BISC209/S11: Lab8 - Revision history

http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&feed=atom&action=history BISC209/S11: Lab8 - Revision history 2013-05-24T14:39:25Z Revision history for this page on the wiki MediaWiki 1.13.2 http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499291&oldid=prev Tucker Crum: /* Finishing the term project */ 2011-03-16T15:31:18Z

<p><span class="autocomment">Finishing the term project</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:31, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 5:</td> <td colspan="2" class="diff-lineno">Line 5:</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;"></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>==Finishing the <del class="diffchange diffchange-inline">term </del>project==</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>==<ins class="diffchange diffchange-inline">LAB 8 </ins>Finishing the project<ins class="diffchange diffchange-inline">!</ins>==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is your last wet lab! Please discard all cultures as soon as you have recorded all your results and photographed your evidence. If you have positive antibiotic producers or AI producers, or cool interactions please show them to your lab instructor so they can be shared with the class and saved. Please do not leave any cultures in the lab while we are away for break. You will receive 5 "clean-up points" if we do not find any evidence of your cultures or tests. If we have to discard and clean-up later after you, you will not receive any of those 5 points. <BR> <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>This is your last wet lab! Please discard all cultures as soon as you have recorded all your results and photographed your evidence. If you have positive antibiotic producers or AI producers, or cool interactions please show them to your lab instructor so they can be shared with the class and saved. Please do not leave any cultures in the lab while we are away for break. You will receive 5 "clean-up points" if we do not find any evidence of your cultures or tests. If we have to discard and clean-up later after you, you will not receive any of those 5 points. <BR> <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>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499288&oldid=prev Tucker Crum: /* SIM TESTS DEVELOPMENT AND ANALYSIS */ 2011-03-16T15:11:33Z

<p><span class="autocomment">SIM TESTS DEVELOPMENT AND ANALYSIS</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:11, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 49:</td> <td colspan="2" class="diff-lineno">Line 49:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test.</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test.</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><LI>'''Hydrogen Sulfide Test.'''  When hydrogen sulfide gas is produced, the gas reacts with the ferrous ammonium sulfate precipitating as ferrous sulfide.  An insoluble black precipitate in the medium indicates the organism produces H<sub>2</sub>S .</UL></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><LI>'''Hydrogen Sulfide Test.'''  When hydrogen sulfide gas is produced, the gas reacts with the ferrous ammonium sulfate precipitating as ferrous sulfide.  An insoluble black precipitate in the medium <ins class="diffchange diffchange-inline">(usually in the butt of the tube) </ins>indicates the organism produces H<sub>2</sub>S .</UL></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;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499286&oldid=prev Tucker Crum: /* SIM TESTS DEVELOPMENT AND ANALYSIS */ 2011-03-16T15:11:05Z

