Writing the self-contained universe

Hi all,

You are not sitting next to me right now as I type these ideas. You’re most likely not in New Jersey, and you might not even be in the U.S. The fact that it’s even possible for you to be reading these words right now highlights an ever-growing need to be able to communicate ideas through writing. It’s the difference between you growing bored and leaving halfway to explore other parts of the internet, and you finishing this blog post (before moving on to explore the rest of the internet!).

In essence, writing is just a means of getting info from Point A to Point B. No matter how many amazing and intelligent ideas you may have in your head, they will have to stay there if you don’t know how to communicate them. Here are a few tips on bridging the gap between you and your reader’s mind when it comes to e-mailing a professor or potential collaborator, writing a grant, or explaining your ideas in general.

1. Who is your reader? Why should they care about your message?
Example: e-mail
As often as possible, put yourself in the head of the person reading what you wrote. Let’s say you’re e-mailing a professor to potentially do a PhD with them. They’ll want to know:

– Who is this person? Is he/she currently an undergraduate? If not, what has she done since then?
– What are his research interests? Of my work, what interests him?
– What are her research qualifications? Has she done research before, or is she just applying to grad school because she hasn’t considered other options?
– Has this applicant actually read up about my lab and thinks he’s a good fit, or is he just sending a template e-mail to every researcher he can find?

The more of these you can answer, the more willing the professor will be to respond. Remember that professors are incredibly busy people. Chances are, they enjoy talking with new people and exchanging ideas. But, their schedules are so packed that the easier you can make an e-mail exchange for them, the less time they have to spend answering these questions themselves. You want a researcher to be nodding her head as she reads the e-mail, her questions being answered as she reads so that by the end, the work has been done for her and she can now focus on writing her response.

2. Does your writing actually address what you wanted to say / the prompt?
Example: grant writing, lab reports
Say you’re working on an NSF-GRFP grant (the National Science Foundation Graduate Research Fellowship). You have phenomenal research ideas that would explain a genetic basis for sociability in humans, and you have told a heartwarming story on how you discovered and decided to pursue science. A few months later, you’re surprised to find your revolutionary ideas were not funded by NSF. What happened?

It’s likely that you didn’t answer every part of the application to the degree NSF was looking for. Consider an introductory biology lab in which the students dissect fish and chicken hearts (diagrams on the right). In their report, they are asked to compare the two hearts and explain how these hearts differ in the ability to support different levels of metabolic demand. Unless they provide comparisons between the two hearts and explain how those differences affect ability to support varying metabolisms, they will not get full credit (no matter how detailed either component of their answers are). Think of it as:

10 points total:
5 – provide 3 differences between the 2 hearts
5 – explain each difference in terms of metabolic potential

You can slam dunk those first 5 points, but if you don’t address the second section, it’s likely you won’t even get a passing grade. Similarly, for the GRFP, regardless of how incredible your ideas are, if you don’t explain how your work has any relevance outside of bullet points in a textbook only people in your field will read, even the very best ideas will get passed down. Again, think from the GRFP officer’s viewpoint: every applicant has good ideas, but NSF wants research fellows who will not only advance science but also help spread its ideas beyond the scientific sphere. Even if you would do outreach if you had the opportunity, if you don’t write about it, the GRFP officer can’t assume you would.

3. If your writing was an isolated universe, would that universe make sense?
Example: course exam
This is one I repeatedly tell my introductory biology students for their lab reports and exams. Imagine your mom somehow stumbled across your biology midterm essays (of all the things she could have discovered in your room) and was reading them. Would she be able to understand what you wrote? In this situation, you have someone who most likely hasn’t taken college-level biology in a few decades, if ever. Do they get lost in your jargon, or is your answer self-contained enough for anyone to be able to pick it up and learn something from it? One of the biggest road blocks to a good scientific talk is losing your audience part way because you assume they understand something they actually don’t. Being able to grab a listener from any background and pull them to a new level of understanding is challenging, but it’s critical for teaching.

