EBOLA VACCINE: MULTIPLE PEPTIDE-EPITOPE LOADED VACCINE FORMULATION FROM PROTEOME USING REVERSE VACCINOLOGY APPROACH

Objective: The present study was carried out to identify the peptide epitopes with high immunogenicity in the surface proteins of four pathogenic Ebola virus (viz. Bundibugyo virus, Sudan virus, Tai Forest virus and Zaire Ebola virus) using modern reverse vaccinology approach through in silico analysis of proteome for use as Ebola vaccine candidates. Methods: Hexapeptide epitopes based on maximum hydrophilicity were identified in eight surface proteins which were separated from a pool of 160 Ebola virus proteins using a covariant discriminant function and the Mahalanobis D2 statistic. Heptapeptide B cell epitopes were predicted from the surface proteins using the AbDesigner algorithm. Immunogenicity score of each identified epitope was estimated on the basis of hydropathy index and Chou-Fasman conformation. Results: Four continuous (linear) hexapeptide epitopes namely RRKRRD (position 497-502), DEDDED (489-494), RRTRRE (497-502) and KTGKKG (221-226) with maximum hydrophilicity score were identified from different surface proteins for use as Ebola vaccine components. For use as B cell epitopes eight linear heptapeptide epitopes viz. PTSPPQD (418-424) and SHYEPPN (385-391) against Bundibugyo virus, PDYDDCH (309-315) and DYDDCHS (310-316) against Sudan virus, QPKCNPN (508-514) against Tai Forest virus and EYTYPDS (685-691), HLGLDDQ (365-371) and DQEKKIL (370-376) against Zaire Ebola virus with high immunogenicity were identified from different surface proteins of Ebola virus. Conclusion: Four hexapeptide and eight heptapeptide epitopes can be loaded along with T cell or B cell signal peptides in virus like particle (vlp) or formulated as subunit vaccine by pharmaceutical industry to raise humoral immunity against Ebola virus in African population as well as in other human populations across the globe as therapeutics in the same way the Hepatitis B therapeutic vaccine based on multiple peptide-epitopes was designed nearly a decade ago

Codon usage bias analysis for the coding sequences of Camellia sinensis and Brassica campestris

Codon usage bias plays an important role in the regulation of gene expression. A couple of measures are widely used to quantify the codon usage in genes. On the other hand, no quantitative endeavour has been made to compare the pattern of codon usage diversity within and between different genes of Camellia sinensis and Brassica campestris. Nucleotide composition and its relationship with codon usage bias were analyzed. Additionally, the rare codons were identified by computing the recurrence of event of all codons in coding sequences of C. sinensis and B. campestris. The host cell, Escherichia coli used universally, failed to express smoothly many eukaryotic genes. For this, the authors prognosticated the codons showing the highest and the lowest expressivity of the coding sequences of C. sinensis and B. campestris, in E. coli K12 strain to improve the expression level of the genes.Key words: Codon usage bias, gene expressivity, codon usage pattern, residual value, synonymous codon

IMPACT OF tAI IN TRANSLATIONAL DYNAMICS OF HOMO SAPIENS GENES IN ESCHERICHIA COLI GENOME

Objective: Translation of mRNA to protein is a central biological process, and its regulation is vital for cell growth, development and differentiation. It is known that the tRNA molecules play a role of nearly 40% in the process of translation. The objective of this study was to find out the major DNA and protein determinants that play major role in heterologous expression of human genes in a prokaryote (E. coli K12 strain) for pharmaceutical applications.Methods: In this article, we have analyzed the expression of 40 randomly chosen genes of Homo sapiens in E. coli K12 strain with tAI (tRNA adaptation index) as an expression measure in the background of E. coli tRNA gene pool using bioinformatic tools. We have studied how three major local features of a gene's coding sequence (namely coding sequence adaptation to the tRNA pool, nuleobases at three positions in codons and codon encoded-amino acid) affect the translation elongation process.Results: Correlation analysis revealed T3 (r = 0.52**), and T1 (r= 0.51**) are positively correlated with tAI. The anticodon of tRNA genes refers the nucleobase T in the mRNA for translation efficiency. Moreover, AT1 (r= 0.28) and GC2 (r= 0.18) contents showed positive correlation with tAI indicating the role of AT composition at first position and the GC composition at third position of codon in human transgene expression in a bacterium. Several amino acids namely, Asp, Ile, Thr and Tyr showed highly significant positive correlation with tAI.Conclusion: Our results suggest that nucleobase compositional dynamics is a determinant of transcriptional dynamics in heterologous gene expression.Â

