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323 results on '"Plevani, P."'

53. In vivo and in silico analysis of PCNA ubiquitylation in the activation of the Post Replication Repair pathway in S. cerevisiae

Author

Amara, F, Colombo, R, Cazzaniga, P, Pescini, D, Csikász Nagy, A, Falconi, M, Besozzi, D, Plevani, P, BESOZZI, DANIELA, Plevani, P., COLOMBO, RICCARDO, CAZZANIGA, PAOLO, PESCINI, DARIO, Amara, F, Colombo, R, Cazzaniga, P, Pescini, D, Csikász Nagy, A, Falconi, M, Besozzi, D, Plevani, P, BESOZZI, DANIELA, Plevani, P., COLOMBO, RICCARDO, CAZZANIGA, PAOLO, and PESCINI, DARIO

Abstract

Background: The genome of living organisms is constantly exposed to several damaging agents that induce different types of DNA lesions, leading to cellular malfunctioning and onset of many diseases. To maintain genome stability, cells developed various repair and tolerance systems to counteract the effects of DNA damage. Here we focus on Post Replication Repair (PRR), the pathway involved in the bypass of DNA lesions induced by sunlight exposure and UV radiation. PRR acts through two different mechanisms, activated by mono- and poly-ubiquitylation of the DNA sliding clamp, called Proliferating Cell Nuclear Antigen (PCNA).Results: We developed a novel protocol to measure the time-course ratios between mono-, di- and tri-ubiquitylated PCNA isoforms on a single western blot, which were used as the wet readout for PRR events in wild type and mutant S. cerevisiae cells exposed to acute UV radiation doses. Stochastic simulations of PCNA ubiquitylation dynamics, performed by exploiting a novel mechanistic model of PRR, well fitted the experimental data at low UV doses, but evidenced divergent behaviors at high UV doses, thus driving the design of further experiments to verify new hypothesis on the functioning of PRR. The model predicted the existence of a UV dose threshold for the proper functioning of the PRR model, and highlighted an overlapping effect of Nucleotide Excision Repair (the pathway effectively responsible to clean the genome from UV lesions) on the dynamics of PCNA ubiquitylation in different phases of the cell cycle. In addition, we showed that ubiquitin concentration can affect the rate of PCNA ubiquitylation in PRR, offering a possible explanation to the DNA damage sensitivity of yeast strains lacking deubiquitylating enzymes.Conclusions: We exploited an in vivo and in silico combinational approach to analyze for the first time in a Systems Biology context the events of PCNA ubiquitylation occurring in PRR in budding yeast cells. Our findings highlighted

Published
2013

54. Effect of Target Fortification on Osmolality and Microbiological Safety of Human Milk Over Time

Author

Piemontese, Pasqua, Liotto, Nadia, Menis, Camilla, Mallardi, Domenica, Tabasso, Chiara, Perrone, Michela, Bezze, Elena, Plevani, Laura, Roggero, Paola, and Mosca, Fabio

Abstract

The fortification of human milk can result in increased osmolality, which may be associated with adverse effects for preterm infants. To evaluate the effect of target fortification on the osmolality and microbiological safety of donor human milk and raw mature milk during the first 72 hours of storage. Methods: We performed target fortification of 63 pasteurized donor human milk (PDHM) and 54 raw mature milk (RMM) samples in a laminar flow hood. Osmolality (mOsm/kg) was evaluated before fortification (T0), immediately after fortification (T1), at 6 (T2), 24 (T3), 48 (T4), and 72 hours (T5) after fortification. Microbiological analysis was performed at T0, T4, and T5. During the study, all samples were stored at 4°C. Mean osmolality at each study point for PDHM and RMM were, respectively: T0: 291.4 ± 11.0 versus 288.4 ± 5.6 (P= 0.06); T1: 384.8 ± 16.7 versus 398.3 ± 23.7; T2: 393.9 ± 17.7 versus 410.1 ± 27.0; T3: 397.8 ± 17.6 versus 417.9 ± 26.1; T4: 400.0 ± 16.5 versus 420.2 ± 24.9; T5: 399.6 ± 16.5 versus 425.2 ± 25.8 (P< 0.001 from T1 to T5). Microbiological analyses were negative at each study points for PDHM. At T0 16.1% of RMM samples had positive cultures, whereas the bacterial count remained stable thought the study. PDHM's osmolality increases during the first 6 hours after fortification and remains stable and safe until 72 hours. RMM's osmolality increases during the first 24 hours and remains stable and safe until 72 hours. The storage at 4°C and the manipulation of PDHM and RMM samples in a laminar flow hood seem to be safe and preserve the microbiological safety of fortified pasteurized human milk until 72 hours.

Published
2020
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55. The Yeast Genome Directory

