J/Psi mass shift in nuclear matter

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

J/Ψ mass shift and J/Ψ-nuclear bound state

We calculate mass shift of the J/Ψ meson in nuclear matter arising from the modification of DD, DD* and D*D* meson loop contributions to the J/Ψ self-energy. The estimate includes the in-medium D and D* meson masses consistently. The J/Ψ mass shift (scalar potential) calculated is negative (attractive), and is complementary to the attractive potential obtained from the QCD color van der Waals forces. Some results for the J/Ψ -nuclear bound state energies are also presented. © 2011 American Institute of Physics.

A New Method for Analysis of Disulfide-Containing Proteins by Matrix-Assisted Laser Desorption Ionization (MALDI) Mass Spectrometry

A simple and high-throughput method for the identification of disulfide-containing peptides utilizing peptide-matrix adducts is described. Some commonly used matrices in MALDI mass spectrometry were found to specifically react with sulfhydryl groups within peptide, thus allowing the observation of the peptide-matrix adduct ion [M + n + n' matrix + H](+) or [M + n + n' matrix + Na](+) (n = the number of cysteine residues, n' = 1, 2, ..., n) in MALDI mass spectra after chemical reduction of disulfide-linked peptides. Among several matrices tested, alpha-cyano-4-hydroxycinnamic acid (CHCA, molecular mass 189 Da) and alpha-cyano-3-hydroxycinnamic acid (3-HCCA) were found to be more effective for MALDI analysis of disulfide-containing peptides/proteins. Two reduced cysteines involved in a disulfide bridge resulted in a mass shift of 189 Da per cysteine, so the number of disulfide bonds could then be determined, while for the other matrices (sinapinic acid, ferulic acid, and caffeic acid), a similar addition reaction could not occur unless the reaction was carried out under alkaline conditions. The underlying mechanism of the reaction of the matrix addition at sulfhydryl groups is proposed, and several factors that might affect the formation of the peptide-matrix adducts were investigated.

Short distance QCD contribution to the electroweak mass difference of pions

It is known that the short distance QCD contribution to the mass difference of pions is quadratic on the quark masses, and irrelevant with respect to the long distance part. It is also considered in the literature that its calculation contains infinities, which should be absorbed by the quark mass renormalization. Following a prescription by Craigie, Narison, and Riazuddin of a renormalization-group-improved perturbation theory to deal with the electromagnetic mass shift problem in QCD, we show that the short distance QCD contribution to the electroweak pion mass difference (with mu=md≠0) is finite and, of course, its value is negligible compared to other contributions.

Squeezed correlations of strange particles-antiparticles

Squeezed correlations of hadron-antihadron pairs are predicted to appear if their masses are modified in the hot and dense medium formed in high-energy heavy ion collisions. If discovered experimentally, they would be an unequivocal evidence of in-medium mass shift found by means of hadronic probes. We discuss a method proposed to search for this novel type of correlation, illustrating it by means of D(s)-mesons with in-medium shifted masses. These particles are expected to be more easily detected and identified in future upgrades at RHIC.

SQUEEZED PARTICLE-ANTIPARTICLE CORRELATIONS

A novel type of correlation involving particle-antiparticle pairs was found out in the 1990's. Currently known as squeezed or Back-to-Back Correlations (BBC), they should be present if the hadronic masses are modified in the hot and dense medium formed in high energy heavy ion collisions. Although well-established theoretically, such hadronic correlations have not yet been observed experimentally. In this phenomenological study we suggest a promising way to search for the BBC signal, by looking into the squeezed correlation function of phi phi and K(+)K(-) pairs at RHIC energies, as function of the pair average momentum, K(12) = (k(1) + k(2))/2. The effects of in-medium mass-shift on the identical particle correlations (Hanbury-Brown and Twiss effect) are also discussed.

J/Ψ in nuclear matter

We report on recent estimates of the J/Ψ mass shift in infinite nuclear matter and finite nuclei arising from in-medium D and D* meson loops. The density dependence of the J/Ψ mass shift is evaluated employing medium-modified D and D* meson masses derived within the quark-meson coupling model. Using a local density approximation, J/Ψ-nuclear bound state energies are calculated for a range of nuclei. We predict that J/Ψ-nuclear bound states should be observed with a clear signal in experiments, provided the J/Ψ meson is produced in recoilless kinematics. © Published under licence by IOP Publishing Ltd.

