Immunoinformatics is a science that helps to create significant immunological information using bioinformatics softwares and applications. One of the most important applications of immunoinformatics is the prediction of a variety of specific epitopes for B cell recognition and T cell through MHC class I and II molecules. This method reduces costs and time compared to laboratory tests. In this state-of-the-art review, we review about 50 papers to find the latest and most used immunoinformatic tools as well as their applications for predicting the viral, bacterial and tumoral structural and linear epitopes of B and T cells. In the clinic, the main application of prediction of epitopes is for designing peptide-based vaccines. Peptide-based vaccines are a considerably potential alternative to low-cost vaccines that may reduce the risks related to the production of common vaccines.
Zaire ebolavirus, a member of family Filoviridae is the cause of hemorrhagic fever. Due to lack of appropriate antiviral or vaccine, this disease is very lethal. In this study, we tried to find epitopes for superficial glycoprotein and nucleoprotein of Zaire ebolavirus (that have high antigenicity for MHC I, II and B cells) by using in silico methods and immunoinformatics approach. By using CTLPred, SYFPEITHI and ProPred web applications for MHC class I and SYFPEITHI and ProPred1 web applications for MHC class II, we had been able to find epitopes (peptides) that have the highest score. Also ElliPro, IgPred and DiscoTope web tools had been performed to predict B cells conformational epitopes. Linear epitope prediction for B cell was performed with six methods from IEDB. All of the results that including candidate epitopes for T cells and B cells were reported. It was expected that these peptides could be stimulated immune response and used for designing the multipeptide vaccine against ZEV but these results should be reliable with experimental analysis.
SummaryThis study was conducted to determine the prevalence of Clostridium difficile in raw milk in Iran. From January to August 2013, a total of 430 raw milk samples from bovine (n=135), ovine (n=100), caprine (n=80), buffalo (n=49) and camel (n=66) were purchased from randomly selected from 111 dairy farm in Iran and were evaluated for the presence of C. difficile. In this study, only 2 of 135 bovine milk samples (1.43%) were contaminated with C. difficile. One of the two C. difficile strains was positive for tcdA and tcdB toxin genes that was classified as ribotype 078. Susceptibilities of isolates were determined for 11 antimicrobial drugs using the disk diffusion assay. None of the isolates was resistant to vancomycin, metronidazole, chloramphenicol and tetracycline. To our knowledge, this study is the first report of direct identification of C. difficile in bulk milk samples from dairy herds in Iran and the first report of direct identification of C. difficile in bulk milk samples from dairy bovine herds.
Keywords: Clostridium difficile, Raw milk, Camel, Buffalo, Bovine, Antimicrobial resistance
İran'da Sığır, Koyun, Keçi, Deve ve Manda Çiğ SütlerindeClostridium difficile'nin Tespiti
ÖzetBu çalışma İran'da çiğ sütlerde Clostridium difficile'nin prevalansını belirlemek amacıyla yapılmıştır. Çalışmada, rastgele seçilmiş 111 süt çiftliğinden toplanmış sığır (n=135), koyun (n=100), keçi (n=80), manda (n=49) ve deve (n=66) toplam 430 çiğ süt örneği C. difficile'nin varlığını ortaya koymak maksadıyla incelendi. Çalışmada, sığır süt örneklerinden 135'inden sadece 2'sinde (1.43%) C. difficile kontaminasyonu tespit edildi. İki C. difficile suşundan birisi ribotip 078 olarak sınıflandırılan tcdA ve tcdB toksin genine pozitiflik gösterdi. Disk difüzyon testi kullanılarak 11 antimikrobial ilaca karşı izolatların hassasiyetlikleri belirlendi. İzolatların hiçbiri vankomisin, metronidazol, kloramfenikol ve tetrasikline karşı dayanıklı değildi. Bilgimiz dahilinde, bu çalışma İran'da sütçü sürülerden ve sığırlardan elde edilen ham süt örneklerinde C. difficile'nin direkt olarak tespit edildiği ilk çalışmadır.
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