Tag Archives: fisheries

The Puzzle of Puffy Snout

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!

Global ocean modeling, with a microscope on Micronesia

How could an equation developed by a German mathematician in 1909 help Micronesian conservation networks plan for the future in the face of climate change? 

In this week’s episode, we interview Dr. Steven Johnson, a graduate of Oregon State University’s Geography graduate program. Steven completed his doctorate earlier in 2021, under the guidance of Dr. James Watson, a professor in the College of Earth, Ocean, and Atmospheric Sciences. He’s now a postdoctoral fellow at Arizona State University. During his time at Oregon State, the focus of his work was oceans. “I study the ocean – in particular, people’s relationship with the ocean. The condition of the ocean has implications for people all over the world and millions depend on it for their livelihood,” he explains.

Steven Johnson, a recent graduate of OSU and now a postdoctoral fellow at Arizona State University

“There used to be this idea that the ocean was ‘too big to fail’, but Oregon State University Distinguished Professor and White House Deputy Director for Climate and the Environment Jane Lubchenco made the point that ‘the ocean is too big to fail, but too big to ignore,’” Steven recounts. “Not a single part of the ocean has not been impacted by people.” Plastic waste, rising temperatures, increasing acidification, and other byproducts of human activity have been changing the ocean as we know it, and it will continue to worsen if the problem can’t be solved. One challenge that arises as a result of these changes is the future of aquatic resource management and conservation programs, which are designed to work in current ocean and climate conditions.

So how does Steven’s research tackle these problems? In the first chapter of his thesis, he developed a novel model for predicting the way the ocean will change due to climate change. This approach is titled the Ocean Novelty Index, or the ONo Index. The Ocean Novelty Index quantifies the relative impact of climate change across all parts of the ocean, using a statistical metric applied to six different ocean surface variables (chlorophyll, O2, pH, sea surface temperature, silica, and zooplankton.) The metric is derived from the Hellinger distance, developed by a German mathematician in 1909, which is a nonparametric analysis that measures the similarity and dissimilarity between two distributions and their overlap. The baseline, or ‘normal’, conditions are derived from the period between 1970-2014, a 50 year period which recognizes 1970 as the birth of the modern Western climate movement. The model can then be used to assess and predict what climate change will do to one part of the ocean, and compare it to how that part of the ocean looked previously. The model better encapsulates the dynamic and unpredictable changes of the ocean resulting from climate change, as opposed to just rising temperatures. 

In addition to the development of this climate change index, Steven’s research also focused on conservation networks and initiatives across Micronesia, the Caribbean, and Southeast Asia. These networks and cooperatives are collaborative efforts between regional governments to meet certain conservation goals, taking into account the differing social, cultural, and economic needs of the different countries involved. Part of Steven’s work has focused on applying the ONo index on a local scale, to help determine what changes may occur in the regions as well as where. What will the regions of these networks look like at different points as the climate changes, and how can we create strong policies and political relationships in these cooperatives and their respective countries to ameliorate potential issues in the future? Steven discusses these topics and more with us on this week’s ID podcast.

If you are interested in learning more about the ONo index and Steven’s work, you can read his paper here.

This post was written by Grace Deitzler

Characterizing off-channel habitats in the Willamette River: Fish need to cool off too!

During the summer, when the mercury clears triple digits on the Fahrenheit scale, people seek out cooler spaces. Shaded parks, air conditioned ice cream parlors, and community pools are often top places to beat the heat. If you’re a resident of Corvallis, Oregon, you may head downtown to dip your toes in the Willamette River. Yet while the river offers a break from the hot temperatures for us, it is much too warm for the cold water fishes that call it home.

Where do fish go to cool off?

As a master’s student in the Water Resources Graduate Program at Oregon State University, Carolyn Gombert is working to understand where cold water habitat is located along the Willamette River. More importantly, she is seeking to understand the riverine and geomorphic processes responsible for creating the fishes’ version of our air conditioned ice cream parlors. By placing waterproof temperature loggers along sites in the upper Willamette, she hopes to shed light both on the temporal and spatial distribution of cold water patches, as well as the creation mechanisms behind such habitats.


The cart before the horse: seeking to reconcile science and policy

Because the Willamette Basin is home to Cutthroat trout and Chinook salmon, the river is subject to the temperature standard adopted by the state of Oregon in 2003. Between May through October, Cutthroat and Chinook require water cooler than 18 degrees Celsius (64.4 degrees Fahrenheit). Currently, the main channel of the Willamette regularly exceeds this threshold. The coolest water during this time is found in side channels or alcoves off the main stem. While Oregon law recognizes the benefits these “cold water refuges” can provide, our scientific understanding of how these features change over time is still in its early stages.

