Current Stillman Laboratory Members

Principal Investigator: Dr. Jonathon Stillman

Professor of Biology
Romberg Tiburon Center for Environmental Studies
San Francisco State University

Adjunct Assistant Professor of Integrative Biology
University of California Berkeley

voice: (415) 338-3790
fax: (415) 435-7120
e-mail: stillmaj_at_sfsu.edu, jstillman_at_berkeley.edu

Curriculum Vitae

In the news

photo credit: Marine Forte

Postdoctoral Researchers

Dr. Alex Gunderson (alexrgunderson@gmail.com)

I am a physiological ecologist interested in the intersection of physiology, evolution, and behavior. Previously, I studied the thermal biology of Caribbean Anolis lizards with respect to two broad topics: 1) climate change vulnerability and 2) the contribution of physiological evolution to adaptive radiations. In the Stillman Lab, I am investigating mechanisms of thermal adaptation at the molecular level using Petrolisthes crabs.

Hear Alex talk about his Thermal Plasticity paper here: https://clyp.it/kspkklpj

For more about Alex: http://sites.google.com/site/alexrgunderson/

Graduate Students
Chelsea

Metadel Abegaz (e-mail). I'm a new MS student starting in Summer 2015.

Chelsea

Eric Armstrong (armstrong@berkeley.edu)

I’m interested in understanding how changes in the abiotic environment (especially alterations in temperature and pH) influence physiological processes in marine invertebrates, both across taxa, and across life history stages within a single species. I am also interested in biological questions related to organism-environment interactions and scale - how do a species' physiological tolerances influence its performance and distribution and what effect do these variations have on whole ecosystem features and processes? I’ve taken a broadly integrative approach to investigate these types of questions, utilizing both whole organism and functional genomics tools to address physiological hypotheses in a diverse array of taxa (porcelain crabs, giant clams, and sea hares).

For more about Eric: https://www.ocf.berkeley.edu/~earmst/index.html

Chelsea

Alma Ceja (aceja1@mail.sfsu.edu). I'm a new MS student starting in Fall 2015

Lindsay Faye (lfaye@mail.sfsu.edu)

I am a second year graduate student researcher working with Phyllaplysia taylori, a sea hare living on the eelgrass beds in San Francisco Bay. I am studying the impacts of climate change, specifically temperature and salinity increases, on the ability of these marine mollusks to successfully live and reproduce on eelgrass blades, where they participate in an important mutualistic relationship in which they consume epiphytic algae off of the blades and in turn keep eelgrass plants healthy.

For more about me: http://714889070861077878.weebly.com

 

Emily Lam (elam2@mail.sfsu.edu)

I am a graduate student who started during Summer 2015. My first projects involve field work and examination of behavioral responses to temperature in porcelain crabs.

Elize Papineau (papineau@sfsu.edu)

My research uses Daphnia pulex as a model to measure the capacity of estuarine organisms to adapt to temperature and salinity stress predicted to occur with future climate change. I employed a transcriptomic approach, using next-generation sequencing technology, so these data may contribute to the building of a universal stress-response framework.

For more about me, see here: http://epapineau.weebly.com

Haydee

Jennifer Souther (jsouther@mail.sfsu.edu)

In a changing climate, I am interested in determining whether porcelain crabs behaviorally thermoregulate. If so, what are some possible implications? To learn more about my graduate work, please visit my website: http://www.jennifersouther.com

I also have a blog where I write about what I'm reading or doing at http://www.achievingnerdvana.com

Chelsea

Richelle Tanner ()

I’m a new PhD student starting in Fall 2015.

Haydee

Carley Turner (cturner@mail.sfsu.edu)

I'm examining whether growth of newly settled porcelain crabs is impacted by conditions of variable pH and temperature.

Tomas "TJ" Yockachonis (tyoke@yahoo.com)

I am interested in the link between genetic diversity and phenotypic stress response. Currently, I am focused on identifying advantages of intraspecies variation in porcelain crabs when faced with thermal stress.

Research Technician

Adam Paganini (paganini@mail.sfsu.edu)

I completed my MS research on on understanding the synergistic effects of thermal and pH variation on adult porcelain crab metabolic physiology and thermal tolerance. Before that I spent a year working on understanding how the metabolism and metabolic enzymes of the invasive Asian clam Corbula amurensis responds to environmental salinity. I have worked on a project involving the thermal physiology of porcelain crab larvae, specifically examining how thermal stress brought on by climate change will alter their metabolic and energetic demands at different life history stages. Now I just do everything.

