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The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease. [ABSTRACT FROM AUTHOR]

Research has been conducted on the creatine kinase which catalyzes creatine reversible conversion and adenosine triphosphate to phosphocreatine and adenosine diphosphate. The X-ray structure of creatine kinase bound to a transition-state analogue complex has been investigated and the details are reported.

Research has been conducted on the human muscle creatine kinase. The use of the site-directed mutagenesis in replacing the Cys282 of the human muscle creatine kinase with serine and methionine is discussed.

The guanidine substrate creatine undergoes reversible phosphorylation catalyzed by the creatine kinase and magnesium-adenosine triphosphate. Crystallographic analysis and site-directed mutagenesis of the enzyme identify Glu232 as the likely catalytic residue and Asp326 aiding in the proper assignment of substrates for catalysis.

Research reveals that benzoylformate decarboxylase reaction with p-nitrobenzoylformic acid shows two transient states of the enzyme-substrate complex yielding a chromophoric product exhibiting absorbance in the visible spectrum. Analysis of the variant enzyme's His70Ala active-site, indicates the role of histidine70 in the decarboxylation pathway of the enzyme.

Two hydrophilic, charged amphipathic alpha-helical peptides, one acidic and one basic (QAPAYEEAAEELAKS and QAPAYKKAAKKLAES, respectively), and structures were studied using NMR and CD. Results made it possible to suggest a working model of the basic peptide-sodium dodecyl sulfate (SDS) complex as well as a mechanism for SDS-induced alpha-helical folding. Although folding of peptides is mostly driven by hydrophobic effects, electrostatic interactions have a significant role in formation/stabilization of SDS-induced structure.

Research has been conducted on the T4 lysozyme folding. The use of CD and 2D (super)1 H NMR spectroscopy to identify the initiation sites is described.

The evolution and diversification of ssRNA plant viruses are often examined under reductionist conditions that ignore potentially much wider biotic interactions. The host range of a plant virus is central to interactions at higher levels that are organized by both fitness and ecological criteria. Here we employ a strategy to minimize sampling biases across distinct plant communities and combine it with a high‐throughput sequencing approach to examine the influence of four habitats on the evolution of Watermelon mosaic virus (WMV). Local, regional and global levels of genetic diversity that correspond to spatial and temporal extents are used to infer haplotype relationships using network and phylogenetic approaches. We find that the incidence and genetic diversity of WMV were structured significantly by host species and habitat type. A single haplotype that infected 11 host species of a total of 24 showed that few constraints on host species use exist in the crop communities. When the evolution of WMV was examined at broader levels of organization, we found variation in genetic diversity and contrasting host use footprints that broadly corresponded to habitat effects. The findings demonstrated that nondeterministic ecological factors structured the genetic diversity of WMV. Habitat‐driven constraints underlie host use preferences. [ABSTRACT FROM AUTHOR]

The crystal structure of the thiamin diphosphate (ThDP)-dependent enzyme benzoylformate decarboxylase (BFD) was determined at 1.6 angstrom resolution. BFD when compared to other ThDP-dependent enzymes displayed similar architecture to the enzymes. While the cofactor- and metal-binding sites were well conserved, the active site residues not directly bound to the cofactor were not. However, it was also observed that the position of functional groups in the functional sites may be well conserved.

CD and H NMR spectroscopy were used to examine the solution conformation of peptide LYS(11-36), corresponding to the beta-sheet region in T4 lsozyme, in aqueous solution, TFE and SDS micelles. Some beta-sheet and turn character in aqueous solution was indicated, but a helical conformation was predicted in a more hydrophobic environment. The peptide was able to form helical, sheet or extended structure depending on concentrations of TFE or SDS.

1H NMR and circular dichroism studies help determine the conformation of a peptide corresponding to T4 lysozyme residues 59-81 in solution. Secondary structure predictions suggest that in a more hydrophobic environment, the peptide adopts a helical conformation. Spectroscopic studies reveal the unstructured nature of the peptide in aqueous solution and the peptide exhibits significant helicity in the presence of TFE or SDS micelles.

Circular dichroism and NMR spectroscopy reveal the aggregation of eledoisin to an average conformation in water and to monomeric forms in sodium dodecyl sulfate (SDS) micelles and trifluoroethanol (TFE). The entire message domain and part of the address domain of eledoisin undergo folding in the hydrophobic medium. The helical core of eledoisin in SDS is more stable in TFE.

Abstract Background The interaction between insects and plants takes myriad forms in the generation of spectacular diversity. In this association a species host range is fundamental and often measured using an estimate of phylogenetic concordance between species. Pollinating fig wasps display extreme host species specificity, but the intraspecific variation in empirical accounts of host affiliation has previously been underestimated. In this investigation, lineage delimitation and codiversification tests are used to generate and discuss hypotheses elucidating on pollinating fig wasp associations with Ficus. Results Statistical parsimony and AMOVA revealed deep divergences at the COI locus within several pollinating fig wasp species that persist on the same host Ficus species. Changes in branching patterns estimated using the generalized mixed Yule coalescent test indicated lineage duplication on the same Ficus species. Conversely, Elisabethiella and Alfonsiella fig wasp species are able to reproduce on multiple, but closely related host fig species. Tree reconciliation tests indicate significant codiversification as well as significant incongruence between fig wasp and Ficus phylogenies. Conclusions The findings demonstrate more relaxed pollinating fig wasp host specificity than previously appreciated. Evolutionarily conservative host associations have been tempered by horizontal transfer and lineage duplication among closely related Ficus species. Independent and asynchronistic diversification of pollinating fig wasps is best explained by a combination of both sympatric and allopatric models of speciation. Pollinator host preference constraints permit reproduction on closely related Ficus species, but uncertainty of the frequency and duration of these associations requires better resolution.

