http://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&feed=atom&action=historyTeam:Osaka/Project - Revision history2024-03-28T20:37:56ZRevision history for this page on the wikiMediaWiki 1.16.0http://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=272695&oldid=prevToshi: /* Radiation detection */2012-10-21T14:26:01Z<p><span class="autocomment">Radiation detection</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== SOS response ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== SOS response ====</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>[[File:<del class="diffchange diffchange-inline">SOS </del>response.png|left|sos responce|350px]]</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>[[File:<ins class="diffchange diffchange-inline">Sos </ins>response.png|left|sos responce|350px]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>When DNA is significantly damaged (e.g. by exposure to UV radiation or chemicals), several DNA damage-related proteins are synthesized quickly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>When DNA is significantly damaged (e.g. by exposure to UV radiation or chemicals), several DNA damage-related proteins are synthesized quickly.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This reaction to DNA damage is known as SOS response.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This reaction to DNA damage is known as SOS response.</p></div></td></tr>
</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=272689&oldid=prevToshi: /* The effects of ionizing radiation */2012-10-21T14:22:01Z<p><span class="autocomment">The effects of ionizing radiation</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Ionizing radiation <del class="diffchange diffchange-inline">causes atoms and molecules to become ionized or excited. These excitations and ionizations </del>can</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">When cells are exposed to </ins>Ionizing radiation<ins class="diffchange diffchange-inline">, it </ins>can produce <ins class="diffchange diffchange-inline">reactive oxygen and </ins>break chemical bonds<ins class="diffchange diffchange-inline">. To induce such kinds of DNA damages</ins>, <ins class="diffchange diffchange-inline">we used </ins>chemical <ins class="diffchange diffchange-inline">agents such as mitomycine C </ins>and <ins class="diffchange diffchange-inline">hydrogen peroxide</ins>. </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>produce <del class="diffchange diffchange-inline">free radicals, </del>break chemical bonds, <del class="diffchange diffchange-inline">and may produce new </del>chemical <del class="diffchange diffchange-inline">bonds </del>and <del class="diffchange diffchange-inline">cross-linkage between macromolecules</del>. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Mitomycin C'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Mitomycin C'''</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Hydrogen peroxide'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Hydrogen peroxide'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Hydrogen peroxide is known as a highly reactive compound. Therefore, when hydrogen peroxide is introduced into a cell, it breaks not only DNA molecules but also various substances in the cell, such as <del class="diffchange diffchange-inline">organelles</del>. This is contrasting to the fact that MitomycinC specifically breaks DNA molecules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Hydrogen peroxide is known as a highly reactive compound. Therefore, when hydrogen peroxide is introduced into a cell, it breaks not only DNA molecules but also various substances in the cell, such as <ins class="diffchange diffchange-inline">cell membrane, cytoplasm</ins>. This is contrasting to the fact that MitomycinC specifically breaks DNA molecules.</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td></tr>
</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=233888&oldid=prevToshi at 02:41, 27 September 20122012-09-27T02:41:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter needs some visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter needs some visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene (red), carrot has carotene (orange), and xanthophyll (yellow) is found in almost all plants.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene (red), carrot has carotene (orange), and xanthophyll (yellow) is found in almost all plants.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP (FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate (IPP) and dimethylallylpyrophosphate(DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP (FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate (IPP) and dimethylallylpyrophosphate (DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=233854&oldid=prevToshi at 02:41, 27 September 20122012-09-27T02:41:27Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Lycopene biosynthesis.jpg|280px|right]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Lycopene biosynthesis.jpg|280px|right]]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter needs some visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter needs some visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange), and xanthophyll(yellow) is found in almost all plants.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene (red), carrot has carotene (orange), and xanthophyll (yellow) is found in almost all plants.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP (FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate (IPP) and dimethylallylpyrophosphate(DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=233136&oldid=prevToshi at 02:27, 27 September 20122012-09-27T02:27:11Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further improved that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>.For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further improved that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>. For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
