There are many adjectives used to describe the taste of different kinds of cheese: mild, tangy, buttery, nutty, sharp, smoky, I could continue but I won’t. Our preferences between these different characteristics will then drive what cheese we look for in stores and buy. But I would wager that most people (or dare I say anyone?) are rarely looking for a bitter cheese. I had never thought about how cheese could be bitter; probably because it’s something that I’ve never tasted before and that’s because the cheese production industry actively works to prevent cheese from being bitter. Intrigued? Good, because our guest this week researches why and how cheese can become bitter.
Paige in the lab
Paige Benson is a first year Master’s student advised by Dr. David Dallas in the Food Science Department. For her research, Paige is trying to understand how starter cultures affect the bitterness in aged gouda and cheddar cheeses. The cheese-making process begins with ripening milk, during which milk sugar is converted to lactic acid. To ensure that this process isn’t random, cheese makers use starter cultures of bacteria to control the ripening process. The bitterness problems don’t appear until the very end when a cheese is in its aging stage, which can take anywhere from 0-90 days. During this aging process, casein proteins (one of the main proteins in milk and therefore cheese) are being broken down into smaller peptides and it’s during this step that bitterness can arise. Even though this bitter cheese problem has been widely reported for decades (probably centuries), there are many different hypotheses about what causes the bitterness. Some say it might be the concentration of peptides, while others believe it’s a result of the starter culture used, and a third school of thought is that it’s the specific types of peptides. Paige is trying to bring some clarity to this problem by focusing on the bitterness that might be coming from the peptides.
To accomplish this work, Paige will be making lots of mini cheeses from different starter cultures, then aging them and extracting the peptides from the cheese to investigate the peptide profiles through genome sequencing. Scaling down the size of the cheeses will allow Paige to investigate starter cultures in isolation as well as in combination with different strains to see how this may affect peptide profiles, and therefore potentially bitterness.
Some of the mini cheeses Paige makes for her research
Besides Paige’s research in cheese, we will also be discussing her background which also features lots of dairy! As a Minnesotan, Paige grew up surrounded by the best of the best dairy. In fact, her grandparents owned and ran a dairy farm, where Paige spent many of her summers and holidays. Her passion for food science was solidified when she started working as an organic farmer during her senior year of high school and she hasn’t ever looked back. Join us on Sunday, April 16th at 7 pm live on 88.7 FM or on the live stream. Missed the live show? You can listen to the recorded episode on your preferred podcast platform!
When you think of a coral reef, what do you picture? Perhaps you imagine colorful branching structures jutting out of rock and the sea floor, with flourishing communities of fish swimming about. Or if you’ve been paying attention to news about global warming for the past decade or two, maybe you picture desolate expanses of bleached corals, their bone-like structures eerily reminiscent of a mass graveyard.
What you might not picture is a zoomed-in view of the coral ecosystem: the multitude of bacteria, fungi, viruses, and algae that occupy the intricate crevices of every coral. While corals are indeed animals in their own right, they belong to a complex symbiotic relationship with these microorganisms: the algae, which are more specifically dinoflagellates, provide energy to the coral through the process of photosynthesis. Bacteria occupying the mucus layers cycle nutrients and play a role in defense against pathogen invasion through the production of antimicrobial peptides.
One lesser-known member of this community, or the coral ‘holobiont’ as it is called, are the viruses. It’s probable that, like other members of the holobiont, they contribute to the health of the coral in some way, but this role is as of yet unclear. Our guest this week is Emily Schmeltzer, a fifth year PhD student in the Vega Thurber lab in the Department of Microbiology, and these elusive viruses are exactly what she is trying to uncover.
Emily Schmeltzer, PhD candidate in Rebecca Vega-Thurber’s lab, takes a sample of a coral
“We don’t know a ton about viruses on coral reefs,” says Schmeltzer. “ We know that some probably cause disease or mortality through infections, but we don’t really know exactly what a lot of them are doing, because marine viral ecology is such a relatively new field,” she explains.
It’s not surprising: viruses, while the most abundant and diverse entity on earth, are incredibly tiny and difficult to detect in environments where other organisms also thrive. Part of the challenge is that they have no universally conserved genes: that is, no easy way to tell the genes from viruses apart from the genes of other organisms. When studying bacteria, a gene called the 16S rRNA gene can be used as a sort of ‘name tag’ – every bacteria has this gene, whereas other organisms do not. There’s no such thing for viruses, making them difficult to study if you don’t already know what you’re looking for.
