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We welcome you to join this symposium, where you will experience a variety of live presentations from top-ranked scientists on the wide-ranging applications of stable isotopes. These include metabolic tracing, quantification, qualification, structure determination, imaging, and more!
During the break, we will also be hosting Isotope Trivia via Kahoot for all participants. This will be a mix of questions about isotopes, CIL, our speakers, science, and general knowledge. Prizes will be awarded to the winners!
Wednesday, June 2, 2021
9:00 AM – 3:00 PM (EDT)
Isotope Day is a virtual event hosted on ZOOM. Space is limited.
We will be incorporating some trivia and recommend downloading
the Kahoot app to participate. Prizes will be awarded to the top players.
2021 Isotope Day Program
9:00 AM
Opening Remarks
Greg Whitney | Cambridge Isotope Laboratories, Inc.
NMR Session
9:15 - 9:30 AM
Kevin Millis, PhD | Cambridge Isotope Laboratories, Inc.
Stable Isotopes in Biomolecular Nuclear Magnetic Resonance Research: A critical technology
9:30 - 9:55 AM
Robert G. Griffin, PhD | M.I.T.
Atomic Resolution Structures of Amyloid Fibrils:
Magic Angle Spinning (MAS), Dynamic Nuclear Polarization (DNP)1H Detected NMR
9:55 - 10:20 AM
Jan Marchant, PhD | University of Maryland
Structural characterization of large RNAs from HIV-1 using NMR
10:20 - 10:45 AM
Haribabu Arthanari, PhD | Harvard Medical School and
Dana Farber Cancer Institute
Leveraging tailored isotope labeling and novel pulse
design to encode amino acid selective line shapes.
10:45 - 11:10 AM
Lewis Kay, PhD | University of Toronto
Without isotopes there is no fancy NMR
11:10 - 11:35 AM
Christoffer Laustsen, PhD | Aarhus University Hospital
Translation of hyperpolarized carbon-13 and deuterium imaging
11:35 AM - 12:00 PM
Break for Lunch
12:00 PM
Trivia with prizes!
Mass Spectrometry Session
12:30 - 12:45 PM
Andrew Percy, PhD | Cambridge Isotope Laboratories, Inc.
Example MS Applications of Stable Isotope Standards and their Mixtures
12:45 - 1:10 PM
Matthew Vander Heiden, MD, PhD | M.I.T.
Using Stable Isotopes to Study Proliferating Cell Metabolism
1:10 - 1:35 PM
David Muddiman, PhD | North Carolina State University
Quantifying Human Exposure to Emerging Contaminants of Concern using Mass Spectrometry
1:35 - 2:00 PM
Lingjun Li, PhD | University of Wisconsin
High Resolution FTMS Enabled Mass Defect-based Chemical Tags for Multiplex Quantitative Omics
2:00 - 2:25 PM
John Yates, PhD | Scripps Research Institute
Quantitative Bioorthogonal Chemistry for Proteomics
2:25- 2:50 PM
Gary Patti, PhD | Washington University
Big Data from Heavy Molecules
2:50 PM
Closing Remarks
Greg Whitney | Cambridge Isotope Laboratories, Inc.
Biographies and Abstracts
Kevin Millis, PhD | Cambridge Isotope Laboratories, Inc.
Kevin Millis, PhD, has been with CIL for over 20 years and is a Senior Scientist and a member of the CIL Technical Services Team. Kevin holds a BS in chemistry, biochemistry emphasis, from California State University, Fullerton; an MS in analytical chemistry; and a PhD in analytical chemistry from the University of California, Riverside.
Talk Title: Stable Isotopes in Biomolecular Nuclear Magnetic Resonance Research: A critical technology
Most communications that pertain to NMR-based research on biopolymers, such as protein or nucleic acids, will devote no more than a few words, if any at all, to describe the isotope labeling scheme or methods used in producing the molecules under study. Although it is true that enriching biopolymers with stable isotopes, such as 13C, 15N and 2H, is not always needed, as in the case for short-stranded peptides and nucleic acids, it is more often the case than not that samples do in fact require enrichment with at least a subset of these three stable isotopes. Enrichment allows for correlations to be measured, which are crucial for the determination of inter-atomic distances, torsion angles, and relative orientations of domains within the molecule. Enrichment also can be critical to obtain an isolated spin system for which dynamics can be investigated, for an assessment of protein folding, for detection of signals in large proteins and supramolecular complexes, and for 15N-based chemical shift perturbation experiments. This short talk will highlight the common reagents and labeling schemes for enriching protein and nucleic acids for most types of NMR investigations.
