Calling all bio-stats ppl

8 01 2014

Ok folks, I need help and trying to describe what I need on twitter isn’t really working because of the whole 140 character thing. So has many of you know, I am a drosophilist, which means I work on the best model organism EVAH, unless of course you work on something else but can still help me. cough *not* cough….

Seriously, though I’m going to ask some Qs without giving away any specific details because this isn’t published yet etc. I work on the imaginal wing disc of the drosophila and because flies are the most awesomist organism ever, we use the UAS-GAL4  which allows us to knock down genes in specific regions of the disc, which is really cool because we always have an internal wildtype control. You can do a google search of imaginal disc with uas gal 4 and you’ll find amazing images like these ones

So I use a driver to knockdown geneA and look at its effect. I’m specifically interested in looking at the effects, more specifically if any changes occur in the distrubution of proteinB after RNAi knockdown of geneA. I’ve done this experiment multiple times and imaged alot of discs. I’ve taken z-projections and looked at the mean gray values of ProteinB in the z-projection analysis

I’m not looking at the solid red lines, I’m looking at the red dashes within each box. I’m asking if the mean gray value of the WT box is different than the mean gray value of the RNAi box? IE are there less dashes in RNAi box vs the WT.  I did this analysis in ImageJ and recognize its a crude estimate as there is a lot of white space one both sides, which may mask changes but a girl can’t be picky.

So say  I have done this analysis on 30 discs, each with a WT and RNAi mean gray value (MGV). I’ve used Prism to set up a 1 variable group, with WT in ColumnA and RNAi in ColumnB. I ran a pair-wise t-test but I don’t think that is correct because a pair-wise T-test is asking if the differences between the WT and RNAi is consistent. I don’t care if the differences are consistent because there are many factors which may make 1 disc have a greater difference than another disc. I want to know if the difference is important. If I divide each RNAi MGV by the its WT  by its internal MGV, I get a value that is different than 1. How do I test if this is significant? Do I use a ratio t test? or is any difference significant?

Any ideas on how to do this analysis? Because proteinB is a phospho proteins its staining is very punctate so if you have better idea for how to analysis the images that would be awesome too.

thanks!





Seven

6 01 2014

Seven years ago I became a mother, for the first time. I’m not sure how you went from the a scrawny, ashy 7 lb baby to a 7 year old star wars loving, video game obessed boy. A boy who’s head touches my shoulders. At seven. Every year, I write these letters to you. Every year I amazed at your capacity to think and reason. But this year, I’m amazed at not only your capacity to love but your capacity and to move forward. This year, I am learning from you.

Its been another hard year for you.. Its started normal enough, but then we had some family issues, we had the horrible break in and then of course our beloved SMDog had to say good bye. These are hard issues you’ve had to deal with. You’ve forgiven these people for the harm they’ve done you with. You did this not blindly but after careful consideration. You asked very hard questions to try and understand why things happen. This ability to try to understand another persons perspective amazes me. You’re 7 and have more empathy than many adults I know.  You stick by your family, making sure your little sisters and cousins are involved in your birthday. Going so far as to share your birthday with your sister.

Yet you’re not a pushover. As easy going and laid back as you are, you will not be pushed into doing something you don’t want to do. You have a quiet determination that both excites and terrifies me. You will do what you want.

I hope you maintain your empathy through your life. You’re always this sympathetic, that life and the world doesn’t jade you. Happy 7th birthday monkey. I love you

 





#StandingwithDNlee and I’m #StandingwithMonicaByrne

15 10 2013

By now, most of you know what went down over this Canadian Thanksgiving weekend. If not click over to <a href="http://isisthescientist.com/2013/10/

    11/tell-someone-no-get-called-a-whore-standingwithdnlee-batsignal/”>Dr.Isis’s blog for the low down of how a WoC scientist was called a whore for asking to be paid to do her professional science job.

    When Dr.Isis sent out the batsignal, the majority of science bloggers, male, female, white and all other hues responded. They were pissed. This was an easy one to get right; really who name calls on email to a stranger?! Especially one who is a prominent and well known diversity advocate in the science communication sphere. I found out about the lovely little fuck up by some random editor via twitter, when some of my favourite tweeters were talking about brawls. In the few spare moments I had, I retweeted some of there very awesome posts on the matter. When I checked my Newsify, a lot of bloggers had reblogged DNLee’s original SciAm post. As you can see it’s now up and running. Through this weekend I kept wondering why Bora Zivkovic, the SciAm blog editor hadn’t said anything.

    I awoke this am with intention of also reblogging Dr.Lees post even if I was late to the party. I wanted to support my fellow scientist but I was distracted by this happened:

    UPDATE, 10/14/13: The man is Bora Zivkovic, Blogs Editor for Scientific American. There’s no reason for me anymore not to name him publicly, which I’d long wanted to do anyway. Reading about this incident is what reminded me (independent of whether or not he had anything to do with that post’s original deletion, which I don’t know).

