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Zhang T, Zhao Y, Juntheikki I, Mouhu K, Broholm SK, Rijpkema AS, Kins L, Lan T, Albert VA, Teeri TH, Elomaa P. Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida. THE NEW PHYTOLOGIST 2017; 216:939-954. [PMID: 28742220 DOI: 10.1111/nph.14707] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 06/17/2017] [Indexed: 05/20/2023]
Abstract
The pseudanthial inflorescences of the sunflower family, Asteraceae, mimic a solitary flower but are composed of multiple flowers. Our studies in Gerbera hybrida indicate functional diversification for SEPALLATA (SEP)-like MADS box genes that often function redundantly in other core eudicots. We conducted phylogenetic and expression analysis for eight SEP-like GERBERA REGULATOR OF CAPITULUM DEVELOPMENT (GRCD) genes, including previously unstudied gene family members. Transgenic gerbera plants were used to infer gene functions. Adding to the previously identified stamen and carpel functions for GRCD1 and GRCD2, two partially redundant genes, GRCD4 and GRCD5, were found to be indispensable for petal development. Stepwise conversion of floral organs into leaves in the most severe RNA interference lines suggest redundant and additive GRCD activities in organ identity regulation. We show conserved and redundant functions for several GRCD genes in regulation of flower meristem maintenance, while functional diversification for three SEP1/2/4 clade genes in regulation of inflorescence meristem patterning was observed. GRCD genes show both specialized and pleiotropic functions contributing to organ differentiation and flower meristem fate, and uniquely, to patterning of the inflorescence meristem. Altogether, we provide an example of how plant reproductive evolution has used conserved genetic modules for regulating the elaborate inflorescence architecture in Asteraceae.
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Chen GH, Mai KJ, Zhou L, Wu RT, Tang XY, Wu JL, He LL, Lan T, Xie QM, Sun Y, Ma JY. Detection and genome sequencing of porcine circovirus 3 in neonatal pigs with congenital tremors in South China. Transbound Emerg Dis 2017; 64:1650-1654. [DOI: 10.1111/tbed.12702] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Indexed: 11/28/2022]
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Chen H, Liu JZ, Hu GJ, Shi LL, Lan T. Promotion of proliferation and metastasis of hepatocellular carcinoma by LncRNA00673 based on the targeted-regulation of notch signaling pathway. EUROPEAN REVIEW FOR MEDICAL AND PHARMACOLOGICAL SCIENCES 2017; 21:3412-3420. [PMID: 28829500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
OBJECTIVE To investigate the relative expression of long non-coding RNA 00673 (lncRNA 00673) in hepatocellular carcinoma (HCC) and HCC cells and study its regulation on the malignant phenotype of HCC cells PATIENTS AND METHODS: Samples of HCC and adjacent tissues from January 2013 to December 2015 were collected. The expression level of lncRNA00673 in HCC tissues and cells was detected by quantitative Real-time polymerase chain reaction (qRT-PCR) assays. lncRNA00673 specific interference sequences were transiently transfected into HCC cells and the effect of HCC cells on the biological behavior of HCC cells was examined by in vitro experiments ((3-(4,5-Dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT assay), flow cytometry, transwell, etc.). A tumor model of nude mice with HCC was established for the study of tumor growth condition of tumor-bearing mice after the interference with lncRNA00673 expression. Changes in expression levels of molecular markers on Notch signaling pathway after the interference with lncRNA00673 were detected by Western blot. RESULTS lncRNA00673 was highly expressed in HCC tissues and cells. MTT results showed that interfering with lncRNA00673 inhibited cell proliferation. Flow cytometry results showed that HCC cell cycle was retarded in G1-G0 phase, thus promoting apoptosis after the interference with lncRNA00673. Western blot results showed that expression levels of molecular markers on Notch signaling pathway were changed after the interference with lncRNA00763. CONCLUSIONS lncRNA00673 is highly expressed in HCC tissues and cells, and can promote the proliferation and metastasis of HCC by the regulation on Notch signaling pathway. lncRNA00673 may be a potential target for the treatment of HCC.
