Kody Clausius/Anh Nguyen Blog Post

(Kody)

9:00- Arrive

Dr. Good, my partner Anh, and I usually start to come in around 9 everyday. We will get settled and ready for the day while Dr. Good checks his email. We get the laser and the plasma chamber up and running if they aren’t already, so we are ready to roll into experiments when we want to. In fact, the laser doesn’t always run the same way daily, even if we do not make any changes to it. A realignment of the dye laser cavity is needed to get our experiment running for most parts. If there is some down time, there is usually a little bit of reading to do. Most of the time it’s textbooks or manuals of the machines that we are using.

10:00- Experiments

Around 10 we start to get our work for the day going. Right now, research has proven to be very day to day. There is a decent bit of maintenance to be done with parts of the plasma chamber and dye laser that we work with, so we could be doing that all morning. There are also a number of things we can do with the dye laser to familiarize ourselves with it. Working with the dye laser is very tedious, as there are many mirrors and lenses that have to be carefully aligned in order for it to operate. Most recently, we have been messing with the alignment of the dye laser, and then practicing realigning. If these activities are being done, there is more reading to do.

Image of the dye laser

12:00- Lunch

We all take an hour lunch break at 12:00 everyday.

1:00- More experiments

At 1 we get back to work and continue what we started in the morning, whether that be maintenance, more trials and experiments, or more ready. Most recently, we have run a trial to get some voltage data while studying laser induced fluorescence. We have aligned our laser to go through a tube filled with gas, and then connected a photo detector to a computer where we are running a logger pro graph of the voltage. 

(Anh)

Our project is to use laser-induced fluorescence (LIF) to diagnose ion-acoustic waves – a phenomenon happens in plasma physics. Plasma is known as the fourth state of matter, which consists of an ionized gas (typically Argon). We use a Langmuir probe to study the characteristics of plasma at different spatial positions. We create plasma in a magnetic-confined chamber, by applying voltage to an incandescent filament that launches electrons to collide with gas atoms and ionize them. Our device consists of two such setups, divided into a source and a target chamber. Ion-acoustic waves are created in the low frequency regime, and it is known to be a collisionless wave (no particle physical interactions needed to create perturbation, but just Coulomb forces). We fluctuate the source chamber voltage in the positive regime and ground the target chamber so particles can flow from source to target chamber. There is a negatively-biased grid in the middle to keep the electrons from going through, which leaves only a net flow of ions. We would then shine a laser to the waves and use the re-emitted light from it to study the wave’ speed distribution, due to Doppler broadening. Basically, when a photon from the laser beam hits a particle, that particle is excited to higher energy states, and quickly decays and emits a photon with longer wavelength (the re-emitted light). 

  • Upgrades: 
  • Computer-controlled stepping motor

Previous experiments involved changing the Langmuir probe’s positions manually. However, after intensive research (the stepping motor is a relatively old device which is not well-supported anymore), we have installed software and drivers that enabled connections between our computer and the motor. And now just with simple commands, we can bring the probe to whichever position we want, making the process of acquiring plasma data much more convenient. 

  • Photomultiplier tube supply

 My current task has been to make a power supply box for the photomultiplier (PMT) tube. The PMT tube simply reads light signals (photons) and gives a voltage output proportional to the number of photons coming in. This is done by the multiplication of electrons when they hit the dynodes (Figure 1). Each subsequent dynode has a more negative potential to attract the electrons. A series of dynodes eventually draw all of the electrons to follow a zigzag pattern. I have modified the output of our PMT tube to have a BNC connection, so we can easily monitor it on an oscilloscope. I am also installing PMT signal connections to the power supply, as well as making a potential meter (just a knob) that modulates the voltage that comes in the PMT tube. Previous student researchers already made one, but we want to make a new portable supply that can be brought to anywhere! In this experiment, the PMT is useful in studying the ion-acoustic wave through reading the light emitted from the ion waves that were excited by the laser beam.

PMT (in a box to trap lights in)

A Small Fixer-Upper: The Gettysburg College Observatory

From Left to Right – Jamir Wesley, Sophia Marrone, Ethan Foote, Professor Milingo

Project Synopsis

Located just past the Painted Turtle Farm, the Gettysburg College observatory has been on our campus since 1967. In the past few years the observatory hasn’t been used much, so our goal this summer is to create a user manual for future research students so they can have a step-by-step guide on how to use the observatory.  In the past, the Gettysburg College Observatory has been used for many research projects including variable star research, binary star research, exoplanet transits, follow-up photometry of supernovae, and asteroid astrometry (carefully measuring the changing positions of asteroids to better understand and predict their orbits).   The Gettysburg College Observatory is a designated Minor Planet Center with the International Astronomical Union.

The Gettysburg College Observatory

Our jobs this summer also include making sure everything at the observatory is functioning well, checking the telescope’s abilities, its limits, and generally just cleaning up to make it a better space to work in.  There are three rooms at the Observatory – the classroom, the dome, and the warm room. The classroom is a large space that holds our smaller telescopes which are used on piers just outside the observatory. We also keep all extra equipment in this space because it is much larger than the dome or warm room. 

Jamir working in the observatory classroom.

The dome is where the telescope is. The telescope is a 16-inch reflecting telescope. Attached to the telescope is a CCD (Charged-Coupled Device) camera.  While we do not have a spectrograph, which would be used to identify energy that is absorbed or emitted from an object as a function of wavelength, we do have a filter wheel which allows us to do photometry. Photometry is the measurement of how much light comes out of an object within a given wavelength band. These filters also allow us to combine different images to make a  colorful picture, also known as astrophotography. 

The last room in the observatory is the warm room. All observatories have a warm room where the computers that control the telescope and the camera are kept at a regulated temperature to prevent damage to the electronics and keep the astronomers comfortable. Typically, observatories are located in dry areas that tend to get cooler at night so these rooms are known as “warm rooms”. Our warm room holds our two computers, the CCD computer that controls the camera and the Telescope control computer that controls the telescope. This room is not only heated in the winter but air-conditioned in the summer, which gave us a nice break from the heat while working. 

Ethan in the warm room

The two pieces of software that we use to observe are MaxIm DL and the ACE controller. MaxIm DL is the software that controls the CCD camera and allows us to collect digital images and different calibration frames with our telescope. The ACE controller software is the system that controls the movement and tracking of the telescope and dome. Our first step in making sure the observatory was in working condition was to check to see if these programs are still functioning and communicating with their respective hardware. In addition, there are many components in the observatory that had to be checked such as the dome. In the dome, there is a box that opens and closes the dome slit and also rotates the dome.  We tested this box when we first got into the observatory and found that it was working properly. The dome slit can also be opened from the telescope control computer through the ACE software which allows the telescope and dome to communicate with each other.  It’s necessary that the dome knows where the telescope is pointing so it can follow while the telescope tracks an astronomical target.  

After checking the dome we checked to see if the telescope control system, camera, and filter wheel were all working properly. As stated previously, the telescope has not been used for a few years so we had to make sure everything was working as expected. During our time we found that one of the photometric filters that we use to take images had become damaged from humidity and age, therefore making it unusable.  We’ve ordered a replacement that will be shipped in August and will be in place shortly after. 

