How sweet it is – forty bonus years of life, and still going

Well, I am not really sure when it all started but I am sure when we figured out what was going on. It was July 22, 1984. Forty years ago today. In some ways you could say it was a good day, because I did not die. In other ways, it was a bad day, because I nearly died and also found out what had been going so wrong with my body for some time.

Though as I said I am not sure when it all started, I do know that for a few months my health was deteriorating. I had told my father, who was a doctor (though he did research at the NIH and was not a practicing clinician), that I just did not feel right. I had been mentioning this for a month or more. But in July I mentioned it more. And he did not seem to think there was anything to worry about.

I was a pretty active kid then and was quite athletic – at least – before my body started having issues. I think this is partly why my dad thought that I must be fine. I played soccer, baseball, street hockey and various other sports.

I had even made the Varsity Baseball team as a sophomore and had done OK.

As an aside, it is kind of fun to see discussion of how I played baseball with Anthony Dilweg who went on to play QB for the Green Bay Packers. Anyway … back to the story. And as another aside, it is cool to me that I am still in touch, at least a tiny bit, with a few people from this team (e.g., Tom Nylen, Andy Keith).

Anyway – more on that in a bit. It was now the summer. And I was still pretty active. Most days went something like this. I was taking Driver’s Ed classes in downtown Bethesda getting ready to get my drivers license. I would bike to the class. Then I biked over to work at the Carey Winston Company where I did data entry, in a job that my friend Ross Kaminsky helped me get. Then I would bike to my High School (Walt Whitman) where I had baseball practice for a summer league team. And then I would bike home. On days when I had a game I think I would bike home, get my uniform on, and then either bike (if the game was nearby) or get a ride from my mom or brother. With all this activity it made a little bit of sense that I might also feel tired all the time, and also that I was pretty skinny. So I think my dad thought “Oh, he must be fine.”

But I knew something was up. Something definitely was not right. And a few days before July 22, I had decided I was going to force the issue. In part, this was because I was feeling worse and worse. But also in part it was because my brother and I had our first backpacking trip planned, with a friend Matt Smith. I was excited about this but also a bit worried due to my health issues. Basically, I was just really really tired. That was the number one symptom. Just crazy tired. And I felt weak. Really weak. (I had other symptoms but more on those later). So here I was – getting ready for my first real outdoor adventure – to hike up Old Rag Mountain with Matt (and Eagle Scout) and my brother and to camp overnight and then get picked up the next day. This did not seem like an ideal time to do that, given that I felt like I could barely walk some of the time.

You see, despite being really active, and doing OK at some of these activities, I just knew something was wrong. In retrospect, something had been going wrong for actually quite some time. Amazingly, I even found that I discussed this pretty openly with people writing stories for our school paper about the Varsity Baseball team in the Spring. For example:

I had a good throwing arm as a pitcher so I could do ok. But I was tired all the time. Like really really tired. For every game. And things had been getting worse over the Summer. So – even though my dad did not think something was wrong, I did. So as I said, I was going to force the issue.

But then somewhere July 18th or 19th, I was the starting pitcher for our team in a baseball game and I pitched phenomenally well – a two hit shutout. I felt awful through the whole thing, but the result was excellent. And I felt like, if I could do that, I must be fine. So we decided to go ahead with the backpacking trip.

So – anyway – back to the summer league game. I pitched well and decided that it was OK to go on this trip. Here is what I wrote about that in a school essay (with corrections from my English Teacher)

This was unquestionably one of the dumbest decisions I have ever made. My mom and dad drove us to the trailhead for Old Rag Mountain, I think on Saturday morning. And then eventually me, Mike and Matt headed up the mountain.

And here is where the shit truly hit the fan. I did not tell you one of the key other symptoms I had, which was thirst. Just devastating thirst. I could not imbibe enough liquid. I basically drank my 2 day supply of water in like 30 minutes and then basically polished off as much of the water of my companions that they would let me have. So just like that, we were out of water basically. Oh, and I was also peeing all the time too. Yay.

