People

 

 

Current Members


Martin Jonikas

 

PI


 

I obtained my Ph.D. from UC San Francisco where I was mentored by Jonathan Weissman, Peter Walter and Maya Schuldiner. In my thesis project, we developed a novel high-throughput genetic strategy for identifying new genes with roles in protein folding in the secretory pathway, and for accurately predicting their functions.

I believe in a healthy work/life balance: work hard, play hard. Vacation and rest gives one a fresh perspective on one's projects and career, allowing one to be more productive in the long run.

I am committed to providing a nurturing training environment for everyone in my lab. When I cannot provide mentorship or expertise myself, I will strive to help my lab members find additional mentors and resources.

CV


Ute Armbruster

 

Postdoc


 

Photosynthesis is the biological process that harnesses light energy from the sun to allow life on earth. While the electron transfer reactions of photosynthesis are well understood, there is a large number of genes with so far unknown functions that are associated with this process by conservation in the “green” lineage and/or on the basis of co-expression with known photosynthesis genes. During my Ph.D. thesis in the lab of Dario Leister at the University of Munich, I studied such novel photosynthetic proteins and characterized assembly factors, RNA-binding proteins, and thylakoid network “morphogens,” all of which are important to sustain the basics of photosynthetic electron transport.

Now, I aim to find novel regulatory factors of photosynthesis within this set of undescribed photosynthesis-associated genes. With my project in the Jonikas lab I am following the hypothesis that thylakoid ion channels and transporters are important to adapt the photosynthetic machinery to changes in light intensities.

Since November 2013 I have also joined the lab of Kris Niyogi at UC Berkeley.


Outside of lab I love watching and helping my baby son discovering the world around him. I also enjoy skiing, hiking and surfing, for which the Bay Area is a prime spot to live in.


Liz Freeman

 

Stanford Biology Graduate Student


 

I graduated from Washington University in St. Louis in 2011 with a B.A. in Biology with a focus on Biochemistry.  While studying there I worked in the lab of Dr. Ursula Goodenough and wrote my senior thesis on late-zygotic microRNAs in Chlamydomonas.

I enjoy research because it is the ultimate logic puzzle.  Nature has solved complex problems billions of years before humans stumbled upon the same questions, and the ability to uncover the secrets of the world we think we know so well amazes me. For my graduate work I am studying the carbon concentration mechanism (CCM) of Chlamydomonas reinhardtii. This mechanism allows for more efficient photosynthesis than in many crop plants, but it is currently not well understood. Together with Luke Mackinder, I am developing a novel Förster Resonance Energy Transfer (FRET) fluorescent biosensor for inorganic carbon. I am also using pH sensitive fluorophores to study inorganic carbon localization and dynamics. It is possible that if we better understood the Chlamydomonas CCM, we could engineer crop plants to fix more carbon and have higher yield.

Outside of the lab I enjoy digital photography, hiking, reading, exploring the Bay area, and watching reality TV cooking shows – especially those involving dessert.


Nina Ivanova

 

Technician


 

I graduated from Williams College, MA in 2009 with a BA in Biology. While an undergraduate, I worked with Dr. Dan Lynch and wrote my thesis on characterizing Arabidopsis thaliana sphingolipid mutants. Following the fashion of studying completely unrelated things at liberal arts institutions, my other major was Art; fortunately, it has come in handy on a few occasions in my scientific endeavours. After college, I started working as a research associate at Aurora Biofuels (now Aurora Algae, Inc.), a company developing technologies for farming algae in open ponds for production of high-value pharmaceuticals and biofuels. After three years of industry experience, I am happy to join the Jonikas lab and continue supporting research in an academic setting.

I enjoy scientific research because I am fascinated by the microcosms that make up our enormous macroscopic world. I like seeing how processes at the molecular and cellular level percolate into organisms on a much larger scale.

My main effort in this lab concerns the design and execution of a photosynthesis screen of the entire mutant library, together with Ru Zhang, Arthur Grossman, and Martin Jonikas. In addition, I contribute to maintaining the library and experimenting with storage conditions.

In my free time, I dabble in entirely too many hobbies. Some of my long-time favorites include a few different styles of dancing, as well as being a maker. I am especially fond of sewing historical costume reproductions for the many costume events in the Bay Area.


Xiaobo Li

 

Project Leader (Mutant Library Project)


 

I obtained my Ph.D. from Michigan State University. During my Ph.D., I worked with Christoph Benning and Min-Hao Kuo on the biochemistry and genetics of lipid metabolism in Chlamydomonas. I also had a side project to study aging with Baker's yeast as a model system.

In the Jonikas lab, I am working together with several colleagues on the generation of an indexed mutant library for the Chlamydomonas community. I am also going to use this library to answer questions in plant lipid metabolism.


