Article
Multidisciplinary Sciences
Anita Talbot, Laura Gargan, Grainne Moran, Louis Prudent, Ian O'Connor, Luca Mirimin, Jens Carlsson, Eugene MacCarthy
Summary: This study investigated the pre-clinical stage of Amoebic Gill Disease (AGD) using RNA-sequencing technology, identifying a significant number of differentially expressed genes, some of which are related to immune response. The pathogen may evade host immune surveillance by interfering with signal transduction pathways.
SCIENTIFIC REPORTS
(2021)
Article
Biotechnology & Applied Microbiology
Thu Thi Minh Vo, Tuan Viet Nguyen, Gianluca Amoroso, Tomer Ventura, Abigail Elizur
Summary: The reduction in flesh pigmentation of farmed Atlantic salmon was investigated using RNA sequencing. Differential gene expression analysis between different flesh color phenotypes revealed associations with metal ion transport, oxidation-reduction processes, immune responses, and lipid metabolism. The study compared two library preparation methods and found similarities in the trend of differentially expressed genes validated by qPCR.
Article
Biotechnology & Applied Microbiology
Carlo C. Lazado, Marianne Iversen, Arvind Y. M. Sundaram
Summary: This study provides the first insight into the basal transcriptome of the olfactory rosette in Atlantic salmon. Comparative transcriptomic analysis with gills, another organ possessing MALT, reveals shared cytokine-cytokine interaction and neuroactive ligand-receptor interaction pathways. The immunological characteristics of both organs are further characterized by the overrepresentation of immune-related pathways, particularly important for pathogen recognition. The differential regulation of markers for interleukins, extracellular matrix, antimicrobial peptides, and complement highlights the immunological differences between the two organs. The basal transcriptome of the Atlantic salmon olfactory rosette is a valuable molecular toolbox for understanding nasal immunity in teleost fish.
Article
Multidisciplinary Sciences
Asia Mendelevich, Svetlana Vinogradova, Saumya Gupta, Andrey A. Mironov, Shamil R. Sunyaev, Alexander A. Gimelbrant
Summary: The study demonstrates that relying on a single RNA-seq library for allele-specific analysis can lead to variable error rates. Therefore, the development of a computational tool like Qllelic, which accurately accounts for technical noise by utilizing replicate RNA-seq libraries, greatly decreases false positive rates and improves reproducibility of AI estimates.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Qiang Fu, Yuqing Li, Hao Zhang, Min Cao, Lu Zhang, Chengbin Gao, Xin Cai, Defeng Chen, Ziying Yang, Jie Li, Ning Yang, Chao Li
Summary: This study conducted RNA-seq analysis on spleen tissue of Atlantic salmon after Aeromonas salmonicida subsp. masoucida (ASM) vaccination to reveal genes, their expression patterns, and pathways involved in immune protections. The results showed that differentially expressed genes were involved in cytokine-cytokine receptor interaction, HTLV-I infection, MAPK signaling pathway, PI3K-Akt signaling pathway, and TNF signaling pathway. The study provided insights into gene regulation and pathways involved in immune response to the vaccine.
MARINE BIOTECHNOLOGY
(2022)
Article
Fisheries
Christine Klykken, Lauris Boissonnot, Anne Katrine Reed, Paul Whatmore, Kari Attramadal, Rolf Erik Olsen
Summary: Nephrocalcinosis is a common disorder in farmed Atlantic salmon and has significant physiological consequences, including decreased metabolism and energy production, upregulation of important signaling pathways, and increased inflammatory responses.
JOURNAL OF FISH DISEASES
(2022)
Article
Biochemical Research Methods
Wancen Mu, Hirak Sarkar, Avi Srivastava, Kwangbom Choi, Rob Patro, Michael Love
Summary: The study introduces a statistical method called airpart for identifying differential cell-type-specific allelic imbalance from single-cell RNA-sequencing data, or dynamics allelic imbalance from other spatially or time-resolved datasets. The method accurately detects common mechanisms of cis-genetic regulation and shows lower error rates in single-cell data.