This is an image of the 16” reflecting telescope in its dome

In addition, we must create a proper focus and flat routine to get good quality scientific images. Proper focus is important because it helps to get a clear image when using the telescope for research. It is very challenging to get a perfect image given the humidity in our area and the light pollution coming from town. Finding a flat routine is also very challenging due to the time frame since flats are meant to be done during dusk (shortly after civil twilight when the sun is 6° below the horizon).  Flats are calibration frames that allow us to characterize the response of the pixel array in the camera. You have to take many of these frames in a short period of time in every filter that will be used for the night, so one of our goals includes designing a smart and efficient process for taking flat field images. 

Since the observatory is only made up of sheet metal and plaster and doesn’t get much attention, we have spent much of our time cleaning it up.  We also spent some of our time updating the warm room (which is the main place we work) and taking down old corkboards and replacing them with whiteboards. There are also many creatures that find their way into the observatory so we worked with facilities to combat the flies, wasps, and mice within the observatory (this is common at observatories since they’re in remote locations).  With that overview, we’ll introduce ourselves and go into a bit more detail about our work.  

Who We Are

My name is Jamir Wesley and I am a rising sophomore majoring in Physics and Environmental Science, hopeful of becoming a professional engineer by 2030. I’ve always wanted to be an architect from a child and I think I’ve found my groove here through these programs offered at Gettysburg College! My favorite part about our research so far has been all the stargazing! I’ve lived in Philadelphia for my entire life and have never gotten a clear view of the night sky! I’ve recently seen the big dipper for the first time and cannot get it off my mind! I hope that writing a user manual for the observatory’s telescope will provide me with a background into how large telescopes function. I believe that this research is important because the science behind telescopes and their observations are so important to fields beyond astronomy. 

My name is Sophia Marrone and I am a rising sophomore majoring in Physics and Studio Art. I grew up in West Chester PA and I plan on becoming an architect. I have always been interested in space ever since I was a little girl, especially after I was given a book on astronomy which inspired me to go into Physics. After research this summer I have developed more of an understanding of how to stargaze and utilize telescopes. I find it interesting to look up into the sky and be able to point out the constellations to my friends and family. My favorite part of the research has been learning how to use the different types of technology in the observatory. There are many different computer programs we have to use to work the telescope and the camera that captures images.  I find it fun to work with them. While there are some interesting troubleshooting problems, I like to sit down and find answers! 

Hello! I’m Ethan Foote, a rising sophomore and an aspiring Physics and Math double major. Astronomy is a special topic for me because it never ceases to capture my imagination. So far my favorite part of our project was the moment my brain finally was able to contextualize the sky, where not only could I see the constellations, but I could also understand where they were going to move and why. This came from our usage of different spherical coordinates for astronomical objects that were confusing at first but helped lead to a better understanding, especially in the context of how it changes due to the Earth’s rotation. Now of course operating our large telescope has been quite fun as there’s that feeling of grandeur getting to use something that can absorb information from distant objects in space. I look forward to being able to combine all that I have learned to observe some celestial objects for science!

SIMBAD and Aladin, Focusing the Telescope, and Calibration Images

During our research experience, we’ve learned about many resources that have helped us prepare for observing. The darkest hours that are void of clouds and low in humidity make it great for observing at the Gettysburg College Observatory. While Weather Underground provides us with great forecasts of cloud cover and humidity in our community, Clear Dark Sky gives us forecast information regarding all things useful for astronomical observing like cloud cover, humidity, seeing (related to atmospheric turbulence), and more.  We also used two tools, the SIMBAD astronomical database, and the Aladin sky atlas, to help us while observing.  SIMBAD is an online astronomical database that allows us to look up the coordinates, basic data such as brightnesses in various filters, other physical measurements, and links to published peer-reviewed papers for astronomical objects. Aladin is an interactive sky atlas, powered by SIMBAD and other astronomical databases, which allows us to generate finding charts so we can identify targets while we’re observing.  One vital characteristic of the targets we identify is their brightness, which we have to consider when taking images.  A very bright star, those we may find with the naked eye, may saturate the CCD camera giving us an image that we can’t use for scientific purposes.  One of the projects we all worked on used SIMBAD and Aladin to create a list of stars that could be used to focus the telescope.  So these were stars that had to be bright enough for a short exposure (a few seconds) but dim enough to not saturate the camera. We needed enough stars that we could use throughout the night to check how the focus changed with temperature. Focusing on the telescope is just one part of the observing process, we also worked on obtaining calibration frames – such as bias frames and flat field images – that allow us to remove the instrumental signatures from our scientific target frames (the astronomical objects we’re interested in studying).  

A Day In The Life

A day for us begins with a debriefing in the morning in Master’s Hall. Our discourse often starts with checking in and talking about how things are going, then what work we have to do, and if the weather forecast is favorable for observing. Due to a longstanding pause in research at the Gettysburg College Observatory, our mornings are often filled with ideas on how we may be able to bring new life into the observatory. Although these conversations often include requests for pest control and computing support; we also determine when and how we should prepare for the rest of our day while considering the weather, cloud cover, and humidity. 

The greatest part of our work has been concentrated on creating a welcoming environment in the Gettysburg College Observatory!  Aside from critter removal (which is constant at most observatories, ours is no exception), we’re working to make the Observatory into a friendly space for astronomical research projects with students. Within the past two weeks, we’ve spent time searching through online databases to compile a directory of observable stars present during the summer nights. We’ve captured images of the faintest stars noticed by our eyes at night and have so far examined how changes in humidity and temperature change the telescope’s focus.  This allows us to direct students using our telescope on how to properly focus the camera images throughout the night.  We are also spending some time with the small hand-operated telescopes at the Observatory so we can host open house observing nights and possibly start an astronomy club!

This image shows a search for focus stars using SIMBAD

We think it is fair to say that our research journey this summer has been no simple task. With each day we all have persisted through unique problems and unforeseen challenges and we will continue to do so until the end.  We’re excited for the future of the observatory and the students who will work in this space with the help of our observing manual. A day in the life with our team is full of wonder for what the next day (or night) may bring!

More About Our Focus Routine:

Creating a focus routine for the telescope has been a unique challenge. For us to focus the telescope we need to take a series of images of a star, with a particular magnitude range, with a lack of other bright stars in its proximity, so that the camera can take a clear picture of that isolated star.  From there the camera control software takes a slice of pixels from the image that includes the most illuminated pixel, creating a graph that charts brightness by pixel position. That graph should create a bell curve shape. The computer then finds the width of that curve at half of the max brightness. Full Width at Half Max, or FWHM for short, allows us to quantify the focus. The smaller the FWHM the better the focus, we found that a good focus has a FWHM in the ballpark of 9 to 7 pixels. However, there is no absolute standard for a ‘good’ or ‘bad’ FWHM as the maximum focus will vary depending on temperature, humidity, and the seeing conditions (how much the atmosphere smears out an image while we’re exposing).

MaxIm DL 5 which we use to take images of the sky

In an effort to help future observers know where to start with a good focus position, we are creating a chart of the best FWHM we found at every temperature. We want to have this guide to reduce the time it takes to reach a good focus.  Good observing conditions can be few and far between in the mid-Atlantic, so the time in the observatory needs to be used diligently.   We are creating a simple focus chart that accounts for variations in temperature.  We focus the telescope by moving the secondary mirror of the telescope with a small motor.  The position of this secondary mirror can be read as an encoder position on the motor.  We’ve spent a lot of time during clear nights changing the secondary mirror position, taking an image of the target star, and measuring the FWHM over and over to determine the lowest FWHM.  Our work (and work continued into the colder months) should allow future observers to quickly adjust the focus throughout the night while observing.  We will continue working on this focus routine until we gain a clear understanding of what affects how well-focused our images are.

