Identifying novel components of human tumour suppressor networks

The p53 pathway plays a central role in protecting cells from becoming tumorigenic. Reactivation of the pathway is under extensive study in the development of anti-cancer drugs. Although a lot is known about the pathway, the way it is inactivated in human tumours harbouring the wild-type p53 gene is in many cases unknown. This raises the question if we indeed know all the components of this important tumour suppressor pathway. In this thesis, we aimed to identify novel components of the p53 tumour suppressor network. Besides focussing on protein-coding genes, we also set out to identify non-coding gene components. To reach these goals, we made use of genetic screens and genome-wide p53-binding analysis. First, we describe the identification of the bromodomain-containing protein BRD7 as a transcriptional cofactor of p53 and show that BRD7 is required for proper p53 activation in response to certain cellular stresses. We further demonstrate that BRD7 expression is low and the gene encoding BRD7 is frequently deleted in human breast tumours harbouring wild-type p53, implying that loss of BRD7 expression is a way to neutralize the p53 pathway. Second, genome-wide p53-binding profiling reveals specific interactions of p53 with promoter regions of nearby genes. Interestingly, we found p53 binding at nongenic regions that possess evolutionary highly conserved p53-binding sites and all known hallmarks of enhancer regions. We demonstrate that these p53-bound domains indeed have p53-dependent enhancer activity and produce non-coding transcripts, termed enhancer RNAs (eRNAs). Importantly, the domains interact with multiple distantly located genes and we show that eRNA production is required for transcriptional induction of some of these genes. Third, we discuss the involvement of an oncogenic microRNA cluster, miR-17-92, in the neoplastic transformation of human primary cells. We propose that the microRNAs in this cluster cooperate to dampen the retinoblastoma tumour suppressor pathway

The asymptotic structure of nearly unstable non-negative integer-valued AR(1) models

This paper considers non-negative integer-valued autoregressive processes where the autoregression parameter is close to unity. We consider the asymptotics of this `near unit root' situation. The local asymptotic structure of the likelihood ratios of the model is obtained, showing that the limit experiment is Poissonian. To illustrate the statistical consequences we discuss efficient estimation of the autoregression parameter and efficient testing for a unit root.Comment: Published in at http://dx.doi.org/10.3150/08-BEJ153 the Bernoulli (http://isi.cbs.nl/bernoulli/) by the International Statistical Institute/Bernoulli Society (http://isi.cbs.nl/BS/bshome.htm

Preliminary Results on Chemical Thinning of Apple Blossoms with Ammonium Thiosulphate, NAA, and Ethephon

Preliminary tests were carried out using ammonium thiosulphate as a chemical thinning agent for apple ('Cox's Orange Pippin' and 'Braeburn') blossoms. Ethephon and NAA (1-napthylacetic acid) were included for comparison. Whole tree sprays of 37g/l ammonium thiosulphate over-thinned 'Cox's Orange Pippin' blossoms and severely scorched blossoms, foliage, and apical meristems. Ethephon at 0.35 g/l also over-thinned, and NAA thinned to an intermediate extent when compared with the controls. When the lower concentration of 3.7 g/l ammonium thiosulphate was directly applied to stamens and styles of 'Braeburn' blossoms by brush, initial fruit set was only 30% that of untreated blossoms. When 0.35 g/I ethephon was directly applied by brush to spur leaves or petals of 'Braeburn' blossoms at pink bud, initial fruit set was only 23% that of untreated blossoms. lt is concluded that ammonium thiosulphate has the potential to thin apple blossoms. Further experiments to define optimum concentrations and spray volumes are needed

Fossil biomass preserved as graphitic carbon in a late paleoproterozoic banded iron formation metamorphosed at more than 550°C

Metamorphism is thought to destroy microfossils, partly through devolatilization and graphitization of biogenic organic matter. However, the extent to which there is a loss of molecular, elemental and isotope signatures from biomass during high-temperature metamorphism is not clearly established. We report on graphitic structures inside and coating apatite grains from the c. 1850 Ma Michigamme silicate banded iron formation from Michigan, metamorphosed above 550°C. Traces of N, S, O, H, Ca and Fe are preserved in this graphitic carbon and X-ray spectra show traces of aliphatic groups. Graphitic carbon has an expanded lattice around 3.6 Å, forms microscopic concentrically-layered and radiating polygonal flakes and has homogeneous δ13C values around −22‰, identical to bulk analyses. Graphitic carbon inside apatite is associated with nanometre-size ammoniated phyllosilicate. Precursors of these metamorphic minerals and graphitic carbon originated from ferruginous clayrich sediments with biomass. We conclude that graphite coatings and inclusions in apatite grains indicate fluid remobilization during amphibolite-facies metamorphism of precursor biomass. This new evidence fills in observational gaps of metamorphosed biomass into graphite and supports the existence of biosignatures in the highly metamorphosed iron formation from the Eoarchean Akilia Association, which dates from the beginning of the sedimentary rock record

Worry and rumination : underlying processes and transdiagnostic characteristics

Worry and rumination are cognitive processes that have been proposed to constitute a driving force across many psychological disorders, emotional disorders in particular. The two concepts are often referred to by the overarching term repetitive negative thinking (RNT), however whether they are indeed representations of the same process is debated. The main aim of the present thesis is to contribute to the ongoing worry-rumination debate by investigating whether worry and rumination are indeed transdiagnostic processes and whether they represent a shared underlying process. In accordance with this aim several studies were designed covering two lines of research; i) epidemiological studies comparing worry and rumination in their relationship with each other and with emotional disorders; ii) experimental studies examining worry at a more functional/process level. Overall the studies presented in this thesis yield support for both accounts: worry and rumination are highly related, are present across emotional disorders and show both similarities and differences at process level. Especially at a general, abstract, level similarities between worry and rumination seem to predominate. However, at a more concrete and specific level both similarities and differences are observed. Such differences can be relevant for research as well as therapeutic interventions. Depending on the questions in a certain research or clinical context emphasis on a more general-abstract or concrete-specific perspective on worry and rumination seems warranted.FSW - Self-regulation models for health behavior and psychopathology - ou