Article
Fisheries
Chang-Ming Bai, Xiang Zhang, Paola Venier, Li Gu, Ya-Nan Li, Chong-Ming Wang, Lu-Sheng Xin, Umberto Rosani
Summary: This study investigated the transcriptional changes in blood clam during OsHV-1 infection using miRNA and total RNA-seq data. It was found that the down-regulation of host metabolic and energetic processes mediated by miRNA may be a possible antiviral strategy during early infection stages, while the activation of immune genes mainly occurred in the late stage of infection.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Microbiology
Xianjun Lai, Haiyan Wang, Caiyun Wu, Wen Zheng, Jing Leng, Yizheng Zhang, Lang Yan
Summary: Viral disease in potatoes is a major problem worldwide. By analyzing the viral composition and sequence variation of potatoes, we found differences in viral infection between introduced and indigenous varieties, as well as tissue-specific infection patterns.
FRONTIERS IN MICROBIOLOGY
(2022)
Article
Multidisciplinary Sciences
Jeongwoong Yoon, Wen-Bin Gu, Mizuki Konuma, Mutsuko Kobayashi, Hayato Yokoi, Makoto Osada, Kazue Nagasawa
Summary: In this study, a primary cell culture from a marine bivalve mollusc, Mizuhopecten yessoensis, was established. A strong promoter sequence derived from a bivalve-infectious virus, ostreid herpesvirus-1 (OsHV-1), was discovered and showed higher activity than commonly used promoters in bivalves. The OsHV-1 promoter can drive gene expression not only in scallop cells but also in other cell types. This finding enables functional analysis of marine molluscan genes and can contribute to understanding gene regulatory networks.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biochemistry & Molecular Biology
Yeonhwa Jo, Hoseong Choi, Jeong Hun Lee, Sang Hyun Moh, Won Kyong Cho
Summary: This study provides a comprehensive overview of viromes in 15 major pepper cultivars through RNA sequencing. Bean broad wilt virus 2 (BBWV2) and cucumber mosaic virus (CMV) were identified as the major viruses infecting pepper plants, with different cultivars showing variations in virus infection and symptoms.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Plant Sciences
Shuxia Li, Zhihao Cheng, Shiman Dong, Zhibo Li, Liangping Zou, Pingjuan Zhao, Xin Guo, Yan Bao, Wenquan Wang, Ming Peng
Summary: This study identified a novel cold-responsive intergenic lncRNA 1 (CRIR1) in cassava, which acts as a positive regulator of cold stress response by enhancing cold tolerance and modulating the translation efficiency of messenger RNA through interaction with cassava cold shock protein 5 (MeCSP5).
PLANT CELL AND ENVIRONMENT
(2022)
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
Biology
Yu-Yi Zhang, Yicong Chen, Xiaoman Wei, Jie Cui
Summary: This study utilized a meta-transcriptomic approach to characterize the viromes of marine invertebrates, identifying 315 newly discovered RNA viruses in nine viral families or orders. The research revealed a hidden diversity of marine invertebrate RNA viruses, including evidence for possible host sharing and switch events during virus evolution.
SCIENCE CHINA-LIFE SCIENCES
(2022)
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
Biology
Madeleine Birgersson, Rajitha Indukuri, Linnea Lindquist, Lina Stepanauskaite, Qing Luo, Qiaolin Deng, Amena Archer, Cecilia Williams
Summary: By analyzing the genome-wide binding, gene regulation, and interaction between ERβ and LRH-1, this study provides a genome-wide mechanistic understanding of ovarian physiology and fertility.
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
Cell Biology
Bo Wang, Xin Xu, Xi Liu, Dong Wang, Hao Zhuang, Xin He, Tong Han, Jian Hong
Summary: The newly identified enzyme ENOPH1 plays a crucial role in promoting the proliferation and migration of glioma cells, with high expression associated with shorter overall survival in high-grade glioma patients. Knockdown of ENOPH1 inhibits tumor growth capacity and prolongs survival, possibly by regulating the PI3K/AKT/mTOR signaling pathway.
JOURNAL OF CELLULAR PHYSIOLOGY
(2021)
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)
Review
Immunology
Marco Gerdol, Paulina Schmitt, Paola Venier, Gustavo Rocha, Rafael Diego Rosa, Delphine Destoumieux-Garzon
FRONTIERS IN IMMUNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Umberto Rosani, Miriam Abbadi, Timothy Green, Chang-Ming Bai, Edoardo Turolla, Giuseppe Arcangeli, K. Mathias Wegner, Paola Venier
Review
Biology
Umberto Rosani, Enrico Bortoletto, Chang-Ming Bai, Beatriz Novoa, Antonio Figueras, Paola Venier, Bastian Fromm
Summary: Bivalves are an important group of mollusks with significant resilience to pollution and extreme environments. Research on bivalve microRNAs provides insights into gene expression regulation. The identification of new miRNA families in bivalves contributes to future comparative studies.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Biochemistry & Molecular Biology
Riccardo Frizzo, Enrico Bortoletto, Tobia Riello, Luigi Leanza, Elisabetta Schievano, Paola Venier, Stefano Mammi
Summary: The hemolymph metabolome of Mytilus galloprovincialis injected with live Vibrio splendidus bacteria showed significant changes in metabolites related to osmoregulation and aerobic respiration. Injection of Vibrio splendidus caused a decrease in amino acids and sugars in mussels acclimated at 18 degrees C, with dynamic metabolic adjustments observed in response to stressful stimuli. NMR-based metabolomics is confirmed as a feasible analytical approach complementary to other omics techniques for studying mussel responses to environmental challenges.
