Hey guys!I wanted to take this opportunity to talk about the research my experience getting funding through a summer undergraduate research funding (SURF) award from the American Society of Plant Biologists (ASPB) to do research at the U of I last summer with Dr.Heath and Dr.Marshall-Colon, and what I spent the summer doing.
To understand the work I was doing, you first have to know a little bit about the legume-rhizobium mutualism, and why we care about it. The legume-rhizobium mutualism is a huge part of the nitrogen cycle in natural and some agricultural systems. The partnership is initiated when a rhizobium cell (a soil living bacteria) infects the root of a legume, triggering a chain of molecular signaling steps that end with the legume forming a specialized structure on its root called a nodule. Once in the nodule, the rhizobium begins replicating and converting atmospheric nitrogen into a form that the plant can use ,which the plant can’t do on its own. In return, the plant supplies the rhizobia in the nodule with various sugars from photosynthesis and amino acids that the rhizobia could not produce on their own.
It sounds like everything is hunky dory right? The plant gets nitrogen to use to grow, and the rhizobia gets all sorts of nutrients it needs to reproduce, everyone walks away happy every time! But that isn’t the whole story. In nature we find a wide range of rhizobia partner qualities between different strains, so while some rhizobia get along great with their plant hosts and provide a great service that helps the plant grow, other strains provide almost no nitrogen to their partners and take just as much sugar from the plant as the high quality rhizobia, hurting the plant more than they help. That variation is interesting to both evolutionary biology and to applied agricultural scientists. It’s interesting to evolutionary biologists because it seems like in natural systems, if bad partners can get just as much energy from their host to reproduce, and spend less of that energy producing useful nitrogen to the plant, they should be able to reproduce more than good partners and take over, wiping out high quality partners, but that’s not what we see in nature. This gets at what I think is one of the most interesting questions in biology, that is, how mutualisms remain stable in evolutionary time against bad partners who take advantage of the system. It’s interesting to agricultural scientists because nitrogen fertilizers have a huge monetary and environmental cost, if we can figure out why high quality rhizobia are good partners and low quality rhizobia are bad partners, we can use that to introduce high quality partner strains to agricultural systems and reduce, nitrogenous fertilizer usage.
Last summer I had the pleasure of starting work on a project studying the mutualism between legumes and rhizobium. The goal of the work I spent the summer doing, and will be working on throughout my graduate studies here at UIUC, is to understand the molecular basis of partner quality variation between rhizobia strains. We’re specifically interested in connecting data on plant health (phenotypic data) with data on the genomes of both the rhizobia strains and legumes we are using, as well as gene expression data within nodule tissue, and metabolism data within nodules. The long term goal is to take all of the data we are collecting (there is a lot!) and eventually put it all together to be able to look at a rhizobium strain genome and say weather it will be a high or low quality partner, and why. With that information, we should be able to find specific regions of genetic diversity to target for further study, and test for different evolutionary forces. We will also be able to move towards designing an optimal rhizobium for applications in agricultural settings.
As anyone who has done research knows, the grand plan style goals don’t happen in the first summer of work on a project, but last summer, and in the time since, we’ve made some really exciting progress. Over the summer we ran our first greenhouse experiment with two different rhizobia strains and two different lines of the model legume Medicago trucatula, and troubleshooted our methods of avoiding contamination between treatments, as well as our methods for metabolite extraction. We also have since gotten RNA sequencing data (gene expression data) from that project and are in the process of combining all of our data types, and coming up with a pipeline to process future projects. While two rhizobia strains, and two line of legume may not seem like a lot, it was critical to run a small experiment first to get our methods to a solid place, and based on what we learned this summer, we are currently harvesting our second experiment from the greenhouse, consisting of 2 legume lines, and 100 strains of rhizobia.
My work last summer was important for the project I’m working on, and that’s of course important, but it was also really critical to my development as a biologist. I learned so many techniques this summer that each could have taken a whole semester to learn with constant stresses and interruptions from classes. I also got the opportunity to read more scientific literature in three months than I think I had in the whole year before, not to mention how much time I got one on one with graduate students and postdocs, which is of course harder to come by during the mad shuffle that is the academic year.