Emerging stories

Data collection for Carolyn’s project is slated to wrap up during September of 2017. However, preliminary results from temperature monitoring efforts suggest the subsurface flow of river water through gravel and sediment plays a critical role in determining water temperature. By pairing results from summer field work with historical data such as air photos and laser-based mapping techniques (LiDAR) like in the image below, it will be possible to link geomorphic change on the Willamette to its current temperature distributions.

Between 1994 and 2000, the Willamette River near Harrisburg, Oregon shifted from a path along the left bank to one along the right bank. This avulsion would have happened during a high flow event, likely the 1996 flood.

No stranger to narratives

Prior to beginning her work in hydrology at OSU, Carolyn earned a bachelor’s in English and taught reading at the middle school level. Her undergraduate work in creative writing neither taught her how to convert temperature units from Fahrenheit to Celsius nor how to maneuver in a canoe. But the time she spent crafting stories did show her that characters are not to be forced into a plot, much like data is not to be forced into a pre-meditated conclusion. Being fortunate enough to work with Stephen Lancaster as a primary advisor, Carolyn looks forward to exploring the subtleties that surface from the summer’s data.

If you’d like to hear more about the results from Carolyn’s work, she will be at the OSU Hydrophiles’ Pacific Northwest Water Research Symposium, April 23-24, 2018. Feel free to check out past Symposiums here. Additionally, to hear more about Carolyn’s journey through graduate school, you can listen to her interview on the Happie Heads podcast.

Carolyn conducting field work on the Willamette.

Carolyn Gombert wrote the bulk of this post, with a few edits contributed by ID hosts.

Learn the past. Speak the present. Guide the future.

Lake Victoria, sitting just below the equator in eastern Africa, shared between the countries of Kenya, Uganda, and Tanzania is the second largest freshwater lake in the world. To put that into

Early 20th century map of Lake Victoria

Colonial territories surrounding Lake Victoria in the early 20th Century

perspective, at 68,800 square kilometers, Lake Victoria is larger than the country of Switzerland (41,285 sq. km.). Beyond its immense size and grandeur, it is also one of the most important sites on earth for our current understanding of evolution because of one rapidly-diversifying group of fishes: the cichlids, which include both tilapia, an important food source, and aquarium fish such as angelfish.


The cichlids in Lake Victoria are especially interesting because that body of water dried out and refilled less than 15,000 years ago. This may seem like a long time, but on a geologic and evolutionary timescale, that’s less than the blink of an eye. Consider that before 1980, itwas estimated that there were over 500 species of cichlids in Lake Victoria. To contrast that with our own timeframe, the speciation time from our last common ancestor with chimps was on the order of millions of years ago. The fish in this lake are evolving at record speeds.

Traditionally haplochromines were harvested and dried as a food source for indigenous peoples Most of these practices were outlawed in 1908 Most subsistence fishing on Lake Victoria today is illegal

Traditionally haplochromines were harvested and dried as a food source for indigenous peoples Most of these practices were outlawed in 1908 Most subsistence fishing on Lake Victoria today is illegal

Today, the populations of cichlids in Lake Victoria have plummeted and many species are either endangered or extinct. The extinction was due to environmental pressures and invasive species such as the nile perch, a large predator game fish with an appetite for a group of small cichlid fish known as Haplochromis. Like many invasive species, the introduction of the nile perch was no accident. It was introduced to stem the overfishing of tilapia in the 1920s. This worked, but at the price of hundreds of species of Haplochromis. Now that the biodiversity in the lake is reduced, there are efforts to protect these species that are informed by scientific inquiry, but who gets a say in how management decisions are made? How did the focus of inquisition change over the past hundred years?


Cat. Man. Do.

Matt his cat work on writing Matt’s thesis

Our guest, Matt McConnell, is trying to answer these questions and trying to understand how communication between scientists and non-scientists affect how science is done. As a Masters Student in the History of Science department or Oregon State University, he is digging through the archives, trying to understand the changing scientific values surrounding Lake Victoria in the 20th century. Is the lake important as a resource or as a haven for species? Why should we care? Our current notion of science is that it is objective, but as we look into its history, science is value-driven, which is culturally laden; the question is, who’s culture is asking the questions and who’s culture is affected? In our current time, we are hearing about resource management and those are informed by scientific inquiry. Science is the answer, but it affects farmers and fishermen and their opinions are often denigrated in favor of science. Science is considered an objective measure, but it is really a cultural decision. Practitioners of science not only need to communicate their values, but they need to listen.

Matt and the 2016 History of Science cohort enjoy a day in the sun in Seattle at an Environmental Humanities Conference

Matt and the 2016 History of Science cohort enjoy a day in the sun in Seattle at an Environmental Humanities Conference

Tune in Sunday, July 3rd at 7PM PDT on 88.7FM or live stream to hear Matt talk about his journey with the history of science and science communication.