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  1. Article ; Online: Prediction of promiscuous epitopes in ORF2 of Hepatitis E virus: an

    Samavia, Noor / Fahed, Parvaiz / Yasir, Waheed / Tasneem, Anwar / Syeda, Nasreen

    African health sciences

    2023  Volume 22, Issue 3, Page(s) 626–639

    Abstract: Background: Vaccine development against emerging infections is essentially important for saving people from increasing viral infections. In developing countries, Hepatitis E (HEV) is a common infection affecting millions of people worldwide. Based on In- ...

    Abstract Background: Vaccine development against emerging infections is essentially important for saving people from increasing viral infections. In developing countries, Hepatitis E (HEV) is a common infection affecting millions of people worldwide. Based on In-silico analysis, different approaches have been targeted.
    Objectives: Rationale of this study is to design an epitope-based vaccine candidates with the help of immunoinformatics that can predict promiscuous B-cell and T-cell epitopes of the most antigenic HEV-ORF2 capsid protein.
    Materials & methods: This study suggests potential T-cell and B-cell epitopes of the highly antigenic HEV ORF2 capsid protein while using various In-silico tools such as NCBI-BLAST, Expassy, CLC workbench, Ellipro and Discotope.
    Results: Potential antigenic and immunogenic CD8+ T-cell epitopes were predicted from the global consensus sequence of ORF2-HEV. Furthermore, twenty-two linear B-cell epitopes were predicted. Among these, "SLGAGPV" at position 587-593 and "LEFRNLTPGNTNTRVSRYSS" at position 306-325 were most antigenic with antigenicity score 1.4206 and 1.3600 respectively. Discontinuous B-cell epitopes were found by three-dimensional capsid protein structure. Epitopes predicted in this study reveal high antigenicity and promiscuity for HLA classes.
    Conclusion: Collectively, our data suggests promiscuous epitopes that can potentially acts as new candidates for the design of HEV peptide vaccine.
    MeSH term(s) Humans ; Capsid Proteins ; Epitopes, B-Lymphocyte/chemistry ; Epitopes, T-Lymphocyte ; Hepatitis E ; Hepatitis E virus
    Chemical Substances Capsid Proteins ; Epitopes, B-Lymphocyte ; Epitopes, T-Lymphocyte ; ORF2 protein, Hepatitis E virus
    Language English
    Publishing date 2023-02-28
    Publishing country Uganda
    Document type Journal Article
    ZDB-ID 2240308-5
    ISSN 1729-0503 ; 1680-6905
    ISSN (online) 1729-0503
    ISSN 1680-6905
    DOI 10.4314/ahs.v22i3.67
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  2. Article ; Online: Green synthesised AuNps using Ajuga Bracteosa extract and AuNps-Free supernatant exhibited equivalent antibacterial and anticancerous efficacies.

    Raja, Sadaf Azad / Andleeb, Saiqa / Javed, Aneela / Sabahat, Sana / Parvaiz, Fahed / Mureed, Hafsah / Ahmad, Sohaib / Naz, Falak

    PloS one

    2023  Volume 18, Issue 8, Page(s) e0282485

    Abstract: The current study is designed to synthesize gold nanoparticles using Ajuga bracteosa extract, which is a highly known medicinal herb found in the northern Himalayas. The synthesized gold nanoparticles were initially characterized by UV-Vis ... ...

