Permanent Genetic Resources added to Molecular Ecology Resources Database 1 May 2009-31 July 2009

This article documents the addition of 512 microsatellite marker loci and nine pairs of Single Nucleotide Polymorphism (SNP) sequencing primers to the Molecular Ecology Resources Database. Loci were developed for the following species: Alcippe morrisonia morrisonia, Bashania fangiana, Bashania fargesii, Chaetodon vagabundus, Colletes floralis, Coluber constrictor flaviventris, Coptotermes gestroi, Crotophaga major, Cyprinella lutrensis, Danaus plexippus, Fagus grandifolia, Falco tinnunculus, Fletcherimyia fletcheri, Hydrilla verticillata, Laterallus jamaicensis coturniculus, Leavenworthia alabamica, Marmosops incanus, Miichthys miiuy, Nasua nasua, Noturus exilis, Odontesthes bonariensis, Quadrula fragosa, Pinctada maxima, Pseudaletia separata, Pseudoperonospora cubensis, Podocarpus elatus, Portunus trituberculatus, Rhagoletis cerasi, Rhinella schneideri, Sarracenia alata, Skeletonema marinoi, Sminthurus viridis, Syngnathus abaster, Uroteuthis (Photololigo) chinensis, Verticillium dahliae, Wasmannia auropunctata, and Zygochlamys patagonica. These loci were cross-tested on the following species: Chaetodon baronessa, Falco columbarius, Falco eleonorae, Falco naumanni, Falco peregrinus, Falco subbuteo, Didelphis aurita, Gracilinanus microtarsus, Marmosops paulensis, Monodelphis Americana, Odontesthes hatcheri, Podocarpus grayi, Podocarpus lawrencei, Podocarpus smithii, Portunus pelagicus, Syngnathus acus, Syngnathus typhle,Uroteuthis (Photololigo) edulis, Uroteuthis (Photololigo) duvauceli and Verticillium albo-atrum. This article also documents the addition of nine sequencing primer pairs and sixteen allele specific primers or probes for Oncorhynchus mykiss and Oncorhynchus tshawytscha; these primers and assays were cross-tested in both species.

EXPERIMENTAL INVESTIGATION OF LINEAR BUBBLE DYNAMICS IN A VISCOELASTIC XANTHAN GEL

Oceanic bubble plumes caused by ship wakes or breaking waves disrupt sonar communi- cation because of the dramatic change in sound speed and attenuation in the bubbly fluid. Experiments in bubbly fluids have suffered from the inability to quantitatively characterize the fluid because of continuous air bubble motion. Conversely, single bubble experiments, where the bubble is trapped by a pressure field or stabilizing object, are limited in usable frequency range, apparatus complexity, or the invasive nature of the stabilizing object (wire, plate, etc.). Suspension of a bubble in a viscoelastic Xanthan gel allows acoustically forced oscilla- tions with negligible translation over a broad frequency band. Assuming only linear, radial motion, laser scattering from a bubble oscillating below, through, and above its resonance is measured. As the bubble dissolves in the gel, different bubble sizes are measured in the range 240 – 470 μm radius, corresponding to the frequency range 6 – 14 kHz. Equalization of the cell response in the raw data isolates the frequency response of the bubble. Compari- son to theory for a bubble in water shows good agreement between the predicted resonance frequency and damping, such that the bubble behaves as if it were oscillating in water.

