Inheritance and Variation of Cytosine Methylation in Three Populus Allotriploid Populations with Different Heterozygosity

DNA methylation is an epigenetic mechanism with the potential to regulate gene expression and affect plant phenotypes. Both hybridization and genome doubling may affect the DNA methylation status of newly formed allopolyploid plants. Previous studies demonstrated that changes in cytosine methylation levels and patterns were different among individual hybrid plant, therefore, studies investigating the characteristics of variation in cytosine methylation status must be conducted at the population level to avoid sampling error. In the present study, an F1 hybrid diploid population and three allotriploid populations with different heterozygosity [originating from first-division restitution (FDR), second-division restitution (SDR), and post-meiotic restitution (PMR) 2n eggs of the same female parent] were used to investigate cytosine methylation inheritance and variation relative to their common parents using methylation-sensitive amplification polymorphism (MSAP). The variation in cytosine methylation in individuals in each population exhibited substantial differences, confirming the necessity of population epigenetics. The total methylation levels of the diploid population were significantly higher than in the parents, but those of the three allotriploid populations were significantly lower than in the parents, indicating that both hybridization and polyploidization contributed to cytosine methylation variation. The vast majority of methylated status could be inherited from the parents, and the average percentages of non-additive variation were 6.29, 3.27, 5.49 and 5.07% in the diploid, FDR, SDR and PMR progeny populations, respectively. This study lays a foundation for further research on population epigenetics in allopolyploids.     

Livin in synergy with Ras induces and sustains corticosteroid resistance in the airway mucosa

Rationale: Corticosteroid resistance (CR) seriously affects the therapeutic effects of steroids on many chronic inflammatory disorders, including airway allergy. The mechanism of CR development is unclear. Recent research indicates that livin, an apoptosis inhibitor, is associated with the regulation in cell activities. This study investigates the role of livin in the inducing and sustaining CR in the airway mucosa.Methods: Nasal epithelial cells (NECs) were isolated from surgically removed nasal mucosal tissues of patients with allergic rhinitis (AR) and nasal polyps with or without CR. Differentially expressed genes in NECs were analyzed by the RNA sequencing. A CR mouse model was developed to test the role of livin in CR development.Results: The results showed that NECs of AR patients with CR expressed high levels of livin, that was positively correlated with the thymic stromal lymphopoietin (TSLP) expression and the high Ras activation status in NECs. Livin and Ras activation mutually potentiating each other in the inducing and sustaining the TSLP expression in NECs. TSLP induced eosinophils and neutrophils to express glucocorticoid receptor-β (GRβ). Eosinophils and neutrophils with high CRβ expression were resistant to corticosteroids. Depletion of livin or inhibition of TSLP markedly attenuated CR and airway allergy.Conclusions: Livin facilitates CR development in the airways by promoting TSLP expression in epithelial cells and the GRβ expression in eosinophils and neutrophils. Depletion of livin or inhibiting TSLP attenuates CR development and inhibits airway allergy, this has the translational potential to be used in the treatment of airway allergy.     

Backbone assignment of the little finger domain of a Y-family DNA polymerase

Sulfolobus solfataricus DNA polymerase IV (Dpo4), a prototype Y-family DNA polymerase, contains a unique little finger domain besides a catalytic core. Here, we report the chemical shift assignments for the backbone nitrogens, α and β carbons, and amide protons of the little finger domain of Dpo4. This work and our published backbone assignment for the catalytic core provide the basis for investigating the conformational dynamics of Dpo4 during catalysis using solution NMR spectroscopy.     

Significant improvement of pig cloning efficiency by treatment with LBH589 after somatic cell nuclear transfer