Here is what I wrote about that in that school essay mentioned above (with corrections from my English Teacher)

Somehow, yes, we made it up Old Rag Mountain and ended up sleeping near the top. The whole time, I felt like I was dying. And in fact, I was. Somehow I made it through the night. Also – despite what I said in the essay – my brain was not functioning particularly well and I really do not remember much about that night. Maybe my brother or Matt Smith can chime in at some point. I vaguely remember that we could not find any water and that Matt had brought some adult beverage to drink which he consumed and my brother had to try and figure out how to deal with the drinker and the dying person at the same time. Anyway – it was not a good night. But I did make it through the night.

I do not have any pictures from the trip but if you are interested – here is some information about hiking up Old Rag:

From https://www.nps.gov/thingstodo/old-rag-summit-berry-hollow.htm

Although I was alive the next morning, I was not doing well. I was so so so so so so so tired. And so confused. And so so so so so so thirsty. And since we were basically out of water, things were not good. On our hike down the other side of the mountain, I started drinking from puddles and trickling baby streams of water. Anything I could find. I slurped from muddy puddles like a dog. And I could barely move. My body hurt like never before. My legs were so weak. And my brain was not all there.

Finally we got down to near where we were to be picked up and there was a house and maybe a farm down there. But most importantly, something there I think saved my life. A hose. I turned it on. And drank. And drank. And drank. And drank. And then peed. And drank some more. And then peed more. And then drank. We waited there for a bit for Matt’s parents to pick us up but the water I got from that hose I am fairly certain saved me.

Clearly, the next thing to do was to go to the hospital. But that was not to be. We got dropped off in the early evening and my dad’s lab had some sort of party that we went to. I barely remember this but I do know they were playing volleyball and despite this being one of my favorite activities normally I did not play. I just sat on the ground nearby, not moving. And at some point I think my parents / my dad realized there was in fact something really wrong.

I vaguely remember that we left the party and went to a drug store (I think People’s) to buy a urine sugar testing kit. And at some point we tested my urine and it was off the scale – literally filled with sugar. And so my dad said something to the effect of – “You have diabetes, we have to go to the hospital.” And off we went to Bethesda Naval Hospital to the emergency room (because my dad worked at the NIH and was a commissioned officer in the Navy, we got our medical care there).

I think I was pretty much not fully alert during all of this. But eventually I was transferred to a bed in the pediatrics unit and then spent many days in the hospital recovering and learning how to treat myself as a diabetic.

In many ways, I was lucky to be alive. I easily could have died on that backpacking trip and if I had not found that hose at the end of the trip, I think I might have died out there. I was in rough shape and things had been going poorly for a while. I looked like a famine victim. I had lost something like 40-50 pounds over a few months. I was in full blown diabetic ketoacidosis and slipping away until they gave me IV fluids and eventually insulin in the ER. Here is the page from my admissions (missing some details on various tests they ran, but suffice it to say I was not doing well)

So in retrospect again, it is pretty crazy that I had not gone in to get checked out before this crisis. Certainly, my dad, an endocrinologist (though again, one who did research in a lab at the NIH and did not practice) probabiy should have caught this earlier. We even had just been in Quebec where my dad was attending the Endocrine Society Annual Meeting and I had been surrounded at various events by world leading endocrinologists.

At dinners, I was getting up all the time to pee, but I did not announce this. And if anyone noticed me seeming fidgety, they probably either thought I was a typical bored teenager or maybe thought I was on drugs.


See https://academic.oup.com/edrv/article-abstract/5/2/370/2548924?redirectedFrom=fulltext

I note – one of the issues with my deteriorating health was that it came along slowly, over many many months. It was like the proverbial frog in the frying pan story – I just kept adjusting and adjusting and adjusting my baseline expectations about what was normal and what was OK slowly over time. And I did not even notice really all the issues. The one I noticed most was fatigue and weakness. What I did not really notice, which seems really bizarre in retrospect, was two key other symptoms that had gotten worse and worse and worse over the months. These were thirst, and the need to pee all the time.

For example, by that time in Mid July, my daily routine was not quite as I laid it out above. This was the daily routine with the full details with the extra new details highlighted with underlining and bolding.

Most days went something like this. I got up in the morning early because I had to pee. Then I went downstairs and made a large two liter pitcher of orange juice from a frozen can. And I drank most of it. I was taking Driver’s Ed classes in downtown Bethesda getting ready to get my drivers license. I would bike to the class. Although it was only about a 20 minute bike ride to the class, I would stop on the way at Montgomery Donuts to get a drink and use the bathroom.

