Detection of human papillomavirus in laryngeal squamous cell carcinoma: systematic review and meta-analysis

Background: Recent studies have reported a human papillomavirus (HPV) prevalence of 20% to 30% in laryngeal squamous cell carcinoma (LSCC), although clinical data on HPV involvement remain largely inconsistent, ascribed by some to differences in HPV detection methods or in geographic origin of the studies. Objective To perform a systematic review and formal meta-analysis of the literature reporting on HPV detection in LSCC. Methods Literature was searched from January 1964 until March 2015. The effect size was calculated as event rates (95% confidence interval [CI]), with homogeneity testing using Cochran's Q and I2 statistics. Meta-regression was used to test the impact of study-level covariates (HPV detection method, geographic origin) on effect size. Potential publication bias was estimated using funnel plot symmetry. Results One hundred seventy nine studies were eligible, comprising a sample size of 7,347 LSCCs from different geographic regions. Altogether, 1,830 (25%) cases tested HPV-positive considering all methods, with effect size of 0.269 (95% CI: 0.242 to 0.297; random-effects model). In meta-analysis stratified by the 1) HPV detection technique and 2) geographic study origin, the between-study heterogeneity was significant only for geographic origin (P = .0001). In meta-regression, the HPV detection method (P = .876) or geographic origin (P = .234) were not significant study-level covariates. Some evidence for publication bias was found only for studies from North America and those using non–polymerase chain reaction methods, with a marginal effect on adjusted point estimates for both. Conclusions Variability in HPV detection rates in LSCC is explained by geographic origin of study but not by HPV detection method. However, they were not significant study-level covariates in formal meta-regression

Pyrearinus termitilluminans larval click beetle luciferase: Active site properties, structure and function relationships and comparison with other beetle luciferases

Several beetle luciferases have been cloned and sequenced. However, most studies on structure and function relationships and bioanalytical applications were done with firefly luciferases, which are pH sensitive. Several years ago we cloned Pyrearinus termitilluminans larval click beetle luciferase, which displays the most blue-shifted bioluminescence among beetle luciferases and is pH insensitive. This enzyme was expressed in E. coli, purified, and its properties investigated. This luciferase shows slower luminescence kinetics, KM values comparable to other beetle luciferases and high catalytic constant. Fluorescence studies with 8-anilino-1-naphtalene-sulfonic acid (1,8-ANS) and modeling studies suggest that the luciferin binding site of this luciferase is very hydrophobic, supporting the solvent and orientation polarizability effects as determining mechanisms for bioluminescence colors. Although pH insensitive in the range between pH 6-8, at pH 10 this luciferase displays a remarkable red-shift and broadening of the bioluminescence spectrum. Modeling studies suggest that the residue C312 may play an important role in bioluminescence color modulation. Compared to other beetle luciferases, Pyrearinus termitilluminans luciferase also displays higher thermostability and sustained luminescence in a bacterial cell environment, which makes this luciferase particularly suitable for in vivo cell analysis and bioimaging. © The Royal Society of Chemistry and Owner Societies 2009

Oligomerization, Membrane Association, And In Vivo Phosphorylation Of Sugarcane Udp-glucose Pyrophosphorylase

