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1. cAMP和钙离子信号循环效应对枣生长发育的影响
WANG Li-xin, WANG Lin-xia, ZHANG Meng-ling, QU Ying-yue, YUAN Ye, Ehsan SADEGHNEZHAD, GAO Meng-jiao, ZHAO Ruo-yu, QI Chao-feng, GUO Xiao-xue, ZHU Wen-hui, LI Rui-mei, DAI Li, LIU Meng-jun, LIU Zhi-guo
Journal of Integrative Agriculture    2023, 22 (7): 2094-2110.   DOI: 10.1016/j.jia.2023.04.039
摘要179)      PDF    收藏

3',5'-环磷酸腺苷(cAMP)是一种重要的代谢产物,特别在枣中高效积累。然而,cAMP在枣细胞中的功能尚未得到系统研究。因此,我们通过枣细胞悬浮系的建立、原生质体分离及荧光强度分析研究了cAMP与钙离子信号的关系。首先,外源cAMP处理可以促进枣的生长和内源cAMP的积累。通过对过表达腺苷酸环化酶(ZjAC)的转基因拟南芥转录组分析鉴定出60个与钙离子信号相关的差异表达基因(DEG),发现这些基因参与钙离子信号转导及细胞间/内的反应。另外,外源cAMP和钙离子促进剂A23187等药物处理可以诱导枣细胞中ZjAC的表达、cAMP的积累及钙离子向细胞质中的流入,而钙离子螯合剂EGTA或腺苷酸环化酶抑制剂bithionol处理抑制了这种增加。此外,外源cAMP处理可以激活钙离子通道及相关下游基因,如ZjCNGC2ZjMAPK2ZjMAPKK2ZjMAPKK4。总之,该研究结果表明cAMP的合成依赖于钙离子信号内流,钙离子信号和cAMP之间的级联放大效应参与细胞内信号转导从而促进枣的生长发育。

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2. JIA-2021-1935 鸡源大肠杆菌共存blaCTX-M-3blaKPC-2blaTEM-1B耐药基因IncN型质粒的特性
WANG Wen-jing, WANG Yi-fu, JIN Ya-jie, SONG Wu-qiang, LIN Jia-meng, ZHANG Yan, TONG Xin-ru, TU Jian, LI Rui-chao, LI Tao
Journal of Integrative Agriculture    2023, 22 (1): 320-324.   DOI: 10.1016/j.jia.2022.08.075
摘要338)      PDF    收藏

目的:分析我国鸡源重要致病菌大肠杆菌耐药性及耐药基因,解析潜在的水平扩散风险。方法:规模化养鸡场棉拭子泄殖腔取样,麦康凯培养基分离单菌,Phoenix-100 全自动细菌鉴定/药敏系统鉴定细菌种类,K-B纸片法检测目的细菌药物敏感性,牛津纳米孔测序技术构建细菌基因组精细图,生物信息学软件及平台解析基因环境及水平转移元件,细菌结合实验验证耐药基因扩散风险。结果201910-202010月,共采集671个泄殖腔样本,分离出302株大肠杆菌单菌,鉴定出一株广泛耐药(An extensively drug-resistant, XDR)大肠杆菌(命名为258E)。MLST分析结果表明,大肠杆菌258E属于ST602型,该分型目前仅见于国外文献报道。K-B纸片法检测结果显示,258E菌株对磷霉素、四环素、β-内酰胺类、氨基糖苷类、喹诺酮类、利福霉素、甲氧苄啶、大环内酯类和头孢菌素类药物均表现出高度耐药。全基因组测序结果表明,大肠杆菌258E染色体全长4,715,664 bp,含有三个质粒(pEC258-1、pEC258-2、pEC258-3,其中pEC258-1和 pEC258-2不含有常见耐药基因,而pEC258-3除了含有常见耐药基因,如qnrS1、 dfrA14、 arr-3acc (6')-Ib等,还含有blaCTX-M-3、 blaKPC-2blaTEM-1B三个重要的耐药基因。质粒分型结果表明,pEC258-3为ST7型,属于质粒不相容群N (incompatibility group N, IncN)。同源性分析结果显示pEC258-3序列与人源肺炎克雷伯菌质粒pCRKP-1-KPC同源性高达99.96%,其不同之处在于:相对pEC258-3,pCRKP-1-KPC质粒在31kb-32kb位点缺失了一个整合酶TinR蛋白编码框。细菌结合实验证实,pEC258-3可使得宿主菌显著提高药物敏感性。同时,流行病学溯源分析结果显示,大肠杆菌258E与英国菌株具有相近的亲缘关系。结论:本研究第一次报道了一株动物源ST602型广泛耐药大肠杆菌,其所含有的质粒可介导宿主菌对多种抗生素产生耐药性,暗示其潜在的耐药性水平扩散风险,也间接证明动物源细菌是耐药性基因的重要储存库和风险传播源头之一。