Article
Multidisciplinary Sciences
Peijie Zhou, Shuxiong Wang, Tiejun Li, Qing Nie
Summary: MuTrans is a method based on multiscale reduction technique that can identify the underlying stochastic dynamics governing cell-fate transitions, construct cell-fate dynamical manifold, distinguish stable and transition cells, and quantify transition probabilities between cell states. The method is consistent with Langevin equation and transition rate theory, and has been shown to robustly unravel complex cell fate dynamics induced by transition cells in various systems. It bridges data-driven and model-based approaches for single-cell resolution analysis of cell-fate transitions.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
Weijun Jiang, Jiajia Shi, Jingjie Zhao, Qiu Wang, Dan Cong, Fenghua Chen, Yu Zhang, Yuhan Liu, Junzheng Zhao, Qian Chen, Linhao Gu, Wenjia Zhou, Chenhang Wang, Zhaoyuan Fang, Shuhui Geng, Wei Xie, Luo-Nan Chen, Yang Yang, Yun Bai, Haodong Lin, Xiajun Li
Summary: ZFP57 is a master regulator of genomic imprinting, which controls the expression of target imprinted genes by maintaining differential DNA methylation at ICRs. Mutations in Zfp57 lead to allelic expression switches in target imprinted genes and genes associated with the NOTCH signaling pathway.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biochemistry & Molecular Biology
A. J. Bowden, M. B. Adams, S. J. Andrewartha, N. G. Elliott, P. B. Frappell, T. D. Clark
Summary: The study found that as amoebic gill disease progresses, the basal energy requirements of Atlantic salmon increase, aerobic scope decreases, and hypoxia tolerance weakens.
COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY A-MOLECULAR & INTEGRATIVE PHYSIOLOGY
(2022)
Article
Biology
Yuqi Cheng, Xingyu Fan, Jianing Zhang, Yu Li
Summary: scBalance is an integrated sparse neural network framework that incorporates adaptive weight sampling and dropout techniques to handle noise and imbalanced datasets, achieving high classification accuracy for both rare and major cell types.
COMMUNICATIONS BIOLOGY
(2023)
Article
Horticulture
Yanli Yao, Mingwei Li, Wenqiu Lin, Shenghui Liu, Qingsong Wu, Qiong Fu, Zhuying Zhu, Yuyao Gao, Xiumei Zhang
Summary: Watercore is a physiological disorder in pineapples that affects fruit quality and storage life. This study, using transcriptome analysis, revealed the molecular mechanism of watercore for the first time and identified key genes related to this disorder.
Article
Immunology
Natasha A. Botwright, Amin R. Mohamed, Joel Slinger, Paula C. Lima, James W. Wynne
Summary: Through studying the pathogenesis of amoebic gill disease in Atlantic salmon, the localized and systemic immune responses of the host and parasite were identified, along with transcription factors and gene networks significantly altered in disease states. This dual transcriptomic study provides novel molecular insights into the pathology of AGD, offering alternative theories for future research and improved management strategies.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Multidisciplinary Sciences
Mizuki Honda, Shinya Oki, Ryuichi Kimura, Akihito Harada, Kazumitsu Maehara, Kaori Tanaka, Chikara Meno, Yasuyuki Ohkawa
Summary: This study introduces a transcriptome profiling method utilizing photo-isolation chemistry to analyze gene expression specifically from photo-irradiated regions in mouse embryos, demonstrating its potential in elucidating cell interactions and functions at subcellular resolutions.
NATURE COMMUNICATIONS
(2021)
Article
Biotechnology & Applied Microbiology
Hiroki Ura, Sumihito Togi, Yo Niida
Summary: This study compared the advantages and disadvantages of three RNA-Seq library preparation methods and found that TruSeq detected transcripts and splicing events better than the other methods, accurately measuring gene expression levels and splicing events. TeloPrime had higher coverage at the transcription start site, while SMARTer performed better than TeloPrime in terms of the number of detected transcripts and splicing events among the studied full-length double-stranded cDNA methods.
