Review
Plant Sciences
Minhang Yuan, Bruno Pok Man Ngou, Pingtao Ding, Xin Xiu-Fan
Summary: Plants have innate immune responses to resist pathogen attacks, involving pattern-recognition receptors (PRRs) and nucleotide-binding domain leucine-rich repeat containing receptors (NLRs) that lead to pattern-triggered immunity (PTI) and effector-triggered immunity (ETI). Despite different activation mechanisms, PTI and ETI converge into similar downstream responses, with evidence of interactions and shared components between PRR-mediated and NLR-mediated signaling cascades. Future research on signal collaboration between PRR-initiated and NLR-initiated immunity will provide a more comprehensive understanding of the plant immune system.
CURRENT OPINION IN PLANT BIOLOGY
(2021)
Article
Plant Sciences
Sangrea Shim, Chung-Mo Park, Pil Joon Seo
Summary: Gene expression is intricately regulated by multilayered genetic and epigenetic mechanisms. iRegNet is a web application that analyzes the upstream regulatory network for user-queried genes or genomic regions of interest in the Arabidopsis genome, providing comprehensive information on DNA-protein interactions and histone modifications.
Review
Microbiology
John P. DeLong, Maitham A. Al-Sammak, Zeina T. Al-Ameeli, David D. Dunigan, Kyle F. Edwards, Jeffry J. Fuhrmann, Jason P. Gleghorn, Hanqun Li, Kona Haramoto, Amelia O. Harrison, Marcia F. Marston, Ryan M. Moore, Shawn W. Polson, Barbra D. Ferrell, Miranda E. Salsbery, Christopher R. Schvarcz, Jasmine Shirazi, Grieg F. Steward, James L. Van Etten, K. Eric Wommack
Summary: This review discusses the traits of viral cells and viral particles, as well as how to categorize virus phenotypes; the foundational goal in biology is understanding how phenotypes emerge from genotypes; identifying the features that constitute a virus's phenotype is crucial for comprehensive interpretation of viral genome sequences and for advancing our understanding of viral evolution and ecology.
NATURE REVIEWS MICROBIOLOGY
(2022)
Article
Psychiatry
Miaomiao Jiang, Ziqi Wang, Tianlan Lu, Xianjing Li, Kang Yang, Liyang Zhao, Dai Zhang, Jun Li, Lifang Wang
Summary: This study identified a novel lncRNA (MIR600HG) associated with autism spectrum disorder (ASD) and explored its role in regulating synaptogenesis through the ASD-associated miRNA-mRNA axes.
TRANSLATIONAL PSYCHIATRY
(2023)
Article
Computer Science, Software Engineering
Bipul Mohanto, A. B. M. Tariqul Islam, Enrico Gobbetti, Oliver Staadt
Summary: Foveated rendering adapts the image synthesis process to the user's gaze, utilizing the limitations of the human visual system to provide high-quality visual experiences at reduced costs. Despite significant progress, there are still open research problems in this field.
COMPUTERS & GRAPHICS-UK
(2022)
Article
Nutrition & Dietetics
Guangqing Fu, Yanhua Ren, Jun Kang, Bo Wang, Junxiang Zhang, Jinggui Fang, Weimin Wu
Summary: Anthocyanins, total phenols, soluble sugar and fruit shape are important factors in determining fruit quality and customer preference. However, little is known about the transcriptomics and underlying regulatory networks that control overall quality during fruit growth and ripening. This study used quality-related transcriptome data from different ecological zones to build a regulatory network that identifies key genes and transcription factors controlling these quality traits in grapes. Overall, this research provides a basis for improving grape quality and offers new insights on quality control during grape development and ripening.
