Article
Biotechnology & Applied Microbiology
Xiaoyu Yang, Bo Song, Jie Cui, Lina Wang, Shuoshuo Wang, Linlin Luo, Lei Gao, Beixin Mo, Yu Yu, Lin Liu
Summary: This study reveals that translational reprogramming plays an important role in rice's response to salt stress, with the salt-tolerant cultivar SR86 adopting a more flexible translational adaptive strategy compared to the salt-sensitive cultivar NB. The differences in translational dynamics under salt stress between NB and SR86 may be due to their varying levels of ribosome stalling.
Article
Biochemistry & Molecular Biology
Pauline Francois, Hugo Arbes, Stephane Demais, Agnes Baudin-Baillieu, Olivier Namy
Summary: Ribosome profiling, a powerful tool for studying translation regulation, suffers from a lack of standardization in the bioinformatics part, hindering result reproducibility. A unique tool has been proposed to standardize the general steps of RiboSeq analysis, aiming to unify bioinformatics pipelines for translation research.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2021)
Article
Biochemical Research Methods
Michaela Frye, Susanne Bornelov
Summary: CONCUR is a standalone tool written in Perl for codon usage analysis in ribosome profiling experiments. It estimates codon counts at the ribosome E-, P- and A-sites using aligned reads in BAM format, and is freely available on https://github.com/susbo/concur.
Article
Multidisciplinary Sciences
Aleksandar Radakovic, Saurja DasGupta, Tom H. Wright, Harry R. M. Aitken, Jack W. Szostak
Summary: Research shows that aminoacylated RNAs can assemble into chimeric amino acid-RNA polymers with active ribozyme function under template guidance, potentially introducing new functionalities in ribozyme catalysis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Qiuyue Ma, Yuxiao Wang, Shushun Li, Jing Wen, Lu Zhu, Kunyuan Yan, Yiming Du, Shuxian Li, Liping Yan, Zhijun Xie, Yunzhou Lyu, Fei Shen, Qianzhong Li
Summary: This study conducted ribosome footprint profiling and multi-omics strategy to investigate the lipid metabolism in Acer truncatum seed development. The transcriptional and proteomic features of the oil accumulation process were characterized. Additionally, key regulators influencing lipid biosynthesis were identified, and the role of post-translational regulation in lipid metabolism was revealed.
Article
Biochemical Research Methods
Hsin-Yen Larry Wu, Polly Yingshan Hsu
Summary: This study describes a custom library construction method for super-resolution Ribo-seq in Arabidopsis, which can be applied to study genome-wide mRNA translation.
Article
Biochemical Research Methods
Alexander L. Cope, Felicity Anderson, John Favate, Michael Jackson, Amanda Mok, Anna Kurowska, Junchen Liu, Emma MacKenzie, Vikram Shivakumar, Peter Tilton, Sophie M. Winterbourne, Siyin Xue, Kostas Kavoussanakis, Liana F. Lareau, Premal Shah, Edward W. J. Wallace
Summary: riboviz 2 is an updated software package for comprehensive analysis and visualization of Ribo-seq data. It utilizes the Nextflow workflow management system for end-to-end processing and has been extensively tested on diverse species and library preparation strategies.
Article
Biochemistry & Molecular Biology
Shing-Yau Tam, Md Zahirul Islam Khan, Ju-Yu Chen, Jerica Hiu-Yui Yip, Hong-Yiu Yan, Tsz-Yan Tam, Helen Ka-Wai Law
Summary: The study aimed to investigate the differences in chemotherapy responses between FOLFOX-resistant and wild-type colorectal cancer cells using proteomic profiling. FOLFOX-resistant cells (DLD1-R and HCT116-R) were developed through chronic exposure to progressive FOLFOX doses. Analysis of the proteomic profiles revealed significantly altered pathways in FOLFOX-resistant cells, with up-regulations in the ribosomal process and actin cytoskeleton. These findings suggest potential novel treatment targets for overcoming chemoresistance in colorectal cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Gastroenterology & Hepatology
Shilin Yuan, Guanghong Liao, Menghuan Zhang, Yuanfei Zhu, Kun Wang, Weidi Xiao, Caiwei Jia, Minhui Dong, Na Sun, Axel Walch, Ping Xu, Jiming Zhang, Qiang Deng, Ronggui Hu
Summary: This study identified multiple self-restricting HBV-host interactions, including a negative feedback mechanism of SRSF2-HpZ/P'. Targeting host splicing machinery might represent a strategy to intervene in HBV-host interactions.
