Productive, pregnant, postdoc - Post I

My major goal at work right now is to get myself to a point where I can work on two manuscripts during maternity leave, IF it’s possible. To do this, I need to get a certain number of things accomplished. Unless the baby decides to make a very early appearance, I think I can get all of the following items accomplished in the next 7-8 weeks. I will post on my progress each week.

Manuscript A: This is a manuscript from graduate school that I started writing in June. I need to verify some in silico promoter analyses using semi-quantitative RT-PCR. To complete this task I will need to do the following, in triplicate:

• Order primers. (not in triplicate :))
• Grow strain under inducing and non-inducing conditions.
• Harvest cells at a specific time point and extract RNA.
• DNAse-treat samples, quantitate and perform RT-PCR

Not too bad, really. The only hold up here is an issue with strain availability, and this should get resolved shortly.

Manuscript B: This is my first paper from my post-doc. Originally I thought we might get this paper out near the end of last year, but I decided to add some experiments and broaden the scope of the paper. These extras are exactly what I need to accomplish.

I need to make two sets of 13 strains (yes, that’s 26 strains) for some in vitro and in vivo work.

Currently, I am cloning as I must create 26 constructs. For each construct, I must combine 3 PCR products. So far, I am about half way through this PCR nightmare. I’ve included the cartoon I put together to help all the non-cloners in my lab understand what I am doing. (Yes, there are some errors in my math regarding the cycles, just ignore it if you can.)

My short-term goal for the end of this week/early next week is to get all PCR products combined (resulting in 26 final products) and ligated into the first cloning vector.

So you're funny now?

I think we’ve all experienced instances where our PI’s say something that makes us want to laugh in their face, particularly when it comes to experiments. For example, “Microbiologist XX, I know you just told me you were going map the 5’ end of your favorite transcript using primer extension, but do you think that will be finished by tomorrow?” Microbiologist XX suppresses laughter and replies “Well, our protocol requires at least two days to complete assuming that you already extracted your RNA, which I haven’t.”

The more time a PI spends away from the bench, the more they forget how long a particular protocol takes to complete. It’s amusing if things are going well, but if you’re already working your ass off and things aren't going as planned, it’s more likely to make you wish you could impale your PI with rusty spatula dipped in nitric acid.

Apparently, my post doc mentor is quite the comedian as well, but not intentionally. My goal is to submit grants by the end of this year/beginning of next year and obviously, more publications are better than less. Magnum, PI asked if I was working on a second manuscript with my graduate school PI and I informed him that I was indeed working on the second paper. Then, Magnum, PI asked me something terribly funny. He wanted to know if the paper would get submitted before my grant? It was all I could do not to laugh. He, of course, does not know that writing a paper with grad. school PI takes at least a year, if not more. He doesn’t know that we will go through 50 revisions. He doesn’t know that the last 25 revisions will center around rearranging 5 to 10 sentences and he also doesn’t know that the 40^th version of the manuscript is almost identical to the 27^th version. I do know these things, and the only way I can keep from losing my mind during the process is to find the humor.

Then it was my turn to accidentally make a joke. I asked Magnum, PI if he thought the paper we were working on would get submitted before my grant. He looked surprised at my question and I am pretty sure he wanted to laugh, but all he said was, “Of course it will. Why wouldn’t it be?” I almost fell out of my chair. Write and submit a manuscript in less than four months? Seriously?

I really hope that this is true. One of my biggest disappointments about grad school lab was how fucking long it took to get papers written and submitted and the fact that I graduated with 3 papers needing to get pushed out the door. I understand going through several revisions, but nitpicking individual sentences where the outcome is basically the same sentence is extremely frustrating.

The Lips and Assholes Paper

I've spent a large part of my day writing a manuscript from using data obtained from graduate school and I'm ready to explode. I blame this on two things: (1) Half of this paper is negative data and (2) The data is what I consider "left-overs."

Writing a paper half-full of negative data sucks ass for the obvious reasons. It is generally not as interesting as a paper based on positive data and, unfortunately, it takes a lot more effort to write. Plus, it seems like you are constantly justifying why the data is important which makes me feel a little more like a used car sales person than a scientist.

