Undergraduate Research Fellows Blog

  • The Secrets of Tree Rings

    A sliver of a tree core with dark bands separating the tree rings
    A portion of a black walnut tree core as seen through the lens of a microscope

    I’ve spent the a majority of my time since my last blog peering down a microscope at tree rings, so I figured now was as good a time as any to share what I’ve learned.

    For starters, trees grow out, not up. A branch that was five feet off the ground in 1998 will still be five feet off the ground tomorrow. Furthermore, trees grow from the outside, laying down layers of new wood just underneath the bark; rather than from the center. Especially in places like the midwest that have distinct seasons, trees alternate between periods of growth in the summer and dormancy in the winter. The harsh lines formed between growing seasons are what cause the visual rings.

    Since trees create a new ring every year, by counting backwards from the bark you can determine how old a tree is! I wouldn’t be surprised if many of you already knew this, but this isn’t all tree rings can tell us.

    The width of a tree ring can also tell us a lot about how the tree grew in that particular year. Large rings mean that tree was able to grow a lot; this could mean lots of sunlight, copious amounts of rain, or appropriate pruning. Similarly, small rings are from years that the tree didn’t do as well, often from injury or lack of rain. Most of the trees I’ve measured have had distinctly small rings in 2012 due to the drought.

    Thus, tree rings allow scientists to look into the history of both a tree and it’s environment. In my particular case, I’m comparing the tree rings of trees from parts of the forest under different prescribed burning treatments in order to see if the varying fire regimes have any effect on tree growth. Fire is an important management tool in midwest oak forests so I’m excited to know if it is actually as good for the trees as we think is.


  • It Happens

    A collage of five different tubes containing various liquids.
    Five snapshots during the process of DNA, start from the top-left and go clock-wise until you hit the bottom-left.

    Hi everyone!


    I previously published a blog post called Going through the Alphabet, where I talked about the trials and tribulations that I faced during the process of nailing down my project.


    Since then, I’ve learned that the same persistence is required for the data collection stage.


    My project has three major components: 1) testing Mongolian Oaks for bacterial leaf scorch by extracting DNA and using a polymerase chain reaction (PCR), 2) determining moisture content by measuring fresh and dry weight, and 3) determining the percentage of foliar Nitrogen present.


    The first and third components in particular require several steps and depend on a variety of factors. Extracting DNA and using PCR involves a tremendous amount of pipetting small volumes of liquids. To visualize your results, you must run a gel electrophoresis, which can be finicky at times. In addition to the hours of benchwork required by these three steps, you must account for the time required for instruments to run. Once you have amplified your DNA using PCR, you must put your samples in the thermocycler for about two hours. Gels take at least an hour to set up and run. Use of instruments is also limited by availability and space within the instrument. I have fifty samples, which translates to three rounds of DNA extraction, four rounds of PCR, and three gels. The number of steps within each of these three stages, coupled with the repetitions required by the number of samples I am testing and the mistakes that I have made with pipetting, results in a very exhausting and time-consuming process.



    A beadbeater whirring as the tubes inside are shaken until they are just a blur.
    The new beadbeater in the herbarium lab that I began to use halfway through my extractions, as the old beadbeater did not work very well.
    Alyssa Gao

    A machine, its screen lit up, with a piece of paper draped over the top.
    The thermocycler that the tubes go in after PCR and before gel electrophoresis.
    Alyssa Gao


    Determining foliar N levels has three stages as well. First, leaves must be ground to dust using a coffee grinder and a mortar and pestle. Then, you wrap 5 mg of each sample into a tiny tin boat. Finally, you run these tinned samples through an Elementar, which burns them at an extremely high temperature. Technically, this analysis does not require rounds like my genetic work does. However, due to mistakes that I have made and technical issues with the Elementar, my samples have had to be re-tinned twice.


