Functional and evolutionary genomic inferences in <i>Populus</i> through genome and population sequencing of American and European aspen

Lin, Yao-Cheng,Wang, Jing,Delhomme, Nicolas,Schiffthaler, Bastian,Sundströ,m, Gö,rel,Zuccolo, Andrea,Nystedt, Bjö,rn,Hvidsten, Torgeir R.,de la Torre, Amanda,Cossu, Rosa M.,Hoeppner, Marc National Academy of Sciences 2018 PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF Vol.115 No.46

<▼1><P><B>Significance</B></P><P>We performed de novo, full-genome sequence analysis of two <I>Populus</I> species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding regions. The strength of selection and rates of sequence divergence were strongly related to differences in gene expression and coexpression network connectivity. These results highlight the importance of both positive and negative selection in shaping genome-wide levels of genetic variation in an obligately outcrossing, perennial plant. The resources we present establish aspens as a powerful study system enabling future studies for understanding the genomic determinants of adaptive evolution.</P></▼1><▼2><P>The <I>Populus</I> genus is one of the major plant model systems, but genomic resources have thus far primarily been available for poplar species, and primarily <I>Populus trichocarpa</I> (Torr. & Gray), which was the first tree with a whole-genome assembly. To further advance evolutionary and functional genomic analyses in <I>Populus</I>, we produced genome assemblies and population genetics resources of two aspen species, <I>Populus tremula</I> L. and <I>Populus tremuloides</I> Michx. The two aspen species have distributions spanning the Northern Hemisphere, where they are keystone species supporting a wide variety of dependent communities and produce a diverse array of secondary metabolites. Our analyses show that the two aspens share a similar genome structure and a highly conserved gene content with <I>P. trichocarpa</I> but display substantially higher levels of heterozygosity. Based on population resequencing data, we observed widespread positive and negative selection acting on both coding and noncoding regions. Furthermore, patterns of genetic diversity and molecular evolution in aspen are influenced by a number of features, such as expression level, coexpression network connectivity, and regulatory variation. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).</P></▼2>

논문(論文) : 장지동(張之洞)의 「근학편(勤學篇)」 분석

요전덕 ( Chuan De Yao ) 중국사학회 2010 中國史硏究 Vol.64 No.-

Induction of Forkhead Class box O3a and apoptosis by a standardized ginsenoside formulation, KG-135, is potentiated by autophagy blockade in A549 human lung cancer cells

Yao, Chih-Jung,Chow, Jyh-Ming,Chuang, Shuang-En,Chang, Chia-Lun,Yan, Ming-De,Lee, Hsin-Lun,Lai, I-Chun,Lin, Pei-Chun,Lai, Gi-Ming The Korean Society of Ginseng 2017 Journal of Ginseng Research Vol.41 No.3

Background: KG-135, a standardized formulation enriched with Rk1, Rg3, and Rg5 ginsenosides, has been shown to inhibit various types of cancer cells; however, the underlying mechanisms are not fully understood. In this study, we explored its effects in A549 human lung cancer cells to investigate the induction of Forkhead Class box O3a (FOXO3a) and autophagy. Methods: Cell viability was determined by sulforhodamine B staining. Apoptosis and cell cycle distribution were analyzed using flow cytometry. The changes of protein levels were determined using Western blot analysis. Autophagy induction was monitored by the formation of acidic vesicular organelles stained with acridine orange. Results: KG-135 effectively arrested the cells in G1 phase with limited apoptosis. Accordingly, a decrease of cyclin-dependent kinase-4, cyclin-dependent kinase-6, cyclin D1, and phospho-retinoblastoma protein, and an increase of p27 and p18 proteins were observed. Intriguingly, KG-135 increased the tumor suppressor FOXO3a and induced the accumulation of autophagy hallmark LC3-II and acidic vesicular organelles without an increase of the upstream marker Beclin-1. Unconventionally, the autophagy adaptor protein p62 (sequestosome 1) was increased rather than decreased. Blockade of autophagy by hydroxychloroquine dramatically potentiated KG-135-induced FOXO3a and its downstream (FasL) ligand accompanied by the cleavage of caspase-8. Meanwhile, the decrease of Bcl-2 and survivin, as well as the cleavage of caspase-9, were also drastically enhanced, resulting in massive apoptosis. Conclusion: Besides arresting the cells in G1 phase, KG-135 increased FOXO3a and induced an unconventional autophagy in A549 cells. Both the KG-135-activated extrinsic FOXO3a/FasL/caspase-8 and intrinsic caspase-9 apoptotic pathways were potentiated by blockade of autophagy. Combination of KG-135 and autophagy inhibitor may be a novel strategy as an integrative treatment for cancers.

