Its always something

Yesterday when taking data I was fighting with DNA issues. First there was too much and then it all but practically vanished. Then today, I had absolutely no problem obtaining a good coverage of DNA, but the NucS was practically nonexistant. I was using half the amount of buffer to combat this issue and twice the volume of the protein and yet I am still not really satisfied with the number of interactions I could see while filming.

I just started the analysis of the first video from today, so I will soon see if enough data points came out of it. It could be that the very few proteins I do see are actually the only ones interacting and that for some strange reason, BSA is being very robust today in preventing the non-specific interactions. I checked the concentration of the NucS on a slide all by itself and it really did seem fine so I do not think thats the problem.

Swan Song

Yesterday I analyzed all of Friday's data and saw a decent portion of interactions but most of them were really short as in only one frame which is not good for us because it could very easily be a nonspecific interaction if we observe it for such a short time frame.

Today I also had bad luck but in the lab. Experiment after experiment after experiment was bad. I wasn't breaking slides or anything but first I couldnt see any DNA, then I saw so much DNA the screen was practically white, then I couldnt see DNA again. After 18 of these, I gave up and switched to just taking videos of photobleaching. Which came out...okay.
Its not helping that both of today's lunch options included fries. I cant believe its harder to eat healthy in Paris than it is at college in America.

Tomorrow's my last day working, so I'm already getting nostalgic for the pipetting ;-)

Week in Review

So Tuesday I worked on my presentation so theres little to report there except i got a lot of advice and changes from Rachid and then in the afternoon from Cedric as well. On Wednesday I presented it to both of them as well as Antigone, a post doc, and two other grad students. I got some good feedback from everyone and made more changes to my powerpoint/spiel from what they said and the questions they asked. The main thing I have to keep in mind is not rushing through the whole presentation. Then we all went and had a nice homemade delicious lunch at Antigone's. It was just course after course after course of GREAT food. Four hours later we were back at work and completely unmotivated after such a long break with so many laughs.
But I made the latest recommended changes to my presentation and Rachid worked on the analysis of his data.

Thursdaym I did some experiments but they didnt turn out that great so we deleted the results. Then that afternoon I went to the musee d'orsay with two other interns which was a lot of fun and very impressive. We all became huge fans of Monet.

Today i started the day off by revising my Paper for this summer and then began on some experiments. Bumped into and had lunch with Haviland and Ginny for a change which was a ton of fun!

Putting it all together

My Presentation is pretty close to being done. We're still trying to fit a model to the latest data but so far the numbers aren't being too cooperative. I'll most likely update the graphs with next week's data before giving the presentation to my fellow interns and their advisors.
I also worked on my paper today and barring any huge developments over the next week, it too is done. Rachid has already read and approved it but I am looking forward to Cedric's opinions on my presentation on Wednesday.
Then we can get back to experiments!

Ye Olde Blog

I'm working on my presentation today. I'm giving it on Wednesday to Rachid, Antigone, and Cedric. I was supposed to do some experiments this morning first with one of our newest buffers but everyone in the lab with the plasma cleaner apparantly took this day off and half of our lab did too including the one person from LOB who also has a key to the plasma cleaner lab. I did help Rachid out with an attempted alignment of another laser but it did not work out even after hours and he believes there must be something subtly wrong with the setup somewhere that doesn't allow us to become precise enough.

Yesterday was Bastille Day so everyone had the day off from work. Kara and I took the opportunity to go get a really nice lunch and then afterwards some gelato! Then in the evening I went with half the group to go see the fireworks.

Tuesday and Wednesday were the usual mix of experimenting with buffers and performing analysis on the resultant data. Trends have been identified and recorded but we still have plenty of experiments to accomplish.

Pipettes for the win!

So after a long week of catching up on analysis, I spent today purely in the lab performing experiments. Today luck was on my side. Of the 12 slides I cleaned, none broke or leaked, and only two didnt produce good videos! I have now got 5 more trials with the NucS in water, 4 trials of NucS in buffer with 100 NaClm and a whopping 12 videos from photobleaching the NucS in the same buffer!

I am starting the analysis already and maybe will get at least one done before going home for the day.