Nuclear charge radius of the halo nucleus lithium-11

Nuclear charge radii of short-lived isotopes can be probed in a nuclear-model independent way via isotope shift measurements. For this purpose a novel technique was developed at GSI, Darmstadt. It combines two-photon laser spectroscopy in the 2s-3s electronic transition of lithium, resonance ionization, and detection via quadrupole mass spectrometry. In this way an accuracy of 5e-5 which is necessary for the extraction of nuclear charge radii, and an overall detection efficiency of 1e-4 is reached. This allowed an isotope shift measurement of Li-11 for the first time at the TRIUMF facility in Vancouver. Additionally, uncertainties in the isotope shift for all other lithium isotopes were reduced by about a factor of four compared to previous measurements at GSI. Results were combined with recent theoretical mass shift calculations in three-electron systems and root-mean-square nuclear charge radii of all lithium isotopes, particulary of the two-neutron halo nucleus Li-11, were determined. Obtained charge radii decrease continuously from Li-6 to Li-9, while a strong increase between Li-9 and Li-11 is observed. This is compared to predictions of various nuclear models and it is found that a multicluster model gives the best overall agreement. Within this model, the increase in charge radius between Li-9 and Li-11is to a large extend caused by intrinsic excitation of the Li-9-like core while the neutron-halo correlation contributes only to a small extend.

Nuclear charge radii of light isotopes based on frequency comb measurements

Optical frequency comb technology has been used in this work for the first time to investigate the nuclear structure of light radioactive isotopes. Therefore, three laser systems were stabilized with different techniques to accurately known optical frequencies and used in two specialized experiments. Absolute transition frequency measurements of lithium and beryllium isotopes were performed with accuracy on the order of 10^(−10). Such a high accuracy is required for the light elements since the nuclear volume effect has only a 10^(−9) contribution to the total transition frequency. For beryllium, the isotope shift was determined with an accuracy that is sufficient to extract information about the proton distribution inside the nucleus. A Doppler-free two-photon spectroscopy on the stable lithium isotopes (6,7)^Li was performed in order to determine the absolute frequency of the 2S → 3S transition. The achieved relative accuracy of 2×10^(−10) is improved by one order of magnitude compared to previous measurements. The results provide an opportunity to determine the nuclear charge radius of the stable and short-lived isotopes in a pure optical way but this requires an improvement of the theoretical calculations by two orders of magnitude. The second experiment presented here was performed at ISOLDE/CERN, where the absolute transition frequencies of the D1 and D2 lines in beryllium ions for the isotopes (7,9,10,11)^Be were measured with an accuracy of about 1 MHz. Therefore, an advanced collinear laser spectroscopy technique involving two counter-propagating frequency-stabilized laser beams with a known absolute frequency was developed. The extracted isotope shifts were combined with recent accurate mass shift calculations and the root-mean square nuclear charge radii of (7,10)^Be and the one-neutron halo nucleus 11^Be were determined. Obtained charge radii are decreasing from 7^Be to 10^Be and increasing again for 11^Be. While the monotone decrease can be explained by a nucleon clustering inside the nucleus, the pronounced increase between 10^Be and 11^Be can be interpreted as a combination of two contributions: the center-of-mass motion of the 10^Be core and a change of intrinsic structure of the core. To disentangle these two contributions, the results from nuclear reaction measurements were used and indicate that the center-of-mass motion is the dominant effect. Additionally, the splitting isotope shift, i.e. the difference in the isotope shifts between the D1 and D2 fine structure transitions, was determined. This shows a good consistency with the theoretical calculations and provides a valuable check of the beryllium experiment.

Stabilising suppressor of cytokine signalling 3 (SOCS3) protein levels to limit neointimal hyperplasia