4. How long do you think your reader will spend on your writing? If they skimmed it, would they still get your message?
Example: lab report, scientific articles
Many science majors in college are under the misconception that a longer lab report is a better one. The idea, which seems reasonable at first, is that the more information you put down, the larger the net you are casting, which has a better chance of catching the answer your TA is looking for. Unfortunately, it’s not quite like that. Aside from giving yourself more opportunities to write something incorrect and actually lose points, in the scientific world you will almost never be in the situation where you’ve written everything you need and should keep writing more.

Again, think about writing as a communication of ideas. Short and sweet (i.e. efficient) is always preferable to long and winding in science. Scientific articles have abstracts so readers can get the gist of the article without needing the motivation, background, and time to read the entire thing (remember how busy many researchers are!). Articles in the journal Science actually have one-sentence summaries for the particularly busy and researchers in related fields who may want a simplified version of the abstract. Brevity is a much better skill to have than the ability to list everything you know about a topic.

Consider the reader, consider your miniature universe. And if all else fails, just call your reader on Skype.

Photo credits:
– Thinking: Basic College English blog (http://uppampangaenglish.blogspot.com)
– Chicken heart: University of Illinois at Urbana-Champaign Chickscope (http://chickscope.beckman.uiuc.edu/explore/embryology/day02/comparative.html)
– Fish heart: Stanford University Environmental Science Investigation (http://esi.stanford.edu/circulation/circulation5.htm)

Matt Grobis is a PhD student at Princeton University and an alumnus of the IB Honors program at the University of Illinois. For more information about academia advice, summaries of scientific articles, and discourses on metal music, check out mattgrobis.blogspot.com or e-mail him at matt.grobis[at]gmail[dot]com.

Fungus that causes white-nose syndrome in bats proves hardy survivor

Written by Diana Yates, Life Sciences Editor | 217-333-5802; diya@illinois.edu

CHAMPAIGN, Ill. — After taking an in-depth look at the basic biology of a fungus that is decimating bat colonies as it spreads across the U.S., researchers report that they can find little that might stop the organism from spreading further and persisting indefinitely in bat caves.

additional photoPhoto by L. Brian Stauffer

Graduate student Daniel Raudabaugh, left, and mycologist Andrew Miller, of the Illinois Natural History Survey, conducted the first in-depth study of the basic biology of P. destructans, the fungus that causes white-nose syndrome in bats.

Their report appears in the journal PLOS ONE.

The aptly named fungus Pseudogymnoascus (Geomyces) destructans causes white-nose syndrome in bats. The infection strikes bats during their winter hibernation, leaving them weakened and susceptible to starvation and secondary infections. The fungus, believed to have originated in Europe, was first seen in New York in the winter of 2006-2007, and now afflicts bats in more than two dozen states. According to the U.S. Fish and Wildlife Service, P. destructans has killed more than 5.5 million bats in the U.S. and Canada.

The fungus thrives at low temperatures, and spreads to bats whose body temperature drops below 20 degrees Celsius (68 degrees Fahrenheit) when they are hibernating in infected caves. Previous research has shown that the fungus persists in caves even after the bats are gone.

The new study, from researchers at the Illinois Natural History Survey at the University of Illinois, found that the fungus can make a meal out of just about any carbon source likely to be found in caves, said graduate student Daniel Raudabaugh, who led the research under the direction of survey mycologist Andrew Miller.

“It can basically live on any complex carbon source, which encompasses insects, undigested insect parts in guano, wood, dead fungi and cave fish,” Raudabaugh said. “We looked at all the different nitrogen sources and found that basically it can grow on all of them. It can grow over a very wide range of pH; it doesn’t have trouble in any pH unless it’s extremely acidic.”

“P. destructans appears to create an environment that should degrade the structure of keratin, the main protein in skin,” Raudabaugh said. It has enzymes that break down urea and proteins that produce a highly alkaline environment that could burn the skin, he said. Infected bats often have holes in their skin, which can increase their susceptibility to other infections.

