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Lab 9: PCR and Gel Electrophoresis

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Lab 9:  PCR and Gel Electrophoresis (Photo: Chris Madden Cartoons) Introduction     The purpose of the first lab was to first familiarize ourselves with the process of the Polymerase Chain Reaction (PCR). If there is isolated DNA, but not very much, PCR is used to make multiple copies of the DNA of interest. From initially creating the solution with the DNA intended for replication along with various other ingredients and then putting it through a temperature cycle many times, we will then be left with a highly concentrated solution of a specific DNA section. The critical point in this process is choosing the correct species specific primer that depends on the downstream application and what exactly we are looking for. For this part, we used DNA from a pure E. coli culture previously prepared in an earlier lab.     The purpose of the second lab was to put the DNA that we previously separated in an earlier lab through an electrophoresis process that separates the DNA fragments
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Literature Review Blog II

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Title:  Effects of temperature warming during a bioremediation study of natural and nutrient-amended hydrocarbon-contaminated sub-Antarctic soils 1. What is the study’s objective/hypothesis/question? The study looked into the use of in-situ bioremediation using microorganisms to degrade petroleum contaminated soils at sub-Arctic conditions, including soils, temperature and vegetation. Temperature was the most important variable, in that the hydrocarbon mineralization rate was assessed on artificially contaminated soils that mimicked Arctic conditions. 2. What is the rationale and relevance of the question? (i.e. why was the study done?)  The Arctic is recognized as the last pristine zone, "almost uncontaminated by anthroprogenic hydrocarbons". However, due to petroleum contamination, identified as the most significant, both coastal marine and terrestrial areas are becoming polluted.  Bioremediation, for now, is the only cost effective and plausible technique feasib
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Lab 8: DNA Isolation

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Lab 8:  DNA Isolation (Photo: HSHP Biology) Introduction     The purpose of this lab was ultimately to familiarize ourselves with the PowerSoil DNA Isolation Kit to successfully purify a DNA sample from a pure E. coli culture in LB broth.. The first step will be obtaining the cells, then through use of the kit and instructions we will break down the membrane and release the DNA from the cells. The next step will be to precipitate the DNA and finally, purify the sample. "The PowerSoil DNA is intended for use with environmental samples containing a high humid acid content including difficult soil types such as compost, sediment and manure...The isolated DNA has a high level of purity allowing for more successful PCR amplification of organisms from the sample." (MoBio) Since the sample we are using is already a pure E. coli sample, all of the purification is a tad overkill but will be done anyways according to the provided instructions. Another important thing to note i
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Lab 6: Coliform Determination by the Membrane Filter Technique

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Lab 6:  Lab Coliform Determination by the Membrane Filter Technique (Photo: Steve Nease) Introduction     The purpose of this lab will ultimately be to familiarize ourselves with counting coliform microorganism colonies as well as another plating method called the membrane filter technique.     The total viable count is based upon the ability of a microorganism placed in a nutrient environment to grow.  While individual microorganisms cannot be seen with the naked eye, they can grow in colonies which are visible to any plain Jane.  Counting the colonies gives an indication of the number of viable colony forming units (CFU) present in the original sample.  However, the appropriate growth medium must be chosen first to get to the counting phase.  This part is crucial because the accuracy will be best if the chosen medium is as similar as possible to the sample environment.     The membrane filter technique uses the semi permeable membrane and a vacuum to trap the microorganis
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Lab 5: Enumeration of Microorganisms

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Lab 5:  Enumeration of Microorganisms (Photo: Cafe Press) Introduction     The purpose of this lab will ultimately be to familiarize ourselves with counting microorganism colonies.  In the process, we will learn another plating method called spread plating and learn our strengths and weaknesses using these techniques.     The total viable count is based upon the ability of a microorganism placed in a nutrient environment to grow.  While individual microorganisms cannot be seen with the naked eye, they can grow in colonies which are visible to any plain Jane.  Counting the colonies gives an indication of the number of viable colony forming units (CFU) present in the original sample.  However, the appropriate growth medium must be chosen first to get to the counting phase.  This part is crucial because the accuracy will be best if the chosen medium is as similar as possible to the sample environment.     Plate counting is the oldest technique in the book, so why teach an old do
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