Article
Engineering, Biomedical
Pulasta Chakrabarty, Pallavi Gupta, Kavitha Illath, Srabani Kar, Moeto Nagai, Fan-Gang Tseng, Tuhin Subhra Santra
Summary: Efficient intracellular delivery strategies are crucial for biomedical applications, with recent advancements in micro/nanotechnology leading to research on microfluidic device-based strategies. Mechanoporation techniques, specifically advantageous due to their high efficiency and cell viability without external energy sources, have seen significant progress in the past two decades.
MATERIALS TODAY BIO
(2022)
Article
Biochemical Research Methods
Antoine Moniot, Yann Guermeur, Sjoerd Jacob de Vries, Isaure Chauvot de Beauchene
Summary: This article introduces a new pipeline for designing searchable databases on the 2D and 3D structures of protein-bound nucleic acids (NA), selecting context-specific NA structures, and creating corresponding fragment libraries. The strength of this pipeline lies in its modularity, allowing it to be adapted to various specific modeling problems.
Review
Pharmacology & Pharmacy
Natalia Teresa Jarzebska, Mark Mellett, Julia Frei, Thomas M. Kundig, Steve Pascolo
Summary: Protamine is a natural cationic peptide mixture used for heparin neutralization and slow-release insulin formulations. It is also employed for cellular delivery of nucleic acids. Protamine plays a dual role in RNA stabilization, protecting against degradation and enhancing cell penetration.
Article
Chemistry, Physical
Qiyao Zhu, Tamar Schlick
Summary: Novel RNA motif design is crucial for technology and medicine, with computational methods playing an increasingly important role. By clustering RNA graphs and utilizing new design features, the accuracy and efficiency of RNA design can be significantly improved.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Biochemistry & Molecular Biology
Xiaomin Ni, Andreas C. Joerger, Apirat Chaikuad, Stefan Knapp
Summary: FUBP-interacting repressor (FIR) is a suppressor of the proto-oncogene MYC's transcription, by binding to the far upstream element (FUSE) of the MYC promoter. Competition with FUSE-binding protein 1 (FUBP1) is a crucial mechanism for MYC transcriptional regulation.
Article
Multidisciplinary Sciences
Mai Shiokawa, Ryotaro Miura, Aki Okubo, Yujiro Hagita, Itaru Yoshimura, Hiroshi Aoki
Summary: Bovine endometrium-derived cells showed high transfection efficiency using lipofection, indicating their suitability for this method in veterinary research. Through controlled passaging, BE-1 cells could be obtained, proving to be a valuable tool for introducing multiple DNAs in reporter assays and contributing to the advancement of veterinary research.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Ryan J. Andrews, Warren B. Rouse, Collin A. O'Leary, Nicholas J. Booher, Walter N. Moss
Summary: The identification of RNA elements in genomes and transcriptomes is a major challenge in target discovery for research and intervention. ScanFold 2.0, a revised version of the original algorithm, uses machine learning to estimate folding energy and significantly improves prediction speeds for large sequences. Comparative tests demonstrate the consistency and efficiency of ScanFold 2.0 compared to the original version.
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)
Article
Chemistry, Multidisciplinary
Florica Adriana Jerca, Cristina Muntean, Katrien Remaut, Valentin Victor Jerca, Koen Raemdonck, Richard Hoogenboom
Summary: Poly(2-isopropenyl-2-oxazoline) (PiPOx) is a functional polymer that shows great potential for developing smart biomaterials. In this study, PiPOx-based cationic charged polymethacrylamides with amino acid side chains were synthesized, which can complex siRNA and promote in vitro transfection. The structures and properties of the (co)polymers were investigated through various analyses, and cationic copolymers with tryptophan and valine or proline side chains showed high transfection efficiency and potent gene silencing.
JOURNAL OF CONTROLLED RELEASE
(2023)
Article
Multidisciplinary Sciences
Yuan Rui, David R. Wilson, Stephany Y. Tzeng, Hannah M. Yamagata, Deepti Sudhakar, Marranne Conge, Cynthia A. Berlinicke, Donald J. Zack, Anthony Tuesca, Jordan J. Green
Summary: Nanoparticle-based mRNA therapeutics show great promise, but cellular internalization and endosomal escape pose challenges for cytosolic delivery. Researchers developed a dual nanoparticle uptake and endosomal disruption assay, which can detect cellular internalization and endosomal disruption. The study found that this assay has higher predictive capacity for mRNA delivery compared to conventional polymer and nanoparticle characteristics.