For more about me visit: www.laplebe.com or here

Undergraduate Students
Chelsea

Emily King. BREED REU student from CSU Monterey Bay.

I am an undergraduate at California State University, Monterey Bay studying marine science. I conducted research in the Stillman Lab in summer 2015. I examined the stress response gene expression profile of porcelain crabs during interspecific and intraspecific interactions.

Chelsea

Kirsten Boyer. NSF REU student from CSU Monterey Bay.

I am currently pursuing a BS in Marine Science at CSU Monterey Bay. My research interests include marine environmental physiology and the effects of global climate change on marine organisms. I spent the 2015 summer investigating the expression patterns of cellular stress response genes in porcelain crabs (Petrolisthes cinctipes) living at different densities.

Chelsea

Kayley You Mak. Undergraduate volunteer from Barnard College of Columbia University.

Other Current Lab Members
Chelsea

Catarina Morerira (Visiting graduate student from Portugal). CIBIO - Research Center in Biodiversity and Genetic Resources Campus Agrário de Vairão, Portugal

Stillman Lab Alumni

Graduate students who completed their theses mage

Tessa Page,MS student 2012-2014; MS THESIS:

I am working on understanding how porcelain crab exoskeletons and embryos change during exposure to lower pH.

For more about Tessa: http://tessampage.weebly.com/
tpage@sfsu.edu

Chelsea

Rachel Diner, Master's student 2011-2013; MS THESIS: Variable negative effects of ocean acidification in the coccolithophore genus Calcidiscus.

Prior to joining the Stillman Lab I worked in a freshwater ecology lab at the University of Georgia as an undergraduate, and later studied coastal environmental law and policy at the University of San Diego. I am currently working on projects that examine how climate change and nutrient availability affect the physiology and functional genomics of phytoplankton. I work mostly with calcifying marine phytoplankton known as coccolithophores, and am addressing the following questions: How will future increases in ocean temperature and CO2 affect the transcriptome of the world’s most abundant coccolithophore, Emiliania huxleyi? How will different coccolithophore species (e.g., Calcidiscus leptoporus) respond to changes in ocean CO2 and shifts in the marine nitrogen cycle?

Some other projects that I have worked on include: The effect of nutrient additions on phytoplankton growth and community composition in the Amazon River Basin (project with Edward Carpenter’s Lab). Heat shock protein (HSP) gene expression in two species of juvenile porcelain crabs (with REU student Carley Turner).

Now I'm a PhD student in Andy Allen's laboratory at the Scripps Institute of Oceanography at UC San Diego. For more about Rachel: http://www.racheldiner.com/home/working-at-jcvi-starting-at-sio

mageDiner, R.E., I. Benner I, U. Passow, T. Komada, E.J Carpenter, J.H. Stillman. 2015. Negative effects of ocean acidification on calcification vary within the coccolithophore genus Calcidiscus. Mar Biol. DOI: 10.1007/s00227-015-2669-x

mageBenner, I., R.E. Diner, S.C. Lefebvre, D.Li MS, T. Komada, E.J Carpenter, J.H. Stillman. 2013. Emiliania huxleyi increases calcification but not expression of calcification- related genes in long-term exposure to elevated temperature and pCO2. Phil. Trans. Roy. Soc. B 368: 20130049

to contact Rachel: (rdiner@jcvi.org)

Chelsea

Adam Paganini, Master's student 2009-2013; MS THESIS: Physiological Responses of Porcelain Crabs to Ocean Acidification and Warming.

mage
Paganini, A.W., N.A. Miller, J.H. Stillman. Temperature and acidification variability reduce physiological performance in the intertidal zone porcelain crab Petrolisthes cinctipes. J. Exp. Biol. 217, 3974-3980

See above, Research Technician, for more about Adam.

Chelsea

Claudia Tomas-Miranda, Master's student 2009-2013; MS THESIS: Cardiac transcriptome responses to heat stress in the porcelain crab, Petrolisthes cinctipes.

Claudia's thesis used microarrays to discover that gene responsiveness to thermal stress depends on the mean temperature and the thermal variability conditions to which the crabs were exposed. She is presently working at UCSF in a clinical research setting.

Chelsea

Lina Ceballos, Master's student 2009-2012; MS THESIS: Developmental Effects of Ocean Acidification on Porcelain Crab, Petrolisthes cinctipes.