创新性:本论文是我国第一例动物源ST602型广泛耐药大肠杆菌的报道,丰富和充实了“同一健康” 框架下细菌耐药性对人类公共健康的风险研究。

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3. JIA-2021-0269 IbGGPS基因显著提高转基因甘薯的类胡萝卜素含量
LI Rui-jie, ZHAI Hong, HE Shao-zhen, ZHANG Huan, ZHAO Ning, LIU Qing-chang
Journal of Integrative Agriculture    2022, 21 (9): 2538-2546.   DOI: 10.1016/j.jia.2022.07.029
摘要234)      PDF    收藏

牻牛儿基牻牛儿基焦磷酸合酶(GGPS)在类胡萝卜素的生物合成中起着重要作用。在之前的研究中,我们从一个高类胡萝卜素含量的甘薯品系农大辐14中克隆得到IbGGPS基因, 但其在甘薯类胡萝卜素生物合成中的作用及其调控机制尚未研究。在本研究中,我们将IbGGPS基因导入甘薯品种栗子香中,发现该基因显著增加转基因甘薯块根中的β-胡萝卜素、β-隐黄质、玉米黄质和叶黄素含量。进一步研究表明,IbGGPS基因的过表达使糖酵解途径、MEP途径和类胡萝卜素途径相关基因的表达系统上调,从而增加了转基因植株的类胡萝卜素含量。这些结果表明,IbGGPS基因具有提高甘薯和其他植物类胡萝卜素含量的利用价值


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4. PPAR gamma2:正调控鸡Plin1基因表达的PPARγ主要蛋白亚型
SUN Yu-hang, ZHAI Gui-ying, PANG Yong-jia, LI Rui, LI Yu-mao, CAO Zhi-ping, WANG Ning, LI Hui, WANG Yu-xiang
Journal of Integrative Agriculture    2022, 21 (8): 2357-2371.   DOI: 10.1016/S2095-3119(21)63896-0
摘要152)      PDF    收藏

本研究的目的旨在确定鸡PPARγPlin1基因调控作用,并阐明其确切的分子机制。本研究首先利用RT-qPCR技术检测PPARγ激动剂对cPlin1基因表达的影响,而后通过双荧光素酶报告基因和RT-qPCR技术分析PPARγcPlin1基因启动子活性和mRNA表达的影响,再通过免疫共沉淀和双荧光素酶报告基因技术研究PPARγ与RXRα的协同作用对cPlin1基因启动子活性的影响,最后通过启动子截短和突变分析以及凝胶阻滞技术确定cPlin1基因启动子中PPARγ2的具体调控位点。基因表达分析结果表明,PPARγ的特异性激动剂—曲格列酮可以显著增强(P<0.05)PPARγ的靶基因LPLA-FABPFAS基因Plin1基因的mRNA表达水平,提示cPlin1基因的表达可能受PPARγ的调控;进一步的报告基因和基因表达分析结果表明,PPARγ2能够显著促进P<0.01)cPlin1基因启动子活性及mRNA表达水平,但PPARγ1却无此作用;免疫共沉淀和报告基因结果表明,PPARγ与RXRα之间存在蛋白质相互作用;与单独过表达RXRα相比,共表达PPARγ2和RXRα显著增强(P<0.01)cPlin1基因的启动子活性,但共表达PPARγ1和RXRα则没有表现出类似的现象;启动子的截短及突变分析以及凝胶阻滞结果表明,PPARγ2可以cPlin1基因启动子的-1126/-1116位点结合促进P<0.01)cPlin1基因表达。与哺乳动物相似,(i)鸡PPARγPlin1基因的转录具有正调控作用,其中PPARγ2是发挥此调控作用的主要蛋白亚型;(ii)PPARγ2是通过与cPlin1基因启动子区域的-1126/-1116位点结合来实现促进cPlin1基因表达作用的。本研究的创新性是明确了鸡PPARγPlin1基因表达的调控作用并揭示了PPARγ2调控Plin1基因转录的分子机制


