Characterisation of genome-wide association epistasis signals for serum uric acid in human population isolates

Genome-wide association (GWA) studies have identified a number of loci underlying variation in human serum uric acid (SUA) levels with the SLC2A9 gene having the largest effect identified so far. Gene-gene interactions (epistasis) are largely unexplored in these GWA studies. We performed a full pair-wise genome scan in the Italian MICROS population (n = 1201) to characterise epistasis signals in SUA levels. In the resultant epistasis profile, no SNP pairs reached the Bonferroni adjusted threshold for the pair-wise genome-wide significance. However, SLC2A9 was found interacting with multiple loci across the genome, with NFIA - SLC2A9 and SLC2A9 - ESRRAP2 being significant based on a threshold derived for interactions between GWA significant SNPs and the genome and jointly explaining 8.0% of the phenotypic variance in SUA levels (3.4% by interaction components). Epistasis signal replication in a CROATIAN population (n = 1772) was limited at the SNP level but improved dramatically at the gene ontology level. In addition, gene ontology terms enriched by the epistasis signals in each population support links between SUA levels and neurological disorders. We conclude that GWA epistasis analysis is useful despite relatively low power in small isolated populations.     

Optical switches and triggers for the manipulation of ion channels and pores

Like fluorescence sensing techniques, methods to manipulate proteins with light have produced great advances in recent years. Ion channels have been one of the principal protein targets of photoswitched manipulation. In combination with fluorescence detection of cell signaling, this has enabled non-invasive, all-optical experiments on cell and tissue function, both in vitro and in vivo. Optical manipulation of channels has also provided insights into the mechanism of channel function. Optical control elements can be classified according to their molecular reversibility as non-reversible phototriggers where light breaks a chemical bond (e.g. caged ligands) and as photoswitches that reversibly photoisomerize. Synthetic photoswitches constitute nanoscale actuators that can alter channel function using three different strategies. These include (1) nanotoggles, which are tethered photoswitchable ligands that either activate channels (agonists) or inhibit them (blockers or antagonists), (2) nanokeys, which are untethered (freely diffusing) photoswitchable ligands, and (3) nanotweezers, which are photoswitchable crosslinkers. The properties of such photoswitches are discussed here, with a focus on tethered photoswitchable ligands. The recent literature on optical manipulation of ion channels is reviewed for the different channel families, with special emphasis on the understanding of ligand binding and gating processes, applications in nanobiotechnology, and with attention to future prospects in the field.     

The rarest and least protected forests in biodiversity hotspots

The goal of biodiversity hotspots is to identify regions around the world where conservation priorities should be focused. We undertake a geographic information system and remote sensing analysis to identify the rarest and least protected forests in biodiversity hotspots. World Wildlife Fund ecoregions with terrestrial forest were subset from 34 biodiversity hotspots and forest cover calculated from GlobCover data at a 300?m pixel resolution. There were 276 ecoregions in 32 biodiversity hotspots classified as containing terrestrial forests. When the first quartile of forest ecoregions was subset based on smallest extent of forest cover in protected areas, there were 69 rare forests identified within 20 biodiversity hotspots. Most rare forest ecoregions (45) occurred on islands or island archipelagos and 47 rare forest ecoregions contained less than 10?% forest cover in protected areas. San Félix-San Ambrosio Islands Temperate Forests, Tubuai Tropical Moist Forests, Maldives-Lakshadweep-Chagos Archipelago Tropical Moist Forests, and Yap Tropical Dry Forests were identified as the least protected and possibly most vulnerable forests within biodiversity hotspots. These ecoregions cover less than 500?km², forest cover is less than 50?km², and there are no protected areas. There is a need to update classifications and boundaries of protected areas, insure that islands are included in global land cover datasets, and identify levels of endemism and endangerment within forest ecoregions. This should improve our ability to compare, prioritize, and monitor forests in biodiversity hotspots.     

