Amazing IB undergrads!

undergrad research week
This week is Undergraduate Research Week, a celebration of student excellence in research across campus. The signature event is the eighth annual campus-wide Undergraduate Research Symposium (URS), held on Thursday, April 23rd.

We are pleased to highlight some of the great research our undergraduates are doing in IB!  The following IB students are presenting at this year’s Symposium:

Behavioral Freeze Avoidance Strategy in an Antarctic Fish
Mateusz Grobelny, Senior

Efficacy of Common Disinfectants Against Ophidiomyces Ophiodiicola, the Causative Agent of Snake Fungal Disease
Marta Rzadkowska, Senior

RNAi Knockdown: The Role of unc-25 in Mediating Nicotine Resistance in Caenorhabditis elegans
Andrew Tran, Sophomore
Emily Yaniz, Sophomore
Stephanie Martynenko, Sophomore

Community Inference
Zachary Cohen, Sophomore

Modeling Threat Assessment in Prey
Nicholas Sutton, Senior

Molecular Evolution for the Chemoreceptor Gene Families in the Common Eastern Bumblebee, Bombus impatiens
Yihui Zhu, Senior

DNA Fragment Length Heterozygosity PCR: Lab-on-a-Chip Method for Testing Bias in Prairie Root Metagenomics
Taylor Pederson, Senior

Electrophysiological and Mass-Spectrometric Investigation of Aplysia L1-L7 Neurons
Feng Zhu, Senior

Elucidation of Dopamine’s Influence in Peripheral Sensing in Pleurobranchaea.
Megan Flanagan, Junior
Andrew Tran, Sophomore

Genetic Analysis of Cellobiohydrolase I (cbhI) Gene Sequences and Production of Other Wood Degradation Enzymes in Tropical Aquatic Fungal Communities
Matthew Boyce, Senior

Improving the Accuracy of Photosynthetic Compensation Point Measurements
Jessica Ayers, Junior

Hox Gene Expression in Mammalian Limb Development
Paige Oboikovitz, Senior

Did you know you can “hack” photosynthesis?

According to IB profs Stephen Long, Amy Marshall-Colon, and Donald Ort, using high-performance computing and genetic engineering to boost the photosynthetic efficiency of plants offers the best hope of increasing crop yields enough to feed a planet expected to have 9.5 billion people on it by 2050.

Read more at: http://phys.org/news/2015-03-photosynthesis-hack-world.html#jCp

A Foundation for Modern Teaching and Research

courtesy LAS News Magazine, Winter 2015 edition

In the late 1800s, with the University of Illinois facing growing enrollments and limited space, renowned University architect Nathan Ricker designed a distinctive teaching and research building at the heart of campus that he hoped would endure through the ages. He produced a gem—the Natural History Building.

This historic structure has hosted generations of students studying geology, biology, and other disciplines. Distinguished scholars have taught, established laboratories, and conducted groundbreaking research within its walls.

But designs and infrastructure that worked for the 19th and 20th centuries do not meet today’s teaching and research demands. The Natural History Building has reached a critical juncture and it must evolve dramatically to continue to serve our campus. Thus, the University has begun a $70 million renovation that preserves the building’s historic exterior while transforming the interior into a new world of state-of-the-art classrooms, laboratories, and meeting spaces.nhbA Vision

The renovation of the Natural History Building will create a dynamic education and research center. It will house classrooms, laboratories, and offices for current and future generations of geologists, geographers, and atmospheric scientists, and will be the center for biological and environmental education for students from across campus.

IB students will gain skills to examine challenges such as the outbreak of a new infectious disease or the causes and consequences of declining biodiversity. They will combine an understanding of basic natural history with new technologies that will bring breakthroughs in fields such as genomics. The holistic approach of the School of Integrative Biology will prepare students to tackle complex problems ranging from understanding evolutionary processes to developing biofuels.

For more on the NHB Renovation, including naming opportunities, and the story of a mysterious time capsule, please visit LAS News magazine.

