Being a Positive sense RNA virus the recent reemergence of Chikungunya and Mayaro virus has taken the concern of the leading scientific communities of the world. Though the outbreak of Mayaro virus is limited to Neotropical region only, Chikungunya is already identified in over 60 countries around the world. Besides, the lack of a strong protective treatment, misdiagnosis issue and co-circulation of both the viruses calls for a new strategy which could potentially prevent these infections from spreading. In this study, we therefore, identified the peptide based vaccine candidates e.g. epitopes for B cell and T cell from Chikungunya virus which also showed to be homologous to the Mayaro virus through immuno-informatics and computational approaches. Final epitopes identified from the most antigenic structural polyprotein of both the viruses were 5 for CD8+ T cell Epitopes ( 209 KPGDSGRPI 217 , 219 TGTMGHFIL 227 , 239 ALSVVTWNK 247 , 98 KPGRRERMC 106 and 100 GRRERMCMK 108 ), 2 epitopes for CD4+ T cell ( 105 MCMKIENDCIFEVKH 119 and 502 DRTLLSQQSGNVKIT 516 ) and a single epitope for B cell ( 504 GGRFTIPTGAGKPGDSGRPI 518 ). Analysis of our predicted epitopes for population coverage showed prominent population coverage (92.43%) around the world. Finally, molecular docking simulation of the foreseen T cell epitopes with respondent HLA alleles secured good HLA-epitope interaction. This study was directed towards the discovery of potential antigenic epitopes which can open up a new skyline to design novel vaccines for combating both of the diseases at the same time.
Random Amplified Polymorphic DNA (RAPD) analysis was performed to assess the genetic variability in sixteen selected germplasms of rice, Oryza sativa L. using eight decamer RAPD primers. The data obtained from this investigation reveals a high level of polymorphism between cultivars. The primers produced a total of 255 bands of which all 255 bands were polymorphic indicating 100% polymorphism. The size of the amplified bands ranged from 220 bp to 2290 bp. The number of polymorphic fragments ranged from 24 to 49 with an average of 32 polymorphic fragments for each primer. The primer OPX04 produced the maximum number (49) of polymorphic bands while the OPB04 and OPB17 produced the minimum number (24) of polymorphic bands. The polymorphic information content (PIC) values ranged from 0.6616 to 0.8845 with an average of 0.832. The highest PIC value (0.8845) was obtained for primer OPL03. The RAPD data was analyzed to determine the pair-wise genetic similarity coefficients which ranged from 0.00 to 0.83. The BRRIdhan 23 and the BRRIdhan 41 varieties were the closest genotypes with the highest similarity index of 83%. This was followed by 77% similarity between a pair of cultivars Kalamona and Horkuch. On the other hand, 100% dissimilarity was seen between BRRIdhan 53, BRRIdhan 50, BRRIdhan 10, BRRIdhan 70, BRRIdhan 54, BRRIdhan 40, BRRIdhan 23, BRRIdhan 47, BRRIdhan 41 and Dadsail respectively and between BRRIdhan 53 and Horkuch; indicating a high level of variability between paired genotypes. Cluster analysis was performed using Unweighted Paired Group of Arithmetic Means (UPGMA). The UPGMA dendrogram resolved the selected rice cultivars into four clusters.
In-vitro callus induction and regeneration method was developed using different plant growth regulators (PGRs), and basal media (Murashige and Skoog (MS), CHU (N6) and Gamborg (B5) media) of Citrus sinensis (L.) Osbeck. Observations of the effect of PGRs were carried out using different concentrations of 2,4-dichlorophenoxyacetic acid (2,4-D),1-naphthalene acetic acid (NAA) and combinations of 2,4-D and NAA using different basal media. This study found Citrus sinensis (L.) Osbeck exhibited a high frequency of callus induction on MS medium supplemented with 3 mg/L 2,4-D and callus induction frequency was 86.7% ± 3.4% whereas N6 and B5 showed lower callus induction frequency of 83.3% ± 8.8% and 82.2% ± 1.9% respectively compared to that of MS media with supplementation of the same hormone. Among the induced calli, the morphological analysis showed only 40% -50% was embryogenic calli. Regeneration of plantlets from calli was done using different concentrations and combinations of auxin and cytokinin. The study showed that 3 mg/L 6-benzylaminopurine (BAP) supplemented medium has the maximum potential to promote regeneration of Citrus sinensis (L.) Osbeck from embryogenic calli with the frequency of 89.3% ± 8.8% but no regeneration occurred from the non-embryogenic calli. The regenerated plantlets were rooted on MS medium with supplementation of 5 mg/l NAA.These observations in Citrus sinensis (L.) Osbeck regeneration will be helpful for genetic improvement with desired traits.
Cycline-dependent kinase 4 (CDK4), an enzyme of the cycline dependent or Ser/Thr protein kinase family, plays a role in cell cycle progression (G1 phase) by phosphorylating a tumor suppressor protein called pRB. Alteration of this enzyme due to missense mutation/ nonsynonymous single nucleotide polymorphisms (nsSNPs) are responsible for various types of cancer progression, e.g. melanoma, lung cancer, and breast cancer. Hence, this study is designed to identify the malignant missense mutation of CDK4 from the single nucleotide polymorphism database (dbSNP) by incorporating computational algorithms. Out of 239 nsSNPs; G15S, D140Y and D140H were predicted to be highly malignant variants which may have a devastating impact on protein structure or function. We also found defective binding motif of these three mutants with the CDK4 inhibitor ribociclib and ATP. However, by incorporating molecular dynamic simulation, our study concludes that the superiority of G15S than the other two mutants (D140Y and D140H) in destabilizing proteins nature.
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