Rainforest Cafe but in Real Life

Welcome to the Caldwell Lab!

About the Caldwell Lab

In the Caldwell lab, we primarily focus on communication via bimodal acoustic calls, which are a way that sounds and vibrations work together to send information from one animal to another. An emphasis in our research this summer has been testing whether vibrations made by calling frogs attract predatory snakes.

Hello! I have been part of the Caldwell lab since my first year and am now a rising senior Biology major. This year, I traveled with Dr. Caldwell to conduct my X-SIG project in the Panamanian rainforest. I really love seeing and hearing so many types of tropical animals that I’ve never encountered before. Experiencing the intense rain and thunder here, though, has probably been one of the most exciting things – aside from being under a moving troop of howler monkeys – and it all reminds me of Rainforest cafe (a chain restaurant that is rainforest themed with rainforest sound effects)!

Research in Gamboa, Panama

In Panama, we are working at the Gamboa laboratory facilities of the Smithsonian Tropical Research Institute (STRI). The Trillo Lab, also from Gettysburg College, is working here this summer (see their X-SIG blog!). Gamboa is a town bordered by the Chagres River and the Panama Canal. The Panama Canal, which was completed in 1914, allows ships to travel between the Atlantic and Pacific oceans. The Smithsonian began conducting studies here in 1910 that looked at the environmental impact the Panama Canal would create on the flora and fauna of the tropics that surround the area. Now, STRI facilities are a base for scientists from around the world to conduct research on the tropical rainforest and marine ecosystems. STRI provides many facilities such as butterfly insectaries, growth chambers, flight cages for bats, and an experimental pond. We work at Experimental Pond, which is man-made, surrounded by vegetation, and adjacent to Soberanía National Park. This site gives us quick access to great diversity of forest creatures, all with a space nearby sheltered from rain and wired with electricity. Dr. Caldwell has been conducting research at STRI for nearly 20 years, and at Experimental Pond for more than 15 years.

Snake Vibrotaxis

My main project this summer builds on research from an earlier X-SIG project, in 2019. We have two related research questions: 1) Do snakes use vibrations produced by calling frogs to find these prey?, and 2) Can snakes tell which direction plant vibrations are coming from?

To answer these questions, we first must train non-venomous wild tree snakes to forage in our experimental arena. This is done by offering them frog egg clutches. I put a snake in the arena and check on it every half-hour to see if it has eaten. In total, we have collected three snakes: Nimbus (Leptophis), Sunshine (Leptodeira), and Tigo (Leptodeira) for the project.

Nimbus, named after the model of the bathroom vent found in our apartment, was released after we realized they had no interest in the all-you-can-eat-buffet of egg clutches.

Sunshine, which is the first snake I caught, has been very cooperative. It went up and ate a clutch on the first night of training! I was so excited that I sang “Walking on Sunshine,” hence the name.

The picture I took when I got Sunshine

We also recently caught Tigo, named after a phone service here in Panama, who is as nice as Sunshine. As Tigo is still going through training, I’m getting to know their personality and have noted that Tigo likes to go swimming in their water bowl.

Once trained, we play snake pre-recorded sound and vibration from the calls of hourglass treefrogs (Dendropsophus ebraccatus). Sound is played from a speaker overhead, while vibrations are filtered using MATLAB to ensure they are played with realistic spectral and amplitude properties, and then played through one of two Y-shaped branches in the arena using an electrodynamic shaker. During trials, if snakes forage more often on the branch vibrating with frog calls, we will conclude these vibrations are used to find prey. If snakes travel to the side of the vibrating branch from which call vibrations are played, we will conclude that snakes can extract localization information from these vibrations.

Other Projects

In addition to the snake vibrotaxis work, I am also spending time working on other projects. One of them looks at the Dear Enemy Effect in red-eyed treefrogs (Agalychnis callidryas). In that experiment, I’m trying to determine whether the frogs are less aggressive to neighboring frogs that they are already familiar with. I’ve also been conducting censuses at Experimental Pond of red-eyed treefrogs and another frog, Hyla rosenbergi. Many of these frogs were tagged in 2021, and we would like to know which frogs return to the pond and if they reclaim the same territories in subsequent rainy seasons.

Experiencing Panama

When we are not doing research, we try and make time to explore much of our surroundings. Sometimes this includes Sunday hikes, where we get to see monkeys and other critters. We’ve also made trips to Panama City, where I got to celebrate my birthday, and grooved our way out of restaurants. I’ve enjoyed my time here and all the animals I’ve seen!

Macrophages and Evil Rubber Chickens

Hello everyone, welcome to the Solis Lab! This summer, we are working on understanding inflammation and potential factors affecting it. Inflammation is known to play a role in the onset of many diseases, such as Alzheimer’s disease, diabetes, and cancer. In order to understand the role of inflammation to a greater extent, it is essential to closely examine macrophages. Macrophages are differentiated cells that eat dead cells and bacteria, and are typically responsible for driving the inflammatory response.

We work with a mouse leukemia cell line called RAW264.7, and we have two ongoing projects this summer. Rose is working on understanding how macrophages respond to light and learning if/how it might play a role in the regulation of inflammation. Bryce is working on learning about the impact of heavy metals on inflammatory responses.

In addition to the work in lab, our workday typically includes a game of Wordle and Dr. Solis showing off his dabbing skills. Our work is strictly supervised by 6 miniature evil rubber chicks residing in an undisclosed location within the lab.

Meet The Team

Dr. Angel Solis

What do you find to be the most challenging part about research?

Most experiments will fail, either because you added something at the wrong time, or you misread an instruction, or most commonly, because it does not support the hypothesis you had. It can be demotivating to set up another experiment when your results are confusing or the hypothesis you were really excited about that explains all your data turns out to be incorrect. The only thing you can do is remind yourself that even when you disprove your hypothesis, you’re still learning something relevant, and hope your next experiment will be more clear!

What motivated you to become a scientist?

When I was in middle school, I was diagnosed with Crohn’s disease. That made me read as much as I could about what Crohn’s disease was, and why it was happening to me. Learning about all the different pathways that became activated in the cells, and how they can become dysregulated was so beautiful to me, and it made me want to learn as much as I can about cells and the molecules they had. During this time, I read a lot about the immune system as well. Reading about inflammation and immune cells was (and still can be) quite confusing, but still utterly mesmerizing.

What is your favorite amino acid?

(Incredulously) Lysine, obviously!

What type of bear is best?

That’s a ridiculous question.


Rose Ankeriasniemi

I am an international student from Finland, a member of class of 2024. My major is Biology and minor is Educational Studies. In my free time I like to do jigsaw puzzles, bike, play the violin and practice badminton with my friends. Right now I am working on the fifth puzzle of the summer; it’s a 1000-piece puzzle featuring a bookcase with cats playing on the shelves.

What motivated you to become a scientist?

I come from a country that has the highest rate of type 1 diabetes in the world, and a handful of my loved ones are affected by it. I myself have an autoimmune condition called localized scleroderma, which is caused by inflammation in certain parts of the skin. The exact causes of many autoimmune diseases, like T1D and scleroderma, are still unknown, and although we have a good idea of how the immune system works (or doesn’t), we often don’t know what has initiated such a response. I have always been invested in understanding the immune system; focusing on inflammation in particular is an excellent approach to learning more about the pathogenesis of certain conditions, because many conditions involve some level of inflammation. Working in the Solis lab has provided me with a way to discover my intellectual curiosity, and I look forward to continuing my work in the lab beyond this summer.

