TOFF, a database of traits of fish to promote advances in fish aquaculture

Functional traits can be valuable pieces of information for aquaculture research and management. Although fish traits have been the focus of an abundant research, trait datasets for these organisms are difficult to access and often unpractical to achieve meta-analyses without a time-consuming extensive review. Already available large-scale compilations include trait information for many fish species but not as detailed as required for aquaculture purpose. Here, we introduce the TOFF (i.e. Traits OF Fish), a database focusing on fish functional traits that aims at bringing together behavioral, morphological, phenological, and physiological traits always coupled to environmental measurement context into a single open-source access repository. TOFF hosts data from published field and experimental studies. Here, we release data for 228 traits for 174 species extracted from 165 publications and present a collaborative platform. We ultimately aim at providing an inclusive and accessible data resource to facilitate advances in aquaculture developmen

The negative charge of phosphorylated Y291 can promote clathrin-dependent endocytosis (CDE) of Fas upon FasL engagement.

<p>(A) Flow cytometry analysis of internalized FasL in SW480 cells overexpressing AcGFP or AcGFP-tagged Fas proteins (as indicated). The extent of FasL internalization was evaluated in cells that expressed equivalent levels of Fas by gating based on the expression level of AcGFP. Results are presented as intensity of internalized FasL in indicated cell lines at different expression levels of AcGFP-tagged Fas or control AcGFP. Note an increase in FasL internalization in SW480 cells overexpressing Y291D.AcGFP Fas. Means ± SEM from three independent experiments are shown (* <i>p</i> < 0.05, unpaired <i>t</i> test). (B) SW480 cells overexpressing indicated AcGFP-tagged Fas proteins were transiently transfected with AP180-C or control vector before subjected to the internalization assay and imaged by a spinning disk confocal microscope. Color-combined images are presented (green, Fas.AcGFP; red, crosslinked FasL; blue nucleus, scale bar = 10 μm, arrows indicate perinuclear region). Unmerged images showing each channel separately are provided in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s006" target="_blank">S5 Fig</a>. (C) SW480 cells expressing indicated AcGFP-tagged Fas proteins were pretreated with vehicle (DMSO) or 100 μM dynasore 30 min before FasL internalization assay and flow cytometry analysis. Fluorescence intensity of internalized FasL of cells with equivalent AcGFP or AcGFP-tagged Fas expression is presented (AcGFP intensity ~600). Means ± SEM are shown (* <i>p</i> < 0.05, paired <i>t</i> test). (D) Postnuclear supernatants from SW480 cells expressing V5-tagged LacZ or Fas proteins were subjected to coimmunoprecipitation with anti-Fas antibody, SDS-PAGE, and immunoblotting by indicated antibodies. Note that the low level of immunoprecipitated Fas from the LacZ sample could be visualized on the image from longer exposure. (E) SW480 cells expressing V5-tagged wild-type Fas protein pretreated with vehicle (DMSO) or 10 μM dynasore for 30 min were incubated with 10 ng/ml FasL crosslinked with M2 for 24 h before cell viability test by WST-1 assay. Percentage of viability compared to untreated control cells is shown. Means ± SEM from three independent experiments are presented (* <i>p</i> < 0.05, unpaired <i>t</i> test). Numerical values underlying the data summary displayed in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s001" target="_blank">S1 Data</a>.</p

Fas death domain pY is important for non-death functions of Fas.

<p>(A) SW480 cells were transiently transfected with control or Fas siRNA before BrdU incorporation analysis by using microplate-based method. Means ± SEM of three independent experiments are shown (*** <i>p</i> < 0.001, unpaired <i>t</i> test). Typical reduction of Fas level, based on immunoblot, is shown in the inset. (B) SW480 cells stably expressing control (LacZ) or indicated Fas proteins carrying silent mutations at the site targeted by an siRNA against Fas were transiently transfected with control or Fas siRNA for 48 h. They were subsequently synchronized to G1 phase by serum deprivation for 24 h and then treated with 1 ng/ml of sFasL for 30 min before analysing the increase in proliferation by BrdU incorporation measurement using microplate-based method. Means ± SEM of three independent experiments are shown (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, unpaired <i>t</i> test). (C) Fluorescently prelabeled SW480 cells were subjected to Boyden chamber migration assay using FluoroBlok membrane inserts. Cells were untreated or induced to migrate by 1 ng/ml sFasL for 2 h. Cells that migrated through the membrane were fixed, imaged, and counted. Data were presented as percentage of cells that migrated through the membrane compared to control cells (LacZ). Means ± SEM of three independent experiments are shown (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, unpaired <i>t</i> test). Numerical values underlying the data summary displayed in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s001" target="_blank">S1 Data</a>.</p

Fas death domain tyrosine phosphorylation is regulated by Src family kinases (SFKs), Src and Yes-1, and protein tyrosine phosphatase SHP-1.

