Specific Nature of Hydrolysis of Insulin and Tobacco Mosaic Virus Protein by Thermolysin

Oxidized bovine insulin and tobacco mosaic virus protein used to determine hydrolysis specificity of thermolysi

Specific recognition of a multiply phosphorylated motif in the DNA repair scaffold XRCC1 by the FHA domain of human PNK.

Short-patch repair of DNA single-strand breaks and gaps (SSB) is coordinated by XRCC1, a scaffold protein that recruits the DNA polymerase and DNA ligase required for filling and sealing the damaged strand. XRCC1 can also recruit end-processing enzymes, such as PNK (polynucleotide kinase 3'-phosphatase), Aprataxin and APLF (aprataxin/PNK-like factor), which ensure the availability of a free 3'-hydroxyl on one side of the gap, and a 5'-phosphate group on the other, for the polymerase and ligase reactions respectively. PNK binds to a phosphorylated segment of XRCC1 (between its two C-terminal BRCT domains) via its Forkhead-associated (FHA) domain. We show here, contrary to previous studies, that the FHA domain of PNK binds specifically, and with high affinity to a multiply phosphorylated motif in XRCC1 containing a pSer-pThr dipeptide, and forms a 2:1 PNK:XRCC1 complex. The high-resolution crystal structure of a PNK-FHA-XRCC1 phosphopeptide complex reveals the basis for this unusual bis-phosphopeptide recognition, which is probably a common feature of the known XRCC1-associating end-processing enzymes

Seafood safety and quality: an analysis of the supply chain in the Sultanate of Oman

The globalization of trade in fish has created many challenges for the developing world specifically with regard to food safety and quality. International organisations have established a good basis for standards in international trade. Whilst these requirements are frequently embraced by the major importers (such as Japan, the EU and the USA), they often impose additional safety requirements and regularly identify batches which fail to meet their strict standards. Creating an effective national seafood control system which meets both the internal national needs as well the requirements for the export market can be challenging. Many countries adopt a dual system where seafood products for the major export markets are subject to tight control whilst the majority of the products (whether for the local market or for more regional trade) are less tightly controlled. With regional liberalization also occurring, deciding on appropriate controls is complex. In the Sultanate of Oman, fisheries production is one of the countries' chief sources of economic revenue after oil production and is a major source of the national food supply. In this paper the structure of the fish supply chain has been analysed and highlighted the different routes operating for the different markets. Although much of the fish are consumed within Oman, there is a major export trade to the local regional markets. Much smaller quantities meet the more stringent standards imposed by the major importing countries and exports to these are limited. The paper has considered the development of the Omani fish control system including the key legislative documents and the administrative structures that have been developed. Establishing modern controls which satisfy the demands of the major importers is possible but places additional costs on businesses. Enhanced controls such as HACCP and other management standards are required but can be difficult to justify when alternative markets do not specify these. These enhanced controls do however provide additional consumer protection and can bring benefits to local consumers. The Omani government is attempting to upgrade the system of controls and has made tremendous progress toward the implementation of HACCP and introducing enhanced management systems into its industrial sector. The existence of strengthened legislative and government support, including subsidies, has encouraged some businesses to implement HACCP. The current control systems have been reviewed and a SWOT analysis approach used to identify key factors for their future development. The study shows that seafood products in the supply chain are often exposed to lengthy handling and distribution process before reaching the consumers, a typical issue faced by many developing countries. As seafood products are often perishable, they safety is compromised if not adequately controlled. The enforcement of current food safety laws in the Sultanate of Oman is shared across various government agencies. Consequently, there is a need to harmonize all regulatory requirements, enhancing the domestic food protection and to continue to work towards a fully risk-based approach in order to compete successfully in the global market

Hazard analysis and critical control point (HACCP) in seafood processing: an analysis of its application and use in regulation in the Sultanate of Oman

