Life of a Biologist
From the Field to the Lab
Cassandra Ziegler
Cassandra Ziegler
How good are you at identifying plants? I’m guessing most of you can ID at least one type of plant by a specific feature such as the leaves, bark, fruits, location, etc. And, even if you’re trying to learn, there’s great resources to help such as ID books and iNaturalist. Over the last 10 years I’ve gotten semi-decent at identifying a variety of plants based on these characteristics and aids from simple curiosity while hiking, classes I’ve taken, and for various research projects that required vegetation sampling to assess the layout and composition of a habitat, mostly for birds. Even with my current research there is a vegetation survey component. However, I’m encountering a new level of plant identification: seeds. Do you think you could ID a plant by just looking at the seed? And I mean identifying it on its own, no fruit to provide helpful hints. It’s quite hard unless you are an expert in the field, I have to say.
My research focuses on bird diet in northwestern Pennsylvania forests during the post-breeding/post-fledging season when birds are wrapping up the breeding season, successfully or not, and start preparing for fall migration. To be able to make such a long journey that can be very difficult physically, birds have to prepare accordingly, particularly through their diets. During the breeding season, many songbirds tend to favor insects for their diets and to feed their nestlings due to the high amounts of protein that insects provide, a great source to help growing babies and to support the adults. However, when the breeding season ends and birds need to increase their body mass for the long migratory flights, birds will also incorporate more berries into their diets to increase their fat stores on their bodies, which they use as an energy source and will burn off as they fly. Long story short, I want to see what insects and fruits two species of birds are eating during this critical time.. How do I do this? I collect their poop, short and simple. While it appears that the birds digest the insects relatively well and leave behind mostly exoskeleton in the samples, seeds stay completely intact as they pass through the digestive system so I can clearly see them. This is great to help identify the berries being eaten to support the DNA sequencing I do, but it’s only helpful if I can actually identify the seeds. Last fall, I created an interactive engagement table display to talk to people with various backgrounds about my research. One of these activities was a seed key, asking if people could identify the seed by itself before lifting a square of paper to reveal the answer. In creating this activity, I sneakily began to create my own seed ID key to use for my samples. Last summer, I collected berries from pretty much every plant I saw that produces berries and removed the seeds. Pretty cool, right? Entertaining AND helpful. Recently, I’ve been taking pictures of seeds I’ve been finding in the fecal samples under a dissecting microscope to help match them with the key I’ve created and it’s definitely been helpful! I’ve seen cherry seeds, seeds from the genus Rubus (blackberry, red raspberry, etc), and elderberry seeds. Fun fact: the birds eat cherries but they spit the pit back out. This is for 2 reasons: first, cherry pits are rather large compared to the size of a bird’s gut and it doesn’t make sense for them to swallow the pits; second, the hard pit is poisonous due to the prussic acid or cyanide it contains at the center. Don’t fret! It’s only poisonous if you bite into the center of the pit, but if you just happen to accidentally swallow a cherry pit, you’re okay because of the resiliency of the hard outer shell. The other helpful part of this key is that it also makes me aware of when I don’t have a key for a seed that I’m seeing in the fecal samples. What do I do with those seeds, you say? Well, I have a few options. I’ve taken various pictures of them, taken some measurements, and saved some of those seeds when the fecal sample had plenty of them to spare. I tried to see if iNaturalist would be able to identify them, but that was unfortunately unsuccessful (and maybe something to consider going forward for iNaturalist identification abilities). Next is to contact a local expert to see if they can assist with the identification. And lastly, germinate and grow the plants! Why not, right? If I can’t identify it from the seed then I should be able to identify it from growing the actual plant, which will be very cool to see.
