Zinc binuclear cluster proteins (ZBC; Zn(II)2Cys6) are unique to the fungi kingdom and associated with a series of functions, viz., the utilization of macromolecules, stress tolerance, and most importantly, host–pathogen interactions by imparting virulence to the pathogen. Codon usage bias (CUB) is the phenomenon of using synonymous codons in a non-uniform fashion during the translation event, which has arisen because of interactions among evolutionary forces. The Zn(II)2Cys6 coding sequences from nine Ascomycetes plant pathogenic species and model system yeast were analysed for compositional and codon usage bias patterns. The clustering analysis diverged the Ascomycetes fungi into two clusters. The nucleotide compositional and relative synonymous codon usage (RSCU) analysis indicated GC biasness toward Ascomycetes fungi compared with the model system S. cerevisiae, which tends to be AT-rich. Further, plant pathogenic Ascomycetes fungi belonging to cluster-2 showed a higher number of GC-rich high-frequency codons than cluster-1 and was exclusively AT-rich in S. cerevisiae. The current investigation also showed the mutual effect of the two evolutionary forces, viz. natural selection and compositional constraints, on the CUB of Zn(II)2Cys6 genes. The perseverance of GC-rich codons of Zn(II)2Cys6 in Ascomycetes could facilitate the invasion process. The findings of the current investigation show the role of CUB and nucleotide composition in the evolutionary divergence of Ascomycetes plant pathogens and paves the way to target specific codons and sequences to modulate host–pathogen interactions through genome editing and functional genomics tools.

/pdf/composition-and-codon-usage-pattern-results-in-divergence-of-1hsu575t.pdf

Composition and Codon Usage Pattern Results in Divergence of the Zinc Binuclear Cluster (Zn(II)2Cys6) Sequences among Ascomycetes Plant Pathogenic Fungi

Abstract Codon usage bias (CUB) is a ubiquitous phenomenon perseveres in genome of all the organisms. It impinges the gene expression and other genetic intricacies within a genome. The present study explicates the pattern of codon usage in the protein coding sequence of Crocus sativus and its relation with gene expression. Gene expression analysis in C. sativus showed genes with high expression had a preference of G base at third position. CUB had an inverse relation with gene expression. Coding sequences with ENC &lt; 50 had low FPKM value while low codon bias group (ENC &gt; 50) possessed high FPKM value. The low tAI values showed the low translation efficiency of genes in C. sativus . The non-significant MELP and ENC correlation analysis suggested that expression of genes might not be associated with CUB. ENC and PR-2 plot revealed mutation pressure and natural selection played role in shaping CUB. However, neutrality plot conclusively depicted the dominance of natural selection in regulating the configuration of codons in all three species. In addition, the role of CUB regarding the predilection of fungal pathogens Aspergillus fumigatus and Fusarium oxysporum towards host plant C. sativus has also been expounded. We found a similar trend of codon usage pattern operative in plant and fungal pathogens as both the fungal pathogens and host plant showed similar GC rich genomic content as well as preference for GC ending codons at third codon position. This concurrence might be attributed for the colonization of fungal pathogens in C. sativus . Overall, different CUB indices reflected a weak codon bias in the C. sativus , F. oxysporum and A. fumigatus genome. 

/pdf/deciphering-the-role-of-codon-usage-bias-on-gene-expression-14xdsz4m.pdf

Deciphering the role of codon usage bias on gene expression and pathogen colonization in Crocus sativus

The porous spherical alumina (γ-Al2O3) as catalyst support was prepared by sol-gel method, and FeCl3/γ-Al2O3 materials were prepared by impregnation method. The FeCl3/γ-Al2O3 materials were used as catalyst in the Solketal production process by acetalization of acetone and glycerol, showing considerable catalytic performance. When the molar ratio of glycerol and acetone was 1 : 10, 0.2 mol% FeCl3/γ-Al2O3 was used as the catalyst, and the reaction was carried out at 25 °C for 30 min, the conversion of glycerol was 99.89 %, the selectivity of Solketal was 98.36 %, and the yield of Solketal reached 98.25 %. The mechanism is due to the spherical γ-Al2O3 support has high thermal stability, large specific surface area, and rich pore structure, encouraging abundant active sites and high catalytic activity of FeCl3 for the acetalization reaction. Thereafter, the experimental results prove that the prepared FeCl3/γ-Al2O3 catalyst can be easily recovered and reused many times, indicating its great value for large-scale research and application in the future. 

