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2. Functional and structural characterization of AntR, an Sb(III) responsive transcriptional repressor

Author

Viswanathan, Thiruselvam, Chen, Jian, Wu, Minghan, An, Lijin, Kandavelu, Palani, Sankaran, Banumathi, Radhakrishnan, Manohar, Li, Mingshun, and Rosen, Barry P

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Amino Acid Sequence, Antimony, Arsenic, Arsenicals, Binding Sites, Comamonas testosteroni, Gene Expression Regulation, Bacterial, Protein Conformation, Repressor Proteins, Transcription Factors, Transcription, Genetic, antimony, AntR, ArsR family, Comamonas testosterone, gene regulation, transcriptional repressor, Agricultural and Veterinary Sciences, Medical and Health Sciences, Microbiology, Biological sciences
Abstract

The ant operon of the antimony-mining bacterium Comamonas testosterone JL40 confers resistance to Sb(III). The operon is transcriptionally regulated by the product of the first gene in the operon, antR. AntR is a member of ArsR/SmtB family of metal/metalloid-responsive repressors resistance. We purified and characterized C. testosterone AntR and demonstrated that it responds to metalloids in the order Sb(III) = methylarsenite (MAs(III) >> As(III)). The protein was crystallized, and the structure was solved at 2.1 Å resolution. The homodimeric structure of AntR adopts a classical ArsR/SmtB topology architecture. The protein has five cysteine residues, of which Cys103a from one monomer and Cys113b from the other monomer, are proposed to form one Sb(III) binding site, and Cys113a and Cys103b forming a second binding site. This is the first report of the structure and binding properties of a transcriptional repressor with high selectivity for environmental antimony.

Published
2021

3. Genomic prediction of yield performance among single-cross maize hybrids using a partial diallel cross design

Author

Luo, Ping, Wang, Houwen, Ni, Zhiyong, Yang, Ruisi, Wang, Fei, Yong, Hongjun, Zhang, Lin, Zhou, Zhiqiang, Song, Wei, Li, Mingshun, Yang, Jie, Weng, Jianfeng, Meng, Zhaodong, Zhang, Degui, Han, Jienan, Chen, Yong, Zhang, Runze, Wang, Liwei, Zhao, Meng, Gao, Wenwei, Chen, Xiaoyu, Li, Wenjie, Hao, Zhuanfang, Fu, Junjie, Zhang, Xuecai, and Li, Xinhai

Published
2023
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6. Nivolumab plus chemotherapy or ipilimumab in gastro-oesophageal cancer

Author

Shitara, Kohei, Ajani, Jaffer A., Moehler, Markus, Garrido, Marcelo, Gallardo, Carlos, Shen, Lin, Yamaguchi, Kensei, Wyrwicz, Lucjan, Skoczylas, Tomasz, Bragagnoli, Arinilda Campos, Liu, Tianshu, Tehfe, Mustapha, Elimova, Elena, Bruges, Ricardo, Zander, Thomas, de Azevedo, Sergio, Kowalyszyn, Ruben, Pazo-Cid, Roberto, Schenker, Michael, Cleary, James M., Yanez, Patricio, Feeney, Kynan, Karamouzis, Michalis V., Poulart, Valerie, Lei, Ming, Xiao, Hong, Kondo, Kaoru, Li, Mingshun, and Janjigian, Yelena Y.

Published
2022
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12. ZmADF5, a Maize Actin-Depolymerizing Factor Conferring Enhanced Drought Tolerance in Maize.

