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Grad school hangups - poll! [Dec. 17th, 2012|10:10 pm]
Lab Rats

Hi all:

I'm polling scientists (mostly grad students) for personal experience -- any comments or insight on the following would be great.

Throughout the grad school process, what do you wish people had just sat down and taught you beforehand?
What are some skills that you sort of had to learn on your own?
How to read papers effectively?
How to ask for help?
How to acquire new skills? (perhaps more effectively?)
How to network with collaborators?
Oral presentation skills?
How to use particular machines?
How to write grants?
Particular milestones in the process, such as the qualifying exam or the proposal?
How to achieve a work-life balance (or for someone to even tell you that it's okay to have this?)
How to elevator-pitch to a collaborator or to a famous scientist?
How to negotiate a postdoc or a faculty position?

I'm thinking about how we can better facilitate these "extraneous things" that prevent us from doing what we came to grad school to do - good creative science. So, any advice on how you might have done these things, or lessons you've learned, would be fantastic.
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OMG [Jun. 29th, 2012|12:58 pm]
Lab Rats

The title of this post just about sums up everything that I heard yesterday:

I went to Maastricht at the request of the committee investigating the plagiarism issue, and they were nice enough (they seemed to believe me, at any rate, though it was a bit disconcerting that one of them didn't realize that it's standard to leave everything behind when you leave a lab). Then I went to the university for a bit of business--I've been copyediting papers for a professor there, and he's occasionally advised me on how to handle the paper thing--and once business wound down, he dropped the bomb: An Moens was fired from the university that morning. I don't think my plagiarism claim had much to do with it, since the outcome still hasn't been decided yet, but I don't think it helped much, either.

Anyway, then I ran into one of the students who used to work with An, and the poor girl ranted for two hours about everything that An did after I left (which included a smear campaign against me, apparently, to which I've responded on my blog), which in turn led to her discussing....MORE plagiarism. This time, by one of the co-authors. Unfortunately for me, this co-author is also a co-author on my review, meaning that some of the five paragraphs of not-my-writing is probably stolen, whether line-by-line or wholesale.

I told the committee this morning about my concerns, and told them that if they do recognize me as the rightful first author, I want the paper retracted (they might not decide until the end of summer). You can't win, even if you've won, apparently. But that's the beauty of my position: I don't need this article on my CV. And God knows, I don't need a plagiarism charge against me.
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Help me lab gripes, you're my only hope [May. 24th, 2012|02:11 am]
Lab Rats

So I'm doing long-term fluorescent studies on Hela cells. Well, I used to do them in another lab, ever since we moved nothing is working anymore.

Whenever I now try to image, my cells die. I tried everything; different cell batches, different buffers, gentler transfection methods, but nothing works. Whenever I set up the cells on the microscope, they bleb and die. And I mean all of them. And even if I manage to image some before they die, that's really not the point of long-term measuring, you know? I am completely clueless, and the boss is getting impatient. I have installed a heating stage and use phenol-red RPMI supplemented with Glutamate and 15mM HEPES. I only remove FBS, which I don't want to interfere with my measurments. This has always worked before, a little starvation was always okay, but not anymore... any idea what could cause this? The cells look fine in the flask, but when I transfer them onto glass my problems start. :(
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Just an update [May. 22nd, 2012|08:53 am]
Lab Rats

OK, so I decided to play hardball: first author, or take it down. Well, I didn't put it quite that way in the email to the editor, but I did say that nothing except first author would be acceptable at this point, considering that I was kind enough to wait for her (rude) response before dashing off the emails to everybody and their grandmother.

Secondly: the universsity has begun legal proceedings. I'm not sure what this means--I very much doubt that a court would be involved, though if it does and I end up testifying, it could get interesting. I wonder if she'll try to slander me in open court...

Anyway, the moral of the story is, if you're trying to get back at someone in the sciences, plagarism is a really shitty way to go about it, especially since they could always have a backup on gmail.
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(no subject) [May. 20th, 2012|08:37 pm]
Lab Rats

So I finally heard back from the editor (meaning that An finally got back to him, meaning that at least one other co-author has spoken with her about this, or else she's gotten wind of what I've done somehow and is desperate for damage control).

An is willing to give me 4th author. On the one hand, I realize that this is a major improvement. On the other, well...as I said before, 85% of the text is mine.

