The role of the adenovirus DNA binding protein in DNA replication and recombination

Replication of adenovirus DNA in infected cells is an efficient process that, compared to cellular replication, has the use of a protein primer as a hallmark. The mechanism of this DNA replication process and especially the role of one of the replication proteins, the DNA binding protein DBP, is the main subject of this thesis. Adenovirus DNA replication can be reconstituted in vitro, using three viral proteins, adenovirus DNA polymerase (pol), precursor terminal protein (pTP), and DBP. Optimal replication efficiency is obtained when two cellular transcription factors are added, nuclear factor I (NFI) and Oct-1. The adenoviral dsDNA genome contains two terminal proteins (TP) covalently linked to the 5. ends. The inverted terminal repeats contain the origins of replication. pTP and pol are tightly associated in solution. During initiation of replication pTP functions as a primer to which the first nucleotide, dCTP, is covalently coupled. Both NFI and Oct-1 stimulate the initiation by recruiting the pTP-pol complex to the origin of replication. Initiation starts opposite position 4 of the template strand. After formation of a pTP-trinucleotide (pTP-CAT), the complex jumps back and CAT becomes paired with template residues 1.3. Shortly after jumping back, the polymerase dissociates from pTP and elongation proceeds via strand displacement. The adenovirus DNA binding protein is an important player in adenovirus DNA replication, where it serves multiple functions. In the first step of adenovirus DNA replication DBP stimulates the coupling of the first nucleotide to pTP. Also binding of NFI to the origin is stimulated by DBP. Subsequently, during elongation DBP unwinds the dsDNA ahead of pol and removes secondary structures. Adenovirus DBP binds with high affinity and cooperativity to ssDNA, whereas binding to dsDNA is non- cooperative and with lower affinity. These differences in binding affinity are the driving force for dsDNA unwinding which is required for processive DNA chain elongation by pol. DBP is a 529 amino acids long protein with a molecular weight of 59 kD. The structure of adenovirus DBP possesses a remarkable feature; the C-terminal arm (aa. 512-529), which is important for the cooperative binding of DBP to another DBP molecule. In addition, the C-terminal arm is flexible and can rotate around a fixed point, called the hinge-region (aa. 512-515). In Chapter 1, an introduction to the adenovirus DNA replication machinery and the role of several single stranded DNA binding proteins originating from different organisms is presented. In Chapter 2 we present data on the function of the flexibility of the C-terminal arm of DBP and we discuss the implications of an altered flexibility on adenovirus DNA replication by mutating several aa in the hinge-region. In Chapter 3, we present data on the function of DBP in the stimulation of initiation. In contrast to a direct protein-protein interaction of DBP with pol we demonstrate that DBP stimulates the binding of pol to the dsDNA origin. We assume that the structure of the dsDNA template is changed by DBP in such a way that polymerase binds more efficiently to the dsDNA. In Chapter 4 we demonstrate that DBP functions in unwinding of the dsDNA donor and that it has an additional role in renaturation of the unwound donor with the complementary acceptor ssDNA. For the first time we were able to demonstrate a direct role for an adenovirus replication protein in homologous recombination. Finally, in Chapter 5 new questions, that have surfaced as a result of the research presented in this thesis, are discussed

A high-resolution stable isotope record from a Peruvian stalagmite

Speleothems are known as carbonate formations in caves. The last few years there is a growing scientific interest in speleothems for climate reconstruction (McDermott, in press; Sancho et al., in press; Jirnénez de Cisneros et al., 2003; Genty et al., 2003; Baker et al., 2002; Proctor et al., 2002; Linge et al., 2001; Wang et al., 2001). Speleothems have proven their potential to create a terrestrial high-resolution paleo-temperature record (Schwarcz, 1986). The advantage of caves for paleoclimatic studies is the yearly stability of climatic conditions in the cave (Jirnénez de Cisneros et al., 2003). Observations have shown that the temperature in any deep cave is clase to the mean annual temperature of the surrounding (Schwarcz et al., 1976; Yonge et al., 1985). This makes speleothems a successful too! paleo-temperature reconstruction (Hendy and Wilson, 1968). The carbonate, ofwhich the speleothem is build, can be used for stable isotope measurements (o13C and o180). Oxygen isotopes are world-wide used to reconstruct paleo-temperatures, especially for biogenic carbonate in marine cores. Precise age-dating on speleothems can be done by U-Th measurements on TIMS, which makes it possible to calculate absolute ages for the isotope record

Association of cardiovascular risk factors with carotid intima media thickness in patients with rheumatoid arthritis with low disease activity compared to controls: A cross-sectional study

Objectives Rheumatoid arthritis (RA) has been identified as an independent cardiovascular risk factor. The importance of risk factors such as hypertension and hyperlipidemia in the generation of atherosclerosis in RA patients is unclear. This study analyzed clinical parameters associated with carotid intima media thickness (cIMT) in patients with RA. Methods Subjects with RA and healthy controls without RA, both without known cardiovascular disease, were included. Participants underwent a standard physical examination and laboratory measurements including a lipid profile. cIMT was measured semi-automatically by ultrasound. Results In total 243 RA patients and 117 controls were included. The median RA disease duration was 7 years (IQ

