Science picks

April 25th, 2015

4/25/2015

Links to three awesome papers on Neuregulin 1 signaling in heart regeneration
http://www.nature.com/nature/journal/v520/n7548/full/520445a.html

Now onto "not science but important anyway" stuff

For all of you trying to decide between Grad School and Med School:
Being a doctor is a career
http://finance.yahoo.com/news/heres-much-money-doctors-actually-110000302.html
While college teaching is more of a hobby. See page 3 in the first link and page 1 in the second
http://laborcenter.berkeley.edu/pdf/2015/the-high-public-cost-of-low-wages.pdf
https://nces.ed.gov/programs/coe/indicator_cuf.asp

That’s likely after you do a postdoc:
http://www.nature.com/news/the-future-of-the-postdoc-1.17253
The last sentence obviously applies to those thinking about graduate school, too.

If you are a woman competing for a tenure track job in the academia, perhaps you will not be discriminated against:
http://www.nature.com/news/leading-scientists-favour-women-in-tenure-track-hiring-test-1.17322
There has been a pro-male bias for a long time. Remember McClintock?

Positions in academia are of course few and far between. So brush up on your computer skills:
http://www.nature.com/nature/journal/v520/n7546/full/nj7546-253a.html

Enjoy!

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April 4, 2015

4/4/2015

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This time we will zoom in on a few worthwhile technical development papers:

In vivo visualization of transcripts in zebrafish
http://dev.biologists.org/content/142/7/1368.full
Has been done in other systems, but cool nonetheless.

Tissue-specific CRISPR/Cas9:
http://www.cell.com/developmental-cell/fulltext/S1534-5807%2815%2900075-1
Same here. The race for fully conditional CRISPR/Cas9 is on…

Smaller Cas9 for packaging into AAV
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14299.html
All these sequences of semi-random genomes are good for something after all...

And here is an exercise in futility:
http://www.sciencemag.org/content/348/6230/18.full
Why would anyone care?

Now onto “career stuff".
Some pharma jobs are moving out of Philly:
http://www.philly.com/philly/business/20150403_GlaxoSmithKline_moving_Philly_vaccine_R_D_jobs_to_Maryland.html
Fortunately not too far.

As career advice goes, this is pretty good:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_03_31/caredit.a1500080
I suppose one could call her a grad school dropout. But then again, she clearly had a more rewarding career than many of her fellow students who did not drop out.

I keep bringing up the tough job market for PhDs. Here the postdoc seems to have just realized that:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_03_30/caredit.a1500078
But while much of the advise is spot on, there is a little too much feel-good baloney for my liking.

Enjoy.

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A very nice paper on head skeleton evolution:
http://www.nature.com/nature/journal/v518/n7540/full/nature14000.html
Maybe someone will pick this paper for the journal club...

One of the “new” big questions in biology that is also a bit of a recurring theme here: how does an enhancer know which promoter to activate?
http://www.nature.com/nature/journal/v518/n7540/full/nature13994.html

I know we have not made a plasmid in a while, but this is a cool method nonetheless:
http://nar.oxfordjournals.org/content/42/20/e154.long

Apparently there has been a dramatic increase in animal usage in biomed research:
http://news.sciencemag.org/plants-animals/2015/02/peta-study-finds-dramatic-rise-use-lab-animals-united-states
Here is a “funny" thing: by head count, my lab may have as many animals as the rest of Temple University. Hereby I copyright “show skin, not scales” slogan.

Apparently it is very hard to teach things you don’t know:
http://www.sciencemag.org/content/347/6226/1054.full
Who knew?

But things you do know can be tricky to communicate, too:
http://www.sciencemag.org/content/347/6226/1047.full
Can something useful be learned by watching other students give talks and poster presentations?

If birds can do it, students should be able to do it too, right?
http://www.nature.com/nature/journal/v518/n7540/full/nature13998.html
This applies to things other than posters, too. Just a hint.

Have a good weekend.