The fungus can subsist on other proteins and lipids on the bats’ skin, as well as glandular secretions, the researchers said.

“P. destructans can tolerate naturally occurring inhibitory sulfur compounds, and elevated levels of calcium have no effect on fungal growth,” Raudabaugh said.

The only significant limitation of the fungus besides temperatures above 20 degrees Celsius has to do with its ability to take up water, Raudabaugh said. Its cells are leaky, making it hard for the fungus to absorb water from surfaces, such as dry wood, that have a tendency to cling to moisture. But in the presence of degraded fats or free fatty acids, like those found on the skin of living or dead animals, the fungus can draw up water more easily, he said.

“All in all the news for hibernating bats in the U.S. is pretty grim,” Miller said.

“When the fungus first showed up here in Illinois earlier this year we went from zero to 80 percent coverage in a little more than a month,” he said. The team led by U. of I. researchers that discovered the fungus in the state found a single infected bat in one northern Illinois cave, he said. Several weeks later most of the bats in that cave were infected.

Although many studies have been done on the fungal genome and on the bats, Miller said, Raudabaugh is the first to take an in-depth look at the basic biology of the fungus.

“Dan found that P. destructans can live perfectly happily off the remains of most organisms that co-inhabit the caves with the bats,” Miller said. “This means that whether the bats are there or not, it’s going to be in the caves for a very long time.”

The Illinois Natural History Survey is a division of the Prairie Research Institute at the U. of I.

This study was funded through awards given by the Illinois Department of Natural Resources State Wildlife Grants Program (project number T-78-R-1) and the Section 6 Endangered and Threatened Species Program (project number E-54-R-1) to the Illinois Natural History Survey.

Alumni Profile: Colleen Stoyas

Colleen Stoyas on the Beach

Graduated: May 2011

Favorite IB class and why: I loved my Ecology and Evolution class and the field work it entailed, my Organismal Biology class because of its labs, Coral Reef Ecology and its mandatory lab in Belize, Genes and Behavior, and so many others. I think the class I find myself continually applying to my every day “life” choices is Ecology and Human Health, taught by Dr. Brian Allan. This course investigates human health issues from an ecological perspective and regularly influences my perception of infectious disease outbreaks, grocery purchases, choice of where within a city or area to live (did you know lyme disease most commonly occurs in communities of moderate population size and not in rural areas?), and more.

Favorite extra curricular activities (undergraduate research, clubs, etc) and why: My favorite activity was definitely my undergraduate research on yeast genetics in the Freeman Lab (dept of MCB), and I submitted a distinction project prior to graduation. Outside of the lab I was in a co-ed Honor Fraternity, Phi Sigma Pi, that allowed me to make a great group of friends outside of my science courses and participate in service projects in the Champaign-Urbana community.

Why you chose IB: I chose IB over other Life Sciences majors because of the emphasis on analytical thinking and problem solving. In IB courses you are required to memorize less facts and instead given a set of information and asked to apply the principles you learned to answer questions on that information. This type of learning is extremely engaging and affected not only my studies, but how I approach any information given to me in life. I entered Illinois generally interested in science and was told growing up that I would make a good physician. While taking IB150, I realized that my interest in medicine had been in the discovery portion all along, and not in actually treating patients.

Colleen Stoyas with turtle

How you feel IB helped prepare you for your career: As I mentioned above, IB focuses on teaching analytical thinking and problem solving skills. I once had a project where I was asked to pick a plant on campus, and I had to email my professor a paragraph on that plant every week. Sometimes it seems hard to find a difference in a dormant magnolia tree from week-to-week in January and February, but “no change” was unacceptable. By the end of that semester I was at that tree every single day noticing so many differing events in its immobile life. IB taught me to be observant, patient, and responsive to my environment in addition to the value the knowledge the coursework provided me. These skills have been invaluable in my current career as a PhD student in Biomedical Sciences.

