scholarly journals The tropical coral Pocillopora acuta has a mosaic DNA methylome, an unusual chromatin structure and shows histone H3 clipping

2019 ◽  
Author(s):  
David Roquis ◽  
Ariadna Picart Picolo ◽  
Kelly Brener Raffalli ◽  
Pascal Romans ◽  
Patrick Masanet ◽  
...  
Keyword(s):  
Chromatin Structure ◽  
Cytosine Methylation ◽  
Histone H3 ◽  
Simple Method ◽  
Intracellular Location ◽  
Mutualistic Symbiosis ◽  
Worldwide Distribution ◽  
Unicellular Algae ◽  
Ecological Importance ◽  
The Impact

AbstractPocillopora acuta is a hermatypic coral with a worldwide distribution and a strong ecological importance. Anthropogenic disturbances and global warming threaten it. Thermal stress can induce coral bleaching, a phenomenon in which the mutualistic symbiosis between the coral polyps host and its endosymbiotic unicellular algae is disrupted, and can lead to the death of entire colonies. Previous works have shown that soma clonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. The clonal nature of a colony and the possibility of generating genetically identical colonies through propagation make corals an attractive model to study the impact of the environment on the epigenome. However, until now, no work had been published on the P. acuta epigenome. One of the main problems is caused by the intracellular location of Symbiodinium, which makes it complicated to isolate coral chromatin free of contamination by endiosymbiotic biological material. Here, (i) we describe a simple method to purify P. acuta chromatin, (ii) we provide the first description of a coral methylome, with a mosaic pattern of cytosine methylation principally in a CpG context (4% of all CpG), and (iii) we show that P. acuta, but not all corals, has an unusual chromatin structure, and displays histone H3 clipping.

scholarly journals The tropical coral Pocillopora acuta displays an unusual chromatin structure and shows histone H3 clipping plasticity upon bleaching

2021 ◽  
Vol 6 ◽  
pp. 195
Author(s):  
David Roquis ◽  
Céline Cosseau ◽  
Kelly Brener Raffalli ◽  
Pascal Romans ◽  
Patrick Masanet ◽  
...  
Keyword(s):  
Western Blot ◽  
Histone Modifications ◽  
Chromatin Structure ◽  
Histone H3 ◽  
Micrococcal Nuclease ◽  
Coral Host ◽  
Mutualistic Symbiosis ◽  
Ecological Importance ◽  
Endosymbiotic Algae ◽  
Insight Into

Background: Pocillopora acuta is a hermatypic coral with strong ecological importance. Anthropogenic disturbances and global warming are major threats that can induce coral bleaching, the disruption of the mutualistic symbiosis between the coral host and its endosymbiotic algae. Previous works have shown that somaclonal colonies display different levels of survival depending on the environmental conditions they previously faced. Epigenetic mechanisms are good candidates to explain this phenomenon. However, almost no work had been published on the P. acuta epigenome, especially on histone modifications. In this study, we aim at providing the first insight into chromatin structure of this species. Methods: We aligned the amino acid sequence of P. acuta core histones with histone sequences from various phyla. We developed a centri-filtration on sucrose gradient to separate chromatin from the host and the symbiont. The presence of histone H3 protein and specific histone modifications were then detected by western blot performed on histone extraction done from bleached and healthy corals. Finally, micrococcal nuclease (MNase) digestions were undertaken to study nucleosomal organization. Results: The centri-filtration enabled coral chromatin isolation with less than 2% of contamination by endosymbiont material. Histone sequences alignments with other species show that P. acuta displays on average ~90% of sequence similarities with mice and ~96% with other corals. H3 detection by western blot showed that H3 is clipped in healthy corals while it appeared to be intact in bleached corals. MNase treatment failed to provide the usual mononucleosomal digestion, a feature shared with some cnidarian, but not all; suggesting an unusual chromatin structure. Conclusions: These results provide a first insight into the chromatin, nucleosome and histone structure of P. acuta. The unusual patterns highlighted in this study and partly shared with other cnidarian will need to be further studied to better understand its role in corals.

scholarly journals Histone H3 Lysine 4 Methylation Marks Postreplicative Human Cytomegalovirus Chromatin

2012 ◽  
Vol 86 (18) ◽  
pp. 9817-9827 ◽  
Author(s):  
Alexandra Nitzsche ◽  
Charlotte Steinhäußer ◽  
Katrin Mücke ◽  
Christina Paulus ◽  
Michael Nevels
Keyword(s):  
Dna Replication ◽  
Dna Synthesis ◽  
Histone Modification ◽  
Dna Polymerase ◽  
Human Cytomegalovirus ◽  
Viral Genome ◽  
Histone H3 ◽  
Viral Dna ◽  
The Impact ◽  
Preferential Incorporation