Schmeltzer is studying the viruses that live on corals and their response to climate change. To do this, her PhD research has involved a massive spatiotemporal study (spatio = across different locations, temporal = across multiple time points) looking at nearly 400 individual coral colonies of three different species over 3 years. All of these colonies are off the coast of the Moorea, a small island in French Polynesia in the South Pacific. The ultimate goal of the project is to contribute to the ongoing data collection for the Moorea Coral Reef Long Term Ecological Research project, and to characterize virus community diversity and potential function in the health of these corals.
Studying coral reefs is a big leap for Schmeltzer, who hails from the land-locked deserts of New Mexico. She was always interested in biology, which she attributes to her dad bringing home dead scorpions to look at together when she was a child. Arthropods ultimately ended up becoming her first research subjects: as an undergraduate at the University of New Mexico, she worked in an insect and spider taxonomy lab, before pivoting to working on West Nile virus.
So how did this insect-loving desert-dweller end up studying viruses that live on corals in the ocean? To learn more about Schmeltzer’s career trajectory, her love of corals, and the challenges of viral research, tune in to Inspiration Dissemination this Sunday, April 2nd at 7 PM. Listen live at 88.7 FM or on the live stream, or catch the episode after the show wherever you get your podcasts!
Rue Dickey (they/he) is a returning guest to ID this week. You may remember Rue from last year as the organizer who helped raise over $400,000 for two trans rights organizations in Texas via Tabletop Role Playing Games (TTRPGs). Well, they’re back at it this year and we’re here to tell you all about it!
In February, 2022 Texas governor Greg Abbott called for teachers and members of the public to report parents of transgender children to authorities, equating providing support and medical care for trans youth to child abuse. This combined with a climate of increasing anti-trans legislation across the US, led Rue to take action. Rue is an Oregon State University alumnus and a freelance game developer, designing games for Hitpoint Press, Cobalt Press, and publishing independent work on game hosting platforms such as itch.io. Wanting to do something to help children and transgender people living in Texas, Rue decided to turn his passion for TTRPGs into a fundraiser. The online indie game hosting platform itch.io has been used in the past to create fundraisers for charities by bundling together and selling games. A few of Rue’s friends who run a BIPOC tabletop server have had experience with creating profit-sharing bundles using the platform in the past, so after he consulted them and walked through the steps, he set up a bundraiser. By the time of our interview with Rue in April, 2022 they had raised over $400,000 for TENT (Transgender Education Network of Texas, a trans-led group that works to combat misinformation on the community level through the corporate level, offering workshops as well as emergency relief funds for trans folks in need) and OLTT (Organización Latina Trans in Texas, a Latina trans woman-led organization focusing on transgender immigrants in Texas, assisting with the legal processes of immigration, name changes, and paperwork.) In addition to this they had been interviewed by several national news outlets, including NBC, Gizmodo, and The Mary Sue, as well as gaming-centric websites like Polygon, Dicebreaker, and GamesHub.
Rue is a 2019 graduate of OSU’s Communications and Microbiology programs.
This year Rue is continuing the fundraiser, but focusing on Florida which has garnered national attention for anti-trans legislation such as the Parental Rights in Education Act, which restricts schools from including LGBTQ+ topics in curricula. The proposed expanded provisions to the act would ban teachers from addressing students by pronouns that differ from those they were assigned at birth, and staff would also be unable to share their own preferred pronouns if they deviate from those assigned at birth. Additionally, the Florida Board of Medicine enacted a rule that bars minors from starting puberty blockers or hormone therapy, essentially banning transition for those under the age of 18.
The organizations benefiting from the bundraiser this year are Zebra Youth Coalition (a network serving youth ages 13-24, that run shelters for youth that need safety and resources) and Transinclusive Group (a trans women of color-led coalition aimed at offering peer support, access to resources like HRT, and educating care providers in how to better take care of trans youth.) The current bundle launched on March 13th and has 505 game supplements and zines, the base price of which is $5 but the top donation is $1000. The fundraising goal for this year’s bundle is $250k, but in the couple of weeks since launching there’s already been $208k raised.
The bundle is live through April 6th, so there is still time to help reach their fundraising goal! To learn more about the fundraiser, tune into Rue’s episode this upcoming Sunday, March 26th at 7 PM! Be sure to listen live on KBVR 88.7FM, or download the podcast if you missed it.
