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Zou M, Bhatia A, Dong H, Jayaprakash P, Guo J, Sahu D, Hou Y, Tsen F, Tong C, O'Brien K, Situ AJ, Schmidt T, Chen M, Ying Q, Ulmer TS, Woodley DT, Li W. Correction: Evolutionarily conserved dual lysine motif determines the non-chaperone function of secreted Hsp90alpha in tumour progression. Oncogene 2024; 43:1397-1398. [PMID: 38575761 PMCID: PMC11065679 DOI: 10.1038/s41388-024-03017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/06/2024]
Affiliation(s)
- M Zou
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Endocrinology and Metabolism, and Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - A Bhatia
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - H Dong
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Endocrinology and Metabolism, and Department of Respiratory and Critical Care Medicine, Chronic Airways Diseases Laboratory, Nanfang Hospital, Southern Medical University, Guangzhou, 510515, China
| | - P Jayaprakash
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - J Guo
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - D Sahu
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - Y Hou
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - F Tsen
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - C Tong
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research and Department of Cell and Neurobiology, Los Angeles, CA, USA
| | - K O'Brien
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
| | - A J Situ
- Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute University of Southern California Keck Medical Center, Los Angeles, CA, USA
| | - T Schmidt
- Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute University of Southern California Keck Medical Center, Los Angeles, CA, USA
| | - M Chen
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Medical Research, Greater Los Angeles Veterans Affairs Heath Care System, Los Angeles, CA, USA
| | - Q Ying
- Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research and Department of Cell and Neurobiology, Los Angeles, CA, USA
| | - T S Ulmer
- Department of Biochemistry and Molecular Biology and Zilkha Neurogenetic Institute University of Southern California Keck Medical Center, Los Angeles, CA, USA
| | - D T Woodley
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA
- Department of Medical Research, Greater Los Angeles Veterans Affairs Heath Care System, Los Angeles, CA, USA
| | - W Li
- Department of Dermatology and the Norris Comprehensive Cancer Center, Los Angeles, CA, USA.
- Department of Medical Research, Greater Los Angeles Veterans Affairs Heath Care System, Los Angeles, CA, USA.
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Zhao C, Zhang Y, Gao L, Xie M, Zhang X, Zeng L, Liu J, Liu Y, Zhang Y, Tong C, Hu Q, Cheng X, Liu L, Liu S. Genome editing of RECEPTOR-LIKE KINASE 902 confers resistance to necrotrophic fungal pathogens in Brassica napus without growth penalties. Plant Biotechnol J 2024; 22:538-540. [PMID: 38047432 PMCID: PMC10893935 DOI: 10.1111/pbi.14253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 11/06/2023] [Accepted: 11/17/2023] [Indexed: 12/05/2023]
Affiliation(s)
- Chuanji Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Yi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Lixia Gao
- State Key Laboratory of Agricultural MicrobiologyHuazhong Agricultural UniversityWuhanHubeiChina
| | - Meili Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Xiong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Lingyi Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Jie Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Yueying Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Yuanyuan Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Qiong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Xiaohui Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Lijiang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
| | - Shengyi Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural AffairsWuhanChina
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Zhao C, Cui X, Xie M, Zhang Y, Zeng L, Liu Y, Huang J, Zhang X, Tong C, Hu Q, Liu L, Liu S. Chromosome-scale genome assembly-assisted identification of Brassica napus BnDCPA1 for improvement of plant architecture and yield heterosis. Plant Commun 2024:100854. [PMID: 38419333 DOI: 10.1016/j.xplc.2024.100854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/25/2024] [Accepted: 02/26/2024] [Indexed: 03/02/2024]
Affiliation(s)
- Chuanji Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiaobo Cui
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Meili Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yi Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Lingyi Zeng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yueying Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Junyan Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Xiong Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Lijiang Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Shengyi Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, China.
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Zhou Z, Tong C, Tian L, Zhang X, Li Y, Xiao Y, Yan L. Retraction Note: Retrospective study of preservation and transection of the round ligament of uterus during laparoscopic transabdominal preperitoneal inguinal hernia repair in adult women. Hernia 2023; 27:1627. [PMID: 37792104 DOI: 10.1007/s10029-023-02906-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Affiliation(s)
- Z Zhou
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Yan'an University, Yan'an, China
| | - C Tong
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - L Tian
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - X Zhang
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Y Li
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Y Xiao
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - L Yan
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China.
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Raman B, McCracken C, Cassar MP, Moss AJ, Finnigan L, Samat AHA, Ogbole G, Tunnicliffe EM, Alfaro-Almagro F, Menke R, Xie C, Gleeson F, Lukaschuk E, Lamlum H, McGlynn K, Popescu IA, Sanders ZB, Saunders LC, Piechnik SK, Ferreira VM, Nikolaidou C, Rahman NM, Ho LP, Harris VC, Shikotra A, Singapuri A, Pfeffer P, Manisty C, Kon OM, Beggs M, O'Regan DP, Fuld J, Weir-McCall JR, Parekh D, Steeds R, Poinasamy K, Cuthbertson DJ, Kemp GJ, Semple MG, Horsley A, Miller CA, O'Brien C, Shah AM, Chiribiri A, Leavy OC, Richardson M, Elneima O, McAuley HJC, Sereno M, Saunders RM, Houchen-Wolloff L, Greening NJ, Bolton CE, Brown JS, Choudhury G, Diar Bakerly N, Easom N, Echevarria C, Marks M, Hurst JR, Jones MG, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Howard LS, Jacob J, Man WDC, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Singh SJ, Thomas DC, Toshner M, Lewis KE, Heaney LG, Harrison EM, Kerr S, Docherty AB, Lone NI, Quint J, Sheikh A, Zheng B, Jenkins RG, Cox E, Francis S, Halling-Brown M, Chalmers JD, Greenwood JP, Plein S, Hughes PJC, Thompson AAR, Rowland-Jones SL, Wild JM, Kelly M, Treibel TA, Bandula S, Aul R, Miller K, Jezzard P, Smith S, Nichols TE, McCann GP, Evans RA, Wain LV, Brightling CE, Neubauer S, Baillie JK, Shaw A, Hairsine B, Kurasz C, Henson H, Armstrong L, Shenton L, Dobson H, Dell A, Lucey A, Price A, Storrie A, Pennington C, Price C, Mallison G, Willis G, Nassa H, Haworth J, Hoare M, Hawkings N, Fairbairn S, Young S, Walker S, Jarrold I, Sanderson A, David C, Chong-James K, Zongo O, James WY, Martineau A, King B, Armour C, McAulay D, Major E, McGinness J, McGarvey L, Magee N, Stone R, Drain S, Craig T, Bolger A, Haggar A, Lloyd A, Subbe C, Menzies D, Southern D, McIvor E, Roberts K, Manley R, Whitehead V, Saxon W, Bularga A, Mills NL, El-Taweel H, Dawson J, Robinson L, Saralaya D, Regan K, Storton K, Brear L, Amoils S, Bermperi A, Elmer A, Ribeiro C, Cruz I, Taylor J, Worsley J, Dempsey K, Watson L, Jose S, Marciniak S, Parkes M, McQueen A, Oliver C, Williams J, Paradowski K, Broad L, Knibbs L, Haynes M, Sabit R, Milligan L, Sampson C, Hancock A, Evenden C, Lynch C, Hancock K, Roche L, Rees M, Stroud N, Thomas-Woods T, Heller S, Robertson E, Young B, Wassall H, Babores M, Holland M, Keenan N, Shashaa S, Price C, Beranova E, Ramos H, Weston H, Deery J, Austin L, Solly R, Turney S, Cosier T, Hazelton T, Ralser M, Wilson A, Pearce L, Pugmire S, Stoker W, McCormick W, Dewar A, Arbane G, Kaltsakas G, Kerslake H, Rossdale J, Bisnauthsing K, Aguilar Jimenez LA, Martinez LM, Ostermann M, Magtoto MM, Hart N, Marino P, Betts S, Solano TS, Arias AM, Prabhu A, Reed A, Wrey Brown C, Griffin D, Bevan E, Martin J, Owen J, Alvarez Corral M, Williams N, Payne S, Storrar W, Layton A, Lawson C, Mills C, Featherstone J, Stephenson L, Burdett T, Ellis Y, Richards A, Wright C, Sykes DL, Brindle K, Drury K, Holdsworth L, Crooks MG, Atkin P, Flockton R, Thackray-Nocera S, Mohamed A, Taylor A, Perkins E, Ross G, McGuinness H, Tench H, Phipps J, Loosley R, Wolf-Roberts R, Coetzee S, Omar Z, Ross A, Card B, Carr C, King C, Wood C, Copeland D, Calvelo E, Chilvers ER, Russell E, Gordon H, Nunag JL, Schronce J, March K, Samuel K, Burden L, Evison L, McLeavey L, Orriss-Dib L, Tarusan L, Mariveles M, Roy M, Mohamed N, Simpson N, Yasmin N, Cullinan P, Daly P, Haq S, Moriera S, Fayzan T, Munawar U, Nwanguma U, Lingford-Hughes A, Altmann D, Johnston D, Mitchell J, Valabhji J, Price L, Molyneaux PL, Thwaites RS, Walsh S, Frankel A, Lightstone L, Wilkins M, Willicombe M, McAdoo S, Touyz R, Guerdette AM, Warwick K, Hewitt M, Reddy R, White S, McMahon A, Hoare A, Knighton A, Ramos A, Te A, Jolley CJ, Speranza F, Assefa-Kebede H, Peralta I, Breeze J, Shevket K, Powell N, Adeyemi O, Dulawan P, Adrego R, Byrne S, Patale S, Hayday A, Malim M, Pariante C, Sharpe C, Whitney J, Bramham K, Ismail K, Wessely S, Nicholson T, Ashworth A, Humphries A, Tan AL, Whittam B, Coupland C, Favager C, Peckham D, Wade E, Saalmink G, Clarke J, Glossop J, Murira J, Rangeley J, Woods J, Hall L, Dalton M, Window N, Beirne P, Hardy T, Coakley G, Turtle L, Berridge A, Cross A, Key AL, Rowe A, Allt AM, Mears C, Malein F, Madzamba G, Hardwick HE, Earley J, Hawkes J, Pratt J, Wyles J, Tripp KA, Hainey K, Allerton L, Lavelle-Langham L, Melling L, Wajero LO, Poll L, Noonan MJ, French N, Lewis-Burke N, Williams-Howard SA, Cooper S, Kaprowska S, Dobson SL, Marsh S, Highett V, Shaw V, Beadsworth M, Defres S, Watson E, Tiongson GF, Papineni P, Gurram S, Diwanji SN, Quaid S, Briggs A, Hastie C, Rogers N, Stensel D, Bishop L, McIvor K, Rivera-Ortega P, Al-Sheklly B, Avram C, Faluyi D, Blaikely J, Piper Hanley K, Radhakrishnan K, Buch M, Hanley NA, Odell N, Osbourne R, Stockdale S, Felton T, Gorsuch T, Hussell T, Kausar Z, Kabir T, McAllister-Williams H, Paddick S, Burn D, Ayoub A, Greenhalgh A, Sayer A, Young A, Price D, Burns G, MacGowan G, Fisher H, Tedd H, Simpson J, Jiwa K, Witham M, Hogarth P, West S, Wright S, McMahon MJ, Neill P, Dougherty A, Morrow A, Anderson D, Grieve D, Bayes H, Fallon K, Mangion K, Gilmour L, Basu N, Sykes R, Berry C, McInnes IB, Donaldson A, Sage EK, Barrett F, Welsh B, Bell M, Quigley J, Leitch K, Macliver L, Patel M, Hamil R, Deans A, Furniss J, Clohisey S, Elliott A, Solstice AR, Deas C, Tee C, Connell D, Sutherland D, George J, Mohammed S, Bunker J, Holmes K, Dipper A, Morley A, Arnold D, Adamali H, Welch H, Morrison L, Stadon L, Maskell N, Barratt S, Dunn S, Waterson S, Jayaraman B, Light T, Selby N, Hosseini A, Shaw K, Almeida P, Needham R, Thomas AK, Matthews L, Gupta A, Nikolaidis A, Dupont C, Bonnington J, Chrystal M, Greenhaff PL, Linford S, Prosper S, Jang W, Alamoudi A, Bloss A, Megson C, Nicoll D, Fraser E, Pacpaco E, Conneh F, Ogg G, McShane H, Koychev I, Chen J, Pimm J, Ainsworth M, Pavlides M, Sharpe M, Havinden-Williams M, Petousi N, Talbot N, Carter P, Kurupati P, Dong T, Peng Y, Burns A, Kanellakis N, Korszun A, Connolly B, Busby J, Peto T, Patel B, Nolan CM, Cristiano D, Walsh JA, Liyanage K, Gummadi M, Dormand N, Polgar O, George P, Barker RE, Patel S, Price L, Gibbons M, Matila D, Jarvis H, Lim L, Olaosebikan O, Ahmad S, Brill S, Mandal S, Laing C, Michael A, Reddy A, Johnson C, Baxendale H, Parfrey H, Mackie J, Newman J, Pack J, Parmar J, Paques K, Garner L, Harvey A, Summersgill C, Holgate D, Hardy E, Oxton J, Pendlebury J, McMorrow L, Mairs N, Majeed N, Dark P, Ugwuoke R, Knight S, Whittaker S, Strong-Sheldrake S, Matimba-Mupaya W, Chowienczyk P, Pattenadk D, Hurditch E, Chan F, Carborn H, Foot H, Bagshaw J, Hockridge J, Sidebottom J, Lee JH, Birchall K, Turner K, Haslam L, Holt L, Milner L, Begum M, Marshall M, Steele N, Tinker N, Ravencroft P, Butcher R, Misra S, Walker S, Coburn Z, Fairman A, Ford A, Holbourn A, Howell A, Lawrie A, Lye A, Mbuyisa A, Zawia A, Holroyd-Hind B, Thamu B, Clark C, Jarman C, Norman C, Roddis C, Foote D, Lee E, Ilyas F, Stephens G, Newell H, Turton H, Macharia I, Wilson I, Cole J, McNeill J, Meiring J, Rodger J, Watson J, Chapman K, Harrington K, Chetham L, Hesselden L, Nwafor L, Dixon M, Plowright M, Wade P, Gregory R, Lenagh R, Stimpson R, Megson S, Newman T, Cheng Y, Goodwin C, Heeley C, Sissons D, Sowter D, Gregory H, Wynter I, Hutchinson J, Kirk J, Bennett K, Slack K, Allsop L, Holloway L, Flynn M, Gill M, Greatorex M, Holmes M, Buckley P, Shelton S, Turner S, Sewell TA, Whitworth V, Lovegrove W, Tomlinson J, Warburton L, Painter S, Vickers C, Redwood D, Tilley J, Palmer S, Wainwright T, Breen G, Hotopf M, Dunleavy A, Teixeira J, Ali M, Mencias M, Msimanga N, Siddique S, Samakomva T, Tavoukjian V, Forton D, Ahmed R, Cook A, Thaivalappil F, Connor L, Rees T, McNarry M, Williams N, McCormick J, McIntosh J, Vere J, Coulding M, Kilroy S, Turner V, Butt AT, Savill H, Fraile E, Ugoji J, Landers G, Lota H, Portukhay S, Nasseri M, Daniels A, Hormis