Influence of the earth rotation on the interfacial wave solutions and wave-induced tangential stress in a two-layer fluid system

Interfacial waves and wave-induced tangential stress are studied for geostrophic small amplitude waves of two-layer fluid with a top free surface and a flat bottom. The solutions were deduced from the general form of linear fluid dynamic equations of two-layer fluid under the f-plane approximation, and wave-induced tangential stress were estimated based on the solutions obtained. As expected; the solutions derived from the present work include as special cases those obtained by Sun et al. (2004. Science in China, Set. D, 47(12): 1147-1154) for geostrophic small amplitude surface wave solutions and wave-induced tangential stress if tire density of the upper layer is much smaller than that of the lower layer. The results show that the interface and the surface will oscillate synchronously, and the influence of the earth's rotation both on the surface wave solutions and the interfacial wave solutions should be considered.

Interactions between the bloom-forming dinoflagellates Prorocentrum donghaiense and Alexandrium tamarense in laboratory cultures

Interactions between Prorocentrum donghaiense and Alexandrium tamarens, two bloom-forming dinoflagellates, were investigated using bi-algal cultures. All R donghaiense died, but A. tamarense was hardly affected by the end of the experiment when the initial cell density was set at 1.0 X 10(4) cells mL(-1) for P. donghaiense and 0.28 x 10(4) cells mL(-1) for A. tamarense. However, significant growth suppression occurred in either species when the initial cell density of P donghaiense increased to I. 0 X 105 Cells mL(-1) in the bi-algal culture, but no out-competement was observed. The simultaneous assay on the culture filtrates showed that P donghaiense filtrate prepared at a lower initial density (1.0 X 10(4) cells mL(-1)) stimulated growth of the co-cultured A. tanzarense (0.28 x 10(4) cells mL(-1)), but filtrate at a higher initial density (1.0 x 10(5) cells mL(-1)) depressed its growth. The filtrate of A. tamarense at a density of 0.28 x 10(4) cells mL(-1) killed all R donghaiense at a lower density (1.0 x 10(4) cells mL(-1)), but only exhibited an inhibitory effect on it at a higher density (1.0 x 10(5) cells mL(-1)). It is likely that these two species of microalgae interfere with each other mainly by releasing allelochemical substance(s) into the culture medium, and a direct cell-to-cell contact was not necessary for their mutual interaction. The allelopathic test further proved that A. tamarense could affect the growth of co-cultured P. donghaiense by producing allelochemical(s); moreover, A. tamarense culture filtrate at the stationary growth phase (SP) had a strongly inhibitory effect on P donghaiense compared to that at the exponential phase (EP). Results also demonstrated a dose-dependent relationship between the microalgal initial cell density and the degree of the allelopathic effect. The growth of R donghaiense and A. tamarense in the bi-algal cultures was simulated using a mathematical model to quantify the interaction. The estimated parameters from the model showed that the inhibition exerted by A. tamarense on P. donghaiense was about 17 and 8 times stronger than the inhibition P. donghaiense exerted on A. tamarense, when the initial cell density was set at 1.0 X 10(4) and 1.0 X 10(5) cells mL(-1) for P donghaiense, respectively. and 0.28 x 10(4) cells mL(-1) for A. tamarense in the bi-algal cultures. A. tamarense seems to have a survival strategy that is superior to that of P. donghaiense in bi-algal cultures under controlled laboratory conditions. (c) 2006 Elsevier B.V. All rights reserved.

Two trichodinid ectoparasites from marine molluscs in the Yellow Sea, off China, with the description of Trichodina caecellae n. sp (Protozoa : Ciliophora : Peritrichia)

The morphology and infraciliature of two ectoparasitic ciliates, Trichodina caecellae n. sp. and T. ruditapicis Xu, Song & Warren, 2000, parasitising the gills of marine molluscs from the Shandong coast of the Yellow Sea, China, were investigated following wet silver nitrate and protargol impregnation. T. caecellae was found on the small marine sand clam Caecella chinensis Deshayes and is distinguished mainly by the acute triangle-like blade, the very delicate central part and the needle-shaped ray. T. ruditapicis was studied based on four populations from three clams: two populations from Ruditapes philippinarum (Adams) and one each from Saxidomus purpuratus (Sowerby) and Solen grandis Dunker. All four populations fell within the range of morphometry and agreed closely in the overall appearance of the adhesive disc. However, variability was found in the denticle structure, especially in populations from different host clams. Our observations suggest that denticle morphology may be more or less variable between and within populations, and that such minor differences should not be overestimated. It should be emphasised that, except for the denticle morphology, the bright granules or circles in the centre of the adhesive disc represent another important feature facilitating the identification of this trichodinid species.

