[This blog was written by Briana Sobecks, an undergraduate student majoring in Chemical Engineering. It is part of the SIB Student Research Experience, a blog series that offers a closer look at students and their research.]
Over the summer, I had the amazing opportunity to work as an undergraduate field assistant in Dr. Gene Robinson’s lab. I first met Dr. Robinson at a presentation about the Earth Biogenome Project, a global initiative to sequence the DNA of all species on earth. When I spoke to him afterwards, he said his lab hired undergraduates as summer researchers at the Bee Research Facility. I applied for the position later that year and was ecstatic when I was hired.
I had several responsibilities around the Bee Research Facility. One was taking care of small indoor bee colonies. Each colony had a queen who could lay up to sixty eggs a day. I supplied food for the colonies and extracted these eggs, which were given CRISPR injections to manipulate their neurological development. I also prepared small cages of bees and monitored them in behavioral assays. These assays are used to determine how either aggressive or nurturing behavior in bees is affected by a difference in internal chemicals. Depending on which chemical is used, the bees may be more responsive in attacking an intruder or more observant in watching their queen eggs.
The task I spent the most time on was bee barcoding. Bee barcoding involves creating a colony of 1200 individually identifiable bees by gluing a unique QR code to the back of each one. This task was highly difficult since the tags had to be oriented perfectly to be read by the computer. However, the more I practiced, the easier it became. Once the colonies were made, the computer system was able to track each individual bee, measuring how different environmental factors affected both specific bees and the colony as a whole.
This research job was an informative experience that helped me further my career goals and improve my scientific skills. I am a chemical engineering major with hopes to work in biochemistry research after I graduate. Working in an Integrative Biology lab helped me improve not only my biology skills, but my scientific skills as a whole. I received a firsthand look at what considerations are necessary for real research.
For example, I learned about the controls necessary for a biological experiment. In chemistry, experiments often have a lot of consistency, so a difference between two trials is easily explained by manipulation of one variable. In biology, however, the samples are living organisms, and a vast amount of variation is possible between two samples. Experiments must control as many factors as possible, and high-level data analysis techniques are needed to ensure measured trends are not a result of random variation. These same techniques can be applied to complicated biochemical reactions. As I move forward in my career, I will remember the lessons I learned in Integrative Biology research and apply them towards my own projects.
[This blog was written by Claire Dust, an alumna from the Integrative Biology with Honors program. It is part of the SIB Student Research Experience, a blog series that offers a closer look at our students and their research.]
Hi all! My name is Claire Dust and
in May of this year, I graduated from Illinois with my bachelor’s degree in
Integrative Biology Honors (IBH) and a minor in chemistry. I was originally
admitted to Illinois as a student in the Division of General Studies (DGS), and
my sophomore year I started in IBH, where I immediately began searching for
One of my professors invited me to
work in her lab, which focused on the relationship between the insect aphids
and their endosymbiotic bacteria, Buchnera.
I was very excited at this prospect, and during my short time in this lab, I
worked with a team of undergraduates from my program to develop and implement a
novel procedure to deliver CRISPR/Cas-9 into aphids and silence the tor gene, a gene which is hypothesized
to affect exoskeleton formation, in subsequent offspring. To our delight, we
were modestly successful in this task (although many aphids gallantly gave
their lives during our scientific pursuit).
I only remained in this lab for
roughly a semester; however, my friends and mentors in IBH helped me to find a
new research opportunity. One of my good friends worked in the Allan lab under then
PhD student Allison Parker (now Dr. Allison Parker, assistant professor in
environmental science at Northern Kentucky University in the greater Cincinnati
area). Allison was looking for undergraduate students to help with her summer
field season, and I was very happy to come on as a part time student researcher
during the summer of 2017. A field season with Allison was not what I initially
expected, I’ll admit. It involved going out to houses to collect mosquito eggs
from the field and then bringing back these eggs to count under a microscope
and then hatch. That first summer, I went out to houses and counted eggs three
days a week with Allison and other members of the research team.
Allison taught us how to identify
mosquito species, different fly species, and she taught us to always wear bug
spray when doing field work in mid-July. I think that summer I was doing some
of the least technical work I’d ever done in lab (or ever would do during
undergrad), but I had by far the most fun, and I learned so much more about
insects, the research process, and study design.
