Uncovering BRCA1-regulated signalling pathways by microarray-based expression profiling

The introduction of microarray technology to the scientific and medical communities has dramatically changed the way in which we now address basic biomedical questions. Expression profiling using microarrays facilitates an experimental approach where alterations in the transcript level of entire transcriptomes can be simultaneously assayed in response to defined stimuli. We have used microarray analysis to identify downstream transcriptional targets of the BRCA1 (Breast Cancer 1) tumour-suppressor gene as a means of defining its function. BRCA1 has been implicated in the predisposition to early onset breast and ovarian cancer and while its exact function remains to be defined, roles in DNA repair, cell-cycle control and transcriptional regulation have been implied. In the current study we have generated cell lines with tetracycline-regulated, inducible expression of BRCA1 as a tool to identify genes, which might represent important effectors of BRCA1 function. Oligonucleotide array-based expression profiling identified a number of genes that were upregulated at various times following inducible expression of BRCA1 including the DNA damage-responsive gene GADD45 (Growth Arrest after DNA Damage). Identified targets were confirmed by Northern blot analysis and their functional significance as BRCA1 targets examined.

Uncovering functionally relevant signaling pathways using microarray-based expression profiling

The introduction of microarray technology to the scientific and medical communities has fundamentally altered the way in which we now address basic biomedical questions. Microarrays technology facilitates a more complete and inclusive experimental approach where alterations in the transcript level of entire genomes can be simultaneously assayed in response to a variety of stimuli. Conceptually different approaches to the development of microarray technology have resulted in the generation of two different array formats: oligonucleotide arrays and cDNA arrays. The application of microarray and related technologies to identify specific targets of defined genes that have clearly been implicated in cancer progression requires a specific experimental approach. The objective of tiffs approach is to define changes in transcriptional profile that occur in response to modulating the expression level of the gene to be studied. The resulting altered expression profile can then be viewed as a blueprint by which that gene effects its cellular function. We have used oligonucleotide array-based expression profiling in collaboration with Affymetrix to identify downstream transcriptional targets of the BRCA1 tumor-suppressor gene as a means of defining its function. BRCA1 has been implicated in at least three functional pathways, namely, mediating the cellular response to DNA damage, as a cell cycle checkpoint protein and in the regulation of transcription. The physiological significance of these properties and their implications for the function of BRCA1 as a tumor-suppressor gene remain to be defined.

RNA expression analysis from formalin fixed paraffin embedded tissues

Formalin fixation and paraffin embedding (FFPE) is the most commonly used method worldwide for tissue storage. This method preserves the tissue integrity but causes extensive damage to nucleic acids stored within the tissue. As methods for measuring gene expression such as RT-PCR and microarray are adopted into clinical practice there is an increasing necessity to access the wealth of information locked in the Formalin fixation and paraffin embedding archives. This paper reviews the progress in this field and discusses the unique opportunities that exist for the application of these techniques in the development of personalized medicine.

The energetics of tetrahydrocarbazole aromatization over Pd(111): A computational analysis

The carbazole moiety is a component of many important pharmaceuticals including anticancer and anti-HIV agents and is commonly utilized in the production of modern polymeric materials with novel photophysical and electronic properties. Simple carbazoles are generally produced via the aromatization of the respective tetrahydrocarbazole (THCZ). In this work, density functional theory calculations are used to model the reaction pathway of tetrahydrocarbazole aromatization over Pd(111). The geometry of each of the intermediate surface species has been determined and how each structure interacts with the metal surface addressed. The reaction energies and barriers of each of the elementary surface reactions have also been calculated, and a detailed analysis of the energetic trends performed. Our calculations have shown that the surface intermediates remain fixed to the surface via the aromatic ring in a manner similar to that of THCZ. Moreover, the aliphatic ring becomes progressively more planer with the dissociation of each subsequent hydrogen atom. Analysis of the reaction energy profile has revealed that the trend in reaction barriers is determined by the two factors: (i) the strength of the dissociating ring-H bond and (ii) the subsequent gain in energy due to the geometric relaxation of the aliphatic ring. (c) 2008 American Institute of Physics.

Analysis and Design of Class-E3F and Transmission-Line Class-E3F2 Power Amplifiers

In this paper, analysis and synthesis approach for two new variants within the Class-EF power amplifier (PA) family is elaborated. These amplifiers are classified here as Class-E3 F2 and transmission-line (TL) Class-E3 F 2. The proposed circuits offer means to alleviate some of the major issues faced by existing topologies such as substantial power losses due to the parasitic resistance of the large inductor in the Class-EF load network and deviation from ideal Class-EF operation due to the effect of device output inductance at high frequencies. Both lumped-element and transmission-line load networks for the Class-E 3 F PA are described. The load networks of the Class-E3 F and TL Class-E 3 F2amplifier topologies developed in this paper simultaneously satisfy the Class-EF optimum impedance requirements at fundamental frequency, second, and third harmonics as well as simultaneously providing matching to the circuit optimum load resistance for any prescribed system load resistance. Optimum circuit component values are analytically derived and validated by harmonic balance simulations. Trade-offs between circuit figures of merit and component values with some practical limitations being considered are discussed. © 2010 IEEE.

Analysis of nine NSAIDs in ungulate tissues available to critically endangered vultures in India

In 2006, India, Pakistan, and Nepal banned the manufacture of veterinary formulations of the nonsteroidal anti-inflammatory drug (NSAID) diclofenac. This action was taken to halt the unprecedented decline of three Gyps vulture species that were being poisoned by diclofenac residues commonly present in carcasses of domestic livestock upon which they scavenged. To assess the affect of this ban and evaluate residue prevelances of other NSAIDs, we present a method to detect diclofenac and eight more NSAIDs by liquid chromatography-mass spectrometry and apply this to 1488 liver samples from carcasses of livestock taken across seven Indian states. Diclofenac was present in 11.1% of samples taken between April and December 2006, and meloxicam (4%), ibuprofen (0.6%), and ketoprofen (0.5%) were also detected. Although meloxicam is safe for a range of avian scavengers, including Gypsvultures, data regarding the safety of other NSAIDs is currently limited. If wild Gyps on the Indian subcontinent are to survive, diclofenac bans must be completely effective, and NSAIDs that replace it within the veterinary drug market must be of low toxicity toward Gyps and other scavenging birds.