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714 results on '"C Y Li"'

701. Revisiting the intraseasonal, interannual and interdecadal variability of tropical cyclones in the western North Pacific

Author

Richard C. Y. LI and Wen ZHOU

Subjects
Tropical cylones, intraseasonal oscillation, ENSO, Pacific–Japan teleconnection, Environmental sciences, GE1-350, Oceanography, GC1-1581
Abstract

This paper reviews the recent progress and research on the variability of tropical cyclones (TCs) at different time scales. Specific focus is placed on how different types of external forcings or climatic oscillations contribute to TC variability in the western North Pacific (WNP). At the intraseasonal scale, recent advances on the distinctive impacts of the Madden–Julian Oscillation (MJO), the Quasi-biweekly Oscillation, and the asymmetric MJO modulation under different El Niño–Southern Oscillation (ENSO) states, as well as the influences of the Pacific–Japan teleconnection, are highlighted. Interannually, recent progress on the influences of the ENSO cycle, different flavors of ENSO, and impacts of Indian Ocean warming is presented. In addition, the uncertainty concerning interdecadal TC variations is discussed, along with the recently proposed modulation mechanisms related to the zonal sea surface temperature gradient, the North Pacific Gyre Oscillation, and the Pacific Decadal Oscillation (PDO). It is hoped that this study can deepen our understanding and provide information that the scientific community can use to improve the seasonal forecasting of TCs in the WNP.

Published
2018
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702. Shrimp (Pandalopsis dispar) waste hydrolysate as a source of novel β–secretase inhibitors

Author

Eunice C. Y. Li-Chan, Imelda W. Y. Cheung, and Hee-Guk Byun

Subjects
Alzheimer’s disease, β–secretase inhibitory activity, Shrimp waste hydrolysates, Peptide, Aquaculture. Fisheries. Angling, SH1-691
Abstract

Abstract In this study, purified peptides from shrimp waste hydrolysates (SWHs) were examined for their inhibitory effects against β–secretase. During consecutive purification using a Sephadex G–25 column chromatography and high performance liquid chromatography on a C18 column, a potent β–secretase inhibitory peptide Asp–Val–Leu–Phe–His (629 Da) was isolated and identified from SWH24 by Q–TOF MS/MS and the IC50 value was determined to be 92.70 μM. The β–secretase inhibition patterns of the purified peptides were found to be competitive. Among synthesized β–secretase inhibitory peptides, Leu–Phe–His had higher β–secretase inhibitory activity than the others. The result of this study suggests that the β–secretase inhibitory peptide derived from SWH24 could be potential candidates to develop nutraceuticals and pharmaceuticals.

Published
2016
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703. FTTH and Two-Band RoF Transport Systems Based on an Optical Carrier and Colorless Wavelength Separators

Author

C. H. Chang, P. C. Peng, Q. Huang, W. Y. Yang, H. L. Hu, W. C. Wu, J. H. Huang, C. Y. Li, H. H. Lu, and H. H. Yee

Subjects
Radio over fiber (RoF), phase modulation, polarization modulation, polarization beam splitter, Applied optics. Photonics, TA1501-1820, Optics. Light, QC350-467
Abstract

A hybrid fiber-to-the-home (FTTH) and radio-over-fiber (RoF) transport system is proposed to transmit one wired signal and two wireless signals simultaneously through an optical lightwave. By properly utilizing the polarization characteristic of a phase-remodulated and polarization-remodulated optical lightwave, the first- and second-order sidebands of the lightwave can be colorlessly separated for optical double- and quadruple-frequency RoF transmissions. Experimental results prove that the independent FTTH and two-band RoF signals can be simultaneously generated and separated by relatively low-frequency radio-frequency devices, optical modulators, and polarization beam splitters. The transmission performances are proven by proper bit error rate (BER) performance and clear eye and constellation diagrams. The interference among the transmitted wired signal and double- and quadruple-frequency RoF signals is acceptable. In this case, the wavelength of the optical carrier can be flexibly assigned, and the frequency of the transmitted wireless signals can be easily adjusted without affecting the functionality of the developed optical fiber transport system. The presented architecture can be flexibly employed to support various types of FTTH and microwave and millimeter-wave over fiber transmissions.

Published
2016
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704. An overview of in-orbit radiometric calibration of typical satellite sensors

Author

G. Q. Zhou, C. Y. Li, T. Yue, L. J. Jiang, N. Liu, Y. Sun, and M. Y. Li

Subjects
Technology, Engineering (General). Civil engineering (General), TA1-2040, Applied optics. Photonics, TA1501-1820
Abstract

This paper reviews the development of in-orbit radiometric calibration methods in the past 40 years. It summarizes the development of in-orbit radiometric calibration technology of typical satellite sensors in the visible/near-infrared bands and the thermal infrared band. Focuses on the visible/near-infrared bands radiometric calibration method including: Lamp calibration and solar radiationbased calibration. Summarizes the calibration technology of Landsat series satellite sensors including MSS, TM, ETM+, OLI, TIRS; SPOT series satellite sensors including HRV, HRS. In addition to the above sensors, there are also summarizing ALI which was equipped on EO-1, IRMSS which was equipped on CBERS series satellite. Comparing the in-orbit radiometric calibration technology of different periods but the same type satellite sensors analyzes the similarities and differences of calibration technology. Meanwhile summarizes the in-orbit radiometric calibration technology in the same periods but different country satellite sensors advantages and disadvantages of calibration technology.