Suppressor of cytokine signalling 3 (SOCS3) is a potent inhibitor of the mitogenic, migratory and pro-inflammatory pathways responsible for the development of neointimal hyperplasia (NIH), a key contributor to the failure of vascular reconstructive procedures. However, the protein levels of SOCS3, and therefore its potential to reduce NIH, is limited by its ubiquitylation and high turnover by the proteasome. I hypothesised that stabilisation of endogenous SOCS3 by inhibiting its ubiquitylation has the potential to limit vascular inflammation and NIH. Consequently, the aim of this PhD was to identify the mechanisms promoting the rapid turnover of SOCS3. Initial experiments involved the identification of residues involved in regulating the turnover of SOCS3 at the proteasome. I assessed the ubiquitylation status of a panel of FLAG tagged SOCS3 truncation mutants and identified a C-terminal 44 amino acid region required for SOCS3 ubiquitylation. This region localised to the SOCS box which is involved in binding Elongin B/C and the formation of a functional E3 ubiquitin ligase complex. However, the single lysine residue at position 173, located within this 44 amino acid region, was not required for ubiquitylation. Moreover, Emetine chase assays revealed that loss of either Lys173 or Lys6 (as documented in the literature) had no significant effect on SOCS3 stability 8 hrs post emetine treatment. As mutagenesis studies failed to identify key sites of ubiquitylation responsible for targeting SOCS3 to the proteasome, LC-MS-MS analysis of a SOCS3 co-immunoprecipitate was employed. These data were searched for the presence of a Gly-Gly doublet (+114 Da mass shift) and revealed 8 distinct sites of ubiquitylation (Lys23, Lys28, Lys40, Lys85, Lys91, Lys173, Lys195, Lys206) on SOCS3 however Lys6 ubiquitylation was not detected. As multiple Lys residues were ubiquitylated, I hypothesised that only a Lys-less SOCS3, in which all 8 Lys residues were mutated to Arg, would be resistant to ubiquitylation. Compared to WT SOCS3, Lys-less SOCS3 was indeed found to be completely resistant to ubiquitylation, and significantly more stable than WT SOCS3. These changes occurred in the absence of any detrimental effect on the ability of Lys-less SOCS3 to interact with the Elongin B/C components required to generate a functional E3 ligase complex. In addition, both WT and Lys-less SOCS3 were equally capable of inhibiting cytokine-stimulated STAT3 phosphorylation upon co-expression with a chimeric EpoR-gp130 receptor. To assess whether SOCS3 auto-ubiquitylates I generated an L189A SOCS3 mutant that could no longer bind the Elongins and therefore form the E3 ligase complex required for ubiquitylation. A denaturing IP to assess the ubiquitylation status of this mutant was performed and revealed that, despite an inability to bind the Elongins, the L189A mutant was poly-ubiquitylated similar to WT SOCS3. Together these data suggested that SOCS3 does not auto-ubiquitylate and that a separate E3 ligase must regulate SOCS3 ubiquitylation. This study sought to identify the E3 ligase and deubiquitylating (DUB) enzymes controlling the ubiquitylation of SOCS3. Our initial strategy was to develop a tool to screen an E3 ligase/DUB library, using an siARRAY, to sequentially knockdown all known E3 ligases in the presence of a SOCS3-luciferase fusion protein or endogenous SOCS3 in a high content imaging screening platform. However, due to a poor assay window (<2) and non-specific immunoreactivity of SOCS3 antibodies available, these methods were deemed unsuitable for screening purposes. In the absence of a suitable tool to screen the si-ARRAY, LC-MS-MS analysis of a SOCS3 co-immunoprecipitate (co-IP) was investigated. I performed a SOCS3 under conditions which preserved protein-protein interactions, with the aim of identifying novel E3 ligase and/or DUBs that could potentially interact with SOCS3. These data were searched for E3 ligase or DUB enzymes that may interact with SOCS3 in HEK293 cells and identified two promising candidates i) an E3 ligase known as HectD1 and ii) a DUB known as USP15. This thesis has demonstrated that in the presence of HectD1 overexpression, a slight increase in K63-linked polyubiquitylation of SOCS3 was observed. Mutagenesis also revealed that an N-terminal region of SOCS3 may act as a repressor of this interaction with HectD1. Additionally, USP15 was shown to reduce SOCS3 polyubiquitylation in a HEK293 overexpression system suggesting this may act as a DUB for SOCS3. The C-terminal region of SOCS3 was also shown to play a major role in the interaction with USP15. The original hypothesis of this thesis was that stabilisation of endogenous SOCS3 by inhibiting its ubiquitylation has the potential to limit vascular inflammation and NIH. Consistent with this hypothesis, immunohistochemistry visualisation of SOCS3, in human saphenous vein tissue derived from CABG patients, revealed that while SOCS3 was present throughout the media of these vessels the levels of SOCS3 within the neointima was reduced. Finally, preliminary data supporting the hypothesis that SOCS3 overexpression may limit the proliferation, but not migration, of human saphenous vein smooth muscle cells (HSVSMCs) is presented. It is expected that multiple E3 ligases and DUBs will contribute to the regulation of SOCS3 turnover. However, the identification of candidate E3 ligases or DUBs that play a significant role in SOCS3 turnover may facilitate the development of peptide disruptors or gene therapy targets to attenuate pathological SMC proliferation. A targeted approach, inhibiting the interaction between SOCS3 and identified E3 ligase, that controls the levels of SOCS3, would be expected to reduce the undesirable effects associated with global inhibition of the E3 ligase involved.

Mass spectrometry-based thermal shift assay for protein-ligand binding analysis.

Described here is a mass spectrometry-based screening assay for the detection of protein-ligand binding interactions in multicomponent protein mixtures. The assay utilizes an oxidation labeling protocol that involves using hydrogen peroxide to selectively oxidize methionine residues in proteins in order to probe the solvent accessibility of these residues as a function of temperature. The extent to which methionine residues in a protein are oxidized after specified reaction times at a range of temperatures is determined in a MALDI analysis of the intact proteins and/or an LC-MS analysis of tryptic peptide fragments generated after the oxidation reaction is quenched. Ultimately, the mass spectral data is used to construct thermal denaturation curves for the detected proteins. In this proof-of-principle work, the protocol is applied to a four-protein model mixture comprised of ubiquitin, ribonuclease A (RNaseA), cyclophilin A (CypA), and bovine carbonic anhydrase II (BCAII). The new protocol's ability to detect protein-ligand binding interactions by comparing thermal denaturation data obtained in the absence and in the presence of ligand is demonstrated using cyclosporin A (CsA) as a test ligand. The known binding interaction between CsA and CypA was detected using both the MALDI- and LC-MS-based readouts described here.