A, Ingham J, Zeidan L, Osborne L, Chablani M, Banerjee A, David A, Pakzad A, Rangelov B, Williams B, Denneny E, Willoughby J, Xu M, Mehta P, Batterham R, Bell R, Aslani S, Lilaonitkul W, Checkley A, Bang D, Basire D, Lomas D, Wall E, Plant H, Roy K, Heightman M, Lipman M, Merida Morillas M, Ahwireng N, Chambers RC, Jastrub R, Logan S, Hillman T, Botkai A, Casey A, Neal A, Newton-Cox A, Cooper B, Atkin C, McGee C, Welch C, Wilson D, Sapey E, Qureshi H, Hazeldine J, Lord JM, Nyaboko J, Short J, Stockley J, Dasgin J, Draxlbauer K, Isaacs K, Mcgee K, Yip KP, Ratcliffe L, Bates M, Ventura M, Ahmad Haider N, Gautam N, Baggott R, Holden S, Madathil S, Walder S, Yasmin S, Hiwot T, Jackson T, Soulsby T, Kamwa V, Peterkin Z, Suleiman Z, Chaudhuri N, Wheeler H, Djukanovic R, Samuel R, Sass T, Wallis T, Marshall B, Childs C, Marouzet E, Harvey M, Fletcher S, Dickens C, Beckett P, Nanda U, Daynes E, Charalambou A, Yousuf AJ, Lea A, Prickett A, Gooptu B, Hargadon B, Bourne C, Christie C, Edwardson C, Lee D, Baldry E, Stringer E, Woodhead F, Mills G, Arnold H, Aung H, Qureshi IN, Finch J, Skeemer J, Hadley K, Khunti K, Carr L, Ingram L, Aljaroof M, Bakali M, Bakau M, Baldwin M, Bourne M, Pareek M, Soares M, Tobin M, Armstrong N, Brunskill N, Goodman N, Cairns P, Haldar P, McCourt P, Dowling R, Russell R, Diver S, Edwards S, Glover S, Parker S, Siddiqui S, Ward TJC, Mcnally T, Thornton T, Yates T, Ibrahim W, Monteiro W, Thickett D, Wilkinson D, Broome M, McArdle P, Upthegrove R, Wraith D, Langenberg C, Summers C, Bullmore E, Heeney JL, Schwaeble W, Sudlow CL, Adeloye D, Newby DE, Rudan I, Shankar-Hari M, Thorpe M, Pius R, Walmsley S, McGovern A, Ballard C, Allan L, Dennis J, Cavanagh J, Petrie J, O'Donnell K, Spears M, Sattar N, MacDonald S, Guthrie E, Henderson M, Guillen Guio B, Zhao B, Lawson C, Overton C, Taylor C, Tong C, Mukaetova-Ladinska E, Turner E, Pearl JE, Sargant J, Wormleighton J, Bingham M, Sharma M, Steiner M, Samani N, Novotny P, Free R, Allen RJ, Finney S, Terry S, Brugha T, Plekhanova T, McArdle A, Vinson B, Spencer LG, Reynolds W, Ashworth M, Deakin B, Chinoy H, Abel K, Harvie M, Stanel S, Rostron A, Coleman C, Baguley D, Hufton E, Khan F, Hall I, Stewart I, Fabbri L, Wright L, Kitterick P, Morriss R, Johnson S, Bates A, Antoniades C, Clark D, Bhui K, Channon KM, Motohashi K, Sigfrid L, Husain M, Webster M, Fu X, Li X, Kingham L, Klenerman P, Miiler K, Carson G, Simons G, Huneke N, Calder PC, Baldwin D, Bain S, Lasserson D, Daines L, Bright E, Stern M, Crisp P, Dharmagunawardena R, Reddington A, Wight A, Bailey L, Ashish A, Robinson E, Cooper J, Broadley A, Turnbull A, Brookes C, Sarginson C, Ionita D, Redfearn H, Elliott K, Barman L, Griffiths L, Guy Z, Gill R, Nathu R, Harris E, Moss P, Finnigan J, Saunders K, Saunders P, Kon S, Kon SS, O'Brien L, Shah K, Shah P, Richardson E, Brown V, Brown M, Brown J, Brown J, Brown A, Brown A, Brown M, Choudhury N, Jones S, Jones H, Jones L, Jones I, Jones G, Jones H, Jones D, Davies F, Davies E, Davies K, Davies G, Davies GA, Howard K, Porter J, Rowland J, Rowland A, Scott K, Singh S, Singh C, Thomas S, Thomas C, Lewis V, Lewis J, Lewis D, Harrison P, Francis C, Francis R, Hughes RA, Hughes J, Hughes AD, Thompson T, Kelly S, Smith D, Smith N, Smith A, Smith J, Smith L, Smith S, Evans T, Evans RI, Evans D, Evans R, Evans H, Evans J. Multiorgan MRI findings after hospitalisation with COVID-19 in the UK (C-MORE): a prospective, multicentre, observational cohort study. Lancet Respir Med 2023; 11:1003-1019. [PMID: 37748493 PMCID: PMC7615263 DOI: 10.1016/s2213-2600(23)00262-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 06/16/2023] [Accepted: 06/30/2023] [Indexed: 09/27/2023]
Abstract
INTRODUCTION The multiorgan impact of moderate to severe coronavirus infections in the post-acute phase is still poorly understood. We aimed to evaluate the excess burden of multiorgan abnormalities after hospitalisation with COVID-19, evaluate their determinants, and explore associations with patient-related outcome measures. METHODS In a prospective, UK-wide, multicentre MRI follow-up study (C-MORE), adults (aged ≥18 years) discharged from hospital following COVID-19 who were included in Tier 2 of the Post-hospitalisation COVID-19 study (PHOSP-COVID) and contemporary controls with no evidence of previous COVID-19 (SARS-CoV-2 nucleocapsid antibody negative) underwent multiorgan MRI (lungs, heart, brain, liver, and kidneys) with quantitative and qualitative assessment of images and clinical adjudication when relevant. Individuals with end-stage renal failure or contraindications to MRI were excluded. Participants also underwent detailed recording of symptoms, and physiological and biochemical tests. The primary outcome was the excess burden of multiorgan abnormalities (two or more organs) relative to controls, with further adjustments for potential confounders. The C-MORE study is ongoing and is registered with ClinicalTrials.gov, NCT04510025. FINDINGS Of 2710 participants in Tier 2 of PHOSP-COVID, 531 were recruited across 13 UK-wide C-MORE sites. After exclusions, 259 C-MORE patients (mean age 57 years [SD 12]; 158 [61%] male and 101 [39%] female) who were discharged from hospital with PCR-confirmed or clinically diagnosed COVID-19 between March 1, 2020, and Nov 1, 2021, and 52 non-COVID-19 controls from the community (mean age 49 years [SD 14]; 30 [58%] male and 22 [42%] female) were included in the analysis. Patients were assessed at a median of 5·0 months (IQR 4·2-6·3) after hospital discharge. Compared with non-COVID-19 controls, patients were older, living with more obesity, and had more comorbidities. Multiorgan abnormalities on MRI were more frequent in patients than in controls (157 [61%] of 259 vs 14 [27%] of 52; p<0·0001) and independently associated with COVID-19 status (odds ratio [OR] 2·9 [95% CI 1·5-5·8]; padjusted=0·0023) after adjusting for relevant confounders. Compared with controls, patients were more likely to have MRI evidence of lung abnormalities (p=0·0001; parenchymal abnormalities), brain abnormalities (p<0·0001; more white matter hyperintensities and regional brain volume reduction), and kidney abnormalities (p=0·014; lower medullary T1 and loss of corticomedullary differentiation), whereas cardiac and liver MRI abnormalities were similar between patients and controls. Patients with multiorgan abnormalities were older (difference in mean age 7 years [95% CI 4-10]; mean age of 59·8 years [SD 11·7] with multiorgan abnormalities vs mean age of 52·8 years [11·9] without multiorgan abnormalities; p<0·0001), more likely to have three or more comorbidities (OR 2·47 [1·32-4·82]; padjusted=0·0059), and more likely to have a more severe acute infection (acute CRP >5mg/L, OR 3·55 [1·23-11·88]; padjusted=0·025) than those without multiorgan abnormalities. Presence of lung MRI abnormalities was associated with a two-fold higher risk of chest tightness, and multiorgan MRI abnormalities were associated with severe and very severe persistent physical and mental health impairment (PHOSP-COVID symptom clusters) after hospitalisation. INTERPRETATION After hospitalisation for COVID-19, people are at risk of multiorgan abnormalities in the medium term. Our findings emphasise the need for proactive multidisciplinary care pathways, with the potential for imaging to guide surveillance frequency and therapeutic stratification. FUNDING UK Research and Innovation and National Institute for Health Research.
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Zhou Z, Tong C, Tian L, Zhang X, Li Y, Xiao Y, Yan L. Retrospective study of preservation and transection of the round ligament of uterus during laparoscopic transabdominal preperitoneal inguinal hernia repair in adult women. Hernia 2023; 27:1195-1202. [PMID: 36949269 PMCID: PMC10533639 DOI: 10.1007/s10029-023-02765-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 03/01/2023] [Indexed: 03/24/2023]
Abstract
PURPOSE The processing of the round ligament of uterus in laparoscopic transabdominal preperitoneal (TAPP) repair of inguinal hernia in women has contended. This study aimed to explore whether there is any difference in the surgical outcome and postoperative complications between the two processing modalities, preservation, and transection of the round ligament of uterus, in adult female inguinal hernia patients undergoing TAPP. METHODS Retrospective analysis of 84 female patients (117 sides) who underwent TAPP in XXX Hospital from July 2013 to August 2022. Patient characteristics and technical details of the surgical procedure were collected and divided into two groups according to whether the round ligament of uterus was severed intraoperatively or not. There were 52 cases (77 sides) in the group with preservation of the round ligament of uterus and 32 cases (40 sides) in the group with transection of the round ligament of uterus, comparing the general condition, surgical condition, and the occurrence of postoperative related complications between the 2 groups. RESULTS The operative time for unilateral primary inguinal hernia was (129.2 ± 35.1) and (89.5 ± 42.6) minutes in the preservation and transection groups, respectively. There were no statistical differences between the two groups in terms of age, length of hospital stay, ASA, BMI, history of lower abdominal surgery, type and side of hernia, intraoperative bleeding, and time to surgery for primary bilateral hernia (P > 0.05). In addition, there was likewise no statistical difference in the occurrence of postoperative Clavien-Dindo classification, VAS, seroma, mesh infection, labia majora edema, chronic pain or abnormal sensation in the inguinal region, and hernia recurrence in the two groups as well (P > 0.05). CONCLUSION There is no evidence that the transection of the round ligament of the uterus during TAPP has an impact on postoperative complications in patients. However, given the important role of the uterine round ligament in the surgical management of patients with uterine prolapse and the high incidence of uterine prolapse in older women, hernia surgeons should also be aware of the need to protect the round ligament of uterus in older women.
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Affiliation(s)
- Z Zhou
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
- Yan'an University, Yan'an, China
| | - C Tong
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - L Tian
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - X Zhang
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Y Li
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - Y Xiao
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China
| | - L Yan
- Department of General Surgery, Shaanxi Provincial People's Hospital, Xi'an, 710068, China.
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Cui X, Hu M, Yao S, Zhang Y, Tang M, Liu L, Cheng X, Tong C, Liu S. BnaOmics: A comprehensive platform combining pan-genome and multi-omics data from Brassica napus. Plant Commun 2023; 4:100609. [PMID: 37098652 PMCID: PMC10504585 DOI: 10.1016/j.xplc.2023.100609] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 04/11/2023] [Accepted: 04/23/2023] [Indexed: 06/01/2023]
Affiliation(s)
- Xiaobo Cui
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan 430023, China
| | - Yuanyuan Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), College of Forestry, Hainan University, Haikou 570228, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China.
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Hu M, Xie M, Cui X, Huang J, Cheng X, Liu L, Yan S, Liu S, Tong C. Characterization and Potential Function Analysis of the SRS Gene Family in Brassica napus. Genes (Basel) 2023; 14:1421. [PMID: 37510325 PMCID: PMC10379590 DOI: 10.3390/genes14071421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/07/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
SRS (SHI-related sequence) transcription factors play a crucial role in plant growth, development, and abiotic stress response. Although Brassica napus (B. napus) is one of the most important oil crops in the world, the role of SRS genes in B. napus (BnSRS) has not been well investigated. Therefore, we employed a bioinformatics approach to identify BnSRS genes from genomic data and investigated their characteristics, functions, and expression patterns, to gain a better understanding of how this gene family is involved in plant development and growth. The results revealed that there were 34 BnSRS gene family members in the genomic sequence of B. napus, unevenly distributed throughout the sequence. Based on the phylogenetic analysis, these BnSRS genes could be divided into four subgroups, with each group sharing comparable conserved motifs and gene structure. Analysis of the upstream promoter region showed that BnSRS genes may regulate hormone responses, biotic and abiotic stress response, growth, and development in B. napus. The protein-protein interaction analysis revealed the involvement of BnSRS genes in various biological processes and metabolic pathways. Our analysis of BnSRS gene expression showed that 23 BnSRS genes in the callus tissue exhibited a dominant expression pattern, suggesting their critical involvement in cell dedifferentiation, cell division, and tissue development. In addition, association analysis between genotype and agronomic traits revealed that BnSRS genes may be linked to some important agronomic traits in B. napus, suggesting that BnSRS genes were widely involved in the regulation of important agronomic traits (including C16.0, C18.0, C18.1, C18.2 C18.3, C20.1, C22.1, GLU, protein, TSW, and FFT). In this study, we predicted the evolutionary relationships and potential functions of BnSRS gene family members, providing a basis for the development of BnSRS gene functions which could facilitate targeted functional studies and genetic improvement for elite breeding in B. napus.