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Haase EM, Kou Y, Sabharwal A, Liao YC, Lan T, Lindqvist C, Scannapieco FA. Erratum to: comparative genomics and evolution of the amylase-binding proteins of oral streptococci. BMC Microbiol 2017; 17:149. [PMID: 28673236 PMCID: PMC5496400 DOI: 10.1186/s12866-017-1060-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 06/27/2017] [Indexed: 11/10/2022] Open
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Wang MY, Liu AD, Zhou C, Hu JQ, Li H, Lan T, Xie JL, Ding WX, Liu WD, Yu CX. A novel approach to estimating the Doppler shift frequency from quadrature mixer output. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:073503. [PMID: 28764541 DOI: 10.1063/1.4991018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Doppler backscattering systems (DBSs) have been widely used in magnetic confinement fusion devices to measure the density fluctuations and propagation velocity of turbulence. However, the received signals of a DBS usually include both zero-order reflection and backscattering components, which results in interference in calculating the Doppler shift frequency from the backscattering components. A novel method is introduced here for estimating the Doppler shift frequency by separating the zero-order reflection and backscattering components using the cross-phase spectrum between the I-signal and Q-signal from a quadrature mixer, based on the difference in symmetrical characteristics between the zero-order reflection and backscattering signal spectra. It is proven that this method is more effective than traditional approaches, such as multiple signal classification and fast Fourier transformation, for extracting Doppler shift information.
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Lin P, Pan P, Lan T. MEDICAL OUTCOME AND UTILIZATION FOR HIP FRACTURE PATIENTS WITH OR WITHOUT OUTPATIENT REHABILITATION. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.847] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Hu JQ, Zhou C, Liu AD, Wang MY, Doyle EJ, Peebles WA, Wang G, Zhang XH, Zhang J, Feng X, Ji JX, Li H, Lan T, Xie JL, Ding WX, Liu WD, Yu CX. An eight-channel Doppler backscattering system in the experimental advanced superconducting tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:073504. [PMID: 28764527 DOI: 10.1063/1.4991855] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Doppler backscattering system can measure the perpendicular velocity and fluctuation amplitude of the density turbulence with intermediate wavenumber. An eight-channel Doppler backscattering system has been installed in the Experimental Advanced Superconducting Tokamak (EAST), which can probe eight different radial locations simultaneously by launching eight fixed frequencies (55, 57.5, 60, 62.5, 67.5, 70, 72.5, 75 GHz) into plasma. The quasi-optical system consists of circular corrugated waveguide transmission, a fixed parabolic mirror, and a rotatable parabolic mirror which are integrated with quasi-optics front-end of the profile reflectometer inside the vacuum vessel. The incidence angle can be chosen from 5° to 12°, and the wavenumber range is 2-15/cm with the wavenumber resolution Δk/k≤0.21. Ray tracing simulations are used to calculate the scattering locations and the perpendicular wavenumber. The dynamic range of this new eight-channel Doppler backscattering system can be as large as 40 dB in the EAST. In this article, the hardware design, the ray tracing, and the preliminary experimental results in the EAST will be presented.
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Haase EM, Kou Y, Sabharwal A, Liao YC, Lan T, Lindqvist C, Scannapieco FA. Comparative genomics and evolution of the amylase-binding proteins of oral streptococci. BMC Microbiol 2017; 17:94. [PMID: 28427348 PMCID: PMC5399409 DOI: 10.1186/s12866-017-1005-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Accepted: 04/08/2017] [Indexed: 01/19/2023] Open
Abstract
Background Successful commensal bacteria have evolved to maintain colonization in challenging environments. The oral viridans streptococci are pioneer colonizers of dental plaque biofilm. Some of these bacteria have adapted to life in the oral cavity by binding salivary α-amylase, which hydrolyzes dietary starch, thus providing a source of nutrition. Oral streptococcal species bind α-amylase by expressing a variety of amylase-binding proteins (ABPs). Here we determine the genotypic basis of amylase binding where proteins of diverse size and function share a common phenotype. Results ABPs were detected in culture supernatants of 27 of 59 strains representing 13 oral Streptococcus species screened using the amylase-ligand binding assay. N-terminal sequences from ABPs of diverse size were obtained from 18 strains representing six oral streptococcal species. Genome sequencing and BLAST searches using N-terminal sequences, protein size, and key words identified the gene associated with each ABP. Among the sequenced ABPs, 14 matched amylase-binding protein A (AbpA), 6 matched amylase-binding protein B (AbpB), and 11 unique ABPs were identified as peptidoglycan-binding, glutamine ABC-type transporter, hypothetical, or choline-binding proteins. Alignment and phylogenetic analyses performed to ascertain evolutionary relationships revealed that ABPs cluster into at least six distinct, unrelated families (AbpA, AbpB, and four novel ABPs) with no phylogenetic evidence that one group evolved from another, and no single ancestral gene found within each group. AbpA-like sequences can be divided into five subgroups based on the N-terminal sequences. Comparative genomics focusing on the abpA gene locus provides evidence of horizontal gene transfer. Conclusion The acquisition of an ABP by oral streptococci provides an interesting example of adaptive evolution. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-1005-7) contains supplementary material, which is available to authorized users.
