Hi everyone, I can't believe this is over, actually my lab work ended one week ago, but I moved to a student dorm and haven't had internet access since then, finally got my LAN cable. What is there left to say? Well, we got the sequences right on time, so the very last day I got to use some sequencing programs and got to see some bioinformatics (well...), too. Beautiful results, just the way we had expected, or hoped we would get, only one slight mistake in one line so far. Well, but then it was time to say goodbye, at least to my bench and the lab. Friday and Saturday GMI hosted the GMI Opening Sympossium, featuring some very very interesting lectures by some very interesting people... And the GMI "A Plant's Night Out" - party, of course.
I started my studies on Monday, so far nothing spectacular, but I'm convinced it will get more challenging very soon.
Day 20 1/2 was yesterday, when I finally handed back my keys and said goodbye to everyone, copied my lab journal... Time passed so quick, and I will forever be extremely grateful for the wonderful internship, the experiences, everything.... I had a 3 hour break before my next course, so I helped harvesting Arabidopsis seeds, sort of a nice, quiet round-off to a wonderful lab time.

Thank you so so so much everyone of the Mittelsten Scheid group, Ortrun, Andrea, Tuncay, Bonnie, Martina, Ales, Marc, it has been a blast! Thanks for your patience, your enthusiasm, your help,... for being funny, down-to-earth colleagues to work with. As Bonnie said, I definitely got to know how a lab can be, and I hope I will encounter many labs as this one, although this has been very special. I would have been even more sad leaving the building, had I not known, that my studies might get me to a place similar to the GMI one day. What a nice prospect! :D

Thanks summerschool, Keep it up! Wonderful idea to get young people into labs. Theory is one thing, but to actually be able to relate to the world of science has been amazing.

See you around,
Hannah

Remember when I spread the sterile seeds on hygomycin media? Well, today was time for some statistics. I counted the resistant plants (the ones that were able to grow on the hygomycin medium), the ones that had germinated, but then died, and the ones that didn't germinate at all.

The purpose of the whole thing: Epigeneticly modified tetraploid plants behave differently from what would be expected from Mendelian inheritance laws. I have been using three approaches in trying to test these differences, Southern Blot and Bisulfite I have already talked about, and today we had a look at the phenotype of these tetraploid plants. Very interesting stuff! I hope I will be able not only use these phenotype data, but also compare them to my Southern Blot and BS data. So, there's mostly computer work left to do!

Last day tomorrow, can't believe it.

See you!

As predicted yestereday, I started a new PCR with our missing line, new everything. New primer dilutions, new Taq buffer, new Taq, new nucleotides, new water, even a set of brand new pipettes that the lab just bought for PCR mastermixes and use with fiter tips only (no DNA!), I was even the first one to use them. Well, and guess what lucky Hannah got on her gel: ... Nothing. Hm.

I was able to proudly present the fresh picture of the gel at the lab meeting.... At least we can be certain now, that the problem lies in the primer stocks. There must be some sort of contaminaion in there, so the same piece is amplified again and again, no matter if we're talking about the actual sample, the controls or the water blank. Well, that's life. So I guess C2S did win the war after all!!! Too little time left to wait for new primers, but still loads of other things that will keep me busy the last 2 days.

See you!

Good Andrea spent way too much time in the lab on Sunday again, so she started the bisulfite treatment, conversion over night in the thermocycler. All that was left for me to do was the clean up, I ended up with (hopefully!) converted DNA, and to save time (and nerves), I let the control PCR run at the same time as the promoter specific PCR.

The good news: Conversion wored beautifully.
The bad news: Promoter specific PCR didn't. Not at all! I got beautiful DNA bands, just that they were all the same size, including in the blank and control.

Well, that was ireally it for yesterday, time consuming work without good results :(

Tomorrow's plan: Super sterile, new everything, under the hood PCR., We'll see if it's any better.

See you!

After getting 2 more samples of our last miniprep (the only two of 24 that had the insert :( ) to the sequencing lab, Tuncay helped me get started on the genomic DNA extraction, using the PhytoPure kit again. It seems like months have passed since Day 2, when I did my first gDNA extraction, so many things that I've seen in between, yet I was surprised by how well I got on. Afrer all, I'm a MiniPrep expert by now ;) and there's a lot of lab routine that's part of many protocols. I ended up with 8 nice DNA peletts, I'm still amazed, each time I finish a protocol, by how those things actually really work! It's not just textbook theory, it's real, nd there's so much more to find out.

Andrea was undergoing some little surgery in the hospital (I hope you're well! :)) so we will resume our work on Monday, trying to finish the missing callus lines by starting a new bisulfite. I know we have little time, but I'll definitely try my best, I can't believe I only have 4 lab days left! Plus sequence analysis... Wow, time flies when you're having fun ;)

See you!

Long time, no see. Bonnie officially declared Andrea and my bench "Miniprep City", because that's what we've been doing the last 4 days ;)

Andrea and I are trying hard to find positive clones (E. coli's that have the insert) using LB Amp plates and the wonderful Isopropanol plasmid precipitation protocol, 48 minipreps a day, run a restriction sigestion, run a gel, check for inserts, send samples for sequencing, having too few positive clones or unreliable sequencing results, running another 48 minipreps, restriction, gel, inserts, sequencing, ..... So, in case you have any questions on isopropanol precipitation, go ahead and ask! I've become quie a bit of an expert in that field :D

So, 2 lines remained their usual stubborn selves up until the 3rd Miniprep, so we picked another 12 colonies each, and ran another miniprep today. This time the express version of a miniprep ;) Using the QIAprep kit. Nice, fast and easy ;) and still 1 clone missing, one to have a complete set of 5 sequences of different cloes to compare. And some nonsense sequences that we got for another plant line, but: to all the stubborn clones out there, we're not giving up! C2S, plant and callus, you might have won the battle, but you will not win the war! :)

Very important to mention: Yesterday's lab meeting at the Heurigen in Grinzing. Bonnie, our Heurigen expert's insider tip. That was a really nice evening! To al you Upper Austrians out there, remember, if you ever go to a Heurigen in Vienna, you're OK to order a Most, you will not get that aweful Uper Austrian type of Most (Do avoid Sturm, though!) And it even got zünftig with the original Heurigenmusi, wonderful. The outcome of the meeting: Tuncay and Heike don't fancy zünftig and Ales wears tights ;)

See you!