Article
Agronomy
Maxime Durand, Baiba Matule, Alexandra J. Burgess, T. Matthew Robson
Summary: The study investigated the characteristics of sunflecks and how different plant canopies produce sunflecks with varying properties. High-frequency irradiance measurements revealed that shorter wind-induced sunflecks contribute significantly to the irradiance available for photosynthesis, and variations in sunfleck properties were observed related to canopy depth and species.
AGRICULTURAL AND FOREST METEOROLOGY
(2021)
Article
Plant Sciences
Zhuang Xiong, Zhigang Dun, Yucheng Wang, Desheng Yang, Dongliang Xiong, Kehui Cui, Shaobing Peng, Jianliang Huang
Summary: Stomatal morphology plays an important role in regulating leaf gas exchange and photosynthetic efficiency under fluctuating light conditions. Smaller and denser stomata lead to faster stomatal response to light fluctuations but lower intrinsic water use efficiency. Stomatal morphology has less impact on stomatal conductance, and there is minimal correlation between steady-state and non-steady-state stomatal conductance among different genotypes. These findings highlight the significance of stomatal morphology in optimizing photosynthetic efficiency and plant growth under fluctuating light.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Hu Sun, Yu-Qi Zhang, Shi-Bao Zhang, Wei Huang
Summary: This study reveals that the decrease in leaf N content delays the induction speeds of net CO2 assimilation, stomatal conductance, and mesophyll conductance upon transition from low to high light in tomato seedlings. The photosynthetic induction kinetics are mainly affected by the induction response of mesophyll conductance rather than stomatal conductance.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Plant Sciences
Nicole Salvatori, Fabrizio Carteni, Francesco Giannino, Giorgio Alberti, Stefano Mazzoleni, Alessandro Peressotti
Summary: Photosynthesis is mainly studied under steady-state conditions, but this assumption is inadequate for assessing biochemical responses to rapid variations in natural environments. This study presents a leaf-level System Dynamics photosynthesis model validated on two soybean varieties, and provides relevant conclusions on their different dynamic responses.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Cell Biology
Peipei Xu, Jinbo Hu, Haiying Chen, Weiming Cai
Summary: Karrikins (KARs) derived from smoke promote seed germination, but the underlying mechanism is still unclear. This study identifies the involvement of KAR signaling, SMAX1, and DELLA proteins in the transcriptional activation of gibberellin (GA) biosynthesis and regulation of seed germination in Arabidopsis. The crosstalk between KAR and GA signaling pathways is mediated by the SMAX1-DELLA module.
Article
Plant Sciences
Chien-Chang Wang, Hsin-Yu Hsieh, Hsu-Liang Hsieh, Shih-Long Tu
Summary: The study demonstrates that H3K36me3 rapidly and differentially responds to light at specific gene loci, leading to light-regulated intron retention in transcripts. The chromatin adaptor PpMRG1 potentially participates in light-mediated alternative splicing in plants.
Article
Plant Sciences
Jiancan Du, Xiang Zhu, Kunrong He, Mengyi Kui, Juping Zhang, Xiao Han, Qiantang Fu, Yanjuan Jiang, Yanru Hu
Summary: CONSTANS (CO) plays a critical role in regulating flowering in Arabidopsis by integrating photoperiodic and circadian signals. A study shows that CO also responds to salt stress and negatively modulates salt tolerance under long-day conditions. The interaction between CO and the ABF transcription factors, as well as their suppressive effect on salinity-responsive genes, contributes to the regulation of salinity responses in Arabidopsis.
Article
Biophysics
Jason T. George
Summary: Phenotypic adaptation is a common feature in biological systems navigating variable environments. Recent empirical data support the role of memory-driven decision making in cellular systems navigating uncertain nutrient landscapes. A mathematical model is developed to describe memory-driven cellular adaptation, showing that growth reductions in fluctuating environments result from optimal decision making and the trade-off between adaptation speed and accuracy imposed by memory capacity.
BIOPHYSICAL JOURNAL
(2023)
Article
Cell Biology
Zhi-Lan Zeng, Hu Sun, Xiao-Qian Wang, Shi-Bao Zhang, Wei Huang
Summary: This study reveals that the regulation of leaf angle is an important strategy used by young leaves to protect PSI against photoinhibition under fluctuating light conditions. The vertical leaf angle decreases light absorption and lowers the amplitude of low/high light intensity, thus reducing PSI photoinhibition.
