Article
Biotechnology & Applied Microbiology
Huiqin Niu, Yifan Pang, Lingli Xie, Qiaozhen Yu, Yubang Shen, Jiale Li, Xiaoyan Xu
Summary: This study investigates the evolutionary background and expression regulation of grass carp miRNAs. Multiple novel miRNAs have emerged during grass carp evolution, and both duplication and de novo production contribute to miRNA cluster formation, with de novo creation being more prevalent. Clustered miRNAs are more conserved and change slower, while unique miRNAs tend to have higher evolution rates and lower expression levels.
Editorial Material
Multidisciplinary Sciences
Matt Friedman
Summary: Scarce evidence suggests that important evolutionary developments for jawed vertebrates may have taken place during or prior to the Silurian period. Fossil discoveries unveil insights into this particular interval.
Review
Endocrinology & Metabolism
Yorgui Santiago-Andres, Matan Golan, Tatiana Fiordelisio
Summary: The pituitary gland, a master endocrine gland in vertebrates, has recently been found to consist of tightly wired large-scale networks of cells that communicate with each other in homo and heterotypic manners, optimizing hormone pulse generation in response to changing physiological demands. The development of 3D imaging methods and transgenic models has allowed for further research into functional pituitary networks across different vertebrate classes.
FRONTIERS IN ENDOCRINOLOGY
(2021)
Article
Multidisciplinary Sciences
Andrea Baucon, Annalisa Ferretti, Chiara Fioroni, Luca Pandolfi, Enrico Serpagli, Armando Piccinini, Carlos Neto de Carvalho, Mario Cachao, Thomas Linley, Fernando Muniz, Zain Belaustegui, Alan Jamieson, Girolamo Lo Russo, Filippo Guerrini, Sara Ferrando, Imants Priede
Summary: This study reveals that fish have been inhabiting the deep seafloor since the Early Cretaceous, using various techniques to feed on prey. These findings shed light on the evolutionary history of deep-seafloor fishes and the availability of new food sources in the deep sea.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Review
Ecology
M. E. McNamara, V Rossi, T. S. Slater, C. S. Rogers, A-L Ducrest, S. Dubey, A. Roulin
Summary: This study integrates fossil data with current understanding of melanin function, biochemistry, and genetics to identify potential genomic controls on melanin evolution. Taxonomic trends in the anatomical location, geometry, and chemistry of vertebrate melanosomes are linked to the evolution of endothermy, suggesting fundamental links between melanization and vertebrate ecology. Tissue-specific and taxonomic trends in melanin chemistry support evidence for evolutionary tradeoffs between function and cytotoxicity.
TRENDS IN ECOLOGY & EVOLUTION
(2021)
Article
Immunology
Elizabeth A. Holzhausen, Allison Kupsco, Bridget N. Chalifour, William B. Patterson, Kelsey A. Schmidt, Pari Mokhtari, Andrea A. Baccarelli, Michael I. Goran, Tanya L. Alderete
Summary: Breast milk contains bioactive compounds such as EV-miRNAs, which may regulate infant immune system development and metabolism. This study examined the associations between EV-miRNA expression and various factors, and identified factors such as sequencing quality indicators, breastfeeding practices, and maternal characteristics that are associated with EV-miRNA expression. These findings provide important insights for future breast milk miRNA research.
FRONTIERS IN IMMUNOLOGY
(2023)
Article
Multidisciplinary Sciences
Lusheng Fan, Bin Gao, Ye Xu, Nora Flynn, Brandon Le, Chenjiang You, Shaofang Li, Natalia Achkar, Pablo A. Manavella, Zhenbiao Yang, Xuemei Chen
Summary: The study reveals a dual role of AAR2 in plant growth and development by promoting miRNA biogenesis and premessenger RNA splicing. AAR2 interacts with HYL1 and regulates its activity and the accumulation of miRNA.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Biology
Diyan Li, Mengnan He, Qianzi Tang, Shilin Tian, Jiaman Zhang, Yan Li, Danyang Wang, Long Jin, Chunyou Ning, Wei Zhu, Silu Hu, Keren Long, Jideng Ma, Jing Liu, Zhihua Zhang, Mingzhou Li
Summary: The three-dimensional architecture of the genome plays a crucial role in gene expression regulation and conservation across species. This study compares the 3D genomes of fish, chickens, and 10 mammalian species, and reveals that genome size and chromosome length influence the higher hierarchical organization of the genome, while local transcriptional availability is selected through vertebrate evolution. Additionally, conservation of topologically associating domains is associated with modularity of expression profiles, and LINE and SINE transposable elements contribute to heterochromatin and euchromatin organization during genome evolution.