During winter months, a few days after the full moon, thousands of fish make their way to the warm tropical waters off the west coast of Little Cayman, Cayman Island. Nassau Grouper are typically territorial and don’t interact often, but once per year, they gather in the same spot where they all spawn to carry on the tradition of releasing gametes, in the hopes that some of them will develop to adulthood and carry on the population.
Our guest this week is Janelle Layton, a Masters (and soon to be PhD) student in Dr. Scott Heppel’s lab in the Department of Fisheries, Wildlife, and Conservation Sciences. Janelle’s research focuses on this grouper, which is listed as near threatened under the Endangered Species Act. Overfishing has been the largest threat to Nassau Grouper populations, but another threat looms: warming waters due to climate change. This threat is what Janelle is interested in studying – how does the warming water temperature affect the growth and development of grouper larvae?
Janelle with a curious sea turtle
Each winter Janelle travels to this aggregation site in the Cayman Islands, where these large groups of grouper (grouper groups?) aggregate for a few days to reproduce. During this time, she collects thousands of fertilized Nassau Grouper eggs to take back to the lab and study. These eggs will develop in varying water temperatures for 6 days, where each day a subset of samples are preserved for future analysis.
Spawning groupers
So far, Janelle is finding that the larvae raised in higher temperatures tend to demonstrate not only an increase in mortality, but an increase in variability in mortality. What does this mean? Basically, eggs from some females are able to survive and develop under these stressful conditions better than eggs from other females – so is there a genetic component to being able to survive these temperature increases?
The answer may lie in proteins
Aside from development and mortality, Janelle is investigating this theory by measuring the expression of heat shock proteins in the fertilized eggs and larvae. Heat shock proteins are expressed in response to environmental stressors such as increased temperatures, and can be measured through RNA sequencing. The expression of these proteins might hold the key to understanding why some grouper are more likely to survive than others. Janelle’s work is a collaborative effort between Oregon State University, Scripps Institute of Oceanography, Reef Environmental Education Foundation and the Cayman Islands Department of Environment.
To learn more about Nassau Grouper, heat shock proteins, and what it’s like being a Black woman in marine science, tune into Janelle’s episode this upcoming Sunday, March 12th at 7 PM! Be sure to listen live on KBVR 88.7FM, or download the podcast if you missed it. You can also catch Janelle on TikTok or at her website.
This week we have a Fisheries and Wildlife Master’s student and ODFW employee, Gabriella Brill, joining us to discuss her research investigating the impact of dams on the movement and reproduction habits of the White Sturgeon here in Oregon. Much like humans, these fish can live up to 100 years and can take 25 years to fully mature. But the similarities stop there, as they can also grow up to 10 ft long, haven’t evolved much in 200 million years, and can lay millions of eggs at a time (makes the Duggar family’s 19 Kids and Counting not seem so bad).
Despite being able to lay millions of eggs at a time, the White Sturgeon will only do so if the conditions are right. This fish Goldilocks’ its way through the river systems, looking for a river bed that’s just right. If it doesn’t like what it sees, the fish can just choose not to lay the eggs and will wait for another year. When the fish don’t find places they want to lay their eggs, it can cause drastic changes to the overall population size. This can be a problem for people whose lives are intertwined with these fish: such as fishermen and local Tribal Nations (and graduate students).
The white sturgeon was once a prolific fish in the Columbia River and holds ceremonial significance to local Tribal Nations, however, post-colonialization a fishery was established in 1888 that collapsed the population just four years later in 1892. Due to the long lifespan of these fish, the effects of that fishery are something today’s populations have still not fully recovered from.
White Sturgeon
Can you hear me now
Gabriella uses sound transmitters to track the white sturgeon’s movements. Essentially, the fish get a small sound-emitting implant that is picked up by a series of receivers – as long the receivers don’t get washed away by a strong current. By monitoring the fish’s journey through the river systems, she can then determine if the man-made dams are impacting their ability to find a desirable place to lay eggs.
Journey to researching a sturgeon’s journey
Gabriella always gravitated towards ecology due to the ways it blends many different sciences and ideas – and Fish are a great system for studying ecology. She started with studying Salmon in undergrad which eventually led to a position with the ODFW. Working with the ODFW inspired her to get a Master’s degree so that she could gain the necessary experience and credentials to be a more effective advocate for changes in conservation efforts that are being made. One way to get clout in the fish world: study a highly picky fish with a long life cycle. Challenge accepted.