Article
Cell Biology
Wuming Gong, Satyabrata Das, Javier E. Sierra-Pagan, Erik Skie, Nikita Dsouza, Thijs A. Larson, Mary G. Garry, Edgar Luzete-Monteiro, Kenneth S. Zaret, Daniel J. Garry
Summary: Gong et al. report that ETV2 functions as a pioneer factor in regulating endothelial genes and remodeling chromatin, which provides potential therapeutic applications for cardiovascular diseases and solid tumors.
NATURE CELL BIOLOGY
(2022)
Article
Limnology
Alexis Lucas Norbert Guislain, Jan Koehler
Summary: This study found that different mixing depths have an impact on the production and photosynthesis of phytoplankton. Mixing phytoplankton better utilize short periods of surface illumination, while the growth capability of plants in Lake TaiHu is affected by light fluctuations. Photosynthesis and respiration are more tightly connected under fluctuating light.
LIMNOLOGY AND OCEANOGRAPHY
(2022)
Article
Plant Sciences
Hu Sun, Qi Shi, Shi-Bao Zhang, Wei Huang
Summary: The study found that leaf nitrogen content significantly influenced the response of PSI to fluctuating light in tomatoes grown under nitrogen deficiency. High-nitrogen plants were more susceptible to over-reduction of PSI compared to low-nitrogen plants, which gradually increased PSII electron flow to avoid this issue.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Rashedul Islam, Catherine E. Jenkins, Qi Cao, Jasper Wong, Misha Bilenky, Annaick Carles, Michelle Moksa, Andrew P. Weng, Martin Hirst
Summary: Runt-related transcription factor 1 (RUNX1) is oncogenic in various leukemias and epithelial cancers, and its expression is associated with poor prognosis. It cooperates with other oncogenic factors to drive the expression of proto-oncogenes in T cell acute lymphoblastic leukemia (T-ALL), but the specific molecular mechanisms and cooperation with other factors are not well understood.
Article
Plant Sciences
Zhuang Xiong, Dongliang Xiong, Detian Cai, Wei Wang, Kehui Cui, Shaobing Peng, Jianliang Huang
Summary: In this study, the leaf photosynthetic induction and underlying mechanism were compared between tetraploid and diploid rice for the first time. After polyploidization, tetraploid rice displayed slower stomatal opening in response to increasing light intensity. Stomatal opening, rather than biochemical processes, was found to be the most important factor contributing to the difference in photosynthetic induction between tetraploid and diploid rice. Tetraploid rice showed lower stomatal conductance and intercellular CO2 concentration, resulting in lower photosynthetic efficiency during light induction.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Plant Sciences
Ruben Tenorio Berrio, Kevin Verstaen, Niels Vandamme, Julie Pevernagie, Ignacio Achon, Julie Van Duyse, Gert Van Isterdael, Yvan Saeys, Lieven De Veylder, Dirk Inze, Marieke Dubois
Summary: Profiling young Arabidopsis leaves at the single-cell level provides insights into the distribution, development, and sensitivity to drought of different cell populations. The study identified 14 cell populations in young leaves, including subpopulations with distinct identity or metabolic activity.
Article
Plant Sciences
Vaclav Bacovsky, Radim Cegan, Eva Tihlarikova, Vilem Nedela, Vojtech Hudzieczek, Lubomir Smrza, Tomas Janicek, Vladimir Benes, Roman Hobza
Summary: This study identified the regulatory pathways involved in sex-specific flower development in the dioecious plant Silene latifolia. These pathways include previously hypothesized and unknown female-regulator genes, as well as a negative regulator of anther development.
JOURNAL OF EXPERIMENTAL BOTANY
(2022)
Article
Multidisciplinary Sciences
Isabel Duarte, Gil Carraco, Nayara T. D. de Azevedo, Vladimir Benes, Raquel P. Andrade
Summary: MicroRNAs in chick embryos have been identified and shown to potentially play important roles in regulating early vertebrate embryo development. This discovery is significant for the avian research community and can lead to further experimental testing of new miRNAs.
