The Membrane Protein Data Bank

The Membrane Protein Data Bank (MPDB) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. Data originates from the Protein Data Bank and other databases, and from the literature. Structures are based on X-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. The MPDB is searchable online by protein characteristic, structure determination method, crystallization technique, detergent, temperature, pH, author, etc. Record entries are hyperlinked to the PDB and Pfam for viewing sequence, three-dimensional structure and domain architecture, and for downloading coordinates. Links to PubMed are also provided. The MPDB is updated weekly in parallel with the Protein Data Bank. Statistical analysis of MPDB records can be performed and viewed online. A summary of the statistics as applied to entries in the MPDB is presented. The data suggest conditions appropriate for crystallization trials with novel membrane proteins

A novel approach to aquatic weed control and habitat restoration using biodegradable jute matting

This technical paper presents results from pilot field trials conducted on the novel use of a biodegradable jute material to eradicate the highly invasive aquatic macrophyte Lagarosiphon major Ridley from Lough Corrib, Ireland. The results demonstrate the ability of the jute material to comprehensively kill L. major and to restore native macrophyte communities to areas of the lake that were previously overgrown with this priority invasive species. To date, eight indigenous plant species (four charophytes and four angiosperms) have been recorded growing through the loose-weave jute fabric. However, no Lagarosiphon has been recorded as doing so. This material has the potential for broader application in the management of nuisance aquatic weeds and in the restoration of native flora extirpated by these alien species

Electronically tuned optical filters

Electro-optical effect of light modifying type for electronically controlling colo

Current status of Ireland's newest invasive species -the Asian clam Corbicula fluminea (Müller, 1774)

The Asian clam Corbicula fluminea was first discovered in Ireland in the Rivers Barrow and Nore in 2010. Scuba diving surveys were the primary sampling method used to determine the detailed distribution of this species in the two rivers. Sustainable populations of Asian clam were present in the tidal freshwater reaches of both rivers. No clams were present upstream of the tidal limit. A maximum density of 9,636 individuals m-2 was recorded in the River Barrow. This paper presents some basic metrics in relation to the populations present in these two connected river systems

Genetic structure of pike (Esox lucius) reveals a complex and previously unrecognized colonization history of Ireland

Aim: We investigated genetic variation of Irish pike populations and their relationship with European outgroups, in order to elucidate the origin of this species to the island, which is largely assumed to have occurred as a human-mediated introduction over the past few hundred years. We aimed thereby to provide new insights into population structure to improve fisheries and biodiversity management in Irish freshwaters. Location: Ireland, Britain and continental Europe. Methods: A total of 752 pike (Esox lucius) were sampled from 15 locations around Ireland, and 9 continental European sites, and genotyped at six polymorphic microsatellite loci. Patterns and mechanisms of population genetic structure were assessed through a diverse array of methods, including Bayesian clustering, hierarchical analysis of molecular variance, and approximate Bayesian computation. Results: Varying levels of genetic diversity and a high degree of population genetic differentiation were detected. Clear substructure within Ireland was identified, with two main groups being evident. One of the Irish populations showed high similarity with British populations. The other, more widespread, Irish strain did not group with any European population examined. Approximate Bayesian computation suggested that this widespread Irish strain is older, and may have colonized Ireland independently of humans. Main conclusions: Population genetic substructure in Irish pike is high and comparable to the levels observed elsewhere in Europe. A comparison of evolutionary scenarios upholds the possibility that pike may have colonized Ireland in two ‘waves’, the first of which, being independent of human colonization, would represent the first evidence for natural colonization of a non-anadromous 42 freshwater fish to the island of Ireland. Although further investigations using comprehensive genomic techniques will be necessary to confirm this, the present results warrant a reappraisal of current management strategies for this species

Management of Lagarosiphon major (ridley) moss in lough corrib-a review

Lagarosiphon major is a priority invasive species first recorded in a natural Irish watercourse, Lough Corrib, in April 2005. The weed has subsequently expanded its range significantly within the upper and middle lake but, as of 2010, has not been recorded in the large lower lake. In Lough Corrib the temporal growth pattern exhibited by L. major is at variance with that displayed in its country of origin. In southern Africa the plant grows most vigorously in summer, whereas in Corrib it achieves its best vegetative expression during the colder and darker winter months. This temporal growth pattern significantly influences practical weed control programmes, as it has proved to be far more efficient to cut and harvest L. major stands when the stems are erect and buoyant, even if it does mean that cutting operations must be conducted during the more inclement winter months. A combination of traditional and innovative weed control methods are used to control L. major in the lake. These include manual removal using scuba divers, mechanical cutting and harvesting, chemical control and light exclusion using a natural jute matting material. In 2008 L. major occupied c. 92ha of lake bed, while some 8,500ha is deemed to be suitable for its establishment and growth. Control work to date has reduced the area of lake occupied by this aggressive weed to c. 35.9ha