To anyone looking at summer opportunities and wondering if they’re worth applying for, if you’re anywhere close to fitting the target audience for an award or position and you feel like it’s something that could help you grow as a biologist, go for it! The two things that I learned while applying for summer funding are that there are so many opportunities both on and off campus to make money over the summer doing independent science through awards available to undergraduates! There really is something to apply for for everyone and if you put in the time to write a good application, odds are great that something will be a good fit!. The other major take away was that the people around you want you to succeed and will do everything they can to help you achieve your goals if you reach out for help. With lots of writing help from the professors I work with, Dr.Marshall-Colon and Dr.Heath, I was able to earn awards from the school of integrative biology and a summer REU position from ASPB, none of which I would likely have qualified for had I submitted my original application without ample comments and editing help.
If you’re interested in the ASPB SURF in future years, you can look for information on each years application and deadlines at https://aspb-surf.secure-platform.com/a/, feel free to contact me to ask about my application, or any questions you may have!
I would like to thank Dr.Heath and Dr.Marshall-Colon for their constant help and guidance, as well as the University of Illinois at Urbana-Champaign School of integrative biology, and the American Society of Plant Biologists for the funding that made my time on campus this summer possible, and finally Dr.Cheng, for allowing me to share my experience with all of you.
The Information Meeting last night was a fun gathering. We have a great turnout - 32 freshmen interested in the program attended.
A couple of images on everyone partaking delectable Manolo's pizzas!
A big shout out to our IBH juniors who made the program presentation - Emily Davis, Josh Nielsen, Alex Riley and Ahmed Radwan! Especially to Josh who updated the PPTX file! Excellent job, and thank you!
Also, thanks to all the IBH students who came to help answer questions - see them in the jpg, plus Yesha Patel (sophomore) who I don't have a picture of.
Thanks to Eric Hauser (senior) who spoke to the James Scholar students in IB150 about the IBH program the same afternoon.
Last but not least, a big thanks to Dr. Ben Clegg for his enthusiastic help in getting the word out about IBH, and also attending the information meeting and giving insightful answers!
If you were unable to attend the informational session and would still be interested in hearing more about the program please contact Dr. Chris Cheng at firstname.lastname@example.org.
Some of you may know me and some of you may not. It's okay if you don't. However, keep reading if you're thinking about senior thesis, interested in finding a job right after graduation, or just want to know what I'm up to. I'm part of the awesome cohort that graduated last spring, but I was one of those few that had no idea what I was going to do after graduation. I was always on the pre-med track, so it weighed heavily on my mind until I decided in June-July to rescind what offers I had. I won't go into detail about that.
So I started the job search very late, but even then, I had offers left and right. I graduated with a double degree in Chemistry and IBH with a high distinction on my senior thesis, so there were a lot of positions I qualified to apply for. From microbiologists to scientist I's, you name it. If you want a job right out of college, or thinking about testing the industry before getting your phd, it's definitely possible. Although I don't recommend the career center for resume building, I do recommend UIUC's simplicity I-link website for job openings (not much variety) and internships. However, I found it most useful to google a list of companies in the field you're interested in, and visiting their career section of the website. Sometimes, it doesn't hurt to send an inquiry or apply for a position even if you don't meet their degree requirements. Experience is what counts. If you want more details on this, message me privately.
So you're probably thinking what I got out of applying so late in the job search without a phd or masters. Within ~3 weeks, I had multiple interviews, and 2 solid offers that had annual bonuses (so salary and not hourly). One was a Chemist position, and the other was a Genomic Analyst position. I don't know if I got lucky, but my double degree helped A LOT. With the jobs that I applied for, I was tested on simple lab skills, such as pipetting and knowledge about certain concepts. They will test on accuracy of the skills. Since my senior thesis was in genetics, I qualified for the Genomic Analyst position even though they preferred someone with a master's degree. So if you're ever wondering whether to go for that time consuming, tiring, and terribly hard project in your final year, I'd say go for it. Just having it on your resume makes a big impact.
If you're job searching, it doesn't hurt to ask the company to give you more time to decide because if they really want you, they will negotiate (even salary). So in the end, I'm out here in Baltimore, working for a great company as a cancer genomic analyst in the ever-growing personalized medicine field. Yep... I didn't even know there was such a thing. The company has tuition reimbursements for going back to school, and since it's founded by JHU oncologists, going back to medicine is also an option. Anything is possible! Going into industry can be daunting, but if you look around, there will be a company that meets your needs.
