Category Archives: April 2020

Humans of Tufts Boston: Logan Schwartz, “I am interested in helping an aging population”

Humans of Tufts Boston, 9 Apr 2020

Logan Schwartz, Genetics (JAX), Second-year Ph.D. “I am interested in helping an aging population”

JH: Thank you so much for agreeing to answer some questions! What were you doing before graduate school?

LS: I started my scientific career as a summer intern at Regeneron Pharmaceuticals for three summers right after high school and through college. I worked in the VelociGene Department aimed at developing genetically modified mammalian models of gene function and disease! I attended the University of Rochester and studied Molecular Genetics and Chemistry. After completing undergrad, I was working for Dana Farber Cancer Institute and MGH as a research technician studying the functional genetics and molecular mechanisms of chronic lymphocytic leukemia and cystic fibrosis.

The Trowbridge lab

JH: What drew you to the JAX program?

LS: I was drawn to the JAX program by the opportunity to work with Dr. Jennifer Trowbridge and the novel mouse models for studying clonal hematopoiesis (CH). The Genetics program at JAX is a unique graduate program with the freedom to take courses at The Jackson Laboratory in topics ranging from systems genetics to different computational languages. I really enjoy the close and collaborative community at JAX and I am happy to be a part of it!

Dr. Trowbridge is a leader in the field of hematopoietic stem cell (HSC) research and she is fearless with respect to developing and employing the new and best techniques to address scientific questions. She is an inspiring investigator to be mentored by, having navigated herself the challenges of achieving success as a woman in science.

The Trowbridge lab hikes in Acadia

I am particularly excited to work in this field of research because I am interested in helping an aging population. With the growing population of elderly individuals worldwide, preventative strategies to reduce aging-associated diseases are urgently needed. We acquire somatic mutations in our HSCs as we age, some of which can confer a competitive advantage and cause clonal HSC expansion, known as clonal hematopoiesis (CH). This is present in 10-15% of individuals aged 70 years or older. My thesis work in the Trowbridge lab strives to identify novel mechanisms that can be used as interventions to prevent aging-associated diseases and disorders of the hematopoietic system, with a specific focus on HSCs, which are responsible for the lifelong maintenance of a functional hematopoietic system.

Riding a camel with Rebecca Brown (Genetics program) in Israel

JH: Is there anything you think is under-appreciated in the field of genetics?

LS: Genetic Diversity! Many diseases are studied by using models on a single genetic background when no two humans with the same disease are genetically identical. My lab is using genetically diverse mice to determine if inherited genetic variants increase the likelihood of developing CH and that there are population differences in clonal advantages gained by specific mutations in particular genetic and environmental contexts. CH is most commonly driven by somatic mutations in the gene encoding DNA methyltransferase (DNMT3A), so we are testing the hypothesize that variation in genetic background dictates whether DNMT3A-mutant HSCs acquire a selective advantage. The work is still in progress so we will have to wait and see!

Logan’s cat, Eugene!

JH: What do you like to do outside of lab?

LS: Outside of the lab, I enjoy hiking/exploring Acadia national park, running, painting and trivia nights, and taking care of my fifty house plants! A couple of years ago, my friend gave me my first house plant, a snake plant. He told me they were impossible to kill, and somehow I still managed to kill it. I decided to try again, and somehow I was able to keep it alive. After that, it has become a sort of obsession, although I still kill succulents from time to time. The thing I love most about having plants is how much life they can bring into your home. I also love watching them grow and change over time!

Some of Logan’s many house plants!

How Do You Figure?: Graphic Design Software For Scientists

As I sit at home writing what will (hopefully) be my very first first-author manuscript, I began to wonder how scientists go about making their figures for a paper. Like many things in academia, it was probably going to be lab-specific: someone would have started using a particular software, taught the next graduate student how to use it before they left, and that student would teach the next. And so on, and so forth.

With this in mind, I took to Twitter to ask students (and @AcademicChatter), how, exactly, were they figuring?

BioRender (@vanesque89, @Nicole_Paulk)

Price: Free for personal/educational (limited) use, various paid plans
Platform: Web-based

Think of BioRender as your scientific clip-art library. BioRender has a collection of over 20,000 different icons covering more than 30 fields of the life sciences. The colors of each icon can be customized, and the drag-and-drop functionality makes figure creation very quick. Even better, there’s nothing to download! It’s right there in your browser, ready whenever and wherever you are working.

CorelDraw (@AdemaRibic)

Price: $249/year or $499 (one-time purchase)*
Platform: Windows, Mac

Originating in Ottawa, Canada, CorelDRAW touts vector illustration, layout, photo editing, and typography tools. It works on both Windows and MacOS.

*Editor’s note: Corel Education Edition is a one-time payment of $109 (thanks to Adema Ribić for this correction!)

Adobe Photoshop and Illustrator (@Nicole_Paulk)

Price: $20/month for the first year, $30/month after that (student pricing, includes all Adobe apps)
Platform: Windows, Mac, some apps available for iOS and Android

Almost everyone is familiar, at this point, with Adobe Creative Cloud, Adobe’s suite of software for designing things (literally, any and all of the things). Photoshop is useful for raw images (such as overlaying fluorescent images and stitching together microscope images). Illustrator, in contrast, is for creating vector art and illustrations, but it’s also useful for aligning the different panels for a cohesive figure. The most updated version of Illustrator seems to have kept this in mind: the Adobe website specifically mentions its use in making infographics, including the ability to edit data through a charts function.

GraphPad Prism
Price: $108/year (student pricing)
Platform: Windows, Mac

Prism is less for making figures and more for making graphs, but it’s worth mentioning here since many of us include graphs in our figures. In Prism 8, you can draw lines or brackets on graphs to indicate significance. A centered text box is automatically included for your asterisks! These graphs can be exported as images and then arranged easily in another application as panels of a figure.

Affinity Photo and Designer (@SimonWad)
Price: $50 per app, one-time purchase
Platform: Windows, Mac, iPad

These are popular alternatives to Adobe Photoshop and Illustrator. One of the major complaints about Adobe was its movement to a cloud-based subscription model. Affinity uses a one-time purchase model, and is also considerably more affordable. The company also has an alternative to Adobe InDesign (called Publisher).

This is by no means an exhaustive list of all the possible software you could use to make a figure. Many people swear by PowerPoint as their favorite way of assembling figures. Here are a few other pieces of software to check out that are free to all:

Price: Free!
Platform: Windows, Mac, Linux

Gimp is a high-quality raster image editor. Think of this as the free version of Photoshop. It can do a lot of the same things, but it’s missing some of the advanced tools, such as using adjustment layers to non-destructively edit images.

Price: Free!
Platform: Windows, Mac, Linux

Inkscape is a vector graphics editor with shapes, layers, text on paths, and the ability to align and distribute objects. If you’re looking for something like Illustrator to handle vector graphics but don’t want to shell out the money, this is a great option!

Price: Free!
Platform: Windows, Mac, Linux

Scribus is an open-source alternative to Adobe InDesign. It has many of the same features as InDesign, but unfortunately can’t open InDesign files.

Thank you to everyone who responded, and happy figuring!

Cover image by Mudassar Iqbal from Pixabay