    A coffee grinder, with its lid containing the ground leaf samples beside it.
    Leaf samples after they have been ground my a coffee grinder.
    Alyssa Gao

    An open vial, a funnel, and a mortar and pestle.
    Leaf samples being ground by a mortar and pestle, with its vial beside it and the funnel used to transfer the powder.
    Alyssa Gao

    A microbalance with a tin boat in the center.
    Weighing a 5 mg sample of ground leaf in a tin boat using a microbalance.
    Alyssa Gao

    A 96 well-plate with folded tin samples in each well.
    The majority of my tinned samples, ready to be run in the Elementar.
    Alyssa Gao

    My project has been further hindered by mistakes that I have made. Although several of my first attempts did not succeed due to mistakes I made with pipetting and with tinning, and other attempts have gone awry due to malfunctions with instruments, I have gained from my experiences and learned a great deal from my mistakes. I think the most important realization I have made during my time here is that research requires more than just persistence, attention to detail, and a willingness to ask questions. It requires optimism - the ability to remain positive and keep trying when things fail or when you make mistakes.

    Even though research can be incredibly painful at times, it definitely pays off. Nothing is more satisfying than looking at the raw data you collected and knowing that it was a product of your hard work and determination, as well as the support of others. Even though roadblocks and mistakes are bound to happen, if you stay positive and keep trying, success in research will eventually happen too.

  • Oak Identifying Fun

    Oak Identifying Fun
    An oak tree at Pleasant Valley Conservancy in WI

    Welcome Back!

    I thought I would use this post as a way to give people more of an insight into what I am doing in the field. Before starting this internship, I had very little experience with tree identification, and I never really paid too much attention to trees when I was walking around outside. Now, that’s ALL I do. Pretty much anytime I am walking outside, I look to see if I can spot any oaks. It’s like I have oak-vision glasses on!


    Because I want all of you to be able to join in on the identifying fun, here are three of my favorite species of oak that I have encountered on my collecting trips and how to identify them:


    Quercus macrocarpa (bur oak)


    This is the species that I am using for my study. The leaves of a bur oak tend to be broad and flat, have a distinctive “waist”, and have several lobes. The bark of a bur oak tree tends to have deep furrows that you can see from a distance. Although this is how bur oaks tend to look, there is often lots of variation between different trees, and sometimes even within a single tree, which is why I am studying them.


    Quercus muehlenbergii (chinkapin oak)


    I really enjoy how symmetrical muehlenbergii leaves tend to be. They have teeth, rather than rounded lobes. The base of the leaf appears truncate (cut short) and the top appears pointed. The bark of a muehlenbergii tree is light-gray, thin, and scaly.

    Quercus stellata (post oak)


    I think that the leaves on this tree are are so unique and look really cool from a distance and up close. The leaves of a post oak tend to resemble a cross, and tend to be thick and waxy. The bark tends to be gray and scaly. You probably won’t see too many of these in the Chicago area, but if you go a little more south you might!



    Next time you are walking around outside, see if you can spot any of these oaks! Not only are oak trees aesthetically pleasing, but they are also environmentally important, providing habitat and resources for several mammals, birds, and insects, and assisting in removing carbon dioxide from the atmosphere.  

  • Lights, Camera, Action!

    Pink "X"s spray painted on the trunk of a Pin oak
    Spray paint mapping out where sap flow meters will be installed

    These past few week I have been working on setting the stage for my experiment. My project has changed a bit since my first post, and I am now studying the impact of an injury on the rate of sap flow in Pin oaks. Choosing the trees and installing the sap flow meters was a process that was completely new to me.


    Even before we went outside, we mapped out where we wanted to put the sap flow meters.

    A white board with a diagram of a tree, and where on the tree the sensors will be, drawn in blue
    Mapping sensor location


    Once outside, we measured the diameter of the Pin oaks. This was important because we wanted to install the sap flow sensors in trees that were of comparable size. This was my first time using a DBH tape, which tells you the diameter of the tree based on the circumference. This is Alyssa, another fellow at the Arboretum, measuring the DBH.

    Using a yellow tape to measure the diameter of a Pin oaks
    Alyssa measuring the DBH of a Pin oak


    Next we spray painted where the injury and sensors would be.

    Pink "X"s spray painted on a tree to shows where sensors will be installed
    Spray painting where the sensors will go

    Then we began chiseling away the bark. The sap flow sensors only work if they are installed in the sapwood located behind the bark.

    A person using a orange chisel to remove the bark of the tree
    Alyssa chiseling away the bark


    After that we drilled holes for the sensor’s needles to go inside. We practiced drilling the hole in a severed piece of tree trunk before moving on to the Pin oaks.

