Friday, October 4, 2019

The excitement and energy of a new job at 60!

Bobcat (UC Merced mascot) on the Vernal Pool Reserve 2013
       Although I cried for about half an hour when Chris and I pulled out of our neighborhood on our way across the country to California, the sadness didn’t last long before excitement took its place. We wound our way across the continent stopping to see relatives, Stephanie and Jim in St. Louis and Judy and Peter in Albuquerque. But I was anxious to pick up the pace. I’d purchased our new house in Mariposa by myself. Chris hadn’t seen the quirky property from the inside, and I was a bit nervous. Also, classes were starting fairly soon, and I’d never really taught a full on course before. We arrived in Mariposa around dusk after over a week on the road. Tied to the top of our Subaru Outback were sleeping bags and pads, a few pots and pans, a coffee maker, and clothes for a week.
            Our first few days were magical. The house in Mariposa is a rambling, multi-story home with 7 acres of large granite rocks, two ponds, and a small forest. Our moving van was fast in coming. David, our driver who packed up a full 55-foot van with all of our possessions and my lab gear, made two drop offs at the Castle and the house in Mariposa. Miraculously, only two things were broken—a lamp and the frame of an old Swarth family painting.
House in Mariposa, Evan in pond, 2015

            We both reported for work the following Monday, and I began to move into my new office. Campus building specialist Steve Rabideaux had reserved a nice, full window corner office at the Castle building, UC Merced’s out post in the small town of Atwater adjacent to the former Castle Air Force base. I was shown my mega-laboratory space. You could literally hold a square dance in the room. One side had black and blue lab benches that looked like they came straight out of a junior high school science lab. One older fume hood was located in a back room. There was no running water, no lab sink. I was also assigned two support rooms to serve as offices when I hired folks to people the lab. I slowly unpacked the boxes of samples, put away files, and looked at the rag-tag bunch of stuff I’d brought from Carnegie. It was fun to carry out the renovations to make this a working laboratory. 
Marilyn in Castle Lab, 2013

            At the Castle, I was alone. Alone! After the whirlwind fall at the Geophysical Lab where I was never alone, always busy with a constant stream of people coming through to get their last minute bits of advice and give some out as well. I also had a shared office on campus. Jessica Blois, the other new ecology professor, and I shared a nice office so that we could meet with students, get to know the campus, and have a small foothold with our colleagues. We both started teaching right away. I was nervous for my first class in Ecology. Heck, I had been practicing ecology for decades, but I’d come from an earth science and astrobiology laboratory. It didn’t take long for me to lean into the teaching and enjoy it. (For more on my experience with students, see a forthcoming blog.)
Selfie after first class--big smiles, 2013

            Again, because I was far removed from my Carnegie people, I got to know the students that year, even recognizing their hand writing on quizzes and tests. I met many of my best students that semester. Meanwhile, Chris was excited to work half time as Director of a new UC natural reserve property adjacent to campus. He was also team teaching a large general education course in Earth System Science. He’d been a college instructor many times in the past, including teaching grad classes at Johns Hopkins when he worked at Jug Bay Wetlands Sanctuary, but this was The University of California! At night and on the long drives to and from campus to our house in Mariposa, we discussed our common employer—the University of California Merced. We were working together! Commuting together after 26 years of separate lives. It was a lot of fun.
            After 9 short months, I became the Chair of our embryonic Life and Environmental Science Department. I loved and embraced the job. I started work at 5:00 in the morning, with a cup of Peet’s coffee, sitting at our kitchen table. I wrote emails, organized my lectures, and prepared for the day. We left the house around 8:15 am arriving on campus to drop off Chris by 9. I continued another 15 minutes to the Castle laboratory. Our drive, so different from our DC and Maryland commutes, went through miles of blue oak foothills and grasslands. Often we saw eagles soaring over the small creeks. Daily, we drove through agricultural fields where our nation’s food is grown. Different species of hawks—red tails, ferruginous, Swainson’s, and red shouldered—flew overheard every day.
            I was able to hire and retain almost half of the faculty in the department. I walked several through the demanding tenure process. I negotiated lab spaces for new assistant professors. I served on leadership campus committees and met everyone from the Provost to the night cleaning staff. It took 16 months for my first isotope mass spectrometer to be operational on April 1st, 2014. I’d hired a former undergrad, David Araiza, and a postdoc, Christina Bradley. We were going places! What a relief to hear vacuum pumps gurgling away again. I had garnered a generous start up package and was having fun buying all new “toys”. 
L-R: David Araiza, Marilyn, Christina Bradley, mass spec boxes 2014

