Deep RNA sequencing of the skeletal muscle transcriptome in swimming fish

Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swim-flume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15-17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (>500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an up-regulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids

Deep RNA Sequencing of the Skeletal Muscle Transcriptome in Swimming Fish

Deep RNA sequencing (RNA-seq) was performed to provide an in-depth view of the transcriptome of red and white skeletal muscle of exercised and non-exercised rainbow trout (Oncorhynchus mykiss) with the specific objective to identify expressed genes and quantify the transcriptomic effects of swimming-induced exercise. Pubertal autumn-spawning seawater-raised female rainbow trout were rested (n = 10) or swum (n = 10) for 1176 km at 0.75 body-lengths per second in a 6,000-L swimflume under reproductive conditions for 40 days. Red and white muscle RNA of exercised and non-exercised fish (4 lanes) was sequenced and resulted in 15–17 million reads per lane that, after de novo assembly, yielded 149,159 red and 118,572 white muscle contigs. Most contigs were annotated using an iterative homology search strategy against salmonid ESTs, the zebrafish Danio rerio genome and general Metazoan genes. When selecting for large contigs (.500 nucleotides), a number of novel rainbow trout gene sequences were identified in this study: 1,085 and 1,228 novel gene sequences for red and white muscle, respectively, which included a number of important molecules for skeletal muscle function. Transcriptomic analysis revealed that sustained swimming increased transcriptional activity in skeletal muscle and specifically an upregulation of genes involved in muscle growth and developmental processes in white muscle. The unique collection of transcripts will contribute to our understanding of red and white muscle physiology, specifically during the long-term reproductive migration of salmonids.Fil: Palstra, Arjan P.. Universidad de Barcelona. Facultad de Biología; España;Fil: Beltran, Sergi. Universitat de Barcelona. Centres Cientifics i Tecnològics. Unitat de Bioinformàtica; España;Fil: Burgerhout, Erik. Leiden University. Institute of Biology. Molecular Cell Biology; Países Bajos; ZF-screens; Países Bajos;Fil: Brittijn, Sebastiaan A.. Leiden University. Institute of Biology. Molecular Cell Biology; Países Bajos; ZF-screens; Países Bajos;Fil: Magnoni, Leonardo Julián. Universidad de Barcelona. Facultad de Biología; España; Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico La Plata. Instituto de Investigaciones Biotecnológicas - Instituto Tecnológico Chascomús. Instituto de Investigaciones Biotecnológicas (sede Chascomús); Argentina;Fil: Henkel, Christiaan V.. ZF-screens; Países Bajos;Fil: Jansen, Hans J.. ZF-screens; Países Bajos;Fil: Van Den Thillart, Guido E. E. J. M.. Leiden University. Institute of Biology. Molecular Cell Biology; Países Bajos; ZF-screens; Países Bajos;Fil: Spaink, Herman P.. Leiden University. Institute of Biology. Molecular Cell Biology; Países Bajos; ZF-screens; Países Bajos;Fil: Planas, Josep V.. Universidad de Barcelona. Facultad de Biologia; España

Dramatic effect of pop-up satellite tags on eel swimming

The journey of the European eel to the spawning area in the Sargasso Sea is still a mystery. Several trials have been carried out to follow migrating eels with pop-up satellite tags (PSATs), without much success. As eels are very efficient swimmers, tags likely interfere with their high swimming efficiency. Here we report a more than twofold increase in swimming cost caused by a regular small satellite tag. The impact was determined at a range of swimming speeds with and without tag in a 2-m swimming tunnel. These results help to explain why the previous use of PSATs to identify spawning sites in the Sargasso Sea was thus far unsuccessful

The human pathogen Mycobacterium tuberculosis and the fish pathogen Mycobacterium marinum trigger a core set of late innate immune response genes in zebrafish larvae

