Molecular and Cellular Biology

I am interested in how cells adjust their intrinsic state (especially cell growth, metabolism and proliferation) to extrinsic conditions (especially nutrient cues). TOR signaling is a central controller connecting these inputs and outputs and highly conserved in all eukaryotes. I have been studying this pathway over the last four years, with a particular focus on the interplay of the two TOR-complexes TORC1 and TORC2 and their relationship to other cellular signaling systems (Plank, 2020). This research was undertaken in Prof. Loewith's lab, a lab that contributed several of the initial discoveries in TOR signaling. In early 2020, I joined Prof. Capaldi's lab, which is dedicated to a holistic perspective of TOR signaling, both with respect to the various inputs to this pathway and how its outputs may differ depending on the combination of inputs received. Two central characteristics of my approach are the use of a Systems Biology perspective and heavily employing mass spectrometry-based proteomics as an experimental approach. By the former, I understand a quantitative description of the signaling pathway as well as observing components (especially proteins) in their interplay with each other, rather than in isolation. Mass spectrometry is a well-suited tool in this respect as it allows the quantitative measurement of hundreds to thousands of proteins or post-translational modifications in a single experiment. TOR-signaling and many other signaling pathways signal mainly through protein phosphorylation. It therefore indicates an untapped opportunity that most research in this field has been performed using genetic and transcriptomic, but not (phospho)-proteomic methods. My first work using this method dates back to my undergraduate days, before employing it during my PhD research on protein methylation, a technically challenging post-translational modification (Plank, 2015) and during my first PostDoc on a TOR-signaling project (Plank, 2020) and in collaborative work (Serbyn, 2020; Liu, 2021). Recently, mass spectrometry has also proven an invaluable tool for exploring the interaction of proteins in complexes. As it is becoming increasingly clear that TOR-signaling is regulated by changes in the composition and orientation of the TOR-complexes themselves and upstream regulatory protein complexes, I intend to utilize mass spectrometry also in this respect. Furthermore, my work in bioinformatic analysis of high-throughput data (Plank, 2012) and training in Systems Biology during my PhD will also provide an asset in this project. Both the laboratories of my first and second PostDoc use baker's yeast as their main model organism, which to this date yields novel discoveries in TOR-signaling research, many of which hold true also in higher eukaryotes. I will make use of this organism`s unique potential for genetic screens, several examples of which have been demonstrated by the Capaldi lab in recent years. I have gained proficiency in S. cerevisiae biology during my first PostDoc, that allow me to perform experiments in weeks that would take months in other organisms. Nonetheless, the projects planned for my second PostDoc involve highly conserved systems and I will follow up leads obtained in yeast in human cell lines.

Dr. Solange Duhamel, Ph.D., is an Associate Professor in the Molecular and Cellular Biology Department at the University of Arizona. She is also affiliated with Columbia University and the American Museum of Natural History in New York. She and her team study the role of microorganisms as agents of biogeochemical transformations, and how microbes adapt to different environments and respond to stress. They are interested in the effects of climate as well as nutrient and energy availability on the distribution, growth and productivity of microplankton but also in the potential of life to adapt to extreme environments and the implications for astrobiology. They use experimental approaches to answer some of the most pressing questions in microbial ecophysiology and biogeochemistry. In particular, Duhamel develops and uses state-of-the-art techniques to study microbial processes at the taxonomic group and single cell levels. Her work has led to the publication of many peer-reviewed journal articles and book chapters.

The Horton lab uses a variety of biochemical and biophysical methods to investigate DNA binding proteins. Recent projects include the discovery of a novel mechanism of regulation of enzyme activity using filamentation. Filamentation, or self-association into polymers of varied lengths, by enzymes has only recently been appreciated as a widespread phenomenon, although the purpose of filamentation is not known in most cases. We discovered this phenomenon in 2010 in a sequence specific endonuclease, SgrAI, and have now determined its high resolution structure via cryo-electron microscopy. We have also performed a full kinetic analysis showing that filamentation greatly expedites the activation of the enzyme, and also allows for the sequestration of enzyme activity onto only a subset of available substrates. The other major project in the lab concerns the triggering of autoimmune diseases in genetically susceptible individuals. We study proteins from the human parvovirus B19, a virus which often precedes the development of autoimmune diseases like rheumatoid arthritis, autoimmune hepatitis, and lupus. We study how these proteins interact with cellular components to modulate the immune system into loss of self-tolerance.

Fragile-X syndrome, which includes mental and physical defects and is the most common form of inherited mental retardation. Keywords: Neurodegeneration, ALS, Aging

George Sutphin, PhD, studies the molecular basis of aging. Individual age is the primary risk factor for the majority of the top causes of death in the United States and other developed nations. As our population grows older, aging is increasingly a central problem for both individual quality of life and the economics of societal health. Understanding the molecular architecture that drives aging will reveal key intervention points to extend healthy human lifespan, simultaneously delay onset of multiple categories of age-associated disease, and develop targeted treatments for specific pathologies. The Sutphin Lab uses a combination of systems biology, comparative genetics, and molecular physiology to identify new genetic and environmental factors in aging and characterize their molecular role in age-associated disease. Keywords: Aging/Age-Related Disease, Comparative Genetics, Systems Genetics

