"We got different social norms than yoooo-oouuuu..."

(by AmasianV) Jul 19 2013

Just a few things to clarify about the "Asians Eat Weird Things" music video:

1. Drinking fish sauce straight from the bottle? No one can handle that umami bomb.

umami-bomb_4764860_GIFSoup.com

2. That's doesn't look like nem nuong (nem nướng) @ 2:45. Nem nướng is grilled pork, that looks more like nem chua which is fermented, cured pork...and delicious.

Nem chua

3. "Hell no we ain't eating no dogs..." Maybe not in America, but in some parts of Vietnam my peoples do.

4. And how are the Fung Bros going to leave out tasty Lethocerus indicus pheromones (cà cuống)? or even the imitation stuff?

Lethocerus indicus

9 responses so far

Editing the third chapter of my thesis

(by AmasianV) Jul 18 2013

2 responses so far

A font even better than Comic Sans for my thesis defense

(by AmasianV) Jul 11 2013

If only it came with a β symbol...

Chinese Takeaway

 

5 responses so far

Maybe I was a little bit harsh...

(by AmasianV) Jun 18 2013

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

No responses yet

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

(by Dr Becca) Jun 13 2013

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.

 

 

5 responses so far

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

(by Dr Becca) Jun 12 2013

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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3 responses so far

One week left to double your money through DonorsChoose!

(by Dr Becca) May 31 2013

DonorsChoose

DonorsChoose has teamed up with Scientopia in an end-of-the-school-year drive to help raise $$$ for needy classrooms! For a limited time (until June 7), your donations of up to $100 will be matched if you enter SCIENTOPIA in the "match or gift code" field (See here for screenshot).

With one week left, I'm happy to report that 11 of the projects on the Scientopia Bloggers Giving Page have been completed. That means Mr. Mead will be able to purchase Zometools to help make learning geometry hands-on and fun! And it means Mrs. Mohlar can use math manipulatives to help students who struggle with math learn in non-traditional ways.

But there are plenty more projects that still need our help and don't think you're limited to the projects on our giving page--the SCIENTOPIA match code can be use for ANY project.

Let's do this y'all!

 

No responses yet

Any advice for a Ph.D. student contemplating a leave of absence?

(by Dr Becca) May 31 2013

Folks, I have a friend who just finished her first year of grad school and is wondering whether she rushed into this whole Ph.D. business (sound familiar?). Now she wants to take a leave of absence to get some "real world experience" before committing the next 5-6 years to finishing her Ph.D. I counseled her as best I could and told her to consider several things: 1) her department's policy wrt to taking a leave of absence, 2) how long of a leave did she want to take and whether "real world experience" jobs would hire her for that length of time, and 3) whether to do it before or after finishing her qualifying exam.

Thoughts?

31 responses so far

Racial disparities in accruing debt during graduate school

(by Dr Becca) May 09 2013

According to a new report from the American Institutes for Research, black and Hispanic STEM PhD students are more likely to accrue larger amounts of debt during grad school than their non-underrepresented minority (URM) peers (read: white, Asian, & biracial). The Chronicle of Higher Education article is a little clunky in trying to summarize a report that compares debt incurred by graduate students in STEM programs versus those in social, behavioral, and economic (SBE) programs. I suggest reading the actual report itself.

Figure 5. Graduate Student Debt for STEM Phd Recipients by Race-Ethnicity and Gender- 2010

The report also found that these disparities existed regardless of the source of funding (institutional vs external) or the time it took students to complete their PhD studies.

Other factors that may be worth exploring include the distance that students travel to attend graduate school, spending patterns during graduate school, the family commitments of PhD students during graduate school (e.g., marital status and number of dependents), and salary expectations after leaving graduate school. If graduate students’ spending patterns during graduate school are related to the expected financial pay-off of their PhDs, then differences in graduate student debt may be related to differences in students’ inflated estimates of their future salaries.

I'd add socioeconomic and debt status upon entering grad school to that list. Identifying which factors contribute to debt could help us better position students to shoulder less of it.

As graduate programs make more of an effort to recruit underrep'ed minorities, however, I wonder whether these disparities will become greater or smaller...

6 responses so far

How is your PI training you to write grants?

(by Dr Becca) May 07 2013

An interesting thing happened during last week's lab meeting. Rather than spending the first 30-40 minutes on mundane lab issues like who left the dishes in the sink or who's responsible for teaching the undergrad how to dissect Drosophila larvae, my PI held an impromptu Q&A session on grantsmanship. Being the old-blood, gray-beard, grad student that I am and having lived through (and helped in the process of) writing grants, progress reports, and renewals with my PI, I've heard her thoughts and experiences at various points during my grad school career. But, I could see that her advice on to how to craft each one of these things as well as cultivating a relationship with your program officer was enlightening to the newer students and foreign postdoc in the lab.

It got me thinking about if and how other PIs were directly preparing their trainees in successful grant writing.

7 responses so far

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