Gabriella Brill holding a smaller sturgeon while on a boat.
To hear more about these finicky fish be sure to listen live on Sunday February 26th at 7PM on 88.7FM, or download the podcast.
This week we have a robotics PhD student, Everardo Gonzalez, joining us to discuss his research on coordinating robots with artificial intelligence (AI). That doesn’t mean he dresses them up in matching bow ties (sadly), but instead he works on how to get a large collective of robots, also called a swarm, to work collectively towards a shared goal.
Why should we care about swarming robots?
Aside from the potential for an apocalyptic robot world domination, there are actually many applications for this technology. Some are just as terrifying. It could be applied to fully automated warfare – reducing accountability when no one is to blame for pulling the trigger (literally).
However, it could also be used to coordinate robots used in healthcare and with organizing fleets of autonomous vehicles, potentially making our lives, and our streets, safer. In the case of the fish-inspired Blue Bots, this kind of coordinated robot system can also help us gather information about our oceans as we try to resolve climate change.
Depiction of how the fish-inspired Blue Bots can observe their surroundings in a shared aquatic space, then send that information and receive feedback from the computer system. Driving the Blue Bots’ behavior is a network model, as depicted in the Agent A square.
#Influencer
Having a group of intelligent robots behaving intelligently sounds like it’s a problem of quantity, however, it’s not that simple. These bots can also suffer from there being “too many cooks in the kitchen”, and, if all bots in the swarm are intelligent, they can start to hinder each other’s progress. Instead, the swarm needs both a few leader bots, that are intelligent and capable of learning and trying new things, along with follower bots, which can learn from their leader. Essentially, the bots play a game of “Follow the Leaders”.
All robots receive feedback with respect to a shared objective, which is typical of AI training and allow the bots to infer which behaviors are effective. In this case, the leaders will get additional feedback on how well they are influencing their followers.
Unlike social media, one influencer with too many followers is a bad thing – and the bots can become ineffective. There’s a famous social experiment in which actors in a busy New York City street stopped to stare at a window to determine if strangers would do the same. If there are not enough actors staring at the window, strangers are unlikely to respond. But as the number of actors increases, the likeness of a stranger stopping to look will also increase. The bot swarms also have an optimal number of leaders required to have the largest influence on their followers. Perhaps we’re much more like robots than the Turing test would have us believe.
Dot to dot
We’re a long way from intelligent robot swarms, though, as Everardo is using simplified 2D particle simulations to begin to tackle this problem. In this case the particles replace the robots, and are essentially just dots (rodots?) in a shared environment that only has two dimensions. The objectives or points of interest for these dot bots are more dots! Despite these simplifications, translating system feedback into a performance review for the leaders is still a challenging problem to solve computationally. Everardo starts by asking the question “what if the leader had not been there”, but then you have to ask “what if the followers that followed that leader did something else?” and then you’ve opened a can of worms reminiscent of Smash Mouth where the “what if”’s start coming and they don’t stop coming.
Everardo Gonzalez
What if you wanted to know more about swarming robots? Be sure to listen live on Sunday February 26th at 7PM on 88.7FM, or download the podcast if you missed it. To learn a bit more about Everardo’s work with swarms and all things robotics, check out his portfolio at everardog.github.io.
This week we have a MS (but soon to be PhD) student from the department of Fisheries and Wildlife, Charles Nye, joining us to discuss their work examining the dietary and environmental DNA of whales. So that begs the question – how exactly does an environment, or a diet, have DNA? Essentially, the DNA of many organisms can be isolated from samples of ocean water near the whales, or in the case of dietary DNA, can be taken from the whales’ fecal matter – that’s right, there’s a lot more you can get from poop than just an unpleasant smell.
Why should we care about what whales eat?
As the climate changes, so too does the composition of creatures and plants in the oceans. Examining environmental DNA gives Charles information on the nearby ecological community – which in turn gives information about what is available for the whale to eat plus what other creatures they may be in resource competition with. He is working to identify the various environmental DNA present to assist with conservation efforts for the right whale near Cape Cod – a whale that they hold as dear to their hearts on the East Coast as the folks of Depoe Bay hold the grey whale to theirs.
