What killed the harbor seals?

My time as a Ph.D. student in the Vega-Thurber lab has come to an end. Completing my dissertation was a very exciting and relieving moment in my life.  To add to this excitement, just a few days after my latest paper from my dissertation was published in the Journal PeerJ. This paper was an extension of the work that I talked about on a previous blog.


Celebrating the completion of my P.h.D

Celebrating the completion of my P.h.D

In my last paper, I looked at the bacteria and viruses from a group of seven young harbor seals that died from some unknown brain disease. When veterinarians performed a necropsy (the animal version of an autopsy), it appeared that these animals were infected with viruses. Although, when we used high-throughput sequencing (sequencing of large amounts of DNA or RNA) to identify a virus we did not find any. The lack of viruses in my results was very surprising as well as disheartening. See I wanted my research to revolve around characterizing viruses, but given that, I could not find any viruses this inhibited my grand research plans.

This situation is very common in research; our hypotheses are not always correct and we often get negative results. It’s one of the aspects that makes the work of a scientist challenging, but it also keeps us thinking and generating new ideas.

My next step was to refocus my question and approach. If a virus did not kill this group of animals something else did. Now I had a new question to answer. What killed the harbor seals? To answer this, I examined the genes of the seven harbor seals. I used a sequencing technique that is known as transcriptomics or RNA-sequencing. This technique is a high-throughput sequencing approach looking at all the genes in a sample. In my case, I was examining the genes in each of the seven seals that died from the mysterious brain disease.

I then analyzed the genes of the harbor seals using computer programs, statistics, and biological principles (bioinformatics). To my surprise, all these animals had high levels of genes related to fatty acid metabolism. Unexpected results are also a common occurrence in research. I initially believed that these animals died from a virus, but my results were suggesting that they likely died from a metabolic disease!

What does high levels of fatty acids in the brain signify?  Generally, fatty acids are important for building cells and providing energy to cells. Fatty acid gene activity typically takes place in fat and the liver cells, and large production of these gene types may indicate a metabolic disease. Things that trigger high fatty acid production includes poor nutrition intake or exposure to toxins. So, we think that these animals either did not absorb proper nutrients or encountered a toxin that caused high fatty acid metabolism production in their brains, which may have led to their death.

So now that we know that fatty acid metabolism dysfunction can occur in the brains of marine mammals we can begin to monitor these genes in other marine mammals. We can look for the same fatty acid genes that we found in our study in other animals. This will help us better understand this disease and hopefully prevent the deaths of other animals. Interestingly, when I began this research question, I envisioned the final results of my study very differently. I didn’t expect to examine marine mammal genes and metabolic pathways, but research has a mind of its own and leads us to unexpected and exciting findings.

Ever wonder what’s inside of the brain of a harbor seal?

As promised I am here to provide some new information about marine mammals. I know you’ve waited too long. This time I will be telling you about my very own research that was just published in PLOS ONE!!! This is my first, first author publication so there was a steep learning curve on data analysis, graphing, and the publication process. In future post I plan on taking the reader on the journey of my first publication. Especially the struggles, since the public often doesn’t hear about that side of science.

For this blog I will  give a quick synopsis of my paper for those who just really want to know what I found inside the brains of Pacific harbor seals.  Although, before I get to the nitty gritty of my story I like to tell you a bit about my study subjects, the harbor seals. I mostly worked with pups (< 1 month) and weaned (1 -12 months) harbor seals, which tend to be born between February and April. Their mothers wean them for about 3-4 weeks and soon after they begin to catch small fish and shrimp. During these early stages of life, they encounter many dangerous situations for example, being preyed, starvation, and disease.


Popeye a Pacific harbor seal not related to this study. Photo by me

I am particularly interested in the diseases of young harbor seals, since understanding this may increase their survival rates during this fragile stage of their lives. About 44% of marine mammal diseases remain a mystery. That means that many harbor seals die and we have no idea what’s killing them. So, I wanted to help discover possible culprits that cause marine mammal diseases.

