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Team:Groningen/Notebook/Wetwork 10July2012 - Revision history
2024-03-28T10:32:33Z
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Jparrish at 21:32, 26 September 2012
2012-09-26T21:32:58Z
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Jparrish
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=176128&oldid=prev
Alicja at 17:06, 25 September 2012
2012-09-25T17:06:20Z
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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;">PCR AlsT promotor with Pfu polymerase and primers 150, 250, 300, 500 bp from AlsT gene at 58 °C and 59 °C.</del></div></td><td colspan="2"> </td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">Result: PCR products were obtained for all primers except the 500 bp at both temperatures.</del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"></style></ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Arjan/Renske</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><p class="margin"></ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (see below). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline">PCR AlsT promotor with Pfu polymerase and primers 150, 250, 300, 500 bp from AlsT gene at 58 °C and 59 °C.<br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Dyed cDNA was purified and concentration was measured (see table). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline">Result: PCR products were obtained for all primers except the 500 bp at both temperatures.<br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>7 uL H2O and 35 uL Ambion hybridization buffer (37 degrees Celsius) where added to the dried cDNA mixture. The mixture was brought onto cleaned, pre-heated Bacillus subtilis slides. The slides used were provided by the Molgen research group. They were probed as described previously by Kloosterman et al., 2006 and produced as decribed Kuipers et al., 2002. The slides contained three technical replicates of the B.s. sp168 genome.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>The cDNA was hybridized on the probed slides O/N at 48 degrees Celsius.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Arjan/Renske<ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></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>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (see below). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.<ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Emeraldo / Nisa</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Dyed cDNA was purified and concentration was measured (see table). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.<ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></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>7 uL H2O and 35 uL Ambion hybridization buffer (37 degrees Celsius) where added to the dried cDNA mixture. The mixture was brought onto cleaned, pre-heated Bacillus subtilis slides. The slides used were provided by the Molgen research group. They were probed as described previously by Kloosterman et al., 2006 and produced as decribed Kuipers et al., 2002. The slides contained three technical replicates of the B.s. sp168 genome.<ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>O/N culture of the plated biobricks from yesterday, each in 5ml LB+100 mikrogram/ul</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><br></ins></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>The cDNA was hybridized on the probed slides O/N at 48 degrees Celsius.<ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
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<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>Emeraldo / Nisa<ins class="diffchange diffchange-inline"><br></ins></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>---------------<ins class="diffchange diffchange-inline"><br></ins></div></td></tr>
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<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><ins class="diffchange diffchange-inline"><img src="https://static.igem.org/mediawiki/2012/d/de/Groningen2012_RR_Hybridizationscheme_micarray.PNG" width="600", height="200"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><i></ins>Kuipers, O., de Jong, A., Baerends, R., van Hijum, S., Zomer, A., Karsens, H., den Hengst, C., Kramer, N., Buist, G., & Kok, J. (2002). Transcriptome analysis and related databases of lactococcus lactis. Antonie Van Leeuwenhoek, 82(1-4), 113-122.<ins class="diffchange diffchange-inline"><br></ins></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><ins class="diffchange diffchange-inline"><br></ins></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>Kloosterman, T. G., Hendriksen, W. T., Bijlsma, J. J. E., Bootsma, H. J., van Hijum, S. A. F. T., Kok, J., Hermans, P. W. M., & Kuipers, O. P. (2006)." Regulation of glutamine and glutamate metabolism by GlnR and GlnA in streptococcus pneumoniae." Journal of Biological Chemistry, 281(35): 25097-25109.<ins class="diffchange diffchange-inline"><br></i></ins></div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">''</del>Kuipers, O., de Jong, A., Baerends, R., van Hijum, S., Zomer, A., Karsens, H., den Hengst, C., Kramer, N., Buist, G., & Kok, J. (2002). Transcriptome analysis and related databases of lactococcus lactis. Antonie Van Leeuwenhoek, 82(1-4), 113-122.<del class="diffchange diffchange-inline">'' </del></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: #ffa; color:black; font-size: smaller;"><div><del class="diffchange diffchange-inline">''</del>Kloosterman, T. G., Hendriksen, W. T., Bijlsma, J. J. E., Bootsma, H. J., van Hijum, S. A. F. T., Kok, J., Hermans, P. W. M., & Kuipers, O. P. (2006)." Regulation of glutamine and glutamate metabolism by GlnR and GlnA in streptococcus pneumoniae." Journal of Biological Chemistry, 281(35): 25097-25109.<del class="diffchange diffchange-inline">''</del></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><A HREF="https://2012.igem.org/Team:Groningen/Notebook"><FONT COLOR=#ff6700>Back to notebook</FONT></A></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><A HREF="https://2012.igem.org/Team:Groningen/Notebook"><FONT COLOR=#ff6700>Back to notebook</FONT></A></div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:SponsorsGroningen2012}}</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>{{Template:SponsorsGroningen2012}}</div></td></tr>
