The begomoviruses (BGVs) are plant pathogens that evolved in the Old World during the Cretaceous and arrived to the New World (NW) in the Cenozoic era. A subgroup of NW BGVs, the “Squash leaf curl virus (SLCV) lineage” (S-Lin), includes viruses with unique characteristics. To get clues on the evolutionary origin of this lineage, a search for divergent members was undertaken. Four novel BGVs were characterized, including one that is basal to the group. Comparative analyses led to discover a ~670 bp genome module that is nearly exclusive of this lineage, encompassing the replication origin, the AC4 gene, and 480 bp of the Rep gene. A similar DNA module was found in two curtoviruses, hence suggesting that the S-Lin ancestor acquired its distinctive genomic segment by recombination with a curtovirus. This hypothesis was definitely disproved by an in-depth sequence analysis. The search for homologs of S-Lin Rep uncover the common origin of Rep proteins encoded by diverse Geminiviridae genera and viral “fossils” integrated at plant genomes. In contrast, no homolog of S-Lin Rep was found in public databases. Consequently, it was concluded that the SLCV clade ancestor evolved by a recombination event between a primitive NW BGV and a virus from a hitherto unknown lineage.
Anthocyanidins under the effects of solvents water, ethanol, n-hexane, and methanol are interesting due to their suitability as natural dyes for photocatalytic applications. In this chapter, DFT and TDDFT methodologies are used to study their electronic structure. The results displayed include HOMO, LUMO, HOMO-LUMO gap, chemical properties, and reorganization energies for the ground states, and excited state data are also displayed. Malvidin in gas phase has lower gap energy. After addition of solvents, gap energy increases in all cases but malvidin with n-hexane presents narrower gap. Conceptual DFT results show that cyanidin and malvidin may have good charge transfer. Cyanidin presented lower electron reorganization energy (λ e) using solvent water; however, ethanol and methanol had similar values. TDDFT is used to calculate excited states, and absorption data show wavelength main peak between 479.1 and 536.4 nm. UV-Vis absorption spectra were generated and solvent effects on each molecule is discussed. Anthocyanidins work well in the visible region with the stronger peak at the green region. These pigments are good options for photocatalysis application and cyanidin and malvidin, in this order, may be the best choices for dye sensitization applications.
A novel begomovirus isolated from a Sida rhombifolia plant collected in Sinaloa, Mexico, was characterized. The genomic components of sida mosaic Sinaloa virus (SiMSinV) shared highest sequence identity with DNA-A and DNA-B components of chino del tomate virus (CdTV), suggesting a vertical evolutionary relationship between these viruses. However, recombination analysis indicated that a short segment of SiMSinV DNA-A encompassing the plus-strand replication origin and the 5´-proximal 43 codons of the Rep gene was derived from tomato mottle Taino virus (ToMoTV). Accordingly, the putative cis- and trans-acting replication specificity determinants of SiMSinV were identical to those of ToMoTV but differed from those of CdTV. Modeling of the SiMSinV and CdTV Rep proteins revealed significant differences in the region comprising the small β1/β5 sheet element, where five putative DNA-binding specificity determinants (SPDs) of Rep (i.e., amino acid residues 5, 8, 10, 69 and 71) were previously identified. Computer-assisted searches of public databases led to identification of 33 begomoviruses from three continents encoding proteins with SPDs identical to those of the Rep encoded by SiMSinV. Sequence analysis of the replication origins demonstrated that all 33 begomoviruses harbor potential Rep-binding sites identical to those of SiMSinV. These data support the hypothesis that the Rep β1/β5 sheet region determines specificity of this protein for DNA replication origin sequences.
Heat effects in photocatalytic reactor applications are discussed and a case study is analyzed where sunlight is used to activate a chemical reaction to degrade water pollutants. Heat is produced in the light-capturing process, and heat effects need to be better understood during the device design process. Radiative transfer equation (RTE) is the guiding equation used to calculate radiation proliferation in participating media, and it is used to describe the balance of radiative energy transport in the participating media including the interactions caused by different processes such as absorption, scattering, and emission, which also are subject to additional phenomena like weakening and magnification. This equation plays an important role in the design process since it may be included in the simulation process to represent the sunlight heat effects in the different photocatalytic reactor components. In this chapter, it is explained how to build a simplified algorithm to incorporate the RTE in a numerical calculation during the design of a photocatalytic reactor using the commercial software ANSYS®. In addition, simplifications are explained that enable the program to coordinate some coefficients such as absorption and dispersion so their effects are included within the numerical calculation. A user-defined function is presented in the end of the chapter as a usable algorithm in ANSYS® program with acceptable results for photocatalytic reactors.
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