Complex Interactions between Dioxin-Like and Non-Dioxin-Like Compounds for in Vitro Cellular Responses: Implications for the Identification of Dioxin Exposure Biomarkers

Despite considerable advances in reducing the production of dioxin-like toxicants in recent years, contamination of the food chain still occasionally occurs resulting in huge losses to the agri-food sector and risk to human health through exposure. Dioxin-like toxicity is exhibited by a range of stable and bioaccumulative compounds including polychlorinated dibenzo-p-dioxins (PCDDs) and dibenzofurans (PCDFs), produced by certain types of combustion, and man-made coplanar polychlorinated biphenyls (PCBs), as found in electrical transformer oils. While dioxinergic compounds act by a common mode of action making exposure detection biomarker based techniques a potentially useful tool, the influence of co-contaminating toxicants on such approaches needs to be considered. To assess the impact of possible interactions, the biological responses of H4IIE cells to challenge by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) in combination with PCB-52 and benzo-a-pyrene (BaP) were evaluated by a number of methods in this study. Ethoxyresorufin-O-deethylase (EROD) induction in TCDD exposed cells was suppressed by increasing concentrations of PCB-52, PCB-153, or BaP up to 10 mu M. BaP levels below 1 mu M suppressed TCDD stimulated EROD induction, but at higher concentrations, EROD induction was greater than the maximum observed when cells were treated with TCDD alone. A similar biphasic interaction of BaP with TCDD co-exposure was noted in the AlamarBlue assay and to a lesser extent with PCB-52. Surface enhanced laser desorption/ionization-time of flight mass spectrometry (SELDI-TOF) profiling of peptidomic responses of cells exposed to compound combinations was compared. Cells co-exposed to TCDD in the presence of BaP or PCB-52 produced the most differentiated spectra with a substantial number of non-additive interactions observed. These findings suggest that interactions between dioxin and other toxicants create novel, additive, and non-additive effects, which may be more indicative of the types of responses seen in exposed animals than those of single exposures to the individual compounds.

Disinfection of Burkholderia cepacia complex from non-touch taps in a neonatal nursery

Burkholderia cepacia complex (Bcc) comprises nine closely related species or genomovars. It is an important causative agent of opportunistic infections and waterborne nosocomial infections. B. cepacia (formerly genomovar I) was identified from the blood culture of a baby in our neonatal unit (NU) in March 2005. B. cepacia was isolated four times from clinical specimens since the introduction of non-touch taps in the NU from 2000 to 2005 and only once from 1994 to 2000. Environmental samples were collected from the NU, including tap water from non-touch taps. Clinical and environmental isolates of Bcc were characterized using molecular identification and strain typing. A literature review was undertaken to delineate a method for eradication of Bcc. Several variations for hot water eradication of the organism from the taps were attempted. Genotyping and molecular analysis revealed that tap water isolates were B. cenocepacia which was a different species from the B. cepacia isolated from blood cultures of the neonate. However, B. cenocepacia has been known to cause nosocomial outbreaks and it was eventually eradicated from the NU by using repeated thermal shock (hot water at 65 degrees C for 10 min), changing taps and decolonizing sinks with hypochlorite. Molecular typing is useful in assisting the investigation of Bcc nosocomial infections.

Efficient Non-Linear Idealisations of Aircraft Fuselage Panels in Compression

Aircraft fuselages are complex assemblies of thousands of components and as a result simulation models are highly idealised. In the typical design process, a coarse FE model is used to determine loads within the structure. The size of the model and number of load cases necessitates that only linear static behaviour is considered. This paper reports on the development of a modelling approach to increase the accuracy of the global model, accounting for variations in stiffness due to non-linear structural behaviour. The strategy is based on representing a fuselage sub-section with a single non-linear element. Large portions of fuselage structure are represented by connecting these non-linear elements together to form a framework. The non-linear models are very efficient, reducing computational time significantly

Genomic organization, complex splicing pattern and expression of a human septin gene on chromosome 17q25.3

