Slowly but surely.

Checking in to see how I did with my to-do list last week:

1. Finish rough draft of intro chapter
Done and done. I'm going to leave this alone for awhile, and revisit when more is written
2. Keep working on book chapter
Got a fair amount done, still a lot to be done because it's due at the end of the month.
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
I'm not willing to cross this off yet - I started to outline possible ideas, but it's hard...
4. Keep looking for people to work for.
Still have more people to look for- after awhile, everyone's work sounds the same...sigh.
5. Try to get some of this cloning to work
Got some cloning to work- now I just hope the construct works---will find out today and tomorrow, I suppose.
6. Control for conjugation
I have done the control, now I just need to figure out if it worked....
7. Design more oligos for transcription
Just a couple more sets to design, and I can put the order in.

I guess I did ok last week! Still soooo much to accomplish, though.

For the next couple days, I just have some experiments to check for the plasmid constructs I made, and then a lot of computery work before I head to Newport News for my friends wedding. :-)

Stacks and stacks

I printed out what I've been working on lately, and it's a substantial amount of paper I suppose. I printed the intro chapter, the second paper (Chapter 3), and the eight pages of the book chapter I've spat out so far.

Revised goals for the week:
1. Finish rough draft of intro chapter
2. Keep working on book chapter
3. Get as much done on Chapter 3 and 4 as possible, but this will be tricky in general
4. Keep looking for people to work for.

5. Try to get some of this cloning to work
6. Control for conjugation
7. Design more oligos for transcription

8. I got my mass spec back, and it actually makes some sense...what to do with this information now eludes me, of course.

The LeStrange Gringott's vault

That's what my work feels like. You know, when you touch something and it multiplies into many more of the same thing. I swear I got a lot of writing done Friday and today. But it just feels like there is so much more to do!!

I actually got about 8 pages of the book chapter done, which I'm pretty proud of. I have also written a couple more sections of my intro chapter. I think I need to print what I have so far and figure out what is left. I also need to deal with the other papers---so much easier said than done.

Time flies...

....even when you're not having that much fun. Ack. How is it mid-August already!?

My to-do lists aren't getting shorter fast enough. I think I need to find a way to do less in lab and more writing because I want to defend before my boyfriend might end up on a geological expedition of sorts in November. It'd be nice to spend a few days with him thesis-free, and also for him to be there to help celebrate my defense. Fingers crossed. I also need some experiments to work. Sheesh.

However, we are at least aiming to submit (re-submit) the paper this week before the boss heads out for another vacation. So...yay! Maybe this time it will be accepted. Our collaborator in Argentina said that it was "beautifully written." After putting all this extra work in , it's tempting to ask to be listed first, but I'm unsure of the politics of it all. Hm...

Things I need to accomplish in the next week:

Writing:
1. Read and write for the book chapter as much as possible. This is technically due at the end of September, which means the advisor and I need to start going back and forth soon. It will be an appendix in my thesis.

2. Work on organization of the other two papers/thesis chapters. There are so many different ways to package the data, and I need to come up with the best option.

3. Draft more emails to send to faculty for post-docs so that advisor can check them out when she gets back from vacation #2.

Lab:
1. Complementation or die!

2. Look at supernatants of strains for possible differential expression of things like T3SS effectors.
    Easier said than done, by the way....hard to concentrate the supernatants, even in TCA.

3. Should be getting back mass spec data on my differentially expressed protein.

4. Should also be getting some RNA-seq data on my favorite mutant to help a) bolster the array data we already have and b) possibly help us identify SigE-regulated sRNAs.

Yep. Gonna be so much fun.

A lot has happened in the last week, and yet not enough has gotten done.

First, I will be teaching next semester. My advisor's small grant got dried up paying for me and the other student in the spring and summer. I got so many apologies from her. She tried to ask my collaborator to pay for me, but apparently he can't either, so teaching it is. We chatted on the phone while she was at a meeting last week, and basically said that the professor who changed the no-teaching-in-your-defending-semester policy likes to punish faculty that are struggling to get funding, and "is just a dick." Sigh. But, I gave her a couple suggestions for which classes might be easier for me to teach. My first choice is a 400-level micro class that I taught my second year. The prof who teaches it is really awesome, and is there during lab. It's less outside work than the 100-level labs because I don't have to design my own quizzes or anything, I just have to grade 10 lab reports and show up ready to answer questions. Hopefully I will get that one. But still. Boo.