Published
2015
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705. Effects of Defaunation on Fermentation Characteristics and Methane Production by Rumen Microbes When Incubated with Starchy Feed Sources

Author

W. Z. Qin, C. Y. Li, J. K. Kim, J. G. Ju, and M. K. Song

Subjects
Defaunation, Grains, Fermentation, Degradation, Total Gas, CH, Animal culture, SF1-1100, Animal biochemistry, QP501-801
Abstract

An in vitro experiment was conducted to examine the effects of defaunation (removal of protozoa) on ruminal fermentation characteristics, CH4 production and degradation by rumen microbes when incubated with cereal grains (corn, wheat and rye). Sodium lauryl sulfate as a defaunation reagent was added into the culture solution at a concentration of 0.000375 g/ml, and incubated anaerobically for up to 12 h at 39°C. Following defaunation, live protozoa in the culture solution were rarely observed by microscopic examination. A difference in pH was found among grains regardless of defaunation at all incubation times (p

Published
2012
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706. Observation of a Dissipative Phase Transition in a One-Dimensional Circuit QED Lattice

Author

Mattias Fitzpatrick, Neereja M. Sundaresan, Andy C. Y. Li, Jens Koch, and Andrew A. Houck

Subjects
Physics, QC1-999
Abstract

Condensed matter physics has been driven forward by significant experimental and theoretical progress in the study and understanding of equilibrium phase transitions based on symmetry and topology. However, nonequilibrium phase transitions have remained a challenge, in part due to their complexity in theoretical descriptions and the additional experimental difficulties in systematically controlling systems out of equilibrium. Here, we study a one-dimensional chain of 72 microwave cavities, each coupled to a superconducting qubit, and coherently drive the system into a nonequilibrium steady state. We find experimental evidence for a dissipative phase transition in the system in which the steady state changes dramatically as the mean photon number is increased. Near the boundary between the two observed phases, the system demonstrates bistability, with characteristic switching times as long as 60 ms—far longer than any of the intrinsic rates known for the system. This experiment demonstrates the power of circuit QED systems for studying nonequilibrium condensed matter physics and paves the way for future experiments exploring nonequilbrium physics with many-body quantum optics.

Published
2017
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707. Resummation for Nonequilibrium Perturbation Theory and Application to Open Quantum Lattices

Author

Andy C. Y. Li, F. Petruccione, and Jens Koch

Subjects
Physics, QC1-999
Abstract

Lattice models of fermions, bosons, and spins have long served to elucidate the essential physics of quantum phase transitions in a variety of systems. Generalizing such models to incorporate driving and dissipation has opened new vistas to investigate nonequilibrium phenomena and dissipative phase transitions in interacting many-body systems. We present a framework for the treatment of such open quantum lattices based on a resummation scheme for the Lindblad perturbation series. Employing a convenient diagrammatic representation, we utilize this method to obtain relevant observables for the open Jaynes-Cummings lattice, a model of special interest for open-system quantum simulation. We demonstrate that the resummation framework allows us to reliably predict observables for both finite and infinite Jaynes-Cummings lattices with different lattice geometries. The resummation of the Lindblad perturbation series can thus serve as a valuable tool in validating open quantum simulators, such as circuit-QED lattices, currently being investigated experimentally.

Published
2016
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708. Imaging Photon Lattice States by Scanning Defect Microscopy

Author

D. L. Underwood, W. E. Shanks, Andy C. Y. Li, Lamia Ateshian, Jens Koch, and A. A. Houck

Subjects
Physics, QC1-999
Abstract

Microwave photons inside lattices of coupled resonators and superconducting qubits can exhibit surprising matterlike behavior. Realizing such open-system quantum simulators presents an experimental challenge and requires new tools and measurement techniques. Here, we introduce scanning defect microscopy as one such tool and illustrate its use in mapping the normal-mode structure of microwave photons inside a 49-site kagome lattice of coplanar waveguide resonators. Scanning is accomplished by moving a probe equipped with a sapphire tip across the lattice. This locally perturbs resonator frequencies and induces shifts of the lattice resonance frequencies, which we determine by measuring the transmission spectrum. From the magnitude of mode shifts, we can reconstruct photon field amplitudes at each lattice site and thus create spatial images of the photon-lattice normal modes.

Published
2016
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709. Electrochemical Deposition and Formation Mechanism of Single-Crystalline Cu2O Octahedra on Aluminum

Author

Q. T. Du, J. S. Tan, Q. T. Wang, C. Y. Li, X. H. Liu, R. S. Cai, Y. H. Ding, and Y. Q. Wang

Subjects
Analytical chemistry, QD71-142
Abstract

A simple electrochemical deposition was developed to synthesize the cuprous oxide (Cu2O) octahedra on aluminum foils. The average edge length of the octahedra is about 300 nm. The chemical composition of the octahedra was determined using energy dispersive X-ray spectroscopy and electron energy-loss spectroscopy. The microstructure of the octahedra was investigated using transmission electron microscopy. The formation mechanism of the octahedra is proposed.

