Carcinoma of the breast with malignant epithelial giant cells. Needle aspiration cytology, immunocytochemistry and electron microscopy in a rare case in a woman under 30.

Needle aspiration cytology, immunocytochemistry and electron microscopic findings are described in a case of rare breast carcinoma with bizarre, malignant giant cells in a young female under age 30. The malignant tumors were found in both breasts; the first one was diagnosed when the patient was 23 years of age and the second one in the contralateral breast four years later. Based on our present findings, and in keeping with a similar case recently described by us as occurring in an elderly female, we thought that the bizarre giant cells in this rare breast carcinoma were of epithelial origin. The differential diagnosis of other conditions that may be associated with giant cells in breast aspirates is discussed.     

PyCogent: a toolkit for making sense from sequence

We have implemented in Python the COmparative GENomic Toolkit, a fully integrated and thoroughly tested framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics. PyCogent includes connectors to remote databases, built-in generalized probabilistic techniques for working with biological sequences, and controllers for third-party applications. The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent.     

A Bayesian mixture model for partitioning gene expression data

In recent years there has been great interest in making inference for gene expression data collected over time. In this article, we describe a Bayesian hierarchical mixture model for partitioning such data. While conventional approaches cluster the observed data, we assume a nonparametric, random walk model, and partition on the basis of the parameters of this model. The model is flexible and can be tuned to the specific context, respects the order of observations within each curve, acknowledges measurement error, and allows prior knowledge on parameters to be incorporated. The number of partitions may also be treated as unknown, and inferred from the data, in which case computation is carried out via a birth-death Markov chain Monte Carlo algorithm. We first examine the behavior of the model on simulated data, along with a comparison with more conventional approaches, and then analyze meiotic expression data collected over time on fission yeast genes.     

Oxygen consumption, ammonia excretion and protein use in response to thermal changes in juvenile Atlantic salmon Salmo salar

Experiments were designed to examine the effects of various temperature challenges on oxygen consumption and ammonia excretion rates and protein utilization in juvenile Atlantic salmon Salmo salar . Fish acclimated to 15° C were acutely and abruptly exposed to either 20 or 25° C for a period of 3 h. To simulate a more environmentally relevant temperature challenge, a third group of fish was exposed to a gradual increase in temperature from 15 to 20° C over a period of 3 h ( c. 1·7° C h⁻¹). Oxygen consumption and ammonia excretion rates were monitored before, during and after the temperature shift. From the ammonia excretion and oxygen consumption rates, protein utilization rates were calculated. Acute temperature changes (15–20° C or 15–25° C) caused large and immediate increases in the oxygen consumption rates. When the temperature was gradually changed ( i.e. 1·7° C h⁻¹), however, the rates of oxygen consumption and ammonia excretion were only marginally altered. When fish were exposed to warmer temperatures ( i.e. 15–20° C or 15–25° C) protein use generally remained at pre-exposure (15° C) levels. A rapid transfer back to 15° C (20–15° C or 25–15° C) generally increased protein use in S. salar . These results indicate that both the magnitude and the rate of temperature change are important in describing the physiological response in juvenile salmonids.     

Specific Isolation of RNA from the Grape Powdery Mildew Pathogen Erysiphe necator, an Epiphytic, Obligate Parasite

RNA expression profiling of obligately parasitic plant microbes is hampered by the requisite interaction of host and parasite. This can be especially problematic in the case of powdery mildews, such as Erysiphe necator (syn. Uncinula necator ), which grow superficially but tightly adhere to the plant epidermis. We developed and refined a simple and efficient technique in which nail polish was used to remove conidia, appressoria, hyphae, conidiophores, and developing ascocarps of E. necator from grapevine ( Vitis vinifera ) leaves and showed that RNA isolated after removal was not contaminated with V. vinifera RNA. This approach can be applied to expression analyses throughout fungal development and could be extended to other epiphytic pathogens and saprophytes.     

Characterisation of CpG methylation in the upstream control region of mouse Nat2: Evidence for a gene–environment interaction in a polymorphic gene implicated in folate metabolism

Human arylamine N-acetyltransferase 1 (NAT1), a polymorphic xenobiotic metabolising enzyme, has been investigated in relation to susceptibility and prognosis in certain types of cancer. Both human NAT1 and its murine equivalent NAT2 have previously been shown to play roles in the catabolism of folate, which is required for the synthesis of S-adenosylmethionine, the methyl donor for cellular methylation reactions. We have tested whether the expression of mouse Nat2 is subject to epigenetic regulation, specifically CpG methylation in the promoter region, by determining levels of 5-methylcytosine by bisulphite sequencing and methylation-specific PCR. Under normal conditions, methylation levels of the Nat2 promoter were low, and varied in different tissues. However, CpG methylation was significantly increased by dietary folate supplementation, and increased methylation corresponded to decreased use of the core promoter. Functional deletion of the Nat2 gene gave rise to a significant increase in Nat2 methylation, extending our previous observations that folate catabolism is decreased in Nat2 null mice. Mouse NAT2 is likely to influence epigenetic gene control, particularly of its own locus, and this is consistent with recent evidence associating aberrant mouse Nat2/human NAT1 gene expression with certain developmental malformations and cancers.     

Annual, lunar and diel reproductive periodicity of a spawning aggregation of snapper Pagrus auratus (Sparidae) in a marine embayment on the lower west coast of Australia

Ichthyoplankton sampling and ovarian characteristics were used to elucidate whether the reproductive cycles of a spawning aggregation of snapper Pagrus auratus in a nearshore marine embayment were temporally and spatially specific and related with environmental conditions. The reproductive dynamics of this aggregation were studied over four consecutive years (2001-2004). Spawning occurred between September and January each year, when water temperatures ranged from 15·8 to 23·1° C. In all 4 years, the cumulative egg densities in Cockburn Sound were highest when water temperatures were between the narrow range of 19-20° C. The spawning fraction of females was monthly bimodal and peaked during new and the full moons at 96-100% and c. 75%, respectively. The backcalculated ages of P. auratus eggs collected from 16 ichthyoplankton surveys demonstrated that P. auratus in Cockburn Sound spawn at night during the 3 h following the high tide. The spatial distributions of P. auratus eggs in Cockburn Sound during the peak reproductive period in all 4 years were consistent, further implying spawning was temporally and spatially specific. High concentrations of recently spawned eggs (8-16 h old) demonstrated spawning also occurred within the adjacent marine embayments of Owen Anchorage and Warnbro Sound. Water circulation in Cockburn and Warnbro Sounds resembled an eddy that was most prominent during the period of highest egg densities, thereby facilitating the retention of eggs in these areas. The reproductive cycles of P. auratus described in this study have assisted managers with the appropriate temporal and spatial scale for a closed fishing season to protect these spawning aggregations.     

Centaurin-alpha(1) associates with and is phosphorylated by isoforms of protein kinase C

Centaurin-alpha(1) is a member of the family of ADP-ribosylation factors (ARF) GTPase activating proteins (GAPs), although ARF GAP activity has not yet been demonstrated. The human homologue, centaurin-alpha(1) functionally complements the ARF GAP activity of Gcs1 in yeast. Although Gcs1 is involved in the formation of actin filaments in vivo, the function of centaurin remains elusive. We have identified a number of novel centaurin-alpha(1) binding partners; including CKIalpha and nucleolin. In this report, we have focused on the interaction of centaurin-alpha(1) with PKC. All groups of PKC associate directly through their cysteine rich domains. Centaurin-alpha(1) is also a substrate for all PKC classes and we have identified the two sites of phosphorylation. This is the first report of a kinase that phosphorylates centaurin-alpha(1).