Robert G. Griffin, PhD | M.I.T.
Our scientific goals are twofold: (1) to develop new methods based on solid state NMR to determine the structure and function of biological systems, and (2) to apply these techniques to interesting problems involving the structure and function of proteins, membranes, nucleic acids and macromolecular systems. We focus on problems that are largely inaccessible with XRD and solution NMR techniques.We were one of the first groups to initiate biological solid state NMR experiments, a field that is now a rapidly expanding scientific enterprise. Initially, we began by studying 2H and 31P spectra of static samples of membrane lipids, but the absence of resolution and low sensitivity stimulated us to develop (1) methods for magic angle spinning (MAS), (2) dipolar recoupling to measure distances and torsion angles, and (3) instrumentation for high frequency dynamic nuclear polarization (DNP) and EPR instrumentation to increase sensitivity by factors of 100-300. To date the primary applications of these techniques is to problems in structural biology of membrane and amyloid proteins. Our successful efforts in developing recoupling and high frequency DNP MAS experiments and applications to membrane and amyloid proteins were recently recognized by the following awards: the Guenther Laukien Prize (2007), the Eastern Analytical Society Prize (2007), the International Society of Magnetic Resonance (ISMAR) Prize (2010), the Sacconi Medal (2011), the ACS E.B. Wilson Prize for Spectroscopy (2016), the EUROMAR R.R. Ernst Prize in Magnetic Resonance (2017), the Bijvoet Medal (2018), election to the US National Academy of Sciences (2021).
Talk Title: Atomic Resolution Structures of Amyloid Fibrils:
Magic Angle Spinning (MAS), Dynamic Nuclear Polarization (DNP)
1H Detected NMR
Abstract: Many peptides and proteins form amyloid fibrils whose detailed molecular structure is of considerable functional and/or pathological importance. For example, amyloid is closely associated with the neurodegenerative diseases such as Alzheimer’s and Parkinson’s diseases. In this presentation we review the macroscopic structural properties of fibrils and outline approaches to determining the microscopic structure of these systems to atomic resolution using magic angle spinning (MAS) NMR in combination with cryoEM. In particular, we discuss a series of 2D and 3D heteronuclear and homonuclear dipole recoupling experiments involving spectral assignments and distance and torsion angle measurements aimed at accomplishing this goal. Key to obtaining high resolution is the ability to measure a sufficient number of NMR structural constraints (13C-13C and 13C-15N distances and torsion angles per residue). We discuss the structures of different systems determined using these approaches but focusing on (1) fibrils formed by Aβ1-42, the toxic species in Alzheimer’ discases, using a set of >500 distance constraints; and (2) a structure of fibrils forned by β2-microglobulin, the 99 amino acid protein associated with dialysis related amylosis, using ~1200 constraints. The spectra also provide information on the arrangement of the monomers in the strands that form sheets, and the sheets that ultimately form the fibrils. Contrary to conventional wisdom, the spectral data indicate that the molecules in the fibril are microscopically well ordered.
Jan Marchant, PhD | University of Maryland
Jan Marchant is a Research Assistant Professor at the University of Maryland Baltimore County. He develops and applies NMR methods for studying structure and dynamics of large RNA molecules, with a focus on elements of the HIV-1 genome.
Talk Title: Structural characterization of large RNAs from HIV-1 using NMR
Abstract: The application of NMR spectroscopy to the study of large, biologically relevant RNAs is complicated by a number of factors, including limited chemical shift dispersion, undesirable relaxation parameters and a relative lack of long-range distance constraints. This talk will describe a number of NMR approaches we use to mitigate these difficulties, with a focus on nucleotide-specific deuterium labeling schemes and multiple bond heteronuclear couplings.