Illness and elevated Human Mortality in Europe Coincident with the Laki Fissure eruption

Grattan, J. Durand, M. Taylor, S., Illness and elevated Human Mortality in Europe Coincident with the Laki fissure eruption. In: 'Volcanic Degassing: Geological Society, Special Publication 213', Oppenheimer, C., Pyle, D.M. and Barclay, J. (eds). Geological Society, London, Special Publications, 410-414, 2003.

An exploration of the positive and negative relationships associated with the development of asthma and atopic disorders in primary school children in Cork

Childhood asthma, allergic rhinitis and eczema are complex heterogenic chronic inflammatory allergic disorders which constitute a major burden to children, their families. The prevalence of childhood allergic disorders is increasing worldwide and merely rudimentary understanding exists regarding causality, or the influence of the environment on disease expression. Phase Three of the International Study of Asthma and Allergy in Childhood (ISAAC) reported that Irish adolescents had the 4th highest eczema and rhinoconjunctivitis prevalence and 3rd highest asthma prevalence in the world. There are no ISAAC data pertaining to young Irish children. In 2002, Sturley reported a high prevalence of current asthma in Cork primary school children aged 6-9 years. This thesis comprises of three cross-sectional studies which examined the prevalence of and associations with childhood allergy and a quasi-retrospective cohort study which observed the natural history of allergy from 6-9 until 11-13 years. Although not part of ISAAC, data was attained by parentally completed ISAAC-based questionnaires, using the ISAAC protocol. The prevalence, natural history and risk factors of childhood allergy in Ireland, as described in this thesis, echo those in worldwide allergy research. The variations of prevalence in different populations worldwide and the recurring themes of associations between childhood allergy and microbial exposures, from farming environments and/or gastrointestinal infections, as shown in this thesis, strengthen the mounting evidence that microbial exposure on GALT may hold the key to the mechanisms of allergy development. In this regard, probiotics may be an area of particular interest in allergy modification. Although their effects in relation to allergy, have been investigated now for several years, our knowledge of their diversity, complex functions and interactions with gut microflora, remain rudimentary. Birth cohort studies which include genomic and microbiomic research are recommended in order to examine the underlying mechanisms and the natural course of allergic diseases.

Eco-evolutionary feedbacks in community and ecosystem ecology: interactions between the ecological theatre and the evolutionary play.

Interactions between natural selection and environmental change are well recognized and sit at the core of ecology and evolutionary biology. Reciprocal interactions between ecology and evolution, eco-evolutionary feedbacks, are less well studied, even though they may be critical for understanding the evolution of biological diversity, the structure of communities and the function of ecosystems. Eco-evolutionary feedbacks require that populations alter their environment (niche construction) and that those changes in the environment feed back to influence the subsequent evolution of the population. There is strong evidence that organisms influence their environment through predation, nutrient excretion and habitat modification, and that populations evolve in response to changes in their environment at time-scales congruent with ecological change (contemporary evolution). Here, we outline how the niche construction and contemporary evolution interact to alter the direction of evolution and the structure and function of communities and ecosystems. We then present five empirical systems that highlight important characteristics of eco-evolutionary feedbacks: rotifer-algae chemostats; alewife-zooplankton interactions in lakes; guppy life-history evolution and nutrient cycling in streams; avian seed predators and plants; and tree leaf chemistry and soil processes. The alewife-zooplankton system provides the most complete evidence for eco-evolutionary feedbacks, but other systems highlight the potential for eco-evolutionary feedbacks in a wide variety of natural systems.

Receptor and G betagamma isoform-specific interactions with G protein-coupled receptor kinases.