Sugarcane is a monocot plant that accumulates sucrose to levels of up to 50% of dry weight in the stalk. The mechanisms that are involved in sucrose accumulation in sugarcane are not well understood, and little is known with regard to factors that control the extent of sucrose storage in the stalks. UDP-glucose pyrophosphorylase (UGPase; EC 2.7.7.9) is an enzyme that produces UDP-glucose, a key precursor for sucrose metabolism and cell wall biosynthesis. The objective of this work was to gain insights into the ScUGPase-1 expression pattern and regulatory mechanisms that control protein activity. ScUGPase-1 expression was negatively correlated with the sucrose content in the internodes during development, and only slight differences in the expression patterns were observed between two cultivars that differ in sucrose content. The intracellular localization of Sc UGPase-1 indicated partial membrane association of this soluble protein in both the leaves and internodes. Using a phospho-specific antibody, we observed that Sc UGPase-1 was phosphorylated in vivo at the Ser-419 site in the soluble and membrane fractions from the leaves but not from the internodes. The purified recombinant enzyme was kinetically characterized in the direction of UDP-glucose formation, and the enzyme activity was affected by redox modification. Preincubation with H2O2 strongly inhibited this activity, which could be reversed by DTT. Small angle x-ray scattering analysis indicated that the dimer interface is located at the C terminus and provided the first structural model of the dimer of sugarcane UGPase in solution.289483336433377NSF; National Science FoundationWaclawovsky, A.J., Sato, P.M., Lembke, C.G., Moore, P.H., Souza, G.M., Sugarcane for bioenergy production: An assessment of yield and regulation of sucrose content (2010) Plant Biotechnol. J., 8, pp. 263-276Matsuoka, S., Ferro, J., Arruda, P., The Brazilian experience of sugarcane ethanol industry (2009) Vitr. Cell. Dev. Biol. Plant, 45, pp. 372-381Arruda, P., Genetically modified sugarcane for bioenergy generation (2012) Curr. Opin. Biotechnol., 23, pp. 315-322Botha, F.C., Black, K.G., Sucrose phosphate synthase and sucrose synthase activity during maturation of internodal tissue in sugarcane (2000) Funct. Plant Biol., 27, pp. 81-85Chen, R., Zhao, X., Shao, Z., Wei, Z., Wang, Y., Zhu, L., Zhao, J., He, G., Rice UDP-glucose pyrophosphorylase1 is essential for pollen callose deposition (2007) Plant Cell, 19, pp. 847-861Amor, Y., Haigler, C.H., Johnson, S., Wainscott, M., Delmer, D.P., A membrane-associated form of sucrose synthase and its potential role in synthesis of cellulose and callose in plants (1995) Proc. Natl. Acad. Sci. U.S.A., 92, pp. 9353-9357Park, J.-I., Ishimizu, T., Suwabe, K., Sudo, K., Masuko, H., Hakozaki, H., Nou, I.-S., Watanabe, M., UDP-glucose pyrophosphorylase is rate limiting in vegetative and reproductive phases in Arabidopsis thaliana (2010) Plant Cell Physiol., 51, pp. 981-996Kleczkowski, L.A., Geisler, M., Ciereszko, I., Johansson, H., UDP-glucose pyrophosphorylase: An old protein with new tricks (2004) Plant Physiol., 134, pp. 912-918Coleman, H.D., Canam, T., Kang, K.-Y., Ellis, D.D., Mansfield, S.D., Over-expression of UDP-glucose pyrophosphorylase in hybrid poplar affects carbon allocation (2007) J. Exp. Bot., 58, pp. 4257-4268Decker, D., Meng, M., Gornicka, A., Hofer, A., Wilczynska, M., Kleczkowski, L.A., Substrate kinetics and substrate effects on the quaternary structure of barley UDP-glucose pyrophosphorylase (2012) Phytochemistry, 79, pp. 39-45Meng, M., Fitzek, E., Gajowniczek, A., Wilczynska, M., Kleczkowski, L.A., Domain-specific determinants of catalysis/substrate binding and the oligomerization status of barley UDP-glucose pyrophosphorylase (2009) Biochim. Biophys. Acta, 1794, pp. 