy of these waves is localized in rarefied region of the gas. The waves of the third family were not specified before. They propagate exactly along the rotational axis with the conventional sound velocity. These waves are polarized only along the rotational axis. Radial and azimuthal motions are not excited. Energy of the waves is concentrated near the wall of the rotor where the density of the gas is largest.

  10. Strong regularizing effect of integrable systems

    SciTech Connect

    Zhou, Xin

    1997-11-01

    Many time evolution problems have the so-called strong regularization effect, that is, with any irregular initial data, as soon as becomes greater than 0, the solution becomes C{sup {infinity}} for both spacial and temporal variables. This paper studies 1 x 1 dimension integrable systems for such regularizing effect. In the work by Sachs, Kappler [S][K], (see also earlier works [KFJ] and [Ka]), strong regularizing effect is proved for KdV with rapidly decaying irregular initial data, using the inverse scattering method. There are two equivalent Gel`fand-Levitan-Marchenko (GLM) equations associated to an inverse scattering problem, one is normalized at x = {infinity} and another at x = {infinity}. The method of [S][K] relies on the fact that the KdV waves propagate only in one direction and therefore one of the two GLM equations remains normalized and can be differentiated infinitely many times. 15 refs.

  11. Model reduction of strong-weak neurons

    PubMed Central

    Du, Bosen; Sorensen, Danny; Cox, Steven J.

    2014-01-01

    We consider neurons with large dendritic trees that are weakly excitable in the sense that back propagating action potentials are severly attenuated as they travel from the small, strongly excitable, spike initiation zone. In previous work we have shown that the computational size of weakly excitable cell models may be reduced by two or more orders of magnitude, and that the size of strongly excitable models may be reduced by at least one order of magnitude, without sacrificing the spatio–temporal nature of its inputs (in the sense we reproduce the cell's precise mapping of inputs to outputs). We combine the best of these two strategies via a predictor-corrector decomposition scheme and achieve a drastically reduced highly accurate model of a caricature of the neuron responsible for collision detection in the locust. PMID:25566048

  12. Scaled Strong Field Interactions at Long Wavelengths

    NASA Astrophysics Data System (ADS)

    Sistrunk, Emily Frances

    The strong field regime describes interactions between light and matter where the electric field of the laser is a significant fraction of the binding field of the atom. Short pulsed lasers are capable of producing local fields on the order of the atomic unit of electric field. Under the influence of such strong fields, the ionization regime and electron dynamics are highly dependent on the wavelength used to drive the interaction. Few studies have been performed in the mid-infrared (MIR) spectral range. Using MIR wavelengths, the ponderomotive energy, Up, imposed on the electrons can be a factor of 20 greater than in the visible and near-infrared. Experiments on above threshold ionization (ATI) of cesium, nonsequential ionization (NSI) of noble gases, and high harmonic generation (HHG) in condensed phase media highlight the benefits of performing strong field investigations in the MIR. The photoelectron energy spectrum from above threshold ionization (ATI) of atoms provides details about the strong field interaction. Cesium atoms driven by a 3.6 mum laser indicate that excited states can play a large role in ionization from the ground state. Previous experiments on argon in the near-infrared can be compared to cesium at 3.6 im due to their similar Keldysh-scaling. Unlike argon, the measured ionization yield in cesium saturates at a higher intensity than predicted due to the Stark shift of the ground state. Such shifts have not been detected in argon. The low-lying 6P excited states of cesium produce a strong effect on the photoelectron energy spectrum, resulting in a splitting of each ATI peak. Enhancements in the photoelectron energy spectrum similar to those found in argon are observed in cesium. These enhancements are relatively insensitive to ellipticity of the drive laser. To take advantage of the large ponderomotive energy associated with Mid-IR lasers, ionization of argon, krypton and xenon is studied at 3.6 im. The factor of 20 increase in Up between the

  13. Solvable model of a strongly driven micromaser

    SciTech Connect

    Lougovski, P.; Walther, H.; Casagrande, F.; Lulli, A.; Englert, B.-G.; Solano, E.

    2004-02-01

    We study the dynamics of a micromaser where the pumping atoms are strongly driven by a resonant classical field during their transit through the cavity mode. We derive a master equation for this strongly driven micromaser, involving the contributions of the unitary atom-field interactions and the dissipative effects of a thermal bath. We find analytical solutions for the temporal evolution and the steady state of this system by means of phase-space techniques, providing an unusual solvable model of an open quantum system, including pumping and decoherence. We derive closed expressions for all relevant expectation values, describing the statistics of the cavity field and the detected atomic levels. The transient regime shows the buildup of mixtures of mesoscopic fields evolving towards a super-Poissonian steady-state field that, nevertheless, yields atomic correlations that exhibit stronger nonclassical features than the conventional micromaser.

  14. Temperature equilibration in strongly coupled plasma

    SciTech Connect

    Thode, L. E.; Chang, C. H.; Snell, C. M.; Daughton, W. S.; Csanak, G. Y.

    2002-01-01

    A laser-driven experiment investigating electron-ion equilibration in strongly coupled plasma was performed in 1995. At that time, standard estimates for the electron-ion equilibration time were two-to-three orders of magnitude faster than observed experimentally. As a result, the electron-ion equilibration time was taken as a fitting parameter to understand the experimental results. Based upon guidance from nonequilibrium molecular dynamics mixture calculations 121 and comparison with strongly coupled resistivity experiments, we have developed a consistent binary collision model to understand the electron-ion equilibration experiment. The model has been implemented in a newly developed multi-species, multi-temperature physics code, which was used for simulation of the experiment. The resulting electron-ion exchange rate is close to the experiment, which is about three orders-of-magnitude slower than given by standard estimates, most of which is the result of a modified coulomb logarithm.

  15. Evolution on a Lattice under Strong Mutation

    NASA Astrophysics Data System (ADS)

    Otwinowski, Jakub; Boettcher, Stefan

    2011-03-01

    The most common approach to study biological evolution in a population considers mutations to arise one at a time, and spread to the whole population. However, recent experimental work has shown that under conditions of strong mutation and strong selection, multiple mutations may arise simultaneously. Such overlapping mutations compete with each other and make the results difficult to analyse. Theorists are working on understanding the relationships between different parameters such as population size, mutation rate, and selection coefficients, in the way they affect observables such as the speed of evolution, and the probability of fixation. We have shown with simulations that under additional spatial constraints the dynamics are very different compared to well-mixed populations. A surface in fitness space evolves, akin to surface growth phenomena, with non-trivial power-law exponents. The result is that the speed of evolution is restricted and the probability of fixation is reduced. With support from the NSF through grant DMR-0812204.

  16. Anomalous retroreflection from strongly absorbing nanoporous semiconductors.

    PubMed

    Prislopski, S Ya; Naumenko, E K; Tiginyanu, I M; Ghimpu, L; Monaico, E; Sirbu, L; Gaponenko, S V

    2011-08-15

    Pronounced retroreflection behavior is reported for a fishnet nanoporous strongly absorbing semiconductor material. Retroreflection features a half-cone about 0.35 rad along with diffusive specular reflection for all angles of incidence. Retroreflection is apparent by the naked eye with daylight illumination and exhibits no selectivity with respect to wavelength and polarization of incident light featuring minor depolarization of retroreflected light. The reflectance in the backward direction measures 12% with respect to a white scattering etalon. The phenomenon can be classified neither as coherent backscattering nor as Anderson localization of light. The primary model includes light scattering from strongly absorptive and refractive superwavelength clusters existing within the porous fishnet structure. A reasonable qualitative explanation is based on the fact that strict retroreflection obeys shorter paths inside absorbing medium, whereas all alternative paths will lead to stronger absorption of light. PMID:21847216

  17. Photon scattering from strongly driven atomic ensembles

    SciTech Connect

    Jin Luling; Evers, Joerg; Macovei, Mihai

    2011-10-15

    The second-order correlation function for light emitted from a strongly and near-resonantly driven dilute cloud of atoms is discussed. Because of the strong driving, the fluorescence spectrum separates into distinct peaks, for which the spectral properties can be defined individually. It is shown that the second-order correlations for various combinations of photons from different spectral lines exhibit bunching together with super-Poissonian or sub-Poissonian photon statistics, tunable by the choice of the detector positions. Additionally, a Cauchy-Schwarz inequality is violated for photons emitted from particular spectral bands. The emitted light intensity is proportional to the square of the number of particles, and thus can potentially be intense. Three different averaging procedures to model ensemble disorder are compared.

  18. Photoneutrino energy losses in strong magnetic fields.

    NASA Technical Reports Server (NTRS)

    Canuto, V.; Fassio-Canuto, L.

    1973-01-01

    Previously computed rates of energy losses (Petrosian et al., 1967) ignored the presence of strong magnetic fields, hence the change brought in when such a field (about 10 to the 12th to 10 to the 13th power G) is included is studied. The results indicate that for T about 10 to the 8th power K and densities rho of about 10,000 g/cu cm, the presence of a strong H field decreases the energy losses by at the most a factor between 10 and 100 in the region up to rho = 1,000,000 g/cu cm. At higher densities the neutrino emissivities are almost identical.

  19. Strong Transverse Coupling in the Tevatron

    NASA Astrophysics Data System (ADS)

    Syphers, Michael

    2004-05-01

    During the 20 years since it was first commissioned, the Fermilab Tevatron has developed strong coupling between the two transverse degrees of freedom. A distributed zeroth harmonic skew quadrupole circuit has traditionally been used to correct for transverse coupling, and the strength required of this circuit has increased since 1983 by more than an order of magnitude. In recent years changes to the Tevatron for colliding beams operation have altered the skew quadrupole corrector distribution and strong local coupling has become evident, often encumbering routine operation. In February 2003 it was discovered that the superconducting coils within the main bending magnets of the Tevatron had become vertically displaced within their iron yokes relative to their measured positions in the early 1980's during construction. The ensuing systematic skew quadrupole field introduced by this displacement accounts for the required corrector settings and observed beam behavior. Beam observations, explanations, and remedial measures are presented.

  20. Strong ground motion prediction using virtual earthquakes.

    PubMed

    Denolle, M A; Dunham, E M; Prieto, G A; Beroza, G C

    2014-01-24

    Sedimentary basins increase the damaging effects of earthquakes by trapping and amplifying seismic waves. Simulations of seismic wave propagation in sedimentary basins capture this effect; however, there exists no method to validate these results for earthquakes that have not yet occurred. We present a new approach for ground motion prediction that uses the ambient seismic field. We apply our method to a suite of magnitude 7 scenario earthquakes on the southern San Andreas fault and compare our ground motion predictions with simulations. Both methods find strong amplification and coupling of source and structure effects, but they predict substantially different shaking patterns across the Los Angeles Basin. The virtual earthquake approach provides a new approach for predicting long-period strong ground motion. PMID:24458636

  1. Basic properties of strongly code disjoint checkers

    NASA Astrophysics Data System (ADS)

    Nicolaidis, M.

    1990-09-01

    In order to ensure total self checking, checkers have been introduced by Carter and defined by Anderson to be totally self checking: that is they are code disjoint, self testing, and fault secure. Checkers which are only code disjoint and self testing are also discussed. Strongly code disjoint checkers are not fault secure. Some researchers feel that the fault secure property is indeed necessary. This lack of agreement about the basic concepts of checkers is an important drawback in further research on self checking checkers. The various arguments used in the debate are presented. Aspects of the problem over which there is the most disagreement are highlighted. Some important points concerning strongly code disjoint checkers are discussed.

  2. Physics of protein motility and motor proteins

    NASA Astrophysics Data System (ADS)

    Kolomeisky, Anatoly B.

    2013-09-01

    Motor proteins are enzymatic molecules that transform chemical energy into mechanical motion and work. They are critically important for supporting various cellular activities and functions. In the last 15 years significant progress in understanding the functioning of motor proteins has been achieved due to revolutionary breakthroughs in single-molecule experimental techniques and strong advances in theoretical modelling. However, microscopic mechanisms of protein motility are still not well explained, and the collective efforts of many scientists are needed in order to solve these complex problems. In this special section the reader will find the latest advances on the difficult road to mapping motor proteins dynamics in various systems. Recent experimental developments have allowed researchers to monitor and to influence the activity of single motor proteins with a high spatial and temporal resolution. It has stimulated significant theoretical efforts to understand the non-equilibrium nature of protein motility phenomena. The latest results from all these advances are presented and discussed in this special section. We would like to thank the scientists from all over the world who have reported their latest research results for this special section. We are also grateful to the staff and editors of Journal of Physics: Condensed Matter for their invaluable help in handling all the administrative and refereeing activities. The field of motor proteins and protein motility is fast moving, and we hope that this collection of articles will be a useful source of information in this highly interdisciplinary area. Physics of protein motility and motor proteins contents Physics of protein motility and motor proteinsAnatoly B Kolomeisky Identification of unique interactions between the flexible linker and the RecA-like domains of DEAD-box helicase Mss116 Yuan Zhang, Mirkó Palla, Andrew Sun and Jung-Chi Liao The load dependence of the physical properties of a molecular motor

  3. Geometry and physics of proteins

    NASA Astrophysics Data System (ADS)

    Banavar, Jayanth R.; Cieplak, Marek; Hoang, Trinh X.; Maritan, Amos

    2005-03-01

    We recall some of the key lessons of protein research over the last several decades and show that they strongly suggest a new framework for understanding proteins. The unified framework is useful for understanding protein folding, amyloid formation and protein interactions and has important implications for natural selection. The experimental data and our new approach, supported by computer simulations, reveal an astonishing simplicity underlying the protein problem. REFERENCES: Banavar, J. R. and Maritan, A. (2003). Colloquium: Geometrical approach to protein folding: A tube picture. Rev. Mod. Phys. 75, 23. Banavar, J. R., Hoang, T. X., Maritan, A., Seno, F. and Trovato, A., (2004). A unified perspective on proteins -- a physics approach. Phys. Rev. E 70, 041905. Banavar, J. R., Cieplak, M. and Maritan, A., (2004). Lattice tube model of proteins, Phys. Rev. Lett. (in press).

  4. Quantum states with strong positive partial transpose

    SciTech Connect

    Chruscinski, Dariusz; Jurkowski, Jacek; Kossakowski, Andrzej

    2008-02-15

    We construct a large class of bipartite M x N quantum states which defines a proper subset of states with positive partial transposes (PPTs). Any state from this class has PPT but the positivity of its partial transposition is recognized with respect to canonical factorization of the original density operator. We propose to call elements from this class states with strong positive partial transposes (SPPTs). We conjecture that all SPPT states are separable.

  5. Bose polarons in the strongly interacting regime

    NASA Astrophysics Data System (ADS)

    Kedar, Dhruv; Hu, Ming-Guang; van de Graaff, Michael; Corson, John; Cornell, Eric; Jin, Deborah

    2016-05-01

    Impurities immersed in and interacting with a Bose-Einstein condensate (BEC) are predicted to form quasiparticle excitations called Bose polarons. I will present experimental evidence of Bose polarons in cold atoms obtained using radio-frequency spectroscopy to measure the excitation spectrum of fermionic K-40 impurities interacting with a BEC of Rb-87 atoms. We use an interspecies Feshbach resonance to tune the interactions between the impurities and the bosons, and we take data in the strongly interacting regime.

  6. Concepts in strong Langmuir turbulence theory

    SciTech Connect

    DuBois, D.F.; Rose, H.A.

    1990-01-01

    Some of the basic concepts of strong Langmuir turbulence (SLT) theory are reviewed. In SLT system, a major fraction of the turbulent energy is carried by local, time-dependent, nonlinear excitations called cavitons. Modulational instability, localization of Langmuir fields by density fluctuations, caviton nucleation, collapse, and burnout and caviton correlations are reviewed. Recent experimental evidence will be presented for SLT phenomena in the interaction of powerful HF waves with the ionosphere and in laser-plasma interaction experiments. 38 refs., 11 figs.

  7. Cosmological Applications of Strong Gravitational Lensing

    NASA Astrophysics Data System (ADS)

    Paraficz, Danuta

    2009-11-01

    One of the most intriguing recent results in physics is the growing evidence that an unknown energy field and an unknown kind of matter are the major components of the Universe (70% and 30%, respectively; see e.g. Riess et al. 1998, Spergel et al. 2007). Understanding and estimating the precise value of the energy density of the two above components, together with measuring the Hubble constant that determines the age of the Universe, is a major goal of modern astrophysics. An interesting method for estimating these parameters is strong gravitational lensing of quasars (QSOs). As shown by Refsdal (1964), H0, !m and !! can be measured based on the time delay ("t) between multiply lensed images of QSOs, because "t depends on H0 and on the distances to lens and source, hence!m and !!. Determination of cosmological parameters using gravitational lensing suffers from some degeneracies, but it is based on well understood physics and unlike distance ladder methods there are no calibration issues. Moreover, it has an advantage over some of the leading methods (such as Type Ia SNe) in that it is a purely cosmological approach. In this thesis, the property of strong gravitational lensing - time delay - is extensively explored. Strong gravitational lensing, and in particular time delays, are investigated here both theoretically and observationally. The focus is on the time delay as a cosmological and astrophysical tool to constrain H0, !m, !!, and to measure the masses of lensing galaxies. The first Chapter presents a historical background of gravitational lensing. It explains the process involved in creating the theory of gravitational lenses. It shows how Newton and then Einstein developed the concept and how Refsdal and others made it a cosmological tool. We present in more detail how gravitational lensing influenced the history of physics by being the first proof of Einstein's theory of gravity. The Chapter ends by discussing the first observational discovery of a strong

  8. Dirac particle spin in strong gravitational fields

    NASA Astrophysics Data System (ADS)

    Obukhov, Yu. N.; Silenko, A. J.; Teryaev, O. V.

    2014-01-01

    Dynamics of the Dirac particle spin in general strong gravitational fields is discussed. The Hermitian Dirac Hamiltonian is derived and transformed to the Foldy-Wouthuysen (FW) representation for an arbitrary metric. The quantum mechanical equations of spin motion are found. These equations agree with corresponding classical ones. The new restriction on the anomalous gravitomagnetic moment (AGM) by the reinterpretation of Lorentz invariance tests is obtained.

  9. Kinetic Characterization of Strongly Coupled Systems

    SciTech Connect

    Knapek, C. A.; Ivlev, A. V.; Klumov, B. A.; Morfill, G. E.; Samsonov, D.

    2007-01-05

    We propose a simple method to determine the local coupling strength {gamma} experimentally, by linking the individual particle dynamics with the local density and crystal structure of a 2D plasma crystal. By measuring particle trajectories with high spatial and temporal resolution we obtain the first maps of {gamma} and temperature at individual particle resolution. We employ numerical simulations to test this new method, and discuss the implications to characterize strongly coupled systems.

  10. Strong interaction studies with kaonic atoms

    NASA Astrophysics Data System (ADS)

    Marton, J.; Bazzi, M.; Beer, G.; Berucci, C.; Bosnar, D.; Bragadireanu, A. M.; Cargnelli, M.; Clozza, A.; Curceanu, C.; d'Uffizi, A.; Fiorini, C.; Ghio, F.; Guaraldo, C.; Hayano, R.; Iliescu, M.; Ishiwatari, T.; Iwasaki, M.; Levi Sandri, P.; Okada, S.; Pietreanu, D.; Piscicchia, K.; Ponta, T.; Quaglia, R.; Romero Vidal, A.; Sbardella, E.; Scordo, A.; Shi, H.; Sirghi, D. L.; Sirghi, F.; Tatsuno, H.; Vazquez Doce, O.; Widmann, E.; Zmeskal, J.

    2016-03-01

    The strong interaction of antikaons (K-) with nucleons and nuclei in the low-energy regime represents an active research field connected intrinsically with few-body physics. There are important open questions like the question of antikaon nuclear bound states - the prototype system being K-pp. A unique and rather direct experimental access to the antikaon-nucleon scattering lengths is provided by precision X-ray spectroscopy of transitions in low-lying states of light kaonic atoms like kaonic hydrogen isotopes. In the SIDDHARTA experiment at the electron-positron collider DAΦNE of LNF-INFN we measured the most precise values of the strong interaction observables, i.e. the strong interaction on the 1s ground state of the electromagnetically bound K-p atom leading to a hadronic shift ɛ1s and a hadronic broadening Γ1s of the 1s state. The SIDDHARTA result triggered new theoretical work which achieved major progress in the understanding of the low-energy strong interaction with strangeness. Antikaon-nucleon scattering lengths have been calculated constrained by the SIDDHARTA data on kaonic hydrogen. For the extraction of the isospin-dependent scattering lengths a measurement of the hadronic shift and width of kaonic deuterium is necessary. Therefore, new X-ray studies with the focus on kaonic deuterium are in preparation (SIDDHARTA2). Many improvements in the experimental setup will allow to measure kaonic deuterium which is challenging due to the anticipated low X-ray yield. Especially important are the data on the X-ray yields of kaonic deuterium extracted from a exploratory experiment within SIDDHARTA.

  11. Kummer solitons in strongly nonlocal nonlinear media

    NASA Astrophysics Data System (ADS)

    Zhong, Wei-Ping; Belić, Milivoj

    2009-01-01

    We solve the three-dimensional (3D) time-dependent strongly nonlocal nonlinear Schrödinger equation (NNSE) in spherical coordinates, with the help of Kummer's functions. We obtain analytical solitary solutions, which we term the Kummer solitons. We compare analytical solutions with the numerical solutions of NNSE. We discuss higher-order Kummer spatial solitons, which can exist in various forms, such as the 3D vortex solitons and the multipole solitons.

  12. Strong cosmic censorship and Misner spacetime

    NASA Astrophysics Data System (ADS)

    Denaro, Pedro; Dotti, Gustavo

    2015-07-01

    Misner spacetime is among the simplest solutions of Einstein's equation that exhibits a Cauchy horizon with a smooth extension beyond it. Besides violating strong cosmic censorship, this extension contains closed timelike curves. We analyze the stability of the Cauchy horizon and prove that neighboring spacetimes in one parameter families of solutions through Misner's in pure gravity, gravity coupled to a scalar field, or Einstein-Maxwell theory end at the Cauchy horizon developing a curvature singularity.

  13. Strong coupling QED with two fermionic flavors

    SciTech Connect

    Wang, K.C.

    1990-11-01

    We report the recent results of our simulation of strong coupling QED, with non-compact action, on lattices 10{sup 4} and 16{sup 4}. Since we are dealing with two staggered fermionic flavors, we use hybrid algorithm to do the simulation. In addition to the measurement of the chiral order parameter {l angle}{bar {psi}}{psi}{r angle}, we also measure magnetic monopole susceptibility, {chi}, throughout the region of chiral transition. 6 refs., 6 figs.

  14. Strong, Ductile Rotor For Cryogenic Flowmeters

    NASA Technical Reports Server (NTRS)

    Royals, W. T.

    1993-01-01

    Improved magnetic flowmeter rotor resists cracking at cryogenic temperatures, yet provides adequate signal to magnetic pickup outside flowmeter housing. Consists mostly of stainless-steel alloy 347, which is ductile and strong at low temperatures. Small bead of stainless-steel alloy 410 welded in groove around circumference of round bar of stainless-steel alloy 347; then rotor machined from bar. Tips of rotor blades contain small amounts of magnetic alloy, and passage of tips detected.

  15. Ultrafiltration of pegylated proteins

    NASA Astrophysics Data System (ADS)

    Molek, Jessica R.

    groups in the PEGylated proteins. Ultrafiltration experiments were performed using PEGylated alpha-lactalbumin, ovalbumin, and bovine serum albumin. In contrast to the size exclusion chromatography data, the sieving coefficient of the PEGylated proteins depended upon both the number and size of the attached PEG chains due to the elongation or deformation of the PEG associated with the filtrate flux. Sieving coefficients at low filtrate flux were in good agreement with predictions of available hydrodynamic models, with significant elongation occurring when the Deborah number for the PEG chain exceeded 0.001. The effects of electrostatic interactions on the ultrafiltration of PEGylated proteins were examined using electrically-charged membranes generated by covalent attachment of sulphonic acid groups to the base cellulosic membrane. Transmission of PEGylated proteins through charged membranes was dramatically reduced at low ionic strength due to strong electrostatic interactions, despite the presence of the neutral PEG. The experimental results were in good agreement with model calculations developed for the partitioning of charged spheres into charged cylindrical pores. The experimental and theoretical results provide the first quantitative analysis of the effects of PEGylation on transport through semipermeable ultrafiltration membranes. The results from small-scale ultrafiltration experiments were used to develop a two-stage diafiltration process to purify PEGylated alpha-lactalbumin. The first-stage used a neutral membrane to remove the unreacted protein by exploiting differences in size. The second stage used a negatively-charged membrane to remove hydrolyzed PEG, with the PEGylated product retained by strong electrostatic interactions. This process provided a purification factor greater than 1000 with respect to the unreacted protein and greater than 20-fold with respect to the PEG with an overall yield of PEGylated alpha-lactalbumin of 78%. These results provide

  16. Implication of Terminal Residues at Protein-Protein and Protein-DNA Interfaces.

    PubMed

    Martin, Olivier M F; Etheve, Loïc; Launay, Guillaume; Martin, Juliette

    2016-01-01

    Terminal residues of protein chains are charged and more flexible than other residues since they are constrained only on one side. Do they play a particular role in protein-protein and protein-DNA interfaces? To answer this question, we considered large sets of non-redundant protein-protein and protein-DNA complexes and analyzed the status of terminal residues and their involvement in interfaces. In protein-protein complexes, we found that more than half of terminal residues (62%) are either modified by attachment of a tag peptide (10%) or have missing coordinates in the analyzed structures (52%). Terminal residues are almost exclusively located at the surface of proteins (94%). Contrary to charged residues, they are not over or under-represented in protein-protein interfaces, but strongly prefer the peripheral region of interfaces when present at the interface (83% of terminal residues). The almost exclusive location of terminal residues at the surface of the proteins or in the rim regions of interfaces explains that experimental methods relying on tail hybridization can be successfully applied without disrupting the complexes under study. Concerning conformational rearrangement in protein-protein complexes, despite their expected flexibility, terminal residues adopt similar locations between the free and bound forms of the docking benchmark. In protein-DNA complexes, N-terminal residues are twice more frequent than C-terminal residues at interfaces. Both N-terminal and C-terminal residues are under-represented in interfaces, in contrast to positively charged residues, which are strongly favored. When located in protein-DNA interfaces, terminal residues prefer the periphery. N-terminal and C-terminal residues thus have particular properties with regard to interfaces, which cannot be reduced to their charged nature. PMID:27611671

  17. Dynamics of strongly-coupled spiking neurons.

    PubMed

    Bressloff, P C; Coombes, S

    2000-01-01

    We present a dynamical theory of integrate-and-fire neurons with strong synaptic coupling. We show how phase-locked states that are stable in the weak coupling regime can destabilize as the coupling is increased, leading to states characterized by spatiotemporal variations in the interspike intervals (ISIs). The dynamics is compared with that of a corresponding network of analog neurons in which the outputs of the neurons are taken to be mean firing rates. A fundamental result is that for slow interactions, there is good agreement between the two models (on an appropriately defined timescale). Various examples of desynchronization in the strong coupling regime are presented. First, a globally coupled network of identical neurons with strong inhibitory coupling is shown to exhibit oscillator death in which some of the neurons suppress the activity of others. However, the stability of the synchronous state persists for very large networks and fast synapses. Second, an asymmetric network with a mixture of excitation and inhibition is shown to exhibit periodic bursting patterns. Finally, a one-dimensional network of neurons with long-range interactions is shown to desynchronize to a state with a spatially periodic pattern of mean firing rates across the network. This is modulated by deterministic fluctuations of the instantaneous firing rate whose size is an increasing function of the speed of synaptic response. PMID:10636934

  18. Inflationary magnetogenesis without the strong coupling problem

    SciTech Connect

    Ferreira, Ricardo J.Z.; Jain, Rajeev Kumar; Sloth, Martin S. E-mail: jain@cp3.dias.sdu.dk

    2013-10-01

    The simplest gauge invariant models of inflationary magnetogenesis are known to suffer from the problems of either large backreaction or strong coupling, which make it difficult to self-consistently achieve cosmic magnetic fields from inflation with a field strength larger than 10{sup −32}G today on the Mpc scale. Such a strength is insufficient to act as seed for the galactic dynamo effect, which requires a magnetic field larger than 10{sup −20}G. In this paper we analyze simple extensions of the minimal model, which avoid both the strong coupling and back reaction problems, in order to generate sufficiently large magnetic fields on the Mpc scale today. First we study the possibility that the coupling function which breaks the conformal invariance of electromagnetism is non-monotonic with sharp features. Subsequently, we consider the effect of lowering the energy scale of inflation jointly with a scenario of prolonged reheating where the universe is dominated by a stiff fluid for a short period after inflation. In the latter case, a systematic study shows upper bounds for the magnetic field strength today on the Mpc scale of 10{sup −13}G for low scale inflation and 10{sup −25}G for high scale inflation, thus improving on the previous result by 7-19 orders of magnitude. These results are consistent with the strong coupling and backreaction constraints.

