Team:Columbia-Cooper-NYC/Columbia notebook 1

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<a href="#">Overview</a>
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         <li><a href="#" onmouseover="mopen('m6')" onmouseout="mclosetime()">Human Practice</a>
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                 <a href="http://2012.igem.org/Team:Columbia-Cooper-NYC/Sponsor_Us">Sponsor Us</a>
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<a href="http://2012.igem.org/Team:Columbia-Cooper-NYC/Acknowledgements">Acknowledgements</a>
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Revision as of 20:00, 15 September 2012



Contents

Columbia Copper Experiment Notebook

Copper Experiment 1

Friday, June 22nd

Outline of activity today:

  • Met with Jason, who showed us how to make A. ferrooxidans liquid media, prepared Copper 1 and 2 samples (with and without bacteria) and placed on shaker. Will be periodically checked until June 25 twice a day for activity.
  • Showed us recipe for solid media, and made enough for two samples, 20 mL (one control with no bacteria). Copper samples were submerged in agarose (see Steven’s pictures). Also learned protocols listed below.

Starting Sample masses:

Copper 1: (liquid media only)
Sample Mass (g)
1 0.0092
2 0.0107.
Copper 2: (liquid media only)
Sample Mass (g)
1 0.1318
2 0.1286.
Copper 2: (solid media)
Sample Mass (g)
1 0.1272
2 0.1282.


Liquid media and flasks were placed in shaker at 11:35 am, 225 rpm, 30C. Solid media and petri dishes were placed in incubator at 12:42 pm, 30C.


Saturday, June 23

  • Checked the progress of all copper samples that included Copper 2 samples in solid media with and without bacteria, Copper 1 and 2 samples in liquid media each containing two samples of with and without bacteria.
  • Observations were made for all samples. Optical density was measured for all of the samples submerged in liquid basal AFM low pH solution. Mass was weighed only copper 2 in liquid media with and without bacteria.
Solid Media Samples:


Copper 2- Sample 1 (fully submerged, without bacteria)
  • Observations: Solid media mostly clear except for the outer edges of the Copper which appeared to be a light golden yellow color (note picture below). Copper turned to a dark brown color. No observable size change to the copper.
Copper 2- Sample 2 (half submerged, with bacteria)
  • Observations: Solid media turned from clear to a light golden yellow color (similar to that of the outer edges of the Copper from sample 1 mentioned above). Copper turned to a dark brown color. No observable size change to the copper.


Liquid Media Samples:


Copper 1- Sample 1 (with bacteria)
  • Observations: Noticeable 7+ small pieces of copper sample within liquid media (note picture below). Conclude to not take mass for this sample.
  • Cuvette reading2: 0.003 A
  • Current mass: N/A, Previous mass: 0.0092g, Initial mass: 0.0092g
  •  % Mass Lost: N/A
Copper 1- Sample 2 (without bateria)
  • Observations: No significant copper pieces visible in liquid media (note picture). Conclude to not take mass for this sample.
  • Cuvette reading: 0.004 A
  • Current mass reading: N/A, Previous mass: 0.0107g, Initial mass: 0.0107g
  •  % Mass lost: N/A
Copper 2- Sample 1 (with bacteria)
  • Observations: No observable change (see photo below).
  • Cuvette reading: .004A
  • Current mass: 0.1063g, Previous mass: 0.1318g, Initial mass: 0.1318g
  •  % Mass Lost: 19.35%
Copper 2- Sample 2 (without bacteria)
  • Observations: No observable change to copper (see picture below).
  • Cuvette reading: 0.040 A**
  • Cuvette reading: 0.018 A***
  • Current mass reading: 0.0953g, Previous mass: 0.1286g, Initial mass: 0.1286g*
  •  % Mass lost: 25.89%


Sunday, June 24

  • Took out all four samples for standard check of OD and mass of copper 2 samples. Solid media was also examined. All samples (liquid and solid) were photographed.
  • No visible copper 1 samples present in either sample (see Observations)


Solid Media Samples:


Copper 2- Sample 1 (fully submerged, without bacteria)
  • Observations: A tint of green color on copper surface, the immediate radius of the copper has brown color, outside of the previously mentioned radius is a yellow tinge to the solid media. The rest of the solid media was clear. No observable size change.


Copper 2- Sample 2 (half submerged, with bacteria)
  • Observations: A darker more present shade of green on copper, compared to that of sample 1 mentioned above. Outer edges of the copper appeared black. Media was a uniformed amber color. No observable size change.


