Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

We introduce a Python-based program that utilizes the large database of (13)C and (15)N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D (13)C-(13)C, (15)N-(13)C, or 3D (15)N-(13)C-(13)C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D (13)C-(13)C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-Cα-Cβ or N-Cα-Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Thymosin beta-4 promotes mesenchymal stem cell proliferation via an interleukin-8-dependent mechanism

Mesenchymal stem cells (MSCs) hold great promise for the field of tissue regeneration. Because only a limited number of MSCs can be obtained from each donor site, it is important to establish standard methods for MSC expansion using growth and trophic factors. Thymosin β4 (Tβ4) is a novel trophic factor that has antimicrobial effects and the potential to promote tissue repair. Tβ4 is a ubiquitous, naturally-occurring peptide in the wound bed. Therefore, the relationship between Tβ4 and MSCs, especially adjacent adipose tissue-derived stem cells (ASCs), merits consideration. Exogenous Tβ4 treatment enhanced the proliferation of human ASCs, resulting in prominent nuclear localization of PCNA immunoreactivity. In addition, exogenous Tβ4 also increased IL-8 secretion and blocking of IL-8 with neutralizing antibodies decreased Tβ4-induced ASC proliferation, suggesting that IL-8 is a critical mediator of Tβ4-enhanced proliferation. Moreover, Tβ4 activated phosphorylation of ERK1/2 and increased the nuclear translocation of NF-κB. These observation provide that Tβ4 promotes the expansion of human ASCs via an IL-8-dependent mechanism that involves the ERK and NF-κB pathways. Therefore, Tβ4 could be used as a tool for MSC expansion in cell therapeutics.

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Yamauchi K, Yamazaki T, Yamazaki Y, Yan Z, Yang H, Yang H, Yang UK, Yang Y, Yang Z, Yanush S, Yao L, Yasu Y, Yatsenko E, Ye J, Ye S, Yen AL, Yilmaz M, Yoosoofmiya R, Yorita K, Yoshida R, Yoshihara K, Young C, Young CJS, Youssef S, Yu D, Yu DR, Yu J, Yu J, Yuan L, Yurkewicz A, Zabinski B, Zaidan R, Zaitsev AM, Zambito S, Zanello L, Zanzi D, Zaytsev A, Zeitnitz C, Zeman M, Zemla A, Zenin O, Ženiš T, Zerwas D, Zevi della Porta G, Zhang D, Zhang H, Zhang J, Zhang L, Zhang X, Zhang Z, Zhao L, Zhao Z, Zhemchugov A, Zhong J, Zhou B, Zhou N, Zhou Y, Zhu CG, Zhu H, Zhu J, Zhu Y, Zhuang X, Zhuravlov V, Zibell A, Zieminska D, Zimin NI, Zimmermann R, Zimmermann S, Zimmermann S, Zinonos Z, Ziolkowski M, Zitoun R, Živković L, Zmouchko VV, Zobernig G, Zoccoli A, zur Nedden M, Zutshi V, Zwalinski L. Measurement of kT splitting scales in W→ℓν events at [Formula: see text] with the ATLAS detector

A measurement of splitting scales, as defined by the kT clustering algorithm, is presented for final states containing a W boson produced in proton-proton collisions at a centre-of-mass energy of 7 TeV. The measurement is based on the full 2010 data sample corresponding to an integrated luminosity of 36 pb-1 which was collected using the ATLAS detector at the CERN Large Hadron Collider. Cluster splitting scales are measured in events containing W bosons decaying to electrons or muons. The measurement comprises the four hardest splitting scales in a kT cluster sequence of the hadronic activity accompanying the W boson, and ratios of these splitting scales. Backgrounds such as multi-jet and top-quark-pair production are subtracted and the results are corrected for detector effects. Predictions from various Monte Carlo event generators at particle level are compared to the data. Overall, reasonable agreement is found with all generators, but larger deviations between the predictions and the data are evident in the soft regions of the splitting scales.

