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Foundations of Programmable Process Structures for the unified modeling and simulation of agricultural and aquacultural systems

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Information Processing in agriculture 2024年第1期11卷 91-108页

作者： Monika Varga Bela Csukas Hungarian University of agriculture and Life Sciences Kaposvar Campus40 Guba S7400 KaposvarHungary

This research paper defines the theoretical foundations and computational implementation of a non-conventional modeling and simulation methodology,inspired by the needs of problem solving for biological,agricultural,aquacultural and environmental *** challenging practical problem is to develop a framework for automatic generation of causally right and balance-based,unified models that can also be applied for the effective coupling amongst the various(sophisticated field-specific,sensor data processing-based,upper level optimization-driven,etc.)*** scientific problem addressed in this innovation is to develop Programmable Process Structures(PPS)by combining functional basis of systems theory,structural approach of net theory and computational principles of agent based *** offers a novel framework for the automatic generation of easily extensible and connectible,unified models for the underlying complex *** models can be generated from one state and one transition meta-prototypes and from the transition oriented description of process *** models consist of unified state and transition *** local program containing prototype elements,derived also from the meta-prototypes,are responsible for the case-specific *** integrity and consistency of PPS architecture are based on the meta-prototypes,prepared to distinguish between the conservation-laws-based measures and the *** simulation is based on data flows amongst the state and transition elements,as well as on the unification based data transfer between these elements and their calculating *** architecture and its AI language-based(Prolog)implementation support the integration of various field-and task-specific models,*** better understanding is helped by a simple *** capabilities of the recently consolidated general methodology are discussed on the basis of some preliminary applications,focusing on the recently studied

关键词： Unified process model Meta-prototype-based architecture Transition-based structure representation Locally programmable functionality prototypes Agricultural systems Aquacultural systems

Sugarcane transcription factor ScWRKY4 negatively regulates resistance to pathogen infection through the JA signaling pathway

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The Crop Journal 2024年第1期12卷 164-176页

作者： Dongjiao Wang Wei Wang Shoujian Zang Liqian Qin Yanlan Liang Peixia Lin Yachun Su Youxiong Que Key Laboratory of Sugarcane Biology and Genetic Breeding Ministry of Agriculture and Rural AffairsKey Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationCollege of AgricultureFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina National Key Laboratory for Tropical Crop Breeding Institute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesSanya 572024HainanChina

WRKY transcription factors,transcriptional regulators unique to plants,play an important role in defense response to pathogen ***,the resistance mechanisms of WRKY genes in sugarcane remain *** the present study,gene ontology(GO)enrichment analysis revealed that WRKY gene family in sugarcane was extensively involved in the response to biotic stress and in defense *** identified gene ScWRKY4,a classⅡc member of the WRKY gene family,in sugarcane cultivar *** gene was induced by salicylic acid(SA)and methyl jasmonate(MeJA)***,expression of ScWRKY4 was down-regulated in smut-resistant sugarcane cultivars but up-regulated in smutsusceptible sugarcane cultivars infected with Sporisorium ***,stable overexpression of the ScWRKY4 gene in Nicotiana benthamiana enhanced susceptibility to Fusarium solani *** and caused down-regulated expression of immune marker-related *** analysis indicated suppressed expression of most JAZ genes in the signal transduction ***4 interacted with ScJAZ13 to repress its *** thus hypothesized that the ScWRKY4 gene was involved in the regulatory network of plant disease resistance,most likely through the JA signaling *** present study depicting the molecular involvement of ScWRKY4 in sugarcane disease resistance lays a foundation for future investigation.

关键词： Disease resistance Expression profile Transcriptome analysis WRKY transcription factors

Mechanism of action of cordycepin in the treatment of hepatocellular carcinoma via regulation of the Hippo signaling pathway

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Food Science and Human Wellness 2024年第2期13卷 1040-1054页

作者： Xiaomin Li Qing Liu Songyu Xie Xiaoping Wu Junsheng Fu College of Life Sciences Mycological Research CenterFujian Agriculture and Forestry UniversityFuzhou 350002China

