Patrick Collins

Innate immunity in the deep sea hydrothermal vent mussel Bathymodiolus azoricus

The interaction between microorganisms and host defense mechanisms is a decisive factor for the survival of marine bivalves. They rely on cell-mediated and humoral reactions to overcome the pathogens that naturally occur in the marine environment. In order to understand host defense reactions in animals inhabiting extreme environments we investigated some of the components from the immune system of the deep sea hydrothermal vent mussel Bathymodiolus azoricus. Cellular constituents in the hemolymph and extrapallial fluid were examined and led to the identification of three types of hemocytes revealing the granulocytes as the most abundant type of cell. To further characterize hemocyte types, the presence of cell surface carbohydrate epitopes was demonstrated with fluorescent WGA lectin, which was mostly ascribed to the granulocytes. Cellular reactions were then investigated by means of phagocytosis and by the activation of putative MAPKs using the microbial compounds zymosan, glucan, peptidoglycan and lipopolysaccharide. Two bacterial agents, Bacillus subtilis and Vibrio parahaemolyticus, were also used to stimulate hemocytes. The results showed that granulocytes were the main phagocytic cells in both hemolymph and extrapallial fluid of B. azoricus. Western blotting analyses using commercially available antibodies against ERK, p38 and JNK, suggested that these putative kinases are involved in signal transduction pathways during experimental stimulation of B. azoricus hemocytes. The fluorescent Ca(2+) indicator Fura-2 AM was also insightful in demonstrating hemocyte stimulation in the presence of laminarin or live V. parahaemolyticus. Finally, the expression of the antibacterial gene mytilin was analyzed in gill tissues by means of RT-PCR and whole-mount in situ hybridization. Mytilin transcripts were localized in hemocytes underlying gill epithelium. Moreover, mytilin was induced by exposure of live animals to V. parahaemolyticus. These findings support the premise of a conserved innate immune system in B. azoricus. Such system is comparable to other Bivalves and involves the participation of cellular and humoral components.

Bone-eating marine worms: habitat specialists or generalists?

We are happy to see the acknowledgement by [Glover et al . (2008)][1] ‘that absence of evidence cannot in itself lend support to the theory that Osedax are exclusively whale-fall specialists’. [Jones et al . (2008)][2] reported that bone-eating marine worms of the genus Osedax will grow on cow

Information Age Ireland: The Attraction, the Reality and Never Ending Geography

Abstract This paper is an attempt to probe deeper behind the well-documented success story of the Irish economy over the 1990s. Over the decade, the country experienced unparalleled levels of economic growth that saw unemployment levels plummet, inflation levels stabilize and inward investment rise at a substantial rate. Growth rates of gross national product (GNP) best surmise the Irish case, the tigerish performance brought the country from one with a per capita GNP two-thirds of the European Union (EU) average in 1987, to one which exceeded the average 10 years later. An exposition of Irelands pursuit of a foreign direct investment (FDI) development model forms a major part of this work. Recognizing the importance of FDI in Ireland, and FDI in the software sector in particular, this paper shows how and why investors flocked into the country over the golden era of the 1990s. Exogenously, Irelands place on the outskirts of one of the worlds biggest markets made it an alluring option for outside investors. Endogenously, the rationale behind the pursuit of high-tech FDI policy, beyond employment creation was the expected spill-over effects of multinational companies (MNCs) on the local economy. Questions are asked about the nature of positive externalities both in terms of the growth of an indigenous sector alongside a foreign-owned one as well as the sustainability of this type of investment. Changes in the organizational structures of MNCs over the 1990s, through decentralization of activities and outsourcing are integral to the Irish success story. Organizational transformation resulting in networks of global production have helped Ireland, as a peripheral region, to reposition itself as an access point to the lucrative European market. The geographic alteration on the national level however, has not been recreated on the sub-national scale. Contrary to the writings of many technology determinists, Irelands pursuit of an information economy has had a very real impact in terms of regional economic divergence within the country. The lack of coherent regional or spatial planning is to blame along with a telecommunications infrastructure that has exacerbated the regional woes of an economy with an explicit focus on high-technology industries.

Innovation systems in the European periphery: The policy approaches of Ireland and Greece

In this paper, we chart the historical evolution of the national innovation systems of Ireland and Greece, under the light of contemporaneous economic, technological and institutional developments. We argue that, among other things, the drafting of policy and the consequent shaping of their institutions has been an important delineator. We observe that importing solutions from abroad, with Greece looking to Brussels and Ireland to the USA, was central to their respective experiences. We conclude that effective innovation policy must also take into account of novel, context-specific approaches to governance. Copyright , Beech Tree Publishing.

