Summer Intern Program 2019

The Bhaya Lab:

Devaki Bhaya, Senior Staff Scientist

Research in my lab is driven by an interest in understanding how photosynthetic microorganisms perceive and evolve in response to environmental stressors, such as light, nutrients and viral attack. We focus on cyanobacteria which are abundant, globally relevant and have been used to probe environmentally important processes ranging from photosynthesis to symbioses to circadian rhythms. We work both with model organisms and with cyanobacteria in naturally occurring communities. Recently,we have started to develop synthetic biology-inspired approaches to use in cyanobacteria.



Rick Kim, Postdoctoral Research Associate in the Bhaya Lab

Rick's project: The Bhaya Lab is interested in understanding how photosynthetic organisms respond to various environmental conditions. The three main research focuses are 1) metagenome sequence analysis, 2) Engineering thermophilic cyanobacteria, and 3) synthetic biology. We have sequenced DNAs of samples from the nature (the hot springs in Yosemite). We are taking bioinformatic approaches to get the distribution and abundance information of the entire microbes in the samples and analyze the CRISPR sequences to discover the interactions between bacteria and bacteriophage (viral attacks). Also, we are engineering the thermophilic cyanobacteria to understand the features and functions of the genes and  apply to protein engineering at high temperature. Lastly, we are also developing synthetic biology tools in cyanobacteria to enable various applications in agriculture and microbiology. In our internship training, you’ll be able to gain experience in molecular cloning, PCR, Western blot, and bioinformatic analysis.

Kriti Shukla, Undergraduate at UCLA, working with Dr. Rick Kim

A few words from Kriti: I am a 1st year Biochemistry and Applied Mathematics major at UCLA. She has experience researching the species prunus subhirtella as part of a Plant Biology lab at Johns Hopkins, hummingbird wing movement as part of a Biomechanics lab at Stanford, fish microbiota as part of an EEB lab at UCLA, and human stress responses as part of an Anthropology lab also at UCLA. In the future, she hopes to pursue a career in pediatric medicine. 




The Ehrhardt Lab:

David Ehrhardt, Senior Staff Scientist

We investigate plant cell development and morphogenesis, utilizing live cell imaging techniques and moelcular genetics  to visualize and investigate the organization and dynamic behaviors of molecules and organelles. Problems of special interest include how cells generate asymmetries and specific shapes. A current focus is how the cortical microtubule cytoskeleton acquires organization and how this organization in turn functions to organize the plasma membrane and cell wall to guide patterns of cell growth and division.


Suryapta Jha, Postdoctoral Research Associate in the Ehrhardt Lab

Sury's project: Intrinsically Disordered Proteins (IDPs), found widely in eukaryotes, are characterized by their lack of a tertiary structure. These proteins instead form multiple alternative conformations based on their interaction with other proteins. In both plant and mammalian systems, IDPs have been implicated to act as sensors because of their ability to phase separate and assemble into proteinaceous droplets under various environmental and physiological stressors. Moreover, recent studies have demonstrated that IDPs may interact with cellular organelles to facilitate the activation and regulation of different stress response pathways.

Despite recent progress in the functional studies of IDPs in general, some significant questions remain to be addressed. I am interested in a group of previously uncharacterized IDPs in Arabidopsis thaliana, that are predicted to be transported to the cell periphery. I am interested in understanding whether these putatively secreted IDPs are involved in the organization of cell wall and/or formation of extracellular vesicles essential for cell-to-cell communication during plant development, to regulate plants’ response to environmental changes.

The Plant Biology Summer Internship Project will involve characterizing two of these novel IDPs, At2G05510 and At1G27710, that encode disordered proteins enriched in amino acid glycine. Glycine rich proteins in Arabidopsis have been reported to function in stress response pathways. We will characterize these two candidates by analyzing growth phenotypes of t-DNA mutants under different conditions. Additionally, using confocal microscopy, we will look at the subcellular localization patterns in the transgenic lines expressing the GFP-tagged fusion proteins.

The intern will be responsible for generating preliminary data and hypothesis about the function of these two proteins in plant development.

