Replication stress affects the fidelity of nucleosome-mediated epigenetic inheritance

The fidelity of epigenetic inheritance or, the precision by which epigenetic information is passed along, is an essential parameter for measuring the effectiveness of the process. How the precision of the process is achieved or modulated, however, remains largely elusive. We have performed quantitative measurement of epigenetic fidelity, using position effect variegation (PEV) in Schizosaccharomyces pombe as readout, to explore whether replication perturbation affects nucleosome-mediated epigenetic inheritance. We show that replication stresses, due to either hydroxyurea treatment or various forms of genetic lesions of the replication machinery, reduce the inheritance accuracy of CENP-A/Cnp1 nucleosome positioning within centromere. Mechanistically, we demonstrate that excessive formation of single-stranded DNA, a common molecular abnormality under these conditions, might have correlation with the reduction in fidelity of centromeric chromatin duplication. Furthermore, we show that replication stress broadly changes chromatin structure at various loci in the genome, such as telomere heterochromatin expanding and mating type locus heterochromatin spreading out of the boundaries. Interestingly, the levels of inheritable expanding at sub-telomeric heterochromatin regions are highly variable among independent cell populations. Finally, we show that HU treatment of the multi-cellular organisms C. elegans and D. melanogaster affects epigenetically programmed development and PEV, illustrating the evolutionary conservation of the phenomenon. Replication stress, in addition to its demonstrated role in genetic instability, promotes variable epigenetic instability throughout the epigenome

Effects of irrigation and fertilization on the emission factors and emission intensities of nitrous oxide in alkaline soil

Environmental damage attributed to nitrous oxide (N _2 O) emissions have received widespread attention. Agricultural sources release substantial amounts of N _2 O into the atmosphere. However, comparative studies on the effects of different irrigation and fertilization methods, namely, drip fertigation (a combination of fertilizing and irrigation), sprinkler fertigation, and traditional furrow irrigation with chemical fertilizer spraying, on N _2 O emissions in alkaline soil have been limited. Therefore, three-year in situ field observations were conducted to investigate the effect of these three irrigation and fertilization modes on N _2 O emissions using the static chamber method over the period 2015–2017. There are significant seasonal variations in soil N _2 O emission fluxes among alkaline soils under different fertilization and irrigation modes, with emissions peaking in July and August, but no significant difference in yearly variations. The N _2 O emission intensity of drip fertigation soil was 0.20 kg N t ^−1 year ^−1 , of sprinkler fertigation soil was 0.38 kg N t ^−1 year ^−1 , respectively, while of furrow irrigation was 0.91 kg N t ^−1 year ^−1 , respectively. Moisture and temperature of soil were key factors driving the observed nitrous oxide variations. Compared with traditional furrow irrigation, drip and sprinkler fertigation significantly increased potato yield and decreased N _2 O emissions in alkaline soil, thus satisfying both yield and environmental protection

Bioaccumulation of Pyraoxystrobin and Its Predictive Evaluation in Zebrafish

This paper aims to understand the bioaccumulation of pyraoxystrobin in fish. Using a flow-through bioconcentration method, the bioconcentration factor (BCF) and clearance rate of pyraoxystrobin in zebrafish were measured. The measured BCF values were then compared to those estimated from three commonly used predication models. At the exposure concentrations of 0.1 μg/L and 1.0 μg/L, the maximum BCF values for pyraoxystrobin in fish were 820.8 and 265.9, and the absorption rate constants (K1) were 391.0 d−1 and 153.2 d−1, respectively. The maximum enrichment occurred at 12 d of exposure. At the two test concentrations, the clearance rate constant (K2) in zebrafish was 0.5795 and 0.4721, and the half-life (t1/2) was 3.84 d and 3.33 d, respectively. The measured BCF values were close to those estimated from bioconcentration predication models

Sprinkler Irrigation Is Effective in Reducing Nitrous Oxide Emissions from a Potato Field in an Arid Region: A Two-Year Field Experiment

In arid and semi-arid regions, water-saving irrigation is the primary mode of local agricultural production. Since the chemical fertilizer is the principal source of nitrous oxide (N2O) emissions, we present results from a two-year (2016−2017) field experiment on a potato field to verify the general influence of water-saving irrigation on N2O emissions. A split-plot experiment was established with two irrigation systems and two fertilizer treatments, which give a total of four treatments. Two different irrigation systems were investigated: (i) flood irrigation with nitrogen fertilizer (NF-FI) combined with a control without any fertilizer (C-FI) and (ii) overhead sprinkler irrigation with a nitrogen fertilizer (NF-SI) accompanied with a control without any fertilizer (C-SI). The N2O emissions of the fertilizer treatment were greater than those of the control under each irrigation system. In plots where the fertilizers were applied, using overhead sprinkler irrigation reduced the average cumulative N2O emissions between 40.72% and 59.65% compared with flood irrigation. This was mainly due to the lower amount of water applied and the lower availability of NO3−-N and NH4+-N of soil associated with an overhead sprinkler irrigation. This work shows that the overhead sprinkler irrigation is an effective strategy to use to save water and mitigate emissions of the atmospheric pollutants N2O in comparison to flood irrigation

Apoptotic mechanism of propofol-induced developmental toxicity in zebrafish embryos.