Published
2012
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710. Macromolecular Interactions in Food Technology

Author

NICHOLAS PARRIS, AKIO KATO, LAWRENCE K. CREAMER, JOHN PEARCE, Vladimir Tolstoguzov, Eunice C. Y. Li-Chan, M. G. Semenova, D. J. Oldfield, Harjinder Singh, M. W. Taylor, K. N. Pearce, H. M. Farrell, P. H. Cooke, G. King, P. D. Hoagland, M. L. Groves, T. F. Kumosinski, B. Chu, Susan D. Arntfield, N. Matsudomi, T. Oshita, Yoshinori Mine, Jacquiline Gezimati, S. F. Wang, A. B. Smyth, D. M. Smith, Tara Habig McHugh, M. Shimizu, M. Saito, Harold E. Swaisgood, Xiaolin L. Huang, George L. Catignani, V. B. Galazka, D. A. Ledward, Eric Dickinson, Fakhrieh Vojdani, John R. Whitaker, Takayoshi Aoki, S. Nakamura, H. Takasaki, S. Maki, S. Utsumi, A. B. Gidamis, Y. Takenaka, N. Maruyama, M. Adachi, B. Mikami, Katsuya Seguro, Noriki Nio, Masao Motoki, Jeremy P. Hill, Mike J. Boland, Skelte G. Anema, Don E. Otter, Geoff R. Paterson, Ruth Lowe, Rose L. Motion, Wayne C. Thresher, NICHOLAS PARRIS, AKIO KATO, LAWRENCE K. CREAMER, JOHN PEARCE, Vladimir Tolstoguzov, Eunice C. Y. Li-Chan, M. G. Semenova, D. J. Oldfield, Harjinder Singh, M. W. Taylor, K. N. Pearce, H. M. Farrell, P. H. Cooke, G. King, P. D. Hoagland, M. L. Groves, T. F. Kumosinski, B. Chu, Susan D. Arntfield, N. Matsudomi, T. Oshita, Yoshinori Mine, Jacquiline Gezimati, S. F. Wang, A. B. Smyth, D. M. Smith, Tara Habig McHugh, M. Shimizu, M. Saito, Harold E. Swaisgood, Xiaolin L. Huang, George L. Catignani, V. B. Galazka, D. A. Ledward, Eric Dickinson, Fakhrieh Vojdani, John R. Whitaker, Takayoshi Aoki, S. Nakamura, H. Takasaki, S. Maki, S. Utsumi, A. B. Gidamis, Y. Takenaka, N. Maruyama, M. Adachi, B. Mikami, Katsuya Seguro, Noriki Nio, Masao Motoki, Jeremy P. Hill, Mike J. Boland, Skelte G. Anema, Don E. Otter, Geoff R. Paterson, Ruth Lowe, Rose L. Motion, and Wayne C. Thresher

Subjects
Macromolecules--Congresses, Food--Composition--Congresses, Food industry and trade--Congresses
Published
1996

711. Imatinib for systemic mast-cell disease.

Author

Pardanani, A., Elliott, M., Reeder, T., C-Y Li, Baxter, E. J., Cross, N. C. P., and Tefferi, A.

Subjects
*IMATINIB, *ONCOGENES, *GENETIC mutation, *PROTEIN-tyrosine kinases, *DRUG therapy, *RESEARCH methodology
Abstract

Imatinib has shown to be effective against malignant disease driven by ckit. We prospectively treated 12 adults with symptomatic systemic mast-cell disease at a dose of either 100 mg or 400 mg per day. Of the ten patients who we could assess for response, five (50%) had a measurable response to the drug, four of whom had important mast-cell cytoreduction and two who had complete clinical and histological remission. In the five patients with eosinophilia, three had complete clinical and haematological remission. The other two, who did not respond to treatment, were the only patients with the ckit D816V mutation. Our results suggest that imatinib either inhibits the growth-promoting role of wild type ckit, or targets an oncogenic kinase. [ABSTRACT FROM AUTHOR]

Published
2003
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712. The tomato genome sequence provides insights into fleshy fruit evolution