My laboratory investigates the normal biology of the Epidermal Growth Factor Receptor (EGFR, and its family members, HER2 and ErbB3), as well as their role in transformation and metastasis. These oncogenes are a family of transmembrane tyrosine kinases that drive a wide-variety of cancers including HER2 positive and triple negative breast cancer, squamous cell lung cancer and glioblastoma. Our work focuses on kinase-independent activities of these receptors (such as modulation of calcium signaling and functions as transcriptional co-factors) and how the receptors are mis-regulated during cancer progression (by a loss of lysosomal degradation). These studies include investigations into receptor trafficking, nuclear translocation and protein-protein interactions that are unique to cancer survival and metastasis. We are currently focused on understanding how EGFR enters the retrotranslocation pathway that allows for it to traffic to the nucleus and directly affect gene transcription, as well as understanding how these events drive migration and survival. Based on these studies, we have developed peptide-based therapeutics for cancer that block protein-protein interactions that promote EGFR retrotranslocation. We are developing these peptide-based therapeutics for clinical applications through peptide stability studies including hydrocarbon stapling and mutational analyses. To promote the clinical translation of these discoveries, the biotech start-up company Arizona Cancer Therapeutics was founded in my lab at the Arizona Cancer Center. We are currently performing toxicity testing of our compounds with the goal of applying for approval from the FDA for clinical trials. These studies have been accomplished through the hard work and dedication of the over 50 undergraduate students, 2 MS and 11 PhD students who have studied in my lab since 2002.

The Gutenkunst group studies the function and evolution of the complex molecular networks that comprise life. To do so, they integrate computational population genomics, bioinformatics, and molecular evolution. They focus on developing new computational methods to extract biological insight from genomic data and applying those methods to understand population history and natural selection.

Lisa Elfring is an Associate Specialist in the Department of Molecular and Cellular Biology and currently serves as Associate Vice Provost for Instruction and Assessment. In this administrative role, she leads the Office of Instruction and Assessment (OIA), which supports teaching and learning across campus. The office supports technology-enabled teaching (D2L, Panopto, Adobe Connect, VoiceThread); provides professional development and courses on evidence-based teaching for all UA instructors; produces media products (web pages, videos) that support instructors in their teaching; helps departments to carry out assessment of learning outcomes; and helps to connect instructors across departmental and college boundaries. Dr. Elfring is currently involved in two teaching-related research projects. In one, she and her collaborators are investigating a model to train instructors in large, collaborative STEM classes to utilize a team of graduate and undergraduates to improve student learning. In the other, the team is investigating the effects on students on creating and improving models in biological systems, in the context of an Introductory Biology lab course. Both projects are funded by awards from the National Science Foundation. Dr. Elfring's teaching experiences range from large courses in introductory cell/molecular biology and cell biology, to courses focusing on helping undergraduate students to prepare for doing laboratory research. Her research interests are integrated with her teaching role. She is interested in process of systemic change in educational systems, and particularly in how the university can promote the adoption, use, and assessment of research-based teaching strategies across the entire range of STEM (science, technology, engineering, and math) courses. In biology education, she has been involved in research on how students come to make sense of the key biological concept that genes code for RNAs which (mostly) encode proteins to form the structural and catalytic molecules of the cell, a process that is termed the central dogma of molecular biology. She and her collaborators were involved in efforts to introduce more quantitative problem-solving work in the Introductory Biology course and across the undergraduate life-sciences curriculum. Her undergraduate, graduate, and post-doctoral training is in molecular, cell, and developmental biology; she has done research using humans, mice, and fruit flies as experimental systems to investigate embryonic development and cancer. Keywords: Biology education, Faculty professional development

Our research focuses on the signal transduction pathways and molecular mechanisms controlling directed cell migration, or chemotaxis, in eukaryotic cells. Chemotaxis is central to many biological processes, including the embryonic development, wound healing, the migration of white blood cells (leukocytes) to sites of inflammation or bacterial infection, as well as the metastasis of cancer cells. Cells can sense chemical gradients that are as shallow as a 2% difference in concentration across the cell, and migrate towards the source of the signal, the chemoattractant. This is achieved through an intricate network of intracellular signaling pathways that are triggered by the chemoattractant signal. These pathways ultimately translate the detected chemoattractant gradient into changes in the cytoskeleton that lead to cell polarization and forward movement. In addition, many cells such as leukocytes and Dictyostelium, transmit the chemoattractant signal to other cells by themselves secreting chemoattractants, which increases the number of cells reaching the chemoattractant source.To investigate key mechanisms of signal transduction underlying chemotaxis, we are using the social amoeba Dictyostelium discoideum as well as human cancer cell models. Cell motility and chemotaxis of Dictyostelium cells is very similar to that of leukocytes and cancer cells, using the same underlying cellular processes as these higher eukaryotic cells. Dictyostelium is amenable to cell biological, biochemical, and genetic approaches that are unavailable in more complex systems. The discoveries we make using Dictyostelium are then confirmed in human cells and, in particular, in the context of directed cancer cell migration and metastasis. Our aim is to understand the molecular foundation of directed cell migration, which is expected to guide the design of efficient anti-metastatic treatments.Our approach is interdisciplinary, in which we combine molecular genetics and proteomics to identify new signaling proteins and pathways involved in the control of chemotaxis, with live cell imaging using fluorescent reporters to understand the spatiotemporal dynamics of the signaling events, as well as biochemical analyses and proximity assays [including Bioluminescence Resonance Energy Transfer (BRET) and FRET] to understand how proteins interact and function within the signaling network. In addition, in collaboration with Dr. Wouter-Jan Rappel at UC San Diego, we generate quantitative models of the chemotactic signaling networks to help identify key regulatory mechanisms and link them to whole cell behavior

Andrew Capaldi, PhD, researches the signaling pathways and transcription factors in a cell that are organized into circuits. They allow cells to process information and make decisions. For Dr. Capaldi, the work arises in understanding both how these circuits are built from their components, and how they function and malfunction. To address these questions, he is working to reverse engineer the circuitry that controls cell growth in budding yeast using a combination of genomic, proteomic and computational methods. http://capaldilab.mcb.arizona.edu