Mícheál Coimín agus a shaothar

Is é a chuirim romham a dhéanamh sa tráchtas seo ná eagar a chur ar shaothar liteartha Mhíchíl Coimín; file agus údar próis a bhí ag saothrú na litríochta i gCill Chorcoráin, Contae an Chláir san ochtú haois déag. D’éag sé sa bhliain 1760 nuair a bhí sé beagnach 90 bliain d’aois. Is féidir a rá go bhfuil an Coimíneach, ó thaobh chanóin litríocht na Gaeilge de i measc na mionscríbhneoirí, agus níl aon dabht faoi ach go bhfuil an-chuid de léitheoirí na Gaeilge sa lá atá inniu ann dall ar a chuid scríbhneoireachta. Tá cáil air mar údar ‘Laoi Oisín i dTír na n-Óg’ ach mar a léireofar sa tráchtas seo, tá gach cuma ar an scéal nárbh é a scríobh. Tá againn óna pheann dornán beag dánta agus dhá scéal rómánsaíochta (‘Eachtra Thoroilbh Mhic Stairn’ agus ‘Eachtra a Thriúr Mac’) a scríobh sé nuair a bhí an traidisiún sin próis ar an dé deiridh. Níl aon chuid dá shaothar ar fáil in eagráin a shásódh léitheoirí an lae inniu ná na critéir scolártha atá i bhfeidhm anois. Níor tháinig aon lámhscríbhinn, i lámh an Choimínigh, anuas chugainn agus dá bhrí sin bhí dúshlán áirithe ag baint leis an bpróiseas eagarthóireachta. Sa tráchtas rinne mé an suirbhé is iomláine go dtí seo ar a shaothar i dtraidisiún na lámhscríbhinní agus ar na scríobhaithe a rinne é a sheachadadh. Bhí sé mar aidhm agam teacht ar na lámhscríbhinní is údarásaí sa traidisiún d’fhonn eagráin a réiteach a bheadh dílis dá bhunshaothar. Chomh maith leis sin tabharfar cuntas ar a bheatha agus ar a chúlra liteartha, agus déanfar iniúchadh criticiúil ar a shaothar próis agus fileata.

The impact of whey protein isolate on energy balance regulation

Using C57BL/6J mice fed whey protein isolate (WPI) enriched high fat (HFD) or low-fat diets (LFD), this study tested the hypothesis that WPI directly impacts on adiposity by influencing lipid metabolism. WPI suppressed HFD-induced body fat and increased lean mass at 8 weeks of dietary challenge despite elevated plasma triacylglycerol (TAG) levels, suggesting reduced TAG storage. WPI reduced HFD-associated hypothalamic leptin and insulin receptor (IR) mRNA expression, and prevented HFD-associated reductions in adipose tissue IR and glucose transporter 4 expression. These effects were largely absent at 21 weeks of HFD feeding, however WPI increased lean mass and cause a trend towards decreased fat mass, with notable increased Lactobacillus and decreased Clostridium gut bacterial species. Increasing the protein to carbohydrate ratio enhanced the above effects, and shifted the gut microbiota composition away from the HFD group. Seven weeks of WPI intake with a LFD decreased insulin signalling gene expression in the adipose tissue in association with an increased fat accumulation. WPI reduced intestinal weight and length, suggesting a potential functional relationship between WPI, gastro-intestinal morphology and insulin related signalling in the adipose. Extending the study to 15 weeks, did not affect adipose fat weight, but decreased energy intake, weight gain and intestinal length. The functionality of protein sensing lysophosphatidic acid receptor 5 (LPA5) in 3T3-L1 pre-adipocytes was assessed. Over-expression of the receptor in 3T3-L1 pre-adipocytes provided a growth advantage to the cells and suppressed cellular differentiation into mature fat cells. In conclusion, the data demonstrates WPI impacts on adiposity by influencing lipid metabolism in a temporal manner, resulting possibly due to changes in lean mass, hypothalamic and adipose gene expression, gut microbiota and gastrointestinal morphology. The data also showed LPA5 is a novel candidate in regulating of preadipocyte growth and differentiation, and may mediate dietary protein effects on adipose tissue.

Novel insights into the expression and function of p38δ MAPK in oesophageal squamous cell carcinoma

Oesophageal cancer is an aggressive malignancy which is resistant to conventional therapy and has a poor prognosis. A greater understanding of the underlying molecular biology of oesophageal cancer and the identification of novel targets is necessary for the future treatment of this disease. This thesis focuses specifically on the ill-defined and understudied p38δ mitogen-activated protein kinase (MAPK) and its function(s) in oesophageal squamous cell carcinoma (OESCC). In contrast to the three other p38 isoforms (p38α, -β and –γ which have to-date been relatively well-studied), p38δ MAPK signalling is poorly understood. Thus, this research elucidates some of the role(s) played by p38δ MAPK in cancer progression. This work outlines how loss of p38δ MAPK expression confers greater tumourigenicity in oesophageal cancer. Restoration of p38δ MAPK expression, however, has anti-proliferative and anti-migratory effects and decreases OESCC capacity for anchorageindependent growth. Using a novel application of an enzyme-substrate fusion approach, the effect of phosphorylated p38δ (p-p38δ) MAPK expression is also considered. The work goes onto describe the effect(s) of p38δ MAPK status on the chemosensitivity of OESCC to conventional cisplatin and 5-fluorouracil (CF) versus the effectiveness of doxorubicin, cisplatin and 5-fluorouracil (ACF). ACF treatment of p38δ MAPK-negative OESCC results in decreased proliferation, migration and recovery, and increased apoptosis when compared with CF treatment. This thesis examines the potential mechanisms by which p38δ MAPK expression is lost in OESCC and identifies epigenetic regulation as the probable cause of differential p38δ MAPK expression. Also analysed is the role p38δ MAPK and p-p38δ MAPK play in the cell cycle. In summary, this research identifies p38δ MAPK as a possible molecular target and a potential predictor of response to chemotherapy in OESCC patients.

