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Theuretzbacher U, Baraldi E, Ciabuschi F, Callegari S. Challenges and shortcomings of antibacterial discovery projects. Clin Microbiol Infect 2022; 29:610-615. [PMID: 36503116 PMCID: PMC10160915 DOI: 10.1016/j.cmi.2022.11.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 11/18/2022] [Accepted: 11/29/2022] [Indexed: 12/14/2022]
Abstract
OBJECTIVES Antibacterial drug discovery activities are essential for filling clinical pipelines with promising clinical candidates. Little information is available about the challenges and shortcomings of small companies and academic institutions in performing these important discovery tasks. METHODS We performed a content analysis of 463 reviewer comments on 91 funding applications of antibacterial drug discovery projects submitted to two major global funders between 2016 and 2020 that had not proceeded further in the selection process. This quality assessment was complemented with the inputs (via e-mail) from a panel involving six antibiotic research and development (R&D) experts with long-standing expertise and experience in antibiotic drug discovery. RESULTS Common critical comments of reviewers are grouped into three main categories: scientific and technical shortcomings, unclear potential societal impact, and insufficient capability and expertise of the project team regarding the R&D process. Insufficient characterization of in vitro activity and/or testing of the hits/leads and insufficient antibacterial activity were the most common critical comments. Other areas of concern were insufficient or lack of differentiation from available drugs or projects with a long R&D history, and the research team's insufficient knowledge of a structured streamlined R&D process as reflected in severe gaps in the expertise of the R&D team. Little appreciation for the problem of the emergence of target-based resistance, especially in single-target approaches, and little awareness of toxicological issues, including approaches with historical liabilities were also commonly mentioned. The shortcomings identified through the analysis of funding applications are echoed by the results of the expert panel. DISCUSSION Our analysis identified an urgent need of strengthening the support for antibacterial drug discovery teams to help more projects reach such a quality to be eligible for global funders and private investors.
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Affiliation(s)
| | - Enrico Baraldi
- Department of Civil and Industrial Engineering, Uppsala University, Uppsala, Sweden
| | | | - Simone Callegari
- Department of Informatics and Media, Uppsala University, Uppsala, Sweden
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Iacoviello P, Bacigaluppi S, Callegari S, Rossello C, Antonini A, Gramegna M, Da Rold M, Signorini G, Verrina G. Optimization of Vascular Supply in Free Flaps for Head and Neck Reconstruction: Analysis of a Young Team’s Experience. Front Surg 2022; 9:912010. [PMID: 35846955 PMCID: PMC9280031 DOI: 10.3389/fsurg.2022.912010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
BackgroundFor head and neck reconstructive procedures, free flap survival depends on microsurgical and anatomical choices besides multimodal clinical management. The aim of the present study is to identify relevant variables for flap survival in our initial consecutive series.MethodsA single-center, novel reconstructive team consecutive surgical series was revised. The outcome was analyzed in terms of flap survival observing variables considered more relevant: flap type, recipient artery, vein(s), and graft interposition were discussed for facial thirds to be reconstructed. Statistical analysis was performed with Chi-square, Mann–Whitney, and Odds ratio.ResultsA total of 118 free flaps were performed in 115 microsurgical procedures (93.9% for malignancies) on 109 patients, with a flap survival rate of 91.5%. For reconstruction of the middle and lower third of the face, the facial artery was privileged, because it was already transected during lymph node dissection in order to save the superior thyroid artery for further microsurgical needs. Flap failure was 50% venous. Double vein anastomosis was not related to flap survival. Deep venous drainage (as the internal jugular vein system) required fewer revisions. Half of the re-explorations saved the flap. Grafts were a risk for flap survival. Bony flaps were more critical.ConclusionAt comparable reconstructive quality, flap choice should avoid a vascular graft. The facial artery is a preferable recipient vessel, since it saves other arteries both in the case of an arterial revision and in the case of recurrence, for further free flap reconstruction. For venous anastomosis, a deep venous recipient is safer, since it offers the possibility to choose the level of anastomosis optimizing the vascular pedicle geometry. A close postsurgical flap monitoring is advisable up to 7 days postoperatively to allow for timely flap salvage.
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Affiliation(s)
- Paolo Iacoviello
- Department of Maxillofacial and Plastic Reconstructive Surgery, E.O. Ospedali Galliera, Genoa, Italy
- Correspondence: Susanna Bacigaluppi Paolo Iacoviello
| | - Susanna Bacigaluppi
- Department of Neurosurgery, E.O. Ospedali Galliera, Genoa, Italy
- Department of Neurosurgery and Neurotraumatology, IRCCS Policlinico San Martino, Genoa, Italy
- DINOGMI, Neurosurgery and Neurotraumatology, University of Genoa, Genoa, Italy
- Correspondence: Susanna Bacigaluppi Paolo Iacoviello
| | - Simone Callegari
- Burn Unit and Plastic Surgery, Villa Scassi Hospital, Genoa, Italy
| | | | | | - Marco Gramegna
- Department of Maxillofacial and Plastic Reconstructive Surgery, E.O. Ospedali Galliera, Genoa, Italy
| | - Mariano Da Rold
- Department of Maxillofacial and Plastic Reconstructive Surgery, E.O. Ospedali Galliera, Genoa, Italy
| | - Giuseppe Signorini
- Department of Maxillofacial and Plastic Reconstructive Surgery, E.O. Ospedali Galliera, Genoa, Italy
| | - Giuseppe Verrina
- Department of Maxillofacial and Plastic Reconstructive Surgery, E.O. Ospedali Galliera, Genoa, Italy
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Okhravi C, Callegari S, McKeever S, Kronlid C, Baraldi E, Lindahl O, Ciabuschi F. Simulating Market Entry Rewards for Antibiotics Development. J Law Med Ethics 2018; 46:32-42. [PMID: 30146961 DOI: 10.1177/1073110518782913] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We design an agent based Monte Carlo model of antibiotics research and development (R&D) to explore the effects of the policy intervention known as Market Entry Reward (MER) on the likelihood that an antibiotic entering pre-clinical development reaches the market. By means of sensitivity analysis we explore the interaction between the MER and four key parameters: projected net revenues, R&D costs, venture capitalists discount rates, and large pharmaceutical organizations' financial thresholds. We show that improving revenues may be more efficient than reducing costs, and thus confirm that this pull-based policy intervention effectively stimulates antibiotics R&D.