  19. Systematic errors in strong lens modeling

    NASA Astrophysics Data System (ADS)

    Johnson, Traci Lin; Sharon, Keren; Bayliss, Matthew B.

    2015-08-01

    The lensing community has made great strides in quantifying the statistical errors associated with strong lens modeling. However, we are just now beginning to understand the systematic errors. Quantifying these errors is pertinent to Frontier Fields science, as number counts and luminosity functions are highly sensitive to the value of the magnifications of background sources across the entire field of view. We are aware that models can be very different when modelers change their assumptions about the parameterization of the lensing potential (i.e., parametric vs. non-parametric models). However, models built while utilizing a single methodology can lead to inconsistent outcomes for different quantities, distributions, and qualities of redshift information regarding the multiple images used as constraints in the lens model. We investigate how varying the number of multiple image constraints and available redshift information of those constraints (ex., spectroscopic vs. photometric vs. no redshift) can influence the outputs of our parametric strong lens models, specifically, the mass distribution and magnifications of background sources. We make use of the simulated clusters by M. Meneghetti et al. and the first two Frontier Fields clusters, which have a high number of multiply imaged galaxies with spectroscopically-measured redshifts (or input redshifts, in the case of simulated clusters). This work will not only inform upon Frontier Field science, but also for work on the growing collection of strong lensing galaxy clusters, most of which are less massive and are capable of lensing a handful of galaxies, and are more prone to these systematic errors.

  20. Diphotons, new vacuum angles, and strong CP

    NASA Astrophysics Data System (ADS)

    Draper, Patrick; McKeen, David

    2016-04-01

    The Standard Model contains a well-understood, natural, spin-0 diphoton resonance: the π 0. Numerous studies have pointed out that the hint of a new diphoton resonance at 750 GeV could be a pion analog, identified with the pseudo-Nambu-Goldstone boson of a chiral symmetry spontaneously broken by new strong dynamics at the TeV scale. These "hypercolor" models are generically expected to violate parity through a topological angle tilde{θ} . We discuss the physics of tilde{θ} and its impact on the phenomenology of the new sector. We also describe some of the theoretical implications of a nonzero tilde{θ} . In particular, tilde{θ} can generate an O(1) threshold correction to the QCD vacuum angle θ near the TeV scale, sharply constraining ultraviolet solutions to the strong CP problem. Alternatively, finding that tilde{θ} is small may be interpreted as evidence in favor of UV solutions to strong CP, particularly those based on spontaneously broken P or CP symmetries.

  1. A Strong Merger Shock in Abell 665

    NASA Astrophysics Data System (ADS)

    Dasadia, S.; Sun, M.; Sarazin, C.; Morandi, A.; Markevitch, M.; Wik, D.; Feretti, L.; Giovannini, G.; Govoni, F.; Vacca, V.

    2016-03-01

    Deep (103 ks) Chandra observations of Abell 665 have revealed rich structures in this merging galaxy cluster, including a strong shock and two cold fronts. The newly discovered shock has a Mach number of M = 3.0 ± 0.6, propagating in front of a cold disrupted cloud. This makes Abell 665 the second cluster, after the Bullet cluster, where a strong merger shock of M ≈ 3 has been detected. The shock velocity from jump conditions is consistent with (2.7 ± 0.7) × 103 km s-1. The new data also reveal a prominent southern cold front with potentially heated gas ahead of it. Abell 665 also hosts a giant radio halo. There is a hint of diffuse radio emission extending to the shock at the north, which needs to be examined with better radio data. This new strong shock provides a great opportunity to study the re-acceleration model with the X-ray and radio data combined.

  2. Cosmological test using strong gravitational lensing systems

    NASA Astrophysics Data System (ADS)

    Yuan, C. C.; Wang, F. Y.

    2015-09-01

    As one of the probes of universe, strong gravitational lensing systems allow us to compare different cosmological models and constrain vital cosmological parameters. This purpose can be reached from the dynamic and geometry properties of strong gravitational lensing systems, for instance, time-delay Δτ of images, the velocity dispersion σ of the lensing galaxies and the combination of these two effects, Δτ/σ2. In this paper, in order to carry out one-on-one comparisons between ΛCDM universe and Rh = ct universe, we use a sample containing 36 strong lensing systems with the measurement of velocity dispersion from the Sloan Lens Advanced Camera for Surveys (SLACS) and Lens Structure and Dynamic survey (LSD) survey. Concerning the time-delay effect, 12 two-image lensing systems with Δτ are also used. In addition, Monte Carlo simulations are used to compare the efficiency of the three methods as mentioned above. From simulations, we estimate the number of lenses required to rule out one model at the 99.7 per cent confidence level. Comparing with constraints from Δτ and the velocity dispersion σ, we find that using Δτ/σ2 can improve the discrimination between cosmological models. Despite the independence tests of these methods reveal a correlation between Δτ/σ2 and σ, Δτ/σ2 could be considered as an improved method of σ if more data samples are available.

  3. Strong convergence for reduced free products

    NASA Astrophysics Data System (ADS)

    Pisier, Gilles

    2016-06-01

    Using an inequality due to Ricard and Xu, we give a different proof of Paul Skoufranis’s recent result showing that the strong convergence of possibly non-commutative random variables X(k) → X is stable under reduced free product with a fixed non-commutative random variable Y. In fact we obtain a more general fact: assuming that the families X(k) = {X i(k)} and Y(k) = {Y j(k)} are ∗-free as well as their limits (in moments) X = {Xi} and Y = {Yj}, the strong convergences X(k) → X and Y(k) → Y imply that of {X(k),Y(k)} to {X,Y }. Phrased in more striking language: the reduced free product is “continuous” with respect to strong convergence. The analogue for weak convergence (i.e. convergence of all moments) is obvious. Our approach extends to the amalgamated free product, left open by Skoufranis.

  4. Spectral models of strongly inhomogeneous turbulence

    NASA Astrophysics Data System (ADS)

    Bragg, Andrew; Kurien, Susan; Clark, Timothy

    2015-11-01

    We compare results from a spectral model for inhomogeneous turbulence (Besnard et al., Theor. Comp. Fluid. Dyn., vol. 8, pp 1-35, 1996) with DNS data of a shear-free mixing layer (SFML) (Tordella et al., Phys. Rev. E, vol. 77, 016309, 2008). The SFML is used as a test case in which the efficacy of the model closure for the physical-space energy transport can be tested in a flow with strong inhomogeneity, without the additional complexity of mean-flow coupling. The model is able to capture certain features of the SFML quite well for intermediate to long-times, including the evolution of the mixing-layer width and turbulent kinetic energy. At short-times, and for more sensitive statistics such as the generation of the velocity field anisotropy, the model does not work so well. It may be argued that the discrepancy arises due to the local approximation to the intrinsically non-local pressure transport in physical-space, the effect of which would be particularly strong at short-times when the inhomogeneity of the SFML is strongest. Motivated by these results, we briefly discuss a new model that captures the non-local transport effects, for arbitrarily strong inhomogeneities of the flow.

  5. Strong CP, Flavor, and Twisted Split Fermions

    SciTech Connect

    Harnik, Roni; Perez, Gilad; Schwartz, Matthew D.; Shirman, Yuri

    2004-11-10

    We present a natural solution to the strong CP problem in the context of split fermions. By assuming CP is spontaneously broken in the bulk, a weak CKM phase is created in the standard model due to a twisting in flavor space of the bulk fermion wavefunctions. But the strong CP phase remains zero, being essentially protected by parity in the bulk and CP on the branes. As always in models of spontaneous CP breaking, radiative corrections to theta bar from the standard model are tiny, but even higher dimension operators are not that dangerous. The twisting phenomenon was recently shown to be generic, and not to interfere with the way that split fermions naturally weaves small numbers into the standard model. It follows that out approach to strong CP is compatible with flavor, and we sketch a comprehensive model. We also look at deconstructed version of this setup which provides a viable 4D model of spontaneous CP breaking which is not in the Nelson-Barr class.

  6. 77 FR 53212 - Notice of Proposed Information Collection: Comment Request Strong Cities Strong Communities...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-08-31

    ... Communities National Resource Network AGENCY: Office of the Assistant Secretary for Policy Development and... Proposal: Strong Cities Strong Communities National Resource Network. OMB Control Number, if applicable... National Resource Network. The U.S. Department of Housing and Urban Development Appropriations Act,...

  7. 77 FR 16131 - Establishing a White House Council on Strong Cities, Strong Communities

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-20

    ... From the Federal Register Online via the Government Publishing Office #0; #0; #0; Presidential Documents #0; #0; #0;#0;Federal Register / Vol. 77 , No. 54 / Tuesday, March 20, 2012 / Presidential Documents#0;#0; #0; #0;Title 3-- #0;The President ] Executive Order 13602 of March 15, 2012 Establishing a White House Council on Strong Cities, Strong Communities By...

  8. Prevention of strong earthquakes: Goal or utopia?

    NASA Astrophysics Data System (ADS)

    Mukhamediev, Sh. A.

    2010-11-01

    In the present paper, we consider ideas suggesting various kinds of industrial impact on the close-to-failure block of the Earth’s crust in order to break a pending strong earthquake (PSE) into a number of smaller quakes or aseismic slips. Among the published proposals on the prevention of a forthcoming strong earthquake, methods based on water injection and vibro influence merit greater attention as they are based on field observations and the results of laboratory tests. In spite of this, the cited proofs are, for various reasons, insufficient to acknowledge the proposed techniques as highly substantiated; in addition, the physical essence of these methods has still not been fully understood. First, the key concept of the methods, namely, the release of the accumulated stresses (or excessive elastic energy) in the source region of a forthcoming strong earthquake, is open to objection. If we treat an earthquake as a phenomenon of a loss in stability, then, the heterogeneities of the physicomechanical properties and stresses along the existing fault or its future trajectory, rather than the absolute values of stresses, play the most important role. In the present paper, this statement is illustrated by the classical examples of stable and unstable fractures and by the examples of the calculated stress fields, which were realized in the source regions of the tsunamigenic earthquakes of December 26, 2004 near the Sumatra Island and of September 29, 2009 near the Samoa Island. Here, just before the earthquakes, there were no excessive stresses in the source regions. Quite the opposite, the maximum shear stresses τmax were close to their minimum value, compared to τmax in the adjacent territory. In the present paper, we provide quantitative examples that falsify the theory of the prevention of PSE in its current form. It is shown that the measures for the prevention of PSE, even when successful for an already existing fault, can trigger or accelerate a catastrophic

  9. Gutzwiller approximation in strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Li, Chunhua

    Gutzwiller wave function is an important theoretical technique for treating local electron-electron correlations nonperturbatively in condensed matter and materials physics. It is concerned with calculating variationally the ground state wave function by projecting out multi-occupation configurations that are energetically costly. The projection can be carried out analytically in the Gutzwiller approximation that offers an approximate way of calculating expectation values in the Gutzwiller projected wave function. This approach has proven to be very successful in strongly correlated systems such as the high temperature cuprate superconductors, the sodium cobaltates, and the heavy fermion compounds. In recent years, it has become increasingly evident that strongly correlated systems have a strong propensity towards forming inhomogeneous electronic states with spatially periodic superstrutural modulations. A good example is the commonly observed stripes and checkerboard states in high- Tc superconductors under a variety of conditions where superconductivity is weakened. There exists currently a real challenge and demand for new theoretical ideas and approaches that treats strongly correlated inhomogeneous electronic states, which is the subject matter of this thesis. This thesis contains four parts. In the first part of the thesis, the Gutzwiller approach is formulated in the grand canonical ensemble where, for the first time, a spatially (and spin) unrestricted Gutzwiller approximation (SUGA) is developed for studying inhomogeneous (both ordered and disordered) quantum electronic states in strongly correlated electron systems. The second part of the thesis applies the SUGA to the t-J model for doped Mott insulators which led to the discovery of checkerboard-like inhomogeneous electronic states competing with d-wave superconductivity, consistent with experimental observations made on several families of high-Tc superconductors. In the third part of the thesis, new

  10. Dietary Proteins

    MedlinePlus

    ... grains and beans. Proteins from meat and other animal products are complete proteins. This means they supply all of the amino acids the body can't make on its own. Most plant proteins are incomplete. You should eat different types of plant proteins every day to get ...

  11. Protein Analysis

    NASA Astrophysics Data System (ADS)

    Chang, Sam K. C.

    Proteins are an abundant component in all cells, and almost all except storage proteins are important for biological functions and cell structure. Food proteins are very complex. Many have been purified and characterized. Proteins vary in molecular mass, ranging from approximately 5000 to more than a million Daltons. They are composed of elements including hydrogen, carbon, nitrogen, oxygen, and sulfur. Twenty α-amino acids are the building blocks of proteins; the amino acid residues in a protein are linked by peptide bonds. Nitrogen is the most distinguishing element present in proteins. However, nitrogen content in various food proteins ranges from 13.4 to 19.1% (1) due to the variation in the specific amino acid composition of proteins. Generally, proteins rich in basic amino acids contain more nitrogen.

  12. Strong electron correlation and nonlinear optics

    NASA Astrophysics Data System (ADS)

    Ghosh, Haranath

    2012-07-01

    Based on experimental and theoretical research during the last decade, giant optical nonlinearities found in Mott-Hubbard insulators like Sr2CuO3,Ca2CuO3, Nickel halides ([Ni(chxn)2X]X2 where X = Br, Cl and `chxn' refers to cyclohexanediamine) are presented. These materials are reported to be potential materials for all optical switching devices. The occurrence of nearly degenerate lowest one- and two-photon states, strong Coulomb correlation and strong dipole coupling between the one- and two-photon states are believed to be the reason for such colossal optical nonlinearities in these systems. In some of these materials (at least), the two photon state is below the one-photon state. This leads to the possibility that such material can be excited to the lowest optical state by shinning laser of suitable wavelength, the populations thus generated decays to the two-photon state at ultrafast short time. Thus nonlinear measurements can be made from an excited state (we call as excited state nonlinear optical properties). One dimensional strongly correlated materials are predicted to have several orders-of-magnitude larger excited state optical non-linearities in comparison to that from the ground state, in the wavelength region suitable for terahertz communications. A large number of measurable nonlinear optical properties like Two Photon absorption, Photo induced absorption, Third Harmonic generation, Stimulated Raman Scattering are obtained theoretically and compared with available experimental observations. Then a large number excited state nonlinear optical properties are predicted which are experimentally measurable. We emphasize that the mechanism of nonlinear optics in one dimensional Mott-Hubbard insulators is different from that of the π-conjugated polymers — in the former spin excitation play an important role. We argue from detailed understanding of nonlinear optics of π-conjugated systems that some features in the Third Harmonic Generation

  13. (1+2)-dimensional strongly nonlocal solitons

    SciTech Connect

    Ouyang Shigen; Guo Qi

    2007-11-15

    Approximate solutions of (1+2)-dimensional strongly nonlocal solitons (SNSs) are presented. It is shown that the power of a SNS in a nematic liquid crystal is in direct proportion to the second power of the degree of nonlocality, the power of a SNS in a nonlocal medium with a logarithmic nonlocal response is in inverse proportion to the second power of its beamwidth, and the power of a SNS in a nonlocal medium with an sth-power decay nonlocal response is in direct proportion to the (s+2)th power of the degree of nonlocality.

  14. Bose Polarons in the Strongly Interacting Regime.

    PubMed

    Hu, Ming-Guang; Van de Graaff, Michael J; Kedar, Dhruv; Corson, John P; Cornell, Eric A; Jin, Deborah S

    2016-07-29

    When an impurity is immersed in a Bose-Einstein condensate, impurity-boson interactions are expected to dress the impurity into a quasiparticle, the Bose polaron. We superimpose an ultracold atomic gas of ^{87}Rb with a much lower density gas of fermionic ^{40}K impurities. Through the use of a Feshbach resonance and radio-frequency spectroscopy, we characterize the energy, spectral width, and lifetime of the resultant polaron on both the attractive and the repulsive branches in the strongly interacting regime. The width of the polaron in the attractive branch is narrow compared to its binding energy, even as the two-body scattering length diverges. PMID:27517776

  15. Thermalization of Strongly Coupled Field Theories

    SciTech Connect

    Balasubramanian, V.; Bernamonti, A.; Copland, N.; Craps, B.; Staessens, W.; Boer, J. de; Keski-Vakkuri, E.; Mueller, B.; Schaefer, A.; Shigemori, M.

    2011-05-13

    Using the holographic mapping to a gravity dual, we calculate 2-point functions, Wilson loops, and entanglement entropy in strongly coupled field theories in d=2, 3, and 4 to probe the scale dependence of thermalization following a sudden injection of energy. For homogeneous initial conditions, the entanglement entropy thermalizes slowest and sets a time scale for equilibration that saturates a causality bound. The growth rate of entanglement entropy density is nearly volume-independent for small volumes but slows for larger volumes. In this setting, the UV thermalizes first.

  16. Thermalization of strongly coupled field theories.

    PubMed

    Balasubramanian, V; Bernamonti, A; de Boer, J; Copland, N; Craps, B; Keski-Vakkuri, E; Müller, B; Schäfer, A; Shigemori, M; Staessens, W

    2011-05-13

    Using the holographic mapping to a gravity dual, we calculate 2-point functions, Wilson loops, and entanglement entropy in strongly coupled field theories in d=2, 3, and 4 to probe the scale dependence of thermalization following a sudden injection of energy. For homogeneous initial conditions, the entanglement entropy thermalizes slowest and sets a time scale for equilibration that saturates a causality bound. The growth rate of entanglement entropy density is nearly volume-independent for small volumes but slows for larger volumes. In this setting, the UV thermalizes first. PMID:21668141

  17. SENTINEL-1 Image Matching Using Strong Scatters

    NASA Astrophysics Data System (ADS)

    Ghannadi, M. A.; Saadatseresht, M.; Motagh, M.

    2015-12-01

    The availability of new radar spaceborne sensors offers new interesting potentialities for the geomatics application: spatial and temporal change detection, generation of Digital Elevation Model(DEM) using radargrametry and interferometry. Since the start of the sentinel-1 mission to take images from different regions all over the world, the ability to use these images in variety domains has been treasured. This paper suggests a method for image matching using strong scatters. all the experiments are done on sentinel-1 stereo images from Jam, Bushehr, Iran.

  18. Fundamental Structure of Matter and Strong Interaction

    SciTech Connect

    Jian-Ping Chen

    2011-11-01

    More than 99% of the visible matter in the universe are the protons and neutrons. Their internal structure is mostly governed by the strong interaction. Understanding their internal structure in terms of fundamental degrees-of-freedom is one of the most important subjects in modern physics. Worldwide efforts in the last few decades have lead to numerous surprises and discoveries, but major challenges still remain. An overview of the progress will be presented with a focus on the recent studies of the proton and neutron's electromagnetic and spin structure. Future perspectives will be discussed.

  19. Strong correlations in actinide redox reactions

    NASA Astrophysics Data System (ADS)

    Horowitz, S. E.; Marston, J. B.

    2011-02-01

    Reduction-oxidation (redox) reactions of the redox couples An(VI)/An(V), An(V)/An(IV), and An(IV)/An(III), where An is an element in the family of early actinides (U, Np, and Pu), as well as Am(VI)/Am(V) and Am(V)/Am(III), are modeled by combining density functional theory with a generalized Anderson impurity model that accounts for the strong correlations between the 5f electrons. Diagonalization of the Anderson impurity model yields improved estimates for the redox potentials and the propensity of the actinide complexes to disproportionate.

  20. Bose polarons in the strongly interacting regime

    NASA Astrophysics Data System (ADS)

    Hu, Ming-Guang; van de Graaff, Michael; Kedar, Dhruv; Cornell, Eric; Jin, Deborah

    Impurities immersed in and interacting with a Bose-Einstein condensate (BEC) are predicted to form quasiparticle excitations called Bose polarons. I will present experimental evidence of Bose polarons in cold atoms obtained using radio-frequency spectroscopy to measure the excitation spectrum of fermionic 40K impurities interacting with a BEC of 87Rb atoms. We use an interspecies Feshbach resonance to tune the interactions between the impurities and the bosons, and we take data in the strongly interacting regime. This work is supported by NSF, NASA and NIST.

  1. Obama Indicates Strong Support for Science

    NASA Astrophysics Data System (ADS)

    Showstack, Randy

    2009-05-01

    In remarks delivered at the U.S. National Academy of Sciences (NAS) annual meeting on 27 April, U.S. President Barack Obama indicated his administration's strong support for science and for pursuing a clean energy economy. He also announced a goal that the United States “will devote more than 3% of our [gross domestic product] to research and development.” “This represents the largest commitment to scientific research and innovation in American history,” Obama said, noting that the American Recovery and Reinvestment Act already is providing the nation with its largest single boost to investment in basic research.

  2. Empirical prediction of strong ground motion

    USGS Publications Warehouse

    Boore, David M.; Joyner, William B.

    1993-01-01

    In 1982, we published equations for the prediction of various measures of ground motion as a function of earthquake magnitude, distance from the earthquake rupture, and site geology. Many more strong-motion recordings have been obtained since we published our equations. The predictions of the ground motions from our published equations are in reasonable agreement with the peak accelerations from the new data. The increased number of data, however, allow us to refine our predictions for some regions of magnitude and distance space, and perhaps for other variables.

  3. Generation of strong MHD Alfvenic turbulence

    NASA Technical Reports Server (NTRS)

    Akimoto, K.; Winske, D.

    1990-01-01

    Strong Alfvenic turbulence containing a number of solitonlike structures propagating at super-Alfvenic speeds is generated self-consistently and studied by means of computer simulation. A one-dimensional hybrid (kinetic ions, fluid electrons) code is used to investigate the nonlinear evolution of an electromagnetic ion-beam instability that generates low-frequency Alfven-like waves. As the instability develops, the field-aligned hydromagnetic waves steepen, forming a soliton that bifurcates several times, leading to a fully turbulent state.

  4. A geodesic principle for strong coupling gravity

    NASA Astrophysics Data System (ADS)

    Niedermaier, Max

    2015-11-01

    Strong coupling gravity arises from general relativity by a scaling limit that preserves the number of physical degrees of freedom as well as covariance under the group of spatio-temporal diffeomorphisms. An intrinsic geodesic principle for it is formulated and justified. Geodesic congruences and the test bodies following them are, according to the principle, unaffected by nonlinear gravitational waves and can be gauged-fixed so as to never depart from their initial values. Among other consequences this offers a new perspective on gravitational coarse graining.

  5. Classical scattering in strongly attractive potentials

    NASA Astrophysics Data System (ADS)

    Khrapak, S. A.

    2014-03-01

    Scattering in central attractive potentials is investigated systematically, in the limit of strong interaction, when large-angle scattering dominates. In particular, three important model interactions (Lennard-Jones, Yukawa, and exponential), which are qualitatively different from each other, are studied in detail. It is shown that for each of these interactions the dependence of the scattering angle on the properly normalized impact parameter exhibits a quasiuniversal behavior. This implies simple scaling of the transport cross sections with energy in the considered limit. Accurate fits for the momentum transfer cross section are suggested. Applications of the obtained results are discussed.

  6. Development of a strong electromagnet wiggler

    SciTech Connect

    Burns, M.J.; Deis, G.A.; Holmes, R.H.; Van Maren, R.D.; Halbach, K.

    1987-01-01

    The Strong Electromagnet (SEM) wiggler is a permanent magnet-assisted electromagnet under development at the Lawrence Livermore National Laboratory (LLNL) as part of the Induction Linac Free-Electron-Laser (IFEL) program. This concept uses permanent magnets within the wiggler to provide a reverse bias flux in the iron and thus delay the onset of magnetic saturation. The electromagnet coils determine the wiggler field and operate at low current densities by virtue of their placement away from the midplane. We describe here the design approach used and test data from a 7-period wiggler prototype that includes curved pole tips to provide wiggle-plane focusing. 7 refs.

  7. Classical scattering in strongly attractive potentials.

    PubMed

    Khrapak, S A

    2014-03-01

    Scattering in central attractive potentials is investigated systematically, in the limit of strong interaction, when large-angle scattering dominates. In particular, three important model interactions (Lennard-Jones, Yukawa, and exponential), which are qualitatively different from each other, are studied in detail. It is shown that for each of these interactions the dependence of the scattering angle on the properly normalized impact parameter exhibits a quasiuniversal behavior. This implies simple scaling of the transport cross sections with energy in the considered limit. Accurate fits for the momentum transfer cross section are suggested. Applications of the obtained results are discussed. PMID:24730827

  8. Dynamical simulations of strongly correlated electron materials

    NASA Astrophysics Data System (ADS)

    Kress, Joel; Barros, Kipton; Batista, Cristian; Chern, Gia-Wei; Kotliar, Gabriel

    We present a formulation of quantum molecular dynamics that includes electron correlation effects via the Gutzwiller method. Our new scheme enables the study of the dynamical behavior of atoms and molecules with strong electron interactions. The Gutzwiller approach goes beyond the conventional mean-field treatment of the intra-atomic electron repulsion and captures crucial correlation effects such as band narrowing and electron localization. We use Gutzwiller quantum molecular dynamics to investigate the Mott transition in the liquid phase of a single-band metal and uncover intriguing structural and transport properties of the atoms.

  9. Bose Polarons in the Strongly Interacting Regime

    NASA Astrophysics Data System (ADS)

    Hu, Ming-Guang; Van de Graaff, Michael J.; Kedar, Dhruv; Corson, John P.; Cornell, Eric A.; Jin, Deborah S.

    2016-07-01

    When an impurity is immersed in a Bose-Einstein condensate, impurity-boson interactions are expected to dress the impurity into a quasiparticle, the Bose polaron. We superimpose an ultracold atomic gas of 87Rb with a much lower density gas of fermionic 40 impurities. Through the use of a Feshbach resonance and radio-frequency spectroscopy, we characterize the energy, spectral width, and lifetime of the resultant polaron on both the attractive and the repulsive branches in the strongly interacting regime. The width of the polaron in the attractive branch is narrow compared to its binding energy, even as the two-body scattering length diverges.

  10. Strongly nonlinear magnetosonic waves and ion acceleration

    SciTech Connect

    Rau, B.; Tajima, T.

    1997-11-01

    The electromagnetic fields associated with a nonlinear compressional Alfven wave propagating perpendicular to an external magnetic field of arbitrary strength are derived. For the strongly magnetized and high phase velocity case relevant for ion acceleration to high energies, we show that the electric field increases proportionally only to the external magnetic field O (B{sub ext}[in T] MV/cm) and the electrostatic potential increases with the square root of the ion-to-electron mass ratio {radical}M{sub i}/m{sub e}.