FRONTIERS IN MOLECULAR BIOSCIENCES
(2021)
Article
Fisheries
Giulia Blasi, Enrico Bortoletto, Matteo Gasparotto, Francesco Filippini, Chang-Ming Bai, Umberto Rosani, Paola Venier
Summary: ZNFX1 is an interferon-stimulated protein found in the outer mitochondrial membrane, capable of binding dsRNAs and interacting with MAVS proteins to stimulate the early antiviral response. Phylogenetic analysis revealed a diverse distribution of ZNFX1 in metazoans, with structural conservation in the helicase region and presence of intrinsically disordered regions in selected proteins. Over-expression of ZNFX1 in bivalve and gastropod mollusks during dsDNA virus infection highlights its antiviral role, while functional diversification in other metazoan proteins remains to be determined.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Virology
Chang-Ming Bai, Umberto Rosani, Xiang Zhang, Lu-Sheng Xin, Enrico Bortoletto, K. Mathias Wegner, Chong-Ming Wang
Summary: The research investigated the full-length viral genomes and transcriptional dynamics of two herpesviruses infecting invertebrates, revealing differences in genome structure, transcriptomic architectures, and transcriptional dynamics between the two viruses, especially the higher transcript variability and extended antisense gene transcription in HaHV-1. Both viruses were found to be heavily affected by post-transcriptional modifications by ADAR1, but they displayed different transcriptional strategies in response to these modifications, potentially to evade the host's immune response in different virus-host combinations.
Article
Fisheries
Chang-Ming Bai, Xiang Zhang, Paola Venier, Li Gu, Ya-Nan Li, Chong-Ming Wang, Lu-Sheng Xin, Umberto Rosani
Summary: This study investigated the transcriptional changes in blood clam during OsHV-1 infection using miRNA and total RNA-seq data. It was found that the down-regulation of host metabolic and energetic processes mediated by miRNA may be a possible antiviral strategy during early infection stages, while the activation of immune genes mainly occurred in the late stage of infection.
FISH & SHELLFISH IMMUNOLOGY
(2022)
Article
Multidisciplinary Sciences
Umberto Rosani
Summary: A meta-transcriptome assembly was performed on RNA sequencing data from 35 nudibranch species, resulting in the identification of 20 bona fide viral genomes. These viruses showed similarity with viruses identified in other RNA sequencing experiments and may be associated with bacteria, plants, and arthropod hosts. Additionally, nudibranchs are found to possess diversified and mostly unknown viral communities.
Article
Microbiology
Umberto Rosani, Enrico Bortoletto, Caroline Montagnani, Paola Venier
Summary: OsHV-1 is a harmful pathogen of bivalve species, such as oysters, with host RNA editing enzyme massively modifying OsHV-1 transcripts during infection. While about 0.5% of the oyster transcriptome is consistently enzymatically modified by ADAR, genes related to antiviral response, miRNA maturation, and epigenetic regulation are hyper-edited only in specific conditions. Despite technical challenges, further research is needed for a comprehensive understanding of the bivalve RNA editome.
Article
Biology
Antonino Di Stefano, Umberto Rosani, Stefano Levra, Isabella Gnemmi, Paola Brun, Mauro Maniscalco, Silvestro Ennio D'Anna, Vitina Carriero, Francesca Bertolini, Fabio L. M. Ricciardolo
Summary: This study found an imbalance between BMP proteins and their antagonists in the lungs of stable COPD patients, which may play a role in airway remodeling and the regenerative-reparative responses of diseased bronchioles and lung parenchyma.
Article
Immunology
E. Bortoletto, P. Venier, A. Figueras, B. Novoa, U. Rosani
Summary: Research on the fp-3 alpha gene family in byssogenic bivalve mollusks reveals insights into the evolution and functional diversification of these genes, providing clues to the molecular mechanisms behind mussel adhesion.
ISJ-INVERTEBRATE SURVIVAL JOURNAL
(2021)
Article
Biotechnology & Applied Microbiology
Marco Gerdol, Rebeca Moreira, Fernando Cruz, Jessica Gomez-Garrido, Anna Vlasova, Umberto Rosani, Paola Venier, Miguel A. Naranjo-Ortiz, Maria Murgarella, Samuele Greco, Pablo Balseiro, Andre Corvelo, Leonor Frias, Marta Gut, Toni Gabaldon, Alberto Pallavicini, Carlos Canchaya, Beatriz Novoa, Tyler S. Alioto, David Posada, Antonio Figueras