After working hours, I like cooking, watching movies and playing badminton. The nice weather in the Bay area also motivates me to bike everyday, as a way of relaxation as well as transportation.


Luke Mackinder

 

Postdoc


 

My scientific passion lies in understanding the fundamental mechanisms behind
cellular processes. My research at Carnegie focuses on the Chlamydomonas carbon
concentrating mechanism (CCM). Chlamydomonas has a high affinity CCM that
raises the CO2 concentration around Rubisco through the use of carbonic anhydrases,
inorganic carbon transporters and pH gradients. Chlamydomonas has the best-
characterized eukaryotic CCM, however, there are still large gaps in our knowledge
of the cellular components, where they operate and how inorganic carbon flows
through the cell. My work focuses on the cellular distribution of CCM components and
developing novel tools to measure intracellular inorganic carbon concentrations to
understand cellular carbon fluxes.


Jason Middleton

 

Stanford Undergraduate Student


 

I am junior at Stanford University pursuing a bachelor’s degree in biology, with plans to work in
healthcare or academia. In my most recent research experience I studied self-assembling semi-
conducting crystals in the Materials Science and Engineering Department at Stanford.

I am drawn to research in biology because I find it has a unique complexity unparalleled to any
other science. Specifically, I am fascinated by the intricate regulatory systems that govern life
and arose naturally from billions of years of evolution. My goal is help improve the scientific
understanding of an important regulatory pathway in Chlamydomonas.

In my free time I enjoying running, hiking, skiing, downhill longboarding, music, and
spontaneous day trips.


Leif Pallesen

 

Postdoc


 

The pursuit of understanding life at the molecular level has been an exciting journey. The similarities of living systems at the molecular level are indeed remarkable. This potentiates the integration of pathways of various organisms to create living systems that are optimized for specific functions. My overall goal as a scientist is to generate understanding of relevant pathways and use this understanding to guide the engineering of novel living systems.

Enhancing photosynthetic efficiency is one approach to increasing food and biofuel production. Currently I am developing and implementing a high-throughput growth screen to identify genes related to photosynthesis in Chlamydomonas reinhardtii. Specifically, I want to identify genes that increase carbon fixation rates. This understanding could then be used to engineer photosynthetic organisms with increased rates of biomass production.


Weronika Patena

 

Bioinformatics Analyst


 

I graduated from Caltech with B.S. degrees in Biology and Computer Science.  I spent over 4 years in the McManus lab at UCSF, researching shRNA design and developing a data analysis pipeline for RNAi screens. 

I started out doing more benchwork than bioinformatics, but my interest has shifted to applying my programming skills to analysis of experimental data and developing tools for others to use.  New large-scale screens made possible by the advances in deep-sequencing provide a lot of data that we’re still learning how to get the most from, and plenty of interesting computational problems. I very much enjoy both thinking about the best way to do the analysis, and the process of writing efficient and flexible programs. My favorite programming language is Python.

I have too many hobbies, including rock-climbing, hiking, role-playing games, skiing, various crafts, and occasional photography - but most of the time I just stay in to read and relax in the evenings. I love to travel to visit friends and family in Poland and all over the US when I have the time, but Northern California is my favorite place to live.


Matt Prior

 

Stanford Biology Graduate Student


 

I graduated from UCLA with a B.S. in Microbiology, Immunology, and Molecular Genetics in 2010. I was fortunate to train in the laboratory of Dr. David Campbell and Dr. Nancy Sturm and completed my department honor thesis on the maturation process of small RNAs in Trypanosoma brucei, a single cell flagellated parasite from Africa.

I enjoy research because it offers the potential to ask and then answer some of the most exciting questions about organisms and their dynamic responses to change and challenge. At the same time, I value how these insights can help us address many problems that require new biologically based solutions.

 I am huge fan of being outside in the Bay Area with my friends and family. I love hiking and birdwatching in the foothills during the evenings, spearfishing in Carmel with my siblings, and hanging out at night after finishing up in lab.


Silvia Ramundo

 

Collaborating Postdoc, Walter Lab, UCSF


 

There is ample evidence that cells sense the functional state of chloroplasts. Thus, retrograde signals must travel from the chloroplast to the host nucleus to trigger reprogramming of gene expression. I am very curious to understand, at the mechanistic level, how conditions inside the organelle are sensed, how signals are triggered, how they cross compartmental boundaries, and to what extent they are self-sufficient or integrated with other signalling pathways. To this aim, I am in the process of designing a high-throughput genetic screen in close collaboration with the laboratory of Dr. Martin Jonikas.