1734-1742Alexander, R.D., Morris, P.C., A proteomic analysis of 14-3-3 binding proteins from developing barley grains (2006) Proteomics, 6, pp. 1886-1896Grose, J.H., Smith, T.L., Sabic, H., Rutter, J., Yeast PAS kinase coordinates glucose partitioning in response to metabolic and cell integrity signaling (2007) EMBO J., 26, pp. 4824-4830Varkonyi-Gasic, E., Wu, R., Wood, M., Walton, E.F., Hellens, R.P., Protocol: A highly sensitive RT-PCR method for detection and quantification of microRNAs (2007) Plant Methods, 3, p. 12Papini-Terzi, F.S., Rocha, F.R., Vêncio, R.Z.N., Felix, J.M., Branco, D.S., Waclawovsky, A.J., Del Bem, L.E.V., Souza, G.M., Sugarcane genes associated with sucrose content (2009) BMC Genomics, 10, p. 120Pabinger, S., Thallinger, G.G., Snajder, R., Eichhorn, H., Rader, R., Trajanoski, Z., QPCR: Application for real-time PCR data management and analysis (2009) BMC Bioinformatics, 10, p. 268Töpfer, R., Matzeit, V., Gronenborn, B., Schell, J., Steinbiss, H.H., A set of plant expression vectors for transcriptional and translational fusions (1987) Nucleic Acids Res., 15, p. 5890Begcy, K., Mariano, E.D., Gentile, A., Lembke, C.G., Zingaretti, S.M., Souza, G.M., Menossi, M., A novel stress-induced sugarcane gene confers tolerance to drought, salt and oxidative stress in transgenic tobacco plants (2012) PLoS One, 7, p. e44697Fusari, C., Demonte, A.M., Figueroa, C.M., Aleanzi, M., Iglesias, A.A., Acolorimetric method for the assay of ADP-glucose pyrophosphorylase (2006) Anal. Biochem., 352, pp. 145-147Kellermann, G., Vicentin, F., Tamura, E., Rocha, M., Tolentino, H., Barbosa, A., Craievich, A., Torriani, I., The small-angle x-ray scattering beamline of the Brazilian Synchrotron Light Laboratory (1997) J. Appl. Crystallogr., 30, pp. 880-883Orthaber, D., Bergmann, A., Glatter, O., SAXS experiments on absolute scale with Kratky systems using water as a secondary standard (2000) J. Appl. Crystallogr., 33, pp. 218-225Mylonas, E., Svergun, D.I., Accuracy of molecular mass determination of proteins in solution by small-angle x-ray scattering (2007) J. Appl. Crystallogr., 40, pp. s245-s249Hammersley, A.P., Svensson, S.O., Hanfland, M., Fitch, A.N., Hausermann, D., Two-dimensional detector software: From real detector to idealised image or two-θ scan (1996) High Press. Res., 14, pp. 235-248Petoukhov, M.V., Franke, D., Shkumatov, A.V., Tria, G., Kikhney, A.G., Gajda, M., Gorba, C., Svergun, D.I., New developments in the ATSAS program package for small-angle scattering data analysis (2012) J. Appl. Crystallogr., 45, pp. 342-350Mertens, H.D.T., Svergun, D.I., Structural characterization of proteins and complexes using small-angle X-ray solution scattering (2010) J. Struct. Biol., 172, pp. 128-141Svergun, D.I., Determination of the regularization parameter in indirect-transform methods using perceptual criteria (1992) J. Appl. Crystallogr., 25, pp. 495-503Rambo, R.P., Tainer, J.A., Characterizing flexible and intrinsically unstructured biological macromolecules by SAS using the Porod-Debye law (2011) Biopolymers, 95, pp. 559-571Doniach, S., Changes in biomolecular conformation seen by small angle x-ray scattering (2001) Chem. Rev., 101, pp. 1763-1778Semisotnov, G.V., Kihara, H., Kotova, N.V., Kimura, K., Amemiya, Y., Wakabayashi, K., Serdyuk, I.N., Kuwajima, K., Protein globularization during folding: A study by synchrotron small-angle x-ray scattering (1996) J. Mol. Biol., 262, pp. 559-574Fischer, H., De Oliveira Neto, M., Napolitano, H.B., Polikarpov, I., Craievich, A.F., Determination of the molecular weight of proteins in solution from a single small-angle x-ray scattering measurement on a relative scale (2009) J. Appl. Crystallogr., 43, pp. 101-109Svergun, D.I., Petoukhov, M.V., Koch, M.H., Determination