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1. JIA-2022-0425 MRUNet:一种复杂环境下昆虫小目标的两阶段分割模型
WANG Fu-kuan, HUANG Yi-qi, HUANG Zhao-cheng, SHEN Hao, HUANG Cong, QIAO Xi, QIAN Wan-qiang
Journal of Integrative Agriculture    2023, 22 (4): 1117-1130.   DOI: 10.1016/j.jia.2022.09.004
摘要316)      PDF    收藏

田间害虫在线自动识别是农田害虫防治的重要辅助手段。在实际应用中,由于目标小、物种相似性高、背景复杂等因素,昆虫在线识别系统往往无法对目标进行准确定位和识别。为方便昆虫幼虫的识别,本研究提出了一种两阶段分割方法MRUNet。在结构上,MRUNet借鉴了Mask R-CNN在进行语义分割之前先进行目标检测的做法,并且使用改进的轻量级UNet进行语义分割。为了可靠地评价所提出模型的分割结果,除了常用的语义分割评价指标外,本研究还引入了统计方法来衡量模型在样本间性能的稳定性。实验结果表明,所提出的两阶段图像分割策略能有效处理复杂背景下的小目标。与现有的语义分割方法相比,MRUNet在相同条件下具有更好的稳定性和细节处理能力。本研究可以为昆虫幼虫识别提供高质量的图像数据。

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2. The impact of tandem duplication on gene evolution in Solanaceae species
HUANG Yi-le, ZHANG Ling-kui, ZHANG Kang, CHEN Shu-min, HU Jian-bin, CHENG Feng
Journal of Integrative Agriculture    2022, 21 (4): 1004-1014.   DOI: 10.1016/S2095-3119(21)63698-5
摘要300)      PDF    收藏

在植物基因组进化中普遍发生的全基因组加倍 (WGD) 和串联复制 (TD) 是基因扩增和功能创新的重要形式。我们分析了三个茄科物种 (番茄、辣椒和矮牵牛) 的基因组,这些茄科物种相对于与葡萄、可可和咖啡经历了一次额外的全基因组三倍化 (WGT) 事件。我们发现没有经历过这次WGT事件的葡萄比经历过WGT事件的茄科物种保留了相对更多和更长的串联复制基因簇 (TDG),并且发现较长TDG簇的形成往往来自于较古老的TD事件,这表明连续TD的基因(绝对剂量效应)在进化过程中长期积累。此外,茄科WGD和TD在基因保留的功能类别上表现出明显的偏向。WGD倾向于保留与生物过程有关的剂量敏感基因,包括DNA结合和转录因子活性等。TD倾向于保留参与逆境胁迫的绝对剂量基因。WGD和TD还通过基因融合和分裂为基因功能创新提供了更多途径。含有抗番茄镰刀菌枯萎病基因I3的TDG簇包含了15个串联重复基因,其中Solyc07g055560在串联重复事件后还经历了基因融合事件。这些结果为阐明TDG在适应环境变化中的新功能形成提供了依据。


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3. Comprehensive characterization of yam tuber nutrition and medicinal quality of Dioscorea opposita and D. alata from different geographic groups in China
SHAN Nan, WANG Pu-tao, ZHU Qiang-long, SUN Jing-yu, ZHANG Hong-yu, LIU Xing-yue, CAO Tian-xu, CHEN Xin, HUANG Ying-jin, ZHOU Qing-hong
Journal of Integrative Agriculture    2020, 19 (11): 2839-2848.   DOI: 10.1016/S2095-3119(20)63270-1
摘要179)      PDF    收藏
China is an important domestication center of yams, and two main yam species of Dioscorea opposita and D. alata are commonly cultivated in China.  However, the differences of nutritional and medicinal characteristics between the two species and their subgroups remain unclear, which would greatly affect the resource conservation and commercial utilization of yams.  In this study, typical yam resources including the species of D. opposita (wild and cultivated Ruichang yam from southern China, and Tiegun yam from northern China) and two landraces of D. alata (Longyan yam and Anyuan yam from southern China) were selected as materials.  Nutritional traits and medicinal characteristics were determined and analyzed respectively.  The results showed that there was no significant differences in the content of most nutrients between D. opposita and D. alata, but most cultivated Ruichang yam of D. opposita showed higher levels of starch, soluble sugar, sucrose, and ascorbate in tuber than that in yam from D. alata.  Moreover, an UPLC-MS method was developed for identification and determination of medicinal characteristics in the two species.  The results showed that allantoin can be detected in all selected samples.  Cultivated Ruichang yam of D. opposita possessed the highest allantoin content among the tested materials, and was significantly different with that in Tiegun yam and D. alata. Dioscin was not detected in D. alata. Overall, there was little difference in nutritional composition between D. opposita and D. alata, but the medicinal quality of D. opposita was better than that of D. alata.  Due to the outstanding comprehensive quality, the local variety of cultivated Ruichang yam can be further developed and utilized.