Investigation of the Photoinduced Anisotropy of the Bacteriorhodopsin/Polymer Composite Film by Using Probing-Pumping Beams of Various Wavelengths

Liang-Yao Chen,Su-Xing Pan,Yun-Fei Wu,Lai Wei,Yu-Xiang Zheng,You-Yuan Zhao,De-Wang Ma 한국물리학회 2008 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.53 No.4

We have investigated the probing beam transmitance due to the photon-induced anisotropy effect in the bacteriorhodopsin/polymer composite film(bR/PC film) by using the probing-pumping beam method under different laser wavelengths. By using a theoretical simulation, we give the characteristics of the birefringence Δn and the dichroism ΔD for various wavelengths of the probing and the pumping beams.

Sensor-less external force detection for industrial manipulators to facilitate physical human-robot interaction

Bitao Yao,Zu-De Zhou,Lihui Wang,Wenjun Xu,Quan Liu 대한기계학회 2018 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.32 No.10

Sensor-less external force detection is important for industrial robots which are usually not equipped with external force sensors to be applied in physical human-robot interaction (pHRI). This paper adopts the dynamic models of the robot in both dynamic mode and quasistatic mode to detect the external force. In the dynamic mode, the inertia and friction parameters of the robot are identified with the weighted least squares. The excitation trajectory for parameter identification is optimised. The un-modelled peak points in the joint torque residual are removed by a statistical method. The torque changes of joints in quasi-static mode which are equivalent to the joint pre-sliding friction is modelled with a lumped parameter model, generalised Maxwell slip (GMS) element model. Therefore, there is no need for the switching between the friction models in different modes and this and facilitates the application of dynamic model in the external force detection. The dynamic models of robots both in dynamic mode and quasi-static mode and their effectiveness for external force detection in pHRI are verified by experimental results.

Use of DNA Methylation for Cancer Detection and Molecular Classification (Reviews)

Jing De Zhu,Xue Biao Yao 한국생화학분자생물학회 2007 BMB Reports Vol.40 No.2

Vector Control of Stator-Permanent Magnet Memory Machine Based on Three Magnetization State Manipulations

Gong-De Yang,Ming-Yao Lin,Nian Li,Li Hao 대한전기학회 2019 Journal of Electrical Engineering & Technology Vol.14 No.1

Owing to the estimated permanent magnet (PM) flux linkage fluctuation, the stator-PM memory machine employing the continuous magnetization state (MS) manipulation may suffer from frequent MS manipulations and the accidental inverter damage in its extended speed range. In order to deal with this issue, in this paper, a novel vector control based on three MS manipulations is proposed and implemented on the existing hybrid PM axial field flux-switching memory machine. After a brief analysis of the researched machine configuration, the principle of the three MS manipulations, the remedial sliding mode speed regulator and the current distribution strategy are discussed. The simulated results show that the proposed scheme reduces the speed and electromagnetic torque overshoot and improves the dynamic performance. Meanwhile, compared with the flux-weakening control, the wide speed range can be obtained. Finally, the experiment is carried out to verify the validity of the theory.

Aberrant Expression of miR-20a and miR-203 in Cervical Cancer

Zhao, Shan,Yao, De-Sheng,Chen, Jun-Ying,Ding, Nan Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.4

MicroRNAs (miRNAs) are small, non-coding RNAs that are critical regulators of various diseases. MicroRNA-20a (miR-20a) and microRNA-203 (miR-203) have previously shown significant alteration in a range of cancers. In this study, the expression levels of miR-20a and miR-203 in 100 cervical cancer tissues were detected by qRT-PCR and compared to patient matched-nontumor cervical tissues. Correlations between expression level and clinicopathologic characteristics of cervical cancer were also analyzed. Finally, we studied the effect of miR-20a and miR-203 on cell proliferation in cervical cancer cell lines by MTT. We found that the expression level of miR-20a (P<0.001) was significantly higher in cervical cancer patients than in healthy controls, while that of miR-203 (P<0.001) was lower. Aberrant expression of miR-20a was correlated with lymph node metastasis (LNM), histological grade and tumor diameter, but down-regulated miR-203 was correlated with LNM only. Furthermore, we found that over-expression of miR-203 decreased cell proliferation, while reduction of miR-20a also prevented tumor progression. Our results support the involvement of miR-20a and miR-203 in cervical tumorigenesis. We propose that miRNAs might be used as therapeutic agents for cervical cancer.

