Question: Help with Masters Dragon.
1
gravatar for biology.dex
20 months ago by
biology.dex10
biology.dex10 wrote:

I went hard on myself the first year of my MSc (studied ALL day every day for a whole year, in a foreign, cold, COLD country) and got really sick, but before that, took up this giant task of assembling a never-before- assembled genome of an extremophile. I know, I took it upon myself and now regretting it. I figured out once I have the draft genome (which back then, my naive self-thought would be a proper, submitting it to NCBI genome-genome), I would find some PUFA related genes and compare them with those found in other extremophiles and build a story about the adaptation mechanisms in my organism.

Long story short, I was bed-ridden for two years and have severe anxiety now. I feel really shy with my incredibly nice supervisor, I have some questions about building my thesis story though, wondering if someone can brain-storm with me a bit. I have a draft de-novo assembled genome. I know which genes to target, I reciprocal blasted them to check their identity, and based on literature, they are part of the Pufa pathway (Pufa genes are connected to adaptaion to extreme temperatures)..But now what? What next? I am aware that my experiment wasn't set up properly, I have no proof of connecting these genes with adaptation to an extreme environment unless I observe their expression, but is there a way I can make a good Masters thesis of the mess that is my situation?

One option is to obviously present the Genome characteristics, GC content comparisons etc but I still feel something is amiss.

Asking because I feel safe here :)

ADD COMMENTlink written 20 months ago by biology.dex10
1

You could try 1) some simple genome annotation on the newly assembled genome 2) run synteny analysis with the closest available genome and as suggested in the previous comment 3) run gene level phylogenetic analysis. Don't be too hard on yourself, it sounds like you have enough data for a masters thesis.

ADD REPLYlink written 20 months ago by Sej Modha4.6k
1

(Pufa genes are connected to adaptaion to extreme temperatures)..But now what? What next?

Next would be gene knock-outs to see if the mutants fail to survive in the extreme temps that the extremophile normally lives in and then decrease the temp to see how that changed for the mutant. That said, it won't be a sure bet since bacteria are resourceful creatures and knocking out one gene at a time may not have a immediately measurable effect.

As others have already said you must have enough material (tie up any loose ends) to write a MSc thesis. You may even be able to get a publication out of it at Genome Announcements.

ADD REPLYlink written 20 months ago by genomax78k

I'd say that assembling a genome is already an impressive accomplishment for a master thesis project.

Could you perhaps extract similar genes from other species and do some phylogeny (not exactly my cup of tea)?

ADD REPLYlink written 20 months ago by WouterDeCoster43k

and metabolic reconstruction after comparing with other species or closest organism.

ADD REPLYlink written 20 months ago by cpad011212k
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