<p><span class="autocomment">SIM TESTS DEVELOPMENT AND ANALYSIS</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:11, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR>Another way to test for indole (we will NOT use this method) is to use amyl alcohol, the main ingredient in Kovacs reagent. It acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR>Another way to test for indole (we will NOT use this method) is to use amyl alcohol, the main ingredient in Kovacs reagent. It acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><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: #ffa; color:black; font-size: smaller;"><div>'''PROTOCOL:'''<BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''<ins class="diffchange diffchange-inline">Reading the tests </ins>PROTOCOL:'''<BR></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfate/ indole/ motility) medium enable detection of two other metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide. These characteristics are sometimes used to differentiate Gram-negative rods of the ''Enterobactericaea'' group of enteric bacteria can be differentiated: '''Sulfur Reduction and /Indole Production'''.  SIM medium contains nutrients, iron, and sodium thiosulfate. <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfate/ indole/ motility) medium enable detection of two other metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide. These characteristics are sometimes used to differentiate Gram-negative rods of the ''Enterobactericaea'' group of enteric bacteria can be differentiated: '''Sulfur Reduction and /Indole Production'''.  SIM medium contains nutrients, iron, and sodium thiosulfate. <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 colspan="2" class="diff-lineno">Line 47:</td> <td colspan="2" class="diff-lineno">Line 47:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''hydrogen sulfide test''' relies on the use of sodium thiosulfate and ferrous ammonium sulfate as indicators of '''hydrogen sulfide''' production. Ferrous ammonium sulfate reacts with H<sub>2</sub>S gas to produce ferrous sulfide, a black precipitate found in the butt of the tube. <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''hydrogen sulfide test''' relies on the use of sodium thiosulfate and ferrous ammonium sulfate as indicators of '''hydrogen sulfide''' production. Ferrous ammonium sulfate reacts with H<sub>2</sub>S gas to produce ferrous sulfide, a black precipitate found in the butt of the tube. <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: #ffa; color:black; font-size: smaller;"><div><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test. <del class="diffchange diffchange-inline"> <BR></del></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test.</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>'''Hydrogen Sulfide Test.'''  When hydrogen sulfide gas is produced, the gas reacts with the ferrous ammonium sulfate precipitating as ferrous sulfide.  An insoluble black precipitate in the medium indicates the organism produces H<sub>2</sub>S .</UL></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><LI></ins>'''Hydrogen Sulfide Test.'''  When hydrogen sulfide gas is produced, the gas reacts with the ferrous ammonium sulfate precipitating as ferrous sulfide.  An insoluble black precipitate in the medium indicates the organism produces H<sub>2</sub>S .</UL></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;"></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499285&oldid=prev Tucker Crum: /* SIM TESTS DEVELOPMENT AND ANALYSIS */ 2011-03-16T15:10:15Z

<p><span class="autocomment">SIM TESTS DEVELOPMENT AND ANALYSIS</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:10, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 40:</td> <td colspan="2" class="diff-lineno">Line 40:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR>Another way to test for indole (we will NOT use this method) is to use amyl alcohol, the main ingredient in Kovacs reagent. It acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR>Another way to test for indole (we will NOT use this method) is to use amyl alcohol, the main ingredient in Kovacs reagent. It acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><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: #ffa; color:black; font-size: smaller;"><div>'''<del class="diffchange diffchange-inline">TEST FOR TRYPTOPHASE and SULFUR REDUCTION by SIMS</del>'''<BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>'''<ins class="diffchange diffchange-inline">PROTOCOL:</ins>'''<BR></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfate/ indole/ motility) medium enable detection of two other metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide. These characteristics are sometimes used to differentiate Gram-negative rods of the ''Enterobactericaea'' group of enteric bacteria can be differentiated: '''Sulfur Reduction and /Indole Production'''.  SIM medium contains nutrients, iron, and sodium thiosulfate. <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfate/ indole/ motility) medium enable detection of two other metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide. These characteristics are sometimes used to differentiate Gram-negative rods of the ''Enterobactericaea'' group of enteric bacteria can be differentiated: '''Sulfur Reduction and /Indole Production'''.  SIM medium contains nutrients, iron, and sodium thiosulfate. <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>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499284&oldid=prev Tucker Crum: /* SIM TESTS DEVELOPMENT AND ANALYSIS */ 2011-03-16T15:08:13Z

