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<export-example>
  <doc>
    <id>615</id>
    <completedYear>2012</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst>69</pageFirst>
    <pageLast>96</pageLast>
    <pageNumber/>
    <edition/>
    <issue>6</issue>
    <volume>2012</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>1</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations</title>
    <abstract language="eng">Tardigrades have unique stress-adaptations that allow them to survive extremes of cold, heat, radiation and vacuum.&#13;
To study this, encoded protein clusters and pathways from an ongoing transcriptome study on the tardigrade Milnesium tardigradum were analyzed using bioinformatics tools and compared to expressed sequence tags (ESTs) from Hypsibius dujardini, revealing major pathways involved in resistance against extreme environmental conditions.&#13;
ESTs are available on the Tardigrade Workbench along with software and databank updates. Our analysis reveals that RNA stability motifs for M. tardigradum are different from typical motifs known from higher animals. M. tardigradum and H. dujardini protein clusters and conserved domains imply metabolic storage pathways for glycogen, glycolipids and specific secondary metabolism as well as stress response pathways (including heat shock proteins, bmh2, and specific repair pathways). Redox-, DNA-, stress- and protein protection pathways complement specific repair capabilities to achieve the strong robustness of M. tardigradum.&#13;
These pathways are partly conserved in other animals and their manipulation could boost stress adaptation even in human cells. However, the unique combination of resistance and repair pathways make tardigrades and M. tardigradum in particular so highly stress resistant.</abstract>
    <parentTitle language="eng">Bioinformatics and Biology Insights</parentTitle>
    <identifier type="issn">1177-9322</identifier>
    <identifier type="urn">urn:nbn:de:kobv:526-opus4-6153</identifier>
    <enrichment key="SourceTitle">Förster et al. Transcriptome Analysis in Tardigrade Species Reveals Specific Molecular Pathways for Stress Adaptations. Bioinformatics and Biology Insights 2012:6 69-96</enrichment>
    <enrichment key="DOI_VoR">https://doi.org/10.4137/BBI.S9150</enrichment>
    <licence>Das Dokument ist urheberrechtlich geschützt.</licence>
    <author>Frank Förster</author>
    <author>Daniela Beisser</author>
    <author>Markus Grohme</author>
    <author>Chunguang Liang</author>
    <author>Brahim Mali</author>
    <author>Alexander Matthias Siegl</author>
    <author>Julia C. Engelmann</author>
    <author>Alexander Shkumatov</author>
    <author>Elham Schokraie</author>
    <author>Tobias Müller</author>
    <author>Martina Schnölzer</author>
    <author>Ralph O. Schill</author>
    <author>Marcus Frohme</author>
    <author>Thomas Dandekar</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>RNA</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>expressed sequence tag</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>cluster</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>protein family</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>adaptation</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>tardigrada</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>transcriptome</value>
    </subject>
    <collection role="ddc" number="570">Biowissenschaften; Biologie</collection>
    <collection role="institutes" number="">Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014)</collection>
    <collection role="open_access" number="">open_access</collection>
    <collection role="green_open_access" number="1">Gold Open Access</collection>
    <thesisPublisher>Technische Hochschule Wildau</thesisPublisher>
    <file>https://opus4.kobv.de/opus4-th-wildau/files/615/3147-BBI-Transcriptome-Analysis-in-Tardigrade-Species-Reveals-Specific-Molecula.pdf</file>
  </doc>
  <doc>
    <id>646</id>
    <completedYear>2009</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>10</pageNumber>
    <edition/>
    <issue>469</issue>
    <volume>10</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>1</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades</title>
    <abstract language="eng">Background&#13;
Tardigrades represent an animal phylum with extraordinary resistance to environmental stress.&#13;
&#13;
Results&#13;
To gain insights into their stress-specific adaptation potential, major clusters of related and similar proteins are identified, as well as specific functional clusters delineated comparing all tardigrades and individual species (Milnesium tardigradum, Hypsibius dujardini, Echiniscus testudo, Tulinus stephaniae, Richtersius coronifer) and functional elements in tardigrade mRNAs are analysed. We find that 39.3% of the total sequences clustered in 58 clusters of more than 20 proteins. Among these are ten tardigrade specific as well as a number of stress-specific protein clusters. Tardigrade-specific functional adaptations include strong protein, DNA- and redox protection, maintenance and protein recycling. Specific regulatory elements regulate tardigrade mRNA stability such as lox P DICE elements whereas 14 other RNA elements of higher eukaryotes are not found. Further features of tardigrade specific adaption are rapidly identified by sequence and/or pattern search on the web-tool tardigrade analyzer http://waterbear.bioapps.biozentrum.uni-wuerzburg.de. The work-bench offers nucleotide pattern analysis for promotor and regulatory element detection (tardigrade specific; nrdb) as well as rapid COG search for function assignments including species-specific repositories of all analysed data.&#13;
