Article
Biochemistry & Molecular Biology
Rui Tao, Yanhong Wang, Yun Hu, Yaoge Jiao, Lifang Zhou, Lurong Jiang, Li Li, Xingyu He, Min Li, Yamei Yu, Qiang Chen, Shaohua Yao
Summary: A novel prime editor, WT-PE, was designed in this study by fusing reverse transcriptase (RT) to nuclease wild-type Cas9, enabling efficient editing of large genomic fragments. The WT-PE system introduced a double strand break (DSB) and a single 3' extended flap in the target site, and coupled with paired prime editing guide RNAs (pegRNAs), it achieved bi-directional prime editing, allowing versatile and efficient large-scale genome editing. This WT-PE system has great potential for modeling or treating diseases related to large-fragment aberrations.
SIGNAL TRANSDUCTION AND TARGETED THERAPY
(2022)
Article
Multidisciplinary Sciences
Marc Teufel, Carlo A. Klein, Maurice Mager, Patrick Sobetzko
Summary: CRISPR SWAPnDROP is a novel genome editing technology that enables large-scale in-vivo DNA transfer between bacterial species. It offers a modular platform and a multi-color scarless co-selection system, facilitating genome editing in various species.
NATURE COMMUNICATIONS
(2022)
Article
Neurosciences
Martin Vinck, Cem Uran, Georgios Spyropoulos, Irene Onorato, Ana Clara Broggini, Marius Schneider, Andres Canales-Johnson
Summary: This article explores the mechanisms underlying flexible inter-areal communication in the cortex, discussing four mechanisms: oscillatory synchronization, communication-through-resonance, non-linear integration, and linear signal transmission. The authors argue that resonance and non-linear integration are viable alternative mechanisms for computation and selective communication. Furthermore, they propose a new hypothesis regarding feedforward and feedback communication frequencies.
Article
Multidisciplinary Sciences
Guiquan Zhang, Yao Liu, Shisheng Huang, Shiyuan Qu, Daolin Cheng, Yuan Yao, Quanjiang Ji, Xiaolong Wang, Xingxu Huang, Jianghuai Liu
Summary: This study developed an upgraded prime editor platform (xrPE) by adding a viral xrRNA motif to pegRNAs, resulting in significantly enhanced editing efficiencies in multiple cell lines. The xrPE exhibited similar edit:indel ratios and minimal off-target editing compared to the canonical PE3, and showed comparable editing performance to the epegRNA-based PE system.
NATURE COMMUNICATIONS
(2022)
Article
Multidisciplinary Sciences
Hongru Shen, Jilei Liu, Jiani Hu, Xilin Shen, Chao Zhang, Dan Wu, Mengyao Feng, Meng Yang, Yang Li, Yichen Yang, Wei Wang, Qiang Zhang, Jilong Yang, Kexin Chen, Xiangchun Li
Summary: tGPT is a method for learning feature representation of transcriptomes, which efficiently handles the exponential growth of single-cell transcriptome data. It shows good performance on tasks such as single-cell analysis and tumor tissue analysis.
Article
Biochemistry & Molecular Biology
Bernadette Liemberger, Johannes Bischof, Michael Ablinger, Stefan Hainzl, Eva M. Murauer, Nina Lackner, Patricia Ebner, Thomas Kocher, Alexander Nystroem, Verena Wally, Elisabeth Mayr, Christina Guttmann-Gruber, Josefina Pinon Hofbauer, Johann W. Bauer, Ulrich Koller
Summary: Mutations in the COL7A1 gene can cause skin problems by affecting type VII collagen (C7) in the basement membrane zone. The researchers used an RNA therapy called spliceosome-mediated RNA trans-splicing (SMaRT) to correct mutations in COL7A1. They successfully corrected mutations in RDEB keratinocytes and RDEB skin equivalents by introducing a repair molecule called RTM-S6m.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
F. Vanessa Loiacono, Dirk Walther, Stefanie Seeger, Wolfram Thiele, Ines Gerlach, Daniel Karcher, Mark Aurel Schoettler, Reimo Zoschke, Ralph Bock
Summary: RNA editing is an important process in converting cytidines to uridines in plant organellar transcripts. This study investigates the evolution and recognition of a recently gained editing site, demonstrating that changes in RNA recognition motifs allow an ancient PPR protein, QED1, to specifically target this site. The study also finds that the target specificity of PPR proteins depends on the RNA:protein ratio and the low expression levels of PPR proteins are necessary to ensure editing site selection specificity.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Computer Science, Artificial Intelligence
Anastasia Drozdova, Ekaterina Trofimova, Polina Guseva, Anna Scherbakova, Andrey Ustyuzhanin
Summary: The use of program code as a data source is becoming more common among data scientists for various purposes. However, the application of machine learning models is limited without annotated code snippets. To address this issue, the Code4ML corpus is introduced, which consists of annotated code snippets collected from Kaggle. This dataset can assist in solving software engineering or data science challenges through a data-driven approach, such as semantic code classification and code generation based on natural language specifications for ML tasks.
