Gemini Planet Imager Spectroscopy of the Dusty Substellar Companion HD 206893 B

We present new near-infrared Gemini Planet Imager (GPI) spectroscopy of HD 206893 B, a substellar companion orbiting within the debris disk of its F5V star. The J, H, K1, and K2 spectra from GPI demonstrate the extraordinarily red colors of the object, confirming it as the reddest substellar object observed to date. The significant flux increase throughout the infrared presents a challenging atmosphere to model with existing grids. Best-fit values vary from 1200 to 1800 K for effective temperature and from 3.0 to 5.0 for log(g), depending on which individual wavelength band is fit and which model suite is applied. The extreme redness of the companion can be partially reconciled by invoking a high-altitude layer of submicron dust particles, similar to dereddening approaches applied to the peculiar red field L dwarf population. However, reconciling the HD 206893 B spectra with even those of the reddest low-gravity L dwarf spectra still requires the contribution of additional atmospheric dust, potentially due to the debris disk environment in which the companion resides. Orbit fitting from 4 yr of astrometric monitoring is consistent with a ∼30 yr period, an orbital inclination of 147 , and a semimajor axis of 10 au, well within the estimated disk inner radius of ∼50 au. As one of a very few substellar companions imaged interior to a circumstellar disk, the properties of this system offer important dynamical constraints on companion-disk interaction and provide a benchmark for substellar and planetary atmospheric study

Circumstellar discs: What will be next?

This prospective chapter gives our view on the evolution of the study of circumstellar discs within the next 20 years from both observational and theoretical sides. We first present the expected improvements in our knowledge of protoplanetary discs as for their masses, sizes, chemistry, the presence of planets as well as the evolutionary processes shaping these discs. We then explore the older debris disc stage and explain what will be learnt concerning their birth, the intrinsic links between these discs and planets, the hot dust and the gas detected around main sequence stars as well as discs around white dwarfs.Comment: invited review; comments welcome (32 pages

A Key Commitment Step in Erythropoiesis Is Synchronized with the Cell Cycle Clock through Mutual Inhibition between PU.1 and S-Phase Progression

During red blood cell development, differentiation and cell cycle progression are intimately and uniquely linked through interdependent mechanisms involving the erythroid transcriptional suppressor PU.1 and the cyclin-dependent kinase inhibitor p57KIP2

Gemini Planet Imager spectroscopy of the dusty substellar companion HD 206893 B

We present new near-infrared Gemini Planet Imager (GPI) spectroscopy of HD 206893 B, a substellar companion orbiting within the debris disk of its F5V star. The J, H, K1, and K2 spectra from GPI demonstrate the extraordinarily red colors of the object, confirming it as the reddest substellar object observed to date. The significant flux increase throughout the infrared presents a challenging atmosphere to model with existing grids. Best-fit values vary from 1200 to 1800 K for effective temperature and from 3.0 to 5.0 for log(g), depending on which individual wavelength band is fit and which model suite is applied. The extreme redness of the companion can be partially reconciled by invoking a high-altitude layer of submicron dust particles, similar to dereddening approaches applied to the peculiar red field L dwarf population. However, reconciling the HD 206893 B spectra with even those of the reddest low-gravity L dwarf spectra still requires the contribution of additional atmospheric dust, potentially due to the debris disk environment in which the companion resides. Orbit fitting from 4 yr of astrometric monitoring is consistent with a ∼30 yr period, an orbital inclination of 147°, and a semimajor axis of 10 au, well within the estimated disk inner radius of ∼50 au. As one of a very few substellar companions imaged interior to a circumstellar disk, the properties of this system offer important dynamical constraints on companion-disk interaction and provide a benchmark for substellar and planetary atmospheric study.Publisher PDFPeer reviewe