    Abstract The current study is designed to synthesize gold nanoparticles using Ajuga bracteosa extract, which is a highly known medicinal herb found in the northern Himalayas. The synthesized gold nanoparticles were initially characterized by UV-Vis spectrophotometer, SEM, FTIR, pXRD, and, GC-MS. Antibacterial efficacy of A. bracteosa extract, AuNps, and AuNps-free supernatant activity was checked against highly pathogenic clinical isolates of Escherichia coli, Staphylococcus aureus, and Pseudomonas aeruginosa via agar well diffusion method, assuming that supernatant might have active compounds. The Nps-free supernatant showed the maximum antibacterial activity against E. coli (20.8±0.3 mm), Staphylococcus aureus (16.5±0.5), and Pseudomonas aeruginosa (13±0.6). While green synthesized AuNps showed effective antibacterial activity (Escherichia coli (16.4±0.3mm), Staphylococcus aureus (15.05±0.5mm), and Pseudomonas aeruginosa (11.07±0.6mm)) which was high compared to A. bracteosa extract. Anticancer activity was assessed by MTT assay on U87 and HEK293 cell lines. Aj-AuNps have an antigrowth effect on both the cell lines however Aj-AuNps-free supernatant which was also evaluated along with the Aj-AuNps, showed high toxicity toward HEK293 cell line compared to U87. Further, the GC-MS analysis of supernatant showed the presence of resultant toxic compounds after the reduction of gold salt, which include Trichloromethane, Propanoic acid, 2-methyl-, methyl ester, Methyl isovalerate, Pentanoic acid, 2-hydroxy-4-methyl-, Benzene-propanoic acid, and alpha-hydroxy. Based on the observation small molecular weight ligands of Ajuga bracteosa were analyzed in-silico for their binding efficacy towards selected membrane proteins of our target pathogens. RMSD is also calculated for the best docked protein ligand pose. The results revealed that among all listed ligands, Ergosterol and Decacetylajugrin IV have high virtuous binding affinities towards the membrane proteins of targeted pathogens. The current findings revealed that the Aj-AuNps are good antibacterial as well as anticancerous agents while the Nps-free supernatant is also exceedingly effective against resistant pathogens and cancer cell lines.
    MeSH term(s) Humans ; Ajuga/chemistry ; Propionates ; Gold/chemistry ; Escherichia coli ; Ligands ; HEK293 Cells ; Metal Nanoparticles/chemistry ; Anti-Bacterial Agents/pharmacology ; Anti-Bacterial Agents/chemistry ; Staphylococcus aureus ; Plant Extracts/pharmacology ; Plant Extracts/chemistry ; Microbial Sensitivity Tests ; Green Chemistry Technology/methods
    Chemical Substances propionic acid (JHU490RVYR) ; Propionates ; Gold (7440-57-5) ; Ligands ; Anti-Bacterial Agents ; Plant Extracts
    Language English
    Publishing date 2023-08-07
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0282485
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  3. Article ; Online: Multifaceted role of cancer educated platelets in survival of cancer cells.

    Asghar, Sidra / Parvaiz, Fahed / Manzoor, Sobia

    Thrombosis research

    2019  Volume 177, Page(s) 42–50

    Abstract: Platelets, the derivatives of megakaryocytes, pose dynamic biological functions such as homeostasis and wound healing. The mechanisms involved in these processes are utilized by cancerous cells for proliferation and metastasis. Platelets through their ... ...

    Abstract Platelets, the derivatives of megakaryocytes, pose dynamic biological functions such as homeostasis and wound healing. The mechanisms involved in these processes are utilized by cancerous cells for proliferation and metastasis. Platelets through their activation establish an aggregate termed as Tumor cell induced platelet aggregation (TCIPA) that aids in establishing a niche for the primary tumor at secondary site while recruiting granulocytes and monocytes. The study of these close interactions between the tumor and the platelets can be exploited as biomarkers in liquid biopsy for early cancer detection, thereby increasing the life expectancy of cancer patients.
    MeSH term(s) Animals ; Blood Platelets/cytology ; Blood Platelets/pathology ; Cell Communication ; Humans ; Liquid Biopsy ; Neoplasm Metastasis/pathology ; Neoplasms/complications ; Neoplasms/diagnosis ; Neoplasms/pathology ; Neovascularization, Pathologic/complications ; Neovascularization, Pathologic/pathology ; Platelet Aggregation ; Thrombosis/complications ; Thrombosis/pathology
    Language English
    Publishing date 2019-02-26
    Publishing country United States
    Document type Journal Article ; Review
    ZDB-ID 121852-9
    ISSN 1879-2472 ; 0049-3848
    ISSN (online) 1879-2472
    ISSN 0049-3848
    DOI 10.1016/j.thromres.2019.02.026
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  4. Article ; Online: Computational design of experimentally validated multi-epitopes vaccine against hepatitis E virus