My junior year, in addition to our
fieldwork with mosquitoes, Allison asked me about conducting an independent
study of my own for IB 490 credit (which is a requirement for graduation in
IBH). She encouraged me to read different papers on topics that could be
encompassed within the realm of the work done in the Allan lab, but she made
sure to tell me to look for something that I
found interesting, not just something I thought would be quick and easy
(and boring). I kept coming up with ideas that were potentially larger and more
involved than an undergraduate thesis, but Allison helped me to cull my
interests into a more “bite size” amount of work and we eventually together
came up with my research project: “Differential hatch rates of Aedes albopictus (Diptera: Culicidae)
eggs inoculated with common bacterial species”.
Basically, I inoculated mosquito
eggs with two different species of bacteria and saw how that affected hatching
rates. This was really fun for me, because I got to work with different people
from the Illinois Natural History Survey (INHS) in order to learn various new laboratory
techniques. I was taught how to culture bacteria, how to make a bacterial
suspension from my culture, how to work in an aseptic environment, among other
skills. I came up with my own experimental procedure, of course with lots of
help from Allison.
We applied for a joint grant, which
we ended up getting; this allowed me to go with her (and other entomologists
from SIB at Illinois) to present my findings at the Entomological Society of
America, ESC, and ESBC Joint Annual Meeting in Vancouver, BC in November of
2018. I never thought I’d be able to present my research at an international
conference as an undergraduate researcher, yet there I was.
I worked with Allison up until I
graduated, working with her the summer before my senior year and then into my
senior year. She helped me analyze my data (or in a lot of cases, she analyzed
in for me and taught me how she did it, so I could do it myself next time) and
she helped me write up a manuscript for my research that is now in the process
of being submitted for publication. Working with Allison in the Allan lab
provided me with countless opportunities that I don’t know I would have gotten
Because of my robust research
background, I got a great offer from the graduate school I wanted. Starting
late this August, I will be attending the Gilings School of Public Health at
the University of North Carolina – Chapel Hill to earn my Master of Science in
Public Health, and hopefully I will stay on to get my PhD here as well. So many
of the things I learned and skills I gained were a direct result of working
with Allison and benefiting from her mentorship.
I feel sure I will remain in
contact with Allison even though we no longer work together. Through all of the
research and field work and manuscript editing, we became very good friends and
I don’t intend to throw that away just because we’re in different states now.
My parents still live in the Champaign area, and I know Cincinnati is on the
way from Chapel Hill to Champaign; she doesn’t know it yet, but I’ll be
sleeping on her couch soon enough.
[This blog was written by Scott Clem, a PhD student in the Harmon-Threatt Lab in the Department of Entomology. It is part of the SIB Student Research Experience, a blog series that offers a closer look at our students and their research.]
Hello blog readers! My name is Scott Clem and I am a doctoral candidate studying entomology at the University of Illinois. How did I end up studying insects do you ask? Well, I suppose I have always been interested in these critters, but the major defining moment was when I took my first entomology class and learned about their fascinating diversity and major ecological importance. This solidified my fate to become an entomologist. I proceeded to get my undergraduate degree in zoology with a minor in entomology at Auburn University. I then stayed at Auburn for my master’s where I studied interactions between caterpillar communities and native/non-native trees. Once I finished, I decided that I wanted to pursue a PhD at the University of Illinois’ Department of Entomology. So, here I am today!
I want to share a little bit about my research at the University of Illinois, and some of my summer experiences. My dissertation is focused around a group of insects known as hover flies (Family Syrphidae). These insects are best known for visiting flowers and having yellow and black coloration, which is an attempt to mimic various bees and wasps. They’re quality pollinators as adults while the larvae of many species are predacious and feed on pesky insects like aphids. So, this is definitely a useful insect to have in the garden! My research is focused on a behavior that is not well understood in these insects: long-distance migration. How the heck does one study fly migration do you ask? Well, I can’t just give them a little radio transmitter (they don’t make them small enough), so I use stable deuterium isotopic ratios found within their tissues. Isotopes are variations of the same chemical element, in this case hydrogen, that have the same number of protons but different numbers of neutrons.
The idea is that ratios of light to heavy deuterium isotopes in water vary geographically due to differences in temperature, humidity, and other climate variables. You know the saying you are what you eat? Well, larval hover flies inadvertently consume these isotopes from water while they feed, which become permanently fixed in wing and leg tissues once the flies emerge as adults. We can then examine these isotopic ratios and estimate where the flies developed as larvae and whether they are local or foreign. If a fly exhibited isotopic ratios that were highly negative, for example, we might conclude that it developed somewhere in Canada and flew south. For my work this summer, I spent much of my time walking around in local parks with a net, looking for specific species of hover flies (mainly Eupeodes americanus and Allograpta obliqua).