FRONTIERS IN NUTRITION
(2023)
Article
Biochemistry & Molecular Biology
Florian Schmidt, Alexander Marx, Nina Baumgarten, Marie Hebel, Martin Wegner, Manuel Kaulich, Matthias S. Leisegang, Ralf P. Brandes, Jonathan Goeke, Jilles Vreeken, Marcel H. Schulz
Summary: STITCHIT is a novel approach to dissect epigenetic variation in a gene-specific manner for the detection of regulatory elements (REMs) without relying on peak calls in individual samples, leading to a more accurate and refined REM detection compared to standard methods across multiple samples. The approach also predicts thousands of putative REMs, suggesting a large portion of the regulome might be uncharted water.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Plant Sciences
Carla Pereira, Pedro Costa, Larindja Pinheiro, Victor M. Balcao, Adelaide Almeida
Summary: This study highlights phage-based biocontrol strategies as an effective alternative to control Psa-induced bacterial canker of kiwifruit. Current treatments for Psa infections are limited, and it is crucial to avoid the use of copper products and antibiotics to prevent the development of bacterial resistance. Therefore, developing new approaches to combat Psa is essential for sustainable agriculture production.
Review
Cell Biology
Glaucia Noeli Maroso Hajj, Paula Borzino Cordeiro Nunes, Martin Roffe
Summary: Gliomas, particularly glioblastoma, exhibit deregulation of translational control due to overactivation of signaling pathways such as PI3K/AKT/mTORC1 and Ras/ERK1/2. Transcriptome analysis can provide important insights into gene expression patterns in gliomas.
CELLULAR SIGNALLING
(2021)
Review
Food Science & Technology
Javier Vicente, Eva Navascues, Fernando Calderon, Antonio Santos, Domingo Marquina, Santiago Benito
Summary: The interest in Lachancea thermotolerans, a yeast species with unusual characteristics, has notably increased in all ecological, evolutionary, and industrial aspects. One key characteristic of L. thermotolerans is its production of high quantities of lactic acid compared to other yeast species. Its evolution has been influenced by the environment and domestication, allowing several metabolic traits to arise. The molecular regulation of the fermentative process in L. thermotolerans reveals interesting routes that play a complementary or protective role against fermentative stresses.
Article
Multidisciplinary Sciences
Liang-Yu Fu, Tao Zhu, Xinkai Zhou, Ranran Yu, Zhaohui He, Peijing Zhang, Zhigui Wu, Ming Chen, Kerstin Kaufmann, Dijun Chen
Summary: ChIP-Hub is an integrated web platform that provides rich resources of plant regulome and epigenome data for visualization and meta-analysis. By manually curating and evaluating the data quality, it allows in-depth investigation of the co-association of different regulators and the dynamic activity of tissue-specific regulatory elements.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hao Li, Changyuan Wang, Yue Jin, Yuanqing Cai, Huijun Sun, Mozhen Liu
Summary: The ceRNA mechanism involving circRNAs, miRNAs, and mRNAs may play an important role in the occurrence and development of osteoporosis (OP). Potential therapeutic options for OP were identified through a drug-target gene network. This study provides insights into the potential links between circRNAs, miRNAs, and mRNAs in OP and highlights the importance of the ceRNA mechanism.
SCIENTIFIC REPORTS
(2022)
Review
Plant Sciences
Shan Kothari, Anna K. Schweiger
Summary: Spectroscopy has been widely used in plant ecology to infer plant traits and processes at individual or community levels. However, understanding the phenotypic information contained in spectra can be challenging due to the complexity of structural and chemical factors. Different approaches, such as radiative transfer and empirical models, have been used to estimate plant traits from spectra, each with their strengths and limitations. In addition, treating spectral data as analogous to trait space can provide valuable insights into the processes structuring plant communities, although it may be more difficult to interpret specific biological processes.
JOURNAL OF ECOLOGY
(2022)
Article
Biochemical Research Methods
Dong-Xu Li, Peng Zhou, Bo-Wei Zhao, Xiao-Rui Su, Guo-Dong Li, Jun Zhang, Peng-Wei Hu, Lun Hu
Summary: BioCAIV is a webserver dedicated to clustering analysis of biological networks, aiming to maximize accessibility and applicability with a user-friendly interface. This tool enables biological researchers to perform accurate clustering analysis for biological networks and identify functionally significant modules.
BMC BIOINFORMATICS
(2023)
Article
Mathematics, Applied
Dilan Ozturk, Hitay Ozbay
Summary: This paper explores the analysis of an extended gene regulatory network model with time delayed negative feedback. The stability of the extended model is investigated using different design parameters, and a local stability condition is derived. Numerical examples are provided to illustrate the stability characteristics of the delayed extended GRN model, and the results are compared with a benchmark homogeneous gene regulatory network.
