Abstracts & Bios

(Will be updated)


Christopher BARNES – Where are we now? One year of COVID-19 structural biology

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BIO: Dr. Christopher Barnes is a newly appointed Assistant Professor of Biology and ChEM-H Institute Scholar at Stanford University. Before arriving at Stanford, Dr. Barnes earned degrees in Chemistry and Psychology from the University of North Carolina at Chapel Hill and completed his PhD thesis at the University of Pittsburgh. It was during his doctoral work that Dr. Barnes begin to develop the structural tools necessary to understand the complexity of macromolecular interactions. Recently, in the lab of Dr. Pamela Bjorkman at the California Institute of Technology, he expanded his skillset to include cryo-electron microscopy techniques to help define the structural correlates of antibody-mediated neutralization of HIV-1 and SARS-CoV-2. As a recipient of the prestigious HHMI Hanna Gray Fellowship and Chan-Zuckerberg Biohub Investigator award, Dr. Barnes hopes to use structural methods to rationally design protein-based immunogens capable of eliciting broad and potent neutralizing antibodies against emerging zoonotic viruses.

Ariane BRIEGEL Exploring the structure and function of microbial motility with cryo-electron tomography

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BIO: Ariane Briegel is a professor at the Leiden University (The Netherlands) and Co-director of The Netherlands Center for Electron Nanoscopy (NeCEN). She has over 20 years of experience using cryo-electron microscopy to study bacterial and archaeal ultrastructure. The Briegel laboratory focuses on investigating how microbes sense and respond to their environment. In order to gain insight into the structure and function of the molecular complexes involved in these behaviors, the lab uses electron cryotomography and correlative microscopy methods.

Mihnea BOSTINA – TBA

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Shujun CAI – Cryo-electron tomography study of a lipid transfer protein VPS13 in situ

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BIO: Shujun Cai is a postdoctoral fellow at Yale University. She was trained as a structural biologist in her PhD, with expertise in cellular cryo-electron tomography and chromatin biology. Her current work uses cryo-electron tomography as a tool to study lipid-transfer mechanisms in mammalian cells including neurons.

Yao CONG – TBA

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Shangyu DANG – TBA

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Danny HSU – Game of spike: the battle between mutations and antibodies

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BIO: Danny obtained his PhD in Chemistry in 2004 from the Utrecht University, the Netherlands, specializing in the applications of solution state NMR spectroscopy and molecular dynamics to study bimolecular interactions. He coined the term pyrophosphate cage to describe how a highly cyclized lanthionine-containing antibiotic, nisin, targets bacterial cell wall precursor, Lipid II, to achieve efficient membrane pore formation. He was awarded a Royal Netherlands Ramsay Memorial Fellowship and subsequently a Long-term fellowship from the Human Frontier Science Program to study co-translational folding of nascent polypeptide chains on the ribosome by NMR at Cambridge University. His work led to a Young Investigator Award from the International Society of Magnetic Resonance in 2007. He also applied NMR spectroscopy to investigate the folding dynamics of DNA and RND G-quadruplexes, and how ions and small molecules modulate the folding topologies and stabilities. He returned to Taiwan in 2010 with a Career Development Award from the Human Frontier Science Program to study folding mechanisms and functions of topologically knotted proteins. Danny is since 2017 a tenured Associate Research Fellow at the Institute of Biological Chemistry, Academia Sinica. His recent research interests focus on the integration of cryo-EM, mass spectrometry and complementary biophysical tools to study highly glycosylated proteins, including the spike protein of SARS-CoV-2.