What do you wish was illegal?

Bullying or laughing at someone’s expense is never OK. Not at school, not at home, not at work. You never know what the other person is going through, and not everyone shares the same sense of humor. Please check in with your loved ones and make sure they know you care about them.

What do you value the most?

I am eternally grateful for the friendships I have developed over the years. I met some of the kindest people in high school when I first came to the USA. There were a few other new *international students at my school, whom I connected with immediately. It hits you differently when you are experiencing a culture shock, and you have someone to share those challenging feelings with.

*Feeney, if you are reading this, I love you! You’re famous now 😊

What are your two truths and a lie?

1. My dad has my name and birthday tattooed on his shoulder

2. I can solve the Rubik’s cube

3. I absolutely loathe seafood and cilantro

Good luck guessing 🙂


Bryce Weigartz

The Name is Bryce William Allen Weigartz and I’m from Gloucester Virginia, which is an hour south of Richmond. I am technically a rising senior who will be living in the depths of Apple with 5 other fellas come the fall/spring. As a guy with a major in Biology, and a minor in Chemistry, I guess you could say I’m a fan of learning. My other interests include the following: sleeping, showering, eating, gym, tennis, pottery, wood turning, reading obscure books on mechanics, bicycling (with the one wheeled variant), not cooking, tree climbing, piano, video games, and YouTube.

What has been the most injured you have ever been?

It’s a toss-up between having appendicitis in the third grade and being in a tree stand that fell and breaking my whole wrist/arm along with lacerating my spleen.

What has your diet consisted of during XSIG?

I keep it simple with plain chicken in a pan, maple oatmeal, chocolate bars, milk, water, mac n’ cheese, cheese crisps (a Weigartz classic) Pepsi, yogurt, and eggs. This is/has been my diet. I went home the other weekend and brought back actual food, a meatloaf and barbecue smoked pig butt, and it was stupendous.

What possession of yours is the most valuable?

Monetarily it is either my Stihl ms250 chainsaw with the bars and chains or it is my Hp omen laptop, in this market I don’t know which is worth more. To myself however, my most valuable object is my ”2-door hatchback 1996 Ford Escort Lx painted in the wonderful bright Calypso Metalic Green”. Her name is Hellen, after the Trojan’s, because this is a beauty to goto war over (look up what I put in quotations and, you’ll be forced to agree with me). I would say that this was my most valuable possession monetarily, but apparently the government estimates the value of this American Classic at a measly 500 pieces as per my property tax letter I got when I last visited home.

Glossary

  • Incubator: a closed cabinet-like space for cells to grow in where the temperature and CO2 are controlled for optimized cell growth
  • Cell culture media: cell food (contains glucose, glutamine, calf serum and pen strep)
  • Macrophage: a differentiated cell that eats dead cells, bacteria, and mediates parts of the immune response
  • ELISA: a technique to measure the amount of proteins or other substances
  • Cell plate & wells: a flat plastic piece that has indents on it where the cells and cell culture media are placed in for cells to grow
  • LPS & Poly I:C: substances that initiate an immunological response. We use these substances to activate our cells, which results in a production of cytokines
  • Cytokines: cytokines are produced by macrophages to act as signals for the rest of the immune system to recruit more immune cells when an invading pathogen is detected
  • Pathogen: a virus, bacteria or other organism that is harmful to the body and can cause disease
  • Antibody: a protein in blood produced in response to foreign substances like a pathogen

Techniques In the Lab

ELISA (Enzyme-linked immunoassay)

Cytokines are indicators of inflammation, and to quantify the cells’ immune response, cytokines can be analyzed. They are produced by the cells (macrophages) and their presence can be tested for with ELISA from the culture media in which the cells are growing. ELISA is a multi-step process that uses antibodies and other molecules to bind to the cytokines, eventually indicating the amount of cytokines present through the strength of a colored reaction product.

We use 96-well plates for ELISA (see below what it looks like—it’s a lot of tiny wells!!), where one well is dedicated for one sample. Below on the left is an illustration on how the cytokine is detected in each well. The more cytokines there are in the sample, the more of these structures are present, which leads to a greater production of the colored product in that well. The absorbance of each well is then read on a spectrophotometer. The data is compared to standard proteins, which we always include on the plate. The process from harvesting cells to collecting the samples is described in detail in Rose’s light project section.

Isolation of RNA

One might isolate RNA from cells to learn how well the cell performs its job. Rose has been isolating RNA from her cells that have been growing in the dark and the light environments. Specifically to compare the two environments, her cells are divided into small wells on plates after which those plates are placed in an incubator overnight for cells to acclimate. The next day, the cells are treated with immunological response initiators (LPS and Poly I:C). The plates are then placed in the corresponding light treatment in incubators. We specifically used an LED light taped in the incubator. After six hours, the plates are taken out of the incubators and the cell culture media is discarded with a pipette. The cells are lysed with TRIzol reagent, after which the liquid from the wells is pipetted into tubes. In short, the mixture is separated by polarity using chloroform, the RNA precipitate is formed by presence of isopropanol, and the formed RNA pellet is resuspended in water and then heated up on a heat block.

CRISPR

The CRISPR method is used to delete a specific gene from the cell line DNA, and a knockout (KO) cell line is created by targeting the macrophages with plasmids. An inflammatory response is induced with the KO cell line, and the aspects of the response are measured by qPCR and ELISA. For instance, if a KO cell line that is missing a gene called RABGGTB presents a different inflammatory response from cells that have the gene, it can be suggested that the gene RABGGTB plays a role in inflammation. In that case, we would want to learn about the function of the gene in order to understand its exact role in inflammation.

Western Blot

A western blot is very similar to the aforementioned ELISA, but where an ELISA detects proteins outside of the cell, a western blot detects proteins WITHIN the cell. The process in our lab is a 3 day one. First the media the cells are grown in is discarded, leaving the cells stuck to the bottom of the plate. Then the cell membrane gets popped open by a solution called RIPA. Once this occurs, the cells are centrifuged down to get rid of any cellular debris, leaving, among other things, proteins that can then be targeted. the samples are loaded into a gel which then has a current applied to it that draws the proteins down through the gel. All of the proteins end up separating out by size within this gel. From here the proteins are transferred over to an easier to handle membrane, where they are then stained for whatever protein you are looking for. This staining is done through the use of protein specific antibodies, which bind to the protein. The result of this process is a membrane that, hopefully, has a few marks where you expect to have seen the protein you stained for.

Rose’s Light Project

The role of light in inflammation can be interpreted as a natural stimulant; when one gets a wound, light has easier way to access the contents under the skin when compared to the gut, for instance. In my project, I am specifically interested in learning the response macrophages produce in response to light. Light therapy is commonly used to treat conditions involving inflammation, such as rheumatoid arthritis and depression; light has been shown to reduce the amount of proinflammatory cytokines, reducing inflammation and furthermore the symptoms associated with these conditions. The goal of this project is to eventually identify new genes that are responsible for mediating macrophages’ response to light.

What are macrophages?

In short, macrophages are immune cells that get activated to kill pathogens. Some of the common ways for macrophages to get activated are ‘communication’ with a T-cell and the presence of cytokines. Once activated, macrophages are able to recognize the pathogen that needs to be destroyed. Macrophages also produce more cytokines to mediate the inflammatory response. Cytokines act as signals for the rest of the immune system to recruit more immune cells when an invading pathogen is detected. When macrophages are activated by exposing them to light (and LPS & Poly I:C), we would expect them to release more anti-inflammatory cytokines, or less proinflammatory cytokines when compared to the dark environment, our control. This hypothesis is based on the use of light therapy to reduce the production of proinflammatory cytokines during low-grade inflammation.


