Matthew Akamatsu, Ph.D. | University of Washington

Talk title: "Self-organization and load adaptation by endocytic actin networks"
Abstract: Ensembles of polymerizing cytoskeletal protein complexes assemble in cells to produce directional force on cellular membranes. During clathrin-mediated endocytosis, networks of branched actin filaments assemble on the plasma membrane to push, pull, and reshape the endocytic pit. The underlying principles that permit the self-assembly of polarized branched actin networks in stochastic cellular environments are not well-understood. Integrating quantitative models with quantitative experimentation allows us to iteratively propose and test such mechanistic hypotheses.  We combined agent-based computational modeling with quantitative live-cell fluorescence microscopy of genome-edited human induced pluripotent stem cells to identify mechanisms by which branched actin networks organize to produce force at sites of mammalian endocytosis. We constrained our model with measurements from purified proteins and tested mechanistic predictions with super-resolution microscopy and cryo-electron tomography. With this combination of approaches, we found that the locations of key actin-binding proteins at sites of endocytosis permit branched actin networks to self-organize into a polarized array radially focused on the clathrin-coated pit. This organization of filaments enables the network to dynamically respond to increases in load, such as elevated membrane tension, by nucleating additional filaments and storing elastic energy in bent filaments. Regular binding of actin-branching and linking proteins on actin filaments leads to sparse asymmetric actin networks that, by continually rebinding to the pit and rearranging, produce sufficient force for endocytic internalization. We propose that these principles of self-organization and load adaptation likely apply broadly to ensembles of self-organizing protein complexes that produce directional force on cellular membranes.

Bio: Matt Akamatsu joins the faculty at the University of Washington’s Department of Biology in June 2022. Matt received his PhD in the department of Molecular Biophysics and Biochemistry at Yale University in Yale's Integrated Graduate Program in Physics, Engineering and Biology. He worked in Tom Pollard's lab to study the mechanisms by which fission yeast cells assemble and position their cytokinetic contractile ring for symmetrical cell division. He carried out postdoctoral work as an Arnold O. Beckman researcher at UC Berkeley in the department of Molecular and Cellular Biology, coadvised by Padmini Rangamani (UC San Diego) and David Drubin. There, he combined computational modeling with live-cell quantitative fluorescence microscopy to study the mechanisms by which the actin cytoskeleton organizes, produces force, and responds to resistance during mammalian endocytosis. At the University of Washington, Matt’s lab will combine mathematical modeling, human stem cell genome-editing, and fluorescence microscopy to study the mechanical relationship between the actin cytoskeleton and membrane deformation during mammalian endocytosis.  Matt is a recipient of the K99 Pathway to Independence Award, UC Berkeley Outstanding Postdoc Award in the Department of Molecular and Cellular Biology, and the 2020 Porter Prize for Research Excellence from the American Society for Cell Biology.


Brian Beliveau, Ph.D. | University of Washington

Talk Title: "Oligo-based technologies for programmed spatial biology"
Abstract: Approaches such as genomics, transcriptomics, and proteomics can provide rich information about the presence and abundance of biomolecules in large populations of cells and more recently even in single cells. However, both the ensemble and single-cell versions of these techniques require the dissociation of complex structures like tissues during their experimental workflows, resulting in a loss of spatial information. Multiplexed imaging approaches capable of visualizing multiple DNA, RNA, or protein species in the same sample can provide a valuable complementary approach to the “-omics” methods, particularly in the context of tissues. We have introduced SABER—Signal Amplification by Exchange Reaction. SABER enables the multiplexed amplification of DNA and RNA fluorescent in situ hybridization (FISH) and immunofluorescence signals in fixed cells and tissues, allowing spatial patterns of gene and protein expression and chromosome organization to be mapped in their native contexts. We have also introduced “PaintSHOP”, an interactive web-based resource that facilitates the design and ordered of oligonucleotide-based FISH probe sets. Together, these tools provide researchers with an accessible and modular framework for executing spatial imaging experiments.

Bio: Brian Beliveau (he/him/his) is an Assistant Professor of Genome Sciences at the University of Washington. Prior to starting his lab in 2018, Brian did his postdoctoral work in the lab of Peng Yin at the Wyss Institute / Harvard Medical School, his PhD training with Ting Wu at Harvard Medical School, and his BS/MS research with Brendan Cormack at Johns Hopkins. The Beliveau lab develops and applies enabling technologies to study spatial patterns of 3D genome organization, gene expression, and protein function in cells and tissues. We also investigate how chromosomes fold and how their structure regulates DNA transactions in the nucleus such as transcription, replication, and repair.