JOURNAL OF HEPATOLOGY
(2021)
Article
Biochemical Research Methods
Rick Gelhausen, Teresa Mueller, Sarah L. Svensson, Omer S. Alkhnbashi, Cynthia M. Sharma, Florian Eggenhofer, Rolf Backofen
Summary: This study aimed to evaluate the performance of tools using Ribo-seq data to detect bacterial ORFs. The results showed that DeepRibo and REPARATION_blast accurately predicted translated ORFs, while start codon predictions with smORFer improved the sensitivity of ORF prediction tools in bacteria.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Genetics & Heredity
Yanyan Li, Honghong Zhou, Xiaomin Chen, Yu Zheng, Quan Kang, Di Hao, Lili Zhang, Tingrui Song, Huaxia Luo, Yajing Hao, Runsheng Chen, Peng Zhang, Shunmin He
Summary: Small proteins, translated from small open reading frames (sORFs), have been recognized for their diverse functions in recent years. However, systematic annotation of small proteins is still insufficient. SmProt offers a curated database of unique small proteins for free access, with increased data volume and updated features.
GENOMICS PROTEOMICS & BIOINFORMATICS
(2021)
Article
Biochemical Research Methods
Mingzhe Xie, Ludong Yang, Gennong Chen, Yan Wang, Zhi Xie, Hongwei Wang
Summary: RiboChat is an interactive web platform for analyzing and annotating Ribo-seq data, which enables convenient decoding of translation information embedded within the data. It features a user-friendly interface and a cloud computing service, utilizing a chat conversation style to analyze data and find the best-matching analytics module.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biology
Andrew D. Bailey, Jason Talkish, Hongxu Ding, Haller Igel, Alejandra Duran, Shreya Mantripragada, Benedict Paten, Manuel Ares
Summary: In this study, a reliable method was developed to track the modification status of single rRNA molecules using yeast genetics and nanopore direct RNA sequencing. The results revealed concerted modification of nucleotides near functional centers of the ribosome and the accumulation of undermodified rRNA subpopulations upon loss of certain RNA helicases involved in ribosome biogenesis. Furthermore, modification profiles were found to be resistant to changes caused by various genetic and acute environmental conditions affecting translation, ribosome biogenesis, and pre-mRNA splicing.
Article
Biochemical Research Methods
Danying Shao, Nabeel Ahmed, Nishant Soni, Edward P. O'Brien
Summary: The article discusses the importance of Translation and Ribosome profiling, and points out the need for accurately identifying A-site locations in analyzing Ribo-Seq data. It introduces a web application RiboA that can achieve this accurately and easily.
BMC BIOINFORMATICS
(2021)
Article
Chemistry, Analytical
Xuanwen Li, Divya Chandra, Simon Letarte, Gregory C. Adam, Jonathan Welch, Rong-Sheng Yang, Shannon Rivera, Smaranda Bodea, Alex Dow, An Chi, Christopher A. Strulson, Douglas D. Richardson
Summary: Polysorbate is widely used in pharmaceutical formulation development to maintain the stability of biotherapeutic proteins, but its degradation can cause particle formation in drug products, posing a major quality issue and patient risk factor. This study successfully identified and confirmed active host cell enzymes responsible for polysorbate degradation using an activity-based protein profiling (ABPP) approach, bridging the gap between lipase abundance and activity.
ANALYTICAL CHEMISTRY
(2021)
Review
Anatomy & Morphology
Yousef A. Almajed, Andrew C. Hall, Thomas H. Gillingwater, Abduelmenem Alashkham
Summary: The glenohumeral joint is the most mobile joint in the human skeleton, with the glenoid labrum playing an important role as a passive stabiliser. Studies have investigated the anatomical features and biomechanical function of the labrum, emphasizing the need for further research to understand its role and mechanics. The relationship between the labrum and surrounding structures is crucial for glenohumeral stability, warranting more investigation into its microanatomy.