    Tasneem Anwar / Saba Ismail / Fahed Parvaiz / Sumra Wajid Abbasi / Fahad A. Al-Abbasi / Amira M. Alghamdi / Khalid Al-Regaiey / Asad Ul-Haq / Imdad Kaleem / Shahid Bashir / Yasir Waheed

    PLoS ONE, Vol 18, Iss

    An immunological approach

    2023  Volume 12

    Keywords Medicine ; R ; Science ; Q
    Language English
    Publishing date 2023-01-01T00:00:00Z
    Publisher Public Library of Science (PLoS)
    Document type Article ; Online
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  5. Article ; Online: Computational design of experimentally validated multi-epitopes vaccine against hepatitis E virus: An immunological approach.

    Anwar, Tasneem / Ismail, Saba / Parvaiz, Fahed / Abbasi, Sumra Wajid / A Al-Abbasi, Fahad / M Alghamdi, Amira / Al-Regaiey, Khalid / Ul-Haq, Asad / Kaleem, Imdad / Bashir, Shahid / Waheed, Yasir

    PloS one

    2023  Volume 18, Issue 12, Page(s) e0294663

    Abstract: Hepatitis E virus (HEV) is one of the leading acute liver infections triggered by viral hepatitis. Patients infected with HEV usually recover and the annual death rate is negligible. Currently, there is no HEV licensed vaccine available globally. This ... ...

    Abstract Hepatitis E virus (HEV) is one of the leading acute liver infections triggered by viral hepatitis. Patients infected with HEV usually recover and the annual death rate is negligible. Currently, there is no HEV licensed vaccine available globally. This study was carried out to design a multi-epitope HEV peptide-based vaccine by retrieving already experimentally validated epitopes from ViPR database leading to epitope prioritization. Epitopes selected as potential vaccine candidates were non-allergen, immunogenic, soluble, non-toxic and IFN gamma positive. The epitopes were linked together by AAY linkers and the linker EAAAK was used to join adjuvant with epitopes. Toll-like receptor (TLR)-4 agonist was used as an adjuvant to boost efficacy of the vaccine. Furthermore, codon optimization followed by disulfide engineering was performed to analyse the designed vaccine's structural stability. Computational modeling of the immune simulation was done to examine the immune response against the vaccine. The designed vaccine construct was docked with TLR-3 receptor for their interactions and then subjected to molecular dynamic simulations. The vaccine model was examined computationally towards the capability of inducing immune responses which showed the induction of both humoral and cell mediated immunity. Taken together, our study suggests an In-silico designed HEV based multi-epitope peptide-based vaccine (MEPV) that needs to be examined in the wet lab-based data that can help to develop a potential vaccine against HEV.
    MeSH term(s) Humans ; Hepatitis E virus ; Epitopes, T-Lymphocyte ; Vaccines, Subunit ; Molecular Dynamics Simulation ; Peptides ; Computational Biology ; Molecular Docking Simulation ; Epitopes, B-Lymphocyte
    Chemical Substances Epitopes, T-Lymphocyte ; Vaccines, Subunit ; Peptides ; Epitopes, B-Lymphocyte
    Language English
    Publishing date 2023-12-14
    Publishing country United States
    Document type Journal Article
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0294663
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  6. Article ; Online: Bacterial vaginosis: An insight into the prevalence, alternative treatments regimen and it's associated resistance patterns.

    Javed, Ayesha / Parvaiz, Fahed / Manzoor, Sobia

    Microbial pathogenesis

    2018  Volume 127, Page(s) 21–30

    Abstract: Bacterial Vaginosis (BV) is a complex polymicrobial infection of vagina that shifts the paradigms of vaginal flora from lactobacilli to opportunistic pathogens. BV is catagorized by greyish white discharge, pH greater than 4.5. It results in the preterm ... ...