Article
Plant Sciences
Adrian F. Powell, Ari Feder, Jie Li, Maximilian H. -W. Schmidt, Lance Courtney, Saleh Alseekh, Emma M. Jobson, Alexander Vogel, Yimin Xu, David Lyon, Kathryn Dumschott, Marcus McHale, Ronan Sulpice, Kan Bao, Rohit Lal, Asha Duhan, Asis Hallab, Alisandra K. Denton, Marie E. Bolger, Alisdair R. Fernie, Sarah R. Hind, Lukas A. Mueller, Gregory B. Martin, Zhangjun Fei, Cathie Martin, James J. Giovannoni, Susan R. Strickler, Bjoern Usadel
Summary: Wild relatives of tomato, such as Solanum lycopersicoides, are valuable sources for tomato breeding due to their natural variation. However, few genome sequences of these wild relatives have been produced. This study presents a chromosome-scale genome assembly of S. lycopersicoides LA2951, which provides important resources for studying fruit nutrient/quality traits, pathogen resistance, and environmental stress tolerance.
Review
Plant Sciences
Seyyedeh-Sanam Kazemi-Shahandashti, Ludwig Mann, Abdullah El-nagish, Doerte Harpke, Zahra Nemati, Bjoern Usadel, Tony Heitkam
Summary: This article traces the evolutionary origin of saffron crocus through ancient arts and recent genetics, focusing on the domestication and cultivation of saffron, and discussing its presumed autopolyploid origin involving cytotypes of wild Crocus cartwrightianus. Both ancient arts and modern genetic research converge in tracing the origin of saffron crocus to ancient Greece.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biochemistry & Molecular Biology
Julia Jessica Reimer, Basel Shaaban, Noud Drummen, Sruthy Sanjeev Ambady, Franziska Genzel, Gernot Poschet, Anika Wiese-Klinkenberg, Bjoern Usadel, Alexandra Wormit
Summary: The plant kingdom contains a wide variety of bioactive compounds, some of which have health-supporting and industrial uses. The pepper plant, in particular, synthesizes many valuable compounds, and the leftover biomass from pepper production provides an opportunity to extract and utilize these metabolites. In addition, the synthesis of these compounds is induced as a defense mechanism against abiotic stresses.
Article
Plant Sciences
Constantin Eiteneuer, David Velasco, Joseph Atemia, Dan Wang, Rainer Schwacke, Vanessa Wahl, Andrea Schrader, Julia J. Reimer, Sven Fahrner, Roland Pieruschka, Ulrich Schurr, Bjoern Usadel, Asis Hallab
Summary: Next-generation sequencing and metabolomics data need to be visualized and further analyzed, but existing tools often require installation or manual programming. Therefore, we developed GXP, a web-based RNAseq and metabolomics data visualization and analysis tool that does not require any custom installation, manual programming, or uploading of confidential data. GXP enables users to interact with the data, perform knowledge-driven analyses, and identify candidates through visualization and data exploration. It can support and accelerate complex interdisciplinary omics projects and downstream analyses, and offers an easy way to publish data and analysis results.
Article
Multidisciplinary Sciences
Sven Schrinner, Rebecca Serra Mari, Richard Finkers, Paul Arens, Bjoern Usadel, Tobias Marschall, Gunnar W. Klau
Summary: This article presents a genetic phasing method for plant breeding that can phase the haplotype sequences of parental samples using a large number of low-depth progeny samples. By integrating weak Mendelian progeny signals with a Bayesian log-likelihood model and utilizing an interval scheduling approach, the method can compute high-quality sparse phasings.
Article
Genetics & Heredity
Adrian Fragoso-Luna, Raquel Romero-Bueno, Michael Eibl, Cristina Ayuso, Celia Munoz-Jimenez, Vladimir Benes, Ildefonso Cases, Peter Askjaer
Summary: Control of gene expression in specific tissues and/or at certain stages of development allows precise study and manipulation of gene function. The addition of FLP lines that drive recombination specifically in certain cells in C. elegans expands this toolkit. This enables simultaneous gene inactivation and transcriptomic profiling, facilitating the investigation of gene function in complex biological processes.
Review
Plant Sciences
Songtao Gui, Felix Juan Martinez-Rivas, Weiwei Wen, Minghui Meng, Jianbing Yan, Bjoern Usadel, Alisdair R. R. Fernie
Summary: Deep sequencing has become popular in recent years due to the collection and release of large amounts of high-quality genomic and transcriptomic data. This approach has greatly advanced our understanding of plant physiology, evolution, and crop domestication through both broad and deep sequencing.
