Advances in Transcriptomic Technologies and Their Applications in Fisheries Science

Use of Single-Cell -Omic Technologies to Study the Gastrointestinal Tract and Diseases, From Single Cell Identities to Patient Features

Open-access databases with utility in fisheries science have grown exponentially in quantity and scope over the past decade, with profound impacts to our discipline. The management, distillation, and sharing of an exponentially growing stream of open-access data represents several fundamental challenges in fisheries science. Many of the currently available open-access resources may not be universally known among fisheries scientists. We therefore introduce many national- and global-scale open-access databases with applications in fisheries science and provide an example of how they can be harnessed to perform valuable analyses without additional field efforts. We also discuss how the development, maintenance, and utilization of open-access data are likely to pose technical, financial, and educational challenges to fisheries scientists. Such cultural implications that will coincide with the rapidly increasing availability of free data should compel the American Fisheries Society to actively address these problems now to help ease the forthcoming cultural transition. RESUMEN en la última década, el número de bases de datos de acceso abierto con utilidad para la ciencia pesquera ha crecido exponencialmente en cantidad y alcance y su impacto ha sido considerado como muy importante en esta disciplina. El manejo, depuración e intercambio de datos de acceso abierto representa retos fundamentales en la ciencia pesquera. Muchos de los recursos actualmente disponibles de acceso abierto pueden no ser conocidos por los científicos pesqueros. Por lo tanto, aquí se presentan varias bases de datos a nivel nacional e internacional de libre acceso con aplicación en las ciencias pesqueras y se da un ejemplo de cómo pueden ser aprovechadas para realizar valiosos análisis sin hacer esfuerzos adicionales de trabajo de campo. También se discute cómo el desarrollo, mantenimiento y uso de las base de datos de libre acceso muy posiblemente representarán retos importantes para los científicos de la pesca en cuanto a las dimensiones técnica, financiera y educativa. Tales implicaciones culturales, que coincidirán con la disponibilidad cada vez mayor de datos gratuitos, debieran servir de impulso a la Sociedad Americana de Pesquerías a que volcara activamente su atención sobre estos problemas con el fin de facilitar la transición cultural que se avecina.

2 - Work of fishery scientists

Chapter 3 - Work of Fishery Scientists

Retinal ganglion cells, a crucial component of the central nervous system, are often affected by irreversible visual impairment due to various conditions, including trauma, tumors, ischemia, and glaucoma. Studies have shown that the optic nerve crush model and glaucoma model are commonly used to study retinal ganglion cell injury. While these models differ in their mechanisms, both ultimately result in retinal ganglion cell injury. With advancements in high-throughput technologies, techniques such as microarray analysis, RNA sequencing, and single-cell RNA sequencing have been widely applied to characterize the transcriptomic profiles of retinal ganglion cell injury, revealing underlying molecular mechanisms. This review focuses on optic nerve crush and glaucoma models, elucidating the mechanisms of optic nerve injury and neuron degeneration induced by glaucoma through single-cell transcriptomics, transcriptome analysis, and chip analysis. Research using the optic nerve crush model has shown that different retinal ganglion cell subtypes exhibit varying survival and regenerative capacities following injury. Single-cell RNA sequencing has identified multiple genes associated with retinal ganglion cell protection and regeneration, such as Gal , Ucn , and Anxa2 . In glaucoma models, high-throughput sequencing has revealed transcriptomic changes in retinal ganglion cells under elevated intraocular pressure, identifying genes related to immune response, oxidative stress, and apoptosis. These genes are significantly upregulated early after optic nerve injury and may play key roles in neuroprotection and axon regeneration. Additionally, CRISPR-Cas9 screening and ATAC-seq analysis have identified key transcription factors that regulate retinal ganglion cell survival and axon regeneration, offering new potential targets for neurorepair strategies in glaucoma. In summary, single-cell transcriptomic technologies provide unprecedented insights into the molecular mechanisms underlying optic nerve injury, aiding in the identification of novel therapeutic targets. Future researchers should integrate advanced single-cell sequencing with multi-omics approaches to investigate cell-specific responses in retinal ganglion cell injury and regeneration. Furthermore, computational models and systems biology methods could help predict molecular pathways interactions, providing valuable guidance for clinical research on optic nerve regeneration and repair.

Author response: A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity

Genomic and transcriptomic analysis of the Whirling disease-resistant Gunnison River Rainbow Trout.

To explore the molecular mechanisms of the Litopenaeus vannamei response to infection by Photobacterium damselae, reveal its immune response and energetic metabolic effect, and provide a valuable genetic data source for the scientific prevention and control of Vibrio infection, transcriptomic analysis, RT-qPCR, and physiological and biochemical tests were conducted. The results showed that the expression of key genes involved in lipid and carbohydrate transport, such as apolipoprotein and TPS, was upregulated after pathogenic infection, which brought the accumulation of triacylglycerol and trehalose into the hemolymph. Additionally, the pathogenic infection selectively triggered an immune response in infected L. vannamei, activating certain immune pathways, such as the serpins and MAPK pathways. The pathogenic infection suppressed the activity of phenoloxidase (PO), and the prophenoloxidase (PPO) cascade responses were suppressed by the invasive bacteria. This paper will help us understand the energetic metabolism, immune response, and activation of the immune recognition response after pathogenic infection by P. damselae, and it lays a theoretical foundation for the biological prevention and control of P. damselae infection.