PEERJ COMPUTER SCIENCE
(2023)
Article
Chemistry, Multidisciplinary
Marcin Ryczek, Martyna Pluta, Leszek Blaszczyk, Agnieszka Kiliszek
Summary: This article provides an overview of methods for large-scale RNA synthesis, with a focus on chemical synthesis and in vitro transcription. Chemical synthesis and in vitro transcription can be used to obtain a large quantity of RNA samples for structural studies, providing convenience for studying the function and structure of RNA.
APPLIED SCIENCES-BASEL
(2022)
Article
Computer Science, Software Engineering
Yiqian Wu, Yong-Liang Yang, Qinjie Xiao, Xiaogang Jin
Summary: This paper investigates how to automatically remove double chin effects in portrait images and presents a novel method based on training a fine classification boundary in the latent space of portrait images. By carefully designing the training stage, a fine separation boundary is generated for editing chin appearance while preserving original features and ensuring the consistency of neck structure and facial characteristics.
ACM TRANSACTIONS ON GRAPHICS
(2021)
Article
Chemistry, Analytical
Zhihao Luo, Jingju Liu, Guozheng Yang, Yongheng Zhang, Zijun Hang
Summary: This paper proposes a large-scale network path probing approach to improve the efficiency of network path probing and reduce probing redundancy and network load. The approach improves the packet delivery order and the update strategy of time-to-live field values, resulting in a more efficient tool for path probing.
Article
Biology
Mona I. M. Ibrahim, Ahmed M. Ramadan, Marwa Amer, Thana K. Khan, Nermin G. Mohamed, Osama A. Said
Summary: This article investigates the relationship between RNA editing and plant cellular stress as well as electron transport organelles. Through the analysis of cDNAs from the mitochondrial atp1 gene of two wheat cultivars, it was found that RNA editing is influenced by drought stress conditions and leads to changes in synonymous amino acids of the protein without altering its tertiary structure.
SAUDI JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Francesca Tasca, Marcella Brescia, Qian Wang, Jin Liu, Josephine M. Janssen, Karoly Szuhai, Manuel A. F. Goncalves
Summary: This study investigates the use of viral gene-deleted adenovector particles (AdVPs) as sources of CRISPR-Cas9 nucleases and donor DNA constructs for targeted chromosomal insertion in human cells. The researchers found that donors prone to homology-mediated end joining (HMEJ) yielded higher genome editing frequencies in muscle progenitor cells, while in induced pluripotent stem cells (iPSCs), both homologous recombination (HR) and HMEJ substrates showed similar editing levels. Furthermore, p53 inhibition increased HMEJ-based genome editing in iPSCs. Overall, AdVPs provide a robust platform for large genomic edits in human cells.
NUCLEIC ACIDS RESEARCH
(2022)
Review
Biochemical Research Methods
Tianzhen Liu, Xuening Zhang, Kai Li, Qi Yao, Dating Zhong, Qi Deng, Yuming Lu
Summary: CRISPR/Cas, as a powerful genome editing technology, is revolutionizing fundamental research and crop breeding. Its large-scale editing tools, which are efficient, simple and programmable, have led to a rapid increase in genome-edited crops. This article describes the general workflow of a CRISPR screen in plants and explores its applications, challenges, and limitations, as well as envisioning a virus-mediated strategy to improve CRISPR screens.