  11. Fractional effective action at strong electromagnetic fields

    NASA Astrophysics Data System (ADS)

    Kleinert, Hagen; Strobel, Eckhard; Xue, She-Sheng

    2013-07-01

    In 1936, Weisskopf [K. Dan. Vidensk. Selsk. Mat. Fys. Medd. XIV (1936)] showed that for vanishing electric or magnetic fields the strong-field behavior of the one-loop Euler-Heisenberg effective Lagrangian of quantum electro dynamics (QED) is logarithmic. Here we generalize this result for different limits of the Lorentz invariants E→2-B→2 and B→·E→. The logarithmic dependence can be interpreted as a lowest-order manifestation of an anomalous power behavior of the effective Lagrangian of QED, with critical exponents δ=e2/(12π) for spinor QED, and δS=δ/4 for scalar QED.

  12. Oriented fibrin gels formed by polymerization in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Torbet, J.

    1981-01-01

    Fibrinogen is a soluble plasma protein which, after cleavage by the specific proteolytic enzyme thrombin, polymerizes to form the filamentous fibrin network during blood clotting (see refs 1 and 2 for reviews). Fibrinogen has a molecular weight of 340,000 and is composed of two identical halves, each containing three peptide chains designated Aα, Bβ and γ. Fibrin monomers are produced by thrombin which releases the small negatively charged fibrinopeptides A and B. The overall shape of the fibrinogen molecule has not been unequivocally established1,2. The trinodular, elongated (~450 Å long) structure proposed by Hall and Slayter3 is the most widely accepted model and it has obtained additional support from recent work4-6. Fibrin monomers are also about 450 Å long7 and in fibres they probably have a half-staggered arrangement along the axis7,8. The fibres are an assembly of protofibrils whose structure and packing are not reliably known. We report here that highly oriented fibrin gels are formed when polymerization takes place slowly in a strong magnetic field. It is shown that the protofibrils pack into a three-dimensional crystalline lattice. We introduce magnetically induced birefringence as a potential tool for studying polymerization and briefly speculate on the applications of strong magnetic fields.

  13. Indoor concentration modeling of aerosol strong acidity

    SciTech Connect

    Zelenka, M.; Waldman, J.; Suh, H.; Koutrakis, P.

    1993-01-01

    A model for estimating indoor concentrations of acid aerosol was applied to data collected during the summer of 1989, in a densely populated location in New Jersey. The model, from a study of a semi-rural community in Pennsylvania, was used to estimate indoor concentrations of aerosol strong acidity (H+) at an elderly care residence in suburban New Jersey. The purpose of the present work is to assess the applicability of the model for predicting H+ exposures in a suburban environment and to evaluate the models performance for daytime and nighttime periods. Indoor and outdoor samples were taken at an elderly care home between June 20 and July 30, 1989. The indoor and outdoor monitoring schedule collected two 12-h samples per day. Samples were taken with the Indoor Denuder Sampler (IDS). Samples were analyzed for indoor and outdoor concentrations of aerosol strong acidity (H+), ammonia (NH3), and anion determination. The model generally underestimated the indoor H+ concentration. Slight improvement was seen in the model estimate of H+ for the nighttime period (7:00 pm to 7:00 am, local time). The model applied to the site in New Jersey did not predict the indoor H+ concentrations as well as it did for the experiment from which it was developed.

  14. Cold Rydberg atoms in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Guest, J. R.; Choi, J.-H.; Povilus, A.; Raithel, G.

    2003-05-01

    The combination of laser-cooling and trapping methods with Rydberg-atom spectroscopy has opened the door to the study of novel ultracold atomic and plasma systems. In particular, the study of Rydberg atoms in strong magnetic fields, which has previously been restricted to optically accessible low azimuthal quantum numbers |m|, has been expanded to include high azimuthal quantum numbers |m| through new collisional and recombinative processes which can play a role in this regime. We describe our efforts to realize this new regime experimentally with a superconducting atom and plasma trap. In theoretical work, we have implemented an efficient method to calculate the spectra of Rydberg atoms in strong magnetic fields. We use adiabatic basis sets that reflect the disparate time scales of the electronic motion parallel and transverse to the magnetic field. We find that, with increasing absolute value of |m|, non-adiabatic corrections become negligible, the adiabatic basis states and their energies become exact solutions, and the level statistics evolve from a Wigner to a Possonian distribution of the nearest-neighbor energy separations. The analogy between the adiabatically separable regime of large |m| and the behavior of charged particles in Penning traps will be discussed.

  15. Relativistically strong electromagnetic radiation in a plasma

    NASA Astrophysics Data System (ADS)

    Bulanov, S. V.; Esirkepov, T. Zh.; Kando, M.; Kiriyama, H.; Kondo, K.

    2016-03-01

    Physical processes in a plasma under the action of relativistically strong electromagnetic waves generated by high-power lasers have been briefly reviewed. These processes are of interest in view of the development of new methods for acceleration of charged particles, creation of sources of bright hard electromagnetic radiation, and investigation of macroscopic quantum-electrodynamical processes. Attention is focused on nonlinear waves in a laser plasma for the creation of compact electron accelerators. The acceleration of plasma bunches by the radiation pressure of light is the most efficient regime of ion acceleration. Coherent hard electromagnetic radiation in the relativistic plasma is generated in the form of higher harmonics and/or electromagnetic pulses, which are compressed and intensified after reflection from relativistic mirrors created by nonlinear waves. In the limit of extremely strong electromagnetic waves, radiation friction, which accompanies the conversion of radiation from the optical range to the gamma range, fundamentally changes the behavior of the plasma. This process is accompanied by the production of electron-positron pairs, which is described within quantum electrodynamics theory.

  16. Emergent quasicrystals in strongly correlated systems

    NASA Astrophysics Data System (ADS)

    Sagi, Eran; Nussinov, Zohar

    2016-07-01

    Commensurability is of paramount importance in numerous strongly interacting electronic systems. In the fractional quantum Hall effect, a rich cascade of increasingly narrow plateaux appear at larger denominator filling fractions. Rich commensurate structures also emerge, at certain filling fractions, in high temperature superconductors and other electronic systems. A natural question concerns the character of these and other electronic systems at irrational filling fractions. Here we demonstrate that quasicrystalline structures naturally emerge in these situations, and trigger behaviors not typically expected of periodic systems. We first show that irrationally filled quantum Hall systems cross over into quasiperiodically ordered configuration in the thin-torus limit. Using known properties of quasicrystals, we argue that these states are unstable against the effects of disorder, in agreement with the existence of quantum Hall plateaux. We then study analogous physical situations in a system of cold Rydberg atoms placed on an optical lattice. Such an experimental setup is generally disorder free, and can therefore be used to detect the emergent quasicrystals we predict. We discuss similar situations in the Falicov-Kimball model, where known exact results can be used to establish quasicrystalline structures in one and two dimensions. We briefly speculate on possible relations between our theoretical findings and the existence of glassy dynamics and other features of strongly correlated electronic systems.

  17. Multi-ion equilibrium with strong rotation

    NASA Astrophysics Data System (ADS)

    Galeotti, L.; Barnes, D. C.; Ceccherini, F.; Pegoraro, F.

    2010-11-01

    We describe a new formulation of the multiple ion species, quasi-neutral, axisymmetric equilibrium problem which includes the possibility of strong (sonic or supersonic) rotation about the geometric axis. This new work is more applicable to well confined, hot plasmas. In contrast to previous related work [1.2] which considered steady states with arbitrary isentropic mass flow, we impose the physically more realistic constraints of uniform temperature and negligible poloidal mass flow. It is shown that there exist three surface functions which are related by a single ordinary differential equation (per species), leaving two surface functions per species. These may be taken to be T and Ω for each species. Equilibria have been obtained by the LR/eq MI code which simultaneously solves a set of 2+3 Ni (where Ni is the number of ion species) nonlinear equations at each point, along with Ampere's law and very flexible boundary conditions. Along with the derivation of the model and profiles, some examples of D-T low aspect, elongated tokamak equilibria with and without strong toroidal rotation are given. [4pt] [1] L. C. Steinhauer, {Phys. Plasmas} {6}, 2734 (1999). [0pt] [2] J. P. Goedbloed, {Phys. Plasmas} {11}, 81 (2004).

  18. Axions and the strong CP problem

    SciTech Connect

    Kim, Jihn E.; Carosi, Gianpaolo

    2010-01-15

    Current upper bounds on the neutron electric dipole moment constrain the physically observable quantum chromodynamic (QCD) vacuum angle |{theta}|(less-or-similar sign)10{sup -11}. Since QCD explains a great deal of experimental data from the 100 MeV to the TeV scale, it is desirable to explain this smallness of |{theta}| in the QCD framework; this is the strong CP problem. There now exist two plausible solutions to this problem, one of which leads to the existence of a very light axion. The axion decay constant window, 10{sup 9}(less-or-similar sign)F{sub a}(less-or-similar sign)10{sup 12} GeV for an O(1) initial misalignment angle {theta}{sub 1}, has been obtained from astrophysical and cosmological data. For F{sub a}(greater-or-similar sign)10{sup 12} GeV with {theta}{sub 1}strong CP problem introduces its superpartner the axino, which might have affected the evolution of the Universe significantly. The very light axion (theory, supersymmetrization, and models) using recent particle, astrophysical, and cosmological data, and present prospects for its discovery is reviewed here.

  19. Low energy strong electroweak sector with decoupling

    SciTech Connect

    Casalbuoni, R.; Dominici, D. |; Deandrea, A.; Gatto, R.; De Curtis, S.; Grazzini, M. |

    1996-05-01

    We discuss possible symmetries of effective theories describing spinless and spin-1 bosons, mainly to concentrate on an intriguing phenomenological possibility: that of a hardly noticeable strong electroweak sector at relatively low energies. Specifically, a model with both vector and axial vector strong interacting bosons may possess a discrete symmetry imposing degeneracy of the two sets of bosons (degenerate BESS model). In such a case its effects at low energies become almost invisible and the model easily passes all low energy precision tests. The reason lies essentially in the fact that the model automatically satisfies decoupling, contrary to models with only vectors. For large mass of the degenerate spin-one bosons the model becomes identical at the classical level to the standard model taken in the limit of infinite Higgs boson mass. For these reasons we have thought it worthwhile to fully develop the model, together with its possible generalizations, and to study the expected phenomenology. For instance, just because of its invisibility at low energy, it is conceivable that degenerate BESS has low mass spin-one states and gives quite visible signals at existing or forthcoming accelerators. {copyright} {ital 1996 The American Physical Society.}

  20. The Athens Acropolis Strong Motion Array

    NASA Astrophysics Data System (ADS)

    Kalogeras, I. S.; Evangelidis, C. P.; Melis, N. S.; Boukouras, K.

    2012-04-01

    During the last decades, extensive restoration works through a dedicated "Acropolis Restoration Service" (YSMA) take place in the Acropolis, the greatest sanctuary of ancient Athens. Since 2008, a permanent strong motion array was deployed by the Institute of Geodynamics, National Observatory of Athens (NOA-IG) in collaboration with YSMA. Free field installations were decided at sites showing various characteristics, aiming to investigate differences in geotechnical properties as well as the structure response of Parthenon itself. The installation phase is presented, with the techniques used to overcome difficulties (i.e. extreme weather conditions, power and communication limitations, restoration works and visitors) and the special care taken for the specific archaeological site. Furthermore, indicative examples of seismic events recorded by the array are analyzed and the complexity of the hill and the monument is made apparent. Among them, the long distance events of Tohoku, Japan 2010 and Van, Turkey 2011, some regional moderate earthquakes in Greece and some weak earthquakes from the vicinity. Continuous ambient noise monitoring using PQLX software gives some first indicative results, showing a variety of characteristics at installation sites. Finally, further developments and future steps are presented such as: the extension of the array, the integration of seismic data within the GIS platform of YSMA at the site and the use of strong motion records, in conjunction with data from other monitoring systems operating in Acropolis for the study of specific monuments.

  1. STRONG FIELD PHYSICS WITH MID INFRARED LASERS.

    SciTech Connect

    POGORELSKY,I.V.

    2001-08-27

    Mid-infrared gas laser technology promises to become a unique tool for research in strong-field relativistic physics. The degree to which physics is relativistic is determined by a ponderomotive potential. At a given intensity, a 10 {micro}m wavelength CO{sub 2} laser reaches a 100 times higher ponderomotive potential than the 1 {micro}m wavelength solid state lasers. Thus, we can expect a proportional increase in the throughput of such processes as laser acceleration, x-ray production, etc. These arguments have been confirmed in proof-of-principle Thomson scattering and laser acceleration experiments conducted at BNL and UCLA where the first terawatt-class CO{sub 2} lasers are in operation. Further more, proposals for the 100 TW, 100 fs CO{sub 2} lasers based on frequency-chirped pulse amplification have been conceived. Such lasers can produce physical effects equivalent to a hypothetical multi-petawatt solid state laser. Ultra-fast mid-infrared lasers will open new routes to the next generation electron and ion accelerators, ultra-bright monochromatic femtosecond x-ray and gamma sources, allow to attempt the study of Hawking-Unruh radiation, and explore relativistic aspects of laser-matter interactions. We review the present status and experiments with terawatt-class CO{sub 2} lasers, sub-petawatt projects, and prospective applications in strong-field science.

  2. Ionization degree for strong evaporation of metals

    SciTech Connect

    Gusarov, Andrey V.; Aoki, Kazuo

    2005-08-15

    Kinetic equations for ions and neutrals are numerically solved in the plasma sheath formed at a condensed phase when strong evaporation is taking place. The Boltzmann distribution is assumed for electrons. A weakly ionized vapor with the Debye length much shorter than the mean free path is considered. This is typical for laser evaporation of metals. Under these conditions, the sheath consists of a Knudsen layer and a thin charge separation layer between the Knudsen layer and the condensed phase. The self-consistent electrostatic field in the Knudsen layer is obtained from the quasineutrality condition. The potential barrier in the charge separation layer is determined by the charge balance. Kinetic boundary conditions for neutrals and charges are estimated by the detailed balance principle from the parameters of the saturated vapor. The transport of charges in the sheath is controlled by ions and depends on ion-neutral collisions and the self-consistent electrostatic field. Ionization degree in the vapor formed by strong evaporation increases with the Mach number and can attain values about 30% higher than the ionization degree in the saturated vapor. Two factors contribute to this increase. The first is the drop of the potential barrier in the charge separation layer and the second is the strengthening of the field in the Knudsen layer. The ionization equilibrium may be disturbed by a considerable excess of charges.

  3. The thermoelectric properties of strongly correlated systems

    NASA Astrophysics Data System (ADS)

    Cai, Jianwei

    Strongly correlated systems are among the most interesting and complicated systems in physics. Large Seebeck coefficients are found in some of these systems, which highlight the possibility for thermoelectric applications. In this thesis, we study the thermoelectric properties of these strongly correlated systems with various methods. We derived analytic formulas for the resistivity and Seebeck coefficient of the periodic Anderson model based on the dynamic mean field theory. These formulas were possible as the self energy of the single impurity Anderson model could be given by an analytic ansatz derived from experiments and numerical calculations instead of complicated numerical calculations. The results show good agreement with the experimental data of rare-earth compound in a restricted temperature range. These formulas help to understand the properties of periodic Anderson model. Based on the study of rare-earth compounds, we proposed a design for the thermoelectric meta-material. This manmade material is made of quantum dots linked by conducting linkers. The quantum dots act as the rare-earth atoms with heavier mass. We set up a model similar to the periodic Anderson model for this new material. The new model was studied with the perturbation theory for energy bands. The dynamic mean field theory with numerical renormalization group as the impurity solver was used to study the transport properties. With these studies, we confirmed the improved thermoelectric properties of the designed material.

  4. Electrodynamics of strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Dordevic, Sasa V.

    2002-09-01

    In this thesis we study a variety of condensed matter systems with strongly correlated electrons, i.e. systems in which the electron-electron interactions cannot be ignored like in conventional metals, (gold, aluminum, copper, etc.). Infrared spectroscopy has proven to be a powerful tool for studying such systems. The latter experimental technique probes all excitations is solids that have a dipole moment associated with them, such as gap excitations, interband transitions, phonons, polarons, magnons etc. Strong electron correlations lead to a variety of interesting physical phenomena at low temperatures. In copper ox ides superconductivity sets in below an unprecedently high critical temperature, Tc. The mechanism of this unusual phenomenon is still unclear. In this thesis we discuss energy scales from which the superconducting condensate is collected and the response of cuprates to an external magnetic field applied parallel to the CuO2 planes. In so-called heavy fermion metals a coherent ground state develops at low temperatures where the electrons appear to have large effective mass, typically 50--1,000 free electron masses. We show that magnetic interactions play an important role for the mass renormalization in heavy fermion metals. In transition metal dichalcogenides reduced dimensionality of the electron gas leads to significant anisotropy of the electron-phonon interaction.

  5. An adaptive SPH method for strong shocks

    NASA Astrophysics Data System (ADS)

    Sigalotti, Leonardo Di G.; López, Hender; Trujillo, Leonardo

    2009-09-01

    We propose an alternative SPH scheme to usual SPH Godunov-type methods for simulating supersonic compressible flows with sharp discontinuities. The method relies on an adaptive density kernel estimation (ADKE) algorithm, which allows the width of the kernel interpolant to vary locally in space and time so that the minimum necessary smoothing is applied in regions of low density. We have performed a von Neumann stability analysis of the SPH equations for an ideal gas and derived the corresponding dispersion relation in terms of the local width of the kernel. Solution of the dispersion relation in the short wavelength limit shows that stability is achieved for a wide range of the ADKE parameters. Application of the method to high Mach number shocks confirms the predictions of the linear analysis. Examples of the resolving power of the method are given for a set of difficult problems, involving the collision of two strong shocks, the strong shock-tube test, and the interaction of two blast waves.

  6. Survival of atoms in strong microwave fields

    NASA Astrophysics Data System (ADS)

    Arakelyan, Alexandr; Gallagher, Thomas F.

    2014-05-01

    Recent experimental work on the ionization of atoms by intense laser and microwave fields has shown that bound atoms in highly excited states remain after the intense radiation pulse, even though the orbital period of the detected atoms exceeds the duration of the laser or microwave pulse. In both cases the fields are orders of magnitude larger than required for static field ionization of the highly excited atoms. Here we report a large population (10-25%) left bound in the states with n >350, when atoms are exposed to strong 16.9-GHz microwave fields in the presence of a well-controlled static field of 6 mV/cm. A production of such extremely high lying states is observed for a wide range of initial Rydberg states, as low as n = 21, for Li and Na, and is, in fact, a general feature of microwave ionization. As well as the survival of the highly excited states in quasi stable orbits, threshold ionization fields also appear to depend strongly on the static field during the experiment. We observe the 1/3n5 dependence only if the static fields are non-zero, and larger fields are required to ionize 50% of atoms if the static field is canceled out.

  7. Efimov correlations in strongly interacting Bose gases

    NASA Astrophysics Data System (ADS)

    Hofmann, Johannes; Barth, Marcus

    A series of recent hallmark experiments have demonstrated that Bose gases can be created in the strongly interacting unitary limit in the non-degenerate high-temperature regime. These systems display the three-body Efimov effect, which poses a theoretical challenge to compute observables including these relevant three-body correlations. In this talk, I shall present our results for the virial coefficients, the contact parameters, and the momentum distribution of a strongly interacting three-dimensional Bose gas obtained by means of a virial expansion up to third order in the fugacity, which takes into account three-body correlations exactly. Our results characterize the non-degenerate regime of the interacting Bose gas, where the thermal wavelength is smaller than the interparticle spacing but the scattering length may be arbitrarily large. In addition, we provide a calculation of the momentum distribution at unitarity, which displays a universal high-momentum tail with a log-periodic momentum dependence - a direct signature of Efimov physics. In particular, we provide a quantitative description of the momentum distribution at high momentum as measured by the JILA group [Makotyn et al., Nat. Phys. 10, 116 (2014)]. Our results allow the spectroscopy of Efimov states at unitarity.

  8. Strongly coupled quark gluon plasma (SCQGP)

    NASA Astrophysics Data System (ADS)

    Bannur, Vishnu M.

    2006-07-01

    We propose that the reason for the non-ideal behaviour seen in lattice simulation of quark gluon plasma (QGP) and ultrarelativistic heavy ion collision experiments is that the QGP near Tc and above is a strongly coupled plasma (SCP), i.e., a strongly coupled quark gluon plasma (SCQGP). It is remarkable that the widely used equation of state of SCP in QED (quantum electrodynamics) very nicely fits lattice results on all QGP systems, with proper modifications to include colour degrees of freedom and the running coupling constant. Results on pressure in pure gauge, 2-flavours and 3-flavours QGP can all be explained by treating QGP as SCQGP, as demonstrated here. Energy density and speed of sound are also presented for all three systems. We further extend the model to systems with finite quark mass and reasonably good fits to lattice results are obtained for (2+1)-flavours and 4-flavours QGP. Hence it is a unified model, namely SCQGP, to explain the non-ideal QGP seen in lattice simulations with just two system dependent parameters.

  9. Multiscale hyporheic exchange through strongly heterogeneous sediments

    NASA Astrophysics Data System (ADS)

    Pryshlak, Timothy T.; Sawyer, Audrey H.; Stonedahl, Susa H.; Soltanian, Mohamad Reza

    2015-11-01

    Heterogeneity in hydraulic conductivity (K) and channel morphology both control surface water-groundwater exchange (hyporheic exchange), which influences stream ecosystem processes and biogeochemical cycles. Here we show that heterogeneity in K is the dominant control on exchange rates, residence times, and patterns in hyporheic zones with abrupt lithologic contrasts. We simulated hyporheic exchange in a representative low-gradient stream with 300 different bimodal K fields composed of sand and silt. Simulations span five sets of sand-silt ratios and two sets of low and high K contrasts (1 and 3 orders of magnitude). Heterogeneity increases interfacial flux by an order of magnitude relative to homogeneous cases, drastically changes the shape of residence time distributions, and decreases median residence times. The positioning of highly permeable sand bodies controls patterns of interfacial flux and flow paths. These results are remarkably different from previous studies of smooth, continuous K fields that indicate only moderate effects on hyporheic exchange. Our results also show that hyporheic residence times are least predictable when sand body connectivity is low. As sand body connectivity increases, the expected residence time distribution (ensemble average for a given sand-silt ratio) remains approximately constant, but the uncertainty around the expectation decreases. Including strong heterogeneity in hyporheic models is imperative for understanding hyporheic fluxes and solute transport. In streams with strongly heterogeneous sediments, characterizing lithologic structure is more critical for predicting hyporheic exchange metrics than characterizing channel morphology.

  10. SS{sub p}G: A strongly orthogonal geminal method with relaxed strong orthogonality

    SciTech Connect

    Cagg, Brett A. Rassolov, Vitaly A.

    2014-10-28

    Strong orthogonality is an important constraint placed on geminal wavefunctions in order to make variational minimization tractable. However, strong orthogonality prevents certain, possibly important, excited configurations from contributing to the ground state description of chemical systems. The presented method lifts strong orthogonality constraint from geminal wavefunction by computing a perturbative-like correction to each geminal independently from the corrections to all other geminals. The method is applied to the Singlet-type Strongly orthogonal Geminals variant of the geminal wavefunction. Comparisons of this new SS{sub p}G method are made to the non-orthogonal AP1roG and the unconstrained Geminal Mean-Field Configuration Interaction method using small atomic and molecular systems. The correction is also compared to Density Matrix Renormalization Group calculations performed on long polyene chains in order to assess its scalability and applicability to large strongly correlated systems. The results of these comparisons demonstrate that although the perturbative correction is small, it may be a necessary first step in the systematic improvement of any strongly orthogonal geminal method.

  11. Using Tremor to Predict Strong Ground Motion

    NASA Astrophysics Data System (ADS)

    Baltay, A.; Asawachaisujja, S.; Beroza, G. C.

    2012-12-01

    Due to its widespread occurrence, frequency content, and location, tectonic tremor presents an exceptional opportunity to test and improve strong ground motion attenuation relations for subduction zones. We characterize the amplitude of thousands of individual tremor events to constrain the distance attenuation relationship of peak ground acceleration (PGA) and peak ground velocity (PGV) of tremor for application to strong ground motion prediction. Ground motion prediction equations (GMPE) relate ground motion amplitude to earthquake magnitude and distance, and are critically important for creating seismic hazard maps. In practice, GMPEs are determined empirically with earthquake data, recorded at many stations. In some areas of high earthquake hazard, such as Cascadia, the data set of recorded earthquakes for ground motion prediction is extremely sparse. Tectonic tremor, however, occurs frequently and abundantly in many subduction zones, including Cascadia. Moreover, the tremor band of 1-10 Hz, corresponds precisely to the frequency band of greatest interest for engineering seismology. Finally, tremor is thought to occur at or near the down-dip limit of rupture in large megathrust earthquakes, which is the area that is likely to control high frequency shaking in large earthquakes. Tremor in Cascadia is strong enough to be recorded at borehole stations of the Plate Boundary Observatory to distances of nearly 200 km, which is sufficient to place important constraints on ground motion decay with distance. We characterize the amplitude of thousands of individual tremor events occurring nearly continuously throughout an ETS event, using tremor locations and timings from independently determined catalogs [Wech and Creager, 2008]. Because tremor bursts do not have a defined absolute magnitude, we normalize all events to a reference magnitude. PGA and PGV for tremor shows a distance decay that is similar to subduction-zone-specific GMPEs developed from both data and

  12. Strong correlations in gravity and biophysics

    NASA Astrophysics Data System (ADS)

    Krotov, Dmitry

    The unifying theme of this dissertation is the use of correlations. In the first part (chapter 2), we investigate correlations in quantum field theories in de Sitter space. In the second part (chapters 3,4,5), we use correlations to investigate a theoretical proposal that real (observed in nature) transcriptional networks of biological organisms are operating at a critical point in their phase diagram. In chapter 2 we study the infrared dependence of correlators in various external backgrounds. Using the Schwinger-Keldysh formalism we calculate loop corrections to the correlators in the case of the Poincare patch and the complete de Sitter space. In the case of the Poincare patch, the loop correction modifies the behavior of the correlator at large distances. In the case of the complete de Sitter space, the loop correction has a strong dependence on the infrared cutoff in the past. It grows linearly with time, suggesting that at some point the correlations become strong and break the symmetry of the classical background. In chapter 3 we derive the signatures of critical behavior in a model organism, the embryo of Drosophila melanogaster. They are: strong correlations in the fluctuations of different genes, a slowing of dynamics, long range correlations in space, and departures from a Gaussian distribution of these fluctuations. We argue that these signatures are observed experimentally. In chapter 4 we construct an effective theory for the zero mode in this system. This theory is different from the standard Landau-Ginsburg description. It contains gauge fields (the result of the broken translational symmetry inside the cell), which produce observable contributions to the two-point function of the order parameter. We show that the behavior of the two-point function for the network of N genes is described by the action of a relativistic particle moving on the surface of the N - 1 dimensional sphere. We derive a theoretical bound on the decay of the correlations and

  13. Possible adaptation to strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Nakhilnitskaya, Z. N.; Klimovskaya, L. D.; Kuzmina, Z. F.; Mastryukova, V. M.; Smirnova, N. P.; Strzhizhovsky, A. D.; Cherkasov, G. V.

    Animal adaptation to a strong magnetic field was investigated. Mice were exposed to 30-day total-body continuous effects of a constant magnetic field (CMF) of 1.6 T, and their physiological responses were assessed. Analysis of the data obtained showed that different parameters varied in a dissimilar manner. Red blood changes returned to normal in the course of the experiment. Leucocytosis and increased content of catecholamines and corticosterone of blood and adrenals persisted throughout the exposure. Changes in the spermatogenic epithelium were most distinct after the exposure. The recovery of certain parameters during the CMF exposure is indicative of adaptation of some physiological systems. The adaptation is, however, incomplete as suggested by the long persisting stress manifestations. Reticulocytopenia and spermatogenetic abnormalities found after the exposure are of particular importance.

