Difference between revisions of "Team:Rheda Bielefeld/Methods"

Revision as of 14:09, 17 October 2018

Short Overview

DNA Extraction from plant leaves:

DNA extraction kit Macherey & Nagel. Extraction was performed according to protocol. The leaf pieces were either frozen with liquid nitrogen and afterwards added to the mortar and pestle or water was added.

Open the Pollen:

Ribolyser:

6500 rpms* two times performed *30 seconds duration of the rotation *30 seconds pause

Media (cultivating bacteria):

LB = 20g LB powder filled up to 1L
Competent cells KRX from promega were used for transformation. Heat shock transformation were tested with the promega provided protocol and with the protocol from the iGEM Bielefeld team 2014:
Transformation via heat shock
Thaw 200 μL Chemo competent E.coli cells on ice
Add 0.5-5μL plasmid to 200 μL chemocompetent cells
Store cells on ice for 10-30 minutes
Heatshock for (60-)90 seconds at 42°C
Transfer transformation reaction to 1 mL SOC or LB Medium and incubate 1 hour at 37°C
Centrifuge 30 seconds at 11000 rpm and plate on selective LB Medium
Incubate overnight at 37°C

Plasmid isolation was performed with the analytic Jena plasmid isolation kit. The enclosed protocol was used. It was changed a bit as the elution step was done with water instead of elution buffer.

PCR:

Plant PCR were performed with Synadorme mastermix with the following protocol:

1µl Forward Primer
1µl Reverse Primer
4µl Master Mix (nucleotides, Taq polymerase)
12µl H2O
2µl Template DNA

Phusion PCR for cloning was performed with fermentas Phusion enzyme and the following protocol:

5x Phusion HF buffer (4µl)
10mM dNTPs (0,4µl)
Forward primer (1µl)
Reverse Primer (1µl)
Template DNA (1µl)
Phusion DNA polymerase (0,2µl)
H2O (add to 20µl)

Gel electrophoresis:

TAE, 50x stock solution (provided by the supervisors); working solution 1x TAE
0,8%-2% agarose (welche?) dissolved in 1x TAE
50x TAE:
242 g Tris Base
57.1 mL Glacial Acetic Acid
100 mL 0.5 M EDTA
pH:7.8

Nanodrop 2000 from XY was used for DNA measurements.
Restrictionsenzyme?
The experiments with liquid nitrogen and trypsin as well as the primer design strategy were especially supported by the supervisors. No antibiotics were handled by team members.

Methods

We have used various different methods for our experiments. Here is an overview of the methods we have used.

Pollen

For our experiments with pollen, we have used two methods. The first method was using trypsin. Trypsin is an enzyme mostly found in the digestive system of many animals and can hydrolyze proteins. We have used it here in the hope that the trypsin would hydrolyze the proteins in the pollen´s outer wall and therefore making the pollen break. The Ribolyser consists of many little balls of ceramics and is used to homogenize biological samples. It works simple: you put a sample into the ribolyser and shake it well, in the best case with a mechanical shaker. By shaking it, the little ceramic balls fly around in the container and by crashing into the sample, a lot of damage can be done to your biological sample. A negative side effect of using the ribolyser is that a lot of heat is produced when the balls fly around. We used the ribolyser to break the pollens wall with both heat and the mechanical damage done. Another way we tried to break open the wall of a pollen was by using liquid nitrogen. When you put liquid nitrogen onto cells, they break because all liquids touching that extremely cold substance freeze and eventually break. We enhanched this process by using a mortar.

PCR

When we extracted the DNA from the leaves, we used a mortar, water, and some ethanol to gap their cellular wall. After crushing them we used filters from the "Nucleospin DNA Extraction Kit" to extract the DNA from the remains. When using this kit, you need two filters, one container for the flow-through, liquids included in the kit and a centrifuge. The kit basically binds the DNA to the filter, washes out everything else through the filter and in the end, you use an elution buffer to elute the DNA from the filter. For the PCR, you have to prepare your sample by adding the nucleotides, the primer, the polymerase, and some water. Afterward, you put the samples into the PCR machine. It goes through many cycles of changing temperatures. In that process, the DNA parts into two strings and the primers bind onto their complimentary sequence and "shows" the polymerase where it has to start sythetising on. Next, the polymerase goes along the string and copies the sequences with the opposite nucleotides. By that process, the DNA was multiplied. When the PCR was finished, we performed a gel electrophoresis. The gel electrophoresis consists of an agarose gel, TAE-buffer, an anode and a cathode, and a connection to electricity. Since the DNA has a negative charge, it moves towards the anode. The gel electrophoresis can be evaluated by putting it into a bath of a coloring chemical. The gel is afterward put into a dark chamber and gets lit by UV-Light. Hereby, the gel electrophoresis pictures resolve.

Assays

The cracking of pollen is related with destruction of pectin and cellulose. Therefore we need enzymes like pectinase and cellulase. At first it is important to prove the content of cellulose and pectin in specific substances. Therefore we used both natural and pure alcohol. If there were small bubbles in the substances to see, then we successfully proved pectin and celluose in the samples. This is important for proving the appearance of pollen. After a while pectinase and cellulase should have destructed the pectin and cellulose. The experiment is successfully performed if there are not any bubbles in the samples.

NCBI

We visited the website of the National Center for Biotecnology Information (NCBI) to get some information from their data base. With them we got to know the sequence of the amino acids in the DNA of the tree leaves we used. Afterwards we were able to check whether our results are correct.