Author

Goffeau, A., Aert, R., Agostini-Carbone, M. L., Ahmed, A., Aigle, M., Alberghina, L., Albermann, K., Albers, M., Aldea, M., Alexandraki, D., Aljinovic, G., Allen, E., Alt-Mörbe, J., André, B., Andrews, S., Ansorge, W., Antoine, G., Anwar, R., Aparicio, A., Araujo, R., Arino, J., Arnold, F., Arroyo, J., Aviles, E., Backes, U., Baclet, M. C., Badcock, K., Bahr, A., Baladron, V., Ballesta, J. P. G., Bankier, A. T., Banrevi, A., Bargues, M., Baron, L., Barreiros, T., Barrell, B. G., Barthe, C., Barton, A. B., Baur, A., Bécam, A.-M., Becker, A., Becker, I., Beinhauer, J., Benes, V., Benit, P., Berben, G., Bergantino, E., Bergez, P., Berno, A., Bertani, I., Biteau, N., Bjourson, A. J., Blöcker, H., Blugeon, C., Bohn, C., Boles, E., Bolle, P. A., Bolotin-Fukuhara, M., Bordonné, R., Boskovic, J., Bossier, P., Botstein, D., Bou, G., Bowman, S., Boyer, J., Brandt, P., Brandt, T., Brendel, M., Brennan, T., Brinkman, R., Brown, A., Brown, A. J. P., Brown, D., Brückner, M., Bruschi, C. V., Buhler, J. M., Buitrago, M. J., Bussereau, F., Bussey, H., Camasses, A., Carcano, C., Carignani, G., Carpenter, J., Casamayor, A., Casas, C., Castagnoli, L., Cederberg, H., Cerdan, E., Chalwatzis, N., Chanet, R., Chen, E., Chéret, G., Cherry, J. M., Chillingworth, T., Christiansen, C., Chuat, J.-C., Chung, E., Churcher, C., Churcher, C. M., Clark, M. W., Clemente, M. L., Coblenz, A., Coglievina, M., Coissac, E., Colleaux, L., Connor, R., Contreras, R., Cooper, J., Copsey, T., Coster, F., Coster, R., Couch, J., Crouzet, M., Cziepluch, C., Daignan-Fornier, B., Dal Paro, F., Dang, D. V., D’Angelo, M., Davies, C. J., Davis, K., Davis, R. W., De Antoni, A., Dear, S., Dedman, K., Defoor, E., De Haan, M., Delaveau, Th., Del Bino, S., Delgado, M., Delius, H., Delneri, D., Del Rey, F., Demolder, J., Démolis, N., Devlin, K., de Wergifosse, P., Dietrich, F. S., Ding, H., Dion, C., Dipaolo, T., Doignon, F., Doira, C., Domdey, H., Dover, J., Du, Z., Dubois, E., Dujon, B., Duncan, M., Durand, P., Düsterhöft, A., Düsterhus, S., Eki, T., El Bakkoury, M., Eide, L. G., Entian, K.-D., Eraso, P., Erdmann, D., Erfle, H., Escribano, V., Esteban, M., Fabiani, L., Fabre, F., Fairhead, C., Fartmann, B., Favello, A., Faye, G., Feldmann, H., Fernandes, L., Feroli, F., Feuermann, M., Fiedler, T., Fiers, W., Fleig, U. N., Flöth, M., Fobo, G. M., Fortin, N., Foury, F., Francingues-Gaillard, M. C., Franco, L., Fraser, A., Friesen, J.D., Fritz, C., Frontali, L., Fukuhara, H., Fulton, L., Fuller, L. J., Gabel, C., Gaillardin, C., Gaillon, L., Galibert, F., Galisson, F., Galland, P., Gamo, F.-J., Gancedo, C., Garcia-Cantalejo, J. M., García-Gonzalez, M. I., Garcia-Ramirez, J. J., García-Saéz, M., Gassenhuber, H., Gatius, M., Gattung, S., Geisel, C., Gent, M. E., Gentles, S., Ghazvini, M., Gigot, D., Gilliquet, V., Glansdorff, N., Gómez-Peris, A., Gonzaléz, A., Goulding, S. E., Granotier, C., Greco, T., Grenson, M., Grisanti, P., Grivell, L. A., Grothues, D., Gueldener, U., Guerreiro, P., Guzman, E., Haasemann, M., Habbig, B., Hagiwara, H., Hall, J., Hallsworth, K., Hamlin, N., Hand, N. J., Hanemann, V., Hani, J., Hankeln, T., Hansen, M., Harris, D., Harris, D. E., Hartzell, G., Hatat, D., Hattenhorst, U., Hawkins, J., Hebling, U., Hegemann, J., Hein, C., Hennemann, A., Hennessy, K., Herbert, C. J., Hernandez, K., Hernando, Y., Herrero, E., Heumann, K., Heuss- Neitzel, D., Hewitt, N., Hiesel, R., Hilbert, H., Hilger, F., Hillier, L., Ho, C., Hoenicka, J., Hofmann, B., Hoheisel, J., Hohmann, S., Hollenberg, C. P., Holmstrøm, K., Horaitis, O., Horsnell, T. S., Huang, M.-E., Hughes, B., Hunicke-Smith, S., Hunt, S., Hunt, S. E., Huse, K., Hyman, R. W., Iborra, F., Indge, K. J., Iraqui Houssaini, I., Isono, K., Jacq, C., Jacquet, M., Jacquier, A., Jagels, K., Jäger, W., James, C. M., Jauniaux, J. C., Jia, Y., Jier, M., Jimenez, A., Johnson, D., Johnston, L., Johnston, M., Jones, M., Jonniaux, J.