Danika Ferguson, Undergraduate at UC Irvine, working with Dr. Sury Jha

A few words from Danika: My name is Danika Ferguson and I am a third year biological sciences undergraduate student at UC Irvine. I really wanted to go into biology because I have always looked up to Jane Goodall, and I thought biology would be general enough to get into a lot of different fields in the future. I plan to graduate UCI in Spring of 2020 and then enter the science field to further explore my interests in plant biology and drug discovery. In my free time I like reading, drawing and playing with my dog when I’m home. My hometown is San Mateo, CA, where my parents, brother and dog all live.  



Heather Meyer, Postdoctoral Fellow in the Ehrhardt Lab

Heather's background: Heather received a B.A. in premedical sciences in 2011 from Sarah Lawrence College and a Ph.D. in genetics, genomics, and development in 2016 from Cornell University. She has been a postdoctoral fellow in David Ehrhardt’s Plant Biology lab since 2016,  and she was awarded Carnegie’s twelfth Postdoctoral Innovation and Excellence Award in 2019. These prizes are given to postdocs for their exceptionally creative approaches to science, strong mentoring, and contributing to the sense of campus community. The nominations are made by the departments and are chosen by the Office of the President. 

Heather initiated a pioneering scientific project to identify the molecular mechanisms that plants use to sense and respond to seasonal temperatures in order to regulate flowering time and reproduction. Timing of reproduction is critical for plant success and is particularly important with global temperature rise. This project is an interdepartmental collaboration between the Ehrhardt lab and Yixian Zheng’s lab at the Department of Embryology initiated with a Carnegie Venture Grant.

Heather obtained preliminary data that allowed her to receive two competitive fellowships to continue this project, including the highly competitive Life Science Research Fellowship. She also was chosen to present her results to the Carnegie trustees at the May 2018 meeting.

Heather’s outstanding leadership and outreach includes co-founding a campus-wide interest group on the biology of intrinsically disordered proteins, which meets once a month and fosters cross-departmental and Carnegie-Stanford interactions.  Heather and three other group members also took the program to the California Academy of Sciences for an outreach night where they taught the public about these proteins using hands-on activities with simple household ingredients.

Heather is also a leader in the Carnegie Institution Postdoc Association. She organizes community events and helps to draft the letters sent to Carnegie’s leadership.

Ethan Trans, Graduate of UC Santa Cruz, working with Dr. Heather Meyer

A few words from Ethan: I just graduated with a Molecular, Cellular, and Developmental Biology B.S. from UCSC. I worked in a neuroscience lab for 2 years when I was at UCSC in Yi Zuo's Lab. I am currently interested working in research, industry, or pursuing medicine but I have no idea what to do with my life. Currently, I'm unsure as to what specific career path I want to pursue, but hopefully this experience can shed some light. 

I'm originally from East San Jose, but I'm living in Los Gatos at the moment. Some of my hobbies include cooking, camping, reading manga, and olympic weightlifting. I just got a fishing rod and just started fishing/crabbing and foraging so I'm still an amateur.


Jacob Moe-Lange, Postdoctoral Research Associate, in the Ehrhardt Lab

Jacob's project: Though plants lack a nervous system, they use long distance signaling in ways analogous to animals. Herbivory and mechanical damage trigger long distance electrical signals emanating from the source of damage, which propagate to distal unwounded leaves and trigger defense mechanisms. These signals are fast, traveling at 4-8cm min-1 and only travel to leaves that are vascularly connected to the wounded leaf. However, the molecular components and mechanisms underlying this long distance signaling is poorly understood. Deciphering long distance signaling in plants could have profound implications in agriculture by giving us the tools necessary to understand intra-organ communication in plants.

We are looking for highly motivated, creative applicants who are interested in advancing plant research. Broadly, the interns will screen a series of candidate mutants using an electrophysiological assay. We will identifying mutant lines that have altered signaling phenotypes and further characterize them. Interns will develop reporter lines to spatially identify candidates’ tissue and cellular localization. Interns will also receive extensive training in live cell fluorescence microscopy. By the end of summer, we expect that interns have learned multiple advanced cloning and molecular techniques, plant electrophysiology, and fluorescence microscopy.