What you’re up to now and what you like about it: I am currently starting my third year as a PhD student in the Biomedical Sciences program at the University of California, San Diego. I am a member of the La Spada Laboratory, a large and diverse environment that studies the genetics of inherited neurodegenerative diseases such as Huntington’s disease. My favorite part of my schooling/job is engaging with leaders in the neurodegeneration field and working at the cutting-edge of scientific discovery.

SIB creates new joint center in genomics with Fujian University.

Professor Ray Ming (plant biology) will direct the new joint center in genomics and biotechnology – the center is a collaboration between Integrative Biology and Fujian Agriculture and Forestry University. With an initial investment of $30 million US, the new center promises to open new collaborations between the two institutions and create new opportunities for student exchanges. Professor Feng Sheng Hu, head of plant biology, was instrumental in negotiating the creation of the new center, which will be open for business in the next two months.

Gap years: trying things out

Hi all,Matt

In the sciences it’s easy to get in the mindset of “go to college, go to grad school, get a post doc, be a professor” for your career. While this path works, I want to talk about the crazy idea of breaking from the path for a year or two before you throw yourself into a PhD program. (Note: this applies to people applying to professional schools like medicine or law, as well.)

To preface, going into grad school straight out of college does work. There’s a lot of people who do it and do it well. If you want to make a career as a researcher, starting grad school early lets you throw yourself at the rigors of a PhD while you’re young and energetic. But grad school is a huge commitment. Do you like fieldwork enough to get up at 7am on a Sunday if you have to? How do you react to the concept of motivating yourself to read a textbook, as opposed to it being assigned reading, for (probably) the first time? Are you ok with cutting your free time to the point that it’ll be a challenge to be simultaneously in that weekly journal club and working on that novel you’ve always thought about?

If you like your subject and are motivated, none of these questions should be that intimidating. But there’s nothing forcing you to throw yourself into all that straight out of college. Dr. John Cheeseman, the former head of IB Honors, continually tried drilling into my head the idea that I don’t have to go to grad school right away, that there are literally dozens of other cool options to consider. Your post-college path can veer wildly away from research, taking you across the world and letting you try things you’ve never had the chance to do before.

Yeah, I didn’t believe him. If you’re anything like I was as an undergrad, all of that will sound like a nice what-if, the cool life of someone who’s not in your shoes. Applying to a PhD program as a senior in college meant having knowledge and stability on what would happen in the half decade (at least) after college. With unemployment as high as it is right now, let’s just take what we can get, right? And with literally the whole world open for the first time, I found myself surprisingly drawn to the idea of “settling down” into a PhD program, where I know what I’m doing in a month, this summer, next year.

The point of this post is to pull a Cheeseman and encourage you to think outside the box. The following alternatives to immediately starting grad school are applicable to new graduates looking for something to fill a few months before more permanent plans, new seniors looking for stuff to do after graduation, and sophomores and juniors looking for summer plans.

1. Teach English or do research in another country on a Fulbright grant
Starting with the option that deviates the least from the research path, the Fulbright is something I highly recommend students interested in research consider. The Fulbright is funding for one year to teach English or do research with a local organization in another country (i.e. you can’t work with an American researcher stationed in Panama). If you want to do research someday, this is a fantastic opportunity to try independent research out, not have it go as you expected, and then learn how to better conduct research. When you enter grad school for real, you’ll have the knowledge of your Fulbright year as a head start on learning to do quality work. Also, the experience of living in another country for a year, especially fresh out of college, teaches you a lot about yourself. (If you’re interested, visit topscholars.illinois.edu or e-mail topscholars@illinois.edu for more information. The priority deadline is July 1.)

2. Work as a field assistant / do a lab internship
Part-time work in the area of research that interests you, especially if you can find something that pays or at least breaks even (e.g. housing is paid for), is awesome. For biology fieldwork, job boards like those of University of Texas A&M, the Ornithological Societies of North America, and Partners in Amphibian and Reptile Conservation constantly have researchers looking for people to help with fieldwork.

