A DNA test for routine prediction in breeding of peach blush,Ppe-R<Subscript>f</Subscript>-SSR

Blush, the proportion of red overcolor on the skin surface of fruit, is highly variable in peach breeding germplasm and is important in the marketing of peach fruit. The fresh market peach industry demands a high level of blush to entice consumers, while the processing peach industry requires minimal blush. Therefore, blush is a major selection criterion in breeding programs. The use of DNA-based information could improve breeding efficiency and accuracy for fruit blush coverage, but a predictive DNA test is required. The objective of this study was to develop a DNA test for the prediction of blush coverage by targeting the major locus, R _f , associated with blush variation. Initially, haplotypes were developed based on five SNP markers associated with variation in blush coverage. To convert the 5-SNP haplotype test into a single, simple PCR-based assay, 11 simple sequence repeat markers were designed and used to screen individuals representing all SNP haplotypes. The most informative assay, named Ppe-R_f-SSR, was chosen to screen 200 individuals of the RosBREED peach reference germplasm set that incorporated germplasm from four breeding programs. Ppe-R_f-SSR accurately differentiated individuals with high-, medium-, and low-blush coverage in most lineages. Outcomes highlighted that DNA tests can be quite predictive for some breeding programs or specific germplasm sets, while for others the predictiveness can falter. Therefore, the confirmation of genotype effects for any DNA test is recommended in new germplasm before routine use. The prediction accuracy and breeding utility of Ppe-R_f-SSR in the University of Arkansas breeding program were subsequently confirmed by screening 443 seedlings, independent of the initial DNA test development process, derived from 18 cross-combinations of 28 parents. Ppe-R_f-SSR can be used to efficiently and accurately predict fruit blush coverage, especially in fresh market germplasm, and has been deployed for routine use in the University of Arkansas peach breeding program.     

Computational investigation of proton transfer,pKa shifts and pH‐optimum of protein–DNA and protein–RNA complexes

Protein–nucleic acid interactions play a crucial role in many biological processes. This work investigates the changes of pKa values and protonation states of ionizable groups (including nucleic acid bases) that may occur at protein–nucleic acid binding. Taking advantage of the recently developed pKa calculation tool DelphiPka, we utilize the large protein–nucleic acid interaction database (NPIDB database) to model pKa shifts caused by binding. It has been found that the protein's interfacial basic residues experience favorable electrostatic interactions while the protein acidic residues undergo proton uptake to reduce the energy cost upon the binding. This is in contrast with observations made for protein–protein complexes. In terms of DNA/RNA, both base groups and phosphate groups of nucleotides are found to participate in binding. Some DNA/RNA bases undergo pKa shifts at complex formation, with the binding process tending to suppress charged states of nucleic acid bases. In addition, a weak correlation is found between the pH‐optimum of protein–DNA/RNA binding free energy and the pH‐optimum of protein folding free energy. Overall, the pH‐dependence of protein–nucleic acid binding is not predicted to be as significant as that of protein–protein association. Proteins 2017; 85:282–295. © 2016 Wiley Periodicals, Inc.     

Elasto-regenerative properties of polyphenols

Abdominal aortic aneurysms (AAA) are progressive dilatations of infra-renal aorta causing structural weakening rendering the aorta prone to rupture. AAA can be potentially stabilized by inhibiting inflammatory enzymes such as matrix metalloproteinases (MMP); however, active regression of AAA is not possible without new elastic fiber regeneration. Here we report the elastogenic benefit of direct delivery of polyphenols such as pentagalloyl glucose (PGG), epigallocatechin gallate (EGCG), and catechin, to smooth muscle cells obtained either from healthy or from aneurysmal rat aorta. Addition of 10 μg/ml PGG and ECGC induce elastin synthesis, organization, and crosslinking while catechin does not. Our results indicate that polyphenols bind to monomeric tropoelastin and enhance coacervation, aid in crosslinking of elastin by increasing lysyl oxidase (LOX) synthesis, and by blocking MMP-2 activity. Thus, polyphenol treatments leads to increased mature elastin fibers synthesis without increasing the production of intracellular tropoelastin.     

Optimal climbing speed explains the evolution of extreme sexual size dimorphism in spiders

Several hypotheses have been put forward to explain the evolution of extreme sexual size dimorphism (SSD). Among them, the gravity hypothesis (GH) explains that extreme SSD has evolved in spiders because smaller males have a mating or survival advantage by climbing faster. However, few studies have supported this hypothesis thus far. Using a wide span of spider body sizes, we show that there is an optimal body size (7.4 mm) for climbing and that extreme SSD evolves only in spiders that: (1) live in high‐habitat patches and (2) in which females are larger than the optimal size. We report that the evidence for the GH across studies depends on whether the body size of individuals expands beyond the optimal climbing size. We also present an ad hoc biomechanical model that shows how the higher stride frequency of small animals predicts an optimal body size for climbing.     