APPLIED AND COMPUTATIONAL MATHEMATICS
(2023)
Article
Plant Sciences
Pavel Kerchev, Frank Van Breusegem
Summary: Reactive oxygen species (ROS), once considered harmful metabolic byproducts, are now seen as integral to cellular programs, activating signaling pathways that regulate plant growth, development, and defense. Adverse environmental conditions can lead to excessive ROS levels, causing oxidative stress and negative impacts on cellular components. Research efforts have focused on enhancing antioxidant mechanisms to improve oxidative stress resilience in both model and crop species.
Article
Plant Sciences
Ruben Tenorio Berrio, Hilde Nelissen, Dirk Inze, Marieke Dubois
Summary: This passage discusses the impact of drought on global agriculture and how new strategies are being researched to enhance crop tolerance to drought. The focus has shifted from simply enhancing drought resistance to aiming to maintain plant growth and yield in drought conditions.
Review
Agronomy
Alain Gojon, Laurent Nussaume, Doan T. Luu, Erik H. Murchie, Alexandra Baekelandt, Vandasue Lily Rodrigues Saltenis, Jean-Pierre Cohan, Thierry Desnos, Dirk Inze, John N. Ferguson, Emmanuel Guiderdonni, Anne Krapp, Rene Klein Lankhorst, Christophe Maurel, Hatem Rouached, Martin A. J. Parry, Mathias Pribil, Lars B. Scharff, Philippe Nacry
Summary: Plant scientists and farmers are facing challenges in providing food security while preserving natural resources and adapting to climate change. Breeding resilient crops and improving nutrient use efficiency are crucial for sustainable agriculture. Understanding the physiological and molecular bases of plant environmental responses is essential, as well as exploring genetic resources and utilizing technological advancements.
FOOD AND ENERGY SECURITY
(2023)
Article
Biochemistry & Molecular Biology
Natallia Ashykhmina, Kai Xun Chan, Henning Frerigmann, Frank Van Breusegem, Stanislav Kopriva, Ulf-Ingo Fluegge, Tamara Gigolashvili
Summary: Plants have highly compartmentalized eukaryotic cells, with plastids and mitochondria relying on the flow of information to and from the nuclei. Retrograde and anterograde signals, such as the retrograde signaling molecule PAP, play a role in coordinating intracellular functions in response to biotic and abiotic stresses. The SAL1 protein, which dephosphorylates PAP to AMP, has different stability and impacts in different cell compartments. Further research is needed to understand the role of the SAL1-PAP pathway in various cellular processes under stress conditions.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2022)
Article
Plant Sciences
Jonas Blomme, Ward Develtere, Ayse Kose, Julia Arraiza Ribera, Christophe Brugmans, Jessica Jaraba-Wallace, Ward Decaestecker, Debbie Rombaut, Alexandra Baekelandt, Alvaro Daniel Fernandez Fernandez, Frank Van Breusegem, Dirk Inze, Thomas Jacobs
Summary: This study presents a simplified heat stress assay that can effectively increase the mutagenesis efficiency of CRISPR in plants and in some cases improve the recovery of mutant progeny.
Correction
Biochemistry & Molecular Biology
Kaoru Urano, Kyonoshin Maruyama, Tomotsugu Koyama, Nathalie Gonzalez, Dirk Inze, Kazuko Yamaguchi-Shinozaki, Kazuo Shinozaki
PLANT MOLECULAR BIOLOGY
(2022)
Editorial Material
Plant Sciences
Oana Dima, Yana Heyvaert, Dirk Inze
Summary: European R&D in plant breeding is falling behind due to strict regulations on genetically modified organisms (GMO) that apply to all crop varieties obtained through genome editing techniques. To support conclusions and facilitate science-based policy making, we have developed an online database of worldwide genome editing applications in crops.