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Affiliation(s)
- Ming Hu
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Meili Xie
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Shunping Yan
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetics Improvement of Oil Crops, Oil Crops Research Institute of Chinese Academy of Agricultural Sciences, Ministry of Agriculture and Rural Affairs, Wuhan 430062, China
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Crichton J, Cox S, Tong C, Leow P, Field X, Welsh F. Observation versus intervention for incidental common bile duct stones at intraoperative cholangiogram: a systematic review. ANZ J Surg 2023; 93:1839-1846. [PMID: 37381094 DOI: 10.1111/ans.18581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Revised: 06/15/2023] [Accepted: 06/20/2023] [Indexed: 06/30/2023]
Abstract
BACKGROUND The natural history of incidental common bile duct stones (CBDS) is poorly understood. Current evidence is conflicting, with several studies suggesting the majority may pass spontaneously. Despite this, guidelines recommend routine removal even if asymptomatic. This study aimed to systematically review the outcomes of expectant management for CBDS detected on operative cholangiography during cholecystectomy. METHODS MEDLINE, Embase and CINAHL databases were systematically searched. Participants were adult patients with CBDS identified by intraoperative cholangiography. Intervention was regarded as any perioperative effort to remove common bile duct stones, including endoscopic retrograde cholangiopancreatography (ERCP), laparoscopic and open bile duct exploration. This was compared to observation. Outcomes of interest included rates of spontaneous stone passage, success of duct clearance and complications. Risk of bias was assessed using the ROBINS-I tool. RESULTS Eight studies were included. All studies were non-randomized, heterogeneous and at serious risk of bias. In patients observed after a positive IOC, 20.9% went on to have symptomatic retained stones. In patients directed to ERCP for positive IOC, persistent CBDS were found in 50.6%. Spontaneous passage was not associated with stone size. Meta-analysis is dominated by the results from one large database, which recommends intervention for incidental stones, despite low rates of persistent stones seen at postoperative ERCP. CONCLUSIONS Further evidence is required before a definitive recommendation on observation can be made. There is some evidence that asymptomatic stones may be safely observed. In clinical scenarios where the risks of biliary intervention are considered high, a conservative strategy could be more widely considered.
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Affiliation(s)
- J Crichton
- Department of General Surgery, Te Whatu Ora Waitaha Canterbury, Christchurch Hospital, Christchurch, New Zealand
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
| | - S Cox
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
| | - C Tong
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
| | - P Leow
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
| | - X Field
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
| | - F Welsh
- Department of General Surgery, Te Whatu Ora Waikato, Waikato Hospital, Hamilton, New Zealand
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Yao S, Xie M, Hu M, Cui X, Wu H, Li X, Hu P, Tong C, Yu X. Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus. Front Plant Sci 2023; 14:1118339. [PMID: 37021309 PMCID: PMC10067767 DOI: 10.3389/fpls.2023.1118339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 03/07/2023] [Indexed: 06/19/2023]
Abstract
Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin-proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.
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Affiliation(s)
- Shengli Yao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - XiaoBo Cui
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Haoming Wu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Xiaohua Li
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Peng Hu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaoli Yu
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, Hubei, China
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Gill RA, Helal MMU, Tang M, Hu M, Tong C, Liu S. High-Throughput Association Mapping in Brassica napus L.: Methods and Applications. Methods Mol Biol 2023; 2638:67-91. [PMID: 36781636 DOI: 10.1007/978-1-0716-3024-2_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/15/2023]
Abstract
Oil seed rape (Braasica napus L.) is ranked second among oil seed crops cultivated globally for edible oil for human, and seed cake for animal consumption. Recent genetic and genomics advancements highlighted the diversity that exists within B. napus, which is largely discovered using the most promising genetic markers called single nucleotide polymorphism (SNP). Their calling rate is also enhanced to ~100 folds after the continuous advancements in the next generation sequencing (NGS) technologies. As the high throughput of NGS resulted in multi-Giga bases data, the detailed quality control (QC) prior to downstream analyses is a pre-requisite. It mainly involved the removal of false positives, missing proportions, filtering of low-quality SNPs, and adjustments of minor-allele frequency and heterozygosity. After marker-trait association, for conformation of target SNPs, validations of SNPs can be performed using various methods, especially allele-specific PCR assay-based methods have been utilized for SNP genotyping of genes targeting agronomic traits and somaclonal variations occurred during transgenic studies. In the present study, the authors mainly argue on the genotypic progress, and pipelines/methods that are being used for detection, calling, filtering, and validation of SNPs. Also, insight is provided into the application of SNPs in linkage and association mapping, including QTL mapping and genome-wide association studies targeting mainly developmental traits related to the root system and plant architecture, flowering time, silique, and oil quality. Briefly, the present study provides the recent information and recommendations on the SNP genotyping methods and its applications, which can be useful for marker-assisted breeding in B. napus and other crops.
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Affiliation(s)
- Rafaqat Ali Gill
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.
| | - Md Mostofa Uddin Helal
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, College of Forestry, Hainan University, Haikou, China
| | - Ming Hu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Yu R, Leung G, Lai D, Tong C, Tam LY, Cheng C, Kong S, Woo J. Assessing the Readiness for Implementing the World Health Organization's ICOPE Approach in Hong Kong: Perspectives from Social Care and Policy Stakeholders. J Frailty Aging 2023; 12:126-133. [PMID: 36946709 DOI: 10.14283/jfa.2023.3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Although integrated care has been considered a key strategy in reforming health systems around the world, it seems hard to realise in practice, particularly in the part of medical social integration. Worse still, little is known about the capacity of social care professionals who implement it, or their perceived roles and responsibilities, as well as the barriers and facilitators that stakeholders from the health and social sectors identify as factors affecting the ICOPE implementation process. Therefore, the present study was performed to probe into these issues. Data were collected from an online survey based on the WHO ICOPE scorecard (N = 34), and focus groups with policy makers, managers, health and social care professionals (N = 47). Inductive analyses were performed in accordance with the service and system levels within the WHO ICOPE implementation framework. While the findings from the scorecard survey highlight the gap in actualizing the ICOPE approach within the existing social services and care structures, we found support for a model of integrated care underpinned by the WHO ICOPE approach. Factors that may hinder and facilitate ICOPE implementation include workforce capacity-building, coordinated networks and partnerships, and financial mechanisms. This finding can help inform subsequent actions that further support health and social care advancement and collaboration, and the implementation of the ICOPE approach.
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Affiliation(s)
- R Yu
- Ruby Yu, The Chinese University of Hong Kong, Hong Kong,
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Yu R, Lai D, Leung G, Tong C, Yuen S, Woo J. A Dyadic Cooking-Based Intervention for Improving Subjective Health and Well-Being of Older Adults with Subjective Cognitive Decline and Their Caregivers: A Randomized Controlled Trial. J Nutr Health Aging 2023; 27:824-832. [PMID: 37960905 DOI: 10.1007/s12603-023-1990-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 09/04/2023] [Indexed: 11/15/2023]
Abstract
OBJECTIVES Evidence on the effectiveness of cooking activities as a well-being promotion intervention for older adults with subjective cognitive decline (SCD) and their caregivers is scarce. In view of this, a randomized controlled trial was conducted to examine whether a dyadic cooking-based intervention can improve the subjective health and well-being of older adults with SCD and their caregivers, as well as the cooking competence of the former group. DESIGN Randomized controlled trial. SETTING Community. PARTICIPANTS Sixty pairs of community-dwelling older adults aged 60 years or above with SCD (mean age = 78.4 years) and their caregivers (mean age = 65.3 years) were randomly assigned to the intervention group (N = 30 pairs) and the wait-list control group (N = 30 pairs). INTERVENTION The intervention was an innovative 5-week (two hours per week) dyadic cooking-based intervention employing procedural learning methods specifically adapted for older adults with SCD. MEASUREMENTS The outcome measures included 1) a well-being index composed by four indicators: life satisfaction, feeling of happiness, sense of purpose and meaning in life, and perceived health, and 2) cooking competence. RESULTS For both older adults with SCD and their caregivers, the increases in the well-being index were significantly greater in the intervention group than in the control group (β = 0.508, 95% CI [0.036, 0.980]). For older adults with SCD, the increases in the cooking competence score were significantly greater in the intervention group than in the control group (β = 1.629, 95% CI [0.165, 3.071]). CONCLUSION The dyadic cooking-based intervention resulted in improvements in the cooking competence and well-being of older adults with SCD, as well as the well-being of caregivers.
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Affiliation(s)
- R Yu
- Ruby Yu, Jockey Club Institute of Ageing, The Chinese University of Hong Kong, Hong Kong,
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Yu R, Lai D, Leung G, Tam LY, Cheng C, Kong S, Tong C, Cheung B, Woo J. Moving towards the ICOPE Approach: Evaluation of Community-Based Intervention Activities on Improving Intrinsic Capacity. J Nutr Health Aging 2023; 27:1028-1037. [PMID: 37997725 DOI: 10.1007/s12603-023-2003-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 09/12/2023] [Indexed: 11/25/2023]
Abstract
OBJECTIVES Different types of community-based intervention activities may have differential effects in improving the intrinsic capacity (IC) of older people. This study aims to (i) identify subgroups of older people based on their IC impairments, (ii) examine the differential associations between different types of activity participations and change in IC across subgroups, and (iii) assess whether the activity participation patterns of older people align with the way that would benefit them the most. METHODS Participants were community-dwelling older people aged 60 years or above. They were screened for IC impairments at baseline, and their participation records of different types (cognitive, physical, nutritional, mental, and social) of intervention activities were collected for one year. An aggregated IC score was created based on four IC domains including cognitive (self-rated memory), locomotor (self-rated difficulties in walking), vitality (self-rated weight loss), and psychological (subjective well-being). Cluster analysis was used to group homogenous participants. Mixed-effects regression was used to examine the associations between activity counts (i.e., number of sessions participated) and change in IC. Activity participation patterns were also compared across subgroups. RESULTS Data were obtained from 7,357 participants (mean age = 74.72 years). Four clusters were identified, including those who were relatively robust (cluster 1, N = 4,380, 59.5%), those who had cognitive decline (cluster 2, N = 2,134, 29.0%), those who had impaired mobility and vitality (cluster 3, N = 319, 4.3%), and those with poor psychological well-being (cluster 4, N = 524, 7.1%). Overall, activity count was associated with IC improvement (β = 0.073, 95% CI [0.037, 0.108]). However, as regards the cluster-specific results, different types of activities were associated with IC improvement for different specific clusters. For instance, cognitive activity count was associated with IC improvement only for cluster 2 (β = 0.491, 95% CI [0.258, 0.732]). Notably, none of the activity types were associated with IC improvement for cluster 1. Regarding the activity participation patterns, there were no significant differences across the four clusters (Wilk's Λ = 0.997, F = 1.400, p = .138). CONCLUSIONS AND IMPLICATIONS IC improvement depended on the activity types and IC status of older people. In view of this, a people-centred and targeted approach should be adopted to maximize the overall benefits of intervention activities.
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Affiliation(s)
- R Yu
- Ruby Yu, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong, E-mail:
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Dong Z, Tang M, Cui X, Zhao C, Tong C, Liu Y, Xiang Y, Li Z, Huang J, Cheng X, Liu S. Integrating GWAS, linkage mapping and gene expression analyses reveal the genetic control of first branch height in Brassica napus L. Front Plant Sci 2022; 13:1080999. [PMID: 36589070 PMCID: PMC9798901 DOI: 10.3389/fpls.2022.1080999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Rapeseed (Brassica napus L.) is a crucial oil crop cultivated worldwide. First branch height, an essential component of rapeseed plant architecture, has an important effect on yield and mechanized harvesting; however, the underlying genetic mechanism remains unclear. In this study, based on the 60K single nucleotide polymorphism array and a recombinant inbred lines population derived from M083 and 888-5, a total of 19 QTLs were detected in five environments, distributed on linkage groups A02, A09, A10, C06, and C07, which explained phenotypic variation ranging from 4.87 to 29.87%. Furthermore, 26 significant SNPs were discovered on Chr.A02 by genome-wide association study in a diversity panel of 324 re-sequencing accessions. The major QTL of the first branch height trait was co-located on Chr.A02 by integrating linkage mapping and association mapping. Eleven candidate genes were screened via allelic variation analysis, inter-subgenomic synteny analysis, and differential expression of genes in parental shoot apical meristem tissues. Among these genes, BnaA02g13010D, which encodes a TCP transcription factor, was confirmed as the target gene according to gene function annotation, haplotype analysis, and full-length gene sequencing, which revealed that TATA insertion/deletion in the promoter region was closely linked to significantly phenotypic differences BnaA02.TCP1 M083 overexpression resulted in decreased branch height and increased branch number in Arabidopsis. These results provide a genetic basis for first branch height and the ideal architecture of B. napus.
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Affiliation(s)
- Zhixue Dong
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants, Ministry of Education, School of Forestry, Hainan University, Haikou, China
| | - Xiaobo Cui
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yueying Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Science, Guiyang, China
| | - Zaiyun Li
- National Key Lab of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the People's Republic of China (PRC), Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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16
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Hu M, Xie M, Cui X, Huang J, Cheng X, Liu L, Liu S, Tong C. Genome-Wide Characterization of Trehalose-6-Phosphate Synthase Gene Family of Brassica napus and Potential Links with Agronomic Traits. Int J Mol Sci 2022; 23:ijms232415714. [PMID: 36555357 PMCID: PMC9779256 DOI: 10.3390/ijms232415714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/07/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
Trehalose and trehalose-6 phosphate played important roles in floral organ development, embryonic development, cell morphogenesis, and signal transduction under abiotic stress. However, little is known about the trehalose-6-phosphate synthase (TPS) gene family in Brassica napus. In this study, in total, 26 TPS genes in B. napus (BnTPS genes) were identified and classified into two groups. In each group, the BnTPS genes showed relatively conserved gene structures. The protein-protein interaction (PPI) network and enrichment analysis indicated that BnTPS genes were involved in the glycolysis/gluconeogenesis, fructose and mannose metabolism, galactose metabolism, pentose phosphate pathway, carbohydrate transmembrane transport, trehalose-phosphatase activity, etc. The expression of BnTPS genes varied greatly across different tissues, while most of the BnTPS genes showed a considerable improvement in expression under different abiotic stresses, indicating that BnTPS genes were significantly responsive to the abiotic treatments. In addition, the association mapping analysis revealed that eight BnTPS genes were potential regulators of particular agronomic traits. Among them, the gene BnTPS23 was significantly associated with the primary flowering time (PFT), full flowering time (FFT1), and final flowering time (FFT2), suggesting that BnTPS genes may play an important role in regulating key agronomic traits in B. napus. In summary, our research provides a better understanding of BnTPS genes, facilitates the breeding of superior B. napus varieties, and paves the way for future functional studies.
