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Brazilian Journal of Medical and Biological Research (0100879X)37(5)pp. 675-681
We describe the impact of subtype differences on the seroreactivity of linear antigenic epitopes in envelope glycoprotein of HIV-1 isolates from different geographical locations. By computer analysis, we predicted potential antigenic sites of envelope glycoprotein (gp120 and gp41) of this virus. For this purpose, after fetching sequences of proteins of interest from data banks, values of hydrophilicity, flexibility, accessibility, inverted hydrophobicity, and secondary structure were considered. We identified several potential antigenic epitopes in a B subtype strain of envelope glycoprotein of HIV-1 (IIIB). Solid-phase peptide synthesis methods of Merrifield and Fmoc chemistry were used for synthesizing peptides. These synthetic peptides corresponded mainly to the C2, V3 and CD4 binding sites of gp120 and some parts of the ectodomain of gp41. The reactivity of these peptides was tested by ELISA against different HIV-1-positive sera from different locations in India. For two of these predicted epitopes, the corresponding Indian consensus sequences (LAIERYLKQQLLGWG and DIIGDIRQAHCNISEDKWNET) (subtype C) were also synthesized and their reactivity was tested by ELISA. These peptides also distinguished HIV-1-positive sera of Indians with C subtype infections from sera from HIV-negative subjects.
This study was conducted to determine the location of DNA segment with homology to the rat conserved genomic DNA in human chromosomes. The labeled rat genomic DNA was hybridized with normal human (male) metaphases. The study of 74 metaphases after fluorescence in situ hybridization showed 371 twin-spot signals on human chromosomes. Statistical analysis indicated that the specific accumulation of signals on 1q22-qter, 2p2, 3p21-p23, 4q3, 6q2, 8p12-pter, 11p12-pter, 11q12-qter, 12q2, 13p, 15p, 16q2, 21q12-qter, Yq1-qter, and Xq2 was not random. Results of stepwise multiple linear regressions indicated that number of mapped oncogenes (Beta = 1.092; t = 7.552; P<0.001) and density of mapped oncogenes on chromosomes (Beta = -0.832; t = -5.751; P<0.001) have significant effects on number of double-spots on human chromosomes. These data reflects the evolutionary conservation between rat DNA and human DNA at the above-mentioned bands.
Saudi Medical Journal (16583175)27(8)pp. 1121-1124
Objective: Human T-cell leukemia virus type 1 (HTLV-1) is an enveloped retrovirus, which is associated with a T-cell malignancy known as adult T-cell leukemia (ATL). Variation in the HTLV-1 envelope nucleotide sequence has been extensively documented and has been used to classify HTLV-1 isolates into different subtypes. The virus occurs in at least 3 subtypes, which have been named A, B, and C. We conducted this study to compare the antigenic proprieties of the Iranian isolate of HTLV-1 with the homologous region of different subtypes of the virus. Methods: This study took place in the Department of Biology, College of Sciences, Shiraz University, Iran in 2005. The predicted antigenic sites and secondary structure of the envelope glycoprotein of HTLV-1, present in Iran, have been compared with the antigenic sites and secondary structure of the homologous domains in subtypes A, B, C of the virus. To predict the epitopes of glycoproteins, 21 different scales were used. Results: The number of helices in the Iranian isolate was equal to the number of these regions in all 3 subtypes, but the number of β-sheets was more than other viruses. One potential glycosylation site, on all these studied envelope glycoproteins, was predicted. Antigenic sites in the Iranian isolate were almost similar to subtype A of the virus and the Iranian isolate of HTLV-1 may be belongs to subtype A. Conclusion: Our results indicate the similarities and differences between the Iranian and other subtypes of HTLV-1. Antigenic sites represent potential candidates for use in a peptide vaccine against HTLV-1 glycoproteins and since most of the properties of a particular protein depend on its structural properties, this type of study can help in better understanding of HTLV-1 isolates present in Iran.
Nanoscale Research Letters (1556276X)2(1)pp. 24-27
Computer-aided design plays a fundamental role in both top-down and bottom-up nano-system fabrication. This paper presents a bottom-up nano-filter patterning process based on DNA self-assembly. In this study we designed a new method to construct fully designed nano-filters with the pores between 5 nm and 9 nm in diameter. Our calculations illustrated that by constructing such a nano-filter we would be able to separate many molecules.
Asian Pacific Journal of Cancer Prevention (15137368)8(4)pp. 602-606
HPV-16 is the HPV most often linked to cervical carcinoma. E6 of the HPV-16 which expressed early in cancer cells is a target for immune therapeutic methods. In the present study, after fetching the sequence of HPV-16 E6 (accession No: ABC48950) from NCBI databank, by using hydrophilicity, flexibility, accessibility, turns, exposed surface, polarity and antigenic propensity scales, B cell epitopes of the protein were predicted. In addition, MHCPred version 2.0 program was used to predict MHC Class I and Class II alleles. The sequences of the epitopes were also found out. According to this computer-based prediction the results from A0203 and DRB0101 reveal lower IC50 than other alleles. For A0203 allele, peptide with the best binding affinity was 25ELQTTIHDI33. For DRB0101 allele, the peptide was 39YCKQQLLRR47. Different structural features of the protein were also predicted. These features were including glycosylation, kinase C phosphorylation, Casein kinase II phosphorylation and N-myristylation sites, and disulfide bonding states. By using these computational scales and programs, 0 glycosylation, 3 kinase C phosphorylation, 2 casein kinase II phosphorylation and 1 Nmyristylation sites and 2 disulfide bonds were predicted. Development and approval of new vaccines are keys for control of cancer. Epitopes and structural features of proteins can be predicted and this information can help us in molecular and medical studies of viruses.