I graduated from Bologna University, in Italy, with a degree in Pharmaceutical Biotechnology. I carried out my master thesis project on splicing regulation in the model yeast S. cerevisiae at the Center for Genomic Regulation, in Barcelona, Spain. In summer 2006, I trained in the laboratory of Dr. Jim Umen at the Salk Institute, in San Diego, USA, where I learned about regulation of cell cycle in the green algae C reinhardtii. Later on, I joined the International PhD Program in Life Sciences at the University of Geneva, in Switzerland. As a major achievement of my research studies in the laboratory of Prof. Jean-David Rochaix, I developed a riboswitch-mediated gene expression system. This genetic tool made it possible, for the first time, to achieve a specific, conditional and reversible knock-down of any essential chloroplast gene. Since autumn 2013, I am a postdoctoral scholar at UCSF, in the laboratory of Prof. Peter Walter.


Gregory Reeves

 

Visiting Researcher


 

I graduated from New Mexico State University (NMSU) with a B.S. degree in Genetics in 2011 and again with an M.S. in Horticulture in 2013. I worked in the NMSU Chile Pepper Breeding and Genetics Program under Dr. Paul W. Bosland. My master’s work involved characterizing a novel disease resistance inhibitor gene and breeding for increased pungency (spicy flavor) in chile pepper, and as a result generated the world’s hottest pepper. Additionally, I was involved in the Chile Pepper Genome Sequencing Project.

As a visiting researcher in the Jonikas Lab, I am assisting in generating a large scale mutant library for high-throughput characterization of unknown genes in photosynthesis, in particular genes that are associated with the Chlamydomonas carbon concentrating mechanism. I hope to gain a better understanding of photosynthesis for biotechnology applications for increased yield potential in economically important crops.

Outside of the lab, I thoroughly enjoy hanging out with friends, gardening and playing video games. I routinely go camping, hiking and skiing in the winter.


Rebecca Yue

 

Technician


 

I graduated from UC Berkeley in 2013 where I majored in Molecular and Cell Biology. During my time at Cal, I worked in the Lu lab, where I also did my undergraduate thesis on protein interactions involved in Salmonella pathogenesis. I really enjoyed my time as an undergraduate researcher and am excited to learn more about Chlamydomonas throughout my time here at the Jonikas lab.

I am drawn to research because it challenges you to think critically and to tackle things from all perspectives. It is also exciting (and really pretty!) to explore the world at the microscopic level.

In my free time, I enjoy biking, hiking, and exploring my way around the Bay Area. When I’m not outdoors, I love watching TV shows and playing board/card games with friends.


Ru Zhang

 

Postdoc


 

I got my Ph.D. from University of Wisconsin-Madison in 2009. During my graduate study, I worked with Dr. Tom Sharkey to investigate the effects of moderate heat stress on thylakoid reactions of photosynthesis in light-adapted, intact Arabidopsis and tobacco leaves.

Science research is enjoyable. Interesting and puzzling phenomena in my research work drive me to propose hypotheses and design experiments to test them. It is this process that gives me huge excitement about research and makes me feel like a science detective. I am also impressed by elegant and complex regulatory mechanisms in biological organisms, and amazed by how they respond to changing environment to protect themselves.

My project is to develop a high throughput genotyping tool in the unicellular green alga Chlamydomonas to enable genome-wide screens for mutants deficient in photosynthesis and the generation of an indexed mutant library. The tool is now established and is called ChlaMmeSeq (Chlamydomonas MmeI-based insertion site Sequencing). I'm using ChlaMmeSeq to screen for mutants of interest.

Outside lab, I like cooking, gardening, and traveling. Balanced and tasteful meals make me healthy and energetic. My favorite place for relaxation is a beautiful garden where I feel fresh and appreciate the beauty of the world. One of my biggest dreams is to travel around world with my family. The time I spend with my family is rewarded with passion for life and enthusiasm for work.

     
     



     

Former Members

   

Saman Parsa

Technician, 2013-2014


I graduated with my bachelor’s degree in plant genetics from UC Davis in 2008. Afterwards, I worked in Dr. Wolf Frommer’s lab at Carnegie. During my time there I worked on developing a comprehensive interactome map for Arabidopsis membrane proteins. I then decided to pursue a career in winemaking, on which I am currently working when the grapes are in season. I have joined the Jonikas lab to work on the high-throughput phenotyping screen. When I’m not working, I enjoy listening to jazz music, cooking, and walking around the beautiful city of San Francisco.

Mia Terashima

Post-Doc, 2011-2013


I attended the University of Münster, Germany for my graduate studies, finishing my doctorate in the spring of 2011. During my dissertation research, I was mentored by Michael Hippler, and I studied the anaerobic response and changes occurring in the chloroplast proteome of Chlamydomonas.I attended the University of Münster, Germany for my graduate studies, finishing my doctorate in the spring of 2011. During my dissertation research, I was mentored by Michael Hippler, and I studied the anaerobic response and changes occurring in the chloroplast proteome of Chlamydomonas.

In my free time, I like to spend time outdoors, cook together with friends and travel whenever possible.