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Tong C, Li Q, Kong L, Ni X, Halengbieke A, Zhang S, Wu Z, Tao L, Han Y, Zheng D, Guo X, Yang X. Sex-specific metabolic risk factors and their trajectories towards the non-alcoholic fatty liver disease incidence. J Endocrinol Invest 2022; 45:2233-2245. [PMID: 35896944 DOI: 10.1007/s40618-022-01848-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/21/2022] [Indexed: 11/28/2022]
Abstract
PURPOSE Non-alcoholic fatty liver disease (NAFLD) is a common chronic liver disease. This study examined sex-specific associations between NAFLD and metabolic factors and investigated the trajectory of risk factors. METHODS We retrospectively investigated 16,140 individuals from Beijing Health Management Cohort. Univariate and multivariate time-dependent Cox regression analyses were performed to identify independent risk factors for new-onset NAFLD. The trajectory of risk factors was investigated using the latent growth curve model and growth mixture model. RESULTS Over a median follow-up of 3.15 years, 2,450 (15.18%) participants developed NAFLD. The risk factors for NAFLD in men were increased body mass index (BMI); waist circumference (WC); triglyceride (TG), low-density lipoprotein cholesterol (LDL-C), haemoglobin (Hb), and serum uric acid (SUA) levels; and platelet (PLT) count and decreased serum creatinine-to-body weight (sCr/bw) and high-density lipoprotein cholesterol (HDL-C) levels. In women, the risk factors were increased BMI, WC, and fasting plasma glucose (FPG), TG, LDL-C, SUA, white blood cell (WBC), and PLT and decreased sCr/bw and HDL-C levels. In addition, BMI, LDL-C, sCr/bw and PLT changing trajectories were associated with NAFLD in men; BMI, WC, TG, LDL-C, SUA and sCr/bw trends was associated with NAFLD risk in women. CONCLUSIONS Development of NAFLD is associated with BMI, LDL-C, sCr/bw and PLT changing trajectories in men; BMI, WC, TG, LDL-C, SUA and sCr/bw trends are associated an increased risk of NAFLD in women. Deterioration of metabolic risk factors status can be a predictor of NAFLD many years before its occurrence.
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Affiliation(s)
- C Tong
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Q Li
- Science and Education Section, Beijing Physical Examination Center, No. 59, Beiwei Road, Xicheng district, Beijing, China
| | - L Kong
- Information Center, Beijing Physical Examination Center, No. 59, Beiwei Road, Xicheng district, Beijing, China
| | - X Ni
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - A Halengbieke
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - S Zhang
- Medical Records Statistics Office, Peking University First Hospital, Beijing, 100034, China
| | - Z Wu
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - L Tao
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - Y Han
- Science and Education Section, Beijing Physical Examination Center, No. 59, Beiwei Road, Xicheng district, Beijing, China
| | - D Zheng
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - X Guo
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China
| | - X Yang
- School of Public Health, Capital Medical University, 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China.
- Beijing Municipal Key Laboratory of Clinical Epidemiology, No. 10 Xitoutiao, Youanmen, Fengtai District, Beijing, 100069, China.
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Zhao C, Yang L, Tang M, Liu L, Huang J, Tong C, Xiang Y, Liu S, Cheng X, Xie M. Genome-wide association study reveals a GLYCOGEN SYNTHASE KINASE 3 gene regulating plant height in Brassica napus. Front Plant Sci 2022; 13:1061196. [PMID: 36407634 PMCID: PMC9666772 DOI: 10.3389/fpls.2022.1061196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Rapeseed (Brassica napus) is an allotetraploid crop that is the main source of edible oils and feed proteins in the world. The ideal plant architecture breeding is a major objective of rapeseed breeding and determining the appropriate plant height is a key element of the ideal plant architecture. Therefore, this study aims to improve the understanding of the genetic controls underlying plant height. The plant heights of 230 rapeseed accessions collected worldwide were investigated in field experiments over two consecutive years in Wuhan, China. Whole-genome resequencing of these accessions yielded a total of 1,707,194 informative single nucleotide polymorphisms (SNPs) that were used for genome-wide association analysis (GWAS). GWAS and haplotype analysis showed that BnaA01g09530D, which encodes BRASSINOSTEROID-INSENSITIVE 2 and belongs to the GLYCOGEN SYNTHASE KINASE 3 (GSK3) family, was significantly associated with plant height in B. napus. Moreover, a total of 31 BnGSK3s with complete domains were identified from B. napus genome and clustered into four groups according to phylogenetic analysis, gene structure, and motif distribution. The expression patterns showed that BnGSK3s exhibited significant differences in 13 developmental tissues in B. napus, suggesting that BnGSK3s may be involved in tissue-specific development. Sixteen BnGSK3 genes were highly expressed the in shoot apical meristem, which may be related to plant height or architecture development. These results are important for providing new haplotypes of plant height in B. napus and for extending valuable genetic information for rapeseed genetic improvement of plant architecture.
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Affiliation(s)
- Chuanji Zhao
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Li Yang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Minqiang Tang
- Key Laboratory of Genetics and Germplasm Innovation of Tropical Special Forest Trees and Ornamental Plants (Ministry of Education), School of Forestry, Hainan University, Haikou, China
| | - Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, Guizhou, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
| | - Meili Xie
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, Hubei, China
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Xie M, Zhao C, Song M, Xiang Y, Tong C. Genome-wide identification and comparative analysis of CLE family in rapeseed and its diploid progenitors. Front Plant Sci 2022; 13:998082. [PMID: 36340404 PMCID: PMC9632860 DOI: 10.3389/fpls.2022.998082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/29/2022] [Indexed: 06/16/2023]
Abstract
Crop genomics and breeding CLAVATA3/EMBRYO SURROUNDING REGION-RELATED (CLE) proteins belong to a small peptide family in plants. During plant development, CLE gene family members play a pivotal role in regulating cell-to-cell communication and stem cell maintenance. However, the evolutionary process and functional importance of CLEs are unclear in Brassicaceae. In this study, a total of 70 BnCLEs were identified in Brassica napus (2n = 4x = 38, AnCn): 32 from the An subgenome, 36 from the Cn subgenome, and 2 from the unanchored subgenome. Meanwhile, 29 BrCLE and 32 BoCLE genes were explored in Brassica rapa (2n = 2x = 20, Ar) and Brassica oleracea (2n = 2x = 18, Co). Phylogenetic analysis revealed that 163 CLEs derived from three Brassica species and Arabidopsis thaliana can be divided into seven subfamilies. Homology and synteny analyses indicated whole-genome triplication (WGT) and segmental duplication may be the major contributors to the expansion of CLE family. In addition, RNA-seq and qPCR analysis indicated that 19 and 16 BnCLEs were more highly expressed in immature seeds and roots than in other tissues. Some CLE gene pairs exhibited different expression patterns in the same tissue, which indicated possible functional divergence. Furthermore, genetic variations and regional association mapping analysis indicated that 12 BnCLEs were potential genes for regulating important agronomic traits. This study provided valuable information to understand the molecular evolution and biological function of CLEs in B. napus and its diploid progenitors, which will be helpful for genetic improvement of high-yield breeding in B. napus.
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Affiliation(s)
- Meili Xie
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Min Song
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
- College of Life Science, Qufu Normal University, Qufu, China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
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Yang L, Yang L, Zhao C, Liu J, Tong C, Zhang Y, Cheng X, Jiang H, Shen J, Xie M, Liu S. Differential alternative splicing genes and isoform co-expression networks of Brassica napus under multiple abiotic stresses. Front Plant Sci 2022; 13:1009998. [PMID: 36311064 PMCID: PMC9608124 DOI: 10.3389/fpls.2022.1009998] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Alternative splicing (AS) is an important regulatory process that affects plant development and stress responses by greatly increasing the complexity of transcriptome and proteome. To understand how the AS landscape of B. napus changes in response to abiotic stresses, we investigated 26 RNA-seq libraries, including control and treatments with cold, dehydration, salt, and abscisic acid (ABA) at two different time points, to perform comparative alternative splicing analysis. Apparently, AS events increased under all stresses except dehydration for 1 h, and intron retention was the most common AS mode. In addition, a total of 357 differential alternative splicing (DAS) genes were identified under four abiotic stresses, among which 81 DAS genes existed in at least two stresses, and 276 DAS genes were presented under only one stress. A weighted gene co-expression network analysis (WGCNA) based on the splicing isoforms, rather than the genes, pinpointed out 23 co-expression modules associated with different abiotic stresses. Among them, a number of significant hub genes were also found to be DAS genes, which encode key isoforms involved in responses to single stress or multiple stresses, including RNA-binding proteins, transcription factors, and other important genes, such as RBP45C, LHY, MYB59, SCL30A, RS40, MAJ23.10, and DWF4. The splicing isoforms of candidate genes identified in this study could be a valuable resource for improving tolerance of B. napus against multiple abiotic stresses.
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Affiliation(s)
- Lingli Yang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Yang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Biosystematics Group, Wageningen University and Research, Wageningen, Netherlands
| | - Chuanji Zhao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Huifang Jiang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jinxiong Shen
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
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Evans RA, Leavy OC, Richardson M, Elneima O, McAuley HJC, Shikotra A, Singapuri A, Sereno M, Saunders RM, Harris VC, Houchen-Wolloff L, Aul R, Beirne P, Bolton CE, Brown JS, Choudhury G, Diar-Bakerly N, Easom N, Echevarria C, Fuld J, Hart N, Hurst J, Jones MG, Parekh D, Pfeffer P, Rahman NM, Rowland-Jones SL, Shah AM, Wootton DG, Chalder T, Davies MJ, De Soyza A, Geddes JR, Greenhalf W, Greening NJ, Heaney LG, Heller S, Howard LS, Jacob J, Jenkins RG, Lord JM, Man WDC, McCann GP, Neubauer S, Openshaw PJM, Porter JC, Rowland MJ, Scott JT, Semple MG, Singh SJ, Thomas DC, Toshner M, Lewis KE, Thwaites RS, Briggs A, Docherty AB, Kerr S, Lone NI, Quint J, Sheikh A, Thorpe M, Zheng B, Chalmers JD, Ho LP, Horsley A, Marks M, Poinasamy K, Raman B, Harrison EM, Wain LV, Brightling CE, Abel K, Adamali H, Adeloye D, Adeyemi O, Adrego R, Aguilar Jimenez LA, Ahmad S, Ahmad Haider N, Ahmed R, Ahwireng N, Ainsworth M, Al-Sheklly B, Alamoudi A, Ali M, Aljaroof M, All AM, Allan L, Allen RJ, Allerton L, Allsop L, Almeida P, Altmann D, Alvarez Corral M, Amoils S, Anderson D, Antoniades C, Arbane G, Arias A, Armour C, Armstrong L, Armstrong N, Arnold D, Arnold H, Ashish A, Ashworth A, Ashworth M, Aslani S, Assefa-Kebede H, Atkin C, Atkin P, Aung H, Austin L, Avram C, Ayoub A, Babores M, Baggott R, Bagshaw J, Baguley D, Bailey L, Baillie JK, Bain S, Bakali M, Bakau M, Baldry E, Baldwin D, Ballard C, Banerjee A, Bang B, Barker RE, Barman L, Barratt S, Barrett F, Basire D, Basu N, Bates M, Bates A, Batterham R, Baxendale H, Bayes H, Beadsworth M, Beckett P, Beggs M, Begum M, Bell D, Bell R, Bennett K, Beranova E, Bermperi A, Berridge A, Berry C, Betts S, Bevan E, Bhui K, Bingham M, Birchall K, Bishop L, Bisnauthsing K, Blaikely J, Bloss A, Bolger A, Bonnington J, Botkai A, Bourne C, Bourne M, Bramham K, Brear L, Breen G, Breeze J, Bright E, Brill S, Brindle K, Broad L, Broadley A, Brookes C, Broome M, Brown A, Brown A, Brown J, Brown J, Brown M, Brown M, Brown V, Brugha T, Brunskill N, Buch M, Buckley P, Bularga A, Bullmore E, Burden L, Burdett T, Burn D, Burns G, Burns A, Busby J, Butcher R, Butt A, Byrne S, Cairns P, Calder PC, Calvelo E, Carborn H, Card B, Carr C, Carr L, Carson G, Carter P, Casey A, Cassar M, Cavanagh J, Chablani M, Chambers RC, Chan F, Channon KM, Chapman K, Charalambou A, Chaudhuri N, Checkley A, Chen J, Cheng Y, Chetham L, Childs C, Chilvers ER, Chinoy H, Chiribiri A, Chong-James K, Choudhury N, Chowienczyk P, Christie C, Chrystal M, Clark D, Clark C, Clarke J, Clohisey S, Coakley G, Coburn Z, Coetzee S, Cole J, Coleman C, Conneh F, Connell D, Connolly B, Connor L, Cook A, Cooper B, Cooper J, Cooper S, Copeland D, Cosier T, Coulding M, Coupland C, Cox E, Craig T, Crisp P, Cristiano D, Crooks MG, Cross A, Cruz I, Cullinan P, Cuthbertson D, Daines L, Dalton M, Daly P, Daniels A, Dark P, Dasgin J, David A, David C, Davies E, Davies F, Davies G, Davies GA, Davies K, Dawson J, Daynes E, Deakin B, Deans A, Deas C, Deery J, Defres S, Dell A, Dempsey K, Denneny E, Dennis J, Dewar A, Dharmagunawardena R, Dickens C, Dipper A, Diver S, Diwanji SN, Dixon M, Djukanovic R, Dobson H, Dobson SL, Donaldson A, Dong T, Dormand N, Dougherty A, Dowling R, Drain S, Draxlbauer K, Drury K, Dulawan