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4. Transcriptomic analyses reveal new genes and networks response to H5N1 influenza viruses in duck (Anas platyrhynchos)
HUANG Yin-hua, FENG Hua-peng, HUANG Li-ren, YI Kang, RONG En-guang, CHEN Xiao-yun, LI Jian-wen, WANG Zeng, ZHU Peng-yang, LIU Xiao-juan, WANG Xiao-xue, HU Jia-xiang, LIU Xin, CHEN Hua-lan, WANG Jun...
Journal of Integrative Agriculture    2019, 18 (7): 1460-1472.   DOI: 10.1016/S2095-3119(19)62646-8
摘要205)      PDF    收藏
H5N1 influenza represents one of the great challenges to public health.  Some H5N1 viruses (i.e., A/goose/Hubei/65/05, GS/65) are weakly pathogenic, while the others (i.e., A/duck/Hubei/49/05, DK/49) are highly pathogenic to their natural hosts.  Here, we performed brain and spleen transcriptomic analyses of control ducks and ones infected by the DK/49 or the GS/65 H5N1 virus.  We demonstrated that, compared to the GS/65 virus, the DK/49 virus infection changed more numerous immune genes’ expression and caused continuous increasing of immune pathways (i.e., RIG-I and MDA5) in ducks.  We found that both H5N1 virus strains might escape or subvert host immune response through affecting alternative translation of immune genes, while the DK/49 virus seemed to induce alternative translation of more immune genes than the GS/65 virus.  We also identified five co-expressional modules associated with H5N1 virus replication through the weight correlation network analysis (WGCNA).  Moreover, we first demonstrated that the duck BCL2L15 and DCSTAMP in one of these five modules inhibited both the highly pathogenic and weakly pathogenic H5N1 virus replication efficiently.  These analyses, in combination with our comprehensive transcriptomic data, provided global view of the molecular architecture for the interaction between host and H5N1 viruses. 