Efficient Synthesis of Solketal from Glycerol and Acetone Catalyzed by FeCl
 3
 /γ‐Al
 2
 O
 3
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Chemical Composition and In Vitro Biological Activity of Angelica Root and Hop Strobile Essential Oils and Hydrolates

Gold Nanoblackbodies-based Multifunctional Nanocomposite for Multimodal Cancer Therapy.

Abstract Meloidogyne incognita (Root-knot nematode) and Alternaria alternata (fungus) were among the dominant parasites of the medicinal plant Withania somnifera . Despite the fatal nature of their infection, a comprehensive study to explore their evolution and adaptation is lacking. The present study elucidates evolutionary and codon usage bias analysis of W. somnifera (host plant), M. incognita (root-knot nematode) and A. alternata (fungal parasite). The results of the present study revealed a weak codon usage bias prevalent in all the three organisms. Based on the nucleotide analysis, genome of W. somnifera and M. incognita was found to be A-T biased while A. alternata had GC biased genome. We found high similarity of CUB pattern between host and its nematode pathogen as compared to the fungal pathogen. Inclusively, both the evolutionary forces influenced the CUB in host and its associated pathogens. However, neutrality plot indicated the pervasiveness of natural selection on CUB of the host and its pathogens. Correspondence analysis revealed the dominant effect of mutation on CUB of W. somnifera and M. incognita while natural selection was the main force affecting CUB of A. alternata . Taken together the present study would provide some prolific insight into the role of codon usage bias in the adaptability of pathogens to the host’s environment for establishing parasitic relationship. 

/pdf/comprehensive-analysis-of-codon-usage-pattern-in-withania-2h327vai.pdf

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

Aim: Gold nanoblackbodies (AuNBs)-mediated plasmonic photothermal cancer therapy was investigated through melanoma-bearing mice. Materials & methods: Polydopamine-coated Au nanoclusters were synthesized, termed AuNBs and PEGylated AuNBs (AuNBs-PEG). The photothermal response of AuNBs-PEG was evaluated upon low-intensity broadband near-infrared irradiation (785/62 nm; 0.9 Wcm-2), and cytotoxicity was assessed on B16-F10 cells. Further, the therapeutic potential of intravenously administered AuNBs-PEG was evaluated on B16-F10 melanoma in C57BL/6 mice. Results: AuNBs-PEG showed an excellent photothermal response (photothermal conversion efficiency of 60.3%), robust photothermal stability and no cytotoxicity. For AuNB-mediated plasmonic photothermal therapy, an average temperature of 63°C was attained within 5 min of irradiation, and tumors were eradicated. Conclusion: AuNBs-PEG are promising photothermal agents for treating melanoma through low-intensity broadband near-infrared irradiation.

Gold nanoblackbodies mediated plasmonic photothermal cancer therapy for melanoma.

Valorization of Distillation Wastes of Aromatic Crops for the Cultivation of Biofortified Pleurotus florida

Our dependence on finite fossil fuels and the insecure energy supply chains have stimulated intensive research for sustainable technologies. Upcycling glycerol, produced from biomass fermentation and as a biodiesel formation byproduct, can substantially contribute in circular carbon economy. Here, we report glycerol's solvent-free and room-temperature conversion to high-added-value chemicals via a reusable graphene catalyst (G-ASA), functionalized with a natural amino acid (taurine). Theoretical studies unveil that the superior performance of the catalyst (surpassing even homogeneous, industrial catalysts) is associated with the dual role of the covalently linked taurine, boosting the catalyst's acidity and affinity for the reactants. Unlike previous catalysts, G-ASA exhibits excellent activity (7508 mmol g-1 h-1) and selectivity (99.9%) for glycerol conversion to solketal, an additive for improving fuels' quality and a precursor of commodity and fine chemicals. Notably, the catalyst is also particularly active in converting oils to biodiesel, demonstrating its general applicability. 

/pdf/acidic-graphene-organocatalyst-for-the-superior-ub3blrvp.pdf

Deepika Singh

Papers

Comprehensive analysis of codon usage pattern in Withania somnifera and its associated pathogens: Meloidogyne incognita and Alternaria alternata

Gold nanoblackbodies mediated plasmonic photothermal cancer therapy for melanoma.

Valorization of Distillation Wastes of Aromatic Crops for the Cultivation of Biofortified Pleurotus florida

Acidic graphene organocatalyst for the superior transformation of wastes into high-added-value chemicals