In the nuclei of permissive cells, human cytomegalovirus genomes form nucleosomal structures initially resembling heterochromatin but gradually switching to a euchromatin-like state. This switch is characterized by a decrease in histone H3 K9 methylation and a marked increase in H3 tail acetylation and H3 K4 methylation across the viral genome. We used ganciclovir and a mutant virus encoding a reversibly destabilized DNA polymerase to examine the impact of DNA replication on histone modification dynamics at the viral chromatin. The changes in H3 tail acetylation and H3 K9 methylation proceeded in a DNA replication-independent fashion. In contrast, the increase in H3 K4 methylation proved to depend widely on viral DNA synthesis. Consistently, labeling of nascent DNA using “click chemistry” revealed preferential incorporation of methylated H3 K4 into viral (but not cellular) chromatin during or following DNA replication. This study demonstrates largely selective epigenetic tagging of postreplicative human cytomegalovirus chromatin.

scholarly journals Epigenetic Changes in Host Ribosomal DNA Promoter Induced by an Asymptomatic Plant Virus Infection

Biology ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 91 ◽  
Author(s):  
Miryam Pérez-Cañamás ◽  
Elizabeth Hevia ◽  
Carmen Hernández
Keyword(s):  
Gene Silencing ◽  
Ribosomal Dna ◽  
Plant Virus ◽  
Dna Methyltransferase ◽  
Cytosine Methylation ◽  
De Novo ◽  
Methylation Pattern ◽  
Transcriptional Gene Silencing ◽  
Post Transcriptional Gene Silencing ◽  
The Impact

DNA cytosine methylation is one of the main epigenetic mechanisms in higher eukaryotes and is considered to play a key role in transcriptional gene silencing. In plants, cytosine methylation can occur in all sequence contexts (CG, CHG, and CHH), and its levels are controlled by multiple pathways, including de novo methylation, maintenance methylation, and demethylation. Modulation of DNA methylation represents a potentially robust mechanism to adjust gene expression following exposure to different stresses. However, the potential involvement of epigenetics in plant-virus interactions has been scarcely explored, especially with regard to RNA viruses. Here, we studied the impact of a symptomless viral infection on the epigenetic status of the host genome. We focused our attention on the interaction between Nicotiana benthamiana and Pelargonium line pattern virus (PLPV, family Tombusviridae), and analyzed cytosine methylation in the repetitive genomic element corresponding to ribosomal DNA (rDNA). Through a combination of bisulfite sequencing and RT-qPCR, we obtained data showing that PLPV infection gives rise to a reduction in methylation at CG sites of the rDNA promoter. Such a reduction correlated with an increase and decrease, respectively, in the expression levels of some key demethylases and of MET1, the DNA methyltransferase responsible for the maintenance of CG methylation. Hypomethylation of rDNA promoter was associated with a five-fold augmentation of rRNA precursor levels. The PLPV protein p37, reported as a suppressor of post-transcriptional gene silencing, did not lead to the same effects when expressed alone and, thus, it is unlikely to act as suppressor of transcriptional gene silencing. Collectively, the results suggest that PLPV infection as a whole is able to modulate host transcriptional activity through changes in the cytosine methylation pattern arising from misregulation of methyltransferases/demethylases balance.

scholarly journals Assessing an Atmospheric Correction Algorithm for Time Series of Satellite-Based Water-Leaving Reflectance Using Match-Up Sites in Australian Coastal Waters

2021 ◽  
Vol 13 (10) ◽  
pp. 1927
Author(s):  
Fuqin Li ◽  
David Jupp ◽  
Thomas Schroeder ◽  
Stephen Sagar ◽  
Joshua Sixsmith ◽  
...  
Keyword(s):  
Coastal Waters ◽  
Atmospheric Correction ◽  
Correction Method ◽  
In Situ Measurements ◽  
Landsat 8 ◽  
Correction Algorithm ◽  
Simple Method ◽  
North East ◽  
The Impact

