List 229: Irish and English Dendrochronology

These results cover dating undertaken since the last published list of dated building from Ireland (Brown (2002)); one English church building is also included in the list. Thanks are due to the owners of the buildings and especially to everyone who assisted in taking of the samples: Phil Barrett, Sapphire Mussen, Charles Lyons, Jon Pilcher and Mike Baillie, Amanda Pedlow, Caimin O’Brien and Martin Timoney. Most of the descriptions of the buildings are taken from the National Inventory of Architectural Heritage http://www.buildingofi reland.ie/. The correlation values were generated by CROSS84 (Munro, 1984), which provides a signifi cance level for the date to be correct; *** (extremely signifi cant), ** (very signifi cant), * (signifi cant), nsm (not signifi cant). Estimated felling date ranges are based on the Belfast sapwood estimate of 32 ± 9 years. Date ranges have been calculated by adding and subtracting 9 years from the calculated estimated felling dates. Timbers from the following buildings could not be dated. Cork: St Finbarre’s Cathedral (W 675 715); Dublin: Christchurch Cathedral (O 152 341); Galway: Cloghan Castle (M 972 119); Kilkenny: Rothe House (S 506 563); Offaly: Boveen House (S 075 956); Waterford: Christchurch Cathedral (S 616 121). Generally only single oak samples were recovered from these structures. References: D.Brown, ‘Dendrochronological dating building from Ireland’, VA 33 (2002), 71–3; M. Munro, ‘An improved algorithm for crossdating tree-ring series’, Tree-Ring Bulletin 44 (1984), 17–27.

Resolving genetic functions within microbial populations: In situ analyses using rRNA and mRNA stable isotope probing coupled with single-cell raman-fluorescence in situ hybridization

Prokaryotes represent one-half of the living biomass on Earth, with the vast majority remaining elusive to culture and study within the laboratory. As a result, we lack a basic understanding of the functions that many species perform in the natural world. To address this issue, we developed complementary population and single-cell stable isotope (C-13)-linked analyses to determine microbial identity and function in situ. We demonstrated that the use of rRNA/mRNA stable isotope probing (SIP) recovered the key phylogenetic and functional RNAs. This was followed by single-cell physiological analyses of these populations to determine and quantify in situ functions within an aerobic naphthalene-degrading groundwater microbial community. Using these culture-independent approaches, we identified three prokaryote species capable of naphthalene biodegradation within the groundwater system: two taxa were isolated in the laboratory (Pseudomonas fluorescens and Pseudomonas putida), whereas the third eluded culture (an Acidovorax sp.). Using parallel population and single-cell stable isotope technologies, we were able to identify an unculturable Acidovorax sp. which played the key role in naphthalene biodegradation in situ, rather than the culturable naphthalene-biodegrading Pseudomonas sp. isolated from the same groundwater. The Pseudomonas isolates actively degraded naphthalene only at naphthalene concentrations higher than 30 mu M. This study demonstrated that unculturable microorganisms could play important roles in biodegradation in the ecosystem. It also showed that the combined RNA SIP-Raman-fluorescence in situ hybridization approach may be a significant tool in resolving ecology, functionality, and niche specialization within the unculturable fraction of organisms residing in the natural environment.

Development of a novel DNA microarray to detect bacterial pathogens in patients with chronic obstructive pulmonary disease (COPD)

A novel microarray was constructed with DNA PCR product probes targeting species specific functional genes of nine clinically significant respiratory pathogens, including the Gram-positive organisms (Streptococcus pneumoniae, Streptococcus pyogenes), the Gram-negative organisms (Chlamydia pneumoniae, Coxiella burnetii Haemophilus spp., Legionella pneumophila, Moraxella catarrhalis, and Pseudomonas aeruginosa), as well as the atypical bacterium, Mycoplasma pneumoniae. In a "proof-of-concept" evaluation of the developed microarray, the microarray was compared with real-time PCR from 14 sputum specimens from COPD patients. All of the samples positive for bacterial species in real-time PCR were also positive for the same bacterial species using the microarray. This study shows that a microarray using PCR probes is a potentially useful method to monitor the populations of bacteria in respiratory specimens and can be tailored to specific clinical needs such as respiratory infections of particular patient populations, including patients with cystic fibrosis and bronchiectasis. (C) 2010 Elsevier B.V. All rights reserved.