P, Dunleavy A, Dunn S, Earley J, Edwards S, Edwardson C, El-Taweel H, Elliott A, Elliott K, Ellis Y, Elmer A, Evans D, Evans H, Evans J, Evans R, Evans RI, Evans T, Evenden C, Evison L, Fabbri L, Fairbairn S, Fairman A, Fallon K, Faluyi D, Favager C, Fayzan T, Featherstone J, Felton T, Finch J, Finney S, Finnigan J, Finnigan L, Fisher H, Fletcher S, Flockton R, Flynn M, Foot H, Foote D, Ford A, Forton D, Fraile E, Francis C, Francis R, Francis S, Frankel A, Fraser E, Free R, French N, Fu X, Furniss J, Garner L, Gautam N, George J, George P, Gibbons M, Gill M, Gilmour L, Gleeson F, Glossop J, Glover S, Goodman N, Goodwin C, Gooptu B, Gordon H, Gorsuch T, Greatorex M, Greenhaff PL, Greenhalgh A, Greenwood J, Gregory H, Gregory R, Grieve D, Griffin D, Griffiths L, Guerdette AM, Guillen Guio B, Gummadi M, Gupta A, Gurram S, Guthrie E, Guy Z, H Henson H, Hadley K, Haggar A, Hainey K, Hairsine B, Haldar P, Hall I, Hall L, Halling-Brown M, Hamil R, Hancock A, Hancock K, Hanley NA, Haq S, Hardwick HE, Hardy E, Hardy T, Hargadon B, Harrington K, Harris E, Harrison P, Harvey A, Harvey M, Harvie M, Haslam L, Havinden-Williams M, Hawkes J, Hawkings N, Haworth J, Hayday A, Haynes M, Hazeldine J, Hazelton T, Heeley C, Heeney JL, Heightman M, Henderson M, Hesselden L, Hewitt M, Highett V, Hillman T, Hiwot T, Hoare A, Hoare M, Hockridge J, Hogarth P, Holbourn A, Holden S, Holdsworth L, Holgate D, Holland M, Holloway L, Holmes K, Holmes M, Holroyd-Hind B, Holt L, Hormis A, Hosseini A, Hotopf M, Howard K, Howell A, Hufton E, Hughes AD, Hughes J, Hughes R, Humphries A, Huneke N, Hurditch E, Husain M, Hussell T, Hutchinson J, Ibrahim W, Ilyas F, Ingham J, Ingram L, Ionita D, Isaacs K, Ismail K, Jackson T, James WY, Jarman C, Jarrold I, Jarvis H, Jastrub R, Jayaraman B, Jezzard P, Jiwa K, Johnson C, Johnson S, Johnston D, Jolley CJ, Jones D, Jones G, Jones H, Jones H, Jones I, Jones L, Jones S, Jose S, Kabir T, Kaltsakas G, Kamwa V, Kanellakis N, Kaprowska S, Kausar Z, Keenan N, Kelly S, Kemp G, Kerslake H, Key AL, Khan F, Khunti K, Kilroy S, King B, King C, Kingham L, Kirk J, Kitterick P, Klenerman P, Knibbs L, Knight S, Knighton A, Kon O, Kon S, Kon SS, Koprowska S, Korszun A, Koychev I, Kurasz C, Kurupati P, Laing C, Lamlum H, Landers G, Langenberg C, Lasserson D, Lavelle-Langham L, Lawrie A, Lawson C, Lawson C, Layton A, Lea A, Lee D, Lee JH, Lee E, Leitch K, Lenagh R, Lewis D, Lewis J, Lewis V, Lewis-Burke N, Li X, Light T, Lightstone L, Lilaonitkul W, Lim L, Linford S, Lingford-Hughes A, Lipman M, Liyanage K, Lloyd A, Logan S, Lomas D, Loosley R, Lota H, Lovegrove W, Lucey A, Lukaschuk E, Lye A, Lynch C, MacDonald S, MacGowan G, Macharia I, Mackie J, Macliver L, Madathil S, Madzamba G, Magee N, Magtoto MM, Mairs N, Majeed N, Major E, Malein F, Malim M, Mallison G, Mandal S, Mangion K, Manisty C, Manley R, March K, Marciniak S, Marino P, Mariveles M, Marouzet E, Marsh S, Marshall B, Marshall M, Martin J, Martineau A, Martinez LM, Maskell N, Matila D, Matimba-Mupaya W, Matthews L, Mbuyisa A, McAdoo S, Weir McCall J, McAllister-Williams H, McArdle A, McArdle P, McAulay D, McCormick J, McCormick W, McCourt P, McGarvey L, McGee C, Mcgee K, McGinness J, McGlynn K, McGovern A, McGuinness H, McInnes IB, McIntosh J, McIvor E, McIvor K, McLeavey L, McMahon A, McMahon MJ, McMorrow L, Mcnally T, McNarry M, McNeill J, McQueen A, McShane H, Mears C, Megson C, Megson S, Mehta P, Meiring J, Melling L, Mencias M, Menzies D, Merida Morillas M, Michael A, Milligan L, Miller C, Mills C, Mills NL, Milner L, Misra S, Mitchell J, Mohamed A, Mohamed N, Mohammed S, Molyneaux PL, Monteiro W, Moriera S, Morley A, Morrison L, Morriss R, Morrow A, Moss AJ, Moss P, Motohashi K, Msimanga N, Mukaetova-Ladinska E, Munawar U, Murira J, Nanda U, Nassa H, Nasseri M, Neal A, Needham R, Neill P, Newell H, Newman T, Newton-Cox A, Nicholson T, Nicoll D, Nolan CM, Noonan MJ, Norman C, Novotny P, Nunag J, Nwafor L, Nwanguma U, Nyaboko J, O'Donnell K, O'Brien C, O'Brien L, O'Regan D, Odell N, Ogg G, Olaosebikan O, Oliver C, Omar Z, Orriss-Dib L, Osborne L, Osbourne R, Ostermann M, Overton C, Owen J, Oxton J, Pack J, Pacpaco E, Paddick S, Painter S, Pakzad A, Palmer S, Papineni P, Paques K, Paradowski K, Pareek M, Parfrey H, Pariante C, Parker S, Parkes M, Parmar J, Patale S, Patel B, Patel M, Patel S, Pattenadk D, Pavlides M, Payne S, Pearce L, Pearl JE, Peckham D, Pendlebury J, Peng Y, Pennington C, Peralta I, Perkins E, Peterkin Z, Peto T, Petousi N, Petrie J, Phipps J, Pimm J, Piper Hanley K, Pius R, Plant H, Plein S, Plekhanova T, Plowright M, Polgar O, Poll L, Porter J, Portukhay S, Powell N, Prabhu A, Pratt J, Price A, Price C, Price C, Price D, Price L, Price L, Prickett A, Propescu J, Pugmire S, Quaid S, Quigley J, Qureshi H, Qureshi IN, Radhakrishnan K, Ralser M, Ramos A, Ramos H, Rangeley J, Rangelov B, Ratcliffe L, Ravencroft P, Reddington A, Reddy R, Redfearn H, Redwood D, Reed A, Rees M, Rees T, Regan K, Reynolds W, Ribeiro C, Richards A, Richardson E, Rivera-Ortega P, Roberts K, Robertson E, Robinson E, Robinson L, Roche L, Roddis C, Rodger J, Ross A, Ross G, Rossdale J, Rostron A, Rowe A, Rowland A, Rowland J, Roy K, Roy M, Rudan I, Russell R, Russell E, Saalmink G, Sabit R, Sage EK, Samakomva T, Samani N, Sampson C, Samuel K, Samuel R, Sanderson A, Sapey E, Saralaya D, Sargant J, Sarginson C, Sass T, Sattar N, Saunders K, Saunders P, Saunders LC, Savill H, Saxon W, Sayer A, Schronce J, Schwaeble W, Scott K, Selby N, Sewell TA, Shah K, Shah P, Shankar-Hari M, Sharma M, Sharpe C, Sharpe M, Shashaa S, Shaw A, Shaw K, Shaw V, Shelton S, Shenton L, Shevket K, Short J, Siddique S, Siddiqui S, Sidebottom J, Sigfrid L, Simons G, Simpson J, Simpson N, Singh C, Singh S, Sissons D, Skeemer J, Slack K, Smith A, Smith D, Smith S, Smith J, Smith L, Soares M, Solano TS, Solly R, Solstice AR, Soulsby T, Southern D, Sowter D, Spears M, Spencer LG, Speranza F, Stadon L, Stanel S, Steele N, Steiner M, Stensel D, Stephens G, Stephenson L, Stern M, Stewart I, Stimpson R, Stockdale S, Stockley J, Stoker W, Stone R, Storrar W, Storrie A, Storton K, Stringer E, Strong-Sheldrake S, Stroud N, Subbe C, Sudlow CL, Suleiman Z, Summers C, Summersgill C, Sutherland D, Sykes DL, Sykes R, Talbot N, Tan AL, Tarusan L, Tavoukjian V, Taylor A, Taylor C, Taylor J, Te A, Tedd H, Tee CJ, Teixeira J, Tench H, Terry S, Thackray-Nocera S, Thaivalappil F, Thamu B, Thickett D, Thomas C, Thomas S, Thomas AK, Thomas-Woods T, Thompson T, Thompson AAR, Thornton T, Tilley J, Tinker N, Tiongson GF, Tobin M, Tomlinson J, Tong C, Touyz R, Tripp KA, Tunnicliffe E, Turnbull A, Turner E, Turner S, Turner V, Turner K, Turney S, Turtle L, Turton H, Ugoji J, Ugwuoke R, Upthegrove R, Valabhji J, Ventura M, Vere J, Vickers C, Vinson B, Wade E, Wade P, Wainwright T, Wajero LO, Walder S, Walker S, Walker S, Wall E, Wallis T, Walmsley S, Walsh JA, Walsh S, Warburton L, Ward TJC, Warwick K, Wassall H, Waterson S, Watson E, Watson L, Watson J, Welch C, Welch H, Welsh B, Wessely S, West S, Weston H, Wheeler H, White S, Whitehead V, Whitney J, Whittaker S, Whittam B, Whitworth V, Wight A, Wild J, Wilkins M, Wilkinson D, Williams N, Williams N, Williams J, Williams-Howard SA, Willicombe M, Willis G, Willoughby J, Wilson A, Wilson D, Wilson I, Window N, Witham M, Wolf-Roberts R, Wood C, Woodhead F, Woods J, Wormleighton J, Worsley J, Wraith D, Wrey Brown C, Wright C, Wright L, Wright S, Wyles J, Wynter I, Xu M, Yasmin N, Yasmin S, Yates T, Yip KP, Young B, Young S, Young A, Yousuf AJ, Zawia A, Zeidan L, Zhao B, Zongo O. Clinical characteristics with inflammation profiling of long COVID and association with 1-year recovery following hospitalisation in the UK: a prospective observational study. Lancet Respir Med 2022; 10:761-775. [PMID: 35472304 PMCID: PMC9034855 DOI: 10.1016/s2213-2600(22)00127-8] [Citation(s) in RCA: 144] [Impact Index Per Article: 72.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 03/23/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND No effective pharmacological or non-pharmacological interventions exist for patients with long COVID. We aimed to describe recovery 1 year after hospital discharge for COVID-19, identify factors associated with patient-perceived recovery, and identify potential therapeutic targets by describing the underlying inflammatory profiles of the previously described recovery clusters at 5 months after hospital discharge. METHODS The Post-hospitalisation COVID-19 study (PHOSP-COVID) is a prospective, longitudinal cohort study recruiting adults (aged ≥18 years) discharged from hospital with COVID-19 across the UK. Recovery was assessed using patient-reported outcome measures, physical performance, and organ function at 5 months and 1 year after hospital discharge, and stratified by both patient-perceived recovery and recovery cluster. Hierarchical logistic regression modelling was performed for patient-perceived recovery at 1 year. Cluster analysis was done using the clustering large applications k-medoids approach using clinical outcomes at 5 months. Inflammatory protein profiling was analysed from plasma at the 5-month visit. This study is registered on the ISRCTN Registry, ISRCTN10980107, and recruitment is ongoing. FINDINGS 2320 participants discharged from hospital between March 7, 2020, and April 18, 2021, were assessed at 5 months after discharge and 807 (32·7%) participants completed both the 5-month and 1-year visits. 279 (35·6%) of these 807 patients were women and 505 (64·4%) were men, with a mean age of 58·7 (SD 12·5) years, and 224 (27·8%) had received invasive mechanical ventilation (WHO class 7-9). The proportion of patients reporting full recovery was unchanged between 5 months (501 [25·5%] of 1965) and 1 year (232 [28·9%] of 804). Factors associated with being less likely to report full recovery at 1 year were female sex (odds ratio 0·68 [95% CI 0·46-0·99]), obesity (0·50 [0·34-0·74]) and invasive mechanical ventilation (0·42 [0·23-0·76]). Cluster analysis (n=1636) corroborated the previously reported four clusters: very severe, severe, moderate with cognitive impairment, and mild, relating to the severity of physical health, mental health, and cognitive impairment at 5 months. We found increased inflammatory mediators of tissue damage and repair in both the very severe and the moderate with cognitive impairment clusters compared with the mild cluster, including IL-6 concentration, which was increased in both comparisons (n=626 participants). We found a substantial deficit in median EQ-5D-5L utility index from before COVID-19 (retrospective assessment; 0·88 [IQR 0·74-1·00]), at 5 months (0·74 [0·64-0·88]) to 1 year (0·75 [0·62-0·88]), with minimal improvements across all outcome measures at 1 year after discharge in the whole cohort and within each of the four clusters. INTERPRETATION The sequelae of a hospital admission with COVID-19 were substantial 1 year after discharge across a range of health domains, with the minority in our cohort feeling fully recovered. Patient-perceived health-related quality of life was reduced at 1 year compared with before hospital admission. Systematic inflammation and obesity are potential treatable traits that warrant further investigation in clinical trials. FUNDING UK Research and Innovation and National Institute for Health Research.
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He Y, Li Y, Bai Z, Xie M, Zuo R, Liu J, Xia J, Cheng X, Liu Y, Tong C, Zhang Y, Liu S. Genome-wide identification and functional analysis of cupin_1 domain-containing members involved in the responses to Sclerotinia sclerotiorum and abiotic stress in Brassica napus. Front Plant Sci 2022; 13:983786. [PMID: 35979083 PMCID: PMC9377217 DOI: 10.3389/fpls.2022.983786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 07/11/2022] [Indexed: 06/15/2023]
Abstract
Cupin_1 domain-containing proteins (CDPs) are ubiquitously present in higher plants, which are known to play essential roles in various biological processes. In this study, we carried out genome-wide characterization and systematic investigation of the CDP genes in Brassica napus. A total of 96 BnCDPs, including 71 germin-like proteins (GLPs; proteins with a single cupin_1 domain) and 25 CDP bicupins (proteins with two cupin_1 domains), were identified and clustered into six distinct subfamilies (I-VI) based on the phylogenic analysis, gene structure and motif distribution. Further analysis indicated that whole-genome duplication (WGD) and segmental duplication are main contributors to the species-specific expansion of the BnCDP gene family, and all the duplicated genes subsequently underwent strong purification selection. The promoter region of BnCDPs showed enrichment of cis-regulatory elements associated with development, hormone and stress, as well as transcription factor binding sites, which validates the prediction that BnCDPs are widely involved in plant growth and biotic and abiotic stress responses. The BnCDPs in different subfamilies exhibited obvious differences in expression among 30 developmental tissues/stages of B. napus, implying that BnCDPs may be involved in tissue- and stage-specific developmental processes. Similar trends in expression of most BnCDPs were observed under Sclerotinia sclerotiorum inoculation and four abiotic stresses (dehydration, cold, ABA and salinity), particularly the BnGLPs in subfamily I and III with single cupin_1 domain, revealing that BnCDPs are of great importance in the environmental adaption of B. napus. We then performed a genome-wide association study (GWAS) of 274 B. napus core germplasms on S. sclerotiorum resistance and identified four significantly associated loci harboring five BnGLPs. The expression levels of two candidate genes, BnGLP1.A08 and BnGLP1.C08, were significantly correlated with S. sclerotiorum resistance. Their functional responses to multiple stages of S. sclerotiorum inoculation and four abiotic stresses were further examined through qPCR. Overall, this study provides rich resources for research on the function and evolutionary playground of CDP genes.