Modelling carbon stocks and fluxes in the wood product sector: a comparative review

In addition to forest ecosystems, wood products are carbon pools that can be strategically managed to mitigate climate change. Wood product models (WPMs) simulating the carbon balance of wood production, use and end of life can complement forest growth models to evaluate the mitigation potential of the forest sector as a whole. WPMs can be used to compare scenarios of product use and explore mitigation strategies. A considerable number of WPMs have been developed in the last three decades, but there is no review available analysing their functionality and performance. This study analyses and compares 41 WPMs. One surprising initial result was that we discovered the erroneous implementation of a few concepts and assumptions in some of the models. We further described and compared the models using six model characteristics (bucking allocation, industrial processes, carbon pools, product removal, recycling and substitution effects) and three model‐use characteristics (system boundaries, model initialization and evaluation of results). Using a set of indicators based on the model characteristics, we classified models using a hierarchical clustering technique and differentiated them according to their increasing degrees of complexity and varying levels of user support. For purposes of simulating carbon stock in wood products, models with a simple structure may be sufficient, but to compare climate change mitigation options, complex models are needed. The number of models has increased substantially over the last ten years, introducing more diversity and accuracy. Calculation of substitution effects and recycling has also become more prominent. However, the lack of data is still an important constraint for a more realistic estimation of carbon stocks and fluxes. Therefore, if the sector wants to demonstrate the environmental quality of its products, it should make it a priority to provide reliable life cycle inventory data, particularly regarding aspects of time and location.     

Simultaneous α/β spin-state selection for <Superscript>13</Superscript>C and <Superscript>15</Superscript>N from a time-shared HSQC-IPAP experiment

Two novel HSQC-IPAP approaches are proposed to achieve α/β spin-state editing simultaneously for ¹³C and ¹⁵N in a single NMR experiment. The pulse schemes are based on a time-shared (TS) 2D ¹H,¹³C/¹H,¹⁵N-HSQC correlation experiment that combines concatenated echo elements for simultaneous J(CH) and J(NH) coupling constants evolution, TS evolution of ¹³C and ¹⁵N chemical shifts in the indirect dimension and heteronuclear α/β-spin-state selection by means of the IPAP principle. Heteronuclear α/β-editing for all CH _n (n = 1–3) and NH _n (1–2) multiplicities can be achieved in the detected F2 dimension of a single TS-HSQC-F2-IPAP experiment. On the other hand, an alternative TS-HSQC-F1-IPAP experiment is also proposed to achieve α/β-editing in the indirect F1 dimension. Experimental and simulated data is provided to evaluate these principles in terms of sensitivity and performance simultaneously on backbone and side-chain CH, CH₂, CH₃, NH, and NH₂ spin systems in uniformly ¹³C/¹⁵N-labeled proteins and in small natural-abundance peptides.     

Bromelain: an overview of industrial application and purification strategies

This review highlights the use of bromelain in various applications with up-to-date literature on the purification of bromelain from pineapple fruit and waste such as peel, core, crown, and leaves. Bromelain, a cysteine protease, has been exploited commercially in many applications in the food, beverage, tenderization, cosmetic, pharmaceutical, and textile industries. Researchers worldwide have been directing their interest to purification strategies by applying conventional and modern approaches, such as manipulating the pH, affinity, hydrophobicity, and temperature conditions in accord with the unique properties of bromelain. The amount of downstream processing will depend on its intended application in industries. The breakthrough of recombinant DNA technology has facilitated the large-scale production and purification of recombinant bromelain for novel applications in the future.     

The structure of Prp40 FF1 domain and its interaction with the crn-TPR1 motif of Clf1 gives a new insight into the binding mode of FF domains

The yeast splicing factor Prp40 (pre-mRNA processing protein 40) consists of a pair of WW domains followed by several FF domains. The region comprising the FF domains has been shown to associate with the 5' end of U1 small nuclear RNA and to interact directly with two proteins, the Clf1 (Crooked neck-like factor 1) and the phosphorylated repeats of the C-terminal domain of RNA polymerase II (CTD-RNAPII). In this work we reported the solution structure of the first FF domain of Prp40 and the identification of a novel ligand-binding site in FF domains. By using chemical shift assays, we found a binding site for the N-terminal crooked neck tetratricopeptide repeat of Clf1 that is distinct and structurally separate from the previously identified CTD-RNAPII binding pocket of the FBP11 (formin-binding protein 11) FF1 domain. No interaction, however, was observed between the Prp40 FF1 domain and three different peptides derived from the CTD-RNAPII protein. Indeed, the equivalent CTD-RNAPII-binding site in the Prp40 FF1 domain is predominantly negatively charged and thus unfavorable for an interaction with phosphorylated peptide sequences. Sequence alignments and phylogenetic tree reconstructions using the FF domains of three functionally related proteins, Prp40, FBP11, and CA150, revealed that Prp40 and FBP11 are not orthologous proteins and supported the different ligand specificities shown by their respective FF1 domains. Our results also revealed that not all FF domains in Prp40 are functionally equivalent. We proposed that at least two different interaction surfaces exist in FF domains that have evolved to recognize distinct binding motifs.