Oscillating enzyme-bound NADH in glycolysis

AbstractIn glycolyzing cell-free cytoplasmic medium extracted from yeast Saccharomyces cerevisiae, the action spectrum of oscillation has an absorption maximum around 335 nm, nearly coinciding with that of the yeast alcohol dehydrogenase (ADH)-NADH complex due to its bound NADH. Our approximate calculations based on the amount of this enzyme and coenzyme NADH present in the extract suggest that the ADH-NADH complex alone can account for 90% or more of the total absorbance change

Synthetic Studies With Pinus Elliottiis' Rosin Derivatives. Oxidation Of Maleopimaric Anhydride Methyl Ester And Trimethyl Fumaropimarate

Ozonolysis of maleopimaric anhydride methyl ester in the presence of tetracyanoethylene led to an epoxide and an ozonide. Ozonolysis of the trimethyl fumaropimarate, followed by treatment with Me2S, led to an epoxide, a diene, a keto-acid and an allylic oxidation product. Some of the compounds obtained were active against Staphylococcus aureus, Bacillus subtilis and Micrococcus luteus.1115963Seebacher, W., Hüfner, A., Haslingeer, E., Weis, R., (1995) Monatsh. Chem., 129, p. 697. , and references cited thereinKsabati, M.B., Schimtz, F.J., (1987) J. Org. Chem., 52, p. 3766Miyamoto, T., Sakamoto, K., Arao, K., Komori, T., Higuchi, R., Sasaki, T., (1996) Tetrahedron, 52, p. 8187Zalkow, L.H., Ford, R.A., Kutney, J.P., (1962) J. Org. Chem., 27, p. 3535Zalkow, L.H., Brannon, D.R., (1964) J. Org. Chem., 29, p. 1296Zalkow, L.H., Girotra, N.N., (1963) J. Org. Chem., 28, p. 2033Zalkow, L.H., Kulkarni, M.V., Girotra, N.N., (1965) J. Org. Chem., 30, p. 1679Halbrook, N.J., Lawrence, R.V., Dressler, R.L., Blackstone, R.C., Herz, W., (1964) J. Org. Chem., 29, p. 1017Santos, C., Rosso, C.R.S., Imamura, P., (1999) M. Synth. Commun., 29, p. 1903Bailey, P.S., (1978) Ozonization in Organic Chemistry, 1. , Academic Press, New YorkHerz, W., Blackstone, R.C., (1969) Atmos Environ, 34, p. 1257Atmos Environ, p. 135Masaki, Y., Miura, T., Ochiai, M., (1996) Bull. Chem. Soc. Jpn., 69, p. 195. , and references cited thereinThe ozonide could be stored in a freezer without decomposition at -5°C for few weeksShiojima, K., Masuda, K., Ageta, K., (1990) Chem. Pharm. Bull., 38, p. 79Li, T., Yang, Y., Li, Y., (1993) J. Chem. Res. (S), p. 30Carlsen, P.H.J., Katsuki, T., Martin, V.S., Sharpless, K.B., (1981) J. Org. Chem., 46, p. 3936Funk, R.L., Abelman, M.M., (1986) J. Org. Chem., 51, p. 3247For convenience, the numbering of carbons for 14 was used the same given for 3Sam, D.J., Simmons, H.F., (1972) J. Am. Chem. Soc., 94, p. 4024Ferreira, J.T.B., Cruz, W.O., Vieira, P.C., Yonashiro, M., (1987) J. Org. Chem., 52, p. 3698Mitra, R.B., Muljiani, Z., Deshmukh, A.R.A., (1982) S. Synth. Commun., 12, p. 1063Aristoff, P.A., Johnson, P.D., Harrison, A.W., (1985) J. Am. Chem. Soc., 107, p. 7961Homans, A.L., Fuchs, A., (1970) J. Chromatogr., 75, p. 327Hamburger, M.O., Cordell, G.A., (1987) J. Nat. Prod., 50, p. 19Bruch, M.K., (1991) Methods of Testing Antiseptics: Antimicrobials Used Topically in Humans and Procedures for Hand Scrubs, in Disinfection, Sterilization and Preservation, 4th. Ed., , Lea & Febinger, PhiladelphiaHalbrook, N.J., Lawrence, R.V., (1958) J. Am. Chem. Soc., 80, p. 36

