Skip navigation

The NaturePlus Forums will be offline from mid August 2018. The content has been saved and it will always be possible to see and refer to archived posts, but not to post new items. This decision has been made in light of technical problems with the forum, which cannot be fixed or upgraded.

We'd like to take this opportunity to thank everyone who has contributed to the very great success of the forums and to the community spirit there. We plan to create new community features and services in the future so please watch this space for developments in this area. In the meantime if you have any questions then please email:

Fossil enquiries:
Life Sciences & Mineralogy enquiries:
Commercial enquiries:

Currently Being Moderated

Summer student Josi has been working with Dr Anne Jungblut on the Museum's cyanobacteria collections. Her next post on cyanobacterial diversity is all about DNA lab work.


At the end of my last post, we determined which cyanobacteria isolates were unialgal by microscopy and suitable for DNA analysis. These samples were initially collected during the Antarctic fieldwork featured on this blog, stored, and brought back to the Museum. Now we want to know what type of cyanobacteria we’re dealing with! One method to determine the species is by DNA sequencing. For cyanobacteria it is really important to use DNA analysis, as cyanobacteria have very varible morphologies that can change under under different growth conditions.


Analysing DNA


The first step of preparing the samples is to carry out a DNA extraction. This step destroys the cell wall of cyanobacterial cells, and removes everything but the DNA from the test tube. A cyanobacterial genome is fairly large, around 1-10 megabases. That’s as much information as fits on a CD-ROM! Therefore we want to look only at a smaller section of DNA at this stage. The step after DNA extraction is called a PCR (polymerase chain reaction), which amplifies a small part of the DNA and generates multiple copies of it. We are using a cyanobacteria-specific protocol that only targets the DNA of cyanobacteria.


Sounds straightforwards, right? Well, this summer I was the victim of the PCR ghoul - none of the reactions worked...or rather, they worked too well. Below you can see the results of one of my (many…) failed PCRs. Each white stripe corresponds to the amplified DNA after PCR of each sample. The 'ladders' on each side are the equivalent of rulers to allow you to verify the size of your amplified DNA. Looks pretty good, right? We’ve got a good yield for each reaction!


Wrong - unfortunately, the white stripe on the far right is a negative control. I set up the PCR for that reaction without any DNA, so actually, there shouldn’t be any stripe showing up at all! So what’s going wrong here?


pos neg control blog.jpgPCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica and contamination in negative control.


Well, the PCR amplifies only cyanobacteria DNA - so there can be only one explanation for the 'positive' negative control. One of the reagents for the PCR has DNA contamination! The only solution to this is trial-and-error elimination - each reagent must be replaced individually to figure out the culprit. Unfortunately, a PCR reaction requires about 8 different reagents to work, and any one of them could contain a  tiny trace amount of cyanobacterial DNA.


You can imagine that this process takes time, and can at times be disheartening, especially as the contaminants cannot be seen with the naked eye. However, luckily, the PCR ghoul finally released me from my odyssey and my negative control was finally 'negative' without  a white strip, and I was able to send my samples for DNA sequencing. More on the results next time!


PCR blog.jpg

PCR results from Cyanobacteria (16S rRNA gene) isolated from Antarctica without contamination.

Comments (0)
Anne D Jungblut

Anne D Jungblut

Member since: Sep 2, 2010

I'm Anne Jungblut from the Botany Department. Join me as I head to Antarctica to study cyanobacterial diversity in ice-covered lakes of the Dry Valleys and Ross Island where already scientists on Scott's and Shakleton's expeditions made many discoveries.

View Anne D Jungblut's profile

Bookmarked by (0)