I started my search with the brain tissue of 14 harbor seals that were found sick on the California coast. I first looked into the viral world and I found viruses in four of the animals from the family Herpesviridae, which have previously been found in harbor seal brains in European and North American waters. A virus from this family (Phocine herpesvirus-1,  PhV-1) are particularly harmful for young seals since they have an undeveloped immune system.

However, the bacteria side of the story proved to be a bit more interesting. One of our significant discoveries was the presence of Burkholderia along with a high amount of Burkholderia genes that are known to cause disease. Burkholderia is an interesting genus of bacteria that can be zoonotic (passed from animals to humans), but it is also ubiquitous and can be harmless. While this is not the first time someone has looked for bacteria in the brains of marine mammals and found Burkholderia, it is the first time that this bacteria was found in harbor seals in the USA. So where else were Burkholderia found in the brains of marine mammals? Well in Southeast Asia, this bacteria was found in an aquarium, which caused the death of marine mammals.

Our other interesting finding on bacteria comes from Coxiella burnetiiSimilar to Burkholderia, it was found at a high abundance with high amounts of disease causing genes. Unlike, Burkholderia it was not found in all our harbor seals, but only in three of our animals. Meaning this pathogen may be less common in harbor seal populations compared to Burkholderia. 

C. burnetii is a known pathogen that needs to replicate within a cell (obligate intracellular pathogen). It is best known for causing Q fever, but in marine mammals it causes inflammation of the placenta (placentitis) and it has never been found in the brain of harbor seals. We think since these harbor seals were young animalsthe placenta may be a source of C. burnetii infection for pups, but this is just a hypothesis that needs some testing!

So what exactly did we learn from all this? Well our study adds to our knowledge about the distribution of Burkholderia in marine mammals and like in Southeast Asia it may also be causing the death of harbor seals in the USA. Also, now we know that C.burnetii  can infect the brains of harbor seals and we should investigate the source of this infection. Finally, we can now begin to monitor for these bacteria in the brains of these animals as possible sources of infections.

Lab Accomplishments: Aliens, Predators, and Brains

I’m a little tardy in writing this, but our lab has a few pieces of stellar news from the last couple of weeks. First off, the most exciting:

Photo from Stephanie Rosales

Meet the man formerly known as Mr. Rory Welsh. He will now be referred to as Dr. Rory Welsh. Or, more likely, still just Rory. This guy is one of the most humble and most awesome guys around. Since he successfully defended his PhD dissertation last week, he is now also formally recognized as an expert in our field, and the foremost expert in his particular corner of it. I know I speak for our whole lab and many others when I say congratulations – you deserve it.

In the course of our tenure as PhD students, we must take classes, teach classes, perform research, and share that research through a number of public presentations. And, most importantly, we must make some verifiable contribution to the collective knowledge of our field. Which brings me to the other fun lab news. During Rory’s dissertation defense preparation, he wrapped up a couple of projects and wrote multiple papers. One was accepted to the influential ISME Journal and became available online just before his defense. Another (which was co-authored by a certain blogging scientist we all know…), he recently submitted to the open-access journal PeerJ and is undergoing the review process. Though it hasn’t yet been accepted, the pre-print also became available online last week. Both of these papers deal with the fascinating ecology of a particular coral-associated bacterial predator called Halobacteriovorax. I could tell you more about it, but I think it’d be best to hear that story straight from the Doctor’s mouth. Rory will tell you about them, soon!

Last week also saw the publication of yet another paper from the lab! Stephanie, who has previously written a post for the blog, had her paper published on the metagenomics of seal brains! It’s available now at another open-access journal, PLOS ONE. Stephanie is also working on a blog post talking about that paper.

Whew! The rest of the lab’s been quite prolific. I definitely feel like I need to step up my game…