Author

Sato, Shusei, Tabata, Satoshi, Hirakawa, Hideki, Asamizu, Erika, Shirasawa, Kenta, Isobe, Sachiko, Kaneko, Takakazu, Nakamura, Yasukazu, Shibata, Daisuke, Aoki, Koh, Egholm, Michael, Knight, James, Bogden, Robert, Changbao, Shuang, Yang, Xun, Pan, Shengkai, Cheng, Shifeng, Liu, Xin, Ren, Yuanyuan, Wang, Jun, Albiero, Alessandro, Dal Pero, Francesca, Todesco, Sara, Van Eck, Joyce, Buels, Robert M., Bombarely, Aureliano, Gosselin, Joseph R., Huang, Minyun, Leto, Jonathan A., Menda, Naama, Strickler, Susan, Mao, Linyong, Gao, Shan, Tecle, Isaak Y., York, Thomas, Zheng, Vrebalov, Julia T., Lee, JeMin, Zhong, Silin, Mueller, Lukas A., Stiekema, Willem J., Ribeca, Paolo, Alioto, Tyler, Wencai, Sanwen, Yongchen, Zhang, Zhonghua, Jianchang, Guo, Yanmei, Xiaoxuan, Ying, Chuanyou, Zhukuan, Zuo, Jianru, Jianfeng, Zhao, Jiuhai, Yan, Liuhua, Jiang, Hongling, Bao, Hongshuang, Zhenjun, Fuyou, Chen, Bingtang, Han, Bin, Feng, Fan, Danlin, Ling, Hongqing, Xue, Yongbiao, Ware, Doreen, McCombie, W. Richard, Lippman, Zachary B., Chia, Jer-Ming, Pasternak, Shiran, Gelley, Laura, Kramer, Melissa, Anderson, Lorinda K., Chang, Song-Bin, Royer, Suzanne M., Shearer, Lindsay A., Stack, Stephen M., Rose, Jocelyn K. C., Yimin, Eannetta, Nancy, Matas, Antonio J., McQuinn, Ryan, Tanksley, Steven D., Camara, Francisco, Guigo, Roderic, Rombauts, Stephane, Fawcett, Jeffrey, Van de Peer, Yves, Zamir, Dani, Liang, Chunbo, Spannagl, Manuel, Gundlach, Heidrun, Bruggmann, Remy, Mayer, Klaus, Jia, Zhiqi, Junhong, Zhibiao, Bishop, Gerard J., Butcher, Sarah, Lopez-Cobollo, Rosa, Buchan, Daniel, Filippis, Ioannis, Abbott, Dixit, Rekha, Singh, Manju, Archana, Pal, Jitendra Kumar, Pandit, Awadhesh, Pradeep Kumar, Mahato, Ajay Kumar, Dogra, Vivek, Gaikwad, Kishor, Sharma, Tilak Raj, Mohapatra, Trilochan, Nagendra Kumar, Causse, Mathilde, Rothan, Christophe, Schiex, Noirot, Celine, Bellec, Arnaud, Klopp, Delalande, Corinne, Berges, Helene, Mariette, Jerome, Frasse, Pierre, Vautrin, Sonia, Zouine, Mohamed, Latche, Alain, Rousseau, Christine, Regad, Farid, Pech, Jean-Claude, Philippot, Murielle, Bouzayen, Mondher, Pericard, Osorio, Fernandez del Carmen, Asuncion, Monforte, Antonio, Granell, Fernandez-Munoz, Rafael, Conte, Mariana, Lichtenstein, Gabriel, Carrari, Fernando, De Bellis, Gianluca, Fuligni, Fabio, Peano, Clelia, Grandillo, Silvana, Termolino, Pasquale, Pietrella, Marco, Fantini, Elio, Falcone, Giulia, Fiore, Alessia, Giuliano, Giovanni, Lopez, Loredana, Facella, Perrotta, Gaetano, Daddiego, Loretta, Bryan, Glenn, Orozco, Modesto, Pastor, Xavier, Torrents, David, van Schriek, Keygene N. V. Marco G. M., Feron, Richard M. C., van Oeveren, Jan, de Heer, Peter, daPonte, Lorena, Jacobs-Oomen, Saskia, Cariaso, Mike, Prins, Marcel, van Eijk, Michiel J. T., Janssen, Antoine, van Haaren, Mark J. J., Sung-Hwan, Kim, Jungeun, Kwon, Suk-Yoon, Sangmi, Koo, Dal-Hoe, Sanghyeob, Hur, Cheol-Goo, Clouser, Christopher, Rico, Hallab, Asis, Gebhardt, Christiane, Klee, Kathrin, Joecker, Anika, Warfsmann, Jens, Goebel, Ulrike, Kawamura, Shingo, Yano, Kentaro, Sherman, Jamie D., Fukuoka, Hiroyuki, Negoro, Satomi, Bhutty, Sarita, Chowdhury, Parul, Chattopadhyay, Debasis, Datema, Erwin, Smit, Sandra, Schijlen, Eliog. W. M., van de Belt, Jose, van Haarst, Jan C., Peters, Sander A., van Staveren, Marjo J., Henkens, Marleen H. C., Mooyman, Paul J. W., Hesselink, Thamara, van Ham, Roeland C. H. J., Guoyong, Droege, Marcus, Choi, Doil, Kang, Byung-Cheol, Byung Dong, Park, Minkyu, Seungill, Yeom, Seon-In, Yong-Hwan, Yang-Do, Guangcun, Jianwei, Yongsheng, Shengxiong, Fernandez-Pedrosa, Victoria, Collado, Carmen, Zuniga, Sheila, Guoping, Cade, Rebecca, Dietrich, Robert A., Rogers, Jane, Knapp, Fei, Zhangjun, White, Ruth A., Thannhauser, Theodore W., Giovannoni, James J., Angel Botella, Miguel, Gilbert, Louise, Gonzalez, Ramon, Goicoechea, Jose Luis, Yeisoo, Kudrna, Collura, Kristi, Wissotski, Marina, Wing, Rod, Schoof, Heiko, Meyers, Blake C., Gurazada, Aishwarya Bala, Green, Pamela J., Mathur, Saloni, Vyas, Shailendra, Solanke, Amolkumar U., Kumar, Rahul, Gupta, Vikrant, Arun K., Khurana, Paramjit, Jitendra P., Tyagi, Akhilesh K., Dalmay, Tamas, Mohorianu, Irina, Walts, Brandon, Chamala, Srikar, Barbazuk, W. Brad, Jingping, Hui, Tae-Ho, Yupeng, Dong, Paterson, Andrew H., Xiyin, Tang, Haibao, Barone, Amalia, Chiusano, Maria Luisa, Ercolano, Maria Raffaella, D'Agostino, Nunzio, Di Filippo, Miriam, Traini, Alessandra, Sanseverino, Walter, Frusciante, Luigi, Seymour, Graham B., Elharam, Mounir, Hua, Axin, Kenton, Steven, Lewis, Jennifer, Lin, Shaoping, Najar, Fares, Lai, Hongshing, Qin, Baifang, Chunmei, Shi, Ruihua, Douglas, Xing, Yanbo, Keqin, Jing, Yao, Ziyun, Zhou, Liping, Roe, Bruce A., Vezzi, D'Angelo, Michela, Zimbello, Rosanna, Schiavon, Riccardo, Caniato, Elisa, Rigobello, Chiara, Campagna, Davide, Vitulo, Nicola, Valle, Giorgio, Nelson, David R., De Paoli, Emanuele, Szinay, Dora, de Jong, Hans H., Bai, Yuling, Visser, Richard G. F., Lankhorst, Rene M. Klein, Beasley, Helen, McLaren, Karen, Nicholson, Riddle, Claire, Gianese, Giulio, Tomato Genome Consortium, S., Sato, S., Tabata, H., Hirakawa, E., Asamizu, K., Shirasawa, S., Isobe, T., Kaneko, Y., Nakamura, D., Shibata, K., Aoki, M., Egholm, J., Knight, R., Bogden, C. B., Li, Y., Shuang, X., Xu, S. K., Pan, S. F., Cheng, X., Liu, Y. Y., Ren, J., Wang, A., Albiero, F. D., Pero, S., Todesco, J. V., Eck, R. M., Buel, A., Bombarely, J. R., Gosselin, M. Y., Huang, J. A., Leto, N., Menda, S., Strickler, L. Y., Mao, S., Gao, I. Y., Tecle, T., York, Y., Zheng, J. T., Vrebalov, J., Lee, S. L., Zhong, L. A., Mueller, W. J., Stiekema, P., Ribeca, T., Alioto, W. C., Yang, S. W., Huang, Y. C., Du, Z. H., Zhang, J. C., Gao, Y. M., Guo, X. X., Wang, Y., Li, J., He, C. Y., Li, Z. K., Cheng, J. R., Zuo, J. F., Ren, J. H., Zhao, L. H., Yan, H. L., Jiang, B., Wang, H. S., Li, Z. J., Li, F. Y., Fu, B. T., Chen, B., Han, Q., Feng, D. L., Fan, Y., Wang, H. Q., Ling, Y. B., A., D., Ware, W. R., Mccombie, Z. B., Lippman, J. M., Chia, K., Jiang, S., Pasternak, L., Gelley, M., Kramer, L. K., Anderson, S. B., Chang, S. M., Royer, L. A., Shearer, S. M., Stack, J. K., C., Y. M., Xu, N., Eannetta, A. J., Mata, R., Mcquinn, S. D., Tanksley, F., Camara, R., Guigo, S., Rombaut, J., Fawcett, Y. V., De, D., Zamir, C. B., Liang, M., Spannagl, H., Gundlach, R., Bruggmann, K., Mayer, Z. Q., Jia, J. H., Zhang, Z. B., A., G. J., Bishop, S., Butcher, R., Lopez