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Lan T, Naguib HE, Coolens C. Development of a permeable phantom for dynamic contrast enhanced (DCE) imaging quality assurance: material characterization and testing. Biomed Phys Eng Express 2017. [DOI: 10.1088/2057-1976/aa6486] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Zou Z, Liu H, Ding W, Brower D, Li W, Lan T, Zeng L, Yao Y, Yang Y, Jie Y. Opto-Mechanical systems design for polarimeter-interferometer on EAST. FUSION ENGINEERING AND DESIGN 2016. [DOI: 10.1016/j.fusengdes.2016.09.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Liu HQ, Qian JP, Jie YX, Ding WX, Brower DL, Zou ZY, Li WM, Lian H, Wang SX, Yang Y, Zeng L, Lan T, Yao Y, Hu LQ, Zhang XD, Wan BN. Initial measurements of plasma current and electron density profiles using a polarimeter/interferometer (POINT) for long pulse operation in EAST (invited). THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:11D903. [PMID: 27910346 DOI: 10.1063/1.4963378] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
A double-pass, radially viewing, far-infrared laser-based POlarimeter-INTerferometer (POINT) system utilizing the three-wave technique has been implemented for diagnosing the plasma current and electron density profiles in the Experimental Advanced Superconducting Tokamak (EAST). POINT has been operated routinely during the most recent experimental campaign and provides continuous 11 chord line-integrated Faraday effect and density measurement throughout the entire plasma discharge for all heating schemes and all plasma conditions (including ITER relevant scenario development). Reliability of both the polarimetric and interferometric measurements is demonstrated in 25 s plasmas with H-mode and 102 s long-pulse discharges. Current density, safety factor (q), and electron density profiles are reconstructed using equilibrium fitting code (EFIT) with POINT constraints for the plasma core.
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Zou ZY, Liu HQ, Li WM, Lian H, Wang SX, Yao Y, Lan T, Zeng L, Jie YX. Optical configuration optimization and calibration for the POINT system on EAST. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2016; 87:11E121. [PMID: 27910327 DOI: 10.1063/1.4961272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Calibration of the polarimeter system is one of the key elements to determine the overall measurement accuracy. The anisotropic reflection and transmission properties of the mesh beam splitters can easily distort the polarization state of the circularly polarized beams. Using a rotating crystal quartz λ/2-waveplate to replace the plasma can effectively allow us to obtain the ratio of the measured Faraday rotation angle to the known rotation angle of the waveplate. This ratio is used to estimate the calibration factor for each chord to be accurately determined and help to minimize distortions introduced by the wire-mesh beam splitters. With the novel configuration optimization, the distortion of polarization state is effectively eliminated.