What's worse than writing about negative data is the fact that this paper seems to consist entirely of left over data. I previously hijacked a portion of the results and placed them into a paper that was recently accepted. Obviously this was a good idea, but now I am left with a hodge-podge of data that is related, but difficult to make into a cohesive story. The results outline I put together with my grad advisor regarding this paper seemed like a good idea at the time, but translating that discussion into a paper is not going so well.

I am so freaking irritated. I keep reminding myself that writing is a frustrating process, but I still want to smash my laptop.

Writers on the storm

Clearly, writing is an important part of science. I get this, but holy shit people, I can't believe the amount of writing that is in store for me.

First of all, I just started another manuscript from my dissertation. The last piece of data from my collaborators finally arrived and my grad. advisor is raring to get started on this paper, as am I. Fortunately, I have a decent rough draft of the results and materials and methods sections.

In my current lab, it looks like yet another first author paper is on the horizon. Initially, I thought that this data would add to another existing manuscript, resulting in a quick second-author publication. However, my results are starting to take over and Magnum, PI is leaning heavily toward changing the direction of the paper. I am likely to get the first author slot. Of course, this means I write the paper (as it should).

In addition to the paper, I am about to embark on my first grant-writing extravaganza. I am very excited about this and I am looking forward to getting all my ideas together. Even if I don't get funding, the process of writing the grant or fellowship is good experience and has the added bonus of forcing me to think about my project more thoroughly than I do on a day-to-day basis. But...the amount of time, effort and writing is certainly daunting considering everything else that is on my plate.

As of this morning, I felt ready for the challenge and confident that I could find enough hours in the day to write two first author manuscripts, a grant/fellowship and continue to churn out data. By the end of the day, those feelings were starting to disappear because Magnum, PI informed me that he wants me to write a review and soon.

This seems like a shit-ton of writing. Sure, it's not all starting on the same day, but based on my calculations, there is going to be some serious overlap.

Now, I am not quite sure how I am going to get all of this done and bust ass in the lab. Failure isn't an option, so I need to get organized and I need to get a plan. Unfortunately, all my thoughts right now contain multiple expletives and whining about how I hate organizing and planning.

I know, I know. Quite your damn complaining and get your shit together.

Tuesday Kicks Monday's Booty

On Monday, I got out of bed late, put on a shirt with multiple stains down the front and made it into to work to find three, yes three, plates chock-full of contaminants. (Contaminants at this stage of the game are so embarrassing.)

On Tuesday, I get out of bed on time, put on clothes containing no visible stains and made it into work early enough to beat Magnum, PI to our meeting. Once he arrived, we discussed the paper I am working on and finalized experiments for the last figure. At this point, I am pretty happy. I've barely been awake two hours and a new paper is on the horizon.

Then........

I return to my computer and check my email only to find that my manuscript was accepted for publication with minor revisions, where minor revisions equal semantics.

o.O.

That's right people. Tuesday is looking up.

Microbiologist XX reviews her first paper

While in graduate school I helped my PI review a couple of papers, but informally. This usually involved me reading the manuscript and then discussing my criticisms with her. What she did with them, I have no idea. Now, Magnum PI wants me to review a paper. He is going to review this one with me, but after that I am pretty much on my own.

He sent me the abstract of the paper today and from that alone I could find some obvious problems with the experiments. Another thing that was abundantly clear upon reading the abstract was that English is not the native language of the authors. In fact, some parts were so poorly written that I had to make assumptions about what the authors were saying. This brings me to my question:

How much does a reviewer get involved with the writing?

For my own papers, I've seen reviewers correct the random spelling or grammatical error, but I have a feeling this paper is going go way beyond this. If I am confronted with sentence after sentence of bad grammar and spelling, as in the abstract, what should I do? Where do you draw the line? The journalist in me wants to correct everything, but obviously I don't have time to rewrite a paper and that is probably not a reviewer’s job.

If there is a limit to how much spelling and grammar a reviewer should correct, does the quality or the science influence this limit?

Anyone care to put in his or her two cents on this one?

Paper Jam

Here I am, post Ph.D., knee-deep in papers that need to go out the door. This situation occurs frequently in my graduate school lab. Usually a student from my current lab leaves with one first author paper and publishes the remaining two papers during their post-doc time. I know this is common in other places as well. However, I was sure I would avoid a similar fate for two reasons.

1. Unlike advisor, I can think in a paper-based manner. Actually, think is not the right word. Advisor can think in a paper-based manner, she just gets off track quickly and easily.
2. I inherited a project with compelling preliminary data and the person I inherited it from had already made several mutants and constructs. I thought I would hit the ground running.

