PCR-based diagnosis of Naegleria sp. infection in formalin-fixed and paraffin-embedded brain sections

We developed a real-time PCR which allowed the highly sensitive detection of Naegleria fowleri in histological brain tissue sections from experimentally infected mice. This genus-specific small-subunit (18S) rRNA gene-based PCR can complement conventional (immuno-) histology for the diagnosis of primary amoebic meningoencephalitis in paraffin-embedded brain necropsy specimens that had been fixed in formalin buffered with phosphate-buffered saline.

Gene expression variation between distinct areas of breast cancer measured from paraffin-embedded tissue cores

BACKGROUND: Diagnosis and prognosis in breast cancer are mainly based on histology and immunohistochemistry of formalin-fixed, paraffin-embedded (FFPE) material. Recently, gene expression analysis was shown to elucidate the biological variance between tumors and molecular markers were identified that led to new classification systems that provided better prognostic and predictive parameters. Archived FFPE samples represent an ideal source of tissue for translational research, as millions of tissue blocks exist from routine diagnostics and from clinical studies. These should be exploited to provide clinicians with more accurate prognostic and predictive information. Unfortunately, RNA derived from FFPE material is partially degraded and chemically modified and reliable gene expression measurement has only become successful after implementing novel and optimized procedures for RNA isolation, demodification and detection. METHODS: In this study we used tissue cylinders as known from the construction of tissue microarrays. RNA was isolated with a robust protocol recently developed for RNA derived from FFPE material. Gene expression was measured by quantitative reverse transcription PCR. RESULTS: Sixteen tissue blocks from 7 patients diagnosed with multiple histological subtypes of breast cancer were available for this study. After verification of appropriate localization, sufficient RNA yield and quality, 30 tissue cores were available for gene expression measurement on TaqMan(R) Low Density Arrays (16 invasive ductal carcinoma (IDC), 8 ductal carcinoma in situ (DCIS) and 6 normal tissue), and 14 tissue cores were lost. Gene expression values were used to calculate scores representing the proliferation status (PRO), the estrogen receptor status and the HER2 status. The PRO scores measured from entire sections were similar to PRO scores determined from IDC tissue cores. Scores determined from normal tissue cores consistently revealed lower PRO scores than cores derived from IDC or DCIS of the same block or from different blocks of the same patient. CONCLUSION: We have developed optimized protocols for RNA isolation from histologically distinct areas. RNA prepared from FFPE tissue cores is suitable for gene expression measurement by quantitative PCR. Distinct molecular scores could be determined from different cores of the same tumor specimen.

The verb slot in causative constructions. Finding the best fit

Using the technique of multiple distinctive collexeme analysis, this paper seeks to determine the verbs that are distinctively associated with the non-finite verb slot of English periphrastic causative constructions. Not only does the analysis reveal that the various causative constructions are attracted to essentially different verbs, but by examining how these verbs fall into semantic classes, it also hints at subtle differences in meaning between the constructions. In addition, the paper shows how the technique of multiple distinctive collexeme analysis can be usefully combined with other, complementary methods, and briefly discusses a number of factors which influence the results of multiple distinctive collexeme analysis and should therefore ideally be taken into account.

The construal of constructions: causal and temporal interpretations in change constructions

In this paper I first discuss some non-causal change constructions which have largely gone unnoticed in the literature, such as The butler bowed the guests in (which is said to code mild causation) and The supporters booed Newcastle off at the interval (which only codes temporal coextension between its two constitutive subevents). Since the same structure (i.e. the transitive object-oriented change construction) can be used to code a wide spectrum of causal and temporal relations, the question arises of what cognitive mechanisms may be involved in such meaning shifts. I argue that variation can be motivated on the basis of the figure/ground segregation which the conceptualiser can impose upon the integrated scene coded by the change construction. The integrated scene depicts a force-dynamic scenario but also evokes a unique temporal setting (i.e. temporal overlap or coextension between the constitutive subevents). Such a “bias” towards temporal overlap can be used by the conceptualiser to background causation and highlight temporal overlap interpretations. It is also shown that figure/ground segregation can be appealed to to account for the causal interpretation of intransitive change constructions, e.g. The kettle boiled dry. If the conceptual distance between the verbal event and the non-verbal event is (relatively) great, causality can be highlighted even in intransitive patterns.