Liquid Media Samples:


Copper 1- Sample 1 (with bacteria)
  • Observations: Liquid media copper brown, that may include ions that are not copper. No visible copper pieces, and conclude to not take mass for this sample. During procedure, centrifuged for another 1 minute to original 2 minutes at sane speed (due to the lack of expected visible pellets of some kind*)
  • Cuvette reading1: 0.025 A
  • Current mass: N/A, Previous mass: N/A, Initial mass: 0.0092g
  •  % Mass Lost: N/A


Copper 1- Sample 2 (without bateria)
  • Observations: Slight light green color to the media, and media appeared slightly cloudy. No significant copper pieces visible in liquid media. Conclude to not take mass for this sample.
  • Cuvette reading: 0.033 A
  • Current mass reading: N/A, Previous mass: N/A, Initial mass: 0.0107g
  •  % Mass lost: N/A


Copper 2- Sample 1 (with bacteria)
  • Observations: Visible brown copper color to liquid media. Pellets formed when the media was centrifuged. Many fluctuations in mass was seen, possible sources of error maybe water droplets or cleanness of the tweezers.
  • Cuvette reading: .667A
  • Current mass 1: 0.0550g, Current mass 2: 0.0388g, Current mass 3: 0.0285g
  • Previous mass: 0.1063g, Initial mass: 0.1318g
  •  % Mass Lost 1: 48.26%,  % Mass Lost 2: 63.50%, % Mass Lost 3: 73.19%


Copper 2- Sample 2 (without bacteria)
  • Observations: Copper is visible in faint blue-green liquid media. No observable change to copper. Observable pellets after centrifuging (Unknown origin). Note the varied measurements in the masses, although not of a significant drop as in Copper 2 liquid media sample 1.
  • Cuvette reading: 0.040 A
  • Current mass reading1: 0.0907g, Current mass reading2: .0842g
  • Previous mass: 0.0953g, Initial mass: 0.1286g
  •  % Mass lost 1: 4.83%, % Mass lost 2: 11.65%


Monday, June 25

  • Took out all four samples for standard check of OD and mass of copper samples. Solid media was also examined. All samples (liquid and solid) were photographed.
  • Only sample 2 of copper 2 in liquid media was able to be measured for the other samples were either etched by bacteria or physically torn apart by shaking or by the AMF media.


Solid Media Samples:


Copper 2- Sample 1 (without bacteria) Removal: 9:51, Return: 9:55 Observations: Green copper sample on surface. No clear media visible. (see photo below).

Copper 2- Sample 2 (with bacteria) Removal: 9:51, Return: 9:55 Observations: A light shade of green on copper. Outer edges of the copper appeared black. Media was a uniformed amber color. No observable size change. (see photo below).

Note: One or both of the solid media samples dried up, therefore requiring another set of experiments.


Liquid Media Samples:


Copper 2- Sample 1 (with bacteria) Removal1: 9:56, Return1: 10:23, Removal2: 10:41, Return2: 10:54* Observations: Visible brown and murky copper color to liquid media. Pellets formed when the media was centrifuged. Copper appeared to turn into little powder, pellet form, and conclude mass is difficult to measure and may alter data. (see photo below). Cuvette reading1: .034A, Cuvette reading2: .057A* Today’s mass (fourth day): N/A Third day’s mass1: 0.0550g, Third day’s mass2: 0.0388g, Third day’s mass3: 0.0285g Second day’s mass: 0.1063g, Initial mass: 0.1318g % Mass Lost: N/A (All of the copper was etched)

  • Note: Since the spectrophotometer reading was significantly lower than that of yesterday (.667 A), the sample’s OD was read twice

Copper 2- Sample 2 (without bacteria) Removal: 10:24, Return: 10:58 Observations: Copper is visible in muddy but faint blue-green liquid media. No observable change to copper (see picture below). Observable pellets after centrifuging (Unknown origin again like yesterday). Note the varied measurements in the masses, although not of a significant drop as in Copper 2 liquid media sample 1 which turned to nothing. Cuvette reading: 0.118 A Current (fourth day) mass1: .0400g Current (fourth day) mass2: .0324g Third day’s mass reading1: 0.0907g, Third day’s mass reading2: .0842g Second day’s mass: 0.0953g, Initial mass: 0.1286g

  •  %Mass change1: 55.90%, % Mass change2: 64.28%
    •  %Mass change1: 52.49%, % Mass change2: 61.52%
  • Note: Based on first reading from yesterday
    • Note: Based on second reading from yesterday

Copper 1- Sample 1 (with bacteria) Removal1: 10:55, Return: 11:04 Observations: Liquid media copper brown, that may include ions that are not copper (note picture below). Some visible tiny fragments of original sample, but conclude to not take mass for this sample. After centrifuging there were visible pellets (bacteria). Cuvette reading1: 0.094 A Current mass: N/A, Previous mass: N/A, Initial mass: 0.0092g % Mass Lost: N/A

Copper 1- Sample 2 (without bateria) Removal: 10:24, Return: 11:19 Observations: Slight light green color to the media, and media appeared slightly cloudy. No significant copper pieces visible in liquid media (note picture). Conclude to not take mass for this sample. Cuvette reading: 0.022 A Current mass reading: N/A, Previous mass: N/A, Initial mass: 0.0107g % Mass lost: N/A


July, 2012