The G protein-coupled receptor (GPCR) kinases (GRKs) phosphorylate and desensitize agonist-occupied GPCRs. GRK2-mediated receptor phosphorylation is preceded by the agonist-dependent membrane association of this enzyme. Previous in vitro studies with purified proteins have suggested that this translocation may be mediated by the recruitment of GRK2 to the plasma membrane by its interaction with the free betagamma subunits of heterotrimeric G proteins (G betagamma). Here we demonstrate that this mechanism operates in intact cells and that specificity is imparted by the selective interaction of discrete pools of G betagamma with receptors and GRKs. Treatment of Cos-7 cells transiently overexpressing GRK2 with a beta-receptor agonist promotes a 3-fold increase in plasma membrane-associated GRK2. This translocation of GRK2 is inhibited by the carboxyl terminus of GRK2, a known G betagamma sequestrant. Furthermore, in cells overexpressing both GRK2 and G beta1 gamma2, activation of lysophosphatidic acid receptors leads to the rapid and transient formation of a GRK/G betagamma complex. That G betagamma specificity exists at the level of the GPCR and the GRK is indicated by the observation that a GRK2/G betagamma complex is formed after agonist occupancy of the lysophosphatidic acid and beta-adrenergic but not thrombin receptors. In contrast to GRK2, GRK3 forms a G betagamma complex after stimulation of all three GPCRs. This G betagamma binding specificity of the GRKs is also reflected at the level of the purified proteins. Thus the GRK2 carboxyl terminus binds G beta1 and G beta2 but not G beta3, while the GRK3 fusion protein binds all three G beta isoforms. This study provides a direct demonstration of a role for G betagamma in mediating the agonist-stimulated translocation of GRK2 and GRK3 in an intact cellular system and demonstrates isoform specificity in the interaction of these components.

A complex intronic enhancer regulates expression of the CFTR gene by direct interaction with the promoter.

Genes can maintain spatiotemporal expression patterns by long-range interactions between cis-acting elements. The cystic fibrosis transmembrane conductance regulator gene (CFTR) is expressed primarily in epithelial cells. An element located within a DNase I-hypersensitive site (DHS) 10 kb into the first intron was previously shown to augment CFTR promoter activity in a tissue-specific manner. Here, we reveal the mechanism by which this element influences CFTR transcription. We employed a high-resolution method of mapping DHS using tiled microarrays to accurately locate the intron 1 DHS. Transfection of promoter-reporter constructs demonstrated that the element displays classical tissue-specific enhancer properties and can independently recruit factors necessary for transcription initiation. In vitro DNase I footprinting analysis identified a protected region that corresponds to a conserved, predicted binding site for hepatocyte nuclear factor 1 (HNF1). We demonstrate by electromobility shift assays (EMSA) and chromatin immunoprecipitation (ChIP) that HNF1 binds to this element both in vitro and in vivo. Moreover, using chromosome conformation capture (3C) analysis, we show that this element interacts with the CFTR promoter in CFTR-expressing cells. These data provide the first insight into the three- dimensional (3D) structure of the CFTR locus and confirm the contribution of intronic cis-acting elements to the regulation of CFTR gene expression.

Predictions of segregation of granular material with the aid of PHYSICA, a 3-D unstructured finite-volume modelling framework

In this paper a continuum model for the prediction of segregation in granular material is presented. The numerical framework, a 3-D, unstructured grid, finite-volume code is described, and the micro-physical parametrizations, which are used to describe the processes and interactions at the microscopic level that lead to segregation, are analysed. Numerical simulations and comparisons with experimental data are then presented and conclusions are drawn on the capability of the model to accurately simulate the behaviour of granular matter during flow.

Low temperature crystal structure of N-Acetyl-L-Glutamic acid: comparison with the DFT calculated structure

N-acetyl-L-glutamic acid, crystallizes in the orthorhombic space group P2(1)2(1)2(1) with unit cell parameters a = 4.747(3), b = 12.852(7), c = 13.906(7) Å, V = 848.5(8) Å3, Z = 4, density (calculated) = 1.481 mg/m3, linear absorption coefficient 0.127 mm−1. The crystal structure determination was carried out with MoKalpha X-ray data measured with liquid nitrogen cooling at 100(2) K temperature. In the final refinement cycle the data/restraints/parameter ratios were 1,691/0/131; goodness-of-fit on F(2) = 1.122. Final R indices for [I > 2sigma(I)] were R1 = 0.0430, wR2 = 0.0878 and R indices (all data) R1 = 0.0473, wR2 = 0.0894. The largest electron density difference peak and hole were 0.207 and −0.154 eÅ(−3). Details of the molecular geometry are discussed and compared with a model DFT structure calculated using Gaussian 98.