The Ov/Br septin gene, which is also a fusion partner of MLL in acute myeloid leukaemia, is a member of a family of novel GTP binding proteins that have been implicated in cytokinesis and exocytosis. In this study, we describe the genomic and transcriptional organization of this gene, detailing seventeen exons distributed over 240 kb of sequence. Extensive database analyses identified orthologous rodent cDNAs that corresponded to new, unidentified 5' splice variants of the Ov/Br septin gene, increasing the total number of such variants to six. We report that splicing events, occurring at non-canonical sites within the body of the 3' terminal exon, remove either 1801 bp or 1849 bp of non-coding sequence and facilitate access to a secondary open reading frame of 44 amino acids maintained near the end of the 3' UTR. These events constitute a novel coding arrangement and represent the first report of such a design being implemented by a eukaryotic gene. The various Ov/Br proteins either differ minimally at their amino and carboxy termini or are equivalent to truncated versions of larger isoforms. Northern analysis with an Ov/Br septin 3' UTR probe reveals three transcripts of 4.4, 4 and 3 kb, the latter being restricted to a sub-set of the tissues tested. Investigation of the identified Ov/Br septin isoforms by RT-PCR confirms a complex transcriptional pattern, with several isoforms showing tissue-specific distribution. To date, none of the other human septins have demonstrated such transcriptional complexity.

The complex array of bradykinin-related peptides (BRPs) in the peptidome of pickerel frog (Rana palustris) skin secretion is the product of transcriptional economy.

Previous peptidomic analyses of the defensive skin secretion from the North American pickerel frog, Rana palustris, have established the presence of canonical bradykinin and multiple bradykinin-related peptides (BRPs). As a consequence of the multiplicity of peptides identified and their diverse primary structures, it was speculated that they must represent the products of expression of multiple genes. Here, we present unequivocal evidence that the majority of BRPs (11/13) identified in skin secretion by the peptidomic approach can be generated by differential site-specific protease cleavage from a single common precursor of 321 amino acid residues, named skin kininogen 1, whose primary structure was deduced from cloned skin secretion-derived cDNA. The organization of skin kininogen 1 consists of a hydrophobic signal peptide followed by eight non-identical domains each encoding a single copy of either canonical bradykinin or a BRP. Two additional splice variants, encoding precursors of 233 (skin kininogen 2) or 189 amino acid residues (skin kininogen 3), were also cloned and were found to lack BRP-encoding domains 5 and 6 or 4, 5 and 6, respectively. Thus, generation of peptidome diversity in amphibian defensive skin secretions can be achieved in part by differential protease cleavage of relatively large and multiple-encoding domain precursors reflecting a high degree of transcriptional economy.

Ion-acoustic waves in a plasma consisting of adiabatic warm ions, non-isothermal electrons and a weakly relativistic electron beam: linear and higher-order nonlinear effects

The nonlinear propagation of finite amplitude ion acoustic solitary waves in a plasma consisting of adiabatic warm ions, nonisothermal electrons, and a weakly relativistic electron beam is studied via a two-fluid model. A multiple scales technique is employed to investigate the nonlinear regime. The existence of the electron beam gives rise to four linear ion acoustic modes, which propagate at different phase speeds. The numerical analysis shows that the propagation speed of two of these modes may become complex-valued (i.e., waves cannot occur) under conditions which depend on values of the beam-to-background-electron density ratio , the ion-to-free-electron temperature ratio , and the electron beam velocity v0; the remaining two modes remain real in all cases. The basic set of fluid equations are reduced to a Schamel-type equation and a linear inhomogeneous equation for the first and second-order potential perturbations, respectively. Stationary solutions of the coupled equations are derived using a renormalization method. Higher-order nonlinearity is thus shown to modify the solitary wave amplitude and may also deform its shape, even possibly transforming a simple pulse into a W-type curve for one of the modes. The dependence of the excitation amplitude and of the higher-order nonlinearity potential correction on the parameters , , and v0 is numerically investigated.

Genetic association analyses of non-synonymous single nucleotide polymorphisms in diabetic nephropathy

Aims/hypothesis: Diabetic nephropathy, characterised by persistent proteinuria, hypertension and progressive kidney failure, affects a subset of susceptible individuals with diabetes. It is also a leading cause of end-stage renal disease (ESRD). Non-synonymous (ns) single nucleotide polymorphisms (SNPs) have been reported to contribute to genetic susceptibility in both monogenic disorders and common complex diseases. The objective of this study was to investigate whether nsSNPs are involved in susceptibility to diabetic nephropathy using a case-control design.

Methods: White type 1 diabetic patients with (cases) and without (controls) nephropathy from eight centres in the UK and Ireland were genotyped for a selected subset of nsSNPs using Illumina's GoldenGate BeadArray assay. A ? 2 test for trend, stratified by centre, was used to assess differences in genotype distribution between cases and controls. Genomic control was used to adjust for possible inflation of test statistics, and the False Discovery Rate method was used to account for multiple testing.

Results: We assessed 1,111 nsSNPs for association with diabetic nephropathy in 1,711 individuals with type 1 diabetes (894 cases, 817 controls). A number of SNPs demonstrated a significant difference in genotype distribution between groups before but not after correction for multiple testing. Furthermore, neither subgroup analysis (diabetic nephropathy with ESRD or diabetic nephropathy without ESRD) nor stratification by duration of diabetes revealed any significant differences between groups.