-L., Kaback, D. B., Kallesøe, T., Kalman, S., Kalogeropoulos, A., Karpfinger-Hartl, L., Kashkari, D., Katsoulou, C., Kayser, A., Kelly, A., Keng, T., Keuchel, H., Kiesau, P., Kirchrath, L., Kirsten, J., Kleine, K., Kleinhans, U., Klima, R., Komp, C., Kordes, E., Korol, S., Kötter, P., Krämer, C., Kramer, B., Kreisl, P., Kucaba, T., Kuester, H., Kurdi, O., Laamanen, P., Lafuente, M. J., Landt, O., Lanfranchi, G., Langston, Y., Lashkari, D., Latreille, P., Lauquin, G., Le, T., Legrain, P., Legros, Y., Lepingle, A., Lesveque, H., Leuther, H., Lew, H., Lewis, C., Li, Z. Y., Liebl, S., Lin, A., Lin, D., Logghe, M., Lohan, A. J. E., Louis, E. J., Lucchini, G., Lutzenkirchen, K., Lyck, R., Lye, G., Maarse, A. C., Maat, M. J., Macri, C., Madania, A., Maftahi, M., Maia e Silva, A., Maillier, E., Mallet, L., Mannhaupt, G., Manus, V., Marathe, R., Marck, C., Marconi, A., Mardis, E., Martegani, E., Martin, R., Mathieu, A., Maurer, C. T. C., Mazón, M. J., Mazzoni, C., McConnell, D., McDonald, S., McKee, R. A., McReynolds, A. D. K., Melchioretto, P., Menezes, S., Messenguy, F., Mewes, H. W., Michaux, G., Miller, N., Minenkova, O., Miosga, T., Mirtipati, S., Möller-Rieker, S., Möstl, D., Molemans, F., Monnet, A., Monnier, A-L., Montague, M. A., Moro, M., Mosedale, D., Möstl, D., Moule, S., Mouser, L., Murakami, Y., Müller-Auer, S., Mulligan, J., Murphy, L., Muzi Falconi, M., Naitou, M., Nakahara, K., Namath, A., Nasr, F., Navas, L., Nawrocki, A., Nelson, J., Nentwich, U., Netter, P., Neu, R., Newlon, C. S., Nhan, M., Nicaud, J.-M., Niedenthal, R. K., Nombela, C., Noone, D., Norgren, R., Nußbaumer, B., Obermaier, B., Odell, C., Öfner, P., Oh, C., Oliver, K., Oliver, S. G., Ouellette, B. F., Ozawa, M., Paces, V., Pallier, C., Pandolfo, D., Panzeri, L., Paoluzi, S., Parle-Mcdermott, A. G., Pascolo, S., Patricio, N., Pauley, A., Paulin, L., Pearson, B. M., Pearson, D., Peluso, D., Perea, J., Pérez-Alonso, M., Pérez-Ortin, J. E., Perrin, A., Petel, F. X., Pettersson, B., Pfeiffer, F., Philippsen, P., Piérard, A., Piravandi, E., Planta, R. J., Plevani, P., Poch, O., Poetsch, B., Pohl, F. M., Pohl, T. M., Pöhlmann, R., Poirey, R., Portetelle, D., Portillo, F., Potier, S., Proft, M., Prydz, H., Pujol, A., Purnelle, B., Puzos, V., Rajandream, M. A., Ramezani Rad, M., Rasmussen, S. W., Raynal, A., Rechmann, S., Remacha, M., Revuelta, J. L., Rice, P., Richard, G-F., Richterich, P., Rieger, M., Rifken, L., Riles, L., Rinaldi, T., Rinke, M., Roberts, A. B., Roberts, D., Rodriguez, F., Rodriguez-Belmonte, E., Rodriguez-Pousada, C., Rodriguez-Torres, A. M., Rose, M., Rossau, R., Rowley, N., Rupp, T., Ruzzi, M., Saeger, W., Saiz, J. E., Saliola, M., Salom, D., Saluz, H. P., Sánchez-Perez, M., Santos, M. A., Sanz, E., Sanz, J. E., Saren, A.-M., Sartorello, F., Sasanuma, M., Sasanuma, S-I., Scarcez, T., Schaaf-Gerstenschläger, I., Schäfer, B., Schäfer, M., Scharfe, M., Scherens, B., Schroff, N., Sen-Gupta, M., Shibata, T., Schmidheini, T., Schmidt, E. R., Schneider, C., Scholler, P., Schramm, S., Schreer, A., Schröder, M., Schwager, C., Schwarz, S., Schwarzlose, C., Schweitzer, B., Schweizer, M., Sdicu, A-M., Sehl, P., Sensen, C., Sgouros, J. G., Shogren, T., Shore, L., Shu, Y., Skala, J., Skelton, J., Slonimski, P. P., Smit, P. H. M., Smith, V., Soares, H., Soeda, E., Soler-Mira, A., Sor, F., Soriano, N., Souciet, J. L., Soustelle, C., Spiegelberg, R., Stateva, L. I., Steensma, H. Y., Stegemann, J., Steiner, S., Stellyes, L., Sterky, F., Storms, R. K., St. Peter, H., Stucka, R., Taich, A., Talla, E., Tarassov, I., Tashiro, H., Taylor, P., Teodoru, C., Tettelin, H., Thierry, A., Thireos, G., Tobiasch, E., Tovan, D., Trevaskis, E., Tsuchiya, Y., Tzermia, M., Uhlen, M., Underwood, A., Unseld, M., Urbanus, J. H. M., Urrestarazu, A., Ushinsky, S., Valens, M., Valle, G., Van Broekhoven, A., Vandenbol, M., Van Der Aart, Q. J. M., Van Der Linden, C. G., Van Dyck, L., Vanoni, M., Van Vliet-Reedijk, J. C., Vassarotti, A., Vaudin, M., Vaughan, K., Verhasselt, P., Vetter, I., Vierendeels, F., Vignati, D., Vilela, C., Vissers, S., Vleck, C., Vo, D. T., Vo, D. H., Voet, M., Volckaert, G., Von Wettstein, D., Voss, H., Vreken, P., Wagner, G., Walsh, S. V., Wambutt, R., Wang, H., Wang, Y., Warmington, J. R., Waterston, R., Watson, M. D., Weber, N., Wedler, E., Wedler, H., Wei, Y., Whitehead, S., Wicksteed, B. L., Wiemann, S., Wilcox, L., Wilson, C., Wilson, R., Winant, A., Winnett, E., Winsor, B., Wipfli, P., Wölfl, S., Wohldman, P., Wolf, K., Wolfe, K. H., Wright, L. F., Wurst, H., Xu, G., Yamasaki, M., Yelton, M. A., Yokohama, K., Yoshikawa, A., Yuping, S., Zaccaria, P., Zagulski, M., Zimmermann, F. K., Zimmermann, J., Zimmermann, M., Zhong, W-W., Zollner, A., and Zumstein, E.