Isotopic composition of inorganic carbon as an indicator of benzoate degradation by Pseudomonas putida: temperature, growth rate and pH effects.

Degradation experiments of benzoate by Pseudomonas putida resulted in enzymatic carbon isotope fractionations. However, isotopic temperature effects between experiments at 20 and 30 °C were minor. Averages of the last three values of the CO2 isotopic composition (δ13CCO2(g)) were more negative than the initial benzoate δ13C value (−26.2‰ Vienna Pee Dee Belenite (VPDB)) by 3.8, 3.4 and 3.2‰ at 20, 25 and 30 °C, respectively. Although the maximum isotopic temperature difference found was only 0.6‰, more extreme temperature variations may cause larger isotope effects. In order to understand the isotope effects on the total inorganic carbon (TIC), a better measure is to calculate the proportions of the inorganic carbon species (CO2(g), CO2(aq) and HCO3−) and to determine their cumulative δ13CTIC. In all three experiments δ13CTIC was more positive than the initial isotopic composition of the benzoate at a pH of 7. This suggests an uptake of 12C in the biomass in order to match the carbon balance of these closed system experiments.

Community Cohesion and Social Inclusion: Unravelling a Complex Relationship

In a global context of an emphasis on identity politics and a ‘cultural turn’ in social analysis, deep concern has been expressed about multiethnic Britain becoming a broken society with many ‘sleepwalking’ into segregation and separatism. Given the close correspondence between areas of acute ethnic segregation and those of multiple deprivation, intercommunal tensions have included disputes about the equitable allocation of scarce urban resources across ethnicity. This creates the possibility that urban programmes may inadvertently accentuate intercommunal tension and confound efforts to synchronise cohesion and inclusion agendas. Following recent debates about the implications of increased diversity, influenced by arguments that multiculturalism has encouraged ‘parallel lives’, an emergent policy framework emphasises more proactive integration to promote ‘common belonging’. Criticism of this agenda includes its confusion between community and social cohesion, and its disproportionate focus on cultural aspects such as identity formation and recognition, relative to structural issues of income and class. In exploring this contested terrain in Britain, the article suggests that the longer-term debate about segregation, deprivation and community differentials in Northern Ireland can offer useful insight for Britain’s policy discourse.

Genomes of "phiKMV-like viruses" of Pseudomonas aeruginosa contain localized single-strand interruptions

The "phiKMV-like viruses" comprise an important genus of T7 related phages infecting Pseudomonas aeruginosa. The genomes of these bacteriophages have localized single-strand interruptions (nicks), a distinguishing genomic trait previously thought to be unique for T5 related coliphages. Analysis of this feature in the newly sequenced phage fkF77 shows all four nicks to be localized on the non-coding DNA strand. They are present with high frequencies within the phage population and are introduced into the phage DNA at late stages of the lytic cycle. The general consensus sequence in the nicks (5'-CGACxxxxxCCTAoh pCTCCGG-3') was shown to be common among all phiKMV-related phages.

Resource access needs and capabilities as mediators of the relationship between VC firm size and syndication

Drawing from the resource-based view and transaction costs economics, we develop a theoretical framework to explain why small and large firms face different levels of resource access needs and resource access capabilities, which mediate the relationship between firm size and hybrid governance. Employing a sample of 317 venture capital firms, drawn across six European countries, we empirically assess our framework in the context of venture capital syndication. We estimate a path model using structural equation modeling and find, consistent with our theoretical framework, mediating effects of different types of resource access needs and resource access capabilities between VC firm size and syndication frequency. These findings advance the small business literature by highlighting the trade-offs that size imposes on firms that seek to manage their access to external resources through hybrid governance strategies.