Article
Biochemistry & Molecular Biology
Brad T. Sherman, Ming Hao, Ju Qiu, Xiaoli Jiao, Michael W. Baseler, H. Clifford Lane, Tomozumi Imamichi, Weizhong Chang
Summary: DAVID, a popular bioinformatics resource system, has undergone updates in 2021, including the rebuilding of the DAVID Gene system, increasing the number of gene-term records for annotation types, adding new annotations, assigning specific subgroups, and adding a species parameter for improved user experience.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Computer Science, Artificial Intelligence
Georgios Stratogiannis, Panagiotis Kouris, Georgios Alexandridis, Georgios Siolas, Giorgos Stamou, Andreas Stafylopatis
Summary: This article introduces a novel framework for semantic enrichment of documents by utilizing hierarchical ontological knowledge and classification techniques. The main contributions include the definition of a theoretical model, a method for handling class imbalance, a methodology for assigning semantic labels, and the introduction of novel metrics for evaluating performance. Extensive experiments on popular datasets show promising results and robustness of the approach.
KNOWLEDGE AND INFORMATION SYSTEMS
(2021)
Article
Biology
Tzu-Hsien Yang, Chia-Wei Hsu, Yan-Xiang Wang, Chien-Hung Yu, Jagat Rathod, Yan-Yuan Tseng, Wei-Sheng Wu
Summary: In this research, the YMLA (Yeast Multiple List Analyzer) platform was constructed for comparative analysis among multiple gene lists, offering 39 yeast features for analysis and customized feature set reanalysis to help form mechanism hypotheses based on enriched feature subsets. The biological applicability of YMLA was demonstrated using example lists consisting of genes with top/bottom translation efficiency values.
COMPUTERS IN BIOLOGY AND MEDICINE
(2022)
Article
Biology
Foteini Thanati, Evangelos Karatzas, Fotis A. Baltoumas, Dimitrios J. Stravopodis, Aristides G. Eliopoulos, Georgios A. Pavlopoulos
Summary: In this article, FLAME, a web application for combining multiple gene lists prior to enrichment analysis, is introduced. Users can upload several lists and utilize interactive UpSet plots to handle unions or intersections among the given input files.
Article
Biochemical Research Methods
Rui Fan, Qinghua Cui
Summary: The weighted gene set enrichment algorithm and online tool WEAT was proposed, which weights genes using essentiality scores. Its usefulness was confirmed through three case studies, suggesting that it could provide more possibilities for further exploring the functions of given gene lists.
Article
Biochemical Research Methods
Jaesik Kim, Dokyoon Kim, Kyung-Ah Sohn
Summary: The study proposes hierarchical representations of GO and genes using Poincare embedding, which can better capture the hierarchical structure and predict gene interactions compared to previous studies. HiG2Vec demonstrates superior performance in capturing the semantics of GO and genes and in data utilization, making it robust for various biological knowledge manipulation.
Article
Psychology, Mathematical
Tyler M. Ensor, Molly B. MacMillan, Ian Neath, Aimee M. Surprenant
Summary: The study conducted three experiments to evaluate various measures of semantic relatedness and their ability to predict the recall of related and unrelated word lists in immediate memory tests. The results showed that lists of semantically related words are better recalled than lists of unrelated words. Different measures had slightly different predictions on the recall of related and unrelated word lists.
BEHAVIOR RESEARCH METHODS
(2021)
Article
Multidisciplinary Sciences
Karren Dai Yang, Anastasiya Belyaeva, Saradha Venkatachalapathy, Karthik Damodaran, Abigail Katcoff, Adityanarayanan Radhakrishnan, G. Shivashankar, Caroline Uhler
Summary: The authors use autoencoders to learn a probabilistic coupling and map different data modalities to a shared latent space, presenting an approach for integrating vastly different modalities. The integration of imaging and transcriptomics is still an open challenge, but this method provides a framework for diverse applications in biomedical discovery.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Hanxiao Sun, Kai Li, Xiaoting Zhang, Jun'e Liu, Meiling Zhang, Haowei Meng, Chengqi Yi
Summary: m(6)Am-seq is a newly developed method that can distinguish m(6)Am from m(6)A and identify functional methylation sites in the transcriptome.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Zongliang Yue, Eric Zhang, Clark Xu, Sunny Khurana, Nishant Batra, Son Do Hai Deng, James J. Cimino, Jake Y. Chen
Summary: PAGER-CoV is a new web-based database that assists biomedical researchers in interpreting coronavirus-related functional genomic study results using a vast collection of PAGs. By exploring relationships between PAGs, users can gain deeper insights into the research information. This database can help researchers find molecular biology mechanisms and tailored therapeutics for treating COVID-19 patients.