Then I would go to class where every 20 minutes or so I would get up to pee. Then I biked over to work at the Carey Winston Company where I did data entry, in a job that my friend Ross Kaminsky helped me get. While working I would spend a lot of time getting up to use the restroom and to buy sodas to quench my thirst. Then I would bike to my High School (Walt Whitman) where I had baseball practice for a summer league team. And during practice, or even during games, I would have to sneak off all the time to pee in the bushes and to also get a drink. And then I would bike home.

Oh and of course, since I did not know I was a diabetic, I was probably making things worse by drinking sweetened drinks all the time. Yes, they seemed to quench my thirst. But they just added more sugar to the fire.

And again, in retrospect, I had been “building” up to this for some time. During the second semester in high school that Spring, I remember having to pee between classes a lot. I remember even being stressed during classes about needing to pee and get excused all the time even before class.

Yes, clearly, it would have been better to have figured things out sooner. But somehow, I did not die. And that was a good thing. As I was in the Navy Hospital, trying to comprehend what this all meant, for reasons that I am not entirely sure of, I did not spend a lot of time lamenting about “Why me?” I mean, sure, it sucked. And sure, I knew my life was altered. But I somehow just wanted to move forward, get on with my life, and deal with the altered reality.

This moving forward thing in part I think came from my general nature. But there were also a few things that happened while I was in the hospital and shortly after that really really helped my perspective and I mention some of these in the next few paragraphs.

One thing that helped me immensely once I was in the hospital was that the pediatrician who took care of me was Dr. Marion Balsam, who happened to be the mom of a friend Ross Kaminsky. I had hung out a lot with Ross a few years before that and knew his mom and this was just remarkably comforting. Plus she was a just phenomenal doctor.

Another thing that really really helped me move forward was the fact that there was a kid in the bed next to me who had brain damage from some type of accident. I realized that things could be much worse than having to take shots and deal with a defective pancreas.

But even with those two things helping me in ways, I was still not fully in a good place mentally. For example, I was at the Bethesda Naval Hospital and alas I had a painful conversation with one of the orderlies who was taking care of me on Day 2 or so. You see, I had dreams of going to the US Naval Academy and playing baseball there and we were discussing this. I had even had a discussion with the Navy Baseball Coach and had either taken or at least signed up for the ASVAB test (I can’t remember anymore). Alas, the orderly then, matter of factly, told me, you can’t join the Navy as a diabetic. Well, shit, there went that dream.

So, you know, even though physically I was starting to feel better than I had in months (IV fluids and insulin for the win …), mentally I was still not in a completely great place. But fortunately I had a lot of visitors (my family and friends must have worked hard to keep me occupied). This was really really uplifting. Someone – possibly Ross – even took me on my first “outing” to get out of the hospital ward. We went bowling at the Navy Bowling alley nearby).

And one of those visitors definitely changed my mental state. You see there was a girl who I had a bit of a crush on who came to visit me in the hospital because it turned out she was also a diabetic (I had not known that). And, well, eventually we developed a relationship – my first real girlfriend. Honestly, I think she probably is more responsible for me being alive today than anyone else because she taught me about diabetes and I wanted to get my diabetes in control to show her that I could do it.

A fourth thing that definitely helped me was that my family had a trip to Alaska planned for a few weeks from when I went in to the hospital and Dr. Balsam encouraged us to still go on the trip. Since my dad was a doctor, in theory he could help take care of any issues that arose. So I had incentive to show that I could manage my diabetes as soon as possible so they would let me go on this trip. And we did. And the trip was incredible. Here are a few pics from that trip:

Although another time I will tell the story about how I cracked a rib and my dad was worried I had punctured my spleen when I crashed into a fire pit while playing frisbee at a campsite in the middle of nowhere. And we cut our trip short by a day to get me to a hospital for a check up. But another time.

A final thing that helped me move forward is, well, that the medicine (insulin basically) was like magic. When they first gave me some in the hospital, I literally think I could feel my body starting to wake up and work again. And since I was almost 16 and had been a science dork of sorts, I actually already knew what insulin was and what diabetes was. I had not imagined I would get it of course, but knowing what it was all about certainly helped too.

