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Jovanovic-Cupic S, Glisic S, Stanojevic M, Nozic D, Petrovic N, Mandusic V, Krajnovic M. The influence of host factors and sequence variability of the p7 region on the response to pegylated interferon/ribavirin therapy for chronic hepatitis C genotype 1b in patients from Serbia. Arch Virol 2016; 161:1189-98. [PMID: 26860912 DOI: 10.1007/s00705-016-2777-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2014] [Accepted: 01/27/2016] [Indexed: 12/31/2022]
Abstract
The goal of this study was to identify host and viral factors affecting the response to pegylated interferon/ribavirin (PEG-IFN/RBV) treatment in patients with chronic hepatitis C genotype 1b. Baseline characteristics of the patients and sequences within the p7 region were analyzed in pre-treatment serum samples from 53 individuals with chronic hepatitis C genotype 1b and related to the outcome of therapy. We found a significant correlation between age and response to therapy (p < 0.001). Furthermore, the pre-treatment viral load was closely associated with the stage of liver fibrosis (p < 0.001). The presence of fewer than 4 mutations and age above 40 were significantly associated with non-response (NR) (p < 0.001). Our findings may be useful for estimating the likelihood of achieving a sustained virologic response (SVR) in patients who are chronically infected with hepatitis C virus genotype 1b.
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Affiliation(s)
- Snezana Jovanovic-Cupic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia.
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Maja Stanojevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, 11000, Belgrade, Serbia
| | - Darko Nozic
- Clinics of Infectious and Tropical Diseases, Military Medical Academy, 11000, Belgrade, Serbia
| | - Nina Petrovic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Vesna Mandusic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
| | - Milena Krajnovic
- Laboratory for Radiobiology and Molecular Genetics, Institute of Nuclear Sciences, Vinca, University of Belgrade, P.O. Box 522, Belgrade, Serbia
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Veljkovic V, Glisic S, Muller CP, Scotch M, Branch DR, Perovic VR, Sencanski M, Veljkovic N, Colombatti A. In silico analysis suggests interaction between Ebola virus and the extracellular matrix. Front Microbiol 2015; 6:135. [PMID: 25745423 PMCID: PMC4333865 DOI: 10.3389/fmicb.2015.00135] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/05/2015] [Indexed: 11/13/2022] Open
Abstract
The worst Ebola virus (EV) outbreak in history has hit Liberia, Sierra Leone and Guinea hardest and the trend lines in this crisis are grave, and now represents a global public health threat concern. Limited therapeutic and/or prophylactic options are available for people suffering from Ebola virus disease (EVD) and further complicate the situation. Previous studies suggested that the EV glycoprotein (GP) is the main determinant causing structural damage of endothelial cells that triggers the hemorrhagic diathesis, but molecular mechanisms underlying this phenomenon remains elusive. Using the informational spectrum method (ISM), a virtual spectroscopy method for analysis of the protein-protein interactions, the interaction of GP with endothelial extracellular matrix (ECM) was investigated. Presented results of this in silico study suggest that Elastin Microfibril Interface Located Proteins (EMILINs) are involved in interaction between GP and ECM. This finding could contribute to a better understanding of EV/endothelium interaction and its role in pathogenesis, prevention and therapy of EVD.
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Affiliation(s)
- Veljko Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade Belgrade, Serbia
| | - Sanja Glisic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade Belgrade, Serbia
| | - Claude P Muller
- Luxembourg Institute of Health (former Centre de Recherche Public de la Santé)/Laboratoire National de Santé Luxembourg, Luxembourg
| | - Matthew Scotch
- Department of Biomedical Informatics, Arizona State University Scottsdale, AZ, USA ; Center for Environmental Security, Biodesign Institute and Security and Defense Systems Initiative, Arizona State University Tempe, AZ, USA
| | - Donald R Branch
- Canadian Blood Services, Center for Innovation Toronto, ON, Canada
| | - Vladimir R Perovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade Belgrade, Serbia
| | - Milan Sencanski
- Innovation Center of the Faculty of Chemistry, University of Belgrade Belgrade, Serbia
| | - Nevena Veljkovic
- Center for Multidisciplinary Research, Institute of Nuclear Sciences VINCA, University of Belgrade Belgrade, Serbia
| | - Alfonso Colombatti
- Divisione di Oncologia Sperimentale, Centro di Riferimento Oncologico CRO-IRCCS Aviano, Italy
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Graham DJ. A new bioinformatics approach to natural protein collections: permutation structure contrasts of viral and cellular systems. Protein J 2013; 32:275-87. [PMID: 23605224 DOI: 10.1007/s10930-013-9485-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Biological cells and viruses operate by different replication and symmetry paradigms. Cells are able to replicate independently and express little spatial symmetry; viruses require cells for replication while manifesting high symmetry. The author inquired whether different paradigms were reflected in the permutations of amino acid sequences. The hypothesis was that the permutation structure level and symmetry within viral protein collections exceed that of living cells. The rationale was that one symmetry aspect generally accompanies and promotes others in a system. The inquiry was readily answered given abundant sequence archives for proteins. The analysis of collections from diverse viral and cellular sources lends strong support. Additional insights into protein primary structure, the design of collections, and the role of information are provided as well.
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Affiliation(s)
- Daniel J Graham
- Department of Chemistry, Loyola University Chicago, 6525 North Sheridan Road, Chicago, IL 60626, USA.
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Information properties of naturally-occurring proteins: Fourier analysis and complexity phase plots. Protein J 2012; 31:550-63. [PMID: 22814572 DOI: 10.1007/s10930-012-9432-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
In previous work from this lab, the information in natural proteins was investigated with Ribonuclease A (RNase A) serving as the source. The signature traits were investigated at three structure levels: primary through tertiary. The present paper travels further by charting the primary structure information of about half a million molecules. This was feasible given abundant sequence archives for both living and viral systems. Notably, a method is presented for evaluating primary structure information, based on Fourier analysis and spectral complexity. Significantly, the results show certain complexity traits to be universal for living sources. Viruses, by contrast, encode protein collections which are case-specific and complexity-divergent. The results have ramifications for discriminating collections on the basis of sequence information. This discrimination offers new strategies for selecting drug targets.
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