Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state
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{"title"=>"Comparative proteome analysis of Milnesium tardigradum in early embryonic state versus adults in active and anhydrobiotic state", "type"=>"journal", "authors"=>[{"first_name"=>"Elham", "last_name"=>"Schokraie", "scopus_author_id"=>"35111863600"}, {"first_name"=>"Uwe", "last_name"=>"Warnken", "scopus_author_id"=>"6602291311"}, {"first_name"=>"Agnes", "last_name"=>"Hotz-Wagenblatt", "scopus_author_id"=>"6603016293"}, {"first_name"=>"Markus A.", "last_name"=>"Grohme", "scopus_author_id"=>"26648317100"}, {"first_name"=>"Steffen", "last_name"=>"Hengherr", "scopus_author_id"=>"23135121200"}, {"first_name"=>"Frank", "last_name"=>"Förster", "scopus_author_id"=>"57193112993"}, {"first_name"=>"Ralph O.", "last_name"=>"Schill", "scopus_author_id"=>"7003652533"}, {"first_name"=>"Marcus", "last_name"=>"Frohme", "scopus_author_id"=>"6602134282"}, {"first_name"=>"Thomas", "last_name"=>"Dandekar", "scopus_author_id"=>"7006832936"}, {"first_name"=>"Martina", "last_name"=>"Schnölzer", "scopus_author_id"=>"7004187726"}], "year"=>2012, "source"=>"PLoS ONE", "identifiers"=>{"scopus"=>"2-s2.0-84866904169", "sgr"=>"84866904169", "issn"=>"19326203", "doi"=>"10.1371/journal.pone.0045682", "pmid"=>"23029181", "isbn"=>"1932-6203 (Electronic)\\r1932-6203 (Linking)", "pui"=>"365755698"}, "id"=>"22b2b3a5-5ddf-3f2e-9797-b5672be2366f", "abstract"=>"Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.", "link"=>"http://www.mendeley.com/research/comparative-proteome-analysis-milnesium-tardigradum-early-embryonic-state-versus-adults-active-anhyd", "reader_count"=>43, "reader_count_by_academic_status"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>5, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>8}, "reader_count_by_user_role"=>{"Unspecified"=>1, "Professor > Associate Professor"=>6, "Student > Doctoral Student"=>5, "Researcher"=>9, "Student > Ph. D. Student"=>8, "Student > Postgraduate"=>1, "Student > Master"=>4, "Other"=>1, "Student > Bachelor"=>8}, "reader_count_by_subject_area"=>{"Engineering"=>4, "Unspecified"=>2, "Environmental Science"=>1, "Biochemistry, Genetics and Molecular Biology"=>7, "Agricultural and Biological Sciences"=>25, "Medicine and Dentistry"=>1, "Pharmacology, Toxicology and Pharmaceutical Science"=>1, "Physics and Astronomy"=>1, "Computer Science"=>1}, "reader_count_by_subdiscipline"=>{"Engineering"=>{"Engineering"=>4}, "Medicine and Dentistry"=>{"Medicine and Dentistry"=>1}, "Physics and Astronomy"=>{"Physics and Astronomy"=>1}, "Agricultural and Biological Sciences"=>{"Agricultural and Biological Sciences"=>25}, "Computer Science"=>{"Computer Science"=>1}, "Biochemistry, Genetics and Molecular Biology"=>{"Biochemistry, Genetics and Molecular Biology"=>7}, "Unspecified"=>{"Unspecified"=>2}, "Environmental Science"=>{"Environmental Science"=>1}, "Pharmacology, Toxicology and Pharmaceutical Science"=>{"Pharmacology, Toxicology and Pharmaceutical Science"=>1}}, "reader_count_by_country"=>{"Belgium"=>1, "Serbia and Montenegro"=>1, "United Kingdom"=>1, "Germany"=>6}, "group_count"=>2}

