Science News

The NIH continues to run, fund grants. The eleventh-hour fiscal cliff deal delayed planned sequestration of funds for discretionary spending, including research funding, for two months to allow further negotiation. Whether this cut will go into effect as written remains uncertain. The NIH reduced its award rate for non-competitive grant renewals in October of 2012, and will continue to fund renewals at a reduced rate at least until the budget for fiscal year 2013 is finalized.

Nobel laureate Rita Levi-Montalcini has died. The Italian neuroscientist and senator-for-life was 102. She received the 1986 Nobel Prize in Physiology or Medicine for her discovery of nerve growth factor, the first diffusible growth factor to be described.

Sub-absolute-zero temperatures attained. Physicists at the Ludwig-Maximilianus University Munich and the Max Planck Institute of Quantum Optics have generated a stable gaseous system with negative kelvin temperature and extraordinarily high kinetic energy.

Unusually harsh flu season hits area hospitals. The CDC reports an unusually high number of outpatient visits for flu-like symptoms, both nationally and in Maryland. Influenza season usually peaks in late January or early February. Meanwhile, Google Flu Trends has proven useful in predicting local outbreaks weeks in advance.


Thesis-writing tips

It’s that time of year again – the thesis-writing deadline for the May graduation ceremony is approaching (29 March 2013). Like me, many of you will be writing your thesis. I’d like to take a moment from my writing to share with you some things that helped me.

1. Where to work

Apart from accessing data on lab computers and looking up methods in your lab notebooks (which are not allowed to leave the lab), thesis writing can take place in many locations: desk in lab, communal area in lab, Welch library or computer center, cafe… Sometimes it can help the creative process to to switch location. A few things about where you work are important, regardless of location:

  • Make lots of backups via internet and/or with external hard drives or USB thumb drives.
  • Sit comfortably and stretch your hands between long stretches of typing.
My desk in the Cole lab, where I do most of my thesis writing.

My desk in the Cole lab, where I do most of my thesis writing.

2. Making figures

Here are some applications and tools that I used to make some of my figures.

  • When writing out mathematical equationsLaTeX online editor allows you to export .gif files with nicely drawn equations.
Some equations I wrote describing my RT-PCR calculations

Some equations I wrote in LaTeX describing my RT-PCR calculations.


  • When making figures of protein structurePyMol wiki has instructions for how to replicate certain effects.
A figure I made in Pymol highlighting different aspects of a p300 crystal structure

A figure I made in Pymol highlighting different aspects of a p300 crystal structure.

  • When drawing the exon-intron structure of a gene, the Exon-Intron Graphic Maker lets you make and export nice simple diagrams.
One of several gene structures I made for a figure.

One of several gene structures I made for a figure.

  • When making graphs, I highly recommend Graphpad Prism, which has a free demo. When the demo expires, you may need to clean it off your computer (for example, by using CleanApp) before you can download the demo again.

3. Vocabulary

  • When providing recombinant DNA to cells, say “transformed” if it is bacteria, “transfected” if it is mammalian cells and you used lipids or electroporation, and “transduced” if it is mammalian cells and you used viruses. Note that “transformed” for mammalian cells means the conversion of normal cells to a cancerous state.
  • When using C. elegans, phenotypes are non-italicized 3-letter abbreviations with the first letter capitalized (e.g. Glo), genes are 3 italicized letters – hyphen – number (e.g. glo-1), and proteins are 3 non-italicized capital letters – hyphen – number (e.g. GLO-1). There are even more rules, available here.

4. Microsoft Word tricks

  • When you get revisions from more than one person on one Word document (with or without “track changes”) you can consolidate them by clicking Tools -> Merge Documents, and this preserves all the comments and edits and style changes. It does NOT work if you click Tools -> Track Changes -> Compare Documents.
  • If you embed a bunch of pictures in your Word document, they may stop printing when you go File -> Print. If that happens, try going File -> Print Preview and then print from there. Worked for me!
  • For figure legends and table titles, use Insert -> Caption. That way, you can make an automated “list of figures” and “list of tables” (by going Insert -> Index and Tables -> Table of Figures) and automated references to figures within your text (by going Insert -> Cross-reference). These automated features update the figure numbers as you add more, update the page numbers in the list, and embed hyperlinks that make it east to scroll back to the figure.
  • Making backups is key. Hopefully it goes without saying, but still worth mentioning! I use Google Drive (easy drag and drop, access anywhere online), external hard-drive Time Machine, and USB thumb drives religiously. I also print each chapter when it’s done so that I have a physical copy in case I ever need to re-write the text. Without these measures, I don’t think I could sleep at night!

Good luck to you when you write your thesis! I hope something in this article helps you.

Following Their Footsteps: Hopkins HHMI faculty give advice for young investigators

BCMB News has been exploring the the Howard Hughes Medical Institute with a three-part article series.  Part I, published in November, showcased the history of HHMI.  Part II, published in December, contained anecdotes from HHMI faculty in the BCMB program, sharing some of their own experiences.  Part III, the final part, shares advice from these BCMB faculty on how to build a career as a scientist.

BCMB News had the good fortune to sit down and talk to many of the HHMI faculty at Johns Hopkins:  ask them questions, listen to their stories, and learn from their collective years of experience.  One question we were certain you’d like them to answer was, “Do you have any advice for a young scientist, such as a graduate student or postdoc, who aspires to have a successful career in academic science?”

