Late night "research"

I stayed up a little later than usual tonight, not out with friends, but actually being semi-productive after an evening of relaxing. I watched some video and read some about the work of someone I am interested in doing a postdoc with. I also drafted the beginnings of a cover email to inquire about job opportunities. I believe that is nearly 1/2 of one point on my checklist for the week!

I also wrote about 2 pages of my intro chapter today after reading a bunch of papers about my system in Pseudomonas aeruginosa. I will perhaps share some of what I learned tomorrow, or really later today, when it's not 1:40 am.

New work schedule

I'm glad that I got the motivation to do more writing when my advisor is gone. It gives me the chance to adjust to a new schedule without her watching me, which will perhaps give me the confidence to disappear more often once she is back. I have been working part-time and writing part time. Most days that means 6 hours work-3 hours writing, and hopefully some more in the evening (but not always...). But I have to leave lab- I am not that great at writing in lab. Data analysis is fine, but actually focusing on reading papers and writing is hard for me, when there is plenty to be done and people who may or may not ask me questions are everywhere on the edge of distracting me.

My (admittedly ambitious) goals for the next week are:

Writing:
1. Write the discussion section of my second paper.

2. Read a ton and write at least 10 more pages of my intro chapter (I currently have 11 pages written).

3. Start reading for the book chapter.

4. Draft cover email for at least 2 people I might be interested in doing a post-doc with.


Lab:
1. I have some membrane preps to do, possibly this weekend. These are for any westerns I still need to do, and also to get ready for mass spec.

2. Check the mutants I tried to make, should be ready Tuesday.

3. Start the process of trying to clone a couple of genes onto a plasmid as alternative method of complementation; though still not as useful as the phenotypic complementation I'm interested in getting someday, at least it is something.

4. Finish some microarray comparisons so I can present some ideas at the other lab's group meeting in a week and a half.


The other thing I have to confess, which I have mentioned before, is that this is all subject to change because I am really good at productive procrastination. I might not get one of these things done, but will get something else of value done instead. It's just how I am.

Checklist fun

I posted a to-do list a couple weeks ago for while my advisor was gone. A couple things got added to it since, but let's see how I'm doing:

1. A couple more western blots (hopefully done soon?).

I just made more protein to hopefully wrap those up soon. We'll see once I present at the other lab's group meeting. Which leads me to....

2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
Still sounds like a time-waster for the first week or two, but I am going to my first one today...wish me luck! I got a lot of data analysis and a handful of slides made to bring with me for when I do get to present my confusing work.

3. Send one protein for mass spec (and get the post-doc to help me).
Still have to talk to the post-doc about this one. I'm a little concerned because I think my advisor needs to ok something in order to pay for this...

4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
I think I got through the subcloning part, but our sequencing facility isn't exactly awesome right now, and I only got back really degraded and useless sequence from sending my clones in. I guess all I can do is proceed forward with the allelic exchange and just hope it works.

5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
Under this category is where something got added. My advisor sent me a draft of the paper that needs to be re-submitted (long story), and I did edit it and add back in all the references, plus some new ones, and I sent it back to her yesterday. Yay! So now I'm back to writing everything else...

6. Look for jobs. Sigh.
This one is where I have fallen short so far. I got sidetracked a week or so ago, and started looking for just teaching jobs because I still can't decide what I want to do eventually. But I think I should look for a post-doc first.

Could what I use to prevent infection sometimes cause it?

I ran across this article today. It describes how a nasal spray was the cause of a mini-Burkholderia outbreak in a hospital in Denver. As a daily nasal spray user, I do not really like the sound of that. I take a nasal steroid and a nasal antihistimine to prevent myself from getting sinus and ear infections all the time, but if I'm introducing hard-to-treat bacteria into an already inflamed nose, I could run into problems.

This raises a bigger question, which is highlighted toward the end of this article: "'Nasal spray products are among the most widely used over-the-counter pharmaceuticals, but to date they are not required by the FDA to be sterile,' said Susan Dolan, one of the article’s authors." What else is not required to be sterile?

As a microbiologist, I know that it's not usually that beneficial to have things be entirely sterile. Most bacteria are good for you, or at least not bad for you. And if they don't seem to be actively helping you, many of them are just taking up physical space to prevent nastier bacteria from setting up shop. But, I also don't want to inject pathogens directly into my nasal cavity. So where do we draw the line? How do we decide what should be absolutely sterile, and when we need to just let the bacteria do their thing?

I heart the library.

I definitely forgot how much more productive I am at writing in the library than I am in lab. In lab, people come and ask me questions, or I feel compelled to stuff tips or do experiments. I can get so much more accomplished without all that extra distraction around. Also, there is less mold, heat, and humidity in the library than in lab. And, strangely enough, I really love the smell of old books. I may be spending considerably more time here in the near future.

Mural of blots

Firstly, sometime after midnight Monday night, my advisor actually sent me the paper to work on (from vacation?), so I have some referencing to do soon. But at least it will get done!