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Affiliation(s)
- Christopher Okhravi
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Simone Callegari
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Steve McKeever
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Carl Kronlid
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Enrico Baraldi
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Olof Lindahl
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
| | - Francesco Ciabuschi
- Christopher Okhravi, M.S.Sc., is a Ph.D. student of Information Systems. His research concerns simulating the effects of policy intervention on research & development. Simone Callegari, Ph.D., is a Postdoctoral Investigator at Uppsala University in Sweden. His research concerns simulating the effects of policy intervention on antimicrobial agents' research & development. Steve McKeever, D.Phil., is an Associate Professor of Information Systems at Uppsala University in Sweden. He holds a D.Phil. in Mathematics from the University of Oxford. A recent focus has been supporting simulations at the life science interface. Carl Kronlid, M.Sc., is a Ph.D. student of Industrial Engineering & Management at Uppsala University in Sweden. His research is focused on innovation and organizing, with a focus on collaborative high-tech innovation projects. Enrico Baraldi, Ph.D., is a Professor of Industrial Engineering & Management at Uppsala University in Sweden. His research concerns strategies in business networks, innovation, product development and the commercialization of science. Olof Lindahl, Ph.D., is an Assistant Professor of International Business at Uppsala University in Sweden. His research interests lie in the management of multinational firms, particularly in the mechanical engineering and pharmaceutical industries. Francesco Ciabuschi, Ph.D., is a Professor of International Business at Uppsala University in Sweden. His research concerns management of multinationals, corporate strategy, state enterprises, innovation management and entrepreneurship
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Iacovelli N, Facchinetti N, Carrara M, Musio D, De Felice F, Bacigalupo A, Callegari S, Bossi P, Fallai C, Naimo S, Steca P, Greco A, Orlandi E. PO-0707: Impact of HPV status, presence of a caregiver and smoke habit on QoL in HNC patients. Radiother Oncol 2018. [DOI: 10.1016/s0167-8140(18)31017-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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Gupta S, Ylä-Anttila P, Callegari S, Tsai MH, Delecluse HJ, Masucci MG. Herpesvirus deconjugases inhibit the IFN response by promoting TRIM25 autoubiquitination and functional inactivation of the RIG-I signalosome. PLoS Pathog 2018; 14:e1006852. [PMID: 29357390 PMCID: PMC5794190 DOI: 10.1371/journal.ppat.1006852] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 02/01/2018] [Accepted: 01/03/2018] [Indexed: 12/15/2022] Open
Abstract
The N-terminal domains of the herpesvirus large tegument proteins encode a conserved cysteine protease with ubiquitin- and NEDD8-specific deconjugase activity. The proteins are expressed during the productive virus cycle and are incorporated into infectious virus particles, being delivered to the target cells upon primary infection. Members of this viral enzyme family were shown to regulate different aspects of the virus life cycle and the innate anti-viral response. However, only few substrates have been identified and the mechanisms of these effects remain largely unknown. In order to gain insights on the substrates and signaling pathways targeted by the viral enzymes, we have used co-immunoprecipitation and mass spectrometry to identify cellular proteins that interact with the Epstein-Barr virus encoded homologue BPLF1. Several members of the 14-3-3-family of scaffold proteins were found amongst the top hits of the BPLF1 interactome, suggesting that, through this interaction, BPLF1 may regulate a variety of cellular signaling pathways. Analysis of the shared protein-interaction network revealed that BPLF1 promotes the assembly of a tri-molecular complex including, in addition to 14-3-3, the ubiquitin ligase TRIM25 that participates in the innate immune response via ubiquitination of cytosolic pattern recognition receptor, RIG-I. The involvement of BPLF1 in the regulation of this signaling pathway was confirmed by inhibition of the type-I IFN responses in cells transfected with a catalytically active BPLF1 N-terminal domain or expressing the endogenous protein upon reactivation of the productive virus cycle. We found that the active viral enzyme promotes the dimerization and autoubiquitination of TRIM25. Upon triggering of the IFN response, RIG-I is recruited to the complex but ubiquitination is severely impaired, which functionally inactivates the RIG-I signalosome. The capacity to bind to and functionally inactivate the RIG-I signalosome is shared by the homologues encoded by other human herpesviruses.
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Affiliation(s)
- Soham Gupta
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Päivi Ylä-Anttila
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Simone Callegari
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Ming-Han Tsai
- Deutsches Krebsforschungszentrum, Heidelberg, Germany
| | | | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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Tkachenko N, Weissmann JD, Petersen WP, Lake G, Zollikofer CPE, Callegari S. Individual-based modelling of population growth and diffusion in discrete time. PLoS One 2017; 12:e0176101. [PMID: 28426763 PMCID: PMC5398609 DOI: 10.1371/journal.pone.0176101] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 04/05/2017] [Indexed: 11/24/2022] Open
Abstract
Individual-based models (IBMs) of human populations capture spatio-temporal dynamics using rules that govern the birth, behavior, and death of individuals. We explore a stochastic IBM of logistic growth-diffusion with constant time steps and independent, simultaneous actions of birth, death, and movement that approaches the Fisher-Kolmogorov model in the continuum limit. This model is well-suited to parallelization on high-performance computers. We explore its emergent properties with analytical approximations and numerical simulations in parameter ranges relevant to human population dynamics and ecology, and reproduce continuous-time results in the limit of small transition probabilities. Our model prediction indicates that the population density and dispersal speed are affected by fluctuations in the number of individuals. The discrete-time model displays novel properties owing to the binomial character of the fluctuations: in certain regimes of the growth model, a decrease in time step size drives the system away from the continuum limit. These effects are especially important at local population sizes of <50 individuals, which largely correspond to group sizes of hunter-gatherers. As an application scenario, we model the late Pleistocene dispersal of Homo sapiens into the Americas, and discuss the agreement of model-based estimates of first-arrival dates with archaeological dates in dependence of IBM model parameter settings.