Hey all IBH students past and present,
Dr. Cheng thought it'd be cool for me to quickly chronicle my summer experience working at a national park through the Student Conservation Association. I just graduated from the IBH program in May and last winter I was thinking, "what do I want to do the summer after graduating?" Grad school and the search for full-time positions were viable options, but I hoped to enjoy the summer marking the end of 16+ consecutive years of school and go on an adventure.
The Student Conservation Association was founded in 1957 to provide America's youth with a means to participate in national conservation efforts and today still offers students opportunities to serve in the U.S. National Park system or other relevant environmental agencies. There are tons of internship opportunities available, ranging from 1 or 2 months to over a year and they provide stipends for travel and food as well as provide housing for interns.
This past summer I worked as a natural resources intern for the Marsh-Billings-Rockefeller National Historical Park in Woodstock, Vermont. After driving out to Vermont at the end of May, my responsibilities for the next three months mainly included clearing the park of 15+ invasive plant species, GPS tracking of invasive populations, creating GIS maps to visualize the spread and severity of these populations, and formulating invasive management plans for the park and other local spaces.
I had previously done a summer REU program through the Smithsonian Tropical Research Institute down in Panamá and my research of U of I mainly consisted of the ecological interactions between local garden plants and mosquito species that act as disease vectors. I wanted to spend the summer enjoying the outdoors, away from IL, and doing something that could introduce me to the NPS and conservation management work. Although my career plan has shifted slightly (toward international relations, U.S. Dept. of State), the summer position with the SCA was really valuable. The internship was in fact a partnership between the SCA, the National Park Service, and the Dept. of the Interior.
Additionally, many SCA internships include an AmeriCorps option through which after completing a minimum number of service hours, you receive an education award (3 months positions get around $1500). This money is usually applied to student loans or for further education later on. SCA internship hours also count toward something called Public Land Corps hours. Once you complete a minimum of 640 hours of PLC hours, you are eligible for non-competitive hiring status for government positions. So even though I was working for the NPS, I can use this status (meaning I only would compete against other govt. applicants, not civilian ones) to apply for State Dept. positions. In the normally convoluted hiring process for government positions, this expedites the process and makes it much smoother.
I would highly recommend SCA summer internships for those looking to spend a summer outdoors and doing some type of environmental work. This could include invasive species work, interpretation at a visitor's center, curatorial work, maintenance, and many other fields. You can check out the available options at the SCA website:
If anyone has any questions about what I did this summer, feel free to message me. SCA is a highly reputed organization and a great agency to work for if you enjoy environmental work.
Dr. Yolanda Holler is an alumnus from the old Biology Honors program. She is currently a pediatric neurologist at Northwestern University Feinberg School of Medicine.
She met with IBH students today to talk about her professional experience, how her Biology degree led to her career in medicine, and even the possibility of mentoring students in the future.
Thanks to all the IBH students who came to meet Dr. Yolanda Holler and attended her presentation "My Journey into Medicine". She is happy to hear directly from you for questions you may have for her. Send Professor Cheng a note if you wish to have her email address.
Katie Lincoln, IBH class of 2016, M1 at Southern Illinois University med school, getting her short white coat!
Hello, everyone, hope you are enjoying your summer!
Here 's a big CONGRATULATION to Brendan Colon, alumnus of the IBH class of 2013, currently a PhD student at Harvard, on his paper in SCIENCE that he co-first authored - "Water Splitting–Biosynthetic System with CO2 Reduction Efficiencies Exceeding Photosynthesis"
It describes "A biocompatible catalyst in an artificial photosynthesis system leads to efficient solar-to-fuel conversion."
Awesome research! Awesome IBH graduate!
Hello IBH students, alumni, and professors!
Dr. Cheng contacted me in regards to writing a post for the IBH Student Highlight section. I’ll be writing about a little intro on astrobiology and astrochemistry. So, naturally, the first couple questions that will probably arise are “What is astrobiology exactly?” and “What is astrochemistry?”
In regards to astrobiology, the first idea that might pop up in your head is that it is the study of extraterrestrial life. That is partially correct. NASA had a separate term for that back in the day (i.e. exobiology), but it never really caught on seeing as that we only know of terrestrial life so far. While astrobiology would involve studying ET, the field is much bigger than that.