Conclusions/interpretation: The nsSNPs investigated in this study do not appear to contribute significantly to the development of diabetic nephropathy in patients with type 1 diabetes.

Do non-native invasive fish support elevated lamprey populations?

Summary
1: Managing populations of predators and their prey to achieve conservation or resource management goals is usually technically challenging and frequently socially controversial. This is true even in the simplest ecosystems but can be made much worse when predator–prey relationships are in?uenced by complex interactions, such as biological invasions, population trends or animal movements.
2: Lough Neagh in Northern Ireland is a European stronghold for pollan Coregonus autumnalis, a coregonine ?sh and for river lampreyLampetra ?uviatilis, which feeds parasitically as an adult. Both species are of high conservation importance. Lampreys are known to consume pollan but detailed knowledge of their interactions is scant. While pollan is well known to be a landlocked species in Ireland, the life cycle of normally anadromous river lamprey in Lough Neagh has been unclear. The Lough is also a highly perturbed ecosystem, supporting several invasive, non-native ?sh species that have the potential to in?uence lamprey–pollan interactions.
3: We applied stable isotope techniques to resolve both the movement patterns of lamprey and trophic interactions in this complex community. Recognizing that stable isotope studies are often hampered by high-levels of variability and uncertainty in the systems of interest, we employed novel Bayesian mixing models, which incorporate variability and uncertainty.
4: Stable isotope analyses identi?ed troutSalmo trutta and non-native breamAbramis brama as the main items in lamprey diet. Pollan only represented a major food source for lamprey between May and July.
5: Stable isotope ratios of carbon in tissues from 71 adult lamprey showed no evidence of marine carbon sources, strongly suggesting that Lough Neagh is host to a highly unusual, nonanadromous freshwater population. This ?nding marks out the Lough’s lamprey population as of particular scienti?c interest and enhances the conservation signi?cance of this feature of the Lough.
6: Synthesis and applications.Our Bayesian isotopic mixing models illustrate an unusual pattern of animal movement, enhancing conservation interest in an already threatened population. We have also revealed a complex relationship between lamprey and their food species that is suggestive of hyperpredation, whereby non-native species may sustain high lamprey populations that may in turn be detrimental to native pollan.Long-term conservation of lamprey and pollan in this system is likely to require management intervention, but in light of this exceptional complexity, no simple management options are currently supported. Conservation plans will require better characterization ofpopulation-level interactions and simulation modelling of interventions. More generally, our study demonstrates the importance of considering a full range of possible trophic interactions, particularly in complex ecosystems, and highlights Bayesian isotopic mixing models as powerful tools in resolving trophic relationships.
Key-words: Bayesian, conservation dilemma, Coregonus autumnalis, hyperpredation, Lampetra ?uviatilis, pollan, potamodromous, River lamprey, stable isotope analysis in R, stable isotope

Simplification of structured population dynamics in complex ecological communities

Goldstone's idea of slow dynamics resulting from spontaneously broken symmetries is applied to Hubbell's neutral hypothesis of community dynamics, to efficiently simplify stage-structured multi-species models-introducing the quasi-neutral approximation (QNA). Rather than assuming population-dynamical neutrality in the QNA, deviations from ideal neutrality, thought to be small, drive dynamics. The QNA is systematically derived to first and second order in a two-scale singular perturbation expansion. The total reproductive value of species, as computed from the effective life-history parameters resulting from the non-linear interactions with the surrounding community, emerges as the new dynamic variables in this aggregated description. Using a simple stage-structured community-assembly model, the QNA is demonstrated to accurately reproduce population dynamics in large, complex communities. Further, the utility of the QNA in building intuition for management problems is illustrated by estimating the responses of a fish stock to harvesting and variations in fecundity.

NON-GAUSSIAN STATISTICS OF OIL PRICING TIME-SERIES: A CASE STUDY

The stochastic nature of oil price fluctuations is investigated over a twelve-year period, borrowing feedback from an existing database (USA Energy Information Administration database, available online). We evaluate the scaling exponents of the fluctuations by employing different statistical analysis methods, namely rescaled range analysis (R/S), scale windowed variance analysis (SWV) and the generalized Hurst exponent (GH) method. Relying on the scaling exponents obtained, we apply a rescaling procedure to investigate the complex characteristics of the probability density functions (PDFs) dominating oil price fluctuations. It is found that PDFs exhibit scale invariance, and in fact collapse onto a single curve when increments are measured over microscales (typically less than 30 days). The time evolution of the distributions is well fitted by a Levy-type stable distribution. The relevance of a Levy distribution is made plausible by a simple model of nonlinear transfer. Our results also exhibit a degree of multifractality as the PDFs change and converge toward to a Gaussian distribution at the macroscales.