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February 21, 2015

2/21/2015

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One of the classical processes in developmental biology - interdigital apoptosis - turns out to involve vascularization:
http://dev.biologists.org/content/142/4/672.full

The latest issue of Nature is all about epigenetics:
http://www.nature.com/nature/journal/v518/n7539/full/518314a.html

Now onto more "fluffy" stuff

A fine reading at the intersection of genomics and linguistics:
http://www.nature.com/news/steppe-migration-rekindles-debate-on-language-origin-1.16935

I keep hearing about the shortage of girls in STEM fields, especially in academia, with recruitment and retention being thrown around as solutions.
http://www.nature.com/nature/journal/v518/n7539/full/nj7539-447c.html
Or is it that girls are smart enough to realize that as things are, the reward is not worth the effort? Recruitment and retention… Cheap grad student and postdoc labor with a topping of "feel good”.

Here is to those trying to decide: Grad or Med?
http://www.sciencemag.org/content/347/6224/918.full
Does not really help to decide, but encouraging nonetheless.

An if you do decide to become a scientist, you must hurry up not to waste your creative years:
http://www.nature.com/news/young-scientists-lead-the-way-on-fresh-ideas-1.16934
According to Nature, using buzzwords makes you innovative. Indeed.

Have a good weekend everyone.

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February 13, 2015

2/13/2015

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We’ll go easy on the actual hard science his week.

Now, we finally have a gene for Darwin’s finches' beak shape:
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature14181.html
Positive selection is the real deal.

With our Department turning more and more evolutionary, perhaps I should post an evolutionary paper every now and then.
http://www.biotechniques.com/news/biotechniquesNews/biotechniques-356685.html?utm_source=BioTechniques+Newsletters+%26+e-Alerts&utm_campaign=ca37b4ad04-weekly&utm_medium=email&utm_term=0_5f518744d7-ca37b4ad04-87700457#.VN05s3a-8_E
I would not have guessed that 0.5% of males worldwide are descendants of Genghis Khan. My guess is that all Nobel laureates’ stats combined will not be as good a few hundred years from now. Evolution at work?

Many of us have something Rand Paul can only dream about:
http://www.washingtonpost.com/blogs/fact-checker/wp/2015/02/13/rand-pauls-claim-twice-in-one-day-that-he-has-a-biology-degree/
Maybe that explains his recent vaccine BS.

I must point out that there also are some differences between being a crown prince and being a junior biomedical researcher...
http://www.nature.com/news/nih-plan-to-give-ageing-scientists-cash-draws-scepticism-1.16895
One of them is "hidden" in the numbers in the last sentence.

Then there are a few more numbers in this article:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_02_12/caredit.a1500039

Have a great weekend everyone.

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February 9, 2015

2/9/2015

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Better late than never…

A really cool way to monitor nuclear translocation of beta catenin in specific tissues.
http://dev.biologists.org/content/142/3/497.full
In zebrafish of course.

Optogenetics taken to a new level:
http://www.nature.com/nature/journal/v518/n7537/full/nature14128.html

Playing with LEGOS is never a waste of time:
http://news.sciencemag.org/plants-animals/2015/02/lego-contraption-allows-scientists-safely-handle-insects?rss=1

Apparently being a part of highly hierarchical group makes you succeed. Or die trying.
http://www.pnas.org/content/112/5/1338.full
From now on, lab members may no longer address me by first name.

Isn’t it reassuring to know that your graduate school does care about you.
http://www.nature.com/nature/journal/v518/n7537/full/nj7537-129c.html
But only until you graduate…

Which means that you must find a balance between working in the lab and schmoozing:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2015_02_04/caredit.a1500032
And please do not take the urban dictionary literally on this one...

Darius

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January 31, 2015

1/31/2015

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My apologies for dropping this list for a month and a half. Now lets try to ease back.

An absolute must-read paper:
http://www.cell.com/developmental-cell/abstract/S1534-5807%2814%2900735-7
As well as accompanying commentary:
http://www.sciencedirect.com/science/article/pii/S1534580714008338

How do enhancers know which gene to activate?
http://www.nature.com/nature/journal/vaop/ncurrent/full/nature13994.html

Another way how obesity may run in families
http://www.sciencedirect.com/science/article/pii/S0092867414014366
Watch what you eat before you procreate...

Now let’s have some fun:
http://www.biotechniques.com/news/biotechniquesNews/biotechniques-356366.html?utm_source=BioTechniques+Newsletters+%26+e-Alerts&utm_campaign=671dbcbc6f-weekly&utm_medium=email&utm_term=0_5f518744d7-671dbcbc6f-87700457#.VMuvynZNk_F

Or, if singing is not your thing, perhaps reading is. Here is a list of who-is-who in classical Molecular Biology and Genetics, with enough book titles to comprise a high school reading curriculum.
http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1004887

Have a great weekend!