NUCLEIC ACIDS RESEARCH
(2021)
Review
Immunology
Amber Park, Laura K. Harris
Summary: The study used a meta-analysis approach to analyze mRNA expression data from SARS infections, potentially identifying therapeutic targets associated with major SARS infections. By comparing gene signatures from different sources, genes associated with SARS infection were identified, providing potential targets for future therapeutic research.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Genetics & Heredity
Cheng Xu, Xiaowei Liu, Xiaoxin Fang, Lei Yu, Hui Chong Lau, Danlei Li, Xiaoman Liu, Haili Li, Justin Ren, Baohui Xu, Jianjun Jiang, Lijiang Tang, Xiaofeng Chen
Summary: This study utilizes single-cell RNA sequencing technology to reveal the cellular composition and heterogeneity of smooth muscle cells (SMCs) in experimental aortic dissection (AD). The study identified 15 cell clusters and 9 cell types, showing significant changes in the relative numbers of SMCs and identifying 7 core differentially expressed genes (DEGs) in SMCs. The study also found that SMCs can differentiate into 8 different subtypes.
FRONTIERS IN GENETICS
(2022)
Article
Pharmacology & Pharmacy
Sang-Min Park, Aeyung Kim, Haeseung Lee, Su-Jin Baek, No Soo Kim, Musun Park, Jin-Mu Yi, Seongwon Cha
Summary: Pharmacogenomic analysis revealed the molecular mechanisms of action of the herbal medicine Bupleuri Radix (BR) in inhibiting cancer cell proliferation and inducing apoptosis. The study also showed enhanced cell adhesion and migration with BR treatment, indicating its potential therapeutic effects for skin disorders. In addition, BR demonstrated a wound-healing effect in skin and lung cells. The main active ingredients of BR exhibited anti-cancer effects, but further research is needed on the minor ingredients.
FRONTIERS IN PHARMACOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Ke-Jia Kan, Feng Guo, Lei Zhu, Prama Pallavi, Martin Sigl, Michael Keese
Summary: The study identified key modules and genes involved in AAA growth through gene expression analysis, and predicted potential drugs to prevent AAA progression.
Article
Endocrinology & Metabolism
Xiaojian Mao, Liangliang Tang, Hongyi Li, Wen Zhang, Li Liu, Heyong Wang, Abdalbari Headar
Summary: This study aims to explore the functions and gene sets of mutated genes related to hyperthyroidism in children. Through gene ontology and biological signaling pathway analysis, it was found that hormone activity and response to peptide hormone are the most significant gene ontology functions and thyroid hormone signaling pathway is the most significant biological signaling pathway. The identified mutated genes provide insights into the expected effects of multiple mutated genes on hyperthyroidism in children.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Review
Plant Sciences
Franziska Fichtner, Indeewari Madhubhashini Dissanayake, Benoit Lacombe, Francois Barbier
Summary: Sugars and nitrates play crucial roles in providing carbon and nitrogen in plants, and understanding how plants sense these nutrients is essential for crop improvement. The major components of nutrient signaling are relatively conserved across eukaryotes, while the diversification of components like the NRT1 family and SWEET sugar transporters is associated with plant terrestrialization. Nutrient signaling has evolved to interact with hormone signaling for fine-tuning physiological and developmental responses in plants.
TRENDS IN PLANT SCIENCE
(2021)
Article
Plant Sciences
Alaeddine Safi, Anna Medici, Wojciech Szponarski, Florence Martin, Anne Clement-Vidal, Amy Marshall-Colon, Sandrine Ruffel, Frederic Gaymard, Hatem Rouached, Julie Leclercq, Gloria Coruzzi, Benoit Lacombe, Gabriel Krouk
Summary: This study reveals that transcription factors of the HHO subfamily are key regulators of the nitrogen starvation response (NSR) in plants. They directly repress high-affinity nitrate transporters and control reactive oxygen species levels, defining a potential feed-forward signaling pathway for NSR.
