Article
Cell Biology
Martin A. Estermann, Craig A. Smith
Summary: Gonadal sex differentiation in vertebrates involves the fate of a common group of progenitor cells. In birds and egg-laying vertebrates, estrogen plays a central role in ovarian development. The expression of PAX2 in undifferentiated supporting cells is downregulated during gonadal sex differentiation.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2022)
Article
Biotechnology & Applied Microbiology
Ellen M. Weise, Mallory Van Wyngaarden, Cornelia Den Heyer, Joanna Mills Flemming, Tony Kess, Anthony L. Einfeldt, Jonathan A. D. Fisher, Reina Ditta, Guillaume Pare, Daniel E. Ruzzante
Summary: The ability to identify sex is crucial in population biology. In Atlantic halibut, external morphological differences are not significant, making phenotypic sex identification impossible. A SNP panel was developed with 4000 SNPs evenly distributed in the genome, with 176 SNPs selected for genetic identification of male and female individuals. This genomic sex identification allows for non-lethal determination and validation, serving as a resource for fisheries management and stock monitoring.
MARINE BIOTECHNOLOGY
(2023)
Review
Endocrinology & Metabolism
Hanhua Cheng, Rongjia Zhou
Summary: Significant progress has been made in the study of swamp eels' biology since their medicinal value was discovered 440 years ago. They are now considered an important model animal for sexual development research, with implications in economy and pharmaceuticals. Studies on their genomic history have revealed chromosome fission/fusion events and the intriguing natural intersex differentiation, while the identification of progenitors of germline stem cells has provided new insights into sex reversal. This review highlights the advances made in the field and presents unanswered questions for future investigations in vertebrate sexual development using this new model.
TRENDS IN ENDOCRINOLOGY AND METABOLISM
(2022)
Article
Biochemistry & Molecular Biology
Andrew J. Jasonowicz, Anna Simeon, Margot Zahm, Cedric Cabau, Christophe Klopp, Celine Roques, Carole Iampietro, Jerome Lluch, Cecile Donnadieu, Hugues Parrinello, Daniel P. Drinan, Lorenz Hauser, Yann Guiguen, Josep Planas
Summary: This study reports the first generation of a high-quality chromosome-level assembly of the Pacific halibut genome, providing an essential resource for future studies on population structure, evolutionary history, and responses to environmental and anthropogenic influences in Pacific halibut.
MOLECULAR ECOLOGY RESOURCES
(2022)
Article
Fisheries
Robson Campos Silva, Daniella Maria Coelho Britto, Conceicao Aparecida Santos, Samuel Cunha Oliveira Giordani, Marcelo Mattos Pedreira
Summary: The hormone 17 alpha methyltestosterone (MT) is commonly used in tilapia farming to obtain a male mono-sex population for higher profitability. This study found that the sex reversal treatment with MT could be shortened by 5 days, reducing the release of synthetic hormone and its harmful effects on other aquatic organisms.
Article
Environmental Sciences
A-L Ferchaud, E. Normandeau, C. Babin, K. Praebel, Rasmus Hedeholm, C. Audet, J. Morgan, M. Treble, W. Walkusz, P. Sirois, L. Bernatchez
Summary: This study found that Greenland Halibut appear to be panmictic throughout the Northwest Atlantic, with significant genetic differentiation between the Gulf of Saint Lawrence and the remainder of the region. Environmental factors explained 51% of the genetic differentiation between the two stocks, with variables like temperature and oxygen involved. This highlights the importance of functional adaptive divergence to different environmental conditions.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Immunology
Shi-Ji Li, Zhi-Wen Cai, Hong-Fu Yang, Xu-Dong Tang, Xiao Fang, Le Qiu, Fei Wang, Xu-Lin Chen
Summary: The study identified key miRNA-mRNA axes in potential blood-to-tissue interactions at early burn stage, suggesting plasma exosome-derived miRNAs may impact on the alteration patterns of gene expressions in a burn wound.
JOURNAL OF INFLAMMATION RESEARCH
(2021)
Article
Fisheries
Xiaoxia Weng, Yangru Xu, Xingyan Dong, Xuan Luo, Weiwei You, Caihuan Ke, Mingyi Cai
Summary: Based on re-sequencing data, candidate sexually dimorphic loci were identified in small abalone, and two sex-specific markers were successfully developed, providing important clues and tools for studying the sex determination mechanism in small abalone.
Article
Virology
Vladimir Loukachov, Karel A. van Dort, Louis Jansen, Henk W. Reesink, Neeltje A. Kootstra
Summary: A novel Hepatitis B Virus (HBV) encoded miRNA, HBV-miR-6, was identified and validated in liver tissue from chronic hepatitis B (CHB) patients. Its expression was correlated with hepatic HBV-DNA and plasma HBsAg levels, suggesting a potential role in viral excretion or particle formation.