Duane LOH – TBA

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Shee-mei LOK – The interplay between dengue morphological diversity and antibody recognition

ABSTRACT: Dengue virus (DENV) is major human pathogens infecting approximately 400 million people annually worldwide. However, currently there is no highly effective vaccine and therapeutics are non-existent. Here we show that DENV in addition to the presence of four different serotypes, within each serotypes, there is also variation of particle morphology between strains. The changes in particle morphology thus antigenicity, is due to the rearrangement of the surface viral envelope (E) proteins allowing DENV to evade host immunity. This will thus complicated the development of effective vaccines and therapeutics. We will discuss the extensive studies that we have done to examine the different morphologies displayed by various DENV strains and how we identify molecular determinants on the E proteins that lead to different structural changes. By studying the different morphological variants displayed by strains within each serotypes, we may be able to incorporate “representative morphologies” for each serotypes to make a more effective vaccine with greater coverage against all DENV serotypes antigenic structures. We will also discuss how highly potent human antibodies can neutralize all or some of the morphological variants of four DENV serotypes.


BIO: Dr Shee-Mei Lok is a Professor in the Emerging Infectious program in Duke-NUS, Singapore. She was also a National Research Foundation (NRF) fellow (2009-2014) and is now a NRF Investigator. She is a structural virologist specializing in x-ray crystallography and cryo-electron microscopy. Her research interest focus on the structural changes of flavivirus particles during its infection cycle and the effect of anti-viral therapeutics on them. She obtained her Msc and PhD in NUS and did her post-doctoral training in Purdue University under the supervision of the late Hanley Prof Michael Rossmann. Her laboratory made significant discoveries in the understanding of the structures of the Zika and dengue viruses, the morphological variants of dengue viruses, also how potent human antibodies neutralize flaviviruses and the structural changes of flavivirus during maturation.

Naoko MIZUNO – TBA

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Kelly NGUYEN – TBA

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Gaia PIGINO – Title

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Isabelle ROUILLER – TBA

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Carsten SACHSE – Cryo-EM structures of ESCRT membrane remodeling complexes

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BIO: Carsten Sachse is heading the Structural Biology division of the Ernst-Ruska-Centre at the Forschungszentrum Jülich (Germany). He was a Group Leader at the EMBL in Heidelberg from 2010 to 2018. His group determines the three-dimensional cryo-EM structures of multi-protein complexes in isolation and their biological context with a particular focus on elucidating the mechanism of membrane biological processes such as autophagy and endocytosis. In order to further advance the cryo-EM method, he is interested in applying novel hardware and developing software for high-resolution single-particle as well as cellular cryo-EM.

Moran SHALEV-BENAMI – TBA

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BIO: Dr. Shalev-Benami received her bachelor's degree in Molecular Biochemistry from the Technion Institute of Technology in 2006. She holds a M.Sc. degree in Biochemistry from the Hebrew University in Jerusalem, where she conducted her graduate research under the mentorship of Prof. Miriam Altstein. After receiving her M.Sc. in 2008, she returned to the Technion to peruse her Ph.D. in Structural Biology under the supervision of Prof. Timor Baasov and Prof. Noam Adir. Her Ph.D. studies focused on X-ray crystallographic studies of RNA and structure-based drug design. In 2013, she joined the lab of Prof. Ada Yonath at the Weizmann Institute of Science as a postdoctoral fellow, working on structural investigations of eukaryotic ribosomes. In 2015, she joined the lab of Prof. Georgios Skiniotis at the University of Michigan where she further perused her structural studies of eukaryotic ribosomes through single particle electron cryo-microscopy (cryo-EM). In 2017, Dr. Shalev-Benami continued her studies under the supervision of Prof. Skiniotis at Stanford University where she focused on structural characterization of membrane proteins using cryo-EM. In December 2018, Dr. Shalev-Benami joined the Weizmann Institute of Science, where her research focuses on the visualization of macromolecular complexes involved in cell-cell communication by cryo-EM.

Minhaj SIRAJUDDIN – Helical reconstruction of actin cytoskeleton bound with cognate binding proteins

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BIO: Our lab is interested in understanding the mechanism of molecular machinery that mediate biological motility, including but not limited to muscle contraction, cell motility and intracellular cargo transport. We employ biochemistry, in vitro reconstitution, light and electron microscopy to study these active matters across dimensions from molecular, mesoscopic, cellular to tissue and organ scale.