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Affiliation(s)
- Natalie Tkachenko
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- * E-mail:
| | - John D. Weissmann
- Department of Anthropology, University of Zurich, Zurich, Switzerland
| | - Wesley P. Petersen
- Department of Anthropology, University of Zurich, Zurich, Switzerland
- Seminar for Applied Mathematics, ETH Zurich, Zurich, Switzerland
| | - George Lake
- Institute for Computational Science, University of Zurich, Zurich, Switzerland
| | | | - Simone Callegari
- Department of Anthropology, University of Zurich, Zurich, Switzerland
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Li J, Callegari S, Masucci MG. The Epstein-Barr virus miR-BHRF1-1 targets RNF4 during productive infection to promote the accumulation of SUMO conjugates and the release of infectious virus. PLoS Pathog 2017; 13:e1006338. [PMID: 28414785 PMCID: PMC5413087 DOI: 10.1371/journal.ppat.1006338] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Revised: 05/02/2017] [Accepted: 04/06/2017] [Indexed: 12/21/2022] Open
Abstract
Post-translational modification by the Small Ubiquitin-like Modifier (SUMO) regulates a variety of cellular functions, and is hijacked by viruses to remodel the host cell during latent and productive infection. Here we have monitored the activity of the SUMO conjugation machinery in cells productively infected with Epstein-Barr virus (EBV). We found that SUMO2/3 conjugates accumulate during the late phase of the productive virus cycle, and identified several viral proteins as bone fide SUMOylation substrates. Analysis of the mechanism involved in the accumulation of SUMOylated proteins revealed upregulation of several components of the SUMO-conjugation machinery and post-transcriptional downregulation of the SUMO-targeted ubiquitin ligase RNF4. The latter effect was mediated by selective inhibition of RNF4 protein expression by the viral miR-BHRF1-1. Reconstitution of RNF4 in cells expressing an inducible miR-BHRF1-1 sponge or a miR-BHRF1-1 resistant RNF4 was associated with reduced levels of early and late viral proteins and impaired virus release. These findings illustrate a novel strategy for viral interference with the SUMO pathway, and identify the EBV miR-BHRF1-1 and the cellular RNF4 as regulators of the productive virus cycle. We have investigated the activity of the SUMOylation machinery in cells infected with Epstein-Barr virus (EBV), a human herpesvirus that infects B-lymphocytes and is associated with malignancies. We found that activation of the productive virus cycle is accompanied by accumulation of SUMO conjugates, upregulation of components of the SUMO conjugation machinery, and downregulation of the SUMO-targeted ubiquitin ligase RNF4. The decrease of RNF4 is due to post-transcriptional downregulation by miR-BHRF1-1, a member of the BHRF1 microRNA cluster that is upregulated during productive infection. The effect of miR-BHRF1-1 was confirmed in luciferase reported assays, by mutation of the RNF4 3’UTR seed site, by transfection of a synthetic miR-BHRF1-1 mimic, by ectopic expression of miR-BHRF1-1 and by the reversal of RNF4 downregulation in cells expressing a miR-BHRF1-1 sponge. We also found that several early and late viral proteins are bona fide SUMOylation substrates. Reconstitution of RNF4 in productively infected cells was accompanied by proteasome-dependent degradation of the SUMOylated viral protein and by a significantly reduced virus yield. These findings illustrate a new strategy for viral interference with the SUMO pathway, an unexpected contribution of miR-BHRF1-1 to the productive cycle of EBV and a previously unrecognized role of the RNF4 ligase in the regulation of virus production.
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Affiliation(s)
- Jinlin Li
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Simone Callegari
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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Petersen WP, Callegari S, Lake GR, Tkachenko N, Weissmann JD, Zollikofer CPE. A Stable Finite-Difference Scheme for Population Growth and Diffusion on a Map. PLoS One 2017; 12:e0167514. [PMID: 28085882 PMCID: PMC5235379 DOI: 10.1371/journal.pone.0167514] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Accepted: 11/15/2016] [Indexed: 11/18/2022] Open
Abstract
We describe a general Godunov-type splitting for numerical simulations of the Fisher-Kolmogorov-Petrovski-Piskunov growth and diffusion equation on a world map with Neumann boundary conditions. The procedure is semi-implicit, hence quite stable. Our principal application for this solver is modeling human population dispersal over geographical maps with changing paleovegetation and paleoclimate in the late Pleistocene. As a proxy for carrying capacity we use Net Primary Productivity (NPP) to predict times for human arrival in the Americas.
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Affiliation(s)
- W. P. Petersen
- Anthropological Institute and Museum, Univ. of Zürich, Zürich, Switzerland
- Seminar for Applied Mathematics, ETH, Zürich, Switzerland
- * E-mail:
| | - S. Callegari
- Anthropological Institute and Museum, Univ. of Zürich, Zürich, Switzerland
| | - G. R. Lake
- Institute for Computational Science, Univ. of Zürich, Zürich, Switzerland
| | - N. Tkachenko
- Anthropological Institute and Museum, Univ. of Zürich, Zürich, Switzerland
| | - J. D. Weissmann
- Anthropological Institute and Museum, Univ. of Zürich, Zürich, Switzerland
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Rossi S, Buccarello A, Ershler PR, Lux RL, Callegari S, Corradi D, Carnevali L, Sgoifo A, Miragoli M, Musso E, Macchi E. Effect of anisotropy on ventricular vulnerability to unidirectional block and reentry by single premature stimulation during normal sinus rhythm in rat heart. Am J Physiol Heart Circ Physiol 2016; 312:H584-H607. [PMID: 28011584 DOI: 10.1152/ajpheart.00366.2016] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 12/05/2016] [Accepted: 12/20/2016] [Indexed: 11/22/2022]
Abstract
Single high-intensity premature stimuli when applied to the ventricles during ventricular drive of an ectopic site, as in Winfree's "pinwheel experiment," usually induce reentry arrhythmias in the normal heart, while single low-intensity stimuli barely do. Yet ventricular arrhythmia vulnerability during normal sinus rhythm remains largely unexplored. With a view to define the role of anisotropy on ventricular vulnerability to unidirectional conduction block and reentry, we revisited the pinwheel experiment with reduced constraints in the in situ rat heart. New features included single premature stimulation during normal sinus rhythm, stimulation and unipolar potential mapping from the same high-resolution epicardial electrode array, and progressive increase in stimulation strength and prematurity from diastolic threshold until arrhythmia induction. Measurements were performed with 1-ms cathodal stimuli at multiple test sites (n = 26) in seven rats. Stimulus-induced virtual electrode polarization during sinus beat recovery phase influenced premature ventricular responses. Specifically, gradual increase in stimulus strength and prematurity progressively induced make, break, and graded-response stimulation mechanisms. Hence unidirectional conduction block occurred as follows: 1) along fiber direction, on right and left ventricular free walls (n = 23), initiating figure-eight reentry (n = 17) and tachycardia (n = 12), and 2) across fiber direction, on lower interventricular septum (n = 3), initiating spiral wave reentry (n = 2) and tachycardia (n = 1). Critical time window (55.1 ± 4.7 ms, 68.2 ± 6.0 ms) and stimulus strength lower limit (4.9 ± 0.6 mA) defined vulnerability to reentry. A novel finding of this study was that ventricular tachycardia evolves and is maintained by episodes of scroll-like wave and focal activation couplets. We also found that single low-intensity premature stimuli can induce repetitive ventricular response (n = 13) characterized by focal activations.NEW & NOTEWORTHY We performed ventricular cathodal point stimulation during sinus rhythm by progressively increasing stimulus strength and prematurity. Virtual electrode polarization and recovery gradient progressively induced make, break, and graded-response stimulation mechanisms. Unidirectional conduction block occurred along or across fiber direction, initiating figure-eight or spiral wave reentry, respectively, and tachycardia sustained by scroll wave and focal activations.