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Alicja
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=168893&oldid=prev
Emeraldo88 at 11:29, 25 September 2012
2012-09-25T11:29:32Z
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<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;">Emeraldo / Nisa</ins></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>
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<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;">O/N culture of the plated biobricks from yesterday, each in 5ml LB+100 mikrogram/ul</ins></div></td></tr>
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Emeraldo88
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134596&oldid=prev
RenskevR at 12:23, 21 September 2012
2012-09-21T12:23:41Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Arjan/Renske</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Arjan/Renske</div></td></tr>
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<tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (<del class="diffchange diffchange-inline">note: to be added Mo_16_july</del>). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (<ins class="diffchange diffchange-inline">see below</ins>). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.</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>Dyed cDNA was purified and concentration was measured (see table). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Dyed cDNA was purified and concentration was measured (see table). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.</div></td></tr>
</table>
RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134594&oldid=prev
RenskevR at 12:23, 21 September 2012
2012-09-21T12:23:21Z
<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (note: to be added Mo_16_july). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Purified cDNA as [[Team:Groningen/Notebook/Wetwork_5July2012|before]]. cDNA concentrations can be read in the hybridization table (note: to be added Mo_16_july). The cDNA made today and the previously made cDNA were stained using the Cy3 and Cy5 dyes from Ambion and kept in the dark for 90 minutes.</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>Dyed cDNA was purified and concentration was measured (see table<del class="diffchange diffchange-inline">|to be added</del>). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Dyed cDNA was purified and concentration was measured (see table). Equal amounts of target/control where combined and the cDNA mixtures where dried in the speedvac rotor for 40 min, 60 degrees, 2000 rpm.</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>7 uL H2O and 35 uL Ambion hybridization buffer (37 degrees Celsius) where added to the dried cDNA mixture. The mixture was brought onto cleaned, pre-heated Bacillus subtilis slides. The slides used were provided by the Molgen research group. They were probed as described previously by Kloosterman et al., 2006 and produced as decribed Kuipers et al., 2002. The slides contained three technical replicates of the B.s. sp168 genome.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>7 uL H2O and 35 uL Ambion hybridization buffer (37 degrees Celsius) where added to the dried cDNA mixture. The mixture was brought onto cleaned, pre-heated Bacillus subtilis slides. The slides used were provided by the Molgen research group. They were probed as described previously by Kloosterman et al., 2006 and produced as decribed Kuipers et al., 2002. The slides contained three technical replicates of the B.s. sp168 genome.</div></td></tr>
</table>
RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134591&oldid=prev
RenskevR at 12:22, 21 September 2012
2012-09-21T12:22:46Z
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RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134589&oldid=prev
RenskevR at 12:22, 21 September 2012
2012-09-21T12:22:19Z
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RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134588&oldid=prev
RenskevR at 12:21, 21 September 2012
2012-09-21T12:21:45Z
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RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=134586&oldid=prev
RenskevR at 12:21, 21 September 2012
2012-09-21T12:21:15Z
<p></p>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Tom</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>Tom</div></td></tr>
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The cDNA was hybridized on the probed slides O/N at 48 degrees Celsius.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The cDNA was hybridized on the probed slides O/N at 48 degrees Celsius.</div></td></tr>
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RenskevR
http://2012.igem.org/wiki/index.php?title=Team:Groningen/Notebook/Wetwork_10July2012&diff=119689&oldid=prev
RenskevR at 17:12, 16 September 2012
2012-09-16T17:12:43Z
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<tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Kloosterman, T. G., Hendriksen, W. T., Bijlsma, J. J. E., Bootsma, H. J., van Hijum, S. A. F. T., Kok, J., Hermans, P. W. M., & Kuipers, O. P. (2006)." Regulation of glutamine and glutamate metabolism by GlnR and GlnA in streptococcus pneumoniae." Journal of Biological Chemistry, 281(35): 25097-25109.''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>''Kloosterman, T. G., Hendriksen, W. T., Bijlsma, J. J. E., Bootsma, H. J., van Hijum, S. A. F. T., Kok, J., Hermans, P. W. M., & Kuipers, O. P. (2006)." Regulation of glutamine and glutamate metabolism by GlnR and GlnA in streptococcus pneumoniae." Journal of Biological Chemistry, 281(35): 25097-25109.''</div></td></tr>
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