Genevieve Hoopes – Graduated Summer 2021
During my time at Michigan State University, I primarily worked in the plant genomics field, contributing new insights into molecular pathways and gene content via the generation of a genome assembly and several transcriptomic studies. The genome of the medicinal plant Calotropis gigantea was assembled with a near complete representation of the genic space, enabling discovery of novel enzymes involved in the biosynthesis of the anti-cancer cardenolide compounds. Through the development of an expanded gene atlas that profiles maize development and stress responses, tissue-specific and stress-induced gene expression were characterized using co-expression principles. Diurnal and circadian co-expression networks were also characterized in potato leaf and tuber tissue using time course experiments, elucidating circadian rhythms in a heterotrophic tissue and providing the means to explore pathways regulated by the circadian clock.
The PBHS training program provided invaluable opportunities to learn science communication, mentoring, networking, and career preparation skills. Through the annual symposium, I gained confidence in talking about my research in both formal and informal settings, and had the opportunity interact with speakers who had chosen differing career paths. The diverse research areas each of these speakers presented was also invaluable in expanding my view of research and how to tackle difficult scientific questions. As part of the program, I also had the unique opportunity to pursue a summer internship at the J.R. Simplot Company, providing experience in conducting research in a company and building connections with the other employees. Due to the internship experience, I will be joining the Molecular and Cellular Biology team at Simplot in Boise, ID. I look forward to starting a new chapter with Simplot utilizing all of the knowledge and skills I have gained during my time at MSU.
Alyssa Preiser - Graduated Spring 2020
My doctoral research in the Sharkey lab focused on the glucose-6-phosphate shunt and its interaction with other areas of plant metabolism. I characterized two enzymes: glucose 6-phosphate dehydrogenase and phosphoglucoisomerase. Both of these enzymes interact with plastidic and cytosolic glucose 6-phosphate pools. In characterizing these enzymes, we described a pathway that provides an alternative pathway around the Calvin-Benson cycle that is usually assumed to be inactive during the day. We also showed that this pathway provided a significant efflux of CO2 during the day, called light respiration.
Participating in the PBHS program provided avenues for both interacting with a variety of scientific research and engaging with many different career paths. This program was part of what sparked my interest in pursuing science communication and teaching. The speakers and scientists that I was able to talk with were engaging, doing excellent research, and creating innovating solutions. I wanted to be part of making sure that business owners, the public, and other scientists would be aware of the science that impacts their lives. I now work teaching high school biology. I love teaching kids how an understanding of science shapes how they interact with the world around them and inspiring and preparing the next generation of scientists.
Anastasia Lavell - Graduated Fall 2019
My graduate studies in the Benning lab focused on plant lipid metabolism, in particular, the synthesis of thylakoid membranes. Thylakoid membranes house the photosynthetic machinery and have a unique lipid composition relative to other membranes in plant cells. There are two contributing pathways to the synthesis of these membranes in most plants, one routed through the chloroplast and the other through the endoplasmic reticulum. My PhD focused on characterizing a rhomboid-like protein 10 (RBL10) which appears to be important for the functionality of the chloroplast pathway to thylakoid biogenesis.
In addition to my scientific training at the bench, I greatly benefitted from participating in the PBHS training program. The funding provided made my PhD project possible and gave me time to generate data needed to make it a grant-funded project to support work beyond PBHS funding period. Participating in organizing the annual symposia provided hands-on training on how to think about scientific meetings, pick topics, and correspond with invited speakers. The required coursework stimulated my thinking about plant biotechnology deeply and together with meeting scientists from universities and companies at the symposia, provided a broad understanding of the current frontiers in academia and industry. On a more personal note, the PBHS program provided a community of like-minded peers throughout my graduate studies from whom I learned immensely. I am walking away with not just knowledge and skills, but a solid network in the plant biotechnology area which will benefit my career long-term.
I am currently starting a postdoc with Kristen Parent in the Biochemistry and Molecular Biology Department at MSU and will be learning how to use Cryo-EM for solving structures of proteins and viral particles. I hope to use structural information to answer complex biological questions.
