DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome‐wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome‐wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome‐wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution

Discrete Element Analysis of Indirect Tensile Fatigue Test of Asphalt Mixture

In order to investigate the damage to microstructure and some other micromechanical responses during a fatigue test on asphalt mixture, Particle Flow Code (PFC) was used to reconstruct a two-dimensional discrete element model of asphalt mixture, based on computed tomography (CT) images and image-processing techniques. The indirect tensile fatigue test of asphalt mixture was simulated with this image-based microstructural model, and verified in the laboratory. It was found that there were four stages during the fatigue failure: no crack, crack initiation, crack developing, and interconnected crack. Cracks mainly developed between the aggregate and asphalt mortar, near the loading axis. The corresponding stages of failure, the developing trend and the distribution characteristics of the cracks matched well with those in the laboratory test. Furthermore, the trends of both the time-load curve and time-displacement curve from the simulation test were also consistent with those from the experimental test. In short, the distribution characteristics of cracks and internal forces of asphalt mixture show that it is feasible to simulate the fatigue performance of the asphalt mixture by a discrete element method (DEM)

Temperature segregation of warm mix asphalt pavement: Laboratory and field evaluations

© 2017 Elsevier Ltd Temperature segregation refers to as different mixture cooling areas during construction in asphalt pavements. The objective of this study is to evaluate the effect of temperature segregation on warm mix asphalt (WMA) with laboratory and field tests. The performance of WMA compacted at four various temperatures was evaluated in the laboratory. The temperatures were measured during construction in the field sections with infrared thermography and plug-in thermometers. The pavement quality indicator (PQI) was applied to measure the density and the air void content at 216 testing locations the day after construction. In addition, field cores were collected to verify some of the PQI results. The test results showed that temperature segregation of WMA had a remarkable effect on the aggregate structure, density, water stability, high temperature stability, low temperature cracking and tensile strength. The reason for temperature segregation and related preventive measures are recommended at the same time. Based on the study, the preliminary temperature segregation criteria are recommended with the consideration of the field measurement. In application, the temperature segregation of a typical gradation with a nominal maximum aggregate size of 19 mm, referred to as AC-20 WMA, was suggested to be divided into four levels in view of the air void content: no segregation, low-level segregation, medium-level segregation and high-level segregation. The corresponding temperature differences were \u3c 3 °C, 3–8 °C, 8–18 °C and \u3e 18 °C, respectively

Crack resistance of waste cooking oil modified cement stabilized macadam

Application of waste cooking oil (WCO) in transportation infrastructure has great potential to significantly improve clean production practice in industry. In view of the successful use of WCO modified asphalt mixture, this study investigates the potential of incorporating WCO into cement stabilized macadam. The study first investigated the macro and micro structural properties of the WCO modified cement stabilized macadam in the laboratory, then a test road was paved to evaluate its performance. The preliminary results indicated that both the initial compressive strength and splitting strength of the WCO modified macadam was decreased, but their strength results were close to those of the control with age. Oil type had a significant effect on the splitting strength, but only a small influence on the compressive strength. The compressive resilient modulus of the WCO modified macadams was decreased due to the increasing flexibility. The dry shrinkage test showed that WCO could effectively reduce the dry shrinkage coefficient of the cement stabilized macadam. Moreover, the fatigue cracking resistance of WCO modified macadams was better than that of the control. One possible reason for the improved cracking resistance of WCO modified macadams was that cracks were filled or separated into smaller cracks by C–S–H glue with age, as shown by scanning electron microscopy images. The field test application reveals that the WCO modified cement stabilized macadam subbase is an acceptable and economical alternative for roadway construction

Homogeneity evaluation of hot in-place recycling asphalt mixture using digital image processing technique

