Genome-wide analysis of mammalian promoter architecture and evolution

Mammalian promoters can be separated into two classes, conserved TATA box-enriched promoters, which initiate at a welldefined site, and more plastic, broad and evolvable CpG-rich promoters. We have sequenced tags corresponding to several hundred thousand transcription start sites (TSSs) in the mouse and human genomes, allowing precise analysis of the sequence architecture and evolution of distinct promoter classes. Different tissues and families of genes differentially use distinct types of promoters. Our tagging methods allow quantitative analysis of promoter usage in different tissues and show that differentially regulated alternative TSSs are a common feature in protein-coding genes and commonly generate alternative N termini. Among the TSSs, we identified new start sites associated with the majority of exons and with 3' UTRs. These data permit genome-scale identification of tissue-specific promoters and analysis of the cis-acting elements associated with them.

A novel suite of cyclotides from Viola odorata: sequence variation and the implications for structure, function and stability

Cyclotides are a fascinating family of plant-derived peptides characterized by their head-to-tail cyclized backbone and knotted arrangement of three disulfide bonds. This conserved structural architecture, termed the CCK (cyclic cystine knot), is responsible for their exceptional resistance to thermal, chemical and enzymatic degradation. Cyclotides have a variety of biological activities, but their insecticidal activities suggest that their primary function is in plant defence. In the present study, we determined the cyclotide content of the sweet violet Viola odorata, a member of the Violaceae family. We identified 30 cyclotides from the aerial parts and roots of this plant, 13 of which are novel sequences. The new sequences provide information about the natural diversity of cyclotides and the role of particular residues in defining structure and function. As many of the biological activities of cyclotides appear to be associated with membrane interactions, we used haemolytic activity as a marker of bioactivity for a selection of the new cyclotides. The new cyclotides were tested for their ability to resist proteolysis by a range of enzymes and, in common with other cyclotides, were completely resistant to trypsin, pepsin and thermolysin. The results show that while biological activity varies with the sequence, the proteolytic stability of the framework does not, and appears to be an inherent feature of the cyclotide framework. The structure of one of the new cyclotides, cycloviolacin O14, was determined and shown to contain the CCK motif. This study confirms that cyclotides may be regarded as a natural combinatorial template that displays a variety of peptide epitopes most likely targeted to a range of plant pests and pathogens.

Folate supplementation fails to affect vascular function and carotid artery intima media thickness in cyclosporin A-treated renal transplant recipients

Background: Cyclosporin A (CsA)-treated renal transplant recipients (RTR) exhibit relative hyperhomocystinemia and vascular dysfunction. Folate supplementation lowers homocysteine and has been shown to improve vascular function in healthy subjects and patients with coronary artery disease. The aim of this study was to assess the effects of 3 months of folate supplementation (5 mg/day) on vascular function and structure in RTR. Methods: A double-blind, placebo-controlled crossover study was conducted in 10 CsA-treated RTR. Vascular structure was measured as carotid artery intima media thickness (IMT) and function was assessed as changes in brachial artery diameter during reactive hyperemia (RE) and in response to glyceryl trinitrate (GTN). Function data were analyzed as absolute and percent change from baseline and area under the diameter/time curve. Blood samples were collected before and after supplementation and analyzed for total plasma homocysteine, folate, vitamin B-12 and asymmetric dimethyl arginine (ADMA) in addition to regular measures of hemoglobin, hematocrit, mean corpuscular volume (MCV) and serum creatinine. Results: Folate supplementation significantly increased plasma folate by 687% (p < 0.005) and decreased homocysteine by 37% (p < 0.05) with no changes (p > 0.05) in vitamin B 12 or ADMA. There were no significant (p > 0.05) changes in vascular structure or function during the placebo or the folate supplementation phases; IMT; placebo pre mean +/- SD, 0.52 +/- 0.12, post 0.50 +/- 0.11; folate pre 0.55 +/- 0.17, post 0.49 +/- 10.20 mm 5% change in brachial artery diameter (RH, placebo pre 10 +/- 8, post 6 +/- 5; folate pre 9 +/- 7, post 7 +/- 5; GTN, placebo pre 18 +/- 10, post 17 +/- 9, folate pre 16 +/- 9, post-supplementation 18 +/- 8). Conclusion: Three months of folate supplementation decreases plasma homocysteine but has no effect on endothelial function or carotid artery IMT in RTR.

Fighting fit: thermal plasticity of metabolic function and fighting success in the crayfish Cherax destructor

1. We examined the effect of thermal acclimation on fighting success and underlying performance traits in the crayfish Cherax destructor. We tested the hypothesis that animals will be more successful when fighting at their acclimation temperature than at a colder or warmer temperature, and that changes in metabolic capacity underlie differences in behavioural performance. 2. Thermal acclimation (to 20 degrees C and to 30 degrees C) had a significant effect on behavioural contests, and the likelihood of winning was significantly greater when individuals fought at their acclimation temperature against an individual from an alternate acclimation temperature. 3. The ratio of ADP stimulated respiration to proton leak (respiratory control ratio) of isolated mitochondria increased significantly in chelae muscle of the cold-acclimated group, and differences in respiratory control ratio between winners and losers were significantly correlated with the outcome of agonistic encounters. However, acclimation did not affect tall muscle mitochondria or the activity of pyruvate kinase in either chelae or tail muscle. 4. The force produced by closing chelae was thermally insensitive within acclimation groups, and there were no significant differences between acclimation treatments. None the less, differences in chelae width between contestants were significantly correlated with the outcome of agonistic encounters, but this perceived resource holding power did not reflect the actual power of force production. 5. Thermal acclimation in C destructor has beneficial consequences for dominance and competitive ability, and the success of cold acclimated animals at the cold temperatures can be at least partly explained by concomitant up-regulation of oxidative ATP production capacity.

The Function and Consequences of Alternative Fresh Produce Supply Chain Models

Around the world, consumers and retailers of fresh produce are becoming more and more discerning about factors such as food safety and traceability, health, convenience and the sustainability of production systems, and in doing so they are changing the way in which fresh produce supply chains are configured and managed. When consumers demand fresh, safe, convenient, value-for-money produce, retailers in an increasingly competitive environment are attracted to those business models most capable of meeting these demands profitably. Traditional models are proving less and less able to deliver competitive advantage in such an environment. As a result, opportunistic, adversarial, price-based approaches to doing business between chain members are being replaced by approaches that are more strategic, collaborative and value-based. The shaping force behind this change is the need for producers, wholesalers, category managers, retailers and consumers to have more certainty about the performance of the supply chains upon which they rely. Certainty is generated through the supply chain's ability to create, deliver and share value. How to build supply chains that create, deliver and share value is arguably the single biggest challenge to the competitiveness of fresh produce firms, and therefore to the industries to which they belong.