JOURNAL OF EXPERIMENTAL BOTANY
(2021)
Article
Biochemistry & Molecular Biology
Ying Liu, Rodolfo A. Maniero, Ricardo F. H. Giehl, Michael Melzer, Priscille Steensma, Gabriel Krouk, Teresa B. Fitzpatrick, Nicolaus von Wire
Summary: This study found that apoplastic acidification induced by ammonium is associated with iron precipitation and hydrogen peroxide accumulation along the stele in root tips, indicating iron-dependent ROS formation. Through screening ammonium sensitivity in genes, PDX1.1 was identified as an ammonium-responsive gene that is upregulated in the root stele and catalyzes the de novo synthesis of vitamin B-6. Mutants of pdx1.1 exhibit hypersensitivity to ammonium, while chemical complementation or overexpression of PDX1.1 restores root elongation. The synthesis of non-phosphorylated B-6 vitamers mediated by PDX1.1 acts as a primary strategy to protect roots from ammonium-induced ROS formation.
Article
Plant Sciences
Laura Morales de los Rios, Claire Corratge-Faillie, Natalia Raddatz, Imelda Mendoza, Marika Lindahl, Alexis de Angeli, Benoit Lacombe, Francisco J. Quintero, Jose M. Pardo
Summary: Studies have shown that nitrate and potassium nutrition are tightly coordinated in vascular plants, with some nitrate transport proteins also affecting the root/shoot distribution of potassium. However, the biochemical connection between these traits remains controversial, as some proteins are suggested to mediate K+/H+ exchange instead of nitrate fluxes.
PLANT PHYSIOLOGY AND BIOCHEMISTRY
(2021)
Review
Plant Sciences
Rebecca Therby-Vale, Benoit Lacombe, Seung Y. Rhee, Laurent Nussaume, Hatem Rouached
Summary: Understanding the complex relationship between nutrient homeostasis and photosynthesis has great potential for crop improvement.
TRENDS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
David Sere, Oceane Cassan, Fanny Bellegarde, Cecile Fizames, Jossia Boucherez, Geoffrey Schivre, Jacinthe Azevedo, Thierry Lagrange, Alain Gojon, Antoine Martin
Summary: Polycomb-group (PcG) proteins play a crucial role in gene expression regulation, mainly by keeping genes in a transcriptionally silent state during development. Recent studies have shown that PcG proteins may have additional functions, including targeting active genes or acting independently of gene expression regulation. This study reveals that mutations in two Arabidopsis PcG proteins, CURLY LEAF (CLF) and LIKE HETEROCHROMATIN PROTEIN1 (LHP1), result in deregulation of active genes targeted by PcG proteins or enriched in associated chromatin marks. The deregulation is associated with the accumulation of small RNAs, leading to the degradation of active gene transcripts. It is concluded that PcG protein function is essential for maintaining the accurate degradation of RNA and ensuring proper gene expression levels.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Editorial Material
Plant Sciences
Benoit Lacombe
PHYSIOLOGIA PLANTARUM
(2022)
Article
Plant Sciences
Francois Vasseur, Denis Cornet, Gregory Beurier, Julie Messier, Lauriane Rouan, Justine Bresson, Martin Ecarnot, Mark Stahl, Simon Heumos, Marianne Gerard, Hans Reijnen, Pascal Tillard, Benoit Lacombe, Amelie Emanuel, Justine Floret, Aurelien Estarague, Stefania Przybylska, Kevin Sartori, Lauren M. Gillespie, Etienne Baron, Elena Kazakou, Denis Vile, Cyrille Violle
Summary: The trait-based approach in plant ecology aims to understand and classify the diversity of ecological strategies by comparing plant morphology and physiology. However, the major drawback is the high time and financial cost of measuring traits. Combining near-infrared spectroscopy (NIRS) with deep learning overcomes this limitation and allows for quick and accurate measurement of a range of traits, as well as identifying the effect of growth conditions on trait values.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Multidisciplinary Sciences
Rashed Abualia, Krisztina Otvos, Ondrej Novak, Eleonore Bouguyon, Kevin Domanegg, Anne Krapp, Philip Nacry, Alain Gojon, Benoit Lacombe, Eva Benkova
Summary: Plant mineral nutrition, especially nitrate uptake, plays a crucial role in plant growth and development. Roots act as a key regulator in coordinating the growth and development of plant organs in response to nitrate availability, through a complex regulatory mechanism involving cytokinin response factors and auxin transporters.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Huikyong Cho, Michael Banf, Zaigham Shahzad, Jelle Van Leene, Flavia Bossi, Sandrine Ruffel, Nadia Bouain, Pengfei Cao, Gabiel Krouk, Geert De Jaeger, Benoit Lacombe, Federica Brandizzi, Seung Y. Rhee, Hatem Rouached
Summary: Nutrient sensing and signaling play a crucial role in adapting growth to available resources. However, the molecular processes involved in sensing and responding to phosphorus (P) limitation to inhibit root growth are still unclear. In this study, the researchers identified a kinase called ARSK1 that attenuates early root growth inhibition under P limitation. They also discovered that ARSK1 phosphorylates and stabilizes RAPTOR1B, a component of TOR complex 1, to regulate root growth in response to P availability. These findings provide insights into the signaling components that regulate growth in relation to P availability.