Olga SOKOLOVA – Structures of viral chaperonins in complex with substrate proteins

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BIO: Olga S. Sokolova, PhD, D.Sc., Professor of Russian Academy of Sciences. Her main interest lies in the field of structural biology and cryo-electron microscopy. She has a background in biochemistry and structural biology/biophysics, with specific postdoctoral training in single particle EM in the laboratory of Dr Nikolaus Grigorieff (HHMI). As a postdoctoral fellow, she has conducted research on the 3D structure of the Shaker Kv channel. After starting her own laboratory in 2006 in Moscow Lomonosov University, she began to develop an integrated approach to study the structures of large protein complexes using cryo-EM and molecular modeling. She collaborates with numerous scientists from USA and Europe and participates in large multinational consortia that develop methods for investigating the structure of transmembrane proteins: “European Drug Initiative of Channels and Transporters” and “Integrated Biology Infrastructure Life-Science Facility at the European XFEL”. She was awarded the honorary title of Professor of Russian Academy of Sciences in 2016.

Ji-Joon SONG – Molecular mechanism of chromatin dynamics

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BIO: Ji-Joon Song is a Professor in the Department of Biological Sciences at KAIST. He received his. B.S. at Seoul National University, and his Ph.D. in structural biology with Leemor Joshua-Tor at the Cold Spring Harbor Laboratory. During his Ph.D., he determined the first structure of Argonaute involved in RNAi. He then joined in Bob Kingston group as a research fellow at Massachusetts General Hospital, Harvard Medical School. The research in Song Lab at KAIST focuses on understanding the molecular mechanisms of epigenetic gene regulation using cryo-EM and integrative structural approaches.

Elitza TOCHEVA – Evolution and biogenesis of the outer membrane in bacteria

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BIO: Dr. Elitza Tocheva graduated with her PhD in Microbiology and Immunology from the University of British Columbia in 2007, where she worked on characterizing the mechanism of bacterial enzymes involved in denitrification using x-ray crystallography and biochemical methods. She continued her structural biology studies as a postdoctoral scholar in the laboratory of Dr. Grant Jensen at Caltech where she applied cryo electron tomography and correlative microscopy approaches to study the ultrastructure of bacteria. She joined Université de Montréal as an Assistant Professor in June of 2015 and in January of 2019 was recruited to the Department of Microbiology and Immunology at UBC. Her lab combines microbiology, biochemistry and structural biology to study sporulation, membrane biogenesis, and host-pathogen interactions.

Kuang-lei TSAI – TBA

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Ming-Daw TSAI – Cryo-EM in Enzymology

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BIO: Professor Ming-Daw Tsai received B.S. degree from National Taiwan University (1972) and Ph.D. from Purdue University (1978), and served in the faculty of the Department of Chemistry and Biochemistry, The Ohio State University in 1981-2006. Subsequently he moved to the Institute of Biological Chemistry of Academia Sinica, Taiwan. His research interests include mechanistic enzymology of phosphoryl transfer enzymes including DNA polymerases, kinases and phospholipases, and structure-function relationship of proteins in DNA damage response and cancer signaling, including ankyrin repeat proteins and FHA domain proteins. A recent focus is on the roles of TIFA in cancer and immunity. He probes mechanistic problems by applying emerging methodologies in structural biology, including NMR, X-ray crystallography, MS, and recently cryo-EM, leading to close to 300 publications. He was elected to Fellow, American Association for the Advancement of Science (AAAS, 1992), Academician, Academia Sinica (2012), and Fellow, The World Academy of Science (TWAS, 2014).