<p><span class="autocomment">SIM TESTS DEVELOPMENT AND ANALYSIS</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 15:08, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 36:</td> <td colspan="2" class="diff-lineno">Line 36:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfide-indole-motility) medium enable detection of two such metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide.  SIM medium contains nutrients, iron, and sodium thiosulfate. <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfide-indole-motility) medium enable detection of two such metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide.  SIM medium contains nutrients, iron, and sodium thiosulfate. <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: #ffa; color:black; font-size: smaller;"><div>The '''indole test''' is used for detecting '''tryptophanase'''. Casein peptone is rich in tryptophan, which is attacked by certain microorganisms resulting in the production of indole.  Bacteria possessing the enzyme tryptophanase cleave tryptophan, producing three end products. One of these end products is indole, produced in aerobic conditions; another is skatole, produced in anaerobic conditions. <del class="diffchange diffchange-inline">Amyl </del>alcohol in Kovacs reagent acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The '''indole test''' is used for detecting '''tryptophanase'''. Casein peptone is rich in tryptophan, which is attacked by certain microorganisms resulting in the production of indole.  Bacteria possessing the enzyme tryptophanase cleave tryptophan, producing three end products. One of these end products is indole, produced in aerobic conditions; another is skatole, produced in anaerobic conditions. <ins class="diffchange diffchange-inline">Indole combines with the reagent '''p-Dimethylaminoaminocinnamaldehyde''' to form a blue-green compound. The reaction occurs by a condensation process formed by an acid splitting of the protein reagent. A positive test is blue-green color development within three minutes. A ''negative'' test using this reagent is pink color. </ins></div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div> </div></td></tr> <tr><td colspan="2"> </td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline"><BR>Another way to test for indole (we will NOT use this method) is to use amyl </ins>alcohol<ins class="diffchange diffchange-inline">, the main ingredient </ins>in Kovacs reagent<ins class="diffchange diffchange-inline">. It </ins>acts as a solvent for indole or skatole, which then reacts with p-dimethylaminobenzaldehyde to produce a '''red rosindole dye'''. Organisms which do not produce tryptophanase produce no color change in SIM medium when Kovacs is added while bacteria positive for tryptophanase produce a red color when Kovacs reagent is added.<BR><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>'''TEST FOR TRYPTOPHASE and SULFUR REDUCTION by SIMS'''<BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''TEST FOR TRYPTOPHASE and SULFUR REDUCTION by SIMS'''<BR></div></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499280&oldid=prev Tucker Crum: /* SIM TESTS DEVELOPMENT AND ANALYSIS */ 2011-03-16T14:42:59Z