<p>(A) SW480 cells expressing V5-tagged Fas protein were pretreated with vehicle (DMSO), 10 μM PP3 (negative control for PP2), or 10 μM PP2 for 30 min and then incubated with 10 ng/ml FasL crosslinked with M2 for 24 h before subjected to cell viability analysis using WST-1 assay. Percentages of viability compared to untreated control cells are shown as means ± SEM from three independent experiments (* <i>p</i> < 0.05, unpaired <i>t</i> test). (B) SW480 cells were synchronized to G1 phase by serum deprivation for 24 h and then treated with vehicle (DMSO), 10 μM PP3 (negative control for PP2), or 10 μM PP2 for 30 min, followed by 0.1 ng/ml of sFasL for 4 h before analyzing the proliferation by BrdU incorporation measurement using microplate-based method. Means ± SEM of three independent experiments are shown (* <i>p</i> < 0.05, unpaired <i>t</i> test). (C) SW480 cells were transiently transfected with control siRNA or siRNA against Src, Yes-1, or Src and Yes-1 for 72 h. Cell lysates were then collected and subjected to SDS-PAGE and immunoblotting with indicated antibodies. (D) SW480 cells expressing V5-tagged Fas protein were pretreated with vehicle (DMSO) or 50 μM PTPiI for 30 min and then incubated with 10 ng/ml FasL crosslinked with M2 for 24 h before being subjected to cell viability analysis using WST-1 assay. Percentage of viability compared to untreated control cells are shown as means ± SEM from three independent experiments (* <i>p</i> < 0.05, unpaired <i>t</i> test). (E) SW480 cells were synchronized to G1 phase by serum deprivation for 24 h and then treated with vehicle (DMSO) or 50 μM PTPiI for 30 min followed by 0.1 ng/ml of sFasL for 1 h before analyzing the proliferation by BrdU incorporation measurement using microplate-based method. Means ± SEM of three independent experiments are shown (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, unpaired <i>t</i> test). (F) SW480 cells were transfected with control vector or SHP-1 for 24 h and (G) with control siRNA or siRNA against SHP-1 for 48 h, then synchronized in G1 phase by serum deprivation for 24 h before treatment with 0.1 ng/ml FasL for 5 min. Cell lysates were then collected and subjected to SDS-PAGE and immunoblotting with indicated antibodies. The specificity of anti-pY232 and anti-pY291 Fas antibodies is demonstrated in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s012" target="_blank">S11 Fig</a>. Numerical values underlying the data summary displayed in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s001" target="_blank">S1 Data</a>.</p

The charge of the 291 residue is more important for the function of Fas than the size and details of the side chain.

<p>(A) SW480 cells stably expressing control protein (LacZ.V5), V5-tagged wild type Fas, or indicated Y232 phosphorylation mutants were treated with 50 ng/ml FasL crosslinked with 1 μg/ml M2 for 4 h and analysed by flow cytometry. Numbers indicated percentage of cells that underwent apoptosis, having subG1 DNA content due to DNA fragmentation. (B) Cells, as in (A), were treated with 20 ng/ml FasL crosslinked with 1 μg/ml M2 for 24h. The cell viability was measured by WST-1 assay and presented as percentage of cell viability compared to untreated control cells. Values represent means ± SEM from three independent experiments (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, unpaired <i>t</i> test). (C) SW480 cells stably expressing LacZ.V5, V5-tagged wild-type Fas, or indicated Y291 phosphorylation mutants were treated with 10 ng/ml FasL crosslinked with 1 μg/ml M2 for 4 h and analysed for apoptosis as in (A). (D) Cells, as in (C), were treated with 10 ng/ml FasL crosslinked with M2 for 24 h. The cell viability was measured by WST-1 assay as in (B). Values represent means ± SEM from three independent experiments (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, unpaired <i>t</i> test). (E) Cells, as in (C), were treated with 10 ng/ml FasL crosslinked with 1 μg/ml M2 or untreated (control) for 10 min. The lysates were collected and subjected to coimmunoprecipitation with anti-Fas antibody followed by SDS-PAGE and immunoblotting with indicated antibodies. Note that the low level of immunoprecipitated Fas from the LacZ sample could be visualized on an image from long exposure. Equivalent Fas expression levels in different stable cell lines are shown in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s005" target="_blank">S4 Fig</a>. Numerical values underlying the data summary displayed in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s001" target="_blank">S1 Data</a>.</p