Article
Genetics & Heredity
Han Zhao, Lu Zhang, Qiang Li, Zhongmeng Zhao, Yuanliang Duan, Zhipeng Huang, Hongyu Ke, Chao Liu, Huadong Li, Lu Liu, Jun Du, Zhen Wei, Chengyan Mou, Jian Zhou
Summary: In this study, the expression profiles of miRNA and mRNA were analyzed to explore their regulatory roles in the gonadal maturation stage of Leiocassis longirostris, a commercially important fish species. The study identified differentially expressed miRNAs and genes that are involved in gonad development and sex determination, providing valuable genomic information for selective breeding purposes.
FUNCTIONAL & INTEGRATIVE GENOMICS
(2022)
Article
Multidisciplinary Sciences
Arpad Bozsodi, Beata Scholtz, Gergo Papp, Zoltan Sapi, Adam Biczo, Peter Pal Varga, Aron Lazary
Summary: Using RNA sequencing and bioinformatics analysis, we identified significantly dysregulated miRNAs and their target genes in sacral chordoma. We predicted regulatory networks and pathways that are affected by aberrant miRNA expression, which might play a role in the self-renewal of chordoma stem cells and provide potential targets for anti-chordoma therapies.
Article
Fisheries
Senyuan Li, Liqiong Xu, Yuhong Shi, Jiong Chen
Summary: By using the 2b-RAD-seq method, the study identified the sex determination mechanism of ayu fish, isolated male-specific scaffolds, and supported an XX/XY sex determination system in ayu. The multiplex-PCR assay based on male-specific markers was developed for molecular sexing in ayu culture.
Article
Urology & Nephrology
Vuthy Ea, Anne Bergougnoux, Pascal Philibert, Nadege Servant-Fauconnet, Alice Faure, Jean Breaud, Laura Gaspari, Charles Sultan, Francoise Paris, Nicolas Kalfa
Summary: The study evaluated the clinical utility of NGS for patients with hypospadias and found that even mild cases can benefit from advanced sequencing techniques. Some variants of unknown significance (VUSs) were identified, but most cases remain unexplained.
Article
Fisheries
Tone-Kari K. ostbye, Nardos T. Woldemariam, Camilla E. Lundberg, Gerd M. Berge, Bente Ruyter, Rune Andreassen
Summary: This study identified significant differences in hepatic fatty acid composition among different family groups of Atlantic salmon, influenced by experimental conditions such as diet and family selection. Small RNA sequencing revealed 12 differentially expressed microRNAs associated with family groups and diets. In silico predictions indicated potential targets related to lipid metabolism, and further experimental validation is required to fully understand the regulatory role of differentially expressed microRNAs in hepatic lipid metabolism.
JOURNAL OF FISH BIOLOGY
(2021)
Article
Genetics & Heredity
Yudong Shen, Qishuai Wang, Weimin Wang, Yanhe Li
Summary: This study explores the genetic sex determination system of P. clarkii and develops an efficient sex-specific marker using whole-genome resequencing data. The identified marker shows a high sex discrimination rate and can be used for sex control breeding of P. clarkii and potentially for investigating sex determination and molecular markers in other crustacean species based on next-generation sequencing data.
FRONTIERS IN GENETICS
(2022)
Article
Nutrition & Dietetics
Chandrasekar Selvam, Philip Antony J. Prabhu, Esmail Lutfi, Trygve Sigholt, Birgitta Norberg, Grete Baeverfjord, Grethe Rosenlund, Bente Ruyter, Nini H. Sissener
Summary: Increasing levels of EPA + DHA in the diet can enhance trace mineral levels in Atlantic salmon, particularly during mechanical delousing stress and at harvest size. High EPA + DHA diets also significantly increase the expression of antimicrobial peptides in fish, while decreasing transferrin receptor expression levels.
BRITISH JOURNAL OF NUTRITION
(2022)
Article
Genetics & Heredity
Rolf Brudvik Edvardsen, Ola Wallerman, Tomasz Furmanek, Lene Kleppe, Patric Jern, Andreas Wallberg, Erik Kjaerner-Semb, Stig Maehle, Sara Karolina Olausson, Elisabeth Sundstroem, Torstein Harboe, Ragnfrid Mangor-Jensen, Margareth Mogster, Prescilla Perrichon, Birgitta Norberg, Carl-Johan Rubin
Summary: This study reveals the sex chromosomes and sex determination mechanism of Atlantic halibut through genome sequencing analysis. The research found that male halibut have higher gene activity of the gonadal somatic cell derived factor gene, which is due to the enhanced function of mobile DNA sequences on the sex chromosomes. In addition, the study also found that the behavior of halibut chromosomes is similar to sex chromosomes, which may contribute to the rapid turnover of genetic sex determination systems in fish.
