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Plant gene co-expression defines the biosynthetic pathway of neuroactive alkaloids

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Molecular Plant 2024年第3期17卷 372-374页

作者： Fang Liu' al.sdair r.fernie Youjun Zhang Key Laboratory of Seed Innovation Institute of Genetics and Developmental BiologyChinese Academy of Sciences100101 BeijingChina Max Planck Institute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center for Plant Systems Biology and Biotechnology 4000 PlovdivBulgaria University of Chinese Academy of Sciences 100049 BeijingChina

Transcriptomes comprise gene co-expression clustersor modules,showcasing distinct patterns of coordinated expression among groups of genes across independent biological samples(Serin et al.,2016).The"guilt-by-association"hypothesis suggests the functional importance of these clusters;for example,co-expressed genes associated with metabolism typically contain genes encoding several enzymes associated with the same pathways.

关键词： metabolism alkaloids

WTV2.0:A high-coverage plant volatilomics method with a comprehensive selective ion monitoring acquisition mode

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Molecular Plant 2024年第6期17卷 972-985页

作者： Honglun Yuan Yiding Jiangfang Zhenhuan Liu rongxiu Su Qiao Li Chuanying Fang Sishu Huang Xianqing Liu al.sdair r.fernie Jie Luo School of Breeding and Multiplication(Sanya Institute of Breeding and Multiplication)and College of Tropical Agriculture and Forestry Hainan UniversitySanya Hainan 572025China Yazhouwan National Laboratory(YNL) Sanya Hainan 572025China Department of Molecular Physiology Max-Planck-Institute of Molecular Plant PhysiologyAm Mühlenberg 1Potsdam-Golm 14476Germany

Volatilomics is essential for understanding the biological functions and fragrance contributions of plant ***,the annotation coverage achieved using current untargeted and widely targeted volatomics(WTV)methods has been limited by low sensitivity and/or low acquisition ***,we introduce WTV 2.0,which enabled the construction of a high-coverage library containing 2111 plant volatiles,and report the development of a comprehensive selective ion monitoring(cSIM)acquisition method,including the selection of characteristic qualitative ions with the minimal ion number for each compound and an optimized segmentation method,that can acquire the smallest but sufficient number of ions for most plant volatiles,as well as the automatic qualitative and semi-quantitative analysis of cSIM ***,the library and acquisition method we developed can be self-expanded by incorporating compounds not present in the library,utilizing the obtained cSIM *** showed that WTV 2.0 increases the median signal-to-noise ratio by 7.6-fold compared with the untargeted method,doubled the annotation coverage compared with the untargeted and WTV 1.0 methods in tomato fruit,and led to the discovery of menthofuran as a novel flavor compound in passion *** 2.0 is a Python library with a user-friendly interface and is applicable to profiling of volatiles and primary metabolites in any species.

关键词： volatilomics widely targeted methods GC-MS selective ion monitoring plant volatiles

revealing the specific regulations of nitric oxide on the postharvest ripening and senescence of bitter melon fruit

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aBIOTECH 2024年第1期5卷 29-45页

作者： Hongwei Wang Ling Li Lili Ma al.sdair r.fernie Anzhen Fu Chunmei Bai Zhaoze Sang Susu Guo Fan Zhang Qing Wang Yanyan Zheng Jinhua Zuo Key Laboratory of Vegetable Postharvest Processing Ministry of AgricultureBeijing Key Laboratory of Fruits and Vegetable Storage and ProcessingKey Laboratory of Biology and Genetic Improvement of Horticultural Crops(North China)of Ministry of AgricultureKey Laboratory of Urban Agriculture(North)of Ministry of AgricultureBeijing Vegetable Research CenterInstitute of Agro-Products Processing and Food NutritionBeijing Academy of Agriculture and Forestry SciencesBeijing 100097China College of Food Science and Biotechnology Tianjin Agricultural UniversityTianjin 300392China Max Planck Institute of Molecular Plant Physiology 14476 Potsdam GolmGermany Institute of Food Science and Technology Chinese Academy of Agricultural SciencesBeijingChina