Now I explain to you what the process of detecting cytokines produced by the macrophages actually looks like. This experiment specifically involved a drug called vardenafil, which I will talk more about in another section. The macrophage cells are grown on petri dishes with cell culture media (cell food). After a few days of letting the cells sit in the petri dish in an incubator (a warm place for cells to grown in), a small portion of the cell population on the petri dish is transported onto two new dishes for more space to grow. The leftover cells are placed onto 12-well plates: each well has 0.5 million cells and 1 mL of red cell culture media:

The two new petri dishes were placed in an incubator overnight to give the cells some time to acclimate to their environment. The next morning, two of the plates were treated with vardenafil (the drug I was testing for) and the plates then sat in the incubator for 30 minutes to again acclimate for the presence of the drug.

I took those two plates out, in addition to two other plates I had prepared the previous day and treated one row of wells in each plate with LPS and one row with Poly I:C (remember, these substances activate the immunological response in the cells, which causes a production of cytokines). 2 plates, vardenafil-treated and non-treated, were placed in the same incubator the cells spent the previous night, and the other 2 plates were placed in another incubator that had a LED light taped above the plates as seen in the image below.

After 6 hours of sitting in the incubators, the cell culture media (the red stuff, cell food) is carefully taken out of the wells into microcentrifuge tubes by pipetting. At this point, the live cells are stuck on the bottom of the wells, but the cytokines they produce are in the cell culture media. The tubes are centrifuged to push all the extra stuff we don’t need anymore, like dead cells, to the bottom of the tube forming a separate ‘pellet’. The liquid is then taken out of the tubes by pipetting and placed in -20 degrees celsius. ELISA is performed on the samples to determine the cytokine concentration in each sample, and the ELISA results are analyzed on Excel. The absorbance of each sample is compared to the absorbance of the standard proteins. Because we know the concentration of cytokines in the standard proteins, we can extrapolate the concentration of cytokines in each sample.

Rose’s ELISA results for illustrative purposes

TNF and IL-6 are both proinflammatory cytokines. The hypothesis of these light experiments was that with exposure to light, macrophages produce less proinflammatory cytokines. Below are selected results from this experiment. It is evident that proinflammatory cytokine production was not decreased with exposure to light, which does not support our hypothesis. Vardenafil treatment seemed to reduce the production of TNF, but it had the opposite effect on IL-6. LPS and Poly I:C both activate the immunological response; we juts wanted to see which one might be more efficient to work with in these experiments.

Vardenafil is a drug that inhibits a cascade that uses light to moderate the transmembrane Na+ channels. I experimented with this drug to learn if the phototransduction cascade of the cell can be disrupted and what that would look like in presence and absence of light. Below is an illustrative diagram of what that cascade looks like; In short, light stimulation causes PDE to break down cyclic GMP (cGMP) into GMP. Reduced concentrations of GMP cause the sodium channels to close. Vardenafil inhibits PDE, therefore inhibiting the closure of the Na+ channels.

(Neuroscience, Purves et al., 2001)

Why is this research important?

Some genes are known to show a greater prevalence in inflammatory macrophages, although their function is still unknown; knowing the specific function of these genes will help us accept the role and significance of inflammation on human health to a greater extent. I will keep working on this project during the academic year, and ultimately I want to learn how light affects macrophage gene expression that results in an inflammatory response. I have identified genes of interest from literature as well as from a large data set based on their prevalence in neutrophils and macrophages. Primers for those specific genes are waiting in the freezer to be used in our experiments.

The CRISPR method will be used to delete a specific gene from the cell line DNA, and a knockout (KO) cell line is created by targeting the macrophages with plasmids. Right now we are optimizing volumes of puromycin we can use to initiate pyroptosis, cell death, on the cells that were not transfected with the KO DNA; we only want to have cells that have the KO DNA. An inflammatory response is induced with the KO cell line, and the aspects of the response are measured by qPCR and ELISA. For instance, if a KO cell line that is missing a gene called RABGGTB presents a different inflammatory response from cells that have the gene, it can be suggested that the gene RABGGTB plays a role in inflammation. In that case, we would want to learn about the function of that gene in order to understand its exact role in inflammation. This part of the research will be conducted during the academic year.

Bryce’s Heavy Metal Project

Light is cool and all, but whats even cooler is HEAVY METAL. Well, that’s a bit of a click bait to get you interested, in reality I’m only looking at two regular old metals, nickel and aluminum. Similar to how Rose’s main experiment is seeing if light affects the macrophage immune response, my experiment is seeing if nickel or aluminum affect macrophages immune response. I think that this path of research is important to study because with there are many possible routes in which nickel and aluminum can make it into the body. Just to name a few: cooking with aluminum foil, medical equipment/implants with nickel infused in as an anti-corrosive, or mining releasing high levels of both compounds into the air and water. Because these metals are getting into the human body through the aforementioned ways, I think it is both interesting and important to see how they may affect our immune cells.

I test the cells by starting out a 12 well plate with newly added cells, and giving them a few hours to acclimate to the new plate, around 6. Then, I bask the cells in a small amount of metal, around 10uM. The cells then get over night to acclimate again, this time to the metal environment, where then the next morning they activated by either LPS, Poly I:C or both. 6 hours after that, the plates are ready to be processed. Depending on the proteins that I want to look for, I will either collect the supernatent to form an ELISA, as seen in our glorious descriptions above, or I will lyse the cells for a Western blot, again way up there, you’ll see it I can wait whilst you re-educate if you need to.

Awesome, so for the ELISA I am looking at Il-6, TNF, Il-10, and Il-1b. Unfortunately, the Il-1b ELISA test hasn’t worked all semester, and the Il-10 doesn’t differ in treated vs non treated groups. This leaves me with either Il-6 and TNF which do interesting things. In the beginning we saw super low levels of Il-6 in nickel exposed cells, with non-significance in TNF. That was dope. We figured that since TNF was the same with the non-treated cells as the metal cells, that the cells were not dying. Boy were we wrong. We started going through this rabbit hole of experiments, specifically western blots, trying to figure out how Il-6 would go down, while TNF stays the same. We found that Nickel affected a protein called IkBz, and were ecstatic. Then I had to start thinking about the poster, and in preparation for it, me and Dr. Solis were like ” I guesssss we can do a test to make sure the cells aren’t dying or whatever”. And uh yeah, turns out the cells are totally dying. Its okay though don’t get too worried, not all is lost. I didn’t waste the whole summer. Think about it, if before we thought that Il-6 was going way down and TNF was the same, then now what we can see is that Il-6 may not be going down, but something is causing the TNF to spike up, making it appear at the same levels as nice and healthy cells, even though the amount of cells are less with nickel, because they are dead, and much more stressed out, because they are dying. The revelation happened at the end of week 6 beginning of week 7, and we are still trying to come to terms.

We still have pieces to the Nickel puzzle, it is just that before we thought we were making a nice picture of a cat during a family picnic. Whereas now, we have pieces of a cat, a basket, some foods, a family, trees, and the words “What a lovely Picnic”, but we know that it is NOT a picnic. Yeah I know sucks right, but as Dr. Solis likes to say, that’s science for ya. You think you got a nice picnic going so you start doing westerns for a pathway that would potentially reduce il-6 and not affect TNF, through a protein called IkBz, then wham, even after you find out that pathway is true and nickel does indeed influence it, you also find out the cells are dying and you are left with a bunch of broken puzzle pieces that look like they should be a picnic but you know cant be. Sad I know, but that’s Science.

