Chromatin organization is disrupted genome-wide during DNA replication. On newly synthesized DNA, nucleosomes are assembled from new naive histones and old modified histones. It remains unknown ...whether the landscape of histone post-translational modifications (PTMs) is faithfully copied during DNA replication or the epigenome is perturbed. Here we develop chromatin occupancy after replication (ChOR-seq) to determine histone PTM occupancy immediately after DNA replication and across the cell cycle. We show that H3K4me3, H3K36me3, H3K79me3, and H3K27me3 positional information is reproduced with high accuracy on newly synthesized DNA through histone recycling. Quantitative ChOR-seq reveals that de novo methylation to restore H3K4me3 and H3K27me3 levels occurs across the cell cycle with mark- and locus-specific kinetics. Collectively, this demonstrates that accurate parental histone recycling preserves positional information and allows PTM transmission to daughter cells while modification of new histones gives rise to complex epigenome fluctuations across the cell cycle that could underlie cell-to-cell heterogeneity.
Display omitted
•ChOR-seq determines histone PTM occupancy on newly replicated DNA•Histone PTM positional information is preserved through parental histone recycling•Parental H3K27me3 domains are stable and inherited to daughter cells•Restoration of histone PTM levels follows mark- and locus-specific kinetics
Histone modifications are a core component of the epigenome. Reverón-Gómez et al. develop ChOR-seq to profile histone modifications after DNA replication and find that the genomic localization of modified parental histones is preserved on daughter strands while new histone modification to restore pre-replication levels follows mark- and locus-specific kinetics.
Display omitted
•A new Lactobacillus pentosus strain was obtained by adaptive evolution.•Lactic acid yield from xylose at initial pH 7, 6 and 5 was enhanced by 2-fold.•Increase in xylose consumption ...rate was also shown when pH was set at 7.•Lactic acid productivity from wheat straw hydrolysate was increased by 1.4-fold.
Since xylose is the second most abundant sugar in lignocellulose, using microorganisms able to metabolize it into bio-based chemicals like lactic acid is an attractive approach. In this study, Lactobacillus pentosus CECT4023T was evolved to improve its xylose fermentation capacity even at acid pH by adaptive laboratory evolution in repeated anaerobic batch cultures at increasing xylose concentration. The resulting strain (named MAX2) presented between 1.5 and 2-fold more xylose consumption and lactic acid production than the parental strain in 20 g L−1 xylose defined media independently of the initial pH value. When the pH was controlled in bioreactor, lactic acid productivity at 16 h increased 1.4-fold when MAX2 was grown both in xylose defined media and in wheat straw hydrolysate. These results demonstrated the potential of this new strain to produce lactic acid from hemicellulosic substrates at low pH, reducing the need of using neutralizing agents in the process.
With increasing concerns regarding energy and environment, algae biofuel is generating considerable interest around the world. Nevertheless, the harvesting step required before downstream biomass ...processing is a major bottleneck. Commonly employed methods include addition of chemicals or use of mechanical equipment that increase dramatically the biofuel production cost. This review deals with naturally occurring processes that can help offset those costs by causing microalgae flocculation. Interaction theories are briefly reviewed. In addition, operational parameters such as pH, irradiance, nutrients, dissolved oxygen, and temperature effect on microalgae flocculation are evaluated. Finally, microalgae flocculation is also considered from an ecological point of view by taking advantage of their interaction with other microorganisms.
Display omitted
•Successful acclimation of methanogenic culture to extreme ammonia levels in CSTR.•Efficient utilization of a 3rd generation biomass as biomethanation substrate.•The most abundant ...bacterium (Shinella spp.) was not affected by the ammonia levels.•C. ultunense increased significantly its abundance during the acclimation process.•Methanosarcina spp. was the most abundant methanogen at the highest ammonia levels.
Acclimatized anaerobic communities to high ammonia levels can offer a solution to the ammonia toxicity problem in biogas reactors. In the current study, a stepwise acclimation strategy up to 10g NH4+-N L−1, was performed in mesophilic (37±1°C) continuously stirred tank reactors. The reactors were co-digesting (20/80 based on volatile solid) cattle slurry and microalgae, a protein-rich, 3rd generation biomass. Throughout the acclimation period, methane production was stable with more than 95% of the uninhibited yield. Next generation 16S rRNA gene sequencing revealed a dramatic microbiome change throughout the ammonia acclimation process. Clostridium ultunense, a syntrophic acetate oxidizing bacteria, increased significantly alongside with hydrogenotrophic methanogen Methanoculleus spp., indicating strong hydrogenotrophic methanogenic activity at extreme ammonia levels (>7g NH4+-N L−1). Overall, this study demonstrated for the first time that acclimation of methanogenic communities to extreme ammonia levels in continuous AD process is possible, by developing a specialised acclimation AD microbiome.