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There’s two parts to research: doing that actual research and sharing the results of that research with everyone, whether that’s with an oral presentation, a poster, a publication, and more. This month, I had a few experiences sharing a part of the research I’ve been working on for the last year through both a powerpoint presentation and two poster presentations, which was a great experience! Some people feel more comfortable in the research aspect and can sometimes struggle with the public presentation portion of the package deal. Even though I still get nervous sometimes with public speaking, I truly do enjoy public presentations. Depending on the audience, it can provide the opportunity to be creative with the presentations and posters. You want to make them engaging while also informative and I’m all about the visual aspect of the presentations. I’ve also been a very visual learner so I make my presentations the same way to try to engage other visual learners or those that can understand what I’m doing with little to no background knowledge in my area of research. And lucky me, I also have forest and bird pictures that I can include to grab people’s attention as well so I try to take advantage of that when possible.
The first event was Duquesne’s annual Graduate Research Symposium that allows Duquesne grad students from all areas of research to talk about the great work they’re doing, going beyond biology and chemistry to include biomedical engineering, forensics, healthcare ethics, public history, english, performance, communication, and more. When submitting an abstract, it is with the intention of completing a poster presentation session with other graduate students. There is also an option to be considered for an oral presentation in which the presenters are selected by a peer selection committee based on the abstract submission, and I was selected! I had an 8-10 minute window to present as much of my research as I could to an interdisciplinary audience, which was really exciting. After the presentation session, I spent about 2 hours with my poster to discuss my research with anyone passing by that was interested.
Later that same week, I attended the joint meeting of the Pennsylvania Chapter of The Wildlife Society and The Pennsylvania Biological Survey in State College, PA. I co-presented the same poster with an undergraduate student in our lab, Ava, who has also been working closely on the project and contributed to the lab work. We drove there right after we finished classes on Friday to engage in a social mixer with other students and professionals attending the meeting. Then on Saturday, we spent the day immersed in a variety of presentations involving the 3rd Pennsylvania Breeding Bird Atlas that is currently underway (find more information here!: https://www.pgc.pa.gov/Wildlife/Birding/Pages/PA-Bird-Atlas.aspx), the endangered Species Act that turned 50 on December 28, 2023 and the work that has been done and is currently in progress to restore and manage habitat for imperiled species, graduate student and professional research with birds, deer, bats, turtles, and more. After all oral presentation sessions were complete, Ava and I co-presented the poster during the 5-6:30pm session with some other graduate and undergraduate students. I want to express how grateful I am for this particular meeting because while the Duquesne symposium allows for internal sharing of research, these meetings allow everyone to share their work on a wider scale with a variety of schools and organizations. This can lead to great networking opportunities, potential collaboration, but more importantly the ability to discuss the research and troubleshoot through any roadblocks with other people in the field that want to see the research succeed.
Overall, both events were great experiences that I look forward to participating in again in the future!
As a PhD student, we’re not only doing our own research and lab work but also taking classes and teaching classes. As part of the program, PhD students are sometimes paid to be a teaching assistant (TA) for undergraduate classes so that we work solely at the university. For example, 1st year PhD students are all assigned to TA for general biology I lab for mostly freshman undergraduate students in the first fall semester. From there, you might continue teaching general biology II lab, or a variety of other classes that have labs. In my time here thus far, I have TAed for general biology I lab, advanced general biology II lab (for biology majors), anatomy and physiology I & II labs, and am now TAing for what we call “superlab.” These are Capstone Lab courses designed for upper level biology majors to learn advanced laboratory techniques while working on projects. There are several