If you can make it to Australia, Tasmanian devils need research love, too

You could study lizards in the Tucson desert, search for crabs on beaches in Washington state, or even end up in Australia watching fairy wrens through binoculars. The options are out there! A Fulbright alumna I know did the ‘fieldwork rock star’ lifestyle for a year, where she hopped from field project to field project. She barely broke even financially, but she got to spend a year traveling the world while simultaneously advancing her career. This is a great way to get exposed to a lot of types of research, too, and see what you like the best.

3. Ditch research for a bit
As much as you might like biology, it’s only one side of you. Ever wanted to tutor kids in creative writing? Find an apartment in San Francisco and intern at 826 National. Does doing manual labor on a farm in exchange for food and a place to sleep sound awesome? Check out work exchange programs like WorkAway. When I interviewed at Cambridge (conflicted, I applied to do a PhD in Cambridge the same year I applied for the Fulbright. I didn’t get in) and was discussing the potential for gap year(s) before grad school, my proposed adviser there said about 4-5 years without science research should be the upper limit between finishing college and starting grad school. That’s a whole lot of time to pick cocoa fruit and build hiking trails in Costa Rica.

Graduating college is intimidating. Not knowing what happens next is scary. But it can also be exciting. I strongly believe (finally) in the benefit of taking time off, whether it be getting experience with research or trying something totally different. If you like the crazy different path you took, awesome! If it wasn’t what you thought and you miss research, grad schools are accepting applications every year. As I mentioned in the previous blog post, grad schools will care more about your experiences with research than whatever grade you got in physics.This is one of the best times of your life to try something new. Don’t be afraid of trying something different just because you don’t know how it’ll turn out.


For more information about academic advice, summaries of scientific articles, and discourses on metal music, check out my blog (www.mattgrobis.blogspot.com) or e-mail me at matt.grobis[at]gmail[dot]com.

Advice for new SIB grads

Hi all!
My name is Matt Grobis. I graduated in May 2012 from the Integrative Biology Honors major and am currently pursuing a Fulbright grant at the Max Planck Institute for Ornithology. With commencement coming up this weekend (congrats to all IB graduates!), I thought I’d share the three biggest lessons I’ve learned since leaving the college bubble.

1. You’ll make mistakes… and that’s ok!
When I began my Fulbright, I was anxious to make the most of it. I had been on the waitlist for ten weeks, so I felt incredibly lucky to have this opportunity at all. I became involved in three separate research projects: formulating and carrying out an independent project on social foraging in wild great tits, helping a graduate student in a project on sleep and predation risk in wild great tits, and recording and analyzing mate-pair vocalizations in captive ravens. I became essentially buried in work, and the grad school applications, bio GRE, NSF-GRFP funding application, and furniture shopping for a new apartment added layer after layer of stress to my life. I made two crucial mistakes: underestimating how much time fieldwork takes to prepare for and carry out, and overestimating how much I can get done in one day. November was pretty miserable, and it was made so much harder because I wasn’t used to things not going well.

Great tits (Parus major) don’t always cooperate with your planned methodology

What the experience taught me, though, is that it’s totally fine to make mistakes. They’re the best way you learn. In undergrad, academic success has a pretty straightforward formula: pay attention in class, study before the exam, profit. It’s a lot different outside of college, where the path from Point A to Point B isn’t so obvious. You will make mistakes as you try to figure this out, but that’s how you grow. While working at the Institute has been a bit of a “tough love” learning experience, I feel I’ve grown so much as a researcher because there was no one to pull me out when I dug myself into that hole. As much as my research group liked me and wanted to help with my work, ultimately the responsibility was on me to fulfill the promises I made to my adviser and group members. As tough as it was, it’s one of the best things that could have happened to me during my year here.

2. Grades matter(ed), but experiences matter more
While your undergrad grades are important, they rarely come up in conversations in grad school, and probably even less so in the real world. Much more important to your future self (and future employers) are your experiences with what interests you. Interested in science journalism? Start a weekly science blog and see how you like it. Interested in field research? E-mail a university professor and ask to volunteer with the field season. I was amazed to learn that my adviser at the Institute is almost always looking for volunteers to help grad students with their fieldwork. Sometimes the professor can pay for your accommodation, too. In exchange for your help, you learn how to do good research by observing trial and error, master a ton of field techniques, and see whether this is something you want to continue with or not.