Chantell Evans, Ph.D. | Duke University

Talk Title: "Investigating the Spatiotemporal dynamics of neuronal mitophagy"
Abstract: Damaged mitochondria are removed from the cell via mitophagy. This pathway may be important for neuronal homeostasis, as mutations in pathway components cause PD and ALS. We used live imaging to investigate the spatiotemporal dynamics of mitophagy in primary neurons following mild oxidative stress. Mitophagy-associated proteins rapidly translocate to depolarized mitochondria and mitochondria were sequestered in autophagosomes within an hour of damage. Surprisingly, the downstream degradation of engulfed mitochondria was delayed, primarily due to slow acidification of the resulting mitophagosomes. Expression of an ALS-associated mutation disrupted mitochondrial network function, and stress exacerbated this effect. These results suggest that slow turnover of damaged mitochondria may increase neuronal susceptibility to neurodegeneration.

Bio: Chantell Evans is an Assistant Professor of Cell Biology at Duke University. She received her Ph.D. in Molecular and Cellular Pharmacology from the University of Wisconsin and was a Postdoctoral Fellow at the University of Pennsylvania. Her lab uses advanced microscopy and biochemical techniques to gain insight into the molecular mechanisms that regulate mitophagy in primary neurons. She is particularly interested in examining mitochondrial quality control pathways in neurons and the role of mitochondrial regulation in neurodegenerative diseases. Chantell is a Duke Science and Technology Scholar and an inaugural recipient of the Hanna Gray Fellowship from the Howard Hughes Medical Institute.


Shila Ghazanfar, Ph.D. | University of Cambridge

Talk Title: "Data integration for molecule-resolved spatial gene expression of mouse organogenesis"
Abstract: Dissociated transcriptional profiling of single cells has advanced our knowledge of the molecular basis of development. Novel spatial transcriptomics technologies, such as seqFISH, enable sensitive detection of RNA molecules in their native spatial context. Here, we have applied seqFISH to build a high-resolution spatial map of mouse organogenesis, with hundreds of target genes captured in tissue sections. By computationally integrating these spatial context and multiplexed transcriptional measurements with single cell transcriptomic atlases, we are able to uncover axes of cell differentiation that are not immediately apparent from either technology alone. In sum, dissociated single cell and imaging-based transcriptomics along with novel approaches for computational data integration provides a powerful new approach for studying how and when cell fate decisions are made during early mammalian development.

Bio: Dr Ghazanfar is currently a Royal Society Newton International Fellow and Postdoctoral Research Associate at the Cancer Research UK Cambridge Institute, University of Cambridge. In May 2022, she will open her lab as a Lecturer and Australian Research Council Discovery Early Career Research Fellow at The University of Sydney, Australia, where she completed her undergraduate and doctoral studies in pure mathematics and statistics, and statistical bioinformatics respectively. Dr Ghazanfar’s lab will focus on designing statistical approaches for analysis of spatial single cell genomics data, alongside building techniques for effectively integrating spatial molecular-resolved genomics data with dissociated single cell transcriptomics and multiomics data types.


David Goodsell, Ph.D. | Scripps Research

Talk title: "Building Structural Models of a Whole Bacterial Cell"
Abstract: Building on previous artistic approaches for visualizing the molecular structure of living cells, we have built 3D models of a whole bacterial cell that includes all macromolecules. The concentration, positions, and interactions of molecules are taken from recent whole-cell systems biology computational models, integrated with experimental and homology-modeled structures of 482 protein monomers and 201 protein complexes, and lattice-based models of the genome, RNA and associated macromolecules. A computational workflow was developed to streamline gathering and curating these structures, defining a “recipe” that specifies the composition of the cellular model, and building and optimizing models based on this recipe. Visualization methods were also developed to allow exploration of functional characteristics of the genome and proteome.

Bio: David S. Goodsell divides his time between research in computational biology at Scripps Research and science outreach with the RCSB Protein Data Bank at Rutgers. This includes three decades of work on artistic and scientific approaches to exploring the molecular structure of living cells, and his popular "Molecule of the Month" column at the PDB. Recent research in his laboratory has focused on development of computational methods for modeling entire bacterial cells, and development of outreach materials on the biology of coronaviruses.