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Hu X, Lan T, Dai D, Xu RA, Yuan L, Zhou Q, Li Y, Cai J, Hu G. Evaluation of 24 CYP2D6 Variants on the Metabolism of Nebivolol In Vitro. Drug Metab Dispos 2016; 44:1828-1831. [DOI: 10.1124/dmd.116.071811] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 08/17/2016] [Indexed: 11/22/2022] Open
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Deng Z, Wang H, Niu W, Lan T, Wang K, Zhan H. [Development and Validation of a Three-Dimensional Finite Element Model of Inferior Cervical Spinal Segments C(4-7) for a Healthy Person]. SHENG WU YI XUE GONG CHENG XUE ZA ZHI = JOURNAL OF BIOMEDICAL ENGINEERING = SHENGWU YIXUE GONGCHENGXUE ZAZHI 2016; 33:652-658. [PMID: 29714902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
This study aims to develop and validate a three-dimensional finite element model of inferior cervical spinal segments C4-7of a healthy volunteer,and to provide a computational platform for investigating the biomechanical mechanism of treating cervical vertebra disease with Traditional Chinese Traumotology Manipulation(TCTM).A series of computed tomography(CT)images of C4-7segments were processed to establish the finite element model using softwares Mimics 17.0,Geromagic12.0,and Abaqus 6.13.A reference point(RP)was created on the endplate of C4 and coupled with all nodes of C4.All loads(±0.5,±1,±1.5and±2Nm)were added to the RP for the six simulations(flexion,extension,lateral bending and axial rotation).Then,the range of motion of each segment was calculated and compared with experimental measurements of in vitro studies.On the other hand,1Nm moment was loaded on the model to observe the main stress regions of the model in different status.We successfully established a detail model of inferior cervical spinal segments C4-7of a healthy volunteer with 591 459 elements and 121 446 nodes which contains the structure of the vertebra,intervertebral discs,ligaments and facet joints.The model showed an accordance result after the comparison with the in vitro studies in the six simulations.Moreover,the main stress region occurred on the model could reflect the main stress distribution of normal human cervical spine.The model is accurate and realistic which is consistent with the biomechanical properties of the cervical spine.The model can be used to explore the biomechanical mechanism of treating cervical vertebra disease with TCTM.
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Brennan MA, Lan T, Brennan CS. Synergistic Effects of Barley, Oat and Legume Material on Physicochemical and Glycemic Properties of Extruded Cereal Breakfast Products. J FOOD PROCESS PRES 2015. [DOI: 10.1111/jfpp.12617] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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Zhang XH, Liu AD, Zhou C, Hu JQ, Wang MY, Yu CX, Liu WD, Li H, Lan T, Xie JL. Influence of lithium coating on the optics of Doppler backscatter system. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:103503. [PMID: 26520951 DOI: 10.1063/1.4932185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This paper presents the first investigation of the effect of lithium coating on the optics of Doppler backscattering. A liquid lithium limiter has been applied in the Experimental Advanced Superconducting Tokamak (EAST), and a Doppler backscattering has been installed in the EAST. A parabolic mirror and a flat mirror located in the vacuum vessel are polluted by lithium. An identical optical system of the Doppler backscattering is set up in laboratory. The power distributions of the emission beam after the two mirrors with and without lithium coating (cleaned before and after), are measured at three different distances under four incident frequencies. The results demonstrate that the influence of the lithium coating on the power distributions are very slight, and the Doppler backscattering can work normally under the dosage of lithium during the 2014 EAST campaign.
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Yuan JL, Wang SM, Lan T, Liu JZ, Wang GH, Sun QS, Chen H. Studies on Anti-Hepatoma Effect of Gan-Ai-Xiao Decoction. TROP J PHARM RES 2015. [DOI: 10.4314/tjpr.v14i7.18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Chen J, Lan T, Zhang W, Dong L, Kang N, Zhang S, Fu M, Liu B, Liu K, Zhang C, Hou J, Zhan Q. Platelet-activating factor receptor-mediated PI3K/AKT activation contributes to the malignant development of esophageal squamous cell carcinoma. Oncogene 2015; 34:5114-27. [PMID: 25639872 DOI: 10.1038/onc.2014.434] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2014] [Revised: 10/16/2014] [Accepted: 11/08/2014] [Indexed: 12/22/2022]
Abstract
Esophageal squamous cell carcinoma (ESCC) is one of the most common malignancies worldwide and occurs at a relatively high frequency in China, yet the mechanisms underlying its devastating outcome remain unclear. Here we report that platelet-activating factor receptor (PAFR), a type of G-protein-coupled receptor, was upregulated in ESCC tumors and cell lines, compared with controls; PAFR levels were positively correlated with ESCC clinical stages and survival time. Overexpression of PAFR promoted the malignant development of ESCC in vitro and in vivo, whereas depletion of PAFR suppressed these effects. Interestingly, PAFR was observed to activate PI3K/AKT (phosphatidylinositol 3-kinase/AKT) through the upregulation of FAK kinase activity. AKT-triggered nuclear factor-κB transcriptionally activated PAFR expression. This mutual positive regulation between PAFR and AKT was required for the aggressiveness of ESCC cells both in vitro and in vivo. Furthermore, treating mice bearing ESCC tumors with cholesterol-conjugated PAFR small interfering RNA effectively inhibited tumor progression and the expression of AKT-mediated oncogenic proteins. Taken together, we made the first demonstration that dysregulation of PAFR and the positive regulatory loop between PAFR and pAKT contribute to malignant progression of ESCC.