A Novel Method of Microsatellite Genotyping-By-Sequencing Using Individual Combinatorial Barcoding

This study examines the potential of next-generation sequencing based ‘genotyping-by-sequencing’ (GBS) of microsatellite loci for rapid and cost-effective genotyping in large-scale population genetic studies. The recovery of individual genotypes from large sequence pools was achieved by PCR-incorporated combinatorial barcoding using universal primers. Three experimental conditions were employed to explore the possibility of using this approach with existing and novel multiplex marker panels and weighted amplicon mixture. The GBS approach was validated against microsatellite data generated by capillary electrophoresis. GBS allows access to the underlying nucleotide sequences that can reveal homoplasy, even in large datasets and facilitates cross laboratory transfer. GBS of microsatellites, using individual combinatorial barcoding, is potentially faster and cheaper than current microsatellite approaches and offers better and more data.

Building a Knowledge Economy in Ireland Through European Research Networks

The success of the Irish economy, and the technology sector in particular, over the last decade has been well noted. This article seeks to uncover the role that Irish participation in the ESPRIT programme of the European Unions Fourth Framework Programme has played in the building of Irelands knowledge economy through its promotion of research collaboration. The primary goal of ESPRIT was the promotion of networking between organizations of similar interest across Europe, and in this article we examine the effects of the imposition of these more formal networks on organizations. The shift towards the promotion of more informal networks among European organizations in the pursuit of innovation is highlighted. After looking at Irish participation in the programme, we gauge the success of various projects and partners, and note the differences between networks, which were in place before participation in ESPRIT, where personal networking was evident, and the more formal networks created by ESPRIT. What becomes most obvious from analysing Irish participation is the conscious move on the part of those networks with a prior existence to advance their own research agenda by means of ESPRIT.

An eDNA assay for Irish Petromyzon marinus and Salmo trutta and field validation in running water.

This pilot study presents an environmental DNA (eDNA) assay for sea lamprey Petromyzon marinus and brown trout Salmo trutta, two species of economic and conservation importance in the Republic of Ireland. The results demonstrate the effectiveness of eDNA for assessing presence of low-abundance taxa (here, P. marinus) for environmental managers, and they highlight the potential for assessing relative abundance of rare or invasive freshwater species.

Comparison of granulometric methods and sampling strategies used in marine habitat classification and Ecological Status assessment

Sediment particle size analysis (PSA) is routinely used to support benthic macrofaunal community distribution data in habitat mapping and Ecological Status (ES) assessment. No optimal PSA Method to explain variability in multivariate macrofaunal distribution has been identified nor have the effects of changing sampling strategy been examined. Here, we use benthic macrofaunal and PSA grabs from two embayments in the south of Ireland. Four frequently used PSA Methods and two common sampling strategies are applied. A combination of laser particle sizing and wet/dry sieving without peroxide pre-treatment to remove organics was identified as the optimal Method for explaining macrofaunal distributions. ES classifications and EUNIS sediment classification were robust to changes in PSA Method. Fauna and PSA samples returned from the same grab sample significantly decreased macrofaunal variance explained by PSA and caused ES to be classified as lower. Employing the optimal PSA Method and sampling strategy will improve benthic monitoring.

The Galway astronomical Stokes polarimeter: an all-Stokes optical polarimeter with ultra-high time resolution

Many astronomical objects emit polarised light, which can give information both about their source mechanisms, and about (scattering) geometry in their source regions. To date (mostly) only the linearly polarised components of the emission have been observed in stellar sources. Observations have been constrained because of instrumental considerations to periods of excellent observing conditions, and to steady, slowly or periodically-varying sources. This leaves a whole range of interesting objects beyond the range of observation at present. The Galway Astronomical Stokes Polarimeter (GASP) has been developed to enable us to make observations on these very sources. GASP measures the four components of the Stokes Vector simultaneously over a broad wavelength range 400–800 nm., with a time resolution of order microseconds given suitable detectors and a bright source - this is possible because the optical design contains no moving or modulating components. The initial design of GASP is presented and we include some preliminary observational results demonstrating that components of the Stokes vector can be measured to

Multiplexing with three-primer PCR for rapid and economical microsatellite validation.

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