By digging into the whale poop to extract dietary DNA, Charles can look into how the whales’ diets shift over seasonal and yearly intervals – and he is doing precisely that with the West Coast grey whales. These dietary shifts may be important for conservation purposes, and may also be applied to studying behavior. For example, by looking at whether or not there are sex differences in diet and asking the ever-important question: do whales also experience bizarre pregnancy cravings?
Scuba diving underwater.
How does someone even get to study whales?
Like many careers, it starts with an identity crisis. Charles originally thought they’d go into scientific illustration, but quickly realized that they didn’t want to turn a hobby he enjoyed into a job with deadlines and dread. A fortunate conversation with his ecology professor during undergrad inspired him to join a research lab studying intertidal species’ genetics – and eventually become a technician at the Monterey Bay Aquarium Research Institute.
After a while, simply doing the experiments was not enough and they wanted to be able to ask his own questions like “does all the algae found in a gray whale’s stomach indicate they may actually be omnivores, unlike their carnivorous whale peers?” (mmm, shrimp).
Turns out, in order to study whales all you have to do is start small – tiny turban snail small.
Working in the lab.
Excited for more whale tales? Us too. Be sure to listen live on Sunday, February 5th at 7PM on 88.7FM, or download the podcast if you missed it. Want to stay up to date with the world of whales and art? Follow Charles @thepaintpaddock on Twitter/Instagram for his art or @cnyescienceguy on Twitter for his marine biology musings.
You probably already know that skim milk and buttermilk are byproducts of cheese-making. But did you know that whey is another major byproduct of the cheese-making process? Maybe you did. Well, did you know that for each 1 kg of cheese obtained, there are about 9 kg of whey produced as a byproduct?! What in the world is done with all of that whey? And what even is whey? In this week’s episode, Food Science Master’s student Alyssa Thibodeau tells us all about it!
Alyssa making cheese!
Whey is the liquid that remains after milk has been curdled and strained to produce cheese (both soft and hard cheeses) and yoghurt. Whey is mainly water but it also has lots of proteins and fats, as well as some vitamins, minerals, and a little bit of lactose. There are two types of whey: acid-whey (byproduct of yoghurt and soft cheese production) and sweet-whey (byproduct of hard cheese production). Most people are probably familiar with whey protein, which is isolated from whey. The whey protein isolates are only a small component of the liquid though and unfortunately the process of isolating the proteins is very energy inefficient. So, it is not the most efficient or effective way of using the huge quantities of whey produced. This is where Alyssa comes in. Alyssa’s research at OSU is focused on trying to develop a whey-beverage. Because of the small amounts of lactose that are in whey, yeast can be used to ferment the lactose, creating ethanol. This ethanol can then be converted by bacteria to acetic acid. Does this process sound a little familiar? It is! A similar process is involved when making kombucha and the end-product in Alyssa’s mind isn’t too far off of kombucha. She envisions creating an organic, acid-based or vinegar-type beverage from whey.
Morphology of yeast species Brettanomyces anomalus which Alyssa is planning on using for her whey-beverage.
How does one get into creating the potentially next-level kombucha? Alyssa’s route to graduate school has been backwards, one that most students don’t get to experience. While the majority of students get a degree, get a job and then start a family, Alyssa started a family, got a job, and then went to graduate school. On top of being a single mother in graduate school, she is also a first-gen student and Hispanic. To quote Alyssa: “It makes me proud every day that I am able to go back to school as a single mom. In the past, this would have maybe been too hard to do or wouldn’t have been possible for older generations but our generations are progressing and people are making decisions for themselves.”.
Intrigued by Alyssa’s research and personal journey? You can hear all about it on Sunday, January 29th at 7 pm on https://kbvrfm.orangemedianetwork.com/. Missed the live show? You can listen to the recorded episode on your preferred podcast platform!
Correlation does not equal causation. This phrase gets mentioned a lot in science. In part, because many scientists can fall into the trap of assuming that correlation equals causation. Proof that this phrase is true can be found in ice cream and sharks. Monthly ice cream sales and shark attacks are highly correlated in the United States each year. Does that mean eating lots of ice cream causes sharks to attack more people? No. The likely reason for this correlation is that more people eat ice cream and get in the ocean during the summer months when it’s warmer outside, which explain why the two are correlated. But, one does not cause the other. Correlation does not equal causation.