Published
1997
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62. Is the new, noninvasive, continuous cardiorespiratory monitoring reliable during neonatal ECMO?

Author

Raffaeli, Genny, Canesi, Francesco, Conigliaro, Federica, Ghirardello, Stefano, Vanzati, Mara, Baracetti, Chiara, Fumagalli, Monica, Ciralli, Fabrizio, Schena, Federico, Pesenti, Nicola, Plevani, Laura, Mosca, Fabio, and Cavallaro, Giacomo

Abstract

Abstract Background Advances in cardiorespiratory monitoring have made the extracorporeal membrane oxygenation (ECMO) technique safer for the patient. Noninvasive, continuous tools are available, although data on their applications in the neonatal ECMO setting are lacking. Objective We retrospectively described the neonatal clinical application of this continuous, noninvasive ECMO monitor and compared the analyzed parameters from those derived from blood gas analysis. Materials and methods We performed 897 h of cardiorespiratory monitoring during neonatal venoarterial-ECMO (VA-ECMO) for four patients affected by (cardio-) respiratory failure, to compare the reliability of a noninvasive, continuous monitoring Spectrum M4® (M4) (Spectrum Medical, Gloucester, England) to an invasive, intermittent co-monitoring with blood gas analyzer (Radiometer Medical ApS, Brønshøj, Denmark). Results A range of 117 pairs (time-matched BGA-derived vs. M4-derived parameters) was retrospectively analyzed. T -test, linear regression and Bland–Altman analysis for hemoglobin, hematocrit, venous oxygen saturation, oxygen delivery, oxygen consumption, oxygen extraction ratio, oxygen partial pressure, and carbon dioxide partial pressure showed a strong relationship between the two monitors for all parameters analyzed (p < 0.0001). Conclusions Continuous, noninvasive cardiorespiratory monitoring appears to be feasible and reliable, although its accuracy needs to be verified in a more extensive cohort. [ABSTRACT FROM AUTHOR]

Published
2018
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63. Biologia Molecolare

Author

Amaldi, F, Benedetti, P, Pesole, G, and Plevani, P

Subjects
Settore BIO/11
Published
2011

65. The nucleotide sequence of Saccharomyces cerevisiae chromosome VII

Author

Tettelin, H, Agostoni Carbone, ML, Albermann, K, Albers, M, Arroyo J, Backes, U, Barreiros, T, Bertani, I, Bjourson, AJ, Bruckner, M, Bruschi, CV, Carignani, G, Castagnoli, L, Cerdan, E, Clemente, ML, Coblenz, A, Coglievina, M, Coissac, E, Defoor, E, Delbino, S, Delius, H, Delneri, D, Dewergifosse, P, Dujon, B, Durand, P, Goffeau, A, Guerreiro, P, Hani, J, Hansen, M, Hebling, U, Hernandez, K, Heumann, KHF, Hofmann, B, Indge, KJ, James, CM, Klima, R, Kötter, P, Kramer, B, Kramer, W, Lauquin, G, Leuther, H, Louis, EJ, Maillier, E, Marconi, A, Martegani, E, Mazon, MJ, Mazzoni, C, McReynolds, ADK, Melchioretto, P, Mewes, HW, Minenkova, O, Müller-Auer, S, Nawrocki, A, Netter, P, Neu, R, Nombela, C, Oliver, SG, Panzeri, L, Paoluzi, S, Plevani, P, Portetelle, D, Portillo, F, Potier, S, Purnelle, B, Rieger, M, Riles, L, Rinaldi, T, Rodrigues-Pousada, C, Rodriguez-Belmonte, E, Rodriguez-Torres, AM, Rose, M, Ruzzi, M, Saliola, M, Sanchez-Perez, M, Schäfer, B, Schäfer, M, Scharfe, M, Schmidheini, T, Schreer, A, Skala, J, Souciet, JLSHY, Talla, E, Thierry, A, Vandenbol, M, van der Aart, QJM, Van Dyck, L, Vanoni, M, Verhasselt, P, Voet, M, Volckaert, G, Wambutt, R, Watson, MD, Weber, N, Wedler, E, Wedler, H, Wipfli, P, Wolf, K, Wright, LF, Zaccaria, P, Zimmermann, M, Zollner, A, Kleine, K, Tettelin, H, Agostoni Carbone, M, Albermann, K, Albers, M, Arroyo, J, Backes, U, Barreiros, T, Bertani, I, Bjourson, A, Bruckner, M, Bruschi, C, Carignani, G, Castagnoli, L, Cerdan, E, Clemente, M, Coblenz, A, Coglievina, M, Coissac, E, Defoor, E, Delbino, S, Delius, H, Delneri, D, Dewergifosse, P, Dujon, B, Durand, P, Goffeau, A, Guerreiro, P, Hani, J, Hansen, M, Hebling, U, Hernandez, K, Heumann, K, Hofmann, B, Indge, K, James, C, Klima, R, Kötter, P, Kramer, B, Kramer, W, Lauquin, G, Leuther, H, Louis, E, Maillier, E, Marconi, A, Martegani, E, Mazon, M, Mazzoni, C, Mcreynolds, A, Melchioretto, P, Mewes, H, Minenkova, O, Müller-Auer, S, Nawrocki, A, Netter, P, Neu, R, Nombela, C, Oliver, S, Panzeri, L, Paoluzi, S, Plevani, P, Portetelle, D, Portillo, F, Potier, S, Purnelle, B, Rieger, M, Riles, L, Rinaldi, T, Rodrigues-Pousada, C, Rodriguez-Belmonte, E, Rodriguez-Torres, A, Rose, M, Ruzzi, M, Saliola, M, Sanchez-Perez, M, Schäfer, B, Schäfer, M, Scharfe, M, Schmidheini, T, Schreer, A, Skala, J, Souciet, J, Talla, E, Thierry, A, Vandenbol, M, van der Aart, Q, Van Dyck, L, Vanoni, M, Verhasselt, P, Voet, M, Volckaert, G, Wambutt, R, Watson, M, Weber, N, Wedler, E, Wedler, H, Wipfli, P, Wolf, K, Wright, L, Zaccaria, P, Zimmermann, M, Zollner, A, and Kleine, K