Molecular analyses of the gill symbiosis of the bathymodiolin mussel Gigantidas platifrons.

Single-cell sequencing (SCS) has revolutionized the life sciences by enabling high-resolution analysis of individual cell heterogeneity at the genomic, transcriptomic, and epigenomic levels—effectively overcoming the limitations of traditional bulk sequencing. Leveraging next-generation sequencing technologies, SCS provides high-resolution insights into cellular diversity, particularly within complex systems such as tumors. This review outlines the principles, methodologies, and platforms of SCS, with an emphasis on single-cell transcriptome, genome, and epigenome sequencing techniques. We highlight recent advances in the application of SCS for characterizing the tumor immune microenvironment, including immune cell heterogeneity, tumor–stroma interactions, and treatment therapeutic responses profiling. Key challenges, such as technical biases, data integration, and clinical translation, are discussed along with emerging opportunities in precision oncology and immunotherapy. This review aims to serve as a comprehensive resource for researchers applying SCS in tumor biology and related fields.

Single-cell and spatial transcriptomics have diverted researchers' attention from the multicellular level to the single-cell level and spatial information. Single-cell transcriptomes provide insights into the transcriptome at the single-cell level, whereas spatial transcriptomes help preserve spatial information. Although these two omics technologies are helpful and mature, further research is needed to ensure their widespread applicability in plant studies. Reviewing recent research on plant single-cell or spatial transcriptomics, we compared the different experimental methods used in various plants. The limitations and challenges are clear for both single-cell and spatial transcriptomic analyses, such as the lack of applicability, spatial information, or high resolution. Subsequently, we put forth further applications, such as cross-species analysis of roots at the single-cell level and the idea that single-cell transcriptome analysis needs to be combined with other omics analyses to achieve superiority over individual omics analyses. Overall, the results of this review suggest that combining single-cell transcriptomics, spatial transcriptomics, and spatial element distribution can provide a promising research direction, particularly for plant research.

Data exploitation, acquired by medium‐frequency omnidirectional multibeam sonar, enables original studies in fisheries research but is seldom used despite the fact that such equipment is found on most fishing vessels and a number of research vessels. This is the only system for real‐time monitoring of fish schools within a horizontal omnidirectional plane about a vessel or a buoy. Between 1996 and 2001, we used two standard omnidirectional sonars and developed new methodologies for exploiting their specific acoustic data according to two main sampling schemes: ‘prospecting’, including fishing and searching operations, and ‘drifting’, as with an instrumental buoy system or aboard a stationary vessel. We present a complete method for continuous data acquisition from aboard a research vessel or commercial boat, with automated data extraction by picture analysis and a data processing method. Two cases of data analysis are considered: the first on a school‐by‐school basis, the ‘single school’ mode; the second taking into account all fish schools detected within the sonar sampling volume, the ‘cluster’ mode. Elementary sonar information is divided into five categories that comprise 24 survey and sonar parameters and 55 school, cluster and fisher behaviour descriptors. We review the applications of these categories and discuss perspectives for their use in fisheries science. If the sonar system enables the evaluation of the effects of vessel avoidance on fish school biomass assessment, no accurate abundance estimate can be provided by a simple sonar echo‐integration process. Omnidirectional sonar data can be used to analyse collectively the fish schools’ swimming speed, kinematics in terms of diffusion and migration, aggregative dynamics as school splitting and merging indexes, spatial characteristics of clusters such as school density, 2D structure and fisher behaviour. The prospect of integrating such data into a fish school database, including multifrequency echo‐sounder and lateral multibeam (3D) sonar data combined with a species recognition method, will enable a complete view of fish school behaviour and consequently the adoption of accurate fisheries management methods.

Dinucleotide–repeat DNA polymorphisms for rainbow trout, Oncorhynchus mykiss, are described. The potential applications of these markers in fisheries science are discussed.

Scientific assessments are an inextricable part of the management of any natural resource. However, placing too much emphasis on their validity without taking other factors into account can result in poor policy. This is especially true in fisheries science; policy makers who have relied too heavily on even the most sophisticated estimates of fish populations have seen disastrous losses and fishery closures. Explorations into the complex concerns of the international fishing community lead to applications in fisheries science and beyond.

Several methods for the visualization of genetic polymorphisms at the nucleic acid level have been developed. Such polymorphisms promise to be exceedingly numerous, and may form the basis for a number of scientific and practical applications in fisheries science. An expanded number of genetic markers should increase the statistical power of marker-based studies in population genetics, for example, improving the sensitivity of biological stock assessments and of studies assessing the impact of stocking programs upon natural populations. Utilization of such genomic markers could contribute to the rapid elaboration of piscine genomic maps and to development of markers for health- and production-related traits in fishes.