Question: What the hell happened? Why am I, at the tail-end of my graduate career, pushing three papers out the door at the exact same time?

Answer: Because I completely started my project over in March 2007. Yes, completely. I destroyed every single construct and mutant that I started with because they were totally useless. I'll post about the spiral into hell that led up to this mass destruction of plasmids and mutants another time, but suffice it to say, I did not have a choice.

Before surrendering strains and plasmids to the autoclave, I spent two years trouble-shooting and I learned a lot. I also uncovered a couple of pieces of data that I felt confident would become papers 2 and 3.

During this time of trouble-shooting my plan was: Uncover the mystery of this project and why the results were not always reproducible, fix said problems, get data, and write up the paper. Then, I would start investigating the interesting finds for papers 2 and 3. I did figure out the problem, and that is why everything went into the trash and I began again.

I decided that when I started the project over, that I would need to work on the other two portions of the project at the same time, or I would never graduate. Just under two years later, I had enough data for a dissertation and almost three papers. I still hoped that paper 1 would get out early, but it was rejected. So now, I am adding two experiments to that manuscript and resubmitting (to the same journal since the editor says they really liked the work) while putting the finishing touches on papers 2 and 3, so that I can submit them as well.

What's the big deal if I still get three first author papers from my Ph.D.? The big deal is interviewing for post-docs with no publications. I think this might pose a small problem for some.

Fortunately for me, it did not, but my situation is far from typical. Since I decided not to move to another city, I was able to rely on my reputation as an excellent graduate student to get my foot in the door. Post-doc PI is very familiar with graduate PI's work. Furthermore, I chose the most well-respected members of graduate school department to serve on my committee and glowing recommendations from them, made the lack of publications a non-issue. Thankfully, I wanted to work in this lab and had been coveting it from afar for a long time, but what if I hadn't wanted to stay in town where people believed my boss when she told them not to worry, I would have publications? I don't know if someone in another city, at the same caliber as post-doc PI would have given me the time of day.

So, here I am, in exactly the situation I was sure I would avoid, considering myself lucky that I really haven't suffered for it. I am glad that my academic career did not stop before it started and that I did not have to spend the next few years in career limbo repairing damage done from graduate school. Now, if I can just regain a little energy and motivation, I just might pull it off.

Rejected

My advisor (Dr. K) mistakenly listed me as the corresponding author when she submitted our paper a few weeks ago. As a result, the rejection letter arrived in my inbox on Friday. I get the unpleasant task of informing Dr. K on Tuesday, when she gets back from vacation.
I've worked for her long enough to know exactly how things will play out. The initial look of defeat, followed by the sad eyes look of I'm sorry, that quickly melts into the cheery realizations that I pushed for submitting to the better journal, and the work consists of ideas that were 100% mine. Whew. She feels better and the lecture ensues. "Now, microbiologist XX...don't feel bad, we can address the suggestions and submit to the journals I prefer" (The preferred journals are similar to a J Bac.) My rejected paper could probably be submitted, as is, to this type of journal and would likely get accepted, but I would rather address the issues raised by the reviewers and resubmit to this journal or a journal with a similar "rating" for the following reasons:

1. The negative comments were very few and weren't really that negative. All three reviewers felt that the evidence for two particular claims that we make to be "thin." However, the reviewers also stated that they thought the conclusions drawn from said evidence were correct. Fortunately, the same issues occurred to me, and as a result, I've already have some of the data. The new results support the original conclusions of the paper and address all the major points the reviewers listed.

2. The reviewers and the editors all made many positive comments about the relevance of the work. Actually, based on the comments in total, I am kind of surprised that the paper was not accepted with modifications. However, it is a good journal that can probably be that picky, which brings me to my next reason.

3. Getting rejected from a better journal leaves you with some great feed back on your work. Also, the experience teaches you about submitting to different kinds of journals and what different journals expect. Since my previous papers were published in J Bac-type journals, I feel like I know what the expectations are. Resubmitting this paper will teach me more about the expectations of journals with higher impact factors.

4. The turn around time for this particular journal is quick, so why not try again. If its rejected again, we send it to journals that fall within the comfort zone with little time lost.

We'll see how it goes on Tuesday when I discuss things with Dr. K.