Genome-Wide DNA Methylation Profiling in Human Breast Tissue by Illumina TruSeq Methyl Capture EPIC Sequencing and Infinium MethylationEPIC Beadchip Microarray

A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P \u3c 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk

Rapid detection and structural characterization of verapamil metabolites in rats by UPLC-MSE and UNIFI platform.

High-resolution mass spectrometry (HRMS) is an important technology for studying biotransformations of drugs in biological systems. In order to process complex HRMS data, bioinformatics, including data-mining techniques for identifying drug metabolites from liquid chromatography/high-resolution mass spectrometry (LC/HRMS) or multistage mass spectrometry (MSn ) datasets as well as elucidating the detected metabolites’ structure by spectral interpretation software, are important tools. Data-mining technologies have widely been used in drug metabolite identification, including mass defect filters, product ion filters, neutral-loss filters, control sample comparisons and extracted ion chromatographic analysis. However, the metabolites identified by current different technologies are not the same, indicating the importance of technique integration for efficient and complete identification of metabolic products. In this study, a universal, high-throughput workflow for identifying and verifying metabolites by applying the drug metabolite identification software UNIFI is reported, to study the biotransformation of verapamil in rats. A total of 71 verapamil metabolites were found in rat plasma, urine and faeces, including two metabolites that have not been reported in the literature. Phase I metabolites of verapamil were identified as N-demethylation, O-demethylation, N-dealkylation and oxidation and dehydrogenation metabolites; phase II metabolites were mainly glucuronidation and sulfate conjugates, indicating that UNIFI software could be effective and valuable in identifying drug metabolites

Effects of different intrusion patterns during anterior teeth retraction using clear aligners in extraction cases: an iterative finite element analysis

BackgroundOvertreatment design of clear aligner treatment (CAT) in extraction cases is currently primarily based on the clinical experience of orthodontists and is not supported by robust evidence on the underlying biomechanics. This study aimed to investigate the biomechanical effects of overtreatment strategies involving different maxillary anterior teeth intrusion patterns during anterior teeth retraction by CAT in extraction cases.Materials and methodsA finite element model of the maxillary dentition with the first premolar extracted was constructed. A loading method of clear aligners (CAs) based on the initial state field was proposed. The iterative method was used to simulate the long-term orthodontic tooth movement under the mechanical load exerted by the CAs. Three groups of CAs were utilized for anterior teeth retraction (G0: control group; G1: incisors intrusion group; G2: anterior teeth intrusion group). Tooth displacement and occlusal plane rotation tendency were analyzed.ResultsIn G0, CAT caused lingual tipping and extrusion of the incisors, distal tipping and extrusion of the canines, mesial tipping, and intrusion of the posterior teeth. In G1, the incisors showed minimal extrusion, whereas the canines showed increased extrusion and distal tipping tendency. G2 showed the smallest degree of posterior occlusal plane angle rotation, while the inclination tendency of the canines and second premolars decreased.Conclusion1. In CAT, tooth displacement tendency may change with increased wear time. 2. During anterior teeth retraction, the incisor intrusion pattern can provide effective vertical control for the lateral incisors but has little effect on the central incisors. Anterior teeth intrusion patterns can alleviate the inclination of canines and second premolars, resulting in partial relief of the roller-coaster effect

Exogenous Melatonin Improves Cold Tolerance of Strawberry (Fragaria × ananassa Duch.) through Modulation of DREB/CBF-COR Pathway and Antioxidant Defense System

The strawberry (Fragaria × ananassa Duch.) is an important fruit crop cultivated worldwide for its unique taste and nutritional properties. One of the major risks associated with strawberry production is cold damage. Recently, melatonin has emerged as a multifunctional signaling molecule that influences plant growth and development and reduces adverse consequences of cold stress. The present study was conducted to investigate the defensive role of melatonin and its potential interrelation with abscisic acid (ABA) in strawberry plants under cold stress. The results demonstrate that melatonin application conferred improved cold tolerance on strawberry seedlings by reducing malondialdehyde and hydrogen peroxide contents under cold stress. Conversely, pretreatment of strawberry plants with 100 μM melatonin increased soluble sugar contents and different antioxidant enzyme activities (ascorbate peroxidase, catalase, and peroxidase) and non-enzymatic antioxidant (ascorbate and glutathione) activities under cold stress. Furthermore, exogenous melatonin treatment stimulated the expression of the DREB/CBF—COR pathways’ downstream genes. Interestingly, ABA treatment did not change the expression of the DREB/CBF—COR pathway. These findings imply that the DREB/CBF-COR pathway confers cold tolerance on strawberry seedlings through exogenous melatonin application. Taken together, our results reveal that melatonin (100 μM) pretreatment protects strawberry plants from the damages induced by cold stress through enhanced antioxidant defense potential and modulating the DREB/CBF—COR pathway. View Full-Tex