Subjects
Fungal Proteins, Open Reading Frames, Base Sequence, Sequence Homology, Amino Acid, Humans, Saccharomyces cerevisiae, Chromosomes, Fungal, DNA, Fungal, BIO/10 - BIOCHIMICA, genome sequencing, yeast
Abstract

The complete nucleotide sequence of Saccharomyces cerevisiae chromosome VII has 572 predicted open reading frames (ORFs), of which 341 are new. No correlation was found between G+C content and gene density along the chromosome, and their variations are random. Of the ORFs, 17% show high similarity to human proteins. Almost half of the ORFs could be classified in functional categories, and there is a slight increase in the number of transcription (7.0 %) and translation (5.2 %) factors when compared with the complete S. cerevisiae genome. Accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence

Published
1997

66. The interplay among chromatin dynamics, cell cycle checkpoints and repair mechanisms modulates the cellular response to DNA damage

Author

Lazzaro F, Michele Giannattasio, Muzi-Falconi M, and Plevani P

Subjects
DNA Repair, Ultraviolet Rays, Cell Cycle, DNA damage, checkpoints, chromatin, cell cycle, Settore BIO/11 - Biologia Molecolare, Chromatin Assembly and Disassembly, Chromatin, Histones, Animals, Humans, DNA Breaks, Double-Stranded, Protein Processing, Post-Translational, DNA Damage
Abstract

Cells are continuously under the assault of endogenous and exogenous genotoxic stress that challenges the integrity of DNA. To cope with such a formidable task cells have evolved surveillance mechanisms, known as checkpoints, and a variety of DNA repair systems responding to different types of DNA lesions. These lesions occur in the context of the chromatin structure and, as expected for all DNA transactions, the cellular response to DNA damage is going to be influenced by the chromatin enviroment. In this review, we will discuss recent studies implicating chromatin remodelling factors and histone modifications in the response to DNA double-strand breaks (DSBs) and in checkpoint activation in response to UV lesions.

Published
2007

73. Expression of M6 protein of Streptococcus pyogenes on the surface of Streptococcus gordonii Challis

Author

Oggioni MR, Manganelli R, Plevani P, Fischetti VA, Pozzi G, Oggioni MR, Manganelli R, Plevani P, Fischetti VA, and Pozzi G

Subjects
stomatognathic diseases, stomatognathic system, transposon, vaccine
Abstract

The M6 protein of Streptococcus pyogenes was expressed on the cell surface and secreted in Streptococcus gordonii Challis (formerly Streptococcus sanguis) after chromosomal integration of a promoterless M6 protein gene (emm-6.1). The ermC gene, conferring resistance to erythromycin, was cloned downstream of emm-6.1, within the same ClaI fragment. The initiation codon of emm-6.1 was 19 bp downstream of a ClaI site, so that ClaI cleavage would leave the gene promoterless. The ClaI fragment containing the promoterless emm-6.1 and ermC was ligated in vitro with a ClaI digest of S. gordonii chromosomal DNA. Random chromosomal integration of the heterologous DNA was obtained by using the ligation mixture to transform the naturally competent S. gordonii Challis. Twenty-eight percent of transformants selected for erythromycin resistance also expressed M6. Among the best M6 producers, 10 clones were selected for the stability of their phenotype. Nine of the 10 clones were shown to harbour one intact copy of the emm-6.1/ermC ClaI fragment integrated into the chromosome. These strains both expressed M6 protein on the surface and secreted different amounts of the molecule, since in each case the protein was produced after a transcriptional fusion of emm-6.1 with a different chromosomal promoter. A S. gordonii strain expressing large amounts of surface M6 protein, as judged by immunofluorescence and Western blot, was compared to the M- parental strain in a standard opsonophagocytosis assay. Of the isogenic pair, M6+ S. gordonii survived better in human blood and was phagocytosed at a slower rate.

Published
1992

74. Elevated levels of the polo kinase Cdc5 override the Mec1/ATR checkpoint in budding yeast by acting at different steps of the signaling pathway

Author

Donnianni, R, Ferrari, M, Lazzaro, F, Clerici, M, Tamilselvan Nachimuthu, B, Plevani, P, Muzi Falconi, M, Pellicioli, A, Donnianni, RA, CLERICI, MICHELA, Pellicioli, A., Donnianni, R, Ferrari, M, Lazzaro, F, Clerici, M, Tamilselvan Nachimuthu, B, Plevani, P, Muzi Falconi, M, Pellicioli, A, Donnianni, RA, CLERICI, MICHELA, and Pellicioli, A.

