Reproducibility and Consistency of Proteomic Experiments on Natural Populations of a Non-Model Aquatic Insect
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{"title"=>"Reproducibility and consistency of proteomic experiments on natural populations of a non-model aquatic insect", "type"=>"journal", "authors"=>[{"first_name"=>"Amparo", "last_name"=>"Hidalgo-Galiana", "scopus_author_id"=>"36141783000"}, {"first_name"=>"Marta", "last_name"=>"Monge", "scopus_author_id"=>"7005668455"}, {"first_name"=>"David G.", "last_name"=>"Biron", "scopus_author_id"=>"7004185238"}, {"first_name"=>"Francesc", "last_name"=>"Canals", "scopus_author_id"=>"6603024975"}, {"first_name"=>"Ignacio", "last_name"=>"Ribera", "scopus_author_id"=>"7004248462"}, {"first_name"=>"Alexandra", "last_name"=>"Cieslak", "scopus_author_id"=>"56528084300"}], "year"=>2014, "source"=>"PLoS ONE", "identifiers"=>{"isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pmid"=>"25133588", "doi"=>"10.1371/journal.pone.0104734", "pui"=>"373786915", "issn"=>"19326203", "sgr"=>"84929138354", "scopus"=>"2-s2.0-84929138354"}, "id"=>"792d4910-1c59-3d2b-8c8f-04c5bb7354d0", "abstract"=>"Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (Agabus ramblae) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2-3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.", "link"=>"http://www.mendeley.com/research/reproducibility-consistency-proteomic-experiments-natural-populations-nonmodel-aquatic-insect", "reader_count"=>19, "reader_count_by_academic_status"=>{"Librarian"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>4, "Other"=>2, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_user_role"=>{"Librarian"=>1, "Researcher"=>5, "Student > Ph. D. Student"=>4, "Other"=>2, "Student > Master"=>2, "Student > Bachelor"=>2, "Lecturer > Senior Lecturer"=>1, "Professor"=>1, "Professor > Associate Professor"=>1}, "reader_count_by_subject_area"=>{"Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>2, "Agricultural and Biological Sciences"=>13, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>13}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>2}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}}, "reader_count_by_country"=>{"Brazil"=>1, "Spain"=>2}, "group_count"=>0}

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/1641111"], "description"=>"<p>The analysis includes the proteins with significantly different expression for each replicated sample, as measured with ANOVA at <i>P</i><0.01 (see <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104734#pone-0104734-t003\" target=\"_blank\">Tables 3</a>, <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104734#pone-0104734-t004\" target=\"_blank\">4</a>). r1 to r3, replicated samples.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143616, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.g004", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Cluster_analysis_of_the_number_of_significantly_differently_expressed_protein_spots_/1143616", "title"=>"Cluster analysis of the number of significantly differently expressed protein spots.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641112"], "description"=>"<p>All PS, overall number of protein spots with significant differences; PS, number of protein spots with significant differences in the pairwise comparison between treatments; fold >1.5, number of protein spots with fold differences above 1.5.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143617, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.t003", "stats"=>{"downloads"=>1, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Number_of_protein_spots_with_a_significantly_different_level_of_expression_/1143617", "title"=>"Number of protein spots with a significantly different level of expression.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641113"], "description"=>"<p>ANOVA, different groupings of the internal standards for the ANOVA test (see main text). Values, fold change.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143618, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.t002", "stats"=>{"downloads"=>10, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparison_between_the_five_internal_standards_within_each_experiment_population_to_estimate_technical_variation_/1143618", "title"=>"Comparison between the five internal standards within each experiment (population) to estimate technical variation.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641114"], "description"=>"<p>Protein yield obtained from each replicated sample.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143619, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.t001", "stats"=>{"downloads"=>4, "page_views"=>5, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Protein_yield_obtained_from_each_replicated_sample_/1143619", "title"=>"Protein yield obtained from each replicated sample.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641115"], "description"=>"<p>Included are the amino-acid sequence of the identified fragment with its isoelectric point (IP), molecular weight (MW) and the score of the search in the database, the identification, and the NCBI accession number and organism of the best match.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143620, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.t005", "stats"=>{"downloads"=>7, "page_views"=>8, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Exemplary_identified_proteins_/1143620", "title"=>"Exemplary identified proteins.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641116"], "description"=>"<p>See <a href=\"http://www.plosone.org/article/info:doi/10.1371/journal.pone.0104734#pone-0104734-t003\" target=\"_blank\">Table 3</a> for the number of protein spots with significant differences between treatments at each <i>P</i> level.