The response of phytoplankton to climate variability associated with the North Atlantic Oscillation

Inter-annual variability in the timing of phytoplankton spring bloom and phytoplankton community structure in the central North Atlantic Ocean was quantified using ocean color data and continuous plankton recorder (CPR) data. This variability was related to the North Atlantic Oscillation using correlation analysis and multivariate auto-regression models. The initiation of the spring bloom derived from CPR phytoplankton color index data is similar to that derived from satellite chlorophyll, and exhibits a nominal correlation with the sea surface temperature (SST) and the North Atlantic Oscillation (NAO). The extrapolated spring bloom timing suggested later initiation of blooms in the mid-1980s and earlier initiation of blooms in the 1990s. The climatological phytoplankton community structure in the central North Atlantic is dominated by diatoms, except for a shift in community composition favoring dinoflagellates in August. The ratio of diatoms to total phytoplankton abundance and the ratio of dinoflagellates to total phytoplankton abundance are both closely correlated with the NAO and SST. The extended time series of phytoplankton community structure between 1985 and 2009, deduced from the time series of SST and NAO over the same interval, showed a decadal shift away from diatoms towards dinoflagellates. The linkages between the NAO, and changes in stratification and phytoplankton processes occur over a larger scale than previously observed.

Horizon scanning for invasive alien species with the potential to threaten biodiversity in Great Britain

Invasive alien species (IAS) are considered one of the greatest threats to biodiversity, particularly through their interactions with other drivers of change. Horizon scanning, the systematic examination of future potential threats and opportunities, leading to prioritization of IAS threats is seen as an essential component of IAS management. Our aim was to consider IAS that were likely to impact on native biodiversity but were not yet established in the wild in Great Britain. To achieve this, we developed an approach which coupled consensus methods (which have previously been used for collaboratively identifying priorities in other contexts) with rapid risk assessment. The process involved two distinct phases: 1. Preliminary consultation with experts within five groups (plants, terrestrial invertebrates, freshwater invertebrates, vertebrates and marine species) to derive ranked lists of potential IAS. 2. Consensus-building across expert groups to compile and rank the entire list of potential IAS. Five hundred and ninety-one species not native to Great Britain were considered. Ninety-three of these species were agreed to constitute at least a medium risk (based on score and consensus) with respect to them arriving, establishing and posing a threat to native biodiversity. The quagga mussel, Dreissena rostriformis bugensis, received maximum scores for risk of arrival, establishment and impact; following discussions the unanimous consensus was to rank it in the top position. A further 29 species were considered to constitute a high risk and were grouped according to their ranked risk. The remaining 63 species were considered as medium risk, and included in an unranked long list. The information collated through this novel extension of the consensus method for horizon scanning provides evidence for underpinning and prioritizing management both for the species and, perhaps more importantly, their pathways of arrival. Although our study focused on Great Britain, we suggest that the methods adopted are applicable globally.

Progress in satellite remote sensing for studying physical processes at the ocean surface and its borders with the atmosphere and sea-ice

Physical oceanography is the study of physical conditions, processes and variables within the ocean, including temperature-salinity distributions, mixing of the water column, waves, tides, currents, and air-sea interaction processes. Here we provide a critical review of how satellite sensors are being used to study physical oceanography processes at the ocean surface and its borders with the atmosphere and sea-ice. The paper begins by describing the main sensor types that are used to observe the oceans (visible, thermal infrared and microwave) and the specific observations that each of these sensor types can provide. We then present a critical review of how these sensors and observations are being used to study i) ocean surface currents, ii) storm surges, iii) sea-ice, iv) atmosphere-ocean gas exchange and v) surface heat fluxes via phytoplankton. Exciting advances include the use of multiple sensors in synergy to observe temporally varying Arctic sea-ice volume, atmosphere- ocean gas fluxes, and the potential for 4 dimensional water circulation observations. For each of these applications we explain their relevance to society, review recent advances and capability, and provide a forward look at future prospects and opportunities. We then more generally discuss future opportunities for oceanography-focussed remote-sensing, which includes the unique European Union Copernicus programme, the potential of the International Space Station and commercial miniature satellites. The increasing availability of global satellite remote-sensing observations means that we are now entering an exciting period for oceanography. The easy access to these high quality data and the continued development of novel platforms is likely to drive further advances in remote sensing of the ocean and atmospheric systems.

