ABSTRACT
OBJECTIVES@#To do mapping and modeling of conformational B cell epitope regions of highly conserved and protective regions of three merozoitecandidate vaccine proteins of Plasmodium vivax (P. vivax), ie. merozoite purface protein-1 (PvMSP-1), apical membrane antigen -1 domain ∏ (PvAMA1-D∏) and region ∏ of the Duffy binding protein (PvDBP∏), and to analyze the immunogenic properties of these predicted epitopes.@*METHODS@#3-D structures of amino acid haplotypes from Sri Lanka (available in GeneBank) of PvMSP-119 (n=27), PvAMA1-D∏ (n=21) and PvDBP∏ (n=33) were modeled. SEPPA, selected as the best online server was used for conformational epitope predictions, while prediction and modeling of protein structure and properties related to immunogenicity was carried out with Geno3D server, SCRATCH Protein Server, NetSurfP Server and standalonesoftware, Genious 5.4.4.@*RESULTS@#SEPPA revealed that regions of predicted conformational epitopes formed 4 clusters in PvMSP-I19, and 3 clusters each in PvAMA1-D∏ and PvDBP∏, all of which displayed a high degree of hydrophilicity, contained solvent exposed residues, displayed high probability of antigenicity and showed positive antigenic propensity values, that indicated high degree of immunogenicity.@*CONCLUSIONS@#Findings of this study revealed and confirmed that different parts of the sequences of each of the conserved regions of the three selected potential vaccine candidate antigens of P. vivax are important with regard to conformational epitope prediction that warrants further laboratory experimental investigations in in vivo animal models.
ABSTRACT
Objective: Paris fargesii is an important medicinal plant and its secondary metabolites, steroidal saponins, synthesized by the mevalonate pathway are the active ingredients. The study on the gene of the key enzyme 3-hydroxy-3-methyl- glutaryl-coenzyme A reductases (HMGR) in the mevalonate pathway is helpful for the regulation of steroidal saponins syntheses. Methods: In the basis of degenerate primers designed according to mRNA homologous conserved regions of 11 HMGRs from 11 plant species published on NCBI and total RNA extracted from the seedling of P. fargesii, a 404 bp fragment of HMGR was amplified by reverse transcription PCR technology, which is a new cDNA as searching in the Genbank. Results: Sequence analysis showed that the obtained fragment had 76%-81% identification compared with other seven plant species. The deduced amino acid seqence was predicted to have a wider and higher homology with other plants. Conclusion: Protein characteristic zones, conserved regions, and phylogenetic analysis by Prosite and ClustalX could give preliminary evidence for the existence of HMGR in P. fargesi, which is the report of HMGR gene isolated from the plants in Liliaceae for the first time.
ABSTRACT
Exploring genetic variation in Gossypium arboreum L. germplasm is useful as it contains many important genes conferring resistance to different stresses. In limited earlier studies, low level of genetic diversity was found by using conventional DNA marker systems which may impede future genome mapping studies. In the present investigation, we explored the extent of Single Nucleotide Polymorphisms (SNP) among 30 conserved regions of Expressed Sequence Tags (EST) of low copy genes between two genotypes of G. arboreum. A total of 27 SNPs including 21 substitutions and 6 Insertions and deletions (Indels) in 7804 bp were found between these genotypes with a frequency of one SNP per 371 bp and one Indel after every 1300 bp. Out of these SNPs, 52 percent were transitions, whilst 48 percent SNPs were transversion. In conclusion, SNPs are expedient markers that can explore polymorphism in highly conserved sequences where other markers are not effective.