Lucas Pelkmans, Ph.D. | University of Zurich

Talk title: "Multimodal perception links cellular state to decision making in single cells"
Abstract: A fundamental property of cells is that they make decisions adapted to their internal state and surrounding. This context-aware behavior requires the processing of large amounts of information, but it is unclear how cells can reliably achieve this using heterogeneous signaling responses. To study the information processing capacity of human epithelial cells, we here apply epidermal growth factor stimulation, combined with multiplexed quantification of signaling responses and multiple markers of the cellular state across multiple spatial scales. We find that signaling nodes in a network display adaptive information processing, which leads to heterogeneous growth factor responses and enables nodes to capture partially non-redundant information about the cellular state. Collectively, as a multimodal percept, this provides individual cells with a large amount of information to accurately place growth factor concentration within the context of their cellular state and make cellular state-dependent decisions. We propose that heterogeneity and complexity in signaling networks have co-evolved to enable specific and context-aware cellular decision making in a multicellular setting.

Bio: Lucas Pelkmans studied Medical Biology at the University of Utrecht (The Netherlands) and did his PhD in Biochemistry at the ETH Zurich (Switzerland). He was then a postdoctoral fellow at the Max Planck Institute of Molecular Cell Biology and Genetics in Dresden (Germany). At the age of 29, he became assistant professor at the Institute of Molecular Systems Biology of the ETH Zurich. He was elected the Ernst Hadorn-endowed Chair at the University of Zurich 5 years later in the Department of Molecular Life Sciences, where he is currently a full professor. Lucas Pelkmans was chairman of the Scientific Executive Board of SystemsX.ch from 2013-2018 and was elected as a member of the European Molecular Biology Organisation (EMBO) in 2015. Lucas Pelkmans is an inventor on several patents in the area of image-based systems biology and is a co-founder of the biotech company 3V-Biosciences (now Sagimet Biosciences). He received the ETH medal for best PhD thesis, won the European Young Investigator Award, and received an ERC junior, consolidator, and advanced grant.


Sabine Petry, Ph.D.| Princeton University

Talk Title: "How to make microtubules and build the cytoskeleton"
Abstract: How does a cell construct its microtubule cytoskeleton? According to Feynman’s principle “what I cannot create, I do not understand”, my lab pursues this question by building the chromosome segregation machinery from scratch. I will first tell you how the microtubule framework is generated in a cell. Upon deciphering the function of the most important microtubule accessory proteins, I will present how we use those building blocks to reconstitute a spindle substructure in vitro and determine its building plan. Finally, I will outline how we combine spindle substructures like pieces of a puzzle to assemble and thereby understand a functioning spindle that segregates chromosomes.
By studying how the MT cytoskeleton is built, I hope to help explain how hundreds of proteins can self-assemble on the nm scale into a complex molecular machine 1000-fold larger than its constituents, a challenge for the biochemistry of the 21st century.

Bio: Prof. Sabine Petry is originally from Germany and played professional basketball while finishing High School. Sabine then studied Biochemistry at the Goethe University and the Max Planck Institute of Biophysics in Frankfurt, where she became interested in structural biology. She performed her thesis research with Dr. Venki Ramakrishnan (Nobel Prize Chemistry) at the MRC Laboratory of Molecular Biology (UK). During her Ph.D., she solved crystal structures of classical translation factors bound to the entire ribosome, work that helped increase our knowledge of how translation factors drive protein synthesis in the ribosome.
In 2008 Sabine joined the laboratory of Ron Vale (Lasker and Gairdner Awards) at UCSF as a postdoctoral HHMI Fellow of the Life Science Research Foundation, where she pursued the study of a less understood and larger molecular entity, the mitotic spindle. Her research focused on understanding how microtubule nucleation is regulated in the mitotic spindle, which is poorly understood. It led to the discovery of a new microtubule nucleation mechanism, in which microtubules arise by nucleation from existing microtubules. Microtubule branching helps explain many unresolved aspects of how the mitotic spindle is assembled, and raises new questions about its role in building the microtubule cytoskeleton of the cell.
Since 2013, Sabine has been an Assistant Professor in the Department of Molecular Biology, and is Associated Faculty of the Departments of Chemical and Biological Engineering, as well as Chemistry. In her lab, she is tackling how the microtubule cytoskeleton builds cellular structures by combining single molecule imaging and cell biological methods with high-resolution structural techniques. Sabine has been recognized with the NIH Pathway to Independence Award, the Kimmel Scholar Award for Cancer Research, the Packard Award for Science and Engineering, and the NIH New Innovator Award. She is also a Pew Fellow of the Biomedical Sciences.
In 2019, she received the Women in Cell Biology Junior Award for Excellence in Research by the American Society of Cell Biology.