  14. Strong mechanical squeezing and its detection

    NASA Astrophysics Data System (ADS)

    Agarwal, G. S.; Huang, Sumei

    2016-04-01

    We report an efficient mechanism to generate a squeezed state of a mechanical mirror in an optomechanical system. We use an especially tuned parametric amplifier (PA) inside the cavity and the parametric photon phonon processes to transfer quantum squeezing from photons to phonons with almost 100% efficiency. We get 50% squeezing of the mechanical mirror which is limited by the PA. We present analytical results for the mechanical squeezing thus enabling one to understand the dependence of squeezing on system parameters like gain of PA, cooperativity, and temperature. As in cooling experiments the detrimental effects of mirror's Brownian and zero point noises are strongly suppressed by the pumping power. By judicious choice of the phases, the cavity output is squeezed only if the mirror is squeezed thus providing us a direct measure of the mirror's squeezing. Further considerable larger squeezing of the mirror can be obtained by adding the known feedback techniques.

  15. Scaling of chaos in strongly nonlinear lattices

    SciTech Connect

    Mulansky, Mario

    2014-06-15

    Although it is now understood that chaos in complex classical systems is the foundation of thermodynamic behavior, the detailed relations between the microscopic properties of the chaotic dynamics and the macroscopic thermodynamic observations still remain mostly in the dark. In this work, we numerically analyze the probability of chaos in strongly nonlinear Hamiltonian systems and find different scaling properties depending on the nonlinear structure of the model. We argue that these different scaling laws of chaos have definite consequences for the macroscopic diffusive behavior, as chaos is the microscopic mechanism of diffusion. This is compared with previous results on chaotic diffusion [M. Mulansky and A. Pikovsky, New J. Phys. 15, 053015 (2013)], and a relation between microscopic chaos and macroscopic diffusion is established.

  16. Formation and damping of relativistic strong shocks

    NASA Astrophysics Data System (ADS)

    Anile, A. M.; Miller, J. C.; Motta, S.

    1983-06-01

    Results are presented from a detailed study of the formation of strong relativistic shocks from simple waves and their subsequent damping. Basic results in relativistic hydrodynamics are first reviewed, and the transport equation for the shock amplitude is derived which permits the exact calculation of the characteristic damping time for an arbitrary initial shock profile. A basic formalism for the numerical treatment of the problem is set up using a Lagrangian formulation with the rest mass as a distance coordinate. Some results derived directly from the Rankine-Hugoniot relations are presented, and numerical results are given for the case of a purely compressive initial sine pulse propagating into a static uniform medium. The calculations confirm the qualitative nature of the effect fund by Liang and Baker (1977).

  17. Weak and strong typicality in quantum systems.

    PubMed

    Santos, Lea F; Polkovnikov, Anatoli; Rigol, Marcos

    2012-07-01

    We study the properties of mixed states obtained from eigenstates of many-body lattice Hamiltonians after tracing out part of the lattice. Two scenarios emerge for generic systems: (i) The diagonal entropy becomes equivalent to the thermodynamic entropy when a few sites are traced out (weak typicality); and (ii) the von Neumann (entanglement) entropy becomes equivalent to the thermodynamic entropy when a large fraction of the lattice is traced out (strong typicality). Remarkably, the results for few-body observables obtained with the reduced, diagonal, and canonical density matrices are very similar to each other, no matter which fraction of the lattice is traced out. Hence, for all physical quantities studied here, the results in the diagonal ensemble match the thermal predictions. PMID:23005351

  18. Towards Integrated Marmara Strong Motion Network

    NASA Astrophysics Data System (ADS)

    Durukal, E.; Erdik, M.; Safak, E.; Ansal, A.; Ozel, O.; Alcik, H.; Mert, A.; Kafadar, N.; Korkmaz, A.; Kurtulus, A.

    2009-04-01

    Istanbul has a 65% chance of having a magnitude 7 or above earthquake within the next 30 years. As part of the preparations for the future earthquake, strong motion networks have been installed in and around Istanbul. The Marmara Strong Motion Network, operated by the Department of Earthquake Engineering of Kandilli Observatory and Earthquake Research Institute, encompasses permanent systems outlined below. It is envisaged that the networks will be run by a single entity responsible for technical management and maintanence, as well as for data management, archiving and dissemination through dedicated web-based interfaces. • Istanbul Earthquake Rapid Response and Early Warning System - IERREWS (one hundred 18-bit accelerometers for rapid response; ten 24-bit accelerometers for early warning) • IGDAŞ Gas Shutoff Network (100 accelerometers to be installed in 2010 and integrated with IERREWS) • Structural Monitoring Arrays - Fatih Sultan Mehmet Suspension Bridge (1200m-long suspension bridge across the Bosphorus, five 3-component accelerometers + GPS sensors) - Hagia Sophia Array (1500-year-old historical edifice, 9 accelerometers) - Süleymaniye Mosque Array (450-year-old historical edifice,9 accelerometers) - Fatih Mosque Array (237-year-old historical edifice, 9 accelerometers) - Kanyon Building Array (high-rise office building, 5 accelerometers) - Isbank Tower Array (high-rise office building, 5 accelerometers) - ENRON Array (power generation facility, 4 acelerometers) - Mihrimah Sultan Mosque Array (450-year-old historical edifice,9 accelerometers + tiltmeters, to be installed in 2009) - Sultanahmet Mosque Array, (390-year-old historical edifice, 9 accelerometers + tiltmeters, to be installed in 2009) • Special Arrays - Atakoy Vertical Array (four 3-component accelerometers at 25, 50, 75, and 150 m depths) - Marmara Tube Tunnel (1400 m long submerged tunnel, 128 ch. accelerometric data, 24 ch. strain data, to be installed in 2010) - Air-Force Academy

  19. Designing asymmetric multiferroics with strong magnetoelectric coupling

    NASA Astrophysics Data System (ADS)

    Lu, X. Z.; Xiang, H. J.

    2014-09-01

    Multiferroics offer exciting opportunities for electric-field control of magnetism. Single-phase multiferroics suitable for such applications at room temperature need much more study. Here, we propose the concept of an alternative type of multiferroics, namely, the "asymmetric multiferroic." In asymmetric multiferroics, two locally stable ferroelectric states are not symmetrically equivalent, leading to different magnetic properties between these two states. Furthermore, we predict from first principles that a Fe-Cr-Mo superlattice with the LiNbO3-type structure is such an asymmetric multiferroic. The strong ferrimagnetism, high ferroelectric polarization, and significant dependence of the magnetic transition temperature on polarization make this asymmetric multiferroic an ideal candidate for realizing electric-field control of magnetism at room temperature. Our study suggests that the asymmetric multiferroic may provide an alternative playground for voltage control of magnetism and find its applications in spintronics and quantum computing.

  20. Designing asymmetric multiferroics with strong magnetoelectric coupling

    NASA Astrophysics Data System (ADS)

    Lu, Xuezeng; Xiang, Hongjun; Rondinelli, James; Materials Theory; Design Group Team

    2015-03-01

    Multiferroics offer exciting opportunities for electric-field control of magnetism. Single-phase multiferroics suitable for such applications at room temperature need much more study. Here, we propose the concept of an alternative type of multiferroics, namely, the ``asymmetric multiferroic.'' In asymmetric multiferroics, two locally stable ferroelectric states are not symmetrically equivalent, leading to different magnetic properties between these two states. Furthermore, we predict from first principles that a Fe-Cr-Mo superlattice with the LiNbO3-type structure is such an asymmetric multiferroic. The strong ferrimagnetism, high ferroelectric polarization, and significant dependence of the magnetic transition temperature on polarization make this asymmetric multiferroic an ideal candidate for realizing electric-field control of magnetism at room temperature. Our study suggests that the asymmetric multiferroic may provide an alternative playground for voltage control of magnetism and find its applications in spintronics and quantum computing.

  1. Circuit electromechanics with single photon strong coupling

    SciTech Connect

    Xue, Zheng-Yuan Yang, Li-Na; Zhou, Jian

    2015-07-13

    In circuit electromechanics, the coupling strength is usually very small. Here, replacing the capacitor in circuit electromechanics by a superconducting flux qubit, we show that the coupling among the qubit and the two resonators can induce effective electromechanical coupling which can attain the strong coupling regime at the single photon level with feasible experimental parameters. We use dispersive couplings among two resonators and the qubit while the qubit is also driven by an external classical field. These couplings form a three-wave mixing configuration among the three elements where the qubit degree of freedom can be adiabatically eliminated, and thus results in the enhanced coupling between the two resonators. Therefore, our work constitutes the first step towards studying quantum nonlinear effect in circuit electromechanics.

  2. Magnetocaloric effect in strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Tishin, A. M.

    Calculations of magnetic entropy change, Δ SM, and magnetocaloric effect, Δ T, in 3d and 4f magnetics have been carried out, based on the molecular field theory. Δ SM and Δ T have been studied as a function of Debye temperature, θ D, Lande factor, gj, quantum number of total mechanical momentum, J, and also of magnetic phase transition temperatures. Limiting values of Δ SM and Δ T have been determined in extremely strong magnetic fields. The results obtained are compared with experimental data. It is shown that the use of ferromagnetic alloys Tb x Gd 1-x as operating devices of magnetic refrigerating machines in the room temperature range is more efficient than the use of pure Gd. These alloys have been found to have high specific refrigerant capacity over a wide range of fields from 0.1 to 6 T, which enables one to develop highly economic refrigeration devices in which weak fields are applied.

  3. Strong Localization of Positive Charge in DNA

    NASA Astrophysics Data System (ADS)

    Uskov, Dmitry; Burin, Alex

    2008-05-01

    The positive charge transfer in a DNA molecule is determined by two main factors: the structure and composition of specific DNA strand, and interaction of a positive charge with the DNA environment. In this letter we present results of microscopic linear response theory for balance of charge transfer reaction in synthetic strands GAGG and GAGGG, where experimental data on the rates of electron hole migration has been reported by Lewis et al Nature, 406, 51-53 (2000). Our theoretical predictions, based on experimental data for the ratio of reaction rates G^+A(G)n<->GA(G)n^+ , n=2,3, suggest that charge in DNA is strongly localized within the single base pair because of the self-induced reorganization of classical environment. The onset of localization has a threshold behavior characteristic to quantum bistability. We also demonstrate that our conclusion does not depend on details of the model.

  4. Strong crystal size effect on deformation twinning.

    PubMed

    Yu, Qian; Shan, Zhi-Wei; Li, Ju; Huang, Xiaoxu; Xiao, Lin; Sun, Jun; Ma, Evan

    2010-01-21

    Deformation twinning in crystals is a highly coherent inelastic shearing process that controls the mechanical behaviour of many materials, but its origin and spatio-temporal features are shrouded in mystery. Using micro-compression and in situ nano-compression experiments, here we find that the stress required for deformation twinning increases drastically with decreasing sample size of a titanium alloy single crystal, until the sample size is reduced to one micrometre, below which the deformation twinning is entirely replaced by less correlated, ordinary dislocation plasticity. Accompanying the transition in deformation mechanism, the maximum flow stress of the submicrometre-sized pillars was observed to saturate at a value close to titanium's ideal strength. We develop a 'stimulated slip' model to explain the strong size dependence of deformation twinning. The sample size in transition is relatively large and easily accessible in experiments, making our understanding of size dependence relevant for applications. PMID:20090749

  5. Transient Heat Conduction in Strongly Correlated Systems

    NASA Astrophysics Data System (ADS)

    Aghjayan, Rita; Luniewski, Arthur; Walczak, Kamil; Nanoscale Physics Division Team

    2015-03-01

    We analyze heat transport carried by electrons via quantum dots, modeled as strongly-correlated systems with discrete spectrum of available energy levels, which couple to two heat reservoirs of different temperatures. Our computational method for the electronic heat flux is based on the density matrix formalism, while the transition rates between particular quantum states are determined within the Fermi's golden rule. By taking into consideration the non-steady-state solutions for probabilities, we examine the influence of initial conductions and contact-induced time delays onto the rapid thermal switching response of the quantum system under investigation. Specifically, we use several different models for quantum dot, where the Zeeman splitting, Coulomb blockade, and the concept of dark-state are explicitly included. A special attention is devoted to thermal memory effects and the relationship between all the quantum transport expressions and the hyperbolic Cattaneo-Vernotte equation. This research is supported by Pace University Start-up Grant.

  6. Inhomogeneous thermalization in strongly coupled field theories.

    PubMed

    Balasubramanian, V; Bernamonti, A; de Boer, J; Craps, B; Franti, L; Galli, F; Keski-Vakkuri, E; Müller, B; Schäfer, A

    2013-12-01

    To describe theoretically the creation and evolution of the quark-gluon plasma, one typically employs three ingredients: a model for the initial state, nonhydrodynamic early time evolution, and hydrodynamics. In this Letter we study the nonhydrodynamic early time evolution using the AdS/CFT correspondence in the presence of inhomogeneities. We find that the AdS description of the early time evolution is well matched by free streaming. Near the end of the early time interval where our analytic computations are reliable, the stress tensor agrees with the second order hydrodynamic stress tensor computed from the local energy density and fluid velocity. Our techniques may also be useful for the study of far-from-equilibrium strongly coupled systems in other areas of physics. PMID:24476254

  7. Strong imploding shock - The representative curve

    NASA Astrophysics Data System (ADS)

    Mishkin, E. A.; Alejaldre, C.

    1981-02-01

    The representative curve of the ideal gas behind the front of a spherically or cylindrically asymmetric strong imploding shock is derived. The partial differential equations of mass, momentum and energy conservation are reduced to a set of ordinary differential equations by the method of quasi-separation of variables, following which the reduced pressure and density as functions of the radius with respect to the shock front are explicit functions of coordinates defining the phase plane of the self-similar solution. The curve in phase space representing the state of the imploded gas behind the shock front is shown to pass through the point where the reduced pressure is maximum, which is located somewhat behind the shock front and ahead of the tail of the shock.

  8. Compton scattering in strong magnetic fields

    NASA Technical Reports Server (NTRS)

    Daugherty, Joseph K.; Harding, Alice K.

    1986-01-01

    The relativistic cross section for Compton scattering by electrons in strong magnetic fields is derived. The results confirm and extend earlier work which has treated only transitions to the lowest or first excited Landau levels. For the teragauss field strengths expected in neutron star magnetospheres, the relative rates for excited state transitions are found to be significant, especially for incident photon energies several times the cyclotron frequency. Since these transitions must result in the rapid emission of one or more cyclotron photons as well as the Compton-scattered photon, the scattering process actually becomes a photon 'splitting' mechanism which acts to soften hard photon spectra, and also provides a specific mechanism for populating higher Landau levels in the electron distribution function. The results should be significant for models of gamma-ray bursters and pulsating X-ray sources.

  9. Strongly Interacting Matter at High Energy Density

    SciTech Connect

    McLerran,L.

    2008-09-07

    This lecture concerns the properties of strongly interacting matter (which is described by Quantum Chromodynamics) at very high energy density. I review the properties of matter at high temperature, discussing the deconfinement phase transition. At high baryon density and low temperature, large N{sub c} arguments are developed which suggest that high baryonic density matter is a third form of matter, Quarkyonic Matter, that is distinct from confined hadronic matter and deconfined matter. I finally discuss the Color Glass Condensate which controls the high energy limit of QCD, and forms the low x part of a hadron wavefunction. The Glasma is introduced as matter formed by the Color Glass Condensate which eventually thermalizes into a Quark Gluon Plasma.

  10. Strongly trapped two-dimensional quantum walks

    NASA Astrophysics Data System (ADS)

    Kollár, B.; Kiss, T.; Jex, I.

    2015-02-01

    Discrete time quantum walks (DTQWs) are nontrivial generalizations of random walks with a broad scope of applications. In particular, they can be used as computational primitives, and they are suitable tools for simulating other quantum systems. DTQWs usually spread ballistically due to their quantumness. In some cases, however, they can remain localized at their initial state (trapping). The trapping and other fundamental properties of DTQWs are determined by the choice of the coin operator. We introduce and analyze a type of walks driven by a coin class leading to strong trapping, complementing the known list of walks. This class of walks exhibits a number of exciting properties with possible applications ranging from light pulse trapping in a medium to topological effects and quantum search.

  11. Strong gravity and structure of topological solitons

    NASA Astrophysics Data System (ADS)

    Rybakov, Yu. P.

    The unification of Skyrme and Faddeev chiral models describing baryons and leptons respectively as topological solitons is suggested within the framework of 16-spinor field ψ = ψ1 ⊕ ψ2 nonlinear model containing two 8-semispinors ψ1 and ψ2. Using Brioschi identity for 8-spinors and special structure of the Higgs potential V implying the spontaneous symmetry breaking, it is possible to realize topological soliton-like excitations of two kinds due to the choice of S2- or S3- manifolds as phase spaces. The interactions with electromagnetic, Yang--Mills and gravitational fields are exhibited through the extention of derivatives via gauge invariance principle. Specific inclusion in the Higgs potential of the Kretschmann gravitational invariant K = RμνσλRμνσλ/48 permits one to obtain the strong gravity behavior at small distances and guarantee the correspondence with Quantum Mechanics at large distances.

  12. Strongly Acidic Auxin Indole-3-Methanesulfonic Acid

    PubMed Central

    Cohen, Jerry D.; Baldi, Bruce G.; Bialek, Krystyna

    1985-01-01

    A radiochemical synthesis is described for [14C]indole-3-methanesulfonic acid (IMS), a strongly acidic auxin analog. Techniques were developed for fractionation and purification of IMS using normal and reverse phase chromatography. In addition, the utility of both Fourier transform infrared spectrometry and fast atom bombardment mass spectrometry for analysis of IMS has been demonstrated. IMS was shown to be an active auxin, stimulating soybean hypocotyl elongation, bean first internode curvature, and ethylene production. IMS uptake by thin sections of soybean hypocotyl was essentially independent of solution pH and, when applied at a 100 micromolar concentration, IMS exhibited a basipetal polarity in its transport in both corn coleoptile and soybean hypocotyl sections. [14C]IMS should, therefore, be a useful compound to study fundamental processes related to the movement of auxins in plant tissues and organelles. PMID:16664007

  13. Utilizing Nanofabrication to Construct Strong, Luminescent Materials

    SciTech Connect

    Chen, Wei; Huang, Gang; Lu, Hong B.; McCready, David E.; Joly, Alan G.; Bovin, Jan-Olov

    2006-05-28

    Luminescent materials have been utilized widely in applications from lighting to sensing. The new development of technologies based on luminescence properties requires the materials to have high luminescence efficiency and mechanical strength. In this article, we report the fabrication of luminescent materials possessing high mechanical strength by nanofabrication with polyvinyl alcohol used as a stabilizer or coupling agent. X-ray diffraction and high resolution transmission microscope observations reveal that the nanocomposite sample contains ZnS and ZnO nanoparticles as well as kozoite and sodium nitrate. The mechanical strength and hardness of these nanocomposite materials are higher than polycarbonate and some carbon nanotube reinforced nanocomposites. Strong luminescence is observed in the new nanocomposites and the luminescence intensity does not degrade following up to 30 minutes of X-ray irradiation. Our results indicate that nanofabrication may provide a good method to improve the mechanical strength of luminescent materials for some applications in which high strength luminescent materials are needed.

  14. Strong mobility in weakly disordered systems

    SciTech Connect

    Ben-naim, Eli; Krapivsky, Pavel

    2009-01-01

    We study transport of interacting particles in weakly disordered media. Our one-dimensional system includes (i) disorder, the hopping rate governing the movement of a particle between two neighboring lattice sites is inhomogeneous, and (ii) hard core interaction, the maximum occupancy at each site is one particle. We find that over a substantial regime, the root-mean-square displacement of a particle s grows superdiffusively with time t, {sigma}{approx}({epsilon}t){sup 2/3}, where {epsilon} is the disorder strength. Without disorder the particle displacement is subdiffusive, {sigma} {approx}t{sup 1/4}, and therefore disorder strongly enhances particle mobility. We explain this effect using scaling arguments, and verify the theoretical predictions through numerical simulations. Also, the simulations show that regardless of disorder strength, disorder leads to stronger mobility over an intermediate time regime.

  15. Bound states in a strong magnetic field

    SciTech Connect

    Machado, C. S.; Navarra, F. S.; Noronha, J.; Oliveira, E. G.; Ferreira Filho, L. G.

    2013-03-25

    We expect a strong magnetic field to be produced in the perpendicular direction to the reaction plane, in a noncentral heavy-ion collision . The strength of the magnetic field is estimated to be eB{approx}m{sup 2}{sub {pi}}{approx} 0.02 GeV{sup 2} at the RHIC and eB{approx} 15m{sup 2}{sub {pi}}{approx} 0.3 GeV{sup 2} at the LHC. We investigate the effects of the magnetic field on B{sup 0} and D{sup 0} mesons, focusing on the changes of the energy levels and of the mass of the bound states.

  16. Isolation of strong constitutive promoters from Lactococcus lactis subsp. lactis N8.

    PubMed

    Zhu, Duolong; Liu, Fulu; Xu, Haijin; Bai, Yanling; Zhang, Xiuming; Saris, Per Erik Joakim; Qiao, Mingqiang

    2015-08-01

    The synthesis of heterologous proteins in Lactococcus lactis is strongly influenced by the promoter selected for the expression. The nisin A promoter is commonly used for induced expression of proteins in L. lactis, whereas few constitutive promoters (P45 and the weaker P32) have been used for protein expression studies. In this study, eight different putative strong constitutive promoters were identified through transcriptional analysis of L. lactis N8 and were investigated for their capability to drive nisZ gene expression with promoters P45 and P32 as control. Four strong promoters (P8, P5, P3 and P2) were identified as having a transcriptional activity that was higher than that of P45 through RT-qPCR and agar-diffusion experiments. In addition, these four promoters were fused to the erythromycin resistant gene (ermC) with promoter P45 as control and inserted into the backbone of the pNZ8048 vector. The transcriptional efficiencies of promoters P8, P5, P2 and P3 were all higher than promoter P45 based on the obtained MIC50 values and they all showed different activity levels. In conclusion, four strong constitutive promoters with a wide range of promoter activities were identified and are suitable for protein production in L. lactis. PMID:26156144

  17. Hydrophilic Strong Anion Exchange (hSAX) Chromatography for Highly Orthogonal Peptide Separation of Complex Proteomes

    PubMed Central

    2013-01-01

    Due to its compatibility and orthogonality to reversed phase (RP) liquid chromatography (LC) separation, ion exchange chromatography, and mainly strong cation exchange (SCX), has often been the first choice in multidimensional LC experiments in proteomics. Here, we have tested the ability of three strong anion exchanger (SAX) columns differing in their hydrophobicity to fractionate RAW264.7 macrophage cell lysate. IonPac AS24, a strong anion exchange material with ultralow hydrophobicity, demonstrated to be superior to other materials by fractionation and separation of tryptic peptides from both a mixture of 6 proteins as well as mouse cell lysate. The chromatography displayed very high orthogonality and high robustness depending on the hydrophilicity of column chemistry, which we termed hydrophilic strong anion exchange (hSAX). Mass spectrometry analysis of 34 SAX fractions from RAW264.7 macrophage cell lysate digest resulted in an identification of 9469 unique proteins and 126318 distinct peptides in one week of instrument time. Moreover, when compared to an optimized high pH/low pH RP separation approach, the method presented here raised the identification of proteins and peptides by 10 and 28%, respectively. This novel hSAX approach provides robust, reproducible, and highly orthogonal separation of complex protein digest samples for deep coverage proteome analysis. PMID:23294059

  18. Strong curvature effects in Neumann wave problems

    SciTech Connect

    Willatzen, M.; Pors, A.; Gravesen, J.

    2012-08-15

    Waveguide phenomena play a major role in basic sciences and engineering. The Helmholtz equation is the governing equation for the electric field in electromagnetic wave propagation and the acoustic pressure in the study of pressure dynamics. The Schroedinger equation simplifies to the Helmholtz equation for a quantum-mechanical particle confined by infinite barriers relevant in semiconductor physics. With this in mind and the interest to tailor waveguides towards a desired spectrum and modal pattern structure in classical structures and nanostructures, it becomes increasingly important to understand the influence of curvature effects in waveguides. In this work, we demonstrate analytically strong curvature effects for the eigenvalue spectrum of the Helmholtz equation with Neumann boundary conditions in cases where the waveguide cross section is a circular sector. It is found that the linear-in-curvature contribution originates from parity symmetry breaking of eigenstates in circular-sector tori and hence vanishes in a torus with a complete circular cross section. The same strong curvature effect is not present in waveguides subject to Dirichlet boundary conditions where curvature contributions contribute to second-order in the curvature only. We demonstrate this finding by considering wave propagation in a circular-sector torus corresponding to Neumann and Dirichlet boundary conditions, respectively. Results for relative eigenfrequency shifts and modes are determined and compared with three-dimensional finite element method results. Good agreement is found between the present analytical method using a combination of differential geometry with perturbation theory and finite element results for a large range of curvature ratios.

  19. Cyclotron resonance cooling by strong laser field

    SciTech Connect

    Tagcuhi, Toshihiro; Mima, Kunioka

    1995-12-31

    Reduction of energy spread of electron beam is very important to increase a total output radiation power in free electron lasers. Although several cooling systems of particle beams such as a stochastic cooling are successfully operated in the accelerator physics, these cooling mechanisms are very slow and they are only applicable to high energy charged particle beams of ring accelerators. We propose here a new concept of laser cooling system by means of cyclotron resonance. Electrons being in cyclotron motion under a strong magnetic field can resonate with circular polarized electromagnetic field, and the resonance take place selectively depending on the velocity of the electrons. If cyclotron frequency of electrons is equal to the frequency of the electromagnetic field, they absorb the electromagnetic field energy strongly, but the other electrons remain unchanged. The absorbed energy will be converted to transverse kinetic energy, and the energy will be dumped into the radiation energy through bremastrahlung. To build a cooling system, we must use two laser beams, where one of them is counter-propagating and the other is co-propagating with electron beam. When the frequency of the counter-propagating laser is tuned with the cyclotron frequency of fast electrons and the co-propagating laser is tuned with the cyclotron frequency of slow electrons, the energy of two groups will approach and the cooling will be achieved. We solve relativistic motions of electrons with relativistic radiation dumping force, and estimate the cooling rate of this mechanism. We will report optimum parameters for the electron beam cooling system for free electron lasers.

  20. Bodrum Strong Motion Network, Mugla, Turkey

    NASA Astrophysics Data System (ADS)

    Alcik, H. A.; Tanircan, G.; Korkmaz, A.

    2015-12-01

    The Gulf of Gökova is located in southwestern Turkey near the Aegean Sea and surrounded by Datça Peninsula to the south, the island of Kos to the west and Bodrum Peninsula to the north. The Bodrum peninsula with a population of one million in summer season is one of the most populated touristic centers of Turkey. This region is also surrounded by numerous active seismic entities such as Ula-Ören Fault Zone, Gökova Graben etc.. and demonstrates high seismic hazard. In the past, many destructive earthquakes have occurred in southwestern Turkey. One of the destructive historical earthquakes is 1493 Kos event (Mw=6.9) caused heavy damage in Bodrum. In the instrumental period seismic activity in the Gökova region includes the Ms>6.0 earthquakes of 23 April 1933 (Ms=6.4), 23 May 1941 (Ms=6.0), 13 December 1941 (Ms=6.5) events. Intense earthquake activity (Mw5+) occurred in Gulf of Gökova in August 2004 and January 2005. Considering the high seismicity and population of this region, a strong ground motion monitoring system stationed in dense settlements in the Bodrum Peninsula: Bodrum, Turgutreis, Yalıkavak, Çiftlik and Ortakent was deployed on June 2015. The network consists of 5 strong motion recorders, has been set up with the aim of monitoring of regional earthquakes, collecting accurate and reliable data for engineering and scientific research purposes, in particular to provide input for future earthquake rapid reporting and early warning implementation projects on urban environments in the Bodrum peninsula and the surrounding areas. In this poster presentation, we briefly introduce the Bodrum Network and discuss our future plans for further developments.

