Review
Plant Sciences
Yoko Mizuta
Summary: Two-photon excitation microscopy (2PEM) allows deep imaging of living tissues with reduced autofluorescence compared to confocal microscopy, achieving higher resolution. Fluorescent proteins with long emission wavelengths, such as orange-red fluorescent proteins, are suitable for high-quality two-photon live imaging in plants.
PLANT AND CELL PHYSIOLOGY
(2021)
Review
Biotechnology & Applied Microbiology
Diego F. Fiol, Maria C. Terrile, Jesica Frik, Florencia A. Mesas, Vera A. alvarez, Claudia A. Casalongue
Summary: Nanotechnology applications in agriculture are increasing and have the potential to be a valuable tool for sustainable food production globally. However, limited understanding of the mechanisms of nanomaterial action restricts their widespread use.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Rahul Shaw, Xin Tian, Jian Xu
Summary: The adoption of single-cell RNA sequencing technology has revolutionized the transcriptome analysis, allowing for better understanding of tissue and cellular heterogeneity and rapid identification of rare cell types. In the field of plant sciences, single-cell transcriptome profiling is in its early stages and presents exciting challenges to overcome.
Review
Plant Sciences
Noriyoshi Yagi, Akira Yoshinari, Ryu J. Iwatate, Reika Isoda, Wolf B. Frommer, Masayoshi Nakamura
Summary: Fluorescent probes are essential tools for visualizing cellular structures and molecular dynamics in living cells, with a wide variety of small-molecule dyes synthesized for labeling purposes. Self-labeling technologies allow these probes to be attached to cellular domains or specific proteins, and are now being increasingly utilized in plant research.
PLANT AND CELL PHYSIOLOGY
(2021)
Review
Biochemistry & Molecular Biology
Daishin Ueno, Shotaro Yamasaki, Ko Kato
Summary: This review discusses the findings and limitations of RNA degradation sequencing methods, and suggests further experiments needed to accurately understand RNA degradation intermediates. It provides direction for future research on RNA degradation and serves as a reference for RNA degradome studies in other species.
Article
Plant Sciences
Kevin L. Cox, Sai Guna Ranjan Gurazada, Keith E. Duncan, Kirk J. Czymmek, Christopher N. Topp, Blake C. Meyers
Summary: Plant cells communicate through transcriptional regulation and gene networks to control development and respond to external stresses. Acquiring high resolution, multi-dimensional spatial transcriptomic data and placing it within a cellular and organismal context is crucial for understanding gene regulation across plant tissues and organs. Combining spatial transcriptomics with 3D imaging technologies can provide insights into how genes are regulated in a multi-dimensional space.
Review
Cell Biology
Tao Wang, Xiaojun Li, Xiaojing Zhang, Qing Wang, Wenqian Liu, Xiaohong Lu, Shunli Gao, Zixi Liu, Mengshuang Liu, Lihong Gao, Wenna Zhang
Summary: A large number of RNA molecules have been found in the phloem of higher plants, where specific RNA motifs and structures facilitate their mobility, while RNA methylation, such as m5C, plays a crucial role in RNA transport. These studies provide a theoretical foundation for uncovering the mechanism of RNA transportation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Review
Forestry
Pengqing Wang, Guo Wei, Liguo Feng
Summary: This paper summarizes the research advances of the main members of the OSC family in plants, their structure and function, the biosynthesis of triterpenes, and the molecular evolution of OSC.
Article
Biochemistry & Molecular Biology
Ruben Dries, Jiaji Chen, Natalie Del Rossi, Mohammed Muzamil Khan, Adriana Sistig, Guo-Cheng Yuan
Summary: Spatial transcriptomics is a rapidly growing field that characterizes tissue organization and architecture comprehensively at single-cell or subcellular resolution, providing a foundation for mechanistic understanding of biological processes. Computational methods play crucial roles in extracting biological signals from data, while various approaches have been developed to overcome technology-specific limitations. Downstream analysis tools quantify spatial organization and cell-cell communications, and integrative pipelines assemble multiple tools for convenient data analysis.
Review
Optics
Vivek Boominathan, Jacob T. Robinson, Laura Waller, Ashok Veeraraghavan
Summary: This article reviews recent advances in lensless imaging technology and describes the design principles to be considered when developing and using lensless imaging systems.
Review
Biotechnology & Applied Microbiology
Malihe Mirzaee, Zhila Osmani, Jitka Frebortova, Ivo Frebort
Summary: Plant molecular farming, known as the heterologous synthesis of proteins or peptides in plant-based systems, is a practical and safe approach for the large-scale and cost-effective production of therapeutic biomolecules. Monocotyledonous plants, especially cereals, are considered attractive platforms for producing high-value recombinant proteins. The endosperm, as the largest grain storage compartment, provides a suitable environment for long-lasting protein accumulation.
BIOTECHNOLOGY ADVANCES
(2022)
Review
Biochemical Research Methods
Ryley Dorney, Bijay P. Dhungel, John E. J. Rasko, Lionel Hebbard, Ulf Schmitz
Summary: This review highlights the importance of gene fusions in cancer, including chromosomal rearrangement-independent fusion transcripts and complex fusion structures. It proposes a classification system for gene and transcript fusions and discusses the use of long-read sequencing and bioinformatic tools to detect and characterize fusions.
BRIEFINGS IN BIOINFORMATICS
(2023)
Review
Plant Sciences
Andrzej T. Wierzbicki, Todd Blevins, Szymon Swiezewski
Summary: Plants have a diverse range of transcription machineries, with four dedicated RNA polymerases involved in producing long noncoding RNAs (lncRNAs) that play various regulatory roles in gene expression and response to environmental stimuli. These lncRNAs can impact gene expression by controlling chromatin accessibility, transcription, splicing, and translation.
ANNUAL REVIEW OF PLANT BIOLOGY, VOL 72, 2021
(2021)
Article
Plant Sciences
Yubing He, Michael Mudgett, Yunde Zhao
Summary: This article introduces several strategies to eliminate transgene residuals in edited plants, including direct editing of plant genomes with DNA-free reagents, using fluorescent markers, pigments, and chemical treatments to distinguish transgenic plants from transgene-free plants, and triggering self-elimination of transgenic plants through suicide genes. Additionally, it discusses the methods of excising transgenes from plant genomes using site-specific recombination, transposition, or gene editing nucleases, as well as the combination of haploid induction and gene editing for editing recalcitrant plants.
Review
Chemistry, Medicinal
Ka Hin Chan, Yakun Wang, Bo-Xin Zheng, Wei Long, Xinxin Feng, Wing-Leung Wong
Summary: RNA structures, including coding and noncoding RNAs, are promising targets of small molecules for drug discovery against human diseases. mRNA-targeting small molecules may regulate the synthesis of disease-related proteins, and RNA-ligand interaction is an attractive approach to address the challenge of undruggable proteins. This review focuses on the recent research on RNA-specific small molecule ligands for live cell imaging and drug discovery, aiming to provide new insights into future development in this field.