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Affiliation(s)
- S Rossi
- Department of Life Sciences, Università degli Studi, Parma, Italy.,CERT, Center of Excellence for Toxicological Research, Department of Clinical and Experimental Medicine, Università degli Studi, Parma, Italy
| | - A Buccarello
- Department of Life Sciences, Università degli Studi, Parma, Italy
| | - P R Ershler
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - R L Lux
- Nora Eccles Harrison Cardiovascular Research and Training Institute, University of Utah, Salt Lake City, Utah
| | - S Callegari
- Azienda Unità Sanitaria Locale, Unit of Cardiology, Parma, Italy
| | - D Corradi
- Department of Biomedical, Biotechnological, and Translational Sciences, Unit of Pathology, Università degli Studi, Parma, Italy.,CERT, Center of Excellence for Toxicological Research, Department of Clinical and Experimental Medicine, Università degli Studi, Parma, Italy
| | - L Carnevali
- Department of Life Sciences, Università degli Studi, Parma, Italy
| | - A Sgoifo
- Department of Life Sciences, Università degli Studi, Parma, Italy
| | - M Miragoli
- CERT, Center of Excellence for Toxicological Research, Department of Clinical and Experimental Medicine, Università degli Studi, Parma, Italy.,Humanitas Clinical and Research Center, Rozzano (Milan), Italy; and
| | - E Musso
- Department of Life Sciences, Università degli Studi, Parma, Italy.,Cardiac Stem Cell Interdepartmental Center "CISTAC," Università degli Studi, Parma, Italy
| | - E Macchi
- Department of Life Sciences, Università degli Studi, Parma, Italy; .,CERT, Center of Excellence for Toxicological Research, Department of Clinical and Experimental Medicine, Università degli Studi, Parma, Italy.,Cardiac Stem Cell Interdepartmental Center "CISTAC," Università degli Studi, Parma, Italy
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10
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Aluicio-Sarduy E, Callegari S, Figueroa del Valle DG, Desii A, Kriegel I, Scotognella F. Electric field induced structural colour tuning of a silver/titanium dioxide nanoparticle one-dimensional photonic crystal. Beilstein J Nanotechnol 2016; 7:1404-1410. [PMID: 27826514 PMCID: PMC5082530 DOI: 10.3762/bjnano.7.131] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 09/09/2016] [Indexed: 06/06/2023]
Abstract
An electric field is employed for the active tuning of the structural colour in photonic crystals, which acts as an effective external stimulus with an impact on light transmission manipulation. In this work, we demonstrate structural colour in a photonic crystal device comprised of alternating layers of silver nanoparticles and titanium dioxide nanoparticles, exhibiting spectral shifts of around 10 nm for an applied voltage of only 10 V. The accumulation of charge at the metal/dielectric interface with an applied electric field leads to an effective increase of the charges contributing to the plasma frequency in silver. This initiates a blue shift of the silver plasmon band with a simultaneous blue shift of the photonic band gap as a result of the change in the silver dielectric function (i.e. decrease of the effective refractive index). These results are the first demonstration of active colour tuning in silver/titanium dioxide nanoparticle-based photonic crystals and open the route to metal/dielectric-based photonic crystals as electro-optic switches.
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Affiliation(s)
- Eduardo Aluicio-Sarduy
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli 70/3, 20133 Milan, Italy
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Simone Callegari
- Dipartimento di Chimica, Materiali e Ingegneria Chimica "Giulio Natta", Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Diana Gisell Figueroa del Valle
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli 70/3, 20133 Milan, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Andrea Desii
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli 70/3, 20133 Milan, Italy
| | - Ilka Kriegel
- Department of Nanochemistry, Istituto Italiano di Tecnologia (IIT), via Morego 30, 16163 Genova, Italy
| | - Francesco Scotognella
- Center for Nano Science and Technology@PoliMi, Istituto Italiano di Tecnologia, Via Giovanni Pascoli 70/3, 20133 Milan, Italy
- Dipartimento di Fisica, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
- Istituto di Fotonica e Nanotecnologie CNR, Piazza Leonardo da Vinci 32, 20133 Milano
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11
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Carnevali L, Vacondio F, Rossi S, Callegari S, Macchi E, Spadoni G, Bedini A, Rivara S, Mor M, Sgoifo A. Antidepressant-like activity and cardioprotective effects of fatty acid amide hydrolase inhibitor URB694 in socially stressed Wistar Kyoto rats. Auton Neurosci 2015. [DOI: 10.1016/j.autneu.2015.07.057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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12
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Majani G, Callegari S, Pierobon A, Giardini A, Viola L, Baiardini I, Sommaruga M. A New Instrument in Quality-of-Life Assessment. International Journal of Mental Health 2015. [DOI: 10.1080/00207411.1999.11449463] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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13
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Callegari S, Gastaldello S, Faridani OR, Masucci MG. Epstein-Barr virus encoded microRNAs target SUMO-regulated cellular functions. FEBS J 2014; 281:4935-50. [DOI: 10.1111/febs.13040] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 08/11/2014] [Accepted: 09/02/2014] [Indexed: 12/30/2022]
Affiliation(s)
- Simone Callegari
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Stefano Gastaldello
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Omid R. Faridani
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology; Karolinska Institutet; Stockholm Sweden
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14
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Gastaldello S, Chen X, Callegari S, Masucci MG. Caspase-1 promotes Epstein-Barr virus replication by targeting the large tegument protein deneddylase to the nucleus of productively infected cells. PLoS Pathog 2013; 9:e1003664. [PMID: 24130483 PMCID: PMC3795028 DOI: 10.1371/journal.ppat.1003664] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 08/12/2013] [Indexed: 11/17/2022] Open
Abstract
The large tegument proteins of herpesviruses contain N-terminal cysteine proteases with potent ubiquitin and NEDD8-specific deconjugase activities, but the function of the enzymes during virus replication remains largely unknown. Using as model BPLF1, the homologue encoded by Epstein-Barr virus (EBV), we found that induction of the productive virus cycle does not affect the total level of ubiquitin-conjugation but is accompanied by a BPLF1-dependent decrease of NEDD8-adducts and accumulation of free NEDD8. Expression of BPLF1 promotes cullin degradation and the stabilization of cullin-RING ligases (CRLs) substrates in the nucleus, while cytoplasmic CRLs and their substrates are not affected. The inactivation of nuclear CRLs is reversed by the N-terminus of CAND1, which inhibits the binding of BPLF1 to cullins and prevents efficient viral DNA replication. Targeting of the deneddylase activity to the nucleus is dependent on processing of the catalytic N-terminus by caspase-1. Inhibition of caspase-1 severely impairs viral DNA synthesis and the release of infectious virus, pointing a previously unrecognized role of the cellular response to danger signals triggered by EBV reactivation in promoting virus replication.