of domain structure of proteins from x-ray solution scattering (2001) Biophys. J., 80, pp. 2946-2953Franke, D., Svergun, D.I., DAMMIF, a program for rapid abinitio shape determination in small-angle scattering (2009) J. Appl. Crystallogr., 42, pp. 342-346Volkov, V.V., Svergun, D.I., Uniqueness of ab initio shape determination in small-angle scattering (2003) J. Appl. Crystallogr., 36, pp. 860-864Roy, A., Kucukural, A., Zhang, Y., I-TASSER: A unified platform for automated protein structure and function prediction (2010) Nat. Protoc., 5, pp. 725-738Dos Reis, M.A., Aparicio, R., Zhang, Y., Improving protein template recognition by using small-angle x-ray scattering profiles (2011) Biophys. J., 101, pp. 2770-2781Svergun, D., Barberato, C., Koch, M.H.J., CRYSOL: A program to evaluate x-ray solution scattering of biological macromolecules from atomic coordinates (1995) J. Appl. Crystallogr., 28, pp. 768-773McCoy, J.G., Bitto, E., Bingman, C.A., Wesenberg, G.E., Bannen, R.M., Kondrashov, D.A., Phillips, G.N., Structure and dynamics of UDP-glucose pyrophosphorylase from Arabidopsis thaliana with bound UDP-glucose and UTP (2007) J. Mol. Biol., 366, pp. 830-841Kozin, M.B., Svergun, D.I., Automated matching of high- and low-resolution structural models (2001) J. Appl. Crystallogr., 34, pp. 33-41Sayle, R.A., Milner-White, E.J., RASMOL: Biomolecular graphics for all (1995) Trends Biochem. Sci., 20, p. 374Zrenner, R., Willmitzer, L., Sonnewald, U., Analysis of the expression of potato uridinediphosphate-glucose pyrophosphorylase and its inhibition by antisense RNA (1993) Planta, 190, pp. 247-252Gupta, S.K., Sowokinos, J.R., Hahn, I.-S., Regulation of UDP-glucose pyrophosphorylase isozyme UGP5 associated with cold-sweetening resistance in potatoes (2008) J. Plant Physiol., 165, pp. 679-690Becker, M., Vincent, C., Reid, J.S., Biosynthesis of (1,3)(1,4)-β- glucan and (1,3)-β-glucan in barley (Hordeum vulgare L.) (1995) Planta, 195, pp. 331-338Kolodziejski, P.J., Rashid, M.B., Eissa, N.T., Intracellular formation of "undisruptable" dimers of inducible nitric oxide synthase (2003) Proc. Natl. Acad. Sci. U.S.A., 100, pp. 14263-14268Salahpour, A., Bonin, H., Bhalla, S., Petäjä-Repo, U., Bouvier, M., Biochemical characterization of β2-adrenergic receptor dimers and oligomers (2003) Biol. Chem., 384, pp. 117-123Koo, J.H., Gill, S., Pannell, L.K., Menco, B.P.M., Margolis, J.W., Margolis, F.L., The interaction of Bex and OMP reveals a dimer of OMP with a short half-life (2004) J. Neurochem., 90, pp. 102-116Manning, M., Colón, W., Structural basis of protein kinetic stability: Resistance to sodium dodecyl sulfate suggests a central role for rigidity and a bias toward β-sheet structure (2004) Biochemistry, 43, pp. 11248-11254Martínez, L.I., Piattoni, C.V., Garay, S.A., Rodrígues, D.E., Guerrero, S.A., Iglesias, A.A., Redox regulation of UDP-glucose pyrophosphorylase from Entamoeba histolytica (2011) Biochimie, 93, pp. 260-268Cheeseman, J.M., Hydrogen peroxide concentrations in leaves under natural conditions (2006) J. Exp. Bot., 57, pp. 2435-2444Meng, M., Wilczynska, M., Kleczkowski, L.A., Molecular and kinetic characterization of two UDP-glucose pyrophosphorylases, products of distinct genes, from Arabidopsis (2008) Biochim. Biophys. Acta, 1784, pp. 967-972Pua, E.-C., Lim, S.S.-W., Liu, P., Liu, J.