  1. Is It Possible to Predict Strong Earthquakes?

    NASA Astrophysics Data System (ADS)

    Polyakov, Y. S.; Ryabinin, G. V.; Solovyeva, A. B.; Timashev, S. F.

    2015-07-01

    The possibility of earthquake prediction is one of the key open questions in modern geophysics. We propose an approach based on the analysis of common short-term candidate precursors (2 weeks to 3 months prior to strong earthquake) with the subsequent processing of brain activity signals generated in specific types of rats (kept in laboratory settings) who reportedly sense an impending earthquake a few days prior to the event. We illustrate the identification of short-term precursors using the groundwater sodium-ion concentration data in the time frame from 2010 to 2014 (a major earthquake occurred on 28 February 2013) recorded at two different sites in the southeastern part of the Kamchatka Peninsula, Russia. The candidate precursors are observed as synchronized peaks in the nonstationarity factors, introduced within the flicker-noise spectroscopy framework for signal processing, for the high-frequency component of both time series. These peaks correspond to the local reorganizations of the underlying geophysical system that are believed to precede strong earthquakes. The rodent brain activity signals are selected as potential "immediate" (up to 2 weeks) deterministic precursors because of the recent scientific reports confirming that rodents sense imminent earthquakes and the population-genetic model of K irshvink (Soc Am 90, 312-323, 2000) showing how a reliable genetic seismic escape response system may have developed over the period of several hundred million years in certain animals. The use of brain activity signals, such as electroencephalograms, in contrast to conventional abnormal animal behavior observations, enables one to apply the standard "input-sensor-response" approach to determine what input signals trigger specific seismic escape brain activity responses.

  2. Strong curvature effects in Neumann wave problems

    NASA Astrophysics Data System (ADS)

    Willatzen, M.; Pors, A.; Gravesen, J.

    2012-08-01

    Waveguide phenomena play a major role in basic sciences and engineering. The Helmholtz equation is the governing equation for the electric field in electromagnetic wave propagation and the acoustic pressure in the study of pressure dynamics. The Schrödinger equation simplifies to the Helmholtz equation for a quantum-mechanical particle confined by infinite barriers relevant in semiconductor physics. With this in mind and the interest to tailor waveguides towards a desired spectrum and modal pattern structure in classical structures and nanostructures, it becomes increasingly important to understand the influence of curvature effects in waveguides. In this work, we demonstrate analytically strong curvature effects for the eigenvalue spectrum of the Helmholtz equation with Neumann boundary conditions in cases where the waveguide cross section is a circular sector. It is found that the linear-in-curvature contribution originates from parity symmetry breaking of eigenstates in circular-sector tori and hence vanishes in a torus with a complete circular cross section. The same strong curvature effect is not present in waveguides subject to Dirichlet boundary conditions where curvature contributions contribute to second-order in the curvature only. We demonstrate this finding by considering wave propagation in a circular-sector torus corresponding to Neumann and Dirichlet boundary conditions, respectively. Results for relative eigenfrequency shifts and modes are determined and compared with three-dimensional finite element method results. Good agreement is found between the present analytical method using a combination of differential geometry with perturbation theory and finite element results for a large range of curvature ratios.

  3. Immunoprofiling Using NAPPA Protein Microarrays

    PubMed Central

    Sibani, Sahar; LaBaer, Joshua

    2012-01-01

    Protein microarrays provide an efficient method to immunoprofile patients in an effort to rapidly identify disease immunosignatures. The validity of using autoantibodies in diagnosis has been demonstrated in type 1 diabetes, rheumatoid arthritis, and systemic lupus, and is now being strongly considered in cancer. Several types of protein microarrays exist including antibody and antigen arrays. In this chapter, we describe the immunoprofiling application for one type of antigen array called NAPPA (nucleic acids programmable protein array). We provide a guideline for setting up the screening study and designing protein arrays to maximize the likelihood of obtaining quality data. PMID:21370064

  4. A genetic sensor for strong methylating compounds

    PubMed Central

    Moser, Felix; Horwitz, Andrew; Chen, Jacinto; Lim, Wendell A.; Voigt, Christopher A.

    2013-01-01

    Methylating chemicals are common in industry and agriculture and are often toxic, partly due to their propensity to methylate DNA. The Escherichia coli Ada protein detects methylating compounds by sensing aberrant methyl adducts on the phosphoester backbone of DNA. We characterize this system as a genetic sensor and engineer it to lower the detection threshold. By overexpressing Ada from a plasmid, we improve the sensor’s dynamic range to 350-fold induction and lower its detection threshold to 40 µM for methyl iodide. In eukaryotes, there is no known sensor of methyl adducts on the phosphoester backbone of DNA. By fusing the N-terminal domain of Ada to the Gal4 transcriptional activation domain, we built a functional sensor for methyl phosphotriester adducts in Saccharomyces cerevisiae. This sensor can be tuned to variable specifications by altering the expression level of the chimeric sensor and changing the number of Ada operators upstream of the Gal4-sensitive reporter promoter. These changes result in a detection threshold of 28 µM and 5.2-fold induction in response to methyl iodide. When the yeast sensor is exposed to different SN1 and SN2 alkylating compounds, its response profile is similar to that observed for the native Ada protein in E. coli, indicating that its native function is retained in yeast. Finally, we demonstrate that the specifications achieved for the yeast sensor are suitable for detecting methylating compounds at relevant concentrations in environmental samples. This work demonstrates the movement of a sensor from a prokaryotic to eukaryotic system and its rational tuning to achieve desired specifications. PMID:24032656

  5. Total protein

    MedlinePlus

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

  6. Whey Protein

    MedlinePlus

    ... shows that taking whey protein in combination with strength training increases lean body mass, strength, and muscle size. ... grams/kg of whey protein in combination with strength training for 6-10 weeks. For HIV/AIDS-related ...

  7. Protein Microarrays

    NASA Astrophysics Data System (ADS)

    Ricard-Blum, S.

    Proteins are key actors in the life of the cell, involved in many physiological and pathological processes. Since variations in the expression of messenger RNA are not systematically correlated with variations in the protein levels, the latter better reflect the way a cell functions. Protein microarrays thus supply complementary information to DNA chips. They are used in particular to analyse protein expression profiles, to detect proteins within complex biological media, and to study protein-protein interactions, which give information about the functions of those proteins [3-9]. They have the same advantages as DNA microarrays for high-throughput analysis, miniaturisation, and the possibility of automation. Section 18.1 gives a brief overview of proteins. Following this, Sect. 18.2 describes how protein microarrays can be made on flat supports, explaining how proteins can be produced and immobilised on a solid support, and discussing the different kinds of substrate and detection method. Section 18.3 discusses the particular format of protein microarrays in suspension. The diversity of protein microarrays and their applications are then reported in Sect. 18.4, with applications to therapeutics (protein-drug interactions) and diagnostics. The prospects for future developments of protein microarrays are then outlined in the conclusion. The bibliography provides an extensive list of reviews and detailed references for those readers who wish to go further in this area. Indeed, the aim of the present chapter is not to give an exhaustive or detailed analysis of the state of the art, but rather to provide the reader with the basic elements needed to understand how proteins are designed and used.

  8. Strong Motion Seismograph Based On MEMS Accelerometer

    NASA Astrophysics Data System (ADS)

    Teng, Y.; Hu, X.

    2013-12-01

    The MEMS strong motion seismograph we developed used the modularization method to design its software and hardware.It can fit various needs in different application situation.The hardware of the instrument is composed of a MEMS accelerometer,a control processor system,a data-storage system,a wired real-time data transmission system by IP network,a wireless data transmission module by 3G broadband,a GPS calibration module and power supply system with a large-volumn lithium battery in it. Among it,the seismograph's sensor adopted a three-axis with 14-bit high resolution and digital output MEMS accelerometer.Its noise level just reach about 99μg/√Hz and ×2g to ×8g dynamically selectable full-scale.Its output data rates from 1.56Hz to 800Hz. Its maximum current consumption is merely 165μA,and the device is so small that it is available in a 3mm×3mm×1mm QFN package. Furthermore,there is access to both low pass filtered data as well as high pass filtered data,which minimizes the data analysis required for earthquake signal detection. So,the data post-processing can be simplified. Controlling process system adopts a 32-bit low power consumption embedded ARM9 processor-S3C2440 and is based on the Linux operation system.The processor's operating clock at 400MHz.The controlling system's main memory is a 64MB SDRAM with a 256MB flash-memory.Besides,an external high-capacity SD card data memory can be easily added.So the system can meet the requirements for data acquisition,data processing,data transmission,data storage,and so on. Both wired and wireless network can satisfy remote real-time monitoring, data transmission,system maintenance,status monitoring or updating software.Linux was embedded and multi-layer designed conception was used.The code, including sensor hardware driver,the data acquisition,earthquake setting out and so on,was written on medium layer.The hardware driver consist of IIC-Bus interface driver, IO driver and asynchronous notification driver. The

  9. Developing Strong Geoscience Programs and Departments

    NASA Astrophysics Data System (ADS)

    MacDonald, R.; Manduca, C. A.

    2002-12-01

    Strong geoscience programs are essential for preparing future geoscientists and developing a broad public understanding of our science. Faculty working as a department team can create stronger programs than individual faculty working alone. Workshops sponsored by Project Kaleidoscope (www.pkal.org) on departmental planning in the geosciences have emphasized the importance of designing programs in the context of both departmental and student goals. Well-articulated goals form a foundation for designing curriculum, courses, and other departmental activities. Course/skill matrices have emerged as particularly valuable tools for analyzing how individual courses combine in a curriculum to meet learning goals. Integrated programs where students have opportunities to learn and use skills in multiple contexts have been developed at several institutions. Departments are leveraging synergies between courses to more effectively reach departmental goals and capitalize on opportunities in the larger campus environment. A full departmental program extends beyond courses and curriculum. Studies in physics (National Task Force on Undergraduate Physics, Hilborne, 2002) indicate the importance of activities such as recruiting able students, mentoring students, providing courses appropriate for pre-service K-12 teachers, assisting with professional development for a diversity of careers, providing opportunities for undergraduates to participate in research, and making connections with the local industries and businesses that employ graduates. PKAL workshop participants have articulated a wide variety of approaches to undergraduate research opportunities within and outside of class based on their departmental goals, faculty goals, and resources. Similarly, departments have a wide variety of strategies for developing productive synergies with campus-wide programs including those emphasizing writing skills, quantitative skills, and environmental studies. Mentoring and advising

  10. Predictive Capability for Strongly Correlated Systems

    SciTech Connect

    Cyrus Umrigar

    2012-05-09

    Diffusion Monte Carlo methods can give highly accurate results for correlated systems, provided that well optimized trial wave functions with accurate nodal surfaces are employed. The Cornell team developed powerful methods for optimizing all the parameters within a multi-determinant Slater-Jastrow form of the wave function. These include the Jastrow parameters within a flexible electron-electron-nucleus form of the Jastrow function, the parameters multiplying the configuration state functions, the orbital parameters and the basis exponents. The method optimizes a linear combination of the energy and the variance of the local energy. The optimal parameters are found iteratively by diagonalizing the Hamiltonian matrix in the space spanned by the wave function and its first-order derivatives, making use of a strong zero-variance principle. It is highly robust, has become the method of choice for correlated wave function optimization and has been adopted by other QMC groups. This optimization method was used on the first-row atoms and homonuclear diatomic molecules, demonstrating that molecular well depths can be obtained with near chemical accuracy quite systematically at the diffusion Monte Carlo level for these systems. In addition the complete ground-state potential energy curve of the C{sub 2} molecule up to the dissociation limit was obtained, and, size consistency and broken spin-symmetry issues in quantum Monte Carlo calculations were studied. The method was used with a eight-electrons-in-eight-orbitals complete active space CAS(8,8) wave function to study the relative energies of the monocyclic and bicyclic forms of m-benzyne. The DMC calculations show that the monocyclic structure is lower in energy than the bicyclic structure by 1.92 kcal/ mole, which is in excellent agreement with the best coupled cluster results (CCSD(T)) and in disagreement with the CCSD results. QMC methods have for the most part been used only for ground states of a given symmetry. We

  11. Strong transverse coupling in the Tevatron

    SciTech Connect

    Annala, G; Carson, J; Edwards, Don; Gelfand, N; Harding, D; Johnson, T; Johnstone, J; Martens, M; Sen, T; Syphers, Mike

    2003-03-01

    The Tevatron was designed with an extensive set of correction and adjustment magnets built into the spool pieces in recognition of the circumstance that a superconducting synchrotron was not as easy to modify as its conventional forebearers. Recently, concern has mounted at the high excitation of the skew quadrupole correctors. The purpose of this note is to account for this situation. When slow extraction was attempted from the Main Ring in the summer of 1970 horizontal-vertical coupling prevented adequate transverse oscillation growth for efficient slow spill. This situation was corrected by an 8 mrad roll of each of twelve equi-spaced quadrupoles [1]. In order to avoid a repetition of this problem in the Tevatron, an extremely strong skew quadrupole circuit was built in at the outset. When the Tevatron was commissioned only 4$ of the capability of this circuit was required. Now, 20 years later, the excitation of this skew quadrupole circuit is approximately 60%. Other skew quadrupole correctors were installed in the neighborhood of the long straight sections, and for a variety of reasons the number of elements in the strong circuit was reduced from 48 to 42. These are relatively minor changes in the present context. Recall that in the normal Tevatron tuning process the skew quad circuits are adjusted to minimize the difference between the horizontal and vertical tunes to the level of {Delta}{nu}{sub min} {approx} 0.003. Normally the horizontal-vertical coupling is not observed directly by orbit measurements during this procedure. it was recognized that the strength of the skew quadrupole settings would imply an uncorrected minimum tune difference of 0.2 units. Clearly, with the skew quad circuit turned off the coupling of the orbital motion should be easily observable. In the following sections, the authors describe the recent Tevatron studies that exhibit the transverse coupling and the analyses that link these observations to the long term development of a

  12. Protein Structure

    ERIC Educational Resources Information Center

    Asmus, Elaine Garbarino

    2007-01-01

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

  13. Emergent behavior in strongly correlated electron systems.

    PubMed

    Pines, David

    2016-09-01

    I describe early work on strongly correlated electron systems (SCES) from the perspective of a theoretical physicist who, while a participant in their reductionist top-down beginnings, is now part of the paradigm change to a bottom-up 'emergent' approach with its focus on using phenomenology to find the organizing principles responsible for their emergent behavior disclosed by experiment-and only then constructing microscopic models that incorporate these. After considering the organizing principles responsible for the emergence of plasmons, quasiparticles, and conventional superconductivity in SCES, I consider their application to three of SCES's sister systems, the helium liquids, nuclei, and the nuclear matter found in neutron stars. I note some recent applications of the random phase approximation and examine briefly the role that paradigm change is playing in two central problems in our field: understanding the emergence and subsequent behavior of heavy electrons in Kondo lattice materials; and finding the mechanism for the unconventional superconductivity found in heavy electron, organic, cuprate, and iron-based materials. PMID:27484183

  14. Mars nightside electrons over strong crustal fields

    NASA Astrophysics Data System (ADS)

    Shane, Alexander D.; Xu, Shaosui; Liemohn, Michael W.; Mitchell, David L.

    2016-04-01

    We investigated 7 years worth of data from the electron reflectometer and magnetometer aboard Mars Global Surveyor to quantify the deposition of photoelectron and solar wind electron populations on the nightside of Mars, over the strong crustal field region located in the southern hemisphere. Just under 600,000 observations, each including energy and pitch angle distributions, were examined. For solar zenith angles (SZA) less than 110°, photoelectrons have the highest occurrence rate; beyond that, plasma voids occur most often. In addition, for SZA >110°, energy deposition of electrons mainly occurs on vertical field lines with median pitch angle averaged energy flux values on the order of 107-108 eV cm-2 s-1. The fraction of downward flux that is deposited at a given location was typically low (16% or smaller), implying that the majority of precipitated electrons are magnetically reflected or scattered back out. The average energy of the deposited electrons is found to be 20-30 eV, comparable to typical energies of photoelectrons and unaccelerated solar wind electrons. Median electron flux values, from near-vertical magnetic field lines past solar zenith angle of 110°, calculated in this study produced a total electron content of 4.2 × 1014 m-2 and a corresponding peak density of 4.2 × 103 cm-3.

  15. Strong anticipation: complexity matching in interpersonal coordination.

    PubMed

    Marmelat, Vivien; Delignières, Didier

    2012-10-01

    A subtle coordination occurs within complex systems, between multiple nested sub-systems. This intra-system coordination can be detected by the presence of 1/f fluctuations produced by the system. But coordination can occur also between systems. Interpersonal coordination has been studied from a local point of view until now, focusing on macroscopic interactions. But the recent concept of strong anticipation introduced by Dubois (Lect Notes Comput Sci 2684:110-132, 2003) suggests that interactions could occur on multiple levels between complex systems. The hypothesis is that time series in interpersonal synchronization present a matching of the complexity index (fractal exponent). Moreover, it is argued that this matching is not a consequence of short-term adaptations but reveals a global coordination between participants. Eleven pairs of participants oscillated a hand-held pendulum in the in-phase pattern for 11 min, in three conditions where the coupling strength was manipulated by the perceptual feedbacks. The results show a high correlation between fractal exponents irrespective of the coupling strength, and a very low percentage of local cross-correlations between time series appear at lag 0 and lag 1. These results suggest that interpersonal coordination, and more globally synchronization of participants with natural environments, is based on non-local time scales. PMID:22865163

  16. Platinum Nanoparticles Strongly Bonded to Freestanding Graphene

    NASA Astrophysics Data System (ADS)

    Thibado, Paul; Schoelz, J. K.; Ghosh, P. K.; Thompson, J.; Dong, L.; Neek-Amal, M.; Peeters, F. M.

    2015-03-01

    Freestanding graphene membranes were successfully functionalized with platinum nanoparticles (Pt NPs). The membranes were imaged using high-resolution transmission electron microscopy, revealing a homogeneous distribution of uniformly sized, single-crystal Pt NPs that exhibit a preferred orientation and nearest-neighbor distance. The Pt NPs were also found to be partially elevated by the graphene substrate, as deduced from atomic-resolution scanning tunneling microscopy (STM) images. Furthermore, the electrostatic force between the STM tip and sample was utilized to estimate the binding energy of the Pt NPs to the suspended graphene. Local strain accumulation due to strong sp3 bond formation is thought to be the origin of the Pt NP self-organization. Such detailed insight into the atomic nature of this functionalized system was only possible through the cooperation of dual microscopic techniques combined with molecular dynamics simulations. The findings are expected to shape future approaches to develop high-performance electronics based on nanoparticle-functionalized graphene as well as fuel cells using Pt NP catalysts. Financial support provided by the Office of Naval Research under Grant No. N00014-10-1-0181 and the National Science Foundation under Grant No. DMR-0855358.

  17. Developments in strong shock wave position tracking

    NASA Astrophysics Data System (ADS)

    Rae, Philip; Glover, Brain; Perry, Lee; WX-6; WX-7 Team

    2011-06-01

    This poster will highlight several modified techniques to allow the position vs. time to be tracked in strong shock situations (such as detonation). Each is a modification or improvement of existing ideas either making use of advances in specialist materials availability or recent advances in electronics.) Shorting embedded mini-coaxial cable with a standing microwave pattern. This technique is a modified version of an old LANL method of shock position tracking making use of a traveling short imposed in an embedded coaxial cable. A high frequency standing wave (3-8GHz) is present in the cable and the moving short position can be tracked by monitoring the output voltage envelope as a function of time. A diode detector is used to allow the envelope voltage to be monitored on a regular low frequency digitizer significantly reducing the cost. The small and cheap high frequency voltage generators now available allow much greater spatial resolution than possible previously. 2) Very thin shorting resistance track gauges. Parallel tracks of constantan resistance material are etched on a thin dielectric substrate. The gauges are less than 0.2 mm thick. The ionized gas present in a detonation front sweeps up the tracks lowering the measured resistance. A potential divider circuit allows the shock position vs. time to be monitored on a regular digitizer after easy calibration. The novel feature is the thin section of the gauge producing minimal perturbation in the detonation front.

  18. Dispersion discontinuities of strong collisionless shocks

    NASA Technical Reports Server (NTRS)

    Coroniti, F. V.

    1970-01-01

    Linear fluid equations are used to estimate wave train properties of strong collisionless shocks. Fast shocks exhibit several dispersion changes with increasing Mach number. For perpendicular propagation into a finite-beta plasma, an ion cyclotron radius trailing wave train exists only for (M sub F)2 is smaller than 2. Oblique fast shocks have a leading ion inertia wave train if M sub A is smaller than root of M(+)/M(-) cos theta/2 and a trailing electron inertia train if M sub A is greater than root of M(+)/M(-) cos theta/2. If the downstream sound speed exceeds the flow speed, linear wave theory predicts a trailing ion acoustic structure which probably resides within the magnetic shock. For a turbulent shock model in which an effective electron-ion collision frequency exceeds the lower hybrid frequency, ions decouple from the magnetic field; the shock wave train now trails with electron inertia and electron gyroradius lengths. Comparisons of this turbulent model and observations on the earth's bow shock are made.

  19. Delineating parton distributions and the strong coupling

    DOE PAGESBeta

    Jimenez-Delgado, P.; Reya, E.

    2014-04-29

    In this study, global fits for precision determinations of parton distributions, together with the highly correlated strong coupling αs, are presented up to next-to-next-to- leading order (NNLO) of QCD utilizing most world data (charm and jet production data are used where theoretically possible), except Tevatron gauge boson production data and LHC data which are left for genuine predictions. This is done within the 'dynamical' (valencelike input at Q02 = 0.8 GeV2 ) and 'standard' (input at Q02 = 2 GeV2) approach. The stability and reliability of the results are ensured by including nonperturbative higher-twist terms, nuclear corrections as well asmore » target mass corrections, and by applying various (Q2, W2) cuts on available data. In addition, the Q02 dependence of the results is studied in detail. Predictions are given, in particular for LHC, on gauge and Higgs boson as well as for top-quark pair production. At NNLO the dynamical approach results in αs(MZ2) = 0.1136 ± 0.0004, whereas the somewhat less constrained standard fit gives αs(MZ2) = 0.1162 ± 0.0006.« less

  20. Strong washout approximation to resonant leptogenesis

    NASA Astrophysics Data System (ADS)

    Garbrecht, Björn; Gautier, Florian; Klaric, Juraj

    2014-09-01

    We show that the effective decay asymmetry for resonant Leptogenesis in the strong washout regime with two sterile neutrinos and a single active flavour can in wide regions of parameter space be approximated by its late-time limit ɛ=Xsin(2varphi)/(X2+sin2varphi), where X=8πΔ/(|Y1|2+|Y2|2), Δ=4(M1-M2)/(M1+M2), varphi=arg(Y2/Y1), and M1,2, Y1,2 are the masses and Yukawa couplings of the sterile neutrinos. This approximation in particular extends to parametric regions where |Y1,2|2gg Δ, i.e. where the width dominates the mass splitting. We generalise the formula for the effective decay asymmetry to the case of several flavours of active leptons and demonstrate how this quantity can be used to calculate the lepton asymmetry for phenomenological scenarios that are in agreement with the observed neutrino oscillations. We establish analytic criteria for the validity of the late-time approximation for the decay asymmetry and compare these with numerical results that are obtained by solving for the mixing and the oscillations of the sterile neutrinos. For phenomenologically viable models with two sterile neutrinos, we find that the flavoured effective late-time decay asymmetry can be applied throughout parameter space.

  1. Frank Murkowski, a strong voice for energy

    SciTech Connect

    1997-09-01

    American Gas presents another in its series of interviews with influential senators and representatives in Washington. This interview with Sen. Frank Murkowski, R-Alaska, was conducted by Deborah Estes, A.G.A. managing director of government relations, and Jeff Murray, A.G.A. government relations director. Murkowski was elected to the Senate in 1980 and today serves as chairman of the Senate Energy and Natural Resources Committee, where he is known as a strong voice on energy supply issues. He answered the following questions. What are some of the major energy issues you would like to see addressed during the 105th Congress? What are the prospects for developing the natural gas resources in Alaska for export or for use in the United States? What is your view on whether federal legislation on electric restructuring is needed and, if so, what would be the critical components of such legislation? Are you satisfied with the pace of unbundling by natural gas local distribution companies? Do you feel that if federal term limits were imposed, members of Congress from small-population states like Alaska would continue to have the opportunity to chair a full committee? Do you believe the Republicans will retain control of the Senate, and, if so, can they reach the magic 60-seat margin?

  2. Emergent behavior in strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Pines, David

    2016-09-01

    I describe early work on strongly correlated electron systems (SCES) from the perspective of a theoretical physicist who, while a participant in their reductionist top-down beginnings, is now part of the paradigm change to a bottom-up ‘emergent’ approach with its focus on using phenomenology to find the organizing principles responsible for their emergent behavior disclosed by experiment—and only then constructing microscopic models that incorporate these. After considering the organizing principles responsible for the emergence of plasmons, quasiparticles, and conventional superconductivity in SCES, I consider their application to three of SCES’s sister systems, the helium liquids, nuclei, and the nuclear matter found in neutron stars. I note some recent applications of the random phase approximation and examine briefly the role that paradigm change is playing in two central problems in our field: understanding the emergence and subsequent behavior of heavy electrons in Kondo lattice materials; and finding the mechanism for the unconventional superconductivity found in heavy electron, organic, cuprate, and iron-based materials.

  3. Collective phases of strongly interacting cavity photons

    NASA Astrophysics Data System (ADS)

    Wilson, Ryan M.; Mahmud, Khan W.; Hu, Anzi; Gorshkov, Alexey V.; Hafezi, Mohammad; Foss-Feig, Michael

    2016-05-01

    We study a coupled array of coherently driven photonic cavities, which maps onto a driven-dissipative XY spin-1/2 model with ferromagnetic couplings in the limit of strong optical nonlinearities. Using a site-decoupled mean-field approximation, we identify steady state phases with canted antiferromagnetic order, in addition to limit cycle phases, where oscillatory dynamics persist indefinitely. We also identify collective bistable phases, where the system supports two steady states among spatially uniform, antiferromagnetic, and limit cycle phases. We compare these mean-field results to exact quantum trajectories simulations for finite one-dimensional arrays. The exact results exhibit short-range antiferromagnetic order for parameters that have significant overlap with the mean-field phase diagram. In the mean-field bistable regime, the exact quantum dynamics exhibits real-time collective switching between macroscopically distinguishable states. We present a clear physical picture for this dynamics, and establish a simple relationship between the switching times and properties of the quantum Liouvillian. This research was supported in part by the NSF under Grant No. NSF PHY11-25915.

  4. Cooperative phenomena in strongly correlated electron systems

    NASA Astrophysics Data System (ADS)

    Farkašovský, Pavol

    2010-10-01

    In this review we present results of our theoretical study of cooperative phenomena in strongly correlated electron systems obtained within various generalizations of the Falicov-Kimball model. The primary goal of this study was to identify crucial interactions that lead to the stabilization of the specific cooperative phenomenon, and then try to elaborate its comprehensive microscopic description. The main attention is devoted to a discussion of valence and metal-insulator transitions, formation of charge and spin ordering, electronic ferroelectricity, itinerant ferromagmetism and mechanisms leading to their stabilization. Among the major mechanisms we examine the effect of local and nonlocal Coulomb interaction between localized and itinerant electrons, local and nonlocal hybridization, long-range and correlated hopping of itinerant electrons and spin-dependent interaction between localized and itinerant electrons, both for zero and nonzero temperatures, as well as for doped and undoped systems. Finally, the relevance of resultant solutions for a description of rare-earth and transition-metal compounds is discussed.