The factors that sequester transcriptionally repressed heterochromatin at the nuclear periphery are currently unknown. In a genome-wide RNAi screen, we found that depletion of S-adenosylmethionine ...(SAM) synthetase reduces histone methylation globally and causes derepression and release of heterochromatin from the nuclear periphery in Caenorhabditis elegans embryos. Analysis of histone methyltransferases (HMTs) showed that elimination of two HMTs, MET-2 and SET-25, mimics the loss of SAM synthetase, abrogating the perinuclear attachment of heterochromatic transgenes and of native chromosomal arms rich in histone H3 lysine 9 methylation. The two HMTs target H3K9 in a consecutive fashion: MET-2, a SETDB1 homolog, mediates mono- and dimethylation, and SET-25, a previously uncharacterized HMT, deposits H3K9me3. SET-25 colocalizes with its own product in perinuclear foci, in a manner dependent on H3K9me3, but not on its catalytic domain. This colocalization suggests an autonomous, self-reinforcing mechanism for the establishment and propagation of repeat-rich heterochromatin.
Display omitted
► Reduced SAM synthetase levels releases perinuclear arrays of heterochromatin ► Peripheral anchoring of gene arrays and chromosome arms requires H3K9 methylation ► The repressive H3K9me3 mark is established step-wise by the HMTs MET-2 and SET-25 ► H3K9me3 leads to sequestration of SET-25 in perinuclear heterochromatin foci
The identification of two histone methyltransferases that act sequentially on lysine 9 on histone 3 to produce trimethylated lysine 9 reveals a requirement for H3K9me3 for the association of chromatin with the nuclear envelope and suggests the existence of a self-reinforcing loop that ensures robust H3K9 methylation at the nuclear periphery.
Mi trabajo recorre algunas ideas de la filosofía política hegeliana basadas en la convicción comunitaria del autor: la visión de la sociedad civil de su tiempo como el mundo del atomismo, la crítica ...al sufragio como principal método de toma de decisiones políticas, la reflexión sobre la familia, las corporaciones y el Estado como instituciones no regidas por lógicas de contrato entre individuos, y el lugar no prescriptivo que Hegel concedió siempre a la reflexión filosófica.
The advance and stability of replication forks rely on a tight co-regulation of DNA synthesis and nucleosome assembly. We show that mutants affected in parental histone recycling are impaired in the ...recombinational repair of the single-stranded DNA gaps generated in response to DNA adducts that hamper replication, which are then filled in by translesion synthesis. These recombination defects are in part due to an excess of parental nucleosomes at the invaded strand that destabilizes the sister chromatid junction formed after strand invasion through a Srs2-dependent mechanism. In addition, we show that a dCas9∗/R-loop is more recombinogenic when the dCas9∗/DNA-RNA hybrid interferes with the lagging than with the leading strand, and this recombination is particularly sensitive to problems in the deposition of parental histones at the strand that contains the hindrance. Therefore, parental histone distribution and location of the replication obstacle at the lagging or leading strand regulate homologous recombination.
Display omitted
•Parental histone recycling contributes to MMS resistance by homologous recombination•Excess parental histones at the invaded chromatid cause SCJ instability by Srs2•A dCas9∗/R-loop is more recombinogenic at the lagging than at the leading strand•HR is impaired by reduced parental histones at the strand that contains the hindrance
González-Garrido and Prado find that parental histone distribution between sister chromatids plays a role in the repair of ssDNA gaps generated by DNA replication obstacles. They show that parental histone distribution controls the stability of recombination intermediates in a manner dependent on the helicase Srs2 and the hindrance location.
The approximations to the embedding potential in frozen-density embedding theory (FDET) have been assessed for the first time for the calculation of the electric field gradient (EFG) at a nucleus. ...FDET-based methods using a hierarchy of approximations are applied to evaluate the EFG at the nuclei of an HCl molecule in several noncovalently bound clusters chosen to represent potential liquid or molecular crystal systems. A detailed assessment of such approximations is made for the Hartree–Fock treatment of electron–electron correlation (both in FDET and in the reference calculations for the whole cluster). The emerging choice of the optimal set of approximations is reconfirmed in calculations in which electron–electron calculations are treated at the MP2 level. Our optimized protocol produces average errors in the complexation-induced EFG shift on the order of 25% relative to conventional quantum mechanical calculations for the whole cluster. This protocol is shown to be numerically robust and leads to enormous computational savings compared to a complete quantum mechanical treatment of the embedded species and its environment. For a cluster comprising a Na+ cation and up to 24 water molecules, the computation time is reduced by a factor of 30,000 at the expense of introducing an error in the environment-induced EFG shift of 22%.
PDF