Aside from working on my summer research, I also had the opportunity to travel to Los Osos, California for two weeks to attend The Diptera Course, organized and hosted by the LA County Natural History Museum. This was the highlight of my summer, and quite honestly one of the highlights of my entomological career. For all you non-entomologists, Diptera is the order of insects that includes true flies. They are incredibly diverse and come in a huge variety of shapes and sizes, but the major characteristic that differentiates them from other insects is that they only have two wings (hence their etymology: di = two, pteron = wing). Other insects like bees and wasps have four wings.
Insects that are classified in the
order Diptera include mosquitoes, maggots, gnats, midges, house flies, crane
flies, hover flies, robber flies, maggots, keds, bots, and many others. The
Diptera Course was dedicated strictly to learning all about flies from some of
the biggest names in dipterology. We learned about fly morphology, taxonomy,
phylogenetics, behavior, and much much more. There were 25 students total representing
16 countries from all over the world and we were each tasked with collecting,
mounting, and identifying 40 families of flies. To put this in perspective,
there are around 150,000 species of flies described, all classified into 188
families. There are probably around 1,000,000 species in existence today, so
there are A LOT yet to be discovered!
Each morning we attended a lecture
given by one of the instructors. After that, we grabbed our nets, aspirators
(“pooters” as some might call them; devices used to vacuum up small insects via
mouth suction), and any other field gear, and jumped into vans to travel to various
pre-selected collecting sites. We sampled a wide variety of habitats from
coastal sand dunes to mountainous scrub. Once we got back to the camp, we all
unloaded our “fly loot” and started pinning, mounting, labelling, and
identifying the flies we collected. All total, I ended up with 47 families of
flies while the group as a whole had 72! What is the purpose of preserving
flies like this? Well, many of these flies will be deposited into natural
history collections. Each specimen is basically a “natural history snapshot” that
represents the location and date that the fly was collected. This can then be
used to answer questions about taxonomy, conservation, phylogenetics, disease
vector ecology, and many more.
You might be wondering, what’s the coolest fly I collected? Well, I’m split because there are so many stinkin’ cool flies that I saw, but I’ll narrow it down to two. The first one is Eulonchus smaragdinus of the family Acroceridae (small-headed flies). This fly is particularly showy because of its bright blue/green iridescence, yellow legs, and a proboscis (a flexible mouthpart) that is nearly twice its body length! It tucks this proboscis under its body while flying and brings it out to sip nectar from trumpet-like flowers. We collected them on high-altitude mountain slopes feeding on monkey flowers of the genus Diplacus.The biology of this fly is astounding. The adults will conceive up to 5,000 eggs and then deposit them on the ground. Upon hatching, the planidial larva waits to grab onto ground-dwelling spiders which happen to pass by. It will crawl up the spider’s leg and force its way inside the spider’s body where it remains for years as a parasite. It will eventually grow and emerge as an adult to start the cycle over.
Another pretty cool fly we collected is of the genus Cuterebra, which are collectively known as rodent bot flies from the family Oestridae. This insect has a pretty gruesome life cycle. Adult females, which have no mouthparts and more or less resemble bumble bees (see below), will lay their eggs near mammal burrows. The body heat of an unsuspecting mammal host triggers the eggs to hatch. Larvae then attach themselves to that host, and burrow under the skin to feed on flesh. Infected hosts have tumor-like bulges with the larva’s spiracles sticking out to breath. Lucky for us, the closely related human bot fly does not occur in North America! We managed to collect these rare flies at the top of a mountain, a great place to sample because of a behavior known as “hill-topping.” This is where insects including flies, butterflies, dragonflies, etc. will gather at the highest point in an area to compete for mates.
Where am I going with all this insect
knowledge? Well, I will be wrapping up my research and finishing up my program
here at Illinois within the next two years. I hope to continue research that
advocates for insect conservation and sustainable pest management, and to teach
people why insects are awesome and why it is in our best interest to keep them
around. Just by reading this blog, I hope that I have inspired at least some of
you to appreciate these critters!
