Standardizing global gene expression analysis between laboratories and across platforms

To facilitate collaborative research efforts between multi-investigator teams using DNA microarrays, we identified sources of error and data variability between laboratories and across microarray platforms, and methods to accommodate this variability. RNA expression data were generated in seven laboratories, which compared two standard RNA samples using 12 microarray platforms. At least two standard microarray types (one spotted, one commercial) were used by all laboratories. Reproducibility for most platforms within any laboratory was typically good, but reproducibility between platforms and across laboratories was generally poor. Reproducibility between laboratories increased markedly when standardized protocols were implemented for RNA labeling, hybridization, microarray processing, data acquisition and data normalization. Reproducibility was highest when analysis was based on biological themes defined by enriched Gene Ontology (GO) categories. These findings indicate that microarray results can be comparable across multiple laboratories, especially when a common platform and set of procedures are used.     

Testing traditional assumptions about regional migration in bats

While some bats cover long distances during migration, moving thousands of kilometers, most migratory bats are considered regional migrants, thought to move relatively short distances (<?500 km) between hibernacula and maternity sites. However, behavior can vary considerably among species and our understanding of these movements has largely been limited to banding studies or detailed tracking of small numbers of bats by aircraft. Inferring population-wide behavior from small samples is difficult and can introduce bias. We tagged 108 Indiana bats (Myotis sodalis) in the Midwestern US and used a regional network of radiotelemetry receivers to study movement patterns. With this dataset, we tested the following traditional generalizations about regional migrants: (1) bats move away from hibernacula in spring in all directions with known maternity roosts, e.g., in a star-like pattern; (2) bats follow linear landscape features; (3) long-distance movements are uncommon; and (4) autumn migration comprises a single movement from summer maternity site to winter hibernaculum. In spring, bats left the hibernaculum immediately and primarily moved north despite available maternity roosts in all directions. We found no evidence that bats follow rivers, the predominant linear element in the landscape. Only six tagged bats traveled >?100 km, suggesting that longer-distance movements may be outliers. In autumn, only two bats visited multiple known hibernacula, and after swarming, some females moved >?100 km to areas without known hibernacula. Common generalizations about regional migrant movements may not be representative of population behavior and care should be taken with respect to management decisions based on those assumptions.     

A validated method for quantifying macrovesicular hepatic steatosis in chronic hepatitis C

Hepatic steatosis is increasingly seen as an important prognostic factor in chronic hepatitis C infection (HCV). The commonly used semiquantitative method of measuring steatosis is based on a study that excluded patients with HCV. Several potentially useful methods of quantifying steatosis using computer-assisted morphometric analysis have been proposed, but none has been validated against a proposed gold standard other than the method they were intended to replace. We present a novel method and propose a gold standard based on manual measurements. The manual method is time consuming but shows little interobserver error, and the mean value of 3 observations by separate investigators is proposed as the gold standard. The computer-assisted method is fast, with a single interactive step that shows minimal interobserver variation. It accurately identifies biopsies with <1% steatosis (7 of 7) and predicts the gold standard value for biopsies with > 1% steatosis with narrow CIs (geometric mean ratio 0.85 with 95% CIs 0.77-0.95). This novel method of computer-assisted morphometric analysis is fast, reliable, and suitable for future research in HCV steatosis. It may be used to reanalyze previous studies. The semiquantitative method of assessing steatosis remains appropriate for clinical purposes.     

The membrane skeleton--a distinct structure that regulates the function of cells

It has long been known that the red blood cell contains a membrane skeleton that stabilizes the plasma membrane, determines its shape, and regulates the lateral distribution of the membrane glyco-proteins to which it is attached. The way in which these functions are regulated in other cells has not been understood. It has now been shown that platelets also contain a membrane skeleton. In contrast to the membrane skeleton of the red blood cell, the platelet membrane skeleton has actin-binding protein, not spectrin, as a major component. The platelet membrane skeleton regulates the same cellular functions as the red blood cell membrane skeleton. Other cells may contain a membrane skeleton that is critical to their viability and normal functioning.