Article
Agronomy
Huiyan Zhao, Guoxia Shang, Nengwen Yin, Si Chen, Shulin Shen, Haiyan Jiang, Yunshan Tang, Fujun Sun, Yuhan Zhao, Yongchao Niu, Zhi Zhao, Liang Xu, Kun Lu, Dezhi Du, Cunmin Qu, Jiana Li
Summary: In this study, the mechanisms underlying seed coat color formation in Brassica rapa were explored through a multi-omics analysis of the transcriptome, metabolome, and genome. Major and minor loci, as well as candidate genes, for seed coat color were identified. The findings provide a foundation and reference for studying the mechanism of seed coat color in B. rapa and other plants.
THEORETICAL AND APPLIED GENETICS
(2022)
Article
Immunology
Yajuan Fan, Yuan Gao, Qingyan Ma, Zai Yang, Binbin Zhao, Xiaoyan He, Jian Yang, Bin Yan, Fengjie Gao, Li Qian, Wei Wang, Feng Zhu, Xiancang Ma
Summary: Schizophrenia is associated with immune dysfunctions and disturbed intestinal microbiota. This study found that abnormal gut metabolism-immune network exists in schizophrenia, and gut microbiota may influence immune responses by regulating host metabolic processes.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Immunology
Huiqing Long, Li Yan, Juncai Pu, Yiyun Liu, Xiaogang Zhong, Haiyang Wang, Lu Yang, Fangzhi Lou, Shihong Luo, Yingying Zhang, Yang Liu, Peng Xie, Ping Ji, Xin Jin
Summary: Microbiota and chronic stress have significant effects on the morphological structures and molecular function of oral homeostasis. Microbiota reshapes the structure of the oral epithelial barrier and changes the function of molecular biology through the immune response and mitochondrial metabolic process, thus maintaining oral homeostasis. Chronic stress enhances the regulatory effects of microbiota on oral homeostasis.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Xiaolan Huang, Fang Li, Yi Wang, Xinbei Jia, Nan Jia, Fei Xiao, Chunrong Sun, Jin Fu, Min Chen, Xiaodai Cui, Dong Qu, Laurence Don Wai Luu, Jun Tai, Jieqiong Li
Summary: Metabolomics was used to identify potential biomarkers for RSV pneumonia and multi-omics analysis revealed the pathogenies of RSV infection.
Review
Plant Sciences
Milad Alizadeh, Ryan Hoy, Bailan Lu, Liang Song
Summary: Seed development is tightly regulated spatiotemporally, with transcriptional regulation playing a crucial role in shaping major traits during seed maturation. This regulation often involves coordinated recruitment or replacement of multiple transcription factors to achieve combinatorial regulation. Recent progress has been made in understanding the integration of activation and repression of seed maturation genes by transcriptional networks.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Pharmacology & Pharmacy
Chengcheng Wang, Zheng He
Summary: In this study, a multi-omics analysis was conducted to investigate the significance of chloride intracellular channel 1 (CLIC1) in gliomas. The results showed that elevated CLIC1 expression was associated with worse survival outcomes and more advanced stage glioma. CLIC1 was also found to be linked to tumorigenic and anticancer immunity pathways. In vitro experiments demonstrated that suppressing CLIC1 could induce apoptosis and attenuate cell motility of glioma cells. Furthermore, high CLIC1 expression was associated with increased sensitivity to certain drugs and immune cell infiltration in tumors.
FRONTIERS IN PHARMACOLOGY
(2023)
Article
Plant Sciences
Jiajia Luo, Zhijian Chen, Rui Huang, Yuanhang Wu, Chun Liu, Zeping Cai, Rongshu Dong, Jacobo Arango, Idupulapati Madhusudana Rao, Rainer Schultze-Kraft, Guodao Liu, Pandao Liu
Summary: In this study, transcriptomic and proteomic analyses identified Pi starvation-inducible APase genes in stylo. Among them, SgPAP7 was found to be a key gene that plays a major role in stylo adaptation to low-Pi conditions by facilitating the utilization of both exogenous and endogenous organic phosphorus sources.