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Yang Y, Li GS, Liu HQ, Jie YX, Ding WX, Brower DL, Zhu X, Wang ZX, Zeng L, Zou ZY, Wei XC, Lan T. Design of vibration compensation interferometer for Experimental Advanced Superconducting Tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:11D404. [PMID: 25430167 DOI: 10.1063/1.4886455] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A vibration compensation interferometer (wavelength at 0.532 μm) has been designed and tested for Experimental Advanced Superconducting Tokamak (EAST). It is designed as a sub-system for EAST far-infrared (wavelength at 432.5 μm) poloarimeter/interferometer system. Two Acoustic Optical Modulators have been applied to produce the 1 MHz intermediate frequency. The path length drift of the system is lower than 2 wavelengths within 10 min test, showing the system stability. The system sensitivity has been tested by applying a periodic vibration source on one mirror in the system. The vibration is measured and the result matches the source period. The system is expected to be installed on EAST by the end of 2014.
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Zou ZY, Liu HQ, Jie YX, Ding WX, Brower DL, Wang ZX, Shen JS, An ZH, Yang Y, Zeng L, Wei XC, Li GS, Zhu X, Lan T. Optical layout and mechanical structure of polarimeter-interferometer system for Experimental Advanced Superconducting Tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:11D409. [PMID: 25430172 DOI: 10.1063/1.4890400] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A Far-InfaRed (FIR) three-wave POlarimeter-INTerferometer (POINT) system for measurement current density profile and electron density profile is under development for the EAST tokamak. The FIR beams are transmitted from the laser room to the optical tower adjacent to EAST via ∼20 m overmoded dielectric waveguide and then divided into 5 horizontal chords. The optical arrangement was designed using ZEMAX, which provides information on the beam spot size and energy distribution throughout the optical system. ZEMAX calculations used to optimize the optical layout design are combined with the mechanical design from CATIA, providing a 3D visualization of the entire POINT system.
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Liu HQ, Jie YX, Ding WX, Brower DL, Zou ZY, Li WM, Wang ZX, Qian JP, Yang Y, Zeng L, Lan T, Wei XC, Li GS, Hu LQ, Wan BN. Faraday-effect polarimeter-interferometer system for current density measurement on EAST. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2014; 85:11D405. [PMID: 25430168 DOI: 10.1063/1.4889777] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
A multichannel far-infrared laser-based POlarimeter-INTerferometer (POINT) system utilizing the three-wave technique is under development for current density and electron density profile measurements in the EAST tokamak. Novel molybdenum retro-reflectors are mounted in the inside wall for the double-pass optical arrangement. A Digital Phase Detector with 250 kHz bandwidth, which will provide real-time Faraday rotation angle and density phase shift output, have been developed for use on the POINT system. Initial calibration indicates the electron line-integrated density resolution is less than 5 × 10(16) m(-2) (∼2°), and the Faraday rotation angle rms phase noise is <0.1°.
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Denoeud F, Carretero-Paulet L, Dereeper A, Droc G, Guyot R, Pietrella M, Zheng C, Alberti A, Anthony F, Aprea G, Aury JM, Bento P, Bernard M, Bocs S, Campa C, Cenci A, Combes MC, Crouzillat D, Da Silva C, Daddiego L, De Bellis F, Dussert S, Garsmeur O, Gayraud T, Guignon V, Jahn K, Jamilloux V, Joët T, Labadie K, Lan T, Leclercq J, Lepelley M, Leroy T, Li LT, Librado P, Lopez L, Muñoz A, Noel B, Pallavicini A, Perrotta G, Poncet V, Pot D, Priyono, Rigoreau M, Rouard M, Rozas J, Tranchant-Dubreuil C, VanBuren R, Zhang Q, Andrade AC, Argout X, Bertrand B, de Kochko A, Graziosi G, Henry RJ, Jayarama, Ming R, Nagai C, Rounsley S, Sankoff D, Giuliano G, Albert VA, Wincker P, Lashermes P. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis. Science 2014; 345:1181-4. [PMID: 25190796 DOI: 10.1126/science.1255274] [Citation(s) in RCA: 336] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Coffee is a valuable beverage crop due to its characteristic flavor, aroma, and the stimulating effects of caffeine. We generated a high-quality draft genome of the species Coffea canephora, which displays a conserved chromosomal gene order among asterid angiosperms. Although it shows no sign of the whole-genome triplication identified in Solanaceae species such as tomato, the genome includes several species-specific gene family expansions, among them N-methyltransferases (NMTs) involved in caffeine production, defense-related genes, and alkaloid and flavonoid enzymes involved in secondary compound synthesis. Comparative analyses of caffeine NMTs demonstrate that these genes expanded through sequential tandem duplications independently of genes from cacao and tea, suggesting that caffeine in eudicots is of polyphyletic origin.