Astrobiology includes the study of the origin of life here on Earth and for the search for extraterrestrial organisms in our solar system and beyond. It tests the limits of what life is capable of. As you might imagine, the field is pretty interdisciplinary. The University of Illinois was awarded an astrobiology grant relatively recently (see here:http://astrobiology.illinois.edu). The team consisted of biologists, chemists, geologists, physicists, and astronomers.
Each field plays its role. Geologists are usually tasked with unlocking Earth’s geological code and identifying biosignatures, which are mineral depositions that can be traced exclusively to biotic origins. The nasty thing about Earth’s geological historical record is that it does not contain much information about life’s origins. That’s where the chemists and physicists come in: they try to determine how life might form using bottom-up approaches. Put another way, they try to recreate life or prebiotic molecules from simple starting materials. That is a definitely a difficult job to do when you do not have the recipe (i.e. geological history).
Physicists also team up with astronomers to search for more exoplanets, search for hints of life on said exoplanets, and search for life in the solar system. At the moment, our ability to search for life outside the solar system is extremely limited. Our best hope is to identify atmospheres that “look” like Earth’s spectroscopically. Humanity cannot do that well right now, but things may be different when the James Webb telescope is finally launched and put into orbit (see this: http://www.jwst.nasa.gov). In regards to our own solar system, geology-chemistry-physicist-astronomer hybrids called planetary scientists design space missions that record the physical and chemical characteristics of planetary bodies including astrobiologically relevant ones like Mars, Europa, and Enceladus.
So where do biologists fit in within astrobiology? Biologists study the origin of life from a top-down approach, they study extremophiles (organisms that, as the name suggests, love extreme physical and/or chemical environments), and put constraints on where life might actually exist.
In studying the origin of life, biologists are responsible for unraveling the genomes of “primitive” bacterial and archaeal species and deducing what the Last Ultimate Common Ancestor, or LUCA, may have looked like. While LUCA itself was probably quite complex with fully operational ribosomal machinery and the works, knowing how such an organism looked like might give the necessary constraints for the aforementioned chemists/physicists trying to solve the origin of life problem from the bottom-up approach. This is not universally accepted, but it is the prevailing school of thought at the moment.
As mentioned, biologists also study extremophiles. A recent infamous example of this includes the GFAJ-1 microbe from Mono Lake, CA where the study’s authors thought that the bacteria was utilizing arsenic in its DNA backbone. Long story short, they’re not. This led to a number of controversies. However, the study of extremophiles is usually not so dramatic. The best example of this is the study of the thermophile Thermus aquaticus which led to the development of the popular technique called the polymerase chain reaction (PCR). The bacteria’s enzymes are able to withstand high heat and are thus perfect for surviving the high temperature required to denature DNA and to assemble nucleotides. Other examples of interesting extremophiles include electrophiles that can accept electrical currents as source of energy and other bacteria that can produce electricity given a source of organic nutrients. Applications for the latter include the development of microbial fuel cells.
Lastly, biologists also put constraints on where life might be found. This is helped a lot by the previously mentioned extremophile work, but biophysicists also come into play here. These types of biologists put physical constraints to what is actually possible. For example, biophysicists poked holes in the paper that claimed GFAJ-1 uses some arsenic instead of phosphorus in its DNA backbone. They did this by showing that the resulting structure would be thermodynamically unstable and break apart. Similarly, they put limitations on what life requires in order to exist in various environments.
So far, astrobiologists can agree on three basic items necessary for life: (1) a liquid solvent (not necessarily water), (2) a source of nutrients, and (3) a source of free energy. Within our solar system, Mars, Europa, Enceladus, and Titan all meet the aforementioned criteria. Personally, I find moons like Europa and Enceladus most exciting, astrobiologically speaking, because both contain subsurface oceans so, in a way, they are the most “Earth-like” since our planet really is more ocean than it is earth.