Anyway, 40 years ago today, I got knocked down. But I got back up. And it has certainly not been easy. But I am still here. Always looking forward. And looking backwards, from a historical point of view, but rarely from a “why me” point of view. I truly feel blessed to have had these extra forty years. Here’s to forty more.

UPDATE 7/25/2024

Got some nice responses to my post at various social media sites and thought I would share links here.

So I wrote a thing about having a bonus forty years of life.phylogenomics.me/2024/07/22/h…

Jonathan Eisen (@phylogenomics.bsky.social) 2024-07-22T16:38:53.880Z

Cooper’s hawk calling at UC Davis – found with a little help from Merlin

Was at the end of a bike ride to work yesterday and was biking by the UC Davis Vet School when I heard a screeching bird. I was not sure what it was but I knew I had heard something like it before and also that it was not common.

So (1) got off my bike (2) got out my iPhone (3) opened the Merlin App and (4) starting the “Start New Recording” option and very quickly it IDd the bird as a Cooper’s hawk.

So then I got out my camera (I had brought a relatively new travel camera – a Nikon CoolPix) with me on my ride and had been taking pics along the way but put it in my backpack when I got near the Vet School – assuming incoorectly I would not want to take any more pics now that I was close to my office).

And I tried to figure out where the call was coming from. It took a bit but I found the bird and first made a video with my phoen and then took some pics. They are below.

A Semi-Random Day of Mammals

So I got up really early on July 12th to get out and go to Yolo Bypass to go for a hike before it got too hot. The weather prediction was for it to get to above 110 °F so I really wanted to get out early. And I was really looking forward to see what creatures were out early in the AM

I left my house jsut before 6 and the sun had already risen but was quite orange still.

Possibly A Blue Grosbeak Seen on the Way to Yolo Bypass

And then when I got there, alas, the gate was closed, even though it is supposed to be opened at sunrise.

Gate at Yolo Bypass Closed

There was also a woman there in her car waiting to get in. We chatted a bit. She was an artist, from Canada, and was hoping to get in early because the lighting would be nice. She told me about her dogs (that were not with her) and her family. We say a few interesting critters from the levee road outside the gate including a mink. I did not get a picture of the mink alas. But I did get a pic of a hawk.

We saw some pickup trucks driving by that we hoped would be someone to open the gate but after 20 or so minutes I decided I wanted to go SOMEWHERE to go for a hike and was not going to wait for the key person. So I headed off to the Davis Wetlands. Not as much shade there and not really where I wanted to go. But I felt like it was the next best option.

On the drive in to the Wetlands I saw an otter family cross the road (no pics of them). But it seemed to be a good omen. I parked, got my stuff together and headed out for a walk. It was not about 7 AM. And it was already getting pretty warm. And lo and behold, just five minutes into the walk I got a nice sighting of a muskrat, swimming towards me.

And got a little video

And then continued on my walk and got to see some nice birds and got a few good pics of some including these:

My apple watch kept getting annoyed when I stopped to look at birds.

I took a few selfies too …

And on the way back I stopped by the spot where I had seen the muskrat and before I could get my camera ready I startled a beaver (no pics alas). And a few minutes later the muskrat came out.

And then I was off to my car to head home. But on the way out of the wetlands I also saw some deer.

Overall I would say that this was a pretty nice outing. More mammals than I was used to seeing in a day. Mink, otter, muskrat, beaver, and deer. Cool.

And then I headed home. But this was not the end of the story. Because just around sunset my wife said our daugther was a bit bored and had not gotten out all day and I asked if I might be able to take her out to do a quick shopping run. I said sure, espeically since I knew that my daughter was likely willing to do a little drive to look for wildlife afterwards. So we headed out, made a stop to do some quick shopping, and then I asked my daughter if she wanted to drive by the entrance of Yolo Bypass to see if we could catch the bats coming up form under the causeway. See a post I wrote about these bats from 2014 here: https://phylogenomics.me/2014/07/26/bat-tour-at-yolo-basin-wetlands/.