            Chris had the thrill of creating the Merced Vernal Pools and Grasslands Reserve, a 6,500-acre property, as part of the University of California’s Natural Reserve System. He learned an entirely new ecosystem, was breathing the air of his home state, and making new connections with vernal pool biologists across the state that had had an adversarial relationship with previous campus administrators. He traveled out to “the Reserve” daily, driving a small, 4WD off road vehicle--the Gator--on its primitive roads. Chris also had a switched-on crop of undergraduate interns, who made his time on campus worthwhile and tied him into the larger academic scene. Cami Vega, Daniel Toews, and Katherine Cook, all seniors, completed projects and helped out as needed. Together, Chris, his interns, my lab group, and I built a research program starting small and going big. On Friday afternoons, when the campus was eerily quiet, we would rustle any faculty, students or staff to join us in the Gator to view the stark and inspiring vistas of the Reserve.
Bobby Nakamoto on the Reserve, 2015
            After several years of contentious colleagues at the Geophysical Lab, my UC Merced colleagues were a breath of fresh air. Peggy O’Day, founding Professor, was my recruiter. We have a common geochemistry background and many colleagues in common. The soil scientists, Asmeret Berhe, Steve Hart, and Teamrat Ghezzehei, formed a small group that I warmed to with time. Their science was not immediately interesting to me, but eventually I learned its importance and relevance to terrestrial ecology. The biology-oriented colleagues, Carolin Frank, Danielle Edwards, Justin Yeakel, Jessica Blois, Mike Beman, Mark Sistrom, and Mike Dawson, provided a daily influx of scientific juice that I missed at the Geophysical Lab. Furthermore, they were all younger than me—and young, period—a stark contrast to the senior scientists at Carnegie.
Chris showing Danielle Edwards and Mark Sistrom kestrel boxes, 2015

            Probably around 2 years from when we arrived at UC Merced, there developed a number of small annoyances that erupted into soul-draining battles. For example, there was little administrative support to run the department, and almost no money. Furthermore, although my colleagues at the Castle were promised we’d have lab space on campus by a certain date, the times came and went without forward progress. As a senior tenured faculty member, I shouldered the burden of fighting for their inclusion on campus with UC quality facilities. By the start of 2016, about 40% of my time was occupied fighting campus “battles”. I felt like General Dwight D. Eisenhower fighting on the African, Southern, and Eastern fronts. 
New lab on main campus, November 2015

            At the same time, Chris was facing increasing scrutiny dealing with environmental issues and access to the Vernal Pool Reserve. His vision for managing an NRS reserve differed significantly from that of his faculty supervisor. He received little support from the very busy faculty on campus. For a combination of reasons, he retired at the end of 2015.
            When the opportunity presented itself to me to start a new Institute at UC Riverside doing exactly what I had wanted to do at UC Merced, I jumped at the chance to learn more about it. Chris and I were disappointed with our life at Merced. We knew we’d made the right decision to leave the east coast and strike out for California. We were less convinced we landed in the best place.

Tuesday, October 1, 2019

Hydrogen isotopes in Amino Acids tell about an organism’s food and water

Student Patrick Griffin at the Geophysical Lab, circa 2008

In 2008, I received a grant from the W. M. Keck Foundation that provided funding for a new isotope system and the ability to measure the hydrogen isotopes of individual compounds. All of the papers published with hydrogen isotopes in single compounds were focused on lipids (i.e. fats) or hydrocarbons from plants, microbes, and sediments. I wanted to try my hand at measuring them in amino acids, the building blocks of proteins. I wanted to know more about how hydrogen isotopes in animal tissues related to geographic location and diet.
Biochemical Pathways of Amino acid synthesis--complicated!