Funding: H.J.J., S.J.R., A.O., M.I.W., C.V.H., P.I.R., N.T.-K. and R.P.D. received funding from the Innovative Medicines Initiative Joint Undertaking under grant agreement n◦ 115337, resources of which are composed of financial contribution from the European Union’s Seventh Framework Program (FP7/2007-2013) and EFPIA companies’ in kind contribution. M.C.H., T.H.M.O. and H.P.S. were supported by a grant from the Innovative Medicines Initiative 2 Joint Undertaking (IMI2 JU) under the RespiriTB project (Grant No. 853903). The authors declare that this study received funding from ZF-Screens B.V., where several authors were employed.Zebrafish is a natural host of various Mycobacterium species and a surrogate model organism for tuberculosis research. Mycobacterium marinum is evolutionarily one of the closest non-tuberculous species related to M. tuberculosis and shares the majority of virulence genes. Although zebrafish is not a natural host of the human pathogen, we have previously demonstrated successful robotic infection of zebrafish embryos with M. tuberculosis and performed drug treatment of the infected larvae. In the present study, we examined for how long M. tuberculosis can be propagated in zebrafish larvae and tested a time series of infected larvae to study the transcriptional response via Illumina RNA deep sequencing (RNAseq). Bacterial aggregates carrying fluorescently labeled M. tuberculosis could be detected up to 9 days post-infection. The infected larvae showed a clear and specific transcriptional immune response with a high similarity to the inflammatory response of zebrafish larvae infected with the surrogate species M. marinum. We conclude that M. tuberculosis can be propagated in zebrafish larvae for at least one week after infection and provide further evidence that M. marinum is a good surrogate model for M. tuberculosis. The generated extensive transcriptome data sets will be of great use to add translational value to zebrafish as a model for infection of tuberculosis using the M. marinum infection system. In addition, we identify new marker genes such as dusp8 and CD180 that are induced by M. tuberculosis infection in zebrafish and in human macrophages at later stages of infection that can be further investigated.Peer reviewe

Establishing Zebrafish as a Novel Exercise Model: Swimming Economy, Swimming-Enhanced Growth and Muscle Growth Marker Gene Expression

Zebrafish has been largely accepted as a vertebrate multidisciplinary model but its usefulness as a model for exercise physiology has been hampered by the scarce knowledge on its swimming economy, optimal swimming speeds and cost of transport. Therefore, we have performed individual and group-wise swimming experiments to quantify swimming economy and to demonstrate the exercise effects on growth in adult zebrafish

First artificial hybrid of the eel species <it>Anguilla australis </it>and <it>Anguilla anguilla</it>

<p>Abstract</p> <p>Background</p> <p>Studies on artificial hybridization of different <it>Anguilla </it>species were conducted recently, i.e. female <it>A. australis </it>with male <it>A. dieffenbachii</it>, and female <it>A. japonica </it>with male <it>A. anguilla</it>. The existence of these artificial hybrids was however not demonstrated by independent genetic methods. Two species - <it>A. anguilla </it>and <it>A. australis </it>- that are phylogenetically close but have different sexual maturation times (12-25 weeks and 6-8 weeks, respectively), were expected to produce favourable hybrids for reproduction studies.</p> <p>Results</p> <p>A modification of the protocol for the reproduction of <it>Anguilla japonica </it>was used to produce eight-day <it>Anguilla australis </it>larvae, with a success rate of 71.4%. Thus ten out of 14 females produced eggs that could be fertilized, and three batches resulted in mass hatching. Hybrid larvae from female <it>A. australis </it>x male <it>A. Anguilla </it>survived for up to seven days post fertilization (dpf). The early development of the hybrid showed typical characteristics of <it>A. anguilla </it>tail pigmentation at 50 hours post fertilization (hpf), indicating expression of genes derived from the father.</p> <p>Conclusions</p> <p>In this paper we describe the first production of hybrid larvae from male <it>A. anguilla </it>and female <it>A. australis </it>and their survival for up to 7 dpf. A species-specific nucleotide difference in the 18 S rDNA gene confirmed that genes from both <it>A. australis </it>and <it>A. anguilla </it>were present in the hybrids. The developmental stages of the hybrid eel embryos and larvae are described using high resolution images. Video footage also indicated a heart beat in 5-dpf larva.</p

Establishing Zebrafish as a Novel Exercise Model: Swimming Economy, Swimming-enhanced Growth and Muscle Growth Marker Gene Expression

Zebrafish has been largely accepted as a vertebrate multidisciplinary model but its usefulness as a model for exercise physiology has been hampered by the scarce knowledge on its swimming economy, optimal swimming speeds and cost of transport. Therefore, we have performed individual and group-wise swimming experiments to quantify swimming economy and to demonstrate the exercise effects on growth in adult zebrafish