Abstract

Checkpoints are surveillance mechanisms that constitute a barrier to oncogenesis by preserving genome integrity. Loss of checkpoint function is an early event in tumorigenesis. Polo kinases (Plks) are fundamental regulators of cell cycle progression in all eukaryotes and are frequently overexpressed in tumors. Through their polo box domain, Plks target multiple substrates previously phosphorylated by CDKs and MAPKs. In response to DNA damage, Plks are temporally inhibited in order to maintain the checkpoint-dependent cell cycle block while their activity is required to silence the checkpoint response and resume cell cycle progression. Here, we report that, in budding yeast, overproduction of the Cdc5 polo kinase overrides the checkpoint signaling induced by double strand DNA breaks (DSBs), preventing the phosphorylation of several Mec1/ATR targets, including Ddc2/ATRIP, the checkpoint mediator Rad9, and the transducer kinase Rad53/CHK2. We also show that high levels of Cdc5 slow down DSB processing in a Rad9-dependent manner, but do not prevent the binding of checkpoint factors to a single DSB. Finally, we provide evidence that Sae2, the functional ortholog of human CtIP, which regulates DSB processing and inhibits checkpoint signaling, is regulated by Cdc5. We propose that Cdc5 interferes with the checkpoint response to DSBs acting at multiple levels in the signal transduction pathway and at an early step required to resect DSB ends. © 2010 Donnianni et al.

Published
2010

75. Physical and functional interactions between nucleotide excision repair and DNA damage checkpoint

Author

Giannattasio, M, Lazzaro, F, Longhese, M, Plevani, P, Muzi Falconi, M, Muzi Falconi M., LONGHESE, MARIA PIA, Giannattasio, M, Lazzaro, F, Longhese, M, Plevani, P, Muzi Falconi, M, Muzi Falconi M., and LONGHESE, MARIA PIA

Abstract

The mechanisms used by checkpoints to identify DNA lesions are poorly understood and may involve the function of repair proteins. Looking for mutants specifically defective in activating the checkpoint following UV lesions, but proficient in the response to methyl methane sulfonate and double-strand breaks, we isolated cdu1-1, which is allelic to RAD14, the homolog of human XPA, involved in lesion recognition during nucleotide excision repair (NER). Rad14 was also isolated as a partner of the Ddc1 checkpoint protein in a two-hybrid screening, and physical interaction was proven by co-immunoprecipitation. We show that lesion recognition is not sufficient for checkpoint activation, but processing, carried out by repair factors, is required for recruiting checkpoint proteins to damaged DNA. Mutations affecting the core NER machinery abolish G1 and G2 checkpoint responses to UV, preventing activation of the Mec1 kinase and its binding to chromosomes. Conversely, elimination of transcription-coupled or global genome repair alone does not affect checkpoints, suggesting a possible interpretation for the heterogeneity in cancer susceptibility observed in different NER syndrome patients.

Published
2004

76. The complete sequence of the yeast chromosome III

Author

Oliver, S. G., van der Aart, Q. J. M., Agostoni Carbone, M. L., Aigle, M., Alberghina, L., Alexandraki, D., Antoine, G., Anwar, R., Ballesta, J. P. G., Benit, P., Berben, G., Bergantino, Elisabetta, Biteau, N., Bolle, P. A., Bolotin Fukuhara, M., Brown, A., Brown, A. J. P., Buhler, J. M., Carcano, C., Carignani, G., Cederberg, H., Chanet, R., Contreras, R., Crouzet, M., Daignan Fornier, B., Defoor, E., Delgado, M., Demolder, J., Doira, C., Dubois, E., Dujon, B., Dusterhoft, A., Erdmann, D., Esteban, M., Fabre, F., Fairhead, C., Faye, G., Feldmann, H., Fiers, W., Francingues Gaillard, M. C., Franco, L., Frontali, L., Fukuhara, H., Fuller, L. J., Galland, P., Gent, M. E., Gigot, D., Gilliquet, V., Glansdorff, N., Goffeau, A., Grenson, M., Grisanti, P., Grivell, L. A., de Haan, M., Haasemann, M., Hatat, D., Hoenicka, J., Hegemann, J., Herbert, C. J., Hilger, F., Hohmann, S., Hollenberg, C. P., Huse, K., Iborra, F., Indje, K. J., Isono, K., Jacq, C., Jacquet, M., James, C. M., Jauniaux, J. C., Jia, Y., Jimenez, A., Kelly, A., Kleinhans, U., Kreisl, P., Lanfranchi, Gerolamo, Lewis, C, Vanderlinden, C. G., Lucchini, G., Lutzenkirchen, K, Maat, M. J., Mallet, L., Mannhaupet, G., Martegani, E., Mathieu, A., Maurer, C. T. C., Mcconnell, D., Mckee, R. A., Messenguy, F., Mewes, H. W., Molemans, F., Montague, M. A., Muzi Falconi, M., Navas, L., Newlon, C. S., Noone, D., Pallier, C., Panzeri, L., Pearson, B. M., Perea, J., Philippsen, P., Pierard, A., Planta, R. J., Plevani, P., Poetsch, B., Pohl, F., Purnelle, B., Ramezani Rad, M., Rasmussen, S. W., Raynal, A., Remacha, M., Richterich, P., Roberts, A. B., Rodriguez, F., Sanz, E., Schaaff Gerstenschlager, I., Scherens, B., Schweitzer, B., Shu, Y., Skala, J., Slonimski, P. P., Sor, F., Soustelle, C., Spiegelberg, R., Stateva, L. I., Steensma, S., Steiner, H. Y., Thierry, A., Thireos, G., Tzermia, M., Urrestarazu, L. A., Valle, Giorgio, Vetter, I., van Vliet Reedijk, J. C., Voet, M., Volckaert, G., Vreken, P., Wang, H., Warmington, J. R., von Wettstein, D., Wicksteed, B. L., Wilson, C., Wurst, H., Xu, G., Yoshikawa, A., Zimmermann, F. K., and Sgouros, J. G.