Regulation of cyclin D1 by the BRCA1-BARD1 complex

Background BRCA1 and cyclin D₁ are both essential for normal breast development and mutation or aberration of their expression is associated with breast cancer [1,2]. Cyclin D₁ is best known as a G₁ cyclin where it regulates the G₁ to S phase transition by acting as a rate-limiting subunit of CDK4/6 kinase activity. More recently, however, Stacey has demonstrated that cyclin D₁ levels in G₂/M determine whether a cell continues to proliferate or exits the cell cycle [3]. The majority of BRCA1 in the cell is bound to BARD1 through their N-terminal RING domains. Heterodimerization is essential for the stability and correct localization of the complex and confers ubiquitin ligase activity to BRCA1. The importance of the ligase activity of BRCA1 to breast cancer development is inferred from the fact that N-terminal diseaseassociated mutations are proposed to reduce ligase activity [4]. Methods Protein–protein interactions were demonstrated using yeast-two-hybrid and coimmunoprecipitation. Protein levels were altered through overexpression, siRNA and antisense technology. The effect of proteasome inhibitors and cycloheximide treatment was also examined. Results We initially identified cyclin D₁ as a binding partner of BARD1 in a yeast-two-hybrid screen and defined the minimal binding region as the N-terminus of BARD1. This interaction was confirmed in vivo by coimmunoprecipitation. The N-terminus of BARD1 also binds BRCA1 and imparts ubiquitin ligase activity to the complex. Covalent modification of proteins with ubiquitin is a common regulatory mechanism in eukaryotic cells. Traditionally polyubiquitin chains linked through lysine 48 target proteins for degradation by the 26 S proteasome. We have demonstrated that cyclin D₁ protein levels are inversely related to BRCA1 and BARD1 levels in several model systems. Furthermore, regulation of cyclin D1 levels occurs through a post-transcriptional mechanism and requires the ligase activity of BRCA1. Interestingly, this phenomenon is cell-cycle regulated, occurring in G₂/M. Conclusion We propose that cyclin D₁ is a potential substrate for BRCA1 ubiquitination and that this targets cyclin D₁ for proteasomal-mediated degradation. Future work will focus on ascertaining the functional consequence of cyclin D₁ regulation by the BRCA1–BARD1 complex; in particular, the impact of BRCA1, mediated through regulation of cyclin D₁, on the proliferation versus differentiation decision.

Raman spectroelectrochemical studies and crystal structure of a binuclear copper(I) complex with a bridging diimine ligand

Raman spectroelectrochemical and X-ray crystallographic studies have been made for the binuclear copper(I) complex, [(Ph(3)P)(2)Cu(dpq)Cu(PPh(3))(2)][BF4](2), where dpq is the bridging ligand 2,3-di(2-pyridyl)quinoxaline. The X-ray data show that the pyridine rings are twisted out of plane with respect to the quinoxaline ring which is itself non-planar. The UV/VIS spectra of the metal-to-ligand charge-transfer excited state and those of the electrochemically reduced complex are similar. The resonance-Raman spectrum of the latter species exhibits little change in the frequency of the pyridinylquinoxaline inter-ring C-C bond stretching mode, compared to the ground electronic state. This suggests minimum change in the inter-ring C-C bond order in the electrochemically or charge-transfer generated radical anion. Semiempirical molecular-orbital calculations on both the neutral dpq and radical anion show two near-degenerate lowest unoccupied orbitals in the neutral species. One is strongly bonding across the inter-ring C-C bond while the other is almost nun-bonding. The Raman data suggest that it is this latter orbital which is populated in the transient and electrochemical experiments.

Joint complex diversity coding and channel coding over space, time and frequency

This study provides a general diversity analysis for joint complex diversity coding (CDC) and channel coding-based space-time-frequency codeing is provided. The mapping designs from channel coding to CDC are crucial for efficient exploitation of the diversity potential. This study provides and proves a sufficient condition of full diversity construction with joint three-dimensional CDC and channel coding, bit-interleaved coded complex diversity coding and symbol-interleaved coded complex diversity coding. Both non-iterative and iterative detections of joint channel code and CDC transmission are investigated. The proposed minimum mean-square error-based iterative soft decoding achieves the performance of the soft sphere decoding with reduced complexity.