TRENDS IN PLANT SCIENCE
(2022)
Review
Plant Sciences
Dirk Inze, Hilde Nelissen
Summary: Comparative analyses of growth-regulatory mechanisms between Arabidopsis and maize show that transferring knowledge from model species to crops is not straightforward even when gene space is conserved. Based on these insights, future opportunities to enhance the interpretation of curiosity-driven research towards crop improvement are formulated.
Article
Biochemistry & Molecular Biology
Christian Damian Lorenzo, Kevin Debray, Denia Herwegh, Ward Develtere, Lennert Impens, Dries Schaumont, Wout Vandeputte, Stijn Aesaert, Griet Coussens, Yara De Boe, Kirin Demuynck, Tom Van Hautegem, Laurens Pauwels, Thomas B. Jacobs, Tom Ruttink, Hilde Nelissen, Dirk Inze
Summary: Ensuring food security while adapting to climate change is the main challenge for agriculture in the 21st century. Recent advances in CRISPR/Cas9 gene engineering have provided a way to accelerate plant breeding to meet the increasing demand. The gene discovery pipeline BREEDIT combines multiplex genome editing with crossing schemes to improve complex traits such as yield and drought tolerance.
Article
Agronomy
Alexandra Baekelandt, Vandasue L. R. Saltenis, Mathias Pribil, Philippe Nacry, Jeremy Harbinson, Norbert Rolland, Ralf Wilhelm, Jessica Davies, Dirk Inze, Martin A. J. Parry, Rene Klein Lankhorst
Summary: To meet the increasing demand for food and feed and mitigate climate change, the world needs to double its agricultural productivity by 2050. Developing and integrating new crops adapted to the future climate can help achieve this goal. The H2020 CropBooster-P project aims to identify and prioritize breeding options for sustainable crop yield increases, taking into account socio-economic and environmental factors.
FOOD AND ENERGY SECURITY
(2023)
Review
Plant Sciences
Heng Zhou, Jingjing Huang, Patrick Willems, Frank Van Breusegem, Yanjie Xie
Summary: Reactive electrophilic species are widely present in plant cells and play a role in specific redox-regulated signaling events. Redox signaling is known to regulate gene expression during various biological processes, including plant growth, development, and stress responses. Recent data has shown that transcription factors are a major target of cysteine thiol-based oxidative post-translational modifications, which can affect their activity and transmit redox information to the nucleus. This review discusses the progress made in characterizing these modifications, their biochemical properties, and their effects on plant transcription factors, as well as the underlying mechanism of redox regulation and the challenges that remain in understanding the redox regulation of plant gene expression.
TRENDS IN PLANT SCIENCE
(2023)
Review
Biochemistry & Molecular Biology
Alvaro Daniel Fernandez-Fernandez, Simon Stael, Frank Van Breusegem
Summary: Proteolysis in plants is a significant field of study because proteases play crucial roles in plant cell death, disease, and development. Proteolytic activities are tightly regulated to ensure precise activity and minimize unwanted effects. Only a few plant proteases and their activation mechanisms have been extensively studied.
CELL DEATH AND DIFFERENTIATION
(2023)
Article
Biochemistry & Molecular Biology
Patrick Willems, Valerie Van Ruyskensvelde, Takanori Maruta, Robin Pottie, Alvaro D. Fernandez-Fernandez, Jarne Pauwels, Matthew A. Hannah, Kris Gevaert, Frank Van Breusegem, Katrien Van der Kelen
Summary: Alternative splicing is an important gene regulatory process in plants, and its inhibition can alleviate cell death and enhance tolerance to oxidative stress.
FREE RADICAL BIOLOGY AND MEDICINE
(2023)
Editorial Material
Plant Sciences
Oana Dima, Rene Custers, Lindsy De Veiman, Dirk Inze
Summary: The European Commission has published a legislative proposal that suggests a science-based approach to regulate genome-editing applications in EU crops, aligning with the legislation in other countries. However, further science-based advice is necessary for implementation.
TRENDS IN PLANT SCIENCE
(2023)
Review
Plant Sciences
Michele Schneider, Michiel Van Bel, Dirk Inze, Alexandra Baekelandt
Summary: This article focuses on the genetic networks governing leaf cell proliferation and discusses the evolutionary conservation among species. It also explores the interconnectedness between these genetic pathways.