I also presented my work at my collaborator's group meeting. It took about an hour, but I got a few decent suggestions of things to do, which is the good/bad thing about group meetings. You get feedback, but then you have a mountain of other things to test, and feel like you have no time to accomplish it in. I guess that's what working Saturdays are for. :-(

I think that's plenty for now. I have plenty more crazy going on in my life, but these are the initial insanity. Figuring out what to do next semester can wait for its own post....

The fun just doesn't stop.

I found out yesterday that, in addition to writing a massive dissertation, looking for (and hopefully interviewing for) a postdoc, finishing up experiments, presumably moving, and hopefully getting to go home for a few days, I will be teaching this semester!

It used to be departmental policy that if your advisor is lacking the funds to pay your stipend, you teach...except in the semester you defend. The new "assistant dept. head of graduate students" has decided to change this policy because they're desperate for TAs. So not fair. I may still be too angry to really talk about it.

Not bad...

I'm actually pretty proud of my work today...I even added to one of the goals, even if I didn't quite get to a couple of them yet. I also accidentally took an hour nap in the middle of the afternoon, and had to walk the dog and such in the evening. Not too shabby.

1. Take Roo to the park in the morning, then come back and run myself.
2. Laundry
3. Clean kitchen

4. Read/write about P. syringae AlgU for intro chapter
   also read/wrote about V. cholerae RpoE for intro chapter
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
6. Start discussion section for RseAB paper
    I started, but I won't promise that it's any good...
7. Work on some kind of alignment figure for intro chapter

8. Lab: overnights for colony PCR, finish destaining gel, change ice

Busy busy.

Today's ambitious to-do list...I'll check in later tonight or tomorrow to see how I did:

1. Take Roo to the park in the morning, then come back and run myself.
2. Laundry
3. Clean kitchen

4. Read/write about P. syringae AlgU for intro chapter
5. Read about 2-3 potential postdoc advisor's work, finish draft of at least one cover email.
6. Start discussion section for RseAB paper
7. Work on some kind of alignment figure for intro chapter

8. Lab: colony PCR, finish destaining gel, change ice

Floodwaters

Sunday, I came in to start prepping outer membranes from my various strains. Bordetella bronchiseptica takes most of the day to lyse, so I figured I could get some writing done between snap-freezes.

Apparently the building had other plans.

I walked into the lab, got to my bench and stopped short. The area around my bench, which is in the middle of the room, had a lake, with no bridge to cross to my desk. I looked up. No water on the ceiling. I looked under the sink. The floor was wet, but nothing near the pipes was. Where had this water come from? There was no trail of trickling water coming from anywhere. My bench is the lowest point in the lab, so no matter where the flood starts, it ends up there, but there was no evidence water had traveled from anywhere else.

It was Sunday, so I called the physical plant emergency number, and someone came over to shop-vac it up pretty quickly. As they did, we noticed that water was seeping out from under the cabinets. Two plumbers came, and couldn't figure out where the water was coming from. After they left, it started seeping out slowly again, so I called again. The plumber cleaned up under the cabinets a little more thoroughly, but still couldn't figure out where the water had come from.

He had some explanation for when it might have happened, but we're still not sure how it got to where it did without leaving any obvious trail to follow:
This building apparently had a huge water problem on Saturday. The elevators and autoclave rooms had water EVERYWHERE. You can still see the water spots in the elevator today, actually. He called the person in charge of that clean-up, who said that there was only water up to our door. But, he said that the guy who did that 'doesn't go looking for extra work,' and quite possibly had not looked in our lab at my bench, so the water could have been sitting there since Saturday. But it still doesn't explain how it got there...sigh. Needless to say, everything took a lot longer yesterday, so even less got accomplished.