Article
Genetics & Heredity
Betty M. N. Furulund, Bard O. Karlsen, Igor Babiak, Peik Haugen, Steinar D. Johansen
Summary: Group I introns in myxomycetes, a distinct protist phylum, exhibit dynamic structures and complex inheritance patterns. The consensus secondary structure reveals a conserved core and RNA sequence complexity in the peripheral regions. These introns possess various structural organizations, including twintron organization and direct repeat arrays. Phylogenetic analyses indicate both vertical and horizontal transfers. The evolutionary history involves the insertion of mobile-type introns, degradation of homing endonuclease genes, and ultimately complete loss of the introns.
Article
Environmental Sciences
Ioannis Konstantinidis, Joana P. Firmino, Alberto Ruiz, Bruno Inarra, David San Martin, Alicia Estevez, Jorge M. O. Fernandes, Enric Gisbert
Summary: This study evaluated the replacement of dietary protein sources with Brewer's spent dry yeast (SDY) in gilthead sea bream and found that SDY had a modulatory effect on the host's immunity, oxygen carrier capacity, steroidogenesis, metabolism, and digestion. The results indicate that SDY can be considered as both a sustainable raw material and a functional ingredient.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Ecology
Omid Jafari, Mehrshad Zeinalabedini, Diego Robledo, Jorge M. O. Fernandes, Ali-Akbar Hedayati, Babak Arefnezhad
Summary: Understanding the population structure and genetic diversity of wild populations is crucial for stock management and conservation. This study investigated the population structure and genetic diversity of common carp in the Southern Caspian basin using genotyping-by-sequencing. The results showed low differentiation between populations and high within population variation. Frequent migration events were observed, but each population still had distinct genetic profiles. However, high inbreeding and low heterozygosity were detected, indicating the need for additional conservation efforts.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Biology
Omid Jafari, Mansour Ebrahimi, Seyed Ali-Akbar Hedayati, Mehrshad Zeinalabedini, Hadi Poorbagher, Maryam Nasrolahpourmoghadam, Jorge M. O. Fernandes
Summary: This study used data mining algorithms to investigate the population classification of common carp in the southern Caspian basin and identified the most important characteristic for distinguishing between Iranian and farmed common carp. The results showed that machine learning methods had higher prediction rates, with head height on eye area being the best marker. The study contributes to the understanding of domestication syndrome in common carp and provides a novel approach for automated detection of farmed fish.
Article
Genetics & Heredity
Eugenia Boulygina, Fedor Sharko, Maksim Cheprasov, Maria Gladysheva-Azgari, Natalia Slobodova, Svetlana Tsygankova, Sergey Rastorguev, Lena Grigorieva, Martina Kopp, Jorge M. O. Fernandes, Gavril Novgorodov, Gennady Boeskorov, Albert Protopopov, Woo-Suk Hwang, Alexei Tikhonov, Artem Nedoluzhko
Summary: This study demonstrates the maternal philopatry of the Northeastern Eurasian U. arctos population during the several thousand years of the Holocene through ancient DNA analysis and comparative phylogenetic analysis.
Article
Immunology
Saima Rehman, Adnan H. Gora, Shubham Varshney, Jorge Dias, Pal A. Olsvik, Jorge M. O. Fernandes, Sylvia Brugman, Viswanath Kiron
Summary: The study reveals the effects of soybean meal-induced inflammation model on the behavior of zebrafish, including reduced locomotor activity, induced developmental defects, and increased oxygen demand. Furthermore, beta-glucan can counteract the negative effects of a soybean diet on behavior and phenotype.
FRONTIERS IN IMMUNOLOGY
(2022)
Review
Biology
Marco Albano, Claudio D'Iglio, Nunziacarla Spano, Jorge Manuel de Oliveira Fernandes, Serena Savoca, Gioele Capillo
Summary: The distribution of Lampriformes fish is important for understanding their contribution to the ecological balance in marine areas. This review aims to describe their biological and ecological characteristics, as well as compile existing literature on their distribution. Lampriformes are of high biological and ecological importance, but their knowledge is limited due to their low commercial value and rarity. The Mediterranean Sea is home to four families of Lampriformes, with a total of six species. This review serves as a baseline to increase knowledge of these rare and important species and encourages further studies in this area.