    I was shocked at 6:00am. I didn’t know what to think. I know who Bora is, I was so excited when he started following me on twitter, bloggers who inspired me into this blogging endeavour wrote about how much they respected him. I quickly looked on my twitter stream and except for two tweets, I saw nada. Then I saw some of Dr.Isiss tweets. I read her post. I thought to myself “Is this why Bora hadn’t said anything about the DNLee situation?” I looked at Boras twitter feed and didn’t see anything.

    It was early in the morning, I had to get out of the house and into a busy day in the lab. Randomly during dinner and the kids bedtime I checked my Newsify / twitter feeds. There is no outrage or shock. Yes DrugMonkey and Odyssey had posts that made me think they were talking about it but they didn’t really make it clear that Bora had sexually harassed someone and used a lame ass excuse. Except of this tweet from @MarkCC, I haven’t really seen any outrage. Why? Where is it? Unless I’ve missed it. Perhaps all the posts have gone up in the 45 minutes it took me to tap this out on my iPad? Or is it because Bora still has power in the Sci Communication field? I mean I saw tweets of people saying they support their friend Bora. WTF?! I’m not saying he can’t be sorry or he isn’t remorseful and can’t be reformed, but that doesn’t mean you excuse or treat him lightly. As a person that has experienced sexual harassment, I call bullshit on the kid gloves that the community is using. I’m sure “odjek” friends and family think he’s a swell guy too. He’s probably going through “stuff” and wasn’t thinking.

    Sexual harassment does major harm and it does even more harm when the harassers colleagues know. Other PIs knew what was going on in my case, they “offered” sympathy. No one ever punished my harasser. It doesn’t look like Bora is receiving any either.





    Happy place

    17 09 2013

    Today will hopefully end up being a productive day. I’ve left biochem for the last couple of days and have gone back to my happy place -> cell biology. And data analysis. It’s amazing how much better one can feel when they feel like their day resulted in some answers. Proteins xyz and epsilon are / are not affected when you remove protein c. Immunofluorescence FTW.

    Tonight dinner is left overs so I should be able to work after putting bear to bed and the house doesn’t look like a tornado went through it. Yay for not getting sucked into watching crap tv. Tomorrow is more swimming. So I’m feeling sorta better….





    A failed experiment is NOT indicative of your intelligence

    12 09 2013

    Or your ability to do science, or to graduate, or any other things. The only thing a failed experiment can tell you is that the experiment did not work.  An experiment not working is VERY different from an experiment not giving you the data you want. An experiment not working is an SDS-Page Gel not running for the 4th week in a row, all for different reasons.  The experiment not workings is not getting a signal on your membrane and you don’t know if its because the protein didn’t transfer, the antibody concentration is correct or the 2ndary is off.

    Thats not entirely true. I know the protein transfer efficiency was enough to have protein1 detected. I know that 1 of the secondaries work fine. That is all I know. Oh that have 3 days of washing and probing, ponceaus S (1% w/v) picks up ZERO bands on the membrane.

    So for all the newbie graduate students that started over the summer and the last couple weeks. The title was kinda for you. But mostly its the mantra I need to tell myself on an hourly basis as I struggle with biochemistry.

    I will publish this damn story and I will graduate.

     

     

     

     





    Baby Steps still get you there

    9 09 2013

    Just maybe slower,

    One of the hard things about science, or at least for me is the inability to see the small success. The experiment didn’t work because I didn’t get quality, usuable data. That is not always true. So I’m going to focus on the things that did go my way or the things I’ve figured out:

    The SDS-Page ran, just slowly. Most likely due to the leak in the chamber because I used the plastic blocker as opposed to making an extra gel. I will now just make extra gels.

    1/x  primary / secondary antibody combos’ I need is working. I got clear, specific bands

    a fresh aliquot of goat anti-rb secondary still did not give a signal, suggesting the primary ab was off I can probe with a known to work rabbit primary.

    I figured out how to distinguish between Bar & Dr. I need the Bar+ Dr- flies but since both eyes look very similar its kinda hard. With the help of a former student, I figured out a plan that was quick and easy.

    I went swimming on sunday morning

    I went for a walk this evening. Score on the getting healthier front.

    I looked at my crosses and figured out somethings I need to do in the am and after class to answer what is going on with the rabbit channel.

    I’m getting better at the fluorescent western blot detection using the Licor. If anyone has sure fire tips that would be much appreciated!

    baby steps folks baby steps





    September Reset

    6 09 2013

    Where to begin? lets start off by saying you all are amazing. You have no idea how encouraging it is to know there are people in my corner.

    I’m resetting this weekend. The summer was not the most productive or ideal. My sister caused some oscar worthy drama that had me drunk blogging, we were robbed and science was generally non-data producing. I’m not going to say unproductive because learning new techniques and trouble shooting is doing something. It just doesn’t make figures or give me something to show my PI, all i can say every week is I tried x, it didn’t work. Learning and troubleshooting something new can be incredibly demoralizing and frustrating. I’m feeling that at the moment. Having a leak in my gel sent me into a tailspin yesterday. As much as my head tells me I can’t let that happen, I can’t help but feel as if I’m hitting my head into a wall.

    So I’m resetting. I’m not going to focus on just getting this technique / data. I’m going back to cell biology. Getting useful data, making figs. Fingers crossed that I can actually meet some goals this semester.








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