Cobollo, D., Buchan, I., Filippi, J., Abbott, R., Dixit, M., Singh, A., Singh, J. K., Pal, A., Pandit, P. K., Singh, A. K., Mahato, V., Dogra, K., Gaikwad, T. R., Sharma, T., Mohapatra, N. K., Singh, M., Causse, C., Rothan, T., Schiex, C., Noirot, A., Bellec, C., Klopp, C., Delalande, H., Berge, J., Mariette, P., Frasse, S., Vautrin, M., Zouine, A., Latche, C., Rousseau, F., Regad, J. C., Pech, M., Philippot, M., Bouzayen, P., Pericard, S., Osorio, A. F., Del, A., Monforte, A., Granell, R., Fernandez Munoz, M., Conte, G., Lichtenstein, F., Carrari, G. D., Belli, F., Fuligni, C., Peano, S., Grandillo, P., Termolino, M., Pietrella, E., Fantini, G., Falcone, A., Fiore, G., Giuliano, L., Lopez, P., Facella, G., Perrotta, L., Daddiego, G., Bryan, M., Orozco, X., Pastor, D., Torrent, K. N. V., R. M. C., J. v., Oeveren, P. d., Heer, L., Daponte, S., Jacobs Oomen, M., Cariaso, M., Prin, M. J., T., A., Janssen, M. J., J., S. H., Jo, J., Kim, S. Y., Kwon, S., Kim, D. H., Koo, S., Lee, C. G., Hur, C., Clouser, A., Rico, A., Hallab, C., Gebhardt, K., Klee, A., Jocker, J., Warfsmann, U., Gobel, S., Kawamura, K., Yano, J. D., Sherman, H., Fukuoka, S., Negoro, S., Bhutty, P., Chowdhury, D., Chattopadhyay, E., Datema, S., Smit, E. W., M., J. v., De, J. C., Van, S. A., Peter, M. J., Van, M. H. C., P. J. W., T., Hesselink, R. C., H., G. Y., Jiang, M., Droege, D., Choi, B. C., Kang, B. D., Kim, M., Park, S. I., Yeom, Y. H., Lee, Y. D., Choi, G. C., Li, J. W., Gao, Y. S., Liu, S. X., Huang, V., Fernandez Pedrosa, C., Collado, S., Zuniga, G. P., Wang, R., Cade, R. A., Dietrich, J., Roger, S., Knapp, Z. J., Fei, R. A., White, T. W., Thannhauser, J. J., Giovannoni, M. A., Botella, L., Gilbert, R., Gonzalez, J. L., Goicoechea, Y., Yu, D., Kudrna, K., Collura, M., Wissotski, R., Wing, H., Schoof, B. C., Meyer, A. B., Gurazada, P. J., Green, S., Mathur, S., Vya, A. U., Solanke, R., Kumar, V., Gupta, A. K., Sharma, P., Khurana, J. P., Khurana, A. K., Tyagi, T., Dalmay, I., Mohorianu, B., Walt, S., Chamala, W. B., Barbazuk, J. P., Li, H., Guo, T. H., Lee, Y. P., Wang, D., Zhang, A. H., Paterson, X. Y., Wang, H. B., Tang, Barone, Amalia, Chiusano, MARIA LUISA, Ercolano, MARIA RAFFAELLA, D'Agostino, Nunzio, M. D., Filippo, A., Traini, W., Sanseverino, Frusciante, Luigi, G. B., Seymour, M., Elharam, Y., Fu, A., Hua, S., Kenton, J., Lewi, S. P., Lin, F., Najar, H. S., Lai, B. F., Qin, C. M., Qu, R. H., Shi, D., White, J., White, Y. B., Xing, K. Q., Yang, J., Yi, Z. Y., Yao, L. P., Zhou, B. A., Roe, A., Vezzi, M., D'Angelo, R., Zimbello, R., Schiavon, E., Caniato, C., Rigobello, D., Campagna, N., Vitulo, G., Valle, D. R., Nelson, E. D., Paoli, D., Szinay, H. H., De, Y. L., Bai, R. G. F., R. M. K., H., Beasley, K., Mclaren, C., Nicholson, C., Riddle, G., Gianese, Kazusa DNA Research Institute (KDRI), 454 Life Sciences, Amplicon Express Inc., Beijing Academy of Agriculture and Forestry Sciences, Chinese Academy of Sciences (CAS), Beijing Genomics Institute [Shenzhen] (BGI), BMR Genomics S.R.L., Partenaires INRAE, Boyce Thompson Inst Plant Res, Cornell University [New York], Centre for Biosystems Genomics, CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08028 Barcelona, Spain, China Agricultural University (CAU), Chinese Academy of Agricultural Sciences (CAAS), Inst Genet & Dev Biol, State Key Lab Plant Cell & Chromosome Engn, Chinese Academy of Sciences [Beijing] (CAS), Cold Spring Harbor, Cold Spring Harbor Laboratory, Colorado State University [Fort Collins] (CSU), National Taiwan University, Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Unité de Biométrie et Intelligence Artificielle (UBIA), Centre National de Ressources Génomiques Végétales (CNRGV), This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture (‘948’ Program: 2007-Z5), National Natural Science Foundation (36171319), Postdoctoral Science Foundation (20070420446). European Union: FP6 Integrated Project EU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence Nationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India, Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects), Ministry of Agriculture (Agronanotech and Biomassval projects), FILAS foundation, ENEA, CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST. Netherlands: Centre for BioSystems Genomics, Netherlands Organization for Scientific Research. Spain: Fundación Genoma España, Cajamar, FEPEX, Fundación Séneca, ICIA, IFAPA, Fundación Manrique de Lara, Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1, DEFRA, SEERAD. USA: NSF (DBI-0116076, DBI-0421634, DBI-0606595, IOS-0923312, DBI-0820612, DBI-0605659, DEB-0316614, DBI 0849896 and MCB 1021718), USDA (2007-02773 and 2007-35300-19739), USDA-ARS. We acknowledge the Potato Genome Sequencing Consortium for sharing data before publication, potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project, tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof, the Amplicon Express team for BAC pooling services, construction of the Whole Genome Profiling (WGP) physical map was supported by EnzaZaden, RijkZwaan, Vilmorin & Cie, and Takii & Co. Keygene N.V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies, AFLP and Keygene are registered trademarks of Keygene N.V. The following individuals are also acknowledged for their contribution to the work described: J. Park, B. Wang, C. Niu, D. Liu, F. Cojutti, S. Pescarolo, A. Zambon, G. Xiao, J. Chen, J. Shi, L. Zhang, L. Zeng, M. Caccamo, D. Bolser, D. Martin, M. Gonzalez, P. A. Bedinger, P. A. Covey, P. Pachori, R. R. Pousada, S. Hakim, S. Sims, V. Cahais, W. Long, X. Zhou, Y. Lu, W. Haso, C. Lai, S. Lepp, C. Peluso, H. Teramu, H. De Jong, R. Lizarralde, E. R. May and Z. Li. M. Zabeau is thanked for his support and encouragement and S. van den Brink for her secretarial support., Institut National Polytechnique de Toulouse - Toulouse INP (FRANCE), Institut National de la Recherche Agronomique - INRA (FRANCE), Université de Bordeaux 1 (FRANCE), Université de Bordeaux 2 - Victor Segalen (FRANCE), Institut National Polytechnique de Toulouse - INPT (FRANCE), and Universitat de Barcelona