What I learned as a First Year Medical Student

Amanda Ilag is a 2013 IB graduate and is our guest blogger this week!

amanda ilagRemember how you felt studying for the MCAT, taking that organic chemistry final, or going to a volunteer service event all in one day? This is the kind of stress and stamina needed to get through medical school. Year one of medical school takes everything you need to know about the basic sciences and applies it to human anatomy and physiology all in one year. That’s why they tell you to be organized, efficient with your time, and good at assessing your weaknesses and strengths. Studying for medical school is a full time job. You need to find new test taking skills, reform your old ones or in some cases group yourself up with fellow peers so that you get the most out of the learning experience.

In medical school you are working with an even more selective group of students so the pressure to do well is even higher. The way you need to study and take tests needs to be more efficient than it has ever been in your life. What I liked about SIU in Carbondale is that they counted our first exam lower than all other exams because they understood undergraduate to medical school could be a transition. It was also less pressure to compete for the best grades because our curriculum was a satisfactory/concern/unsatisfactory grading scale instead of actual grades. The good news is if you have the motivation and stamina to succeed; you will succeed! Get excited about testing yourself to the maximal potential of understanding! You’ll be pleased by how much you will have learned and even more curious about all there is to come.

A big part of learning now in any medical school curriculum is through “problem based learning.” This style of learning was crucial in SIU’s curriculum. It was discussion based and really challenged students to help each other understand material in a non-confrontational (group of 6-8 students) and moderated setting (tutor group leader, either a doctorate faculty member in the basic sciences or an actual physician). It was so different than undergraduate lectures where the lecturer told you most things and there was little or no discussion between students before exams. With problem based learning, students were the ones discussing what could be wrong with a “fake patient” in the computer system whose “labs, physical exam, and history information” were based on a compilation of actual patient records. It is a chance to explain material in your own words, to see if you are on the right track, and helps solidify material into memory.

I learned a lot about myself by talking with fellow students. Not all of your classmates are fresh out of college, in fact some may already be married with kids, so it was neat to gain new perspectives on life by talking with fellow classmates who are different from me. I made a lot of new friends that I hadn’t expected to make based on age, diverse background, previous work experiences, etc. We got to know our peers well because of our small class size, making it easy to be studious and to get together when we needed to have fun.

There is some clinical experience involved in year one. First years got a mentor to shadow in a specialty of your choice (mine was family medicine) where I would go once a week to observe and learn how to talk to patients from the surrounding community. You learn techniques for doing physical exam, what type of questions to ask to lead you to a list of possible diagnoses, and you learn to communicate this information concisely both verbally and in writing.

You still have time for hobbies, significant others, and relaxation you just have to be smart with your time; and be ready to adjust as necessary. And when you do find yourself in stressful situations get help from people you know and trust. There were many people on our faculty and fellow students that helped me deal with stress. And my family continued to be a strong means of support.

If you are applying to medical school or thinking about applying consider this… IS the lifestyle of a medical student something you can work with? CAN you imagine doing anything else? If you answered YES, then NO, go for it.  If you have applied but are not sure whether you want to go, take some time off to think about it. Year one of medical school is a life-changing experience for anyone so be really sure you want to go before doing it.  If you have been accepted and are sure you want to go, congratulations there is so much more you will learn about yourself along the way, and you are that much closer to being the doctor you’ve always wanted to be. Sometimes people find they don’t want to go AFTER they’ve already been there, and that’s ok too. The skills you will learn from a year of medical school will stay with you for the rest of your life and will surely make you a better person for it! Just consider all the options and learn as much as you can about it before diving into it.

Applying for a Fulbright Research Grant

IMG_7191My name is Sally Feng. I graduated with a B.S. in Integrative Biology in May 2014. I am currently doing work on coral restoration in the Philippines under a Fulbright research grant. If you are interested in applying for a Fulbright, here is my experience.