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5. Identification of novel genes associated with duck OASL in response to influenza A virus
WANG Xiao-xue, LU Chang, RONG En-guang, HU Jia-xiang, XING Yan-ling, LIU Zheng-yu, GAO Chu-ze, LIU Jin-hua, HUANG Yin-hua
Journal of Integrative Agriculture    2019, 18 (7): 1451-1459.   DOI: 10.1016/S2095-3119(19)62685-7
摘要201)      PDF    收藏
2´-5´-Oligoadenylate synthetase like protein (OASL) plays a key role in response to viral infections through selectively activating the OAS/RNase L or OASL/RIG-I signaling pathway.  Although classic pathway of OASL is well-known, its regulated genes or co-actors are largely unknown.  To study the possible molecular mechanism of duck OASL (dOASL), we performed RNA-sequencing (RNA-seq) and immunoprecipitation and mass spectrometry (IP-MS) at the level of mRNA and protein, respectively.  For RNA-seq, we used DF1 cell lines (DF1dOASL+/+, DF1cOASL–/–, and DF1) with or without the CK/0513 H5N1 virus (A/chicken/huabei/0513/2007) infection.  1 737 differentially expressed genes (DEGs) were identified as candidate target genes regulated by dOASL.  Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis and Weighted Correlation Network Analysis (WGCNA) were performed.  We identified one important yellow co-expression module correlated with antiviral immune response.  In this module, Ankyrin repeat and FYVE domain containing 1 (ANKFY1), harboring a BTB domain similar to the methyl CpG-binding protein 1 (MBD1) which bound to OASL in human, was regulated by dOASL.  At protein level, 133 host proteins were detected.  Interestingly, ANKFY1 was one of them binding to dOASL protein.  Further phylogenomic and chromosomal syntenic analysis demonstrated MBD1 was absent in birds, while mammals retained.  It is suggested that OASL-ANKFY1 interaction might act as a compensatory mechanism to regulate gene expression in birds.  Our findings will provide a useful resource for the molecular mechanism research of dOASL.
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6. More children nutrition distribution, less labor incentive: Evidence from Chinese collective agriculture
HUANG Ying-wei, MAO Pei, LI Jun
Journal of Integrative Agriculture    2019, 18 (10): 2422-2433.   DOI: 10.1016/S2095-3119(19)62733-4
摘要162)      PDF    收藏
Distribution system will affect the labor incentive that has been heatedly discussed by recent literatures. Using a unique micro dataset, this paper demonstrates that the equalitarian distribution system is one of the reasons for the insufficient labor incentive during the Chinese Collective Agriculture period. Specifically speaking, in the distribution of basic rations, the proportion for children (aged 1–3 and 4–7 years) was often beyond their nutrition demand, resulting the dissatisfaction of other families with more laborers and less children, thus these households will reduce their labor supply gradually. At the same time, the existence of outstanding accounts makes it a failure to use work points to buy distributions, which is the mechanism of the distribution system and insufficient labor incentive. All the results have been accepted by the robustness tests. The study will help to understand the distribution system and labor incentive, as well as the failure of the Chinese collective agriculture.
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7. Overexpression of the Suaeda salsa SsNHX1 gene confers enhanced salt and drought tolerance to transgenic Zea mays
HUANG Ying, ZHANG Xiao-xia, LI Yi-hong, DING Jian-zhou, DU Han-mei, ZHAO Zhuo, ZHOU Li-na, LIU Chan, GAO Shi-bin, CAO Mo-ju, LU Yan-li, ZHANG Su-zhi
Journal of Integrative Agriculture    2018, 17 (12): 2612-2623.   DOI: 10.1016/S2095-3119(18)61998-7
摘要300)      PDF    收藏
Maize is one of the most important crops worldwide, but it suffers from salt stress when grown in saline-alkaline soil. There is therefore an urgent need to improve maize salt tolerance and crop yield. In this study, the SsNHX1 gene of Suaeda salsa, which encodes a vacuolar membrane Na+/H+ antiporter, was transformed into the maize inbred line 18-599 by Agrobacterium-mediated transformation. Transgenic maize plants overexpressing the SsNHX1 gene showed less growth retardation when treated with an increasing NaCl gradient of up to 1%, indicating enhanced salt tolerance. The improved salt tolerance of transgenic plants was also demonstrated by a significantly elevated seed germination rate (79%) and a reduction in seminal root length inhibition. Moreover, transgenic plants under salt stress exhibited less physiological damage. SsNHX1-overexpressing transgenic maize accumulated more Na+ and K+ than wild-type (WT) plants particularly in the leaves, resulting in a higher ratio of K+/Na+ in the leaves under salt stress. This result revealed that the improved salt tolerance of SsNHX1-overexpressing transgenic maize plants was likely attributed to SsNHX1-mediated localization of Na+ to vacuoles and subsequent maintenance of the cytosolic ionic balance. In addition, SsNHX1 overexpression also improved the drought tolerance of the transgenic maize plants, as rehydrated transgenic plants were restored to normal growth while WT plants did not grow normally after dehydration treatment. Therefore, based on our engineering approach, SsNHX1 represents a promising candidate gene for improving the salt and drought tolerance of maize and other crops.
