The tagged microarray marker (TAM) method for high-throughput detection of single nucleotide and indel polymorphisms

The tagged microarray marker (TAM) method allows high-throughput differentiation between predicted alternative PCR products. Typically, the method is used as a molecular marker approach to determining the allelic states of single nucleotide polymorphisms (SNPs) or insertion-deletion (indel) alleles at genomic loci in multiple individuals. Biotin-labeled PCR products are spotted, unpurified, onto a streptavidin-coated glass slide and the alternative products are differentiated by hybridization to fluorescent detector oligonucleotides that recognize corresponding allele-specific tags on the PCR primers. The main attractions of this method are its high throughput (thousands of PCRs are analyzed per slide), flexibility of scoring (any combination, from a single marker in thousands of samples to thousands of markers in a single sample, can be analyzed) and flexibility of scale (any experimental scale, from a small lab setting up to a large project). This protocol describes an experiment involving 3,072 PCRs scored on a slide. The whole process from the start of PCR setup to receiving the data spreadsheet takes 2 d.

Crocodiles in the regulatory swamp: navigating the dangers of outsourcing, SaaS and shadow IT

Corporates are entering the brave new world of the internet and digitization without much regard for the fine print of a growing regulation regime. More traditional outsourcing arrangements are already falling foul of the regulators as rules and supervision intensifies. Furthermore, ‘shadow IT’ is proliferating as the attractions of SaaS, mobile, cloud services, social media, and endless new ‘apps’ drive usage outside corporate IT. Initial cost-benefit analyses of the Cloud make such arrangements look immediately attractive but losing control of architecture, security, applications and deployment can have far reaching and damaging regulatory consequences. From research in financial services, this paper details the increasing body of regulations, their inherent risks for businesses and how the dangers can be pre-empted and managed. We then delineate a model for managing these risks specifically focused on investigating, strategizing and governing outsourcing arrangements and related regulatory obligations

Disabled access and heritage attractions

In a UK context, the importance of heritage tourism, the potential of the disabled market, and government policies concerning tourism, social inclusion, and the historic environment provide the setting within which access improvements at heritage attractions for disabled visitors are studied. At issue is how disabled access and conservation can be reconciled. The stakeholders range from the central actors, the disabled tourists and the heritage tourism service providers, through to the gatekeeper and lobby players in the conservation, disability, and tourism contexts. The critical power structures are identified. Changes to the historic environment are managed through the conservation planning system in which disability interests are not formally represented. Recent disability discrimination legislation has not altered this balance of power, and is a source of uncertainty over the access standards that should apply to heritage attractions. An evaluation of progress in implementing access improvements at heritage attractions reveals the limited extent of improvements undertaken to date. Consideration is given not only to physical access but also to alternative methods (intellectual access) of providing the heritage tourism service. In conclusion, the situation is examined from three perspectives. From the disabled tourists' perspective, choice of heritage attractions to visit remains restricted compared to that of nondisabled tourists. The lack of consultation with disabled stakeholders in the access improvements decision-making process is discussed, including the acceptability of alternative methods of service delivery to disabled tourists. The uncertainties facing heritage tourism service providers arising from the disability discrimination legislation are considered but, to ensure a more balanced recognition of disability interests, both conservation planning and disability discrimination legislation need to be amended, adjusting the roles of the legislative gatekeepers.

The role of meat as a source of n-3 polyunsaturated fatty acids in the human diet

It is considered that consumption of very long chain (VLC, carbon chain length >= 20) n - 3 PUFAs in most Western populations is sub-optimal and benefits in relation to chronic disease would be gained from increased consumption. This review examines the current contribution that meat makes to dietary intake of VLC n - 3 PUFA and given its current low contribution, how ruminant meat may be enriched. Enrichment both directly with VLC n - 3 fatty acids and indirectly by increasing intake by the animals of alpha-linolenic acid (ALNA; C 18:3 n - 3) are considered. Since it now appears that dietary ALNA is a very limited source of VLC n - 3 PUFA in humans, the indirect route is controversial but since some forages-are rich sources of ALNA this route has many sustainability and environmental attractions. Consideration is also given to the increased concentrations of trans and conjugated fatty acids that will arise from enriching ruminant meat with PUFA.