Darius

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November 14, 2014

11/14/2014

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A very cool study of recombination hot spots in humans:
http://www.sciencemag.org/content/346/6211/1256442.abstract
I guess it is much more enjoyable to read than to donate tissue to…

The title oversells it a bit, but mind controlled cellular factories is a great concept:
http://www.nature.com/ncomms/2014/141111/ncomms6392/full/ncomms6392.html
Not to be out-done by Nature, Science also has a great idea to oversell - DNA memory:
http://www.sciencemag.org/content/346/6211/1256272.abstract
I suppose both papers are major breakthroughs.

Different (publication) trajectories of different model systems:
http://www.genetics.org/content/198/3/787.full
The part that surprises me (probably because of my ignorance) is the difference between C. elegans and D. melanogaster.

I know quite a few female faculty who would strongly disagree with the assessment that sexism no longer exists in academia:
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_11_06/caredit.a1400279
http://www.sciencemag.org/content/346/6211/798.full
Being underrepresented by choice (“underrepresentation … rooted in … choices") is a concept that I can’t quite wrap my mind around. But it sounds like something on the Colbert Report.

Have a great weekend.

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November 07th, 2014

11/7/2014

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A fantastic paper on FGF signaling in lateral line development:
http://www.nature.com/nature/journal/v515/n7525/full/nature13852.html
My little summary sentence doesn’t do it justice.

It turns out Argonaute plays a role in RNA splicing. By binding enhancers.
http://www.pnas.org/content/111/44/15622.full
Do not try this during an exam, but “it’s complicated” is often the correct answer...

Should you really aspire to get a Ph.D.?
http://sciencecareers.sciencemag.org/career_magazine/previous_issues/articles/2014_11_05/caredit.a1400277
Or will you need to spend a lot of time reminiscing about your undergrad days? Why?

Because happy thoughts make you … (drum roll) … Happy!
http://www.nature.com/nature/journal/v515/n7525/full/515011c.html
And you may actually end up working on a really important scientific problem.

Because Guy Noir is not the only one trying to answer life’s persistent questions. Scientists do, too:
http://news.sciencemag.org/biology/2014/11/mystery-solved-where-penis-comes
I am surprised major news outlets have not picked up on the story…

Enjoy your weekend.

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October 31, 2014

10/31/2014

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The latest issue of Cell has plenty of treats and tricks...

How nerves in the retina prevent vascular growth:
http://www.sciencedirect.com/science/article/pii/S009286741401174X

Multiple enhancers cooperate - in trans - to activate one gene:
http://www.sciencedirect.com/science/article/pii/S0092867414011829

A virtual in situ hybridization for all transcripts at once:
http://www.sciencedirect.com/science/article/pii/S0092867414012264

A very cool - if not always practical - trick to image single protein:
http://www.sciencedirect.com/science/article/pii/S0092867414012276

I must admit I find quality and breadth of these papers haunting...

This adds to the long and sometimes contentious literature on sirtuins in aging:
http://onlinelibrary.wiley.com/doi/10.1111/acel.12220/abstract;jsessionid=EAEB65E032A1930B93083989FD7D84FF.f03t02
Many days I think I could use some of that SRT2104 thing

OK, so Michael Douglas must have known what he was talking about a couple of years back:
http://www.pnas.org/content/111/43/15544.full
Bad genes…

Perception is reality, even when it comes to quality of science:
http://www.pnas.org/content/111/43/15316.full
But really, why should science be different from all other human enterprises?

It’s that time of year again.
http://news.sciencemag.org/people-events/2014/10/dance-your-ph-d-finalists-announced
Think about it: you could have been watching these instead of that baseball stuff… Scary, isn’t it?

Have a fun Halloween everyone.

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Weekly sciencey bits

Disclaimer: This started as a "weekend reading list" meant to encourage students in the lab to think about science and their own future in it. Do not take it seriously: I myself may no longer agree with whatever I wrote here last week.
- Darius

April 25th, 2015

April 4, 2015

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