&#13;
Conclusion&#13;
Different protein clusters and regulatory elements implicated in tardigrade stress adaptations are analysed including unpublished tardigrade sequences.</abstract>
    <parentTitle language="eng">BMC Genomics</parentTitle>
    <identifier type="issn">1471-2164</identifier>
    <identifier type="urn">urn:nbn:de:kobv:526-opus4-6461</identifier>
    <enrichment key="SourceTitle">F. Förster et al. Tardigrade workbench: comparing stress-related proteins, sequence-similar and functional protein clusters as well as RNA elements in tardigrades. BMC Genomics 2009, 10:469</enrichment>
    <enrichment key="DOI_VoR">https://doi.org/10.1186/1471-2164-10-469</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 2.0 Generic</licence>
    <author>Frank Förster</author>
    <author>Chunguang Liang</author>
    <author>Alexander Shkumatov</author>
    <author>Daniela Beisser</author>
    <author>Julia C. Engelmann</author>
    <author>Martina Schnölzer</author>
    <author>Marcus Frohme</author>
    <author>Tobias Müller</author>
    <author>Ralph O. Schill</author>
    <author>Thomas Dandekar</author>
    <collection role="ddc" number="570">Biowissenschaften; Biologie</collection>
    <collection role="institutes" number="">Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014)</collection>
    <collection role="open_access" number="">open_access</collection>
    <collection role="green_open_access" number="1">Gold Open Access</collection>
    <thesisPublisher>Technische Hochschule Wildau</thesisPublisher>
    <file>https://opus4.kobv.de/opus4-th-wildau/files/646/2F1471-2164-10-469.pdf</file>
  </doc>
  <doc>
    <id>614</id>
    <completedYear>2012</completedYear>
    <publishedYear/>
    <thesisYearAccepted/>
    <language>eng</language>
    <pageFirst/>
    <pageLast/>
    <pageNumber>13</pageNumber>
    <edition/>
    <issue>72</issue>
    <volume>6</volume>
    <type>article</type>
    <publisherName/>
    <publisherPlace/>
    <creatingCorporation/>
    <contributingCorporation/>
    <belongsToBibliography>1</belongsToBibliography>
    <completedDate>--</completedDate>
    <publishedDate>--</publishedDate>
    <thesisDateAccepted>--</thesisDateAccepted>
    <title language="eng">Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum</title>
    <abstract language="eng">Tardigrades are multicellular organisms, resistant to extreme environmental changes such as heat, drought, radiation and freezing. They outlast these conditions in an inactive form (tun) to escape damage to cellular structures and cell death. Tardigrades are apparently able to prevent or repair such damage and are therefore a crucial model organism for stress tolerance. Cultures of the tardigrade Milnesium tardigradum were dehydrated by removing the surrounding water to induce tun formation. During this process and the subsequent rehydration, metabolites were measured in a time series by GC-MS. Additionally expressed sequence tags are available, especially libraries generated from the active and inactive state. The aim of this integrated analysis is to trace changes in tardigrade metabolism and identify pathways responsible for their extreme resistance against physical stress.</abstract>
    <parentTitle language="eng">BMC Systems Biology</parentTitle>
    <identifier type="issn">1752-0509</identifier>
    <identifier type="urn">urn:nbn:de:kobv:526-opus4-6146</identifier>
    <enrichment key="SourceTitle">Beisser et al.:Integrated pathway modules using time-course metabolic profiles and EST data from Milnesium tardigradum. BMC Systems Biology 2012 6:72.</enrichment>
    <enrichment key="DOI_VoR">https://doi.org/10.1186/1752-0509-6-72</enrichment>
    <licence>Creative Commons - CC BY - Namensnennung 2.0 Generic</licence>
    <author>Daniela Beisser</author>
    <author>Markus Grohme</author>
    <author>Joachim Kopka</author>
    <author>Marcus Frohme</author>
    <author>Ralph O. Schill</author>
    <author>Steffen Hengherr</author>
    <author>Thomas Dandekar</author>
    <author>Gunnar W. Klau</author>
    <author>Marcus Dittrich</author>
    <author>Tobias Müller</author>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>integrated network analysis</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>functional module</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metabolic profile</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>metabolic pathway</value>
    </subject>
    <subject>
      <language>eng</language>
      <type>uncontrolled</type>
      <value>trend test</value>
    </subject>
    <collection role="ddc" number="570">Biowissenschaften; Biologie</collection>
    <collection role="institutes" number="">Fachbereich Ingenieurwesen / Wirtschaftsingenieurwesen (bis 8/2014)</collection>
    <collection role="open_access" number="">open_access</collection>
    <collection role="green_open_access" number="1">Gold Open Access</collection>
    <thesisPublisher>Technische Hochschule Wildau</thesisPublisher>
    <file>https://opus4.kobv.de/opus4-th-wildau/files/614/2F1752-0509-6-72.pdf</file>
  </doc>
</export-example>