Take it or leave it?
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Pissed as hell, and naming names [May. 18th, 2012|10:10 pm]
Lab Rats

In 2010 I worked at Maastricht University, under Dr. An Moens. During my time there, I wrote a monster review, but we couldn't find a journal that would publish it (at 11,000+ words, I can't blame them). When I left the lab, she was still looking for a publisher. I was aware that it would probably be extensively edited, and if that was the case, I might not be first-author on it anymore. Fine. Just get it out there.

Just this week, I learned that it's just been published. And that my name is nowhere on the author list.

Incensed, I contacted the editor at the journal. He sent me a PDF, to show me that I was, in fact, acknowledged--in the acknowledgements, for my "technical expertise, editorial assistance". Editorial assistance my @$$. 85% of the text is mine, with minor edits at best. As in, huge sections of the review were copy-pasted from the original. And the parts that have been changed? "It is apparent" becomes "Apparently"--that sort of thing. There are maybe 5 original paragrpahs in the entire thing--and I'm being generous. If someone wants to check this, I can forward you my last version of the review, and you can compare it to what's online.

The editor-in-chief is a decent guy--he got back to me the same day (editors tend to do that when you subject an email with "plagarism"). I forwarded him the original 11,000 word beast, which I still had on gmail, to show him that I was not joking when I said that most of the words that are in that review are mine. I think he wants to get both sides of the story. I don't think he will, because she's good at ignoring things she doesn't like to hear.

The article, FWIW, is the J Mol Cell Cardiol. 2012 Jun;52(6):1213-25. Epub 2012 Mar 21, and is titled "Doxorubicin-induced cardiomyopathy: From molecular mechanisms to therapeutic strategies." If anybody wants to read the original in all its glory, let me know.

EDIT: I should also add that this is not a spur-of-the-moment post. I waited until she responded. And her response, basically, was, "I don't think you made any significant contributions." So this goes up. Spread the word.
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Protocol Hunt [Feb. 13th, 2012|12:37 pm]
Lab Rats

[mood |determined]

For various reasons, I find myself without my own lab protocols (I'm not currently working in a lab, much as I wish I was). I was hoping folks here would either be willing/able to share their protocols or have online resources they like to use. I'm looking particularly for cell culture, transformation/infection, cloning, immunohistochemistry, and cellular assay (e.g. ELISA) protocols, but certainly wouldn't mind protocols for extraction, purification, and analysis of DNA, RNA, and proteins as well. All help is very much appreciated!
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Working days of a scientist [Dec. 26th, 2011|03:47 pm]
Lab Rats

[mood |aggravatedaggravated]

It is cold. Those unsung heroes that still make it to the lab are sitting in overcoats and typing in gloves. There are two portable heaters per student, but they don't help very much. The ink in our pens doesn't freeze only because we do not use pens. Lasers and computers are happy, they don't overheat. Other instruments don't really care: they have their own heaters. We are warming our hands on mugs of hot tea and reading e-mails from our administration. They send us reminders from the the warm South that we should be grateful, because electricity could be shut off, as well.

Our high-resolution TEM  (transmission electron microscope), worth a handsome but unspecified sum money (more than a million), shut off for the umpteenth time. Starting it up takes a few days. Like every other electrical device more complicated than an iron, it requires stability. It also needs cooling water. The water pump is on the roof. Some times it is blown away by the wind, other times it drowns in rain water and short-circuits. In other words, many times we have no microscope.

On the positive side, we can now keep precious reagents right on our lab benches: the temperature is about the same as in the fridge. That is what I call freedom!
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Sales Reps [Jul. 29th, 2011|03:19 pm]
Lab Rats

Is it my imagination or do sales reps, more often than not, suck?  When you need to talk to them they don't return calls or emails.  When you don't need to talk to them they interrupt whatever you're doing in the lab. 
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Reverse Transcription PCR [Jul. 26th, 2011|11:51 pm]
Lab Rats

Why does my RT-PCR suck? Because the RT-extension primer has a nasty hairpin Tm one degree below the protocol's RNA-to-DNA temp. Why didn't I know this? I assumed the previous worker checked the primer design before placing the order. Why didn't using the alternate primers help? Because they were designed by a second person who hadn't checked their design for secondary structures. What's the lesson? Don't assume anything's been checked unless the analysis is written down.

The good news is, now I know why my experiments were broken, and I'm getting up to speed on primer design damn fast.
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