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5. JIA-2021-1253 秸秆带状覆盖:旱地冬小麦节水增效的可持续生产技术
LI Rui, CHAI Shou-xi, CHAI Yu-wei, LI Ya-wei, CHANG Lei, CHENG Hong-bo
Journal of Integrative Agriculture    2022, 21 (12): 3556-3568.   DOI: 10.1016/j.jia.2022.08.098
摘要177)      PDF    收藏

秸秆覆盖模式改良可以通过废弃秸秆资源循环利用改善土壤水肥环境,可能是一种可持续的农业生产技术。2015-2019年,在西北黄土高原进行了为期4年的随机区组试验,研究了秸秆带状覆盖(SSM)无覆盖常规平作(CK)对土壤贮水量、耗水特性、水分利用效率、降水利用效率、冬小麦生长、经济效益和养分效益的影响。年的试验结果表明,SSM处理提高了0 ~ 180 cm土层的土壤水分,其中以冬小麦拔节期和开花期0 ~ 60 cm土层的效果尤为明显。CK相比,SSM提高了降水对总耗水的贡献,且在生前期显著提高了20.4个百分点。SSM显著降低了0 ~ 180 cm土层的水分消耗,最终减少生育期耗水11.2 mm。在0 ~ 180 cm土层,SSM~拔节期减少耗水33.1 mm但在拔节期~开花期增加了19.5 mm。此外,SSM提高籽粒产量水分利用效率21.6%,提高籽粒产量降水利用效率18.6%,最终通过提高穗数9.5%、提高穗粒数8.9%,而提高籽粒产量16.5%SSM使生物产量的水分利用效率提高了13.5%,使生物产量的降水利用效率提高了9.9%,最终提高生物产量8.7%增加株高6.5%SSM还增加了413/公顷的净收入,收获后预计秸秆还田总量增加8876~9619千克/公顷。秸秆还田后,SSM显著增加了土壤养分,年后可明显减轻农民施肥负担。因此,秸秆带状覆盖是一种雨养冬小麦生产中节水增效、可持续、实用措施

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6. Detection and enumeration of wheat grains based on a deep learning method under various scenarios and scales
WU Wei, YANG Tian-le, LI Rui, CHEN Chen, LIU Tao, ZHOU Kai, SUN Cheng-ming, LI Chun-yan, ZHU Xin-kai, GUO Wen-shan
Journal of Integrative Agriculture    2020, 19 (8): 1998-2008.   DOI: 10.1016/S2095-3119(19)62803-0
摘要145)      PDF    收藏
Grain number is crucial for analysis of yield components and assessment of effects of cultivation measures.  The grain number per spike and thousand-grain weight can be measured by counting grains manually, but it is time-consuming, tedious and error-prone.  Previous image processing algorithms cannot work well with different backgrounds and different sizes.  This study used deep learning methods to resolve the limitations of traditional image processing algorithms.  Wheat grain image datasets were collected in the scenarios of three varieties, six background and two image acquisition devices with different heights, angles and grain numbers, 1 748 images in total.  All images were processed through color space conversion, image flipping and rotation.  The grain was manually annotated, and the datasets were divided into training set, validation set and test set.  We used the TensorFlow framework to construct the Faster Region-based Convolutional Neural Network Model.  Using the transfer learning method, we optimized the wheat grain detection and enumeration model.  The total loss of the model was less than 0.5 and the mean average precision was 0.91.  Compared with previous grain counting algorithms, the grain counting error rate of this model was less than 3% and the running time was less than 2 s.  The model can be effectively applied under a variety of backgrounds, image sizes, grain sizes, shooting angles, and shooting heights, as well as different levels of grain crowding.  It constitutes an effective detection and enumeration tool for wheat grain.  This study provides a reference for further grain testing and enumeration applications.
 