JOURNAL OF ANATOMY
(2022)
Letter
Medicine, General & Internal
Thomas H. Gillingwater, Catherine McWilliam, Iain Horrocks, Kenneth McWilliam, Mark Hamilton, Elaine Fletcher, Nicola Williams, Sarah Smith, Simon H. Parson
SCOTTISH MEDICAL JOURNAL
(2022)
Article
Oncology
Rana Gbyli, Yuanbin Song, Wei Liu, Yimeng Gao, Giulia Biancon, Namrata S. Chandhok, Xiaman Wang, Xiaoying Fu, Amisha Patel, Ranjini Sundaram, Toma Tebaldi, Padmavathi Mamillapalli, Amer M. Zeidan, Richard A. Flavell, Thomas Prebet, Ranjit S. Bindra, Stephanie Halene
Summary: Treatment options for relapsed/refractory acute myeloid leukemia (AML) and myelodysplastic syndromes (MDS) patients are limited. Our study demonstrates the effectiveness of the PARP inhibitor olaparib in IDH1/2-mutant AML/MDS patients, particularly those who are resistant to IDH(m)i treatment or have relapsed.
Article
Clinical Neurology
Claudia S. Bauer, Rebecca N. Cohen, Francesca Sironi, Matthew R. Livesey, Thomas H. Gillingwater, J. Robin Highley, Daniel J. Fillingham, Ian Coldicott, Emma F. Smith, Yolanda B. Gibson, Christopher P. Webster, Andrew J. Grierson, Caterina Bendotti, Kurt J. De Vos
Summary: A GGGGCC hexanucleotide repeat expansion in the C9ORF72 gene is the main genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. This study shows that C9orf72 protein interacts with the synapsin family of synaptic vesicle proteins, and C9orf72 deficiency reduces the number of excitatory synapses and synapsin levels, leading to synaptic dysfunction.
ACTA NEUROPATHOLOGICA
(2022)
Article
Clinical Neurology
F. E. V. Scheijmans, I. Cuppen, M. M. Zwartkruis, I. Signoria, C. van Ekris, F. Asselman, R. I. Wadman, E. F. Knol, W. L. van der Pol, E. J. N. Groen
Summary: Spinal muscular atrophy (SMA) is a progressive motor neuron disease that affects infants and young children. Recent therapeutic advances have improved survival and motor function in SMA patients. The most commonly used treatment, nusinersen, has been shown to be safe, but long-term effects are still unknown.
EUROPEAN JOURNAL OF PAEDIATRIC NEUROLOGY
(2023)
Article
Neurosciences
Samuele Negro, Fabio Lauria, Marco Stazi, Toma Tebaldi, Giorgia D'Este, Marco Pirazzini, Aram Megighian, Francesca Lessi, Chiara M. Mazzanti, Gabriele Sales, Chiara Romualdi, Silvia Fillo, Florigio Lista, James N. Sleigh, Andrew P. Tosolini, Giampietro Schiavo, Gabriella Viero, Michela Rigoni
Summary: This study identifies the importance of hydrogen peroxide (H2O2) and its downstream effector, Connective Tissue Growth Factor (Ctgf), in promoting neuromuscular junction (NMJ) regeneration. The study also highlights the striking extracellular matrix (ECM) remodeling process during nerve regeneration upon local H2O2 signaling.
ACTA NEUROPATHOLOGICA COMMUNICATIONS
(2022)
Article
Clinical Neurology
Jeroen W. Bos, Ewout J. N. Groen, Kevin Budding, Eveline M. Delemarre, H. Stephan Goedee, Edward F. Knol, Leonard H. van den Berg, W. Ludo van der Pol
Summary: This study aimed to further understand the risk factors and disease modifiers of MMN by studying the innate immune responses to endotoxin in patients with MMN and controls. The results showed no significant differences in immune responses to endotoxin between the two groups, suggesting that altered endotoxin-induced innate immune responses are unlikely to be a susceptibility factor for MMN.
JOURNAL OF THE NEUROLOGICAL SCIENCES
(2023)
Article
Cell Biology
Valeria Savoca, Julieta Rivosecchi, Alice Gaiatto, Annalisa Rossi, Riccardo Mosca, Irene Gialdini, Lorena Zubovic, Toma Tebaldi, Paolo Macchi, Emilio Cusanelli
Summary: This study reveals that the stability of TERRA transcripts is regulated by the RNA-binding protein associated with lethal yellow mutation (RALY). Depletion of RALY leads to decreased levels of TERRA, impaired localization of TERRA at telomeres, and ultimately telomere damage. Furthermore, TERRA interacts with the poly(A)-binding protein nuclear 1 (PABPN1), suggesting an interplay between RALY and PABPN1 in regulating TERRA stability.