Periodic heat production by oscillating glycolysis in a cytoplasmic medium extracted from yeast

AbstractThe rate of heat production in a periodically glycolysing cell-free cytoplasmic medium extracted from yeast Saccharomyces cerevisiae is measured with a batch calorimeter. The rate exhibits periodic variations of approx. 10% of the average heat production rate of about 54 mJml per minute. From this rate and the enthalpy change fro glycolysis a glucose degradation rate of 0.43 mMming is calculated. The value fits into the ‘oscillatory window’ determined by a glucose injection technique

The interfascicular matrix enables fascicle sliding and recovery in tendon, and behaves more elastically in energy storing tendons

While the predominant function of all tendons is to transfer force from muscle to bone and position the limbs, some tendons additionally function as energy stores, reducing the cost of locomotion. Energy storing tendons experience extremely high strains and need to be able to recoil efficiently for maximum energy storage and return. In the equine forelimb, the energy storing superficial digital flexor tendon (SDFT) has much higher failure strains than the positional common digital extensor tendon (CDET). However, we have previously shown that this is not due to differences in the properties of the SDFT and CDET fascicles (the largest tendon subunits). Instead, there is a greater capacity for interfascicular sliding in the SDFT which facilitates the greater extensions in this particular tendon (Thorpe et al., 2012). In the current study, we exposed fascicles and interfascicular matrix (IFM) from the SDFT and CDET to cyclic loading followed by a test to failure. The results show that IFM mechanical behaviour is not a result of irreversible deformation, but the IFM is able to withstand cyclic loading, and is more elastic in the SDFT than in the CDET. We also assessed the effect of ageing on IFM properties, demonstrating that the IFM is less able to resist repetitive loading as it ages, becoming stiffer with increasing age in the SDFT. These results provide further indications that the IFM is important for efficient function in energy storing tendons, and age-related alterations to the IFM may compromise function and predispose older tendons to injury

The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis. Availability: The RNA workbench is available at https://github.com/bgruening/galaxy-rna-workbench

The RNA workbench: Best practices for RNA and high-throughput sequencing bioinformatics in Galaxy

RNA-based regulation has become a major research topic in molecular biology. The analysis of epigenetic and expression data is therefore incomplete if RNA-based regulation is not taken into account. Thus, it is increasingly important but not yet standard to combine RNA-centric data and analysis tools with other types of experimental data such as RNA-seq or ChIP-seq. Here, we present the RNA workbench, a comprehensive set of analysis tools and consolidated workflows that enable the researcher to combine these two worlds. Based on the Galaxy framework the workbench guarantees simple access, easy extension, flexible adaption to personal and security needs, and sophisticated analyses that are independent of command-line knowledge. Currently, it includes more than 50 bioinformatics tools that are dedicated to different research areas of RNA biology including RNA structure analysis, RNA alignment, RNA annotation, RNA-protein interaction, ribosome profiling, RNA-seq analysis and RNA target prediction. The workbench is developed and maintained by experts in RNA bioinformatics and the Galaxy framework. Together with the growing community evolving around this workbench, we are committed to keep the workbench up-to-date for future standards and needs, providing researchers with a reliable and robust framework for RNA data analysis

Model-independent search for CP violation in D0→K−K+π−π+ and D0→π−π+π+π− decays

A search for CP violation in the phase-space structures of D0 and View the MathML source decays to the final states K−K+π−π+ and π−π+π+π− is presented. The search is carried out with a data set corresponding to an integrated luminosity of 1.0 fb−1 collected in 2011 by the LHCb experiment in pp collisions at a centre-of-mass energy of 7 TeV. For the K−K+π−π+ final state, the four-body phase space is divided into 32 bins, each bin with approximately 1800 decays. The p-value under the hypothesis of no CP violation is 9.1%, and in no bin is a CP asymmetry greater than 6.5% observed. The phase space of the π−π+π+π− final state is partitioned into 128 bins, each bin with approximately 2500 decays. The p-value under the hypothesis of no CP violation is 41%, and in no bin is a CP asymmetry greater than 5.5% observed. All results are consistent with the hypothesis of no CP violation at the current sensitivity

