Former Worden lab members
Eleanor (Ellie) Handler – Undergraduate Summer Intern 2017
Ellie joined the lab for the summer following her junior year at Yale. Utilizing a combination of photo-bioreactors and other methods, she characterized the photobiology and light acclimation strategies of arctic species of the green algal genus, Micromonas. She worked from the whole cell level down to the nitty gritty of electron transfer and will be a co-author on our new study of this organism. In the long term she plans to pursue a graduate program in Microbiology.
Yun-Chi Lin – Postdoctoral Fellow 2016-2017
Dr. Lin joined the lab for a 1 year fellowship sponsored by the Taiwanese Government in late summer 2016. Her research during this stay in the lab addresses how the core genome versus the so-called niche defining genes (those that are not shared with close relatives) operate in the environment – and over a strong environmental gradient. It has been great to have Yun-Chi back in the lab!
Susanne Wilken – Marie Curie Fellow and Post-doctoral Researcher, 2013-2017
Dr. Wilken joined the Worden lab after completing her Ph.D. at the Netherlands Institute of Ecology in the group of Professor Ellen van Donk. Susanne undertook a series of innovative, exciting projects while in the lab which have led to greater understanding of the ecology and evolutionary history of mixotrophic eukaryotes. The results are described in several manuscripts (in prep.). She contributed to multiple other publications from the lab and co-authored a review article on the importance of considering microbes from the three domains of life together (Worden et al. Science 2015) as well as a perspective in Science on the importance of time-series measurements for understanding future oceans (Worden & Wilken Science 2016). Susanne left the lab in March 2017 for an Assistant Professorship at the University of Amsterdam where she is in the Institute for Biodiversity and Ecosystem Dynamics.
Magdalena Gutowska – Post-doctoral Researcher, 2014-2017
Dr. Gutowska completed her Ph.D. at the University of Kiel where she also performed a post-doctoral fellowship. She joined the Worden lab as an MBARI post-doctoral fellow from 2014 to 2016 and, after completing the fellowship, has been pursuing ocean policy at the Monterey Bay Aquarium while continuing to participate in several lab projects. Magda’s research has focused on thiamin cycling in the ocean with important discoveries on the usage of precursor molecules (Gutowska et al. 2017). Magda is pursuing her interests in translating science more effectively for use in ocean policy.
Alexander J. (AJ) Limardo – Technician and then Graduate Student 2011-2016
AJ joined the lab after undergraduates studies at the University of Georgia where he worked in the lab of Mary Ann Moran. AJ was a terrific team member and participated in numerous seagoing expeditions. AJ also developed quantitative assays against newly identified open-ocean ecotypes of the prasinophyte Bathycoccus, a genus that is found from tropical to polar oceans. He co-authored an invited perspective in the journal Nature with Alex, participated in Simmons et al. AEM 2016, and is currently finishing a manuscript on quantitative biogeography of prasinophyte algae. AJ received his Master’s in Fall 2016 and is moving to industry.
Charles Bachy – Post-doctoral Researcher, 2013 – 2016
Dr. Bachy joined the lab after completing a Ph.D. with Puri Lopez-Garcia and David Moreira in Paris. Here he performed multiple studies on the evolution and biology of prasinophytes – with two co-first author articles in Molecular Biology and Evolution and PNAS. He also co-authored a perspective on the Rare Biosphere with Alex in Current Biology and is co-author on a Nature Reviews Microbiology article on marine protists. Charles is wrapping up manuscripts on prasinophyte viruses and an exciting new method for estimating viral infection frequency. Charles received a Marie Curie for returning to France where he joined the lab of Fabrice Not, another former Worden lab member!
Amy Zimmerman – Post-doctoral Researcher, 2014 – 2016
Dr. Zimmerman joined the lab after completing her Ph.D. at UC Irvine. In addition to stellar teaching outreach projects and education Amy has been pursuing ecological interactions between viruses and their prasinophyte hosts. She co-authored a major review in Science with Alex, Susanne Wilken and others, that addresses interactions across the three domains of life in the context of the global carbon cycle and marine food webs. She has several manuscripts in preparation on Ostreococcus viruses. Amy joined the faculty of Roosevelt University in September 2016!