Perhaps unsurprisingly, many of them were eager to answer this question, reflecting on their own experiences from when they were students and postdocs, or drawing from their role as a mentor.  The majority agreed that the most important thing was to work on something that was an interesting, compelling question, regardless of how “trendy” the topic may seem.

“I think the main thing is to follow your dreams.  Especially when you’re young, you have to do what really excites you.  If you can do that and if you are passionate about what you’re doing, then the good ideas will just bubble up.  I don’t think there’s any other advice,” says Dr. Jeremy Nathans.

Dr. Cynthia Wolberger talked about her own experiences with the field of x-ray crystallography.   “[Don’t] think about the current trend because whatever the current trend is [now], that won’t be the trend in five or ten years.  I went into x-ray crystallograpy back when, apparently, it was almost impossible to get an academic job. I didn’t know that (laughs), I thought it was just so cool, I loved it!  That turned out in my favor, because suddenly when it became popular there was almost nobody trained in it.”

Others advised generating a tool or technology that could potentially spread to your field or other fields.  Dr. David Ginty explains, “Generating new tools puts you in a strong position of addressing or asking important questions that nobody else can ask, so it gives you a niche.  Over and over again in my career I’ve seen that if you if you generate new tools, you’re in a strong position for success, and it gives you something that that allows you to stand out from the crowd.”

Other faculty emphasized the value of getting well-rounded training in scientific knowledge and concepts.  Dr. DJ Pan commented that, “For students and postdocs I think the very best thing you can do now is just to try to train yourself as much as possible, both technically and also conceptually. Don’t just limit yourself to your own research field. Go to a lot of seminars, read widely, understand your friends’ research. Often the marriage of different fields is a fertile ground for new ideas.”

Being brave in the face of adversity is an important quality for a successful scientist.  “[Don’t] get discouraged, because you’re inevitably going to face grants being rejected, papers being turned down.  It can be very discouraging, but you just have to keep going.  The people who succeed are the people who can just keep doing it and keep being excited,” says Dr. Bob Siliciano.

BCMB News would like to thank all of the HHMI faculty who participated in the interviews for this article series.

-Diedre Ribbens

Kickoff to Student Admissions Season – A Message From Sin Urban


The start of the new year brings the excitement of welcoming our superb new applicants as they visit the BCMB program. I can report that we on the Admission Committee have worked hard over the holiday season discussing our many outstanding applicants, and are now starting preparations to meet these extraordinary young scientists as we host their visits.

Like most of us, I feel these visiting weekends are one of the highlights of the BCMB year: it’s a great opportunity for our >100 faculty and students to enjoy each other’s company, both inside and outside the lab, by sharing our experiences with our many stellar applicants. There is a great deal of excitement among our faculty, as we prepare to schedule ~400 one-on-one 35 minute meetings with our applicants. At the same time, our energetic BCMB students and remarkable staff are planning a fun and memorable visit to Charm City.

But by any measure our challenge is great – we have only 48 hours to convey the special Hopkins spirit that has brought us all here, and ignites our passion at this institution that we call home. The challenge is magnified all the more by the outstanding nature of our applicants – a group that will visit many excellent institutions of higher learning all over the nation and be highly courted. So let’s make sure that we give them a visit to remember, until they join us as official BCMB students at the end of the summer!

-Sin Urban


Publication Spotlight: December 2012

Publication spotlight is a series designed to showcase noteworthy BCMB publications from students and faculty. If you have a recent publication that you are proud of, tell us about it.


Wang JT, Seydoux G. Germ cell specification. Adv Exp Med Biol. 2013;757:17-39. Review. PMID: 22872473.

Baile MG, Claypool SM. The power of yeast to model diseases of the powerhouse of the cell. Front Biosci. 2013 Jan 1;18:241-78. PMID: 23276920.


Wang Y, Rattner A, Zhou Y, Williams J, Smallwood PM, Nathans J. Norrin/Frizzled4 signaling in retinal vascular development and blood brain barrier plasticity. Cell. 2012 Dec 7;151(6):1332-44. PMID: 23217714.

Han L, Ma C, Liu Q, Weng HJ, Cui Y, Tang Z, Kim Y, Nie H, Qu L, Patel KN, Li Z, McNeil B, He S, Guan Y, Xiao B, Lamotte RH, Dong X. A subpopulation of nociceptors specifically linked to itch. Nat Neurosci. 2012 Dec 23. PMID: 23263443.


Tu-Sekine B, Goldschmidt H, Petro E, Raben DM. Diacylglycerol kinase θ: Regulation and stability. Adv Biol Regul. 2012 Sep 20. PMID: 23266086.

Sisk JM, Clements JE, Witwer KW. miRNA Profiles of Monocyte-Lineage Cells Are Consistent with Complicated Roles in HIV-1 Restriction. Viruses. 2012 Sep 25;4(10):1844-64. PMID: 23202444.


Deng K, Zink MC, Clements JE, Siliciano RF. A quantitative measurement of antiviral activity of anti-human immunodeficiency virus type 1 drugs against simian immunodeficiency virus infection: dose-response curve slope strongly influences class-specific inhibitory potential. J Virol. 2012 Oct;86(20):11368-72. PMID: 22875968.

Nalayanda DD, Puleo C, Fulton WB, Sharpe LM, Wang TH, Abdullah F. An open-access microfluidic model for lung-specific functional studies at an air-liquid interface. Biomed Microdevices. 2009 Oct;11(5):1081-9. PMID: 19484389.

If you have publication you would like featured in this month’s Spotlight, please let us know.