The water-gas shift reaction over CeO/CuO:Operando SSITKA-DRIFTS-mass spectrometry study of low temperature mechanism

An inverse CeO2/CuO catalyst has been investigated by operando steady-state isotopic transient kinetic analysis (SSITKA) in combination with diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) under 3% CO +3% H2O reactant mixture at 473 K with the aim of determining intermediates involved in the water gas shift reaction at relatively low temperatures. Among the various species detected in the infrared spectra which may be involved in the reaction, i.e. formates, copper carbonyls and carbonates, a particular type of carbonate species is identified as a reaction intermediate on the basis of detailed analysis of the spectra during isotopic exchange in comparison with the change in the corresponding isotopically labelled CO2 product. 

Дизайнът на взаимодействията, масовата комуникация и предизвикателствата на споделеното експертно знание (Interaction Design, Mass Communication And the Challenge of Distributed Expertise)

This paper considers some of the implications of the rise of design as a master-metaphor of the information age. It compares the terms 'interaction design' and 'mass communication', suggesting that both can be seen as a contradiction in terms, inappropriately preserving an industrial-age division between producers and consumers. With the shift from mass media to interactive media, semiotic and political power seems to be shifting too - from media producers to designers. This paper argues that it is important for the new discipline of 'interactive design' not to fall into habits of thought inherited from the 'mass' industrial era. Instead it argues for the significance, for designers and producers alike, of what I call 'distributed expertise' -including social network markets, a DIY-culture, user-led innovation, consumer co-created content, and the use of Web 2.0 affordances for social, scientific and creative purposes as well as for entertainment. It considers the importance of the growth of 'distributed expertise' as part of a new paradigm in the growth of knowledge, which has 'evolved' through a number of phases, from 'abstraction' to 'representation', to 'productivity'. In the context of technologically mediated popular participation in the growth of knowledge and social relationships, the paper argues that design and media-production professions need to cross rather than to maintain the gap between experts and everyone else, enabling all the agents in the system to navigate the shift into the paradigm of mass productivity.

The knock-on from the knock-off : recent shifts within Australian mass market fashion design practice

Australia’s mass market fashion labels have traditionally benefitted from their peripheral location to the world’s fashion centres. Operating a season behind, Australian mass market designers and buyers were well-placed to watch trends play out overseas before testing them in the Australian marketplace. For this reason, often a designer’s role was to source and oversee the manufacture of ‘knock-offs’, or close copies of Northern hemisphere mass market garments. Both Weller (2007) and Walsh (2009) have commented on this practice. The knock-on effect from this continues to be a cautious, derivative fashion sensibility within Australian mass market fashion design, where any new trend or product is first tested and proved overseas months earlier. However, there is evidence that this is changing. The rapid online dissemination of global fashion trends, coupled with the Australian consumer’s willingness to shop online, has meant that the ‘knock-off’ is less viable. For this reason, a number of mass market companies are moving away from the practice of direct sourcing and are developing product in-house under a Northern hemisphere model. This shift is also witnessed in the trend for mass market companies to develop collections in partnership with independent Australian designers. This paper explores the current and potential effects of these shifts within Australian mass market design practice, and discusses how they may impact on designers, consumers and on the wider culture of Australian fashion.

The knock-on from the knock-off : recent shifts within Australian mass market fashion design practice

Australia's mass market fashion labels have traditionally benefitted from their peripheral location to the world's fashion centres. Operating a season behind, Australian mass market designers and buyers were well-placed to watch trends play out overseas before testing them in the Australian marketplace. For this reason, often a designer's role was to source and oversee the manufacture of 'knock-offs', or close copies of northern hemisphere mass market garments. Both Weller and Walsh have commented on this practice.12 The knock-on effect from this continues to be a cautious, derivative fashion sensibility within Australian mass market fashion design, where any new trend or product is first tested and proved overseas months earlier. However, there is evidence that this is changing. The rapid online dissemination of global fashion trends, coupled with the Australian consumer’s willingness to shop online, has meant that the ‘knock-off’ is less viable. For this reason, a number of mass market companies are moving away from the practice of direct sourcing and are developing product in-house under a northern hemisphere model. This shift is also witnessed in the trend for mass market companies to develop collections in partnership with independent Australian designers. This paper explores the current and potential effects of these shifts within Australian mass market design practice, and discusses how they may impact on both consumers and on the wider culture of Australian fashion.