Identification of Mytilus edulis genetic regulators during early development

Bassim, Sleiman; Tanguy, Arnaud; Genard, Bertrand; Moraga, Dario; Tremblay, Réjean

doi:10.1016/j.gene.2014.08.042

Cited by 25 publications

(24 citation statements)

References 76 publications

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“…Gametes from different individual parents were used in a pool-cross design to produce one random larval family and was conducted at the Aquicole Station of Pointe-aux-Peres for the University of Quebec at Rimouski (UQAR), Quebec. Cultured larvae and postlarvae were reared in a flow-through system following the method described in Bassim et al (2014b). Larvae were fed continuously at 30,000 cells mlˉ¹ (Andersen et al, 2011) either with a cocktail of three different algae species (Isochrysis galbana, Pavlova lutherii, Nannochloropsis oculata) or with a unialgal diet (Nannochloropsis oculata).…”

Section: Larval Collection and Samplingmentioning

confidence: 99%

“…The ratio ω3/ω6 was calculated using the sum of molar proportions (%) of the polar lipid fraction. Total RNA was extracted following the protocol described in Bassim et al (2014b). Quality and quantity assessment of RNA was performed using the NanoDrop ND-8000 UV spectrophotometer designed for high throughput sample evaluation and RNA integrity checks were performed with the Bioanalyzer and the RNA6000 Nano assay kit (Agilent Technologies) designed for minimal sample consumption.…”

Section: Fatty Acids and Rna Quality Controlmentioning

confidence: 99%

“…In this study we extended our previous work (Bassim et al, 2014b) with a set of new Agilent 8x60K microarrays that target early larval stages, given a second dietary treatment condition. The mussel transcriptome was assembled after sequencing eggs (0 DPF), M. edulis trocophores (1 DPF), veligers (18 DPF), pediveligers (28 DPF), and juveniles (42 DPF) of both treatments.…”

Section: Transcriptome Analysismentioning

confidence: 99%

“…It was then used to construct 22 microarrays (n). Sequencing, assembly, and annotation procedures for the transcriptome of M. edulis and microarray chip construction were all covered in detail in Bassim et al (2014b).…”

Section: Transcriptome Analysismentioning

confidence: 99%

“…Despite their ecological and economical importance, bivalves functional genomics started to get more attention only in recent years, e.g., tissue-specific expression (Craft et al, 2010), RNAimediated gene-targeting (You et al, 2012), de novo genome annotation (Zhang et al, 2012;Gerdol et al, 2015), innate immune system discovery (Philipp et al, 2012), whole transcriptome genetic regulatory network inferences (Bassim et al, 2014b), and exploration of bivalve shell layers (Liao et al, 2015). Here we developed a statistical learning pipeline to regularize (reduce) the number of differentially expressed genes between stages of both dietary conditions.…”

Section: Introductionmentioning

confidence: 99%

See 4 more Smart Citations

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

Bassim

Chapman

Tanguy

et al. 2015

Comparative Biochemistry and Physiology Part D: Genomics and Pr

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Section: Larval Collection and Samplingmentioning

confidence: 99%

Section: Fatty Acids and Rna Quality Controlmentioning

confidence: 99%

Section: Transcriptome Analysismentioning

confidence: 99%

Section: Transcriptome Analysismentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

Bassim

Chapman

Tanguy

et al. 2015

Comparative Biochemistry and Physiology Part D: Genomics and Pr

Self Cite

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Networking Omic Data to Envisage Systems Biological Regulation

Kalapanulak

Saithong

Thammarongtham

2016

Advances in Biochemical Engineering/Biotechnology

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To understand how biological processes work, it is necessary to explore the systematic regulation governing the behaviour of the processes. Not only driving the normal behavior of organisms, the systematic regulation evidently underlies the temporal responses to surrounding environments (dynamics) and long-term phenotypic adaptation (evolution). The systematic regulation is, in effect, formulated from the regulatory components which collaboratively work together as a network. In the drive to decipher such a code of lives, a spectrum of technologies has continuously been developed in the post-genomic era. With current advances, high-throughput sequencing technologies are tremendously powerful for facilitating genomics and systems biology studies in the attempt to understand system regulation inside the cells. The ability to explore relevant regulatory components which infer transcriptional and signaling regulation, driving core cellular processes, is thus enhanced. This chapter reviews high-throughput sequencing technologies, including second and third generation sequencing technologies, which support the investigation of genomics and transcriptomics data. Utilization of this high-throughput data to form the virtual network of systems regulation is explained, particularly transcriptional regulatory networks. Analysis of the resulting regulatory networks could lead to an understanding of cellular systems regulation at the mechanistic and dynamics levels. The great contribution of the biological networking approach to envisage systems regulation is finally demonstrated by a broad range of examples.

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β integrin-like protein-mediated adhesion and its disturbances during cell cultivation of the mussel Mytilus trossulus

Maiorova

Odintsova

2015

Cell Tissue Res

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In this study, we focus on the specific contribution of β integrin-like protein to adhesion-mediated events in molluscan larval cells in culture that could not have been investigated within the whole animal. An analysis of disturbances to cell-substratum adhesion, caused by the integrin receptor inhibiting Arg-Gly-Asp-Ser (RGDS)-peptide, the Ca(2+)/Mg(2+)-chelators and the stress influence of freezing-thawing, reveals that all these factors resulted in the partial destruction of the integrin-extracellular matrix (ECM) interaction in culture and, in particular, changes in the distribution and relative abundance of β integrin-positive cells. The experiments, carried out on selected substrates, found that β integrin-positive cells demonstrate different affinities for the substrates. This finding further supports the assumption that epithelial differentiation in cultivated cells of larval Mytilus may be mediated by β integrin-like proteins via binding to laminin; direct binding to other components of the ECM could not be demonstrated. The mussel β integrin-positive cells are not involved in myogenic or neuronal differentiation on any of the substrates but part of them has tubulin-positive cilia, forming some epithelia-like structures. Our data indicate that β integrin-positive cells are able to proliferate in vitro which suggests that they could participate in renewing the digestive epithelium in larvae. The findings provide evidence that the distribution pattern of β integrin-like protein depends on the cell type and the factors influencing the adhesion.

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Identification of Mytilus edulis genetic regulators during early development

Cited by 25 publications

References 76 publications

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

Predicting growth and mortality of bivalve larvae using gene expression and supervised machine learning

Networking Omic Data to Envisage Systems Biological Regulation

β integrin-like protein-mediated adhesion and its disturbances during cell cultivation of the mussel Mytilus trossulus

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