Lexi WALLS – Visualizing the SARS-CoV-2 spike in complex with neutralizing antibodies

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BIO: Lexi received her bachelors of science degree in Biochemistry from the University of Massachusetts Amherst and worked with Dr. Mary Munson and Dr. Lila Gierasch during her time there. She moved to Seattle to pursue her PhD in Biochemistry from the University of Washington in Seattle where she is currently working as a scientist in David Veesler's laboratory. Her work has been foundational for understanding coronavirus structure, function and developing therapeutics both before and during the current pandemic. She has co-authored more than 28 scientific publications, contributed to four US patents, and her work has led to two clinical trials currently being evaluated in humans. When she isn't in the laboratory, she spends her free time hiking and climbing the beautiful mountains of the Pacific Northwest.

Elizabeth WRIGHT – TBA

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Min XU – Automatic analysis of cryo-electron tomography using computer vision and machine learning

ABSTRACT: The cell is the basic structural and functional unit of all living organisms. Understanding how cells function is fundamental to life science. Macromolecules are nano-machines inside cells that govern the cellular processes. To fully understand such processes, it is necessary to know the native structures and spatial organizations of macromolecules inside single cells, and their interactions with other subcellular components. Such information has been extremely difficult to obtain due to a lack of suitable data acquisition techniques. The recent revolution of Cryo-electron tomography (cryo-ET) 3D imaging technology has made collecting such information possible. Cryo-ET captures a 3D image of a single cell's subcellular structures at sub-molecular resolution and in a near-native state. It provides unprecedented opportunities for systematically studying the native spatial organization of subcellular structures, especially macromolecules. However, cryo-ET has a high degree of structural complexity and imaging limits, such as high structural diversity and crowding, low signal-to-noise ratio, and missing values. These have made the automated systematic analysis of such images extremely difficult. Since 2008, we have been developing image analysis methods to address this challenge. In particular, we focus on systematic recognition and recovery of the structures of large numbers (millions) of macromolecules captured by cryo-ET, without relying on external structural knowledge. To do so, we have developed different cryo-ET image registration, classification, segmentation restoration techniques. Our effort is a key step for systematic analysis of macromolecules' structures and spatial organizations inside single cells captured by cryo-ET.


BIO: Dr. Min Xu is an Assistant Professor at the Computational Biology Department in the School of Computer Science at Carnegie Mellon University. He serves as training faculty at the Joint CMU-Pitt Ph.D. Program in Computational Biology. He also serves as a training faculty Master of Science in Computer Vision Program at Robotics Institute. He is an investigator at the National Center for Multiscale Modeling of Biological Systems. Dr. Xu’s career has centered on developing computational methods to study cellular systems using imaging and omics data. He started his research career in the field of Computational Biology and Bioinformatics since 2000. He developed machine learning methods for gene selection for classifying cancer samples, for cancer gene network module discovery, and sample phenotype prediction by integrating hundreds of gene expression datasets. Since 2008, he started working in computational analysis of Cellular Cryo-Electron Tomography (Cryo-ET) data. He designed structural pattern mining methods and first demonstrated the feasibility of De Novo extraction of structures and spatial organizations of macromolecular complexes in single cells using Cryo-ET data. His current research focus on developping computer vision and machine learning techniques for Cryo-ET-derived modeling of the cellular organization at molecular resolution. Dr. Xu has published over 60 research papers. Example publications include top image analysis conference papers such as CVPR and MICCAI, as well as prestigious journals and conference papers in computational biology, such as PNAS and ISMB. He is a recipient of NIH R01, NSF IIBR, and IIS awards. He is currently serving in the editorial board of Statistical Methods in Medical Research. Dr. Xu received an B.E. in Computer Science from the Beihang University, M.Sc from School of Computing at the National University of Singapore, M.A. in Applied Mathematics from the University of Southern California (USC), and Ph.D. in Computational Biology and Bioinformatics from USC. He was a postdoctoral researcher at USC.

Koji YONEKURA – Cryo-EM and EX for high-resolution and high-precision structure analyses

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