different Capstone Labs that students can take and this semester, I’m TAing for the Capstone IV: Microbiology lab. Now, I don’t know if you’ve potentially noticed up to this point, but I am not a microbiologist. When I was asked by a faculty member to TA for this class, they had every confidence in me based on my skills and knowledge in molecular biology (the PhD in biology program here at Duquesne is very focused on molecular biology). However, I also provided a fair warning that I hadn’t done any microbiology techniques in quite some time…about 14 years, to be exact, when I was in a microbiology class as an undergraduate at IUP. Knowing that, there was no problem. I was told that the faculty mainly teaching the lab would provide any assistance along the way and to never be afraid to ask questions, specifically that it would be worse if I didn’t understand and didn’t ask the questions. Never be afraid to ask questions, especially in science! Anyway, I’m going into all of this because we’re now approaching our spring break and the halfway point of the semester. The main teaching instructors for this superlab will be transitioning from one to another, and so will the types of techniques and projects that the students (and myself) will be working on. I figured that this would be a good opportunity to talk about and provide some pictures from part of a project that students were working on. I’m going to give yinz the cliff note version of the background so you have an idea of what is going on, because it can get pretty crazy. First off, we were working with a non-toxic strain of Eschererichia coli, commonly abbreviated as E. coli, a type of bacteria that can be a good model system to use for certain studies. One of the experiments the student were working on was to observe a specific transposon (Tn5), a piece of DNA that can move itself from one piece of DNA to another, go from one strain of E.coli to another strain by something called conjugal transfer. In our experiment, we know that the Tn5 transposon will insert itself somewhere into the lac operon. Some of you may know about the lac operon and some may not, so here is a crash course. Basically, the lac operon has the genes that allow us to metabolize lactose. Here is an image and link to a YouTube video from a channel called the Amoeba Sisters that always do an amazing job explaining biological concepts. From the image above, you can see that the lac operon has 3 main genes: lacZ, lacY, and lacA. After the students did the conjugal transfer experiment from one strain of E.coli with Tn5 (donor) with another strain of E.coli (recipient without Tn5…yet!), the students then spread E.coli on petri dishes that had specific media (this provides the bacteria with specific nutrients and/or antibiotics to either encourage or discourage growth) and allowed colonies of the bacteria to grow for a couple of days. One of the ways to determine if the Tn5 transferred into genes of the lac operon is to look for mutants. When Tn5 inserts into the DNA, the insertion can disrupt the gene and cause a mutation. How are they able to find the mutations, you ask? We used two specific types of media for the bacteria to grow on that will turn certain lac operon mutations different colors!. Let me show you an example of a final demonstration plate a student is using for their lab report: In the picture labeled “Xgal”, the wild type (no Tn5 transposon) is light blue (upper right). If Tn5 is inserted into the lacI gene, the colonies are dark blue (upper left) and if it is inserted into the lacZ gene, the colonies are white (bottom left). Now, you might have noticed that the last area for lacY mutants is also light blue. How can you tell the lacY mutants for the wild type? Glad you asked! That’s where the other plate comes into play, labeled “Mac Lac.” This stands for MacConkey agar and lactose, serving as a pH indicator. If the bacteria do not ferment the lactose, the colonies are white and indicate that they are lacY mutants. Bacteria that ferment lactose cause a decrease in pH (more acidic) and the resulting colonies are pink/red in color. These plates can help to find those last mutants. The plates you see above are the beautiful final demonstration plates after finding the mutants in a sea of wild type (non mutant) colonies and streaking them onto new plates to truly isolate the colonies. Here is what one of the initial plates looks like: You can see that almost every one of the colonies is light blue but there are one or two spots on the left area of the plate that are white. These are lacZ mutants! How cool is that? Science is crazy! In summary, that’s only a small portion of what the class was working on for the first half of the semester and they all did a great job. Even though this is not a comfortable area of biology for me, I definitely