Celia Charlton, Undergraduate at Stanford University, working with Jacob Moe-Lange

A few words from Celia: I am a freshman at Stanford, undeclared, but hoping to study human biology  with a concentration in economics. I have lived in California my entire life, where I have pursued both my passions for the visual arts and athletics as well as discovered my curiosity for the natural world. I am very excited to work at Carnegie, where I will begin learning professional skills that will help me further pursue my interests!


The Grossman Lab:

Arthur Grossman, Senior Staff Scientist

Our activities over the last five years have been extremely diverse, crossing over various disciplines. We have explored research areas ranging from identifying new functions associated with photosynthetic processes including proteins involved in the biosynthesis and regulation of the photosynthetic apparatus (assembly of photosystem I, assembly/stability of the cytochrome b6f complex), mechanism(s) of coral bleaching and the impact of temperature and light on the bleaching process, metabolic switching in algae as they transition from oxic to anoxic conditions, the analyses of algae associated with desert crusts, the regulation of sulfur and nitrogen metabolism in green algae and the role of the acidocalcisome in acclimation to a low nutrient environments, the use of atomic force microscopy to probe the structure and dynamics of the photosynthetic apparatus, pathways for photosynthetic electron flow in microbes in marine and fresh water environments and evolutionary events involved in transitioning from an endosymbiotic association to the establishment of an organelle. We have also focused significant effort on generating a more thorough analysis of the Chlamydomonas genome and establishing various methods for examining the transcriptome and the function of proteins involved in photosynthesis and acclimation processes. The work from the laboratory is given in detail in manuscripts listed under publications.

Weichao Huang, Postdoctoral Research Associate in the Grossman Lab

Weichao's project: NAD(P)H and ATP are the common cellular currencies. Recently, the exportation of energies from chloroplast to the other compartments is becoming a hot topic. Studies on this subject provide promising possibilities for metabolic engineering. Intracellular transport of ATP/NAD(P)H form a complex traffic network, allowing metabolic pathways are connected. Photosynthetic organisms have two ATP producing organelles: chloroplasts and mitochondria. Light stimulates electron flow in chloroplasts that is coupled to the formation of NADPH and ATP. In the dark, the cells depend on mitochondrial electron transport to generate energy; NADH that is primarily generated from the Tricarboxylic Acid or Krebs Cycle is used by mitochondrial electron transport to synthesize ATP. However, these two energetic generating systems can communicate and under various conditions reductant can be shuttled from chloroplasts to mitochondria. Accumulating evidence suggests that under various conditions there is a strong coupling of chloroplast and mitochondrial electron flow that can function in balancing the production of reductant and ATP, dissipating excess excitation energy as heat and diminishing the production of reactive oxygen species. Although chloroplast and mitochondria cooperation was hypothesized, not a lot of experimental quantitative data was presented to support this important notion.  My project is aiming to address how these two energetic generating organelles do cross-talk by applying various genetic and molecular technologies. Metabolic and proteomic analysis will also be used.

Ju Yu (Andrea) Lin, Undergraduate at UC Santa Cruz, working with Dr. Weichao Huang

A few words from Andrea: My name is Andrea, and I will be graduating from the University of California, Santa Cruz this upcoming June, 2019 with a B.S. degree in Molecular Cell and Development Biology.  During my undergrad research, I study toxic RNA biology, mechanism and regulation of alternative pre-mRNA splicing, and post-transcriptional control of gene expression.


Justin Findinier, Postdoctoral Research Associate in the Grossman Lab

Justin's project: Chloroplasts and mitochondria are highly cooperative organelles in a plant cell. In the day time, carbon backbone derived from photosynthetic CO2 fixation are exported from the chloroplast to the mitochondria and participate in respiration. During the night, ATP formed by respiration in the mitochondria will be transferred to the chloroplast to sustain a number of essential functions. This crosstalk between both organelles is challenged by the presence of two physical barriers: the chloroplast envelope (composed of an inner and an outer membrane) and the mitochondrial double membrane. Several transporters allowing the passage of metabolites have already been characterized in plant cell but their number is still limiting in view of the multiplicity of molecules produced in both organelles. One of the aim of my project is to identify new transporters/translocators involved in the interfacing of chloroplasts and mitochondria by directly looking at the protein composition of the membrane through a proteomics approach.