Article
Biochemistry & Molecular Biology
Danyang Chen, Xiaolan Guo, Kaiying Wang, Weigang Zhao, Zhongjuan Chang, Quankai Wang, Chao Xu
Summary: This study investigated the changes in gene and protein expression in raccoon dogs infected with Eperythrozoon using transcriptome and proteome sequencing. The results showed significant alterations in genes related to immunity and metabolism, suggesting that Eperythrozoon infection can affect raccoon dog growth and development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Zhenghao Lv, Dongying Zhou, Xiaolong Shi, Jingyao Ren, He Zhang, Chao Zhong, Shuli Kang, Xinhua Zhao, Haiqiu Yu, Chuantang Wang
Summary: This study investigated the metabolites and regulatory mechanisms associated with pod size in peanut. Comparative metabolome and transcriptome analysis revealed the phenylpropanoid biosynthesis pathway as a major pathway influencing pod size. The differential accumulation of p-coumaryl alcohol, a metabolite in this pathway, was found to be correlated with pod size. The differential expression of gene-LOC112771695, involved in the biosynthesis of monolignols, may explain the differential accumulation of p-coumaryl alcohol. The findings provide valuable insights into the factors influencing peanut pod size and have implications for genetic improvement of peanut.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Mari Spildrejorde, Athina Samara, Ankush Sharma, Magnus Leithaug, Martin Falck, Stefania Modafferi, Arvind Y. M. Sundaram, Ganesh Acharya, Hedvig Nordeng, Ragnhild Eskeland, Kristina Gervin, Robert Lyle
Summary: A study using a multi-omics approach found that prenatal paracetamol exposure may have a detrimental effect on brain development.
Article
Immunology
Qiaoke Li, Mingze Sun, Qi Zhou, Yulong Li, Jinmei Xu, Hong Fan
Summary: This study used gene set enrichment analysis to analyze the transcriptome of sepsis patients and identified 84 differentially expressed KEGG pathways. Among them, 10 pathways were associated with 28-day survival. Some pathways were correlated with immune cell abundance, and five pathways could be used to distinguish systemic inflammatory response syndrome, bacterial sepsis, and viral sepsis with an AUC above 0.80. Furthermore, seven related drugs were screened using survival-related pathways.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Plant Sciences
Hongzhi Liu, Wei Wu
Summary: Seed germination is promoted by overexpression of Tomato Ethylene Responsive Factor 1 (TERF1), leading to increased levels of SA, IAA, ABA, and GAs, and decreased levels of JA in TERF1 seeds. Transcriptome analysis identified differentially expressed genes involved in various biological processes, revealing the regulatory role of TERF1 in the ABA and GA biosynthesis and signaling pathways for seed germination.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2021)
Article
Plant Sciences
Hao Guo, Mengdi Mao, Yuan Deng, Lisong Sun, Ridong Chen, Peng Cao, Jun Lai, Yueran Zhang, Chao Wang, Chun Li, Yiran Li, Qunhang Bai, Tingting Tan, Jun Yang, Shouchuang Wang
Summary: This study identified 176 AP2/ERF genes related to steroidal glycoalkaloids and fruit development in tomato, with SlERF.D6 showing a significant regulatory role in fruit ripening and SGA synthesis pathway gene expression as the fruit matures.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agricultural Engineering
Zhi Zou, Yongguo Zhao, Li Zhang, Yanhua Xiao, Anping Guo
Summary: This study provides a transcriptome-based characterization of the SMP gene family in tigernut and reveals their important expression in late stages of tuber development. These findings improve the understanding of the lineage-specific evolution of the SMP gene family and provide valuable information for functional analysis and genetic improvement in tigernut.