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Affiliation(s)
- Stefano Gastaldello
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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15
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Alpigiani M, Salvati P, Rosina S, Callegari S, Tripodi G, Lorini R, Michelis M, Boero S. AB1171 Use of bone marrow cells (BMCS) added to platelet-rich plasma (PRP) for treatment of bone degenerative processes in jia patient: 18-month follow-up. Ann Rheum Dis 2013. [DOI: 10.1136/annrheumdis-2012-eular.1169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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16
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Coppotelli G, Mughal N, Callegari S, Sompallae R, Caja L, Luijsterburg MS, Dantuma NP, Moustakas A, Masucci MG. The Epstein-Barr virus nuclear antigen-1 reprograms transcription by mimicry of high mobility group A proteins. Nucleic Acids Res 2013; 41:2950-62. [PMID: 23358825 PMCID: PMC3597695 DOI: 10.1093/nar/gkt032] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Viral proteins reprogram their host cells by hijacking regulatory components of protein networks. Here we describe a novel property of the Epstein-Barr virus (EBV) nuclear antigen-1 (EBNA1) that may underlie the capacity of the virus to promote a global remodeling of chromatin architecture and cellular transcription. We found that the expression of EBNA1 in transfected human and mouse cells is associated with decreased prevalence of heterochromatin foci, enhanced accessibility of cellular DNA to micrococcal nuclease digestion and decreased average length of nucleosome repeats, suggesting de-protection of the nucleosome linker regions. This is a direct effect of EBNA1 because targeting the viral protein to heterochromatin promotes large-scale chromatin decondensation with slow kinetics and independent of the recruitment of adenosine triphosphate-dependent chromatin remodelers. The remodeling function is mediated by a bipartite Gly-Arg rich domain of EBNA1 that resembles the AT-hook of High Mobility Group A (HMGA) architectural transcription factors. Similar to HMGAs, EBNA1 is highly mobile in interphase nuclei and promotes the mobility of linker histone H1, which counteracts chromatin condensation and alters the transcription of numerous cellular genes. Thus, by regulating chromatin compaction, EBNA1 may reset cellular transcription during infection and prime the infected cells for malignant transformation.
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Affiliation(s)
- Giuseppe Coppotelli
- Department of Cell and Molecular Biology, Karolinska Institutet, 17177 Stockholm, Sweden
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17
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Gastaldello S, Callegari S, Coppotelli G, Hildebrand S, Song M, Masucci MG. Herpes virus deneddylases interrupt the cullin-RING ligase neddylation cycle by inhibiting the binding of CAND1. J Mol Cell Biol 2012; 4:242-51. [DOI: 10.1093/jmcb/mjs012] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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18
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Alpigiani MG, Salvati P, Callegari S, Bagnis A, Papadia M, Traverso CE, Lorini R. Abatacept for severe anti-TNF-alfa refractory JIA-associated uveitis: one year follow-up. Pediatr Rheumatol Online J 2011. [PMCID: PMC3194545 DOI: 10.1186/1546-0096-9-s1-p189] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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19
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Alpigiani MG, Salvati P, Muraca M, Callegari S, Tripodi G, Lorini R, Michelis MB, Boero S. Use of bone marrow cells (BMCS) added to Platelet-Rich Plasma (PRP) for treatment of bone degenerative processes in JIA patients: a case report. Pediatr Rheumatol Online J 2011. [PMCID: PMC3194544 DOI: 10.1186/1546-0096-9-s1-p188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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20
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Guerra L, Guidi R, Slot I, Callegari S, Sompallae R, Pickett CL, Åström S, Eisele F, Wolf D, Sjögren C, Masucci MG, Frisan T. Bacterial genotoxin triggers FEN1-dependent RhoA activation, cytoskeleton remodeling and cell survival. J Cell Sci 2011; 124:2735-42. [DOI: 10.1242/jcs.085845] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
The DNA damage response triggered by bacterial cytolethal distending toxins (CDTs) is associated with activation of the actin-regulating protein RhoA and phosphorylation of the downstream-regulated mitogen-activated protein kinase (MAPK) p38, which promotes the survival of intoxicated (i.e. cells exposed to a bacterial toxin) cells. To identify the effectors of this CDT-induced survival response, we screened a library of 4492 Saccharomyces cerevisiae mutants that carry deletions in nonessential genes for reduced growth following inducible expression of CdtB. We identified 78 genes whose deletion confers hypersensitivity to toxin. Bioinformatics analysis revealed that DNA repair and endocytosis were the two most overrepresented signaling pathways. Among the human orthologs present in our data set, FEN1 and TSG101 regulate DNA repair and endocytosis, respectively, and also share common interacting partners with RhoA. We further demonstrate that FEN1, but not TSG101, regulates cell survival, MAPK p38 phosphorylation, RhoA activation and actin cytoskeleton reorganization in response to DNA damage. Our data reveal a previously unrecognized crosstalk between DNA damage and cytoskeleton dynamics in the regulation of cell survival, and might provide new insights on the role of chronic bacteria infection in carcinogenesis.
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Affiliation(s)
- Lina Guerra
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Riccardo Guidi
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Ilse Slot
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Simone Callegari
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Ramakrishna Sompallae
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Carol L. Pickett
- Department of Microbiology and Immunology, Chandler Medical Center, University of Kentucky, Lexington, KY 40536-0298, USA
| | - Stefan Åström
- Department of Developmental Biology, Wenner-Grens Institutet, Stockholm University, 106 91 Stockholm, Sweden
| | - Frederik Eisele
- Institute of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Dieter Wolf
- Institute of Biochemistry, University of Stuttgart, 70569 Stuttgart, Germany
| | - Camilla Sjögren
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
| | - Teresa Frisan
- Department of Cell and Molecular Biology, Karolinska Institutet, Box 285, S-171 77 Stockholm, Sweden
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21
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Queirolo P, Morabito A, Piccioli P, Lastraioli S, Callegari S, Camoriano M, Ascierto PA, Laurent S, Dozin B, Pistillo MP. Analysis of CTLA-4 gene polymorphisms in patients with advanced melanoma treated with anti-CTLA-4 therapy. J Clin Oncol 2011. [DOI: 10.1200/jco.2011.29.15_suppl.8588] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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22
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Sompallae R, Callegari S, Kamranvar SA, Masucci MG. Transcription profiling of Epstein-Barr virus nuclear antigen (EBNA)-1 expressing cells suggests targeting of chromatin remodeling complexes. PLoS One 2010; 5:e12052. [PMID: 20706582 PMCID: PMC2919392 DOI: 10.1371/journal.pone.0012052] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2010] [Accepted: 07/13/2010] [Indexed: 12/15/2022] Open
Abstract
The Epstein-Barr virus (EBV) encoded nuclear antigen (EBNA)-1 regulates virus replication and transcription, and participates in the remodeling of the cellular environment that accompanies EBV induced B-cell immortalization and malignant transformation. The putative cellular targets of these effects of EBNA-1 are largely unknown. To address this issue we have profiled the transcriptional changes induced by short- and long-term expression of EBNA-1 in the EBV negative B-cell lymphoma BJAB. Three hundred and nineteen cellular genes were regulated in a conditional transfectant shortly after EBNA-1 induction while a ten fold higher number of genes was regulated upon continuous EBNA-1 expression. Promoter analysis of the differentially regulated genes demonstrated a significant enrichment of putative EBNA-1 binding sites suggesting that EBNA-1 may directly influence the transcription of a subset of genes. Gene ontology analysis of forty seven genes that were consistently regulated independently on the time of EBNA-1 expression revealed an unexpected enrichment of genes involved in the maintenance of chromatin architecture. The interaction network of the affected gene products suggests that EBNA-1 may promote a broad rearrangement of the cellular transcription landscape by altering the expression of key components of chromatin remodeling complexes.