Review
Biochemical Research Methods
Yongxin Zhao, Zheng Kuang, Ying Wang, Lei Li, Xiaozeng Yang
Summary: The past two decades have witnessed a surge in studies on microRNAs (miRNAs) in plants and animals. This review article focuses on the progress and challenges of miRNA annotation in plants, comparing it with the annotation of animal miRNAs. Methods and criteria for plant miRNA annotation are discussed along with the potential solutions to existing difficulties, as well as the advantages and disadvantages of bioinformatics tools used in this field. Additionally, the availability of databases hosting plant miRNAs and potential optimization solutions are summarized, with a look towards future challenges and perspectives in plant miRNA annotations.
BRIEFINGS IN BIOINFORMATICS
(2021)
Article
Physiology
Stacy V. Nguyen, Dominic Lanni, Yongqi Xu, James S. Michaelson, Sarah K. McMenamin
Summary: Zebrafish is a valuable model for studying skeletal development and disorders, and 3D technologies can provide detailed insights into the process. This study generated a high-resolution skeletal reference dataset for zebrafish and analyzed the changes in density and volume during growth. The findings provide quantitative and qualitative assessments of skeletal changes throughout development.
FRONTIERS IN PHYSIOLOGY
(2022)
Review
Biology
Anais N. Bauer, Niska Majumdar, Frank Williams, Smit Rajput, Lok R. Pokhrel, Paul P. Cook, Shaw M. Akula
Summary: Viral outbreaks pose obstacles to human health, and understanding viral pathology is crucial for developing methods to combat infection. The relatively new field of miRNA research in virology has shown that miRNAs play important roles in gene expression regulation. Changes in miRNA expression can either help the host fight infections or be exploited by viruses to enhance infection. Uncovering these interactions and their implications can guide therapeutic and diagnostic advancements. miRNA technology has market potential and is already being used in commercial biopharmaceuticals. Further research into the functions of miRNAs during infection and their therapeutic potential can contribute to strategies against current and future viral pathogens.
Article
Biochemistry & Molecular Biology
Yao Xiao, TingYu M. Liu, Ian J. MacRae
Summary: Argonaute (AGO) proteins use microRNAs (miRNAs) and small interfering RNAs (siRNAs) to regulate gene expression. The functional distinction between AGOs in plants and animals depends on a minor structural difference in the PIWI domain. Swapping a 9-amino acid loop in the PIWI domain can alter the targeting properties and silencing efficiency of AGO proteins.
Review
Biochemistry & Molecular Biology
Jacek Kabzinski, Monika Maczynska, Ireneusz Majsterek
Summary: This article discusses the potential use of microRNAs in the diagnosis of head and neck squamous cell carcinoma, highlighting their application in radiotherapy and immunotherapy, as well as addressing the challenges and future research directions in developing this promising technology.
Review
Plant Sciences
Jayanti Jodder
Summary: miRNAs in plants play a crucial role in controlling growth, development, and stress tolerance by modulating the expression of target genes. Modulating the expression of specific stress/development-related genes can be achieved by targeting the corresponding miRNAs. Understanding the molecular mechanism of miRNA biogenesis, particularly the processing of pri-MIRNAs, is essential for effectively modulating miRNA expression levels and ultimately improving plant yield and stress tolerance.
PLANT CELL REPORTS
(2021)
Article
Biochemistry & Molecular Biology
Iyad Kobeissi, Islam Eljilany, Tala Achkar, William A. LaFramboise, Lucas Santana-Santos, Ahmad A. Tarhini
Summary: This study identified a 4-miRNA signature that is significantly associated with improved relapse-free survival in patients with advanced melanoma. Functional annotation analysis indicated that these miRNAs are involved in cancer-related pathways including cell proliferation regulation, apoptosis, the MAPK signaling pathway, and the positive regulation of T cell activation.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Ecology
Joanna L. Kelley, Thomas Desvignes, Kerry L. McGowan, Marcos Perez, Lenin Arias Rodriguez, Anthony P. Brown, Zach Culumber, Michael Tobler
Summary: The study identified differentially expressed miRNAs in Poecilia mexicana populations adapted to contrasting habitats, suggesting their involvement in H2S adaptation by regulating genes related to sulphide detoxification and mitochondrial function. MiRNAs play a critical role in promoting necessary functions for survival and reducing functions affected by H2S in natural populations.
