daf-12 encodes a nuclear receptor that regulates the dauer diapause and developmental age in C. elegans

The daf-12 gene acts at the convergence of pathways regulating larval diapause, developmental age, and adult longevity in Caenorhabditis elegans. It encodes a nuclear receptor most closely related to two C. elegans receptors, NHR-8 and NHR-48, Drosophila DHR96, and vertebrate vitamin D and pregnane-X receptors. daf-12 has three predicted protein isoforms, two of which contain DNA- and ligand-binding domains, and one of which contains the ligand-binding domain only. Mutations cluster in DNA- and ligand-binding domains, but correspond to distinct phenotypic classes. DAF-12 is expressed widely in target tissues from embryo to adult, but is upregulated during midlarval stages. In the adult, expression persists in nervous system and somatic gonad, two tissues that regulate adult longevity. We propose that DAF-12 integrates hormonal signals in cellular targets to coordinate major life history traits.     

Metabolic pathway profiling of mitochondrial respiratory chain mutants in C. elegans

Caenorhabditis elegans affords a model of primary mitochondrial dysfunction that provides insight into cellular adaptations which accompany mutations in nuclear genes that encode mitochondrial proteins. To this end, we characterized genome-wide expression profiles of C. elegans strains with mutations in nuclear-encoded subunits of respiratory chain complexes. Our goal was to detect concordant changes among clusters of genes that comprise defined metabolic pathways. Results indicate that respiratory chain mutants significantly upregulate a variety of basic cellular metabolic pathways involved in carbohydrate, amino acid, and fatty acid metabolism, as well as cellular defense pathways such as the metabolism of P450 and glutathione. To further confirm and extend expression analysis findings, quantitation of whole worm free amino acid levels was performed in C. elegans mitochondrial mutants for subunits of complexes I, II, and III. Significant differences were seen for 13 of 16 amino acid levels in complex I mutants compared with controls, as well as overarching similarities among profiles of complex I, II, and III mutants compared with controls. The specific pattern of amino acid alterations observed provides novel evidence to suggest that an increase in glutamate-linked transamination reactions caused by the failure of NAD⁺-dependent ketoacid oxidation occurs in primary mitochondrial respiratory chain mutants. Recognition of consistent alterations both among patterns of nuclear gene expression for multiple biochemical pathways and in quantitative amino acid profiles in a translational genetic model of mitochondrial dysfunction allows insight into the complex pathogenesis underlying primary mitochondrial disease. Such knowledge may enable the development of a metabolomic profiling diagnostic tool applicable to human mitochondrial disease.     

A natural history of melanoma: serial gene expression analysis

Ena Wang and Francesco Marincola propose a novel strategy whereby tumor-host interactions are studied within the melanoma microenvironment by serial gene expression analysis. Methodological constraints and ways to circumvent them are discussed. This approach might improve our understanding of the molecular basis of tumor regression in response to immune manipulation.     

daf-28 encodes a C. elegans insulin superfamily member that is regulated by environmental cues and acts in the DAF-2 signaling pathway

In Caenorhabditis elegans, the decision to enter a developmentally arrested dauer larval stage is triggered by a combination of signals from sensory neurons in response to environmental cues, which include a dauer pheromone. These sensory inputs are coupled to the parallel DAF-2/insulin receptor-like and DAF-7/TGFbeta-like signaling pathways. Although sensory inputs have been shown to physiologically regulate DAF-7/TGFbeta expression, no such regulation of insulin-like ligands in the DAF-2 pathway has been reported. We show here that daf-28 encodes an insulin-like protein, which when mutated causes dauer arrest and down-regulation of DAF-2/IR signaling. A daf-28GFP fusion gene is expressed in ASI and ASJ, two sensory neurons that regulate dauer arrest. daf-28GFP expression in ASI and ASJ is down-regulated under dauer-inducing conditions and in mutants of DAF-11/guanylyl cyclase, a predicted component of the dauer-pheromone-sensing pathway. Thus, daf-28 expression in sensory neurons is regulated by the environmental cues that normally trigger dauer arrest. Among the 38 C. elegans insulin genes, daf-28 is so far the only insulin mutant to affect dauer arrest. daf-28 was revealed from this functional redundancy by a dominant-negative allele that disrupts a probable proteolytic processing site required for insulin maturation. This DAF-28 mutant is likely to be poisonous to wild-type DAF-28 and other insulins.     

Fluorodeoxyuridine affects the identification of metabolic responses to daf-2 status in Caenorhabditis elegans

Fluorodeoxyuridine (FUdR) is often used to help maintain synchronous populations of Caenorhabditis elegans adults, for instance as would typically be the case in studying age-related effects. However, given that FUdR inhibits DNA synthesis and therefore reproduction, it will clearly have significant wide-ranging biological effects. It is often assumed that these can be compensated for using appropriate controls. We show here that this is not the case for a metabolomic analysis of a long-lived daf-2 mutant strain: not only were the effects of FUdR much greater than the effects of the mutation, there were clear interactions between FUdR and genotype, such that identification of daf-2-dependent metabolites would have been compromised on FUdR plates. This indicates that FUdR should only be used with caution for C. elegans ageing experiments, and should not be assumed to be independent of other factors being studied.     

基因表达系列分析及其应用前景

基因表达系列分析(Serial analysis of gene expression，SAGE)是一种研究真核细胞表达基因信息的高通量检测技术，它能对细胞内所有表达基因进行定性与定量分析。近年来此技术广泛应用于获得表达基因谱的研究，并且可以发现新基因信息，还可发现基因的靶向定位以及对其它基因的影响，明确表达基因的功能。本文就SAGE的原理、实验方案、技术发展与演变及其应用前景进行详细介绍。