Scopus | Further Information

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Figshare

  • {"files"=>["https://ndownloader.figshare.com/files/568708"], "description"=>"<p>Tardigrades in different states were homogenized directly in lysis buffer. Total protein extracts of tardigrades in early embryonic state and adult tardigrades in active and tun state were separated by 1D gel electrophoresis. After staining gel lanes were sliced and proteins in-gel digested with trypsin. MS/MS data obtained by nanoLC-ESI-MS/MS analysis were searched against the tardigrade specific database. The database was developed by translating EST sequences of <i>M. tardigradum</i>, which were obtained by 454 sequencing. Identified proteins with annotation were classified in different functional groups using the Blast2GO program. Identified proteins without annotation were analyzed with the DomainSweep program to search for specific protein domains.</p>", "links"=>[], "tags"=>["workflow", "proteome"], "article_id"=>239198, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.g003", "stats"=>{"downloads"=>4, "page_views"=>53, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_The_experimental_workflow_to_analyze_the_proteome_of_Milnesium_tardigradum_/239198", "title"=>"The experimental workflow to analyze the proteome of <i>Milnesium tardigradum</i>.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-27 02:33:18"}
  • {"files"=>["https://ndownloader.figshare.com/files/568487"], "description"=>"<p>The Venn diagram illustrates the number of protein identifications in EES, AS and TS. A total of 1301 proteins were found in all three states, 472 proteins are found only in EES (a) and 680 proteins are found only in adult tardigrades in TS and AS (f). Proteins which are non-overlapping (a, b, c) or partially overlapping (d, e, f) between the different states are analyzed using Blast2GO program to determine the involved biological processes. The ten major biological processes for non-overlapping proteins are listed in 2a-2c and for partially overlapping proteins in 2d–2f.</p>", "links"=>[], "tags"=>["proteome", "proteins"], "article_id"=>238971, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.g002", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_proteome_analysis_of_proteins_identified_in_different_states_/238971", "title"=>"Comparative proteome analysis of proteins identified in different states.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-27 02:29:31"}
  • {"files"=>["https://ndownloader.figshare.com/files/303259", "https://ndownloader.figshare.com/files/303812", "https://ndownloader.figshare.com/files/304297", "https://ndownloader.figshare.com/files/304904", "https://ndownloader.figshare.com/files/304975", "https://ndownloader.figshare.com/files/304991"], "description"=>"<div><p>Tardigrades have fascinated researchers for more than 300 years because of their extraordinary capability to undergo cryptobiosis and survive extreme environmental conditions. However, the survival mechanisms of tardigrades are still poorly understood mainly due to the absence of detailed knowledge about the proteome and genome of these organisms. Our study was intended to provide a basis for the functional characterization of expressed proteins in different states of tardigrades. High-throughput, high-accuracy proteomics in combination with a newly developed tardigrade specific protein database resulted in the identification of more than 3000 proteins in three different states: early embryonic state and adult animals in active and anhydrobiotic state. This comprehensive proteome resource includes protein families such as chaperones, antioxidants, ribosomal proteins, cytoskeletal proteins, transporters, protein channels, nutrient reservoirs, and developmental proteins. A comparative analysis of protein families in the different states was performed by calculating the exponentially modified protein abundance index which classifies proteins in major and minor components. This is the first step to analyzing the proteins involved in early embryonic development, and furthermore proteins which might play an important role in the transition into the anhydrobiotic state.</p> </div>", "links"=>[], "tags"=>["comparative", "proteome", "embryonic", "adults", "anhydrobiotic"], "article_id"=>119797, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>["https://dx.doi.org/10.1371/journal.pone.0045682.s001", "https://dx.doi.org/10.1371/journal.pone.0045682.s002", "https://dx.doi.org/10.1371/journal.pone.0045682.s003", "https://dx.doi.org/10.1371/journal.pone.0045682.s004", "https://dx.doi.org/10.1371/journal.pone.0045682.s005", "https://dx.doi.org/10.1371/journal.pone.0045682.s006"], "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/Comparative_proteome_analysis_of_Milnesium_tardigradum_in_early_embryonic_state_versus_adults_in_active_and_anhydrobiotic_state/119797", "title"=>"Comparative proteome analysis of <em>Milnesium tardigradum</em> in early embryonic state <em>versus</em> adults in active and anhydrobiotic state", "pos_in_sequence"=>0, "defined_type"=>4, "published_date"=>"2012-09-27 02:43:17"}