<p><span class="autocomment">SIM TESTS DEVELOPMENT AND ANALYSIS</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:42, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 29:</td> <td colspan="2" class="diff-lineno">Line 29:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==SIM TESTS DEVELOPMENT AND ANALYSIS ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==SIM TESTS DEVELOPMENT AND ANALYSIS ==</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''MOTILITY'''<BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''MOTILITY'''<BR></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Motility detection is possible due to the semisolid nature (low concentration of agar) of the SIM medium. '''Growth radiating out from the central stab inoculation line indicates that the test organism is motile.''' <del class="diffchange diffchange-inline">The motility test should be assessed first. </del> Motile organisms <del class="diffchange diffchange-inline">will </del>exhibit growth radiating from the stab inoculation line. Non motile organisms will exhibit growth only along the stab inoculation line. Would it be useful for some soil community members to be motile? Why? Would having motile members in a soil community be useful to non-motile members, or would that mixture be disadvantageous to one or the other, or could it be both?<BR><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div><ins class="diffchange diffchange-inline">The motility test should be assessed before you add the indicator reagent to test for indole from tryptophanase. </ins>Motility detection is possible due to the semisolid nature (low concentration of agar) of the SIM medium. '''Growth radiating out from the central stab inoculation line indicates that the test organism is motile.'''  <ins class="diffchange diffchange-inline">First look at your ''E. coli'' positive control to see an example of what radiating growth may look like. Hold your SIM tube up to the light so that you can see the difference in the medium and the growth line. Get an uninoculated SIM tube to compare color and turbidity. </ins>Motile organisms <ins class="diffchange diffchange-inline">should </ins>exhibit <ins class="diffchange diffchange-inline">detectable </ins>growth radiating from the stab inoculation line <ins class="diffchange diffchange-inline">towards the periphery. Strictly aerobic organisms may show more growth radiating down from the surface than farther into the stab</ins>. Non motile organisms will exhibit growth only along the stab inoculation line<ins class="diffchange diffchange-inline">. Consult with your instructor if you are having a hard time deciding on the motility results</ins>. Would it be useful for some soil community members to be motile? Why? Would having motile members in a soil community be useful to non-motile members, or would that mixture be disadvantageous to one or the other, or could it be both?<BR><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>'''TEST FOR TRYPTOPHANASE and SULFUR REDUCTION'''<BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''TEST FOR TRYPTOPHANASE and SULFUR REDUCTION'''<BR></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>What functional advantage would bacteria have if they are positive for tryptophanase or able to produce hydrogen sulfide? Would having some soil community members with these functional capacities obviate the need for other members to have the same enzymes? How so? Remember that all metabolic processes are "expensive" in terms of energy and raw materials used. Does this testing give us direct rather than theoretical evidence of a community where members have different metabolic capabilities that contribute to the success of the community? Will direct evidence that community members have the capacity to perform disparate roles be useful in answering one or more of your main investigative questions? Did the assessment we did previously of other exoenzymes and their relative prevalence in your soil community provide direct evidence for functional metabolic diversity as well, better, or just differently than the evidence you obtained from the SIM tests? Do you understand why we are doing these tests as part of this investigation?<BR><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>What functional advantage would bacteria have if they are positive for tryptophanase <ins class="diffchange diffchange-inline">production </ins>or able to produce hydrogen sulfide? Would having some soil community members with these functional capacities obviate the need for other members to have the same enzymes? How so? Remember that all metabolic processes are "expensive" in terms of energy and raw materials used. Does this testing give us direct rather than theoretical evidence of a community where members have different metabolic capabilities that contribute to the success of the community? Will direct evidence that community members have the capacity to perform disparate roles be useful in answering one or more of your main investigative questions? Did the assessment we did previously of other exoenzymes and their relative prevalence in your soil community provide direct evidence for functional metabolic diversity as well, better, or just differently than the evidence you obtained from the SIM tests? Do you understand why we are doing these tests as part of this investigation?<BR><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>The ingredients in SIM (sulfide-indole-motility) medium enable detection of two such metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide.  SIM medium contains nutrients, iron, and sodium thiosulfate. <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The ingredients in SIM (sulfide-indole-motility) medium enable detection of two such metabolic capabilities that some bacteria have and others lack: digestion of tryptophan by the enzyme tryptophanase to indole and/or sulfur reduction with the production of hydrogen sulfide.  SIM medium contains nutrients, iron, and sodium thiosulfate. <BR></div></td></tr> <tr><td colspan="2" class="diff-lineno">Line 43:</td> <td colspan="2" class="diff-lineno">Line 43:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''indole test''' is used for detecting '''tryptophanase'''. Casein peptone is rich in tryptophan, which is attacked by certain microorganisms resulting in the production of indole.  Bacteria possessing the enzyme tryptophanase cleave tryptophan, producing  '''indole'''. Indole combines with dimethyl-aminocinnamaldehyde to form a blue-green compound.  <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>The '''indole test''' is used for detecting '''tryptophanase'''. Casein peptone is rich in tryptophan, which is attacked by certain microorganisms resulting in the production of indole.  Bacteria possessing the enzyme tryptophanase cleave tryptophan, producing  '''indole'''. Indole combines with dimethyl-aminocinnamaldehyde to form a blue-green compound.  <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: #ffa; color:black; font-size: smaller;"><div>The '''hydrogen sulfide test''' relies on the use of sodium thiosulfate and ferrous ammonium sulfate as indicators of '''hydrogen sulfide''' production. Ferrous ammonium sulfate reacts with H<sub>2</sub>S gas to produce ferrous sulfide, a black precipitate. <BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>The '''hydrogen sulfide test''' relies on the use of sodium thiosulfate and ferrous ammonium sulfate as indicators of '''hydrogen sulfide''' production. Ferrous ammonium sulfate reacts with H<sub>2</sub>S gas to produce ferrous sulfide, a black precipitate <ins class="diffchange diffchange-inline">found in the butt of the tube</ins>. <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><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test.  <BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><UL><LI> '''Indole test:''' Dispense 2 drops of the '''remel® spot indole reagent''' into the SIM tube.  Observe for the development of a blue color within 1-3 minutes.  A  pink color indicates a negative test.  <BR></div></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499278&oldid=prev Tucker Crum: /* Complete Antibiotic Production & Sensitivity Testing */ 2011-03-16T14:36:14Z