Hot in-place recycling (HIR) allows 100% reuse of reclaimed asphalt pavement (RAP) directly on a construction site. However, the homogeneity of the HIR is difficult to be evaluated due to the complexity of the material composition and construction process. In this study, in view of the homogeneity of the HIR can be reflected by the mixing quality of virgin and RAP aggregates, the homogeneity of virgin and RAP aggregates was investigated. Firstly, the Marshall test specimens of an HIR asphalt mixture were prepared and saw-cut, and the microstructure of each cross section was extracted using digital image processing (DIP) technique, including image enhancement, iterative threshold segmentation and maximum between-class variance (OTSU threshold), retention of the green channel, and image morphology. Then, each cross section of the specimen was divided into 36 regions of equal area by an annular segmentation with sector segmentation. Based on the coefficient of variation in the area ratio of the virgin aggregate to RAP aggregate, a homogeneity coefficient of HIR asphalt mixture was proposed. Another nine groups of Marshall specimens were prepared and cut, and the homogeneity coefficient of each group was calculated. The results showed that the virgin and RAP aggregates in the cross section could be effectively identified due to different gray values by retaining the green channel. The characteristics of the virgin and RAP aggregates could be comprehensively described using annular segmentation combined with sector segmentation. The related macro qualitative test showed that the aggregate in the asphalt mixture could be accurately extracted by the threshold segmentation method based on annular segmentation combined with the OTSU method. The homogeneity could be accurately and quantitatively evaluated by a homogeneity coefficient based on the area ratio of the virgin and RAP aggregates in each cross section. An improvement in the homogeneity of the virgin and RAP aggregates was achieved with an increase in the heating temperature of RAP and mixing time. However, no further improvement was noticed as the heating temperature and mixing time increased. In short, the quantitative homogeneity evaluation index of virgin and RAP aggregates presented in this study, reflecting the homogeneity of HIR asphalt mixture, is helpful for controlling the quality of the HIR asphalt pavement

DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids

Allopolyploidization, which entails interspecific hybridization and whole genome duplication (WGD), is associated with emergent genetic and epigenetic instabilities that are thought to contribute to adaptation and evolution. One frequent genomic consequence of nascent allopolyploidization is homoeologous exchange (HE), which arises from compromised meiotic fidelity and generates genetically and phenotypically variable progenies. Here, we used a genetically tractable synthetic rice segmental allotetraploid system to interrogate genome‐wide DNA methylation and gene expression responses and outcomes to the separate and combined effects of hybridization, WGD and HEs. Progenies of the tetraploid rice were genomically diverse due to genome‐wide HEs that affected all chromosomes, yet they exhibited overall methylome stability. Nonetheless, regional variation of cytosine methylation states was widespread in the tetraploids. Transcriptome profiling revealed genome‐wide alteration of gene expression, which at least in part associates with changes in DNA methylation. Intriguingly, changes of DNA methylation and gene expression could be decoupled from hybridity and sustained and amplified by HEs. Our results suggest that HEs, a prominent genetic consequence of nascent allopolyploidy, can exacerbate, diversify and perpetuate the effects of allopolyploidization on epigenetic and gene expression variation, and hence may contribute to allopolyploid evolution.This is the peer reviewed version of the following article: Li, Ning, Chunming Xu, Ai Zhang, Ruili Lv, Xinchao Meng, Xiuyun Lin, Lei Gong, Jonathan F. Wendel, and Bao Liu. "DNA methylation repatterning accompanying hybridization, whole genome doubling and homoeolog exchange in nascent segmental rice allotetraploids." New Phytologist (2019), which has been published in final form at doi: 10.1111/nph.15820. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. </p

TET2 is required to suppress mTORC1 signaling through urea cycle with therapeutic potential

Abstract Tumor development, involving both cell growth (mass accumulation) and cell proliferation, is a complex process governed by the interplay of multiple signaling pathways. TET2 mainly functions as a DNA dioxygenase, which modulates gene expression and biological functions via oxidation of 5mC in DNA, yet whether it plays a role in regulating cell growth remains unknown. Here we show that TET2 suppresses mTORC1 signaling, a major growth controller, to inhibit cell growth and promote autophagy. Mechanistically, TET2 functions as a 5mC “eraser” by mRNA oxidation, abolishes YBX1–HuR binding and promotes decay of urea cycle enzyme mRNAs, thus negatively regulating urea cycle and arginine production, which suppresses mTORC1 signaling. Therefore, TET2-deficient tumor cells are more sensitive to mTORC1 inhibition. Our results uncover a novel function for TET2 in suppressing mTORC1 signaling and inhibiting cell growth, linking TET2-mediated mRNA oxidation to cell metabolism and cell growth control. These findings demonstrate the potential of mTORC1 inhibition as a possible treatment for TET2-deficient tumors