Published
1992

82. Autophagy in placentas from acidotic newborns: An immunohistochemical study of LC3 expression.

Author

Avagliano, L., Danti, L., Doi, P., Felis, S., Guala, M., Locatelli, A., Maffeo, I., Mecacci, F., Plevani, C., Simeone, S., and Bulfamante, G.P.

Abstract

Abstract: Autophagy is an inducible catabolic process activated during compromised conditions, such as hypoxia. Neonatal encephalopathy (NE) is a syndrome of disturbed neurological function. No absolute prognostic indicators are available at birth to identify neonates at high risk to develop NE. Immunohistochemical staining with LC3 antibody was performed on 40 placentas from uneventful term singleton pregnancies with umbilical artery pH ≤ 7.00 at birth; semi-quantitative analysis was carried-out to estimate autophagy level. 6/40 (15%) neonates developed NE. Placentas from newborns with NE exhibited a higher LC3 expression. Autophagy protein expression in placentas with severe acidosis is a potential marker for poor outcome. [Copyright &y& Elsevier]

Published
2013
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91. To trim or not to trim: Progression and control of DSB end resection

Author

Granata, Magda, Panigada, Davide, Galati, Elena, Lazzaro, Federico, Pellicioli, Achille, Plevani, Paolo, and Muzi-Falconi, Marco

Abstract

DNA double-strand breaks (DSBs) are the most cytotoxic form of DNA damage, since they can lead to genome instability and chromosome rearrangements, which are hallmarks of cancer cells. To face this kind of lesion, eukaryotic cells developed two alternative repair pathways, homologous recombination (HR) and non-homologous end joining (NHEJ). Repair pathway choice is influenced by the cell cycle phase and depends upon the 5′-3′ nucleolytic processing of the break ends, since the generation of ssDNA tails strongly stimulates HR and inhibits NHEJ. A large amount of work has elucidated the key components of the DSBs repair machinery and how this crucial process is finely regulated. The emerging view suggests that besides endo/exonucleases and helicases activities required for end resection, molecular barrier factors are specifically loaded in the proximity of the break, where they physically or functionally limit DNA degradation, preventing excessive accumulation of ssDNA, which could be threatening for cell survival.

Published
2013
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92. NER and DDR: Classical music with new instruments

Author

Sertic, Sarah, Pizzi, Sara, Lazzaro, Federico, Plevani, Paolo, and Muzi-Falconi, Marco

Abstract

Genomic insults by endogenous or exogenous sources activate the DNA damage response (DDR). After the recognition of damaged DNA by specific factors, repair mechanisms process the lesions, and a surveillance mechanism, known as DNA damage checkpoint, is triggered by single-stranded (ss) DNA covered by RPA. UV light induces DNA lesions, mainly 6,4 photoproducts (6–4PP) and cyclobutane pyrimidine dimers (CPD), which are removed by nucleotide excision repair (NER). Recent reports shed light onto the mechanism connecting NER and DDR after UV irradiation. How does UV-induced DNA damage activate checkpoint kinases? How is ssDNA generated at UV lesions? In yeast, UV lesions persisting during S phase represent a block for the advancing of replication forks, which temporarily stop and then reinitiate downstream of the damage, leaving a ssDNA region containing the lesion. Nonreplicating yeast and human cells with defects in NER are not able to properly activate the checkpoint cascade, indicating that processing of UV lesions is a prerequisite for checkpoint activation. This pathway also requires the function of exonuclease 1, which acts on NER intermediates generating long tracts of ssDNA. Here, we review the connections between NER processing of UV-induced lesions and checkpoint activation, discussing the role of recently identified players in this mechanism.

Published
2012
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95. Alk1 and Alk2 are Two New Cell Cycle-Regulated Haspin-Like Proteins in Budding Yeast

Author

Nespoli, Alessandro, Vercillo, Raffaella, Nola, Lisa di, Diani, Laura, Giannattasio, Michele, Plevani, Paolo, and Muzi-Falconi, Marco

Abstract

Haspin is a protein kinase identified in mouse and human cells, and genes coding forhaspin-like proteins are present in virtually all eukaryotic genomes sequenced so far. Twohaspin homologues, called Alk1 and Alk2, are present in the yeast Saccharomycescerevisiae. Both Alk1 and Alk2 exhibit a weak auto-kinase activity in vitro, arephosphoproteins in vivo and are hyperphosphorylated in response to DNA damage. Theamount and modification of the two proteins is greatly regulated during the cell cycle. Infact, Alk1 and Alk2 levels peak in mitosis and late-S/G2, respectively, and phosphorylationof both proteins is maximal in mitosis. Control of protein stability plays a major role inAlk2 regulation. The half-life of Alk2 is particularly short in G1; mutagenesis and geneticanalysis indicate that its degradation is controlled by the APC pathway. Overexpression ofALK2, but not of ALK1, causes a mitotic arrest, which is correlated to the kinase activity ofthe protein. This finding, together with its cell cycle regulation, suggests a role for Alk2 inthe control of mitosis.