The role of meat as a source of n-3 polyunsaturated fatty acids in the human diet

It is considered that consumption of very long chain (VLC, carbon chain length >= 20) n - 3 PUFAs in most Western populations is sub-optimal and benefits in relation to chronic disease would be gained from increased consumption. This review examines the current contribution that meat makes to dietary intake of VLC n - 3 PUFA and given its current low contribution, how ruminant meat may be enriched. Enrichment both directly with VLC n - 3 fatty acids and indirectly by increasing intake by the animals of alpha-linolenic acid (ALNA; C 18:3 n - 3) are considered. Since it now appears that dietary ALNA is a very limited source of VLC n - 3 PUFA in humans, the indirect route is controversial but since some forages-are rich sources of ALNA this route has many sustainability and environmental attractions. Consideration is also given to the increased concentrations of trans and conjugated fatty acids that will arise from enriching ruminant meat with PUFA.

Hierarchical analysis of production efficiency in a coastal trawl fishery

We present, pedagogically, the Bayesian approach to composed error models under alternative, hierarchical characterizations; demonstrate, briefly, the Bayesian approach to model comparison using recent advances in Markov Chain Monte Carlo (MCMC) methods; and illustrate, empirically, the value of these techniques to natural resource economics and coastal fisheries management, in particular. The Bayesian approach to fisheries efficiency analysis is interesting for at least three reasons. First, it is a robust and highly flexible alternative to commonly applied, frequentist procedures, which dominate the literature. Second,the Bayesian approach is extremely simple to implement, requiring only a modest addition to most natural-resource economist tool-kits. Third, despite its attractions, applications of Bayesian methodology in coastal fisheries management are few.

Regimes of conformational transitions of a diblock polyampholyte

The conformational properties of symmetric flexible diblock polyampholytes are investigated by scaling theory and molecular dynamics simulations. The electrostatically driven coil-globule transition of a symmetric diblock polyampholyte is found to consist of three regimes identified with increasing electrostatic interaction strength. In the first (folding) regime the electrostatic attraction causes the chain to fold through the overlap of the two blocks, while each block is slightly stretched by self-repulsion. The second (weak association or scrambled egg) regime is the classical collapse of the chain into a globule dominated by the fluctuation-induced attractions between oppositely charged sections of the chain. The structure of the formed globule can be represented as a dense packing of the charged chain sections (electrostatic attraction blobs). The third (strong association or ion binding) regime starts with direct binding of oppositely charged monomers (dipole formation), followed by a cascade of multipole formation (quadrupole, hexapole, octupole, etc.), leading to multiplets analogous to those found in ionomers. The existence of the multiplet cascade has also been confirmed in the simulations of solutions of short polymers with only one single charge (either positive or negative) in the middle of each chain. We use scaling theory to estimate the average chain size and the electrostatic correlation length as functions of the chain length, strength of electrostatic interactions, charge fraction, and solvent quality. The theoretically predicted scaling laws of these conformational properties are in very good agreement with our simulation results.

Modelling the rheology of anisotropic particles adsorbed on a two-dimensional fluid interface

We present a general approach based on nonequilibrium thermodynamics for bridging the gap between a well-defined microscopic model and the macroscopic rheology of particle-stabilised interfaces. Our approach is illustrated by starting with a microscopic model of hard ellipsoids confined to a planar surface, which is intended to simply represent a particle-stabilised fluid–fluid interface. More complex microscopic models can be readily handled using the methods outlined in this paper. From the aforementioned microscopic starting point, we obtain the macroscopic, constitutive equations using a combination of systematic coarse-graining, computer experiments and Hamiltonian dynamics. Exemplary numerical solutions of the constitutive equations are given for a variety of experimentally relevant flow situations to explore the rheological behaviour of our model. In particular, we calculate the shear and dilatational moduli of the interface over a wide range of surface coverages, ranging from the dilute isotropic regime, to the concentrated nematic regime.