Abstract Background Insects that feed on plants contribute greatly to the generation of biodiversity. Hypotheses explaining rate increases in phytophagous insect diversification and mechanisms driving speciation in such specialists remain vexing despite considerable attention. The proliferation of plant-feeding insects and their hosts are expected to broadly parallel one another where climate change over geological timescales imposes consequences for the diversification of flora and fauna via habitat modification. This work uses a phylogenetic approach to investigate the premise that the aridification of Australia, and subsequent expansion and modification of arid-adapted host flora, has implications for the diversification of insects that specialise on them. Results Likelihood ratio tests indicated the possibility of hard molecular polytomies within two co-radiating gall-inducing species complexes specialising on the same set of host species. Significant tree asymmetry is indicated at a branch adjacent to an inferred transition to a Plurinerves ancestral host species. Lineage by time diversification plots indicate gall-thrips that specialise on Plurinerves hosts differentially experienced an explosive period of speciation contemporaneous with climatic cycling during the Quaternary period. Chronological analyses indicated that the approximate age of origin of gall-inducing thrips on Acacia might be as recent as 10 million years ago during the Miocene, as truly arid landscapes first developed in Australia. Conclusion Host-plant diversification and spatial heterogeneity of hosts have increased the potential for specialisation, resource partitioning, and unoccupied ecological niche availability for gall-thrips on Australian Acacia.

The genomics era has revolutionized studies of adaptive evolution by monitoring large numbers of loci throughout the genomes of many ~ individuals. Ideally, the investigation of emergence in plant viruses requires examining the population dynamics of both virus and host, their interactions with each other, with other organisms and the abiotic environment. Genetic mechanisms that affect demographic processes are now i. being studied with high-throughput technologies. traditional genetics methods, and new computational tools for big-data. In this review, we discuss ~i the utility of these approaches to monitor and detect changes in virus populations within cells and individuals, and over wider areas across species and communities of ecosystems. The advent of genomics in virology has fostered a multidisciplinary approach to tackling disease risk. The ability to, make sense of the inforination now generated in this integrated setting is by far the most substantial obstacle lu the ultimate goal of plant virology to ~ minimize the threats to food security posed by disease, To achieve this goal, it is imperative to understand and forecast how populations respond to ~ future changes in complex natural systems. [ABSTRACT FROM AUTHOR]

Control strategies for plant viruses cannot eradicate widespread outbreaks of disease, or the emergence of new ones. Most of the reported emerging diseases of plants are caused by viruses, which stresses the need to model and forecast plant virus disease risk. Most of the reported emerging diseases of plants are caused by viruses (Aranda & Freitas-Astúa, [3]), which stresses the need to model and forecast plant virus disease risk. At one level, distributions were shaped by specific host-virus species pairs, and specific virus-virus and host-virus (multiple infection) interactions, which suggests species traits (infectivity and resistance mechanisms at the microlevel) had a role in infection heterogeneity. [Extracted from the article]

The structural relationship between the active site of [beta]-lactam-recognizing enzymes (BLRE) and amidase signature (AS) enzymes which represent a superfamily of largely bacterial proteins exhibiting bacterial resistance to lactam antibiotics is discussed. The close spatial overlap between the two tetrads might be attributed to a process of convergent evolution driven by a mechanistic imperative.

A point mutant, benzaldehyde lyase (BAL) from Pseudomonas putida A28S which is able to catalyze the decarboxylation of benzoylformate and is inactivated by the benzoylformate analogues methyl benzoylphosphonate (MBP) and benzoylphosphonate (BP), similar to benzoylformate decarboxylase (BFDC) is reported. The findings suggested that an appropriately placed nucleophile facilitated the expulsion of carbon dioxide from the active site in many thiamin diphosphate (ThDP-dependent decarboxylases.

The article studies benzoylformate decarboxylase (BFDC) and pyruvate decarboxylase (PDC), which are both thiamin diphosphate-dependent enzymes. Findings revealed that changes in Thr377 and Ala460 results in a substrate spectrum, which included higher activity toward pyruvate.

The various mechanisms involved in the reaction of benzoylformate decarboxylase (BFDC) with methyl benzoylphosphonate (MBP) inhibitors are discussed. The reaction is shown to lead to the formation of a tetrahedral adduct C2[alpha]-mandelyl-thiamin diphosphate.

The mechanism of the enzyme benzoylformate decarboxylase (BFDC), carrying out a thiamin diphosphate (ThDP)-dependent nonoxidative decarboxylation reaction, is analyzed with the chromophoric alternate substrate (E)-2-oxo-4(pyridin-3-yl)-3-butenoic acid (3-PKB). The studies have shown that the ability to directly observe the true enamine intermediate in BFDC using benzaldehyde as a substrate and the stability of this enamine intermediate has made it s potential candidate for crystallization.

An excellent electrostatic analogue of benzoylformic acid, methyl benzoylphosphonate was used to probe the catalytic kinetics of benzaldehyde lyase (BAL). The results obtained provide insight into structure of the BAL in its covalent complex with methyl benzoylphosphonate and the role of His29 and other active site residue Trp163 in catalysis by BAL.

Direct spectroscopic observation of thiamin diphosphate-bound intermediates performed on the enzyme benzaldehyde lyase to understand the reversible and highly enantiospecific conversion of (R)-benzoin to benzaldehyde. The observations from circular dichroism provide insight into all thiamin related intermediates which are in a chiral environment on benzaldehyde lyase.

The pH dependence of tautomeric forms providing the first data for the internal thermodynamic equlibria on thiamin diphosphate enzymes are reported. The dramatic influence of the protein on the internal equilibria points to conditions under which the long-elusive ylide intermediate could be stabilized.