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Plant Sciences
Xiaojuan Xing, Yurong Ding, Jinyu Jin, Aiping Song, Sumei Chen, Fadi Chen, Weimin Fang, Jiafu Jiang
Summary: The study found that melatonin can enhance the heat resistance of chrysanthemum seedlings by reducing oxidative lipid accumulation and increasing antioxidant accumulation. Additionally, melatonin promotes the growth and photosynthetic rate of chrysanthemum seedlings and regulates multiple genes involved in signal transduction and metabolism pathways.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biotechnology & Applied Microbiology
Juan Carlos Fragoso-Jimenez, Rosa Maria Gutierrez-Rios, Noemi Flores, Alfredo Martinez, Alvaro R. Lara, Frank Delvigne, Guillermo Gosset
Summary: In this study, the transcriptomic response of E. coli strains with impaired glucose import capacity was characterized. The results showed that these strains exhibited a consistent transcriptional response consistent with carbon source limitation, involving functions related to transport and metabolism of alternate carbon sources. Additionally, the lower glucose consumption rates were associated with energy limitation and entry into the stationary phase.
MICROBIAL CELL FACTORIES
(2022)
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Physiology
Jeeyun Lee, Marshall C. Phillips, Monica Lobo, Christopher S. Willett
Summary: The study found that acute low salinity conditions caused more deaths in Tigriopus californicus populations than high salinity; molecular processes increasing proline levels were significantly elevated at 7ppt salinity, contrary to other physiological studies; tolerance to salinity fluctuation was not determined by latitude but influenced by a complex interplay of factors including population and duration of salinity stress.
PHYSIOLOGICAL AND BIOCHEMICAL ZOOLOGY
(2021)
Article
Microbiology
Franca Schaefer, Pia Goerner, Sabrina Woltemate, Christina Brandenberger, Robert Geffers, Stefan Ziesing, Dirk Schlueter, Marius Vital
Summary: This study investigated the physiological adaptation of carbapenem-resistant Enterobacteriaceae isolates with different resistance mechanisms during growth with sublethal concentrations of ertapenem. The results showed distinct strategies and gene expression patterns between strains carrying carbapenemase or alterations in porin-encoding genes. The study also observed a survival-like phenotype and reduced growth efficiencies in strains with alterations in porin-encoding genes, indicating costs of resistance.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Plant Sciences
Gabriella Frosi, Jose Ribamar Costa Ferreira-Neto, Joao Pacifico Bezerra-Neto, Valesca Pandolfi, Manasses Daniel da Silva, David Anderson de Lima Morais, Ana Maria Benko-Iseppon, Mauro Guida Santos
Summary: The study revealed that Cenostigma pyramidale has the ability to perceive and regulate ion channels and transporters in response to salt stress at early stages, with a shift towards focusing on the antioxidant system, aquaporins, and hormone responses as the stress progresses. Five selected DEGs were validated through qPCR, providing insights on how this native species modulates gene expression to achieve salt stress tolerance.
PHYSIOLOGIA PLANTARUM
(2021)
Article
Multidisciplinary Sciences
Richard C. Tyser, Elmir Mahammadov, Shota Nakanoh, Ludovic Vallier, Antonio Scialdone, Shankar Srinivas
Summary: The single-cell transcriptional profile of a human embryo between 16 and 19 days after fertilization shows similarities and differences in gastrulation compared to mouse and non-human primate models. This study provides new insights into human development and offers valuable information for directed differentiation of human cells in vitro.
Article
Plant Sciences
Lilan Lu, Siting Chen, Weibo Yang, Yi Wu, Yingying Liu, Xinxing Yin, Yaodong Yang, Yanfang Yang
Summary: Potassium ions (K+) play a crucial role in the growth and yield of coconut seedlings. This study investigated the effects of K+ deficiency on coconut seedlings through various analyses, including physiological, transcriptomic, and metabolomic profiling. The results showed that K+ deficiency led to a reduction in plant height, biomass, and nutrient content, as well as changes in hormone levels and enzyme activities. RNA-sequencing and metabolomic analysis revealed differentially expressed genes and metabolites involved in various pathways related to plant growth and stress response. Overall, this study provides a comprehensive understanding of coconut seedlings' response to K+ deficiency and highlights the importance of K+ for coconut production.
FRONTIERS IN PLANT SCIENCE
(2023)
Editorial Material
Biochemical Research Methods
John P. Chute, Joshua P. Sasine
Summary: Image-seq combines high-resolution microscopy with single-cell transcriptomics to spatially resolve and isolate viable bone marrow and leukemia cells, achieving a long-sought integration of single-cell molecular profiling and cellular spatial localization.
Article
Plant Sciences
Xinyu Zhao, Wei Zheng, Tongfei Qu, Yi Zhong, Jinhui Xu, Yongshun Jiang, Huanxin Zhang, Xuexi Tang, Ying Wang
Summary: Ultraviolet-B (UV-B) is an important factor in the production of reactive oxygen species (ROS) in plants, with the use of chlorofluorocarbons (CFCs) leading to ozone depletion and increased UV-B radiation. This study found that ROS production in Ulva prolifera under UV-B primarily occurred in the chloroplast, leading to oxidative damage in extreme radiation conditions and signaling functions in moderate conditions.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Multidisciplinary Sciences
Kai Battenberg, S. Thomas Kelly, Radu Abu Ras, Nicola A. Hetherington, Makoto Hayashi, Aki Minoda
Summary: Single-cell RNA-sequencing analysis has gained popularity, and UniverSC is a universal tool for processing single-cell RNA-seq data on any platform. It provides a command-line tool, docker image, and containerized graphical application for consistent and comprehensive integration, comparison, and evaluation of data from various platforms. Additionally, a cross-platform application with a graphical user interface is available to address the bottleneck of data processing for researchers without bioinformatics expertise.
NATURE COMMUNICATIONS
(2022)
Article
Biochemical Research Methods
Tal Ashuach, Mariano I. Gabitto, Rohan V. Koodli, Giuseppe-Antonio Saldi, Michael I. Jordan, Nir Yosef
Summary: Jointly profiling the transcriptome, chromatin accessibility, and other molecular properties of single cells can enhance the study of cellular diversity. MultiVI, a probabilistic model, allows the analysis of multiomic data and enhances single-modality datasets by creating a joint representation. It can be accessed at scvi-tools.org.
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
Sonia Garcia-Ruiz, Emil K. Gustavsson, David Zhang, Regina H. Reynolds, Zhongbo Chen, Aine Fairbrother-Browne, Ana Luisa Gil-Martinez, Juan A. Botia, Leonardo Collado-Torres, Mina Ryten
Summary: Dysregulation of RNA splicing is implicated in rare and complex diseases. We have developed IntroVerse, a comprehensive resource for exploring intron usage by providing a catalogue of annotated introns and novel junctions. This dataset, generated from extensive RNA sequencing analysis, offers insights into novel transcripts and assessment of splicing noise in introns.
NUCLEIC ACIDS RESEARCH
(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
Biochemistry & Molecular Biology
Mengwei Li, Xiaomeng Zhang, Kok Siong Ang, Jingjing Ling, Raman Sethi, Nicole Yee Shin Lee, Florent Ginhoux, Jinmiao Chen
Summary: DISCO is an integrated database of single-cell omics data, offering an integrated cell atlas and harmonized metadata that users can utilize for comprehensive single-cell data analysis and exploration.
NUCLEIC ACIDS RESEARCH
(2022)