Bryan Leong - Graduated Fall 2019
My doctoral research focused on enzyme identification in acylsugar biosynthesis. Acylsugars are compounds produced by Solanaceae species that protect against insects and microbes. Specialized metabolic diversity is interesting from an evolutionary and practical perspective. We want to understand how metabolic diversity arises in plants through evolution at the enzyme and species level. This can provide insight into the mechanisms that drive the metabolic diversification in specialized metabolism. Practically, we can test whether the differences in compounds has an effect on insects or pathogens when we have a better understanding of the mechanisms that underlie acylsugar diversity in the Solanaceae family. My work primarily focused on enzyme characterization and evolution in two different Solanaceae species: a South American fruit crop, Solanum quitoense and a wild relative of tomato, Solanum pennellii.
The PBHS program was instrumental in shaping the future of my career. I was not aware of all the career options available after earning my Ph.D. at the beginning of graduate school. However, that changed quickly through my experiences during the PBHS symposia. Speakers that focused their careers on communication, government research, start ups, or industrial research provided insight into the variety of paths available to me after my doctoral work. The breadth of topics and research I experienced – both from my colleagues in the program and from the symposium speakers – is one of the primary factors behind my decision to pursue a postdoc in Andrew Hanson’s group at University of Florida, to enrich my skill set for an ever-evolving job market. One of the other benefits from the PBHS program was soft skill development. There were many opportunities to give talks about my research, develop a network, introduce speakers, and collaborate with other students in my cohort to put together successful symposiums and a retreat. The skills learned from the PBHS program will be invaluable in my career going forward.
Brian St. Aubin – Graduated Fall 2019
Development of glandular trichomes in Solanum lycopersicum highlights the dynamics required to convert one cell type to another. My doctoral research focused on the transition between growing trichome and fully-filled glandular trichome. This transition is important because the metabolites produced and stored in these trichomes important for herbivory deterrence. Understanding the metabolic shift that occurs in these cells could also help us better understand other aspects of metabolic regulation in plants.
The PBHS program provided the classes that were most helpful when starting my project. The extra career development opportunities provided through the PBHS program provided the bridge between learning science and a career in science. Planning meetings, sending letters, meeting other scientists, interviewing, writing reports, presenting…the list goes on.
I am continuing to follow the regulation of metabolic shifts with Dr. Robert VanBuren at MSU. Our lab has the expertise to computationally analyze not just one cell type on a plant, but several species at a time. This more phylogenetic approach to studying plants can highlight the differences and commonalities in plants as they go through stresses such as drought. Insights to the way plants deal with drought will inform future biotechnology to help with a major challenge, water scarcity.
Tomomi Takeuchi – Graduated Fall 2019
I completed my PhD dissertation in the lab of Dr. Christoph Benning in 2019, and my project focused on the molecular switch controlling cellular proliferation and quiescence in the model green alga, Chlamydomonas reinhardtii. In particular, my research focused on an algal protein named Compromised Hydrolysis of Triacylglycerols 7 (CHT7) with a proposed role in the regulation of nitrogen (N) deprivation-induced quiescence. We identified CHT7 as necessary for the repression of cell cycle-related gene expression and the optimal survival cells during N starvation. CHT7 was also necessary for the cells to appropriately resume cell division upon N resupply.
Participating in the PBHS program allowed me to gain valuable insights into the different science career paths available to PhD graduates. By organizing and attending the annual symposia, I was able to interact with speakers from many sectors at different stages of their careers. In addition, I learned first-hand what it was like to work in the industry by completing a summer internship. These experiences and opportunities were helpful in choosing my career path and learning about what to expect in the industry. I now work as a scientist in the Biomarkers and Investigative Pathology Unit of Charles River Laboratories, an early phase contract research organization, at its Mattawan, MI facility.
Angélica V. Medina-Cucurella - Graduated Summer 2019
My doctoral research focused on the application of deep sequencing-guided engineering platforms to address numerous aims relevant to the protein engineering and antibody discovery field. We evaluated multiple protein-protein interactions using a standardized pipeline developed by the Whitehead Lab, which combines comprehensive mutagenesis, yeast surface display, high-throughput screening, and deep sequencing. These informational datasets were applied to understand sequence-function relationships between proteins, which in turn, allow us to develop a protein engineering workflow capable of increasing the production of displayed proteins in a conformation recognizable by the binder partner, to map conformational epitopes of potential monoclonal antibodies, and to determine the binding sites of target antigen receptors. In addition, my research improved current deep mutational scanning methods by using a single oligo pool to construct user-defined single and double mutagenesis libraries from plasmid DNA with low off-target rates.