  5. Bioinspired Strong and Highly Porous Glass Scaffolds

    PubMed Central

    Saiz, Eduardo; Tomsia, Antoni P.

    2011-01-01

    The quest for more efficient energy-related technologies is driving the development of porous and high-performance structural materials with exceptional mechanical strength. Natural materials achieve their strength through complex hierarchical designs and anisotropic structures that are extremely difficult to replicate synthetically. We emulate nature’s design by direct-ink-write assembling of glass scaffolds with a periodic pattern, and controlled sintering of the filaments into anisotropic constructs similar to biological materials. The final product is a porous glass scaffold with a compressive strength (136 MPa) comparable to that of cortical bone and a porosity (60%) comparable to that of trabecular bone. The strength of this porous glass scaffold is ~100 times that of polymer scaffolds and 4–5 times that of ceramic and glass scaffolds with comparable porosities reported elsewhere. The ability to create both porous and strong structures opens a new avenue for fabricating scaffolds for a broad array of applications, including tissue engineering, filtration, lightweight composites, and catalyst support. PMID:21544222

  6. Observed strong currents under global tropical cyclones

    NASA Astrophysics Data System (ADS)

    Chang, Yu-Chia; Tseng, Ruo-Shan; Chu, Peter C.; Chen, Jau-Ming; Centurioni, Luca R.

    2016-07-01

    Global data from drifters of the Surface Velocity Program (Niiler, 2001) and tropical cyclones (TCs) from the Joint Typhoon Warning Center and National Hurricane Center were analyzed to demonstrate strong ocean currents and their characteristics under various storm intensities in the Northern Hemisphere (NH) and in the Southern Hemisphere (SH). Mean TC's translation speed (Uh) is faster in the NH (~ 4.7 m s- 1) than in the SH (~ 4.0 m s- 1), owing to the fact that TCs are more intense in the NH than in the SH. The rightward (leftward) bias of ocean mixed-layer (OML) velocity occurs in the NH (SH). As a result of this slower Uh and thus a smaller Froude number in the SH, the flow patterns in the SH under the same intensity levels of TCs are more symmetric relative to the TC center and the OML velocities are stronger. This study provides the first characterization of the near-surface OML velocity response to all recorded TCs in the SH from direct velocity measurements.

  7. Strong thin membrane structure. [solar sails

    NASA Technical Reports Server (NTRS)

    Frazer, R. E. (Inventor)

    1979-01-01

    A continuous process is described for producing strong lightweight structures for use as solar sails for spacecraft propulsion by radiation pressure. A thin reflective coating, such as aluminum, is applied to a rotating cylinder. A nylon mesh, applied over the aluminum coating, is then coated with a polymerizing material such as a para-xylylene monomer gas to polymerize as a film bound to the mesh and the aluminum. An emissivity increasing material such as chromium or silicon monoxide is applied to the polymer film to disperse such material colloidally into the growing polymer film, or to the final polymer film. The resulting membrane structure is then removed from the cylinder. Alternately, the membrane structure can be formed by etching a substrate in the form of an organic film such as a polymide, or a metal foil, to remove material from the substrate and reduce its thickness. A thin reflective coating (aluminum) is applied on one side of the substrate, and an emissivity increasing coating is applied on the reverse side of the substrate.

  8. Quark matter under strong magnetic fields

    NASA Astrophysics Data System (ADS)

    Peres Menezes, Débora; Laércio Lopes, Luiz

    2016-02-01

    We revisit three of the mathematical formalisms used to describe magnetized quark matter in compact objects within the MIT and the Nambu-Jona-Lasinio models and then compare their results. The tree formalisms are based on 1) isotropic equations of state, 2) anisotropic equations of state with different parallel and perpendicular pressures and 3) the assumption of a chaotic field approximation that results in a truly isotropic equation of state. We have seen that the magnetization obtained with both models is very different: while the MIT model produces well-behaved curves that are always positive for large magnetic fields, the NJL model yields a magnetization with lots of spikes and negative values. This fact has strong consequences on the results based on the existence of anisotropic equations of state. We have also seen that, while the isotropic formalism results in maximum stellar masses that increase considerably when the magnetic fields increase, maximum masses obtained with the chaotic field approximation never vary more than 5.5%. The effect of the magnetic field on the radii is opposed in the MIT and NJL models: with both formalisms, isotropic and chaotic field approximation, for a fixed mass, the radii increase with the increase of the magnetic field in the MIT bag model and decrease in the NJL, the radii of quark stars described by the NJL model being smaller than the ones described by the MIT model.

  9. Thermal Infrared Anomalies of Several Strong Earthquakes

    PubMed Central

    Wei, Congxin; Guo, Xiao; Qin, Manzhong

    2013-01-01

    In the history of earthquake thermal infrared research, it is undeniable that before and after strong earthquakes there are significant thermal infrared anomalies which have been interpreted as preseismic precursor in earthquake prediction and forecasting. In this paper, we studied the characteristics of thermal radiation observed before and after the 8 great earthquakes with magnitude up to Ms7.0 by using the satellite infrared remote sensing information. We used new types of data and method to extract the useful anomaly information. Based on the analyses of 8 earthquakes, we got the results as follows. (1) There are significant thermal radiation anomalies before and after earthquakes for all cases. The overall performance of anomalies includes two main stages: expanding first and narrowing later. We easily extracted and identified such seismic anomalies by method of “time-frequency relative power spectrum.” (2) There exist evident and different characteristic periods and magnitudes of thermal abnormal radiation for each case. (3) Thermal radiation anomalies are closely related to the geological structure. (4) Thermal radiation has obvious characteristics in abnormal duration, range, and morphology. In summary, we should be sure that earthquake thermal infrared anomalies as useful earthquake precursor can be used in earthquake prediction and forecasting. PMID:24222728

  10. Parallel search of strongly ordered game trees

    SciTech Connect

    Marsland, T.A.; Campbell, M.

    1982-12-01

    The alpha-beta algorithm forms the basis of many programs that search game trees. A number of methods have been designed to improve the utility of the sequential version of this algorithm, especially for use in game-playing programs. These enhancements are based on the observation that alpha beta is most effective when the best move in each position is considered early in the search. Trees that have this so-called strong ordering property are not only of practical importance but possess characteristics that can be exploited in both sequential and parallel environments. This paper draws upon experiences gained during the development of programs which search chess game trees. Over the past decade major enhancements of the alpha beta algorithm have been developed by people building game-playing programs, and many of these methods will be surveyed and compared here. The balance of the paper contains a study of contemporary methods for searching chess game trees in parallel, using an arbitrary number of independent processors. To make efficient use of these processors, one must have a clear understanding of the basic properties of the trees actually traversed when alpha-beta cutoffs occur. This paper provides such insights and concludes with a brief description of a refinement to a standard parallel search algorithm for this problem. 33 references.

  11. Particle Acceleration in Superluminal Strong Waves

    NASA Astrophysics Data System (ADS)

    Teraki, Yuto; Ito, Hirotaka; Nagataki, Shigehiro

    2015-06-01

    We calculate the electron acceleration in random superluminal strong waves (SLSWs) and radiation from them using numerical methods in the context of the termination shocks of pulsar wind nebulae. We pursue the orbit of electrons by solving the equation of motion in the analytically expressed electromagnetic turbulences. These consist of a primary SLS and isotropically distributed secondary electromagnetic waves. Under the dominance of the secondary waves, all electrons gain nearly equal energy. On the other hand, when the primary wave is dominant, selective acceleration occurs. The phase of the primary wave for electrons moving nearly along the wavevector changes very slowly compared with the oscillation of the wave, which is “phase-locked,” and such electrons are continuously accelerated. This acceleration by SLSWs may play a crucial role in pre-shock acceleration. In general, the radiation from the phase-locked population is different from the synchro-Compton radiation. However, when the amplitude of the secondary waves is not extremely weaker than that of the primary wave, the typical frequency can be estimated from synchro-Compton theory using the secondary waves. The primary wave does not contribute to the radiation because the SLSW accelerates electrons almost linearly. This radiation can be observed as a radio knot at the upstream of the termination shocks of the pulsar wind nebulae without counterparts in higher frequency ranges.

  12. DYNAMICS OF STRONGLY TWISTED RELATIVISTIC MAGNETOSPHERES

    SciTech Connect

    Parfrey, Kyle; Beloborodov, Andrei M.; Hui, Lam

    2013-09-10

    Magnetar magnetospheres are believed to be strongly twisted due to shearing of the stellar crust by internal magnetic stresses. We present time-dependent axisymmetric simulations showing in detail the evolution of relativistic force-free magnetospheres subjected to slow twisting through large angles. When the twist amplitude is small, the magnetosphere moves quasi-statically through a sequence of equilibria of increasing free energy. At some twist amplitude the magnetosphere becomes tearing-mode unstable to forming a resistive current sheet, initiating large-scale magnetic reconnection in which a significant fraction of the magnetic free energy can be dissipated. This ''critical'' twist angle is insensitive to the resistive length scale. Rapid shearing temporarily stabilizes the magnetosphere beyond the critical angle, allowing the magnetosphere of a rapidly differentially rotating star to store and dissipate more free energy. In addition to these effects, shearing the surface of a rotating star increases the spindown torque applied to the star. If shearing is much slower than rotation, the resulting spikes in spindown rate can occur on timescales anywhere from the long twisting timescale to the stellar spin period or shorter, depending both on the stellar shear distribution and the existing distribution of magnetospheric twists. A model in which energy is stored in the magnetosphere and released by a magnetospheric instability therefore predicts large changes in the measured spindown rate before soft gamma repeater giant flares.

  13. Efimov correlations in strongly interacting Bose gases

    NASA Astrophysics Data System (ADS)

    Barth, Marcus; Hofmann, Johannes

    2015-12-01

    We compute the virial coefficients, the contact parameters, and the momentum distribution of a strongly interacting three-dimensional Bose gas by means of a virial expansion up to third order in the fugacity, which takes into account three-body correlations exactly. Our results characterize the nondegenerate regime of the interacting Bose gas, where the thermal wavelength is smaller than the interparticle spacing but the scattering length may be arbitrarily large. We observe a rapid variation of the third virial coefficient as the scattering length is tuned across the three-atom and the atom-dimer thresholds. The momentum distribution at unitarity displays a universal high-momentum tail with a log-periodic momentum dependence, which is a direct signature of Efimov physics. We provide a quantitative description of the momentum distribution at high momentum as measured by P. Makotyn et al. [Nat. Phys. 10, 116 (2014), 10.1038/nphys2850], and our calculations indicate that the lowest trimer state might not be occupied in the experiment. Our results allow for a spectroscopy of Efimov states in the unitary limit.

  14. Anomalous solutions to the strong CP problem.

    PubMed

    Hook, Anson

    2015-04-10

    We present a new mechanism for solving the strong CP problem using a Z_{2} discrete symmetry and an anomalous U(1) symmetry. A Z_{2} symmetry is used so that two gauge groups have the same theta angle. An anomalous U(1) symmetry makes the difference between the two theta angles physical and the sum unphysical. Two models are presented where the anomalous symmetry manifests itself in the IR in different ways. In the first model, there are massless bifundamental quarks, a solution reminiscent of the massless up quark solution. In the IR of this model, the η^{'} boson relaxes the QCD theta angle to the difference between the two theta angles-in this case zero. In the second model, the anomalous U(1) symmetry is realized in the IR as a dynamically generated mass term that has exactly the phase needed to cancel the theta angle. Both of these models make the extremely concrete prediction that there exist new colored particles at the TeV scale. PMID:25910109

  15. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, F.

    1993-12-07

    Strong liquid-crystalline polymeric (LCP) compositions of matter are described. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment. 27 figures.

  16. Strong liquid-crystalline polymeric compositions

    DOEpatents

    Dowell, Flonnie

    1993-01-01

    Strong liquid-crystalline polymeric (LCP) compositions of matter. LCP backbones are combined with liquid crystalline (LC) side chains in a manner which maximizes molecular ordering through interdigitation of the side chains, thereby yielding materials which are predicted to have superior mechanical properties over existing LCPs. The theoretical design of LCPs having such characteristics includes consideration of the spacing distance between side chains along the backbone, the need for rigid sections in the backbone and in the side chains, the degree of polymerization, the length of the side chains, the regularity of the spacing of the side chains along the backbone, the interdigitation of side chains in sub-molecular strips, the packing of the side chains on one or two sides of the backbone to which they are attached, the symmetry of the side chains, the points of attachment of the side chains to the backbone, the flexibility and size of the chemical group connecting each side chain to the backbone, the effect of semiflexible sections in the backbone and the side chains, and the choice of types of dipolar and/or hydrogen bonding forces in the backbones and the side chains for easy alignment.

  17. Polymer ejection from strong spherical confinement

    NASA Astrophysics Data System (ADS)

    Piili, J.; Linna, R. P.

    2015-12-01

    We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.

  18. Collective phases of strongly interacting cavity photons

    NASA Astrophysics Data System (ADS)

    Wilson, Ryan; Foss-Feig, Michael; Mahmud, Khan; Hafezi, Mohammad

    We study the steady state phases of the Bose-Hubbard model in the presence of dissipation and coherent driving, which in the limit of strong interactions maps onto a driven-dissipative XX spin-1/2 model with transverse and longitudinal fields. Using a site-decoupled mean-field approximation, we identify phases with antiferromagnetic and spin density wave order, in addition to limit cycle phases, where oscillatory dynamics persist indefinitely. We also identify collective bistable phases, where the system supports two steady states among spatially uniform, antiferromagnetic, and limit cycle phases. We compare these mean-field results to exact quantum trajectories for one dimensional cavity arrays. The quantum results exhibit short-range antiferromagnetic and spin density wave order, in good qualitative agreement with the mean-field predictions. In the bistable regime, this system exhibits real-time collective switching between macroscopically distinguishable states. We present a clear physical picture for these dynamics, and establish a simple relationship between the switching times and properties of the quantum Liouvillian.

  19. Stochastic properties of strongly coupled plasmas.

    PubMed

    Morozov, I V; Norman, G E; Valuev, A A

    2001-03-01

    Stochastic properties of equilibrium strongly coupled plasmas are investigated by a molecular dynamics method. The Krylov-Kolmogorov entropy K and the dynamical memory time t(m) are calculated both for electrons and ions with mass ratios 10-10(5). Two values of K entropy for ions are discovered corresponding to electron and ion time scales. The dependence of the K entropy on the number of particles, the nonideality parameter, and the form of the interaction potential is investigated. The problem of the accuracy of molecular dynamics simulations is discussed. A universal relation between Kt(m) and the fluctuation of the total energy of the system is obtained. The relation does not depend on the numerical integration scheme, temperature, density, and the interparticle interaction potential, so that it may be applied to arbitrary dynamic systems. Transition from dynamic to stochastic correlation is treated for both electron and ion velocity autocorrelation functions, for Langmuir and ion-sound plasma wave dynamic structure factors. We point to quantum uncertainty as a physical reason which limits dynamic (Newton) correlation for times greater than t(m). PMID:11308773

  20. Thermal infrared anomalies of several strong earthquakes.

    PubMed

    Wei, Congxin; Zhang, Yuansheng; Guo, Xiao; Hui, Shaoxing; Qin, Manzhong; Zhang, Ying

    2013-01-01

    In the history of earthquake thermal infrared research, it is undeniable that before and after strong earthquakes there are significant thermal infrared anomalies which have been interpreted as preseismic precursor in earthquake prediction and forecasting. In this paper, we studied the characteristics of thermal radiation observed before and after the 8 great earthquakes with magnitude up to Ms7.0 by using the satellite infrared remote sensing information. We used new types of data and method to extract the useful anomaly information. Based on the analyses of 8 earthquakes, we got the results as follows. (1) There are significant thermal radiation anomalies before and after earthquakes for all cases. The overall performance of anomalies includes two main stages: expanding first and narrowing later. We easily extracted and identified such seismic anomalies by method of "time-frequency relative power spectrum." (2) There exist evident and different characteristic periods and magnitudes of thermal abnormal radiation for each case. (3) Thermal radiation anomalies are closely related to the geological structure. (4) Thermal radiation has obvious characteristics in abnormal duration, range, and morphology. In summary, we should be sure that earthquake thermal infrared anomalies as useful earthquake precursor can be used in earthquake prediction and forecasting. PMID:24222728

  1. Protein folds and protein folding

    PubMed Central

    Schaeffer, R. Dustin; Daggett, Valerie

    2011-01-01

    The classification of protein folds is necessarily based on the structural elements that distinguish domains. Classification of protein domains consists of two problems: the partition of structures into domains and the classification of domains into sets of similar structures (or folds). Although similar topologies may arise by convergent evolution, the similarity of their respective folding pathways is unknown. The discovery and the characterization of the majority of protein folds will be followed by a similar enumeration of available protein folding pathways. Consequently, understanding the intricacies of structural domains is necessary to understanding their collective folding pathways. We review the current state of the art in the field of protein domain classification and discuss methods for the systematic and comprehensive study of protein folding across protein fold space via atomistic molecular dynamics simulation. Finally, we discuss our large-scale Dynameomics project, which includes simulations of representatives of all autonomous protein folds. PMID:21051320

  2. Molecular Dynamics Simulations of a Pulmonary Surfactant Protein B Peptide in a Lipid Monolayer

    PubMed Central

    Freites, J. Alfredo; Choi, Yunsoo; Tobias, Douglas J.

    2003-01-01

    Pulmonary surfactant is a complex mixture of lipids and proteins that lines the air/liquid interface of the alveolar hypophase and confers mechanical stability to the alveoli during the breathing process. The desire to formulate synthetic mixtures for low-cost prophylactic and therapeutic applications has motivated the study of the specific roles and interactions of the different components. All-atom molecular dynamics simulations were carried out on a model system composed of a monolayer of palmitic acid (PA) and a surfactant protein B peptide, SP-B1–25. A detailed structural characterization as a function of the lipid monolayer specific area revealed that the peptide remains inserted in the monolayer up to values of specific area corresponding to an untilted condensed phase of the the pure palmitic acid monolayer. The system remains stable by altering the conformational order of both the anionic lipid monolayer and the peptide secondary structure. Two elements appear to be key for the constitution of this phase: an electrostatic interaction between the cationic peptide residues with the anionic headgroups, and an exclusion of the aromatic residues on the hydrophobic end of the peptide from the hydrophilic and aqueous regions. PMID:12668426

  3. Light-Scattering Studies of Protein Solutions: Role of Hydration in Weak Protein-Protein Interactions

    PubMed Central

    Paliwal, A.; Asthagiri, D.; Abras, D.; Lenhoff, A. M.; Paulaitis, M. E.

    2005-01-01

    We model the hydration contribution to short-range electrostatic/dispersion protein interactions embodied in the osmotic second virial coefficient, B2, by adopting a quasi-chemical description in which water molecules associated with the protein are identified through explicit molecular dynamics simulations. These water molecules reduce the surface complementarity of highly favorable short-range interactions, and therefore can play an important role in mediating protein-protein interactions. Here we examine this quasi-chemical view of hydration by predicting the interaction part of B2 and comparing our results with those derived from light-scattering measurements of B2 for staphylococcal nuclease, lysozyme, and chymotrypsinogen at 25°C as a function of solution pH and ionic strength. We find that short-range protein interactions are influenced by water molecules strongly associated with a relatively small fraction of the protein surface. However, the effect of these strongly associated water molecules on the surface complementarity of short-range protein interactions is significant, and must be taken into account for an accurate description of B2. We also observe remarkably similar hydration behavior for these proteins despite substantial differences in their three-dimensional structures and spatial charge distributions, suggesting a general characterization of protein hydration. PMID:15980182

  4. Stretching to Understand Proteins

    NASA Astrophysics Data System (ADS)

    Cieplak, Marek

    2007-03-01

    Mechanical stretching of single proteins has been studied experimentally for about 50 proteins yielding a variety of force patterns and values of the peak forces. We have performed a theoretical survey of 7749 proteins of known native structure and map out the landscape of possible dynamical behaviors unders stretching at constant speed. The model used is constructed based on the native geometry. It is solved by methods of molecular dynamics and validated by comparing the theoretical predictions to experimental results. We characterize the distribution of peak forces and on correlations with the system size and with the structure classification as characterized by the CATH scheme. We identify proteins with the biggest forces and show that they belong to few topology classes. We determine which protein segments act as mechanical clamps and show that, in most cases, they correspond to long stretches of parallel beta-strands, but other mechanisms are also possible. We then consider stretching by fluid flows. We show that unfolding induced by a uniform flow shows a richer behavior than that in the force clamp. The dynamics of unfolding is found to depend strongly on the selection of the amino acid, usually one of the termini, which is anchored. These features offer potentially wider diagnostic tools to investigate structure of proteins compared to experiments based on the atomic force microscopy.

  5. Protein denaturing on Nanospheres

    NASA Astrophysics Data System (ADS)

    Forrest, James; Teichroeb, Jonathan

    2007-03-01

    We have used localized surface plasmon resonance (LSPR) to monitor the structural changes that accompany thermal denaturing of Bovine Serum Albumin(BSA) adsorbed onto gold nanospheres of size 5nm-60nm. The effect of the protein on the LSPR was monitored by visible extinction spectroscopy. The position of the resonance is affected by the conformation of the adsorbed protein layer, and as such can be used as a very sensitive probe of thermal denaturing that is specific to the adsorbed protein. The results are compared to detailed calculations and show that full calculations can lead to significant increases in knowledge where gold nanospheres are used as biosensors. Thermal denaturing on spheres with diameter > 20 nm show strong similarity to bulk calorimetric studies of BSA in solution. BSA adsorbed on nanospheres with d<= 15 nm shows a qualitative difference in behavior, suggesting a sensitivity of denaturing characteristics on local surface curvature. Studies of isothermal denaturing kinetics were used to obtain an activatiuon barrier for thermal denaturing. This activation barrier also exhibited a strong dependence on nanoparticle size. These results may have important implications for other protein-nanoparticle interactions.

  6. Strong Coupling Gauge Theories in LHC ERA

    NASA Astrophysics Data System (ADS)

    Fukaya, H.; Harada, M.; Tanabashi, M.; Yamawaki, K.

    2011-01-01

    Higgs, or techni-dilaton - composite Higgs near conformality / Koichi Yamawaki -- Phase diagram of strongly interacting theories / Francesco Sannino -- Resizing conformal windows / O. Antipin and K. Tuominen -- Nearly conformal gauge theories on the lattice / Zoltan Fodor ... [et al.] -- Going beyond QCD in lattice gauge theory / G. T. Fleming -- Phases of QCD from small to large N[symbol]: (some) lattice results / A. Deuzeman, E. Pallante and M. P. Lombardo -- Lattice gauge theory and (quasi)-conformal technicolor / D. K. Sinclair and J. B. Kogut -- Study of the running coupling constant in 10-flavor QCD with the Schrodinger functional method / N. Yamada ... [et al.] -- Study of the running coupling in twisted Polyakov scheme / T. Aoyama ... [et al.].Running coupling in strong gauge theories via the lattice / Zoltan Fodor ... [et al.] -- Higgsinoless supersymmetry and hidden gravity / Michael L. Graesser, Ryuichiro Kitano and Masafumi Kurachi -- The latest status of LHC and the EWSB physics / S. Asai -- Continuum superpartners from supersymmetric unparticles / Hsin-Chia Cheng -- Review of minimal flavor constraints for technicolor / Hidenori S. Fukano and Francesco Sannino -- Standard model and high energy Lorentz violation / Damiano Anselmi -- Dynamical electroweak symmetry breaking and fourth family / Michio Hashimoto -- Holmorphic supersymmetric Nambu-Jona-Lasino model and dynamical electroweak symmetry breaking / Dong-Won Jung, Otto C. W. Kong and Jae Sik Lee -- Ratchet model of Baryogenesis / Tatsu Takeuchi, Azusa Minamizaki and Akio Sugamoto -- Classical solutions of field equations in Einstein Gauss-Bonnet gravity / P. Suranyi, C. Vaz and L. C. R. Wijewardhana -- Black holes constitute all dark matter / Paul H. Frampton -- Electroweak precision test and Z [symbol] in the three site Higgsless model / Tomohiro Abe -- Chiral symmetry and BRST symmetry breaking, quaternion reality and the lattice simulation / Sadataka Furui -- Holographic techni-dilaton, or

  7. Controlling strongly correlated dust clusters with lasers

    NASA Astrophysics Data System (ADS)

    Thomsen, Hauke; Ludwig, Patrick; Bonitz, Michael; Schablinski, Jan; Block, Dietmar; Schella, André; Melzer, André

    2014-09-01

    Lasers have been used extensively to manipulate matter in a controlled way - from single atoms and molecules up to macroscopic materials. They are particularly valuable for the analysis and control of mesoscopic systems such as few-particle clusters. Here we report on recent work on finite size complex (dusty) plasma systems. These are unusual types of clusters with a very strong inter-particle interaction so that, at room temperature, they are practically in their ground state. Lasers are employed as a tool to achieve excited states and phase transitions. The most attractive feature of dusty plasmas is that they allow for a precise diagnostic with single-particle resolution. From such measurements, the structural properties of finite two-dimensional (2D) clusters and three-dimensional (3D) spherical crystals in nearly harmonic traps—so-called Yukawa balls—have been explored in great detail. Their structural features—the shell compositions and the order within the shells—have been investigated and good agreement to theoretical predictions was found. Open questions on the agenda are the excitation behaviour, the structural changes and phase transitions that occur at elevated temperature. Here we report on recent experimental results where laser heating methods were further improved and applied to finite 2D and 3D dust clusters. Comparing to simulations, we demonstrate that laser heating indeed allows to increase the temperature in a controlled manner. For the analysis of thermodynamic properties and phase transitions in these finite systems, we present theoretical and experimental results on the basis of the instantaneous normal modes, pair distribution function and the recently introduced centre-two-particle correlation function.

  8. Synthetic Strong Ground Motion Validation and Prediction

    NASA Astrophysics Data System (ADS)

    Zeng, Y.

    2003-12-01

    In this paper, I first validate a ground motion simulation procedure against ground motion observation from the Imperial Valley, Loma Prieta, Landers, Northridge, Kobe, and Kocaeli earthquakes. The ground motion simulation procedure follows Zeng et al. (1994) using a composite source model. In that model, the source is taken as a superposition of circular subevents with a constant stress drop. The number of subevents and their radius follows a power law distribution equivalent to the Gutenberg and Richter's magnitude-frequency relation for seismicity. The heterogeneous nature of the composite source model is characterized by its maximum subevent size and subevent stress drop. As rupture propagates through each subevent, it radiates a circular crack rupture pulse. In addition to wave propagation through a layered earth, the model has been improved by including scattering waves from small scale heterogeneity structure of the earth, site specific ground motion prediction using weak motion site amplification, and nonlinear soil response using geotechnical engineering models. In the current validation study, the fixed and free model parameters have been systematically cataloged and the statistical distribution of those free parameters has been carefully identified. A critical component of the study is to define the function of goodness-of-fit. In this investigation I emphasize on goodness-of-fit based on ground motion response spectra. Other forms of goodness-of-fit based on seismic waveform, shake duration, accumulative energies, etc., are also examined. Based on the result, I then conduct broadband ground motion prediction from scenario earthquakes. The objective of this simulation is to argument the existing empirical strong ground motion database on magnitude, distance, and frequency range. The result will be used to test the function forms used in developing the Next-Generation-Attenuation relation initiated by PEER/SCEC/USGS.