 

My Fulbright Timeline

  • May 2, 2013 – Attend Fulbright info session
  • July 1, 2013 – Priority deadline submission
  • September 3, 2013 – Top Scholars deadline submission
  • September 25, 2013 – Fulbright campus interview
  • October 2, 2013 – Fulbright final deadline submission
  • January 31, 2014 – Institute of International Education sends application abroad for final review
  • April 9, 2014 – Selected for Fulbright U.S. Student Award to the Philippines 

General Advice

Before starting the application, you need to decide whether you are willing to commit to the process. You have to be determined, self-motivated and patient. This applies even more so once the scholarship has been awarded. It is not a study abroad program where you take a class with fellow students. You will spend up to a year on your own in a foreign country. Don’t let that scare you; it is well worth the opportunity and a very rewarding experience.

Since it is quite a long journey, it is important to become familiar with the application process and deadlines. All U of I students will apply for the scholarship via the Top Scholars/National International Scholarships Program. The process involves submitting an online application, college transcripts, 1-page personal statement, 2-page grant purpose, 3 letters of recommendation and an affiliation letter. Keep in mind the letters of recommendation have different deadlines and specific submission instructions.

To begin, determine a starting point. What interests you? Where do you want to go? This is your opportunity to be creative. If you need help, there are many resources available. Visit the Top Scholars office and read past submissions. Ask professors if they have contacts abroad that may be willing to accept you in their lab. Have others proofread your essays. I highly recommend submitting a draft for the priority deadline. Be very detailed in your essay to let the reviewers know you have done your research. Plan out the months of what you will be doing during your stay there. Talk about the preparations you will take to become a stronger candidate. Let them know you are interested in the culture and what you hope to gain out of it. Most importantly, convince them why they should fund you to go to this specific country.

My Application Process

My starting point was the location. I wanted to work in water so I narrowed my search to islands. Next I looked into statistics. Based off of the 2013-2014 statistics for Philippines, of the 18 applicants, 8 were awarded. I began looking into universities that specialized in marine sciences. I looked into the research topics of faculty members to see if any were of interest. I found the topic of coral restoration very appealing so I emailed a professor telling him I was applying for a Fulbright and would love to work in his lab. He was willing to accommodate me at his lab considering that I would be fully funded throughout my stay.

That may have sounded easy but couldn’t have been done without help. My initial draft needed a lot of work and I might have given up if it wasn’t for the support provided by my professors and from the Top Scholars office. I was told I had very strong letters of recommendation and my professors were rooting for me. That was encouraging to hear and I did not want to disappoint them. I continued to read research articles to get ideas. I emailed my prospective professor for advice on my grant purpose. I worked on new drafts until I was satisfied with my project. It is extremely important to come up with a project that you are interested in because this could potentially be the next year of your life.

The application process is a rewarding experience by itself. Not only did I learn how to write a grant purpose, I was accepted into a lab at an international university. I have letters of recommendation ready for future references. I learned how to present myself on paper and in person. I gained confidence in the work I accomplished and the effort paid off.

In the coming weeks, I hope to share more about my past and current research experience. If you have questions, feel free to contact me at feng.sally26@gmail.com. Best of luck!

– Sally.

On the job hunt?

Searching for a job can be one of the most stressful ventures in life!  The IB Advisors are here to help with career exploration, finding internships, preparing for the job search, and more!

Be sure to also use The Career Center at Illinois for services related to job hunting like resume reviews, mock interviews, and career fair prep!crying in baseball meme

Check out these additional great resources to help make yourself the best possible candidate and minimize anxiety:

On cover letters via Conservation Careers

On using power words in your resume from Career Bliss

On staying positive from The Muse

On decreasing anxiety via The Career Center at Illinois

On tough interview questions via The Career Center at Illinois

On etiquette via The Career Center at Illinois

Bug Buffet!

Our very own Professor May Berenbaum and PhD student Michelle Duennes were featured in a recent Daily Illini article regarding IB 109: Insects and People, where as part of the class, the students enjoy a “bug buffet.”

