Article
Plant Sciences
Baoyi Zhang, Yuhan Fei, Jiejie Feng, Xueai Zhu, Rui Wang, Hanqing Xiao, Hongsheng Zhang, Ji Huang
Summary: This study constructed a comprehensive rice ncRNA co-expression atlas, RiceNCexp, which provides expression information and co-expression analysis tools for rice ncRNAs in multiple tissues/organs.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Biochemistry & Molecular Biology
Yiyao Zhang, Aining Zhang, Wenhui Yang, Xinyi Jia, Qingjun Fu, Tingting Zhao, Jingbin Jiang, Jingfu Li, Huanhuan Yang, Xiangyang Xu
Summary: In this study, RNA-seq analysis was performed on two stages of tomato flower development, revealing differentially expressed genes related to plant hormone signaling and metabolism. Enrichment analysis indicated that flower development requires a significant amount of energy and material supply. Additionally, some plant hormones may have effects on flower development.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Fengmei Jin, Mingyan Hua, Lanfang Song, Shaojie Cui, Haibo Sun, Weidong Kong, Zhiyu Hao
Summary: Premature senescence of leaves can have a critical impact on tomato yield and quality. The leaf premature senescence mutant MT318 in this study was controlled by a single recessive nuclear gene. Various parameters such as maximum photochemical efficiency, superoxide dismutase, chlorophyll content, and malondialdehyde content were measured in the mutant, showing significant changes. Gene Ontology and pathway analysis revealed the involvement of differentially expressed genes in metabolic processes, cellular processes, single-organism processes, and catalytic activity. The 'plant hormone signal transduction' pathway was found to be the most significantly enriched. Correlation analysis pointed towards the importance of the auxin regulatory pathway and SA signal transduction pathway. These findings contribute to the understanding of the MT318 premature senescence gene and provide insights into tomato leaf senescence research.
PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS
(2022)
Article
Plant Sciences
Simone Landi, Paola Punzo, Roberta Nurcato, Rossella Albrizio, Walter Sanseverino, Riccardo Aiese Cigliano, Pasquale Giorio, Florinda Fratianni, Giorgia Batelli, Sergio Esposito, Stefania Grillo
Summary: 'Corbarino' (COR) and 'Lucariello' (LUC) are Mediterranean long shelf-life tomato landraces that produce high-quality fruits under low water input cultivation. Understanding their unique drought stress tolerance at morpho-physiological and molecular levels may be crucial for their utilization in breeding programs.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2023)
Article
Multidisciplinary Sciences
Amichay Afriat, Vanessa Zuzarte-Luis, Keren Bahar Halpern, Lisa Buchauer, Sofia Marques, Angelo Ferreira Chora, Aparajita Lahree, Ido Amit, Maria M. Mota, Shalev Itzkovitz
Summary: This study characterized the temporal expression programs of the rodent malaria parasite Plasmodium berghei ANKA and the host hepatocyte in a zonally controlled manner using single-cell RNA sequencing and single-molecule transcript imaging. The study identified differences in parasite gene expression in distinct zones and identified a subpopulation of hepatocytes with reduced levels of Plasmodium transcripts and parasitophorous vacuole breakdown. These findings provide insights into the liver stage of Plasmodium infection.
Article
Biotechnology & Applied Microbiology
Huseyin Basim, Esin Basim, Huseyin Tombuloglu, Turgay Unver
Summary: The transcriptome responses of Cmm-resistant and -susceptible tomato lines were compared after inoculation with Clavibacter michiganensis subsp. michiganensis. Differentially expressed genes were identified, with susceptible lines showing more genes involved in biological processes and molecular functions, while resistant lines exhibited distinct defense response and stress-related genes upon inoculation. This study provides insights for molecular breeding studies aiming to control the pathogen in tomato.