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Laboratory of Virology, tomato, 01 natural sciences, Genome, Laboratorium voor Plantenveredeling, Arabidopsis, Genetic Variation, Genome, Plant, Genomics, Lycopersicon esculentum, Molecular Sequence Data, Phylogeny, RNA, Plant, Sequence Analysis, DNA, Solanum tuberosum, Soybeans, Synteny, Evolution, Molecular, Solanum lycopersicum, Génétique des plantes, Tomàquets, Wild tomato, Genome Sequencing, Lycopersicon-esculentum, gene, diversification : arabidopsis, patterns, ortholog, history, sorghum, potato, ComputingMilieux_MISCELLANEOUS, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Solanum chilense, biology, EPS-4, BioSolar Cells, food and beverages, Solanum pimpinellifolium, BIOS Applied Metabolic Systems, Neofunctionalization, Laboratory of Genetics, Sequence Analysis, diversification, Génomique, Transcriptomique et Protéomique, Evolution, Bioinformatics, Laboratorium voor Erfelijkheidsleer, Article, Genètica molecular, Laboratorium voor Virologie, 03 medical and health sciences, BIOS Applied Bioinformatics, Tomatoes, Botany, Bioinformatica, Genetics, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Genomes, Laboratorium voor Nematologie, lycopersicon-esculentum, 030304 developmental biology, fungi, Molecular, Plant, DNA, Genètica evolutiva, 15. Life on land, biology.organism_classification, Tomato genome, Plant Breeding, arabidopsis, Genòmica, RNA, Solanum, Laboratory of Nematology, Plant sciences, 010606 plant biology & botany
Abstract