         I began this work with postdoc Seth Newsome and a graduate student, Patrick Griffin. Patrick, now a student at Indiana University, was training in Steelie’s lab as a microbiologist. Famous for his outrageous, funny, off-color one-liners, Patrick has an interest in astrobiology, broadly, and microbiology, specifically. He kept unusual work hours, often working into the wee hours of the night at the lab bench, harvesting microbes, setting up experiments, and reading scientific papers. I didn’t necessarily approve of this behavior, but Patrick had glimmers of brilliance that we hoped to nurture.
         Although hydrogen is one of the major elements in living organisms, it is not fully understood how organisms incorporate hydrogen from their surroundings into the biochemical compounds that comprise them.  Living systems derive their hydrogen from two primary sources--food and water---and a full understanding of how hydrogen moves through an organism or an ecosystem must consider studies of both sources.  To determine how hydrogen from water is incorporated into living matter, Patrick cultured the common bacteria E. coli in nutrient broths composed of waters of differing isotopic compositions. To determine the influence of the dietary source on hydrogen, we designed experiments with a glucose-based culture broth, as well as a one based on the protein digest, tryptone. Together with Patrick and Seth Newsome, our experiments showed that roughly 25-35% of the hydrogen in E. coli cells originated from the water in which it is grown, but the remainder transfers directly from the diet to cellular biomass (Fogel et al., 2016). It made sense that more hydrogen originates from media water in E. coli grown on the glucose-based medium than from organisms grown on tryptone, because the bacteria had to synthesize more of its cellular biomass with just glucose as its “food”. 
         Our first set of measurements we made with hydrogen in amino acids was in the single protein, tryptone, that we used to feed the E. coli. We were surprised to find that the hydrogen isotopes in the different amino acids varied by a huge amount--nearly the entire natural range of hydrogen isotopic compositions of living organisms on Earth. Amino acids extracted from our E. coli cultures showed even more extreme variations with some amino acids having identical isotopic compositions to those in tryptone and others being enriched or depleted in the heavier isotope of hydrogen. 
         Our results from these simple experiments with E. coli grown on tryptone provided the basis for examining complex organisms, such as birds, mice, and fish.   Tryptone is essentially food for the microbes, and our data showed that the more complex branch-chained amino acids (e.g., isoleucine, valine, and leucine) could be incorporated, or routed, directly into cellular protein. Less than 10% of the hydrogen in these amino acids was sourced from water. Mathematical models suggested that ~40-50% of the hydrogen in one of the simplest amino acids, alanine, was sourced from media water. We had discovered that by analyzing hydrogen isotope values in a suite of amino acids, we could tell what an animal was eating as well as where its drinking water came from.
         We went on to measure the hydrogen isotopes of amino acids in bird feathers. Using some of the Black-throated Blue warbler samples measured previously, we found that there were similar patterns of isotope discrimination among the hydrogen isotopes of individual amino acids similar to those in the bacteria. Amino acid isotope values from feathers in warblers from North Carolina showed that these birds lived in a more southern climate than those amino acids in feathers from warblers collected in Ontario, Canada, showing the influence of geographical location. 
Nathan Wolf mixing up fish diets

         Seth Newsome, then at the University of Wyoming, and his grad student Nathan Wolf carried out a defined diet experiment in which tilapia fish (Oreochromis niloticus) were grown in tanks where the hydrogen isotopes of environmental water and the isotopes of each of the major diet macromolecules of carbohydrates, proteins, and fats was known. We had nine experimental tanks: 3 different isotopically-flavored diets, each tested with three different isotopically labeled waters. About 25% of the hydrogen in fish tissues originated from water. Of the remainder, 34-44% came from dietary protein, 25-30% from carbohydrates, and <1% from lipids (Newsome et al., 2017).
         The individual amino acid data was more complicated. Interpreting the hydrogen isotope composition of individual amino acids required us to measure the carbon isotope composition of the amino acids as well to tease apart our data. Since corn is a C4 plant, and the casein was derived from C3-based milk protein, we could use the carbon isotope values to roughly estimate which proportion of the fish’s amino acids came from C4 plants and which from C3 based casein. We anticipated that the simplest amino acids would show the strongest relationship to the isotopic composition of the water in the tank. Based on carbon incorporation proportions we expected the more complicated amino acids, including those essential for the fish, to be more influenced by the hydrogen isotopes of food rather than water.
The hydrogen isotopes of the tank water significantly influenced only alanine, glycine, and serine—three simple amino acids-- for all of the nine experimental tanks. The remainder of the amino acids had little to no isotope relationship between water and the amino acid. We then linked the carbon isotope data with the hydrogen isotope data to understand and possibly tease out the source of hydrogen to all of the amino acids. What is striking about our results is the fact that very few of the amino acids in the tilapia came from only one dietary carbon or hydrogen source. Interestingly, the origin of essential amino acids was as variable as the non-essential amino acids. Microbial synthesis in the gut must have been a critical component supporting protein synthesis in the fish.  
Tilapia experimental tanks

Publishing this data has been put on hold, because pretty much all of our results point to a greater complexity than we’d originally thought. Seth’s undergraduate student Mariel Curras did another experiment, this time changing the amount of protein in the experimental animal’s diet. He grew some mice, and my student Bobby Nakamoto analyzed the isotopes in the amino acids. We’ve submitted a nice paper explaining the very basics and hopefully, when that manuscript is accepted, it will open up the floodgates for all of the data we’re been collecting for the past 6 years! Scientific research often begins with a simple premise or hypothesis but more often than not, the results lead you in a different, unanticipated direction. In my career, my best work has followed this pathway.

Rounding Third Base and Heading Home

Cards from Franny and Flowers the Rumbles   My daughter Dana is marrying George Goryan on June 25 at our home in Mariposa...