learned a lot and have had a great time with the students along the way. Hope you learned something cool from this too! If someone asked you right now what skill you wish you could do, what would you say? Sing? Fix cars? Dance? Build something? My answer is that I wish I could draw. I like to occasionally be creative, but I wouldn’t call myself a creative or artistic type but sometimes I wish I was more creative. If someone would ask me to draw a picture in this moment, it would probably be an image of a sun in the corner with one tree, a grassy field with some simple flowers, puffy clouds, and some birds flighing by making those outlandish v-shapes to represent the wings. That’s about all I’ve got, but my default tends to be something nature-focused. That being said, I’ve decided that one of my 2024 resolutions is to learn how to draw, specifically drawing nature. Birds, trees, flowers, mushrooms, insects, you name it. I have some books already to help get me started and I’m excited to see what I can learn and create in the next year. Of all the skills, I wish I could draw and will start working on it because I love the mixing of science and art together. It brings together what could potentially be thought of as two different groups of people to produce some of the most beautiful works of art I’ve ever seen and provides another form of science communication. If you were to pick up a Sibley bird field guide, you’d notice that it’s filled with illustrations of birds with such amazing detail as to help anyone differentiate between species, between male and female, and even between juvenile and adult birds. People buy books and posters of vintage botanical and mushroom drawings to display on their coffee tables or to decorate their homes. And some drawings are even turned into permanent art and science communication through tattoos (as mentioned in a previous post!). While I’m not a skilled and practiced artist, I deeply appreciate those that are. I follow a variety of nature artists on social media, mostly through Instagram, and continue to follow more everyday. I’ve even purchased a variety of nature art on Christmas tree ornaments, art prints to hang on walls, printed as stickers. I now have a serious sticker addiction with a Barred Owl on the back of my phone case and several bird stickers on the back window of my car. It’s a slippery slope but so much fun. One of my favorite artists is Rosemary Mosco, a cartoonist and writer known for her comics that make science fun, funny, and informative across all of the kingdoms of life. You can check our her website here at Bird and Moon → https://rosemarymosco.com/comics/bird-and-moon As I’ve been following this wide community of artists over the last year, I constantly see their love for what they do.One artist I’ve purchased stickers from who attends birding festivals is a licensed wildlife rehabilitator, has a blog, and a podcast. Another artist I’ve purchased items from recently collaborated with The American Goshawk Project to create a design and is currently pursuing a degree in science illustration in California - did you know there was a degree for that?! There are many more I could list but it would go on forever! I will provide a list below of the artists I follow and I encourage you to explore Instagram artists to follow as well. I also encourage you to pursue this skill you thought of at the start of this blog. It’s never too late to start learning something new, especially if it will bring joy to your life. Support independent artists! Artist Accounts (Instagram): @rosemarymosco @kaylafiskbirds @katrina_haffner @tinyhousebigwoods @weneedtogooutside @borb.a.day @hootalexarchive @vanessafoley @the_local_naturalist @zoekellerart @muiri_ @annaquarelles https://www.redbubble.com/i/sticker/support-independent-artists-rainbow-quote-sticker-by-glowingly/43357731.EJUG5
Oof. This month has been nothing short of chaotic in so many aspects, but in a good way. Approaching the end of the year, most college students are stressed for their finals but then relieved for the break before the spring semester starts to relax and rejuvenate. For many graduate students, however, it is a month of potential productivity. We are no longer teaching classes, taking classes, having meetings, and fighting for a good parking spot amidst the normal hustle and bustle of a busy campus. This is the time to catch up on the writing or experiments that we now have about 3 weeks to work on with barely anyone on campus. One of my weeks was devoted entirely to preparing 88 samples for DNA sequencing, a long and tedious process, and another week working on grant writing. But in the midst of the serious side of science and grad work, there have also been a lot of fun activities. At Duquesne, we have a Women in STEM organization that will occasionally