A variance-stabilizing transformation for gene-expression microarray data

MOTIVATION: Standard statistical techniques often assume that data are normally distributed, with constant variance not depending on the mean of the data. Data that violate these assumptions can often be brought in line with the assumptions by application of a transformation. Gene-expression microarray data have a complicated error structure, with a variance that changes with the mean in a non-linear fashion. Log transformations, which are often applied to microarray data, can inflate the variance of observations near background. RESULTS: We introduce a transformation that stabilizes the variance of microarray data across the full range of expression. Simulation studies also suggest that this transformation approximately symmetrizes microarray data.     

Turnover of histone acetyl groups in cultured mammalian cells

The relative metobolic turnover rates of labeled histone fractions and of their labeled acetyl groups were determined in random cultures of exponentially-growing mammalian cells. Both the parent histones and their acetyl groups were conserved, neither exhibiting detectable metabolic turnover. The significance of these observations is discussed.     

Spindle assembly checkpoint genes reveal distinct as well as overlapping expression that implicates MDF-2/Mad2 in postembryonic seam cell proliferation in Caenorhabditis elegans

Background

The spindle assembly checkpoint (SAC) delays anaphase onset by inhibiting the activity of the anaphase promoting complex/cyclosome (APC/C) until all of the kinetochores have properly attached to the spindle. The importance of SAC genes for genome stability is well established; however, the roles these genes play, during postembryonic development of a multicellular organism, remain largely unexplored.

Results

We have used GFP fusions of 5' upstream intergenic regulatory sequences to assay spatiotemporal expression patterns of eight conserved genes implicated in the spindle assembly checkpoint function in Caenorhabditis elegans. We have shown that regulatory sequences for all of the SAC genes drive ubiquitous GFP expression during early embryonic development. However, postembryonic spatial analysis revealed distinct, tissue-specific expression of SAC genes with striking co-expression in seam cells, as well as in the gut. Additionally, we show that the absence of MDF-2/Mad2 (one of the checkpoint genes) leads to aberrant number and alignment of seam cell nuclei, defects mainly attributed to abnormal postembryonic cell proliferation. Furthermore, we show that these defects are completely rescued by fzy-1(h1983)/CDC20, suggesting that regulation of the APC/C^CDC20 by the SAC component MDF-2 is important for proper postembryonic cell proliferation.

Conclusion

Our results indicate that SAC genes display different tissue-specific expression patterns during postembryonic development in C. elegans with significant co-expression in hypodermal seam cells and gut cells, suggesting that these genes have distinct as well as overlapping roles in postembryonic development that may or may not be related to their established roles in mitosis. Furthermore, we provide evidence, by monitoring seam cell lineage, that one of the checkpoint genes is required for proper postembryonic cell proliferation. Importantly, our research provides the first evidence that postembryonic cell division is more sensitive to SAC loss, in particular MDF-2 loss, than embryonic cell division.     

Brief debrisoquin administration to assess central dopaminergic function in children

Central dopaminergic (DA) function in children was assessed by monitoring plasma-free homovanillic acid (pHVA) levels after brief (18 hour) administration with debrisoquin sulfate, a peripherally active antihypertensive agent that blocks peripheral, but not central, HVA production. Brief debrisoquin administration resulted in marked reductions in pHVA in each of six patients studied. In five of the six patients, post-debrisoquin pHVA levels remained relatively stable over the six-hour period of observation. No significant cardiovascular or behavioral side effects of debrisoquin were observed. The brief debrisoquin administration method appears to be a safe, simple, and potentially valid peripheral technique for evaluating aspects of central dopaminergic function in children with neuropsychiatric disorders. Additional work is needed to further establish this method's validity and reliability.     

Guanine-rich telomeric sequences stimulate DNA polymerase activity in vitro

Guanine-rich oligonucleotides and short telomeric DNA sequences can self-associate into G-quartet stabilized complexes. We discovered that this self-association can occur in sequencing reactions and that higher-order structures stimulate DNA polymerase to synthesize extended DNA strands. Base analogues were used to identify Hoogsteen base pairings as stabilizing forces in these stimulatory DNA structures. Scanning force microscopy confirmed that quartet-DNA was formed from these oligomers and that these extended, four-stranded structures could be bound by DNA polymerase. Since guanine quartet-stabilized structures are proposed to exist in vivo, such structures may stimulate DNA polymerization in vivo.     

PATTERNS OF VARIATION IN FOLIAR TRICHOMES OF EASTERN NORTH AMERICAN QUERCUS

Scanning electron microscopy of leaf trichomes of the forty two native species of oaks in eastern North America indicates five patterns of variability: 1) Eight trichome types are evident among the species and each species possesses a definite complement of trichome types. Certain trichomes are restricted to particular subgenera and series. 2) An obvious seasonal loss of trichomes occurs during leaf maturation. This loss may be both quantitative in terms of trichome density and qualitative in terms of trichome type. 3) There is an obvious difference between the adaxial and abaxial surfaces. The adaxial side of most oak leaves is dark green, lustrous, and glabrous or glabrate. The abaxial surface either remains pubescent, becomes glabrate or glabrous, or maintains trichomes along the midrib or in the axils of major secondary veins. There are also initial quantitative and qualitative trichome differences between the two sides. 4) Geographical and ecological variations are due in part to non-genetic ecophenic modifications, ecotypic differentiation, and random genetic differences not necessarily correlated with environmental conditions. Trichome types are considered to be less affected by environment than is trichome density. 5) Hybridization and introgression within a subgenus leads to localized variability. Trichomes of hybrids are usually a combination of the parental types. These five patterns of variation are predictable and appear to be held within rather narrow limits. The complement of foliar trichomes, therefore, is a reliable character in the taxonomy of the oaks.     

Skin tight: cell adhesion in the epidermis of Caenorhabditis elegans

The powerful genetics, genomics and microscopy tools available for C. elegans make it well suited to studying how epithelial cells adhere to one another and the extracellular matrix, and how the integrated, simultaneous activities of multiple cell adhesion complexes function to shape an organism. Recent studies using forward and reverse genetics have shed light on how phylogenetically conserved cell adhesion complexes, such as the cadherin/catenin complex, claudins, the Discs large complex and hemidesmosome-like attachment structures, regulate epithelial cell adhesion, providing new insights into conserved cell adhesion mechanisms in higher eukaryotes.     

Mucosal inflammation in a genetic model of spontaneous type I diabetes mellitus

The BioBreeding (BB) rat provides a model of spontaneous type I diabetes mellitus that closely resembles the human disease. Diabetes-prone BB rats demonstrate increased intestinal permeability prior to the development of insulinitis. Studies suggest that alterations in intestinal permeability can lead to increased intestinal inflammatory activity. Diabetes-prone (BBdp) and diabetes-resistant (BBdr) BB rats were examined at 45 days and at >70 days of age following the development of clinical disease (BBd). In separate experiments, tissue was assayed for myeloperoxidase (MPO) or fixed for histological assessment and immunohistochemistry. Blood was obtained for leukocyte MPO measurements and morphological assessment of circulating leukocytes. MPO activity was significantly elevated in the distal small intestine of 45-day-old BBdp rats. In contrast, at >70 days of age, MPO activity was significantly increased throughout the small intestine of BBd and non-diabetic BBdp rats. Subsequently, all measurements were performed in >70-day-old rats. An increase in inflammatory infiltrate was noted in the distal small intestine of BBd rats by light microscopy. Infiltrating cells were identified as bands (a maturing cell type of the neutrophil lineage) and mature neutrophils. The findings suggest diabetes susceptibility is associated with an increase in intestinal inflammatory activity.