  9. Strong washout approximation to resonant leptogenesis

    SciTech Connect

    Garbrecht, Björn; Gautier, Florian; Klaric, Juraj E-mail: florian.gautier@tum.de

    2014-09-01

    We show that the effective decay asymmetry for resonant Leptogenesis in the strong washout regime with two sterile neutrinos and a single active flavour can in wide regions of parameter space be approximated by its late-time limit ε=Xsin(2φ)/(X{sup 2}+sin{sup 2}φ), where X=8πΔ/(|Y{sub 1}|{sup 2}+|Y{sub 2}|{sup 2}), Δ=4(M{sub 1}-M{sub 2})/(M{sub 1}+M{sub 2}), φ=arg(Y{sub 2}/Y{sub 1}), and M{sub 1,2}, Y{sub 1,2} are the masses and Yukawa couplings of the sterile neutrinos. This approximation in particular extends to parametric regions where |Y{sub 1,2}|{sup 2}>> Δ, i.e. where the width dominates the mass splitting. We generalise the formula for the effective decay asymmetry to the case of several flavours of active leptons and demonstrate how this quantity can be used to calculate the lepton asymmetry for phenomenological scenarios that are in agreement with the observed neutrino oscillations. We establish analytic criteria for the validity of the late-time approximation for the decay asymmetry and compare these with numerical results that are obtained by solving for the mixing and the oscillations of the sterile neutrinos. For phenomenologically viable models with two sterile neutrinos, we find that the flavoured effective late-time decay asymmetry can be applied throughout parameter space.

  10. Strong Algerian Earthquake Strikes Near Capital City

    NASA Astrophysics Data System (ADS)

    Ayadi, A.; Maouche, S.; Harbi, A.; Meghraoui, M.; Beldjoudi, H.; Oussadou, F.; Mahsas, A.; Benouar, D.; Heddar, A.; Rouchiche, Y.; Kherroubi, A.; Frogneux, M.; Lammali, K.; Benhamouda, F.; Sebaï, A.; Bourouis, S.; Alasset, P. J.; Aoudia, A.; Cakir, Z.; Merahi, M.; Nouar, O.; Yelles, A.; Bellik, A.; Briole, P.; Charade, O.; Thouvenot, F.; Semane, F.; Ferkoul, A.; Deramchi, A.; Haned, S. A.

    On 21 May 2003, a damaging earthquake of Mw 6.8 struck the region of Boumerdes 40 km east of Algiers in northern Algeria (Figure 1). The mainshock, which lasted ~ 36-40 s, had devastating effects and claimed about 2300 victims, caused more than 11,450 injuries, and left about 200,000 people homeless. It destroyed and seriously damaged around 180,000 housing units and 6000 public buildings with losses estimated at $5 billion. The mainshock was widely felt within a radius of ~ 400 km in Algeria. To the north, the earthquake was felt in southeastern Spain, including the Balearic Islands, and also in Sardinia and in southern France. The mainshock location, which was calculated at 36.91°N, 3.58°E (15 km offshore of Zemmouri; Figure 1), and the local magnitude (Md 6.4) are from seismic records of local stations. International seismological centers obtained Mw 6.8 (NEIC) with a thrust focal mechanism solution and 1.83 × 1026 dyne.cm for the seismic moment. A sequence of aftershocks affected the epicentral area with two strong shocks reaching Mw 5.8 on 27 and 29 May 2003. Field investigations allowed us to assign a maximum intensity X (European Macroseismic Scale 98) and to report rockfalls, minor surface cracks, and liquefaction phenomena. The mainshock was not associated with inland surface faulting, but one of the most striking coseismic effects is the coastal uplift and the backwash along the littoral of the Mitidja basin.

  11. The Strong Lensing Time Delay Challenge (2014)

    NASA Astrophysics Data System (ADS)

    Liao, Kai; Dobler, G.; Fassnacht, C. D.; Treu, T.; Marshall, P. J.; Rumbaugh, N.; Linder, E.; Hojjati, A.

    2014-01-01

    Time delays between multiple images in strong lensing systems are a powerful probe of cosmology. At the moment the application of this technique is limited by the number of lensed quasars with measured time delays. However, the number of such systems is expected to increase dramatically in the next few years. Hundred such systems are expected within this decade, while the Large Synoptic Survey Telescope (LSST) is expected to deliver of order 1000 time delays in the 2020 decade. In order to exploit this bounty of lenses we needed to make sure the time delay determination algorithms have sufficiently high precision and accuracy. As a first step to test current algorithms and identify potential areas for improvement we have started a "Time Delay Challenge" (TDC). An "evil" team has created realistic simulated light curves, to be analyzed blindly by "good" teams. The challenge is open to all interested parties. The initial challenge consists of two steps (TDC0 and TDC1). TDC0 consists of a small number of datasets to be used as a training template. The non-mandatory deadline is December 1 2013. The "good" teams that complete TDC0 will be given access to TDC1. TDC1 consists of thousands of lightcurves, a number sufficient to test precision and accuracy at the subpercent level, necessary for time-delay cosmography. The deadline for responding to TDC1 is July 1 2014. Submissions will be analyzed and compared in terms of predefined metrics to establish the goodness-of-fit, efficiency, precision and accuracy of current algorithms. This poster describes the challenge in detail and gives instructions for participation.

  12. High Concentration Suspensions Under Strong Tidal Flows

    NASA Astrophysics Data System (ADS)

    Kineke, G. C.; Milligan, T. G.; Heath, K. M.; Law, B. A.

    2006-12-01

    An experiment investigating the influence of high-concentration suspensions of fine sediments (fluid muds) on a quasi-steady flow was carried out in the Petitcodiac River, Moncton, New Brunswick, Canada in August 2006. Concurrent measurements of fluid properties (salinity, temperature, density), suspended-sediment concentration, current velocity and shear were made throughout the water column over portions of several tidal cycles. The Petitcodiac was chosen because of consistently high suspended-sediment concentrations (0.5- >200 g/L) and large tidal range (>4 m) producing strong current velocities (> 1.5 m/s). Thus the Peticodiac serves as an ideal natural flume for examining the behavior of muddy suspensions under both accelerating and decelerating flows. Instrumentation included a profiling package with paired electromagnetic current meters mounted 0.6 m apart, a CTD, and an Optical Backscatterance Sensor with a pump system for in situ calibrations. Approximately 1.5 hours after the passage of the tidal bore and a fully mixed turbulent flow, the water column begins to stratify and a high concentration bottom layer forms persisting through the ensuing ebb. Measured suspended-sediment concentrations reached 286 g/L at the bottom and low shear rates of 0.13 s-1 in the upper water column increased to ~0.5 s-1 through the lutocline 1 m above the bed, and decreased to approximately 0 within the fluid mud. Analysis is in progress and the data set provides an excellent means to test threshold conditions regarding suppression of turbulence by sediment-induced stratification and the carrying capacity of turbulent flows.

  13. RELATIONSHIP BETWEEN SEED YIELD AND SEED PROTEIN IN HIGH PROTEIN SOYBEAN POPULATIONS

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Soybean seed yield and protein concentration often show a strong negative correlation. Initial results of our study indicate that development of soybean lines with high yield and high protein concentration is possible by selecting for protein concentration first. We evaluated the relationship of yie...

  14. Competing Orders in Strongly Correlated Systems

    NASA Astrophysics Data System (ADS)

    Ramachandran, Ganesh

    Systems with competing orders are of great interest in condensed matter physics. When two phases have comparable energies, novel interplay effects such can be induced by tuning an appropriate parameter. In this thesis, we study two problems of competing orders - (i) ultracold atom gases with competing superfluidity and Charge Density Wave (CDW) orders, and (ii) low dimensional antiferromagnets with Neel order competing against various disordered ground states. In the first part of the thesis, we study the attractive Hubbard model which could soon be realized in ultracold atom experiments. Close to half-filling, the superfluid ground state competes with a low-lying CDW phase. We study the collective excitations of the superfluid using the Generalized Random Phase Approximation (GRPA) and strong-coupling spin wave analysis. The competing CDW phase manifests as a roton-like excitation. We characterize the collective mode spectrum, setting benchmarks for experiments. We drive competition between orders by imposing superfluid flow. Superflow leads to various instabilities: in particular, we find a dynamical instability associated with CDW order. We also find a novel dynamical incommensurate instability analogous to exciton condensation in semiconductors. In the second part, inspired by experiments on Bi3Mn 4O12(NO3)(BMNO), we first study the interlayer dimer state in spin-S bilayer antiferromagnets. At a critical bilayer coupling strength, condensation of triplet excitations leads to Neel order. In describing this transition, bond operator mean field theory suffers from systematic deviations. We bridge these deviations by taking into account corrections arising from higher spin excitations. The interlayer dimer state shows a field induced Neel transition, as seen in BMNO. Our results are relevant to the quantitative modelling of spin-S dimerized systems. We then study the J1 - J2 model on the honeycomb lattice with frustrating next-nearest neighbour exchange. For J2 >J1

  15. Black Holes Admitting Strong Resonant Phenomena

    NASA Astrophysics Data System (ADS)

    Stuchlík, Z.; Kotrlová, A.; G. Török

    2008-12-01

    High-frequency twin peak quasiperiodic oscillations (QPOs) are observed in four microquasars, i.e., Galactic black hole binary systems, with frequency ratio very close to 3:2. In the microquasar GRS 1915+105 the structure of QPOs exhibits additional frequencies and more than two frequencies are observed in the Galaxy nuclei Sgr A* or in some extragalactic sources (NGC 4051, MCG-6-30-15 and NGC 5408 X-1). The observed QPOs can be explained by a variety of the orbital resonance model versions assuming resonance of oscillations with the Keplerian frequency νK or the vertical epicyclic frequency νθ, and the radial epicyclic frequency νr, or some combinations of these frequencies. Generally, different resonances could arise at different radii of an accretion disk. However, we have shown that for special values of dimensionless black hole spin a strong resonant phenomena could occur when different resonances can be excited at the same radius, as cooperative phenomena between the resonances may work in such situations. The special values of a are determined for triple frequency ratio sets νK:νθ:νr=s:t:u with s,t,u being small integers. The most promising example of such a special situation arises for black holes with extraordinary resonant spin a=0.983 at the radius r=2.395 M, where νK:νθ:νr=3:2:1. We also predict that when combinations of the orbital frequencies are allowed, QPOs with four frequency ratio set 4:3:2:1 could be observed in the field of black holes with a=0.866,0.882 and 0.962. Assuming the extraordinary resonant spin a=0.983 in Sgr A*, its QPOs with observed frequency ratio ≍3:2:1 imply the black hole mass in the interval 4.3×106 Msolar< M< 5.4×106 Msolar, in agreement with estimates given by other, independent, observations.

  16. The Strong Interactions, Flavour Physics and Beyond

    NASA Astrophysics Data System (ADS)

    Zuberi, Saba

    In this thesis we use effective field theories of the strong interactions to improve our understanding of several quantities in the Standard Model of particle physics (SM). We also examine constraints on an extension of the SM scalar sector and study the implications for the Higgs mass. We first examine an approach to extracting the Cabibbo-Kobayashi-Maskawa matrix element |Vub| via the relationship between the B meson decays B → X uℓnul and B → Xsgamma, where Xi is any final state hadron containing a quark of flavour i. Model dependence is reduced in this approach since the non-perturbative shape function at leading order is universal and drops out; however the perturbative expansion at next-to-leading order is found to be poorly behaved. We carry out a renormalon analysis of the relationship between these spectra to examine higher order perturbative corrections and compare the fixed-order and log expansions. Our analysis can be used to estimate the perturbative uncertainty in the extraction of |Vub|, which we show to be relatively small. Next we take a step towards the broader goal of summing large phase space logarithms from a variety of jet algorithms using Soft Collinear Effective Theory (SCET). We develop a consistent approach to implementing arbitrary phase space constraints in SCET and demonstrate the connection between cutoffs in SCET and phase space limits. By considering several jet algorithms at next-to-leading order, we gain some insight into factorization of final state jets. In particular, we point out the connection between the ultraviolet regulator and factorization. Finally we consider a scalar sector that contains a colour-octet electroweak-doublet scalar, in addition to the SM Higgs. This extension contains the only scalar representations that Yukawa-couple to quarks and are consistent with minimal flavour violation. We examine constraints from electroweak precision data, direct production from LEPII and the Tevatron, and from flavour

  17. Flow behavior of mixed-protein incipient gels

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strong protein gel networks may result from synergistic interactions with other proteins or food materials above that achievable with a single protein alone. We determined varying flow and viscoelastic behavior of calcium caseinate (CC) or whey protein isolate (WPI) mixed with egg albumin (EA), fish...

  18. Parallel Simulation Algorithms for the Three Dimensional Strong-Strong Beam-Beam Interaction

    SciTech Connect

    Kabel, A.C.; /SLAC

    2008-03-17

    The strong-strong beam-beam effect is one of the most important effects limiting the luminosity of ring colliders. Little is known about it analytically, so most studies utilize numeric simulations. The two-dimensional realm is readily accessible to workstation-class computers (cf.,e.g.,[1, 2]), while three dimensions, which add effects such as phase averaging and the hourglass effect, require vastly higher amounts of CPU time. Thus, parallelization of three-dimensional simulation techniques is imperative; in the following we discuss parallelization strategies and describe the algorithms used in our simulation code, which will reach almost linear scaling of performance vs. number of CPUs for typical setups.

  19. Effective Theories Of The Strong Interaction

    SciTech Connect

    Dr. Ubirajara van Kolck

    2004-07-31

    This is the final report corresponding to the full funding period (08/01-07/04) in the Department of Energy Outstanding Junior Investigator Grant DE-FG03-01ER41196. The development of an understanding of the interplay between perturbative and non-perturbative effects in strong-interacting systems forms the broad context of this research. The main thrust is the application of effective theories to QCD. Topics included a new power counting in the pionful effective theory, low-energy Compton scattering, charge-symmetry breaking in pion production and in the two-nucleon potential, parity violation, coupled-channel scattering, shallow resonances and halo nuclei, chiral symmetry in the baryon spectrum, existence of a tetraquark state, and molecular meson states. DOE grant DE-FG03-01ER41196 was used to partially support in the period 08/01-07/04 the research activities of the Principal Investigator, Dr. Ubirajara van Kolck, one post-doctoral research associate, Dr. Boris A. Gelman, and one graduate student, Mr. Will Hockings. During the grant period the PI was first Assistant then Associate Professor of Physics at the University of Arizona (UA), and a RHIC Physics Fellow at the RIKEN-BNL Research Center (RBRC). The association with RBRC ended in the Summer of 2004. Since September of 2002 the PI has also been partially supported by a Sloan Research Fellowship. Dr. Boris Gelman was supported by the grant from September 2002 to May 2004. He joined the UA after receiving a Ph.D. from the University of Maryland in the Summer of 2002. He left to take a research associate position in the nuclear theory group of the State University of New York at Stony Brook. The support of a post-doctoral researcher on this grant for two years was only possible by carrying over first- and second-year funds to later years. In addition, Mr. William Hockings started doing research under the PI's guidance. Mr. Hockings took Independent Study courses with the PI, while working as a teaching

  20. Supernova spectra below strong circumstellar interaction

    NASA Astrophysics Data System (ADS)

    Leloudas, G.; Hsiao, E. Y.; Johansson, J.; Maeda, K.; Moriya, T. J.; Nordin, J.; Petrushevska, T.; Silverman, J. M.; Sollerman, J.; Stritzinger, M. D.; Taddia, F.; Xu, D.

    2015-02-01

    We construct spectra of supernovae (SNe) interacting strongly with a circumstellar medium (CSM) by adding SN templates, a black-body continuum, and an emission-line spectrum. In a Monte Carlo simulation we vary a large number of parameters, such as the SN type, brightness and phase, the strength of the CSM interaction, the extinction, and the signal to noise ratio (S/N) of the observed spectrum. We generate more than 800 spectra, distribute them to ten different human classifiers, and study how the different simulation parameters affect the appearance of the spectra and their classification. The SNe IIn showing some structure over the continuum were characterized as "SNe IInS" to allow for a better quantification. We demonstrate that the flux ratio of the underlying SN to the continuum fV is the single most important parameter determining whether a spectrum can be classified correctly. Other parameters, such as extinction, S/N, and the width and strength of the emission lines, do not play a significant role. Thermonuclear SNe get progressively classified as Ia-CSM, IInS, and IIn as fV decreases. The transition between Ia-CSM and IInS occurs at fV ~ 0.2-0.3. It is therefore possible to determine that SNe Ia-CSM are found at the (un-extincted) magnitude range -19.5 >M> -21.6, in very good agreement with observations, and that the faintest SN IIn that can hide a SN Ia has M = -20.1. The literature sample of SNe Ia-CSM shows an association with 91T-like SNe Ia. Our experiment does not support that this association can be attributed to a luminosity bias (91T-like being brighter than normal events). We therefore conclude that this association has real physical origins and we propose that 91T-like explosions result from single degenerate progenitors that are responsible for the CSM. Despite the spectroscopic similarities between SNe Ibc and SNe Ia, the number of misclassifications between these types was very small in our simulation and mostly at low S/N. Combined with

  1. The Commercial TREMOR Strong-Motion Seismograph

    NASA Astrophysics Data System (ADS)

    Evans, J. R.; Hamstra, R. H.; Kuendig, C.; Camina, P.

    2001-12-01

    The emergence of major seismological and earthquake-engineering problems requiring large, dense instrument arrays led several of us to investigate alternate solutions. Evans and Rogers (USGS Open File Report 95-555, 1995) and Evans (USGS Open File Report 98-109, 1998) demonstrated the efficacy of low-cost robust silicon accelerometers in strong-motion seismology, making possible a vast increase in the spatial density of such arrays. The 1998 design displays true 16-bit performance and excellent robustness and linearity---13 of these prototype near-real-time instruments are deployed in Oakland, California, and have recorded data from seven small events (up to 5.7 %g). Since this technology is a radical departure from past efforts, it was necessary for the USGS to develop the sensor and demonstrate its efficacy thoroughly. Since it is neither practical nor appropriate for the USGS to produce instrumentation beyond a demonstration phase, the US Geological Survey and GeoSIG Ltd undertook a collaborative effort (a ``CRAD'') to commercialize the new technology. This effort has resulted in a fully temperature-compensated 16-bit system, the GeoSIG GT-316, announced in April, 2001, combining the ICS-3028 TM-based USGS sensor, temperature compensation technique, and peak ground velocity (PGV) computation with a highly customized 16-bit GeoSIG recorder. The price has not been set but is likely to be around \\2000 in large quantities. The result is a near-real-time instrument telemetering peak ground acceleration (PGA) and PGV about 90 s after onset of the P wave, then minutes later transmitting the waveform. The receiving software, ``HomeBase()'', also computes spectral acceleration, S_{a}. PGA, PGV, S_{a}, and waveforms are forwarded immediately by HomeBase() for ShakeMap generation and other uses. Shaking metrics from the prototypes in Oakland are consistently among the first to arrive for the northern California ShakeMap. For telemetry we use a low-cost always

  2. Improving experimental phases for strong reflections prior to density modification

    SciTech Connect

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-09-20

    Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

  3. Improving experimental phases for strong reflections prior to density modification

    DOE PAGESBeta

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-09-20

    Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number ofmore » strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. Lastly, a computer program,SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.« less

  4. Protein Dynamics

    NASA Astrophysics Data System (ADS)

    Frauenfelder, Hans

    2011-03-01

    Proteins combine properties of solids, liquids, and glasses. Schrödinger anticipated the main features of biomolecules long ago by stating that they had to be solid-like, but able to assume many different conformations. Indeed proteins can assume a gigantic number of conformational substates with the same primary sequence but different conformations. The different substates are described as craters in a very-high-dimensional energy landscape. The energy landscape is organized in a hierarchy of tiers, craters within craters within craters. Protein motions are pictured as transition between substates - jumps from crater to crater. Initially we assumed that these jumps were controlled by internal barriers between substates, but experiments have shown that nature selected a different approach. Proteins are surrounded by one to two layers of water and are embedded in a bulk solvent. Structural motions of the protein are controlled by the alpha fluctuations in the solvent surrounding the protein. Some internal motions most likely involving side chains are controlled electrostatically by beta fluctuations in the hydration shell. The dynamics of proteins is consequently dominated by the environment (H. Frauenfelder et al. PNAS 106, 5129 (2009). One can speculate that this organization permits exchange of information among biomolecules. The energy landscape is not just organized into two tiers, alpha and beta, but cryogenic experiments have revealed more tiers and protein more properties similar to that of glasses. While proteins function at ambient temperatures, cryogenic studies are necessary to understand the physics relevant for biology.

  5. Strong effect of low-dimensional Fe-doped cobalt niobate on a strongly ferrimagnetic system

    NASA Astrophysics Data System (ADS)

    Nlebedim, Cajetan; Jiles, David

    2015-03-01

    In this work, the first investigation of the effect of Fe-doped cobalt niobate (CoNb2O6) imbedded in the matrix of a strongly ferrimagnetic cobalt-iron oxide, is presented. The temperature dependence of the magnetic properties and how they change with variations in the concentration of CoNb2O6 is also presented. CoNb2O6 is a prototypical low-dimensional material belonging to the pyrochlore-type AB2O6 systems. Its low-dimensional magnetic characteristics can help in understanding the magnetic properties of higher order systems. It has been investigated for applications in resonators and capacitors. This work shows that the magnetization of the ferrimagnetic phase is strongly affected by the concentration of Co ions in the low-dimensional phase, below 15 K but changes in coercivity with temperature were predominantly due to the ferrimagnetic phase. The systematic variation in the concentration of both phases and the cation ratio in each phase, enable us to understand the variation of the magnetic properties with temperature. This work provides useful insights into tuning the magnetism in strongly magnetic materials with transition metal AB2O6 systems imbedded in their matrices. This work was supported by the USDoE, Office of Science, Basic Energy Sciences, Materials Science and Engineering Division. The research was performed at Ames Laboratory, operated for the USDoE by Iowa State University (Contract # DE-AC02-07CH11358).

  6. SARCS strong-lensing galaxy groups. II. Mass-concentration relation and strong-lensing bias

    NASA Astrophysics Data System (ADS)

    Foëx, G.; Motta, V.; Jullo, E.; Limousin, M.; Verdugo, T.

    2014-12-01

    Aims: Various studies have shown a lensing bias in the mass-concentration relation of cluster-scale structures that is the result of an alignment of the major axis and the line of sight. In this paper, we aim to study this lensing bias through the mass-concentration relation of galaxy groups, thus extending observational constraints to dark matter haloes of mass ~1013-1014 M⊙. Methods: Our work is based on the stacked weak-lensing analysis of a sample of 80 strong-lensing galaxy groups. By combining several lenses, we significantly increase the signal-to-noise ratio of the lensing signal, thus providing constraints on the mass profile that cannot be obtained for individual objects. The resulting shear profiles were fitted with various mass models, among them the Navarro-Frank-White (NFW) profile, which provides an estimate of the total mass and of the concentration of the composite galaxy groups. Results: The main results of our analysis are the following: (i) the lensing signal does not allow us to firmly distinguish between a simple singular isothermal sphere mass distribution and the expected NFW mass profile; (ii) we obtain an average concentration c200 = 8.6-1.3+2.1 that is much higher than the value expected from numerical simulations for the corresponding average mass M200 = 0.73-0.10+0.11 × 1014 M⊙; (iii) the combination of our results with those at larger mass scales gives a mass-concentration relation c(M) of more than two decades in mass, whose slope disagrees with predictions from numerical simulations using unbiased populations of dark matter haloes; (iv) our combined c(M) relation matches results from simulations that only used haloes with a large strong-lensing cross-section, that is, elongated with a major axis close to the line of sight; (v) for the simplest case of prolate haloes, we estimate a lower limit on the minor-to-major axis ratio a/c = 0.5 for the average SARCS galaxy group with a toy model. Conclusions: Our analysis based on galaxy

  7. Protein-templated peptide ligation.

    PubMed

    Brauckhoff, Nicolas; Hahne, Gernot; Yeh, Johannes T-H; Grossmann, Tom N

    2014-04-22

    Molecular templates bind particular reactants, thereby increasing their effective concentrations and accelerating the corresponding reaction. This concept has been successfully applied to a number of chemical problems with a strong focus on nucleic acid templated reactions. We present the first protein-templated reaction that allows N-terminal linkage of two peptides. In the presence of a protein template, ligation reactions were accelerated by more than three orders of magnitude. The templated reaction is highly selective and proved its robustness in a protein-labeling reaction that was performed in crude cell lysate. PMID:24644125

  8. Cantharidin, a protein phosphatase inhibitor, strongly upregulates detoxification enzymes in the Arabidopsis proteome

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cantharidin is a potent natural herbicide. This work was conducted to probe its mode of action. We previously published its effect on transcription of plant genes (mRNA production) with transcriptomic methods. This paper follows up and looks at cantharidin effects translation of mRNA using proteom...

  9. Plasma waves in a relativistic, strongly anisotropic plasma propagated along a strong magnetic field

    NASA Technical Reports Server (NTRS)

    Onishchenko, O. G.

    1980-01-01

    The dispersion properties of plasma waves in a relativistic homogeneous plasma propagated along a strong magnetic field are studied. It is shown that the non-damping plasma waves exist in the frequency range omega sub p or = omega or = omega sub L. The values of omega sub p and omega sub L are calculated for an arbitrary homogeneous relativistic function of the particle distribution. In the case of a power ultrarelativistic distribution, it is shown that, if the ultrarelativistic tail of the distribution drops very rapidly, slightly damping plasma waves are possible with the phase velocity (omega/K)c.

  10. PPE Antigen Rv2430c of Mycobacterium tuberculosis Induces a Strong B-Cell Response

    PubMed Central

    Choudhary, Rakesh Kumar; Mukhopadhyay, Sangita; Chakhaiyar, Prachee; Sharma, Naresh; Murthy, K. J. R.; Katoch, V. M.; Hasnain, Seyed E.

    2003-01-01

    The variation in sequence and length in the C-terminal region among members of the unique PE (Pro-Glu) and PPE (Pro-Pro-Glu) protein families of Mycobacterium tuberculosis is a likely source of antigenic variation, giving rise to the speculation that these protein families could be immunologically important. Based on in silico analysis, we selected a hypothetical open reading frame (ORF) encoding a protein belonging to the PPE family and having epitopes with predictably higher antigenic indexes. Reverse transcriptase PCR using total RNA extracted from in vitro-cultured M. tuberculosis H37Rv generated an mRNA product corresponding to this gene, indicating the expression of this ORF (Rv2430c) at the mRNA level. Recombinant protein expressed in Escherichia coli was used to screen the sera of M. tuberculosis-infected patients, as well as those of clinically healthy controls (n = 10), by enzyme-linked immunosorbent assay. The panel of patient sera comprised sera from fresh infection cases (category 1; n = 32), patients with relapsed tuberculosis (category 2; n = 30), and extrapulmonary cases (category 3; n = 30). Category 2 and 3 sera had strong antibody responses to the PPE antigen, equal to or higher than those to other well-known antigens, such as Hsp10 or purified protein derivative (PPD). However, a higher percentage of patients belonging to category 1, as opposed to clinically healthy controls, showed stronger antibody response against the PPE protein when probed with anti-immunoglobulin M (IgM) (71 versus 37.5%) or anti-IgG (62.5 versus 28.12%). Our results reveal that this PPE ORF induces a strong B-cell response compared to that generated by M. tuberculosis Hsp10 or PPD, pointing to the immunodominant nature of the protein. PMID:14573653

  11. Strong-field approximation for ionization of a diatomic molecule by a strong laser field

    SciTech Connect

    Milosevic, D. B.

    2006-12-15

    We present a theory of ionization of diatomic molecules by a strong laser field. A diatomic molecule is considered as a three-particle system, which consists of two heavy atomic (ionic) centers and an electron. After the separation of the center-of-mass coordinate, the dynamics of this system is reduced to the relative electronic and nuclear coordinates. The exact S-matrix element for ionization is presented in a form in which the laser-molecule interaction is emphasized. This form is useful for application of the molecular strong-field approximation (SFA). We introduced two forms of the molecular SFA, one with the field-free and the other with the field-dressed initial molecular bound state. We relate these two forms of our modified molecular SFA to the standard molecular SFAs, introduced previously using the length gauge and the velocity gauge. Numerical examples of the ionization rates of N{sub 2} and O{sub 2} molecules are shown and compared for all four versions of the molecular SFA and we suggest that our modified molecular SFA should be used instead of the standard molecular SFA.