Anyways, enough of that sad talk, how is lab usually? Well great question, the first 6 weeks of experimenting were all ELISAs, which was a LOT of pipetting. I am not saying I like doing westerns more, but there is only like 107 instances of pipetting, versus the ELISA at like 2400 pipettes if I do a whole plate. Unfortunately I have nothing too bad to say about the western that the ELISA doesn’t also have. Proteins, check. Lots of waiting? Check. Cold room over night? Check. Nerve wracking feeling of wondering if you messed up a 3 day protocol because you cant tell if you did the assay correct until the last 5 minutes of the entire test? Check. As you can see, they are pretty much the same, though I guess the western does have gel. One thing I can say however is at the end the ELISA gives a nice quantitative answer. See this graph of il-6 for nickel induced cells, great awesome.

 

Look how pretty that is, now compare it to this western I have looking at IkBz, a protein that is one of the few ways to decrease IL-6 while keeping TNF the same.

Just two small lil pencil lines. That’s all a Western blot gives you. I mean it was great for our hypothesize that nickel decreased the amount of IkBz, but I am now on my second attempt at replication, so here is to hoping.
To to end off this blog, I want to make a list of all the things I do when I’m NOT actively Sciencing:

  • Autoclaving
  • Talking to the Craig lab
  • And the Powell Lab
  • Plus the Meiss Lab
  • And you know, Justin
  • And my Lab mate Rose
  • Also who could forget my men tor Dr. Solis

now that I typed it out, I guess I do a lot of talking to peoples…… Oh well that’s Science, thanks for stopping by

Selected pictures from the summer

“Sugar Magnolia, Blossom Blooming, Heads All Empty and I Don’t Care”

“Sugar Magnolia, Blossom Blooming, Heads All Empty and I Don’t Care”

Meet the Ferster Lab! Zach Hoffman ’23, Gabe Guzman ’24, Dr.Ferster, and Jamie Dinella ’24 (from left to right). Here we are at one of our field sites, the Sherfy Garden on the Gettysburg Battlefield.

Where have all the Good Butterflies Gone?: Introduction

Butterfly conservation is a vital but complicated endeavor. These charismatic pollinators are adapted for several ecosystems, including wide and open grassland environments with many nectar plants reliant on them. They act as flagship species, where the conservation of butterflies will benefit all pollinators that coevolved with the native fauna and are thus more vulnerable and a potential indicator of widespread pollinator declines, with cascading ecosystem effects. Unfortunately, these areas have become increasingly restricted by urbanization, improper management, changes in agricultural practices, and suburban sprawl, reducing butterflies to varying patches of habitat few and far between. This isolation is exacerbated by the usage of broad-spectrum pesticides and herbicides. Ecologically, these flowering patches act as islands, from which butterflies are locked within or around, without any suitable habitat between them, within the sea of unusable habitat, such as monoculture lawns, buildings, and farms. Understanding the dynamics between these patches is imperative for effective conservation.

Butterflies interact with their environment in two ways because they are holometabolous insects, with a complete metamorphosis. Thus, their habitat needs must be considered in two ways for conservation, focusing on ample amounts of larval host plants for caterpillars (ranging from wildflowers, grasses, trees, and vines) as well as nectar plants as adults (i.e., milkweed, thistles). Policy makers and land managers must understand the interactions these butterflies have with available plants to diagnose the direct cause of the butterfly decline. Is a lack of host plants the limiting factor? Is it the nectar plants? Is it genetic isolation from isolated patches?

A previous case study in the National Guard training center, Fort Indiantown Gap, has diagnosed one rare native butterfly’s decline as a product of a decline in available nectar plants (Swartz et al. 2015), however replicant studies must be done elsewhere to assess if this is the case elsewhere and for other species. 

Northeastern butterflies exist in a fragile space. The grasslands they live in require frequent disturbance to prevent the growth of a deciduous forest due to the high amount of rainfall we receive in the Pennsylvania area. Therefore, optimal butterfly habitat exists in the middle of secondary ecological succession, a state referred to as a sere (Latham et al. 2007). Historically, this state was kept stable by the now extinct buffalo population (or “iron bison”), trampling and rolling over larger flora, maintaining an open space of wildflowers and grasses (Ferster and Vulinec. 2009).

The Gettysburg National Military Park (GNMP) provides an excellent opportunity to study the make-up of these vulnerable habitat patches, with several long-maintained wet meadows and old successional fields (dating back to the early 1800s) at a larger size than seen elsewhere in the Gettysburg area. Creating inventories and long term surveying of plants and butterflies can answer our core research questions: How do butterflies interact with the plants around them? How can we use our information in the conservation of northeastern grassland butterflies?

(Butter) Fly Me to the Moon: About Our Field Surveys

Once a week, we conduct field surveys of butterfly and flowering plant species across six field sites in the Gettysburg regional area. We hope that through our surveys, we will better understand how butterflies use nectar resources throughout the year, and if this relationship is changing over time (phenology). In order to monitor these trends, we follow specified criteria which are dependent on the weather. These conditions include: 

  • Temperatures between 68 and 98 Fahrenheit degrees
  • Between 9AM and 2PM
  • Wind Speed less than 10mph 
  • Cloud Cover less than 50% 

These criteria are inspired by techniques from Ferster and Vulinec (2009) as well as Harker and Shreeve (2008), and altered to fit field conditions of the national park and surrounding areas.

With a modified Pollard walk technique (Pollard 1977), we follow the same paths each week and record which species of butterflies and plants we observe (GIS figure). Each member of the lab has a specialized job in order to ensure the data collection process runs smoothly. Jamie walks towards the front of the group, and scans the area for any butterfly observations. We try and take a photo of every butterfly species we see to cross reference identifications (photos). To do so, we use two websites: iNaturalist.com a citizen science database, and butterfliesandmoths.org where observations are verified by lepidopterists (butterfly experts). Zach walks alongside Jamie as a second pair of eyes to make sure that she doesn’t miss any (which can happen from time to time since some butterflies, such as low flying grass skippers, can be so small!).

Common sootywing (Pholisora catullus) on white clover (Trifolium repens) near the Painted Turtle Farm.

Gabe and Dr. Ferster are the designated botanists of the group, and are able to identify flowering plant species through their acquired knowledge, supplemented occasionally by conforming species in the lab using our “Plants of Pennsylvania Guide”. In our plant surveys, we look at flowering plants which may contribute to the nectar resource pool. We identify every flowering plant by species and record where it was found. This information helps us understand nectar resource diversity and it allows us to understand the relationship between nectar resource presence and diversity to butterfly abundance and diversity over time. Our plant data also serves as a phenological record or life cycle of the plants in Gettysburg.

We’re about to take you through an island getaway, and not necessarily an island off the coast, but biogeographical islands we have designated in order to compare biodiversity.

Our six field sites: Sherfy Garden, The Wheatfield, New Jersey Brigade, Adams County Agricultural Center, The Painted Turtle Farm, and our own curated Pollinator Garden vary in both land management as well as other site characteristics such as size and age.