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8. Physiological changes and expression characteristics of ZIP family genes under zinc deficiency in navel orange (Citrus sinensis)
XING Fei, FU Xing-zheng, WANG Nan-qi, XI Jian-long, HUANG Yi, ZHOU Wei, LING Li-li, PENG Liang-zhi
Journal of Integrative Agriculture    2016, 15 (4): 803-811.   DOI: 10.1016/S2095-3119(15)61276-X
摘要2014)      PDF    收藏
Zinc (Zn) deficiency is widespread among citrus plants, but information about the mechanisms for Zn deficiency response in these plants is scarce. In the present study, different navel orange (Citrus sinensis (L.) Osbeck) leaves with various yellowing levels were sampled in our experimental orchard, and upon estimation of nutrient contents, Zn deficiencies were diagnosed as mild, moderate, and severe. Further analysis of chlorophyll content, photosynthetic characteristics, antioxidant enzyme activities, and expression levels of Zn/Iron-regulated transporter-like protein (ZIP) family genes were conducted in the sampled Zn-deficient leaves. The results showed that chlorophyll contents and net photosynthetic rate (Pn) seemed to decrease with reduced Zn contents. In addition, comparison of severe Zn-deficient and normal leaves revealed that activities of peroxidase (POD) and catalase (CAT) increased significantly, whereas that of Zn-containing enzymes such as Cu/Zn superoxide dismutase (Cu/Zn-SOD) significantly reduced with decreasing Zn contents. As expected, expression of the ZIP family genes, ZIP1, ZIP3, and ZIP4, was induced by Zn deficiencies. These results deepen our understanding of Zn deficiency in citrus plants as well as provide useful preliminary information for further research.
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9. Muscle Biological Characteristics of Differentially Expressed Genes in Wujin and Landrace Pigs
XU Hong, HUANG Ying, LI Wei-zhen, YANG Ming-hua, GE Chang-rong, ZHANG Xi, LI Liu-an, GAO Shi-zheng , ZHAO Su-mei
Journal of Integrative Agriculture    2014, 13 (10): 2236-2242.   DOI: 10.1016/S2095-3119(13)60605-X
摘要1349)      PDF    收藏
The biological chemistry would be responsible for the meat quality. This study tried to investigate the transcript expression profile and explain the characteristics of differentially expressed genes between the Wujin and Landrace pigs. The results showed that 526 differentially expressed genes were found by comparing the transcript expression profile of muscle tissue between Wujin and Landrace pigs. Among them, 335 genes showed up-regulations and 191 genes showed down-regulations in Wujin pigs compared with the Landrace pigs. Gene ontology (GO) analysis indicated that the differentially expressed genes were clustered into three groups involving in protein synthesis, energy metabolism and immune response. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis found that these differentially expressed genes participated in protein synthesis metabolism, energy metabolism and immune response pathway. The Database for Annotation, Visualization and Integrated Discovery (DAVID) analysis of protein function and protein domains function also confirmed that differentially expressed genes belonged to protein synthesis, energy metabolism and immune response. Genes related protein synthesis metabolism pathway in Landrace was higher than in Wujin pigs. However, differentially expressed genes related energy metabolism and immune response was up-regulated in Wujin pigs compared with Landrace pigs. Quantitative real-time RT-PCR on selected genes was used to confirm the results from the microarray. These suggested that the genes related to protein synthesis, energy metabolism and immune response would contribute to the growth performance, meat quality as well as anti-disease capacity.
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