Article
Biotechnology & Applied Microbiology
Carolina P. Moraleda, Diego Robledo, Alejandro P. Gutierrez, Jorge del-Pozo, Jose M. Yanez, Ross D. Houston
Summary: The resistance to SRS is a polygenic trait, and this study has identified relevant genes and pathways that are likely to play a role in mediating genetic resistance through genome-wide association analysis and RNA-sequencing.
Article
Cell Biology
Ismael Hernandez-Nunez, Diego Robledo, Helene Mayeur, Sylvie Mazan, Laura Sanchez, Fatima Adrio, Anton Barreiro-Iglesias, Eva Candal
Summary: Neurogenesis is the process of generating new neurons by progenitor cells, which is restricted to specific neurogenic niches. The retina of cartilaginous fish such as catsharks shows active proliferation and neurogenesis in juveniles but a reduction in cell proliferation after sexual maturation. RNA-Seq analysis revealed a decrease in gene expression related to cell proliferation and neurogenesis in adult catsharks, providing valuable insight into signaling pathways controlling neurogenesis in vertebrate retinas.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Biotechnology & Applied Microbiology
O. Gervais, A. Barria, A. Papadopoulou, R. L. Gratacap, B. Hillestad, A. E. Tinch, S. A. M. Martin, D. Robledo, R. D. Houston
Summary: The study found that the heritability of ISAV resistance is moderate with a polygenic architecture, but a significant quantitative trait locus was detected on chromosome 13. A mild up-regulation of the interferon pathway characterizes the response to the virus in heart samples from this population of Atlantic salmon, and candidate genes showing differential expression between samples with high and low breeding values for resistance were identified.
Review
Biology
Robert W. A. Potts, Alejandro P. Gutierrez, Carolina S. Penaloza, Tim Regan, Tim P. Bean, Ross D. Houston
Summary: Molluscan aquaculture is important for global seafood production, but faces challenges from infectious disease outbreaks. Selective breeding, genomic technologies, and genome editing show promise in improving genetic resistance to disease in molluscs, with tailored approaches needed due to their unique characteristics.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Review
Biotechnology & Applied Microbiology
Ye Hwa Jin, Diego Robledo, John M. Hickey, Mike J. McGrew, Ross D. Houston
Summary: The use of surrogate broodstock technology provides new opportunities for improving genome editing, preserving aquatic genetic resources, and reducing generation intervals in aquaculture breeding, ultimately expediting genetic gain and dissemination of high quality production animals.
BIOTECHNOLOGY ADVANCES
(2021)
Article
Evolutionary Biology
Tim Regan, Lewis Stevens, Carolina Penaloza, Ross D. Houston, Diego Robledo, Tim P. Bean
Summary: Bivalve molluscs, with 20,000 species globally, are crucial for ecosystem engineering and food security, yet little is known about their evolutionary adaptation strategies. Recent advances in long-read sequencing have allowed for accurate genome assemblies and revealed expansions in gene families across bivalve genomes as a response to evolutionary pressures.
GENOME BIOLOGY AND EVOLUTION
(2021)
Article
Biotechnology & Applied Microbiology
Jon Pavelin, Ye Hwa Jin, Remi L. Gratacap, John B. Taggart, Alastair Hamilton, David W. Verner-Jeffreys, Richard K. Paley, Carl-johan Rubin, Stephen C. Bishop, James E. Bron, Diego Robledo, Ross D. Houston
Summary: The study identified nae1 as the causative gene underlying the major QTL affecting resistance to IPNV in Atlantic salmon, providing further evidence for the critical role of neddylation in host-pathogen interactions. The results also highlight the value of combining high-throughput genomics approaches with targeted genome editing to understand the genetic basis of disease resistance.
Article
Biotechnology & Applied Microbiology
C. Penaloza, T. Manousaki, R. Franch, A. Tsakogiannis, A. K. Sonesson, M. L. Aslam, F. Allal, L. Bargelloni, R. D. Houston, C. S. Tsigenopoulos
Summary: SNP arrays are powerful tools for studying the genetic basis of complex traits in European seabass and gilthead seabream, showing high conversion rates and repeatability. These arrays enable efficient genotyping and exploration of population structure and haplotype sharing in diverse fish populations.
