Highlights d Lysosomal lipid messenger signaling actively regulates mitochondrial ß-oxidation d Mitochondrial ß-oxidation modulates electron transport chain complex II activity d Lysosomal and mitochondrial pro-longevity signaling converge on JUN-1 d Organelle coordination improves metabolic balance, redox homeostasis, and longevity

Rickettsioses are emerging infectious diseases caused by rickettsiae in association with arthropods. We report the detection of spotted fever group rickettsiae (SFGR) in Taiwan using molecular methods. Phylogenetic analyses of the 17-kd protein and citrate synthase (gltA) genes showed that SFGR TwKM01 detected in Rhipicephalus haemaphysaloides ticks was most similar to Rickettsia rhipicephali. Three TwKM01 isolates were obtained from three individual R. haemaphysaloides ticks. Small, intracellular, coccobacillary bacteria were found in infected L929 cells using immunofluorescence antibody testing and transmission electron microscopy. Two other SFGRs, TwKM02 and TwKM03, identified in Leptotrombidium chigger mites, were closely related to R. australis and R. felis URRWXCal(2), respectively. The TwKM03 strain was also detected in Ixodes granulatus ticks and widely distributed in Hualien, Kinmen, and Lienchiang counties in Taiwan. The endonucleases MaeII and HhaI selected for restriction fragment length polymorphism analysis of the gltA and 17-kd polymerase chain reaction products, respectively, were useful for genotyping Rickettsia species TwKM01, TwKM02, TwKM03, and other SFGRs. Although their infectivity and pathogenicity for vertebrates are unknown, the finding of SFGRs raises the possibility that bacteria other than Orientia tsutsugamushi, Coxiella burnetii, and R. typhi may be involved in rickettsial diseases in Taiwan.

BackgroundMicroarray technology can acquire information about thousands of genes simultaneously. We analyzed published breast cancer microarray databases to predict five-year recurrence and compared the performance of three data mining algorithms of artificial neural networks (ANN), decision trees (DT) and logistic regression (LR) and two composite models of DT-ANN and DT-LR. The collection of microarray datasets from the Gene Expression Omnibus, four breast cancer datasets were pooled for predicting five-year breast cancer relapse. After data compilation, 757 subjects, 5 clinical variables and 13,452 genetic variables were aggregated. The bootstrap method, Mann–Whitney U test and 20-fold cross-validation were performed to investigate candidate genes with 100 most-significant p-values. The predictive powers of DT, LR and ANN models were assessed using accuracy and the area under ROC curve. The associated genes were evaluated using Cox regression.ResultsThe DT models exhibited the lowest predictive power and the poorest extrapolation when applied to the test samples. The ANN models displayed the best predictive power and showed the best extrapolation. The 21 most-associated genes, as determined by integration of each model, were analyzed using Cox regression with a 3.53-fold (95% CI: 2.24-5.58) increased risk of breast cancer five-year recurrence…ConclusionsThe 21 selected genes can predict breast cancer recurrence. Among these genes, CCNB1, PLK1 and TOP2A are in the cell cycle G2/M DNA damage checkpoint pathway. Oncologists can offer the genetic information for patients when understanding the gene expression profiles on breast cancer recurrence.