María Corrochano-Luque – Undergraduate Summer Intern – 2016
María joined the lab as part of the MBARI summer intern program following her third year at the University of Seville in Spain. María’s project involved the investigation of potential phagotrophy under different light and nutrient conditions in a polar strain of the prasinophyte green alga, Micromonas.
Valeria Jimenez – Graduate Student, 2010 – 2016
Dr. Jimenez joined the lab after her Master’s degree in Chile. She came to the lab on a Fulbright Scholarship and here participated in a wide range of studies – including at-sea growth experiments and culture based studies of growth and transcriptional responses in eukaryotic algae. She co-authored two articles in PNAS and one in Environmental Microbiology during her Ph.D. and has two first author manuscripts in preparation. Valeria planned to stay on for a mini-postdoc but received an exciting offer from the labs of Daniel Vaulot and Fabrice Not at Station Biologique de Roscoff. In addition to being a fantastic scientists and teammate Valeria joined the lab just before Alex went on maternity leave so provided lots of guidance there over the years!
Jian Guo – Post-doctoral Researcher, 2013 – 2015
Jian also co-authored an article on the transcriptional /proteomic program of Micromonas pusilla (Waltman et al. PLoS One, 2016), a widespread prasinophyte alga. Her experiments on phytoplankton transitions to nutrient limitation include transcriptomic and proteomic responses to conditions that are predicted under future climate change scenarios (Guo et al. in prep.). Jian left the lab in early 2015 to rejoin her family in Canada and returned to Santa Cruz to work on a high risk project on developing a genetic system for marine algae in the lab of Prof. Manny Ares at UCSC in Winter 2015/2016.
Zena Jensvold – Undergraduate Summer Intern 2014
Zena came to under the National Science Foundation’s Research Experiences for Undergraduates (REU) program for the summer after her sophomore year at the University of Oregon. Zena’s project involved testing responses of the smallest free living eukaryote known to growth under low phosphate and nitrogen conditions, as well as investigating cellular quotas of C, N and P. Zena returned in autumn 2014 to participate in the MBARI CANON cruises.
Ashley Maitland – Undergraduate Summer Intern 2014
Ashley joined the MBARI intern program for the summer following her junior year at the University of Arizona where she has worked in the lab of Matt Sullivan. Ashley has been investigated the growth of Micromonas, a prasinophyte green alga that is broadly distributed in the world oceans – and its response to different nutrient conditions.
Marijke (Jeltje) van Baren – Bioinformatician, 2010 – 2014
Dr. van Baren joined the lab after working in human, mouse, and fly genome annotation. Here she developed an evidence based set of criteria for creating and selecting best gene models and developed new model sets for two complete eukaryotic genomes. She also contributed to RNA-seq analyses in the lab and a variety of other projects. Jeltje is now working as an independent bioinformatics contractor.
Melinda P. Simmons – Graduate Student, UCSC 2007 – 2014
Melinda came to the lab after performing an MS at Scripps Institution of Oceanography and a position at the Gordon and Betty Moore Foundation as part of the Marine Microbiology Initiative. Melinda’s research here focused on the ecology of picoeukaryotic green algae. Melinda is a co-author on the 2009 Science genome paper and one of her primary dissertation publications came out in Molecular Biology and Evolution in 2015. The latter shows that there is a polar-adapted Micromonas species with near perfect nucleotide identity present in the Arctic and Antarctic, but not in surface waters in lower latitudes. In collaboration with Post-doc Charles Bachy we also showed that this Micromonas (or its DNA) is present in the North Atlantic Deep Water, providing a connection between populations at the two poles. Melinda defended her Ph.D. thesis, entitled “Mamiellophyceae: phylogenetic and biogeographic insights” in June 2014. Her final paper explores the distribution of picophytoplankton in the eastern North Pacific, and through collaboration with post-doc Adam Monier, shows that two ecotypes of Bathycoccus exist (Simmons et al. Applied and Environmental Microbiology 2016). Melinda joined the faculty of Jacksonville University in Fall 2016!