Article
Plant Sciences
Ngoc Nga Nguyen, Olivier Lamotte, Mohanad Alsulaiman, Sandrine Ruffel, Gabriel Krouk, Nathalie Berger, Vincent Demolombe, Claude Nespoulous, Thi Minh Nguyet Dang, Sebastien Aime, Pierre Berthomieu, Christian Dubos, David Wendehenne, Denis Vile, Francoise Gosti
Summary: Ectopic expression of defensins in plants enhances their ability to withstand biotic and abiotic stresses. However, this study reveals that decreased endogenous defensin expression in Arabidopsis thaliana is associated with increased tolerance to pathogens and zinc toxicity, contrary to previous understanding. The study also discusses additional roles of endogenous plant defensins, opening up new avenues for further research.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Article
Plant Sciences
Amandine Crabos, Yunji Huang, Thomas Boursat, Christophe Maurel, Sandrine Ruffel, Gabriel Krouk, Yann Boursiac
Summary: Deciphering signaling pathways driving plant adaptation to drought, changes in water availability, and salt in the context of climate change is crucial. In this study, the effect of different osmotic treatments on the roots of Arabidopsis plants was investigated. Transcriptome analyses revealed specific and quantitative responses to osmotic and turgor pressure variations, highlighting the role of water-related biophysical parameters in shaping the root transcriptome under stress.
JOURNAL OF EXPERIMENTAL BOTANY
(2023)
Editorial Material
Plant Sciences
Gabriel Krouk, Wojciech Szponarski, Sandrine Ruffel
TRENDS IN PLANT SCIENCE
(2023)
Article
Biochemistry & Molecular Biology
Houssein Zhour, Fabrice Bray, Israa Dandache, Guillaume Marti, Stephanie Flament, Amelie Perez, Maelle Lis, Llorenc Cabrera-Bosquet, Thibaut Perez, Cecile Fizames, Ezekiel Baudoin, Ikram Madani, Loubna El Zein, Anne-Alienor Very, Christian Rolando, Herve Sentenac, Ali Chokr, Jean-Benoit Peltier
Summary: Diazotrophic bacteria isolated from the rhizosphere of a wild wheat ancestor were found to be efficient Plant Growth-Promoting Rhizobacteria (PGPR) in promoting the growth of elite wheat cultivars. They increased nitrogen levels in nitrogen-starved plants and influenced root development. Analysis of bacterial exudates revealed a complex set of secondary metabolites, including phytohormone mimetics and inter-kingdom signaling molecules.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Sandrine Ruffel, Valentin Chaput, Jonathan Przybyla-Toscano, Ian Fayos, Catalina Ibarra, Tomas Moyano, Cecile Fizames, Pascal Tillard, Jose Antonio O'Brien, Rodrigo A. Gutierrez, Alain Gojon, Laurence Lejay
Summary: The transcription factors TGA3, MYC1, and bHLH093 have been identified as regulators of NRT2.4 or NRT2.5 gene expression in response to N or C signals, revealing their important role in controlling the expression of root NRT2 transporter genes.