To date, much of the research that has been conducted on LGBTQ+ health has been correlational. Our guest this week, Kalina Fahey, hopes that her dissertation project will play a part in changing this paradigm as she is trying to get more at causation. Kalina is a 5th year PhD candidate in the School of Psychological Science working with her advisors Drs. Anita Cservenka and Sarah Dermody. Her research broadly investigates LGBTQ+ health disparities and how stress impacts health in LGBTQ+ groups. She is also interested in understanding ways in which spiritual and/or religious identities can influence stress, and thereby, health. To do this, Kalina is employing a number of methods, including undertaking a systematic review to synthesize the existing research on substance use in transgender youth, analyzing large-scale publicly available datasets to look at how religious and spiritual identity relates to health outcomes, and finally developing a safe experiment to look at how specific forms of stress impact substance use-related behaviors in real time.
Most of Kalina’s time at the moment is being spent on the experimental portion of her research as part of her dissertation. For this study, Kalina is adapting the personalized guided induction stress paradigm, with the aim of safely eliciting minor stress responses in a laboratory setting. The experiment involves one virtual study visit and two in-person sessions. During the first visit, participants are asked to describe a minority-induced stressful event that occurred recently, as well as a description of a moment or situation that is soothing or calming. After this session, Kalina and her team develop two meditative scripts – one each to recreate the two events or moments described by the participant. When the participant comes back for their in-person sessions, they listen to one of two different meditative scripts and are asked a series of questions regarding their stress levels. Kalina and her team also are collecting saliva and heart rate readings to look at physiological stress levels. This project is still looking for participants. If you are a sexual-minority woman who drinks alcohol, consider checking out the following website to learn more about the study: https://oregonstate.qualtrics.com/jfe/form/SV_8e443Lq10lgyX66?fbclid=IwAR3XOdECIOvCbx1xn3QA5rrCtHfSezZrR5Ppkpnd9sx1SsicZRQnfYHAqb8. Kalina hopes to continue experiment-based research on LGBTQ+ health disparities in the future as she sees the lack of experimental studies to be a major gap in better understanding, and thereby supporting, the LGBTQ+ community.
Interested in learning more about Kalina’s research, the results, and her background? Listen live on Sunday, January 15, 2023 at 7 PM on 88.7 KBVR FM. Missed the live show? You can download the episode on our Podcast Pages! Also, check out her other work here or finder her on Twitter @faheypsych
Puffy snout syndrome: though it has a cute-sounding name, this debilitating condition causes masses on the face of Scombridae fish (a group of fish that includes mackerel and tuna.) Fish afflicted with puffy snout syndrome (PSS) develop excessive collagenous tumor-like growths around the eyes, snout, and mouth. This ultimately leads to visual impairment, difficulty feeding, and eventual death. PSS is surprisingly confined to just fish raised in captivity – those in aquaculture farms or aquariums, for example. Unfortunately, when PSS is identified in aquaculture, the only option is to cull the entire tank — no treatments or cures currently exist.
Left: a mackerel with puffy snout syndrome. Collagenous growths cover the snout and eye. Right: a healthy mackerel. Photos Emily Miller
PSS was first identified in the 1950s, in a fish research center in Honolulu, Hawaii. Since then, there have only been 9 publications in the scientific literature documenting the condition and possible causes, although the fish community has come to the conclusion that PSS is likely a transmittable condition with an infectious agent as the cause. But despite this conclusion, there’s been no success so far in identifying such a cause – tests for parasites, bacterial growth, and viruses have come up empty-handed. That was until a 2021 paper, using high-resolution electron microscopy, found evidence of viral particles in facial tissues taken from Pacific mackerel. Suddenly, there was a lead: could PSS be caused by a virus that we just don’t have a test for yet?
Electron microscopy images showing viral-like particles (red arrows) in facial tissue from Pacific mackerel (Miller et al 2022).
Putting Together the Pieces
To investigate this hypothesis, this week’s guest Savanah Leidholt (a co-author of the 2021 microscopy study) is using an approach for viral detection known as metatranscriptomics. Leidholt, a fourth year PhD candidate in the Microbiology department, sees this complex approach as a sort of puzzle: “Your sample of RNA has, say, 10 giant jigsaw puzzles in it. But the individual puzzles might not be complete, and the pieces might fit into multiple places, so your job is to reassemble the pieces into the puzzles in a way that gives you a better picture of your story.”
Savanah Leidholt, PhD candidate in Rebecca Vega-Thurber’s lab, is looking for evidence of viruses in the tissues of fish with puffy snout syndrome.