3. Got a question? Send an e-mail
Success is never completely independent. Everyone you look up to has had help along the way, and you’d be surprised at how willing people are to pay it back (especially if you’re thankful and nice to them). Go on LinkedIn and find U of I alumni doing what you want to do and invite them to coffee. E-mail grad students doing the research that sounds cool and hear their story. It’s ok not to get responses; don’t hassle them. But if you’re humble and genuinely interested, people will always be willing to help.

– Matt

For more information about academic advice, summaries of scientific articles, and discourses on metal music, check out my blog (www.mattgrobis.blogspot.com) or e-mail me at matt.grobis@gmail.com.

Congratulations to the IB NSF Graduate Research Fellowship Recipients

As featured in Inside Illinois, Illinois graduate students won a record number of NSF Graduate Research Fellowships this year.  Several students in Integrative Biology are among the awardees.  Let’s congratulate them for their hard work!

This year’s awardees from IB are:

▪Lorena Rios Acosta
▪Matias Cristobal Fernandez
▪Matthew Grobis
▪Daniel Joseph Urban
▪Kevin James Wolz

IB students accorded Honorable Mention are:

▪Cassie Wesseln
▪Kristen Bishop
▪Christopher Holmes-Singh
▪Allen Victor Lawrance
▪John Michael Maddux
▪Selina Ariel Ruzi

These lists come from the NSF-GRF Fastlane database. For additional information on this year’s competition, see the NSF-GRF main page.

Congratulations to the 2013 Biomathematics Research Fellows!

The Illinois Biomathematics Research Experience Program is a year-long research experience in mathematical biology. Despite the strong demand for students that are trained in biomathematics, undergraduate mathematics and biology majors still proceed largely along parallel isolated tracks, with many biology students acquiring very few mathematical skills and concepts, while many mathematics students remain relatively uninformed about biology. The Illinois Biomathematics Research Program brings mathematics and biology students together under joint mentorship by biologists and mathematicians.  Our goal is to contribute a generation of scientists and mathematicians to meet the new challenges at the interface between these two disciplines.  Additional information about the program can be found here: http://www.math.uiuc.edu/biomath/

The 2013 National Science Foundation funded fellows are working on the three projects under the guidance of faculty from the Departments of Mathematics and Animal Biology.

RachelPoeGene Regulation and Limb Development
Kari Kosog (Integrative Biology), Rachel Poe (Mathematics), Dr. Zoi Rapti (Mathematics), Dr. Karen Sears (Animal Biology)

Hi! My name is Rachel Poe, and I’m a sophomore researching mammalian limb development with Dr. Zoi Rapti and Dr. Karen Sears. I’m a mathematics major and a computer science and biology enthusiast. Needless to say, I am really excited to be a part of the U of I BioMath team this year. Before I came to school, I was convinced that I had to choose just one subject to study, and was disappointed that I wouldn’t be able to use multiple areas of interest for one purpose. But I quickly discovered that this was not the case — and now I get to use differential equations to model gene interactions in the process of limb growth! I can’t say that the project is without challenges, and I still have a lot to learn. One of the challenges for me has been connecting the more advanced biological concepts with the math models. Although I really enjoy biology, I don’t have as strong a background in it as I do math. But I’m excited by challenges and am always looking for something new to learn. That’s one of the reasons I’m excited to be working on this project — I’m learning so much along the way, and I know I’ll always have more to learn! I look forward to spending my summer in full-time research and exploring all the things I have yet to discover.