An Investigation Into Human-centred Peer-support Education Systems for Students with Learning Difficulties

This research investigates the potential application and use of ICT in the development of peersupport networks centered on learners with Specific Learning Difficulties at third level education. Utilising a theoretical model based on both the social and medical models of disability, it is intended to develop a system that will allow learners to develop through interaction with their peers actionable education frameworks, adaptive learning strategies and reusable learning resources in a safe and contextualised learning environment. Primary research will be performed with the student population of Waterford Institute of Technology as a case study. The longitudinal goal is the improved retention, resilience and performance of the target population

Measurements of the acid-binding capacity of ingredients used in pig diets

peer-reviewedSome feed ingredients bind more acid in the stomach than others and for this reason may be best omitted from pig starter foods if gastric acidity is to be promoted. The objective of this study was to measure the acid-binding capacity (ABC) of ingredients commonly used in pig starter foods. Ingredients were categorised as follows: (i) milk products (n = 6), (ii) cereals (n = 10), (iii) root and pulp products (n = 5), (iv) vegetable proteins (n = 11), (v) meat and fish meal (n = 2), (vi) medication (n = 3), (vii) amino acids (n = 4), (viii) minerals (n = 16), (ix) acid salts (n = 4), (x) acids (n = 10). A 0.5 g sample of food was suspended in 50 ml distilled de-ionised water with continuous stirring. This suspension was titrated with 0.1 mol/L HCl or 0.1 mol/L NaOH so that approximately 10 additions of titrant was required to reach pH 3.0. The pH readings after each addition were recorded following equilibration for three minutes. ABC was calculated as the amount of acid in milliequivalents (meq) required to lower the pH of 1 kg food to (a) pH 4.0 (ABC-4) and (b) pH 3.0 (ABC-3). Categories of food had significantly different (P < 0.01) ABC values. Mean ABC-4 and ABC-3 values of the ten categories were: (i) 623 (s.d. 367.0) and 936 (s.d. 460.2), (ii) 142 (s.d. 79.2) and 324 (s.d. 146.4), (iii) 368 (s.d. 65.3) and 804 (s.d. 126.7), (iv) 381 (s.d. 186.1) and 746 (s.d. 227.0), (v) 749 (s.d. 211.6) and 1508 (s.d. 360.8), (vi) 120 (s.d. 95.6) and 261 (s.d. 163.2), (vii) 177 (s.d. 60.7) and 1078 (s.d. 359.0), (viii) 5064 (s.d. 5525.1) and 7051 (s.d. 5911.6), (ix) 5057 (s.d. 1336.6) and 8945 (s.d. 2654.1) and (x) -5883 (s.d. 4220.5) and -2591 (s.d. 2245.4) meq HCl per kg, respectively. Within category, ABC-3 and ABC- 4 values were highly correlated: R2 values of 0.80 and greater for food categories i, iv, v, vi, vii and viii. The correlation between predicted and observed ABC values of 34 mixed diets was 0.83 for ABC-4 and 0.71 for ABC-3. It was concluded that complete diets with low ABC values may be formulated through careful selection of ingredients. The final pH to which ABC is measured should matter little as ABC-3 and ABC-4 are highly correlated

Pressure Induced Hydration Dynamics of Membranes

Pressure-jump initiated time-resolved x-ray diffraction studies of dynamics of the hydration of the hexagonal phase in biological membranes show that (i) the relaxation of the unit cell spacing is non-exponential in time; (ii) the Bragg peaks shift smoothly to their final positions without significant broadening or loss in crystalline order. This suggests that the hydration is not diffusion limited but occurs via a rather homogeneous swelling of the whole lattice, described by power law kinetics with an exponent $\beta = 1.3 \pm 0.2$.Comment: REVTEX 3, 10 pages,3 figures(available on request),#