Haribabu Arthanari, PhD | Harvard Medical School and Dana Farber Cancer Institute
Assistant Professor Biological Chemistry and Molecular Pharmacology, Harvard Medical School and Cancer Biology Dana Farber Cancer Institute
Talk Title: Leveraging tailored isotope labeling and novel pulse design to encode amino acid selective line shapes.
Abstract: Solution NMR has the unique capacity to determine structures of proteins and characterize their dynamic states at an atomic resolution. With the maturity of X-ray crystallography and the emergence of cryo-EM, the power of NMR lies in complementing structural information with dynamics and characterizing transient interactions. Such studies have profound implications for protein function and therapeutic drug design. The starting point for most NMR protein investigations is “sequence specific resonance assignment” – matching each observed resonance peak to a particular nucleus in the protein. Currently, resonance assignment of large proteins (> 25 kDa) demands long hours of expert analysis. Studies of proteins with molecular weights above 50 kDa are not routine given two predominant challenges: i) Larger proteins produce more peaks, leading to overlap and degeneracy ii) Large proteins suffer rapid relaxation, which broadens the peaks and diminishes both sensitivity and resolution – especially for experiments with multiple lengthy delays for transfer of magnetization. The HNCA is the most sensitive triple resonance experiment that provides sequential connectivity for resonance assignment. Degeneracy of Cα chemical shifts impedes the complete assignment of large proteins. However, HNCACB and HNCACO, which are typically used to resolve the ambiguities, have poor sensitivity for large systems. We use a mixed pyruvate labeling strategy to modulate the isotope-environment of different amino acids, producing unique signature peak shapes. We design tailored 13C-homonuclear decoupling pulses to generate fingerprint patterns of CO and Cβ resonances directly in the observed Cα peak patterns, suitable for pyruvate or traditional isotope labeled samples. Cβ and CO information will then be collected using the superior resolution and sensitivity of the HNCA.
Lewis Kay, PhD | University of Toronto
Coming Soon
Talk Title: Without Isotopes There Is No Fancy NMR
Abstract: Over the past four decades solution NMR spectroscopy has made huge advances both in terms of the biochemical problems that can be explored as well as the quantitative nature of investigations that can be performed. The use of stable isotopes has been absolutely critical in this process, certainly as important as advances in spectrometer hardware and software, and improvements to NMR experiments that continue to evolve. I will present an overview of methyl labeling as applied to both proteins and DNA, focusing on the nucleosome core particle, the 220 kDa building block of chromatin. Examples from NMR spin relaxation studies of invisible protein states will also be presented, showing that different applications are best performed with different labeling strategies.
Christoffer Laustsen, PhD | Aarhus University Hospital
Christoffer Laustsen is a professor in translational MRI and head of the MR research department at the Clinical Institute of Medicine at Aarhus University. His research interests focus on translation of advanced imaging methods, such as hyperpolarized carbon 13 MRI, DMI and sodium 23 MRI.
Talk Title: Translation of Hyperpolarized Carbon-13 and Deuterium Imaging
Abstract: In this presentation I will introduce hyperpolarized carbon 13C MRI and DMI and discuss the translation and consideration that goes into a good metabolic MRI biomarker.
Andrew Percy, PhD | Cambridge Isotope Laboratories, Inc.
Dr. Andrew Percy obtained a PhD in bioanalytical chemistry at the University of Calgary (Alberta, Canada) in 2011, studying the structure and dynamics of protein complexes through H/DX-MS. After a brief postdoctoral fellowship, he served in the role of Quantitative Proteomics group leader at the UVic-Genome BC Proteomics Centre (BC, Canada), where his research there focused on the development and application of novel, isotope-directed MS-based assays for the qualification/quantification of proteins in human and mouse biosamples. Dr. Percy’s position at Cambridge Isotope Laboratories, Inc (CIL) since early 2016 is Senior Applications Chemist for Mass Spectrometry. At CIL, his responsibilities minimally involve new product identification and development, writing and reviewing marketing literature, and technical training/support in a diverse range of research areas. His focus has been MS ‘omics (proteomics, metabolomics, and lipidomics in particular) and newborn screening, which is facilitated by his practical and hands-on proficiency in MS applications of isotopically labeled analytes. To date, Dr. Percy has published over 40 research articles in peer-reviewed journals, is an active member of the mQACC consortium, acts as an ad-hoc reviewer for an array of scientific journals, and is on the editorial board of Biomedicines.