A common cysteine substitution for tyrosine in the Fas death domain in primates and rodents and site-directed mutagenesis suggest that the tyrosine phosphorylation is dispensable for Fas apoptosis.

<p>(A) Partial sequence alignment of Fas death domain (helices 1 and 5 [<a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.ref009" target="_blank">9</a>]) in vertebrates. Positions 232 and 291 of human Fas are highlighted. Cysteine and alanine at the 291 position of Fas are boxed in red. (B) SW480 cells stably expressing control protein (LacZ.V5) or indicated Fas.V5 proteins were treated with 10 ng/ml FasL crosslinked with anti-FLAG (M2) for 24 h and subsequently subjected to DNA content analysis by flow cytometry. Numbers indicate percentage of cells that underwent apoptosis, having subG1 DNA content due to DNA fragmentation.</p

Introduction of negative charge to the 291 position results in a dominant inter- and intra-molecular anti-apoptotic capacity to Fas.

<p>(A) SW480 cells stably expressing V5-tagged LacZ and “dead-on” Fas proteins (wild-type, Y232F, or Y291F) were transiently transfected with AcGFP-tagged Y291D Fas for 24 h and subsequently treated with 8 ng/ml FasL+M2 or left untreated for 4 h. Cells were then stained with propidium iodide (PI) and analyzed by flow cytometry for cell death based on membrane permeability. The percentages of PI-positive cells (dead cells) due to FasL treatment in the Y291D.AcGFP-positive and Y291D.AcGFP-negative cell populations are compared after subtracting the percentage of spontaneous cell death in untreated cells. Note an increased resistance to FasL-induced cell death when Y291D.AcGFP Fas was introduced in cells that stably expressed “dead-on” Fas. Values represent means ± SEM from three independent experiments (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, unpaired <i>t</i> test, compared to Y291D.AcGFP negative cells). (B) SW480 cells stably expressing V5-tagged LacZ (control) and “dead-off” Fas Y291D were transiently transfected with AcGFP-tagged “dead-on” Fas (wild-type, Y232F, or Y291F) for 24 h and subsequently treated with 8 ng/ml FasL+M2 or left untreated for 4 h. Cells were then stained with PI and analyzed for cell death by flow cytometry. The percentages of PI-positive cells in the “dead-on” Fas.AcGFP-negative and -positive cell populations are compared after subtracting the percentage of spontaneous cell death in untreated cells. Values represent means ± SEM from three independent experiments (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, paired <i>t</i> test, compared to control cells). Note that compared to control cells, cells stably expressing “dead-off” Y291D Fas were more resistant to the increase in FasL-induced cell death brought about by the introduction of “dead-on” Fas.AcGFP species. (C) SW480 and (D) SW620 cells stably expressing AcGFP or AcGFP-tagged wild-type or indicated mutant Fas proteins were left untreated or treated with indicated concentration of FasL crosslinked with M2 for 24 h and subjected to viability measurement by WST-1 assay. Cell viability is presented as percentage compared to untreated control cells. The presence of Y—>D mutations completely inhibited FasL-induced cell death. Values represent means ± SEM from three independent experiments (* <i>p</i> < 0.05, ** <i>p</i> < 0.01, *** <i>p</i> < 0.001, unpaired <i>t</i> test). (E) A diagram depicting different states of Fas, with respect to its ability to transmit an apoptotic signal, as affected by its death domain phosphorylation. Examples of possible dominant-negative scenarios are given. Numerical values underlying the data summary displayed in this figure can be found in <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.1002401#pbio.1002401.s001" target="_blank">S1 Data</a>.</p

Toll-like receptor 3 downregulation is an escape mechanism from apoptosis during hepatocarcinogenesis

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