The Precambrian Khondalite Belt in the Daqingshan area, North China Craton: evidence for multiple metamorphic events in the Palaeoproterozoic era

High-grade pelitic metasedimentary rocks (khondalites) are widely distributed in the northwestern part of the North China Craton and were named the ‘Khondalite Belt’. Prior to the application of zircon geochronology, a stratigraphic division of the supracrustal rocks into several groups was established using interpretative field geology. We report here SHRIMP U–Pb zircon ages and Hf-isotope data on metamorphosed sedimentary and magmatic rocks at Daqingshan, a typical area of the Khondalite Belt. The main conclusions are as follows: (1) The early Precambrian supracrustal rocks belong to three sequences: a 2.56–2.51 Ga supracrustal unit (the previous Sanggan ‘group’), a 2.51–2.45 Ga supracrustal unit (a portion of the previous upper Wulashan ‘group’) and a 2.0–1.95 Ga supracrustal unit (including the previous lower Wulashan ‘group’, a portion of original upper Wulashan ‘group’ and the original Meidaizhao ‘group’) the units thus do not represent a true stratigraphy; (2) Strong tectono-thermal events occurred during the late Neoarchaean to late Palaeoproterozoic, with four episodes recognized: 2.6–2.5, 2.45–2.37, 2.3–2.0 and 1.95–1.85 Ga, with the latest event being consistent with the assembly of the Palaeoproterozoic supercontinent Columbia; (3) During the late Neoarchaean to late Palaeoproterozoic (2.55–2.5, 2.37 and 2.06 Ga) juvenile, mantle-derived material was added to the crust

Genome-wide DNA methylation profiling in human breast tissue by Illumina TruSeq methyl capture EPIC sequencing and infinium methylationEPIC beadchip microarray

A newly-developed platform, the Illumina TruSeq Methyl Capture EPIC library prep (TruSeq EPIC), builds on the content of the Infinium MethylationEPIC Beadchip Microarray (EPIC-array) and leverages the power of next-generation sequencing for targeted bisulphite sequencing. We empirically examined the performance of TruSeq EPIC and EPIC-array in assessing genome-wide DNA methylation in breast tissue samples. TruSeq EPIC provided data with a much higher density in the regions when compared to EPIC-array (~2.74 million CpGs with at least 10X coverage vs ~752 K CpGs, respectively). Approximately 398 K CpGs were common and measured across the two platforms in every sample. Overall, there was high concordance in methylation levels between the two platforms (Pearson correlation r = 0.98, P < 0.0001). However, we observed that TruSeq EPIC measurements provided a wider dynamic range and likely a higher quantitative sensitivity for CpGs that were either hypo- or hyper-methylated (β close to 0 or 1, respectively). In addition, when comparing different breast tissue types TruSeq EPIC identified more differentially methylated CpGs than EPIC-array, not only out of additional sites interrogated by TruSeq EPIC alone, but also out of common sites interrogated by both platforms. Our results suggest that both platforms show high reproducibility and reliability in genome-wide DNA methylation profiling, while TruSeq EPIC had a significant improvement over EPIC-array regarding genomic resolution and coverage. The wider dynamic range and likely higher precision of the estimates by the TruSeq EPIC may lead to the identification of novel differentially methylated markers that are associated with disease risk

Genome sequences reveal global dispersal routes and suggest convergent genetic adaptations in seahorse evolution