Talk Title: Example MS Applications of Stable Isotope Standards and their Mixtures
Abstract: Stable isotope standards provide valuable experimental and informatic solutions to improving the validity of qualitative/quantitative determinations in analytical and diagnostic science. To help enable routine implementation, CIL offers a broad and diverse collection of stable isotope-labeled standards in their individual and mixture forms. Applications of these are innumerable, ranging from exploratory ‘omics research to modern biomedicine. This presentation will provide an overview into example applications of isotopically labeled standards (and their mixtures) in MS-based measurements.
Matt Vander Heiden, MD, PhD | M.I.T.
Matthew Vander Heiden is the Director of the Koch Institute for Integrative Cancer Research and an Associate Professor in the Department of Biology at the Massachusetts Institute of Technology. He is also an Institute Member of the Broad Institute of Harvard and MIT, and an Instructor of Medicine at the Dana-Farber Cancer Institute and Harvard Medical School. Dr. Vander Heiden received his MD and PhD degree from the University of Chicago. He also completed clinical training in Internal Medicine and Medical Oncology at the Brigham and Women’s Hospital / Dana-Farber Cancer Institute prior to completing a post-doctoral fellowship at Harvard Medical School. His laboratory studies how metabolism is regulated to meet the needs of cells in different physiological situations with a focus on understanding the role of metabolism in cancer.
Talk Title: Using Stable Isotopes to Study Proliferating Cell Metabolism
Complex regulatory mechanisms enable cell metabolism to match physiological state.
The major pathways cells use to turn nutrients into energy and to synthesize macromolecules have been elucidated; however, there remain many unanswered questions regarding how metabolism supports cancer cell proliferation and thus how best to target metabolism for cancer treatment. By tracing the fate of isotope labeled nutrients in different cancer contexts, we are working to identify how different cancers use metabolism differently to grow. This includes tracing nutrient use into stable biomass to assess differential pathway use by different cancer cells in tumors, as well as isotope tracing to uncover whether cells use synthesis or salvage pathways to acquire nucleotides.
David Muddiman, PhD | North Carolina State University
David C. Muddiman is the Jacob and Betty Belin Distinguished Professor of Chemistry and Director, Molecular Education, Technology and Research Innovation Center (METRIC) at North Carolina State University in Raleigh, NC. Prior to moving his research group to North Carolina State University in 2005, David was a Professor of Biochemistry and Molecular Biology and Founder and Director of the Proteomics Research Center at the Mayo Clinic College of Medicine in Rochester, MN. Prior to this appointment, David was an Associate Professor of Chemistry at Virginia Commonwealth University. It was there that he began his professional career as an assistant professor with an adjunct appointment in the Department of Biochemistry and Molecular Biophysics and as a member of the Massey Cancer Center in 1997. These academic appointments were preceded by a postdoctoral fellowship at Pacific Northwest National Laboratory in the Environmental Molecular Sciences Laboratory under Richard D. Smith from 1995-1997. David was born in Long Beach, CA in 1967 but spent most of his formative years in a small town in Pennsylvania. David received his B.S. in chemistry from Gannon University (Erie, PA) in 1990 and his Ph.D. in Analytical Chemistry from the University of Pittsburgh in 1995 under the auspices of David M. Hercules. Dr. Muddiman was Editor of Analytical and Biological Chemistry (2015-2020) and he currently serves on the Editorial Advisory Board of Molecular and Cellular Proteomics, Rapid Communications in Mass Spectrometry, and the Journal of Chromatography B. He also serves on the advisory board of the NIH Funded Yale/NIDA Neuroproteomics Center, Yale University. Dr. Muddiman has served as a member of the ASMS Board of Directors (2013-2015) and Treasurer (2013-2015) and President (2015-2017) of the United States Human Proteome Organization. His group has presented over 675 invited lectures and presentations at national and international meetings including 31 plenary/keynote lectures. His group has published over 300 peer-reviewed papers and has received six US patents. He is the recipient of the 2016 Graduate School Outstanding Graduate Faculty Mentor Award in the Mathematical, Physical Sciences, and Engineering, 2015 ACS Award in Chemical Instrumentation, 2010 Biemann Medal (American Society for Mass Spectrometry), 2009 NCSU Alumni Outstanding Research Award, the 2004 ACS Arthur F. Findeis Award, the 1999 American Society for Mass Spectrometry Research Award, and the 1990-1991 Safford Award for Excellence in Teaching (University of Pittsburgh). Dr. Muddiman’s research is at the intersection of innovative mass spectrometry technologies, systems biology, environmental science, and model organisms to understand human disease and is funded by the National Institutes of Health.