INDUSTRIAL CROPS AND PRODUCTS
(2022)
Review
Biochemistry & Molecular Biology
Akiko Kozaki, Takuya Aoyanagi
Summary: Seed formation is a crucial process in plant life cycle, involving embryogenesis and maturation phases. Plants rely on the coordination of multiple signaling pathways, with gibberellin and abscisic acid identified as major hormones that antagonistically regulate seed development and germination. Understanding the complex molecular networks and signaling mechanisms of these hormones in seed development from embryogenesis to maturation is essential for plant survival and propagation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Valentin Verges, Christelle Dutilleul, Beatrice Godin, Boris Collet, Alain Lecureuil, Loic Rajjou, Cyrille Guimaraes, Michelle Pinault, Stephane Chevalier, Nathalie Giglioli-Guivarc'h, Eric Ducos
Summary: Protein farnesylation, regulated by the ERA1 gene, plays a crucial role in Arabidopsis, impacting seed development and quality. The era1 mutants exhibit severe pleiotropic phenotypes, affecting seed traits of agronomic interest.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Statistics & Probability
M. Perrot-Dockes, C. Levy-Leduc, L. Rajjou
Summary: The proposed method offers a novel and fully data-driven approach for estimating large sparse covariance matrices, capable of handling block structures in matrices with unknown permutations, implemented in the 'BlockCov' R package. Through numerical experiments and comparisons with other methods, the statistical and numerical performance of the method is demonstrated.
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES C-APPLIED STATISTICS
(2022)
Article
Plant Sciences
Gwendal Cueff, Loic Rajjou, Hai Ha Hoang, Christophe Bailly, Francoise Corbineau, Juliette Leymarie
Summary: This study compares the proteome of barley embryos induced to secondary dormancy (D2) under different temperature and hypoxia conditions. The results indicate that D2 induction is mainly associated with changes in protein accumulation and co-expression of genes. These findings suggest that temperature and oxygen have similar molecular regulatory mechanisms in dormancy cycling.
PLANT AND CELL PHYSIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Anja Krieger-Liszkay, Ginga Shimakawa
Summary: Light capture by chlorophylls and photosynthetic electron transport can generate reactive oxygen species (ROS), but under normal physiological conditions, the production of these ROS is regulated to non-destructive levels. Photosystem II is more susceptible to photoinhibition but can be quickly repaired, while photosystem I is largely protected. The size of the proton gradient plays a crucial role in preventing photoinhibition. Various antioxidants can quench or scavenge ROS.
BIOCHEMICAL SOCIETY TRANSACTIONS
(2022)
Review
Food Science & Technology
Luiza Avezum, Eric Rondet, Christian Mestres, Nawel Achir, Yann Madode, Olivier Gibert, Charlotte Lefevre, Youna Hemery, Jean-Luc Verdeil, Loic Rajjou
Summary: Germinated pulse-based food is a traditional process and a growing trend in healthy foods. This review examines the physiological and biochemical changes during the germination process in pulses, taking into account various factors that affect their nutritional value, and evaluates the impact of food processing on the nutritional and antinutritional components.
FOOD REVIEWS INTERNATIONAL
(2023)
Article
Plant Sciences
Kevin Baudry, Felix Barbut, Severine Domenichini, Damien Guillaumot, Mai Pham Thy, Helene Vanacker, Wojciech Majeran, Anja Krieger-Liszkay, Emmanuelle Issakidis-Bourguet, Claire Lurin
Summary: This study reveals the role of CBSX proteins in regulating thioredoxins (TRXs) and plant stress adaptation. CBSX2 specifically inhibits the activities of m-type TRXs, and this inhibition can be alleviated in the presence of AMP or ATP.
Article
Plant Sciences
Naoto Sano, Imen Lounifi, Gwendal Cueff, Boris Collet, Gilles Clement, Sandrine Balzergue, Stephanie Huguet, Benoit Valot, Marc Galland, Loic Rajjou
Summary: This study examines the genetic pathways and metabolic changes in the embryo and endosperm of rice seeds during germination using a multi-omics approach. The results show that the early phase of germination is a crucial turning point, and the endosperm and embryo exhibit distinct changes at the protein and metabolite levels. The study also highlights the importance of hormonal metabolism and energy supply-related proteins in rice seed germination.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Ginga Shimakawa, Anja Krieger-Liszkay, Thomas Roach
Summary: In plants, senescence is associated with the production of reactive oxygen species (ROS) and lipid peroxidation. However, lipid peroxidation is not solely linked to stress, as it also plays a role in plant development. The major polyunsaturated fatty acid (PUFA) in senescing leaves is linolenic acid, which is sensitive to peroxidation. Lipid catabolism during senescence leads to a decrease in PUFA levels and an increase in short-chain saturated fatty acids.