Article
Biochemical Research Methods
Fedor Sharko, Golam Rbbani, Prabhugouda Siriyappagouder, Joost A. M. Raeymaekers, Jorge Galindo-Villegas, Artem Nedoluzhko, Jorge M. O. Fernandes
Summary: In this study, the CircPrime web platform was developed, which provides a user-friendly solution for circRNA identification by designing specific circular RNA primers. It works in collaboration with popular bioinformatic predictors of circRNAs.
BMC BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Golam Rbbani, Artem Nedoluzhko, Prabhugouda Siriyappagouder, Fedor Sharko, Jorge Galindo-Villegas, Joost A. M. Raeymaekers, Rajesh Joshi, Jorge M. O. Fernandes
Summary: This study used an integrative omics approach to identify myogenic circular RNAs (circRNAs) in Nile tilapia, and found 1947 mRNAs, 9 miRNAs, and 4 circRNAs that were differentially expressed between fast- and slow-growing individuals. These miRNAs can regulate myogenic genes and have binding sites for the novel circRNA circMef2c. The study suggests that circ-Mef2c may interact with three miRNAs and 65 differentially expressed mRNAs to form multiple competing endogenous RNA networks that regulate growth, providing new insights into the role of circRNAs in muscle growth regulation in teleosts.
Article
Biochemistry & Molecular Biology
Alba Ferre, Francois Chauvigne, Anna Vlasova, Birgitta Norberg, Luca Bargelloni, Roderic Guigo, Roderick Nigel Finn, Joan Cerda
Summary: The aquaporin-mediated oocyte hydration plays a crucial role in the evolution of pelagic eggs and the success of marine teleosts. However, the molecular regulatory mechanisms controlling this process have not been fully understood. Through analyzing over 400 piscine genomes, researchers discovered a teleost-specific aquaporin-1 cluster (TSA1C) consisting of aqp1aa-aqp1ab2-aqp1ab1 genes. Evolutionary analysis revealed that marine species with highly hydrated pelagic eggs retained at least one downstream paralog, and a significant portion of modern marine teleosts retained both aqp1ab-type channels and co-evolved regulatory proteins for membrane trafficking. The selective advantages of these mechanisms were demonstrated to accelerate hydration and facilitate geodispersal in oceanic currents.
MOLECULAR BIOLOGY AND EVOLUTION
(2023)
Article
Multidisciplinary Sciences
Ioannis Konstantinidis, Pal Saetrom, Jorge M. O. Fernandes
Summary: This study presents a genome-wide epigenetic dataset that quantifies DNA hydroxymethylation in Nile tilapia with distinct growth performance. They found several growth-related genes that are differentially hydroxymethylated, especially within gene bodies and promoters. This dataset can be analyzed in various contexts and compared to other epigenomic datasets in the future.
Article
Genetics & Heredity
Likith R. Pinninti, Marius F. Maurstad, Siv N. K. Hoff, Torstein Kristensen, Leslie R. Noble, Sissel Jentoft, Jorge M. O. Fernandes
Summary: The complete mitochondrial genome of the Atlantic spiny lumpsucker (Eumicrotremus spinosus) was sequenced using PacBio Sequel II HiFi platform. It has a length of 19,281 bp and includes 13 protein-coding sequences, 22 tRNA genes, 2 rRNA genes, a control region with D-loop (2383 bp), and a duplicate control region (1133 bp). Phylogenetic analysis indicated that E. spinosus is closely related to Siberian lumpsucker (E. asperrimus). The mitogenome of spiny lumpsucker is valuable for population genomics and systematic studies of Cyclopteridae, Liparidae, and Cottidae.
MITOCHONDRIAL DNA PART B-RESOURCES
(2023)
Article
Fisheries
Giacomo Zaccone, Alessio Alesci, Doaa M. M. Mokhtar, Marialuisa Aragona, Maria Cristina Guerrera, Gioele Capillo, Marco Albano, Jorge de Oliveira Fernandes, Viswanath Kiron, Ramy K. A. Sayed, Marwa M. M. Hussein, Patrizia Lo Cascio, Michal Kuciel, Krystyna Zuwala, Antonino Germana, Jose Manuel Icardo, Eugenia Rita Lauriano
Summary: The recognition and elimination of invading pathogens are essential for host survival. Macrophages, which function similarly to vertebrate macrophages, play a crucial role in host protection in all multicellular organisms. CD14 is a pattern responsible for bacterial recognition found on the surface of macrophages. These cells store antimicrobial molecules and display polarization states similar to mammalian macrophages. The present study reports the presence of various cell markers, including CD14, in the intestinal macrophages of catfish and bonytongue, providing insights into the in vivo function of macrophages in fish.