Talk Title: Quantifying Human Exposure to Emerging Contaminants of Concern using Mass Spectrometry
Abstract: Mass spectrometry offers a versatile and robust platform to discover and subsequently quantify new diagnostic, prognostic, and therapeutic biomarkers for disease as well as understand the role of the environment (exposure) on human health. This presentation will cover two main topics: 1) a CE-MS approach related to human exposure to environmental neurotoxins as well as new discoveries, followed by translation of those findings to a new even more rapid MS-platform; and 2) novel methods for the quantification of per- and poly-fluoroalkyl substances (PFAS) in human serum.
Lingjun Li, PhD | University of Wisconsin
Dr. Lingjun Li is a Vilas Distinguished Achievement Professor and the Charles Melbourne Johnson Distinguished Chair Professor of Pharmaceutical Sciences and Chemistry at the University of Wisconsin-Madison (UW-Madison). Dr. Li received her Ph.D. degree in Analytical Chemistry/Biomolecular Chemistry from the University of Illinois at Urbana-Champaign in 2000. She then did joint postdoctoral research at the Pacific Northwest National Laboratory and Brandeis University before joining the faculty at UW-Madison in December 2002. Dr. Li’s research interests include the development of novel mass spectrometry (MS)-based tools such as new isotopic and isobaric labeling strategies that enable hyperplexing for quantitative proteomics, peptidomics, and glycomics, and their applications in neuroscience and cancer research. She and her team also develop microscale separations, in vivo microdialysis and imaging MS tools for functional discovery of neuropeptides in model organisms and (glyco)protein biomarkers in neurodegenerative diseases with a strong focus on Alzheimer’s disease. Her lab also explores novel use of ion mobility MS to address technical challenges in peptidomic research. Professor Li has established a highly productive research program and published more than 300 peer-reviewed research journal papers and has given more than 200 invited talks. She has successfully trained and graduated 50 PhDs and is currently training 25 PhD graduate students, 4 postdoctoral scientists, and 7 undergraduate students. She has been recognized with numerous awards, including ASMS Research Award, NSF CAREER Award, Sloan Fellowship, PittCon Achievement Award, and ASMS Biemann Medal, and was named one of the Top 50 most influential women in the analytical sciences in 2016 and was recently featured in the 2019 Top 100 Power List by the Analytical Scientist. Dr. Li is currently serving as an Associate Editor for the Journal of the American Society for Mass Spectrometry (JASMS) and sitting on the Advisory Board for Analytical and Bioanalytical Chemistry. She is a member of the Board of Directors for the US Human Proteome Organization (US HUPO) and Chair of the Board of Directors for the Chinese American Society for Mass Spectrometry (CASMS).
Talk Title: High Resolution FTMS Enabled Mass Defect-based Chemical Tags for Multiplex Quantitative Omics
Abstract: Recent advances in mass spectrometry (MS) have made MS-based omics a central technology for biomedical research. Quantification of proteins, peptides and metabolites present in complex biological systems is often key to understanding dynamic changes of many essential physiological and pathological processes. Chemical labeling with multiplex isobaric tags offers an effective strategy for parallel comparative analyses of many samples during liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis. In this presentation, I will present our recent progress on the design and development of several novel chemical tags, including dimethylated leucine (DiLeu) isobaric tagging reagents, which offer cost-effective implementations that enable higher orders of multiplexing. The utilities of these novel chemical tags are further demonstrated through their application in the study of targeted proteomic and glycoproteomic changes in Alzheimer’s disease. Additionally, we report on a multiplexed quantification method for simultaneous proteomics and amine metabolomics analyses via nanoflow reversed phase LC-MS/MS, exploiting mass defect-based DiLeu (mdDiLeu) labeling. Paralleled proteomics and amine metabolomics analyses using mdDiLeu will be presented for application to pancreatic cancer cells. Collectively, we present a versatile chemical tagging toolbox enabled by high solution FTMS platform for system-wide omics studies.