    Drilling a tiny hole in a severed tree trunk
    Practicing drilling holes

    We then attached the sensors and strapped them onto the tree. We also connected the sensors to solar panels that keep them charged and running. The sap flow sensors will be left on for the next week. About half way through the week, we will be injuring the tree and seeing how the data on the rate of sap flow changes.

    Four sensors installed in the side of a Pin oak
    Complete installation of the sap flow meters
  • Collecting Samples from the Canopy

    Four male arborists and young female intern gather for group picture by the golf carts at the end of a busy day collecting samples.
    Arborists and URF collaboration

    Hello again! One of the biggest roadblocks my mentor and I faced while planning my research project was how to access leaves from the canopy of the forest! Luckily, the arborist crew was able to help us out. After 2 busy weeks of setting up all my plots, finding the right tree species, and counting seedlings, I was finally ready for collecting leaf samples!


    The APTA air cannon being loaded with a small bean bag and line.

    For the arborists, work starts early. My mentor and I met with some members of the crew at 7:00 am to start collecting. The arborists used an APTA (Air Powered Tree Access) which was essentially a hand held air cannon to shoot a small line into the canopy to pull down leaves and small branches. Once the leaves fell, we rushed to pick up the bundle of twigs, branches, and individual leaves. While we were working, a photographer came out to take professional pictures of the fun work we were doing! Big thanks to the arborist crew for making time to help me with my research project! I could not have done it without your help!

    Author smiling in the woods wearing a hard hat, holding a bundle of red oak branches.

    At the end of the day, all of the leaves we collected were brought back to the lab for weighing, drying and photographing. I am excited to begin learning new lab skills now that most of my field work is complete!

  • A Long Journey

    A golden yellow slug contrasted against dark wet wood
    I found a slug when we were out doing fieldwork in the East Woods

    These past few weeks, dear readers, have been an exercise in persistence. I’ve spent the better part of my time recently doing intensely repetitive work.

    In my previous blog post I described the permanent plots in the East Woods that I am studying this summer. In addition to those four plots, I also set up six smaller temporary plots. Across the 3,100 square meter area that these plots cover, I have over 100 trees to collect data from!

    These data are in the form of tree cores which are collected using a special hollow-hand drill called an increment borer. The idea is similar to stabbing a straw into a watermelon and retrieving the cylinder of fruit from inside the straw.

    The tree cores are stored in paper straws for transport from the field to the lab. Once the cores are dry they need to be mounted on a block of wood to stabilize them. Each core then needs to be sanded, starting with a very coarse grit of 80 and progressively working towards finer grits, with the finest being 1500. When this has been done, a microscope can be used to measure the tree rings to an accuracy of .001 millimeters!

    Since I collected at least two cores from each tree, I had a total of 225 tree cores, all which needed to be cored, mounted, sanded, dated, and measured. Coring alone took eight days and that was with the help of six other people. There were times when the work seemed endless, but despite that it is definitely worth it and I can't wait to see where the data leads.

    A T-shaped hand drill partially embedded in the bark of a tree
    An increment borer in the process of coring a tree
    A box filled with labeled straws
    All of the tree cores being stored in straws to dry out
    A sliver of wood mounted on a labeled block; the wood is sanded so the tree rings are apparent
    These cores have been mounted and sanded so the rings can be easily seen
  • Sensors, Sap Flow, Science

    a Pin oak with four different sap flow meters attached along the trunk
    a Pin oak with four different sap flow meters attached along the trunk

    In the last few weeks my project has been changing, and now I get to work with an exciting piece of technology, sap flow meters!


    This is the SFM1 Sap Flow Meter.

    Four sap flow meters attached to a tree with orange spray paint markings on it
    Sap flow meters installed in a Pin oak



    There are 2 main parts to the sap flow meter. The data logger, which is silver, and the sensors, which are the red and black pins. Each of the pins has a different job.

    A red pin and two black pins inserted into the trunk of a Pin oak
    The three pins of the sap flow meter


    The pin closest to the data logger measures the ambient temperature of the sap, which is usually flowing upwards. The red pin heats up the sap, and then the top black pin measures the temperature again. Based on the change in temperature, you can get the volume and rate of sap flowing past the sensor. And, if you measure the diameter of the tree, you can get the volume and rate of sap flowing through the entire tree.


