A 15 µm selected sample of hHigh-z starbursts and AGNs

We report results from our Spitzer GO-1 program on IRS spectroscopy of a large sample of Luminous Infrared Galaxies and quasars selected from the European Large Area ISO Survey (ELAIS). The selected ELAIS sources have a wide multi-wavelength coverage, including ISOCAM, ISOPHOT, IRAC and MIPS (from SWIRE), and optical photometry. Here we present the sample selection and results from the IRS spectroscopy

Stops making sense: translational trade-offs and stop codon reassignment

Background Efficient gene expression involves a trade-off between (i) premature termination of protein synthesis; and (ii) readthrough, where the ribosome fails to dissociate at the terminal stop. Sense codons that are similar in sequence to stop codons are more susceptible to nonsense mutation, and are also likely to be more susceptible to transcriptional or translational errors causing premature termination. We therefore expect this trade-off to be influenced by the number of stop codons in the genetic code. Although genetic codes are highly constrained, stop codon number appears to be their most volatile feature. Results In the human genome, codons readily mutable to stops are underrepresented in coding sequences. We construct a simple mathematical model based on the relative likelihoods of premature termination and readthrough. When readthrough occurs, the resultant protein has a tail of amino acid residues incorrectly added to the C-terminus. Our results depend strongly on the number of stop codons in the genetic code. When the code has more stop codons, premature termination is relatively more likely, particularly for longer genes. When the code has fewer stop codons, the length of the tail added by readthrough will, on average, be longer, and thus more deleterious. Comparative analysis of taxa with a range of stop codon numbers suggests that genomes whose code includes more stop codons have shorter coding sequences. Conclusions We suggest that the differing trade-offs presented by alternative genetic codes may result in differences in genome structure. More speculatively, multiple stop codons may mitigate readthrough, counteracting the disadvantage of a higher rate of nonsense mutation. This could help explain the puzzling overrepresentation of stop codons in the canonical genetic code and most variants

Realising the right to data portability for the domestic Internet of Things

There is an increasing role for the IT design community to play in regulation of emerging IT. Article 25 of the EU General Data Protection Regulation (GDPR) 2016 puts this on a strict legal basis by establishing the need for information privacy by design and default (PbD) for personal data-driven technologies. Against this backdrop, we examine legal, commercial and technical perspectives around the newly created legal right to data portability (RTDP) in GDPR. We are motivated by a pressing need to address regulatory challenges stemming from the Internet of Things (IoT). We need to find channels to support the protection of these new legal rights for users in practice. In Part I we introduce the internet of things and information PbD in more detail. We briefly consider regulatory challenges posed by the IoT and the nature and practical challenges surrounding the regulatory response of information privacy by design. In Part II, we look in depth at the legal nature of the RTDP, determining what it requires from IT designers in practice but also limitations on the right and how it relates to IoT. In Part III we focus on technical approaches that can support the realisation of the right. We consider the state of the art in data management architectures, tools and platforms that can provide portability, increased transparency and user control over the data flows. In Part IV, we bring our perspectives together to reflect on the technical, legal and business barriers and opportunities that will shape the implementation of the RTDP in practice, and how the relationships may shape emerging IoT innovation and business models. We finish with brief conclusions about the future for the RTDP and PbD in the IoT

Amino Acid Metabolic Origin as an Evolutionary Influence on Protein Sequence in Yeast

The metabolic cycle of Saccharomyces cerevisiae consists of alternating oxidative (respiration) and reductive (glycolysis) energy-yielding reactions. The intracellular concentrations of amino acid precursors generated by these reactions oscillate accordingly, attaining maximal concentration during the middle of their respective yeast metabolic cycle phases. Typically, the amino acids themselves are most abundant at the end of their precursor’s phase. We show that this metabolic cycling has likely biased the amino acid composition of proteins across the S. cerevisiae genome. In particular, we observed that the metabolic source of amino acids is the single most important source of variation in the amino acid compositions of functionally related proteins and that this signal appears only in (facultative) organisms using both oxidative and reductive metabolism. Periodically expressed proteins are enriched for amino acids generated in the preceding phase of the metabolic cycle. Proteins expressed during the oxidative phase contain more glycolysis-derived amino acids, whereas proteins expressed during the reductive phase contain more respiration-derived amino acids. Rare amino acids (e.g., tryptophan) are greatly overrepresented or underrepresented, relative to the proteomic average, in periodically expressed proteins, whereas common amino acids vary by a few percent. Genome-wide, we infer that 20,000 to 60,000 residues have been modified by this previously unappreciated pressure. This trend is strongest in ancient proteins, suggesting that oscillating endogenous amino acid availability exerted genome-wide selective pressure on protein sequences across evolutionary time

The STF2p Hydrophilin from Saccharomyces cerevisiae Is Required for Dehydration Stress Tolerance

The yeast Saccharomyces cerevisiae is able to overcome cell dehydration; cell metabolic activity is arrested during this period but restarts after rehydration. The yeast genes encoding hydrophilin proteins were characterised to determine their roles in the dehydration-resistant phenotype, and STF2p was found to be a hydrophilin that is essential for survival after the desiccation-rehydration process. Deletion of STF2 promotes the production of reactive oxygen species and apoptotic cell death during stress conditions, whereas the overexpression of STF2, whose gene product localises to the cytoplasm, results in a reduction in ROS production upon oxidative stress as the result of the antioxidant capacity of the STF2p protein

A Calanais myth and an alignment of the east stone-row with both the rising of the Pleiades and crossovers of Venus at sunrise on the summer solstices

Acknowledgements My thanks to Stefan Sagrott of Historic Environment Scotland for his help in obtaining Patrick Ashmore’s data and to David Forrest, School of Geographical and Earth Sciences, University of Glasgow, for providing a copy of David Tait’s map of Calanais.Peer reviewedPublisher PD

A framework physical map for peach, a model Rosaceae species

A genome-wide framework physical map of peach was constructed using high-information content fingerprinting (HICF) and FPC software. The resulting HICF assembly contained 2,138 contigs composed of 15,655 clones (4.3× peach genome equivalents) from two complementary bacterial artificial chromosome libraries. The total physical length of all contigs is estimated at 303 Mb or 104.5% of the peach genome. The framework physical map is anchored on the Prunus genetic reference map and integrated with the peach transcriptome map. The physical length of anchored contigs is estimated at 45.0 Mb or 15.5% of the genome. Altogether, 2,636 markers, i.e., genetic markers, peach unigene expressed sequence tags, and gene-specific and overgo probes, were incorporated into the physical framework and supported the accuracy of contig assembly.This project was supported by the United States Department of Agriculture NRI Award # 2005-35300-15452.Peer reviewe