  • {"files"=>["https://ndownloader.figshare.com/files/568848"], "description"=>"<p>Total emPAI is the sum of emPAI of each protein member. Large lipid transfer protein (LLTP) superfamily belong to major components in all three states. This protein family is highly expressed in EES compared to adults. Semi-quantitative analysis of proteins contributing to the structural integrity of ribosome indicates a significant up-regulation of ribosomal proteins in EES. In contrast proteins involved in cytoskeletal-, muscle- and vitellin membrane structure are not highly abundant at this state compared to adults in AS and TS. Proteins with antioxidant activity such as GSTs are approximately 3 fold higher in adults compared to EES. In contrast Cu-Zn SODs are upregulated in EES.</p>", "links"=>[], "tags"=>["Biochemistry"], "article_id"=>239334, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.g004", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Comparative_expression_analysis_of_selected_proteins_/239334", "title"=>"Comparative expression analysis of selected proteins.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-27 02:35:34"}
  • {"files"=>["https://ndownloader.figshare.com/files/568981"], "description"=>"<p>Comparing the annotated proteins in AS and TS we found the same two major functional groups, protein members of structural constituent of cytoskeleton/muscle and protein members of large lipid transporter family. The contig description is indicated with asterisk, in case we found putative candidates in DomainSweep analysis.</p>", "links"=>[], "tags"=>["components", "tardigrades", "tun", "53", "proteins", "49"], "article_id"=>239458, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.t003", "stats"=>{"downloads"=>1, "page_views"=>10, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Major_protein_components_in_adult_tardigrades_in_active_and_tun_state_53_proteins_were_found_as_major_components_in_adult_tardigrades_in_AS_and_49_in_TS_/239458", "title"=>"Major protein components in adult tardigrades in active and tun state. 53 proteins were found as major components in adult tardigrades in AS and 49 in TS.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-27 02:37:38"}
  • {"files"=>["https://ndownloader.figshare.com/files/569018"], "description"=>"<p>38 proteins were found as major components in EES, 10 of which belong to the large lipid transporter superfamily. Other members are the heat shock protein family, structural constituent of ribosome and cytoskeleton. In addition, 20 proteins are without annotation. The contig description is indicated with asterisk, in case we found putative candidates by DomainSweep analysis. For one contig DomainSweep analysis delivered a significant candidate (indicated with #). Proteins with annotation are ordered by their biological function.</p>", "links"=>[], "tags"=>["components", "embryonic"], "article_id"=>239503, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.t002", "stats"=>{"downloads"=>1, "page_views"=>14, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Major_protein_components_in_early_embryonic_state_EES_/239503", "title"=>"Major protein components in early embryonic state (EES).", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-27 02:38:23"}
  • {"files"=>["https://ndownloader.figshare.com/files/568221"], "description"=>"<p>Lane 1: Rainbow molecular weight marker. Lane 2: Protein extract of adult tardigrades in active state (AS). Lane 3: Protein extract of adult tardigrades in tun state (TS). Lane 4: Protein extract of tardigrades in early embryonic state (EES). Bottom. SEM-images of <i>M. tardigradum</i> in the corresponding states.</p>", "links"=>[], "tags"=>["lysates", "tardigrades", "states", "one-dimensional", "polyacrylamide", "gel"], "article_id"=>238702, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.g001", "stats"=>{"downloads"=>0, "page_views"=>2, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Separation_of_protein_lysates_of_tardigrades_in_three_different_states_by_one_dimensional_polyacrylamide_gel_electrophoresis_/238702", "title"=>"Separation of protein lysates of tardigrades in three different states by one-dimensional polyacrylamide gel electrophoresis.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2012-09-27 02:25:02"}
  • {"files"=>["https://ndownloader.figshare.com/files/568927"], "description"=>"<p>BP: biological process; MF: molecular function.</p>", "links"=>[], "tags"=>["proteins", "processes"], "article_id"=>239416, "categories"=>["Biochemistry"], "users"=>["Elham Schokraie", "Uwe Warnken", "Agnes Hotz-Wagenblatt", "Markus A. Grohme", "Steffen Hengherr", "Frank Förster", "Ralph O. Schill", "Marcus Frohme", "Thomas Dandekar", "Martina Schnölzer"], "doi"=>"https://dx.doi.org/10.1371/journal.pone.0045682.t001", "stats"=>{"downloads"=>1, "page_views"=>4, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Semi_quantitative_analysis_of_selected_proteins_associated_with_diverse_processes_such_as_response_to_stimulus_protection_and_development_/239416", "title"=>"Semi-quantitative analysis of selected proteins associated with diverse processes such as response to stimulus, protection and development.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2012-09-27 02:36:56"}

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Relative Metric

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