JOURNAL OF EVOLUTIONARY BIOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Romain Feron, Qiaowei Pan, Ming Wen, Boudjema Imarazene, Elodie Jouanno, Jennifer Anderson, Amaury Herpin, Laurent Journot, Hugues Parrinello, Christophe Klopp, Verena A. Kottler, Alvaro S. Roco, Kang Du, Susanne Kneitz, Mateus Adolfi, Catherine A. Wilson, Braedan McCluskey, Angel Amores, Thomas Desvignes, Frederick W. Goetz, Ato Takanashi, Mari Kawaguchi, Harry William Detrich, Marcos A. Oliveira, Rafael H. Nobrega, Takashi Sakamoto, Masatoshi Nakamoto, Anna Wargelius, Orjan Karlsen, Zhongwei Wang, Matthias Stoeck, Robert M. Waterhouse, Ingo Braasch, John H. Postlethwait, Manfred Schartl, Yann Guiguen
Summary: RADSex is a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data, with visualization and identification of sex-specific markers. By applying RADSex, we uncovered Y chromosome polymorphism in Japanese medaka, identified sex determination systems and sex-specific markers in six out of 15 fish species.
MOLECULAR ECOLOGY RESOURCES
(2021)
Article
Biochemistry & Molecular Biology
Thomas Desvignes, Jason Sydes, Jerome Montfort, Julien Bobe, John H. Postlethwait
Summary: Following whole-genome duplication in teleosts, miRNA genes are more likely to be retained in ohnologous pairs, while gene losses occur rapidly. Factors such as genomic context, expression patterns, and purifying selection influence the evolution of miRNA genes.
MOLECULAR BIOLOGY AND EVOLUTION
(2021)
Correction
Genetics & Heredity
Yi-Lin Yan, Tom Titus, Thomas Desvignes, Ruth BreMiller, Peter Batzel, Jason Sydes, Dylan Farnsworth, Danielle Dillon, Jeremy Wegner, Jennifer B. Phillips, Judy Peirce, John Dowd, Charles Loren Buck, Adam Miller, Monte Westerfield, John H. Postlethwait
Review
Genetics & Heredity
Emily A. Beck, Hope M. Healey, Clayton M. Small, Mark C. Currey, Thomas Desvignes, William A. Cresko, John H. Postlethwait
Summary: EMMs provide unique avenues to study gene-by-environment interactions and mutations in noncoding regions, improving our understanding of complex diseases. Fish, as the most diverse group of vertebrates, exhibit specialized phenotypes that could be pathogenic in humans but are adaptive in their specialized habitats.
TRENDS IN GENETICS
(2022)
Review
Ecology
Jilda Alicia Caccavo, Henrik Christiansen, Andrew J. Constable, Laura Ghigliotti, Rowan Trebilco, Cassandra M. Brooks, Cedric Cotte, Thomas Desvignes, Tracey Dornan, Christopher D. Jones, Philippe Koubbi, Ryan A. Saunders, Anneli Strobel, Marino Vacchi, Anton P. van de Putte, Andrea Walters, Claire M. Waluda, Briannyn L. Woods, Jose C. Xavier
Summary: Southern Ocean ecosystems are important and vulnerable, with fish and squid playing key roles in the food web. They are uniquely adapted to extreme habitats, but face threats from fisheries and global climate change. Uncertainty about population dynamics and ecosystem structure necessitates caution in management to ensure conservation objectives are met.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2021)
Article
Biology
Emilie Cardona, Cervin Guyomar, Thomas Desvignes, Jerome Montfort, Samia Guendouz, John H. Postlethwait, Sandrine Skiba-Cassy, Julien Bobe
Summary: This study investigated the potential of c-miRNAs as biomarkers of reproductive and metabolic states in female rainbow trout. Results showed significant changes in blood plasma miRNAome under different metabolic and reproductive states, identifying potential biomarkers like myomiRs and miR-202-5p. These promising results suggest the high potential of c-miRNAs as physiologically relevant biomarkers in various fish species, paving the way for non-invasive phenotyping.
Article
Biochemistry & Molecular Biology
Thomas Desvignes, Philippe Bardou, Jerome Montfort, Jason Sydes, Cervin Guyomar, Simon George, John H. Postlethwait, Julien Bobe
Summary: FishmiRNA is a miRNA annotation and expression database for ray-finned fishes, providing detailed manually curated miRNA annotations with orthology relationships, expression data for each mature miRNA, and convenient download formats and search options for user-friendly access.