Author

Liu, Bojuan, Wang, Nan, Yang, Ruisi, Wang, Xiaonan, Luo, Ping, Chen, Yong, Wang, Fei, Li, Mingshun, Weng, Jianfeng, Zhang, Degui, Yong, Hongjun, Han, Jienan, Zhou, Zhiqiang, Zhang, Xuecai, Hao, Zhuanfang, and Li, Xinhai

Subjects
DROUGHT tolerance, GENOME-wide association studies, LOCUS (Genetics), AGRICULTURE, REACTIVE oxygen species, CORN, ABSCISIC acid
Abstract

Drought stress is seriously affecting the growth and production of crops, especially when agricultural irrigation still remains quantitatively restricted in some arid and semi-arid areas. The identification of drought-tolerant genes is important for improving the adaptability of maize under stress. Here, we found that a new member of the actin-depolymerizing factor (ADF) family; the ZmADF5 gene was tightly linked with a consensus drought-tolerant quantitative trait locus, and the significantly associated signals were detected through genome wide association analysis. ZmADF5 expression could be induced by osmotic stress and the application of exogenous abscisic acid. Its overexpression in Arabidopsis and maize helped plants to keep a higher survival rate after water-deficit stress, which reduced the stomatal aperture and the water-loss rate, as well as improved clearance of reactive oxygen species. Moreover, seventeen differentially expressed genes were identified as regulated by both drought stress and ZmADF5, four of which were involved in the ABA-dependent drought stress response. ZmADF5-overexpressing plants were also identified as sensitive to ABA during the seed germination and seedling stages. These results suggested that ZmADF5 played an important role in the response to drought stress. [ABSTRACT FROM AUTHOR]

Published
2024
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14. A plain language summary of the CheckMate 649 study: nivolumab in combination with chemotherapy compared to chemotherapy alone for untreated advanced or metastatic cancer of the stomach or esophagus

Author

Janjigian, Yelena Y, primary, Shitara, Kohei, additional, Moehler, Markus, additional, Garrido, Marcelo, additional, Salman, Pamela, additional, Wyrwicz, Lucjan, additional, Yamaguchi, Kensei, additional, Skoczylas, Tomasz, additional, Bragagnoli, Arinilda Campos, additional, Liu, Tianshu, additional, Schenker, Michael, additional, Yanez, Patricio, additional, Tehfe, Mustapha, additional, Kowalyszyn, Ruben, additional, Karamouzis, Michalis V, additional, Bruges, Ricardo, additional, Zander, Thomas, additional, Pazo-Cid, Roberto, additional, Hitre, Erika, additional, Feeney, Kynan, additional, Cleary, James M, additional, Poulart, Valerie, additional, Cullen, Dana, additional, Lei, Ming, additional, Xiao, Hong, additional, Kondo, Kaoru, additional, Li, Mingshun, additional, and Ajani, Jaffer A, additional

Published
2023
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16. Earthwork allocation optimisation based on cut-fill matching and transportation path planning

Author

Yu, Jing, Huang, You, Xing, Lining, Zhao, Zizhou, and Li, Mingshun

Abstract

Earthwork allocation is a critical component of engineering construction projects, with the objective of reducing costs and shortening the construction period. While previous research has focused on solving the cut-fill matching problem, there is a lack of study on mechanical transportation path planning. This study introduces a matching model for cut-fill that minimises construction costs and mechanical transfer distance. Moreover, a hybrid ant colony-greedy model and algorithm are proposed to address the transportation path planning problem. To demonstrate the effectiveness of the model and algorithm, an earthwork allocation project is examined using the earthwork allocation model and its solution algorithm. Experimental results show that the two-stage allocation model and algorithm successfully address earthwork allocation challenges. Additionally, the AC-GA algorithm provides a superior earthwork allocation scheme.