Hepatocellular carcinoma(HCC)is one of the common most malignant *** study aimed to determine the in vitro and in vivo anticancer activity of cordycepin and elucidate its mechanism of *** results of in vitro and in vivo studies revealed that cordycepin inhibited proliferation and migration in HepG-2 cells and inhibited the growth of HepG-2 xenograft-bearing nude mice by inducing *** sequencing analysis revealed a total of 403 differential genes,which revealed that cordycepin may play an anti-HCC role by regulating Hippo signaling *** regulatory effects of cordycepin on the Hippo signaling pathway was further investigated using a YAP1 *** results demonstrated that cordycepin upregulated the expression of MST1 and LAST1,and subsequently inhibited YAP1,which activated the Hippo signaling *** in turn downregulated the expression of GBP3 and ETV5,and subsequently inhibited cell proliferation and ***,YAP1 regulated the expression of Bax and Bcl-2,regulated the mitochondrial apoptotic pathway,and induced apoptosis by upregulating the expression of the caspase-3 *** summary,this study reveals that cordycepin exerts its anti-hepatocarcinoma effect through regulating Hippo signaling pathway,and GBP3 and ETV5 may be potential therapeutic targets for hepatocarcinoma.

关键词： Cordycepin Hepatocellular carcinoma Hippo signaling pathway GBP3 ETV5

Prediction of the potential distribution and analysis of the freezing injury risk of winter wheat on the Loess Plateau under climate change

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Journal of Integrative agriculture 2024年第9期23卷 2941-2954页

作者： Qing Liang Xujing Yang Yuheng Huang Zhenwei Yang Meichen Feng Mingxing Qing Chao Wang Wude Yang Zhigang Wang Meijun Zhang Lujie Xiao Xiaoyan Song College of agriculture Shanxi Agricultural UniversityTaigu 030801China Smart agriculture College Shanxi Agricultural UniversityTaigu 030801China College of Resources and Environment Shanxi Agricultural UniversityTaigu 030801China

Determining the suitable areas for winter wheat under climate change and assessing the risk of freezing injury are crucial for the cultivation of winter *** used an optimized Maximum Entropy(MaxEnt)Model to predict the potential distribution of winter wheat in the current period(1970-2020)and the future period(2021-2100)under four shared socioeconomic pathway scenarios(SSPs).We applied statistical downscaling methods to downscale future climate data,established a scientific and practical freezing injury index(FII)by considering the growth period of winter wheat,and analyzed the characteristics of abrupt changes in winter wheat freezing injury by using the Mann-Kendall(M-K)*** results showed that the prediction accuracy AUC value of the MaxEnt Model reached *** minimum temperature in the coldest month,precipitation in the wettest season and annual precipitation were the main factors affecting the spatial distribution of winter *** total suitable area of winter wheat was approximately 4.40×10^(7)ha in the current *** the 2070s,the moderately suitable areas had the greatest increase by 9.02×10^(5)ha under SSP245 and the least increase by 6.53×10^(5)ha under *** centroid coordinates of the total suitable areas tended to move *** potential risks of freezing injury in the high-latitude and-altitude areas of the Loess Plateau,China increased *** northern areas of Xinzhou in Shanxi Province,China suffered the most serious freezing injury,and the southern areas of the Loess Plateau suffered the *** factors such as temperature,precipitation and geographical location had important impacts on the suitable area distribution and freezing injury risk of winter *** the future,greater attention should be paid to the northward boundaries of both the winter wheat planting areas and the areas of freezing injury risk to provide the early warning of freezing injury and implement corresponding management strat

关键词： climate change scenarios winter wheat freezing injury risk downscaling MaxEnt

FLOWERING LOCUS T(FT)in Photosensitive Type Chrysanthemum Accelerates Flowering in Arabidopsis

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Phyton-International Journal of Experimental Botany 2024年第4期93卷 819-830页

作者： Fenglan Wang Zhenyuan Cai Zhimei Li Shilong Zhang Honghui Luo Qing Wu Hanhan Xia Yanhong Guo College of Horticulture and Landscape Architecture Zhongkai University of Agriculture and EngineeringGuangzhou510225China