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</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=233098&oldid=prevToshi at 02:26, 27 September 20122012-09-27T02:26:25Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> </div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p> </div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further <del class="diffchange diffchange-inline">inproved </del>that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>.For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further <ins class="diffchange diffchange-inline">improved </ins>that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>.For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
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</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=197527&oldid=prevMol7cks: /* Radiation detection */2012-09-26T13:35:26Z<p><span class="autocomment">Radiation detection</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== SOS response ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== SOS response ====</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:SOS response.png|left|sos responce|350px]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:SOS response.png|left|sos responce|350px]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p><del class="diffchange diffchange-inline">If </del>DNA is significantly damaged (<del class="diffchange diffchange-inline">eg </del>by exposure to UV radiation or chemicals), <del class="diffchange diffchange-inline">synthesis of </del>several DNA damage-related proteins <del class="diffchange diffchange-inline">occurs </del>quickly.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p><ins class="diffchange diffchange-inline">When </ins>DNA is significantly damaged (<ins class="diffchange diffchange-inline">e.g. </ins>by exposure to UV radiation or chemicals), several DNA damage-related proteins <ins class="diffchange diffchange-inline">are synthesized </ins>quickly.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>This reaction to DNA damage is <del class="diffchange diffchange-inline">the </del>SOS response.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>This reaction to DNA damage is <ins class="diffchange diffchange-inline">known as </ins>SOS response.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>RecA <del class="diffchange diffchange-inline">is a 38 kilodalton </del><<del class="diffchange diffchange-inline">I</del>>Escherichia coli</<del class="diffchange diffchange-inline">I</del>> protein essential for <del class="diffchange diffchange-inline">the </del>repair and maintenance of DNA. RecA has multiple activities, all related to DNA repair. In the bacterial SOS response, it has a co-protease function in the autocatalytic cleavage of the LexA repressor and the λ repressor. <del class="diffchange diffchange-inline">LexA </del>is expressed constitutively and prevents expression of damage-related proteins by binding to SOS box as a repressor. RecA is activated by binding to single-stranded DNA, and the activated RecA then turns on LexA protease activity. Self-cleavage of LexA derepresses the expression of damage-related proteins enabling a response to be mounted. </p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>RecA <ins class="diffchange diffchange-inline">of </ins><<ins class="diffchange diffchange-inline">i</ins>>Escherichia coli</<ins class="diffchange diffchange-inline">i</ins>> <ins class="diffchange diffchange-inline">is a 38 kilodalton </ins>protein essential for repair and maintenance of DNA. RecA has multiple activities, all related to DNA repair. In the bacterial SOS response, it has a co-protease function in the autocatalytic cleavage of the LexA repressor and the λ repressor. <ins class="diffchange diffchange-inline">lexA gene </ins>is expressed constitutively and prevents expression of damage-related proteins by binding to <ins class="diffchange diffchange-inline">a </ins>SOS box as a repressor. RecA is activated by binding to single-stranded DNA, and the activated RecA then turns on LexA protease activity. Self-cleavage of LexA derepresses the expression of damage-related proteins enabling a response to be mounted. </p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>We decided to employ the promoter of the <del class="diffchange diffchange-inline">RecA </del>gene ([http://partsregistry.org/wiki/index.php?title=Part:BBa_J22106 BBa J22106]) to detect DNA damage. While RecA is an inducer of SOS genes, it itself is an SOS gene that is auto-induced upon DNA damage. Expression of genes downstream of this promoter is induced by DNA damage.