The low success rate of animal cloning by somatic cell nuclear transfer (SCNT) associates with epigenetic aberrancy, including the abnormal acetylation of histones. Altering the epigenetic status by histone deacetylase inhibitors (HDACi) enhances the developmental potential of SCNT embryos. In the current study, we examined the effects of LBH589 (panobinostat), a novel broad-spectrum HDACi, on the nuclear reprogramming and development of pig SCNT embryos in vitro. In experiment 1, we compared the in vitro developmental competence of nuclear transfer embryos treated with different concentrations of LBH589. Embryos treated with 50 nM LBH589 for 24 hours showed a significant increase in the rate of blastocyst formation compared with the control or embryos treated with 5 or 500 nM LBH589 (32.4% vs. 11.8%, 12.1%, and 10.0%, respectively, P < 0.05). In experiment 2, we examined the in vitro developmental competence of nuclear transfer embryos treated with 50 nM LBH589 for various intervals after activation and 6-dimethylaminopurine. Embryos treated for 24 hours had higher rates of blastocyst formation than the other groups. In experiment 3, when the acetylation of H4K12 was examined in SCNT embryos treated for 6 hours with 50 nM LBH589 by immunohistochemistry, the staining intensities of these proteins in LBH589-treated SCNT embryos were significantly higher than in the control. In experiment 4, LBH589-treated nuclear transfer and control embryos were transferred into surrogate mothers, resulting in three (100%) and two (66.7%) pregnancies, respectively. In conclusion, LBH589 enhances the nuclear reprogramming and developmental potential of SCNT embryos by altering the epigenetic status and expression, and increasing blastocyst quality.     

Unlocking the sugar "steric gate" of DNA polymerases

To maintain genomic stability, ribonucleotide incorporation during DNA synthesis is controlled predominantly at the DNA polymerase level. A steric clash between the 2'-hydroxyl of an incoming ribonucleotide and a bulky active site residue, known as the "steric gate", establishes an effective mechanism for most DNA polymerases to selectively insert deoxyribonucleotides. Recent kinetic, structural, and in vivo studies have illuminated novel features about ribonucleotide exclusion and the mechanistic consequences of ribonucleotide misincorporation on downstream events, such as the bypass of a ribonucleotide in a DNA template and the subsequent extension of the DNA lesion bypass product. These important findings are summarized in this review.     

CircPSMC3 alleviates the symptoms of PCOS by sponging miR‐296‐3p and regulating PTEN expression

Polycystic ovary syndrome (PCOS), the most common female endocrine disease that causes anovulatory infertility, still lacks promising strategy for the accurate diagnosis and effective therapeutics of PCOS attributed to its unclear aetiology. In this study, we determined the abnormal reduction in circPSMC3 expression by comparing the ovarian tissue samples of PCOS patients and normal individuals. The symptom relief caused by up‐regulation of circPSMC3 in PCOS model mice suggested the potential for further study. In vitro functional experiments confirmed that circPSMC3 can inhibit cell proliferation and promote apoptosis by blocking the cell cycle in human‐like granular tumour cell lines. Mechanism study revealed that circPSMC3 may play its role through sponging miR‐296‐3p to regulate PTEN expression. Collectively, we preliminarily characterized the role and possible insights of circPSMC3/miR‐296‐3p/PTEN axis in the proliferation and apoptosis of KGN cells. We hope that this work provides some original and valuable information for the research of circRNAs in PCOS, not only to better understand the pathogenesis but also to help provide new clues for seeking for the future therapeutic target of PCOS.     

Dynamic transition of microbial communities in response to acidification in fixed-bed anaerobic baffled reactors (FABR) of two different flow directions

Two five-compartment fixed-bed anaerobic baffled reactors (FABRs) were operated under deteriorative and stable conditions. The FABRs were identical except for flow direction: one was horizontal (H-reactor) and the other was vertical (V-reactor). The microbial community dynamics in 1, 3 and 5 compartments were analyzed using denaturing gradient gel electrophoresis (DGGE), 16S rRNA gene clone library screening and quantitative PCR. After start-up, the Methanomicrobiales were typically dominant in adhering sludge of 5th compartments of two reactors. Because methanogenesis mainly occurred in the latter compartment, Methanomicrobiales were likely to play important roles in FABRs. FABRs recovered from performance deterioration very quickly. Meanwhile, methanogens and dominant methanogens greatly increased in every compartment of two reactors. Our results indicated that 16S rRNA levels of methanogens in the adhering sludge were higher than those in the deposited sludge and the adhering fraction of V-reactor held up more acid-resistant bacteria and methanogens than that of H-reactor.     