Branching fraction and CP asymmetry of the decays B+→K0Sπ+ and B+→K0SK+

An analysis of B+ → K0 Sπ+ and B+ → K0 S K+ decays is performed with the LHCb experiment. The pp collision data used correspond to integrated luminosities of 1 fb−1 and 2 fb−1 collected at centre-ofmass energies of √ s = 7 TeV and √ s = 8 TeV, respectively. The ratio of branching fractions and the direct CP asymmetries are measured to be B(B+ → K0 S K+ )/B(B+ → K0 Sπ+ ) = 0.064 ± 0.009 (stat.) ± 0.004 (syst.), ACP(B+ → K0 Sπ+ ) = −0.022 ± 0.025 (stat.) ± 0.010 (syst.) and ACP(B+ → K0 S K+ ) = −0.21 ± 0.14 (stat.) ± 0.01 (syst.). The data sample taken at √ s = 7 TeV is used to search for B+ c → K0 S K+ decays and results in the upper limit ( fc · B(B+ c → K0 S K+ ))/( fu · B(B+ → K0 Sπ+ )) < 5.8 × 10−2 at 90% confidence level, where fc and fu denote the hadronisation fractions of a ¯b quark into a B+ c or a B+ meson, respectively

Anisotropic flow of charged hadrons, pions and (anti-)protons measured at high transverse momentum in Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm NN}}=2.76 TeV

The elliptic, $v_2$, triangular, $v_3$, and quadrangular, $v_4$, azimuthal anisotropic flow coefficients are measured for unidentified charged particles, pions and (anti-)protons in Pb-Pb collisions at $\sqrt{s_{\rm NN}} = 2.76$ TeV with the ALICE detector at the Large Hadron Collider. Results obtained with the event plane and four-particle cumulant methods are reported for the pseudo-rapidity range $|\eta|<0.8$ at different collision centralities and as a function of transverse momentum, $p_{\rm T}$, out to $p_{\rm T}=20$ GeV/$c$. The observed non-zero elliptic and triangular flow depends only weakly on transverse momentum for $p_{\rm T}>8$ GeV/$c$. The small $p_{\rm T}$ dependence of the difference between elliptic flow results obtained from the event plane and four-particle cumulant methods suggests a common origin of flow fluctuations up to $p_{\rm T}=8$ GeV/$c$. The magnitude of the (anti-)proton elliptic and triangular flow is larger than that of pions out to at least $p_{\rm T}=8$ GeV/$c$ indicating that the particle type dependence persists out to high $p_{\rm T}$.Comment: 16 pages, 5 captioned figures, authors from page 11, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/186

Centrality dependence of charged particle production at large transverse momentum in Pb-Pb collisions at sNN=2.76\sqrt{s_{\rm{NN}}} = 2.76 TeV

The inclusive transverse momentum ($p_{\rm T}$) distributions of primary charged particles are measured in the pseudo-rapidity range $|\eta|<0.8$ as a function of event centrality in Pb-Pb collisions at $\sqrt{s_{\rm{NN}}}=2.76$ TeV with ALICE at the LHC. The data are presented in the $p_{\rm T}$ range $0.15<p_{\rm T}<50$ GeV/$c$ for nine centrality intervals from 70-80% to 0-5%. The Pb-Pb spectra are presented in terms of the nuclear modification factor $R_{\rm{AA}}$ using a pp reference spectrum measured at the same collision energy. We observe that the suppression of high-$p_{\rm T}$ particles strongly depends on event centrality. In central collisions (0-5%) the yield is most suppressed with $R_{\rm{AA}}\approx0.13$ at $p_{\rm T}=6$-7 GeV/$c$. Above $p_{\rm T}=7$ GeV/$c$, there is a significant rise in the nuclear modification factor, which reaches $R_{\rm{AA}} \approx0.4$ for $p_{\rm T}>30$ GeV/$c$. In peripheral collisions (70-80%), the suppression is weaker with $R_{\rm{AA}} \approx 0.7$ almost independently of $p_{\rm T}$. The measured nuclear modification factors are compared to other measurements and model calculations.Comment: 17 pages, 4 captioned figures, 2 tables, authors from page 12, published version, figures at http://aliceinfo.cern.ch/ArtSubmission/node/284