Fitness reduction and potential extinction of wild populations of Atlantic salmon, Salmo salar, as a result of interactions with escaped farm salmon.

The high level of escapes from Atlantic salmon farms, up to two million fishes per year in the North Atlantic, has raised concern about the potential impact on wild populations. We report on a twogeneration experiment examining the estimated lifetime successes, relative to wild natives, of farm, F1 and F2 hybrids and BC1 backcrosses to wild and farm salmon. Offspring of farm and hybrids (i.e. all F1 , F2 and BC1 groups) showed reduced survival compared with wild salmon but grew faster as juveniles and displaced wild parr, which as a group were significantly smaller. Where suitable habitat for these emigrant parr is absent, this competition would result in reduced wild smolt production. In the experimental conditions, where emigrants survived downstream, the relative estimated lifetime success ranged from 2% (farm) to 89% (BC1 wild) of that of wild salmon, indicating additive genetic variation for survival . Wild salmon primarily returned to fresh water after one sea winter (1SW) but farm and hybrids produced proportionately more 2SW salmon. However, lower overall survival means that this would result in reduced recruitment despite increased 2SW fecundity. We thus demonstrate that interaction of farm with wild salmon results in lowered fitness, with repeated escapes causing cumulative fitness depression and potentially an extinction vortex in vulnerable populations.

Elucidation of the interactions between the transcription factor E2A and the transcriptional co-activator CBP/p300

E2A is a transcription factor that plays a particularly critical role in lymphopoiesis. The chromosomal translocation 1;19, disrupts the E2A gene and results in the expression of the fusion oncoprotein E2A-PBX1, which is implicated in acute lymphoblastic leukemia. Both E2A and E2A-PBX1 contain two activation domains, AD1 and AD2, which comprise conserved ΦxxΦΦ motifs where Φ denotes a hydrophobic amino acid. These domains function to recruit transcriptional co-activators and repressors, including the histone acetyl transferase CREB binding protein (CBP) and its paralog p300. The PCET motif within E2A AD1 interacts with the KIX domain of CBP/p300, the disruption of which abrogates the transcriptional activation by E2A and the transformative properties of E2A-PBX1. The generation of a peptide-based inhibitor targeting the PCET:KIX interaction would serve useful in further assessing the role of E2A and E2A-PBX1 in lymphopoiesis and leukemogenesis. An interaction between E2A AD2 and the KIX domain has also been recently identified, and the TAZ domains of CBP/p300 have been shown to interact with several transcription factors that contain ΦxxΦΦ motifs. Thus the design of an inhibitor of the E2A:CBP/p300 interaction requires the full complement of interactions between E2A and the various domains of CBP/p300 to be elucidated. Here, we have used nuclear magnetic resonance (NMR) spectroscopy to determine that AD2 interacts with KIX at the same site as PCET, which indicates that the E2A:KIX interaction can be disrupted by targeting a single binding site. Using an iterative synthetic peptide microarray approach, a peptide with the sequence DKELQDLLDFSLQY was derived from PCET to interact with KIX with higher affinity than the wild type sequence. This peptide now serves as a lead molecule for further development as an inhibitor of the E2A:CBP/p300 interaction. Fluorescence anisotropy, peptide microarray technology, and isothermal titration calorimetry were employed to characterize interactions between both TAZ domains of CBP/p300 and the PCET motif and AD2 of E2A. Alanine substitution of residues within PCET demonstrated that the ΦxxΦΦ motif is a key mediator of these interactions, analogous to the PCET:KIX interaction. These findings now inform future work to establish possible physiological roles for the E2A:TAZ1 and E2A:TAZ2 interactions.