Superhumps in a Peculiar SU UMa-Type Dwarf Nova ER Ursae Majoris

We report the photometry of a peculiar SU UMa-type dwarf nova - ER UMa for ten nights during 1998 December and 1999 March covering a complete rise to the supermaximum and a normal outburst cycle. Superhumps have been found during the rise to the superoutburst. A negative superhump appeared in Dec.22 light curve, while the superhump on the next night became positive and had large amplitude and distinct waveform from that of the previous night. In the normal outburst we captured, superhumps with larger or smaller amplitudes seem to always exist, although it is not necessarily true for every normal outburst. These results show great resemblance with V1159 Ori (Patterson et al. 1995). It is more likely that superhumps occasionally exist at essentially all phases of the eruption cycles of ER UMa stars, which should be considered in modeling.Comment: 4 pages, 5 figures, Accepted by ApJ Letter

Photometry and Spectroscopy of KS Ursae Majoris during Superoutburst

We report photometric and spectroscopic observations of the SU UMa-type dwarf novae, KS Ursae Majoris, during its 2003 February superoutburst. Modulations with a period of $0.07017\pm0.00021$ day, which is 3.3% larger than the orbital period, have been found during the superoutburst and may be positive superhumps. A maximum trough-to-peak amplitude of around 0.3 magnitude is determined for this superhump. The spectra show broad, absorption-line profiles. The lines display blue and red troughs which alternate in depth. The radial velocity curve of the absorption wings of H$\beta$ has an amplitude of $40\pm11$ km s$^{-1}$ and a phase offset of $0.12\pm0.03$. The $\gamma$ velocity of the binary is $3\pm9$ km s$^{-1}$ and varies on an order of 50 km s$^{-1}$ from day to day. From another clear evidence for a precessing eccentric disk, we obtain a solution to an eccentric outer disk consistent with theoretical works, which demonstrates the validity of the relation between superhumps and tidal effects. The inner part of the disk is also eccentric as evidenced by asymmetric and symmetric wings in the lines. Therefore, the whole disk is eccentric and the variation of $\gamma$ velocity and the evolutionary asymmetric line profiles could be criterions for an precessing eccentric accretion disk.Comment: 12 pages, 8 figures, accpeted for publication in A

Systems consequences of amplicon formation in human breast cancer

Chromosomal structural variations play an important role in determining the transcriptional landscape of human breast cancers. To assess the nature of these structural variations, we analyzed eight breast tumor samples with a focus on regions of gene amplification using mate-pair sequencing of long-insert genomic DNA with matched transcriptome profiling. We found that tandem duplications appear to be early events in tumor evolution, especially in the genesis of amplicons. In a detailed reconstruction of events on chromosome 17, we found large unpaired inversions and deletions connect a tandemly duplicated ERBB2 with neighboring 17q21.3 amplicons while simultaneously deleting the intervening BRCA1 tumor suppressor locus. This series of events appeared to be unusually common when examined in larger genomic data sets of breast cancers albeit using approaches with lesser resolution. Using siRNAs in breast cancer cell lines, we showed that the 17q21.3 amplicon harbored a significant number of weak oncogenes that appeared consistently coamplified in primary tumors. Down-regulation of BRCA1 expression augmented the cell proliferation in ERBB2-transfected human normal mammary epithelial cells. Coamplification of other functionally tested oncogenic elements in other breast tumors examined, such as RIPK2 and MYC on chromosome 8, also parallel these findings. Our analyses suggest that structural variations efficiently orchestrate the gain and loss of cancer gene cassettes that engage many oncogenic pathways simultaneously and that such oncogenic cassettes are favored during the evolution of a cancer.Singapore. Agency for Science, Technology and ResearchNational Science Foundation (U.S.) (East Asia and Pacific Summer Institutes (OISE-1108282)

TNFα signals through specialized factories where responsive coding and miRNA genes are transcribed: Specialized transcription factories

Tumour necrosis factor alpha (TNFα) is a potent cytokine that signals through nuclear factor kappa B (NFκB) to activate a subset of human genes. It is usually assumed that this involves RNA polymerases transcribing responsive genes wherever they might be in the nucleus. Using primary human endothelial cells, variants of chromosome conformation capture (including 4C and chromatin interaction analysis with paired-end tag sequencing), and fluorescence in situ hybridization to detect single nascent transcripts, we show that TNFα induces responsive genes to congregate in discrete ‘NFκB factories'. Some factories further specialize in transcribing responsive genes encoding micro-RNAs that target downregulated mRNAs. We expect all signalling pathways to contain this extra leg, where responding genes are transcribed in analogous specialized factories

Deciphering the regulatory logic of an ancient, ultraconserved nuclear receptor enhancer module.

Cooperative, synergistic gene regulation by nuclear hormone receptors can increase sensitivity and amplify cellular responses to hormones. We investigated thyroid hormone (TH) and glucocorticoid (GC) synergy on the Krüppel-like factor 9 (Klf9) gene, which codes for a zinc finger transcription factor involved in development and homeostasis of diverse tissues. We identified regions of the Xenopus and mouse Klf9 genes 5-6 kb upstream of the transcription start sites that supported synergistic transactivation by TH plus GC. Within these regions, we found an orthologous sequence of approximately 180 bp that is highly conserved among tetrapods, but absent in other chordates, and possesses chromatin marks characteristic of an enhancer element. The Xenopus and mouse approximately 180-bp DNA element conferred synergistic transactivation by hormones in transient transfection assays, so we designate this the Klf9 synergy module (KSM). We identified binding sites within the mouse KSM for TH receptor, GC receptor, and nuclear factor κB. TH strongly increased recruitment of liganded GC receptor and serine 5 phosphorylated (initiating) RNA polymerase II to chromatin at the KSM, suggesting a mechanism for transcriptional synergy. The KSM is transcribed to generate long noncoding RNAs, which are also synergistically induced by combined hormone treatment, and the KSM interacts with the Klf9 promoter and a far upstream region through chromosomal looping. Our findings support that the KSM plays a central role in hormone regulation of vertebrate Klf9 genes, it evolved in the tetrapod lineage, and has been maintained by strong stabilizing selection. Mol Endocrinol 2015 Jun; 29(6):856-72

Selective Wavelength Tuning of Self-assembled InAs Quantum Dots grown on InP

We report the experimental results of tuning the emission wavelength of InAsInP quantum dots (QDs) by varying either the GaAs interlayer thickness or the indium composition of the Inx Ga1-x As interlayer. The InAs QDs are grown on lattice-matched GaInAs