Stair na Gaeilge i gContae Thiobraid Árann 1700-1901

Stair na Gaeilge i gCo. Thiobraid Árann i rith na tréimhse 1700-1901 atá á ríomhadh sa tráchtas seo. Tar éis a cúlra agus a comhthéacs a shuíomh i gCaibidil a hAon, déantar scríobhaithe an cheantair a áireamh, fara tráchtaireacht orthu, i gCaibidil a Dó. I gCaibidlí a Trí agus a Ceathair, féachtar ar thionchar na hEaglaisí Caitlicí agus Eaglais na hÉireann (i measc eaglaisí Protastúnacha eile) ar an dteangain. I gCaibidil a Cúig, faightear spléachadh ar ghnéithe éagsúla de shaíocht an chontae, ag tabhairt léargais ar tháirgí na scríobhaithe, ar leabhair a clóbhualadh sa réigiún, agus ar fhilí móra na háite, leithéidí Liam Daill Uí Ifearnáin, ag sonrú limistéir faoi leith, an t-oirdheisceart, mar shampla. Léirítear éifeacht na gcumann Gaelach agus na ndíograiseoirí iomadúla a bhain leo. Ábhar suime, leis, feidhm na Gaeilge sna cúirteanna dlí. Tugtar faisnéis i gCaibidil a Sé ar fhianaise cuairteoirí ar an Ghaeilge mar urlabhra i dTiobraid Árann. Is anseo chomh maith a deintear anailís ar Dhaonáirimh na mblianta 1861-1901, le mórchuid adhmaid á baint as ceann 1901 go háirithe. Breactar as ainmneacha sagart agus múinteoirí le Gaeilge, agus tráchtar ar aicmí suntasacha eile, na póilíní agus na saighdiúirí a raibh an teanga sin ina mbéal acu. Tugtar le chéile dá réir na snáithíní difriúla eolais ar an dúiche ar bhealach nár tharla cheana don gcontae casta fairsing seo le haghaidh na tréimhse atá idir lámha ag an saothar.

Development and validation of a shipboard system for measuring high-resolution vertical profiles of aqueous dimethylsulfide concentrations using chemical ionization mass spectrometry

A sampling and analytical system has been developed for shipboard measurements of high-resolution vertical profiles of the marine trace gas dimethylsulfide (DMS). The system consists of a tube attached to a CTD with a peristaltic pump on deck that delivers seawater to a membrane equilibrator and atmospheric pressure chemical ionization mass spectrometer (Eq-APCIMS). This allows profiling DMS concentrations to a depth of 50 m, with a depth resolution of 1.3-2 m and a detection limit of nearly 0.1 nmol L-1. The seawater is also plumbed to allow parallel operation of additional continuous instruments, and simultaneous collection of discrete samples for complementary analyses. A valve alternates delivery of seawater from the vertical profiler and the ship�s underway intake, thereby providing high-resolution measurements in both the vertical and horizontal dimensions. Tests conducted on various cruises in the Mediterranean Sea, Atlantic, Indian, and Pacific Oceans show good agreement between the Eq-APCIMS measurements and purge and trap gas chromatography with flame photometric detection (GC-FPD) and demonstrate that the delivery of seawater from the underway pump did not significantly affect endogenous DMS concentrations. Combination of the continuous flow DMS analysis with high-frequency hydrographic, optical, biological and meteorological measurements will greatly improve the spatial/temporal resolution of seagoing measurements and improve our understanding of DMS cycling.

