There are several outer membrane proteins (OMPs) of H. pylori which attach to corresponding receptors on the host gastric epithelium. Exposed AMINO ACID SEQUENCES of outer membrane proteins have important role in interaction with stomach epithelial cell and developing of gastritis, peptic ulcer and gastric adenocarcinoma. Therefore, detection of these SEQUENCES is very useful for locating of corresponding receptors on the surface of gastric epithelial cell. We have systematically analyzed exposed AMINO ACID SEQUENCES for detection of adhesion motifs and possible receptors. Secondary and tertiary structures of membrane proteins including OipA, BabA, BabB, AlpA, AlpB, vacA, SabA and SabB predicted by PHD and GOR 4 servers. The presence and location of signal peptide cleavage sites in AMINO ACIDs SEQUENCES were predicted by SignalP 4.1 Server. PHYRE server was applied for finding of homology modeling. VADAR server was applied for prediction of accessible surface area AMINO ACIDs among SEQUENCES of external loops. Based on our analysis, exposed AMINO ACID SEQUENCES which detected among various outer membrane proteins are including oipa, BabA, BabB, Alpa, AlpB, VacA, SabA and SabB with 6, 4, 2, 5, 4, 7, 5 and 6 SEQUENCES of AMINO ACIDs, respectively. Structural similarity between proteins is a very good predictor of functional similarity. Higher similarity was found between two pair of AlpA - AlpB and SabA - SabB proteins. This structural similarity may be helpful to design new drugs or vaccines with simultaneous interaction against such target sites. Taken together, based on our findings detection of these SEQUENCES will be very useful for specific targeting of cell surface receptors.

The major histocompatibility complex genes (mhc) encode MHC I and II molecules which present peptide fragments to Tcells. Therefore these polymorphic molecules critically influence susceptibility to infectious diseases. At present study potential relationship between AMINO ACID SEQUENCES in the antigen binding groove of different BoLA-DRB3 alleles and susceptibility or resistance to calf diarrhea was investigated. Twelve different DRB3 alleles were found among 171 calves (84 diarrheic and 87 healthy) analyesd by PCR-RFLP method. AMINO ACID SEQUENCES of the encoded peptide binding region were compared. 26 polymorphic positions were detected in this region. A significant association (p< 0.05) was shown between occurrence of diarrhea and the presence of glutamic ACID and tyrosine in pocket 4 and valine, glutamine and leucine in pocket 9 of peptide binding region. Thus it can be concluded that pockets 4 and 9 of the BoLA-DRB3 molecule would be involved in conferring susceptibility of calf to diarrhea.

Introduction: Influenza is a contagious acute viral disease of the respiratory tract that causes fever, headache, muscle aches and cough. One of the unique features of influenza virus is antigenic variation in viral protein neuraminidase (NA) which causes emergence of new virus variants. NA is responsible for the release and spread of progeny virions. Due to the continuous changes of NA genes, vaccine strains must be re-selected annually.Methods: Complete NA AMINO ACID SEQUENCES of 97 strains circulating from 2006 to 2013 in Iran were downloaded from NCBI. The SEQUENCES were edited and classified by the year of isolation and their diversity and important changes as well as changes in the predicted ligand binding sites and their resistance to anti-NA drugs, were analyzed. Bioinformatics software such as MEGA6.0, BioEdit, DNAsisMAX and DNAstar were used for the sequence alignments and phylogenetic analyses. Web-based analysis such as SWISS-MODEL, Phyre2 and 3DLigandSite were used for evaluation of the second and third protein structures and prediction of the ligand binding sites.Results: The results showed that 2009 could be considered as an important transition year which caused to classify the isolates into two different distinct groups. This shows the importance of changes made during possible mutations in the genomic structure of the virus which have made it antigenic ally different from the previous years. Anti-NA drug resistance was observed in 2009. This pandemic strain has become dominant in the following years and is used as a standard vaccine strain from 2010 onwards.Conclusion: The results obtained in this study can aid in better understanding of the antigenic evolution of H1N1 influenza viruses and can potentially accelerate the selection of the vaccine strains.