<p><span class="autocomment">Complete Antibiotic Production & Sensitivity Testing</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:36, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 24:</td> <td colspan="2" class="diff-lineno">Line 24:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Week 3 <BR>'''</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>'''Week 3 <BR>'''</div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><UL><LI></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><UL><LI></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Examine the plates and look for evidence of a zone of inhibition (no growth) of "control" organisms in an area near the putative antibiotic producer's colonial growth. Evidence of antibiotic production should appear as a measurable zone of inhibition (section of a circle of no growth). The size of the zone of inhibition is indicative of the diffusion potential of the antibiotic and/or an indication of how sensitive the test organism is to the secreted inhibitor. Compare your results to other tested isolates in your lab section. Think about why an antibiotic might work differently on a Gram positive vs. a Gram negative organism or between two bacteria that are both Gram positive.  <LI></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Examine the plates and look for evidence of a zone of inhibition (no <ins class="diffchange diffchange-inline">growth or reduced </ins>growth) of <ins class="diffchange diffchange-inline">any of the </ins>"control" organisms in an area near the putative antibiotic producer's colonial growth. Evidence of antibiotic production should appear as a measurable zone of inhibition (section of a circle of no growth <ins class="diffchange diffchange-inline">or reduced growth compared to the growth see on the control plate</ins>). The size of the zone of inhibition is indicative of the diffusion potential of the antibiotic and/or an indication of how sensitive the test organism is to the secreted inhibitor. Compare your results to other tested isolates in your lab section. Think about why an antibiotic might work differently on a Gram positive vs. a Gram negative organism or between two bacteria that are both Gram positive <ins class="diffchange diffchange-inline">or Gram negative</ins>.  <LI></div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Take photos of any plates that show evidence of antibiotic producers in your soil community. If you found that your isolates did not appear to cause measurable inhibition of growth, does that mean that your isolate does not secrete any antimicrobial compounds? <del class="diffchange diffchange-inline">Why or why not</del>? </LI></UL><BR><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Take photos of any plates that show evidence <ins class="diffchange diffchange-inline">of the presence </ins>of antibiotic producers in your soil community. If you found that your isolates did not appear to cause measurable inhibition of growth, does that mean that your isolate does not secrete any antimicrobial compounds? <ins class="diffchange diffchange-inline">Explain</ins>? </LI></UL><BR><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>==SIM TESTS DEVELOPMENT AND ANALYSIS ==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==SIM TESTS DEVELOPMENT AND ANALYSIS ==</div></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499276&oldid=prev Tucker Crum: /* Nitrogen Cycle */ 2011-03-16T14:34:21Z

<p><span class="autocomment">Nitrogen Cycle</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:34, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 18:</td> <td colspan="2" class="diff-lineno">Line 18:</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>==Nitrogen Cycle==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Nitrogen Cycle==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Did you or your partners see a change in the levels of nitrate, nitrite, or ammonia? Please let your instructor know how these tests worked. Do you have a control? If you haven't already done so, please take an uninoculated tube of medium and test it with all three test strips. Be sure to post your final results to your team's DATA folder in Resources in Sakai. Add any final observations. Discuss with your team members the implications of your data.  If you have no change <del class="diffchange diffchange-inline">or </del>no positive tests, <del class="diffchange diffchange-inline">how might </del>you <del class="diffchange diffchange-inline">explain </del>this?</div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Did you or your partners see a change in the levels of nitrate, nitrite, or ammonia? Please let your instructor know how these tests worked. Do you have a control? If you haven't already done so, please take an uninoculated tube of medium and test it with all three test strips. Be sure to post your final results to your team's DATA folder in Resources in Sakai. Add any final observations. Discuss with your team members the implications of your data.  If you have no change<ins class="diffchange diffchange-inline">, </ins>no positive tests, <ins class="diffchange diffchange-inline">or your no-culture media control was positive, </ins>you <ins class="diffchange diffchange-inline">probably don't want to include </ins>this <ins class="diffchange diffchange-inline">test in your M&M, results or discussion</ins>? <ins class="diffchange diffchange-inline">Consult with your instructor about this. </ins></div></td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR><BR></div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div><BR><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>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499275&oldid=prev Tucker Crum: /* Interactions */ 2011-03-16T14:32:09Z