RNA, or ribonucleic acid, is a nucleic acid similar to DNA found in all living organisms, But where DNA is like a blueprint – providing the code that makes you, you; RNA is more like the assembly manual. When a gene is expressed (meaning the corresponding protein is manufactured), the double-stranded DNA is unwound and the information is transcribed into a molecule called messenger RNA. This single-stranded mRNA is now a copy of the gene that can be translated into protein. The process of writing an mRNA copy of the DNA blueprint is called transcription, and these mRNA molecules are the target of this metatranscriptomics approach, with the prefix “meta” meaning all of the RNA in a sample (both the fish RNA and the potential viral RNA, in this case) and the suffix “omics” just referring to the fact that this approach happens on a large scale (ALL of the RNA, not just a single gene, is sequenced here!) When mRNA is sequenced in this manner, the researchers can then conclude that the gene it corresponds to was being expressed in the fish at the time the sample was collected.
The process of transcription: making messenger RNA from DNA. Image from Nature Education.
So far, Leidholt has identified some specific genes in fish that tend to be much more abundant in fish from captive settings versus those found in the wild. Could these genes be related to why PSS is only seen in fish in captivity? It’s likely – the genes identified are immune markers, and the upregulation of immune markers is well-known to be associated with chronic stress. Think about a college student during finals week – stress is high after a long semester, maybe they’ve been studying until late in the night and not eating or sleeping well, consuming more alcohol than is recommended. And then suddenly, on the day of the test, they’re stuck in bed with the flu or a cold. The same thing can happen to fish (well, maybe not the part where they take a test!,) especially in captivity – Pacific mackerel, tuna, and other scombrid species susceptible to PSS are fairly large, sometimes swimming hundreds of miles in a single day in the ocean. But in captivity, they are often in very small tanks, constantly swimming in constrained circles. They’re not exposed to the same diversity of other fish, plankton, prey, and landscape as they would be in the wild. “Captivity is a great place to be if you’re a pathogen, but not great if you’re a fish”, says Leidholt.
The results of Leidholt’s study are an exciting step forward in the field of PSS research, as one of the biggest challenges currently facing aquaculture farms and aquariums is that there is no way to screen for PSS in healthy fish before symptoms begin to show. Finding these marker genes that appear in fish that could later on develop PSS means that in the future a test could be developed. If vulnerable fish could be identified and removed from the population before they begin to show symptoms and spread the condition, then it would mean fish farmers no longer have to cull the entire tank when PSS is noticed.
The elusive virus
One of the challenges that remains is going beyond the identification of genes in the fish and beginning to identify viruses in the samples. Viruses, which are small entities made up of a DNA or RNA core and a protective protein coating, are thought to be the most abundant biological entities on the planet Earth – and the smallest in terms of size. They usually get a bit of a bad reputation due to their association with diseases in humans and other animals, but there are also viruses that play important positive roles in their ecosystems – bacteriophages, for example, are viruses that infect bacteria. In humans, bacteriophages can attack and invade pathogenic or antibiotic-resistance bacteria like E. coli or S. aureus (for more information on phages and how they are actually studied as a potential therapy for infections, check out this November 2021 interview with Miriam Lipton!) Across the entire planet there are estimated to be between 10^7 to 10^9 distinct viral species – that’s between 10 million and 10 billion different species. And fish are thought to host more viruses than any other vertebrate species. Because of technological advancements, these viral species have only really been identified very recently, and identification still poses a significant challenge.
As a group, viruses are very diverse, so one of the challenges is finding a reliable way to identify them in a given sample. For bacteria, researchers can use a marker gene called the 16S rRNA gene – this gene is found in every single bacterial cell, making it universal, but it also has a region of variability. This region of variability allows for identification of different strains of bacteria. “Nothing like 16S exists for viruses,” Leidholt says. “Intense sequencing methods have to be used to capture them in a given sample.” The metatranscriptomic methods that Leidholt is using should allow her to capture elusive viruses by taking a scorched earth approach – targeting and sequencing any little bit of RNA in the sample at all, and trying to match up that RNA to a virus.
To learn more about Savanah’s research on puffy snout syndrome, her journey to Oregon State, and the amazing outreach she’s doing with high school students in the Microbiology Department, tune in to Inspiration Dissemination on Sunday, November 20th at 7 PM Pacific!
