The expanding constellation of histone post-translational modifications in the epigenetic landscape

The emergence of a nucleosome-based chromatin structure accompanied the evolutionary transition from prokaryotes to eukaryotes. In this scenario, histones became the heart of the complex and precisely timed coordination between chromatin architecture and functions during adaptive responses to environmental influence by means of epigenetic mechanisms. Notably, such an epigenetic machinery involves an overwhelming number of post-translational modifications at multiple residues of core and linker histones. This review aims to comprehensively describe old and recent evidence in this exciting field of research. In particular, histone post-translational modification establishing/removal mechanisms, their genomic locations and implication in nucleosome dynamics and chromatin-based processes, as well as their harmonious combination and interdependence will be discussed

An alternate algorithm for correction of the scanning multichannel microwave radiometer polarization radiances using Nimbus-7 observed data

The manner in which Nimbus-7 scanning multichannel microwave radiometer (SMMR) scan radiance data was used to determine its operational characteristics is described. The predicted SMMR scan radiance was found to be in disagreement at all wavelengths with a large area of average measured ocean radiances. A modified model incorporating a different phase shift for each of the SMMR horizontal and vertical polarization channels was developed and found to provide good data correlation. Additional study is required to determine the validity and accuracy of this model

Environmental epigenetics in zebrafish

It is widely accepted that the epigenome can act as the link between environmental cues, both external and internal, to the organism and phenotype by converting the environmental stimuli to phenotypic responses through changes in gene transcription outcomes. Environmental stress endured by individual organisms can also enforce epigenetic variations in offspring that had never experienced it directly, which is termed transgenerational inheritance. To date, research in the environmental epigenetics discipline has used a wide range of both model and non-model organisms to elucidate the various epigenetic mechanisms underlying the adaptive response to environmental stimuli. In this review, we discuss the advantages of the zebrafish model for studying how environmental toxicant exposures affect the regulation of epigenetic processes, especially DNA methylation, which is the best-studied epigenetic mechanism. We include several very recent studies describing the state-of-the-art knowledge on this topic in zebrafish, together with key concepts in the function of DNA methylation during vertebrate embryogenesis

Roles of the Core Components of the Mammalian miRISC in Chromatin Biology

The Argonaute (AGO) and the Trinucleotide Repeat Containing 6 (TNRC6) family proteins are the core components of the mammalian microRNA-induced silencing complex (miRISC), the machinery that mediates microRNA function in the cytoplasm. The cytoplasmic miRISC-mediated post-transcriptional gene repression has been established as the canonical mechanism through which AGO and TNRC6 proteins operate. However, growing evidence points towards an additional mechanism through which AGO and TNRC6 regulate gene expression in the nucleus. While several mechanisms through which miRISC components function in the nucleus have been described, in this review we aim to summarize the major findings that have shed light on the role of AGO and TNRC6 in mammalian chromatin biology and on the implications these novel mechanisms may have in our understanding of regulating gene expression

Diversification of spatiotemporal expression and copy number variation of the echinoid hbox12/pmar1/micro1 multigene family

Changes occurring during evolution in the cis-regulatory landscapes of individual members of multigene families might impart diversification in their spatiotemporal expression and function. The archetypal member of the echinoid hbox12/pmar1/micro1 family is hbox12-a, a homeobox-containing gene expressed exclusively by dorsal blastomeres, where it governs the dorsal/ventral gene regulatory network during embryogenesis of the sea urchin Paracentrotus lividus. Here we describe the inventory of the hbox12/pmar1/micro1 genes in P. lividus, highlighting that gene copy number variation occurs across individual sea urchins of the same species. We show that the various hbox12/pmar1/micro1 genes group into three subfamilies according to their spatiotemporal expression, which ranges from broad transcription throughout development to transient expression in either the animal hemisphere or micromeres of the early embryo. Interestingly, the promoter regions of those genes showing comparable expression patterns are highly similar, while differing from those of the other subfamilies. Strikingly, phylogenetic analysis suggests that the hbox12/pmar1/micro1 genes are species-specific, exhibiting extensive divergence in their noncoding, but not in their coding, sequences across three distinct sea urchin species. In spite of this, two micromere-specific genes of P. lividus possess a TCF/LEF-binding motif in a similar position, and their transcription relies on Wnt/ f-catenin signaling, similar to the pmar1 and micro1 genes, which in other sea urchin species are involved in micromere specification. Altogether, our findings suggest that the hbox12/pmar1/micro1 gene family evolved rather rapidly, generating paralogs whose cis-regulatory sequences diverged following multiple rounds of duplication from a common ancestor

Identification of GABA receptor genes and evidence of GABA signaling during embryogenesis of the sea urchin