I have made science into art. Well, not really...but I printed out all my western blots from this summer and taped them up on the chalkboard so I could see what differences we're interested in are always there (reproducible) vs. some that only show up occasionally, and have about four major differences to take to my collaborator's lab meeting and ask about. Now I just have to convince the postdoc my advisor and her husband share to take me down to the mass spec facility.

I'm afraid to jinx it, but I will say that my cloning looks more promising than it has in awhile- it would be great to make this construct, and for it to actually work to make my mutant, but three years of failure on that front has taught me not to hold my breath. I realize it's not true, but sometimes it feels like there's more superstition to science than there should be. As in, you have to make the appropriate sacrifices to the cloning gods, and do things during the proper phase of the moon wearing your lucky socks or something.

I have spent a lot of this week helping a younger student work on her comprehensive proposal, and helping my boyfriend's sister with her cover letter to get a job in microbiology. That all qualifies as writing, right? I'm hoping this afternoon I can get a couple good hours in at the library before celebrating the one-year anniversary of my boyfriend and my first date. Last night, I went to a send-off dinner for someone else in my class who is moving to CA to get a professional masters in business of sorts, and went to the defense of someone else in my class. Bittersweet on so many levels. I think most of us thought I would be one of the first done. I peaked early, though, and the last couple years have been tough going in the lab. We have all noticed that research either stalls early or late for most of us; I'm lucky enough for it to have gone really well for about 3.5 years, and then the last 2 have been rough, which I believe (though biased) is harder to deal with, because you're so anxious to be done while things aren't working.

Keep your fingers crossed for my mutants!

"I'm all alone....all by myself"

My advisor left for a 2-week vacation. She was supposed to send me the latest draft of my paper so I can add the references in while she's gone. Did she? Ha. Maybe I'll email her at some point, but I doubt I will hear from her these first two weeks or so. I need one of those vacation things. Going to weddings doesn't count- I need something relaxing!

Things to do while she's away:

1. A couple more western blots (hopefully done soon?).
2. Apparently I need to start attending my collaborator's group meeting. Sounds like a little bit of a time waster at first, but maybe they'll have some good ideas for me.
3. Send one protein for mass spec (and get the post-doc to help me).
4. Try and get this silly mutant made. First step: get it sub-cloned into something else. If E. coli could be rebellious, I have the leaders of the revolution right now.
5. WRITE. I agreed last Thursday to help write a book chapter on regulated proteolysis as an appendix to my thesis, so I guess everyone here might be learning a little more about that subject soon. :-)
6. Look for jobs. Sigh.

"What happens in there?"

Thursday, as I was leaving lab, an older couple was sitting on a bench outside my building.
The gentleman says, "Young lady, I have noticed that everyone that comes out that door doesn't look happy - what happens in there?" I replied, "It's a biochemistry building - we're all grad students." His wife interjects, "So - a lot of work."
The gentleman comes back, "But why does NO one look happy?" Instead of all the jaded, cynical quips I could give about grad school, I decide to go with, "Well, we're all inside working on this beautiful day." And he chuckles, and says something like, "Well, when you're retired like us..."

It says something, though, when someone notices that EVERYONE that comes out of the biochemistry building looks unhappy. Maybe we should rethink this. Regardless, this gentleman made my day with his good-natured attitude.

Vaccination conundrum

Saw this come up on my reader today:


Vaccine requirement

It talks about pediatricians who are turning away patients who are not vaccinated. To be honest, I don't know how I feel about this.
On the one hand, I am thrilled that someone is standing up to the people who think vaccines are more dangerous than, say...whooping cough (perhaps my favorite example because I work on its cousin). On the other hand, I'm a little taken aback by the idea of turning patients away.

I understand the reasoning behind it - they don't want to jeopardize the health of the other patients coming in by mixing vaccinated children, children who may carry vaccine-preventable diseases because their parents thought they didn't need to vaccinate their own children, and children with other problems who are medically unable to receive vaccines. If someone who was not vaccinated passes, say whooping cough, to even the aunt or big brother of an infant who has not yet received the full vaccine course, that infant can easily become infected and die. All because they were in the same waiting room as someone who had whooping cough. Read about strategies to prevent this.

I use whooping cough as an example, not only because I work on it, but also because, in older patients, like the aunt I described earlier, it would present more like a cold or flu. Give it to an infant, and suddenly it actually looks like whooping cough, and the baby basically coughs itself to death. I attended a Bordetella conference (whooping cough is caused by Bordetella pertussis or Bordetella parapertussis) last year, and at least two or three presenters forced us to listen to a baby whooping - it may be one of the saddest sounds ever recorded. Whooping cough is also a re-emerging pathogen, which means it's coming back, partly because newer vaccines with even fewer small side effects probably need more boosters to keep immunity high, partly because a closely related bacteria can also cause whooping cough symptoms and doesn't respond as well to the vaccine, and probably partly because many people have stopped vaccinating their children.

