BCMB Rocks!

Wow  — we all know our BCMB graduates are outstanding scientists, but check this out:

In the current issue of Science, two BCMB grads are first authors of RESEARCH ARTICLES!  Clara Bien Peek worked with Peter Espenshade and is currently a postdoc with Joseph Bass at Northwestern.  Jason McLellan worked with Dan Leahy, and recently started as an Assistant Professor at Dartmouth after a postdoc at the NIH with Peter Kwong.

Here are the links to these papers:



Congrats Clara and Jason!

Must Do Around Baltimore: Glassblowing at McFadden Art Glass

BCMB student Risa Burr participated in a Glassblowing workshop at a local artisan’s studio.  If you have done a local activity, visited an attraction, or dined at a restaurant and would like to share your experience, please Contact Us about writing a review!

What: McFadden Art Glass glassblowing “date night”

When: alternate Fridays, 7-10pm, no reservation required

Where: 6800 Eastern Avenue Baltimore, MD 21224

Have you ever wanted to try your hand at the ancient craft of glassblowing, learning to create beautiful pieces of art out of molten silicon dioxide? Then McFadden Art Glass, located right here in Baltimore, is for you. Since 2006, Tim McFadden has been delighting the greater Baltimore community with custom glass art pieces out of his studio on Eastern Ave, including swooping chandeliers and intricate vases. Even better, he has a great affinity for teaching, which he shares in classes for all interest and ability levels. I recently went to one of the “date nights” (anyone is welcome, no date required), which he puts on every other Friday from 7-10pm. They begin with a free glassblowing demonstration, in which Tim makes one of the fantastic works of art on display in the gallery. While you sit and watch the magic happen, you are invited to enjoy any libations you may have brought, either from home or the bar next door.

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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.

In Memoriam: Dr. Bob Cotter

Dr. Bob Cotter, professor of Pharmacology and Biophysics, passed away suddenly on the evening of NovemBS bs-md-ob-robert-cotterber 12. Faculty and students from the Pharmacology and Biophysics departments gathered the following day to remember his career and his larger-than-life presence in the department, and on the nineteenth, a meeting of the Washington/Baltimore Mass Spectrometry Discussion Group, which Dr. Cotter was to have hosted, was held instead as a memorial symposium in his honor.

Dr. Cotter spent the bulk of his academic life at Hopkins. After graduating from the College of the Holy Cross, he completed his doctoral research in the Chemistry department at Homewood. Following a brief stint as a faculty member at Gettysburg College in Pennsylvania, he returned to Hopkins as a research associate and advanced over the years to full professorship. Research over the course of his career substantially advanced the field of time-of-flight mass spectrometry, and garnered him honors from the American Society for Mass Spectrometry and the American Chemical Society. In December of 2008, on the occasion of his sixty-fifth birthday, the International Journal of Mass Spectrometry dedicated an issue to him.

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An Enduring Accomplishment: The Founding of the Howard Hughes Medical Institute

This article is the first in a three-part series on the Howard Hughes Medical Institute (HHMI).  The series will cover the history of HHMI, the careers of some awardees at Johns Hopkins, and the nature and scope of the awards offered by HHMI.  Look for part two and three of the series in forthcoming issues of BCMB News.  This month, we bring you the storied history of the HHMI, and a glimpse of some of the people who have made this institute successful over the last 60 years.  

Howard Robard Hughes, Jr., in his day, was a man known for his sense of adventure and mystery.  A successful film producer and businessman, Hughes accomplished much throughout his lifetime.  Perhaps his most well-known and enduring accomplishment, the one most recognized in the current times, was the creation of the Howard Hughes Medical Institute.

Howard Hughes. Image courtesy of the HHMI website.

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A Career Planning Tool for Trainees & Mentors: myIDP

How many mentors in academic science are well-versed in the career path one takes to be a science policy analyst?  Scientific consultant?  Sales and marketing?  Unless the mentor has undertaken a side venture of their own, chances are that their experience outside academia is limited.  This can be a frustrating situation for both the mentor and their trainee who wishes to explore these non-academic career paths.  Bruce Alberts, editor of Science, and Jim Austin, editor of Science Careers think that they have developed a tool to help both mentors and trainees who find themselves in this situation.

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Question of the Month

We are less than two weeks away from the annual BCMB retreat. The retreat is a time where we take a break from the lab work that keeps us ever so busy, and come out to mingle with our fellow students and faculty. It is a time where we get the opportunity to learn first-hand about the science that is conducted by the BCMB community.  All of this, in a two day retreat!

The retreat takes place locally; the first day is on campus, and the second day is at Sheppard-Pratt conference center ~20 minutes away from campus. It wasn’t always a local event though. My classmates and I, of the class of 2009, were the last class to experience the retreat in its old format: a 3-day retreat at Rocky Gap Resort, a mountain resort ~130 miles west of Baltimore. Although more faculty attend the retreat when it takes place locally, having the retreat at Rocky Gap allowed for more opportunities to bond and mingle through science and outdoor activities alike!

Question of the month: Where do you prefer having the retreat? There is an option for readers to enter their own answer, for those who would like to explain their choice, or submit an answer not listed below.

REMEMBER! If you choose “other” and submit your own answer, you may be selected to have your response featured in the next issue! Start sharing your opinions!

-Saif Al Qassim