<p><span class="autocomment">Interactions</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:32, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 15:</td> <td colspan="2" class="diff-lineno">Line 15:</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>==Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Interactions==</div></td></tr> <tr><td class='diff-marker'>-</td><td style="background: #ffa; color:black; font-size: smaller;"><div>Observe the colonies on your plate, comparing any differences in the appearance of the colony growth of each isolate, alone vs mixed. Note that the inoculum in the diagonal spots is <del class="diffchange diffchange-inline">actually </del>a <del class="diffchange diffchange-inline">single (hopefully </del>pure<del class="diffchange diffchange-inline">) isolate</del>. Note the "edge" effect, a difference in the appearance of the colony growth in the spots along the perimeter of the plate as opposed to those growing in a more protected locations (the diagonal control colonies). <br><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>Observe the colonies on your plate, comparing any differences in the appearance of the colony growth of each isolate, alone vs mixed. Note that the inoculum in <ins class="diffchange diffchange-inline">each of </ins>the diagonal spots is a pure <ins class="diffchange diffchange-inline">culture control as are the spots in the column on the far left</ins>. Note the "edge" effect, a difference in the appearance of the colony growth in the spots along the perimeter of the plate as opposed to those growing in a more protected locations (the diagonal control colonies). <br><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>==Nitrogen Cycle==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Nitrogen Cycle==</div></td></tr>  </table>

Tucker Crum http://www.openwetware.org/index.php?title=BISC209/S11:_Lab8&diff=499274&oldid=prev Tucker Crum: /* Quorum sensing */ 2011-03-16T14:30:49Z

<p><span class="autocomment">Quorum sensing</span></p> <table style="background-color: white; color:black;"> <col class='diff-marker' /> <col class='diff-content' /> <col class='diff-marker' /> <col class='diff-content' /> <tr valign='top'> <td colspan='2' style="background-color: white; color:black;">←Older revision</td> <td colspan='2' style="background-color: white; color:black;">Revision as of 14:30, 16 March 2011</td> </tr> <tr><td colspan="2" class="diff-lineno">Line 12:</td> <td colspan="2" class="diff-lineno">Line 12:</td></tr> <tr><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Quorum sensing==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Quorum sensing==</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>If the isolate produces AI and it is sensed by the CV026 mutant, a purple pigment will be produced by the mutant. What does this tell you about your isolate? <del class="diffchange diffchange-inline">Is there any reason to test the Gram </del>positive <del class="diffchange diffchange-inline">isolates? Why </del>or <del class="diffchange diffchange-inline">why not</del>?<br><BR></div></td><td class='diff-marker'>+</td><td style="background: #cfc; color:black; font-size: smaller;"><div>If the isolate produces AI and it is sensed by the CV026 mutant, a purple pigment will be produced by the mutant. What does this tell you about your isolate? <ins class="diffchange diffchange-inline">What type of autoinducer is being produced if you found a </ins>positive<ins class="diffchange diffchange-inline">: AHL, AI-2, </ins>or <ins class="diffchange diffchange-inline">Oligopeptide? Explain</ins>?<br><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>==Interactions==</div></td><td class='diff-marker'> </td><td style="background: #eee; color:black; font-size: smaller;"><div>==Interactions==</div></td></tr>  </table>

Tucker Crum