Published
2024
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21. Genetic basis of maize kernel protein content revealed by high-density bin mapping using recombinant inbred lines

Author

Lu, Xin, primary, Zhou, Zhiqiang, additional, Wang, Yunhe, additional, Wang, Ruiqi, additional, Hao, Zhuanfang, additional, Li, Mingshun, additional, Zhang, Degui, additional, Yong, Hongjun, additional, Han, Jienan, additional, Wang, Zhenhua, additional, Weng, Jianfeng, additional, Zhou, Yu, additional, and Li, Xinhai, additional

Published
2022
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25. A differentially methylated region of the ZmCCT10promoter affects flowering time in hybrid maize

Author

Zhou, Zhiqiang, Lu, Xin, Zhang, Chaoshu, Li, Mingshun, Hao, Zhuanfang, Zhang, Degui, Yong, Hongjun, Han, Jienan, Li, Xinhai, and Weng, Jianfeng

Abstract

Flowering time (FT) is a key maize domestication trait, variation in which allows maize to grow in a wide range of latitudes. Although previous studies have investigated the genetic control of FT-related traits per se, few studies of FT hybrid performance have been published. We characterized the genomic architecture associated with hybrid performance for FT in a hybrid panel by testcrossing Chang 7–2 with 328 Ye478 × Qi319 recombinant inbred lines (RILs). We identified 11 quantitative trait loci (QTL) for hybrid performance in FT-related traits, including a major QTL qFH10that controls hybrid performance and heterosis in a summer maize-growing region. However, this locus acts in regulating FT traits per seonly in a spring maize-growing region. We validated ZmCCT10as a candidate gene for qFH10and found that differences between hybrids and their parental lines in DNA methylation in the differentially methylated region (DMR, –700 to –1520) of the ZmCCT10promoter affected gene expression pattern and thereby FT in the summer maize-growing region.

Published
2023
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26. Abstract CT023: Nivolumab (NIVO) plus chemotherapy (chemo) vs chemo as first-line (1L) treatment for advanced gastric cancer/gastroesophageal junction cancer/esophageal adenocarcinoma (GC/GEJC/EAC): CheckMate 649 biomarker analyses

Author

Lei, Ming, primary, Janjigian, Yelena Y., additional, Ajani, Jaffer A., additional, Moehler, Markus, additional, Wang, Xuya, additional, Shen, Lin, additional, Garrido, Marcelo, additional, Gallardo, Carlos, additional, Yamaguchi, Kensei, additional, Wyrwicz, Lucjan, additional, Skoczylas, Tomasz, additional, Bragagnoli, Arinilda, additional, Liu, Tianshu, additional, Tehfe, Mustapha, additional, Elimova, Elena, additional, Li, Mingshun, additional, Poulart, Valerie, additional, Wang, Yu, additional, Doshi, Parul, additional, and Shitara, Kohei, additional

Published
2022
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28. Identification and Fine-Mapping of a Novel QTL, qMrdd2, That Confers Resistance to Maize Rough Dwarf Disease

Author

Xu, Zhennan, primary, Wang, Feifei, additional, Zhou, Zhiqiang, additional, Meng, Qingchang, additional, Chen, Yanping, additional, Han, Xiaohua, additional, Tie, Shuanggui, additional, Liu, Changlin, additional, Hao, Zhuanfang, additional, Li, Mingshun, additional, Zhang, Degui, additional, Han, Jienan, additional, Wang, Zhenhua, additional, Li, Xinhai, additional, and Weng, Jianfeng, additional

Published
2022
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31. Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize

Author

Li, Dongdong, primary, Zhou, Zhiqiang, additional, Lu, Xiaohuan, additional, Jiang, Yong, additional, Li, Guoliang, additional, Li, Junhui, additional, Wang, Haoying, additional, Chen, Shaojiang, additional, Li, Xinhai, additional, Würschum, Tobias, additional, Reif, Jochen C., additional, Xu, Shizhong, additional, Li, Mingshun, additional, and Liu, Wenxin, additional

Published
2021
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32. Transcriptome Reveals Allele Contribution to Heterosis in Maize

Author

Wu, Jianzhong, primary, Sun, Dequan, additional, Zhao, Qian, additional, Yong, Hongjun, additional, Zhang, Degui, additional, Hao, Zhuanfang, additional, Zhou, Zhiqiang, additional, Han, Jienan, additional, Zhang, Xiaocong, additional, Xu, Zhennan, additional, Li, Xinhai, additional, Li, Mingshun, additional, and Weng, Jianfeng, additional

