Archive for: June, 2013

Maybe I was a little bit harsh...

Jun 18 2013 Published by under Late-stage PhD student

nmeth.1618-F3

(from B. Wong 2011)

 

That moment during lab meeting when I demand from an undergrad if he's convinced whether 2 proteins really are colocalized based on overlapping red-green immunofluorescence and he frustratingly replies, "I can't tell you that...because I'm color blind."

 

http://www.youtube.com/watch?v=9l7S1hnRPF0%&start=5&w=480

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Should I start patenting the cDNAs I've made in the lab?

Jun 13 2013 Published by under Issues in Science

In a unanimous decision today, the SCOTUS struck down patents for genes by ruling against Myriad Genetics in Association for Molecular Pathology vs. Myriad Genetics. The Court, however, did leave some wiggle room for companies to patent cDNAs, or complementary DNA.

"In Myriad, the high court held cDNA is patentable, because it involves actual work in the laboratory and inverts the normal process found in nature. The synthetic DNA is an edited version of a gene, stripped of non-coding regions that the court said makes it “not naturally occurring.”

Critics say even the edited sequences are directly analogous to naturally occurring DNA."

In many labs, cDNAs are routinely made, manipulated, and used for research. cDNA is DNA that is engineered in reverse using messenger RNA (mRNA) as the template. As the above quote alludes, a cDNA is not a carbon copy of its corresponding gene. Interspersed along the length of a gene are regions of non-coding DNA sequence. These are segments of DNA that aren't represented in the sequence of the encoded protein. When a gene is initially transcribed into mRNA some of these non-coding regions, called introns, are included. Introns, however, are ultimately removed by the cell before the mRNA is translated into protein. Since mRNA is used to make cDNA, the introns are excluded from the cDNA sequence.

gene expression

During gene expression, a gene is first transcribed into a primary RNA transcript, which includes non-coding introns (blue). Through a process called splicing the introns are removed from the transcript resulting in a mature mRNA molecule. The sequences found in mRNA are called exons (red and yellow). The mRNA is  then translated into protein. Since cDNA is made from mature mRNA, it will consist only of exon sequences.

Although gene and cDNA are different, they both carry essentially the same DNA sequence for a protein. (It should be noted, however, that many genes encode multiple forms of a protein, for which each form has its own corresponding cDNA.) So, I'm not sure why the "patentable" emphasis is on cDNAs as opposed to making mutations* to the underlying sequence that result in say, new or altered function of a protein. At least there I could see an inventive process happening--or am I missing something here?

*I'm talking about generating novel mutations. Of course, I'm not sure what should happen if said mutations are discovered to be "naturally occurring" after the fact.

 

 

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What's the gender ratio of your references for letters of recommendation?

Jun 12 2013 Published by under Issues in Science, Late-stage PhD student

A few weeks ago while going through old resumes and updating my CV, I noticed that my references have historically been women-centric. I started wondering what the gender ratios were like for other people's references, so I threw this question out into the Twitterealm.

Here were some of the responses:

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What's the gender ratio of your references?

  1. Peoples - what is the gender ratio of your references?
  2. @AmasianV Mostly men. Most of them seem to be called "Al".
  3. @AmasianV all women currently. Historically about 3/4 women.
  4. Depends on job/app. For any single app my range was 0-33% female. MT @AmasianV: what is the gender ratio of your letter writers?
  5. @AmasianV @27andaphd 50/50. The strongest and most influential = female.
  6. @AmasianV @27andaphd Most of my women colleagues very familiar w/ me and my work are at similar stage as I am, grad students, postdocs, etc.
  7. @AmasianV @27andaphd I've met more senior women who do great work in my field, but I don't know them well enough to ask for reccomendation
  8. @AmasianV @27andaphd Oh, absolutely. In my case it's just a matter of probabilities of being in same place/same time and getting their time
  9. @AmasianV @27andaphd Just like any other important, more senior researcher that I want to know well.
  10. @AmasianV @N3OX fo sho. Sadly, I've only had 1 female mentor in my field since I started grd school 10 yrs ago #structuralbiology

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