Article
Biochemical Research Methods
Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang
Summary: Different types of RNAs have distinct subcellular localizations, and the nucleotide features determining these localizations are not fully understood. This study presents RNAlight, a machine learning model based on LightGBM, to identify nucleotide k-mers that contribute to the subcellular localizations of mRNAs and lncRNAs. By analyzing these nucleotide features and their association with RBPs, the sequence basis for different RNA subcellular localizations is revealed. RNAlight is also proven to be effective in predicting the subcellular localizations of other types of RNAs, indicating its potential for general application in RNA localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biochemical Research Methods
Guo-Hua Yuan, Ying Wang, Guang-Zhong Wang, Li Yang
Summary: In this study, a machine learning model called RNAlight was developed to identify nucleotide features related to the subcellular localizations of mRNAs and lncRNAs. By extracting nucleotide features and mapping them to RBPs, the sequence basis for distinct RNA subcellular localizations was revealed. Furthermore, RNAlight could also predict the subcellular localizations of other types of RNAs, highlighting its generality in RNA subcellular localization prediction.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Materials Science, Multidisciplinary
Pengkai Wu, Shuai Yin, Tianqing Liu, Dan Ding, Kaikai Wang
Summary: By incorporating different functional ligands and linked reductive disulfides into low-molecular-weight PEI 1.8k, this study constructed reductive-responsive PEI-X-SS-X-PEI copolymers to enhance siRNA transfection efficiency. The strategy, named building-block crosslinking, showed a simple and smart way to synthesize new materials and improve gene delivery systems.
SCIENCE CHINA-MATERIALS
(2021)
Article
Biology
Raeann Goering, Ankita Arora, Megan C. Pockalny, J. Matthew Taliaferro
Summary: RNA molecules are localized to specific subcellular regions through interactions between RNA regulatory elements and RNA binding proteins. The localization mechanisms are conserved across different cell types with different morphologies, indicating the presence of broadly similar mechanisms. In the study, it was found that mRNA encoding ribosomal proteins were strongly localized to the basal pole of human intestinal epithelial cells, and the same motifs were also sufficient to drive RNA localization to the neurites of mouse neuronal cells.
Article
Chemistry, Multidisciplinary
Elke Hebisch, Martin Hjort, Diogo Volpati, Christelle N. Prinz
Summary: Fluorescent nanodiamonds (FND) are promising materials for long term cell labeling and tracking due to their stable fluorescence, biocompatibility, and amenability to functionalization. This study successfully achieved direct delivery of FND to the cytosol using nanostraws and low voltage electroporation pulses, showing efficient and rapid transport of FND into cells. Live cell STED microscopy revealed that cell membranes open entirely on top of nanostraws, supporting the hypothesis that many FND are delivered directly to the cytosol, avoiding endocytosis and lysosomal entrapment.
Article
Cell Biology
Juergen Brojatsch, Heriberto Lima, Deborah Palliser, Lee S. Jacobson, Stefan M. Muehlbauer, Raquel Furtado, David L. Goldman, Michael P. Lisanti, Kartik Chandran
Article
Immunology
David C. Zawieja, Sangeetha Thangaswamy, Wei Wang, Raquel Furtado, Cristina C. Clement, Zachary Papadopoulos, Marco Vigano, Eric A. Bridenbaugh, Lello Zolla, Anatoliy A. Gashev, Jonathan Kipnis, Gregoire Lauvau, Laura Santambrogio
JOURNAL OF IMMUNOLOGY
(2019)
Article
Infectious Diseases
Neida K. Mita-Mendoza, Ariel Magallon-Tejada, Priyanka Parmar, Raquel Furtado, Margaret Aldrich, Alex Saidi, Terrie Taylor, Joe Smith, Karl Seydel, Johanna P. Daily
Article
Immunology
Raquel Furtado, Laurent Chorro, Natalie Zimmerman, Erik Guillen, Emily Spaulding, Shu Shien Chin, Johanna P. Daily, Gregoire Lauvau
Summary: In a mouse model of non-lethal P. yoelii infection, blockade of LAG-3 with monoclonal antibodies promoted accelerated control and clearance of blood parasites, independent of PD-1/PD-L1 and LAG-3 deficiency. These results suggest that targeting LAG-3 on parasite-specific CD4(+) T cells unleashes their ability to effectively clear blood parasites, separate from humoral responses.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Cristina C. Clement, Angelo D'Alessandro, Sangeetha Thangaswamy, Samantha Chalmers, Raquel Furtado, Sheila Spada, Giada Mondanelli, Federica Ianni, Sarah Gehrke, Marco Gargaro, Giorgia Manni, Luisa Carlota Lopez Cara, Peter Runge, Wanxia Li Tsai, Sinem Karaman, Jorge Arasa, Ruben Fernandez-Rodriguez, Amanda Beck, Antonio Macchiarulo, Massimo Gadina, Cornelia Halin, Francesca Fallarino, Mihaela Skobe, Marc Veldhoen, Simone Moretti, Silvia Formenti, Sandra Demaria, Rajesh K. Soni, Roberta Galarini, Roccaldo Sardella, Gregoire Lauvau, Chaim Putterman, Kari Alitalo, Ursula Grohmann, Laura Santambrogio
Summary: 3-hydroxy-L-kynurenamine (3-HKA) is a metabolite deriving from a lateral pathway of tryptophan catabolism. The authors identify 3-HKA as a biogenic amine with anti-inflammatory properties, showing its protective effects against psoriasis and nephrotoxic nephritis in mice.
NATURE COMMUNICATIONS
(2021)