An atmospheric correction algorithm for medium-resolution satellite data over general water surfaces (open/coastal, estuarine and inland waters) has been assessed in Australian coastal waters. In situ measurements at four match-up sites were used with 21 Landsat 8 images acquired between 2014 and 2017. Three aerosol sources (AERONET, MODIS ocean aerosol and climatology) were used to test the impact of the selection of aerosol optical depth (AOD) and Ångström coefficient on the retrieved accuracy. The initial results showed that the satellite-derived water-leaving reflectance can have good agreement with the in situ measurements, provided that the sun glint is handled effectively. Although the AERONET aerosol data performed best, the contemporary satellite-derived aerosol information from MODIS or an aerosol climatology could also be as effective, and should be assessed with further in situ measurements. Two sun glint correction strategies were assessed for their ability to remove the glint bias. The most successful one used the average of two shortwave infrared (SWIR) bands to represent sun glint and subtracted it from each band. Using this sun glint correction method, the mean all-band error of the retrieved water-leaving reflectance at the Lucinda Jetty Coastal Observatory (LJCO) in north east Australia was close to 4% and unbiased over 14 acquisitions. A persistent bias in the other strategy was likely due to the sky radiance being non-uniform for the selected images. In regard to future options for an operational sun glint correction, the simple method may be sufficient for clear skies until a physically based method has been established.

Nitrification preservation in activated sludge during curative bulking chlorination

2003 ◽  
Vol 47 (11) ◽  
pp. 85-92 ◽  
Author(s):  
E. Cotteux ◽  
P. Duchene
Keyword(s):  
Activated Sludge ◽  
Pilot Plant ◽  
Wastewater Treatment Plants ◽  
Oxygen Uptake Rate ◽  
Ammonia Concentration ◽  
Synthetic Wastewater ◽  
Biological Wastewater Treatment ◽  
Simple Method ◽  
Method Of Measurement ◽  
The Impact

The bulking that occurs in biological wastewater treatment plants using activated sludge is very often controlled by the injection of sodium hypochlorite into the return activated sludge (RAS) stream. In the present study undertaken at two pilot plants fed with synthetic wastewater, the impact of the pass frequency of the sludge at the chlorine dosing point on the nitrifying flora is analysed. The pass frequency is one for the pilot plant 1 and two for the pilot plant 2. A dose of chlorine of 4.85 ± 0.05 g/kg/MLVSS per day was applied at both pilots. The preservative effect on nitrifying activity of the lowest concentration of chlorine at the dosing point and therefore of the highest pass frequency was evidenced. Among other tools, a simple method of measurement of the oxygen uptake rate enabled us to monitor the effect of chlorination on nitrification before recording an increase in the ammonia concentration in the bulking.

scholarly journals Exploring the Impact of Early Decisions in Variable Ordering for Constraint Satisfaction Problems

2018 ◽  
Vol 2018 ◽  
pp. 1-14
Author(s):  
José Carlos Ortiz-Bayliss ◽  
Ivan Amaya ◽  
Santiago Enrique Conant-Pablos ◽  
Hugo Terashima-Marín
Keyword(s):  
Constraint Satisfaction ◽  
Constraint Satisfaction Problems ◽  
Search Cost ◽  
High Quality ◽  
Simple Method ◽  
Variable Ordering ◽  
It Performance ◽  
The Cost ◽  
The Impact ◽  
Variable Ordering Heuristics

When solving constraint satisfaction problems (CSPs), it is a common practice to rely on heuristics to decide which variable should be instantiated at each stage of the search. But, this ordering influences the search cost. Even so, and to the best of our knowledge, no earlier work has dealt with how first variable orderings affect the overall cost. In this paper, we explore the cost of finding high-quality orderings of variables within constraint satisfaction problems. We also study differences among the orderings produced by some commonly used heuristics and the way bad first decisions affect the search cost. One of the most important findings of this work confirms the paramount importance of first decisions. Another one is the evidence that many of the existing variable ordering heuristics fail to appropriately select the first variable to instantiate. Another one is the evidence that many of the existing variable ordering heuristics fail to appropriately select the first variable to instantiate. We propose a simple method to improve early decisions of heuristics. By using it, performance of heuristics increases.

scholarly journals DEUFRABASE: A Simple Tool for the Evaluation of the Noise Impact of Pavements in Typical Road Geometries

Environments ◽  
2019 ◽  
Vol 6 (3) ◽  
pp. 27 ◽  
Author(s):  
Michel Bérengier ◽  
Judicaël Picaut ◽  
Bettina Pahl ◽  
Denis Duhamel ◽  
Benoit Gauvreau ◽  
...  
Keyword(s):  
Traffic Noise ◽  
Emission Spectra ◽  
Low Noise ◽  
Noise Emission ◽  
Simple Method ◽  
Acceptable Error ◽  
The Road ◽  
Noise Impact ◽  
On The Road ◽  
The Impact