[This blog was written by Stephany Virrueta-Herrera, a PhD student in the Johnson lab at the Illinois Natural History Survey. It is part of the SIB Student Research Experience, a blog series that offers a closer look at our students and their research.]
During undergrad, I took an ornithology course and became interested in studying both birds and conservation, which led me to the PEEC program at Illinois, where I am now starting my third year as a PhD student. In February 2017, I visited the Johnson lab at Illinois, where Kevin Johnson (now my PhD advisor) introduced me to bird lice. Birds are hosts for several different types of parasites, lice being one of them. There are several types of bird lice, which vary based on what part of the bird’s body they live.
My research explores the evolutionary patterns of the lice
found on several different types of birds, with some of my specific projects
including birds that live in the Neotropics.
At the moment, I am wrapping up a manuscript in which I used whole genome data
from lice of an ancient linage of birds, tinamous,
to estimate their evolutionary
origins (ancestry) in relation to other bird lice.
While they are one of the most abundant organisms on the planet, there is still a lot about parasites that we don’t know. There is even less information about parasites in non-temperate climates. Bird lice in particular can help us understand many different things because they live outside their host, but spend their entire lives on the same host. They are also very small, which makes their genome relatively easy to sequence.
As lice spend all, if not most, of their lives on the same hosts, many times there are similarities between host and parasite evolutionary trees. Lice are not limited to humans or birds, and in a recent study I worked on, we found that seals and their lice have coevolved. An interesting finding from this study showed that seal lice with the highest genetic diversity corresponded with seal hosts with the most individuals. We would need further data to confirm these findings, but this case illustrates that parasites can provide information on what’s happening with the host population, as the lice with the lowest genetic diversity corresponded to an endangered seal.
Being a grad student entails a lot of research and working behind a computer in my office, but recently I have been able to go on some cool travels for work. I attended the 2019 Midwest Phylogenetics Workshop at the University of Minnesota’s Itasca Biological Station. During the workshop, I not only gained new skills and knowledge in comparative phylogenetics (methods that allow us to study the history of how organisms evolved and diversified), but also had the opportunity to meet and work with colleagues thinking about similar phylogenetic questions across the country.
Conferences are also a wonderful opportunity to present work and meet with colleagues from around the world. I also recently traveled to Alaska for the American Ornithological Society’s 137th meeting, where I presented my work on tinamou lice, met colleagues and collaborators, and also experienced some of Alaska’s unique habitats.
Being a part of an interdisciplinary department in SIB means that my peers and I study a wide diversity of organisms and systems. Over spring break, I had the opportunity to work with fellow PEEC student, Kira Long, in Panama. Kira studies manakins, but in her work, she also catches several other neotropical birds which also happen to land in her nets. While Kira processed birds for her ongoing studies, I was able to collect feather lice from some of the birds.
Spending time with the birds in their actual habitat was a wonderful experience, and it was truly amazing to be able to see live lice crawling through their hosts’ feathers trying to avoid being removed, in this case, by me.
After being at Illinois for two years, there are still many questions that remain unanswered, and that is one of my favorite parts about being a scientist. Lice are parasites on their hosts, but we also know that most lice are also hosting symbiotic bacteria. Feather lice on birds specifically are thought to host these bacteria because they can help provide nutrients which are limited in their feather-based diets (Smith et al. 2013).
I am currently working with an IB undergrad, Lorenzo D’Alessio, on a project exploring the symbionts found in tinamou lice. So far, we have found evidence for bacteria such as Sodalis (and other genera), which may not be previously described in lice, for which we hope to have more solid results and prepare a manuscript for in the near future. This study will allow us to further knowledge of host parasite systems, and eventually make connections and comparisons from bird (host) to lice (parasite/host) to bacterial symbiont.
Summer is an exciting time for the School of Integrative Biology – many of our faculty and students use this time to travel to their study sites across the US and around the world to set up their experiments, collect data, and gain new experiences that will guide their work.
Student researchers are critical to the success of SIB, and
the collaborative relationships that they develop with our faculty prepare them
for exciting careers in all kinds of industries, such as health care, biotech
and bioinformatics, agriculture and plant biology, ecology, sustainability and
conservation, and more.
Over half of all of SIB undergraduates gain some form of
research experience during their time at Illinois, which provides them with
hands-on skills developed in the field and the lab. Using these skills, our
undergraduates are uniquely poised to tackle complex, interdisciplinary
Faculty benefit immensely from having these dedicated, creative students working with them full-time during the summer. This mentor-mentee relationship goes far beyond a set of extra hands in the laboratory. Students bring with them fresh ways of looking at long-standing problems, boundless energy and infectious enthusiasm. These research-based connections transform the way that our students engage with their undergraduate experience and the relationships are often maintained long after the student has graduated.