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Affiliation(s)
- Yizhou He
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, School of Life Sciences, Hubei University, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
| | - Zetao Bai
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Meili Xie
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Rong Zuo
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jie Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Jing Xia
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yuanyuan Zhang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, School of Life Sciences, Hubei University, Wuhan, China
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Wahid S, Xie M, Sarfraz S, Liu J, Zhao C, Bai Z, Tong C, Cheng X, Gao F, Liu S. Genome-Wide Identification and Analysis of Ariadne Gene Family Reveal Its Genetic Effects on Agronomic Traits of Brassica napus. Int J Mol Sci 2022; 23:ijms23116265. [PMID: 35682945 PMCID: PMC9181464 DOI: 10.3390/ijms23116265] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 05/27/2022] [Accepted: 05/29/2022] [Indexed: 02/04/2023] Open
Abstract
E3 ligases promote protein ubiquitination and degradation, which regulate every aspect of eukaryotic life. The Ariadne (ARI) proteins of RBR (ring between ring fingers) protein subfamily has been discovered as a group of potential E3 ubiquitin ligases. Only a few available research studies show their role in plant adaptations processes against the external environment. Presently, the functions of ARI proteins are largely unknown in plants. Therefore, in this study, we performed genome-wide analysis to identify the ARI gene family and explore their potential importance in B. napus. A total of 39 ARI genes were identified in the B. napus genome and were classified into three subfamilies (A, B and C) based on phylogenetic analysis. The protein–protein interaction networks and enrichment analysis indicated that BnARI genes could be involved in endoreduplication, DNA repair, proteasome assembly, ubiquitination, protein kinase activity and stress adaptation. The transcriptome data analysis in various tissues provided us an indication of some BnARI genes’ functional importance in tissue development. We also identified potential BnARI genes that were significantly responsive towards the abiotic stresses. Furthermore, eight BnARI genes were identified as candidate genes for multiple agronomic traits through association mapping analysis in B. napus; among them, BnaA02g12100D, which is the ortholog of AtARI8, was significantly associated with ten agronomic traits. This study provided useful information on BnARI genes, which could aid targeted functional research and genetic improvement for breeding in B. napus.
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Xie M, Zuo R, Bai Z, Yang L, Zhao C, Gao F, Cheng X, Huang J, Liu Y, Li Y, Tong C, Liu S. Genome-Wide Characterization of Serine/Arginine-Rich Gene Family and Its Genetic Effects on Agronomic Traits of Brassica napus. Front Plant Sci 2022; 13:829668. [PMID: 35251101 PMCID: PMC8889041 DOI: 10.3389/fpls.2022.829668] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
Serine/arginine-rich (SR) proteins are indispensable factors for RNA splicing, and they play important roles in development and abiotic stress responses. However, little information on SR genes in Brassica napus is available. In this study, 59 SR genes were identified and classified into seven subfamilies: SR, SCL, RS2Z, RSZ, RS, SR45, and SC. In each subfamily, the genes showed relatively conserved structures and motifs, but displayed distinct expression patterns in different tissues and under abiotic stress, which might be caused by the varied cis-acting regulatory elements among them. Transcriptome datasets from Pacbio/Illumina platforms showed that alternative splicing of SR genes was widespread in B. napus and the majority of paralogous gene pairs displayed different splicing patterns. Protein-protein interaction analysis indicated that SR proteins were involved in the regulation of the whole lifecycle of mRNA, from synthesis to decay. Moreover, the association mapping analysis suggested that 12 SR genes were candidate genes for regulating specific agronomic traits, which indicated that SR genes could affect the development and hence influence the important agronomic traits of B. napus. In summary, this study provided elaborate information on SR genes in B. napus, which will aid further functional studies and genetic improvement of agronomic traits in B. napus.
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Liu S, Chen H, Wang C, Xu Q, Feng S, Wang Y, Yao J, Zhou Q, Tong C, Yang B, Chen J, Jiang H. POS-340 MAPK1 MEDIATES HIGH GLUCOSE INDUCED RENAL TUBULAR INJURY THROUGH DISRUPTING THE INTEGRITY OF MAM. Kidney Int Rep 2022. [DOI: 10.1016/j.ekir.2022.01.361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Tong C, Wang Y, Han WD. [Structural optimization and prospect of chimeric antigen receptor T cells]. Zhonghua Xue Ye Xue Za Zhi 2021; 42:771-777. [PMID: 34753236 PMCID: PMC8607033 DOI: 10.3760/cma.j.issn.0253-2727.2021.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- C Tong
- The First Medical Center, The Chinese People's Liberation Army General Hospital, Beijing 100853, China
| | - Y Wang
- The First Medical Center, The Chinese People's Liberation Army General Hospital, Beijing 100853, China
| | - W D Han
- The First Medical Center, The Chinese People's Liberation Army General Hospital, Beijing 100853, China
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Reising MM, Tong C, Harris B, Toohey-Kurth KL, Crossley B, Mulrooney D, Tallmadge RL, Schumann KR, Lock AB, Loiacono CM. A review of guidelines for evaluating a minor modification to a validated assay. REV SCI TECH OIE 2021; 40:217-226. [PMID: 34140729 DOI: 10.20506/rst.40.1.3219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Any modification to a validated assay must be evaluated in terms of the impact on the assay's performance characteristics and whether the assay remains fit for the intended purpose. The comparison is referred to as a 'method comparison', 'method comparability', 'method change', or 'comparative validation'. This review presents recommendations and examples of studies found in the current literature as a means of assessing minor modifications. In addition, the authors discuss common statistical approaches used for these comparisons.
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Dong Z, Alam MK, Xie M, Yang L, Liu J, Helal MMU, Huang J, Cheng X, Liu Y, Tong C, Zhao C, Liu S. Mapping of a major QTL controlling plant height using a high-density genetic map and QTL-seq methods based on whole-genome resequencing in Brassica napus. G3 (Bethesda) 2021; 11:6219302. [PMID: 33836054 PMCID: PMC8495924 DOI: 10.1093/g3journal/jkab118] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 04/06/2021] [Indexed: 12/02/2022]
Abstract
Plant height is a crucial element related to plant architecture that influences the seed yield of oilseed rape (Brassica napus L.). In this study, we isolated a natural B. napus mutant, namely a semi-dwarf mutant (sdw-e), which exhibits a 30% reduction in plant height compared with Zhongshuang 11-HP (ZS11-HP). Quantitative trait locus sequencing (QTL-seq) was conducted using two extreme DNA bulks in F2 populations in Wuchang-2017 derived from ZS11-HP × sdw-e to identify QTLs associated with plant height. The result suggested that two QTL intervals were located on chromosome A10. The F2 population consisting of 200 individuals in Yangluo-2018 derived from ZS11-HP × sdw-e was used to construct a high-density linkage map using whole-genome resequencing. The high-density linkage map harbored 4323 bin markers and covered a total distance of 2026.52 cM with an average marker interval of 0.47 cM. The major QTL for plant height named qPHA10 was identified on linkage group A10 by interval mapping and composite interval mapping methods. The major QTL qPHA10 was highly consistent with the QTL-seq results. And then, we integrated the variation sites and expression levels of genes in the major QTL interval to predict the candidate genes. Thus, the identified QTL and candidate genes could be used in marker-assisted selection for B. napus breeding in the future.
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Affiliation(s)
- Zhixue Dong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - Muhammad Khorshed Alam
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Meili Xie
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Li Yang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,Biosystematics Group, Experimental Plant Sciences, Wageningen University and Research, Wageningen, Netherlands
| | - Jie Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China.,National Key Laboratory of Crop Genetic Improvement, National Center of Rapeseed Improvement, Huazhong Agricultural University, Wuhan 430070, P. R. China
| | - M M U Helal
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Junyan Huang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Xiaohui Cheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Yueying Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Chuanji Zhao
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
| | - Shengyi Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences/The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture and Rural Affairs, Wuhan 430062, P. R. China
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Garreis R, Knothe A, Tong C, Eich M, Gold C, Watanabe K, Taniguchi T, Fal'ko V, Ihn T, Ensslin K, Kurzmann A. Shell Filling and Trigonal Warping in Graphene Quantum Dots. Phys Rev Lett 2021; 126:147703. [PMID: 33891439 DOI: 10.1103/physrevlett.126.147703] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Transport measurements through a few-electron circular quantum dot in bilayer graphene display bunching of the conductance resonances in groups of four, eight, and twelve. This is in accordance with the spin and valley degeneracies in bilayer graphene and an additional threefold "minivalley degeneracy" caused by trigonal warping. For small electron numbers, implying a small dot size and a small displacement field, a two-dimensional s shell and then a p shell are successively filled with four and eight electrons, respectively. For electron numbers larger than 12, as the dot size and the displacement field increase, the single-particle ground state evolves into a threefold degenerate minivalley ground state. A transition between these regimes is observed in our measurements and can be described by band-structure calculations. Measurements in the magnetic field confirm Hund's second rule for spin filling of the quantum dot levels, emphasizing the importance of exchange interaction effects.
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Affiliation(s)
- R Garreis
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - A Knothe
- National Graphene Institute, University of Manchester, Manchester M13 9PL, United Kingdom
| | - C Tong
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - M Eich
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - C Gold
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - K Watanabe
- National Institute for Material Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - T Taniguchi
- National Institute for Material Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - V Fal'ko
- National Graphene Institute, University of Manchester, Manchester M13 9PL, United Kingdom
- Henry Royce Institute for Advanced Materials, M13 9PL, Manchester, United Kingdom
| | - T Ihn
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - K Ensslin
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
| | - A Kurzmann
- ETH Zurich (Swiss Federal Institute of Technology in Zurich), 8093 Zurich, Switzerland
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Chen X, Tong C, Zhang X, Song A, Hu M, Dong W, Chen F, Wang Y, Tu J, Liu S, Tang H, Zhang L. A high-quality Brassica napus genome reveals expansion of transposable elements, subgenome evolution and disease resistance. Plant Biotechnol J 2021; 19:615-630. [PMID: 33073445 PMCID: PMC7955885 DOI: 10.1111/pbi.13493] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Revised: 09/21/2020] [Accepted: 10/13/2020] [Indexed: 05/03/2023]
Abstract
Rapeseed (Brassica napus L.) is a recent allotetraploid crop, which is well known for its high oil production. Here, we report a high-quality genome assembly of a typical semi-winter rapeseed cultivar, 'Zhongshuang11' (hereafter 'ZS11'), using a combination of single-molecule sequencing and chromosome conformation capture (Hi-C) techniques. Most of the high-confidence sequences (93.1%) were anchored to the individual chromosomes with a total of 19 centromeres identified, matching the exact chromosome count of B. napus. The repeat sequences in the A and C subgenomes in B. napus expanded significantly from 500 000 years ago, especially over the last 100 000 years. These young and recently amplified LTR-RTs showed dispersed chromosomal distribution but significantly preferentially clustered into centromeric regions. We exhaustively annotated the nucleotide-binding leucine-rich repeat (NLR) gene repertoire, yielding a total of 597 NLR genes in B. napus genome and 17.4% of which are paired (head-to-head arrangement). Based on the resequencing data of 991 B. napus accessions, we have identified 18 759 245 single nucleotide polymorphisms (SNPs) and detected a large number of genomic regions under selective sweep among the three major ecotype groups (winter, semi-winter and spring) in B. napus. We found 49 NLR genes and five NLR gene pairs colocated in selective sweep regions with different ecotypes, suggesting a rapid diversification of NLR genes during the domestication of B. napus. The high quality of our B. napus 'ZS11' genome assembly could serve as an important resource for the study of rapeseed genomics and reveal the genetic variations associated with important agronomic traits.
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Affiliation(s)
- Xuequn Chen
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Xingtan Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Aixia Song
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ming Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Wei Dong
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Fei Chen
- College of HorticultureNanjing Agricultural UniversityNanjingChina
| | - Youping Wang
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Jinxing Tu
- National Key Laboratory of Crop Genetic ImprovementNational Center of Rapeseed ImprovementHuazhong Agricultural UniversityWuhanChina
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil CropsThe Ministry of Agriculture and Rural Affairs of PRCOil Crops Research InstituteChinese Academy of Agricultural SciencesWuhanChina
| | - Haibao Tang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liangsheng Zhang
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems BiologyKey Laboratory of Ministry of Education for Genetics & Breeding and Multiple Utilization of CropsCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhouChina
- Genomics and Genetic Engineering Laboratory of Ornamental PlantsCollege of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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31
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Liu L, Qin L, Cheng X, Zhang Y, Xu L, Liu F, Tong C, Huang J, Liu S, Wei Y. Comparing the Infection Biology of Plasmodiophora brassicae in Clubroot Susceptible and Resistant Hosts and Non-hosts. Front Microbiol 2020; 11:507036. [PMID: 33178139 PMCID: PMC7596292 DOI: 10.3389/fmicb.2020.507036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 09/17/2020] [Indexed: 11/13/2022] Open
Abstract
The potential infection biology of Plasmodiophora brassicae in resistant hosts and non-hosts is still not completely understood. Clubroot resistance assay on European clubroot differentials (ECD) set revealed that ECD10 (Brassica napus) and ECD4 (Brassica rapa) show a complete resistance to the tested P. brassicae isolate in contrast to highly susceptible hosts Westar (B. napus) and ECD5 (B. rapa). Previously, we used fluorescent probe-based confocal microscopy (FCM) to refine the life cycle of P. brassicae and indicate the important time points during its infection in Arabidopsis. Here, we used FCM to systematically investigate the infection of P. brassicae in two resistant host species ECD10 and ECD4 and two non-host crops wheat and barley at each indicated time points, compared with two susceptible hosts Westar and ECD5. We found that P. brassicae can initiate the primary infection phase and produce uninucleate primary plasmodia in both resistant hosts and non-hosts just like susceptible hosts at 2 days post-inoculation (dpi). Importantly, P. brassicae can develop into zoosporangia and secondary zoospores and release the secondary zoospores from the zoosporangia in resistant hosts at 7 dpi, comparable to susceptible hosts. However, during the secondary infection phase, no secondary plasmodium was detected in the cortical cells of both resistant hosts in contrast to massive secondary plasmodia present in the cortex tissue of two susceptible hosts leading to root swelling at 15 dpi. In both non-host crops, only uninucleate primary plasmodia were observed throughout roots at 7 and 15 dpi. Quantitative PCR based on DNA revealed that the biomass of P. brassicae has no significant increase from 2 dpi in non-host plants and from 7 dpi in resistant host plants, compared to the huge biomass increase in susceptible host plants from 2 to 25 dpi. Our study reveals that the primary infection phase in the root epidermis and the secondary infection phase in the cortex tissue are, respectively, blocked in non-hosts and resistant hosts, contributing to understanding of cellular and molecular mechanisms underlying clubroot non-host and host resistance.