    Abstract Bacterial Vaginosis (BV) is a complex polymicrobial infection of vagina that shifts the paradigms of vaginal flora from lactobacilli to opportunistic pathogens. BV is catagorized by greyish white discharge, pH greater than 4.5. It results in the preterm labor, abortion, pelvic inflammatory disorders, post cesarean infections. BV is associated with Sexually Transmitted Diseases (STDs) or immune deficiency disorders like Human Immunodeficiency Virus, Human Papilloma Virus, Herpes Simplex Virus 1 and 2, and Neisseria gonorrhoeae. The prevalence rate is about 21.2 million (29.2%) worldwide. BV is more frequent in black females as compared to white females, independent of geographical distribution. Globally, BV is treated with the current recommended antibiotic therapy including Metronidazole and Clindamycin. The recurrence rates are 76% and occur within 06 months of treatment due to antibiotic resistance against pathogenic bacteria and their biofilms. The antibiotic resistance is a global health issue which directs the attentions towards other treatments. One of these is the treatment of sex partners, thus helping to stop the recurrence rates in females. However, this method does not show any positive results. Probiotic therapy is an incorporation of Lactobacilli orally or intravaginally for the recolonization of healthy microbes. This therapy has exhibited promising results but some studies revealed that Probiotic therapy does not control the recurrence rate. The other methods are in trials period and none of them are used clinically or commercially available for the treatment. The thermoplastic polyurethane (TPU) intravaginal rings contain lactic acid and metronidazole showed promising results in trials of BV treatment. The vaginal acidifiers are used as an alternative method to maintain the vaginal pH but the process of douching is a major limitation. The activated charcoal is used to treat BV patients in clinical trials showed decrease in the pH with only 3.1% loss of lactobacilli. Phage therapy is a reemerging field to overcome the bacterial resistance. They are host specific and easier to handle. They can be used naturally, synthetically; phage cocktails and phage-antibiotics combination can be used. Phages show auspicious results for the treatment of bacterial infections as compared to antibiotics as they also treat biofilms. This is one of the promising therapy in future to treat infections with no side effects. Phage therapy can be used in pharmaceuticals according to Food and Drug Administration (FDA) guidelines. Taken together, it is suggested that large funding is required by pharmaceutical sector or government for further investigation of bacteriophages to be used against BV pathogenesis.
    MeSH term(s) Anti-Infective Agents/pharmacology ; Anti-Infective Agents/therapeutic use ; Bacteria/drug effects ; Bacteria/isolation & purification ; Biological Therapy/methods ; Drug Resistance, Bacterial ; Drug Therapy/methods ; Female ; Global Health ; Humans ; Prevalence ; Recurrence ; Vaginosis, Bacterial/epidemiology ; Vaginosis, Bacterial/microbiology ; Vaginosis, Bacterial/pathology ; Vaginosis, Bacterial/therapy
    Chemical Substances Anti-Infective Agents
    Language English
    Publishing date 2018-11-28
    Publishing country England
    Document type Journal Article ; Review
    ZDB-ID 632772-2
    ISSN 1096-1208 ; 0882-4010
    ISSN (online) 1096-1208
    ISSN 0882-4010
    DOI 10.1016/j.micpath.2018.11.046
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  7. Article: Genetic diversity of cucumber green mottle mosaic virus (CGMMV) infecting cucurbits.

    Asad, Zohaib / Ashfaq, Muhammad / Iqbal, Naeem / Parvaiz, Fahed / Mehmood, Mirza Abid / Hameed, Akhtar / Malik, Amir Humayun / Kayani, Samah Bashir / Al-Kahtani, Mohamed A / Ahmad, Zubair

    Saudi journal of biological sciences

    2022  Volume 29, Issue 5, Page(s) 3577–3585

    Abstract: Cucumber green mottle mosaic ... ...

    Abstract Cucumber green mottle mosaic virus
    Language English
    Publishing date 2022-02-19
    Publishing country Saudi Arabia
    Document type Journal Article
    ZDB-ID 2515206-3
    ISSN 2213-7106 ; 1319-562X
    ISSN (online) 2213-7106
    ISSN 1319-562X
    DOI 10.1016/j.sjbs.2022.02.027
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  8. Article: In-Vitro Transcription analysis of NS5A from HCV-3a circulating in Pakistani patients with chronic hepatitis C and their differential response to antiviral therapy.