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>We decided to employ the promoter of the <ins class="diffchange diffchange-inline">recA </ins>gene <ins class="diffchange diffchange-inline">of <i>D. radiodurans</i> </ins>([http://partsregistry.org/wiki/index.php?title=Part:BBa_J22106 BBa J22106]) to detect DNA damage. While RecA is an inducer of SOS genes, it itself is an SOS gene that is auto-induced upon DNA damage. Expression of genes downstream of this promoter is induced by DNA damage.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><br></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Lycopene biosynthesis ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Lycopene biosynthesis ====</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Lycopene biosynthesis.jpg|280px|right]]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Lycopene biosynthesis.jpg|280px|right]]</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter <del class="diffchange diffchange-inline">must have </del>some <del class="diffchange diffchange-inline">sort of </del>visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Our Bio-dosimeter <ins class="diffchange diffchange-inline">needs </ins>some visible output to alert users to radioactivity (detected as DNA damage). In a previous iGEM project, "colrcoli", we attempted to use <I>E.coli</I> as a paint tool. To that end, we examined biosynthesis of carotenoid pigments as a way of producing color. Here, we attempted to use biosynthesis of the carotenoid lycopene as a reporter for DNA damage.</p></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange)<del class="diffchange diffchange-inline">. Xanthophyll</del>(yellow) is found in almost all plants.</p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p>Carotenoid is a family of natural pigments. Many plants such as fruits and vegetables contain these pigments. For example, tomato has lycopene(red), carrot has carotene(orange)<ins class="diffchange diffchange-inline">, and xanthophyll</ins>(yellow) is found in almost all plants.</p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>Biosynthesis of carotenoid pigments starts from FPP(FARNESYL DIPHOSPHATE). FPP is formed from isopentenylpyrophosphate(IPP) and dimethylallylpyrophosphate(DMAPP), which can be biologically produced by two distinct pathways, the mevalonate and non-mevalonate pathways. In <i>E.coli</i>, FPP is formed through the non-mevalonate pathway. By the introduction of heterologous enzymatic genes colorless FPP is then converted to orange-red lycopene, which has a peak absorbance at 407nm that is easily measured. </p></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><p>As shown in the figure on the right, the heterologous enzymes CrtE, CrtB, CrtI were introduced into <i>E. coli</i> to complete the biosynthesis of lycopene. We used a lycopene biosynthetic gene cluster provided by 2009 Cambridge (<partinfo>K274100</partinfo>).<br></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del style="color: red; font-weight: bold; text-decoration: none;"></del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== References===</div></td></tr>
</table>Mol7ckshttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=197171&oldid=prevToshi at 13:25, 26 September 20122012-09-26T13:25:56Z<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Project Details==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>== Project Details==</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><p></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><p> <ins class="diffchange diffchange-inline"> </ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">====iGEM Osaka 2012 project description==== </del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further inproved that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>.For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>It is still sharp in our memory that, on March 11, 2011, the Great East Japan Earthquake struck off the East coast of Japan's main island and triggered a series of events that led to the nation wide nuclear crisis. Moved by that accident in iGEM 2011, we have built a synthetic biological dosimeter to detect the radiation. In this year we further inproved that "<b>Bio-dosimeter</b>". Our "<b>Bio-dosimeter</b>"consists of two points: <b>damage tolerance</b> and <b>radiation detection</b>. To introduce the tolerance to <i>E. coli</i>, we are trying to put in some radiation resistance genes from <i>Deinococcus radiodurans</i>.For the detection of the radiation, we are trying to connect the native DNA damage response system of <i>E. coli</i> to production of pigment lycopene as an optical reporter. Now, we are attempting to assess its tolerance to various types of DNA damage and to evaluate DNA damage detection more clearly.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div></p></div></td></tr>