Saudi Medical Journal (16583175)28(10)pp. 1520-1524
Objectives: To study primer sequences (1060, 1247, 1254, 1281, 1283, and 1290) for random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR). Methods: Twenty-four clinical Serratia marcescens (S. marcescens) isolates were obtained over a 6-month period from April 2002 to September 2002 from hospitals in the Fars province of Iran. Six primers were used due to S. marcescens genome properties, and RAPD-PCR was carried out. The results were subjected to unweighted pair-group method analysis using NTSYSpc 2.02. The primers were blasted with the S. marcescens genome, and the primers efficiency was estimated. Results: The results of blast primers with S. marcescens genome sequence showed that primer 1283 had the highest homology and primer 1290 had the lowest homology. Comparing the resulted dendrograms showed that the pattern of the primers to separate isolates was closely related to their sequence homology with the genome and their amount of guanine and cytosine nucleotide content. Conclusions: There are clear differences in RAPD-PCR results when different primers are used, and it is recommended to consider genomic properties of an organism to design a primer for RAPD-PCR.
Asian Pacific Journal of Cancer Prevention (15137368)9(4)pp. 631-636
Human papillomaviruses (HPVs) are small DNA tumor viruses that replicate and assemble exclusively in the nucleus. Thus their proteins, including E6, must carry nuclear localization signals (NLSs) to enter the nucleus. To analyze and to predict the nuclear localization signals and several post translational modifications by bioinformatics analysis, we obtained 91 E6 protein sequences from available databases. To investigate the localization of these sequences, we used Hum-Ploc software. Homology and alignment of sequences were performed by Blast software and Multalin server respectively. Prediction of N-glycosylation and serine, threonine and tyrosine phosphorylation sites of HPV E6 protein sequences was accomplished with NetNGlyc and NetPhos software. Out of 91 types, the NLSs of 29 types were predicted by signal-3L and signal-CF software. We tried to predict the NLSs of remaining HPV E6 proteins according to the homology of the already predicted NLSs. However, because of considerable variation between E6 protein sequences, we could not classify the NLSs in monopartite or bipartite. According to the results, all NLSs of HPV E6 proteins could be assigned to 11 categories. NLSs of several HPV E6 protein sequences were also determined by experimental studies. Overall, different types of HPV E6 protein in same category show approximately similar pattern in post translational modifications such as N-glycosylation and phosphorylation. Some HPV "early"genes, such as E6, are known to act as oncogenes that promote tumor growth and malignant transformation. Thus more detailed recognition of nuclear localizing sequences and nucleocytoplasmic transport pathway can play a key role in prevention and treatment of HPV infection and related cancers. The results also show that bioinformatics technology can direct and simplify experimental studies.
Iranian Journal Of Fuzzy Systems (17350654)5(2)pp. 21-33
This paper considers the generation of some interpretable fuzzy rules for assigning an amino acid sequence into the appropriate protein superfamily. Since the main objective of this classifier is the interpretability of rules, we have used the distribution of amino acids in the sequences of proteins as features. These features are the occurrence probabilities of six exchange groups in the sequences. To generate the fuzzy rules, we have used some modified versions of a common approach. The generated rules are simple and understandable, especially for biologists. To evaluate our fuzzy classifiers, we have used four protein superfamilies from UniProt database. Experimental results show the comprehensibility of generated fuzzy rules with comparable classification accuracy.
Glutathione S-transferase is a family of multifunctional detoxification enzymes which are mainly cytosolic that detoxify natural and exogenous toxic compounds by conjugation with glutathione. Glutathione, an endogenous tripeptide, is important as either a reducing agent or a nucleophilic scavenger. This molecule alleviates the chemical toxicity in plants by reaction of glutathione S-transferase, and its conjugates can be transported to vacuole or apoplast. The plant soluble glutathione S-transferases grouped today into seven distinct Phi, Tau, Zeta, Theta, lambda, dehydroascorbate reductase, and tetrachlorohydroquinone dehalogenase classes. In this study, bioinformatics analysis of glutathione S-transferase gene in barley was carried out using Tau-class of barley glutathione S-transferase sequences in NCBI GenBank and isolated sequence. DNA extraction, primer design, PCR, electrophoresis, column purifica-tion, DNA sequencing and analysis by some software led to identify new sequences of Tau-class of glutathione S-transferase from barley, which is similar to Tau GST of the diploid wheat. Comparison of the deduced amino acid sequences of the three barley GST genes showed that they have 99% identity with each other but only 45% identity with the new GST. This sequence was submitted to NCBI GenBank with FI131240 accession number.