A moon like Titan or dwarf planets like Pluto are exciting for different reasons altogether and they finally bring me to the topic of astrochemistry, the study of chemical reactions that occur in space. The reasons why Titan and Pluto are exciting are because of their large amounts of nitrogen and presence of primordial molecules like methane. Titan’s atmosphere is denser than Earth’s and its composition is thought to be similar to early Earth’s. I previously mentioned that we do not have a terrestrial geological record of the origin of life, but I never said anything about an extraterrestrial record. ☺ The problem is getting there. Titan’s atmospheric chemistry is very exciting as it is laced with simple organic building blocks like CO2, CO, and CH4. The atmospheric reactions lead to the formation of large molecules called tholins, a nonspecific group of organic chemicals that could be important in forming prebiotic molecules.
Tholins are also formed on the dwarf planet Pluto where methane laced nitrogen ices exist on the surface. This is important because such ices could have existed closer to the inner solar system before solar fusion began in the Sun and temperatures were much lower. The thinking then goes that some important prebiotic molecules may have formed in space first before raining down on Earth in the form of comets. Time will only tell.
So what are some of the opportunities that I had with astrobiology/astrochemistry? My astrobiology experiences began at the University of Illinois where I worked in Dr. Bruce Fouke’s geomicrobiology laboratory. My main project there involved working on an artificial hot spring with the goal of seeing how microbes affect calcium carbonate deposition in a controlled environment. As an undergraduate, I had two internships at NASA: the first was also at a geomicrobiology laboratory and the second was in something called planetary protection. While the latter does sound like a Men In Black type of job, the protection portion is usually meant for other planetary bodies nowadays. In short, NASA does not want terrestrial microbes to start colonizing astrobiologically relevant sites like Mars or Europa.
The project I most enjoyed working on was at JPL with the planetary protection division. It involved enumerating the amount of bioburden found within spacecraft materials. We used what one of my mentors called „classical techniques” like counting colonies, but also „modern techniques” like qPCR and epifluorescent microscopy to quantify the amount of spores within spacecraft materials. We also had the opportunity to work with a cryogenic mill…it is always fun to grind down material meant to survive the harsh conditions of outer space into a fine powder. ☺
After working on some more biology-related projects, I moved towards astrochemistry. My Master’s research had a number of projects, but the most relevant one to biology involved the chemistry of Pluto-analogue ices. Here we created a gas mixture consisting of a carbon source (CO or CH4), H2O, and N2 to simulate the Pluto-Charon system. We then irradiated the gas mixtures and deposited the products on a 6 Kelvin coldfinger where we were able to identify products using IR spectroscopy. At this point, the ices consisted mostly of nitrogen. Now, nitrogen is interesting because it can be used as a matrix material that separates out reactive species in the solid phase. So, in short, it can trap and accumulate reactive species. Our goal was then to show that with the right sublimation steps we would be able to form new products and trap them in a water ice. We were able to show that, but I’ll leave the details for another day as the work still isn’t published. So in addition to the direct irradiation of ices on Pluto and other planetary bodies, chemicals can also form in relatively large amounts through simple processes like sublimation. The other thing that we formed were the aforementioned tholins! While we did not characterize most of the tholins, these molecules are interesting because they are large organic molecules and many are prebiotically relevant. While Pluto has not officially been confirmed to have tholins yet, the red haze observed by New Horizons is mostly likely due to tholins.
I’m taking a little break from school, but I hope to continue with astrochemistry for my PhD work and work exclusively on tholins!
I hope that the information mentioned here was both informative and inspirational. If you do get hooked by astrobiology, my only major career recommendation would be to not make it your only gig. Funding for space sciences is capricious and life is a lot more fun when you are getting paid for doing what you love! All the scientist types mentioned here do research within other fields so just remember that you do not have to “settle” for one thing or another.
If you have questions on how to get started in astrobio/chem, you can send me an e-mail here: email@example.com
CONGRATULATIONS to our graduated IBH seniors - Class of 2016!
It's been a privilege to be part of your formative education, and to share a bond that will last for all times to come!
Please post graduation pictures you wish to share.
We had our annual IBH spring picnic on reading day yesterday. Couldn't ask for a finer, sunny day. Over 40 people attended. We got to welcome the new students who will start the IBH program this Fall semester, and celebrate the graduating seniors' successes and wishing them the best as they embark on the next stage of their career path.
This is the most awesome picture of the IBH family, EVER!
IBH students travel the world, publish research papers, and do all sorts of amazing things