Expression microarray analysis of papillary thyroid carcinoma and benign thyroid tissue: emphasis on the follicular variant and potential markers of malignancy.

The most common sub-variant of papillary thyroid carcinoma (PTC) is the so-called follicular variant (FVPTC), which is a particularly problematic lesion and can be challenging from a diagnostic viewpoint even in resected lesions. Although fine needle aspiration cytology is very useful in the diagnosis of PTC, its accuracy and utility would be greatly facilitated by the development of specific markers for PTC and its common variants. We used the recently developed Applied Biosystems 1700 microarray system to interrogate a series of 11 benign thyroid lesions and conditions and 14 samples of PTC (six with classic morphology and eight with follicular variant morphology). TaqMan(R) reverse transcriptase-polymerase chain reaction was used to validate the expression portfolios of 50 selected transcripts. Our data corroborates potential biomarkers previously identified in the literature, such as LGALS3, S100A11, LYN, BAX, and cluster of differentiation 44 (CD44). However, we have also identified numerous transcripts never previously implicated in thyroid carcinogenesis, and many of which are not represented on other microarray platforms. Diminished expression of metallothioneins featured strongly among these and suggests a possible role for this family as tumour suppressors in PTC. Fifteen transcripts were significantly associated with FVPTC morphology. Surprisingly, these genes were associated with an extremely narrow repertoire of functions, including the major histocompatibility complex and cathepsin families.

Isolation of plant nuclei.

The isolation of plant nuclei is a useful first step in many experiments concerned with the mechanism and control of gene expression in plants. For example, isolated nuclei can be used for the isolation of nuclear components such as chromosomal proteins (1), for the study of the processing of primary transcripts (2,3), for the assay and characterization of RNA polymerase activities (4-7), or for the measurement of transcription rates of specific genes (8) (see Chapter 37 ). A method is described here for the isolation of a crude preparation of intact plant nuclei, with an additional protocol for nuclei purification on a discontinuous gradient of Percoll (9) (see Note 1 in section 4). Centrifugation of crude nuclei preparations through Percoll gradients removes much of the contaminating cytoplasmic material such as starch grains (10), and the Percoll step appears to reduce the ribonuclease activity associated with nuclei (10). It is therefore recommended for transcription experiments. The crude nuclei preparation alone may be adequate for some work, for example, when attempting RNA polymerase assays for the first time, when very small amounts of tissue are involved, for preliminary experiments on the characterization of enzyme activities, or for the isolation of nuclear components that may be lost during purification.

In vitro transcription in plant nuclei.

Isolated plant nuclei can be used for fundamental studies on the transcription apparatus. Total RNA polymerase activity can be measured using plant nuclei, and by using different α-amanitin concentrations in the enzyme assay, the individual RNA polymerase I, II, and in activities can be measured (1-5). The assay procedure involves the incubation of nuclei in the presence of the four substrates for RNA synthesis: ATP, GTP, CTP, and UTP. If one of these precursors is supplied as a radio-labeled molecule, transcription can be detected as incorporation of radioactivity into acid-insoluble material. Following incubation, transcription products are precipitated with TCA, collected and washed on glass fiber filter discs, and counted by liquid scintillation counting.

Regional quality assessment of pH and blood gas analysers.

The performance of 41 pH and blood gas analysers in 20 hospitals was assessed using commercially available blood gas ampoules provided by seven manufacturers. The stability of the material and the effect of ambient temperature on Po2 was assessed. The overall mean values were outside the manufacturers' assigned values on eight out of 64 values. Using IL413 analysers as a basis for comparison, significant differences were found for Pco2 on ABL1, Corning 168 and 178 analysers and for Po2 on ABL1 and 2 and Corning 178. No significant differences were found for pH. Poor performers were identified in terms of imprecision. Analysers within or associated with clinical biochemistry departments gave better performance than those outside the laboratory. The five analysers that provided insufficient data for inclusion in the study were all situated outside the laboratory. Analysers from different manufacturers performed equally well provided they were used regularly and in accordance with manufacturers' instructions.

Antigenic and molecular characterization of host cell-mediated variants of equine H3N8 influenza viruses.

Antigenic differences between three of six equine influenza virus (H3N8) MDCK cell- and egg-derived pairs have been demonstrated using monoclonal and polyclonal antibodies. Sequencing of the haemagglutinin (HA) genes revealed amino acid changes in four of the six virus pairs. These data contrast with those for human isolates of influenza virus in that it was predominantly tissue culture-isolated equine virus and not egg-derived virus which displayed heterogeneity. Some of the molecular changes involved are located within the vicinity of the cell receptor-binding site (positions 156, 158 and 222) whereas others are in the vicinity of the HA1-HA2 cleavage site (positions 18 and 32 of HA1 and position 12 of HA2). Our results indicate that the host cell can play a part in selecting antigenic variants of equine influenza virus and suggest that the egg, and not cell culture as is the case for human isolates, is the preferred host for vaccine and antigenic studies.

Quantitative detection of HIV-1 drug resistance mutations by automated DNA sequencing.

A comparison has been made between manual and automated DNA sequencing procedures to evaluate the ability to distinguish mixtures of wild-type and mutant sequences. Quantitative detection of such mixtures of HIV-1 drug resistance mutations was best achieved using an automated system that uses fluorescent-labelled sequencing primers. This procedure has a wide range of applications in clinical research, including heterozygote analysis. Software that automatically reports mixed-base positions is presented.