-Z., Expression of a UDPglucose pyrophosphorylase cDNA during fruit ripening of banana (Musa acuminata) (2000) Funct. Plant Biol., 27, pp. 1151-1159Ciereszko, I., Johansson, H., Kleczkowski, L.A., Sucrose and light regulation of a cold-inducible UDP-glucose pyrophosphorylase gene via a hexokinase-independent and abscisic acid-insensitive pathway in Arabidopsis (2001) Biochem. J., 354, pp. 67-72Ciereszko, I., Johansson, H., Hurry, V., Kleczkowski, L.A., Phosphate status affects the gene expression, protein content and enzymatic activity of UDP-glucose pyrophosphorylase in wild-type and pho mutants of Arabidopsis (2001) Planta, 212, pp. 598-605Moore, P., Temporal and spatial regulation of sucrose accumulation in the sugarcane stem (1995) Aust. J. Plant Physiol., 22, p. 661Zhu, Y.J., Komor, E., Moore, P.H., Sucrose accumulation in the sugarcane stem is regulated by the difference between the activities of soluble acid invertase and sucrose phosphate synthase (1997) Plant Physiol., 115, pp. 609-616Ciereszko, I., Johansson, H., Kleczkowski, L.A., Interactive effects of phosphate deficiency, sucrose and light/dark conditions on gene expression of UDP-glucose pyrophosphorylase in Arabidopsis (2005) J. Plant Physiol., 162, pp. 343-353Meng, M., Geisler, M., Johansson, H., Mellerowicz, E.J., Karpinski, S., Kleczkowski, L.A., Differential tissue/organ-dependent expression of two sucrose- and cold-responsive genes for UDP-glucose pyrophosphorylase in Populus (2007) Gene, 389, pp. 186-195Mikami, S., Hori, H., Mitsui, T., Separation of distinct compartments of rice Golgi complex by sucrose density gradient centrifugation (2001) Plant Sci., 161, pp. 665-675Kleczkowski, L., Kunz, S., Wilczynska, M., Mechanisms of UDP-glucose synthesis in plants (2010) CRC Crit. Rev. Plant Sci., 29, pp. 191-203Winter, H., Huber, S.C., Regulation of sucrose metabolism in higher plants: Localization and regulation of activity of key enzymes (2000) Crit. Rev. Biochem. Mol. Biol., 35, pp. 253-289Rutter, J., Probst, B.L., McKnight, S.L., Coordinate regulation of sugar flux and translation by PAS kinase (2002) Cell, 111, pp. 17-28Toroser, D., Athwal, G.S., Huber, S.C., Site-specific regulatory interaction between spinach leaf sucrose-phosphate synthase and 14-3-3 proteins (1998) FEBS Lett., 435, pp. 110-114Stitt, M., Wilke, I., Feil, R., Heldt, H.W., Coarse control of sucrose-phosphate synthase in leaves: Alterations of the kinetic properties in response to the rate of photosynthesis and the accumulation of sucrose (1988) Planta, 174, pp. 217-230Barratt, D.H.P., Derbyshire, P., Findlay, K., Pike, M., Wellner, N., Lunn, J., Feil, R., Smith, A.M., Normal growth of Arabidopsis requires cytosolic invertase but not sucrose synthase (2009) Proc. Natl. Acad. Sci. U.S.A., 106, pp. 13124-13129Yan, S., Tang, Z., Su, W., Sun, W., Proteomic analysis of salt stress-responsive proteins in rice root (2005) Proteomics, 5, pp. 235-244Van Den Ende, W., Valluru, R., Sucrose, sucrosyl oligosaccharides, and oxidative stress: Scavenging and salvaging? (2009) J. Exp. Bot., 60, pp. 9-18Gill, S.S., Tuteja, N., Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants (2010) Plant Physiol. Biochem., 48, pp. 909-930Dixon, D.P., Skipsey, M., Grundy, N.M., Edwards, R., Stressinduced protein S-glutathionylation in Arabidopsis (2005) Plant Physiol., 138, pp. 2233-2244Martz, F., Wilczynska, M., Kleczkowski, L.A., Oligomerization status, with the monomer as active species, defines catalytic efficiency of UDP-glucose pyrophosphorylase (2002) Biochem. J., 367, pp. 295-300Yu, Q., Zheng, X., The crystal structure of human UDP-glucose pyrophosphorylase reveals a latch effect that influences enzymatic activity (2012) Biochem. J., 442, pp. 283-291Roeben, A., Plitzko, J.M., Körner, R., Böttcher, U.M.K., Siegers, K., Hayer-Hartl, M., Bracher, A., Structural basis for subunit assembly in UDP-glucose pyrophosphorylase from Saccharomyces cerevisiae (2006) J. Mol. Biol., 364, pp. 551-560Steiner, T., Lamerz, A.-C., Hess, P., Breithaupt, C., Krapp, S., Bourenkov, G., Huber, R., Jacob, U., Open and closed structures of the UDP-glucose pyrophosphorylase from Leishmania major (2007) J. Biol. Chem., 282, pp. 13003-1301