The PBHS training program gave me valuable skills and experiences that have influenced my future research endeavors and career goals. The opportunity of being able to work with researchers from diverse fields to achieve common goals allowed me to explore new areas of research and to expand my knowledge about new scientific fields. In fact, I became delighted with the idea to pursue a career path on the industrial research area by interacting with the invited speakers and attending to their lectures focused on multiple careers options at the annual symposia. Furthermore, I participated in an industrial summer internship at GigaGen (San Francisco, CA), which focuses on antibody engineering. During this time, I was involved in two different projects to develop new method guided by next-generation sequencing for the selection of enriched antibodies against selected targets. Thanks to this opportunity, I recently began as a senior scientist at GigaGen where I hope to continue the research efforts on improving the techniques used to discover human antibodies for therapeutic applications.
Colleen Friel - Graduated Summer 2018
My PhD research focused on the carbon for nitrogen exchange between plants and nitrogen fixing bacteria called rhizobia. This interaction could provide an alternative to environmentally costly synthetic nitrogen fertilizers. However, not all plants are able to interact with rhizobia, and we do not fully understand the signal exchange and trade negotiations that determine the cost:benefit ratio of this interaction for the plant. My PhD work focused on exploring the factors that determine how many resources plants allocate to their rhizobial partners.
Participating in the PBHS program was particularly valuable to me since my PhD lab was focused on ecology and evolution, with few connections to industry. The classes and symposia that I attended through PBHS helped me learn about the exciting advances happening in plant biotechnology in industry, and to expand my professional network in the field. In fact, I first connected with my current PI at the 2017 PBHS symposium. I am now a postdoc in Cecilia Martinez-Gomez's lab at Michigan State University. I am studying the role of lanthanide biochemistry in the interactions between crops and methylotrophic bacteria. The goal of the project is to elucidate the mechanism of lanthanide-mediated plant growth promotion by methylotrophs and to develop commercial inoculants for various crops.
Emily Wrenbeck - Graduated summer 2017
The focus of my PhD research was to gain better understanding of the constraints of functional enzyme evolution using a research technology pipeline developed by the Whitehead Lab. In brief, the pipeline involved coupling high-throughput screens or selections for protein function to deep sequencing to generate datasets containing information on thousands of mutations of a protein sequence. This was applied to study how enzymes encode substrate specificity, which is currently not well understood, by performing functional selections for an enzyme on multiple substrates. In this work, I found that specificity is globally encoded throughout protein sequence and structure. In addition, during my PhD I co-developed Nicking Mutagenesis, a method for the construction of comprehensive single-site saturation mutagenesis DNA libraries that requires only double-stranded plasmid DNA as input substrate. This method was validated on several gene targets and plasmids and is currently being used in academic, government, and industry laboratories worldwide.
During my time in the training program I was exposed to new areas of research and ways of thinking that undoubtedly influenced my scientific interests and career goals. Specifically, from the material covered in program courses and the lectures given by invited speakers at the annual symposia I became captivated with the idea of biomanufacturing and natural product synthesis in engineered microbes. This led me to pursue a related research project and ultimately to a collaboration between the Whitehead Lab (Dept. of Chemical Engineering) and the Barry Lab (Dept. of Horticulture and another training lab). In brief, this project entailed applying the research pipeline to engineer improved heterologous expression of an enzyme from the Atropa belladonna medicinal Tropane Alkaloids pathway recently discovered by the Barry Lab, with the ultimate goal of improving productivity of an engineered Tropane Alkaloids biosynthetic pathway in yeast. These program-inspired interests will be continued this fall when I begin my career as a scientist at Ginkgo Bioworks (Boston, MA) with the title of Protein Engineer. I hope to expand my knowledge of natural product synthesis and state-of-the-art technologies for engineering biology, be part of developing a world-class protein engineering group, and glean insight into the business workings of a biotechnology company.