Search for supersymmetry in pp collisions at [Formula: see text] TeV in events with a single lepton, jets, and missing transverse momentum

Results are reported from a search for new physics processes in events containing a single isolated high-transverse-momentum lepton (electron or muon), energetic jets, and large missing transverse momentum. The analysis is based on a 4.98 fb-1 sample of proton-proton collisions at a center-of-mass energy of 7 TeV, obtained with the CMS detector at the LHC. Three separate background estimation methods, each relying primarily on control samples in the data, are applied to a range of signal regions, providing complementary approaches for estimating the background yields. The observed yields are consistent with the predicted standard model backgrounds. The results are interpreted in terms of limits on the parameter space for the constrained minimal supersymmetric extension of the standard model, as well as on cross sections for simplified models, which provide a generic description of the production and decay of new particles in specific, topology based final states.

ELECTRONIC SUPPLEMENTARY MATERIAL

The online version of this article (doi:10.1140/epjc/s10052-013-2404-z) contains supplementary material, which is available to authorized users.

Observation of associated near-side and away-side long-range correlations in sqrt[s(NN)]=5.02 TeV proton-lead collisions with the ATLAS detector

Two-particle correlations in relative azimuthal angle (Δø) and pseudorapidity (Δη) are measured in sqrt[s(NN)] = 5.02 TeV p+Pb collisions using the ATLAS detector at the LHC. The measurements are performed using approximately 1 μb(-1) of data as a function of transverse momentum (p(T)) and the transverse energy (ΣE(T)(Pb)) summed over 3.1 < η < 4.9 in the direction of the Pb beam. The correlation function, constructed from charged particles, exhibits a long-range (2 < |Δ η | < 5) "near-side" (Δø ~ 0) correlation that grows rapidly with increasing ΣE(T)(Pb). A long-range "away-side" (Δø ~ π) correlation, obtained by subtracting the expected contributions from recoiling dijets and other sources estimated using events with small ΣE(T)(Pb), is found to match the near-side correlation in magnitude, shape (in Δη and Δø) and ΣE(T)(Pb) dependence. The resultant Δø correlation is approximately symmetric about π/2, and is consistent with a dominant cos2Δø modulation for all ΣE(T)(Pb) ranges and particle p(T).

Open reduction and internal fixation versus external fixation for unstable distal radial fractures: a meta-analysis

PURPOSE

To compare the clinical outcomes of open reduction and internal fixation (ORIF) versus the ones of closed reduction and external fixation (EF) in the treatment of distal radial fractures.

METHODS

We performed a meta-analysis of randomized controlled trials that compared the clinical results of ORIF to EF in the treatment of distal radial fractures. A systemic retrieve from PubMed, EMBASE, OVID and Cochrane Collaboration CENTRAL database resulted in 11 studies with 824 patients. We thus performed data synthesis using RevMan (version 5.1).

RESULTS

Superior statistical differences were observed for DASH scores (at 3, 6 and 12 months follow-up) grip strength (at 3 months follow-up), volar tilt (at 12 months follow-up), flexion and supination (at 3 months follow-up), and extension (at 3 and 6 months follow-up) in ORIF patients group, compared with those in EF group. We also found a significantly higher risk of infection associated with EF. There was no significant difference in the incidence of malunion and median nerve dysfunction.

CONCLUSION

Regarding surgical fixation of unstable distal radius fractures, ORIF yields significantly better subjective outcome (DASH scores) the first year after operation, restoration of anatomic volar tilt, and forearm flexion and extension at the end of the follow-up period. However, EF results in higher incidence of infection compared to ORIF. ORIF is equal to EF for either grip strength, or range of motion of the injured wrist, or incidence of malunion or median nerve dysfunction at the end of the follow-up period.

LEVEL OF EVIDENCE

Level II. Therapeutic study.