    Bhatti, Shameem / Manzoor, Sobia / Parvaiz, Fahed / Ashraf, Javed / Javed, Farakh

    Pakistan journal of medical sciences

    2017  Volume 33, Issue 5, Page(s) 1236–1241

    Abstract: Objective: Mutations in HCV nonstructural protein 5A (NS5A) play a vital role in virus resistance. The aim of this study was to develop a correlation between NS5A mutations (genotype 3a) and virological response towards interferon alpha (IFN-α) plus ... ...

    Abstract Objective: Mutations in HCV nonstructural protein 5A (NS5A) play a vital role in virus resistance. The aim of this study was to develop a correlation between NS5A mutations (genotype 3a) and virological response towards interferon alpha (IFN-α) plus ribavirin therapy.
    Methods: In this study, which was conducted from 09-02-2013 to 25-11-2015 in the rural area of Province Sindh - Pakistan, total patients' responses to peg-IFN therapy were investigated. Patients were given peg-IFN therapy for 24 to 48 weeks and categorized as sustained virologic responders (SVR) or non-responders (NR) to HCV infection. HCV NS5A region (2215-2335) of genotype 3a was identified in both responders and non-responders.
    Results: Twenty-four NR with 24 SVR isolates showed significant mutations within the nonstructural protein 5A region in HCV genotype 3a. The New Zealand (NZL1) (GenBank D17763) differences were observed by using gene. The ISDR mutations for nonstructural protein 5A in non-responders have been reported as a possible explanation of HCV interferon resistance.
    Conclusion: Based on these results, it is suggested that decreased SVR is caused by the increased mutations in nonstructural protein 5A sequences. When the sequence outside the Protein kinases R binding domain (PKRBD) (2281-2335) was examined, significant differentiations were observed among the SVR and NR classes at few amino acid strains.
    Language English
    Publishing date 2017-11-02
    Publishing country Pakistan
    Document type Journal Article
    ZDB-ID 2032827-8
    ISSN 1681-715X ; 1682-024X ; 1017-4699
    ISSN (online) 1681-715X
    ISSN 1682-024X ; 1017-4699
    DOI 10.12669/pjms.335.12973
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    Zs.A 3948: Show issues Location:
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  9. Article ; Online: Genetic diversity of cucumber green mottle mosaic virus (CGMMV) infecting cucurbits

    Zohaib Asad / Muhammad Ashfaq / Naeem Iqbal / Fahed Parvaiz / Mirza Abid Mehmood / Akhtar Hameed / Amir Humayun Malik / Samah Bashir Kayani / Mohamed A. Al-Kahtani / Zubair Ahmad

    Saudi Journal of Biological Sciences, Vol 29, Iss 5, Pp 3577-

    2022  Volume 3585

    Abstract: Cucumber green mottle mosaic virus (CGMMV), a well-known Tobamovirus, infects cucurbits across the globe. To determine its current status, molecular characterization, genetic recombination, gene flow and selection pressure, 10 districts from Punjab ... ...

    Abstract Cucumber green mottle mosaic virus (CGMMV), a well-known Tobamovirus, infects cucurbits across the globe. To determine its current status, molecular characterization, genetic recombination, gene flow and selection pressure, 10 districts from Punjab province of Pakistan were surveyed and a total of 2561 cucurbits samples were collected during 2019–2020. These samples were subjected to virus-specific double antibody sandwich-enzyme linked immunosorbent assay (DAS-ELISA) for the detection of CGMMV. The results revealed that viral disease was prevalent in all surveyed districts of Punjab with an overall 25.69% disease incidence. ELISA positive samples were further confirmed through RT-PCR and sequencing of coat protein (CP) cistron. Sequence analysis showed that the present studied CGMMV isolates have 96–99.5% nucleotide and 94.40–99.50% amino acid identities with those already available in GenBank. Phylogenetic analysis also revealed that understudied isolates were closely related with South Korean (AB369274) and Japanese (V01551) isolates and clustered in a separate clad. Sequence polymorphisms were observed in 663 bp of sequence within 31 CGMMV isolates covering complete CP gene. Total number of sites were 662, of which 610 and 52 sites were monomorphic and polymorphic (segregating), respectively. Of these polymorphic, 24 were singleton variable and 28 were parsimony informative. Overall nucleotide diversity (π) in all the understudied 31 isolates was 0.00010 while a total of 1 InDel event was observed and InDel Diversity (k) was 0.065. Haplotype diversity analysis revealed that there was a total 29 haplotypes with haplotype diversity (Hd) of 0.993458 in all the 31 isolates which provide evidence of less diversity among Pakistani isolates. The statistical analysis revealed the values 2.568, 5.31304 and 4.86698 of Tajima's D, Fu, & Li’s F* and D*, respectively, which witnessed the population of CGMMV was under balanced selection pressure.
    Keywords Coat protein ; CGGMV ; Selection pressure ; Recombination ; Biology (General) ; QH301-705.5
    Subject code 580
    Language English
    Publishing date 2022-05-01T00:00:00Z
    Publisher Elsevier
    Document type Article ; Online
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  10. Article ; Online: Predictive potential of IL-18 -607 and osteopontin -442 polymorphism in interferon-based therapy of HCV infection in the Pakistani population.