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Marine Messant, Umama Hani, Thais Hennebelle, Florence Guerard, Bertrand Gakiere, Andrew Gall, Sebastien Thomine, Anja Krieger-Liszkay
Summary: This study investigates the effects of excess and deficiency of manganese on chloroplast ultrastructure and photosynthetic electron transport in the liverwort Marchantia polymorpha, an emerging model system.
Article
Plant Sciences
Naeif Matar, Catherine Macadre, Gamal A. G. Ammar, Alexis Peres, Boris Collet, Naim El Boustany, Loic Rajjou, Falah As-Sadi, Marie Dufresne, Pascal Ratet
Summary: This study successfully isolated two beneficial Trichoderma strains from wheat in Lebanon, which were found to promote root growth, produce plant growth hormones, and inhibit the growth of pathogenic fungi in vitro. These Trichoderma strains have the potential to be used as organic fertilizers for wheat.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Manuela Nagel, Erwann Arc, Loic Rajjou, Gwendal Cueff, Marlene Bailly, Gilles Clement, Inmaculada Sanchez-Vicente, Christophe Bailly, Charlotte E. Seal, Thomas Roach, Hardy Rolletschek, Oscar Lorenzo, Andreas Boerner, Ilse Kranner
Summary: Seed quality is crucial for agricultural production, but it is affected by climate change. This study investigated the influence of drought and elevated temperature on key seed quality traits in two genotypes of barley. The results showed that different genotypes of barley had varying responses to drought and temperature stress, with differences in seed size, weight, and vigor. Transcription factors associated with environmental responses and seed dormancy were found to be more abundant in one genotype. Drought significantly reduced seed yield in both genotypes, while elevated temperature only affected seed size. Metabolite profiling revealed differences in metabolic processes between the embryos of the two genotypes, with drought affecting amino acid metabolism in both genotypes. This study could support future breeding efforts to develop lodging and drought-resistant barley varieties without compromising stress resistance and dormancy.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Marine Messant, Umama Hani, Thanh-Lan Lai, Adjele Wilson, Ginga Shimakawa, Anja Krieger-Liszkay
Summary: In this study, the role of plastid terminal oxidase PTOX in protecting photosystem I and II was investigated using PTOX mutants in two model plants. The results show that PTOX plays a dual role as both a pro-oxidant and an antioxidant in vivo.
Article
Biology
Sebastien Baud, Massimiliano Corso, Isabelle Debeaujon, Bertrand Dubreucq, Dominique Job, Annie Marion-Poll, Martine Miquel, Helen North, Loic Rajjou, Loic Lepiniec
Summary: This article introduces the research on the mechanisms controlling seed development, metabolism, and physiology, as well as the contributions of Michel Caboche in this field. By updating a review coordinated by Caboche, the review provides an overview of seed biology research and highlights the experimental methods and advancements in the past decade.
COMPTES RENDUS BIOLOGIES
(2022)
Article
Biochemistry & Molecular Biology
Takafumi Shimizu, Yuri Kanno, Shunsuke Watanabe, Mitsunori Seo
Summary: Abscisic acid (ABA) is a plant hormone that plays crucial roles in seed development and germination. The uptake of ABA into the seed coat via NPF5.1 is found to be important for maintaining ABA homeostasis and regulating seed germination.
PLANT SIGNALING & BEHAVIOR
(2022)
Review
Plant Sciences
S. P. Jeevan Kumar, Anjani Devi Chintagunta, Y. Mohan Reddy, Loic Rajjou, Vijay Kumar Garlapati, Dinesh K. Agarwal, S. Rajendra Prasad, Jesus Simal-Gandara
Summary: ROS and RNS play significant roles in seed physiology, influencing germination, dormancy, and longevity. Recent studies show that they induce seed germination through oxidative and nitrosative signaling, and post-translational modifications promote germination. Understanding their interaction with plant hormones, signaling functions, and protection mechanisms can lead to hormone engineering for improved crop productivity.
CURRENT PLANT BIOLOGY
(2021)