Darcy McRose – Summer Intern 2008, MS Student Stanford University 2009 – 2011, Research Assistant until Aug 2012
Darcy spent the summer after her senior year at Stanford University working on growth and photosynthetic activity of axenic strains from the different Micromonas clades as well as Ostreococcus. This beautiful piece of research involved a huge amount of work – for which she spent just about every day of the summer in the lab. Darcy then returned to the lab for her Master’s research and worked as a Research Assistant after the completion of her MS. Darcy’s research focus was on comparative genomics of vitamin genes in marine phytoplankton and vitamin physiology in prasinophytes. Darcy is currently finishing her Ph.D. in the lab of Francois Morel at Princeton University.
Adam Monier – Post-doctoral Researcher, 2009 – 2012
Dr. Adam Monier joined the lab after his Ph.D. on HGT and marine eukaryotic viruses. Adam’s research in the lab focused on analysis of eukaryotic metagenomes, targeted metagenomes from flow sorted populations, HGT and on eukaryotic viral genomes. Adam is the lead author on the first genome sequence of the marine prasinophyte Bathycoccus, sequenced directly from nature using targeted metagenomics; he is also first / co-first author on two ISME J articles, and participated in several other publications. Adam moved to perform a second post-doc at the University of Laval in theTakuvik International Lab in Canada where he used omic approaches to identify metabolic responses of marine microbial communities to the changing Arctic. He then became a Royal Fellow in the UK.
Emily Reistetter – Research Technician II, 2010 – 2012
Emily joined the lab after completing her MS at University of Washington in the lab of Prof. Gabrielle Rocap. Emily performed a series of important chemostat experiments with talent and persistence in a technically challenging system. The experiments address the interaction between CO2 concentration and nutrient limitation on phytoplankton growth. The experiments/samples include complete transcriptome and proteome analyses and the first results were published in PNAS (Duanmu, Bachy et al.) in 2014. Emily is a coauthor on multiple other publications / manuscripts from the lab. Emily is now working in the real estate business in the Bay area and still occassionally consults for the lab!
Yun-Chi Lin – Visiting Graduate Student, UCSC/MBARI 2010-2011
Yun-Chi came to the lab on a fellowship from the Taiwan National Science Council to work on her Ph.D. studies on uncultured stramenopiles (MAST). She published one first author paper from this work in Environmental Microbiology; she also performed qPCR, constructed and analyzed clone libraries for a study of phytoplankton in a frontal system. She received her degree from the National Taiwan Ocean University in 2013. We were all sad to see Yun-Chi leave at the end of her 1 year stay! After her Ph.D. Dr. Lin became a post-doc at the Institute of Marine Biology, National Taiwan Ocean University.
Tracy Campbell – Research Technician I, 2010 – 2012
Tracy joined the lab after completing her MS at the University of Hawaii in the lab of Mike Rappe with an interest of gaining some additional research experience before finding and starting a Ph.D. Program. Tracy contributed data support to Lin et al. 2012, a publication addressing the distribution of Marine Stramenopiles (MAST) in marine systems and enhanced our 16S rRNA alignment database. Tracy started research on invertebrates in fall 2012 at MLML.
Shuang Chun “Jeremy” Yan – Post-doctoral Researcher, 2011 – 2012
Jeremy earned his PhD in plant pathology and physiology from Virginia Tech where he studied interactions between plants and bacteria, virulence mechanisms and host range evolution of the plant pathogen Pseudomonas syringae. At MBARI Jeremy worked on algal physiology in response to changing light fields and temperature as well as host defense systems. Jeremy moved to Harvard University to research novel therapeutics as alternatives to antibiotics in the wake of increasing challenges from multi-drug resistant organisms. Jeremy is a co-author on our Vitamin B1 research (e.g. ISME J 2014).
Hang Yu – Summer Intern and Research Assistant, June – Dec 2010
Hank came to the lab after completing his undergraduate degree at the University of British Columbia. Hank worked on characterizing new phytoplankton isolates and performed a series of experiments for complete transcriptome analysis through RNA-seq on a range of prasinophyte species. Hank started his Ph.D. at Caltech in the lab of Victoria Orphan in autumn 2011.
