Difference between revisions of "Team:Uppsala/Worm Culturing/Design"

Line 432: Line 432:
 
<h1> Design  
 
<h1> Design  
 
</h1>
 
</h1>
−
<p>The idea behind the work of the transcriptomics group is to try and detect any changes in the gene expression when <i>E. coli</i> is grown alongside strongyles as opposed to just being grown in a normal lab environment. The aim for this undertaking is to find any and all genes which might be expressed exclusively in the proximity to the worms - giving us a prime opportunity to work some biotech magic and find a way to make a diagnostics tool for the strongyle parasites out of that very bacteria gene.<br><br>
+
<p>The main goal of our project has been the creation of a diagnostic tool for detecting the level of infestation of small strongyles (cyathostomins) in horse faeces. For this purpose, transcriptomics and phage display analysis have been performed. These techniques, however, require large amounts of clean sterilized strongyles.
 +
For this reason, the first part of our project has been the recovery and the processing of the nematodes, to obtain samples usable for the following segments of the project.  
  
−
The way we decided to approach this was by running a full-scale transcriptome sequencing on the entire <i>E. coli</i> genome, both in bacteria grown normally and grown alongside the worms. By doing this, we would be able to quantitatively determine the differences in gene expression.<br><br>
+
While dealing with this task, however, many times our group has faces one problem: the lack of information. Not much, in fact, has been published about strongyles and techniques to handle them. For this reason, this first part of the project often involved the adaptation of a pre-existing protocol or the creation of entirely new ones.
  
−
For this, we created an eight-step pipeline starting from lysing the bacteria to extracting their RNA contents, to refining and finally sequencing the genetic material using Oxford Nanopore’s MinION device - which you plug in to your laptop. That same laptop will then be used to understand what exactly is going on in the bacteria.
 
 
  </p>  
 
  </p>  
  

Revision as of 11:46, 14 October 2018