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Affiliation(s)
- Lijiang Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China.,Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Li Qin
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Li Xu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Yangdou Wei
- Department of Biology, University of Saskatchewan, Saskatoon, SK, Canada
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32
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Yao S, Liang F, Gill RA, Huang J, Cheng X, Liu Y, Tong C, Liu S. A global survey of the transcriptome of allopolyploid Brassica napus based on single-molecule long-read isoform sequencing and Illumina-based RNA sequencing data. Plant J 2020; 103:843-857. [PMID: 32270540 DOI: 10.1111/tpj.14754] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 03/15/2020] [Accepted: 03/18/2020] [Indexed: 05/21/2023]
Abstract
Brassica napus is a recent allopolyploid derived from the hybridization of Brassica rapa (Ar Ar ) and Brassica oleracea (Co Co ). Because of the high sequence similarity between the An and Cn subgenomes, it is difficult to provide an accurate landscape of the whole transcriptome of B. napus. To overcome this problem, we applied a single-molecule long-read isoform sequencing (Iso-Seq) technique that can produce long reads to explore the complex transcriptome of B. napus at the isoform level. From the Iso-Seq data, we obtained 147 698 non-redundant isoforms, capturing 37 403 annotated genes. A total of 18.1% (14 934/82 367) of the multi-exonic genes showed alternative splicing (AS). In addition, we identified 549 long non-coding RNAs, the majority of which displayed tissue-specific expression profiles, and detected 7742 annotated genes that possessed isoforms containing alternative polyadenylation sites. Moreover, 31 591 AS events located in open reading frames (ORFs) lead to potential protein isoforms by in-frame or frameshift changes in the ORF. Illumina RNA sequencing of five tissues that were pooled for Iso-Seq was also performed and showed that 69% of the AS events were tissue-specific. Our data provide abundant transcriptome resources for a transcript isoform catalog of B. napus, which will facilitate genome reannotation, strengthen our understanding of the B. napus transcriptome and be applied for further functional genomic research.
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Affiliation(s)
- Shengli Yao
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Fan Liang
- Nextomics Biosciences, Wuhan, 430000, Hubei, China
| | - Rafaqat Ali Gill
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Junyan Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Xiaohui Cheng
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Yueying Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture and Rural Affairs of the PRC, Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan, 430062, Hubei, China
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Qi H, Luo X, Zheng Y, Zhang H, Li J, Zou L, Feng L, Chen D, Shi Y, Tong C, Baker PN. Safe delivery for pregnancies affected by COVID-19. BJOG 2020; 127:927-929. [PMID: 32219995 DOI: 10.1111/1471-0528.16231] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2020] [Indexed: 01/30/2023]
Affiliation(s)
- H Qi
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - X Luo
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Y Zheng
- Department of Stem Cell Transplantation and Cell Therapy, MD Anderson Cancer Center, Houston, Texas, USA
| | - H Zhang
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - J Li
- Department of Obstetrics and Gynaecology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei, China
| | - L Zou
- Department of Obstetrics and Gynaecology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - L Feng
- Department of Obstetrics and Gynaecology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China
| | - D Chen
- Department of Obstetrics and Gynaecology, Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Y Shi
- Department of Neonatology, Children's Hospital of Chongqing Medical University, Chongqing, China
| | - C Tong
- Department of Obstetrics and Gynaecology, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - P N Baker
- College of Life Sciences, University of Leicester, Leicester, UK
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Tang M, Tong C, Liang L, Du C, Zhao J, Xiao L, Tong J, Dai X, Helal M, Dai W, Xiang Y. A recessive high-density pod mutant resource of Brassica napus. Plant Sci 2020; 293:110411. [PMID: 32081260 DOI: 10.1016/j.plantsci.2020.110411] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 01/06/2020] [Accepted: 01/07/2020] [Indexed: 05/28/2023]
Abstract
In Brassica napus, pod number and pod density are critical factors to determine seed yield. Although the pod density is an essential yield trait, the regulation of yield formation in oil crops, as well as the genetic and molecular mechanisms, are poorly understood. In this study, we characterized a rapeseed high-density pod mutant (dpt247) from composite hybridization. To shed some light on the nature of this mutation, it was investigated morphologically, anatomically, physiologically, genetically and transcriptomically. The mutant plant showed noticeable phenotypic differences in comparison with the control plant, including reduced plant height and primary branch length, decreased number of primary branches, significantly increased number of pod on the main inflorescence, and more compact pod distribution. Besides, the mutant had higher levels of indole-3-acetic acid (IAA) and zeatin riboside (ZR) in the shoot apical meristem (SAM). The dense pod trait was controlled by two major recessive genes identified in the segregating genetic populations of GRE501 and dpt247. RNA sequencing indicated genes participated in auxin, cytokinin and WUS/CLV signalling pathway in dpt247 were more active in the mutant. These results provide important information for understanding the regulation of yield formation and high yield breeding in rapeseed.
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Affiliation(s)
- Minqiang Tang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China; Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, PR China
| | - Chaobo Tong
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, PR China
| | - Longbin Liang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Caifu Du
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Jixian Zhao
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Langtao Xiao
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, PR China
| | - Jianhua Tong
- Hunan Provincial Key Laboratory of Phytohormones and Growth and Development, Hunan Agricultural University, Changsha 410128, PR China
| | - Xianglai Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Mmu Helal
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan 430062, PR China
| | - Wendong Dai
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China
| | - Yang Xiang
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, PR China.
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35
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Pan Q, Zhu B, Zhang D, Tong C, Ge X, Liu S, Li Z. Gene Expression Changes During the Allo-/Deallopolyploidization Process of Brassica napus. Front Genet 2020; 10:1279. [PMID: 31921314 PMCID: PMC6931035 DOI: 10.3389/fgene.2019.01279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 11/21/2019] [Indexed: 11/21/2022] Open
Abstract
Gene expression changes due to allopolyploidization have been extensively studied in plants over the past few decades. Nearly all these studies focused on comparing the changes before and after genome merger. In this study, we used the uniquely restituted Brassica rapa (RBR, AeAe, 2n = 20) obtained from Brassica napus (AnAnCnCn, 2n = 38) to analyze the gene expression changes and its potential mechanism during the process of allo-/deallopolyploidization. RNA-seq-based transcriptome profiling identified a large number of differentially expressed genes (DEGs) between RBR and natural B. rapa (ArAr), suggesting potential effects of allopolyploidization/domestication of AA component of B. napus at the tetrapolyploid level. Meanwhile, it was revealed that up to 20% of gene expressions were immediately altered when compared with those in the An-subgenome. Interestingly, one fifth of these changes are in fact indicative of the recovery of antecedent gene expression alternations occurring since the origin of B. napus and showed association with homoeologous expression bias between An and Cn subgenomes. Enrichment of distinct gene ontology (GO) categories of the above sets of genes further indicated potential functional cooperation of the An and Cn subgenome of B. napus. Whole genome methylation analysis revealed a small number of DEGs were identified in the differentially methylated regions.
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Affiliation(s)
- Qi Pan
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Bin Zhu
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Dawei Zhang
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Xianhong Ge
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, Wuhan, China.,Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Wuhan, China
| | - Zaiyun Li
- National Key Laboratory of Crop Genetic Improvement, Key Laboratory of Rapeseed Genetics and Breeding of Agriculture Ministry of China, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China
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36
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Yu R, So MC, Tong C, Ho F, Woo J. Older Adults' Perspective towards Participation in a Multicomponent Frailty Prevention Program: A Qualitative Study. J Nutr Health Aging 2020; 24:758-764. [PMID: 32744573 DOI: 10.1007/s12603-020-1369-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
OBJECTIVES This study aimed to explore pre-frail and frail older Chinese people's perspectives on a multi-component, group-based frailty prevention program in Hong Kong, along with their views regarding factors determining participation and sustainability of such program. DESIGN Seven focus groups were conducted. SETTING Community elderly centres. PARTICIPANTS A total of 38 community-dwelling older people aged 54 - 84 (mean age, 64.9 years; female, 58%; married, 68%; retired, 97%) screened with pre-frailty or frailty completing a 12-week multi-component (involving physical, cognitive, and social activities), group-based frailty prevention program were interviewed. MEASUREMENTS Thematic analysis was conducted. RESULTS Using thematic analysis, perceived health benefits, peer support and social networking were identified as key motivators concerning intention to participate in the frailty prevention program; whereas perceived health benefits, socializing, sense of connectedness, expert guidance and sense of dignity were identified as key motivators concerning program adherence. CONCLUSION Majority of participants provided positive feedbacks about the multi-component intervention program in regards to their physical health, psychological well-being and social life. These findings highlighted several important factors for consideration in future design of frailty interventions regarding the needs of pre-frail and frail older adults, which could help to motivate and sustain their participation in community-based frailty prevention programs.
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Affiliation(s)
- R Yu
- Ruby Yu, Department of Medicine and Therapeutics, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, SAR, China, Tel: (852) 3943 5142, Fax: (852) 2637 9215, E-mail:
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Li Y, Dong C, Hu M, Bai Z, Tong C, Zuo R, Liu Y, Cheng X, Cheng M, Huang J, Liu S. Identification of Flower-Specific Promoters through Comparative Transcriptome Analysis in Brassica napus. Int J Mol Sci 2019; 20:ijms20235949. [PMID: 31779216 PMCID: PMC6928827 DOI: 10.3390/ijms20235949] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/20/2019] [Accepted: 11/25/2019] [Indexed: 01/24/2023] Open
Abstract
Brassica napus (oilseed rape) is an economically important oil crop worldwide. Sclerotinia stem rot (SSR) caused by Sclerotinia sclerotiorum is a threat to oilseed rape production. Because the flower petals play pivotal roles in the SSR disease cycle, it is useful to express the resistance-related genes specifically in flowers to hinder further infection with S. sclerotiorum. To screen flower-specific promoters, we first analyzed the transcriptome data from 12 different tissues of the B. napus line ZS11. In total, 249 flower-specific candidate genes with high expression in petals were identified, and the expression patterns of 30 candidate genes were verified by quantitative real-time transcription-PCR (qRT-PCR) analysis. Furthermore, two novel flower-specific promoters (FSP046 and FSP061 promoter) were identified, and the tissue specificity and continuous expression in petals were determined in transgenic Arabidopsis thaliana with fusing the promoters to β-glucuronidase (GUS)-reporter gene. GUS staining, transcript expression pattern, and GUS activity analysis indicated that FSP046 and FSP061 promoter were strictly flower-specific promoters, and FSP046 promoter had a stronger activity. The two promoters were further confirmed to be able to direct GUS expression in B. napus flowers using transient expression system. The transcriptome data and the flower-specific promoters screened in the present study will benefit fundamental research for improving the agronomic traits as well as disease and pest control in a tissue-specific manner.
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Kurzmann A, Eich M, Overweg H, Mangold M, Herman F, Rickhaus P, Pisoni R, Lee Y, Garreis R, Tong C, Watanabe K, Taniguchi T, Ensslin K, Ihn T. Excited States in Bilayer Graphene Quantum Dots. Phys Rev Lett 2019; 123:026803. [PMID: 31386494 DOI: 10.1103/physrevlett.123.026803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Indexed: 05/21/2023]
Abstract
We report ground- and excited-state transport through an electrostatically defined few-hole quantum dot in bilayer graphene in both parallel and perpendicular applied magnetic fields. A remarkably clear level scheme for the two-particle spectra is found by analyzing finite bias spectroscopy data within a two-particle model including spin and valley degrees of freedom. We identify the two-hole ground state to be a spin-triplet and valley-singlet state. This spin alignment can be seen as Hund's rule for a valley-degenerate system, which is fundamentally different from quantum dots in carbon nanotubes, where the two-particle ground state is a spin-singlet state. The spin-singlet excited states are found to be valley-triplet states by tilting the magnetic field with respect to the sample plane. We quantify the exchange energy to be 0.35 meV and measure a valley and spin g factor of 36 and 2, respectively.
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Affiliation(s)
- A Kurzmann
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - M Eich
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - H Overweg
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - M Mangold
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - F Herman
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - P Rickhaus
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - R Pisoni
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Y Lee
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - R Garreis
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - C Tong
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - K Watanabe
- National Institute for Material Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - T Taniguchi
- National Institute for Material Science, 1-1 Namiki, Tsukuba 305-0044, Japan
| | - K Ensslin
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
| | - T Ihn
- Solid State Physics Laboratory, ETH Zurich, CH-8093 Zurich, Switzerland
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Zhang F, Huang J, Tang M, Cheng X, Liu Y, Tong C, Yu J, Sadia T, Dong C, Liu L, Tang B, Chen J, Liu S. Syntenic quantitative trait loci and genomic divergence for Sclerotinia resistance and flowering time in Brassica napus. J Integr Plant Biol 2019; 61:75-88. [PMID: 30506639 DOI: 10.1111/jipb.12754] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 11/26/2018] [Indexed: 06/09/2023]
Abstract
Oilseed rape (Brassica napus) is an allotetraploid with two subgenomes descended from a common ancestor. Accordingly, its genome contains syntenic regions with many duplicate genes, some of which may have retained their original functions, whereas others may have diverged. Here, we mapped quantitative trait loci (QTL) for stem rot resistance (SRR), a disease caused by the fungus Sclerotinia sclerotiorum, and flowering time (FT) in a recombinant inbred line population. The population was genotyped using B. napus 60K single nucleotide polymorphism arrays and phenotyped in six (FT) and nine (SSR) experimental conditions or environments. In total, we detected 30 SRR QTL and 22 FT QTL and show that some of the major QTL associated with these two traits were co-localized, suggesting a genetic linkage between them. Two SRR QTL on chromosome A2 and two on chromosome C2 were shown to be syntenic, suggesting the functional conservation of these regions. We used the syntenic properties of the genomic regions to exclude genes for selection candidates responsible for QTL-associated traits. For example, 152 of the 185 genes could be excluded from a syntenic A2-C2 region. These findings will help to elucidate polyploid genomics in future studies, in addition to providing useful information for B. napus breeding programs.