Bitter melon fruit is susceptible to yellowing,softening,and rotting under room-temperature storage conditions,resulting in reduced commercial *** oxide(NO)is an important signaling molecule and plays a crucial role in regulating the fruit postharvest *** this study,we investigated the effects of NO treatment on changes in sensory and firmness of bitter melon fruit during postharvest ***,transcriptomic,metabolomic,and proteomic analyses were performed to elucidate the regulatory mechanisms through which No treatment delays the ripening and senescence of bitter melon *** results show that differentially expressed genes(DEGs)were involved in fruit texture(CSLE,β-Gal,and PME),plant hormone signal transduction(ACS,JAr4,and AUX28),and fruit flavor and aroma(SUS2,LOX,and GDH2).In addition,proteins differentially abundant were associated with fruit texture(PLY,PME,and PGA)and plant hormone signal transduction(PBL15,JAr1,and PYL9).Moreover,No significantly increased the abundance of key enzymes involved in the phenylpropanoid biosynthetic pathway,thus enhancing the disease resistance and alleviating softening of bitter melon ***,differential metabolites mainly included phenolic acids,terpenoids,and *** results provide a theoretical basis for further studies on the physiological changes associated with postharvest ripening and senescence of bitter melon fruit.

关键词： Bitter melon NO treatment Postharvest ripening and senescence

The light and hypoxia induced gene ZmPOrB1 determines tocopherol content in the maize kernel

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Science China(Life Sciences) 2024年第3期67卷 435-448页

作者： Nannan Liu Yuanhao Du Shijuan Yan Wei Chen Min Deng Shutu Xu Hong Wang Wei Zhan Wenjie Huang Yan Yin Xiaohong Yang Qiao Zhao al.sdair r.fernie Jianbing Yan National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Hubei Hongshan Laboratory Wuhan 430070China Agro-biological Gene research Center Guangdong Academy of Agricultural SciencesGuangzhou 510640China College of Agronomy Hunan Agricultural UniversityChangsha 410128China College of Agronomy Northwest A&F UniversityXi'an 710000China State Key Laboratory of North China Crop Improvement and regulation Hebei Sub-center of National Maize Improvement Center of ChinaCollege of AgronomyHebei Agricultural UniversityBaoding 071001China College of Life Sciences South-Central Minzu UniversityWuhan 430070China Plant Science Facility of the Institute of Botany Chinese Academy of SciencesBeijing 100093China National Maize Improvement Center of China Beijing Key Laboratory of Crop Genetic ImprovementChina Agricultural UniversityBeijing 100093China Shenzhen Key Laboratory of Synthetic Genomics Guangdong Provincial Key Laboratory of Synthetic GenomicsShenzhen Institute of Synthetic BiologyShenzhen Institute of Advanced TechnologyChinese Academy of SciencesShenzhen 518055China Max Planck Institute of Molecular Plant Physiology Potsdam-Golm 14476Germany

Tocopherol is an important lipid-soluble antioxidant beneficial for both human health and plant growth. Here, we fine mapped a major QTLqVE1 affecting γ-tocopherol content in maize kernel, positionally cloned and confirmed the underlying gene ZmPOrB1(por1), as a protochlorophyllide oxidoreductase. A 13.7 kb insertion reduced the tocopherol and chlorophyll content, and the photosynthetic activity by repressing ZmPOrB1 expression in embryos of NIL-K22, but did not affect the levels of the tocopherol precursors HGA(homogentisic acid)and PMP(phytyl monophosphate). Furthermore, ZmPOrB1 is inducible by low oxygen and light, thereby involved in the hypoxia response in developing embryos. Concurrent with natural hypoxia in embryos, the redox state has been changed with NO increasing and H_(2)O_(2) decreasing, which lowered γ-tocopherol content via scavenging reactive nitrogen species. In conclusion, we proposed that the lower lightharvesting chlorophyll content weakened embryo photosynthesis, leading to fewer oxygen supplies and consequently diverse hypoxic responses including an elevated γ-tocopherol consumption. Our findings shed light on the mechanism for fine-tuning endogenous oxygen concentration in the maize embryo through a novel feedback pathway involving the light and low oxygen regulation of ZmPOrB1 expression and chlorophyll content.