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7. Identification and expression of the CEP gene family in apple (Malus×domestica)
LI Rui, AN Jian-ping, YOU Chun-xiang, SHU Jing, WANG Xiao-fei, HAO Yu-jin
Journal of Integrative Agriculture    2018, 17 (2): 348-358.   DOI: 10.1016/S2095-3119(17)61653-8
摘要727)      PDF    收藏
Plant peptide hormones play important roles in plant growth and development.  Among these hormones, the C-TERMINALLYENCODED PEPTIDE (CEP) belongs to a newly found peptide family that regulates root development in Arabidopsis as well as in other species.  However, nothing is known about the CEP genes in apple (Malus×domestica, MdCEP).  In this study, a total of 27 apple CEP genes were identified through a genome-wide analysis and were phylogenetically divided into three classes (I, II and III).  The predicted MdCEP genes were distributed across 10 of 17 chromosomes with different densities.  Next, the gene structures and motif compositions of the MdCEP genes were analyzed.  Subsequently, the expression analysis suggested that the MdCEP genes were highly activated in roots and that MdCEP23 may play an important role in regulating the growth and development of roots.  Moreover, all of the MdCEP genes were responsive to multiple abiotic stresses, indicating that MdCEP genes may be involved with various aspects of physiological processes in apple.  Nearly one-third of MdCEP genes had a significant response to low nitrogen treatment.  Most of the MdCEP genes were up-regulated under stress, including mannitol, polyethylene glycol (PEG) and abscisic acid (ABA), suggesting that MdCEP genes may be involved in the drought stress response.  This study provides insight into the putative functions of the MdCEP genes using a genome-wide analysis of the CEP gene family. 
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8. Gene cloning and expression analyses of WBC genes in the developing grapevine seeds
TANG Yu-jin, WANG Qian, XUE Jing-yi, LI Yan, LI Rui-min, Steve Van Nocker, WANG Yue-jin, ZHANG Chao-hong
Journal of Integrative Agriculture    2018, 17 (06): 1348-1359.   DOI: 10.1016/S2095-3119(17)61827-6
摘要445)      PDF    收藏
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9. Growth performance and rumen microorganism differ between segregated weaning lambs and grazing lambs
JI Shou-kun, JIANG Cheng-gang, LI Rui, DIAO Qi-yu, TU Yan, ZHANG Nai-feng, SI Bing-wen
Journal of Integrative Agriculture    2016, 15 (4): 872-878.   DOI: 10.1016/S2095-3119(15)61267-9
摘要1753)      PDF    收藏
Two feeding patterns of the segregated weaning or grazing in the pasture are carried out worldwide in animal production. To investigate the difference of growth performance and rumen microorganism population related to methane metabolism in the two feeding patterns, three groups of lambs (70 in total) were used: Weaning at 21 days old and being subjected to high-concentration diets (3WK group with 20 lambs), weaning at 35 days old and being subjected to high-concentration diets (5WK group with 20 lambs), or grazing at pasture with the nursing mother (Grazing group with 30 lambs). The growth performance, pH value of rumen content, and the rumen microbes were investigated during weaning period and fattening period with approximately 3 months. Our results showed that lambs in 3WK and 5WK groups demonstrated a better growth performance than the lambs in Grazing group, but no significant difference was observed in the pH value between the three groups (P>0.05). The total rumen bacterial population of the Grazing lambs was significantly lower than that of 3WK lambs (P<0.05) and 5WK lambs (P<0.05); however, the population of methanogens was 4.2- and 2.7-fold lower in the 3wk (P<0.05) and 5wk (P<0.05) lambs compared with Grazing lambs, respectively; protozoa were also 3.5- and 3.4-fold lower in the 3WK (P<0.05) and 5WK (P<0.05) lambs, respectively. The results revealed that segregated weaning lambs may have better growth performance, and reduce methane-producing microbes.
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10. Impacts of Climate Change on Agriculture and Adaptive Strategies in China