Published
2021
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34. Abstract CT184: First-Line (1L) nivolumab (NIVO) plus chemotherapy (chemo) versus chemo in patients (pts) with advanced gastric cancer/gastroesophageal junction cancer/esophageal adenocarcinoma (GC/GEJC/EAC): CheckMate 649 Chinese subgroup analysis

Author

Shen, Lin, primary, Bai, Yuxian, additional, Lin, Xiaoyan, additional, Li, Wei, additional, Wang, Jufeng, additional, Zhang, Xiaochun, additional, Pan, Hongming, additional, Bai, Chunmei, additional, Bai, Li, additional, Cheng, Ying, additional, Zhang, Jingdong, additional, Zhong, Haijun, additional, Ba, Yi, additional, Hu, Wenwei, additional, Xu, Ruihua, additional, Guo, Weijian, additional, Qin, Shukui, additional, Yang, Nong, additional, Lu, Jianwei, additional, Shitara, Kohei, additional, Lei, Ming, additional, Li, Mingshun, additional, Bao, Nicole, additional, Chen, Tian, additional, and Liu, Tianshu, additional

Published
2021
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35. First-line nivolumab plus chemotherapy versus chemotherapy alone for advanced gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma (CheckMate 649): a randomised, open-label, phase 3 trial

Author

Janjigian, Yelena Y. Shitara, Kohei Moehler, Markus Garrido, Marcelo Salman, Pamela Shen, Lin Wyrwicz, Lucjan and Yamaguchi, Kensei Skoczylas, Tomasz Bragagnoli, Arinilda Campos and Liu, Tianshu Schenker, Michael Yanez, Patricio Tehfe, Mustapha Kowalyszyn, Ruben Karamouzis, Michalis V. Bruges, Ricardo Zander, Thomas Pazo-Cid, Roberto Hitre, Erika and Feeney, Kynan Cleary, James M. Poulart, Valerie Cullen, Dana and Lei, Ming Xiao, Hong Kondo, Kaoru Li, Mingshun and Ajani, Jaffer A.

Abstract

Background First-line chemotherapy for advanced or metastatic human epidermal growth factor receptor 2 (HER2)-negative gastric or gastro-oesophageal junction adenocarcinoma has a median overall survival (OS) of less than 1 year. We aimed to evaluate first-line programmed cell death (PD)-1 inhibitor-based therapies in gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma. We report the first results for nivolumab plus chemotherapy versus chemotherapy alone. Methods In this multicentre, randomised, open-label, phase 3 trial (CheckMate 649), we enrolled adults (>= 18 years) with previously untreated, unresectable, non-HER2-positive gastric, gastro-oesophageal junction, or oesophageal adenocarcinoma, regardless of PD-ligand 1 (PD-L1) expression from 175 hospitals and cancer centres in 29 countries. Patients were randomly assigned (1:1:1 while all three groups were open) via interactive web response technology (block sizes of six) to nivolumab (360 mg every 3 weeks or 240 mg every 2 weeks) plus chemotherapy (capecitabine and oxaliplatin every 3 weeks or leucovorin, fluorouracil, and oxaliplatin every 2 weeks), nivolumab plus ipilimumab, or chemotherapy alone. Primary endpoints for nivolumab plus chemotherapy versus chemotherapy alone were OS or progression-free survival (PFS) by blinded independent central review, in patients whose tumours had a PD-L1 combined positive score (CPS) of five or more. Safety was assessed in all patients who received at least one dose of the assigned treatment. This study is registered with ClinicalTrials.gov, NCT02872116. Findings From March 27, 2017, to April 24, 2019, of 2687 patients assessed for eligibility, we concurrently randomly assigned 1581 patients to treatment (nivolumab plus chemotherapy [n=789, 50%] or chemotherapy alone [n=792, 50%]). The median follow-up for OS was 13.1 months (IQR 6.7-19.1) for nivolumab plus chemotherapy and 11.1 months (5.8-16.1) for chemotherapy alone. Nivolumab plus chemotherapy resulted in significant improvements in OS (hazard ratio [HR] 0.71 [98.4% CI 0.59-0.86]; p= 25%) were nausea, diarrhoea, and peripheral neuropathy across both groups. 16 (2%) deaths in the nivolumab plus chemotherapy group and four (1%) deaths in the chemotherapy alone group were considered to be treatment-related. No new safety signals were identified. Interpretation Nivolumab is the first PD-1 inhibitor to show superior OS, along with PFS benefit and an acceptable safety profile, in combination with chemotherapy versus chemotherapy alone in previously untreated patients with advanced gastric, gastro-oesophageal junction, or oesophageal adenocarcinoma. Nivolumab plus chemotherapy represents a new standard first-line treatment for these patients. Funding Bristol Myers Squibb, in collaboration with Ono Pharmaceutical. Copyright (c) 2021 Elsevier Ltd. All rights reserved.