General anesthetics can cause neurological damage and long-term behavioral/cognitive impairment during fetal and early postnatal life. However, the adverse influence on embryo development induced by propofol is unclear. We used embryonic zebrafish to explore the effects of propofol on embryonic and larval growth and development, and the related apoptotic mechanism. Zebrafish embryos were immersed in propofol (1, 2, 3, 4, and 5 μg/ml) dissolved in E3 medium from 6 to 48 hours post fertilization (hpf). The survival rate, locomotion, heart rate, hatchability, deformity rate, and body length were analyzed at defined stages. Terminal deoxynucleotidyl transferase nick-end-labeling was used to detect zebrafish embryo apoptosis, and the expression levels of apoptosis-related genes were determined using quantitative real-time reverse transcription PCR and whole-mount in situ hybridization. Larvae at 48 hpf were anesthetized by immersion in E3 culture medium containing 2 μg/ml propofol, the reasonable anesthetic concentration for zebrafish embryos, which caused significant caudal fin dysplasia, light pigmentation, edema, hemorrhage, and spinal deformity, and decreased the hatchability, body length, and heart rate. The numbers of apoptotic cells in propofol-treated 12, 48 and 72 hpf embryos increased significantly, and the mRNA expression levels of intrinsic apoptosis pathway-related casp3a, casp3b, casp9, and baxb genes were upregulated, mainly in the head and tail. Propofol decreased apoptosis in the head and back of 24 hpf zebrafish, which was consistent with the mRNA expression analysis. Our findings demonstrated that zebrafish embryos and larvae exposed to propofol experienced developmental toxicity, which correlated with the intrinsic apoptosis pathway with casp3a, casp3b, casp9, and baxb as the key genes

Immunogenicity Analysis and Identification of Potential T-Cell Epitopes in C129R Protein of African Swine Fever Virus

The highly conserved C129R protein of AFSV was utilized in the development of an ASFV recombinant adenovirus vaccine, demonstrating strong immunogenicity. In this study, we immunized 6-week-old female C57BL/6J mice via subcutaneous injection with 10 μg of purified C129R protein. Humoral and cellular immune effects were assessed using ELISA, flow cytometry, and ELISpot assays. Additionally, 19 peptides of the C129R protein were synthesized and screened for the use of bioinformatics. Positive T-cell epitopes were screened using ELISpot. The results indicated a higher proportion of CD4+ and CD8+ T lymphocytes in immunized mice compared to control mice. ELISA analysis revealed a serum titer of approximately 1:1, 638, 400 in the experimental group of mice. Additionally, peptides C11(53−61aa), C14(81−89aa), C16(97−105aa), and C18(116−124aa) from the C129R protein were able to activate mice spleen lymphocytes to produce IFN-γ. These findings suggest that the C129R protein significantly enhances both humoral and cellular immunity in immunized mice. Moreover, peptides C11, C14, C16, and C18 may serve as potential T-cell epitopes for the C129R protein. These results lay the groundwork for the further exploration of ASFV C129R protein and the identification of novel ASF vaccine antigens

Replication stress affects white gene PEV in <i>D</i>.<i>melanogaster</i> and vulva development in <i>C</i>.<i>elegans</i>.

<p><b>(A)</b> HU treatment increases the likelihood of <i>In(1)wm4</i> silencing in flies. Male or female flies grown without drug (gray bars) or 6 mM HU (black bars) were separated into five bins based on the degree of eye pigmentation. Bar height is the percentage of the population in that bin for all pooled trials. The error bars are 1 SD of percentages for four or five independent trials. Total flies assayed: > 500. (B-F) HU treatment induces a <i>SynMuv</i> phenotype in an <i>hpl-2</i> mutant worm. <b>(B)</b> Montage of DIC images of a wild-type with one normal valva (arrowhead) and <b>(C)</b> an hpl-2 mutant adult raised on 10mM HU plate, with three vulva-like structures (arrows). Scale bars are 50 mms. <b>(D-F)</b> Synchronized L1 larvae were placed on NGM plates containing HU as labeled, the multivulva phenotype was scored after worms reached adulthood. Each data point is represented as mean ± SD. In (D), the animals for scoring and their mothers were raised at 20°C; in (E), mothers were raised at 20°C, and the animals for scoring were raised at 25°C, start at the embryonic stage; in (F), the animals for scoring and their mothers were all raised at 25°C.</p

Mutations in the replication machinery enhance centromeric PEV correlates with excessive formation of ssDNA.

<p><b>(A)</b> Increased levels of Ssb2-GFP signal in the mutant S phase cells. Cells are grown in the liquid rich media except for Psf1-HBD cells in YE+5S media plus 100nM β-estradiol (proficient condition) or 0.1nM β-estradiol (deficient condition), respectively. <i>mcm4-M68</i> cells are grown in 29^°C for 6 hours. Ssb2-GFP signal is measured as in <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1006900#pgen.1006900.g002" target="_blank">Fig 2A</a>. Left panels, representative images of S phase cells. <b>(B)</b> Quantification of <i>cnt2</i>::<i>ade6</i>⁺ red-to-white switching frequency in the replication mutants. For <i>psf1</i>-HBD (deficient) cells, pedigree analyses are performed on “hybrid” plates, on which three cell generations are tracked at the “deficient”-zone containing 0.1nM β-estradiol. The eight progeny cells are then moved to the “proficient”-zone, containing 100nM β-estradiol, incubated at 25^°C for five days. For <i>mcm4-M68</i> cells, pedigree analysis is performed at 29^°C, and incubated at 25^°C for 5 days before scoring. For each test, 500–800 cell division events are scored. The error bars are 1 SD of percentages for four independent experiments. <i>p</i> values are calculated by t test.</p