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Affiliation(s)
- Fengqi Zhang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Junyan Huang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, China
| | - Minqiang Tang
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Xiaohui Cheng
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Yueying Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Chaobo Tong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, China
| | - Jingyin Yu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Tehrim Sadia
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Caihua Dong
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, China
| | - Lingyan Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
| | - Baojun Tang
- Cereal Crops Research Institute, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Jianguo Chen
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, China
| | - Shengyi Liu
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, the Ministry of Agriculture, Oil Crops Research Institute of CAAS, Wuhan 430062, China
- Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Faculty of Life Science, Hubei University, Wuhan 430062, China
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Lacambra M, Loong H, To K, Feng X, Taylor G, Pleasance E, Laskin J, Marra M, Griffith J, Yeung H, Wong KC, Chow C, Kumta S, Ng W, Tse T, Tong C, Ng T. FUS-NFATc2 sarcoma of bone, a novel molecular entity with aggressive behavior: Clinical and molecular pathology findings of two cases. Ann Oncol 2018. [DOI: 10.1093/annonc/mdy443.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
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Tong C, Danylyshyn T, Kerr S, Swiggum E. USE OF THE BIOMARKER NT-PROBNP TO TRIAGE PATIENTS INTO MULTIDISCIPLINARY HEART FUNCTION CLINIC: SINGLE CENTRE EXPERIENCE WITH CANADIAN APPLICABILITY. Can J Cardiol 2018. [DOI: 10.1016/j.cjca.2018.07.141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Feldman-Stewart D, Tong C, Brundage MD. Evaluation of a widely available patient decision aid for the treatment of prostate cancer. Patient Educ Couns 2018; 101:1761-1766. [PMID: 29729858 DOI: 10.1016/j.pec.2018.04.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 04/20/2018] [Accepted: 04/23/2018] [Indexed: 06/08/2023]
Abstract
BACKGROUND The effectiveness of patient decision aids (PtDA) is rarely evaluated in the "real world" where patients vary in their preferences related to decision support. PURPOSE To determine how Canadian patients use and evaluate our widely available PtDA for early-stage prostate cancer treatment with its 8 components. METHODS Google Analytics and online tracking provided usage information. A Usability Assessment (UA) following the PtDA provided evaluation data; main outcomes [scale: 1 (strongly disagree) to 5 (strongly agree)] were (a) the aid was helpful, and (b) I would recommend it to other patients. RESULTS Usage data were from 993 users, and UAs from 168 of them. Mean "helpfulness" score was 4.1(5 max); mean "recommend" score was 4.2 (5 max). For each PtDA component, there was no significant difference on each main outcome, between those who used it and those who did not. CONCLUSION Overall, patients who completed the UA rated the PtDA as helpful and would recommend it to other patients. The widely available PtDA accommodated expected variation in decision support desired, and helpfulness was not associated with variation in components used. PRACTICE IMPLICATION The internet can be an effective medium for making appropriately designed decision support widely available to prostate cancer patients.
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Affiliation(s)
- D Feldman-Stewart
- Division of Cancer Care and Epidemiology, Cancer Research Institute, Queen's University Kingston, ON, Canada.
| | - C Tong
- Division of Cancer Care and Epidemiology, Cancer Research Institute, Queen's University Kingston, ON, Canada
| | - M D Brundage
- Division of Cancer Care and Epidemiology, Cancer Research Institute, Queen's University Kingston, ON, Canada
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Guo Z, Tong C, Doucet Y, Abaci H, Jackow J, Zeng W, Hansen C, Lumpkin E, Christiano A. 1446 Atopic cytokines IL4/13 perturb iPSC-derived itch-specific sensory neurons. J Invest Dermatol 2018. [DOI: 10.1016/j.jid.2018.03.1464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Kaufman A, Poonia S, Cazzador D, Kohanski M, Kuan E, Tong C, Borsetto D, Emanuelli E, Palmer J, Adappa N. Disorders Involving a Persistent Craniopharyngeal Canal: A Case Series. Skull Base Surg 2018. [DOI: 10.1055/s-0038-1633628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- A. Kaufman
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - S. Poonia
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - D. Cazzador
- Otorhinolaryngology Unit, Department of Neurosciences, University of Padua, Padua, Italy
| | - M. Kohanski
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - E. Kuan
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - C. Tong
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - D. Borsetto
- Otorhinolaryngology Unit, Department of Neurosciences, University of Padua, Padua, Italy
| | - E. Emanuelli
- Otorhinolaryngology Unit, Department of Neurosciences, University of Padua, Padua, Italy
| | - J. Palmer
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
| | - N. Adappa
- Department of Otorhinolaryngology-Head and Neck Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States
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Watier-Grillot S, Boni M, Tong C, Renoult PA, Fournier A, Joie L, Mérens A, Chesnay A, Perelle S, Fraisse A, Ambert-Balay K, Chal D, Larréché S, Michel R, de Santi VP. Challenging Investigation of a Norovirus Foodborne Disease Outbreak During a Military Deployment in Central African Republic. Food Environ Virol 2017; 9:498-501. [PMID: 28674933 DOI: 10.1007/s12560-017-9312-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
In January 2016, a large-scale outbreak of acute gastroenteritis was reported among French armed forces deployed in the Central African Republic. Challenging investigations, conducted from France, made it possible to identify a norovirus genogroup II in both stool and food samples, confirming a norovirus foodborne disease outbreak. Infected food handler management is discussed.
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Affiliation(s)
| | - M Boni
- French Ministry of Defense Joint Logistics and Supply Agency, Pantin, France
| | - C Tong
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France
| | - P-A Renoult
- French Military Health Service, Montauban-Agen Medical Unit, Montauban, France
| | - A Fournier
- French Military Health Service, Montauban-Agen Medical Unit, Montauban, France
| | - L Joie
- Regional Department of the French Military Health Service, Toulon, France
| | - A Mérens
- Bégin Military Teaching Hospital, Paris, France
| | - A Chesnay
- French Armed Forces Food Laboratory, Angers, France
| | - S Perelle
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, 94700, Maisons-Alfort, France
| | - A Fraisse
- French Agency for Food, Environmental and Occupational Health and Safety (ANSES), Laboratory for Food Safety, 94700, Maisons-Alfort, France
| | - K Ambert-Balay
- National Reference Center for Gastroenteritis Viruses, F. Mitterrand Teaching Hospital, Dijon, France
- AgroSup Dijon, PAM UMR A 02.102, 21000, Dijon, France
| | - D Chal
- Military Veterinary Unit, Lyon, France
| | - S Larréché
- Bégin Military Teaching Hospital, Paris, France
| | - R Michel
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France
- Val-de-Grâce Military Health Service Academy, Paris, France
| | - V Pommier de Santi
- French Armed Forces Center for Epidemiology and Public Health (CESPA), Marseille, France
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Girard IJ, Tong C, Becker MG, Mao X, Huang J, de Kievit T, Fernando WGD, Liu S, Belmonte MF. RNA sequencing of Brassica napus reveals cellular redox control of Sclerotinia infection. J Exp Bot 2017; 68:5079-5091. [PMID: 29036633 PMCID: PMC5853404 DOI: 10.1093/jxb/erx338] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 09/14/2017] [Indexed: 05/12/2023]
Abstract
Brassica napus is one of the world's most valuable oilseeds and is under constant pressure by the necrotrophic fungal pathogen, Sclerotinia sclerotiorum, the causal agent of white stem rot. Despite our growing understanding of host pathogen interactions at the molecular level, we have yet to fully understand the biological processes and underlying gene regulatory networks responsible for determining disease outcomes. Using global RNA sequencing, we profiled gene activity at the first point of infection on the leaf surface 24 hours after pathogen exposure in susceptible (B. napus cv. Westar) and tolerant (B. napus cv. Zhongyou 821) plants. We identified a family of ethylene response factors that may contribute to host tolerance to S. sclerotiorum by activating genes associated with fungal recognition, subcellular organization, and redox homeostasis. Physiological investigation of redox homeostasis was further studied by quantifying cellular levels of the glutathione and ascorbate redox pathway and the cycling enzymes associated with host tolerance to S. sclerotiorum. Functional characterization of an Arabidopsis redox mutant challenged with the fungus provides compelling evidence into the role of the ascorbate-glutathione redox hub in the maintenance and enhancement of plant tolerance against fungal pathogens.
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Affiliation(s)
- Ian J Girard
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture, Wuhan 430062, Hubei, China
| | - Michael G Becker
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Xingyu Mao
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Junyan Huang
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture, Wuhan 430062, Hubei, China
| | - Teresa de Kievit
- Department of Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | | | - Shengyi Liu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, The Key Laboratory of Biology and Genetic Improvement of Oil Crops, The Ministry of Agriculture, Wuhan 430062, Hubei, China
| | - Mark F Belmonte
- Department of Biological Sciences, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
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Sun F, Fan G, Hu Q, Zhou Y, Guan M, Tong C, Li J, Du D, Qi C, Jiang L, Liu W, Huang S, Chen W, Yu J, Mei D, Meng J, Zeng P, Shi J, Liu K, Wang X, Wang X, Long Y, Liang X, Hu Z, Huang G, Dong C, Zhang H, Li J, Zhang Y, Li L, Shi C, Wang J, Lee SMY, Guan C, Xu X, Liu S, Liu X, Chalhoub B, Hua W, Wang H. The high-quality genome of Brassica napus cultivar 'ZS11' reveals the introgression history in semi-winter morphotype. Plant J 2017; 92:452-468. [PMID: 28849613 DOI: 10.1111/tpj.13669] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 08/05/2017] [Accepted: 08/11/2017] [Indexed: 05/04/2023]
Abstract
Allotetraploid oilseed rape (Brassica napus L.) is an agriculturally important crop. Cultivation and breeding of B. napus by humans has resulted in numerous genetically diverse morphotypes with optimized agronomic traits and ecophysiological adaptation. To further understand the genetic basis of diversification and adaptation, we report a draft genome of an Asian semi-winter oilseed rape cultivar 'ZS11' and its comprehensive genomic comparison with the genomes of the winter-type cultivar 'Darmor-bzh' as well as two progenitors. The integrated BAC-to-BAC and whole-genome shotgun sequencing strategies were effective in the assembly of repetitive regions (especially young long terminal repeats) and resulted in a high-quality genome assembly of B. napus 'ZS11'. Within a short evolutionary period (~6700 years ago), semi-winter-type 'ZS11' and the winter-type 'Darmor-bzh' maintained highly genomic collinearity. Even so, certain genetic differences were also detected in two morphotypes. Relative to 'Darmor-bzh', both two subgenomes of 'ZS11' are closely related to its progenitors, and the 'ZS11' genome harbored several specific segmental homoeologous exchanges (HEs). Furthermore, the semi-winter-type 'ZS11' underwent potential genomic introgressions with B. rapa (Ar ). Some of these genetic differences were associated with key agronomic traits. A key gene of A03.FLC3 regulating vernalization-responsive flowering time in 'ZS11' was first experienced HE, and then underwent genomic introgression event with Ar , which potentially has led to genetic differences in controlling vernalization in the semi-winter types. Our observations improved our understanding of the genetic diversity of different B. napus morphotypes and the cultivation history of semi-winter oilseed rape in Asia.
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Affiliation(s)
- Fengming Sun
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guangyi Fan
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Qiong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yongming Zhou
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Chaobo Tong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, BeiBei District, Chongqing, 400715, China
| | - Dezhi Du
- Qinghai Academy of Agricultural and Forestry, National Key Laboratory Breeding Base for Innovation and Utilization of Plateau Crop Germplasm, Xining, 810016, China
| | - Cunkou Qi
- Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China
| | - Liangcai Jiang
- Shichun Academy of Agricultural Sciences, Chengdu, 610066, China
| | - Weiqing Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shunmou Huang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Wenbin Chen
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jingyin Yu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Desheng Mei
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Jinling Meng
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Peng Zeng
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiaqin Shi
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Kede Liu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xi Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Xinfa Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yan Long
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinming Liang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Zhiyong Hu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Guodong Huang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Caihua Dong
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - He Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jun Li
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Yaolei Zhang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Liangwei Li
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Chengcheng Shi
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Jiahao Wang
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Simon Ming-Yuen Lee
- State Key Laboratory of Quality Research in Chinese Medicine and Institute of Chinese Medical Sciences, Macao, China
| | - Chunyun Guan
- College of Agronomy, Hunan Agricultural University, Changsha, 410128, China
| | - Xun Xu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
| | - Shengyi Liu
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Xin Liu
- Beijing Genome Institute-Shenzhen, Shenzhen, 518083, China
- BGI-Qingdao, Qingdao, 266555, China
| | - Boulos Chalhoub
- Institut National de Recherche Agronomique (INRA), Unité de Recherche en Génomique Végétale (URGV), UMR1165, Organization and Evolution of Plant Genomes (OEPG), 2 rue Gaston Crémieux, 91057, Evry, France
| | - Wei Hua
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
| | - Hanzhong Wang
- The Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture of the PRC, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan, 430062, China
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Wei D, Cui Y, He Y, Xiong Q, Qian L, Tong C, Lu G, Ding Y, Li J, Jung C, Qian W. A genome-wide survey with different rapeseed ecotypes uncovers footprints of domestication and breeding. J Exp Bot 2017; 68:4791-4801. [PMID: 28992309 PMCID: PMC5853444 DOI: 10.1093/jxb/erx311] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Rapeseed (Brassica napus L.) is an important oilseed crop. Despite a short period of domestication and breeding, rapeseed has formed three diverse ecotype groups, namely spring, winter, and semi-winter. However, the genetic changes among the three ecotype groups have remained largely unknown. To detect selective signals, a set of 327 accessions from a worldwide collection were genotyped using a Brassica array, producing 33 186 high-quality single nucleotide polymorphisms (SNPs). Linkage disequilibrium (LD) was unevenly distributed across the genome. A total of 705 (78.2%) weak LD regions were found in the A subgenome, whereas 445 (72.6%) strong LD regions were in the C subgenome. By calculating the nucleotide diversity and population differentiation indices, a total of 198 selective sweeps were identified across ecotype groups, spanning 5.91% (37.9 Mb) of the genome. Within these genome regions, a few known functional genes or loci were found to be in association with environmental adaptability and yield-related traits. In particular, all 12 SNPs detected in significant association with flowering time among accessions were in the selection regions between ecotype groups. These findings provide new insights into the structure of the B. napus genome and uncover the footprints of domestication and breeding.
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Affiliation(s)
- Dayong Wei
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- College of Horticulture and Landscape Architecture, Southwest University, Chongqing 400715, China
| | - Yixin Cui
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Yajun He
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Qing Xiong
- School of Computer and Information Science, Southwest University, Chongqing 400715, China
| | - Lunwen Qian
- Department of Plant Breeding, IFZ Research Centre for Biosystems, Land Use and Nutrition, Justus Liebig University, Giessen, Germany
| | - Chaobo Tong
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Guangyuan Lu
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430062, China
| | - Yijuan Ding
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
| | - Christian Jung
- Plant Breeding Institute, Christian Albrechts University of Kiel, Olshausenstr. 40, D-24098 Kiel, Germany
| | - Wei Qian
- College of Agronomy and Biotechnology, Southwest University, Chongqing 400715, China
- Correspondence:
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49
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Zhang H, Tong C. ELDERLY ANESTHESIA AND ANALGESIA. Innov Aging 2017. [DOI: 10.1093/geroni/igx004.4506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- H. Zhang
- Chinese PLA General Hospital, Beijing, China
| | - C. Tong
- Wake Forest Baptist Medical Center, Winston-Salem
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50
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Guo Z, Tong C, Doucet Y, Abaci H, Jackow J, Lumpkin E, Christiano A. 908 Keratinocytes and fibroblasts facilitate maturation of sensory neurons differentiated from human induced pluripotent stem cells. J Invest Dermatol 2017. [DOI: 10.1016/j.jid.2017.02.935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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