Exploiting the full power of temporal gene expression profiling through a new statistical test: Application to the analysis of muscular dystrophy data

Background  

The identification of biologically interesting genes in a temporal expression profiling dataset is challenging and complicated by high levels of experimental noise. Most statistical methods used in the literature do not fully exploit the temporal ordering in the dataset and are not suited to the case where temporal profiles are measured for a number of different biological conditions. We present a statistical test that makes explicit use of the temporal order in the data by fitting polynomial functions to the temporal profile of each gene and for each biological condition. A Hotelling T ²-statistic is derived to detect the genes for which the parameters of these polynomials are significantly different from each other.     

Metal resistance and accumulation in bacteria

Recent research on the ecology, physiology and genetics of metal resistance and accumulation in bacteria has significantly increased the basic understanding of microbiology in these areas. Research has clearly demonstrated the versatility of bacteria to cope with toxic metal ions. For example, certain strains of bacteria can efficiently efflux toxic ions such as cadmium, that normally exert an inhibitory effect on bacteria. Some bacteria such as Escherichia coli and Staphylococcus sp. can volatilize mercury via enzymatic transformations. It is also noteworthy that many of these resistance mechanisms are encoded on plasmids or transposons. By expanding the knowledge on metal-resistance and accumulation mechanisms in bacteria, it may be possible to utilize certain strains to recover precious metals such as gold and silver, or alternatively remove toxic metal ions from environments or products where their presence is undesirable.     

Metallic electrodes and leads in simultaneous EEG-MRI: specific absorption rate (SAR) simulation studies

The purpose of this study was to investigate the changes in specific absorption rate (SAR) in human-head tissues while using nonmagnetic metallic electroencephalography (EEG) electrodes and leads during magnetic resonance imaging (MRI). A realistic, high resolution (1 mm(3)) head model from individual MRI data was adopted to describe accurately thin tissues, such as bone marrow and skin. The RF power dissipated in the human head was evaluated using the FDTD algorithm. Both surface and bird cage coils were used. The following numbers of EEG electrodes/leads were considered: 16, 31, 62, and 124. Simulations were performed at 128 and 300 MHz. The difference in SAR between the electrodes/leads and no-electrodes conditions was greater with the bird cage coil than with the surface coil. The peak 1 g averaged SAR values were highest at 124 electrodes, increasing to as much as two orders of magnitude (x172.3) at 300 MHz compared to the original value. At 300 MHz, there was a fourfold (x3.6) increase of SAR averaged over the bone marrow, and a sevenfold (x7.4) increase in the skin. At 128 MHz, there was a fivefold (x5.6) increase of whole head SAR. Head models were obtained from two different subjects, with an inter-subject whole head SAR variability of 3%. .     

Changes in calcineurin expression induced in the rat brain by the administration of antipsychotics

Calcineurin (CN) was recently identified as a susceptibility gene for schizophrenia as well as showing altered RNA expression levels in the post-mortem brains of individuals with schizophrenia. CN knockout mice show a number of behaviours associated with schizophrenia, including deficits in sensorimotor gating, suggesting a link between CN and psychosis. Concurrently, we found, using genome screening techniques, that antipsychotics alter CN expression levels. Therefore, western blotting, in situ hybridization, immunocytochemistry and phosphatase assays were employed to determine what effect antipsychotics have on CN. The results indicate that clozapine, risperidone and haloperidol cause substantial reductions in the A subunit of CN but not CN B at both the RNA and protein levels in the striatum and prefrontal cortex. The changes could only be observed after repeated treatment with antipsychotics but not after acute administration. The alterations in CN protein levels were specific to antipsychotics and mediated by D2 dopamine receptor antagonism. However, despite reductions in CN protein levels, the phosphatase activity of CN was significantly elevated after treatment with antipsychotics. Collectively the results suggest that CN may be a common target for antipsychotics and that antipsychotic-induced alterations in CN may represent one of the mechanisms by which antipsychotics alleviate psychosis.     

The solubility of calcium oxalate in tissue culture media

The equilibrium parameters for calcium oxalate solubility in tissue culture media were investigated because of the current interest in oxalate toxicity. The calcium selective ion electrode methodology was evaluated and calcium concentrations from potentiometric calculations were verified by d-c argon plasma emission spectroscopy. The experimental K(sp)'s at 25 degrees C for Dulbecco's modified Eagle media and McCoys 5A media are equivalent to the literature K(sp) of 2.3 x 10(-9) for low ionic strength. The equilibrium concentration products, [Ca2+] [C2O2-(4)], are ten times higher than the K(sp)'s due to the high ionic strengths of tissue culture media. At 37 degrees C, addition of soluble oxalate at the 10(-3) to 10(-4) M level causes >50% precipitation of the oxalate resulting in equilibrium oxalate concentrations of less than 6 x 10(-5) M. This relatively inexpensive selective ion technique allows the determination of oxalate concentrations in equilibrium-saturated media which are substantially less than those calculated by the amount of soluble oxalate added to the media.     

Use of chromomycin A3 staining in bovine sperm cells for detection of protamine deficiency

Sperm chromatin integrity is essential for accurate transmission of male genetic information, and normal sperm chromatin structure is important for fertilization. Protamine is a nuclear protein that plays a key role in sperm DNA integrity, because it is responsible for sperm DNA stability and packing until the paternal genome is delivered into the oocyte during fertilization. Our aim was to investigate protamine deficiency in sperm cells of Bos indicus bulls (Nelore) using chromomycin A₃ (CMA₃) staining. Frozen semen from 14 bulls were thawed, then fixed in Carnoy's solution. Smears were prepared and analyzed by microscopy. As a positive control of CMA₃ staining, sperm from one bull was subjected to deprotamination of nuclei. The percentage of CMA₃-positive bovine sperm did not vary among batches. Only two bulls showed a higher percentage of CMA₃-positive sperm cells compared to the others. CMA₃ is a simple and useful tool for detecting sperm protamine deficiency in bulls.     

Monitoring of clinical signs in goats with transmissible spongiform encephalopathies

Background  

As there is limited information about the clinical signs of BSE and scrapie in goats, studies were conducted to describe the clinical progression of scrapie and BSE in goats and to evaluate a short clinical protocol for its use in detecting scrapie-affected goats in two herds with previously confirmed scrapie cases. Clinical assessments were carried out in five goats intracerebrally infected with the BSE agent as well as five reported scrapie suspects and 346 goats subject to cull from the two herds, 24 of which were retained for further monitoring. The brain and selected lymphoid tissue were examined by postmortem tests for disease confirmation.