Published
2021

38. First-line nivolumab plus chemotherapy versus chemotherapy alone for advanced gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma (CheckMate 649): a randomised, open-label, phase 3 trial

Author

Janjigian, Yelena Y., Shitara, Kohei, Moehler, Markus, Garrido, Marcelo, Salman, Pamela, Shen, Lin, Wyrwicz, Lucjan, Yamaguchi, Kensei, Skoczylas, Tomasz, Bragagnoli, Arinilda Campos, Liu, Tianshu, Schenker, Michael, Yanez, Patricio, Tehfe, Mustapha, Kowalyszyn, Ruben, Karamouzis, Michalis V., Bruges, Ricardo, Zander, Thomas, Pazo-Cid, Roberto, Hitre, Erika, Feeney, Kynan, Cleary, James M., Poulart, Valerie, Cullen, Dana, Lei, Ming, Xiao, Hong, Kondo, Kaoru, Li, Mingshun, Ajani, Jaffer A., Janjigian, Yelena Y., Shitara, Kohei, Moehler, Markus, Garrido, Marcelo, Salman, Pamela, Shen, Lin, Wyrwicz, Lucjan, Yamaguchi, Kensei, Skoczylas, Tomasz, Bragagnoli, Arinilda Campos, Liu, Tianshu, Schenker, Michael, Yanez, Patricio, Tehfe, Mustapha, Kowalyszyn, Ruben, Karamouzis, Michalis V., Bruges, Ricardo, Zander, Thomas, Pazo-Cid, Roberto, Hitre, Erika, Feeney, Kynan, Cleary, James M., Poulart, Valerie, Cullen, Dana, Lei, Ming, Xiao, Hong, Kondo, Kaoru, Li, Mingshun, and Ajani, Jaffer A.

Abstract

Background First-line chemotherapy for advanced or metastatic human epidermal growth factor receptor 2 (HER2)-negative gastric or gastro-oesophageal junction adenocarcinoma has a median overall survival (OS) of less than 1 year. We aimed to evaluate first-line programmed cell death (PD)-1 inhibitor-based therapies in gastric, gastro-oesophageal junction, and oesophageal adenocarcinoma. We report the first results for nivolumab plus chemotherapy versus chemotherapy alone. Methods In this multicentre, randomised, open-label, phase 3 trial (CheckMate 649), we enrolled adults (>= 18 years) with previously untreated, unresectable, non-HER2-positive gastric, gastro-oesophageal junction, or oesophageal adenocarcinoma, regardless of PD-ligand 1 (PD-L1) expression from 175 hospitals and cancer centres in 29 countries. Patients were randomly assigned (1:1:1 while all three groups were open) via interactive web response technology (block sizes of six) to nivolumab (360 mg every 3 weeks or 240 mg every 2 weeks) plus chemotherapy (capecitabine and oxaliplatin every 3 weeks or leucovorin, fluorouracil, and oxaliplatin every 2 weeks), nivolumab plus ipilimumab, or chemotherapy alone. Primary endpoints for nivolumab plus chemotherapy versus chemotherapy alone were OS or progression-free survival (PFS) by blinded independent central review, in patients whose tumours had a PD-L1 combined positive score (CPS) of five or more. Safety was assessed in all patients who received at least one dose of the assigned treatment. This study is registered with ClinicalTrials.gov, NCT02872116. Findings From March 27, 2017, to April 24, 2019, of 2687 patients assessed for eligibility, we concurrently randomly assigned 1581 patients to treatment (nivolumab plus chemotherapy [n=789, 50%] or chemotherapy alone [n=792, 50%]). The median follow-up for OS was 13.1 months (IQR 6.7-19.1) for nivolumab plus chemotherapy and 11.1 months (5.8-16.1) for chemotherapy alone. Nivolumab plus chemotherapy resulted i