Lina is interested in crustacean biology and environmental studies. Her previous research includes the first report of the reef lobster Enoplometopus antillensis (Lütken 1865) in Colombian Caribbean waters (Ceballos et al. 2005), and a description of its larval stages. Her MS research examined physiological responses to ocean acidification in embryos, larvae and juveniles of the porcelain crab Petrolisthes cinctipes. Presently she is working at the Smithsonian Environmental Research Center in Tiburon.

mageCeballos, L.O., H.A. Carter, N. Miller and J.H. Stillman. 2013. Effects of ocean acidification on early life-history stages of the intertidal porcelain crab Petrolisthes cinctipes . J. Exp. Biol. 216: 1405-1411 (inside JEB featured article)

Chelsea

Hayley Carter, Master's student 2009-2012; MS THESIS: Physiological Effects of Ocean Acidification on Early Life History Stages of Porcelain Crab, Petrolisthes cinctipes.

Hayley is interested in how marine invertebrate organisms respond to environmental stressors. She enjoys working with intertidal organisms and is fascinated with their adaptations to extreme environmetal conditions. Her thesis examined how porcelain crab early life history stages will respond to future global climate change, including changes in ocean acidification.

mageCarter H.A., L.O. Ceballos, N. Miller and J.H. Stillman. 2013. Impact of ocean acidification on the metabolism and energetics of early life stages in the intertidal porcelain crab Petrolisthes cinctipes. J. Exp. Biol. 216: 1412-1422 (inside JEB featured article)

Chelsea

Chelsea Chen, Master's student 2008-2011; MS THESIS: Synergistic Effects of Thermal and Osmotic Stress on Metabolism in Freshwater Zooplankton.

mage Chen, X., and J.H. Stillman. 2012. Multigenerational analysis of temperature and salinity variability: affects on metabolic rate, generation time, and acute thermal and salinity tolerance in Daphnia pulex. Journal of Thermal Biology. 37(3): 185-194.
Chelsea

Andrea Cayenne, Master's student 2008-2010; MS THESIS: Identification of Protein Interactions with Lactate Dehydrogenase in Porcelain Crab Petrolisthes cinctipes

mageCayenne, A.P., B. Gabert, J.H. Stillman. 2011. Identification of proteins interacting with lactate dehydrogenase in claw muscle of the porcelain crab Petrolisthes cinctipes. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 6(4): 393-398. doi:10.1016/j.cbd.2011.09.002. NIHMSID #327871, Publ.ID: CBD243

Chelsea

Eric Galassi, Master's student 2007-2008; MS THESIS: Thermal Influences on Gene Expression in the Intertidal Porcelain Crab, Petrolisthes cinctipes.

Chelsea

Kristen Teranishi, Master's student 2004-2006; MS THESIS: Response to Heat Stress in the Porcelain Crab, Petrolisthes cinctipes.

Teranishi, K.S. and J.H. Stillman. 2007. A cDNA microarray analysis of the response to heat stress in hepatopancreas tissue of the porcelain crab Petrolisthes cinctipes. Comparative Biochemistry and Physiology Part D: Genomics and Proteomics. 2: 53-62.

Following her MS research Kris started a PhD program at UCSF in the pharmacogenomics program. After a year, though, she decided to return to home and Hawaii, where she enrolled in the UH Medical School to become a medical doctor.

Other graduate students who worked in the lab for a while, and their projects:
Bandele Okelana (2014-2015): Stress, atrazine and longevity in Daphnia pulex.
Dave Hurt (2010-2012): Transcriptomic analyses of larval and juvenile crab responses to OA
Tyler Waterson (2007-2010): Environmental physiology of corals
Joanna Lipinski (2006-2007): Neurophysiology of crabs
Laurie Kara (2006-2007): Metabolic physiology of clams
Beth Moore (2005-2006): Transcriptome variation across latitude in crabs

Postdoctoral Fellows who continue to do great things...

Dr. Scott Fay (scott.a.fay |at| gmail |dot| com)

I focus my research on food web ecology, especially in examining links between microbes and higher trophic levels. In the Stillman Lab I'm applying my expertise in molecular ecology to address how the metabolic efficiency of algal grazers, aquatic insects in California Coast Range streams, will be affected by changing climate.

Scott completed two projects at UC Berkeley, one on Insect Ecophysiology, and one on king crab responses to climate change. In both projects, we'll be using RNA-seq to assess physiological reponses to environmental change, and to develop a suite of molecular biomarkers that can be used in larger population studies of response to climate change.

Now Scott is starting a new adventure as a bioinformaticist at Invitae.

For more about Scott: http://www.scott-fay.com/

Dr. Nathan Miller (2008-2013): Currently working in Anne Todgham's laboratory at RTC/SFSU and in Antarctica!

Nate is an environmental physiologist interested in understanding phenotypic plasticity, its role in allowing organisms to respond to environmental stress, and how changes in plasticity during ontogeny may influence stress tolerance.