WHICH EVOLUTIONARY FORCES DICTATE CODON USAGE IN HUMAN TESTIS SPECIFIC GENES?

Objective: Unequal usage of synonymous codons encoding an amino acid is termed as codon usage bias. Synonymous codon usage bias is an inevitable phenomenon in organismic taxa across the three domains of life, i.e. plants, animals and microbes. Here we report the codon usage pattern in human testis-specific genes found in Y chromosome. Testis-specific genes are associated with several dysfunctions, such as gonadal sex reversion, infertility, gonadoblastoma and non-syndromic hearing impairment.Methods: We used bioinformatics approaches to analyze codon usage bias in human testis-specific genesResults: Highly significant negative correlation was found between ICDI and tAI (r=-0.939**, p<0.01). Moreover, highly significant positive correlation between A% and A3% (r =0.774*, p<0.05), T and T3% (r=0.894**, p<0.01), GC% and GC3% (r = 0.897**, p<0.01) suggest that mutation pressure played an important role in codon usage pattern of these genes. However, significant positive correlation between G and G3 % (r =0.936**, p<0.01), G and C3 (r=0.557, p>0.05) but negative correlation between GC and T3 % (r=-0.960**, p<0.01) indicate the role of natural selection on codon bias. Variation of codon usage pattern was also evident in different genes from principal component analysis (PCA).Conclusion: Codon usage bias in human testis-specific genes is low. These genes are rich in GC content. Both natural selection and mutation pressure affect the codon usage bias in these genes.Keywords: Codon usage bias, Mutation pressure, Natural selectio

Effect of moisture and water on thermal protective performance of multilayered fabric assemblies for firefighters

Multilayered protective fabric assemblies comprising a Nomex III woven outer layer, Nomex nonwoven thermal liners and a modacrylic/cotton woven inner layer have been studied for heat protective performance. Effect of conditioning and presence of water on the outer layer fabric has been studied on heat protective performance, against radiant heat flux. It is observed that the radiative heat protective performance of firefighters’ protective clothing assembly can be improved in presence of a water tight barrier layer used just after the outer layer when the outer layer fabric is wet. Conditioning of the assembly in a particular environment can also significantly affect thermal protective performance

Sanity Checks for Saliency Metrics

Saliency maps are a popular approach to creating post-hoc explanations of image classifier outputs. These methods produce estimates of the relevance of each pixel to the classification output score, which can be displayed as a saliency map that highlights important pixels. Despite a proliferation of such methods, little effort has been made to quantify how good these saliency maps are at capturing the true relevance of the pixels to the classifier output (i.e. their "fidelity"). We therefore investigate existing metrics for evaluating the fidelity of saliency methods (i.e. saliency metrics). We find that there is little consistency in the literature in how such metrics are calculated, and show that such inconsistencies can have a significant effect on the measured fidelity. Further, we apply measures of reliability developed in the psychometric testing literature to assess the consistency of saliency metrics when applied to individual saliency maps. Our results show that saliency metrics can be statistically unreliable and inconsistent, indicating that comparative rankings between saliency methods generated using such metrics can be untrustworthy.Comment: Accepted for publication at the Thirty Fourth AAAI conference on Artificial Intelligence (AAAI-20