Tuesday, August 29, 2006
Introductory week
***this was supposed to be posted on Tuesday but for some strange reason my blogger saved it as a draft***
This week is a week of my thesis introduction. I already have detailed outline of this section but I really need to start working on putting up some paragraphs. I'll also have to read a bunch of papers in order to be able to give good background info for the projects that I did.
The results section is still not completely done! I am working on writing up the results for my bionformatics project that I did some time ago (but it really takes time to get back into those thoughts). I also had to redo some analysis for the portion of this project - I wanted to make sure that the data I am presenting in my thesis is correct.
The more I think about this project the more I find it interesting.
The bioinformatics project was done to test whether the secondary structures of sxy RNA in Pasteurellaceae are similar (our famous H. influenzae is a member of this family). The hypothesis was that the RNAs in sxy homologues would fold in similar manner if the secondary structure were the one responsible for regulation of this gene.
Eventhough the analysis suggested that there is no common secondary structure of sxy RNA in this family, it showed that the intergenic regions upstream of this gene are quite long (~600 nt). This implies that a regulatory element (of some kind) could be present in the region just upstream of sxy (perhaps in the untranslated regions of their RNAs). This number (600 nt) is even more striking when compared to the mean length of intergenic regions in E. coli (I think that it is about 55nt ).
Unfortunaly, we have no experimental data of the RNA of sxy homologues in other Pasteurellaceae, (we are not sure if they even have untranslated regions in their RNAs), but as other things in science, it make us wonder and think of new ways to test these interesting questions.
This week is a week of my thesis introduction. I already have detailed outline of this section but I really need to start working on putting up some paragraphs. I'll also have to read a bunch of papers in order to be able to give good background info for the projects that I did.
The results section is still not completely done! I am working on writing up the results for my bionformatics project that I did some time ago (but it really takes time to get back into those thoughts). I also had to redo some analysis for the portion of this project - I wanted to make sure that the data I am presenting in my thesis is correct.
The more I think about this project the more I find it interesting.
The bioinformatics project was done to test whether the secondary structures of sxy RNA in Pasteurellaceae are similar (our famous H. influenzae is a member of this family). The hypothesis was that the RNAs in sxy homologues would fold in similar manner if the secondary structure were the one responsible for regulation of this gene.
Eventhough the analysis suggested that there is no common secondary structure of sxy RNA in this family, it showed that the intergenic regions upstream of this gene are quite long (~600 nt). This implies that a regulatory element (of some kind) could be present in the region just upstream of sxy (perhaps in the untranslated regions of their RNAs). This number (600 nt) is even more striking when compared to the mean length of intergenic regions in E. coli (I think that it is about 55nt ).
Unfortunaly, we have no experimental data of the RNA of sxy homologues in other Pasteurellaceae, (we are not sure if they even have untranslated regions in their RNAs), but as other things in science, it make us wonder and think of new ways to test these interesting questions.
# posted by Okapia Johnstoni @ 5:32 PM 
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Hi Milica!
Did you ever do a blast of just your intergenic region against GenBank? I am just wondering if maybe there is a repeated sequence in that intergenic region, or an uncharacterised orf?
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Did you ever do a blast of just your intergenic region against GenBank? I am just wondering if maybe there is a repeated sequence in that intergenic region, or an uncharacterised orf?
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