</table>Toshihttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=197167&oldid=prevMol7cks: /* The effects of ionizing radiation */2012-09-26T13:25:50Z<p><span class="autocomment">The effects of ionizing radiation</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ionizing radiation causes atoms and molecules to become ionized or excited. These excitations and ionizations can</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ionizing radiation causes atoms and molecules to become ionized or excited. These excitations and ionizations can</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>produce free radicals, break chemical bonds, and produce new chemical bonds and cross-linkage between macromolecules. </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>produce free radicals, break chemical bonds, and <ins class="diffchange diffchange-inline">may </ins>produce new chemical bonds and cross-linkage between macromolecules. </div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Mitomycin C'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Mitomycin C'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The DNA-damaging agent mitomycin C is known to introduce interstrand cross-links into duplex DNA. Mitomycin C is reduced in cells and bonds with the specific base sequence. When the bonding mitomycin C is oxidized <del class="diffchange diffchange-inline">automatically</del>, reactive oxygen <del class="diffchange diffchange-inline">species </del>is produced and it breaks DNA chains near the bond site.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The DNA-damaging agent mitomycin C is known to introduce interstrand cross-links into duplex DNA. Mitomycin C is reduced in cells and bonds with the specific base sequence. When the bonding mitomycin C is oxidized <ins class="diffchange diffchange-inline">autonomically</ins>, <ins class="diffchange diffchange-inline">a </ins>reactive oxygen is produced and it breaks DNA chains near the bond site.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Hydrogen peroxide'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''Hydrogen peroxide'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Hydrogen peroxide is known <del class="diffchange diffchange-inline">to </del>highly reactive <del class="diffchange diffchange-inline">product</del>. Therefore, when hydrogen peroxide is <del class="diffchange diffchange-inline">added to the </del>cell, it breaks not only DNA molecules but also various substances in the cell, such as organelles. This is contrasting to the fact that MitomycinC specifically breaks DNA molecules.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Hydrogen peroxide is known <ins class="diffchange diffchange-inline">as a </ins>highly reactive <ins class="diffchange diffchange-inline">compound</ins>. Therefore, when hydrogen peroxide is <ins class="diffchange diffchange-inline">introduced into a </ins>cell, it breaks not only DNA molecules but also various substances in the cell, such as organelles. This is contrasting to the fact that MitomycinC specifically breaks DNA molecules.</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div> </div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>=== Radiation detection ===</div></td></tr>
</table>Mol7ckshttp://2012.igem.org/wiki/index.php?title=Team:Osaka/Project&diff=197011&oldid=prevMol7cks: /* Radiotolerance genes */2012-09-26T13:21:39Z<p><span class="autocomment">Radiotolerance genes</span></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Radiotolerance genes ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== Radiotolerance genes ====</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The </del><i>D.radiodurans</i> DNA repair system <del class="diffchange diffchange-inline">comprises </del>many unique proteins.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><i>D.radiodurans<ins class="diffchange diffchange-inline">'s</ins></i> DNA repair system <ins class="diffchange diffchange-inline">consist of </ins>many unique proteins.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:DNA repair system.jpg|500px|center|''D.radiodurans'']]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:DNA repair system.jpg|500px|center|''D.radiodurans'']]</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''PprI'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''PprI'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>PprI, which is unique to ''D. radiodurans'', is <del class="diffchange diffchange-inline">invoked by present data </del>as the most important protein for radiation <del class="diffchange diffchange-inline">response mechanism</del>.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>PprI, which is unique to ''D. radiodurans'', is <ins class="diffchange diffchange-inline">regarded </ins>as the most important protein for <ins class="diffchange diffchange-inline">the </ins>radiation <ins class="diffchange diffchange-inline">tolerance</ins>.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PprI can significantly and specifically induce the gene expression of recA and pprA and enhance the enzyme</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PprI can significantly and specifically induce the gene expression of recA and pprA and enhance the enzyme</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>activities of catalases. These results strongly suggest that PprI plays a crucial role in regulating multiple DNA repair and protection</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>activities of catalases. These results strongly suggest that PprI plays a crucial role in regulating multiple DNA repair and protection</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''PprA'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''PprA'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>A pleiotropic protein promoting DNA repair, its role in radiation resistance of ''<del class="diffchange diffchange-inline">Deinococcus </del>radiodurans''</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>A pleiotropic protein promoting DNA repair, its role in radiation resistance of ''<ins class="diffchange diffchange-inline">D. </ins>radiodurans''</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>was demonstrated.