The developmental stage-and erythroid lineage-specific activation of the human embryonic {-and fetal/adult a-globin genes is controlled by an upstream regulatory element [hypersensitive site (HS)-401 with locus control region properties, a process mediated by multiple nuclear factor-DNA complexes. In vitro DNase I protection experiments of the two G+C-rich, adult a-globin promoters have revealed a number of binding sites for nuclear factors that are common to HeLa and K-562 extracts. However, genomic footprinting analysis has demonstrated that only a subset of these sites, clustered between -130 and + 1, is occupied in an erythroid tissue-specific manner. The function of these in vivo-occupied motifs of the x-globin promoters, as well as those previously mapped in the HS-40 region, is assayed by site-directed mutagenesis and transient expression in embryonic/fetaf'erythroid K-562 cells. These studies, together with our expression data on the human embryonic C-globin promoter, provide a comprehensive view of the functional roles of individual nuclear factor-DNA complexes in the final stages of transcriptional activation of the human a-like globin promoters by the HS-40 element. Spl (13,19,20).In contrast to the picture we have of the nuclear factor-DNA interactions that exist within the human HS-40 element, as described above, and in the embryonic~2 promoter (19, 21), our knowledge of such interactions occurring within the human al and a2 globin promoters is relatively sparse. In this regard, more is known about two other mammalian a-globin genes at the promoter level-namely, the mouse and rabbit a-globin promoters (22)(23)(24)(25). To gain further insight into the mechanisms by which the fetal/adult expression of the human a-globin genes in erythroid cells is regulated by HS-40, we have carried out genomic footprinting of the human a-globin promoter. Based on this information and the previously obtained genomic footprints of HS-40, we then used site-directed mutagenesis and transient expression assay to determine the functional contribution of the individual nuclear factorbinding motifs to the transcriptional activation of human a-globin genes by HS-40 in the embryonic/fetal erythroid K-562 cell line. MATERIALS AND METHODSGenomic Footprinting Analysis. The binding of nuclear factors in vivo at the human a-globin promoters was analyzed by dimethyl sulfate (DMS) footprinting. The maintenance of different cell lines, the isolation of cells from human tissues, and the purification of adult human erythroblasts were done by using described procedures (10). Cells were then treated with DMS, and the genomic DNA was purified and subjected to piperidine cleavage (26). These cleavage sites were then mapped by the ligation-mediated PCR (LMPCR) (27, 28), using the same procedures as described (10,29). However, due to the high G+C content (96%) of the human a-globin promoter DNA, dimethyl sulfoxide was included in some of the Abbreviations: DMS, dimethyl sulfate; LCR, locus control region; LMPCR, ligation-mediated PC...

3The HS-40 enhancer is the major cis-acting regulatory element responsible for the developmental stage-and erythroid lineage-specific expression of the human ␣-like globin genes, the embryonic and the adult ␣2/␣/1. A model has been proposed in which competitive factor binding at one of the HS-40 motifs, 3-NA, modulates the capability of HS-40 to activate the embryonic -globin promoter. Furthermore, this modulation was thought to be mediated through configurational changes of the HS-40 enhanceosome during development. In this study, we have further investigated the molecular basis of this model. The interplay among the multiple nuclear factor-DNA complexes formed at the enhancers (enhanceosomes) and their cis-linked promoters (polymerase II [pol II] preinitiation complexes) is essential for the regulation of many eukaryotic genes (reviewed in references 6 and 9). Several modes of actions have been proposed for the enhanceosome function. Some enhanceosomes, such as the locus control region (LCR) of the human ␤-globin locus (reviewed in references 16, 20, and 22) may set up and/or maintain an active chromatin state of a gene or locus domain, thus allowing the formation of active pol II preinitiation complex. On the other hand, enhanceosomes could also facilitate the assembly of active pol II preinitiation complex by direct interaction with, or recruitment of, coactivators and different basal transcription factors (reference 6 and references therein).HS-40 is an element located at 40 kb upstream of the human ␣-globin locus (Fig. 1). Genetic and molecular data have indicated that it is essential for transcriptional regulation of the human embryonic -and adult ␣-globin promoters during erythroid development (21). Most of the ␣-globin gene cluster maintains an open chromatin structure in both erythroid and nonerythroid cells, possibly due to the transcription of certain ubiquitous genes (54). Further remodeling and modification of the chromatin structure must occur in erythroid cells, however, since several new HS sites appear, including those at the HS-40 element and the promoter regions of the -and ␣-globin genes (54, 59). These latter sites apparently result from erythroid lineage-specific binding of nuclear factors to the above transcriptional regulatory elements, as demonstrated by previous genomic footprint analysis of 60) and of the ␣-globin upstream promoters (47).HS-40 acts as a classical enhancer in transient transfection assays (44,46,60), and it confers appropriate developmental control of the human -globin promoter activity in transgenic mice (19,23,45,56). In vitro and in vivo binding studies have shown that the HS-40 enhanceosome consists mainly of six DNA sequence motifs that are bound with nuclear factors in an erythroid lineage-specific manner: two NF-E2/AP1 motifs (5Ј-NA and 3Ј-NA), three GATA-1 motifs (b, c, and d), and a GT motif (26,50,60) (Fig. 1A). Of these, the NF-E2/AP1 motifs could be recognized by the erythroid-enriched factor NF-E2, the ubiquitous AP1, the homodimers of small Maf family, or...