Jeremy Pardo - Graduated Fall 2022
I was a plant biology graduate student in Dr. Robert VanBuren’s lab until graduating in Fall 2022 and am now employed as a computational biologist at Inari Agriculture in Cambridge, MA. The PBHS program allowed me the opportunity to gain exposure to a wide array of plant research. In addition I was able to complete an internship at Inari Agriculture in Cambridge, MA, through PBHS funding, which provided new skills particularly in the realm of software development and computational genomics.
My PhD research focused on understanding the evolution of water-stress tolerance in C4 grasses. Most recently I have been working on a project using a predictive modeling approach to identify conserved drought responses between maize and sorghum. We were able to develop a model that when trained in one species could accurately predict stress level in the other species. Reverse engineering the model allowed us to identify evolutionarily conserved drought responses. This work has been posted on the BioRxiv preprint server and is currently under peer review. I also recently wrote a review on the evolution of drought stress tolerance in C4 grasses with my advisor Dr. Robert VanBuren. The review was published in The Plant Cell in August 2021. I use comparative genomic tools to investigate the dynamics of water stress evolution during historic artificial selection. The goal of this research is to uncover tradeoffs associated with water-stress tolerance to inform breeding of more resilient cereal crops. I previously conducted a comparative study using the desiccation tolerant wild grass Eragrostis nindensis and its sister crop species Eragrostis tef. Previous work on E. nindensis and other desiccation tolerant angiosperms suggested that expression of seed dehydration pathways in leaves is responsible for conferring their extreme tolerance phenotype. However, my results demonstrated that the same seed dehydration pathways are expressed in the leaves of E. tef during extreme water-stress implying that expression of seed dehydration pathways is insufficient to explain the desiccation tolerance phenotype. This work was published in Proceedings of the National Academy of Science in April of 2020.
Reid Longley - Graduated Fall 2022
During my doctoral research, I studied interactions between soybeans and their associated microbiomes. Specifically, my research focused on understanding the impact of agricultural management (tillage regime and fungicide application) on microbiomes associated with all parts of the plant. My research indicated that management techniques impact plant-associated microbes throughout the plants, including those with putative beneficial functions. Additionally, my dissertation work demonstrated that inoculating soybean seeds with microbes that appear to be important to structuring microbial communities can lead to benefits for plant health including increased nodulation, increased expression of genes involved in nitrogen fixation, and increased plant growth.
In 2021 I performed a 6-month internship at Los Alamos National Labs as part of a graduate fellowship through the DOE Office of Science Graduate Student Research (SCGSR) program. During this internship, I worked as a part of Patrick Chain’s bacterial-fungal interactions (BFI) research group. Throughout my internship, I learned computational techniques for analyzing RNASeq data that were generated as part of my thesis project. Additionally, I was able to work alongside other members of the Chain lab BFI team to analyze data from a comparative genomics study on mollicutes related endobacteria (MRE) that reside inside Mortierellaceae fungi. This work revealed that MRE genomes are greatly reduced, ranging in size from 326,000 bp to 600,000 bp and that these genomes have lost various functions including DNA repair which may explain their apparent rapid rate of evolution. This work is important for assessing how relationships between Mortierellaceae and endobacteria formed and how they continue to evolve. My internship at Los Alamos National Labs was valuable for introducing me to the environment at a national laboratory and for introducing me to the types of research occurring within the DOE. The internship also led to a postdoctoral position that started summer 2022.
Participating in the PBHS program was crucial for my development as a scientist throughout graduate school. The annual symposia and other training introduced me to various aspects of plant biology and research outside of academia. Without participating in the PBHS training program, I would not have been exposed to these career opportunities during graduate school. Additionally, as part of the PBHS program, my 6-month internship led to my current position as a postdoctoral researcher at Los Alamos National Labs. The skills I learned as well as the network of scientific peers that the PBHS program helped me develop will continue to serve me throughout my scientific career.
Danielle Young - Graduated Spring 2022
During my doctoral studies at Michigan State University, I studied microalgal lipid metabolism in a model green alga. In conditions of environmental stress, algal growth slows and the cells accumulate oil, which can be chemically modified to make biodiesel fuel. My work focused on elucidating the biochemical pathways leading to algal oil accumulation using isotopic labeling and mass spectrometry. Using these techniques, I was able to quantify the portion of oil that was made from preexisting cellular components versus newly made fatty acids, and to discern the biochemical mechanism by which one of these routes occurs. This has implications for engineering the composition and quantity of algal oil in future biofuel work.
Being a participant in PBHS was highly valuable for my development during graduate school. The funding from the PBHS program allowed me to focus on my research, which allowed me to be more productive. Participating in PBHS’s annual symposium was also an excellent experience, as I was able to be involved in the planning/organization of a symposium, practice giving research talks, and network with the invited speakers. My interaction with one of the symposium speakers enabled me to do an internship at Synthetic Genomics (now Viridos) in La Jolla, California halfway through my PhD. I’m very grateful for PBHS facilitating this internship experience, as without it I would have only been exposed to research in an academic setting. Thanks to my internship, I now have a broader range of experience in both academia and industry, and it gave me a clearer idea of what I wish to pursue after graduate school. I am currently a postdoc in my lab at Michigan State finishing up some projects, but I am in the midst of applying for jobs both inside and outside of academia. For instance, I am currently applying to two fellowships, one in public policy and one at a national lab.
Kody Duhl - Graduated Spring 2022
While working at Michigan State University, I conducted studies within the Biochemistry and Molecular Biology department. My work began as an introductory look into the function of the respiratory chain of the metal reducing bacterium Shewanella oneidensis MR-1 for bioelectrochemical and biotechnological applications. Throughout the development of these projects, my research evolved into a more physiological approach, allowing me to conduct studies on the function of the electron transport chain structure for redox balance and overall efficiency depending on the respiratory complex used. S. oneidensis MR-1 retains a highly branched electron transport chain, allowing it to modulate expression of specific complexes to adapt to differing growth conditions.