[EN] Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera(1) and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium(2), and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness., This work was supported by: Argentina: INTA and CONICET. Belgium: Flemish Institute for Biotechnology and Ghent University. China: The State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences; Ministry of Science and Technology (2006AA10A116, 2004CB720405, 2006CB101907, 2007DFB30080) Ministry of Agriculture ('948' Program: 2007-Z5); National Natural Science Foundation (36171319); Postdoctoral Science Foundation (20070420446). European Union: FP6 Integrated Project EU-SOL PL 016214. France: Institute National de la Recherche Agronomique and Agence Nationale de la Recherche. Germany: the Max Planck Society. India: Department of Biotechnology, Government of India; Indian Council of Agricultural Research. Italy: Ministry of Research (FIRB-SOL, FIRB-Parallelomics, ItaLyco and GenoPOM projects); Ministry of Agriculture (Agronanotech and Biomassval projects); FILAS foundation; ENEA; CNR-ENEA project L. 191/2009. Japan: Kazusa DNA Research Institute Foundation and National Institute of Vegetable and Tea Science. Korea: KRIBB Basic Research Fund and Crop Functional Genomics Research Center (CFGC), MEST. Netherlands: Centre for BioSystemsGenomics, Netherlands Organization for Scientific Research. Spain: Fundacion Genoma Espana; Cajamar; FEPEX; Fundacion Seneca; ICIA; IFAPA; Fundacion Manrique de Lara; Instituto Nacional de Bioinformatica. UK: BBSRC grant BB/C509731/1; DEFRA; SEERAD. USA: NSF (DBI-0116076; DBI-0421634; DBI-0606595; IOS-0923312; DBI-0820612; DBI-0605659; DEB-0316614; DBI 0849896 and MCB 1021718); USDA (2007-02773 and 2007-35300-19739); USDA-ARS. We acknowledge the Potato Genome Sequencing Consortium for sharing data before publication; potato RNA-Seq data was provided by C. R. Buell from the NSF-funded Potato Genome Sequence and Annotation project; tomato RNA-Seq data by the USDA-funded SolCAP project, N. Sinha and J. Maloof; the Amplicon Express team for BAC pooling services; construction of the Whole Genome Profiling (WGP) physical map was supported by EnzaZaden, RijkZwaan, Vilmorin&Cie, and Takii & Co. Keygene N. V. owns patents and patent applications covering its AFLP and Whole Genome Profiling technologies; AFLP and Keygene are registered trademarks of Keygene N. V.