All of our survey sites are uniquely different, from the management practices that go into maintaining the sites or the geography and features of each site such as presence of highways and proximity to other nectar resources. All of these factors affect the ability of butterflies to spread  as well as their survival rates, both aspects of the ecology which we are interested in understanding. We have put sites into three categories depending on how survey sites are maintained: minimally managed sites, human maintained food  gardens, and pollinator gardens. We used this information to better understand the differences and similarities of sites that are alike in terms of management and to understand how management affects biodiversity. 

In order to understand how our sites are related to each other we use Geographical Information Systems (GIS) to see how islands are related in space. This will help us understand the movement of butterflies between our resource (nectar and larval host plant) “islands” (survey sites) by allowing us to visualize the habitat patches between sites.

We encourage you to download iNaturalist on your phone so you can help us contribute to our data collection! Due to the limitations of our surveys, we may miss species sightings. We have created an iNaturalist project page that selects observations that fall inside the national park or college boundary so we can see butterfly species that citizen-scientists upload! Although we don’t factor these observations into our biodiversity calculations, we track where species sightings have occurred in order to make comparisons of the habitat where butterflies may occupy. Please view our iNaturalist page via this link!

Every Rose has its Thorns: Results

We have used  our 2021 field data to calculate butterfly diversity via three diversity metrics as well as a calculation to determine butterfly species evenness. If you’re curious how to interpret each of these indices, we have assembled an equation table for your convenience!

We hypothesize that butterfly diversity will be greater in the old maintained grasslands of Gettysburg National Military Park (GNMP) when compared with cultivated gardens. Although man-made gardens may have a higher species richness, the abundance of the nectar plants in these man-made gardens is significantly lower than in natural areas of the battlefield. For example, we found 174 stems of common milkweed at Sherfy Garden and 1,343 stems at our New Jersey Brigade field site. From an island biogeography perspective, the chance that a butterfly will find a smaller habitat island farther away from the mainland is small. The largest and the oldest of our field sites, the Wheatfield and the New Jersey Brigade, had the highest butterfly diversity in 2021 as predicted.  We are curious to determine why Sherfy Garden has the lowest diversity, given that it is older than our other garden sites, and its distance to the “mainland” sites (the Wheatfield and New Jersey brigade) is relatively small.

We did not find a significant difference in butterfly diversity among sites by category of our field sites; maintained Grassland (Battlefield Sites), Food Gardens (PTF and Sherfy garden), and Pollinator Gardens (pollinator garden and Agriculture center). We performed two distinct ANOVA tests to evaluate if site classification has an effect on butterfly species evenness (F=2.18, df=2, p=0.26) and diversity: Shannon-Wiener (F=3.87, df=2., p=0.15). We fail to reject the null hypothesis that species diversity and evenness differs among site classifications. However, the trends we see indicate still are beneficial in comparing the species composition of our “islands”.

We began surveying these fields in 2020 and found no significant difference between diversity between 2020 and 2021. We plan to conduct these same analyses at the conclusion of our 2022 field season.

Understanding the plant diversity in our sites can help characterize our surveyed areas, to begin looking for differences which may explain butterfly diversity and abundance. The data collected from our plant surveys helps us understand the proportion of native and exotic flowering plant species plant resources and the number of unique plant species per site. 

In both 2020 and 2021, the Wheatfield had the highest percentage of native plant species, yet the lowest number of unique species, followed by the New Jersey Brigade and the Pollinator Garden. These sites contrasted with the Adams County Agricultural and Natural Resource Center Garden and Sherfy Garden, which both had a low percentage of native species, but a high number of unique species.

I Heard it Through the Grapevine: Our Pollinator Garden

Using our survey data and the butterfly literature, our lab is constructing and maintaining a pollinator garden on campus, located next to the Painted Turtle Farm. We spend most mornings maintaining this plot when we aren’t conducting our field surveys. Planting began in April of 2021, when the plot looked open and empty.

Use the slider to compare the pollinator garden in June 2022 to its origin as a mowed lawn in April 2021.

We emphasize a diversity of native host and nectar plants, following pollinator garden recommendations by the Penn State Master Gardener program and the Xerxes society. This literature stresses having a high diversity of larval host and nectar plants to ensure that there is no period during the spring or summer where flowering nectar plants are not available. However, these butterfly garden recommendations don’t address resource abundance. Adopting a scientific model, our aim with this garden is to have a greater abundance of important plants than other pollinator gardens we survey for comparison. Using other gardens as a control (Adam’s County Agricultural and Natural Resource Center Garden and Sherfy Garden), we predict that having a higher abundance of important native plants, primarily milkweeds and thistles, will attract a greater abundance and diversity of butterflies.

Looking at our pollinator garden through the lens of theory of island biogeography, our “island” of butterfly habitat should accrue a higher diversity over time, thus it is early to see significant differences between monitored gardens to support our hypothesis. Despite this expected lag period, the Gettysburg Pollinator Garden has optimistically shown a slightly higher diversity than our two control gardens (Figure). Shown below are some of the species we’ve observed: 

The process of succession from the starting monocultural field has had radiating ecosystem effects, benefiting more than just pollinators. Observing plant colonization post disturbance in the garden hints at the process of succession. Invasives, such as teasel and canada thistle, have proliferated, however, native milkweeds and blue vervain have also proliferated. Ground nesting birds have settled between patches of blue vervain which may act as protection from predators, while feeding on caterpillars which thrive in such areas. Additionally, painted turtles have laid eggs within the garden due to its proximity to Quarry Pond.

Although early on in our long-term surveying, our pollinator garden has shown more than just promise. High densities of important nectar plants within our garden have attracted a higher diversity of butterflies in a shorter time than other pollinator gardens in the same area, and we predict that these numbers will increase with time. Using the same principles, we have been growing seedlings in the greenhouse to be planted in Gettysburg professors’ and faculties’ backyards, increasing butterfly habitat even more. Combatting butterfly biodiversity loss will take more than just one garden, and using the observations we have made about what works well in our garden will inform us about what constitutes good butterfly habitat, allowing the widespread planting of pollinator plants in backyards.

Thank you for reading! Enjoy this sweet video.

Works Cited

Ferster, B. & Vulinec, K.(2008). Population size and conservation of the last eastern remnants of the regal fritillary, Speyeria idalia (Drury) [Lepidoptera, Nymphalidae]; implications for temperate grassland restoration. J Insect Conserv. DOI: 10.1007/s10841-009-9222-5.

Harker, R. & Shreeve, T. (2008) How accurate are single site transect data for monitoring butterfly trends? Spatial and temporal issues identified in monitoring Lasiommata megera. J Insect Conserv.DOI: 10.1007/s10841-007-9068-7

Latham, R.E., Zercher, D., McElhenny, P., Mooreside, P., Ferster, B. (2007). The role of disturbance in habitat restoration and management for the Eastern regal fritillary (Speyeria idalia idalia) at a military installation in Pennsylvania. Ecological Restoration. 25:2. 103-111.

Pollard, E. (1977). A method for assessing changes in the abundance of butterflies. Biological Conservation. 12(2). 115-135. https://doi.org/10.1016/0006-3207(77)90065-9

Swartz, M.T, Ferster, B., Vulinec, B., Paulson, G. (2015). Measuring Regal Fritillary Butterfly (Speyeria idalia) Habitat Requirements in South-Central Pennsylvania: Implications for the Conservation of an Imperiled Butterfly. Northeastern Naturalist. 22(4). 812-829.