Besides, we believe that those exchanges might be promoted by bringing the two membrane systems close together. This is for example the case in high light conditions where the mitochondria switch from a random, central distribution to a peripheral position, surrounding the chloroplast. This tight interaction might involve membrane contact site (MCS) where both the outer mitochondrial membrane and the chloroplast outer envelope membrane are anchored to each other by membrane inserted proteins. The second aim of my project is to prove that these MCS happen in Chlamydomonas reinhardtii using a fluorescence approach.

If you choose to join and help me achieving the goals of my projects, you will get familiar with basic biochemistry and molecular biology techniques such as western blot, PCR, cloning. You will also use DNA sequencing to check you did a great job. Hopefully, you will also have the opportunity to use photosynthesis measurement techniques and fluorescence imaging. Additionally to standard cloning, you will be initiated to Modular Cloning which is a new and powerful tool for manipulation of Chlamydomonas reinhardtii. Don’t hesitate to send me an email for more details.

Alina Ng-Parish, Graduate from UC Berkeley, working with Dr. Justin Findinier

A few words from Alina: I am a recent Genetics and Plant Biology graduate from UC Berkeley with a passion for all things algae. My background includes a broad range of plant based topics like plant physiology and biochemistry to medical ethnobotany. However, my most enjoyable experience was my Biology of Algae course. In the future I hope to do some kind of algal biochemistry work aimed toward pharmaceutical products.




Emanuel Sanz-Luque, Postdoctoral Research Associate in the Grossman Lab

Emanuel's project: My research focuses on how the photosynthetic alga Chlamydomonas copes with stress, specifically nutrient deprivation and excess light. In nature, organisms frequently face harsh conditions and struggle to survive. Polyphosphate, a energy rich molecule conserved from bacteria to humans, is essential for the acclimation to a wide variety of stresses. In Grossman’s lab I am trying to understand how the synthesis of this molecule helps Chlamydomonas cells acclimate to these conditions.  

In this project the intern will learn how to handle Chlamydomonas cultures, will measure different enzyme activities and will acquire some experience in a set of molecular techniques used in our lab.

Inderpreet Kaur, Undergraduate at Coventry University in the UK, working with Dr. Emanuel Sanz-Luque

A few words from Inderpreet: Inderpreet Kaur is currently an undergraduate majoring in Biomedical Science at Coventry University within the United Kingdom. Her previous research consisted of working with Nuffield Research in the field of epidemiology, whereby she was awarded the SWAN Athena for producing a scientific report on interdigital dermatitis during her placement. Further previous experience consists of working within Warwick University’s biology department to examine the induction of B-galactosidase in E.coli by using a colorimetric substrate, ortho-nitrophenolgalactosidase (oNPG). Supporting the medical aspect of her degree, she is qualified and trained within first aid by St John Ambulance, awarded a care certificate for being qualified and trained as a care assistant and awarded by University Hospital Coventry and Warwickshire NHS Trust for completing a clinical program. She has recently joined the Grossman Lab to perform research as an intern at Carnegie Institute of Science, to investigate within molecular biology, how the synthesis of polyphosphate molecules helps Chlamydomonas cells to acclimate within harsh conditions.


Tingting Xiang, Postdoctoral Research Associate in the Wang Lab

Tingting's project: The marine dinoflagellate alga Symbiodinium forms a symbiotic relationship between a variety of marine animals, most notably coral. They provide coral with photosynthetically fixed carbon while the coral supplies Symbiodinium with inorganic nutrients and a haven from predation. However, this symbiotic relationship is particularly susceptible to environmental perturbations, such as heat and ocean acidification. The break-down of this relationship, or ‘coral bleaching’ can ultimately lead to coral death and destruction of the reef ecosystem.

Although coral bleaching has been studied extensively at the ecological level, we know very little about the mechanisms governing the establishment, maintenance and breakdown of the coral-dinoflagellate interaction. Currently we are focusing on establishing the genetic tools (including CRISPR-based genome editing tools) for dinoflagellate alga Symbiodinium, and establishing the genetic system would allow us to understand the fundamental aspects of algal biology and thus greatly enhance our knowledge of algal-coral symbiosis. It is a great opportunity to gain experience in molecular biology, genome editing, and genetics and so on. It is also a wonderful opportunity to work on coral symbiosis in a lab model system. 