@@ Line 85: / Line 85: @@
 <b> <a href="https://2018.igem.org/Team:Rheda_Bielefeld/Pollen" style="color:yellow;font-size:25px;"> Pollen </a> </b> <br/> <br/>
-For our experiments with pollen, we have used two methods. The first method was using trypsin. Trypsin is an enzyme mostly found in the digestive system of many animals and can hydrolyze proteins. We have used it here in the hope that the trypsin would hydrolyze the proteins in the pollen´s outer wall and therefore making the pollen break. The Ribolyser is made up from many little balls of ceramics and is used to homogenize biological samples. It works easily: you put a sample into the ribolyser and shake it well, best with a mechanical shaker. By shaking it, the little ceramic balls fly around in the container and by crashing into the sample, a lot of damage can be done to your biological sample. A negative side effect of using the ribolyser is that a lot of heat is produced when the balls fly around. We used the ribolyser to break the pollens wall with both heat and the mechanical damage done. Another way we tried to break open the wall of a pollen was by using liquid nitrogen. When you put liquid nitrogen onto cells, they break because all liquids touching that extremely cold substance freeze and eventually break. We helped that process by using a mortar.<br/> <br/>
+For our experiments with pollen, we have used two methods. The first method was using trypsin. Trypsin is an enzyme mostly found in the digestive system of many animals and can hydrolyze proteins. We have used it here in the hope that the trypsin would hydrolyze the proteins in the pollen´s outer wall and therefore making the pollen break. The Ribolyser consists of many little balls of ceramics and is used to homogenize biological samples. It works simple: you put a sample into the ribolyser and shake it well, in the best case with a mechanical shaker. By shaking it, the little ceramic balls fly around in the container and by crashing into the sample, a lot of damage can be done to your biological sample. A negative side effect of using the ribolyser is that a lot of heat is produced when the balls fly around. We used the ribolyser to break the pollens wall with both heat and the mechanical damage done. Another way we tried to break open the wall of a pollen was by using liquid nitrogen. When you put liquid nitrogen onto cells, they break because all liquids touching that extremely cold substance freeze and eventually break. We enhanched this process by using a mortar.<br/> <br/>
 <b> <a href="https://2018.igem.org/Team:Rheda_Bielefeld/PCR" style="color:yellow;font-size:25px;"> PCR </a> </b> <br/> <br/>
-When we extracted the DNA from the leaves, we used a mortar, water, and some ethanol to gap the cellular wall of them. After crushing them we used filters from the "Nucleospin DNA Extraction Kit" to extract the DNA from the remains. When using that kit, you need two filters, one container for the flow-through, liquids included in the kit and a centrifuge. The kit basically binds the DNA to the filter, washes out other things in the filter and in the end, you use an elution buffer to elute the DNA from the filter. For the PCR, you have to prepare your sample by adding the nucleotides, the primer, the polymerase, and some water. Afterward, you put the samples into the PCR machine. It goes through many cycles of changing temperatures. In that process, the DNA parts into two strings and the primer binds onto their triplet and "shows" the polymerase where it has to set on. Next, the polymerase goes along the string and copies the sequences with opposing nucleotides. From that process, the DNA was multiplied. When the PCR has finished, we performed a gel electrophoresis. The gel electrophoresis consists of an agarose gel, TAE-buffer, an anode and a cathode, and a connection to electricity. Since the DNA has a positive charge, it is being moved towards the anode. The gel electrophoresis can be evaluated by putting it into a bath of a coloring chemical. The gel is afterward put into a dark chamber and gets lit by UV-Light. From that, the gel electrophoresis pictures resolve. <br/> <br/>
+When we extracted the DNA from the leaves, we used a mortar, water, and some ethanol to gap their cellular wall. After crushing them we used filters from the "Nucleospin DNA Extraction Kit" to extract the DNA from the remains. When using this kit, you need two filters, one container for the flow-through, liquids included in the kit and a centrifuge. The kit basically binds the DNA to the filter, washes out everything else through the filter and in the end, you use an elution buffer to elute the DNA from the filter. For the PCR, you have to prepare your sample by adding the nucleotides, the primer, the polymerase, and some water. Afterward, you put the samples into the PCR machine. It goes through many cycles of changing temperatures. In that process, the DNA parts into two strings and the primers bind onto their complimentary sequence and "shows" the polymerase where it has to start sythetising on. Next, the polymerase goes along the string and copies the sequences with the opposite nucleotides. By that process, the DNA was multiplied. When the PCR was finished, we performed a gel electrophoresis. The gel electrophoresis consists of an agarose gel, TAE-buffer, an anode and a cathode, and a connection to electricity. Since the DNA has a negative charge, it moves towards the anode. The gel electrophoresis can be evaluated by putting it into a bath of a coloring chemical. The gel is afterward put into a dark chamber and gets lit by UV-Light. Hereby, the gel electrophoresis pictures resolve. <br/> <br/>
 <b> <a href="https://2018.igem.org/Team:Rheda_Bielefeld/Assays" style="color:yellow;font-size:25px;"> Assays </a> </b> <br/> <br>
 The cracking of pollen is related with destruction of pectin and cellulose. Therefore we need enzymes like pectinase and cellulase.
-At first it is important to prove the content of cellulose and pectin in specific substances. Therefore we used each natural and pure alcohol. If there were small bubbles in the substances to see, then we successfully proved pectin and celluose in the samples. This is important for proving the appearance of pollen. After a while pectinase and cellulase should have destructed the pectin and cellulose. The experiment is successfully performed if there are not any bubbles in the samples. <br>
+At first it is important to prove the content of cellulose and pectin in specific substances. Therefore we used both natural and pure alcohol. If there were small bubbles in the substances to see, then we successfully proved pectin and celluose in the samples. This is important for proving the appearance of pollen. After a while pectinase and cellulase should have destructed the pectin and cellulose. The experiment is successfully performed if there are not any bubbles in the samples. <br>