The role of cathepsin C in Papillon-Lefèvre syndrome, prepubertal periodontitis, and aggressive periodontitis

We have previously reported that loss-of-function mutations in the cathepsin C gene (CTSC) result in Papillon Lefevre syndrome, an autosomal recessive condition characterized by palmoplantar keratosis and early,onset, severe periodontitis. Others have also reported CTSC mutations in patients with severe prepubertal periodontitis, but without any skin manifestations. The possible role of CTSC variants in more common types of non-mendelian, early-onset, severe periodontitis ("aggressive periodontitis") has not been investigated. In this study, we have investigated the role of CTSC in all three conditions. We demonstrate that PLS is genetically homogeneous and the mutation spectrum that includes three novel mutations (c.386T>A/p. V129E, c.935A>G/p.Q312R, and c.1235A>G/p.Y412C) in 21 PLS families (including eight from our previous study) provides an insight into structure-function relationships of CTSC. Our data also suggest that a complete loss-of-function appears to be necessary for the manifestation of the phenotype, making it unlikely that weak CTSC mutations are a cause of aggressive periodontitis. This was confirmed by analyses of the CTSC activity in 30 subjects with aggressive periodontitis and age-sex matched controls, which demonstrated that there was no significant difference between these two groups (1,728.7 +/- SD 576.8 mu moles/mg/min vs. 1,678.7 +/- SD 527.2 mu moles/mg/min, respectively, p = 0.73). CTSC mutations were detected in only one of two families with prepubertal periodontitis; these did not form a separate functional class with respect to those observed in classical PLS. The affected individuals in the other prepubertal periodontitis family not only lacked CTSC mutations, but in addition did not share the haplotypes at the CTSC locus. These data suggest that prepubertal periodontitis is a genetically heterogeneous disease that, in some families, just represents a partially penetrant PLS. (C) 2004 Wiley-Liss, Inc.

The clinical significance of cathepsin S expression in human astrocytomas

Early local invasion by astrocytoma. cells results in tumor recurrence even after apparent total surgical resection, leading to the poor prognosis associated with malignant astrocytomas. Proteolytic enzymes have been implicated in facilitating tumor cell invasion and the current study was designed to characterize the expression of the cysteine proteinase cathepsin S (CatS) in astrocytomas and examine its potential role in invasion. Immunohistochemical analysis of biopsies demonstrated that CatS was expressed in astrocytoma cells but absent from normal astrocytes, oligodendrocytes, neurones and endothelial cells. Microglial cells and macrophages were also positive. Assays of specific activity in 59 astrocytoma biopsies confirmed CatS expression and in addition demonstrated that the highest levels of activity were expressed in grade IV tumors. CatS activity was also present in astrocytoma cells in vitro and the extracellular levels of activity were highest in cultures derived from grade IV tumors. In vitro invasion assays were carried out using the U251MG cell line and the invasion rate was reduced by up to 61% in the presence of the selective CatS inhibitor 4-Morpholineurea-LeuHomoPhe-vinylsulphone. We conclude that CatS expression is up-regulated in astrocytoma. cells and provide evidence for a potential role for CatS in invasion.

Rheumatologists' judgements about the efficacy of anti-TNF therapy in two neighbouring regions

Objectives: The requirement in Northern Ireland to prescribe biologic agents according to NICE/BSR guidelines and within a fixed budget has created a waiting list for treatment that has no parallel in the Republic of Ireland. The study investigated the bearing this situation may have on had on the consultants’ judgements in the respective areas.

Methods: 78 case vignettes created from the data on real patients with RA treated with biologics in the north and south of Ireland were appraised by 9 southern and 8 northern consultants who judged the clinical benefit and significance of the patients’ condition after a trial of therapy. Quantitative (Clinical Judgement Analysis) and Qualitative (Focus groups) techniques were used.

Results: Northern consultants perceived a slightly greater degree of clinical benefit after a trial of therapy than southern consultants. Judgment models of northern and southern consultants were broadly comparable. The latter tended to be more uniform in their judgments than the southern group. Focus group discussions with consultants largely validated the findings of the quantitative analysis but revealed how clinical judgment analysis might be misled by gaming strategies.

Conclusions: Despite the absence of overt rationing in the south of Ireland, as far as the judgment of therapeutic benefit from biologics was concerned, the clinical judgment policies of practitioners were very similar to those in the north. The adoption of NICE/BSR guidelines in the north may have improved the uniformity of clinical practice in Northern Ireland.