Torfinn Nome » MSc

Le Fin

Torfinn Nome — Sun, 22 Jun 2008 12:05:53 +0000

I actually did it. I defended my thesis last week. Believe it or not. I certainly do not. At least not yet. A summary of the thesis can be seen in the above picture (courtesy of Wordle).

Now what?

Living amongst Barley, Trees and Bees.

Torfinn Nome — Sun, 25 Jun 2006 12:53:42 +0000

The confocal microscopy wasnt’ the blast I was hoping for. Not because 3D visualization using laser and fluourescence isn’t fun and impressive. But, mostly me having high hopes: Looking at living mammal cells. Manipulated proteins with different stains, interacting, colourful images… Oh well. Instead, we watched a dull image of some cells involved in the breaking loose of the leaves of the flower Poinsettia. There are times I really dislike studying at an agricultural university, one of them being now. :)

BIO300 – Mikroskopiteknikker

Torfinn Nome — Wed, 14 Jun 2006 14:36:32 +0000

I’m attending a 3 week long course teaching different microscopy techniques. We are 8 people. Yesterday, I fell hopelessly in love. With their brand new scanning electron microscopy! I was kind of suspecting this to happen, having wanted to work on a SEM for along time, but I was really blown away. I definetly need to integrate it in my thesis. I have a hunch the confocal microscopy might not be too disappointing either…

Using intense lobbying (I believe), two … collegues (Lasse and Marthe) of mine got me a job at the Norwegian Institute of Public Health, all July and most of August. Thanks!

KJM310

Torfinn Nome — Wed, 22 Mar 2006 20:41:42 +0000

I’ve not been able to do much work in the lab lately. Mostly because I’m a Master of Procrastination(TM). But also because I’ve been working on finishing the practical part of a course I’m taking this semester, chromatography. We’re having three lab exercises, using three separation techniques. Ion exchange column, GC (with FID) and HPLC. Instead of the tidious work of writing lab journals, posters are to be presented in plenum. This course is very relevant to my thesis, as I will be using eluation techniques for purifying my precious chitin binding proteins.

Substitute for Love!

Torfinn Nome — Sun, 05 Mar 2006 21:00:57 +0000

Initiating a new transformation process this Friday, I spent most of the weekend in the lab. Mostly … waiting. This evening, at 19:30, looking at the result (after restriction enzyme cutting): The transformation was successfull! Nothing to write home about, really… But. After a week of feeling crappy. Lacking results. Nothing going the way you want them to. Finally looking at a successfull result materialising in front of your eyes somehow makes it all worth while, and then some!

…or lack of.

Torfinn Nome — Mon, 27 Feb 2006 15:04:47 +0000

That is, lack of successfull transformation. I got my colonies on the LB agar, and was happy, everything going on as planned. But, darn, something wasn’t right. Using restriction enzymes to cut the new plasmids, checking if my genes actually had been incorporated, showed … nothing. I’ve spent the last days trying to find out what went wrong. My PCR products seems all right. The plasmid we’re using for transformation has a “suicide” gene which gets transcribed if there is no successful gene incorporation, inhibiting growth. But, I got my colonies, the bacteria did grow. I even tried several different restriction enzymes, and restriction buffers, just to be sure. But, nothing, nada, my gene is not there. Weirdness. I will probably end up doing the transformation from scratch. Albeit I really want to know what went wrong…

Transformation

Torfinn Nome — Mon, 13 Feb 2006 18:02:10 +0000

I’ve learned a lot these first weeks. And the feeling of being totally lost is gradually fading. Still, talking about green fingers, my head definitely feels green sometimes… Anway. I got the primers. I did PCR. I did gel electrophoresis, isolating the genes I multiplied. Today I started the transformation progress, using the Zero Blunt TOPO technology. Tomorrow I will know if my first GMO (Gene Modified Organism) experiment was successfull or not. And later this week I will know if I actually managed to insert the correct sequence into the E. coli or not. Looking forward to checking out the agar plates tomorrow! My other life: Weekend; at our cabin in Valdres. The weather was absolutely perfect. Blue sky, no wind, -5 celcius. I spent the days enjoying cross country skiing, reading a norwegian classic horror book (“Døde menn går i land”), and listening to the Olympics on the radio.

Progress

Torfinn Nome — Fri, 27 Jan 2006 18:31:38 +0000

So. I’m installed in the lab. I’ve done my initial share of mixing up buffers and LB media for the E.coli bacteria (the ever-present lab workhorse). I’ve created a (tiny) stock of vectors (pRSET based), and should work out the primers for PCR amplifying the two chitin binding proteins I will work on. Trying not to drown in protocols and all kind of information these first weeks, I’ve set up a wiki, and I think it will be quite useful. Actually, I think the whole lab should switch to the OpenWetWare system. My supervisor seems to like the idea, at least. But I guess the management is sick and tired of this happening every year, with new students trying to change the lab… (I know I would!) Today, I spent most of the day playing around with PyMOL, which provides “real-time visualization and rapid generation of high-quality molecular graphics images and animations“. It will definitely help trying to understand the chitin binding processes. Oh, and by the way: PubCrawler. “It goes to the library – you go to the pub(TM)”. You gotta love it.

Rolling

Torfinn Nome — Tue, 17 Jan 2006 19:16:29 +0000

I had a meeting with my supervisor today. He gave me a “tour de labs”, and got me installed. Immediate plans involves setting up an array of useful buffers. I will also have to design primers for a couple of potentially interesting genes that codes for proteins involved in chitin degradation. When the constructs (vector with the interesting gene) are integrated into the new E.coli strain, those cute bacterias will hopefully spew out plenty of the two proteins I’m interested in. I might have to use two methods for collecting/purifying these proteins. One is by using an affinity column coated with chitin. Another way is to add a his-tag to the protein, which binds to a metal ion column. Anyway, this is what is scheduled to be finished before easter. But, as Gustav (my supervisor) puts it; “it all depends; if you have green fingers or not”. Oh, and he was kind enough to hand me at least one kilogram of relevant articles. So if you need to contact me, you’ll probably find me at some machine trying copying them…

edit: Easter, not summer.

Plans for next year

Torfinn Nome — Fri, 23 Dec 2005 23:11:39 +0000

My thesis is scheduled to begin in August, but I’m already planning on starting slowly this winter. This autumn I’ve been studying mathematical statistics, molecular biology, protein chemistry, and molecular genome analysis. I’m slightly ahead of my original plan, meaning I will only apply to one course this spring (chromatography), and one intensive course next August (immunology). I need to figure out what techniques I really want to learn, and have already started reading relevant papers, including the ph.d. thesis of my supervisor Gustav Vaaje-Kolstad. His work includes a paper characterising the protein CBP21 from Serratia marcescens, a protein “opening” the structure of the tightly packed chitin, assisting the chitinase degradation. The paper was made Paper of The Week in the Journal of Biological Chemistry: “Chitinase’s Little Helper“. My plan is to work on other related proteins, see if I can find more proteins involved in similar activities. So there will be a lot of protein chemistry activity, hopefully involving scanning electron microscopy, x-ray, nmr, etc. I will also focus on the bioinformatics tools available, as I know that will come in handy.