John Yates, PhD | Scripps Research Institute
John R. Yates is the Ernest W. Hahn Professor in the Departments of Molecular Medicine and Neurobiology at Scripps Research. His research interests include development of integrated methods for tandem mass spectrometry analysis of protein mixtures, bioinformatics using mass spectrometry data, and biological studies involving proteomics. He is the lead inventor of the SEQUEST software for correlating tandem mass spectrometry data to sequences in the database and developer of the shotgun proteomics technique for the analysis of protein mixtures. His laboratory has developed proteomic techniques to analyze protein complexes, posttranslational modifications, organelles and quantitative analysis of protein expression for the study of biology. He has received awards including the ASMS Biemann Medal, HUPO Achievement Award, Christian Anfinsen Award (Protein Society), Analytical Chemistry award (ACS), Ralph N. Adams Award, Thomson Medal (IMSF), John B. Fenn Award (ASMS), HUPO Discovery Award. He is currently the EIC at the Journal of Proteome Research.
Talk Title: Quantitative Bioorthogonal Chemistry for Proteomics
Abstract: Identifying molecular changes associated with disease is a major challenge and to do so at the earliest time point prior to pathology is desired. At early time points, however, molecular changes may be small and difficult to identify hidden by the overwhelming static proteome. The second method is to measure protein degradation in tissues. Traditional methods of using stable isotope labeled amino acids is complicated by a decreasing signal in a high background. One solution we are exploring is to pulse in azidohomoalanine (AHA) into an animal model and then use click chemistry to enrich labeled peptides at various timepoints to plot degradation curves. Azidohomoalanine (AHA) is a modified methionine that is accepted by the endogenous methionine tRNA and inserted into proteins in vivo. AHA can be covalently linked to a biotin alkyne through click chemistry. Thus, AHA proteins or peptides can be enriched and efficiently separated from the whole proteome through avidin bead enrichment. Newly synthesized proteins (NSP) within a discrete time period in conjunction with the development of disease can be identified using this method. We’ve also developed sophisticated software tools to analyze the data.
Gary Patti, PhD | Washington University
Gary Patti is the Michael and Tana Powell Professor at Washington University in St. Louis, where he holds appointments in the department of chemistry and the department of medicine. Dr. Patti is the Director of the Center for Metabolomics and Isotope Tracing and the Co-Director of the Metabolic Kinetics Core in the Nutrition Obesity Research Center. Professor Patti’s research focuses on developing and applying both mass spectrometry- and NMR-based metabolomics technologies to enhance our understanding of human metabolism. Applications of his work range from studies of molecular processes in cell culture to physiological regulation of metabolism at the organ level in animal models and human patients. Professor Patti has been recognized with numerous awards including the Pew Biomedical Scholars Award, the Alfred P. Sloan Award, the Camille Dreyfus Teacher-Scholar Award, the Mallinckrodt Scholar Award, and the NIEHS award for revolutionizing, innovative, and visionary research.
Talk Title: Big Data from Heavy Molecules
Abstract: Stable isotopes are a cornerstone of metabolic research, with applications ranging from quantitation to flux analysis. This presentation will outline three different use cases of stable isotopes in mass spectrometry-based metabolomics. First, an experimental approach called credentialing will be discussed as a strategy for data reduction. Given that only peaks derived from biological compounds can become isotopically labeled, credentialing enables the annotation of signals in metabolomics data that correspond to contaminants and artifacts. Second, an application of stable isotopes to mammalian cell culture will be described. Rapidly dividing cells will be compared to quiescent cells to demonstrate metabolic fluxes that change in support of proliferation. Finally, third, experimental strategies for performing isotope-tracer analysis in animals will be reviewed. An example of metabolic crosstalk, where molecules are exchanged between different tissues, will be highlighted.