KariKosogHello there, my name is Kari Kosog, and I am currently a sophomore majoring in Integrative Biology and German. I took the Biomath class because it sounded interesting and like a fresh way to look at things. I really enjoyed it and decided to apply for the internship, and I am now working on a project under the supervision of Dr. Karen Sears and Dr. Zoi Rapti looking at the gene regulatory network in limb development. One of my favorite things about this project is that mapping gene networks mathematically is a relatively new field. I will be working in the lab with Dr. Sears to evaluate the gene networks. The math portion of the project is definitely new to me. I have a strong math background but have never tried to model anything. This is my first major project in a lab, and I am so excited to gain experience, learn from our advisors, and begin a life of scientific discovery!

We will specifically be looking at the feedback loops of the growth factors including sonic hedgehog, Gremlin 1, fibroblast growth factor (FGF), and Bone Morphogenic Protein 4 (BMP4). We will be comparing the differences between chicken, bats and opossums. The figure (Zellner 2009) shows an example of the network we will be working with. It is also an example of how the genes Sonic Hedgehog, Gremlin 1, BMP4, and FGF work together in regulatory loops. By creating a differential equation to map the feedback and regulatory loops, we can predict the effect of each gene on the system.

ZellerFigure from:
Zeller, R., Lopez-Rios, J., Zuniga, A. December 2009.Vertebrate limb bud development: moving towards integrative analysis of organogenesis. Nature Reviews, 10. 845-858.

Variable Light Environment exampleVisual Ecology of the Two Cone Visual System of Largemouth Bass
Shannon Stanis (Integrative Biology), Nick Sutton (Integrative Biology), Zach Turner (Mathematics), Dr. Lee DeVille (Mathematics), Dr. Becky Fuller (Animal Biology)

Largemouth BassOur group is working hard on developing both a theoretical and a functional mathematical model of the two cone visual system of largemouth bass (Micropterus salmoides) to better understand the predatory behavior of these fish in varying water environments. Now, without further ado, let’s introduce the undergraduate researchers:

Zach TurnerHi everyone, my name is Zach Turner and I am a sophomore studying mathematics. Most of my work on this project thus far has been extracting equations from the paper we are studying and then converting that into a workable code that we can manipulate with various data inputs. To be honest, I actually have really enjoyed doing that! It’s frustrating working with computers when things aren’t going your way, but I love the satisfaction when it’s finally working. My biggest struggle is coping with my extreme lack of biological knowledge, but luckily my fellow group members Nick and Shannon are more than capable of explaining all the science to me. Currently our project is rather preliminary but I am very excited to see how far we can expand it in the future!

Shannon StanisI’m Shannon Stanis, a senior double majoring in Integrative Biology and Psychology. I have been working in Becky Fuller’s lab for three years researching the visual system of killifish and now I am really excited to work with Zach and Nick to research their predator, the largemouth  bass.  Biomath is a perfect way to satisfy my scientific curiosity.   We have been reading papers and sitting down together to talk through figuring out exactly what we want to know and how we are going to figure it out.  I’m looking forward to lots of time with Zach, Nick, and, of course, the bass, to complete our behavioral assays this summer and integrate it into our model.  We have a great team and I’m sure we will find some fascinating results!

Nick SuttonHello, my name is Nick Sutton. I’m a sophomore majoring in Integrative Biology and aiming for a minor in Spatial and Quantitative Methods in Natural Resources and Environmental Sciences. As one of the biologists of the group, I’m working a lot with Shannon and Becky to help ensure the functionality of our mathematical model in order to keep it as realistic as possible. Once the summer hits, I’ll be helping in the design and implementation of the many behavioral assays we will be performing in order to test our model. This project is very exciting for me since I’m getting to experience a lot of visual ecology and mathematical programming at a deeper level than I would have thought possible as an undergrad. Though exciting, the project is not without its challenges, and I’d say that, for me, the most difficult aspect of this project is integrating the math and the biology. While I have a firm grasp of each subject separately, things tend to get a bit more complicated when you combine the two. Regardless of these challenges, I’m looking forward to continuing the project and seeing how well the results of our behavioral assays match up with our models.

