细胞命运抉择的数学模型:活性氧与p53的关系及其意义(英文)

生物体内的细胞生活在复杂的环境中。在生物体内,活性氧是普遍存在的。生物体内的活性氧可以诱导DNA损伤,最终破坏基因组稳定性。其中,对基因组损伤最严重的是DNA双链断裂损伤。肿瘤抑制因子p53是细胞内介导DNA损伤反应的重要因子。p53可以修复损伤DNA,保护轻度受损细胞。而当细胞受到严重损伤时,p53能够诱发细胞凋亡,从而维持机体稳态。p53的动力学对于细胞的反应性具有重要影响,然而对这方面却缺少系统的认识。因此在本文中,我们主要关注运用数学模型方法研究p53脉冲的动力学性质,从而揭示细胞内潜在的生死选择机制。     

Diurnal rhythms of autophagy: Implications for cell biology and human disease

Autophagy is a key mechanism for cell survival under conditions of nutrient limitation. On the organismal level, autophagy is essential for survival of lower eukaryotes during extended periods of starvation, and it is induced in mammals during short-term starvation. As a consequence of the induction of autophagy during short periods of fasting, animals experience diurnal rhythms of autophagy in concert with their circadian cycle. Autophagy has also been identified as a component of the metabolic cycle of yeast, an ultradian rhythm that bears many similarities to the circadian rhythm of plants, flies, and mammals. The circadian clock, which is present in almost all mammalian cell types studied to date, temporally regulates expression of multiple genes, gating cell processes such as nutrient uptake, glycolysis, and proliferation, to particular times of day. Whether the circadian clock directly regulates autophagy in mammalian cells, or whether autophagy may play a role in the cycling of mammalian cell clocks is not yet clear. Nevertheless, the relationship between circadian cycles and autophagy is an intriguing area for future study and has implications for multiple human diseases, including aging, neurodegeneration, and cancer.     

An Integrated Mitochondrial ROS Production and Scavenging Model: Implications for Heart Failure

It has been observed experimentally that cells from failing hearts exhibit elevated levels of reactive oxygen species (ROS) upon increases in energetic workload. One proposed mechanism for this behavior is mitochondrial Ca²⁺ mismanagement that leads to depletion of ROS scavengers. Here, we present a computational model to test this hypothesis. Previously published models of ROS production and scavenging were combined and reparameterized to describe ROS regulation in the cellular environment. Extramitochondrial Ca²⁺ pulses were applied to simulate frequency-dependent changes in cytosolic Ca²⁺. Model results show that decreased mitochondrial Ca²⁺uptake due to mitochondrial Ca²⁺ uniporter inhibition (simulating Ru360) or elevated cytosolic Na⁺, as in heart failure, leads to a decreased supply of NADH and NADPH upon increasing cellular workload. Oxidation of NADPH leads to oxidation of glutathione (GSH) and increased mitochondrial ROS levels, validating the Ca²⁺ mismanagement hypothesis. The model goes on to predict that the ratio of steady-state [H₂O₂]_m during 3Hz pacing to [H₂O₂]_m at rest is highly sensitive to the size of the GSH pool. The largest relative increase in [H₂O₂]_m in response to pacing is shown to occur when the total GSH and GSSG is close to 1 mM, whereas pool sizes below 0.9 mM result in high resting H₂O₂ levels, a quantitative prediction only possible with a computational model.     

Biochemistry of peroxisomes in health and disease

The ubiquitous distribution of peroxisomes and the identification of a number of inherited diseases associated with peroxisomal dysfunction indicate that peroxisomes play an essential part in cellular metabolism. Some of the most important metabolic functions of peroxisomes include the synthesis of plasmalogens, bile acids, cholesterol and dolichol, and the oxidation of fatty acids (very long chain fatty acids > C22, branched chain fatty acids (e.g. phytanic acid), dicarboxylic acids, unsaturated fatty acids, prostaglandins, pipecolic acid and glutaric acid). Peroxisomes are also responsible for the metabolism of purines, polyamines, amino acids, glyoxylate and reactive oxygen species (e.g. O-2 and H2O2). Peroxisomal diseases result from the dysfunction of one or more peroxisomal metabolic functions, the majority of which manifest as neurological abnormalities. The quantitation of peroxisomal metabolic functions (e.g. levels of specific metabolites and/or enzyme activity) has bec ome the basis of clinical diagnosis of diseases associated with the organelle. The study of peroxisomal diseases has also contributed towards the further elucidation of a number of metabolic functions of peroxisomes. (Mol Cell Biochem 167:1-29, 1997)     