Published
2006
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97. The yeast DNA polymerase-primase complex: Genes and proteins

Author

Plevani, P., Foiani, M., Muzi Falconi, M, Pizzagalli, A., Santocanale, C., Francesconi, S., Valsasnini, P., Comedini, A., Piatti, S., Lucchini, G., Falconi, M.Muzi, and Università degli Studi di Milano [Milano] (UNIMI)

Subjects
DNA polymerase, [SDV]Life Sciences [q-bio], MESH: RNA Nucleotidyltransferases, MESH: DNA Replication, MESH: Amino Acid Sequence, DNA-Directed DNA Polymerase, Biochemistry, DNA polymerase delta, MESH: Structure-Activity Relationship, Structural Biology, MESH: DNA-Directed DNA Polymerase, Polymerase, Immunoassay, Genetics, 0303 health sciences, DNA clamp, biology, 030302 biochemistry & molecular biology, RNA Nucleotidyltransferases, MESH: Saccharomyces cerevisiae, MESH: DNA Primase, Electrophoresis, Polyacrylamide Gel, Primase, MESH: Immunoassay, DNA Replication, MESH: Mutation, DNA polymerase II, Biophysics, DNA Primase, Saccharomyces cerevisiae, MESH: Sequence Homology, Nucleic Acid, Structure-Activity Relationship, 03 medical and health sciences, Sequence Homology, Nucleic Acid, MESH: DNA Polymerase II, Humans, Amino Acid Sequence, MESH: DNA Polymerase I, 030304 developmental biology, MESH: Humans, Binding Sites, DNA replication, DNA Polymerase II, DNA Polymerase I, MESH: Binding Sites, Mutation, biology.protein, DNA polymerase I, MESH: Electrophoresis, Polyacrylamide Gel
Abstract

International audience; The yeast DNA polymerase-primase complex is composed of four polypeptides designated p180, p74, p58 and p48. All the genes coding for these polypeptides have now been cloned. By protein sequence comparison we found that yeast DNA polymerase I (alpha) shares three major regions of homology with several DNA polymerases. A fourth region, called region P, is conserved in yeast and human DNA polymerase alpha. The site of a temperature-sensitive mutation in the POL1 gene which causes decreased stability of the polymerase-primase complex has been sequenced and falls in this region. We hypothesize that region P is important for protein-protein interactions. Highly selective biochemical methods might be similarly important to distinguish functional domains in the polymerase-primase complex. An autocatalytic affinity labeling procedure has been applied to map the active center of yeast DNA primase. From this approach we conclude that both primase subunits (p48 and p58) participate in the formation of the catalytic site of the enzyme.

Published
1988
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99. Active polypeptide fragments common to prokaryotic, eukaryotic, and mitochondrial DNA polymerases.

Author

Scovassi, A.I., Torsello, S., Plevani, P., Badaracco, G.F., and Bertazzoni, U.

Abstract

With a procedure that allows the renaturation of the DNA polymerase catalytic activity in situ after SDS‐polyacrylamide gel electrophoresis, we have compared the active polypeptides present in extracts from organisms covering a wide evolutionary range from prokaryotes to eukaryotes, namely: Escherichia coli, Oryza sativa, Daucus carota, Neurospora crassa, Dictyostelium discoideum, Saccharomyces cerevisiae, Ceratitis capitata, Leucophaea maderae, Xenopus laevis, rat tissues and human lymphoblastoid cells. Two main clusters of active peptides are visible in mammalian and adult insect tissues, characterized by a mol. wt. greater than 70000 and less than 50000, respectively. High mol. wt. peptides are heterogeneous in size and correspond to active fragments of DNA polymerase alpha, whereas low mol. wt. peptides show the same migration rate as purified DNA polymerase beta and are not generated by proteolysis of the high mol. wt. cluster, In the three species of fungi studied, only high mol. wt. peptides are found. The same is true in plant cells, where no DNA polymerase beta activity is detectable and the pattern of the high mol. wt. cluster is similar to that observed in E. coli extracts (which also lack low mol. wt. peptides). Also in mitochondria from higher and lower eukaryotes only high mol. wt. species are observed, and the active band(s) range from 70000 to 145000 daltons. Our results indicate that the structure of DNA polymerase has been highly conserved during evolution so that an active fragment of mol. wt. greater than or equal to 70 000 is always found in prokaryotic enzymes and in the replicative species of eukaryotic and mitochondrial DNA polymerases; at a certain stage in evolution, another species of low mol. wt. DNA polymerase (beta or beta‐like) appears.

Published
1982
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100. Initiation, elongation and pausing of in vitro DNA synthesis catalyzed by immunopurified yeast DNA primase: DNA polymerase complex.

Author

Badaracco, G., Bianchi, M., Valsasnini, P., Magni, G., and Plevani, P.

Abstract

Yeast DNA primase and DNA polymerase I can be purified by immunoaffinity chromatography as a multipeptide complex which can then be resolved into its functional components and further reassembled in vitro. Isolated DNA primase synthesizes oligonucleotides of a preferred length of 9‐10 nucleotides and multiples thereof on a poly(dT) template. In vitro reconstitution of the DNA primase:DNA polymerase complex allows the synthesis of long DNA chains covalently linked to RNA initiators shorter than those synthesized by DNA primase alone. The SS (single‐stranded) circular DNA of phage M13mp9 can also be replicated by the DNA primase:DNA polymerase complex. Priming by DNA primase occurs at multiple sites and the initiators are utilized by the DNA polymerase moiety of the complex, so that almost all the SS template is converted into duplex form. The rate of DNA synthesis catalyzed by isolated yeast DNA polymerase I on the M13mp9 template is not constant and is characterized by distinct pausing sites, which partly correlate with secondary structures on the template DNA. Thus, replication of M13mp9 SS DNA with the native primase:polymerase complex gives rise to a series of DNA chains with significantly uniform termini specified by the primase start sites and the polymerase stop sites.

Published
1985
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