Heritability and genetic correlations between enteric methane production and concentration recorded by GreenFeed and sniffers on dairy cows

To reduce methane (CH4) emissions of dairy cows by animal breeding, CH4 measurements have to be recorded on thousands of individual cows. Currently, several techniques are used to phenotype cows for CH4, differing in costs and applicability. However, there is uncertainty about the agreement between techniques. To judge the similarity and repeatability between measurements of different recording techniques, the repeatability, heritability, and genetic correlation are useful metrics. Therefore, our objective was to estimate (1) the repeatability and heritability for CH4 and carbon dioxide production recorded by GreenFeed (GF) and for CH4 and carbon dioxide concentration measured by cost-effective but less accurate sniffers, and (2) the genetic correlation between CH4 recorded with these 2 different on farm and high throughput techniques. Data were available from repeated measurements of CH4 production (grams/day) by GF units and of CH4 concentration (ppm) by sniffers, recorded on commercial dairy farms in the Netherlands. The final data comprised 24,284 GF daily means from 822 cows, 170,826 sniffer daily means from 1,800 cows, and 1,786 daily means from 75 cows by both GF and sniffer (in the same period). Additionally, CH4 records were averaged per week. For daily and weekly mean GF CH4 the heritabilities were 0.19 ± 0.02 and 0.33 ± 0.04, and for daily and weekly mean sniffer CH4 the heritabilities were similar and were 0.18 ± 0.01 and 0.32 ± 0.02, respectively. Phenotypic correlations between GF CH4 production and sniffer CH4 concentration were moderate (0.39 ± 0.03 for daily means and 0.37 ± 0.05 for weekly means). However, genetic correlations were high" 0.71 ± 0.13 for daily means and 0.76 ± 0.15 for weekly means. The high genetic correlation indicates that selection on low CH4 concentrations (ppm) recorded by the cost-effective sniffer method, will result in reduced CH4 production (grams/day) as recorded with GF

Heritability and genetic correlations of enteric methane emissions of dairy cows measured by sniffers and GreenFeed

Before methane (CH4) emission can be mitigated with animal breeding, breath measurements have to be recorded on a large number of cows. Our aim was to estimate heritabilities for, and a genetic correlation between, CH4 recorded by GreenFeed and sniffers. Repeated records were available for CH4 production (g/cow/day) by GreenFeed and for CH4 concentration (ppm) by sniffers. The data included 24,284 GreenFeed daily means from 822 cows, 172,948 sniffer daily means from 1,800 cows, and 1,787 daily means from both devices on the same day from 75 cows. Additionally, records were averaged per week. The datasets were analyzed using bivariate animal models. The results show that CH4 emissions recorded by either device has a moderate heritability (0.18-0.37). Furthermore, the genetic correlation between weekly mean CH4 recorded by GreenFeed or by sniffers was high (0.77). This suggest that the measurements can be used in the same genetic evaluations

Bayesian Cluster Finder: Clusters in the CFHTLS Archive Research Survey

The detection of galaxy clusters in present and future surveys enables measuring mass-to-light ratios, clustering properties, galaxy cluster abundances and therefore, constraining cosmological parameters. We present a new technique for detecting galaxy clusters, which is based on the Matched Filter Algorithm from a Bayesian point of view. The method is able to determine the position, redshift and richness of the cluster through the maximization of a filter depending on galaxy luminosity, density and photometric redshift combined with a galaxy cluster prior that accounts for color-magnitude relations and BCG-redshift relation. We tested the algorithm through realistic mock galaxy catalogs, revealing that the detections are 100% complete and 80% pure for clusters up to z $$20 (Abell Richness $\sim$0, M$\sim4\times10^{14} M_{\odot}$). The completeness and purity remains approximately the same if we do not include the prior information, implying that this method is able to detect galaxy cluster with and without a well defined red sequence. We applied the algorithm to the CFHTLS Archive Research Survey (CARS) data, recovering similar detections as previously published using the same or deeper data plus additional clusters which appear to be real.Comment: Accepted for publication in MNRAS; 17 pages, 38 figure

Sample size calculations for the design of cluster randomized trials: A summary of methodology.