My time with the PBHS training program became integral to my professional development during my graduate studies. While I did not study plants, the program exposed me to a wide variety of research that I was not familiar with, faculty members from a multitude of institutions, and unveiled an assortment of career paths outside of academia. PBHS also expanded my development in career preparation training, such as networking during symposia and mentoring. The exposure to industry in the PBHS program allowed me to widen my career path horizons. My experience at MSU and within the PBHS program allowed me to join the Fortis Life Sciences team in Grand Rapids, MI. I am extremely excited to start the next portion of my career with Fortis, and I plan to use the skills that I have developed at MSU and in the PBHS program to further my career development.
Evan Angelos - Graduated Spring 2021
My graduate studies in Biochemistry and Molecular Biology were performed in the Brandizzi Lab at Michigan State. In my research I studied the cell signaling mechanism known as the unfolded protein response (UPR) in the contexts of plant development and environmental stress. My initial projects focused on the mechanisms by which the core UPR components integrated with other plant signaling mechanisms to regulate endoplasmic reticulum stress outcomes. My later projects and dissertation examined how UPR regulators, which are strongly conserved between mammal and plant models, have divergent signaling outputs tailored to the unique nature of plants. This work included an investigation of UPR activity in plants subjected to spaceflight-associated stresses which launched on the SpaceX-CRS12 mission in collaboration with NASA. Additionally, by studying the physiological functions of the UPR in normal plant development I was also able to demonstrate that the UPR regulator IRE1 limits Target of Rapamycin (TOR) kinase activity to promote proper organ formation in Arabidopsis.
These accomplishments would not have been possible without the financial support, career development, and networking opportunities granted by the PBHS program. PBHS funding allowed me to focus on my scientific training and project development at the bench, while PBHS courses helped me develop a conceptual framework of how fundamental plant research can be translated into applied plant biotechnology. The annual student-run symposium provided opportunities to present my work and learn about cutting-edge developments in academia and industry through direct discussions with leading scientists in the relevant fields. By participating in these symposiums and in the organization of the 2018 PBHS retreat I was able to practice effective leadership and communication skills. The lessons learned from these collective experiences lead me to pursue a postdoc at University of California Riverside in Katie Dehesh’s lab, whom I first met at the 2018 PBHS retreat. In Katie’s lab I will expand my industry-relevant skillsets by studying the metabolic reconfigurations which underpin chloroplast stress responses and learn from a mentor who has worked as a lead scientist in industry and academic settings.
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.
Alshae’ Logan-Jackson - Graduated Summer 2020
Being a member of the PBHS Graduate Training Program has allowed me the opportunity to expand my professional network. Participating in an internship at BASF has allowed me to augment my technical skills as well as enhancing my research skills; while increasing my skill set in the industry sector, this internship has offered the opportunity for me to network with several employees (in crop pipeline department as well as other departments) inside the company. I have not only created a professional network by completing an internship, but I have also increased my research network broadly by attending the annual symposia—which aided my career development. Ultimately, this training program has prepared me to achieve my potential by interacting with many individuals (students and professionals) with both similar and broader biotechnological interests. All these opportunities, together with an opportunity to be a part of a larger learning and practice community of students with similar interests and to participate in the annual symposia, contributed to a more comprehensive preparation for my profession. I am now an Environmental Engineer in the Heat Transfer and Alternative Energy Systems Group within the Building Energy and Environment Division of the Engineering Laboratory at the National Institute of Standards of Technology where I am applying my knowledge gained from MSU to understand how pathogenic bacteria thrive in the plumbing systems of residential buildings.
Daniel Lybrand - Graduated Summer 2020
The PBHS program at Michigan State University highlighted many career paths that are not traditionally presented to graduate students. Through the program’s annual symposium, I got a closer look at careers in government and industry. I was able to meet many of the guest speakers at the five PBHS symposia held during my time at Michigan State and learned much about participating in scientific research outside academia. Just as valuable as the annual symposium was the opportunity to participate in an industrial internship that PBHS funding allowed. I completed my internship at Synthetic Genomics, Inc. in La Jolla, California where I was able to practice techniques in organic chemistry and microbiology. In addition to complementing my graduate research, this experience also gave me an inside look at the workings of a small biotechnology company.
My graduate work in the Last lab focused on specialized metabolites produced in plant trichomes. I studied biosynthesis of natural antifeedant compounds known as acylsugars produced by many species in the nightshade (Solanaceae) family and the pyrethrin insecticides produced by Dalmatian pyrethrum (Tanacetum cinerariifolium). This work included extensive purification and characterization of acylsugars and pyrethrins from natural sources as well as in vitro enzymology to elucidate biosynthetic pathways. I also experimented with engineering pyrethrin biosynthesis into cultivated tomato (Solanum lycopersicum) using trichome-specific promoters. All my work relied heavily on chromatographic separations and mass spectrometry. Over the course of my doctoral work, my interests shifted from the pathways of metabolism to the techniques of mass spectrometry. This prompted me to apply mass spectrometry techniques toward pharmacological research questions during my time as a post-doctoral scholar in the laboratory of Dr. Bruce Hammock at the University of California, Davis.
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 a Computational Biologist at Pairwise, in North Carolina. My job involves developing and performing computational analyses that help us understand the crops we want to work with, and the genes involved in pathways and structures of interest. I rely heavily on things I learned before and during my time as a PBHS trainee. I support the molecular approaches at Pairwise to deliver fruits and vegetables that consumers want to eat.
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.