For more about Nate: http://www.nate-miller.org ; email: namiller_at_sfsu.edu

Chelsea

Stephane Lefebvre (2008-2011): Currently a research scientist at the J. Craig Venter Institute in San Diego, CA.

Stephane's research focuses on the cellular biology and genomics of phytoplankton, and other photosynthetic organisms. In the Stillman lab, Stephane examined physiological and functional genomic responses of coccolithophores and diatoms to simultaneous shifts in dissolved carbon dioxide and nitrogen source (ammonium vs. nitrate) to understand how multiple environmental changes expected in future oceans would impact phytoplankton that play a major role in regulating the Earth's carbon cycle and climate.

Chelsea

Pascale Rossignol (2009-2010): Currently a postdoc at Yale Univ.

Pascale is interested in plant physiology. In the Stillman laboratory, she participated in projects involving transcriptome responses to thermal acclimation, and sequencing and subcloning LDH genes from porcelain crabs.

Chelsea

Mani Tagmount (2005-2009): Currently a research scientist in Chris Vulpe's laboratory at UC Berkeley

Mani is a terrific molecular biologist with interests in environmental stress responses. In the Stillman laboratory he worked on functional genomics of porcelain crabs, including our EST project, and variation in gene expression across ecological gradients in temperature. He also worked on cloning LDH genes from porcelain crabs.

Other Lab Alumni:

Undergraduate students:
Mikaela McCarthy, 2014: qPCR of aquatic insects and intertidal zone biology
Carl Hendrickson, 2013-2014: Aquatic insect ecophysiology and intertidal zone biology
Symphony Yu, 2014: juvenile porcelain crab growth under ocean acidification and warming
Will Neives, 2013-2014: embryonic porcelain crab growth under ocean acidification and warming
Joseph Gapuz, 2013: aquatic insect ecophysiology, thermal incubations
Shima Maddah, PostBac Student at SFSU 2011-2013; porcelain crab embryo experiments and image analysis
Cecilia Tran, 2013: RNA extractions, RNA-seq library construction, and qPCR of aquatic insects.
Jacqueline Nguyen, 2012: Aquatic insect ecophysiology
Trevor Allen, 2012: Aquatic insect ecophysiology
Carley Turner, REU Summer 2012: Porcelain crab heat shock protein expression
Heather Schneider, REU Summer 2012: Crab swelling disease, clam reproduction
Leore Geller, REU Summer 2011: Juvenile Dungeness crab distribution
Audrey Nickles, 2011: Crab larval biology
Jean-Claude Breach, 2010-2011: Ocean acidification effects on porcelain crabs
Garren Piccolo, 2010-2011: Crab larval biology
Cheyenne Snavely, 2011: Expression of extensin-like transcripts in crabs
Shamaila Khan, 2011: Clam enzymology
Jackie Prasad, 2011: Clam enzymology
Elise Latz, 2009: Coccolithophore biology
Anteo Quiroz, 2009: DNA analysis
Paula Robinson, 2008-2009: Microarray analysis of crab responses to thermal stress.
Daria Ronges, 2008-2009 (Dental School, Tufts University): microarray analysis of crab thermal acclimation.
Claudia Tomas Miranda, 2007-2008: microarray analysis of crab responses to thermal stress
Eddy Mazmanian, 2006: Aquarium control system engineering
Dianna Baldwin, REU Summer 2007: Thermal physiology of crab hearts
Morrigan Shaw, 200
6: Response to infection and thermal stress in crabs

High School interns:
Ricky Olivares, 2013: Tridacnid clam biology
Jeanne Shepherd, 2012: C
occolithophore responses to temperature
Sophie McGuinness, 2011: Corbula feeding biology

Other Laboratory Participants:
Trevor Alaurent, MS student from France at UC Berkeley 2014: qPCR of Dicosmoecus gilvipes from different thermal regimes.
Dian Li, MS student in mathematics at SFSU 2012-2013; RNA-seq statistics.
Vincent Leignel, French visiting professor 2013; green crab physiology, aquatic insect RNA-seq
Mudasir Andrabi, Indian CREST visiting professor 2013; red king crab RNA-seq transcriptomics
Melanie Schiffer, DAAD exchange PhD student from Alfred Wegener Institute, 2012: larval crabs and OA
Yoshihiro Tanaka, MS student in computer science at SFSU, 2008-2010: PCAD database
Dan Barshis, visiting PhD student from the University of Hawaii, 2007: Coral thermal acclimation
Jane Winhall-Rice, Technician, 2007