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713. Structural basis of a microbial trimethylamine transporter.

Author

Gao C, Ding H-T, Li K, Cao H-Y, Wang N, Gu Z-T, Wang Q, Sun M-L, Chen X-L, Chen Y, Zhang Y-Z, Fu H-H, and Li C-Y

Subjects
Membrane Transport Proteins metabolism, Membrane Transport Proteins chemistry, Membrane Transport Proteins genetics, Cryoelectron Microscopy, Protein Conformation, Models, Molecular, Biological Transport, Bacterial Proteins metabolism, Bacterial Proteins chemistry, Bacterial Proteins genetics, Protein Binding, Methylamines metabolism
Abstract

Trimethylamine (TMA), a simple trace biogenic amine resulting from the decomposition of proteins and other macromolecules, is ubiquitous in nature. It is found in the human gut as well as in various terrestrial and marine ecosystems. While the role of TMA in promoting cardiovascular diseases and depolarizing olfactory sensory neurons in humans has only recently been explored, many microbes are well known for their ability to utilize TMA as a carbon, nitrogen, and energy source. Here, we report the first structure of a TMA transporter, TmaT, originally identified from a marine bacterium. TmaT is a member of the betaine-choline-carnitine transporter family, and we show that TmaT is an Na + /TMA symporter, which possessed high specificity and binding affinity toward TMA. Furthermore, the structures of TmaT and two TmaT-TMA complexes were solved by cryo-EM. TmaT forms a homotrimer structure in solution. Each TmaT monomer has 12 transmembrane helices, and the TMA transport channel is formed by a four-helix bundle. TMA can move between different aromatic boxes, which provides the structural basis of TmaT importing TMA. When TMA is bound in location I, residues Trp146, Trp151, Tyr154, and Trp326 form an aromatic box to accommodate TMA. Moreover, Met105 also plays an important role in the binding of TMA. When TMA is transferred to location II, it is bound in the aromatic box formed by Trp325, Trp326, and Trp329. Based on our results, we proposed the TMA transport mechanism by TmaT. This study provides novel insights into TMA transport across biological membranes., Importance: The volatile trimethylamine (TMA) plays an important role in promoting cardiovascular diseases and depolarizing olfactory sensory neurons in humans and serves as a key nutrient source for a variety of ubiquitous marine microbes. While the TMA transporter TmaT has been identified from a marine bacterium, the structure of TmaT and the molecular mechanism involved in TMA transport remain unclear. In this study, we elucidated the high-resolution cryo-EM structures of TmaT and TmaT-TMA complexes and revealed the TMA binding and transport mechanisms by structural and biochemical analyses. The results advance our understanding of the TMA transport processes across biological membranes., Competing Interests: The authors declare no conflict of interest.

Published
2025
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714. SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments.

Author

He X-Y, Liu N-H, Liu J-Q, Peng M, Teng Z-J, Gu T-J, Chen X-L, Chen Y, Wang P, Li C-Y, Todd JD, Zhang Y-Z, and Zhang X-Y

Subjects
Carbon-Sulfur Lyases metabolism, Carbon-Sulfur Lyases genetics, Phylogeny, Sulfhydryl Compounds metabolism, Oceans and Seas, Gases metabolism, Sulfonium Compounds metabolism, Seawater microbiology, Gammaproteobacteria metabolism, Gammaproteobacteria genetics, Gammaproteobacteria classification, Sulfides metabolism
Abstract

Importance: Catabolism of dimethylsulfoniopropionate (DMSP) by marine bacteria has important impacts on the global sulfur cycle and climate. However, whether and how members of most oligotrophic bacterial groups participate in DMSP metabolism in marine environments remains largely unknown. In this study, by characterizing culturable strains, we have revealed that bacteria of the SAR92 clade, an abundant oligotrophic group of Gammaproteobacteria in coastal seawater, can catabolize DMSP through the DMSP lyase DddD-mediated cleavage pathway and/or the DMSP demethylase DmdA-mediated demethylation pathway to produce climate-active gases dimethylsulfide and methanethiol. Additionally, we found that SAR92 clade bacteria capable of catabolizing DMSP are widely distributed in global oceans. These results indicate that SAR92 clade bacteria are potentially important DMSP degraders and sources of climate-active gases in marine environments that have been overlooked, contributing to a better understanding of the roles and mechanisms of the oligotrophic bacteria in oceanic DMSP degradation., Competing Interests: The authors declare no conflict of interest.

Published
2023
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