    In the next few weeks, I will be looking at how the rate of sap flow changes when an injury is added to the tree. The completed setup, with the injury, will look similar to this.

    A Pin oak with four different sap flow meters installed in various location along the trunk
    a Pin oak with four sap flow meters installed

    I am excited to get started using the sap flow meters and learn more about how injuries impact a tree!



  • Tools, Tech, and Tests

    Soil samples in glass beakers
    Soil samples are measured into glass beakers and set out for enzyme analysis

    The remaining weeks of my internship will be spent in the lab. I will be running different tests and analyses on my soil and root collections. Below are a few pictures of some of the cool things I get to use in the lab! The analyses I will be performing are soil nitrogen mineralization rates, soil microbial biomass, soil carbon concentration, enzymes, root biomass, root structure and size, and root exudation. All of these tests require the use of many different lab technologies and tools. 

    Cheers to lab work!

    Micropipette with 8 dispensers
    This micropipette was used to quickly dispense solution into soil samples on small trays for enzyme analyses
    Machine called Elementar that analyzes samples for element concentrations
    Machine called Elementar that analyzes samples for different element concentrations
    Centrifuge Machine
    A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., soil and acid) or liquids from solids.
    Licor photosynthesis analyzer machine
    Measuring photosynthesis/carbon by gas exchange
  • Working Towards a Fitbit for Trees

    Boxes of collection tubes alongside a beaker filled with more tubes and a row of bottles.
    Some of the materials used for DNA extraction: collection tubes, various buffers, micropipette tips, and a tube stand.

    Hello again!


    It is now week 6 and things are heating up (literally).


    These past two weeks have been action-packed, as I’ve finally began to collect my samples and run my experiments. My project has two separate components: (1) testing Mongolian Oaks within the Morton Arboretum collection for bacterial leaf scorch and (2) measuring leaf morphological traits including moisture content, foliar nitrogen levels, and leaf area. My project synthesizes these two elements by examining leaf morphology in a pathological context.


    In this post, I wanted to focus on the pathological dimension of my project.


    In most cases, a tree is brought down by a combination of drought and disease. Insects are common vectors which injure trees by allowing bacteria to invade, and spread the infection by traveling from tree to tree. Bacteria like Xylella fastidiosa, which causes bacterial leaf scorch, grows in cavities and blocks water and nutrients from reaching the leaves.


    A butterfly with orange bands on the upper and lower halves of its wings, perched on the edge of a deep canker in a tree trunk.
    A butterfly perched on the edge of a canker in one of the Mongolian Oak specimens I am studying.
    Alyssa Gao


    Just as advancements in STEM research have allowed for doctors to diagnose humans, plant pathology seeks to understand and diagnose plants for disease. However, this requires a baseline knowledge of plant physiology and how plant structure adjusts in response to disease.


    The caps of tubes protruding out in a wheel formation.
    Samples held in a centrifuge in the Plant Pathology lab.
    Alyssa Gao

    In addition to showcasing plant health at the Arboretum, an aspect of plant research that is often overlooked, my research works towards designing a “Fitbit for Trees”. My project seeks to contributes to a baseline of information on trees which would allow us to refine our ability to diagnose the health and growth of trees in the future.


    Until next time!

  • Behind the Scenes of Science

    Undergraduate researcher Sam Panock is being filmed by a camera man while completing lab work,
    Undergraduate researcher Sam Panock (pictured right) is being filmed by camera man Matthew Taylor (pictured left) from the Development Department while completing extractions for soil microbial biomass analyses.

    For the first five weeks of this program, I have been working in the field to collect soil samples, root samples, and root exudates for my 48 individual trees (8 species total). On my last few days of collection, I was being filmed by staff from The Morton Arboretum Development Department. The goal was to capture close ups of some behind the scenes science. The camera man followed me through swarms of mosquitos into the deep forest to film the soil and root collection processes. The lab work and extraction preparations were also filmed the next day.  It was a super cool experience to be able to show off the hard work I have been doing for the past weeks, and it is a great feeling to know others are exited and eager to learn about my research! 

    Stay tuned for the video.

    Cheers to Week 5!


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