The renal cortical interstitium: morphological and functional aspects

The renal interstitial compartment, situated between basement membranes of epithelia and vessels, contains two contiguous cellular networks. One network is formed by interstitial fibroblasts, the second one by dendritic cells. Both are in intimate contact with each other. Fibroblasts are interconnected by junctions and connected to basement membranes of vessels and tubules by focal adhesions. Fibroblasts constitute the “skeleton” of the kidney. In the renal cortex, fibroblasts produce erythropoietin and are distinguished from other interstitial cells by their prominent F-actin cytoskeleton, abundance of rough endoplasmic reticulum, and by ecto-5′-nucleotidase expression in their plasma membrane. The resident dendritic cells belong to the mononuclear phagocyte system and fulfil a sentinel function. They are characterized by their expression of MHC class II and CD11c. The central situation of fibroblasts suggests that signals from tubules, vessels, and inflammatory cells converge in fibroblasts and elicit an integrated response. Following tubular damage and inflammatory signals fibroblasts proliferate, change to the myofibroblast phenotype and increase their collagen production, potentially resulting in renal fibrosis. The acquisition of a profibrotic phenotype by fibroblasts in renal diseases is generally considered a main causal event in the progression of chronic renal failure. However, it might also be seen as a repair process

Gemini Planet Imager Spectroscopy of the Dusty Substellar Companion HD 206893 B

We present new near-infrared Gemini Planet Imager (GPI) spectroscopy of HD 206893 B, a substellar companion orbiting within the debris disk of its F5V star. The J, H, K1, and K2 spectra from GPI demonstrate the extraordinarily red colors of the object, confirming it as the reddest substellar object observed to date. The significant flux increase throughout the infrared presents a challenging atmosphere to model with existing grids. Best-fit values vary from 1200 to 1800 K for effective temperature and from 3.0 to 5.0 for log(g), depending on which individual wavelength band is fit and which model suite is applied. The extreme redness of the companion can be partially reconciled by invoking a high-altitude layer of submicron dust particles, similar to dereddening approaches applied to the peculiar red field L dwarf population. However, reconciling the HD 206893 B spectra with even those of the reddest low-gravity L dwarf spectra still requires the contribution of additional atmospheric dust, potentially due to the debris disk environment in which the companion resides. Orbit fitting from 4 yr of astrometric monitoring is consistent with a ~30 yr period, an orbital inclination of 147°, and a semimajor axis of 10 au, well within the estimated disk inner radius of ~50 au. As one of a very few substellar companions imaged interior to a circumstellar disk, the properties of this system offer important dynamical constraints on companion–disk interaction and provide a benchmark for substellar and planetary atmospheric study

Clustered ChIP-Seq-defined transcription factor binding sites and histone modifications map distinct classes of regulatory elements

<p>Abstract</p> <p>Background</p> <p>Transcription factor binding to DNA requires both an appropriate binding element and suitably open chromatin, which together help to define regulatory elements within the genome. Current methods of identifying regulatory elements, such as promoters or enhancers, typically rely on sequence conservation, existing gene annotations or specific marks, such as histone modifications and p300 binding methods, each of which has its own biases.</p> <p>Results</p> <p>Herein we show that an approach based on clustering of transcription factor peaks from high-throughput sequencing coupled with chromatin immunoprecipitation (Chip-Seq) can be used to evaluate markers for regulatory elements. We used 67 data sets for 54 unique transcription factors distributed over two cell lines to create regulatory element clusters. By integrating the clusters from our approach with histone modifications and data for open chromatin, we identified general methylation of lysine 4 on histone H3 (H3K4me) as the most specific marker for transcription factor clusters. Clusters mapping to annotated genes showed distinct patterns in cluster composition related to gene expression and histone modifications. Clusters mapping to intergenic regions fall into two groups either directly involved in transcription, including miRNAs and long noncoding RNAs, or facilitating transcription by long-range interactions. The latter clusters were specifically enriched with H3K4me1, but less with acetylation of lysine 27 on histone 3 or p300 binding.</p> <p>Conclusion</p> <p>By integrating genomewide data of transcription factor binding and chromatin structure and using our data-driven approach, we pinpointed the chromatin marks that best explain transcription factor association with different regulatory elements. Our results also indicate that a modest selection of transcription factors may be sufficient to map most regulatory elements in the human genome.</p