COVID-19 Again?! Only Data Science This Time

Information About the Author

My name is Giorgi. I am an international student coming from the country of Georgia, double majoring in Mathematical Economics and Data Science at Gettysburg College. I am passionate about capturing, maintaining, processing, analyzing, and communicating data. I find particular interest in finding the answer to the following question – How can we use existing information to make conclusions about the future?

I am also enthusiastic about reading and analyzing news regarding economy, business, and financial markets on The Wall Street Journal, finding the process of applying concepts learned from various courses of economics to real-world scenarios extremely fascinating.

Currently I am working in Dr. Johnson’s lab on a COVID-19 Data Science research project. Besides working, as a member of professor Johnson’s lab group, I engage in everyday 40-minute Hacky Sack sessions that are often characterized by a “sluggish” start and a “competitively” energetic finish. The activity helps me relax, have fun, and socialize with my peers.

Synopsis of the Research Project

Since the beginning of pandemic, copious amounts of data have been collected on the spread of the COVID-19 virus throughout the world’s population. In this data science project, different Python libraries (NumPy, SciPy, Pandas, Matplotlib…) are used to numerically analyze the publicly available demographic data. Specifically, the project uses data from sources, such as usafacts.org – the central repository for all COVID data in the US and the healthdata.gov – one of the most accessible online sources for health data in the United States.

The primary goal of this analysis is to create an interactive data visualization tool that will display temporal correlations between the rates, or peaks, of cases, hospitalizations, and deaths around different parts of the United States.

Methodology

The research is mostly centered on coding with Python programming language in the Jupyter Notebook – a web-based interactive computing platform. Together with other packages, primary Python libraries for effective data science, such as NumPy, Pandas, and Matplotlib, are used to carry out the processes of data mining, cleansing, filtration, manipulation, transformation, processing, and analysis. To create advanced data visualizations, including the generation of interactive choropleth maps, different functions from libraries like Folium, GeoPandas, Plotly, and PyDeck are also used.

Besides the pure numerical side of the project in Jupyter Notebook, the research also makes use of GeoJSON, which is an open standard geospatial data interchange format that represents geographic features and their attributes. Based on JavaScript programming language, GeoJSON serves as a flexible format for generating and encoding variety of geographic data structures. Importantly, the GeoJSON files can be interpreted by Python to provide visualizations through few lines of code.

The research takes inspiration from the DataIsBeautiful subreddit that is an open-source forum where individuals research, share, and discuss various types of data visualizations and analyses, providing detailed methodology, data, and source code through the description of their posts.  

Daily Work and Insight

Every day I use Jupyter Notebook to work with data. My tasks range from data extraction, collection, and processing to coding and generating interactive visualizations for purposes of displaying data and appropriate conclusions.

During the first part of the research, I mainly focused on cleansing and manipulation of the given structures of data for cases, hospitalizations, and deaths. Replacing NA values with zeroes and eliminating outliers caused by misreporting are two good examples of my tasks in the beginning of the research. Since data for cases and deaths were obtained from usafacts.org, the datasets were structured in a similar fashion.

The following images display the organization of data for daily cumulative cases and deaths. 

The data of hospitalizations (from healthdata.gov) was given in a weekly cumulative structure. This data file was granular and required a closer inspection as compared to the previous files of cases and deaths. In fact, in addition to including columns for hospitalizations for different age groups, the file also contained other information, such as the geocoded hospital name, hospital address, number of beds, etc. 

After the cleansing process, I performed operation of aggregation in order to convert the raw county-level data into useful state-level information. As the data for hospitalizations was characterized by granularity, it required more combination and grouping.

Data for cases, hospitalizations, and deaths were all given in a cumulative order. As an example, data for cases on specific date was the sum of cases of previous date and the new cases. To fix this, I converted the cumulative data to daily new data, meaning that each grid in a data frame would display new information related to that specific date.

In order to standardize the data from two different sources, I had to convert the daily scale of cases and deaths to the weekly scale, allowing me to start comparing the dynamics of datasets.

Following this, I calculated the cases, hospitalizations, and deaths in each state per capita by dividing the data by the population of each state.

As soon as this step was finished, Professor Johnson and I decided to make the moving average calculation variable, allowing the future users to indicate the computation of the moving average per X number of days for purposes of observing the final data from different perspectives. Therefore, I wrote a code in Python that allows the user to enter the state FIPS (unique number for each state) and the moving average computation variable by which the data is processed.

After this step, I made slight adjustments to the code so that it combined all three parameters (cases, hospitalizations and deaths) and generated a final array, containing a fully prepared data for each. By aggregating the code for all states, I observed the dates for different peaks on a national scale. Following this, I created the “range of inspection” in which dates for national peaks were serving as the midpoint of the interval. Then, I wrote a code that selects the maximum values (peaks) of cases, hospitalizations, and deaths in the set interval for each state. Following this, I began calculating the approximate time difference (Δt) between the three parameters for the first, second, and third peaks.

Finally, I created a code structure, that allows the user to enter the reference number (state FIPS) for two states and the respective moving average computation variables. After running the code, the figure is generated, comparing the plots of cases, hospitalizations, and deaths for the two states.

The image below displays the figures that compare the cases, hospitalizations, and deaths in addition to showing data frames for states of Mississippi and Texas, including approximate time differences between the parameters.

Important Note – normally, peaks happen in the following order – cases, hospitalizations, and deaths. In such cases, the time difference will have a negative sign. Otherwise, if the order is violated in any way, the sign of the ΔT will be positive, as observed when comparing the second peaks of cases and deaths in the second data frame.

“28” and “48” stand for state FIPS of Mississippi and Texas, respectively. The image displays the plots of new cases/hospitalizations/deaths per 10000/10000/200000 people and the data frames showing approximate temporal difference between the peaks of each state. Although calculated precisely, the height of the peaks and the scaling of y-axis is not essential to the research question since the project holds interest to compare the time difference between the dates of peaks represented by the x-axis.

The following image zooms in on the last (third) peak, caused by the Omicron Variant that is highly contagious but less lethal than the previous Delta Variant.

To make the comparison straightforward, the scaling of y values for each curve has been adjusted. This way the peaks are normalized around the same horizontal level.

What is Next in the Research?

The pure quantitative part of the research is finished. As a checkpoint, I have a working Python code that generates plots and arrays of cases, hospitalization, and deaths for two states that the user wants to use to compare the temporal difference between the different peaks. The remaining time of the research will be spent on creating a user-friendly interactive visualization that will take a form of a US map. To this end, I will be using GeoJSON files and various functions from libraries of Folium, GeoPandas, Plotly, and Pydeck. Besides, I will be constantly going over the code for data processing to make sure that everything is running well and producing the intended results.

Future

As the conclusion of the research, I am willing to publicize the visualization so that individuals from different fields interested in such analysis shall read, share, and discuss the existing work. I am confident that besides serving as an interactive data visualization tool, the research product will act as an instrument of observation and inquiry, raising new questions and inspiring further research in the field. I expect that the research product will definitely generate new data analytics related projects concerned with investigating how different demographic factors, such as political affiliation, socioeconomic status, vaccination rate, race, gender, affect the temporal difference between the peaks of cases, hospitalizations, and deaths throughout the different regions of the United States.

References

  1. Data for Cases, Deaths, and Population https://usafacts.org/visualizations/coronavirus-covid-19-spread-map/
  2. Data for Hospitalizations https://healthdata.gov/dataset/COVID-19-Community-Profile-Report-County-Level/di4u-7yu6/data
  3. DataIsBeautiful subreddit – https://www.reddit.com/r/dataisbeautiful/