关键词： maize tocopherol hypoxia photosynthesis ZmPOrB1

Image Splicing Forgery Detection Using Feature-Based of Sonine Functions and Deep Features

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Computers, Materials & Continua 2024年第1期78卷 795-810页

作者： ala’a r.al-Shamasneh rabha W.Ibrahim Department of Computer Science College of Computer&Information SciencesPrince Sultan UniversityRiyadh11586Saudi Arabia Department of Computer Science and Mathematics Lebanese American UniversityBeirut11022801Lebanon Department of Mathematics Mathematics Research CenterNear East UniversityNicosia99138Turkey Information and Communication Technology research Group Scientific Research CenterAlayen UniversityDhi Qar64001Iraq

The growing prevalence of fake images on the Internet and social media makes image integrity verification a crucial research *** of the most popular methods for manipulating digital images is image splicing,which involves copying a specific area from one image and pasting it into *** were made to mitigate the effects of image splicing,which continues to be a significant research *** study proposes a new splicing detectionmodel,combining Sonine functions-derived convex-based features and deep *** stages make up the proposed *** first step entails feature extraction,then classification using the“support vector machine”(SVM)to differentiate authentic and spliced *** proposed Sonine functions-based feature extraction model reveals the spliced texture details by extracting some clues about the probability of image *** proposed model achieved an accuracy of 98.93% when tested with the CASIA V2.0 dataset“Chinese Academy of Sciences,Institute of Automation”which is a publicly available dataset for forgery *** experimental results show that,for image splicing forgery detection,the proposed Sonine functions-derived convex-based features and deep features outperform state-of-the-art techniques in terms of accuracy,precision,and ***,the obtained detection accuracy attests to the benefit of using the Sonine functions alongside deep feature *** the regions or locations where image tampering has taken place is limited by the *** research will need to look into advanced image analysis techniques that can offer a higher degree of accuracy in identifying and localizing tampering regions.

关键词： Image forgery image splicing deep learning Sonine functions

Provenance and depositional setting of the Late MiocenePleistocene clastic sediments in the eastern Arabian Peninsula and western Iraq using rare earth elements geochemistry

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Acta Geochimica 2024年第2期43卷 399-410页

作者： Salih M.Awadh Zinah S.al-Ankaz Mohanad r.A.al-Owaidi John S.Armstrong-altrin Department of Geology College of ScienceUniversity of BaghdadBaghdadIraq Department of Geology College of ScienceUniversity of WasitWasit 52011Iraq Department of Applied Geology College of ScienceUniversity of BabylonBabylon 51001Iraq Unidad de Procesos Oceanicos y Costeros Instituto de Ciencias del Mar y LimnologíaUniversidad Nacional Autonoma de MexicoCiudad Universitaria04510 Mexico CityCDMXMexico Department of Marine Sciences Bharathidasan UniversityTiruchirapalliTamil Nadu 620024India

The sandstones of the Late miocene–Pliocene Dibdibba Formation in the Najaf–Karbala Plateau and Basra were examined to determine their source rocks and origin. The rare earth elements(rEE) and trace elements(Sc, Co, V, and Th) concentrations in these sandstones revealed that they likely derived from a single source. The steep light rare earth elements(LrEE) and flat, heavy rare earth element(HrEE) patterns, negative Eu anomaly, and high ΣrEE contents in sandstones suggest its derivation from a suggests that a passive continental margin environment and originated from felsic source rocks. The average concentration of ΣrEE is 93.5 ppm, which is lower than that of the average crustal compositions like Upper Continental Crust and Post Archean Australian Shale. The higher proportion of LrEE compared to HrEE implies that these sandstones were recycled and derived from a distal source. The Th/Co, Th/Sc, La/Sc, La/Co, Eu/Eu*and(La/Lu)cn elemental ratios indicated that these Late Miocene–Pliocene sandstones were derived from felsic rocks located in the marginal region of the Arabian Shield.