Catalase-negative peroxisomes in human embryonic liver

Hepatic peroxisomes in human embryos with a menstrual age of 6 and 7 weeks have been examined via catalase cytochemistry. In the younger sample, the organelles show no catalase activity, their matrix being pale and coarsely reticular. In the 7-week specimen, the peroxisome population consists of catalase-positive and catalase-negative organelles. The latter have a morphology identical to that of the 6-week sample and represent 66% of the population. The positive organelles show a pronounced staining hetereogeneity. Together with the simultaneous presence of negative organelles, this might reflect the onset of catalase import into the peroxisomes during this period. Catalase heterogeneity excludes a continuous exchange of matrix contents; moreover, interconnections between peroxisomes have not been observed, and no cluster formation occurs. The data therefore also suggest that catalase is imported into individual, preexisting organelles in embryonic liver. The three peroxisomal -oxidation enzymes become detectable by immunocytochemistry only later during development. Morphological indications for a rapidly dividing population, such as elongated and/or tailed organelles, have not been observed. Morphometry has revealed that, in these early stages, the organelles are significantly smaller than the peroxisomes of fetal and adult human liver.     

Phylogenetic analysis of the thiolase family. Implications for the evolutionary origin of peroxisomes

Summary The thiolase family is a widespread group of proteins present in prokaryotes and three cellular compartments of eukaryotes. This fact makes this family interesting in order to study the evolutionary process of eukaryotes. Using the sequence of peroxisomal thiolase from Saccharomyces cerevisiae recently obtained by us and the other known thiolase sequences, a phylogenetic analysis has been carried out. It shows that all these proteins derived from a primitive enzyme, present in the common ancestor of eubacteria and eukaryotes, which evolved into different specialized thiolases confined to various cell compartments. The evolutionary tree obtained is compatible with the endosymbiotic theory for the origin of peroxisomes. Offprint requests to: J.E. Pérez-Ortín     

Heterogeneity of catalase staining in human hepatocellular peroxisomes

Hepatocellular peroxisomes stained for catalase activity have different electron densities. When measured by scanning transmission electron microscopy, density is inversely linear to diameter. We investigated whether this phenomenon is the result of a staining artifact that reflects more efficient diffusion of substrate into smaller peroxisomes (higher surface-to-volume ratio), or of differences in endogenous enzymatic activity. Measurements of optical density show that the amount of reaction product is proportional to the diaminobenzidine concentration in the medium; this is not the case for H2O2. Modifying the concentration of both substrates does not alter the heterogeneous staining pattern. Heterogeneity persists when the reaction is slowed by inhibitors or when diffusion takes place before the reaction, and in preparations that have not been subjected to cytochemical staining. These data show that catalase activity is different in individual peroxisomes and that the staining differences are not a consequence of variations in substrate diffusion. Some implications of this conclusion are discussed.     

The human secretome atlas initiative: Implications in health and disease conditions

Proteomic analysis of human body fluids is highly challenging, therefore many researchers are redirecting efforts toward secretome profiling. The goal is to define potential biomarkers and therapeutic targets in the secretome that can be traced back in accessible human body fluids. However, currently there is a lack of secretome profiles of normal human primary cells making it difficult to assess the biological meaning of current findings. In this study we sought to establish secretome profiles of human primary cells obtained from healthy donors with the goal of building a human secretome atlas. Such an atlas can be used as a reference for discovery of potential disease associated biomarkers and eventually novel therapeutic targets. As a preliminary study, secretome profiles were established for six different types of human primary cell cultures and checked for overlaps with the three major human body fluids including plasma, cerebrospinal fluid and urine. About 67% of the 1054 identified proteins in the secretome of these primary cells occurred in at least one body fluid. Furthermore, comparison of the secretome profiles of two human glioblastoma cell lines to this new human secretome atlas enabled unambiguous identification of potential brain tumor biomarkers. These biomarkers can be easily monitored in different body fluids using stable isotope labeled standard proteins. The long term goal of this study is to establish a comprehensive online human secretome atlas for future use as a reference for any disease related secretome study. This article is part of a Special Issue entitled: An Updated Secretome.     

Role of excitotoxicity in human neurological disease.

An increasing body of evidence has implicated excitoxicity as a mechanism of neuronal death in both acute and chronic neurological diseases. A major recent advance has been the successful cloning and expression of the non-NMDA, NMDA, and metabotropic glutamate receptors. The cellular mechanisms responsible for cell death following activation of these receptors are still being clarified. A recent advance in conceptualizing excitotoxicity is the notion that a slow excitotoxic process may occur as a consequence of either a receptor abnormality or an impairment of energy metabolism. It is possible that such a mechanism may occur in neurodegenerative illnesses. Recent therapeutic studies have focused on glycine site antagonists and on the efficacy of non-NMDA antagonists in ischemia.     