Eat bugs

From the article…

While many cringe at the idea of eating bugs, which is called “entomophagy,” this practice is widely accepted in many countries around the world. For students enrolled in Professor May Berenbaum’s Integrative Biology 109 course, “Insects and People,” eating insects during the course’s bug buffet lab is anything but accidental.” 

Read on here.

Photo courtesy Anna Hecht via The Daily Illini

Looking for hands-on experience?

Consider registering for ENG 315: Learning in Community

Student teams working on real projects with community partners
Open to all students, all majors, all levels

LINC is an interdisciplinary, inquiry-guided service-learning course in which students provide meaningful service through the conception, development, and implementation of projects in collaboration with non-profits and community partners. Each section of the course is dedicated to a nonprofit organization that has proposed one or more projects of importance to the organization.  There are both new and continuing partners each semester. Choose a section based upon your interests and/or skills or your desire to learn something new!

Early in the semester you will meet a representative from your partner organization, learn more about the organization and its mission, and begin a semester project that addresses the needs of the organization. You will engage in a variety of research, service and fieldwork activities outside of class to gain knowledge needed for the project, and that knowledge is then discussed for understanding, applied, analyzed, synthesized, and evaluated in class. Class time is also used to help students delegate tasks, make decisions, process new information, engage in reflective discussions, learn core course content, collaborate with teammates, and receive guidance and feedback on the projects. Throughout the semester you will identify and explore topics that will assist you with the execution of your project. The semester concludes with a public poster presentation in which teams present the accomplishments of the project, value added to the community organization, and lessons learned.

As a result of this course you can expect to gain knowledge and skills in conducting research, understanding social and environmental issues, analyzing community and organizational needs and assets, defining problems, generating and analyzing solutions, identifying and mobilizing resources, project scoping, planning, and execution, teamwork and leadership, communication, problem-solving, critical thinking, professional writing, and civic responsibility.

For more information and to see projects for Spring ’15, visit http://linc.illinois.edu/spring-15-projects

IB Professor James O’Dwyer improves on 35-year old ecology model

Article courtesy of Biomarker Magazine from the University of Illinois Institute for Genomic Biology.

“Well, in our country,” said Alice, still panting a little, “you’d generally get to
somewhere else — if you run very fast for a long time, as we’ve been doing.”
“A slow sort of country!” said the Queen. “Now, here, you see, it takes all the running you can do, to keep in the same place. If you want to get somewhere else, you must run at least twice as fast as that!”
-Lewis Carroll, Through the Looking GlassODwyerIGB01

Inspired by the Red Queen in Lewis Carroll’s Through the Looking Glass, collaborators from the University of Illinois and National University of Singapore improved a 35-year-old ecology model to better understand how species evolve over decades to millions of years, as reported in Ecology Letters.

The new model, called a mean field model for competition, incorporates the “Red Queen
Effect,” an evolutionary hypothesis introduced by Lee Van Valen in the 1970s that suggests
organisms must constantly increase their fitness in order to compete with other ever-evolving organisms in an ever-changing environment. The mean field model assumes that new species have competitive advantages that allow them to multiply, but over time new species with even better competitive advantages will evolve and outcompete current species, like a conveyor belt constantly moving backwards.

The model gets its name from field theory, which describes how fields, or a value in space and time, interact with matter. A field is like a mark on a map indicating wind speeds at various locations to measure the wind’s velocity. In this ecological context, the “fields” approximate distributions of species abundances. Ecologists can use models to predict what happens next and diagnose sick ecosystems, said Assistant Professor of Plant Biology James O’Dwyer, who co-authored the study.

CREATING A MODEL ECOLOGY MODEL
The mean field model has improved a fundamental ecology model, called neutral
biodiversity theory, which was introduced by Stephen Hubbell in the 1970s. Neutral theory
does not account for competition between different species, thus considering all species to be selectively equal.