Elizabeth Duan, Undergraduate at UC Irvine, working with Dr. Tingting Xiang

A few words from Elizabeth: I am a current undergraduate Biochemistry major at UCI participating in the Carnegie Institute of Plant Biology's summer internship. I am interested in research concerning how climate change affects interactions between organisms and between organisms and the environment. I hope to expand my knowledge of laboratory techniques and the research process during my time here at Carnegie Science.




The Rhee Lab:

Sue Rhee, Senior Staff ScientistOur lab combines computational and experimental approaches to reveal molecular mechanisms underlying adaptive strategies in plants. We focus on metabolic traits at multiple scales including individual genes, pathways, and networks. We also uncover novel functions, mechanisms, and pathways of 'unknown' genes (those that are not similar to any known genes), which is taking us to areas of research we never thought of studying before.


David Hoang, Undergraduate at UC San Diego, working with Dr. Sue Rhee

A few words from David: I am currently an undergraduate student pursuing a bioengineering major at UC San Diego. I've always been fascinated by the mechanisms of the natural world, from the intricate interactions between cellular molecules to the rich beauty of the flora and fauna on this planet. My personal goal is to understand the countless facets of the world we live in, and as such I am always willing to learn about something new regardless of the subject. Recently, I have been working on expanding my technical repertoire through projects including scoliosis modelling through 3D printing and electrogram analysis. In my free time, I love letting my creative side loose through photography, cinematography, graphic design, and writing! My hope is to portray the beauty of science through my artistic capabilities, and to convey a story through my own lens. 


Karine Prado, Postdoctoral Research Associate in the Rhee Lab

Karine's project: Deciphering the mechanisms of thermo-adaptation of an extremophilic desert plant. Global warming is changing the habitability of many places for many species on Earth. Understanding thermo-adaptation in plants is critical and timely for global sustainability, food security and species conservation. In the 1970s, Carnegie scientists studying Tidestromia oblongifolia in Death Valley discovered that this Amaranth is highly adapted to high temperatures. Almost 50 years have passed and the molecular basis of its remarkable thermo-adaptation of photosynthesis remains largely uninvestigated.

The summer intern will be involved to decipher the mechanisms of thermo-adaptation of T. oblongifolia at multiple scales. Specifically, he/she will examine if the trichomes play a substantial role in the mechanisms of thermo-adaptation of T. oblongifolia and compare root architecture of T. oblongifolia with a heat sensitive Amaranth. Plants and material will be ready for the student at the beginning of internship.

Suhyun (Suzie) Lee, Undergraduate at Cal Poly University, working with Dr. Karine Prado

A few words from Suzie: I'm currently a first year student at Cal Poly University studying biology. Molecular biology has always piqued my interest. My long-term goal is to pursue research in organism adaptations to external stimuli and hopefully help out my community through research.




The Wang Lab:

Zhiyong Wang, Acting Director and Senior Staff Scientist

Research in my lab focuses on elucidating the molecular mechanisms underlying growth regulation and environmental adaptation. Plants have evolved high levels of developmental plasticity, which is crucial for their growth and survival. Underlying such developmental plasticity are complex cellular networks that integrate environmental and endogenous signals with gene expression and cell differentiation programs. One goal of our research is to gain a comprehensive understanding of the regulatory systems, and we use a wide range of research approaches, including genetics, genomics, and proteomics to achieve this goal. We are particularly effective in analyzing protein-DNA binding, protein-protein interactions, and posttranslational modifications. We study both the model organism Arabidopsis and major crops such as rice and maize . Our long-term goal is to develop effective strategies and tools for genetic improvement of plant productivity.

Kanako Bessho-Uehara, Postdoctoral Research Associate in the Wang Lab

Kanako's project: Phosphoenolpyruvate carboxykinase 1 (PCK1) is the key gene of gluconeogenesis which catalyzes the step from oxaloacetic acid to phosphoenolpyruvate. PCK1 is common role in animal and plant. Phosphorylated PCK1 is inactive in various plant species but it’s still unclear what the phosphorylation of PCK1 alters its activity in Arabidopsis or not.The summer intern student would be involved in the following aspects: 1) Examine PCK1 activity in Arabidopsis after light treatment. 2) Carry out in vitro kinase assay to determine whether the candidate kinase catalyze the phosphorylation on PCK1. 3) Assess PCK1 degradation under the phosphorylated or dephosphorylated state. I am preparing plant materials and constructs to perform the above-mentioned experiments.