Marie L. Cuvelier – Ph.D. Student, RSMAS University of Miami / MBARI, Fall 2004 – 2010
Marie completed her dissertation entitled “New insights into the diversity, distribution and ecophysiology of marine picoeukaryotes” in 2010. In addition to co-authoring several papers in the lab, Marie is first author on a publication on a novel protistan group in Environmental Microbiology as well as one on the importance of picoplanktonic prymnesiophytes to oceanic systems in PNAS. Marie also performed a series of photophysiology experiments on prasinophytes. During her Ph.D. Marie participated in many cruises and was a wonderful team player. Marie went on for a post-doc in the lab of Rebecca Vega Thurber, Florida International University. Marie is now Adjunct Faculty in the Biological Sciences Department at Nova Southeastern University.
Elif Demir – Post-doctoral Researcher, 2007 – 2010
Elif performed her Ph.D. at the University of Delaware in the laboratory of David Hutchins where she worked on harmful algal species. Elif joined the lab here in autumn 2007 and worked on qPCR primer-probe development for enumerating different pico-prasinophytes from which she is first author on publication in the ISME Journal. Elif participated in several North Pacific cruises as well as one in the Florida Straits and played an active role in mentoring undergraduates who came to the lab. At the end of her 3 year post-doc here, Elif moved to work on the Environmental Sample Processor in the Scholin lab group at MBARI.
Alyssa Gehman – Research Technician, 2008 – 2010
Alyssa performed a master’s at Western Washington University on the rocky intertidal. She joined the lab as a research technician hoping to gain a couple more years research experience before pursuing a Ph.D. in parasitology. Here she ran and analyzed flow cytometry data, performed sorting experiments, participated in cruises and managed the lab! She co-authored two articles from the lab on the dynamics of small phytoplankton. Alyssa has a long standing interest in parasitology and started a Ph.D. at the University of Georgia in Fall 2010 on that topic and where she has been making waves with creative funding mechanisms.
Heather M. Wilcox – Senior Research Technician, 2007 – 2009
Heather moved from the field of immunology to join the lab in 2007. She has been responsible for developing our metagenomic extraction procedures and managing the ever growing axenic culture collection in addition to many other activities in the lab, including master troubleshooter for RNA work. Here she co-authored publications in PNAS and PLoS Biology. Prior to joining the lab, Heather played important roles in brief episodes setting up the lab at Miami, and helping with the move/set up at MBARI. Heather moved back to the ‘human’ world to have direct involvement with patient care.
Harriet Alexander – Undergraduate Summer Intern 2008, Honors Thesis Student 2009 – 2010
Harriet quickly mastered the high speed flow sorter and explored the cell cycles of Micromonas and Ostreococcus, as well as helping all sorts of folks out by running their samples. She then developed her own project. After completing her Biology and Math double major at Wellesley College and honors thesis in the Worden Lab, Harriet went on for a Ph.D. in the MIT-WHOI Joint Program.
Julie Vassar – Undergraduate Summer Intern 2009
Julie came to the lab for the MBARI summer internship after her sophomore summer at Smith College. Julie learned to love PCR – always upbeat and cheery, not to mention ready to run another PCR and Gel ASAP!
Rory M. Welsh – Research Technician, RSMAS University of Miami / MBARI, 2005 – 2008
Rory joined the lab in fall of 2005 and quickly became the fall back guy – maintaining the axenic cultures, mastering the high speed flow sorter and participating in a large number of research expeditions – taking him to the tropical Atlantic, South Pacific and the North Pacific. He is well known for his ‘heart of gold’ and for being a patient teacher. He moved with the lab from UM to MBARI in 2007 and stayed on for a year to get the lab up and running in its new home. Rory co-authored papers in PNAS, Current Biology and Environmental Microbiology while in the lab. Rory went on for a Ph.D. in the lab of Rebecca Vega Thurber, Florida International University.
Sarah McDonald, Ph.D. – Post-Doctoral Associate, RSMAS University of Miami / MBARI, 2007 – 2008
Sarah came to the lab in January of 2007 from the Stazione Zoologica in Napoli, Italy after finishing her Ph.D. in which she explored natural eukaryotic phytoplankton populations using genetic markers. In Miami she entered into the field of genomics and designed experiments to explore Micromonas nitrogen and carbon utilization via genome-informed gene expression. She continued with this project after the move to MBARI – resulting in a publication in Molecular Biology and Evolution and co-authorship on the Micromonas genome paper (Science 2009). Sarah went on for a position at SRI International.