Article
Biochemistry & Molecular Biology
Sue A. Krause, Gayle Overend, Julian A. T. Dow, David P. Leader
Summary: FlyAtlas 2 is a database and web application for studying gene expression in different tissues of Drosophila melanogaster, with enhancements including a 'Profile' search function and a dedicated feature for exploring gene expression in the larval midgut. The database now includes data from 13 tissues, five sex-specific tissues, and eight larval tissues, with major improvements to the interface.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Plant Sciences
Pengyu Guo, Qingling Yang, Yunshu Wang, Zhijie Yang, Qiaoli Xie, Guoping Chen, Xuqing Chen, Zongli Hu
Summary: In this study, the researchers isolated and characterized an atypical bHLH transcription factor gene called SlPRE3, which showed predominant expression in the root and moderate expression in the senescent leaves. Comparative analysis revealed significant changes in plant morphology, increased GA(3) levels, reduced starch accumulation, and alterations in transcript levels of genes involved in gibberellin metabolism and signal transduction, cell expansion, and root development in the 35S:SlPRE3 plants. Physical interactions between SlPRE3 and several other factors were identified using Y2H and BiFC techniques. Overall, this study highlights the crucial role of SlPRE3 in determining plant morphology and root development.
PLANT CELL REPORTS
(2023)
Article
Plant Sciences
D. Tsitsekian, G. Daras, D. Templalexis, F. Avgeri, L. Lotos, C. G. Orfanidou, V. Ntoukakis, V. I. Maliogka, S. Rigas
Summary: Plants have evolved surveillance systems and defense mechanisms to restrict pathogens, with transcription factors (TFs) playing a key role. In this study, a combination of transcriptome analysis, validation, comparative analysis, and co-expression analysis was used to identify 11 highly responsive TFs involved in regulating host responses to PepMV. These findings provide insights into the molecular responses of the tomato-PepMV pathosystem.
Article
Biochemistry & Molecular Biology
Yaoguang Sun, Wenhui Yang, Jinxiu Chen, Dexia Chen, Huanhuan Yang, Xiangyang Xu
Summary: Flowering reversion in tomato may be related to various biological processes, such as cell signal transduction, energy metabolism, and protein post-transcriptional regulation. Endogenous hormone analysis and exogenous hormone treatment revealed the involvement of multiple plant hormones in tomato flowering reversion.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Biochemical Research Methods
Malte D. Luecken, M. Buettner, K. Chaichoompu, A. Danese, M. Interlandi, M. F. Mueller, D. C. Strobl, L. Zappia, M. Dugas, M. Colome-Tatche, Fabian J. Theis
Summary: This study benchmarked 68 method and preprocessing combinations on 85 batches of gene expression data, highlighting the importance of highly variable gene selection in improving method performance. When dealing with complex integration tasks, scANVI, Scanorama, scVI, and scGen consistently performed well, while the performance of single-cell ATAC-sequencing integration was strongly influenced by the choice of feature space.
Article
Biochemistry & Molecular Biology
Xiuming Jiang, Yang Li, Ran Li, Yijie Gao, Zengbing Liu, Huanhuan Yang, Jingfu Li, Jingbin Jiang, Tingting Zhao, Xiangyang Xu
Summary: Tomato leaf mold disease caused by Cladosporium fulvum is a common disease in greenhouse tomato production. The Cf genes play a role in resistance to the disease, but the effectiveness of common Cf genes has decreased due to the rapid mutation of C. fulvum. Ont7813 plants carrying the Cf-13 gene show effective resistance. Transcriptome sequencing revealed differentially expressed genes and enriched gene ontology terms in the response process. Key regulatory genes involved in plant hormone signal transduction, plant-pathogen interaction, and MAPK signaling pathways were identified. The JA and SA contents increased significantly in Ont7813 during C. fulvum infection.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Horticulture
Agustina Paula Fortuny, Diego Alberto Mengarelli, Javier Hernan Pereira da Costa, Gustavo Ruben Rodriguez, Maria Ines Zanor
Summary: This study provides a deeper understanding of the molecular basis of reciprocal effect and heterosis in plant crops by studying the genetic and molecular differences between different parental genotypes and their reciprocal hybrids, as well as the presence of heterosis and reciprocal effects.