Sola Takahashi, Undergraduate at UC San Diego, working with Dr. Kanako Bessho-Uehara

A few words from Sola: I am a third year studying molecular biology at the University of California, San Diego. At UCSD, I am a part of a lab where I work with gene expression for a project focused on neuroscience. I am a part of the Student Sustainability Collective where we work towards running projects aimed at creating a more environmentally conscious campus for the students. With my free time, I enjoy cooking, nature, and traveling! 





Frej Tulin, Postdoctoral Research Associate in the Wang Lab

Frej's project: Characterization of Chlamydomonas GSK3 during cell division. There is only limited knowledge about chlamy GSK3. We know that (1) GSK3 (like BSL1) is found in the proteome of the flagellar “transition zone”, and that (2) knock-down of GSK3, and treatment with lithium ions confers a long flagella phenotype (deletion of GSK3 is likely lethal). It would be worthwhile I think to examine GSK3’s role in cell division. The project would be mostly microscopy-based, with the possibility of some biochemistry.

Main experiments:

-          Treat cells with Li+ at various points in the cell cycle to see if Li­+ produces a specific phenotype. Take advantage of marker strains (microtubules, centrin, BSL1-Venus etc.). Look at morphology, flagella, cell size etc for clues about function.

-          Localize GSK3-GFP through cell cycle in WT and various mutant background (e.g. cdc20, cdkb …)

-          Possibly IP of GSK3-3xFLAG and mass spectrometric analysis to identify interacting proteins.

Maia Granoski, Undergraduate at Bowdoin College, working with Dr. Frej Tulin

A few words from Maia: I am from San Mateo, CA, and I am a rising sophomore at Bowdoin College in Brunswick, ME. I have always had a strong interest in biology, and I plan to major in either biochemistry or neuroscience. I am fascinated by the mechanisms that underlie the natural phenomena that we observe on a daily basis, and I recently combined my love for agriculture with my interest in genetics in a research project studying the correlation between the genetics of dairy cattle and the proteins found in their milk. I also love drawing and painting, and I’m interested in finding new and creative ways to combine science and the arts.



The Xu Lab:

Shouling Xu, Research Scientist

Shouling's project: Nutrient sensing is important to both plants and animals. One important nutrient sensing pathway is through O-linked N-acetylglucosamine transferases (OGTs), which modify and modulate target proteins using donor substrate UDP-GlcNAc derived from nutrients through the hexosamine biosynthetic pathway. Genetic studies have shown essential functions of O-GlcNAc modification in plants. However, the proteins and sites subject to this post-translational modification were largely unknown. Using lectin weak affinity chromatography to enrich modified peptides, followed by mass spectrometry, we reported the first large scale proteomic identification of O-GlcNAc-modified proteins and sites in the model plant Arabidopsis thaliana. Our study generates a snapshot of the O-GlcNAc modification landscape in plants, indicating functions in many cellular regulation pathways and providing a powerful resource for further dissecting these functions at the molecular level. We are currently developing an improved O-GlcNAc TRAP to enrich O-GlcNAc modified proteins, and we will also focus on understanding substrates, function and regulation of O-GlcNAcylation in both Arabidopsis and Maize. 

Clement Bouden, Undergraduate at Stanford University, working with Dr. Shouling Xu


A few words from Clement: I am an undeclared freshman at Stanford pursuing interests in bioengineering, botany, and chemistry, so I am fortunate to be working in Dr. Xu's lab this summer studying nutrient sensing in maize.  I enjoy contemporary dance, nature photography, shoegaze rock, and enhancing objects with googly eyes.




Matthew Webb, Undergraduate at Cal Poly Pomona, working with Dr. Shouling Xu


A few words from Matt: My name's Matthew Webb and I am Biology major entering my 3rd year at Cal Poly Pomona. Although I go to school in SoCal, I grew up as a Bay Area native and I love to sing, cook, hike, and mountain bike. As a returning intern I am eager to continue developing my skills and meeting new faces!