Extracellular and cell-associated forms of beta-glucosidase in Thermomonospora curvata

The thermophilic actinomycete, Thermomonospora curvata , released 16-times the beta-glucosidase when grown on protein-extracted lucerne fibre compared with growth on cellobiose or purified cellulose. The intracellular and extracellular betaglucosidases had the same mol. wts (66 kD), but the extracellular enzyme had higher affinities for both p -nitrophenyl glucoside and cellobiose and was more resistant to thermal inactivation.     

Blood‐feeding ecology of mosquitoes in zoos

To determine if the unique host assemblages in zoos influence blood‐feeding by mosquitoes (Diptera: Culicidae), a sampling programme was conducted in Greenville and Riverbanks Zoos, South Carolina, U.S.A., from April 2009 to October 2010. A total of 4355 female mosquitoes of 14 species were collected, of which 106 individuals of nine species were blood‐fed. The most common taxa were Aedes albopictus (Skuse), Aedes triseriatus (Say), Anopheles punctipennis (Say), Culex erraticus (Dyar & Knab), Culex pipiens complex (L.) and Culex restuans (Theobald). Molecular analyses (cytochrome b) of bloodmeals revealed that mosquitoes fed on captive animals, humans and wildlife, and took mixed bloodmeals. Host species included one amphibian, 16 birds, 10 mammals (including humans) and two reptiles. Minimum dispersal distances after feeding on captive hosts ranged from 15.5 m to 327.0 m. Mosquito–host associations generally conformed to previous accounts, indicating that mosquito behaviour inside zoos reflects that outside zoos. However, novel variation in host use, including new, exotic host records, warrants further investigation. Zoos, thus, can be used as experiment environments in which to study mosquito behaviour, and the findings extrapolated to non‐zoo areas, while providing medical and veterinary benefits to zoo animals, employees and patrons.     

Green tea extracts as ultraviolet protectants for the beet armyworm,Spodoptera exigua,nucleopolyhedrovirus

The addition of a caffeinated green tea, Camellia sinensis L., filtrate (1%) to the nucleopolyhedrovirus (SeMNPV) of the beet armyworm, Spodoptera exigua (Hübner), provided almost complete protection following UVB irradiation (30 min) in laboratory tests. There were few differences in UV protection when extracts were prepared at 27 or at 90°C. Moreover, few differences in UV protection were demonstrated following infusion times of 5, 15, 30, and 60 min at 90°C. At a 1% concentration, decaffeinated and caffeinated green teas were equally effective as UV protectants. At lower concentrations (0.1, 0.01, and 0.001%) caffeinated green tea provided greater UV protection (UVB/UVB 30, 60 min). Virus/tea extracts (caffeinated), under field conditions at 1 and 5%, were ineffective as UV screens. At a 10% concentration, some UV protection was provided and UV protection further increased in a concentration-dependent manner.     

The importance of sourcing enzymes from non-conventional fungi for metabolic engineering and biomass breakdown

A wealth of fungal enzymes has been identified from nature, which continue to drive strain engineering and bioprocessing for a range of industries. However, while a number of clades have been investigated, the vast majority of the fungal kingdom remains unexplored for industrial applications. Here, we discuss selected classes of fungal enzymes that are currently in biotechnological use, and explore more basal, non-conventional fungi and their underexploited biomass-degrading mechanisms as promising agents in the transition towards a bio-based society. Of special interest are anaerobic fungi like the Neocallimastigomycota, which were recently found to harbor the largest diversity of biomass-degrading enzymes among the fungal kingdom. Enzymes sourced from these basal fungi have been used to metabolically engineer substrate utilization in yeast, and may offer new paths to lignin breakdown and tunneled biocatalysis. We also contrast classic enzymology approaches with emerging ‘omics’-based tools to decipher function within novel fungal isolates and identify new promising enzymes. Recent developments in genome editing are expected to accelerate discovery and metabolic engineering within these systems, yet are still limited by a lack of high-resolution genomes, gene regulatory regions, and even appropriate culture conditions. Finally, we present new opportunities to harness the biomass-degrading potential of undercharacterized fungi via heterologous expression and engineered microbial consortia.