    Imran, Muhammad / Manzoor, Sobia / Parvaiz, Fahed

    Viral immunology

    2014  Volume 27, Issue 8, Page(s) 404–411

    Abstract: The adaptive immune system plays an important role in response to interferon plus ribavirin treatment of hepatitis C virus (HCV) infection. Cytokines play a significant role in the adaptive immune system. The production of cytokines may be regulated by ... ...

    Abstract The adaptive immune system plays an important role in response to interferon plus ribavirin treatment of hepatitis C virus (HCV) infection. Cytokines play a significant role in the adaptive immune system. The production of cytokines may be regulated by single nucleotide polymorphisms (SNPs). This study was designed to examine the correlation of some important SNPs of cytokines with interferon plus ribavirin treatment of HCV infection in the Pakistani population. We followed 140 chronic HCV-infected patients in our study. All of these patients had completed their planned course of interferon plus ribavirin treatment. We also considered 120 healthy subjects as controls. The detection of interleukin-18 (IL-18) SNPs was performed by tetra-primers amplification-refectory mutation system polymerase chain reaction, while for genotyping of osteopontin (OPN), transforming growth factor beta (TGFβ), and N-acetylgalactosaminyltransferase 8 (GALNT8) SNPs, allele-specific polymerase chain reaction was performed. The distribution of the IL-18 -607AA genotype varied significantly between healthy control and patient groups. Its distribution was significantly high in healthy subjects than HCV patients (p = 0.031), signifying its potential involvement in the natural clearance of HCV infection. The occurrence of the -607AA genotype of IL-18 was also significantly higher in the sustained virological group (SVR) than in the nonresponder (NR) group (p = 0.046), highlighting its protective involvement in the treatment outcome of chronic HCV infection. The frequency of the OPN -442TT genotype was higher in the SVR group than in the NR group (p = 0.034), indicating a significant possible role of this genotype in therapy for HCV infection. No important association was found between TGFβ and GALNT8 genotypes and the natural clearance and treatment response of HCV infection. IL-18 -607AA and OPN -442TT genotypes can be used as positive predictive markers of interferon plus ribavirin treatment of HCV infection in the Pakistani population.
    MeSH term(s) Adolescent ; Adult ; Female ; Genotype ; Genotyping Techniques ; Hepatitis C, Chronic/drug therapy ; Humans ; Interferon-alpha/therapeutic use ; Interleukin-18/genetics ; Male ; Middle Aged ; Osteopontin/genetics ; Pakistan ; Polymorphism, Single Nucleotide ; Ribavirin/therapeutic use ; Treatment Outcome ; Young Adult
    Chemical Substances IL18 protein, human ; Interferon-alpha ; Interleukin-18 ; Osteopontin (106441-73-0) ; Ribavirin (49717AWG6K)
    Language English
    Publishing date 2014-09-08
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 639075-4
    ISSN 1557-8976 ; 0882-8245
    ISSN (online) 1557-8976
    ISSN 0882-8245
    DOI 10.1089/vim.2014.0044
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