Article
Microbiology
Sophie Fridman, Smaragda Tsairidou, Nilantha Jayasuriya, Halina Sobolewska, Alastair Hamilton, Carlos Lobos, Ross D. Houston, Hamish Rodger, James Bron, Tharangani Herath
Summary: This study aimed to develop a novel gross pathological scoring system for assessing complex or multifactorial gill disease in farmed Atlantic salmon. The scoring system combines presumptive or healed amoebic gill disease (AGD) with other types of gill lesions, providing a standardized approach to characterize severe proliferative pathologies in affected gills.
Article
Biotechnology & Applied Microbiology
Robert Mukiibi, Carolina Penaloza, Alejandro Gutierrez, Jose M. Yanez, Ross D. Houston, Diego Robledo
Summary: This study investigated DNA methylation changes in response to P. salmonis infection in the head kidney and liver tissue of Atlantic salmon, and the interaction between gene expression and DNA methylation in the same tissues. The results suggest that methylation plays an important role in gene expression regulation and response to infectious diseases, providing valuable insights for utilizing epigenetic markers to improve disease resistance and manage fish health in salmon aquaculture.
Review
Fisheries
Nicholas A. Robinson, Diego Robledo, Lene Sveen, Rose Ruiz Daniels, Aleksei Krasnov, Andrew Coates, Ye Hwa Jin, Luke T. Barrett, Marie Lillehammer, Anne H. Kettunen, Ben L. Phillips, Tim Dempster, Andrea Doeschl-Wilson, Francisca Samsing, Gareth Difford, Sarah Salisbury, Bjarne Gjerde, John-Erik Haugen, Erik Burgerhout, Binyam S. Dagnachew, Dominic Kurian, Mark D. Fast, Morten Rye, Marcela Salazar, James E. Bron, Sean J. Monaghan, Celeste Jacq, Mike Birkett, Howard I. Browman, Anne Berit Skiftesvik, David M. Fields, Erik Selander, Samantha Bui, Anna Sonesson, Stanko Skugor, Tone-Kari Knutsdatter Ostbye, Ross D. Houston
Summary: Disease and parasitism pose significant challenges to global aquaculture, and genetic technologies offer potential solutions. Understanding genetic mechanisms, developing tools for boosting host resistance, and applying genetic technologies can improve disease resistance and transform aquaculture.
REVIEWS IN AQUACULTURE
(2023)
Editorial Material
Genetics & Heredity
Wei Huang, Qiang Gao, Kai Fu, Rodrigo Pulgar Tejo, Lucile Maria Floeter-Winter, Alejandro P. Gutierrez
FRONTIERS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
Nidia de Sousa, Diego Robledo, Laura Gonzalez-Llera, Andreia G. Pinho, Diogo J. Santos, Susana Monteiro, Jonas Campos, Jorge R. Cibrao, Nuno A. Silva, Laura Sanchez, Antonio J. Salgado, Anton Barreiro-Iglesias
Summary: Spinal cord injury (SCI) has no available pharmacological treatments for promoting neurological recovery. Baclofen treatment has been shown to promote functional recovery in mice with compression SCI. This study provides transcriptomic data from adult mouse spinal cords collected 7 days after compression SCI and baclofen administration. The data includes raw RNA-seq data and bioinformatic analyses.
Review
Fisheries
Rose Ruiz Daniels, Richard S. S. Taylor, Diego Robledo, Daniel J. J. Macqueen
Summary: Single cell genomics is a rapidly advancing technology that measures the molecular characteristics of individual cells in target samples. It provides more biological information compared to traditional 'bulk' methods and has revolutionized our understanding of cellular biology in humans and model organisms. This review highlights the potential applications of single cell genomics in aquaculture research, discussing the challenges and solutions in its broad adoption. The review focuses on single cell transcriptomics, discussing considerations in experimental design and data analysis tailored to under-characterized aquaculture species.
REVIEWS IN AQUACULTURE
(2023)