participate in outreach activities. This month, a group of chemistry and biology graduate and undergraduate students went to Ringgold North Elementary School to do some hands-on experiments with about 74 4th grade students. On the biology side, we had the kids do a DIY lava lamp with cleaned recycled bottles filled with water and oil. The kids add some food coloring drops to the mixture before adding in an Alka Seltzer tablet, and viola! A DIY lava lamp (which made me nostalgic for the actual lava lamp I used to have when I was a teenager). I’ll say this - if you ever need a quick, fun experiment to do with kids, this is always an absolute hit. (https://www.sciencebuddies.org/stem-activities/make-a-lava-lamp). The other activity was a strawberry DNA experiment using strawberries, water, dishwashing detergent, coffee filters, rubbing alcohol, and a toothpick or wooden skewer. The idea is that you’re extracting DNA from the strawberries but you have to break open the cells so that the DNA is released and observable when the rubbing alcohol makes the DNA strands clump together. This one took a bit more explanation and guidance but with really cool results since strawberries have a LOT of DNA (https://www.sciencebuddies.org/stem-activities/strawberry-dna-extraction). All in all, the kids loved it and we all had a great time together. Our biology department at Duquesne also holds a yearly Christmas party to celebrate the end of the semester by unwinding with some great food and activities. One of the most competitive events we have is a door decorating contest for the labs. Each door that participates has to include elements of science, creativity, and holiday spirit that will be evaluated by a group of judges to determine the winner (the winning door wins a pizza party for the lab). Last year, we were (shocker) too busy to want to participate with the door contest, but this year, even though we were arguably busier than last year, we decided we needed to have some fun and decorate the door. Our theme was The 12 Days of Christmas, entirely science themed in relation to our lab that studies fish, birds, diatoms, and more. We also have a small army of undergraduate students that do research in our lab so we had a lot of options to fill the 12 Days, with our pride and joy being Dr. Porter (our research advisor) in a Pear Tree. It just couldn’t get any better. We also made snowflakes out of centrifuge tubes. Our creativity paid off! Much to our surprise and excitement, we tied for 1st place with another lab. In the end, what I want people to take away from all of this is that being a graduate student is a lot of work and not for the faint of heart, and even though your science might be stressing you out, there are a lot of fun, creative ways to celebrate and experience science. Happy holidays and maybe do a DIY science experiment at home!
Tattoos are such an interesting topic of conversation. There are so many kinds of designs you see (and don’t see) on people. Many people get tattoos that remind them of their family, their beliefs, a significant moment in their lives, a favorite character from a movie or book, or something completely random with no significance other than they thought was really cool. I’m in the group that’s slowly accumulating nature-themed tattoos on myself. Of course, one of those includes an exceptionally large tattoo of a bird (naturally) on my right shoulder of an Eastern Whip-poor-will. Some of you may have heard of this bird, some may have heard its repetitive song that sounds exactly like its name, and some of you might have never heard of this bird. Let me introduce you! The Eastern Whip-poor-will (Antrostomus vociferus) is a nocturnal, ground-nesting bird that breeds in eastern and central North America. These birds are more often heard than seen due to the height of their activity occurring during the night. They have a tiny bill but a huge mouth that they use to catch insects, such as moths and beetles at night. An extremely interesting fact about these birds is that they rely on the moon and the lunar cycle. They use moonlight to help provide enough light for foraging through the night and they also lay their eggs in time with the lunar cycles so that the adults will be able to capture and provide plenty of food to feed the nestlings. They’ll only lay about 1-2 eggs in a nest that doesn’t even look like a nest (you can see a picture from last blog post about nests!) with dead leaves on the ground, located at the edge of a forested area for protection but also close enough to an open area that can allow moonlight through. Why such a simple nest? Their feathers are a mixture of browns and grays that allow them to camouflage with the leaves on the ground. It’s the perfect example of hidden in plain sight and working smarter and not harder, right?
