Genome-wide Analysis using ChIP to Identify Isoform-specific Gene Targets

Recruitment of transcriptional and epigenetic factors to their targets is a key step in their regulation. Prominently featured in recruitment are the protein domains that bind to specific histone modifications. One such domain is the plant homeodomain (PHD), found in several chromatin-binding proteins. The epigenetic factor RBP2 has multiple PHD domains, however, they have different functions (Figure 4). In particular, the C-terminal PHD domain, found in a RBP2 oncogenic fusion in human leukemia, binds to trimethylated lysine 4 in histone H3 (H3K4me3)1. The transcript corresponding to the RBP2 isoform containing the C-terminal PHD accumulates during differentiation of promonocytic, lymphoma-derived, U937 cells into monocytes2. Consistent with both sets of data, genome-wide analysis showed that in differentiated U937 cells, the RBP2 protein gets localized to genomic regions highly enriched for H3K4me33. Localization of RBP2 to its targets correlates with a decrease in H3K4me3 due to RBP2 histone demethylase activity and a decrease in transcriptional activity. In contrast, two other PHDs of RBP2 are unable to bind H3K4me3. Notably, the C-terminal domain PHD of RBP2 is absent in the smaller RBP2 isoform4. It is conceivable that the small isoform of RBP2, which lacks interaction with H3K4me3, differs from the larger isoform in genomic location. The difference in genomic location of RBP2 isoforms may account for the observed diversity in RBP2 function. Specifically, RBP2 is a critical player in cellular differentiation mediated by the retinoblastoma protein (pRB). Consistent with these data, previous genome-wide analysis, without distinction between isoforms, identified two distinct groups of RBP2 target genes: 1) genes bound by RBP2 in a manner that is independent of differentiation; 2) genes bound by RBP2 in a differentiation-dependent manner

Non-homogeneous Behaviour of the Spatial Distribution of Macrospicules

In this paper the longitudinal and latitudinal spatial distribution of macrospicules is examined. We found a statistical relationship between the active longitude determined by sunspot groups and the longitudinal distribution of macrospicules. This distribution of macrospicules shows an inhomogeneity and non-axysimmetrical behaviour in the time interval from June 2010 until December 2012 covered by observations of the Solar Dynamic Observatory (SDO) satellite. The enhanced positions of the activity and its time variation has been calculated. The migration of the longitudinal distribution of macrospicules shows a similar behaviour as that of the sunspot groups

Active region formation through the negative effective magnetic pressure instability

The negative effective magnetic pressure instability operates on scales encompassing many turbulent eddies and is here discussed in connection with the formation of active regions near the surface layers of the Sun. This instability is related to the negative contribution of turbulence to the mean magnetic pressure that causes the formation of large-scale magnetic structures. For an isothermal layer, direct numerical simulations and mean-field simulations of this phenomenon are shown to agree in many details in that their onset occurs at the same depth. This depth increases with increasing field strength, such that the maximum growth rate of this instability is independent of the field strength, provided the magnetic structures are fully contained within the domain. A linear stability analysis is shown to support this finding. The instability also leads to a redistribution of turbulent intensity and gas pressure that could provide direct observational signatures.Comment: 19 pages, 10 figures, submitted to Solar Physic

Automated Detection of EUV Polar Coronal Holes During Solar Cycle 23

A new method for automated detection of polar coronal holes is presented. This method, called perimeter tracing, uses a series of 171, 195, and 304 \AA\ full disk images from the Extreme ultraviolet Imaging Telescope (EIT) on SOHO over solar cycle 23 to measure the perimeter of polar coronal holes as they appear on the limbs. Perimeter tracing minimizes line-of-sight obscurations caused by the emitting plasma of the various wavelengths by taking measurements at the solar limb. Perimeter tracing also allows for the polar rotation period to emerge organically from the data as 33 days. We have called this the Harvey rotation rate and count Harvey rotations starting 4 January 1900. From the measured perimeter, we are then able to fit a curve to the data and derive an area within the line of best fit. We observe the area of the northern polar hole area in 1996, at the beginning of solar cycle 23, to be about 4.2% of the total solar surface area and about 3.6% in 2007. The area of the southern polar hole is observed to be about 4.0% in 1996 and about 3.4% in 2007. Thus, both the north and south polar hole areas are no more than 15% smaller now than they were at the beginning of cycle 23. This compares to the polar magnetic field measured to be about 40% less now than it was a cycle ago.Comment: 18 pagers, 7 figures, accepted to Solar Physic