So we headed over to Yolo Bypass, with some trpidation because of the earlier locked gate. But now the gate was not locked although it was likely to be locked shortly since they close up at sunset. And it was just getting to be sunset. So we parked on the little levee road where I had parked in the morning, got out, and lo and behold got to see the bats flying out from the causeway. I made a short video and then my phone battery died so alas I did not make others. Here is that video. My phone makes it look lighter than it was out — it was actually quite dark.

And then when we had enough of the bats we decided to do a little drive around rural areas to see if we could see any wildlife. We do this often, although never before had we done this after sunset. And we did what we always do on drives. We guess what mammal species we might see. I chose opoosum. She chose coyote. And then changed her mind thinking that was too unlikely so she chose skunk. We drove around slowly on some rural roads and saw a lot of bunnies but no other mammals (we see so many bunnies and their relatives around here that we no longer allow them as one of the guesses).

And then on a rural road between Davis and Woodland we hit the jackpot. Juveniles coyotes. OMG. OMG. OMG.. They were so cutre. Got some videos and a few pics (with my cell phone – my real camera does not do well in low light). Actually fumbled quite a bit and missed a lot of the scene but at least caputred some of it. Here are some pics and videos.

We were SO excited about this. Just amazing to see these juvenile coyotes. And even though my daughter had originally picked coyote but then changed her pick to skunk, we both agreed she deserved credit for the original pick. And though we wanted to stay and see if the coyotes came back, we decided to head back home. And then a few minutes later we struck gold.

A mother and juvenile fox. I have never seen a fox around here. And these two were not exceptionally shy so we got good looks.

Made a few movies – the juvenile headed into the brush.

After the juvenile headed into the shrubs the adult stayed around and just sat there. So amazing.

What a day. It went from a possible disaster with Yolo Bypass being closed to a day where I saw a slew of mammals – a mink, two otters, a muskrat, a beaver, two deer, many bats, two juvenile coyotes and a juvenile and adult fox. Just amazing. And my daughter was beyond thrillled.

New paper from Eisen Lab – on ” The Genome Encyclopedia of Spacecraft Associated Microbes (GESAM)” project 

New data report paper out from my lab and others. Basically this is a report of genome sequences and some other measures such as MLADIMALDI-TOF) of bacteria isolated by NASA from some of their spacecraft (before they were sent to space).

See “Draft Genome Sequences of Spacecraft-Associated Microbes Isolated from Six NASA Missions” https://journals.asm.org/doi/10.1128/mra.01011-22.

Tran MT, Seuylemezian A, Wright A, Coil D, Eisen J, Guan L. Draft Genome Sequences of Spacecraft-Associated Microbes Isolated from Six NASA Missions. Microbiol Resour Announc. 2023 Feb 22:e0101122. doi: 10.1128/mra.01011-22. Epub ahead of print. PMID: 36840549.

This paper was from a collaboration between my lab (Alonna Wright – who was a PhD student in my lab and who just got her doctorate recently, David Coil – who was my lab manager and is now the Public Health Coordinator at UC Davis- and me) and researchers at the Jet Propulsion Lab (Michelle Tran, Arman Seuylemezian and Lisa Guan).

Abstract: Whole-genome sequencing can be used to better understand and assess the functional abilities of microorganisms isolated from spacecraft hardware and associated surfaces for planetary protection (PP) purposes. We sequenced 191 isolates from 6 spaceflight missions with PP requirements and identified them using Illumina-based sequencing methods and matrix-assisted laser desorption ionization–time of flight (MALDI-TOF) mass spectrometry.

New paper from Eisen lab and others … on challenges with relic RNA in SARS-CoV-2 environmental surveys

New paper out from my lab and other labs.

Zuniga-Montanez R, Coil DA, Eisen JA, Pechacek R, Guerrero RG, Kim M, Shapiro K, Bischel HN. The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA? PLoS One. 2022 Apr 22;17(4):e0267212. doi: 10.1371/journal.pone.0267212. PMID: 35452479; PMCID: PMC9032406.

This was a collaboration between my lab and labs of Heather Bischel and Karen Shapiro.

Funding was provided by Healthy Yolo Together/Healthy Davis Together.