Sean Blum

Technician, 2011-2013


I received my B.S. in Biochemistry at UC San Diego.  While studying there I worked in the lab of Dr. Dong-Er Zhang to characterize the translational mechanisms of USP18, a protein involved in interferon treatment for cancer.  Although new to the study of Chlamydomonas, I find the research here to be rewarding—due in equal parts to the fascinating cell biology, the cutting edge techniques employed, and the welcoming lab environment.

Outside the lab, I am a private math tutor, as well as an amateur music producer.  I love tinkering with my music software, watching movies, and playing games with friends.

Sean is currently working towards a Masters degree in bioinformatics at the University of California, Santa Cruz.


Augustine Chemparathy

High School Student, Summer 2013


I am a junior at Dougherty Valley High School in San Ramon, California, where I am working towards a career in science. Ever since my head was lower than what is now my elbow, I’ve adored biology, and it’s fantastic to have a chance to drag my interests out of the realm of the theoretical. Biology is amazing to me because it promises us answers to systems that seem immeasurably complex, allowing us to wade through the intricacies and peccadilloes of life and unravel the truth, one strand at a time.

In my spare time, I like to read just about anything by Kurt Vonnegut, watch movies, and bike.


Rachel Purdon

Visiting Student, Spring 2013


I graduated from Cambridge University in 2012 with a degree in Natural Sciences (Plant Science), and since then have been carrying out algae-related projects in various labs around the world, prior to starting a PhD. I spent 3 months at Rutgers University, NJ, working with Phaeodactylum, but now it's nice to come back to my favorite species - Chlamydomonas. At Cambridge I was involved in the CAPP (Combining Algal and Plant Photosynthesis) project both as a summer student and during my final year research project, so it is a wonderful opportunity to be able to continue to be involved in the same project from Carnegie.

I enjoy cycling, walking in beautiful places, and reading in the sunshine! I am really excited about the opportunity to travel and explore - so I'll definitely be making the most of my time living in California.

 


Graciela Watrous

Stanford Undergraduate Student, Summer 2012


I am currently a Stanford undergraduate in Biology with a particular interest in agricultural engineering. Working in the Jonikas lab is my first experience with hands on scientific research, which makes every step part of an exciting new learning process.

I enjoy the research I have done so far because I have an amazing, patient mentor, Ru Zhang, and because I get to be a very small part of exploring biological processes directly linked to the environment—research that will influence future discovery of biological responses and solutions to climate change.

In my free time, I throw pottery, read, write plays, and hike.

Gracie is currently working towards her bachelor's degree at Stanford University.


Madeline Mitchell

Visiting PhD Student, Summer 2012


I studied a double degree in Arts/Science at the University of Melbourne, Australia, majoring in Botany and Biochemistry/Molecular Biology. I undertook my Honours research project in the Plant Physiology lab, where I investigated the biosynthesis of eucalyptus oil.

I am now finishing my second year of a PhD in the Physiological Ecology group at the University of Cambridge. I am working on the chloroplast pyrenoid and carbon concentrating mechanism in Chlamydomonas so I have come to spend two months in the Jonikas lab as part of a collaboration.

I enjoy being outdoors in my free time so sunny California is a welcome change from less-than-sunny Cambridge! I also enjoy cooking, reading and the opportunity to explore new places.

Maddie is currently continuing her PhD work at the University of Cambridge.


Elisabeth Schmidtmann

Visiting Student, Spring 2012


I obtained my B.S. in Biology from LMU, Munich, Germany. There, I was mentored by Dr. Iris Finkemeier. My bachelor thesis project was on the protein-biochemical characterization of the Arabidopsis citrate synthase.

What I like most about science is the discovery of the previously unknown. I am fascinated by life on earth with its complexity and (im)perfections. There is still so much to find out about it, and I really like the idea that with my work I might contribute to a better understanding of a small or maybe even bigger aspect of it.

Elsie is currently a Masters student at Ludwig Maximilians University Munich. 
 


Spencer Gang

Technician, 2010 - 2012


I graduated from Santa Clara University in 2009 with a B.S. in Cellular and Molecular Biology. While studying at Santa Clara, I worked with Dr. Craig Stephens to develop pathways for metabolism and regulation of common herteropolysaccharides in the freshwater bacterium Caulobacter crescentus.

I enjoy doing research because there are so many unknowns. Any research question can serve as the springboard to hundreds more. It is a constant but rewarding challenge that requires me to think in innovative ways on a daily basis.

When not in the lab I enjoy spending time with close friends and visiting my family. I also love competing in any type of sport or game. My favorites are basketball, football, and snowboarding, but there are few challenges I won’t accept. When I want to relax, or I’m feeling lazy, I like to go to the movies or read a book by the pool.

Spencer is currently a PhD student at the University of California, Los Angeles.