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.


Augustine Chemparathy

High School Student


I am a senior 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.


Chris Chen

Stanford Undergraduate Student


I'm a rising junior at Stanford majoring in Biology and looking to gain a broad, solid foundation in science and hopefully pursue medicine in the future. I'm thrilled to be able to spend this summer in the Jonikas lab working on protein localization as it relates to the CCM in Chlamydomonas. I've always been drawn to biology because it amazes me how such complex organisms in this world live, interact with, and support each other in such complicated ways. The science of life is, to me, the most interesting science of all.

In my free time, I like reading fiction, playing video games, going camping, hiking, and running, and watching movies.


Vivian Chen

Stanford Biology Rotation Student


Born and raised in Southern California, I graduated from UCLA with a B.S. in Molecular Cell and Developmental Biology in 2013 where I worked in Utpal Banerjee's lab studying the regulatory mechanisms of hematopoiesis in Drosophila melanogaster.

Science and research is the field of constant learning and pursuit/generation of knowledge. I consider myself the perpetual student and I love learning new things. So, science is the ultimate playground for me because I can ask questions and have the means to go and answer them. I also get to investigate how this crazy, beautiful, complicated world was created. In the Jonikas Lab, my goal is to help elucidate the structural and molecular regulation of the carbon concentrating mechanism (CCM) in Chlamydomonas reinhardtii in hopes that the knowledge will be applied to further understand photosynthesis and how to improve its efficiency.

Outside of lab, I really enjoy cooking and eating all kinds of delicious food and I am big proponent of trying new things at least once! Hiking, running, and bouldering are what I like to do when I am not being a homebody and watching cooking shows. At the end of the day, I am a yogi at heart and love savasana!


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.


Robert Jinkerson

Postdoc


I am a Life Science Research Foundation Postdoctoral Fellow (sponsored by the Simons Foundation) in the Jonikas Laboratory. My projects are focused on using high-throughput functional genomics to investigate algal lipid metabolism.

I obtained my Ph.D. from the Colorado School of Mines in the laboratory of Matthew Posewitz, where I was a NSF Graduate Research Fellow, and my BS in Biological Engineering at the University of Missouri. My Ph.D research focused on systems biology and genetically engineering algae for biofuel production. Some of my projects included altering starch metabolism in Chlamydomonas reinhardtii and sequencing the genome of Nannochloropsis gaditana.


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.


Matthew Rodman

Stanford Undergraduate Student


I'm a rising Junior majoring in biology and looking to gain valuable skills and critical thinking for my future in science. I'm extremely excited to work in the Jonikas lab this summer on protein localization in Chlamydomonas. I have always found biology so interesting because it unites many different disciplines in unexpected ways, creating fascinatingly complex systems.

In addition to biology, I also enjoy learning and attempting to speak German, hiking, watching TV and movies, and reading the occasional book.


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.


   
   



   

Former Members

 

Former Post-Docs:

Ru Zhang (2010 - 2014)

Mia Terashima (2011 - 2013)

 

Former Visiting Researchers:

Gregory Reeves (2013 - 2014)

 

Former Visiting Students:

Rachel Purdon (Spring 2013)

Madeline Mitchell (Summer 2012)

Elisabeth Schmidtmann (Spring 2012)

 

Former Technicians:

Saman Parsa (2013 - 2014)

Sean Blum (2011 - 2013)

Spencer Gang (2010 - 2012)

 

Former Undergraduate Students:

Jessie Bacha (Summer 2014)

Rachel Vasquez (Summer 2014)

Graciela Watrous (Summer 2012)