Beginning this summer, you’ll be hearing from some of these student researchers through a new series on our blog – The SIB Student Research Experience. They will be telling their stories to put a face and a name behind their data and results. Their accounts show in a very tangible way how their professional journey relates to their research goals, and highlights the wide range of backgrounds and interests we have here in SIB.
From microbes to ecosystems, our students are training to develop and apply their extensive technical knowledge to our most pressing issues as a global community, addressing the challenges of 21st century biology. I hope you enjoy their stories, and be sure to check back for each new blog.
Carla Cáceres, Director, School of Integrative Biology
This May, the School of Integrative Biology celebrated the achievements of our graduating class of 2019! We join your family and friends in congratulating you on your accomplishments, and we hope you keep in touch with us as you take the next steps in your journey!
One of our graduating seniors, Daniel Garza, shared his thoughts on his time with SIB.
What do you value the
most from your experience with SIB?
I value the diversity in education and training I received. From
building phylogenies based on genomic data to crafting an essay in science
communication, SIB offers courses and training in everything a science-oriented
career could need. The truly well-rounded education offered by the School of
Integrative Biology creates an academic community centered on unique career
What was one of the
most important lessons you learned from SIB?
To always be curious and to always seek out answers!
What is something you wish incoming students knew about IB? Do you have any advice for them?
Something that every incoming SIB student should know about is the
various career paths you can pursue with a degree in integrative biology. You
can build your major through electives to be as specific or as broad as you
One piece of advice that a professor told me (freshman year!) that
has stuck with me is to take the courses that sounds interesting to you, not
just the ones that your pre-med or pre-grad school advisor told you to take.
You never know where unique courses and world views will take you; it may end
up becoming your passion.
How do you feel SIB
has prepared you for the next step in your career journey?
SIB has prepared me extremely well for the next steps in my
career. Crafting logical and evidence-based arguments will be of paramount
importance to me as a future attorney. Additionally, the ability to write
coherently and concisely in the presentation of an argument is a skill taught
to all SIB students, and that ability is critical to any career path,
regardless of the field.
What was one of the
most valuable things you gained from SIB?
There are many aspects of my education under the School of
Integrative Biology that will stick with me for life, but most of all is the
ability to have fun while learning and creating scientific discoveries. The
passion and personal nature of the SIB creates an environment where students
are encouraged to grow both personally and professionally. Good natured
professors are abundant in the SIB and the welcoming and fun environment that
they help to create promotes science and learning while reducing the stress and
anxiety normally associated with the college experience.
Do you have any
professors or instructors that made SIB particularly memorable for you? What
kind of impact did they have on your college experience?
Professors Suarez, Berlocher, and Cheng all provided lasting
memories for not only myself but almost everyone who comes into their
classrooms. Each created a classroom where topics were presented in a way that
immediately caught your attention and made learning easy with such passionate
and driven teaching. Where some of my friends in other majors dreaded attending
classes, these 3 professors made attending class worthwhile and
One of my most unforgettable experiences came through working in
Dr. Suarez’s lab. The lab was awarded the opportunity to perform research with
the particle accelerator at Argonne National Laboratory. Filming x-ray footage
of foaming ants, click beetles, and trap-jaw ants through the particle
accelerator was one of the most rewarding experiences I had in college and it
would not have possible without the Suarez lab and the School of Integrative
Where are you going
after graduation and how did SIB prepare you for that?
I will be attending the University of Illinois College of Law
aiming to specialize in biotech, pharmaceutical corporate law. The scientific
background I gained from my degree will be a considerable advantage as I enter
this field. Science-based degrees are at the forefront of the job market and
SIB prepares its students for all career paths through their well-rounded and
Integrative Biology has been working hard this summer, and has a couple of big changes to share with you. Watch the short video below for more information, and then explore the Alumni Mentoring Program home page here: http://go.illinois.edu/AlumniMentorU
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 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 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.
Second-generation biofuel crops like the perennial grasses Miscanthus and switchgrass can efficiently meet emission reduction goals without significantly displacing cropland used for food production, according to a new study. The researchers call it the most comprehensive study on the subject to date.
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