FLOWERING LOCUS T(FT)is an important factor for integrating flowering signals through the photoperiod pathway,which significantly promotes *** chrysanthemum varieties are short-day plants,sensitive to the photoperiod,which limits their ornamental and annual production *** this study,we aim to analyze the nutrients and flowering-related genes of chrysanthemums with different photoperiod types and to clone and verify the function of the flowering-related gene *** found that the formation of floral buds requires the accumulation of starch while consuming soluble sugars and the expression patterns of flowering-related genes GIGANTEA(GI),CONSTANS(CO),and FT in ***‘Zilian’and ***‘Zihongtuogui’had a certain synchronization during floral buds differentiation according to our quantitative validation,and the expression levels of CmGI,CmCO and CmFT in ***‘Zihongtuogui’were higher than those in ***.‘Zilian’in the later stage of *** was cloned from photosensitive ***‘Zihongtuogui’and polypeptide alignment and phylogenetic analysis showed that CmFT was clustered in FT-like *** further functional verification,we obtained two Arabidopsis transgenic *** results showed that CmFT transgenic ft mutant lines can significantly accelerate flowering in ***,we can initially confirm that CmFT plays an important role in promoting flowering,which may be the key reason for the photosensitivity of ***‘Zihongtuogui’.Overall,the results of this study are of great importance in revealing the flowering mechanism of different photoperiod types of chrysanthemums.

关键词： Chrysanthemum morifolium flowering-related genes CmFT photoperiod pathway heterologous expression

Changes in climatic conditions drive variations in arbuscular mycorrhizal fungi diversity and composition in semi-arid oak forests

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Journal of Forestry Research 2024年第5期35卷 106-119页

作者： Nahid Jafarian Javad Mirzaei Reza Omidipour Yahya Kooch Department of Forest Science Faculty of AgricultureIlam UniversityIlam 69315-516Iran Department of Range and Watershed Management Faculty of AgricultureIlam UniversityIlam 69315-516Iran Faculty of Natural Resources and Marine Sciences Tarbiat Modares UniversityNoor 46417-76489MazandaranIran

Arbuscular mycorrhizal fungi(AMF)play a vital role in plant productivity and ecosystem ***,their responses to abiotic factors(i.e.,climate,physiography,and soil properties)are unknown,especially across climatic gradients and slope aspects in arid and semi-arid *** this study,using 60 composite soil samples,direct and indirect effects of climate factors and slope aspects on AMF diversity,composition and spore density were *** findings indicate that climate has a more direct influ-ence on soil properties(P<0.001)in comparison to slope aspect(P=0.449).In contrast,climate significantly affected AMF diversity and composition,with the highest diversity in dryer *** pH had the highest correlation with different facets of AMF *** equation modeling(SEM)indicated that only a small part of the variation in AMF diversity and spore density could be explained by climate characteristics,slope aspect and soil *** on SEM results,climate was the most important determinant of AMF diversity and spore density;slope aspect had a less critical *** outputs suggest that variations in AMF diversity are derived by the direct effects of climate and the indirect effect of soil chemical *** addition,with increasing dryness,sporulation and AMF diversity increased.

关键词： AMF diversity and composition Physiographic factors Semi-arid ecosystems Zagros forest

Genome-Wide Identification of Tomato (Solanum lycopersicum L.) CKX Gene Family and Expression Analysis in the Callus Tissue under Zeatin Treatment

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Phyton-International Journal of Experimental Botany 2024年第6期93卷 1143-1158页

作者： Zhengfeng Lai Dongmei Lian Shaoping Zhang Yudong Ju Bizhen Lin Yunfa Yao Songhai Wu Jianji Hong Zhou Li Subtropical agriculture Research Institute Fujian Academy of Agricultural SciencesZhangzhou363005China