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Affiliation(s)
| | - Simone Callegari
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | | | - Maria G. Masucci
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
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23
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Illergård K, Callegari S, Elofsson A. MPRAP: an accessibility predictor for a-helical transmembrane proteins that performs well inside and outside the membrane. BMC Bioinformatics 2010; 11:333. [PMID: 20565847 PMCID: PMC2904353 DOI: 10.1186/1471-2105-11-333] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2009] [Accepted: 06/18/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In water-soluble proteins it is energetically favorable to bury hydrophobic residues and to expose polar and charged residues. In contrast to water soluble proteins, transmembrane proteins face three distinct environments; a hydrophobic lipid environment inside the membrane, a hydrophilic water environment outside the membrane and an interface region rich in phospholipid head-groups. Therefore, it is energetically favorable for transmembrane proteins to expose different types of residues in the different regions. RESULTS Investigations of a set of structurally determined transmembrane proteins showed that the composition of solvent exposed residues differs significantly inside and outside the membrane. In contrast, residues buried within the interior of a protein show a much smaller difference. However, in all regions exposed residues are less conserved than buried residues. Further, we found that current state-of-the-art predictors for surface area are optimized for one of the regions and perform badly in the other regions. To circumvent this limitation we developed a new predictor, MPRAP, that performs well in all regions. In addition, MPRAP performs better on complete membrane proteins than a combination of specialized predictors and acceptably on water-soluble proteins. A web-server of MPRAP is available at http://mprap.cbr.su.se/ CONCLUSION By including complete a-helical transmembrane proteins in the training MPRAP is able to predict surface accessibility accurately both inside and outside the membrane. This predictor can aid in the prediction of 3D-structure, and in the identification of erroneous protein structures.
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Affiliation(s)
- Kristoffer Illergård
- Center for Biomembrane Research, Stockholm Bioinformatics Center, Dept of Biochemistry and Biophysics, Stockholm University, SE-106 91 Stockholm, Sweden
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24
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Moroni L, Sguazzin C, Filipponi L, Bruletti G, Callegari S, Galante E, Giorgi I, Majani G, Bertolotti G. [Caregiver Need Assessment: a questionnaire for caregiver demand]. G Ital Med Lav Ergon 2008; 30:B84-B90. [PMID: 19288782] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
UNLABELLED Many studies have focused on the importance of the informal care provided by caregivers and on its impact in terms of worsening quality of life and increased burden. The aim of the present study is to analyze the psychometric validity and reliability of the Caregiver Needs Assessment (CNA) questionnaire, which has been built to investigate the needs (related to assistance) perceived by caregivers of severely impaired patients, particularly in the first stages of their illness. METHODS The CNA was administered to 226 family caregivers (24.3% males) of 197 patients (50.8% males) hospitalized for neuromotor rehabilitation after a stroke, head injury, Lateral Amyotrophic Sclerosis, Parkinson or other severely impairing diseases. RESULTS The instrument was tested on a large sample (KMO = 0.83) of heterogeneous caregivers. Explorative and confirmatory factor analysis, performed on a two subgroup random subdivision of the sample, showed the presence of two factors with good internal consistency: the factor "needs of emotional and social support" (alpha = 0.765) and the factor "needs of information and communication" (alpha = 0.742). The structural equation modeling confirms the goodness of fit of the 2-factor structure (RMSEA = 0.073; SRMR = 0.1; CFI = 0.96). We observed a positive correlation (p < 0.01) between the factor "needs of emotional and social support" of the CNA and other questionnaires aimed at assessing psychological wellbeing, and between the factor "needs of information and communication" and the factor "needs for knowledge about the disease" of the Family Strain Questionnaire, showing good convergent validity. We also observed high Pearson correlation coefficients (0.942 and 0.965) between test-retest measurements of both factors in the CNA. CONCLUSION The statistical analysis confirms the good psychometric properties of the CNA questionnaire. For its brevity and ease in compilation the CNA is promising practical tool aimed at assessing caregivers' needs in order to personalize a programme of psychological support, to measure it's outcome and to provide comparison of the different needs in different diseases.
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Affiliation(s)
- L Moroni
- Servizi di Psicologia Fondazione Salvatore Maugeri IRCCS, Istituti Scientifici di Tradate
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25
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Sguazzin C, Baiardi P, Bertolotti G, Bruletti G, Callegari S, Galante E, Giorgi I, Majani G. [Caregiver and care: from needs assessment to alliance in the therapeutic path]. G Ital Med Lav Ergon 2007; 29:118-22. [PMID: 17569434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Affiliation(s)
- C Sguazzin
- Servizi di Psicologia Fondazione Salvatore Maugeri IRCCS, Istituti Scientifici di Pavia sede di Via Boezio, Italy.
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26
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Pierobon A, Callegari S, Mastretta E. [A traumatic brain injury patient: from rehabilitation to social-familial re-integration. Case report focusing on quality of life aspects]. G Ital Med Lav Ergon 2006; 28:119-122. [PMID: 18924302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
WHO recommends that the biopsychosocial model be adopted in the rehabilitation and, particularly, in the multidisciplinary care of Traumatic Brain Injury (TBI) patients. The neuropsychological, psychological, and Quality of Life (QoL) assessment of TBI patients follows the evolution of their clinical conditions. The following evaluation battery is administered in our Unit: Specific Neuropsicological Tests, Wechsler Adult Intelligence Scales Revised (WAIS-R), and the Short Form-36 (SF-36) and Satisfaction Profile (SAT-P), two generic questionnaires measuring respectively health status and subjective aspects of QoL. Mauro is an 18-year old patient with TBI, complicated after one and a half years by epilepsy. The clinical report is divided into three phases (3, 5 and 18 months post-TBI)--ranging from the first psychological-neuropsychological assessment to the patient's socio-educational re-integration--and includes self-reports by the patient and/or his mother, a discussion of the QoL and neuropsychological data, and a presentation of the work carried out in the cognitive behavioural rehabilitation. The psychological topics that emerged are: memories of the traumatic event and the hospitalization period, enthusiasm about the "return to life", and difficulties and suffering due to the fact of "being different". This paper offers an example of both the assessment and treatment of TBI patients--following its course from where it begins in the Rehabilitation Center to its continuation in the patient's social environment. The purpose of such a global clinical management is to effectuate a psychosocial re-integration that is adequate in terms of the patient's cognitive resources and residual behavioural abilities.