SCIENTIA HORTICULTURAE
(2023)
Article
Biochemistry & Molecular Biology
Matthias Flotho, Jeremy Amand, Pascal Hirsch, Friederike Grandke, Tony Wyss-Coray, Andreas Keller, Fabian Kern
Summary: The molecular causes and mechanisms of neurodegenerative diseases are still not well understood. This study introduces ZEBRA, a large single-cell and single-nucleus RNA-seq database, which integrates gene expression and metadata from multiple studies to enhance our understanding of mammalian brain function during aging and disease.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Estanislao Burgos, Maria Belen De Luca, Isidore Diouf, Luis A. de Haro, Elise Albert, Christopher Sauvage, Zhao J. Tao, Luisa Bermudez, Ramon Asis, Adriano N. Nesi, Michel Matringe, Claire Brehelin, Thomas Guiraud, Carine Ferrand, Isabelle Atienza, Joana Jorly, Jean P. Mauxion, Pierre Baldet, Alisdair R. Fernie, Leandro Quadrana, Christophe Rothan, Mathilde Causse, Fernando Carrari
Summary: By studying the genetic determinants of tocochromanol accumulation in tomato fruits and genetically engineering their biosynthetic pathway, a total of 25 quantitative trait loci were identified across the genome. By bypassing specific pathway points, the engineered tomatoes showed increased tocopherols and tocotrienols content, indicating a trade-off between VTE and natural variation in chorismate metabolism.
Article
Biotechnology & Applied Microbiology
Andrea Becchimanzi, Maddalena Avolio, Hamed Bostan, Chiara Colantuono, Flora Cozzolino, Donato Mancini, Maria Luisa Chiusano, Pietro Pucci, Silvia Caccia, Francesco Pennacchio
Article
Plant Sciences
Julien Curaba, Hamed Bostan, Pablo F. Cavagnaro, Douglas Senalik, Molla Fentie Mengist, Yunyang Zhao, Philipp W. Simon, Massimo Iorizzo
FRONTIERS IN PLANT SCIENCE
(2020)
Review
Plant Sciences
Luca Ambrosino, Chiara Colantuono, Gianfranco Diretto, Alessia Fiore, Maria Luisa Chiusano
Article
Biochemistry & Molecular Biology
Miriam Ruocco, Luca Ambrosino, Marlene Jahnke, Maria Luisa Chiusano, Isabel Barrote, Gabriele Procaccini, Joao Silva, Emanuela Dattolo
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Article
Biochemistry & Molecular Biology
Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2020)
Review
Food Science & Technology
Francesco Monticolo, Emanuela Palomba, Rosa De Santis, Lorenzo Assentato, Viviana Triscino, Maria Chiara Langella, Virginia Lanzotti, Maria Luisa Chiusano
TRENDS IN FOOD SCIENCE & TECHNOLOGY
(2020)
Review
Plant Sciences
Francesco Monticolo, Emanuela Palomba, Pasquale Termolino, Pasquale Chiaiese, Elisabetta de Alteriis, Stefano Mazzoleni, Maria Luisa Chiusano
FRONTIERS IN PLANT SCIENCE
(2020)
Article
Cell Biology
Francesco Monticolo, Emanuela Palomba, Maria Luisa Chiusano
Summary: Programmed cell death, involving complex molecular pathways, leads to changes in ribosomal protein expression and organization, influencing cell fate. The differential expression of ribosomal proteins during programmed cell death induced by acetic acid suggests the relevance of reprogramming translational apparatus in yeast cells. Furthermore, exposure to acetic acid affects genes related to translation processes and rRNA maturation, demonstrating the impact of environmental factors on cell death mechanisms.