关键词： rEE Dibdibba formation Clastic sediments Passive continental margin

On the role of the tricarboxylic acid cycle in plant productivity

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Journal of Integrative Plant Biology 2018年第12期60卷 1199-1216页

作者： Youjun Zhang al.sdair r.fernie Max-Planck-lnstitute of Molecular Plant Physiology Am Muhlenberg 114476 Potsdam-GolmGermany Center of Plant System Biology and Biotechnology 4000 PlovdivBulgaria

The tricarboxylic acid(TCA) cycle is one of the canonical energy pathways of living systems, as well as being an example of a pathway in which dynamic enzyme assemblies, or metabolons, are well characterized. The role of the enzymes have been the subject of saturated transgenesis approaches, whereby the expression of the constituent enzymes were reduced or knocked out in order to ascertain their in vivo *** of the resultant plants exhibited improved photosynthesis and plant growth, under controlled greenhouse conditions. In addition, overexpression of the endogenous genes, or heterologous forms of a number of the enzymes, has been carried out in tomato fruit and the roots of a range of species, and in some instances improvement in fruit yield and postharvest properties and plant performance, under nutrient limitation, have been reported, respectively. Given a number of variants, in nature, we discuss possible synthetic approaches involving introducing these variants, or at least a subset of them, into plants. We additionally discuss the likely consequences of introducing synthetic metabolons, wherein certain pairs of reactions are artificially permanently assembled into plants, and speculate as to future strategies to further improve plant productivity by manipulation of the core metabolic pathway.

关键词： On the role of the tricarboxylic acid cycle in plant productivity TCA cycle

De Novo Domestication:An alternative route toward New Crops for the Future

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Molecular Plant 2019年第5期12卷 615-631页

作者： al.sdair r.fernie Jianbing Yan Department of Molecular Physiology Max-Planck-lnstitute of Molecular Plant PhysiologyAm Muhlenberg 114476 Potsdam-GolmGermany National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China

Current global agricultural production must feed over 7 billion ***,productivity varies greatly across the globe and is under threat from both increased competitions for land and climate change and associated environmental ***,the increase in human population size and dietary changes are putting an ever greater burden on *** majority of this burden is met by the cultivation of a very small number of species,largely in locations that differ from their origin of *** technological advances have raised the possibility of de novo domestication of wild plants as a viable solution for designing ideal crops while maintaining food security and a more sustainable lowinput *** we discuss how the discovery of multiple key domestication genes alongside the development of technologies for accurate manipulation of several target genes simultaneously renders de novo domestication a route toward crops for the future.

关键词： De Novo Domestication redomestication New Crops Genome Editing Food Security Sustainable Agriculture

Transition of primary to secondary cell wall synthesis

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Science Bulletin 2016年第11期61卷 838-846页

作者： Zheng Li al.sdair r.fernie Staffan Persson School of Bio Sciences University of Melbourne Max-Planck-Institute of Molecular Plant Physiology ArC Centre of Excellence in Plant Cell Walls School of Bio Sciences University of Melbourne

The construction of a secondary cell wall is an important and necessary developmental decision that sup- ports cell function and plant stature. Unlike the primary cell walls, which are initiated during cell division and develop along with the expansion of the cells, secondary cell walls are constructed after the cells have stopped growing. Hence, the transition from primary to secondary wall synthesis marks an important and distinct metabolic investment by the plant. This transition requires a coordi- nated change of a plethora of cellular processes, including hormonal, transcriptional and post-transcriptional activi- ties, metabolic flux re-distributions and enzymatic activities. In this review, we briefly summarize the hormonal and transcriptional control of the primary to secondary wall transition, and highlight important gaps in our under- standing of the metabolic framework that support the transition. Several tools that may aid in future research efforts to better understand the changes in cell wall synthesis during the trans-differentiation are also discussed.

关键词： Secondary cell wall Primary cell walltransition Hormone Transcriptional network Metabolism