New preprint out from my lab and others about environmental monitoring for SARS-CoV-2 in schools and in part about how difficult this is

New preprint out on from the Eisen Lab and others. This is from a collaboration between David CoilHeather Bischel, Karen Shapiro,  Randi Pechacek, Roque G. Guerrero, Minji Kim, and Rogelio Zuniga-Montanez (first author) at University of California, Davis.  

It is about environmental monitoring for SARS-CoV-2 in schools and, well, in part about how difficult this is.

See https://www.medrxiv.org/content/10.1101/2021.11.12.21266178v1

The challenge of SARS-CoV-2 environmental monitoring in schools using floors and portable HEPA filtration units: Fresh or relic RNA?

Abstract: 

Testing surfaces in school classrooms for the presence of SARS-CoV-2, the virus that causes COVID-19, can provide public-health information that complements clinical testing. We monitored the presence of SARS-CoV-2 RNA in five schools (96 classrooms) in Davis, California (USA) by collecting weekly surface-swab samples from classroom floors and/or portable high-efficiency particulate air (HEPA) units. Twenty-two surfaces tested positive, with qPCR cycle threshold (Ct) values ranging from 36.07–38.01. Intermittent repeated positives in a single room were observed for both floor and HEPA filter samples for up to 52 days, even following regular cleaning and HEPA filter replacement after a positive result. We compared the two environmental sampling strategies by testing one floor and two HEPA filter samples in 57 classrooms at Schools D and E. HEPA filter sampling yielded 3.02% and 0.41% positivity rates per filter sample collected for Schools D and E, respectively, while floor sampling yielded 0.48% and 0% positivity rates. Our results indicate that HEPA filter swabs are more sensitive than floor swabs at detecting SARS-CoV-2 RNA in interior spaces. During the study, all schools were offered weekly free COVID-19 clinical testing. On-site clinical testing was offered in Schools D and E, and upticks in testing participation were observed following a confirmed positive environmental sample. However, no confirmed COVID-19 cases were identified among students associated with classrooms yielding positive environmental samples. The positive samples detected in this study appeared to reflect relic viral RNA from individuals infected before the monitoring program started and/or RNA transported into classrooms via fomites. The high-Ct positive results from environmental swabs further suggest the absence of active infections. Additional research is needed to differentiate between fresh and relic SARS-CoV-2 RNA in environmental samples and to determine what types of results should trigger interventions

Article about Dr. Connie Rojas getting UC Davis Chancellor’s Postdoctoral Fellow Award

See Researcher Studying the Microbiome and Chemical Communication of Cats Named a Chancellor’s Postdoctoral Fellow for an article by Greg Watry about Dr. Connie Rojas who is a post-doc in my lab. Dr. Rojas got a UC Davis Chancellor’s Postdoctoral Fellow Award to come to UC Davis to work on cats and the role of their microbiome in chemical signaling and scent production.

For more about Dr. Rojas see

Twitter: @ConnieLaBiologa

Web Site: conniearojas.weebly.com

The tale of the blue soy products – from contaminated soy milk to a new publication

A new paper is out from my lab. This one is a remarkable story of work by PhD Student Marina E. De León (https://phylogenomics.me/people/marina-de-leon/).

It started with her pouring out some soy milk from her fridge that was blue.

See her Tweet about this here: https://twitter.com/MicrobialFuture/status/1220399781165461504?s=20https://twitter.com/MicrobialFuture/status/1220399781165461504?s=20

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And then she isolated bacteria from the soy milk and from some blue tofu in her fridge, identified them, did experiments to see if these isolated bacteria could cause soy milk to turn blue, found some that did, sequenced their genomes, and analyzed them to show that these ones had similar properties to other bacteria known to cause blue discoloration of food products. A truly remarkable piece of work.

See the paper here: “Draft Genome Sequences and Genomic Analysis for Pigment Production in Bacteria Isolated from Blue Discolored Soymilk and Tofu

And thanks to Guillaume Jospin and Harriet Wilson who helped with the work and all the people in my lab and via social media that encouraged and supported Marina along the way.