CELL DEATH DISCOVERY
(2021)
Article
Cell Biology
Quirino Attilio Vassalli, Chiara Colantuono, Valeria Nittoli, Anna Ferraioli, Giulia Fasano, Federica Berruto, Maria Luisa Chiusano, Robert Neil Kelsh, Paolo Sordino, Annamaria Locascio
Summary: Photoreceptor cells have diversified during evolution, with the homeodomain transcription factor Onecut (Oc) playing a key role in their differentiation and functioning. Downstream genes of Oc are involved in functions such as exocytosis, calcium homeostasis, and neurotransmission in both tunicates and vertebrates.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Public, Environmental & Occupational Health
Vincenzo De Luca, Giovanni Tramontano, Luigi Riccio, Ugo Trama, Pietro Buono, Mario Losasso, Umberto Marcello Bracale, Giovanni Annuzzi, Rosa Zampetti, Francesco Cacciatore, Giannamaria Vallefuoco, Alberto Lombardi, Anna Marro, Mariarosa Anna Beatrice Melone, Cristina Ponsiglione, Maria Luisa Chiusano, Giancarlo Bracale, Gaetano Cafiero, Aurelio Crudeli, Carmine Vecchione, Maurizio Taglialatela, Donatella Tramontano, Guido Iaccarino, Maria Triassi, Regina Roller-Wirnsberger, Jean Bousquet, Maddalena Illario
Summary: Campania in Italy utilizes an innovative strategy with a person-centered, life-course, One Health approach to improve health outcomes by combining demographic change with the opportunities of the Silver Economy. Through research and innovation projects and collaborations with international networks, innovative solutions are transferred to stakeholders in the multi-sectoral ecosystem for health.
FRONTIERS IN PUBLIC HEALTH
(2021)
Article
Plant Sciences
Molla F. Mengist, Hamed Bostan, Elisheba Young, Kristine L. Kay, Nicholas Gillitt, James Ballington, Colin D. Kay, Mario G. Ferruzzi, Hamid Ashrafi, Mary Ann Lila, Massimo Iorizzo
Summary: This study focused on the genetic basis of fruit quality traits in blueberry, constructing a high-density linkage map and identifying 18 loci associated with fruit quality traits over a three-year period. The study also found associations between fruit quality traits and metabolites, providing valuable insights into the genetic factors affecting blueberry fruit quality.
HORTICULTURE RESEARCH
(2021)
Article
Oncology
Francesco Monticolo, Maria Luisa Chiusano
Summary: A healthy diet is widely accepted as a fundamental approach to prevent cancer, with nutrigenomics studies providing valuable information in the search for compounds that can affect gene expression favorably. This computational study selected 23 natural compounds as potential candidates for novel drugs or functional foods for cancer treatment and prevention, based on analyses of gene expression and structure similarity with compounds that had positive effects on cancer types.
Article
Plant Sciences
Maria Luisa Chiusano, Guido Incerti, Chiara Colantuono, Pasquale Termolino, Emanuela Palomba, Francesco Monticolo, Giovanna Benvenuto, Alessandro Foscari, Alfonso Esposito, Lucia Marti, Giulia de Lorenzo, Isaac Vega-Munoz, Martin Heil, Fabrizio Carteni, Giuliano Bonanomi, Stefano Mazzoleni
Summary: Recent research has shown that extracellular DNA has inhibitory effects on the growth of conspecific individuals in plants, with cells being able to distinguish self from nonself DNA. Exposure to self-DNA limits cell permeability and affects chloroplast functioning, while exposure to nonself-DNA triggers a hypersensitive response and systemic acquired resistance. These findings suggest complex cascades of events in response to extracellular self- or nonself-DNA, which are discussed in the context of DAMP and PAMP responses.
Article
Cell Biology
Alfonso Esposito, Luca Ambrosino, Silvano Piazza, Salvatore D'Aniello, Maria Luisa Chiusano, Annamaria Locascio
Summary: This study investigates the presence of thyroid-related proteins in non-vertebrate and vertebrate chordates and determines the conservation and divergence of functional domains at the protein level. The findings support the hypothesis that non-vertebrate chordates have a functional thyroid hormone signaling system and provide insights into its possible evolutionary adaptation.