Epigenetic Mechanisms Regulate Stem Cell Expressed Genes Pou5f1 and Gfra1 in a Male Germ Cell Line

Male fertility is declining and an underlying cause may be due to environment-epigenetic interactions in developing sperm, yet nothing is known of how the epigenome controls gene expression in sperm development. Histone methylation and acetylation are dynamically regulated in spermatogenesis and are sensitive to the environment. Our objectives were to determine how histone H3 methylation and acetylation contribute to the regulation of key genes in spermatogenesis. A germ cell line, GC-1, was exposed to either the control, or the chromatin modifying drugs tranylcypromine (T), an inhibitor of the histone H3 demethylase KDM1 (lysine specific demethylase 1), or trichostatin (TSA), an inhibitor of histone deacetylases, (HDAC). Quantitative PCR (qPCR) was used to identify genes that were sensitive to treatment. As a control for specificity the Myod1 (myogenic differentiation 1) gene was analyzed. Chromatin immunoprecipitation (ChIP) followed by qPCR was used to measure histone H3 methylation and acetylation at the promoters of target genes and the control, Myod1. Remarkably, the chromatin modifying treatment specifically induced the expression of spermatogonia expressed genes Pou5f1 and Gfra1. ChIP-qPCR revealed that induction of gene expression was associated with a gain in gene activating histone H3 methylation and acetylation in Pou5f1 and Gfra1 promoters, whereas CpG DNA methylation was not affected. Our data implicate a critical role for histone H3 methylation and acetylation in the regulation of genes expressed by spermatogonia – here, predominantly mediated by HDAC-containing protein complexes

Mitogen- and Stress-Activated Kinase 1 (MSK1) Regulates Cigarette Smoke-Induced Histone Modifications on NF-κB-dependent Genes

Cigarette smoke (CS) causes sustained lung inflammation, which is an important event in the pathogenesis of chronic obstructive pulmonary disease (COPD). We have previously reported that IKKα (I kappaB kinase alpha) plays a key role in CS-induced pro-inflammatory gene transcription by chromatin modifications; however, the underlying role of downstream signaling kinase is not known. Mitogen- and stress-activated kinase 1 (MSK1) serves as a specific downstream NF-κB RelA/p65 kinase, mediating transcriptional activation of NF-κB-dependent pro-inflammatory genes. The role of MSK1 in nuclear signaling and chromatin modifications is not known, particularly in response to environmental stimuli. We hypothesized that MSK1 regulates chromatin modifications of pro-inflammatory gene promoters in response to CS. Here, we report that CS extract activates MSK1 in human lung epithelial (H292 and BEAS-2B) cell lines, human primary small airway epithelial cells (SAEC), and in mouse lung, resulting in phosphorylation of nuclear MSK1 (Thr581), phospho-acetylation of RelA/p65 at Ser276 and Lys310 respectively. This event was associated with phospho-acetylation of histone H3 (Ser10/Lys9) and acetylation of histone H4 (Lys12). MSK1 N- and C-terminal kinase-dead mutants, MSK1 siRNA-mediated knock-down in transiently transfected H292 cells, and MSK1 stable knock-down mouse embryonic fibroblasts significantly reduced CS extract-induced MSK1, NF-κB RelA/p65 activation, and posttranslational modifications of histones. CS extract/CS promotes the direct interaction of MSK1 with RelA/p65 and p300 in epithelial cells and in mouse lung. Furthermore, CS-mediated recruitment of MSK1 and its substrates to the promoters of NF-κB-dependent pro-inflammatory genes leads to transcriptional activation, as determined by chromatin immunoprecipitation. Thus, MSK1 is an important downstream kinase involved in CS-induced NF-κB activation and chromatin modifications, which have implications in pathogenesis of COPD