When considering the supply of fish products to consumers, the adoption of food safety management systems throughout the 'net to plate' continuum is of a paramount importance. It is essential to safeguard consumers and to facilitate regional and international trade. This study has assessed the technical barriers and benefits associated with the implementation of management system incorporating HACCP and related pre-requisite programmes in the seafood processors in the Sultanate of Oman. A survey, using qualitative surveys and interviews, was conducted out to verify the level of implementation of the seafood safety and quality requirements. A total of 22 (92% returned) HACCP processors, and 15 (83% returned) non-HACCP processors and 15 (75%) officials completed the questionnaires. Differences between processors operating with or without a HACCP system in place have been identified. The survey of local officials provided an additional perspective on the issues involved. The implications of handling practices in the seafood supply chain, seafood trade and the cost implications of implementing HACCP-based food safety management systems were also assessed. In comparison to the non-HACCP processors, the results indicated that HACCP firms were more diversified in their export markets and were able to target the more lucrative markets such as EU, Japan and America. However, the processors felt that the main barrier for exporting to these markets was the restriction imposed by the government on exporting certain species which reduced their ability to meet contracts with these countries. The study has also shown inadequate execution of prerequisite programmes due mainly to lack of training delivered to food handlers and a poor knowledge of food safety concepts. In particular there is an overreliance on the use of CCPs to control hazards when prerequisite programmes would be more appropriate is many situations. When considering whether to implement HACCP-based control systems, the seafood processors identified barriers linked to costs as their main concerns. However, whilst recognising this issue, the officials also highlighted barriers linked to the lack of expertise, skills and commitment of the staff. In general, the study highlighted significant gaps which undermine the effectiveness and success of implementing safety and quality requirements to meet national legislative obligations. These include: poor attitudes and understanding toward HACCP and its pre-requisite programmes, lenient enforcement by the authorities, the lack of training and consultancy organizations in the country, a lack of awareness. The overlapping structure of the regulatory authorities in the country and the distribution of national inspection resources have also been identified as an issue of concern

Turbulent jet from a slender annular slot ventilated by a self-induced flow through the open core

The dynamics of an incompressible turbulent air jet from an annular source into otherwise quiescent surroundings are investigated. Focussing on a slender annulus with an open core, the development of the jet is examined using planar and stereoscopic particle image velocimetry (PIV) from the source to 16 (outer) source diameters downstream. Unique to these annular sources, the jet induces a flow through the open core - in other words, the core is `ventilated'. Our measurements indicate that the volume flux drawn through the core exceeds that from the source by approximately 20%. Based on the streamwise development of the jet, we identify four distinct regions: (i) an internal region of induced flow that is bounded by the jet; (ii) a near-field planar-jet-like region; (iii) a transition region; and, ultimately, (iv) a far- field round-jet-like region. We explore the evolution of the jet towards self-similar behaviour based on cross-stream profiles of time-averaged velocity and turbulence statistics within these different regions. Four distinct length scales are shown to characterise the streamwise extents and behaviours within the regions identified. Finally, to highlight the role of the open-core (ventilated) annular geometry on jet development, comparisons are made with PIV measurements of turbulent jets issuing from circular sources. These comparisons reveal that the ventilated geometry significantly enhances dilution in the near field.The authors G.R.H. and S.P. gratefully acknowledge the financial support of Dyson Technology Ltd and the EPSRC Industrial Case Award programme 13440009

Developing and applying heterogeneous phylogenetic models with XRate

Modeling sequence evolution on phylogenetic trees is a useful technique in computational biology. Especially powerful are models which take account of the heterogeneous nature of sequence evolution according to the "grammar" of the encoded gene features. However, beyond a modest level of model complexity, manual coding of models becomes prohibitively labor-intensive. We demonstrate, via a set of case studies, the new built-in model-prototyping capabilities of XRate (macros and Scheme extensions). These features allow rapid implementation of phylogenetic models which would have previously been far more labor-intensive. XRate's new capabilities for lineage-specific models, ancestral sequence reconstruction, and improved annotation output are also discussed. XRate's flexible model-specification capabilities and computational efficiency make it well-suited to developing and prototyping phylogenetic grammar models. XRate is available as part of the DART software package: http://biowiki.org/DART .Comment: 34 pages, 3 figures, glossary of XRate model terminolog

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

Active flow control systems architectures for civil transport aircraft

Copyright @ 2010 American Institute of Aeronautics and AstronauticsThis paper considers the effect of choice of actuator technology and associated power systems architecture on the mass cost and power consumption of implementing active flow control systems on civil transport aircraft. The research method is based on the use of a mass model that includes a mass due to systems hardware and a mass due to the system energy usage. An Airbus A320 aircraft wing is used as a case-study application. The mass model parameters are based on first-principle physical analysis of electric and pneumatic power systems combined with empirical data on system hardware from existing equipment suppliers. Flow control methods include direct fluidic, electromechanical-fluidic, and electrofluidic actuator technologies. The mass cost of electrical power distribution is shown to be considerably less than that for pneumatic systems; however, this advantage is reduced by the requirement for relatively heavy electrical power management and conversion systems. A tradeoff exists between system power efficiency and the system hardware mass required to achieve this efficiency. For short-duration operation the flow control solution is driven toward lighter but less power-efficient systems, whereas for long-duration operation there is benefit in considering heavier but more efficient systems. It is estimated that a practical electromechanical-fluidic system for flow separation control may have a mass up to 40% of the slat mass for a leading-edge application and 5% of flap mass for a trailing-edge application.This work is funded by the Sixth European Union Framework Programme as part of the AVERT project (Contract No. AST5-CT-2006-030914

The geology of Devizes

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