CURRENT OPINION IN BIOTECHNOLOGY
(2023)
Article
Multidisciplinary Sciences
J. Boutin, J. Rosier, D. Cappellen, F. Prat, J. Toutain, P. Pennamen, J. Bouron, C. Rooryck, J. P. Merlio, I. Lamrissi-Garcia, G. Cullot, S. Amintas, V. Guyonnet-Duperat, C. Ged, J. M. Blouin, E. Richard, S. Dabernat, F. Moreau-Gaudry, A. Bedel
Summary: The study reveals the genotoxicity caused by CRISPR-Cas9 leading to loss of heterozygosity changes, while also highlighting the potential safety concerns of this technology for gene therapy.
NATURE COMMUNICATIONS
(2021)
Article
Biochemistry & Molecular Biology
Ora Haimov, Urmila Sehrawat, Ana Tamarkin-Ben Harush, Anat Bahat, Anna Uzonyi, Alexander Will, Hiroyuki Hiraishi, Katsura Asano, Rivka Dikstein
MOLECULAR AND CELLULAR BIOLOGY
(2018)
Article
Biochemistry & Molecular Biology
Schraga Schwartz
Article
Biochemical Research Methods
Aldema Sas-Chen, Schraga Schwartz
Letter
Multidisciplinary Sciences
Joel Henrique Ellwanger
Article
Biochemistry & Molecular Biology
Markus Mittnenzweig, Yoav Mayshar, Saifeng Cheng, Raz Ben-Yair, Ron Hadas, Yoach Rais, Elad Chomsky, Netta Reines, Anna Uzonyi, Lior Lumerman, Aviezer Lifshitz, Zohar Mukamel, Ayelet-Hashahar Orenbuch, Amos Tanay, Yonatan Stelzer
Summary: The mouse embryonic development model provides insights into mammalian cell fate acquisition. Recent studies show that most lineages exhibit combinatorial multifurcation dynamics rather than hierarchical transcriptional transitions.
Article
Biochemical Research Methods
David Dierks, Miguel Angel Garcia-Campos, Anna Uzonyi, Modi Safra, Sarit Edelheit, Alice Rossi, Theodora Sideri, Radhika A. Varier, Alexander Brandis, Yonatan Stelzer, Folkert van Werven, Ruth Scherz-Shouval, Schraga Schwartz
Summary: m6A-seq2 is a method that uses multiplexed N-6-methyladenosine immunoprecipitation to compare m6A levels at the site, gene, and sample level, increasing throughput and reducing technical variability and cost. It provides sample-level relative quantitation of m6A and gene-level quantitation, showing that m6A is a main driver of RNA stability in mouse embryonic stem cells.
Article
Biochemistry & Molecular Biology
Ronit Nir, Thomas Philipp Hoernes, Hiromi Muramatsu, Klaus Faserl, Katalin Kariko, Matthias David Erlacher, Aldema Sas-Chen, Schraga Schwartz
Summary: RNA can be modified post-transcriptionally with various modifications, including pseudouridine (psi), which has been found in mRNA molecules. This study investigates the possibility of snoRNA-guided pseudouridylation of mRNA targets and provides insights into the factors affecting the efficiency of this modification. The study also explores the potential therapeutic application of pseudouridylation in suppressing translational termination.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Anna Uzonyi, David Dierks, Ronit Nir, Oh Sung Kwon, Ursula Toth, Isabelle Barbosa, Cindy Burel, Alexander Brandis, Walter Rossmanith, Herve Le Hir, Boris Slobodin, Schraga Schwartz
Summary: N6-methyladenosine (m6A) is a widespread destabilizing mark on mRNA with non-uniform distribution across the transcriptome. In this study, the authors propose that m6A deposition is exclusion-based rather than selective. They demonstrate that m6A consensus motifs are methylated by default unless they are near splice junctions. By validating a simple model based on the presence of m6A motifs and exon-intron architecture, they show that mRNA decay is mechanistically mediated via m6A.
Editorial Material
Multidisciplinary Sciences
Ashley Barbara Heim, Tina Bharani, Nikos Konstantinides, Jackson Ross Powell, Sudhakar Srivastava, Xiangkun Elvis Cao, Divyansh Agarwal, Khor Waiho, Teng-Jui Lin, Edgar Virgueez, Wadim Strielkowski, Anna Uzonyi
Article
Biochemical Research Methods
Anna Uzonyi, Ronit Nir, Schraga Schwartz
Summary: This article provides a detailed protocol for cloning DNA oligo pools consisting of tens of thousands of different constructs, which can be used for studying genetic and transcriptomic machinery.
Letter
Multidisciplinary Sciences
Jennifer Sills