Seahorses have a circum-global distribution in tropical to temperate coastal waters. Yet, seahorses show many adaptations for a sedentary, cryptic lifestyle: they require specific habitats, such as seagrass, kelp or coral reefs, lack pelvic and caudal fins, and give birth to directly developed offspring without pronounced pelagic larval stage, rendering long-range dispersal by conventional means inefficient. Here we investigate seahorses’ worldwide dispersal and biogeographic patterns based on a de novo genome assembly of Hippocampus erectus as well as 358 re-sequenced genomes from 21 species. Seahorses evolved in the late Oligocene and subsequent circum-global colonization routes are identified and linked to changing dynamics in ocean currents and paleo-temporal seaway openings. Furthermore, the genetic basis of the recurring “bony spines” adaptive phenotype is linked to independent substitutions in a key developmental gene. Analyses thus suggest that rafting via ocean currents compensates for poor dispersal and rapid adaptation facilitates colonizing new habitats.Fil: Chunyan, Li. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. Chinese Academy of Sciences; República de ChinaFil: Olave, Melisa. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Provincia de Mendoza. Instituto Argentino de Investigaciones de las Zonas Áridas. Universidad Nacional de Cuyo. Instituto Argentino de Investigaciones de las Zonas Áridas; Argentina. University of Konstanz; AlemaniaFil: Hou, Yali. Chinese Academy of Sciences; República de ChinaFil: Geng, Qi. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; ChinaFil: Schneider, Ralf. University Of Konstanz; Alemania. Helmholtz Centre for Ocean Research Kie; AlemaniaFil: Zeixa, Gao. Huazhong Agricultural University; ChinaFil: Xiaolong, Tu. Allwegene Technologies ; ChinaFil: Xin, Wang. Chinese Academy of Sciences; República de ChinaFil: Furong, Qi. China National Center for Bioinformation; China. University of Chinese Academy of Sciences; ChinaFil: Nater, Alexander. University of Konstanz; AlemaniaFil: Kautt, Andreas F.. University of Konstanz; Alemania. Harvard University; Estados UnidosFil: Wan, Shiming. Chinese Academy of Sciences; República de ChinaFil: Yanhong, Zhang. Chinese Academy of Sciences; República de ChinaFil: Yali, Liu. Chinese Academy of Sciences; República de ChinaFil: Huixian, Zhang. Chinese Academy of Sciences; República de ChinaFil: Bo, Zhang. Chinese Academy of Sciences; República de ChinaFil: Hao, Zhang. Chinese Academy of Sciences; República de ChinaFil: Meng, Qu ,. Chinese Academy of Sciences; República de ChinaFil: Shuaishuai, Liu. Chinese Academy of Sciences; República de ChinaFil: Zeyu, Chen. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Zhong, Jia. Chinese Academy of Sciences; República de ChinaFil: Zhang, He. BGI-Shenzhen; ChinaFil: Meng, Lingfeng. BGI-Shenzhen; ChinaFil: Wang, Kai. Ludong University; ChinaFil: Yin, Jianping. Chinese Academy of Sciences; República de ChinaFil: Huang, Liangmin. Chinese Academy of Sciences; República de China. University of Chinese Academy of Sciences; ChinaFil: Venkatesh, Byrappa. Institute of Molecular and Cell Biology; SingapurFil: Meyer, Axel. University of Konstanz; AlemaniaFil: Lu, Xuemei. Chinese Academy of Sciences; República de ChinaFil: Lin, Qiang. Chinese Academy of Sciences; República de China. Southern Marine Science and Engineering Guangdong Laboratory; China. Pilot National Laboratory for Marine Science and Technology; China. University of Chinese Academy of Sciences; Chin

Local axisymmetry-breaking–induced transition of trapped-particle orbit and loss channels in quasi-axisymmetric stellarators

The transition of trapped-particle orbit topologies has been investigated in quasi-axisymmetric (QA) configurations, such as the Chinese First Quasi-axisymmetric Stellarator (CFQS). It is found that the axisymmetry-breaking phenomenon in QA configurations is of great significance at some specific locations, which could easily induce blocked particles to transit into localized particles. A novel aspect is presented to interpret the transition mechanism of trapped-particle orbit topologies in this paper, i.e., as the amplitudes of non-axisymmetric field increase along the radius direction, the region of large toroidal inhomogeneity is gradually generated, which makes the length of the trapped-particle trajectory substantially short, and hence, may restrict particles to a single helical field period. Meanwhile, at such locations the "pseudo-axisymmetric" field results in coupling of the maximum radial drift and the minimum poloidal drift, which enables the transition of trapped-particle orbit topologies considerably and forms specific loss channels, degrading plasma confinement. These results may shed light on the optimization of QA configurations via avoidance of such coupling with respect to energetic particle confinement. Moreover, this work is also relevant to the generation of inhomogeneity of particle flux deposition on the devertor plates