Alejandra Ortiz – Undergraduate Summer Intern, 2008 (2007 & 2006!)
Aleja first joined the lab (while still at University of Miami) the summer after her senior year in high school and then left for Wellesley College. She took on an 18S rRNA gene sequence analysis using consed in her first summer. Aleja returned to the lab for two more summers (one more at UM and one at MBARI) – and orchestrated intense culture based studies on algal response to high light and UV exposure. She is a co-author on several publications / manuscripts. After completing her degree at Wellesley College Aleja went on for a Ph.D. in the MIT-WHOI Joint Program. In May 2015 she accepted a position as Assistant Professor which she will start after completing her post-doc.
Augustin Engman – Undergraduate Researcher, University of Miami / MBARI, 2006 – 2007
Gus joined the lab and went to sea in his first week! He worked on bacterial-algal interactions and participated in Micromonas growth experiments. His research expeditions include the Florida Straits, Florida to Cape Verde and back, and orchestrating our efforts in the North Pacific transects. Gus finished his B.S. in June of 2007 and stayed on for another half year to help the lab transition to MBARI, and perform the North Pacific research. From this research he coauthored our 2012 de novo wild pelagophyte chloroplast genome in Current Biology. Gus went on to study stream ecology at the Department of Marine Sciences, University of Puerto Rico and subsequently for a Ph.D. back on the mainland.
Sharria Scavella – High School Student Researcher, University of Miami, Summer 2007
Sharria’s is interested in the medical field – but joined our lab to learn basic science. She worked on nitrogen growth physiology of Micromonas. At the end of the summer she placed 3rd for her talk on this research at a in a national competition held in Bethesda Maryland.
Heike Moehlig, Ph.D. – Post-Doctoral Associate, RSMAS University of Miami, 2006 – 2007
Heike completed her Ph.D. in Germany in the field of immunology and came to the lab to work on phagocytosis in marine nanoflagellate predators. She also co-authored our work on the distribution of a newly identified protistan group (putatively photosynthetic), the biliphytes. Heike moved into biotech (back in Germany). While in Miami Heike also became a sailing aficionado.
Joshua Lake – Undergraduate Extern, MIT Independent Activities Period 2006
Joshua came to the lab while working on his degree in Materials Science at MIT. He worked to set up a system in the lab for incubating phytoplankton in an isothermal environment where they could be exposed to both high light and UV radiation. He also worked on cell cycle analysis of prasinophytes using flow cytometry and the nucleic acid stain Sybr green.
Jason A. Hilton – Undergraduate Honors Thesis Student, University of Miami, 2005 – 2006
Jason undertook the Florida Straits work, specifically the Fluorescence in situ Hybridizations (under th guidance of Dr. F. Not) on different eukaryotic algae. He organized and performed a large number of the Florida Straits expeditions and is a co-author on Cuvelier et al. PNAS 2010. Jason went on for a Ph.D. program in the Department of Ocean Sciences, University of California Santa Cruz in the lab of Jon Zehr, which he defended in 2014.
Vladimer Cessant – Undergraduate Researcher Summer 2005
Vladimer worked the lab during his junior summer at University of Miami.
Fabrice Not, Ph.D. – Post-Doctoral Associate, RSMAS University of Miami, 2004 – 2005
Fabrice is now a faculty member at the Station Biologique de Roscoff (firstname.lastname@example.org). We had a lucky coincidence of an unexpected award coming in (The Moore Young Investigator Award to AZW) and Fabrice finishing his Ph.D. and still waiting on proposals he had written to stay in Europe. Fabrice initiated the Florida Straits time series and worked on the diversity of picoeukaryotes in the Sargasso Sea – and is first author on the Environmental Microbiology publication from that work. He also co-authored the picoeukaryotes chapter on picoeukaryotes with Alex in Kirchman’s “Microbial Ecology of the Oceans”.