MOLECULAR BIOLOGY AND EVOLUTION
(2022)
Article
Virology
Simona Kraberger, Charlotte Austin, Kata Farkas, Thomas Desvignes, John H. Postlethwait, Rafaela S. Fontenele, Kara Schmidlin, Russell W. Bradley, Pete Warzybok, Koenraad Van Doorslaer, William Davison, Christopher B. Buck, Arvind Varsani
Summary: This study expands the known genomes of fish papillomaviruses and reveals their genetic distance from other papillomaviruses, suggesting a bottleneck event in the evolution of papillomaviruses infecting terrestrial vertebrates.
Article
Anatomy & Morphology
Thomas Desvignes, Amy E. Robbins, Andrew Z. Carey, Raisa Bailon-Zambrano, James T. Nichols, John H. Postlethwait, Kryn Stankunas
Summary: This study explores the development and patterning of caudal skeletal elements in zebrafish and proposes a model for the origins of caudal fin symmetry. It suggests that a central organizer establishes the hypural diastema and patterns the surrounding tissue into two plates of connective tissue and two mirrored sets of central principal rays (CPRs). Additionally, two peripheral organizers specify peripheral principal rays (PPRs) unidirectionally, forming a symmetric composite fin derived from three fields. The findings provide insights into the mechanisms underlying teleost fin morphological variation.
DEVELOPMENTAL DYNAMICS
(2022)
Article
Marine & Freshwater Biology
Manuel Novillo, Thomas Desvignes, Eugenia Moreira, Esteban Barrera-Oro
Summary: This study reports the recent ingestion of emerald notothens eggs by a large specimen of bullhead notothen in Paradise Bay, West Antarctic Peninsula, and discusses aspects of emerald notothen reproductive ecology. The findings suggest a lack of effectiveness in egg protection in this predator-prey interaction between two sympatric notothenioid species.
ESTUARINE COASTAL AND SHELF SCIENCE
(2022)
Review
Biochemistry & Molecular Biology
Scott Hotaling, Thomas Desvignes, John S. Sproul, Luana S. F. Lins, Joanna L. Kelley
Summary: This study utilized long-read sequencing data to generate a high-quality genome assembly for an Antarctic eelpout, Ophthalmolycus amberensis, and compared it to other Antarctic fishes. The study revealed unique evolution and adaptation features in O. amberensis and highlighted the importance of long-read sequencing in understanding genome evolution.
Article
Biochemistry & Molecular Biology
Ming Wen, Qiaowei Pan, Elodie Jouanno, Jerome Montfort, Margot Zahm, Cedric Cabau, Christophe Klopp, Carole Iampietro, Celine Roques, Olivier Bouchez, Adrien Castinel, Cecile Donnadieu, Hugues Parrinello, Charles Poncet, Elodie Belmonte, Veronique Gautier, Jean-Christophe Avarre, Remi Dugue, Rudhy Gustiano, Tran Thi Thuy Ha, Marc Campet, Kednapat Sriphairoj, Josiane Ribolli, Fernanda L. de Almeida, Thomas Desvignes, John H. Postlethwait, Christabel Floi Bucao, Marc Robinson-Rechavi, Julien Bobe, Amaury Herpin, Yann Guiguen
Summary: This study generated novel genomic resources for 12 Pangasiids, characterized their sex determination system, and identified a conserved master sex-determining gene. The findings contribute to a better understanding of the dynamics of sex determination systems.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Multidisciplinary Sciences
Thomas Desvignes, Henrik Lauridsen, Alejandro Valdivieso, Rafaela S. Fontenele, Simona Kraberger, Katrina N. Murray, Nathalie R. Le Francois, H. William Detrich, Michael L. Kent, Arvind Varsani, John H. Postlethwait
Summary: Climate changes can lead to disease outbreaks in remote areas, and the West Antarctic Peninsula is facing rapid climate change. Two notothenioid fish species in this biodiversity hotspot were found to have large skin tumors, caused by X-cell parasitic al-veolates, a genus we call Notoxcellia. These tumors negatively impacted the host's growth and condition, revealing potential biotic threats to vulnerable Antarctic ecosystems.
Article
Genetics & Heredity
Yi-Lin Yan, Tom Titus, Thomas Desvignes, Ruth BreMiller, Peter Batzel, Jason Sydes, Dylan Farnsworth, Danielle Dillon, Jeremy Wegner, Jennifer B. Phillips, Judy Peirce, John Dowd, Charles Loren Buck, Adam Miller, Monte Westerfield, John H. Postlethwait
Summary: People with NR5A1 mutations can experience various reproductive and adrenal issues, and the gene's role in zebrafish may be similar to that in mammals, with mutations resulting in the absence of male or female characteristics.