Photospheric and Subphotospheric Dynamics of Emerging Magnetic Flux

Magnetic fields emerging from the Sun's interior carry information about physical processes of magnetic field generation and transport in the convection zone. Soon after appearance on the solar surface the magnetic flux gets concentrated in sunspot regions and causes numerous active phenomena on the Sun. This paper discusses some properties of the emerging magnetic flux observed on the solar surface and in the interior. A statistical analysis of variations of the tilt angle of bipolar magnetic regions during the emergence shows that the systematic tilt with respect to the equator (the Joy's law) is most likely established below the surface. However, no evidence of the dependence of the tilt angle on the amount of emerging magnetic flux, predicted by the rising magnetic flux rope theories, is found. Analysis of surface plasma flows in a large emerging active region reveals strong localized upflows and downflows at the initial phase of emergence but finds no evidence for large-scale flows indicating future appearance a large-scale magnetic structure. Local helioseismology provides important tools for mapping perturbations of the wave speed and mass flows below the surface. Initial results from SOHO/MDI and GONG reveal strong diverging flows during the flux emergence, and also localized converging flows around stable sunspots. The wave speed images obtained during the process of formation of a large active region, NOAA 10488, indicate that the magnetic flux gets concentrated in strong field structures just below the surface. Further studies of magnetic flux emergence require systematic helioseismic observations from the ground and space, and realistic MHD simulations of the subsurface dynamics.Comment: 21 pages, 15 figures, to appear in Space Science Review

Astrophysical turbulence modeling

The role of turbulence in various astrophysical settings is reviewed. Among the differences to laboratory and atmospheric turbulence we highlight the ubiquitous presence of magnetic fields that are generally produced and maintained by dynamo action. The extreme temperature and density contrasts and stratifications are emphasized in connection with turbulence in the interstellar medium and in stars with outer convection zones, respectively. In many cases turbulence plays an essential role in facilitating enhanced transport of mass, momentum, energy, and magnetic fields in terms of the corresponding coarse-grained mean fields. Those transport properties are usually strongly modified by anisotropies and often completely new effects emerge in such a description that have no correspondence in terms of the original (non coarse-grained) fields.Comment: 88 pages, 26 figures, published in Reports on Progress in Physic

Association of IGF1 and KDM5A polymorphisms with performance, fatness and carcass traits in chickens

Two functional and positional candidate genes were selected in a region of chicken chromosome 1 (GGA1), based on their biological roles, and also where several quantitative trait loci (QTL) have been mapped and associated with performance, fatness and carcass traits in chickens. The insulin-like growth factor 1 (IGF1) gene has been associated with several physiological functions related to growth. The lysine (K)-specific demethylase 5A (KDM5A) gene participates in the epigenetic regulation of genes involved with the cell cycle. Our objective was to find associations of selected single-nucleotide polymorphisms (SNPs) in these genes with performance, fatness and carcass traits in 165 F chickens from a resource population. In the IGF1 gene, 17 SNPs were detected, and in the KDM5A gene, nine SNPs were detected. IGF1 SNP c. 47673G > A was associated with body weight and haematocrit percentage, and also with feed intake and percentages of abdominal fat and gizzard genotype × sex interactions. KDM5A SNP c. 34208C > T genotype × sex interaction affected body weight, feed intake, percentages of abdominal fat (p = 0. 0001), carcass, gizzard and haematocrit. A strong association of the diplotype × sex interaction (p < 0. 0001) with abdominal fat was observed, and also associations with body weight, feed intake, percentages of carcass, drums and thighs, gizzard and haematocrit. Our findings suggest that the KDM5A gene might play an important role in the abdominal fat deposition in chickens. The IGF1 and KDM5A genes are strong candidates to explain the QTL mapped in this region of GGA1

Physics of Solar Prominences: II - Magnetic Structure and Dynamics

Observations and models of solar prominences are reviewed. We focus on non-eruptive prominences, and describe recent progress in four areas of prominence research: (1) magnetic structure deduced from observations and models, (2) the dynamics of prominence plasmas (formation and flows), (3) Magneto-hydrodynamic (MHD) waves in prominences and (4) the formation and large-scale patterns of the filament channels in which prominences are located. Finally, several outstanding issues in prominence research are discussed, along with observations and models required to resolve them.Comment: 75 pages, 31 pictures, review pape