Protein-protein Interactions of the Androgen Receptor in Living Cells

__Abstract__ Natural androgens, testosterone (T) and its derivative dihydrotestosterone (DHT) play a crucial role in the development and maintenance of the male phenotype. Androgens are steroids that exert their function via the androgen receptor (AR), a ligand dependent transcription factor. The human AR gene, is located on the X chromosome, and contains 8 exons, coding for a 110 kDa, 919 amino acids protein (Brinkmann et al., 1989; Hughes and Deeb, 2006). In the classical model of AR action, the unliganded AR is located in the cytoplasm in complex with chaperone proteins (Pratt and Toft, 1997; Prescott and Coetzee, 2006). Upon androgen binding the chaperone complex is modifi ed and the AR translocates to the nucleus (Georget et al., 1997; Tyagi et al., 2000; Black and Paschal, 2004). In the nucleus, the AR binds to specifi c sequences in promoters and enhancers of target genes, interacts with specifi c coregulators and enhances the recruitment of the general transcription machinery, leading to transcription initiation (Fig. 1) (Glass and Rosenfeld, 2000; Claessens et al., 2001; Cosma, 2002; Orphanides and Reinberg, 2002; Heemers and Tindall, 2007). Recently, many reviews on AR function have been published (e.g. Dehm and Tindall, 2007; Heemers and Tindall, 2007; Trapman and Dubbink, 2007; Centenera et al., 2008; Claessens et al., 2008). The focus of this thesis is on molecular mechanisms underlying AR function in living cells

The Non-Coding Transcriptome of Prostate Cancer: Implications for Clinical Practice

Prostate cancer (PCa) is the most common type of cancer and the second leading cause of cancer-related death in men. Despite extensive research, the molecular mechanisms underlying PCa initiation and progression remain unclear, and there is increasing need of better biomarkers that can distinguish indolent from aggressive and life-threatening disease. With the advent of advanced genomic technologies in the last decade, it became apparent that the human genome encodes tens of thousands non-protein-coding RNAs (ncRNAs) with yet to be discovered function. It is clear now that the majority of ncRNAs exhibit highly specific expression patterns restricted to certain tissues and organs or developmental stages and that the expression of many ncRNAs is altered in disease and cancer, including cancer of the prostate. Such ncRNAs can serve as important biomarkers for PCa diagnosis, prognosis, or prediction of therapy response. In this review, we give an overview of the different types of ncRNAs and their function, describe ncRNAs relevant for the diagnosis and prognosis of PCa, and present emerging new aspects of ncRNA research that may contribute to the future utilization of ncRNAs as clinically useful therapeutic targets

Ratios of BB and DD Meson Decay Constants in Relativistic Quark Model

We calculate the ratios of $B$ and $D$ meson decay constants by applying the variational method to the relativistic hamiltonian of the heavy meson. We adopt the Gaussian and hydrogen-type trial wave functions, and use six different potentials of the potential model. We obtain reliable results for the ratios, which are similar for different trial wave functions and different potentials. The obtained ratios show the deviation from the nonrelativistic scaling law, and they are in a pretty good agreement with the results of the Lattice calculations.Comment: 13 pages, 1 Postscript figur

Extended van Royen-Weisskopf formalism for lepton-antilepton meson decay widths within non-relativistic quark models

The classical van Royen-Weisskopf formula for the decay width of a meson into a lepton-antilepton pair is modified in order to include non-zero quark momentum contributions within the meson as well as relativistic effects. Besides, a phenomenological electromagnetic density for quarks is introduced. The meson wave functions are obtained from two different models: a chiral constituent quark model and a quark potential model including instanton effects. The modified van Royen-Weisskopf formula is found to improve systematically the results for the widths, giving an overall good description of all known decays.Comment: 22 pages, 3 figures, RevTex, epsfig. To be published in Nucl. Phys.

Vector Meson Production at HERA

We show that the lowest-order QCD calculation in a simple model of elastic vector-meson production does reproduce correctly the ratios of cross sections for rho, phi and J/psi, both in photoproduction and in high-Q2 quasi-elastic scattering. The dependence of the slopes on the mass of the vector meson is reproduced as well. We examine the lower-energy data, and find that the energy dependence of the cross section does not depend on Q2, but may depend on the vector-meson mass.Comment: 12 pages, Latex, 6 figures. Shortened version of the previous paper, which also includes a clearer criticism of the work by Martin, Ryskin and Teubner, hep-ph/960944

Androgen receptor complexes probe DNA for recognition sequences by short random interactions

Owing to the tremendous progress in microscopic imaging of fluorescently labeled proteins in living cells, the insight into the highly dynamic behavior of transcription factors has rapidly increased over the past decade. However, a consistent quantitative scheme of their action is still lacking. Using the androgen receptor (AR) as a model system, we combined three different fluorescence microscopy assays: single-molecule microscopy, photobleaching and correlation spectroscopy, to provide a quantitative model of the action of this transcription factor. This approach enabled us to distinguish two types of AR-DNA binding: very brief interactions, in the order of a few hundred milliseconds, and hormone-induced longer-lasting interactions, with a characteristic binding time of several seconds. In addition, freely mobile ARs were slowed down in the presence of hormone, suggesting the formation of large AR-co-regulator complexes in the nucleoplasm upon hormone activation. Our data suggest a model in which mobile hormone-induced complexes of transcription factors and co-regulators probe DNA by briefly binding at random sites, only forming relatively stable transcription initiation complexes when bound to specific recognition sequences

Q^2 dependence of diffractive vector meson electroproduction

We give a general formula for the cross section for diffractive vector meson electroproduction, gamma^* p -> Vp. We first calculate diffractive qqbar production, and then use parton-hadron duality by projecting out the J^P = 1^- state in the appropriate mass interval. We compare the Q^2 dependence of the cross section for the diffractive production of rho and J/psi mesons with recent HERA data. We include the characteristic Q^2 dependence associated with the use of the skewed gluon distribution. We give predictions for sigma_L/sigma_T for both rho and J/psi production.Comment: 15 pages, LaTeX, including five PostScript figure

Three-dimensional microscopic analysis of clinical prostate specimens

__Aims:__ Microscopic evaluation of prostate specimens for both clinical and research purposes is generally performed on 5-μm-thick tissue sections. Because cross-sections give a two-dimensional (2D) representation, little is known about the actual underlying three-dimensional (3D) architectural features of benign prostate tissue and prostate cancer (PCa). The aim of this study was to show that a combination of tissue-clearing protocols and confocal microscopy can successfully be applied to investigate the 3D architecture of human prostate tissue. __Methods and results:__ Optical clearing of intact fresh and formalin-fixed paraffin-embedded (FFPE) clinical prostate specimens allowed us to visualize tissue structures up to a depth of 800 μm, whereas, in uncleared tissue, detection of fluorescence was only possible up to 70 μm. Fluorescent labelling with a general nuclear dye and antibodies against cytokeratin (CK) 5 and CK8-18 resulted in comprehensive 3D imaging of benign peripheral and transition prostate zones, as well as individual PCa growth patterns. After staining, clearing, and imaging, samples could still be processed for 2D (immuno)histochemical staining and DNA analysis, enabling additional molecular and diagnostic characterization of small tissue specimens. __Conclusions:__ In conclusion, the applicability of 3D imaging to archival FFPE and fresh clinical specimens offers unlimited opportunities to stud