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Affiliation(s)
- A Pierobon
- Servizio di Psicologia, Fondazione Salvatore Maugeri, Clinica del Lavoro e della Riabilitazione, IRCCS, Istituto Scientifico di Montescano (PV) Pavia, Italy.
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27
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Callegari S, Pierobon A, Viola L, Mastretta E, Majani G. [Neuropsychological course of patients with craniocerebral injuries in rehabilitation]. G Ital Med Lav Ergon 2004; 26:150-5. [PMID: 15270447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
The aim of the present paper is to describe a neuropsychological assessment and intervention model in Traumatic Brain Injury (TBI) patients. The theoretical and methodological frameworks are described and the following diagnostic and rehabilitative flowchart is fully explained: 1. first visit with patient and his relatives; 2. clinical and testing assessment; 3. diagnostic balance and its communication to patient and his relatives; 4. neuropsychological rehabilitation and psychological counseling. Whenever necessary, patient's relatives are involved. Furthermore, TBI patients' health related quality of life is outlined as an important clinical and scientific issue deserving more attention, in spite of the objective methodological difficulties which its evaluation implies.
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Affiliation(s)
- S Callegari
- Fondazione Salvatore Maugeri, Clinica della Lavoro e della Riabilitazione, IRCCS, Istituto Scientifico di Montescano, Servizio di Psicologia, Italy.
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29
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Callegari S, Majani G, Giardini A, Pierobon A, Opasich C, Cobelli F, Tavazzi L. Relationship between cognitive impairment and clinical status in chronic heart failure patients. Monaldi Arch Chest Dis 2002; 58:19-25. [PMID: 12693065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023] Open
Abstract
BACKGROUND In spite of its clinical importance, cognitive functioning is not always taken into account in studies on patients with chronic heart failure. The aim of the present study is to analyse the relationship between cognitive impairment and cardiovascular variables in a sample of patients with chronic heart failure for assessment or candidated for heart transplant. METHODS Sixty-four male patients with chronic heart failure in NYHA class I-III, in a stable clinical condition, underwent cardiological evaluation and neuropsychological assessment by means of a wide battery of tests: Spinnler and Tognoni's tests and WAIS scale. RESULTS Compared to the normative group, only 9% of patients did not have impairment in any cognitive function. 26% of patients had impairment of one cognitive function, and 30% of four or more cognitive functions. The cognitive functions that were most often impaired were short-term verbal memory, short-term visual spatial memory, differed verbal memory and verbal learning and visual spatial logical ability. On the whole, no statistical significant relationship was found between cognitive scores and the considered cardiovascular variables. CONCLUSIONS Our data support the need to take into account the risk of cognitive impairment in CHF patients, regardless of age, disease severity or functional status. The high prevalence of short-term verbal memory impairment has important implications in clinical practice, since CHF patients should be actively involved in the medical management of their disease. Memory deficits could compromise patient's adherence to treatment as well as doctor-patient interactions. The practical consequences of these difficulties require some changes in doctors' behaviour and suggest the need for specific medical staff member training.
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Affiliation(s)
- S Callegari
- Psychology Unit, Fondazione S. Maugeri, Clinica del Lavoro e della Riabilitazione, IRCCS, Scientific Institute of Montescano, PV, Italy
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Moruzzi P, Rossi M, Contini M, Callegari S. [Circadian rhythm in myocardial infarction in relation to the site and the different cases of coronary involvement]. Cardiologia 1999; 44 Suppl 1:237-40. [PMID: 12497914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/28/2023]
Affiliation(s)
- P Moruzzi
- Cattedra di Cardiologia, Università degli Studi, Centro Cardiologico-Fondazione Monzino, IRCCS, Via Carlo Parea, 4, 20138 Milano.
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Majani G, Pierobon A, Giardini A, Callegari S, Opasich C, Cobelli F, Tavazzi L. Relationship between psychological profile and cardiological variables in chronic heart failure. The role of patient subjectivity. Eur Heart J 1999; 20:1579-86. [PMID: 10529326 DOI: 10.1053/euhj.1999.1712] [Citation(s) in RCA: 60] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
AIM To analyse the relationships between the psychological profile, the satisfaction profile and cardiological variables in patients with chronic heart failure. MATERIAL AND METHODS One hundred and fifty-two male patients with chronic heart failure in a stable clinical condition underwent cardiological evaluation and psychological assessment by means of two instruments: the Cognitive Behavioural Assessment 2.0 Battery and the Satisfaction Profile. RESULTS Patients scored higher than healthy subjects in terms of psychophysiological disorders and depression. Patients in NYHA class III reported higher anxiety and depression scores and had more frequent problems in daily life than patients in NYHA classes I and II. Class III patients also reported lower satisfaction levels in many aspects of psychological and physical functioning. Pulmonary resistances >2.5 Wood units, pulmonary capillary wedge pressure >0. 18 mmHg and a diagnosis of ischaemic cardiomyopathy were associated with low satisfaction levels in the Satisfaction Profile 'physical functioning' factor. To be listed for heart transplantation and a history of more than three hospitalizations were related to low satisfaction levels in many items of the Satisfaction Profile. Finally, stepwise multiple regression showed that NYHA class, depression score and pulmonary capillary resistance accounted for 32% of the variance in the Satisfaction Profile physical functioning factor score. CONCLUSION On the basis of chronic heart failure diagnosis only, a generic pattern of psychological distress can be predicted, common to many severe chronic diseases. Shifting from objective mental health measures towards the domain of subjective satisfaction, the only link which emerges is between objective cardiological data and satisfaction with physical functioning. Satisfaction in terms of other life aspects does not seem to be related to cardiological variables. These results support the importance of subjectivity in health related quality of life, as well as objective measures.