LI Rui-li , Shu Geng
Journal of Integrative Agriculture    2013, 12 (8): 1402-1408.   DOI: 10.1016/S1671-2927(00)9053
摘要1354)      PDF    收藏
China is the world’s most populous country and a major emitter of greenhouse gases. Consequently, China’s role in climate change has received a great deal of attention, whereas the impact of climate change on China has been largely ignored. Studies on the impacts of climate change on agriculture and adaptation strategies are increasingly becoming major areas of scientific concern. However, the clear warming that has been sounded in China in recent decades has not been matched with a clear assessment of the impact of climate change on China’s water resources and agriculture. In the present study, we review observations on climate change, hydrology, and agriculture in China and relate these observations to likely future changes. We also analyse the adaptive strategies in China’s agriculture.
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11. Molecular Characterization and Functional Analysis of OsPHY1, a Purple Acid Phosphatase (PAP)-Type Phytase Gene in Rice (Oryza sativa L.)
LI Rui-juan, LU Wen-jing, GUO Cheng-jin, LI Xiao-juan, GU Jun-tao, XIAO Kai
Journal of Integrative Agriculture    2012, 12 (8): 1217-1226.   DOI: 10.1016/S1671-2927(00)8650
摘要1221)      PDF    收藏
As a specific type of acid phosphatses, phytases play diverse roles in plants by catalazing the degradation of phytic acid and its derivatives. In this study, a rice phytase gene referred to OsPHY1 has been functionally characterized. OsPHY1 contains a 1 620 bp of open reading frame, encoding a 539-aa polypeptide. A conserve domain metallophosphatase (MPP) (MPP_PAPs), generally harbored in phytase and purple acid phosphatases (PAP), was identified in OsPHY1 (residue 194- 398). Phylogenetic analysis revealed that OsPHY1 shares high similarities with phytase genes and PAP-type genes that derived from diverse plant species. The OsPHY1 transcripts were detected to be abundant in germinating seeds, suggesting that this gene plays potential roles on degradation of seed phytic acid and its derivatives during the germination process. Biochemical analysis confirmed that OsPHY1 possesses strong catalytic activities on phytic acid-Na2, with optimal temperature of 57°C and suitable pH of 3.5. Based on transgene analysis, the putative role of OsPHY1 in plants on utilization of phytate was assessed. Under the condition that phytic acid-Na2 was used as sole P source, the OsPHY1- overexpressing tobacco plants behaved higher phytase activities, higher concentrations of Pi, more accumulative amount of total phosphorus, and much more improved growth traits than those of the control plants. Therefore, OsPHY1 is acted as an important component on degradation of the phytins during the seed germination process in rice. Also, OsPHY1 has a potential use on generation of elite crop germplasms with improved use efficiencies on phytate and its derivatives.
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12. Assimilation of Remote Sensing and Crop Model for LAI Estimation Based on Ensemble Kalman Filter
LI Rui, LI Cun-jun, DONG Ying-ying, LIU Feng, WANG Ji-hua, YANG Xiao-dong , PAN Yu-chun
Journal of Integrative Agriculture    2011, 10 (10): 1595-1602.   DOI: 10.1016/S1671-2927(11)60156-9
摘要1915)      PDF    收藏
Data assimilation in agricultural remote sensing research is of great significance to integrate with remote sensing observations and model simulations for parameters estimation. The present investigation not only designed and realized the Ensemble Kalman Filtering algorithm (EnKF) assimilation by combing the crop growth model (CERES-Wheat) with remote sensing data, but also optimized and updated the key parameters (LAI) of winter wheat by using remote sensing data. Results showed that the assimilation LAI and the observation ones agreed with each other, and the R2 reached 0.8315. So assimilation remote sensing and crop model could provide reference data for the agricultural production.
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