“The neutral model relies on random chance,” said O’Dwyer, who is a member of the Biocomplexity theme. “It’s like a series of coin flips and a species has to hit heads every time to become very abundant. That doesn’t happen very often.”

Neutral theory can predict static distributions and abundances of species reasonably well, but it breaks down when applied to changes in communities and species over time. For instance, the neutral model estimates that certain species of rainforest trees are older than Earth.

“At one end of the spectrum, we have this neutral model with very few parameters and very simple mechanisms and dynamics, but at the other end, we have models where we try to parameterize every detail,” O’Dwyer said. “What’s been hardest is to take one or
two steps down this spectrum from the neutral model without being sucked down to this very complicated end of the spectrum.”

By creating a more realistic model that incorporates species differences, O’Dwyer and co-author Ryan Chisholm, an assistant professor at National University of Singapore, have taken an important step down that spectrum. “Our model is not the ecological equivalent of Einstein’s General Theory of Relativity, which was a conceptual leap for physics,” O’Dwyer said. “It is an incremental step at this point. But we will need those conceptual leaps that incorporate the best parts of different models to really understand complex ecological systems better.”
The Templeton World Charity Foundation
supported O’Dwyer’s work.

You can view the complete Biomarker magazine here

Reflections on the first year of graduate school

matt grobis 2Thanks to our guest blogger, Matt Grobis, who is in his second year working toward a PhD in the Ecology and Evolutionary Biology department at Princeton, researching how groups filter noise from information in their environment (particularly predators) and how group membership affects how the whole group behaves.  Matt earned his B.S. in IB in 2012.

What I thought grad school would be like during college:
“Grad school is where you show up at noon, plan some experiments, run them the next day, then analyze the data. A PhD takes 5-7 years because it takes a while to plan the perfect experiment, one that hasn’t been done before and that answers a hole in the literature. During your first year, you do 5-6 experiments and publish at least one of them.”
When you’re doing lab reports during college, it’s almost guaranteed that the Discussion section will say something like “the study would benefit from more data.” We had three hours to do the lab; imagine how good the data would look if we had three weeks? Then, during your senior thesis, you continually imagine being able to do your research without juggling hours of lectures and homework at the same time. Grad school seemed like a big expanse of time to think about experiments, try them again and again until they’re perfect, and then publish. Any sub-perfect experiments were the fault of the experimenter not being motivated enough.

What I think grad school is like at the end of my 1st year:
“Grad school has cycles. Sometimes you show up at 10am, read articles all day, teach yourself R, and go home early. Sometimes you show up at 8am because you need to run three trials of experiments, and sometimes you swing by at 2pm because you were up until 4am writing revisions for a manuscript due to the journal that day. A PhD takes 5-7 years because literally everything takes longer than you think it will, and nothing works the first time you try.”
Something I didn’t quite grasp during my senior thesis and the beginning of the Fulbright was how much others had helped in making the experiment work out. It’s the difference between trying to find a store in a huge city you’ve never been in versus someone giving you a crude map and telling you roughly where the store should be. My advisor in college steered my thesis ideas towards a project that would answer a question regardless of what the results were, and my collaborator in Germany was the equivalent of a 4th-year PhD student in the U.S., meaning she’d had a lot of experience with figuring out the right way to do an experiment.

What my 1st year was like:
You frequently feel like you know nothing
An incredibly common feeling in grad school is “hm… I’m not sure how to do this.” The first reaction is to ask someone else, maybe an older grad student in the lab, or your friend who’s a lot better at R or Matlab than you are (hi, Sinead). You just don’t know the answer right now, so let’s find it and move on. For our generation especially, Wikipedia and Google make the answers to most of our questions separated by merely seconds from when we decide we want to find out. Grad school, on the other hand, is about constantly being in this zone of wanting to know an answer but not having it. That’s what research is; if we knew the answer, we’d have passed the info along to someone else (government organizations, the medical world, conservation groups, engineers, etc.) and be focusing on finding the answer to a new question.