 


Johannes Schöeneberg, Ph.D. | University of California San Diego

Talk Title: Coming Soon
Abstract: Coming Soon

Bio: Johannes Schöneberg is an Assistant Professor in the departments of Pharmacology and Chemistry and Biochemistry at the University of California San Diego. He completed a postdoctoral fellowship at the University of California, Berkeley, where he was also a Berkeley Institute for Data Science (BIDS) fellow. He received his PhD in Computer Science and Biophysics from the Free University Berlin and the Max Planck Institute for Molecular Genetics, and his B.Sc. in Bioinformatics from Saarland University. His newly formed research group at UC San Diego uses computational and experimental approaches to study the link between mitochondrial dynamics and neurological diseases that are caused by mitochondrial dysfunction such as Parkinson’s Disease and epilepsy, using 5D adaptive optics lattice light-sheet microscopy, brain organoids, human induced pluripotent stem cells, and machine learning.


Devin Schweppe, Ph.D. | University of Washington

Talk title: "Multiplexed Mapping of Complex Proteomes"
Abstract: Modern high-throughput proteomics enables deep quantitation of up to 10,000 proteins per sample. As we seek to take advantage of the analytical power of this field, we are asking what are the limits of sensitivity, robustness, and accuracy? To address these questions, we developed new methods, termed millisecond informatic pipelines, to reduce acquisition times and improve quantitative analyses. We have now applied these methods to analyze large sample cohorts in half the time as previously needed for canonical analyses. We used these more efficient analytical workflows to profile murine aging across ten tissues and chemical library screening. In our aging study, we established a dataset across hundreds of samples and more than 11,000 proteins in just 18 days of instrument time. These data enabled the determination of quantitative profiles indicative of age-based protein changes in kidney, adipose tissue, and murine brain regions. In our small-molecule interactome work, we are establishing high-throughput profiles of protein-small-molecule interactions across the entire human proteome. Together these large-scale analyses are helping to build common resources for understanding complex biological systems.Coming Soon

Bio: Dr. Schweppe’s research interests focus on the implementation of millisecond informatics to enable intelligent data acquisition strategies. His research group applies these technologies to quantify proteins as a readout for diverse cell states with broad interests spanning microbial protein interactions, small-molecule binding events, pre-clinical proteomics, and profiling primary tissue samples. Dr. Schweppe’s research group builds on the application of sample multiplexing and real-time search to achieve high efficiency instrument acquisition for both discovery and targeted proteomics platforms. Along with the methods and technology development focus, the group has worked to build applications and resources to disseminate large-scale proteomics datasets to the research community, these efforts include work the crosslinking mass spectrometry repository XLinkDB and the BioPlex human interactome explorer.


Sanja Vickovic, Ph.D. | Broad Institute

Talk Title: "SM-Omics as an automated platform for high-throughput spatial multi-omics"
Abstract: The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial Transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. We advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate ST-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.

Bio: Dr. Vickovic is currently a Wallenberg Fellow at the Broad Institute of MIT and Harvard and will soon be starting as an Assistant Professor of Bioengineering at Columbia University. Dr. Vickovic received her PhD in Genetics from the Royal Institute of Technology in Stockholm. Following her graduate work, Dr. Vickovic joined the Broad Institute of MIT and Harvard. Dr. Vickovic pioneered novel spatially resolved transcriptomics and genomics methods that enable massively parallel in situ profiling of intact tissue samples. Dr. Vickovic has vast experience in spatial and single cell genomics, imaging, data analysis and software implementations with focus on developing cheaper and more accessible genomic methods for use in a clinical setting. The spatial organization of cells and molecules plays a key role in tissue function in homeostasis and disease. Spatial Transcriptomics has recently emerged as a key technique to capture and positionally barcode RNAs directly in tissues. We advance the application of spatial transcriptomics at scale, by presenting Spatial Multi-Omics (SM-Omics) as a fully automated, high-throughput all-sequencing based platform for combined and spatially resolved transcriptomics and antibody-based protein measurements. SM-Omics uses DNA-barcoded antibodies, immunofluorescence or a combination thereof, to scale and combine spatial transcriptomics and spatial antibody-based multiplex protein detection. SM-Omics allows processing of up to 64 in situ spatial reactions or up to 96 sequencing-ready libraries, of high complexity, in a ~2 days process. We demonstrate ST-Omics in the mouse brain, spleen and colorectal cancer model, showing its broad utility as a high-throughput platform for spatial multi-omics.