Article
Multidisciplinary Sciences
Martina Paganin, Toma Tebaldi, Fabio Lauria, Gabriella Viero
Summary: expressyouRcell is an easy-to-use R package that visualizes the multi-dimensional variations of transcript and protein levels in dynamic cell pictographs, reducing the complexity of gene expression and protein level changes and improving the quantitative interpretation and communication of results.
Review
Cell Biology
Ilaria Signoria, W. Ludo van der Pol, Ewout J. N. Groen
Summary: Spinal muscular atrophy (SMA) is a severe neuromuscular disease with three gene-targeting therapies developed. The existing animal models of SMA, although recapitulate severe types of the disease, still differ from patients in terms of genetics and phenotypes. Therefore, there is a need to generate model systems that better reflect these developments.
DISEASE MODELS & MECHANISMS
(2023)
Article
Biochemistry & Molecular Biology
Sharon J. Brown, Darija Soltic, Silvia A. Synowsky, Sally L. Shirran, Ellie Chilcott, Hannah K. Shorrock, Thomas H. Gillingwater, Rafael J. Yanez-Munoz, Bernard Schneider, Melissa Bowerman, Heidi R. Fuller
Summary: Structural, functional and molecular cardiac defects have been found in SMA patients and mouse models. Proteomics analysis showed widespread molecular defects in severe SMA mice. This study investigated if similar changes can be found in less severe SMA mouse models, and found that many proteins related to cardiovascular development and function were dysregulated.
HUMAN MOLECULAR GENETICS
(2023)
Article
Medicine, Research & Experimental
Yu-Ting Huang, Hannah R. Crick, Helena Chaytow, Dinja van der Hoorn, Abrar Alhindi, Ross A. Jones, Ralph D. Hector, Stuart R. Cobb, Thomas H. Gillingwater
Summary: Neuromuscular junction stability is crucial for the treatment of various diseases, and this study developed a novel gene delivery vector to achieve targeted overexpression of DOK7 in skeletal muscle. The results showed that this method can safely achieve DOK7 overexpression and enlarge both the pre- and post-synaptic components of the neuromuscular junction without causing denervation.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Oncology
Daniela Brina, Adele Ponzoni, Martina Troiani, Bianca Cali, Emiliano Pasquini, Giuseppe Attanasio, Simone Mosole, Michela Mirenda, Mariantonietta D'Ambrosio, Manuel Colucci, Ilaria Guccini, Ajinkya Revandkar, Abdullah Alajati, Toma Tebaldi, Deborah Donzel, Fabio Lauria, Nahjme Parhizgari, Aurora Valdata, Martino Maddalena, Arianna Calcinotto, Marco Bolis, Andrea Rinaldi, Simon Barry, Jan Hendrik Rueschoff, Marianna Sabbadin, Semini Sumanasuriya, Mateus Crespo, Adam Sharp, Wei Yuan, Mathew Grinu, Alexandra Boyle, Cynthia Miller, Lloyd Trotman, Nicolas Delaleu, Matteo Fassan, Holger Moch, Gabriella Viero, Johann de Bono, Andrea Alimonti
Summary: In prostate cancer, the secretome is rewired at the translational level to recruit MDSCs, with Hgf, Spp1, and Bgn identified as key regulators. By inhibiting the MNK/eIF4E and AKT pathways, this study provides a therapeutic strategy that combines translation inhibition with immunotherapy to restore immune surveillance in prostate cancer.
Article
Biochemical Research Methods
Giulia Biancon, Emma Busarello, Poorval Joshi, Bluma J. Lesch, Stephanie Halene, Toma Tebaldi
Summary: This study presents experimental and computational analysis pipelines of fractionated eCLIP-seq (freCLIP-seq), allowing transcriptome-wide analysis of protein-RNA interactions at single-nucleotide level with increased resolution.
Meeting Abstract
Oncology
Francesco Antonica, Lucia Santomaso, Davide Pernici, Linda Petrucci, Giuseppe Aiello, Alessandro Cutarelli, Luciano Conti, Alessandro Romanel, Evelina Miele, Toma Tebaldi, Luca Tiberi