Implications for Powering Biomarker Discovery Studies

This study examined variations in gene expression between FFPE blocks within tumors of individual patients. Microarray data were used to measure tumor heterogeneity within and between patients and disease states. Data were used to determine the number of samples needed to power biomarker discovery studies. Bias and variation in gene expression were assessed at the intrapatient and interpatient levels and between adenocarcinoma and squamous samples. A mixed-model analysis of variance was fitted to gene expression data and model signatures to assess the statistical significance of observed variations within and between samples and disease states. Sample size analysis, adjusted for sample heterogeneity, was used to determine the number of samples required to support biomarker discovery studies. Variation in gene expression was observed between blocks taken from a single patient. However, this variation was considerably less than differences between histological characteristics. This degree of block-to-block variation still permits biomarker discovery using either macrodissected tumors or whole FFPE sections, provided that intratumor heterogeneity is taken into account. Failure to consider intratumor heterogeneity may result in underpowered biomarker studies that may result in either the generation of longer gene signatures or the inability to identify a viable biomarker. Moreover, the results of this study indicate that a single biopsy sample is suitable for applying a biomarker in nonsmall-cell lung cancer. © 2012 American Society for Investigative Pathology and the Association for Molecular Pathology.

Novel bioassays to examine the host-finding ability of plant-parasitic nematodes

We present two novel bioassays to be used in the examination of plant-parasitic nematode host-finding ability. The host-finding 'pipette-bulb assay' was constructed from modelled Pasteur pipette bulbs and connecting barrels using parafilm fastenings. This assay examines the direction of second-stage juvenile (J2) migration in response to a host seedling, through a moistened sand substrate, which underlies terminal upward-facing 'seedling bulbs', one containing a host seedling in potting compost, the other with only potting compost. An equal watering regime through both upward-facing seedling bulbs creates a directional concentration gradient of host diffusate chemotactic factors. Positive chemotactic stimuli cause the J2 to orientate and migrate towards the host plant. We present validation data collected from assays of the root-knot nematode, Meloidogyne incognita, and the potato cyst nematode, Globodera pallida, which indicate a highly significant positive attraction of J2 of both species to respective host plants. This represents a simple, quick and inexpensive method of assessing host-finding behaviour in the laboratory. We consider that the pipette-bulb assay improves on previous host-finding/chemo-attraction assays through creating a more biologically relevant environment for experimental J2; analysis is quick and easy, allowing the straightforward interpretation of results. In addition, we have developed an 'agar trough' sensory assay variant which we believe can be used rapidly to ratify nematode responses to chemical gustatory or olfactory cues. This was constructed from a water agar substrate such that two counting wells were connected by a raised central trough, all flooded with water. Two small water agar plugs were dehydrated briefly in an oven and then hydrated in either an attractant, repellent or water control; these plugs were then placed in the terminal counting wells and subsequently leached the attractant or repellent to form a concentration gradient along the central trough, which contained the initial J2 innoculum. Our data show that both M. incognita and G. pallida J2 are positively attracted to host diffusates. In addition, they displayed a strong repulsion in response to 1 M NaCl2. J2 of M. incognita displayed a mild aversion to a non-host oak root diffusate, whereas G. pallida J2 displayed a strong aversion to the same non-host diffusate; neither species responded to a compost leachate. We believe that the agar trough assay improves on previous methods by facilitating rapid diffusion of attractant or repellents. Both of the aforementioned assays were designed as tools to assess the impact of RNAi-based reverse genetics screens for gene targets involved in chemosensory orientation.

Children’s perceptions of primary science assessment in England and Wales

This study builds on and contributes to work on assessment of children in primary school, particularly in science. Previous research has examined primary science assessment from different standpoints, but no studies have speci?cally addressed children’s perspectives. This article provides additional insight into issues surrounding children’s assessment in primary school and how the assessment of science might develop in England after the science SATs (Standard Assessment Tests) were abolished in 2009. Some research suggests that primary science assessment via SATs is a major reason for the observed decline in children’s engagement with science in upper primary and lower secondary school. The analytic focus on engaging children as coresearchers to assist in the process of gathering informed views and interpreting ?ndings from a large sample of children’s views enables another contribution. The study, based on a survey of 1000 children in primary and secondary schools in England and Wales, reveals that despite being assessed under two different regimes (high-stakes national tests in England and moderated teacher assessment in Wales), children’s views of science assessment are remarkably consistent. Most appreciate the usefulness of science assessment and value frequent, non-SATs testing for monitoring/improving science progress. There was a largely negative impact, however, of science
assessment on children’s well-being, particularly due to stress. The paper demonstrates that children provide an important perspective on assessment and that including their views can improve policy-making in relation to primary science assessment.

Optical and infrared spectroscopy of the type IInSN1998S: days 3-127

We present contemporary optical and infrared spectroscopic observations of the type IIn SN 1998S covering the period between 3 and 127 days after discovery. During the first week the spectra are characterized by prominent broad H, He and C III/N III emission lines with narrow peaks, superimposed on a very blue continuum (T similar to 24 000 K). In the following two weeks the C III/N III emission vanished, together with the broad emission components of the H and He lines. Broad, blueshifted absorption components appeared in the spectra. The temperature of the continuum also dropped to similar to 14000 K. By the end of the first month the spectrum comprised broad, blueshifted absorptions in H, He, Si II, Fe II and Sc II. By day 44, broad emission components in H and He reappeared in the spectra. These persisted to as late as days similar to 100-130, becoming increasingly asymmetric. We agree with Leonard et al. that the broad emission lines indicate interaction between the ejecta and circumstellar material (CSM) emitted by the progenitor. We also agree that the progenitor of SN 1998S appears to have gone through at least two phases of mass-loss, giving rise to two CSM zones. Examination of the spectra indicates that the inner zone extended to less than or equal to 90 au, while the outer CSM extended from 185 an to over 1800 au.