Temporal and spatial comparison of food web structure in marine pastures in the Pearl River Estuary: Implications for sustainable fisheries management

The biological and ecological integrity of marine ecosystems in the Pearl River Estuary (PRE) has been compromised due to overfishing and water pollution. Fishing moratorium and artificial reef construction have been implemented in Wanshan and Miaowan for resource protection and restoration. Therefore, food web structure and trophic pathways of Wanshan, Miaowan, and Wailingding in different temporal and spatial situation will be determined using the Ecopath model, as well as the keystone species affecting these ecosystems, which can provide a basis for fishery management. The results showed that the energy transfer efficiency of IV and V trophic levels (TL) was higher than that of II and III‐TL before and after fishing moratorium, and the energy transfer efficiency of artificial reefs II and III‐TL was only slightly higher than that of nonartificial reefs in Wanshan. In addition, the mean values of ecosystem property indicators (consumption, respiration flow, total system throughput, and total biomass) after the fishing moratorium were significantly higher than those before the fishing moratorium. The average value of the ecosystem attribute indicators (consumption, respiration flow, total system throughput, and total biomass) of artificial reefs is lower than those of nonartificial reef areas, which may be related to the differences in community composition between artificial reefs and non‐artificial reefs. Finally, Nemipterus japonicus and Gastrophysus spadiceus are keystone species that distinguish the Wanshan and Miaowan artificial reefs from other areas. Overall, the fishing moratorium has a positive effect on the short‐term restoration of fishery resources, mainly restoring short‐life cycle organisms. However, the construction of artificial reefs will be more conducive to the persistence of ecosystem restoration. In addition, reasonable proliferation, release and fishing of N. japonicus and G. spadiceus will be beneficial to the sustainable utilization of fishery resources.     

Mechanically Asymmetrical Triboelectric Nanogenerator for Self‐Powered Monitoring of In Vivo Microscale Weak Movement

Although much effort has been put in the studies of weak in vivo microscale movements due to its importance, the real‐time, long‐time, and accurate monitoring is still a great challenge because of the complexity of the in vivo environment. Here, a new type of mechanically asymmetrical triboelectric nanogenerator with ultrashort working distance and high anti‐interference ability is developed to accurately and real‐timely monitor the microscopically weak movement of intestinal motility at low frequencies even around 0.3 Hz. The intestinal status after the glucose absorption, and physiological states in different times also have been monitored successfully in the complex in vivo environment with many kinds of interference and noises. This work gives a new self‐powered, long‐time and in vivo technical way for the real‐timely gastrointestinal motility monitoring, and contributes to the detection of every kind of gentle movements in various complex bio‐systems.     

Nitric oxide is the shared signalling molecule in phosphorus- and iron-deficiency-induced formation of cluster roots in white lupin (Lupinus albus)

Background and Aims

Formation of cluster roots is one of the most specific root adaptations to nutrient deficiency. In white lupin (Lupinus albus), cluster roots can be induced by phosphorus (P) or iron (Fe) deficiency. The aim of the present work was to investigate the potential shared signalling pathway in P- and Fe-deficiency-induced cluster root formation.

Methods

Measurements were made of the internal concentration of nutrients, levels of nitric oxide (NO), citrate exudation and expression of some specific genes under four P × Fe combinations, namely (1) 50 µm P and 10 µm Fe (+P + Fe); (2) 0 P and 10 µm Fe (–P + Fe); (3) 50 µm P and 0 Fe (+P–Fe); and (4) 0 P and 0 Fe (–P–Fe), and these were examined in relation to the formation of cluster roots.

Key Results

The deficiency of P, Fe or both increased the cluster root number and cluster zones. It also enhanced NO accumulation in pericycle cells and rootlet primordia at various stages of cluster root development. The formation of cluster roots and rootlet primordia, together with the expression of LaSCR1 and LaSCR2 which is crucial in cluster root formation, were induced by the exogenous NO donor S-nitrosoglutathione (GSNO) under the +P + Fe condition, but were inhibited by the NO-specific endogenous scavenger 2-(4-carboxyphenyl)-4, 4, 5, 5-tetramethylimidazoline-1-oxyl- 3-oxide (cPTIO) under –P + Fe, +P–Fe and –P–Fe conditions. However, cluster roots induced by an exogenous supply of the NO donor did not secrete citrate, unlike those formed under –P or –Fe conditions.

Conclusions

NO plays an important role in the shared signalling pathway of the P- and Fe-deficiency-induced formation of cluster roots in white lupin.