The cytokinin oxidase/dehydrogenase(CKX)enzyme is essential for controlling theﬂuctuating levels of endogen-ous cytokinin(CK)and has a signiﬁcant impact on different aspects of plant growth and ***-less,there is limited knowledge about CKX genes in tomato(Solanum lycopersicum L.).Here we performed genome-wide identiﬁcation and analysis of nine SlCKX family members in tomatoes using bioinformatics *** results revealed that nine SlCKX genes were unevenly distributed onﬁve chromosomes(Chr.1,Chr.4,Chr.8,Chr.10,and Chr.12).The amino acid length,isoelectric points,and molecular weight of the nine SlCKX proteins ranged from 453 to 553,5.77 to 8.59,and 51.661 to 62.494 kD,*** localization analysis indi-cated that SlCKX2 proteins were located in both the vacuole and cytoplasmic matrix;SlCKX3 and SlCKX5 pro-teins were located in the vacuole;and SlCKX1,4,6,7,8,and 9 proteins were located in the cytoplasmic ***,we observed differences in the gene structures and phylogenetic relationships of SlCKX proteins among different ***1-9 were positioned on two out of the three branches of the CKX phylogenetic tree in the multispecies phylogenetic tree construction,revealing their strong conservation within phylogenetic *** patterns of expression of CKX genes were noticed in callus cultures exposed to varying con-centrations of exogenous ZT,suggesting their roles in speciﬁc developmental and physiological functions in the regeneration *** results may facilitate subsequent functional analysis of SlCKX genes and provide valu-able insights for establishing an efﬁcient regeneration system for tomatoes.

关键词： Tomato SlCKX gene family phylogenetic relationships trans-zeatin expression pattern

Uncovering key salt-tolerant regulators through a combined eQTL and GWAS analysis using the super pan-genome in rice

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National Science Review 2024年第4期11卷 55-69页

作者： Hua Wei Xianmeng Wang Zhipeng Zhang Longbo Yang Qianqian Zhang Yilin Li Huiying He Dandan Chen Bin Zhang Chongke Zheng Yue Leng Xinglan Cao Yan Cui Chuanlin Shi Yifan Liu Yang Lv Jie Ma Wenchuang He Xiangpei Liu Qiang Xu Qiaoling Yuan Xiaoman Yu Tianyi Wang Hongge Qian Xiaoxia Li Bintao Zhang Hong Zhang Wu Chen Mingliang Guo Xiaofan Dai Yuexing Wang Xiaoming Zheng Longbiao Guo Xianzhi Xie Qian Qian Lianguang Shang Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural Sciences Institute of Wetland agriculture and Ecology Shandong Academy of Agricultural Sciences State Key Laboratory of Rice Biology China National Rice Research Institute National Key Facility for Crop Gene Resources and Genetic Improvement Institute of Crop Science Chinese Academy of Agricultural Sciences Yazhouwan National Laboratory

For sessile plants, gene expression plays a pivotal role in responding to salinity stress by activating or suppressing specific genes. However, our knowledge of genetic variations governing gene expression in response to salt stress remains limited in natural germplasm. Through transcriptome analysis of the Global Mini-Core Rice Collection consisting of a panel of 202 accessions, we identified 22 345 and 27 610expression quantitative trait loci associated with the expression of 7787 and 9361 e Genes under normal and salt-stress conditions, respectively, leveraging the super pan-genome map. Notably, combined with genome-wide association studies, we swiftly pinpointed the potential candidate gene STG5—a major salt-tolerant locus known as q STS5. Intriguingly, STG5 is required for maintaining Na+/K+homeostasis by directly regulating the transcription of multiple members of the Os HKT gene family. Our study sheds light on how genetic variants influence the dynamic changes in gene expression responding to salinity stress and provides a valuable resource for the mining of salt-tolerant genes in the future.

关键词： super pan-genome expression quantitative trait loci GWAS salt tolerance rice

Structural analysis of silk using solid-state NMR

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Magnetic Resonance Letters 2024年第3期4卷 19-34页

作者： Tetsuo Asakura Department of Biotechnology Tokyo University of Agriculture and TechnologyKoganeiTokyo184-8588Japan

Silkworms and spiders are capable of generating fibers that are both highly durable and elastic in a short span of time,using a silk solution stored within their bodies at room temperature and normal atmospheric *** dragline silk fiber,which is essentially a spider's lifeline,surpasses the strength of a steel wire of equivalent ***,humans have yet to replicate this process to produce fibers with similar high strength and elasticity in an eco-friendly ***,it is of utmost importance to thoroughly comprehend the extraordinary structure and fibrillation mechanism of silk,and leverage this understanding in the manufacturing of high-strength,high-elasticity *** review will delve into the recent progress in comprehending the structure of silks derived from silkworms and spiders,emphasizing the distinctive attributes of solidstate NMR.

关键词： Silk Bombyx mori Spider Solid-state NMR Structure