However, I am not convinced that blocking unvaccinated children from being their patients will solve the problem they claim. The other patients of these doctors could run into unvaccinated children in daycare, at the mall, or on the playground. But, if their point is to bring awareness and force some kind of consequence on people who choose not to vaccinate their children, then I guess I say "well-played."

On the Road to Recovery

What a crazy weekend. The only time I didn't have to keep running (sometimes actually running, like to get the garlands for the milni, and to keep the boys away from the shoes we had to steal) was after the mendhi, but that's because no one could use their hands, so we couldn't do anything, which in and of itself was entertaining. It was a pretty great weekend, craziness and all. I'm pretty sure I had fun...looking back. At the time I was a little too busy to notice.

Of course, now that I'm back, I'm heading straight back into the science fray. Here's to hoping some of my experiments start working! It would be nice to be able to get a few things out of the way, so I feel better about getting some writing done, and starting to look for a postdoc and/or job.

I think a reasonable set of goals for while my advisor is gone for three weeks is:
1. Having a draft of the second paper (minus the onery experiment) ready to go.
2. Making a list of people who I am ready to send emails to, and for which I might need recommendations.
3. Be as close to done with these western blots as possible.
4. Send at least one sample to mass spec.
 I'm not going to kid myself that I will have made the mutant that has eluded me for years. Some of the time that my advisor is gone, my boyfriend will also be gone, so we can pretend that means I'll get more work done, when in fact, it probably means less.

Hittin' the road, Jack.

The last major trip of my summer (that I know of) starts tomorrow. I'm maid 0f honor in my friend's wedding this weekend. She's American and he's Indian, and there will be both an American and an Indian ceremony in the same day. It will be a whole lot of crazy, but it will be a good break from lab and thinking about work. Hopefully I can come back relaxed and re-energized to work. Also, hopefully in the meantime my cells rethink their bad behavior and come to their senses so that I can graduate eventually.

Also, my advisor got back from her trip to do a pilot screen. Sounds like I get to do some assays while she's on vacation to earn my pay from the grant that's giving me my stipend. I feel so...used. Oh, well.

Happy 4th of July, everyone!

I am celebrating by taking advantage of something cited in a PhD comic from last year:
http://www.phdcomics.com/comics/archive.php?comicid=1338

Free parking on campus.

Yep--I'm in lab for the bulk of the day - of course, some of what I'm doing didn't work, but "that's what puts the re- in research," right? Then it's home to do laundry, maybe take the dog to the park, grill, and watch some fireworks. Busy busy busy.

Everything but.

I am apparently doing everything in my power not to actually work on my dissertation. Today, I cleaned the entire apartment, went to lab briefly, made dinner, brownies, took a nap, talked to my parents, gave my dog a bath, and only just now starting to do some reading I guess. Oops. It's just hard motivation when it feels like there is so much to do. Maybe it will help to break it down into smaller goals...I will have to think about that.

The future is scary.

Had a great dinner/venting session with a classmate of mine tonight. She and I even rotated in the same lab our first year together. She's had a rough go of it with her advisor lately, but has finally set a date for her defense. Now I'm feeling even further behind. When will I be ready? I don't know if I will ever feel ready.

Need to start thinking about buckling down...

Inspired by the blog of a girl I used to work with in undergrad, I think a list of goals sounds like a good plan. I think the goal of this will be by the start of the school year...

Lab-wise:

1. Make the mutant that has been eluding me for years, or at least come up with some other ways to get it made. It's the last piece of my second paper.

2. Mass-spec some of the proteins we'd talked about doing since forever ago.

3. Continue to identify members of my regulon (this may never truly be complete).

4. Organize my strains, primers, plasmids and make digital spreadsheets of all of them.

5. Start getting protocols ready to leave behind.

6. (and most boring)- make Tables of Contents for all my lab notebooks - something I'm going to seriously regret not doing as I went- I am about to start Notebook #13)

Writing-wise:

1. Get the first paper resubmitted. Basically, bug my advisor until it happens.

2. Get a draft of the second paper done (leaving appropriate holes for when that mutant gets made).

3. Have at least a draft of every chapter of my thesis (This is probably impossible. I could be ok with a draft of my intro chapter and my two main papers, a really rough draft of the third main paper, and outlines of all my appendices).

4. Set a date for my defense. Also going to be tricky to do w/ no advisor around...

Post-doc exploration:

1. Make a short list of people I'm interested in contacting. Read info about them and figure out how I might fit in their research.

2. Update my CV, and start drafting "cover emails."

3. This is the tricky part, because my advisor is gone for three weeks starting the end of July, but decide who will write my recommendation letters, and get their ok to be my references.

Life-wise

1. Survive being maid-of-honor in this crazy wedding next weekend.

2. Keep walking/running, and try not to revert to crazy studying snacking with no exercise. I don't need to gain any thesis weight...

3. Set aside some money for a small trip after my defense.

4. Just try to keep some balance between crazy graduating and sanity.