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Several Organisms (several + organism)
Selected Abstracts,-Synuclein, oxidative stress and apoptosis from the perspective of a yeast model of Parkinson's diseaseFEMS YEAST RESEARCH, Issue 8 2006Stephan N. Witt Abstract The neuronal protein ,-synuclein (,-syn) has been suggested to be one of the factors linked to Parkinson's disease (PD). Several organisms, including the rat, mouse, worm, and fruit fly, are being used to study ,-syn pathobiology. A new model organism was recently added to this armamentarium: the budding yeast Saccharomyces cerevisiae. The yeast system recapitulates many of the findings made with higher eukaryotes. For example, yeast cells expressing ,-syn accumulate lipid droplets, have vacuolar/lysosomal defects, and exhibit markers of apoptosis, including the externalization of phosphatidylserine, the release of cytochrome c, and the accumulation of reactive oxygen species. This MiniReview focuses on the mechanisms by which ,-syn induces oxidative stress and the mechanisms by which yeast cells respond to this stress. Three classes of therapeutics are discussed. [source] The efficiency of mitochondrial electron transport chain is increased in the long-lived mrg19 Saccharomyces cerevisiaeAGING CELL, Issue 6 2009Nitish Mittal Summary Integrity of mitochondrial functionality is a key determinant of longevity in several organisms. In particular, reduced mitochondrial ROS (mtROS) production leading to decreased mtDNA damage is believed to be a crucial aspect of longevity. The generation of low mtROS was thought to be due to low mitochondrial oxygen consumption. However, recent studies have shown that higher mitochondrial oxygen consumption could still result in low mtROS and contribute to longevity. This increased mitochondrial efficiency (i.e. low mtROS generated despite high oxygen consumption) was explained as a result of mitochondrial biogenesis, which provides more entry points for the electrons to the electron transport chain (ETC), thereby resulting in low mtROS production. In this study, we provide evidence for the existence of an alternative pathway to explain the observed higher mitochondrial efficiency in the long-lived mrg19 mutant of Saccharomyces cerevisiae. Although we observe similar amounts of mitochondria in mrg19 and wild-type (wt) yeast, we find that mrg19 mitochondria have higher expression of ETC components per mitochondria in comparison with the wt. These findings demonstrate that more efficient mitochondria because of increased ETC per mitochondria can also produce less mtROS. Taken together, our findings provide evidence for an alternative explanation for the involvement of higher mitochondrial activity in prolonging lifespan. We anticipate that similar mechanisms might also exist in eukaryotes including human. [source] Speciation, hybrid zones and phylogeography , or seeing genes in space and timeMOLECULAR ECOLOGY, Issue 3 2001Godfrey M. Hewitt Abstract The origins and development of the study of speciation, hybrid zones and phylogeography are outlined using evolutionary iconography. This traces the ideas in this field from Lamarck and Darwin through to the present as represented in diagrams and figures. A ,tree of trees' summarizes this growth and current vitality. The new facility to use various DNA sequences from nuclear, mitochondrial and chloroplast genomes to determine genetic variation throughout a species range is examined particularly. There is great genomic subdivision across species distributions, which can be interpreted in the light of the recent demonstrations of severe palaeoclimatic oscillations. Refugia and postglacial colonization routes are proposed for several organisms across Europe. The role of geography in speciation through the Pleistocene is considered. These emerging principles and analyses are applied to data available on a variety of organisms in other regions of the world, such as the Arctic, North America and the Tropics, and including the progress of Homo sapiens through the last ice age. Some suggestions are made for future research directions. [source] Protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster: Large-scale organization and robustnessPROTEINS: STRUCTURE, FUNCTION AND BIOINFORMATICS, Issue 2 2006Dong Li Abstract High-throughput screens have begun to reveal protein interaction networks in several organisms. To understand the general properties of these protein interaction networks, a systematic analysis of topological structure and robustness was performed on the protein interaction networks of Saccharomyces cerevisiae, Caenorhabditis elegans and Drosophila melanogaster. It shows that the three protein interaction networks have a scale-free and high-degree clustering nature as the consequence of their hierarchical organization. It also shows that they have the small-world property with similar diameter at 4,5. Evaluation of the consequences of random removal of both proteins and interactions from the protein interaction networks suggests their high degree of robustness. Simulation of a protein's removal shows that the protein interaction network's error tolerance is accompanied by attack vulnerability. These fundamental analyses of the networks might serve as a starting point for further exploring complex biological networks and the coming research of "systems biology". [source] To SIR with Polycomb: linking silencing mechanismsBIOESSAYS, Issue 2 2005Vivek S. Chopra Yeast SIR2, the most evolutionarily conserved deacetylase, plays an essential role in epigenetic silencing at the silent mating type loci and telomeres. SIR2 has been implicated in chromatin silencing and lifespan determination in several organisms. Discovery that Drosophila SIR2 is also involved in epigenetic silencing mediated by the Polycomb group proteins and is physically associated with a complex containing the E(Z) histone methyltransferase1 has wide implications. These findings suggest possible link of Polycomb system to diverse cellular processes including senescence. BioEssays 27:119,121, 2005. © 2005 Wiley Periodicals, Inc. [source] Bayesian Methods for Predicting Interacting Protein Pairs Using Domain InformationBIOMETRICS, Issue 3 2007Inyoung Kim Summary Protein,protein interactions (PPIs) play important roles in most fundamental cellular processes including cell cycle, metabolism, and cell proliferation. Therefore, the development of effective statistical approaches to predicting protein interactions based on recently available large-scale experimental data is very important. Because protein domains are the functional units of proteins and PPIs are mostly achieved through domain,domain interactions (DDIs), the modeling and analysis of protein interactions at the domain level may be more informative and insightful. However, due to the large number of domains, the number of parameters to be estimated is very large, yet the amount of information for statistical inference is quite limited. In this article we propose a full Bayesian method and a semi-Bayesian method for simultaneously estimating DDI probabilities, the false positive rate, and the false negative rate of high-throughput data through integrating data from several organisms. We also propose a model to associate protein interaction probabilities with domain interaction probabilities that reflects the number of domains in each protein. Our Bayesian methods are compared with the likelihood-based approach (Deng et al., 2002, Genome Research12, 1504,1508; Liu, Liu, and Zhao, 2005, Bioinformatics21, 3279,3285) developed using the expectation maximization algorithm. We show that the full Bayesian method has the smallest mean square error through both simulations and theoretical justification under a special scenario. The large-scale PPI data obtained from high-throughput yeast two-hybrid experiments are used to demonstrate the advantages of the Bayesian approaches. [source] | ||||||||||