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143621, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.t004", "stats"=>{"downloads"=>0, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Results_of_the_ANOVA_comparison_between_populations_/1143621", "title"=>"Results of the ANOVA comparison between populations.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641117", "https://ndownloader.figshare.com/files/1641118", "https://ndownloader.figshare.com/files/1641119", "https://ndownloader.figshare.com/files/1641120"], "description"=>"<div><p>Population proteomics has a great potential to address evolutionary and ecological questions, but its use in wild populations of non-model organisms is hampered by uncontrolled sources of variation. Here we compare the response to temperature extremes of two geographically distant populations of a diving beetle species (<i>Agabus ramblae</i>) using 2-D DIGE. After one week of acclimation in the laboratory under standard conditions, a third of the specimens of each population were placed at either 4 or 27°C for 12 h, with another third left as a control. We then compared the protein expression level of three replicated samples of 2–3 specimens for each treatment. Within each population, variation between replicated samples of the same treatment was always lower than variation between treatments, except for some control samples that retained a wider range of expression levels. The two populations had a similar response, without significant differences in the number of protein spots over- or under-expressed in the pairwise comparisons between treatments. We identified exemplary proteins among those differently expressed between treatments, which proved to be proteins known to be related to thermal response or stress. Overall, our results indicate that specimens collected in the wild are suitable for proteomic analyses, as the additional sources of variation were not enough to mask the consistency and reproducibility of the response to the temperature treatments.</p></div>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143622, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0104734.s001", "https://dx.doi.org/10.1371/journal.pone.0104734.s002", "https://dx.doi.org/10.1371/journal.pone.0104734.s003", "https://dx.doi.org/10.1371/journal.pone.0104734.s004"], "stats"=>{"downloads"=>10, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Reproducibility_and_Consistency_of_Proteomic_Experiments_on_Natural_Populations_of_a_Non_Model_Aquatic_Insect_/1143622", "title"=>"Reproducibility and Consistency of Proteomic Experiments on Natural Populations of a Non-Model Aquatic Insect", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641108"], "description"=>"<p>a) Spanish population, 4°C treatment, Cy5; b) Spanish population, 4°C treatment, Cy3; c) Spanish population, 27°C treatment, Cy3 and d) Moroccan population, 27°C treatment, Cy3. Differences between a) and b) correspond to variation between replicated samples; a) and c) different treatments within the same population; and c) and d) same treatment between different populations. pI, isoelectric point; MW molecular weight (Kilo Daltons).</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143613, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.g001", "stats"=>{"downloads"=>0, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Example_images_of_2D_DIGE_gels_representing_populations_and_temperature_treatments_/1143613", "title"=>"Example images of 2D-DIGE gels representing populations and temperature treatments.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641109"], "description"=>"<p>Data reflect normalised protein spot volume. On the right of each graph the quantile box plot reflects the distribution of the variation, with mean (rhomboid) and median. Vertical axis, fold change.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143614, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.g002", "stats"=>{"downloads"=>2, "page_views"=>16, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_differences_between_the_three_replicated_samples_of_each_treatment_/1143614", "title"=>"Distribution of differences between the three replicated samples of each treatment.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-18 04:35:40"}
  • {"files"=>["https://ndownloader.figshare.com/files/1641110"], "description"=>"<p>On the right, distributions in a quantile box plot, including mean (rhomboid) and median. Vertical axis, fold change.</p>", "links"=>[], "tags"=>["pairwise comparisons", "control samples", "temperature extremes", "protein spots", "protein expression level", "temperature treatments", "specimen", "dige", "variation", "Agabus ramblae", "proteomic analyses", "response", "12 h", "beetle species", "Natural Populations", "expression levels", "Proteomic Experiments"], "article_id"=>1143615, "categories"=>["Biological Sciences", "Ecology"], "users"=>["Amparo Hidalgo-Galiana", "Marta Monge", "David G. Biron", "Francesc Canals", "Ignacio Ribera", "Alexandra Cieslak"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0104734.g003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Distribution_of_pairwise_differences_in_protein_spot_volume_between_temperature_treatments_in_each_population_/1143615", "title"=>"Distribution of pairwise differences in protein spot volume between temperature treatments in each population.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2014-08-18 04:35:40"}

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