Traffic noise is considered by people as one of the most important sources of environmental discomfort. A way to limit the traffic noise is to reduce the noise emission, for example, by using specific low noise pavements, particularly in suburban areas. However, in real situations, it can be difficult to evaluate the impact of a given pavement, because it depends, for example, on the road geometry, the meteorological conditions, or the distance of the receiver position. Finally it can be difficult to select the most appropriate pavement for a given noise reduction objective. In this paper, a simple method is proposed to evaluate the noise impact of a pavement, in typical road geometries and environmental conditions. The proposed approach uses two databases, the first one based on measurements of emission spectra of road vehicles on several typical pavements, the second one made of pre-calculations of noise propagation for typical road configurations. Finally, the method is implemented in an interactive web tool, called DEUFRABASE, which allows one to obtain a fast estimation of the L Aeq (1 h or 24 h) and L den noise levels for various pavements and road configurations, as functions of the traffic flow and composition. By comparing the method with measurements, it is showed that the tool, although based on a restricted number of pavements and on several simplifications, can predict the noise impact of typical road configurations, with an acceptable error, most often less than 2 dB.

scholarly journals Dispersed Mutations in Histone H3 That Affect Transcriptional Repression and Chromatin Structure of the CHA1 Promoter in Saccharomyces cerevisiae

2008 ◽  
Vol 7 (10) ◽  
pp. 1649-1660 ◽  
Author(s):  
Qiye He ◽  
Cailin Yu ◽  
Randall H. Morse
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Chromatin Structure ◽  
Transcriptional Repression ◽  
Histone H3 ◽  
Temperature Sensitive ◽  
Active Chromatin ◽  
Temperature Sensitive Mutants ◽  
Nucleosome Structure ◽  
Lysine Residues ◽  
Chromatin Configuration

ABSTRACT The histone H3 amino terminus, but not that of H4, is required to prevent the constitutively bound activator Cha4 from remodeling chromatin and activating transcription at the CHA1 gene in Saccharomyces cerevisiae. Here we show that neither the modifiable lysine residues nor any specific region of the H3 tail is required for repression of CHA1. We then screened for histone H3 mutations that cause derepression of the uninduced CHA1 promoter and identified six mutants, three of which are also temperature-sensitive mutants and four of which exhibit a sin − phenotype. Histone mutant levels were similar to that of wild-type H3, and the mutations did not cause gross alterations in nucleosome structure. One specific and strongly derepressing mutation, H3 A111G, was examined in depth and found to cause a constitutively active chromatin configuration at the uninduced CHA1 promoter as well as at the ADH2 promoter. Transcriptional derepression and altered chromatin structure of the CHA1 promoter depend on the activator Cha4. These results indicate that modest perturbations in distinct regions of the nucleosome can substantially affect the repressive function of chromatin, allowing activation in the absence of a normal inducing signal (at CHA1) or of Swi/Snf (resulting in a sin − phenotype).

scholarly journals Parameterizing the impact of vegetated urban canopies on wind and temperature fields by using a simple nudging method

2021 ◽  
Author(s):  
Ge Cheng ◽  
David Grawe ◽  
K. Heinke Schlünzen
Keyword(s):  
Mesoscale Model ◽  
Three Dimensional ◽  
Urban Canopy ◽  
Temperature Fields ◽  
Simple Method ◽  
Local Climate ◽  
Local Climate Zones ◽  
Urban Canopy Parameterizations ◽  
The Impact ◽  
Nudging Method

<p>Nudging is a simple method that aims to dynamically adjust the model toward the observations by including an additional feedback term in the model governing equation. This method is widely applied in data assimilation due to its simple implementation and reasonable model results. The basic concept of nudging is similar to that of urban canopy parameterization, in which additional terms are usually added in the conservation equations of momentum and energy aiming to simulate the canopy effects. However, few studies have investigated the implementation of nudging methods in urban canopy parameterizations. In this study we developed a multi-layer urban canopy parameterization (UCP) by using a nudging approach to represent the impacts of vegetated urban canopies on temperatures and winds in mesoscale models.</p><p>The difficulty of developing UCP by using a nudging method lies in defining appropriate values for the nudging coefficients and the forcing fields (e.g. indoor temperature fields for temperature nudging). To determine nudging coefficients, we use three major urban canopy morphological parameters: building height, frontal area density and building density. The ranges of these parameters are taken from the values for the Local Climate Zones datasets, in our case for the city of Hamburg. The UCP is employed in the three -dimensional atmospheric mesoscale model METRAS. Results show that this UCP can well simulate wind-blocking effects induced from obstacles as buildings and trees and urban heat island phenomenon for cities. Thus, nudging is an efficient and effective method that can be used for urban canopy parameterizations. However, as well known for nudging, it is not conserving energy. Therefore, we investigated the energy loss by tracking the reduced kinetic energy and internal energy. The UCP and model results will be presented.</p>

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