And see also:

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Post-Doc Position available in Ecology of Emerging Infectious Disease

Post-Doc Position available in Ecology of Emerging Infectious Disease

The Epicenter for Disease Dynamics at the One Health Institute in the School of Veterinary Medicine at UC Davis is seeking a post-doctoral researcher interested in the impacts of environmental change on the epidemiology, ecology and evolution of zoonotic diseases. Activities will focus on a new National Science Foundation Ecology and Evolution of Infectious Diseases project “Impacts of Rapid Landscape Change and Biodiversity on Virus Host Specificity”.

Primary responsibilities relate to both theoretical and data-informed modeling of virus evolution and transmission across landscape changes in Southeast Asia. This is a 3-year post-doctoral position, expected to begin January 2022 based at UC Davis with opportunities for collaboration and co-mentorship across the PIs on this project including Christine Kreuder Johnson (UCD), Tierra Smiley Evans (UCD), Lark Coffey (UCD), Michael Boots (UC Berkeley), and Rebekah Kading (CSU).

Project Overview:

This study investigates the impacts of deforestation, landscape change, and biodiversity on virus characteristics that determine zoonotic potential, including virus “host plasticity”, which is the diversity of host species a virus can infect in nature. Findings from this research will contribute to ecological theory on the impact of environmental changes on microbial adaptation, with practical implications for management of ecosystems at high risk for pathogen spillover. Investigations will evaluate host range of bat-borne coronaviruses and mosquito- borne arboviruses (flaviviruses, alphaviruses and bunyaviruses) in the biodiverse tropical forests of Southeast Asia. Activities will include theoretical and computational modeling, underpinned by field investigations and in vitro experiments, to develop data and model driven insights into the role that mosquito vectors play in constraining or expanding virus host plasticity and genetic diversity. Characterization of bat-borne coronaviruses and host affinities in an ecosystem with SARS-CoV-related viruses will further inform on coronavirus evolution and emergence of zoonotic potential. This position will conduct research in a team science setting that is especially relevant to development of an evidence-base on the relationship between environmental change, biodiversity, disease outbreaks, and pandemics to underpin public policy.

65% SCIENTIFIC RESEARCH

  • Contribute to designing field studies to investigate virus host plasticity, evolution and transmission across forest gradients in Southeast Asia;
  • Develop methods and analyses to evaluate surveillance strategies to detect zoonotic pathogens at high-risk interfaces for disease emergence;
  • Analyze metadata on emerging zoonotic diseases, high-risk human-animal contact, and ecological risk and conduct data analyses needed to train models for emerging disease prediction;
  • Develop advanced analytical techniques and associated programming capabilities for infectious disease modeling, predictive frameworks, and social network analyses;
  • Conduct independent research and produce high quality scientific manuscripts related to biosurveillance and the ecology of emerging infectious disease.

35% PROJECT IMPLEMENTATION

  • Provide disease expertise, technical support, data analyses, and data-sharing tools for zoonotic disease prediction and biosurveillance projects;
  • Provide epidemiologic expertise to field staff in other countries on study design, data collection, data management, data analysis and interpretation, and publication preparation;
  • Contribute to regular summaries of surveillance data, assist in development of data collection and data management tools; and ensure open communication and coordination with international partners in project implementation;
  • Travel to international field sites to work with field staff, participate in field activities, and attend scientific meetings as needed.

Skills needed:

Background in infectious disease epidemiology or disease ecology and strong quantitative skills in biostatistics, epidemiology, and mathematical modeling with knowledge of animal health and wildlife disease. Experience with statistical software including R and STATA, as well as ability to write code for programming, including Python. Experience conducting independent, applied scientific research on infectious diseases with a promising publication track record.

Education:

PhD in biology, ecology, epidemiology, or related life-science (required)

Application:

Please email cover letter and CV by September 30th to:

Tierra Smiley Evans, DVM, PhD and Christine Kreuder Johnson, VMD, PhD EpiCenter for Disease Dynamics | One Health Institute
School of Veterinary Medicine
University of California
Davis, CA 95616
530-752-1238

tsmevans@ucdavis.edu, ckjohnson@ucdavis.edu

NSF EEID_Post_Doc_Position.pdf

The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies (talk video and slides)

Posted video of a recording I made of a talk for BIATA2021 meeting. Phylogenomic Case Studies: The Benefits (and Occasional Drawbacks) of Integrating Evolutionary and Genomic Studies

Slides here