Published
2021

44. Transcriptomes of early developing tassels under drought stress reveal differential expression of genes related to drought tolerance in maize

Author

Liang Li, Nan Wang, Yong-bo Wu, Hong-jun Yong, Wen-wei Gao, Zhuan-fang Hao, De-gui Zhang, Xin-hai Li, Li Mingshun, and Jianfeng Weng

Subjects
0301 basic medicine, Agriculture (General), Drought tolerance, drought tolerance, Tassel, Plant Science, Biology, Biochemistry, S1-972, Transcriptome, 03 medical and health sciences, Food Animals, Zea mays L, Transcription (biology), Gene, Transcription factor, Genetics, Ecology, fungi, food and beverages, RNA, mRNA surveillance, 030104 developmental biology, Animal Science and Zoology, transcriptome, Agronomy and Crop Science, early developing tassel, Food Science
Abstract

Tassel, the male reproductive organs in maize, its development is adversely affected by drought during tasseling. To determine drought tolerance mechanisms of tassel differentiation at transcriptome level, RNA-Seq was performed using RNA of early developing tassel from 10 maize inbred lines under well-watered (control) and drought-stressed conditions, respectively. Results showed that the most active pathway for drought stress in maize were related to metabolic regulation at RNA level. And some genes, encoding enzymes involved in carbohydrate and lipid metabolism, were significantly down-regulated in drought-stressed plants. While, the transcription factors and genes, encoding catabolic or degradative enzymes, were over-expressed in maize early developing tassels under drought-stressed conditions, and among them, the transcripts of genes encoding exon-junction complexes involved in ‘RNA transcript’ and ‘mRNA surveillance’ pathways were significantly affected by drought stress. In addition, many other genes related to drought stress showed transcriptional changes at the later period of stress.

Published
2018

45. An autosomal dominant cerebellar ataxia linked to chromosome 16q22.1 is associated with a single-nucleotide substitution in the 5' untranslated region of the gene encoding a protein with spectrin repeat and rho guanine-nucleotide exchange-factor domains

Author

Ishikawa, Kinya, Toru, Shuta, Tsunemi, Taiji, Li, Mingshun, Kobayashi, Kazuhiro, Yokota, Takanori, Amino, Takeshi, Owada, Kiyoshi, Fujigasaki, Hiroto, Sakamoto, Masaki, Tomimitsu, Hiroyuki, Takashima, Minoru, Kumagai, Jiro, Noguchi, Yoshihiro, Kawashima, Yoshiyuki, Ohkoshi, Norio, Ishida, Gen, Gomyoda, Manabu, Yoshida, Mari, Hashizume, Yoshio, Saito, Yuko, Murayama, Shigeo, Yamanouchi, Hiroshi, Mizutani, Toshio, Kondo, Ikuko, Toda, Tatsushi, and Mizusawa, Hidehiro

Subjects
Human genetics -- Research, Nervous system -- Degeneration, Genetic disorders, Cerebellar ataxia, Central nervous system diseases, Biological sciences
Published
2005

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