Viruses show noticeable evolution to adapt and reproduce within their hosts. Theoretically, patterns and factors that affect the codon usage of viruses should reflect evolutionary changes that allow them to optimize their codon usage to their hosts. Some software tools can analyze the codon usage of organisms; however, their performance has room for improvement, as these tools do not focus on examining the codon usage co-adaptation between viruses and their hosts. This paper describes the R package, which is a crucial tool used to analyze the co-adaptation vhcub of codon usage between a virus and its host, with several implementations of indices and plots. The tool is available from: https://cran.r-project.org/web/packages/vhcub/. PubMed Abstract | Publisher Full Text | Free Full Text 2. Boël G, Letso R, Neely H, et al.: Codon influence on protein expression in E. coli correlates with mRNA levels. Nature. 2016; 529(7586): 358-363. PubMed Abstract | Publisher Full Text | Free Full Text 3. Burns CC, Shaw J, Campagnoli R, et al.: Modulation of poliovirus replicative fitness in HeLa cells by deoptimization of synonymous codon usage in the capsid region. J Virol. 2006; 80(7): 3259-3272. PubMed Abstract | Publisher Full Text | Free Full Text 4. Cladel NM, Hu J, Balogh KK, et al.: CRPV genomes with synonymous codon optimizations in the CRPV E7 gene show phenotypic differences in growth and altered immunity upon E7 vaccination. PLoS One. 2008; 3(8): e2947. PubMed Abstract | Publisher Full Text | Free Full Text 5. Elek A, Kuzman M, Vlahovicek K: coRdon: Codon Usage Analysis and Prediction of Gene Expressivity. R package version 1.0.3. 2019. Reference Source 6. Novembre JA: Accounting for background nucleotide composition when measuring codon usage bias. Mol Biol Evol. 2002; 19(8): 1390-1394. PubMed Abstract | Publisher Full Text 7. Sharp PM, Li WH: The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 1987; 15(3): 1281-1295. PubMed Abstract | Publisher Full Text | Free Full Text 8. Puigbò P, Aragonès L, Garcia-Vallvé S: RCDI/eRCDI: a web-server to estimate codon usage deoptimization. BMC Res Notes. 2010; 3(1): 87. PubMed Abstract | Publisher Full Text | Free Full Text 9. Zhou JH, Zhang J, Sun DJ, et al.: The distribution of synonymous codon choice in the translation initiation region of dengue virus. PLoS One. 2013; 8(10): e77239. PubMed Abstract | Publisher Full Text | Free Full Text 10. Wan XF, Xu D, Kleinhofs A, et al.: Quantitative relationship between synonymous codon usage bias and GC composition across unicellular genomes.

Background: Cadmium (Cd) is considered a health hazard due to its industrial use. Lungs and kidneys are the primary organs affected by its toxicity. Inflammatory response in lung tissue is mediated by Cd exposure until it becomes dysfunctional. Cd damages DNA indirectly by increasing reactive oxygen species generation, which interacts with DNA defense system leading to genomic instability. Curcumin (C) has multiple health benefits, as well as its Nano-formulation, Nano-curcumin (NC), which has potential to increase biological and pharmacological actions of curcumin. Aim: To focus on Cd-mediated inflammatory response and cell apoptosis in lung tissue of adult male albino rat and use NC as a potential therapeutic agent. Methods and methods: Thirty adult albino male rats were split into three groups, each with ten rats: control (group I), Cd treated (group II), and Cd+NC treated (group III). Rats were sacrificed and lungs were extracted for light microscopic and ultra-structural examination. IL-6 and TNF-α concentration were estimated and lung cellular survival genes; Bax and Bcl2 expression was evaluated by PCR. Results: Alveolar damage with loss of normal lung architecture were seen in H&E-stained sections of group II confirmed by ultrastructural investigation revealing cellular cytoplasmic vacuolations with degenerated mitochondria. In group II, IL-6, TNF-α and Bax gene were increased, whereas Bcl2 gene was decreased with increased Bax/Bcl-2 genes ratio expression. NC treated group showed cellular restoration, decreased pro-inflammatory cytokines and decreased Bax/Bcl-2 genes ratio expression. Conclusions: NC can be taken as a medicinal supplement to ease Cd poisoning risk in lungs.