Ecology of Infectious Disease
Sarah Duple (Integrative Biology Honors), Glynn Davis (Mathematics),Ping Lee (Integrative Biology), Dr. Carla Cáceres (Animal Biology), Dr. Zoi Rapti (Mathematics)

DaphniaThe 2013 BioMath Daphnia Disease team consists of three members, Sarah Duple- junior in Integrative Biology Honors, Ping Lee- senior in Integrative Biology, and Glynn Davis- sophomore in Mathematics. When we first arrived at the University of Illinois Urbana-Champaign as freshmen, we had no idea what we wanted to do for the next four years. Luckily, the U of I offers many courses that help students explore their interests in many different majors and fields. We all made a great decision and signed up for one of these courses, IB/Math 299 (Biomath), and it was the turning point of our college careers.

Throughout the course, we learned and explored the field of biomathematics and developed several research topics related to the ecology of infectious diseases. In 2012 (together with past team-member Adam Koss), we all worked together to study the dilution effect. The dilution effect is a concept in disease research by which biodiversity can potentially reduce disease prevalence. We specifically studied how disease dynamics change between a species of Daphnia, D. dentifera and its fungal pathogen Metschnikowia when a competitor species of D. dentifera, D. pulicaria is added to the system. We modeled the disease system using an ordinary differential equations system and also conducted biological experiments in the lab to obtain data to support our model predictions.

This year, the three of us are continuing to work with the Daphnia project but each focusing on different aspects of the system. Glynn is currently working on a three population mathematical model to determine how different parameters that are associated with negative fitness costs, such as feeding rate reduction, fecundity reduction, and per-spore infectivity affect virulence. Ping is also looking into the per-spore infectivity parameter, but specifically at how successful the spores are at transmitting the disease to different host genotypes, and how that affects the disease prevalence in the host population. Sarah is focusing on how different resource acquisition traits in the host and its competitors affect disease prevalence on different resource qualities.

In the coming months, we will all be working individually and collectively along with our advisors Dr. Carla Cáceres from Department of Animal Biology and Dr. Zoi Rapti from the Department of Mathematics. At the end of the summer we will be presenting our research at the 98th annual Ecological Society of America conference!




Former Student Aims High

One of our undergrads is competing to go into space!  He’ll be on campus for Engineering Open House this weekend.  Go check him out and show your support!

Hi everybody,

So AXE, the deodorant company and not the chemistry fraternity, teamed up with Space Expedition Corporation, a private aerospace company developing a miniature space shuttle, to send a few people from around the world to outer space.  The United States gets two seats.  One of them was assigned with a sweepstakes during the Superbowl.  The other one will be determined at a later date.  The competition I’m in would allow me to get a chance to get that other seat.  I am basically in a popularity contest:  the top two spots with the most amount of votes move on to attend Space Camp.  The two winners will join eight others chosen from other sweepstakes to go to Space Camp.  The last seat for space travel will be chosen from people attending.  Space Camp itself should be fairly exciting:  it covers a ride in a fighter jet, a microgravity flight, and simulator space flight.  I am currently in 24th place in that popularity contest.  I’ve been dressing up as an astronaut everyday at George Mason University (just doing everyday things like doing hw, eating, going to class, etc…) and I’ll do the same at U of I when I visit March 8-10.  That’s during my spring break so I’ll also have time to hand out flyers/pamphlets. The school newspaper there is going to run a story on me fairly soon.

For my graduate studies, I am pursing a Master’s degree in chemistry.  My advisor is Paul Cooper and he specializes in the chemistry of planetary ices.  The research I am conducting involves elucidating the mechanism behind methanol formation in irradiated ice.  Water ice is the most dominant ice in the solar system and that ice is constantly bombarded by high-speed electrons, protons, and ions.  This can lead to the creation of new and more complex chemical species if the ice contains other primordial chemical species like methane or carbon dioxide.  My experiments involve shooting high speed electrons at water ice laced with methane.  We identify various products using IR spectroscopy and mass spectroscopy.  The exact mechanism or mechanisms of formation will be identified by using deuterium that will replace the hydrogen atoms in either the methane or water so that we can trace the movement of the hydrogen atoms.