Okay, so now you might be thinking that this sounds like an interesting bird, but why would I decide to get a large tattoo of it? When I was an young undergraduate, very new to field research and working on my undergraduate thesis, part of my focus was on this bird and it’s habitat. It is a near-threatened species experiencing population declines like many other birds. And like many other birds, loss of habitat is one of the problems. In 2010, I was researching if there is an overlap in habitat management styles between Golden-winged Warblers and Eastern Whip-poor-wills. While the primary focus was on the Golden-winged Warblers, our crew did some evening surveys for Eastern Whip-poor-wills to determine how many were present in the same areas and how many there were at the time. One day, when I was surveying for Golden-winged Warblers in our study area in Sproul State Forest in central PA, I flushed up one of these beautiful birds from it’s nest. Not only had I laid eyes on my first Whip-poor-will, but I had also located its nest with 2 speckled eggs. Over the next week or so, I returned to the same spot and was not only able to capture beautiful picture of this bird and how well it blended in with the ground, but I was also able to see the nestlings after they finally hatched into 2 litter orange (!!!!) fuzzballs. After that, I fell in love. Fast forward to 2013 when I had the tattoo done, and then fast forward to another year after that while working in Fort Morgan, AL during fall migration, we caught an Eastern Whip-poor-will so we HAD to take a picture of it next to my tattoo. And it is still my favorite of my (current) 4 tattoos to this day. Have you ever found a bird nest before? If so, do you know what bird species it belonged to? Do you remember the color of the egg(s)? Where the nest was? What it was made with? I didn’t start noticing bird nests until I was in my 20s. I’m sure there were plenty of nests in my backyard growing up but I was completely oblivious to them until birds became such a large part of my life in college. I was one of the lucky individuals that was being paid to watch birds and to find their nests. Didn’t know that was a job, did you? Unfortunately, it’s only a temporary job when birds are breeding in the spring and summer. In 2010, I was a biology major at the Indiana University of Pennsylvania (IUP) and was part of an undergraduate research program that gave me the opportunity to explore research being conducted by the biology department faculty and allowed me to conduct my own research for the first time. My first experience with field research was studying Golden-winged Warblers in central Pennsylvania. This meant that I was working and hiking outside Monday through Friday from about 6am-4pm searching for these particular birds and their nests. Jealous? It was hard work but it was beautiful, I was spending my days surrounded by nature, and I was able to see and learn so much. If you aren’t familiar with them, Golden-winged Warblers are secretive ground-nesting birds that can make finding their nests very difficult unless you are very patient and observant. I was beyond excited when I discovered my first nest. It was just this tiny cup, almost touching the ground (but not quite) attached to goldenrod, made with leaves and grasses, and with more grasses and ferns surrounding it to hide it. And the eggs? So small, which is to be expected from a 10 gram (0.35 oz) bird. The eggs are pale white/pinkish in color with some small brown speckles on them. A female will typically lay anywhere from 3-6 eggs at a time, but most nests I found had an average of 3-4 eggs. Little did I know that while I was looking for these particular nests that I would also find more nests from several other bird species and how different they would all be from each other. Some of the nests I found were from a Cliff Swallow, a Tree Swallow, and an Eastern Whip-poor-will. The Cliff Swallow builds its nest out of mud, creating a jug-like appearance with a hole for entering and exiting. These swallows tend to form large colonies of nests next to each other so I found dozens of these nests under a small overpass. Then, near a lake, there were several Tree Swallow nest boxes set up that are occupied by pairs of these beautiful birds. Like the Cliff Swallows, these birds are cavity nesters but lack the ability to make their own cavities to nest in so they take advantage of old woodpecker cavities and nest boxes that are placed for them. And finally, one of my favorite nests to have ever found, was the Eastern Whip-poor-will. This is because they are nocturnal birds AND they don’t truly make nests. They nest on dead leaves on the ground near shrubs or saplings for shade, using their brown coloration to blend in with their surroundings to go unnoticed. How cool is that evolutionary advantage? The only reason I even found it was because I accidentally scared the female from the nest when I got too close and spotted the 2 eggs she was incubating. Since my first field season, I’ve encountered a lot more nests but I also think I may not have noticed many of them if I hadn’t started studying birds as closely as I do. I could go on about the other nests I’ve seen but I don’t want to give away the surprise of you finding them. So, this upcoming spring I challenge you to search for at least one bird nest and to explore what species it belongs to, where you found it, and what materials were used to make it. |
AuthorBird Enthusiast and Graduate Student Archives
February 2024
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