As frustrating as it can be not knowing how to fit a quadratic curve on a scatterplot in R or who to e-mail for ordering new syringes for the lab, it is very satisfying the next time you have to do it and you know exactly how. And as you read more articles, go to more lectures, and talk with more people, you start seeing the same concepts reappearing… but this time, you understand them a little better.

You spend a long time figuring out how to find the answer to a question
Do you remember those “If you had a million dollars, how would you spend the money?” essay prompts in high school? One of the biggest hurdles I’ve had in planning experiments in grad school is getting out of this mentality of infinite money and time. You read about experiments where the authors make grandiose claims out of six data points and you vow to never publish something so ridiculous. If you’re going to do science, you’re going to do it right, even if it means fewer publications during your PhD. Your experiments will have at least 30 individuals, each assayed on multiple days to control for between-day variation in behavior, and each individual will be exposed to 5 treatment groups to see the full effect of the variable on behavior.

Those are fantastic intentions, and you can often make it work. But it’s really difficult. If you’re like me in college, “really difficult” sounds like something that applied to people who weren’t you; you’ve faced “really difficult” before and gotten an A in the class. Let me reiterate: it is really freaking hard to do this.

Here’s an example from this week: I’ve started a pilot experiment to figure out how the social environment affects how skittish a fish is in a new environment. The idea is to use 8 fish in 3 different groups of 60 fish. Due to poor planning, the videos ended up really dark, and it’s impossible to distinguish who’s who in the video. Not only can I not use the data; if it wasn’t for some quick thinking by marking all tanks where fish had seen the experimental tank, I might have had to scrap the experiment! (In animal behavior research, novelty to an environment is often extremely important.) So even though I’ve been planning these ideas for a few weeks, I nearly messed everything up within the first two days of actually doing anything. It always seems so obvious before you start, and then it never goes how you plan. (Above right is a video still from a trial I can’t use.)

But… that’s just how it goes. You can’t get to the end result without making mistakes. And you can’t make any progress if you don’t try.

You wait (a lot) for clearance to do research
Animal welfare committees are a crucial part of research by instituting ethical requirements for how research should be conducted. They ensure that the research has a bigger point and that your methods are the most humane way to get there (e.g. if mice have to be euthanized, what’s the calmest and least painful way for the animals? If the crickets suddenly start dying during the experiment, what do you do?). If you’re doing fieldwork, you need to get a license for the work; if it’s in another country, you probably need a visa as well.

Ensuring that research will be done properly takes a lot of time. Animal welfare committees have panels of both scientists and non-scientists to get a range of perspectives on the ethics of the work, which means extra time is needed to exchange and explain the reasoning for different viewpoints. For fieldwork, a lot of people want government approval for permits or visas, and there are only so many people reading the proposals. The only advice I can give on this is to start early, be patient, and be courteous with your e-mails. The waiting time (on the order of months) can really help refine your ideas for when you actually start.

You start to understand what makes for an interesting scientific question
For the first few months of grad school, I told people I was interested in how group composition affects predator evasion behavior in schools of fish. It took a lot of thinking and discussing with others to refine those ideas into a broader framework with more applicability than one species of fish under one type of predation risk.

You spend a lot of time thinking in grad school. Your ideas have to stand up to hundreds of hours of mental chewing; the best ideas are the ones that not only hold strong but also generate new ideas the more you learn about them.

——————————————————————————————————–
Doing research has been challenging but I’ve been really happy so far. It’s really quite amazing to be paid to think about and do experiments asking questions nobody in the world knows the answer to yet. I feel like the incredible amount of time stuck, trying to figure out an impasse, has taught me how to find the answers to things I don’t know. This mentality has given me a lot of confidence to approach things I might have shied away from before because it seemed too difficult (e.g. teaching myself linear algebra, taking a metro or bus in a country where I don’t speak the language, etc.). And most importantly, I constantly feel like I’m gaining a better understanding of how the world works, which only makes me more excited to see where grad school takes me.

-Matt