Analysis of Volatile Compounds of Jasmine Scented Tea during the Orthodox Manufacturing Process Using HS-SPME/GC-MS

Jian Lu,De-Jun Fu,Dong-Fen Wu,Yu Liu,Yao-Ping Luo 한국차학회 2015 한국차학회지 Vol.- No.S

Volatile components of jasmine-scented tea during the orthodox manufacturing process were extracted using Headspace solid-phase microextraction (HS-SPME) and the major flavor compounds were identified by Gas chromatography-mass spectrometry/Retention indices (GC-MS/RI). The major volatile compounds extracted by SDE could also be obtained by HS-SPME, which appears more suitable for extraction of aromatic compounds, for its advantages of simplicity and convenience. The GC-MS chromatograms of tea samples showed that the aromatic constituents of jasmine tea had been identified in composition after 1st scenting, which contained 6 apparently high peaks representing linalool, benzyl acetate, α-farnesene, (Z)-3-hexenyl benzoate, methyl anthranilate, and indole. According to the change of peak area of major volatile compounds, (Z)-3-hexenyl acetate and (Z)-3-hexenyl butyrate with green grass aroma reduced by 71.13% and 63.10% respectively in jasmine tea product, while 7 compounds with favorable flowery fruity aroma-benzyl acetate, (Z)-3-hexenyl benzoate, linalool, benzyl alcohol, α-farnesene, methyl anthranilate and indole- increased by 17.84%, 28.33 times, 32.49%, 1.70 times, 6.67 times, 11.84 times and 21.48 times respectively, comparing to the base tea. Besides, nerolidol (fruity-flowery) and germacrene D (woody), not detected in the base tea also gradually increased. The quality grade of jasmine tea was potentially correlated to the ratio of peak area of the 9 favorable compounds to that of the 2 grass compounds. After 1st scenting, the peak areas of compounds from jasmine flower increased by 1.81×105-18.24×105, and decreased by 36.14%-69.95% after the 1st drying. The peak areas of some components detected in both the base tea and jasmine flowers, like (Z)-3-hexenyl acetate and methyl salicylate, increased by 9.05%-57.60% of those of the base tea after 1st scenting, and lost more than 100% after the 1st drying, while the increased peak areas of some other components both detected, like α-farnesene and indole, were more than peak areas of the base tea, with 30%- 95% loss after the 1st drying. The content change tendency of volatiles during 2nd scenting and the 2nd drying were consistent with those during 1st scenting and the 1st drying. After raising fragrance, the contents of some low boiling point volatiles and compounds not detected in the base tea increased.

Evaluation and Adjustment Based on Broad Learning System for Small Signal Stability Analysis of Power System Integrated with Wind Farms

Yang Yu-De,Yao Wen-Jing,Yang Li-Zhen 대한전기학회 2022 Journal of Electrical Engineering & Technology Vol.17 No.6

This paper primarily focuses on evaluation and adjustment methods for small signal analysis with wind farm integration. The connection of wind farms may aff ect the original oscillation modes of the system, and may also introduce new oscillation modes. To ensure the security and stability of the system, it is necessary to assess the running state of the system and evaluate the development direction of the small signal stability on the premise of taking volatility into account. It is also important to fast adjust the system when an unstable state happened. The method in this paper provides a new way to accurately evaluate and adjust the stability of the system integrated with wind farms. Broad learning system (BLS) is a non-fi xed model and has the potential of incremental learning. A BLS model is trained to evaluate the damping ratio sensitivity in diff erent operating states. The adjustment part will use the optimal adjustment model and damping ratio sensitivity to adjust unstable systems. The superior performance of the model proposed in this paper is tested by the case study based on the IEEE 3-machine, 9-bus, and the New-England 10-machine, 39-bus. The results demonstrate the feasibility, validity, and eff ectiveness of the method proposed in this article.