Presenting

So Cedric will not be here the last week of my internship so I will most likely be doing my presentation twice. Once at LOB for him and probably Rachid and Antigone as well and then another time for the other interns and the advisors back at the University of Michigan.

As a result, I am spending my compiling time today trying to brainstorm what and how I want to present instead of looking up possible career options as a physicist.

I am spending the morning analyzing data which I also spent all yesterday doing. Some of the trials come out great others come out with very very few legitimate points. It has given us a lot of different datasets to compare but we still need to do more experiments so we can have more points under each dataset. Then hopefully our results will become statistcally signficant.
In the meantime, at least I now fully understand stochastic processes.

Pulling out the Big Guns

So Rachid went to talk to Cedric about my badge problem and he came to the rescue. He pulled out the form he had been sent which should have been sent to them as well and now a few minutes later I am in proud posession of an ecole polytechnique badge. My picture is horrendous but no more sandwiches!

Lies.

No badge. Miscommunication somewhere. We went yesterday afternoon and they didnt have it but told us to come back in the morning, we just headed down and the guy said he hadnt recieved any paperwork for it. Looks like I'm stuck eating practically meatless sandwiches for the rest of my time in France.

Lets sing the Xenia's got a badge song!

My badge is finally ready!!! I just have to go to the office and get my picture taken and Ill be able to get in and out of the buiding whenever I want!The theme song for this fortuitious event would be to the tune of Amy's got a gun but a lot funnier.

Spent the first hour this mornign doing analysis and then Matlab lost the connection so all my work was basicaly thrown away and of course since it couldnt connect I lost my license and had to wait for someone else to sign off matlab before I could recommence the analysis. So Rachid and I switched places and he did analysis while I worked on experiments this morning. Out of 7 slides I took 3 videos. We are seeing much fewer protiens than we're used to which means we get fewer good points out of each experiment. We might change the concentration to help remedy this.

Now Matlab is working again so I'm redoing this mornings analysis which got cut short and then after I finish up the data from yesterday, I'll hopefully have time to look at today's data.

Tonight is Girl's night! Inspired by our lovely evening together in Switzerland where we had a nice dinner and couldn't stop laughing, we are going to try and repeat the experience at an Italian restaurant in Paris.

Experiments in the morning and analyzing in the afternoon. The experiments went well, or so we thought until we sat down and started to actually look at the analysis. we're getting so few points on each one. its a real problem.

I also looked at the data from yesterday and those results are coming out horrendous too. I dont have a single point from three of the trials.

We're still experimenting with different salt concentrations so we'll probably redo these 4-6 trials and then analyze them before making a decision on whether higher salt does affect the longevity of NucS in solution.

Today was split up between analyzing data in the morning and performing more experiments in the afternoon. Rachid did the reverse which gave me a lot of independence but also the availability of his expertise for both portions.

In performing the analysis of the photobleaching of the NucS from last Friday , I found that the amount of time they survived was significantly greater (which is good!) than what I had previously found with Monday's data. I printed out the graphs and have saved them as images so theres a half decent chance theyll end up in my final presentation.

In the afternoom I did experiments with the full surface treatment and a different buffer that Rachid had used with his in the morning so that we could compare results. I started out with three slides and treated them all exactly the same as I went through the steps, yet one came out covered in DNA and the other two had a much more sparse density. Rachid doesn't know why this happens but we've seen it time and time again and is one of the reasons why its so difficult to optimize the surface treatment since variables you dont even control also affect each trial.

No four leaf clovers

A seriously unlucky morning as far as the experiments were concerned.

While Rachid worked with the students again, I was trying to do another set of photobleaching trials. I broke two slides just trying to set up, an inauspicious start to be sure. Then every ten minutes I checked the first slide to see how the concentration of NucS on the surface was developing. Even after an hour they were still fairly sparse. Then the laser seemed to exit TIRF mode on its own while I was adjusting the position of the objective lens. When I thought I had it back to how it was supposed to be, I couldnt find anything on the slide. I checked my other two slides but they were also void of NucS spots.

With the second set of trials, I saw no good areas on one. But! with the second one i did take ten videos. Looking at them again back at my desk though I have to say that although the points are very clear, there are so few of them that I'm not sure its a strong analysis either.

Unfortunately matlab is once again giving me the licensing error, so I cant test that theory. Back to reading papers!