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>was demonstrated.</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PprA preferentially binds to double-stranded DNA carrying strand breaks, inhibits ''E. coli'' exonuclease III activity, and stimulates the DNA end-joining reaction catalysed by ATP-dependent and NAD-dependent DNA ligases. These</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>PprA preferentially binds to double-stranded DNA carrying strand breaks, inhibits ''E. coli'' exonuclease III activity, and stimulates the DNA end-joining reaction catalysed by ATP-dependent and NAD-dependent DNA ligases. These</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''RecA'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>*'''RecA'''</div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">The ''</del>D. radiodurans'<del class="diffchange diffchange-inline">' </del>RecA protein has been characterized and its gene has been sequenced; <del class="diffchange diffchange-inline">it shows greater than 50% identity to the ''</del>E. coli'<del class="diffchange diffchange-inline">' RecA protein</del>. <del class="diffchange diffchange-inline">''</del>D. radiodurans'<del class="diffchange diffchange-inline">' </del>recA mutants are highly sensitive to UV and ionizing radiation. <del class="diffchange diffchange-inline">In this context, early work </del>by Carroll et al (1996) <del class="diffchange diffchange-inline">reported </del>that ''E. coli'' <del class="diffchange diffchange-inline">RecA </del>did not complement an IR-sensitive <del class="diffchange diffchange-inline">''</del>D. radiodurans<del class="diffchange diffchange-inline">'' </del>recA point-mutant (rec30) and that expression of <del class="diffchange diffchange-inline">''</del>D. radiodurans<del class="diffchange diffchange-inline">'' RecA </del>in <del class="diffchange diffchange-inline">''</del>E. coli<del class="diffchange diffchange-inline">'' </del>was lethal. <del class="diffchange diffchange-inline">More </del>recently<del class="diffchange diffchange-inline">, however</del>, it <del class="diffchange diffchange-inline">has been </del>reported that <I>E. coli</I> recA can provide partial complementation to a <del class="diffchange diffchange-inline">''</del>D. radiodurans<del class="diffchange diffchange-inline">'' </del>recA null mutant (Schlesinger, 2007).</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><i></ins>D. radiodurans'<ins class="diffchange diffchange-inline">s</i> </ins>RecA protein has been characterized and its gene has been sequenced; <ins class="diffchange diffchange-inline">its gene is homologous with <i></ins>E. coli'<ins class="diffchange diffchange-inline">s</i> recA gene</ins>. <ins class="diffchange diffchange-inline"><i></ins>D. radiodurans'<ins class="diffchange diffchange-inline">s</i> </ins>recA mutants are highly sensitive to UV and ionizing radiation. <ins class="diffchange diffchange-inline">It was repored </ins>by Carroll et al (1996) that ''E. coli'' <ins class="diffchange diffchange-inline">recA </ins>did not complement an IR-sensitive <ins class="diffchange diffchange-inline"><i></ins>D. radiodurans<ins class="diffchange diffchange-inline"></i> </ins>recA point-mutant (rec30) and that expression of <ins class="diffchange diffchange-inline"><i></ins>D. radiodurans<ins class="diffchange diffchange-inline"></i> recA </ins>in <ins class="diffchange diffchange-inline"><i></ins>E. coli<ins class="diffchange diffchange-inline"></i> </ins>was lethal. <ins class="diffchange diffchange-inline"> However </ins>recently, it <ins class="diffchange diffchange-inline">was </ins>reported that <I>E. coli</I> recA can provide partial complementation to a <ins class="diffchange diffchange-inline"><i></ins>D. radiodurans<ins class="diffchange diffchange-inline"></i> </ins>recA null mutant (Schlesinger, 2007).</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Effects of inoing radiation.png|350px|right|''D.radiodurans'']]</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>[[File:Effects of inoing radiation.png|350px|right|''D.radiodurans'']]</div></td></tr>
<tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins style="color: red; font-weight: bold; text-decoration: none;"></ins></div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==== The effects of ionizing radiation ====</div></td></tr>
<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ionizing radiation causes atoms and molecules to become ionized or excited. These excitations and ionizations can</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Ionizing radiation causes atoms and molecules to become ionized or excited. These excitations and ionizations can</div></td></tr>
</table>Mol7cks