Characterization of peroxisomes in Tetrahymena pyriformis

Peroxisomes from Tetrahymena pyriformis contained catalase, d-amino acid oxidase, cyanide-insensitive fatty acyl-CoA oxidizing system, carnitine acetyltransferase, isocitrate lyase, leucine:glyoxylate aminotransferase and phenylalanine:glyoxylate aminotransferase. These activities, except carnitine acetyltransferase, were found at the highest levels in the light mitochondrial fraction, whereas the highest activity of carnitine acetyltransferase was found in the micotchondrial fraction. Sucrose density gradient centrifugation showed that the density of peroxisomes was approx. 1.228 g/ml and that of mitochondria was approx. 1.213 g/ml. When the light mitochondrial fraction was treated with deoxycholate or by freeze-thawing, most of the activities of catalase and isocitrate lyase were solubilized, whereas about half of the original activity of aminotransferase remained in the pellet fraction. Addition of fatty acid and clofibrate increased the activities of the cyanide-insensitive fatty acyl-CoA oxidizing system and isocitrate lyase in the peroxisomes. The activity of catalase was slightly increased by glucose and clofibrate; leucine:glyoxylate aminotransferase activity was significantly increased by clofibrate treatment.     

Post-mortem visualization of peroxisomes in rat and in human liver

Summary This paper describes spontaneous post-mortem changes of peroxisomal staining in normal liver and kidney of rats and in human autopsy liver. At room temperature, regional staining loss is observed at 18h after death in rat kidney, at 24h in human liver and at 48 h in rat liver. Preservation at 4°C delays this phenomenon. In human liver, the peroxisomal volume density is decreased at both temperatures at 48 h. After freezing of fresh tissue in dry ice, peroxisomal staining is decreased homogeneously. Under the electron microscope, peroxisomal alterations suggest a loss of catalase activity. These changes do not necessarily preclude the study of peroxisomal features since, even after 48 h at room temperature, peroxisomes are still well stained in the less affected regions. Catalase and three -oxidation enzymes, namely acyl-CoA oxidase, bifunctional protein (with enoyl-CoA hydratase and 3-hydroxyacyl-CoA dehydrogenase) and 3-oxoacyl-CoA thiolase, could be visualized immunocytochemically in human autopsy livers up to 48 h after death. However, the study of certain peroxisomal features such as catalase activity and peroxisomal distribution, may be hampered as the post-mortem period is prolonged.     

Regulation of G protein function: Implications for heart disease

Heterotrimeric GTP-binding and -hydrolyzing proteins (G proteins) link members of a family of seven-helix transmembrane receptors (G protein-coupled receptors, GPCR) to intracellular effectors. The coupling mechanism involves the G protein completing a cycle of activation, dissociation into and subunits, deactivation, and reassociation. At the center of this cycle is the subunit, in which activation by GPCR, GTPase activity, and regulation of effector are combined. Whereas G's functional domains and residues had already been inferred from mutagenesis studies, the recent solution of the crystal structure has elucidated the structural basis of subunit function. It is now clear that an irregularity in any GPCR pathway component could cause a physiological defect. This is confirmed by the identification of mutations in GPCR and G's in various human diseases. Although several cardiomyopathies are associated with abnormal GPCR function, mutations are unlikely in these disorders. The last few years, other aspects of G protein function have moved into focus: e.g. posttranslational modifications; effector regulation by subunits; GTPase activating protein (GAP) activity of effectors; G protein expression levels etc. When comparing the regulation of G protein functional activity in cAMP and in inositol phosphate generating pathways, an extrapolation can be made to data on the status of these pathways in some cardiovascular diseases.Abbreviations AC adenylate cyclase - GPCR G protein-coupled receptor - PLC phospholipase C - GAP GTPase activating protein - PTX pertussis toxin - Ptdins(4,5)P ₂ phosphatidylinositol 4,5-bisphosphate - Ins(1,4,5)P ₃ inositol 1,4,5-trisphosphate - CCh carbachol     

Role of reactive oxygen species (ROS) in apoptosis induction

Reactive oxygen species (ROS) and mitochondria play an important role in apoptosis induction under both physiologic and pathologic conditions. Interestingly, mitochondria are both source and target of ROS. Cytochrome c release from mitochondria, that triggers caspase activation, appears to be largely mediated by direct or indirect ROS action. On the other hand, ROS have also anti-apoptotic effects. This review focuses on the role of ROS in the regulation of apoptosis, especially in inflammatory cells.