Gene-dependent cell death in yeast.

Caspase-dependent apoptotic cell death has been extensively studied in cultured cells and during embryonic development, but the existence of analogous molecular pathways in single-cell species is uncertain. This has reduced enthusiasm for applying the advanced genetic tools available for yeast to study cell death regulation. However, partial characterization in mammals of additional genetically encoded cell death mechanisms, which lead to a range of dying cell morphologies and necrosis, suggests potential applications for yeast genetics. In this light, we revisited the topic of gene-dependent cell death in yeast to determine the prevalence of yeast genes with the capacity to contribute to cell-autonomous death. We developed a rigorous strategy by allowing sufficient time for gene-dependent events to occur, but insufficient time to evolve new populations, and applied this strategy to the Saccharomyces cerevisiae gene knockout collection. Unlike sudden heat shock, a ramped heat stimulus delivered over several minutes with a thermocycler, coupled with assessment of viability by automated counting of microscopic colonies revealed highly reproducible gene-specific survival phenotypes, which typically persist under alternative conditions. Unexpectedly, we identified over 800 yeast knockout strains that exhibit significantly increased survival following insult, implying that these genes can contribute to cell death. Although these death mechanisms are yet uncharacterized, this study facilitates further exploration.

Mitochondrial fission and fusion dynamics: the long and short of it.

Maintenance of functional mitochondria requires fusion and fission of these dynamic organelles. The proteins that regulate mitochondrial dynamics are now associated with a broad range of cellular functions. Mitochondrial fission and fusion are often viewed as a finely tuned balance within cells, yet an integrated and quantitative understanding of how these processes interact with each other and with other mitochondrial and cellular processes is not well formulated. Direct visual observation of mitochondrial fission and fusion events, together with computational approaches promise to provide new insight.

[Glucocorticoid hypofunction in myotonic dystrophy]. / Hipofunción glucocorticoide en la distrofia miotónica.

INTRODUCTION: Myotonic dystrophy (DM1) is an autosomal dominant disorder whose genetic defect consists of the amplification of an unstable CTG trinucleotide repeat in the 3' untranslated region of the dystrophia myotonica protein kinase gene (DMPK). This is a multi-systemic disease with a well-known endocrinological repercussion. With respect to the adrenal function variable results have been described, although lately they are interpreted as indicators of a hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis. MATERIAL AND METHODS: Twenty-five patients (13 men and 12 women) with DM1 were recruited. They were analysed for: basal cortisol and ACTH, stimulus test with 0.25 mg of ACTH for cortisol and CRH test for cortisol and ACTH. Similarly, the degree of expansion of CTG was evaluated by Southern blot and PCR. Twenty-five healthy individuals, comparable by age and sex, were studied as a control group; the CRH test was carried out on 11 of them. RESULT: One patient was diagnosed with primary non-autoimmune adrenal failure. In the rest of the cases there were no differences between the basal ACTH of patients and controls, and the cortisol response to ACTH was normal. The patients showed a lower level of basal cortisol (p<0.01) and also showed, following stimulation with CRH, a lower cortisol response (p<0.05) with higher average values of ACTH. CONCLUSIONS: Our data differs from the latest publications and point to an adrenal hypofunction due to lack of efficacy of the ACTH on its receptor or at the post-receptor level. We suggest that the etiology might be related to the underlying defect in the gene that codifies DMPK.

Bioinformatics and mass spectrometry for microorganism identification: proteome-wide post-translational modifications and database search algorithms for characterization of intact H. pylori.

MALDI-TOF mass spectrometry has been coupled with Internet-based proteome database search algorithms in an approach for direct microorganism identification. This approach is applied here to characterize intact H. pylori (strain 26695) Gram-negative bacteria, the most ubiquitous human pathogen. A procedure for including a specific and common posttranslational modification, N-terminal Met cleavage, in the search algorithm is described. Accounting for posttranslational modifications in putative protein biomarkers improves the identification reliability by at least an order of magnitude. The influence of other factors, such as number of detected biomarker peaks, proteome size, spectral calibration, and mass accuracy, on the microorganism identification success rate is illustrated as well.

Testing the significance of microorganism identification by mass spectrometry and proteome database search.

We derive and validate a simple statistical model that predicts the distribution of false matches between peaks in matrix-assisted laser desorption/ionization mass spectrometry data and proteins in proteome databases. The model allows us to calculate the significance of previously reported microorganism identification results. In particular, for deltam = +/-1.5 Da, we find that the computed significance levels are sufficient to demonstrate the ability to identify microorganisms, provided the number of candidate microorganisms is limited to roughly three Escherichia coli-like or roughly 10 Bacillus subtilis-like microorganisms (in the sense of having roughly the same number of proteins per unit-mass interval). We conclude that, given the cluttered and incomplete nature of the data, it is likely that neither simple ranking nor simple hypothesis testing will be sufficient for truly robust microorganism identification over a large number of candidate microorganisms.