Cluster randomized trial designs are growing in popularity in, for example, cardiovascular medicine research and other clinical areas and parallel statistical developments concerned with the design and analysis of these trials have been stimulated. Nevertheless, reviews suggest that design issues associated with cluster randomized trials are often poorly appreciated and there remain inadequacies in, for example, describing how the trial size is determined and the associated results are presented. In this paper, our aim is to provide pragmatic guidance for researchers on the methods of calculating sample sizes. We focus attention on designs with the primary purpose of comparing two interventions with respect to continuous, binary, ordered categorical, incidence rate and time-to-event outcome variables. Issues of aggregate and non-aggregate cluster trials, adjustment for variation in cluster size and the effect size are detailed. The problem of establishing the anticipated magnitude of between- and within-cluster variation to enable planning values of the intra-cluster correlation coefficient and the coefficient of variation are also described. Illustrative examples of calculations of trial sizes for each endpoint type are included

Modelling high redshift Lyman-alpha Emitters

We present a new model for high redshift Lyman-Alpha Emitters (LAEs) in the cosmological context which takes into account the resonant scattering of Ly-a photons through expanding gas. The GALICS semi-analytic model provides us with the physical properties of a large sample of high redshift galaxies. We implement a gas outflow model for each galaxy based on simple scaling arguments. The coupling with a library of numerical experiments of Ly-a transfer through expanding or static dusty shells of gas allows us to derive the Ly-a escape fractions and profiles. The predicted distribution of Ly-a photons escape fraction shows that galaxies with a low star formation rate have a f_esc of the order of unity, suggesting that, for those objects, Ly-a may be used to trace the star formation rate assuming a given conversion law. In galaxies forming stars intensely, the escape fraction spans the whole range from 0 to 1. The model is able to get a good match to the UV and Ly-a luminosity function (LF) data at 3 < z < 5. We find that we are in good agreement with both the bright Ly-a data and the faint population observed by Rauch et al. (2008) at z=3. Most of the Ly-a profiles of our LAEs are redshifted by the diffusion in the outflow which suppresses IGM absorption. The bulk of the observed Ly-a equivalent width (EW) distribution is recovered by our model, but we fail to obtain the very large values sometimes detected. Predictions for stellar masses and UV LFs of LAEs show a satisfactory agreement with observational estimates. The UV-brightest galaxies are found to show only low Ly-a EWs in our model, as it is reported by many observations of high redshift LAEs. We interpret this effect as the joint consequence of old stellar populations hosted by UV-bright galaxies, and high HI column densities that we predict for these objects, which quench preferentially resonant Ly-a photons via dust extinction.Comment: 17 pages, 12 figures, 3 tables, accepted for publication in MNRA

The Subaru/XMM-Newton Deep Field - II. The 37 brightest radio sources

We study the 37 brightest radio sources in the Subaru/XMM-Newton Deep Field (SXDF). We have spectroscopic redshifts for 24 of 37 objects and photometric redshifts for the remainder, yielding a median redshift z_med for the whole sample of z_med ~= 1.1 and a median radio luminosity close to the `FRI/FRII' luminosity divide. Using mid-IR (Spitzer MIPS 24 um) data we expect to trace nuclear accretion activity, even if it is obscured at optical wavelengths, unless the obscuring column is extreme. Our results suggest that above the FRI/FRII radio luminosity break most of the radio sources are associated with objects that have excess mid-IR emission, only some of which are broad-line objects, although there is one clear low-accretion-rate object with an FRI radio structure. For extended steep-spectrum radio sources, the fraction of objects with mid-IR excess drops dramatically below the FRI/FRII luminosity break, although there exists at least one high-accretion-rate `radio-quiet' QSO. We have therefore shown that the strong link between radio luminosity (or radio structure) and accretion properties, well known at z ~ 0.1, persists to z ~ 1. Investigation of mid-IR and blue excesses shows that they are correlated as predicted by a model in which, when significant accretion exists, a torus of dust absorbs ~30% of the light, and the dust above and below the torus scatters >~1% of the light.Comment: Accepted for publication by MNRAS; 39 pages, 7 figures, 4 table

The WiggleZ Dark Energy Survey: Survey Design and First Data Release

The WiggleZ Dark Energy Survey is a survey of 240,000 emission line galaxies in the distant universe, measured with the AAOmega spectrograph on the 3.9-m Anglo-Australian Telescope (AAT). The target galaxies are selected using ultraviolet photometry from the GALEX satellite, with a flux limit of NUV<22.8 mag. The redshift range containing 90% of the galaxies is 0.2<z<1.0. The primary aim of the survey is to precisely measure the scale of baryon acoustic oscillations (BAO) imprinted on the spatial distribution of these galaxies at look-back times of 4-8 Gyrs. Detailed forecasts indicate the survey will measure the BAO scale to better than 2% and the tangential and radial acoustic wave scales to approximately 3% and 5%, respectively. This paper provides a detailed description of the survey and its design, as well as the spectroscopic observations, data reduction, and redshift measurement techniques employed. It also presents an analysis of the properties of the target galaxies, including emission line diagnostics which show that they are mostly extreme starburst galaxies, and Hubble Space Telescope images, which show they contain a high fraction of interacting or distorted systems. In conjunction with this paper, we make a public data release of data for the first 100,000 galaxies measured for the project.Comment: Accepted by MNRAS; this has some figures in low resolution format. Full resolution PDF version (7MB) available at http://www.physics.uq.edu.au/people/mjd/pub/wigglez1.pdf The WiggleZ home page is at http://wigglez.swin.edu.au