  12. Is Peroxiredoxin II's peroxidase activity strongly inhibited in human erythrocytes?

    PubMed

    Benfeitas, Rui; Selvaggio, Gianluca; Antunes, Fernando; Coelho, Pedro; Salvador, Armindo

    2014-10-01

    H2O2 elimination in human erythrocytes is mainly carried out by catalase (Cat), glutathione peroxidase (GPx1) and the more recently discovered peroxiredoxin 2 (Prx2). However, the contribution of Prx2 to H2O2 consumption is still unclear. Prx2's high reactivity with H2O2 (kPrx2=10×10(7) M(-1)s(-1), kCat =7×10(7) M(-1)s(-1), kGPx1 =4×10(7) M(-1)s(-1)) and high abundance ([Prx2]= 570µM, [Cat]= 32µM, [GPx1]= 1µM) suggest that under low H2O2 supply rates it should consume >99% of the H2O2. However, extensive evidence indicates that in intact erythrocytes Prx2 contributes no more than Cat to H2O2 consumption. In order for this to be attained, Prx2's effective rate constant with H2O2would have to be just ~10(5) M(-1)s(-1), much lower than that determined in multiple experiments with the purified proteins. Nevertheless, nearly all Prx2 is oxidized within 1min of exposing erythrocytes to a H2O2 bolus, which is inconsistent with an irreversible inhibition. A mathematical model of the H2O2 metabolism in human erythrocytes [Benfeitas et al. (2014) Free Radic. Biol. Med.] where Prx2 either has a low kPrx2 or is subject to a strong (>99%) but readily reversible inhibition achieves quantitative agreement with detailed experimental observations of the responses of the redox status of Prx2 in human erythrocytes and suggests functional advantages of this design (see companion abstract). By contrast, a variant where Prx2 is fully active with kPrx2=10(8) M(-1)s(-1) shows important qualitative discrepancies. Altogether, these results suggest that Prx2's peroxidase activity is strongly inhibited in human erythrocytes. We acknowledge fellowship SFRH/BD/51199/2010, grants PEst-C/SAU/LA0001/2013-2014, PEst-OE/QUI/UI0612/2013, PEst-OE/QUI/UI0313/2014, and FCOMP-01-0124-FEDER-020978 (PTDC/QUI-BIQ/119657/2010) co-financed by FEDER through the COMPETE program and by FCT. PMID:26461310

  13. On strongly GA-convex functions and stochastic processes

    SciTech Connect

    Bekar, Nurgül Okur; Akdemir, Hande Günay; İşcan, İmdat

    2014-08-20

    In this study, we introduce strongly GA-convex functions and stochastic processes. We provide related well-known Kuhn type results and Hermite-Hadamard type inequality for strongly GA-convex functions and stochastic processes.

  14. On strongly GA-convex functions and stochastic processes

    NASA Astrophysics Data System (ADS)

    Bekar, Nurgül Okur; Akdemir, Hande Günay; Işcan, Imdat

    2014-08-01

    In this study, we introduce strongly GA-convex functions and stochastic processes. We provide related well-known Kuhn type results and Hermite-Hadamard type inequality for strongly GA-convex functions and stochastic processes.

  15. Ultrasensitivity of Cell Adhesion to the Presence of Mechanically Strong Ligands

    NASA Astrophysics Data System (ADS)

    Roein-Peikar, Mehdi; Xu, Qian; Wang, Xuefeng; Ha, Taekjip

    2016-01-01

    Integrins, a class of membrane proteins involved in cell adhesion, participate in the cell's sensing of the mechanical environments. We previously showed that, for the initial cell adhesion to occur, single integrins need to experience a threshold force of 40 pico-Newton (pN) through their bond with surface-bound ligands. This force requirement was determined using a series of double-stranded DNA tethers called tension gauge tethers (TGTs), each with a different rupture force, linked to the ligand. Here, we performed cell-adhesion experiments using surfaces coated with two different TGTs, one of a strong rupture force (around 54 pN) and the other of a weak rupture force (around 12 pN). When presented with one type of TGT only, cells adhered to the strong TGT-coated surface but not to the weak TGT-coated surface. However, when presented with both, the presence of the strong TGTs transforms the way cells respond to the weak TGTs such that cells treat both TGTs the same, as if the weak TGTs were strong. Furthermore, a subpopulation of cells can adhere to and spread on a surface displaying just a few molecules of the strong TGTs per cell if, and only if, they are presented along with many weak TGTs. This ultrasensitivity to just a few tethers that can withstand strong forces raises a question of how the cells can achieve such remarkable sensitivity to their mechanical environment without amplifying noise.

  16. Short, strong hydrogen bonds on enzymes: NMR and mechanistic studies

    NASA Astrophysics Data System (ADS)

    Mildvan, A. S.; Massiah, M. A.; Harris, T. K.; Marks, G. T.; Harrison, D. H. T.; Viragh, C.; Reddy, P. M.; Kovach, I. M.

    2002-09-01

    The lengths of short, strong hydrogen bonds (SSHBs) on enzymes have been determined with high precision (±0.05 Å) from the chemical shifts ( δ), and independently from the D/ H fractionation factors ( φ) of the highly deshielded protons involved. These H-bond lengths agree well with each other and with those found by protein X-ray crystallography, within the larger errors of the latter method (±0.2 to±0.8 Å) [Proteins 35 (1999) 275]. A model dihydroxynaphthalene compound shows a SSHB of 2.54±0.04 Å based on δ=17.7 ppm and φ=0.56±0.04, in agreement with the high resolution X-ray distance of 2.55±0.06 Å. On ketosteroid isomerase, a SSHB is found (2.50±0.02 Å), based on δ=18.2 ppm and φ=0.34, from Tyr-14 to the 3-O - of estradiol, an analog of the enolate intermediate. Its strength is ˜7 kcal/mol. On triosephosphate isomerase, SSHBs are found from Glu-165 to the 1-NOH of phosphoglycolohydroxamic acid (PGH), an analog of the enolic intermediate (2.55±0.05 Å), and from His-95 to the enolic-O - of PGH (2.62±0.02 Å). In the methylglyoxal synthase-PGH complex, a SSHB (2.51±0.02 Å) forms between Asp-71 and the NOH of PGH with a strength of ≥4.7 kcal/mol. When serine proteases bind mechanism-based inhibitors which form tetrahedral Ser-adducts analogous to the tetrahedral intermediates in catalysis, the Asp⋯His H-bond of the catalytic triad becomes a SSHB [Proc. Natl Acad. Sci. USA 95 (1998) 14664], 2.49-2.63 Å in length. Similarly, on the serine-esterase, butyrylcholinesterase complexed with the mechanism-based inhibitor m-( N, N, N-trimethylammonio)-2,2,2-trifluoroacetophenone, a SSHB forms between Glu-327 and His-438 of the catalytic triad, 2.61±0.04 Å in length, based on δ=18.1 ppm and φ=0.65±0.10. Very similar results are obtained with (human) acetylcholinesterase. The strength of this SSHB is at least 4.9 kcal/mol.

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

    PubMed

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

    2010-08-31

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

  18. The Conceptual Elements of Strong Interventions in School Settings.

    ERIC Educational Resources Information Center

    Lentz, Francis E., Jr.; And Others

    1996-01-01

    Presents a conceptual model of strong school-based interventions. Notes strong interventions are ecological in nature, naturalistic in scope, contain elements from the research base that are predictive for success, and incorporate the constructs of social validity in a practical manner. Provides suggestions and implications for strong school-based…

  19. 7 CFR 51.906 - Well developed and strong.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 7 Agriculture 2 2011-01-01 2011-01-01 false Well developed and strong. 51.906 Section 51.906 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards....906 Well developed and strong. Well developed and strong means that the main and lateral stems...

  20. 7 CFR 51.906 - Well developed and strong.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 7 Agriculture 2 2010-01-01 2010-01-01 false Well developed and strong. 51.906 Section 51.906 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards....906 Well developed and strong. Well developed and strong means that the main and lateral stems...

  1. Strong monogamy of quantum entanglement for multiqubit W -class states

    NASA Astrophysics Data System (ADS)

    Kim, Jeong San

    2014-12-01

    We provide strong evidence for the strong monogamy inequality of multiqubit entanglement recently proposed [B. Regula et al., Phys. Rev. Lett. 113, 110501 (2014), 10.1103/PhysRevLett.113.110501]. We consider a large class of multiqubit generalized W -class states and analytically show that the strong monogamy inequality of multiqubit entanglement is saturated by this class of states.

  2. Sucralose Destabilization of Protein Structure.

    PubMed

    Chen, Lee; Shukla, Nimesh; Cho, Inha; Cohn, Erin; Taylor, Erika A; Othon, Christina M

    2015-04-16

    Sucralose is a commonly employed artificial sweetener that behaves very differently than its natural disaccharide counterpart, sucrose, in terms of its interaction with biomolecules. The presence of sucralose in solution is found to destabilize the native structure of two model protein systems: the globular protein bovine serum albumin and an enzyme staphylococcal nuclease. The melting temperature of these proteins decreases as a linear function of sucralose concentration. We correlate this destabilization to the increased polarity of the molecule. The strongly polar nature is manifested as a large dielectric friction exerted on the excited-state rotational diffusion of tryptophan using time-resolved fluorescence anisotropy. Tryptophan exhibits rotational diffusion proportional to the measured bulk viscosity for sucrose solutions over a wide range of concentrations, consistent with a Stokes-Einstein model. For sucralose solutions, however, the diffusion is dependent on the concentration, strongly diverging from the viscosity predictions, and results in heterogeneous rotational diffusion. PMID:26263149

  3. Strong ion difference excess and corrected strong ion difference model incorporating the variations in apparent dissociation constant for human blood plasma electro-neutrality equilibria.

    PubMed

    Rana, Amar P S; Rana, Sam Pal; Rana, Jay Pal; Singh, Sumarjeet

    2006-01-01

    We introduce computed value of the corrected Strong Ion Difference (SID) by including the large variability of the apparent dissociation constant pK' in non-logarithmic form on SID in Henderson-Hasselbach bicarbonate ion aqueous equilibria thereby resulting in a significant correction of up to 27% in SID. We further introduce a new concept of Strong Ion Difference Excess (SIDE) as the change in SID from the reference value at pH = 7.4, pCO2 = 5.33 Kpa (or 40 torr). The SIDE is a particularly useful quick measure when one can rule out the effects of hemoglobin, weak proteins and unidentified components for human blood plasma. PMID:17051730

  4. Whey Protein

    MedlinePlus

    ... intolerance, for replacing or supplementing milk-based infant formulas, and for reversing weight loss and increasing glutathione ( ... allergic reactions compared to infants who receive standard formula. However, taking why protein might not be helpful ...

  5. Improving experimental phases for strong reflections prior to density modification

    SciTech Connect

    Uervirojnangkoorn, Monarin; Hilgenfeld, Rolf; Terwilliger, Thomas C.; Read, Randy J.

    2013-10-01

    A genetic algorithm has been developed to optimize the phases of the strongest reflections in SIR/SAD data. This is shown to facilitate density modification and model building in several test cases. Experimental phasing of diffraction data from macromolecular crystals involves deriving phase probability distributions. These distributions are often bimodal, making their weighted average, the centroid phase, improbable, so that electron-density maps computed using centroid phases are often non-interpretable. Density modification brings in information about the characteristics of electron density in protein crystals. In successful cases, this allows a choice between the modes in the phase probability distributions, and the maps can cross the borderline between non-interpretable and interpretable. Based on the suggestions by Vekhter [Vekhter (2005 ▶), Acta Cryst. D61, 899–902], the impact of identifying optimized phases for a small number of strong reflections prior to the density-modification process was investigated while using the centroid phase as a starting point for the remaining reflections. A genetic algorithm was developed that optimizes the quality of such phases using the skewness of the density map as a target function. Phases optimized in this way are then used in density modification. In most of the tests, the resulting maps were of higher quality than maps generated from the original centroid phases. In one of the test cases, the new method sufficiently improved a marginal set of experimental SAD phases to enable successful map interpretation. A computer program, SISA, has been developed to apply this method for phase improvement in macromolecular crystallography.

  6. MafA has strong cell transforming ability but is a weak transactivator.

    PubMed

    Nishizawa, Makoto; Kataoka, Kohsuke; Vogt, Peter K

    2003-09-11

    The maf oncogene of the avian oncogenic retrovirus AS42 encodes a nuclear bZip protein, v-Maf, that recognizes sequences related to the AP-1 target site. The corresponding cellular protein, c-Maf belongs to a family of related bZip proteins together with MafA and MafB. In this paper, we compare the transactivation and cell transforming abilities of MafA and MafB along with two forms of the c-Maf protein. These proteins induce cellular transformation when expressed in chicken embryo fibroblasts. In reporter assays, MafA is a much less effective transactivator than the other Maf proteins, but unexpectedly shows the strongest activity in cell transformation. Chimeras of MafA and MafB correlate the strong cell transforming ability of MafA with its DNA-binding domain. The DNA-binding domain of MafA is also correlated with weak transactivation. Additional mutagenesis experiments show that transactivation and transformation by MafA are also controlled by phosphorylation of two conserved serine residues in the transactivation domain. Finally, we constructed MafA-estrogen receptor fusion molecules that show tightly hormone-dependent cell transforming ability. These regulatable constructs permit a kinetic characterization of target gene responses and facilitate discrimination between direct and indirect targets. PMID:12970735

  7. Membrane tension controls the assembly of curvature-generating proteins

    PubMed Central

    Simunovic, Mijo; Voth, Gregory A.

    2015-01-01

    Proteins containing a Bin/Amphiphysin/Rvs (BAR) domain regulate membrane curvature in the cell. Recent simulations have revealed that BAR proteins assemble into linear aggregates, strongly affecting membrane curvature and its in-plane stress profile. Here, we explore the opposite question: do mechanical properties of the membrane impact protein association? By using coarse-grained molecular dynamics simulations, we show that increased surface tension significantly impacts the dynamics of protein assembly. While tensionless membranes promote a rapid formation of long-living linear aggregates of N-BAR proteins, increase in tension alters the geometry of protein association. At high tension, protein interactions are strongly inhibited. Increasing surface density of proteins leads to a wider range of protein association geometries, promoting the formation of meshes, which can be broken apart with membrane tension. Our work indicates that surface tension may play a key role in recruiting proteins to membrane-remodelling sites in the cell. PMID:26008710

  8. 76 FR 52934 - Request for Comments: Public Input for the Launch of the Strong Cities, Strong Communities...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-08-24

    ... Economic Development Administration Request for Comments: Public Input for the Launch of the Strong Cities, Strong Communities Visioning Challenge AGENCY: Economic Development Administration, U.S. Department of..., 2011, the Economic Development Administration (EDA) published a Federal Register notice...

  9. Protein-protein and protein-salt interactions in aqueous protein solutions containing concentrated electrolytes

    SciTech Connect

    Curtis, R.A.; Blanch, H.W.; Prausnitz, J.M.

    1998-01-05

    Protein-protein and protein-salt interactions have been obtained for ovalbumin in solutions of ammonium sulfate and for lysozyme in solutions of ammonium sulfate, sodium chloride, potassium isothiocyanate, and potassium chloride. The two-body interactions between ovalbumin molecules in concentrated ammonium-sulfate solutions can be described by the DLVO potentials plus a potential that accounts for the decrease in free volume available to the protein due to the presence of the salt ions. The interaction between ovalbumin and ammonium sulfate is unfavorable, reflecting the kosmotropic nature of sulfate anions. Lysozyme-lysozyme interactions cannot be described by the above potentials because anion binding to lysozyme alters these interactions. Lysozyme-isothiocyanate complexes are strongly attractive due to electrostatic interactions resulting from bridging by the isothiocyanate ion. Lysozyme-lysozyme interactions in sulfate solutions are more repulsive than expected, possibly resulting from a larger excluded volume of a lysozyme-sulfate bound complex or perhaps, hydration forces between the lysozyme-sulfate complexes.

  10. Strong aggregation and increased toxicity of polyleucine over polyglutamine stretches in mammalian cells.

    PubMed

    Dorsman, Josephine C; Pepers, Barry; Langenberg, Dennis; Kerkdijk, Henri; Ijszenga, Marije; den Dunnen, Johan T; Roos, R A C; van Ommen, Gert-Jan B

    2002-06-15

    Expansion of a Glutamine (Gln) repeat above a specific critical size in certain proteins gives rise to aggregation-prone proteins that cause neurodegenerative disorders, such as Huntington's disease. However, proteins with long hydrophilic polyglutamine repeats are more frequently found in nature than proteins with long homogeneous repeats of other amino acids, such as hydrophobic (Ala)(n) and (Leu)(n). To explore this finding, the effects of expression in mammalian cells of polyglutamine and polyleucine encoded by mixed DNA repeats were compared. It was found that polyleucine is significantly more toxic than polyglutamine. In addition, we show that polyleucine stretches display a high propensity for aggregation utilizing two complementary biochemical assays and that polyleucine stretches can also be detected by the monoclonal antibody 1C2, which specifically recognizes expanded pathogenic and aggregation-prone glutamine repeats. Together, these results suggest that polyglutamine stretches are in fact relatively well tolerated and that nature may select more strongly against DNA stretches that encode long hydrophobic homopolymeric amino acid stretches, such as polyleucine -- possibly owing to their strong propensity for aggregation. In keeping with this notion, an increasing number of diseases are found to be associated with expansion of stretches of hydrophobic amino acids, including oculopharyngeal muscular dystrophy (OPMD), which is associated with expansion of a hydrophobic polyalanine stretch. PMID:12045202

  11. Protein Adsorption in Three Dimensions

    PubMed Central

    Vogler, Erwin A.

    2011-01-01

    initially-adsorbed protein. Interphase protein concentration CI increases as VI decreases, resulting in slow reduction in interfacial energetics. Steady-state is governed by a net partition coefficient P=(/CBCI). In the process of occupying space within the interphase, adsorbing protein molecules must displace an equivalent volume of interphase water. Interphase water is itself associated with surface-bound water through a network of transient hydrogen bonds. Displacement of interphase water thus requires an amount of energy that depends on the adsorbent surface chemistry/energy. This “adsorption-dehydration” step is the significant free-energy cost of adsorption that controls the maximum amount of protein that can be adsorbed at steady state to a unit adsorbent-surface area (the adsorbent capacity). As adsorbent hydrophilicity increases, protein adsorption monotonically decreases because the energetic cost of surface dehydration increases, ultimately leading to no protein adsorption near an adsorbent water wettability (surface energy) characterized by a water contact angle θ → 65°. Consequently, protein does not adsorb (accumulate at interphase concentrations greater than bulk solution) to more hydrophilic adsorbents exhibiting θ < 65° . For adsorbents bearing strong Lewis acid/base chemistry such as ion-exchange resins, protein/surface interactions can be highly favorable, causing protein to adsorb in multilayers in a relatively thick interphase. A straightforward, three-component free energy relationship captures salient features of protein adsorption to all surfaces predicting that the overall free energy of protein adsorption ΔGadso is a relatively small multiple of thermal energy for any surface chemistry (except perhaps for bioengineered surfaces bearing specific ligands for adsorbing protein) because a surface chemistry that interacts chemically with proteins must also interact with water through hydrogen bonding. In this way, water moderates protein

  12. A strong candidate for the breast and ovarian cancer susceptibility gene BRCA1

    SciTech Connect

    Miki, Y.; Swenson, J.; Yakumo, K.; Lewis, C.; Neuhausen, S.; Goldgar, D.; Shattuck-Eidens, D.; Harshman, K.; Tavtigian, S.; Liu, Q.

    1994-10-07

    A strong candidate for the 17q-linked BRCA1 gene, which influences susceptibility to breast and ovarian cancer, has been identified by positional cloning methods. Probable predisposing mutations have been detected in five of eight kindreds presumed to segregate BRCA1 susceptibility alleles. The mutations include an 11-base pair deletion, a 1-base pair insertion, a stop codon, a missense substitution, and an inferred regulatory mutation. The BRCA1 gene is expressed in numerous tissues, including breast and ovary, and encodes a predicted protein of 1863 amino acids. This protein contains a zinc finger domain in its amino-terminal region, but is otherwise unrelated to previously described proteins. Identification of BRCA1 should facilitate early diagnosis of breast and ovarian cancer susceptibility in some individuals as well as a better understanding of breast cancer biology.

  13. Activation of macrophages by an exopolysaccharide isolated from Antarctic Psychrobacter sp. B-3

    NASA Astrophysics Data System (ADS)

    Yu, Leiye; Sun, Guojie; Wei, Jingfang; Wang, Yingze; Du, Chao; Li, Jiang

    2016-09-01

    An exopolysaccharide (EPS) was isolated and purified from an Antarctic psychrophilic bacterium B-3, identified as Psychrobacter sp., and the activation of RAW264.7 cells by B-3 EPS was investigated. The results show that B-3 EPS, over a certain concentration range, promoted cell viability, nitric oxide production, tumor necrosis factor (TNF)α secretion, and phagocytic ability. Furthermore, TAK-242, an inhibitor of the toll-like receptor 4 (TLR4) significantly reduced nitric oxide production by these cells after stimulation with B-3 EPS. Moreover, B-3 EPS induced p65 phosphorylation and IκBα degradation in these cells. In conclusion, B-3 EPS might have activated RAW264.7 cells by combining with TLR4 on cell surface and triggering activation of NF-κB signaling pathways, implying that this EPS could activate macrophages and regulate initial immune response.

  14. Activation of macrophages by an exopolysaccharide isolated from Antarctic Psychrobacter sp. B-3

    NASA Astrophysics Data System (ADS)

    Yu, Leiye; Sun, Guojie; Wei, Jingfang; Wang, Yingze; Du, Chao; Li, Jiang

    2016-01-01

    An exopolysaccharide (EPS) was isolated and purified from an Antarctic psychrophilic bacterium B-3, identified as Psychrobacter sp., and the activation of RAW264.7 cells by B-3 EPS was investigated. The results show that B-3 EPS, over a certain concentration range, promoted cell viability, nitric oxide production, tumor necrosis factor (TNF)α secretion, and phagocytic ability. Furthermore, TAK-242, an inhibitor of the toll-like receptor 4 (TLR4) significantly reduced nitric oxide production by these cells after stimulation with B-3 EPS. Moreover, B-3 EPS induced p65 phosphorylation and IκBα degradation in these cells. In conclusion, B-3 EPS might have activated RAW264.7 cells by combining with TLR4 on cell surface and triggering activation of NF-κB signaling pathways, implying that this EPS could activate macrophages and regulate initial immune response.

  15. Solving search problems by strongly simulating quantum circuits

    PubMed Central

    Johnson, T. H.; Biamonte, J. D.; Clark, S. R.; Jaksch, D.

    2013-01-01

    Simulating quantum circuits using classical computers lets us analyse the inner workings of quantum algorithms. The most complete type of simulation, strong simulation, is believed to be generally inefficient. Nevertheless, several efficient strong simulation techniques are known for restricted families of quantum circuits and we develop an additional technique in this article. Further, we show that strong simulation algorithms perform another fundamental task: solving search problems. Efficient strong simulation techniques allow solutions to a class of search problems to be counted and found efficiently. This enhances the utility of strong simulation methods, known or yet to be discovered, and extends the class of search problems known to be efficiently simulable. Relating strong simulation to search problems also bounds the computational power of efficiently strongly simulable circuits; if they could solve all problems in P this would imply that all problems in NP and #P could be solved in polynomial time. PMID:23390585

  16. Negativity and strong monogamy of multiparty quantum entanglement beyond qubits

    NASA Astrophysics Data System (ADS)

    Choi, Jin Hyuk; Kim, Jeong San

    2015-10-01

    We propose the square of convex-roof extended negativity (SCREN) as a powerful candidate to characterize strong monogamy of multiparty quantum entanglement. We first provide a strong monogamy inequality of multiparty entanglement using SCREN and show that the tangle-based multiqubit strong-monogamy inequality can be rephrased by SCREN. We further show that the SCREN strong-monogamy inequality is still true for the counterexamples that violate tangle-based the strong-monogamy inequality in higher-dimensional quantum systems other than qubits. We also analytically show that SCREN strong-monogamy inequality is true for a large class of multiqudit states, a superposition of multiqudit generalized W -class states and vacuums. Thus SCREN is a good alternative to characterize the strong monogamy of entanglement even in multiqudit systems.

  17. Protein imprinting in polyacrylamide-based gels

    PubMed Central

    Zayats, Maya; Brenner, Andrew J.; Searson, Peter C.

    2015-01-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  18. Protein imprinting in polyacrylamide-based gels.

    PubMed

    Zayats, Maya; Brenner, Andrew J; Searson, Peter C

    2014-10-01

    Protein imprinting in hydrogels is a method to produce materials capable of selective recognition and capture of a target protein. Here we report on the imprinting of fluorescently-labeled maltose binding protein (MBP) in acrylamide (AAm)/N-isopropylacrylamide (NIPAm) hydrogels. The targeting efficiency and selectivity of protein recognition is usually characterized by the imprinting factor, which in the simplest case is the ratio of protein uptake in an imprinted film divided by the uptake by the corresponding non-imprinted film. Our objective in this work is to study the dynamics of protein binding and elution in imprinted and non-imprinted films to elucidate the processes that control protein recognition. Protein elution from imprinted and non-imprinted films suggests that imprinting results in sites with a distribution of binding energies, and that only a relatively small fraction of these sites exhibit strong binding. PMID:25034963

  19. Designed protein-protein association.

    PubMed

    Grueninger, Dirk; Treiber, Nora; Ziegler, Mathias O P; Koetter, Jochen W A; Schulze, Monika-Sarah; Schulz, Georg E

    2008-01-11

    The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures. PMID:18187656

  20. Evolution of Robustness to Protein Mistranslation by Accelerated Protein Turnover

    PubMed Central

    Farkas, Zoltán; Horvath, Peter; Bódi, Zoltán; Daraba, Andreea; Szamecz, Béla; Gut, Ivo; Bayes, Mónica; Santos, Manuel A. S.; Pál, Csaba

    2015-01-01

    Translational errors occur at high rates, and they influence organism viability and the onset of genetic diseases. To investigate how organisms mitigate the deleterious effects of protein synthesis errors during evolution, a mutant yeast strain was engineered to translate a codon ambiguously (mistranslation). It thereby overloads the protein quality-control pathways and disrupts cellular protein homeostasis. This strain was used to study the capacity of the yeast genome to compensate the deleterious effects of protein mistranslation. Laboratory evolutionary experiments revealed that fitness loss due to mistranslation can rapidly be mitigated. Genomic analysis demonstrated that adaptation was primarily mediated by large-scale chromosomal duplication and deletion events, suggesting that errors during protein synthesis promote the evolution of genome architecture. By altering the dosages of numerous, functionally related proteins simultaneously, these genetic changes introduced large phenotypic leaps that enabled rapid adaptation to mistranslation. Evolution increased the level of tolerance to mistranslation through acceleration of ubiquitin-proteasome–mediated protein degradation and protein synthesis. As a consequence of rapid elimination of erroneous protein products, evolution reduced the extent of toxic protein aggregation in mistranslating cells. However, there was a strong evolutionary trade-off between adaptation to mistranslation and survival upon starvation: the evolved lines showed fitness defects and impaired capacity to degrade mature ribosomes upon nutrient limitation. Moreover, as a response to an enhanced energy demand of accelerated protein turnover, the evolved lines exhibited increased glucose uptake by selective duplication of hexose transporter genes. We conclude that adjustment of proteome homeostasis to mistranslation evolves rapidly, but this adaptation has several side effects on cellular physiology. Our work also indicates that