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Juntheikki-Palovaara I, Tähtiharju S, Lan T, Broholm SK, Rijpkema AS, Ruonala R, Kale L, Albert VA, Teeri TH, Elomaa P. Functional diversification of duplicated CYC2 clade genes in regulation of inflorescence development in Gerbera hybrida (Asteraceae). THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 79:783-96. [PMID: 24923429 DOI: 10.1111/tpj.12583] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 05/26/2014] [Accepted: 06/03/2014] [Indexed: 05/19/2023]
Abstract
The complex inflorescences (capitula) of Asteraceae consist of different types of flowers. In Gerbera hybrida (gerbera), the peripheral ray flowers are bilaterally symmetrical and lack functional stamens while the central disc flowers are more radially symmetrical and hermaphroditic. Proteins of the CYC2 subclade of the CYC/TB1-like TCP domain transcription factors have been recruited several times independently for parallel evolution of bilaterally symmetrical flowers in various angiosperm plant lineages, and have also been shown to regulate flower-type identity in Asteraceae. The CYC2 subclade genes in gerbera show largely overlapping gene expression patterns. At the level of single flowers, their expression domain in petals shows a spatial shift from the dorsal pattern known so far in species with bilaterally symmetrical flowers, suggesting that this change in expression may have evolved after the origin of Asteraceae. Functional analysis indicates that GhCYC2, GhCYC3 and GhCYC4 mediate positional information at the proximal-distal axis of the inflorescence, leading to differentiation of ray flowers, but that they also regulate ray flower petal growth by affecting cell proliferation until the final size and shape of the petals is reached. Moreover, our data show functional diversification for the GhCYC5 gene. Ectopic activation of GhCYC5 increases flower density in the inflorescence, suggesting that GhCYC5 may promote the flower initiation rate during expansion of the capitulum. Our data thus indicate that modification of the ancestral network of TCP factors has, through gene duplications, led to the establishment of new expression domains and to functional diversification.
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Chamala S, Chanderbali AS, Der JP, Lan T, Walts B, Albert VA, dePamphilis CW, Leebens-Mack J, Rounsley S, Schuster SC, Wing RA, Xiao N, Moore R, Soltis PS, Soltis DE, Barbazuk WB. Assembly and Validation of the Genome of the Nonmodel Basal Angiosperm Amborella. Science 2013; 342:1516-7. [DOI: 10.1126/science.1241130] [Citation(s) in RCA: 77] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
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Zhou C, Liu AD, Zhang XH, Hu JQ, Wang MY, Li H, Lan T, Xie JL, Sun X, Ding WX, Liu WD, Yu CX. Microwave Doppler reflectometer system in the Experimental Advanced Superconducting Tokamak. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2013; 84:103511. [PMID: 24182112 DOI: 10.1063/1.4825344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
A Doppler reflectometer system has recently been installed in the Experimental Advanced Superconducting (EAST) Tokamak. It includes two separated systems, one for Q-band (33-50 GHz) and the other for V-band (50-75 GHz). The optical system consists of a flat mirror and a parabolic mirror which are optimized to improve the spectral resolution. A synthesizer is used as the source and a 20 MHz single band frequency modulator is used to get a differential frequency for heterodyne detection. Ray tracing simulations are used to calculate the scattering location and the perpendicular wave number. In EAST last experimental campaign, the Doppler shifted signals have been obtained and the radial profiles of the perpendicular propagation velocity during L-mode and H-mode are calculated.
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