Article
Plant Sciences
Ipek Yildiz, Marlene Gross, Denise Moser, Patrick Petzsch, Karl Koehrer, Juergen Zeier
Summary: N-hydroxypipecolic acid (NHP) accumulates in pathogen-inoculated and distant leaves of Arabidopsis and induces systemic acquired resistance (SAR) through the SA receptor NPR1. The transcription factors TGA2/5/6 and TGA1/4 are required for NHP-triggered SAR gene expression, and also play a role in pathogen-induced SAR. However, the accumulation of NHP and SA at the sites of infection is not fully dependent on TGA factors. Our findings indicate the existence of a TGA- and NPR1-dependent transcriptional module that mediates SAR and systemic defense responses induced by NHP.
PLANT CELL AND ENVIRONMENT
(2023)
Article
Multidisciplinary Sciences
Maximilian Seidel, Natalie Romanov, Agnieszka Obarska-Kosinska, Anja Becker, Nayara Trevisan Doimo de Azevedo, Jan Provaznik, Sankarshana R. Nagaraja, Jonathan J. M. Landry, Vladimir Benes, Martin Beck
Summary: Various cellular quality control mechanisms are involved in maintaining protein homeostasis. In addition to preventing misfolding during translation, ribosome-associated chaperones and importins also play roles in preventing protein aggregation and facilitating nucleocytoplasmic transport. This study suggests that importins can bind to ribosome-associated cargoes in a co-translational manner, including proteins such as ribosomal proteins, chromatin remodelers, and RNA binding proteins that are prone to cytosolic aggregation. The authors also demonstrate that importins act consecutively with other ribosome-associated chaperones, highlighting the interconnectedness of the nuclear import system and nascent chain folding.
NATURE COMMUNICATIONS
(2023)
Article
Ecology
Sebastian C. Treitli, Pavla Hanouskova, Vladimir Benes, Andreas Brune, Ivan Cepicka, Vladimir Hampl
Summary: Pelomyxa is a genus of anaerobic amoebae that form a consortium with multiple prokaryotic endosymbionts. The prokaryotic community associated with P. schiedti consists of two bacteria, Candidatus Syntrophus pelomyxae and Candidatus Vesiculincola pelomyxae, and a methanogen called Candidatus Methanoregula pelomyxae. The consortium relies on the cellulolytic activity of P. schiedti to produce simple sugars for its own metabolism and for Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae obtains energy through the degradation of butyrate and isovalerate from the environment. Methanogenesis carried out by Ca. Methanoregula pelomyxae is essential for the consortium, as inhibiting this process leads to the death of the amoebae.
Article
Plant Sciences
Yuxi Niu, Dusan Lazar, Alfred R. Holzwarth, David M. Kramer, Shizue Matsubara, Fabio Fiorani, Hendrik Poorter, Silvia D. Schrey, Ladislav Nedbal
Summary: The study focused on the rapid regulation of photoprotective mechanisms in response to changing light in plants. It was found that PsbS regulation had the fastest response time to oscillating light with periods longer than 10 seconds. Processes involving violaxanthin de-epoxidase dampened changes in chlorophyll fluorescence in oscillation periods of 2 minutes or longer. Knocking out the PGR5/PGRL1 pathway strongly reduced variations in all monitored parameters, possibly due to congestion in the electron transport. The observed dynamics of photosystem I components were interpreted as being formed by thylakoid remodeling in slow light oscillations.
Article
Biology
Rhowell N. Tiozon Jr, Nese Sreenivasulu, Saleh Alseekh, Kristel June D. Sartagoda, Bjoern Usadel, Alisdair R. Fernie
Summary: Germination of rice enhances its dietary properties, increasing levels of free phenolics and micronutrients. Metabolomic analysis indicates the accumulation of dipeptides, GABA, and flavonoids during germination. Genome-wide association studies reveal the activation of genes CHS1 and UGT associated with the increase of specific flavonoid compounds.
COMMUNICATIONS BIOLOGY
(2023)
Article
Biochemical Research Methods
Anna Pryszlak, Tobias Wenzel, Kiley West Seitz, Falk Hildebrand, Ece Kartal, Marco Raffaele Cosenza, Vladimir Benes, Peer Bork, Christoph A. Merten
Summary: We present a droplet microfluidic method for directly targeting and sorting individual cells from complex microbiome samples, enabling bulk whole-genome sequencing without the need for cultivation. This approach allows for the recovery of bacteria at low ratios and successful enrichment of specific strains for genome assembly. The encapsulation of microbiome samples in microfluidic droplets and the use of custom molecular probes facilitate the selective enrichment of target strains, addressing the lack of cultivated strains and reference genomes.
CELL REPORTS METHODS
(2022)