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Boneyard Creek by IB463

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Every day thousands of students walk along the engineering quad, crossing the bridge over Boneyard Creek. While many students don’t even notice the creek, it is home to a surprising diversity of fish species. Boneyard Creek is a headwater creek which feeds into many drainages, ultimately leading to the Mississippi River. This ecological connectivity provides continuous habitat for fish migration including several species of sunfish, largemouth bass, and catfish. On any given day, you may find as many as 20 (or more!) different species of fish. Despite being the main aquatic feature, it remains an overlooked part of campus.

The Boneyard Creek at Sunset

The Boneyard Creek at Sunset, © All Rights Reserved, by tobiastoennies

The website fishesofboneyardcreek.weebly.com was created to educate unwitting residents and incoming students at the University of Illinois at Urbana- Champaign about the surprising abundance of fish in Boneyard Creek. This website was made by the Ichthyology Classes of 2012, 2014, and 2016. It provides an array of information, including the history of the creek, a list of present fishes, a dichotomous key to identify them, education activities for children, and a volunteering tab that tells how you can contribute to the health of the Boneyard Creek. Many resources are included on this website, and it effectively serves as the information hub for all things Boneyard Creek. Click here to see an underwater video of fish in the creek recorded by Elise Snyder.

 

Male Rainbow Darter

Male Rainbow Darter collected and photographed by Alexander Pane at Phillips Tract

The Fishes of Boneyard Creek website is the result of a unique class project that stretched across three different cohorts of Ichthyology students (IB 463 from years 2012, 2014, and 2016). The 2012 course originally made the site. The 2014 course greatly improved it. The 2016 course created videos that explained how to use a dichotomous key. The 2012 class obtained a list of ‘potential’ fish species that could be found in the creek based on historical records from the Saline Branch, into which the Boneyard Creek feeds. The class has continued to sample the creek and to perform numerous class projects. One project has addressed the question of whether fish use the fish ladder at Scott Park. Another project sampled fish with minnow traps. Another project performed seine hauls to assess the fish community.

Creating this website and the accompanying videos not only taught us about the specific characteristics of the Boneyard Creek fish species – it also taught us how to communicate science to the public. We learned not only how to identify the different species of the Boneyard, but we also learned valuable skills like script writing, video editing, and how to present scientific information in a digestible way. These skills are vital in the modern scientific world where there is a heavy emphasis on communication and presentation of findings. Having scientists who are able to communicate with the public ensures that information can be utilized in a meaningful way. We hope that this project continues to go forward and ask/answer meaningful questions about the Boneyard Creek.

Ichthyology Class of 2016

Ichthyology Class of 2016 in the field

Alumni Profile: Muhammed Fazeel

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Muhammed Fazeel

Graduated: May 2012

Favorite IB class and why: Ecology and Human Health (IB 361). Professor Allan held a fantastic class related to health. I especially liked it since he made a conscious effort of making relevant lectures based on current/recent epidemics.

Favorite extra curricular activities (undergraduate research, clubs, etc) and why: Being part of the Illinois Launch program at the Academy for Entrepreneurial Leadership.

Why you chose IB:  Integrative Biology took a broader approach at understanding the world from a biology perspective which I found very stimulating.

How you feel IB helped prepare you for your career:  My time at U of I has given me the basic skills needed to better understand and address problems.

What you’re up to now: Soon after I graduated, I started a biomedical startup in Chicago. We have set up partnerships with a few clinics and our work is set to help several heart patients across America.

 

Writing the self-contained universe

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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

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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

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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.

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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.

“Girls Do Science!” Summer Camp

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Group Photo of Girls Do Science Summer Camp

For the second year in a row, SIB faculty, students and staff led a week-long “Girls Do Science!” camp for girls entering 2nd – 6th grade, in partnership with Orpheum Children’s Science Museum. Camp co-directors were Carla Cáceres (Animal Biology/SIB), Katy Heath (Plant Biology/SIB), and Katie Hicks (Education Director at the Orpheum). Campers explored the Pollinatarium with Lesley Deem, where they learned about insects and ticks, ran through Meadowbrook Park for a scavenger hunt of prairie plants, and participated in SIB faculty research on microbes (Katy Heath), mammals (Karen Sears) and plankton (Carla Cáceres) at the Natural History Building.

Staff and graduate and undergraduate students (too many to name!) from SIB and other units such as the graduate Program in Ecology, Evolution and Conservation Biology, Natural Resources and Environmental Sciences and the Department of Cell and Developmental Biology also participated. The camp was sponsored by grants from the National Science Foundation (DEB 1120804 and DGE 1069157).

More Pictures of Our Scientists

 

Gap years: trying things out

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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.

Conclusions
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.

-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[at]gmail[dot]com.