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Affiliation(s)
- G Majani
- Psychology Service, 'S. Maugeri' Foundation, IRCCS, Rehabilitation Institute of Montescano, Pavia, Italy
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Callegari S, Pini M, Andreoli L. [Guidelines and clinical practice: anticoagulant therapy and cardioversion in atrial fibrillation]. G Ital Cardiol 1999; 29:1157-63. [PMID: 10546125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
UNLABELLED The cardioversion of atrial fibrillation is linked to a substantial risk of systemic embolization. In an effort to reduce it, the American College of Chest Physicians (ACCP) periodically publishes guidelines for the use of anticoagulation in the conversion of atrial fibrillation. OBJECTIVE Determination of the physician's compliance with the recommendations of the "Fourth ACCP Consensus Conference on Antithrombotic Therapy". METHODS The charts of people admitted to a community hospital in 1998 with a diagnosis of atrial fibrillation (n = 202) were evaluated retrospectively. Consideration was given to the ACCP's recommendation to give anticoagulants 3 weeks before and 4 weeks after elective cardioversion to patients who had been in atrial fibrillation for more than 2 days. RESULTS Ninety-one of the 202 patients admitted with atrial fibrillation reported the onset of arrhythmia more than 48 hours before. Thirty-four of them underwent elective cardioversion and 13 cases (33%) went without anticoagulation in the preceding 2 weeks. Of these 13 cases, 8 were patients aged over 75 (range 78-88, mean 84). After sinus rhythm had been restored in 30 people (spontaneously in 5 of them), the anticoagulant therapy was not administered during the 4 recommended weeks in 10 people (33%), all of them over 75 (range 77.94, mean 84). CONCLUSIONS Anticoagulation for cardioversion of atrial fibrillation is underused, especially among elderly patients. In order not to let age itself be an obstacle to the correct treatment of patients with high embolic risk, our efforts must be improved in order to identify the correct therapeutic choice in each particular case. Initiatives aimed at identifying and removing any impediment to the application of guidelines may contribute to stimulating physicians in the process of evaluating the quality of hospital treatment.
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Affiliation(s)
- S Callegari
- Unità Operativa di Cardiologia, Ospedale di Fidenza
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Majani G, Callegari S, Pierobon A, Viola L, Manera M, Opasich C, Cobelli F, Tavazzi L. [The psychological side of chronic heart failure. A pluriannual experience]. G Ital Cardiol 1997; 27:244-54. [PMID: 9244726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The present study summarizes the authors' experience reached in the last four years with chronic heart failure patients', particularly referring to the psychological aspects. The 218 male patients (age 51.7 +/- 8.3) psychological profile (obtained by means of the CBA 2.0 Primary Scales) has shown higher scores in the anxiety, depression and psychophysiological disorders scales and lower scores in some of the fear scales, compared with the reference normative group. The CBA 2.0 Schedule 4 has enlightened suicidal ideas, eating and sleep disorders, economic and sexual problems. The comparison between the psychological and the many cardiological variables taken into account, has not allowed to highlight significant relationships on the whole. Our data support the necessity to introduce other--likely subjective--variables in the studies aimed at analyzing the relationships between psychological and cardiological factors in the chronic heart failure patients.
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Affiliation(s)
- G Majani
- Servizio di Psicologia, Fondazione Salvatore Maugeri, IRCCS, Istituto di Riabilitazione Montescano (PV)
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Sommaruga M, Spanevello A, Migliori GB, Neri M, Callegari S, Majani G. The effects of a cognitive behavioural intervention in asthmatic patients. Monaldi Arch Chest Dis 1995; 50:398-402. [PMID: 8541826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Abstract
There is evidence that educational programmes may improve patient's compliance with asthma treatment and control symptoms. Whilst medical parameters have been thoroughly studied, few data are available concerning psychological intervention. The aim of our open pilot study was to verify whether any difference in perceived illness and response style to asthma existed in the patients enrolled in an Asthma Rehabilitation Group (ARG) and in a Control Group (CG). Forty consecutive asthmatics were randomly enrolled, all of whom were diagnosed, treated and followed-up according to the International Guidelines. Both groups underwent a psychological assessment at baseline and after one year. A battery of questionnaires was used to obtain data relating to baseline characteristics (anxiety, depression, psychophysiological disorders), emotional reactions to asthma attacks (panic-fear, etc,) and cognitive variables (external control, psychological stigma, internal beliefs, external chance, etc.) involved in the perceived illness. In addition, the Asthma Rehabilitation Group patients underwent an educational programme and a cognitive-behavioural intervention. In both groups, a reduction of anxiety and depression scores was observed, as well as a significant improvement of the medical parameters evaluated. Only the Asthma Rehabilitation Group reported lower scores on the Psychophysiological Questionnaire and on the External Control Subscale after 1 year. The Control Group reported higher score on the External Chance Scale. The data of our study seem to confirm the effectiveness of psychological intervention on the cognitive skills involved in the perception and management of asthma. Larger scale studies on this topic are suggested.
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Affiliation(s)
- M Sommaruga
- Salvatore Maugeri Foundation, Care and Research Institute, Rehabilitation Medical Centre of Tradate (VA), Italy
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Amadori M, Archetti IL, Berneri C, Lodetti E, Salvalai M, Cordioli P, Callegari S. Human lymphoblastoid interferon as vaccine adjuvant in cattle. J BIOL REG HOMEOS AG 1994; 8:9-14. [PMID: 7976493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Human lymphoblastoid interferon from Namalwa cells was purified for clinical use by ethanol fractionation, and used as adjuvant of an inactivated Bovid Herpesvirus 1 vaccine in calves. In agreement with other in vitro and in vivo models, low and high interferon doses were shown to increase and depress the specific antibody response, respectively. The low, effective interferon dose (100 International Units/kg) also reduced the variability of antibody titres after the first vaccine injection. This latter dose had apparently no influence on the regulatory T cell circuits, as opposed to the other doses under study.
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Affiliation(s)
- M Amadori
- Department of Vaccine Research and Development Instituto Zooprofilattico Sperimentale Lombardia ed Emilia, Brescia, Italy
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Pistarini C, Majani G, Callegari S, Viola L. Multiple learning tasks in patients with ideomotor apraxia. Riv Neurol 1991; 61:57-61. [PMID: 1887197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The Authors studied a group of patients with ideomotor apraxia (LBD+) to verify if these patients had some difficulties in multiple learning tasks in respect to non-apraxic patients and normal control subjects. All five groups were submitted to gesture learning task, motor skill learning task, supra-span (Corsi) learning task. The results indicate that learning difficulties were present in LBD+ patients, as demonstrated by their low performance in gesture sequence, motor skill and score of block-tapping supra-span task. This fact may be seen as a basic learning deficit and therefore linked to memory impairment. On the other hand, this could be tied to an aspecific more diffuse deterioration of attention if we consider that our apraxic patients had a greater cerebral lesion than non-apraxic patients.
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Affiliation(s)
- C Pistarini
- Istituto di Ricovero e Cura a Carattere Scientifico, Centro Medico di Riabilitazione di Montescano (PV)
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