Gamma-aminobutyric acid (GABA) is the principal inhibitory neurotransmitter in the mammalian central nervous system and acts via ionotropic (GABAA-Rs) and metabotropic (GABAB-Rs) receptors. GABAA-Rs are Cl- selective hetero-pentameric channels assembled by combinations of 19 distinct gene products. Instead, GABAB-Rs are bi-subunit G-protein coupled receptors linked to K+ or Ca2+ channels. Dysfunctions of GABA-signaling (GS) cause psychotic disorders and correlate with epigenetic alterations, such as over-expression of DNA methyl transferase-1 which in turn imposes iper-methylation of GABA-regulated genes. The sea urchin embryo, which presents a rudimentary nervous system, offers a big opportunity to study the GS and its potential epigenetic implications in a simple eukaryote model. To this purpose, we performed a comprehensive in silico analysis of the sea urchin genome and identified a 450 Kb long cluster containing two genes encoding for the GABAB-R subunits, and two genes respectively encoding for a \u3b1/\u3b3/\u3b5-type and a \u3b2/\u3c1/\u3b4/\u3c4/\u3c0-type GABA B A-R subunit. From an evolutionary perspective, this result revealed a unique genomic organization of these genes in sea urchin. Next, to preliminarily evaluate the role of GS during development, Paracentrotus lividus embryos were cultured in the presence of GABA at concentrations ranging from 0.01 to 1.0 mM. Compared to controls, treated embryos showed aberrations in axial patterning, with a dose-dependent effect. In particular, at 48 hours post-fertilization control embryos were normal bilateral symmetric plutei whereas GABA-treated embryos displayed a radial organization with supranumerary spicules. Washout experiments allowed to determine that the period of sensitivity is restricted from the blastula to the gastrula stage. Altogether, these results suggest that dysregulation of GS affects the polarization of the ectoderm. Although preliminary, this study provide the first evidence of GS activity during development of echinoderms

Jet-edge interaction tones

Motivated by the problem of jet-flap interaction noise, we study the tonal dynamics that occur when a sharp edge is placed in the hydrodynamic nearfield of an isothermal turbulent jet. We perform hydrodynamic and acoustic pressure measurements in order to characterise the tones as a function of Mach number and streamwise edge position. The distribution of spectral peaks observed, as a function of Mach number, cannot be explained using the usual edge-tone scenario, in which resonance is underpinned by coupling between downstream-travelling Kelvin-Helmholtz wavepackets and upstream-travelling sound waves. We show, rather, that the strongest tones are due to coupling between the former and upstream-travelling jet modes recently studied by Towne et al. (2017) and Schmidt et al. (2017). We also study the band-limited nature of the resonance, showing a high-frequency cut-off to be due to the frequency dependence of the upstream-travelling waves. At high Mach number these become evanescent above a certain frequency, whereas at low Mach number they become progressively trapped with increasing frequency, a consequence of which is their not being reflected in the nozzle plane. Additionally, a weaker, low-frequency, forced-resonance regime is identified that involves the same upstream travelling jet modes but that couple, in this instance, with downstream-travelling sound waves. It is suggested that the existence of two resonance regimes may be due to the non-modal nature of wavepacket dynamics at low-frequency.Comment: 21 pages, 15 figure

Coherent pressure structures in turbulent channel flow

Most of the studies on pressure fluctuations in wall-bounded turbulent flows aim at obtaining statistics as power spectra and scaling laws, especially at the walls. In the present study we study energetic coherent pressure structures of turbulent channel flows, aiming at a characterization of dominant coherent structures throughout the channel. Coherent structures are detected using spectral proper orthogonal decomposition (SPOD) and modeled using resolvent analysis, similar to related works dealing with velocity fluctuations, but using pressure fluctuations as the output of interest. The resolvent operator was considered with and without the Cess eddy viscosity model. Direct numerical simulations (DNSs) of incompressible turbulent channel flows at friction Reynolds numbers of approximately 180 and 550 were employed as databases. Three representative dominant structures emerged from a preliminary spectral analysis: near-wall, large-scale and spanwise-coherent structures. For frequency-wavenumber combinations corresponding to these three representative structures, SPOD results show a strong dominance of the leading mode, highlighting low-rank behavior of pressure fluctuations. The leading resolvent mode closely agrees with the first SPOD mode, providing support to studies that showed better performance of resolvent-based estimators when predicting pressure fluctuations compared to velocity fluctuations. The dominant mechanisms of the analyzed modes are seen to be the generation of quasi-streamwise vortices with pressure fluctuations appearing close to vortex centers. A study on the individual contributions of the nonlinear terms (treated as forcing in resolvent analysis) to the pressure output reveals that each forcing component plays a constructive role to the input-output formulation, which also helps understanding the weaker role of forcing color in driving pressure fluctuations.Comment: 24 pages, 23 figure