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  • Pathology from the Molecular Scale on Up.

    Contains 1 Component(s) Recorded On: 02/07/2018

    I will present evidence of deep internal order in immune functionality demonstrating that differentiation and immune activities have evolved with a definable “shape”. Further, specific cellular neighborhoods of immune cells are now definable with unique abilities to affect cellular phenotypes—and these neighborhoods alter in various disease states.

    High parameter single cell analysis has driven deep understanding of immune processes.  Using a next-generation single-cell “mass cytometry” platform we quantify surface and cytokine or drug responsive indices of kinase target with 45 or more parameter analyses (e.g. 45 antibodies, viability, nucleic acid content, and relative cell size).  Similarly, we have developed two advanced technologies that enable deep phenotyping of solid tissue in both fresh frozen and FFPE formats (50 – 100 markers).   I will present evidence of deep internal order in immune functionality demonstrating that differentiation and immune activities have evolved with a definable “shape”.  Further, specific cellular neighborhoods of immune cells are now definable with unique abilities to affect cellular phenotypes—and these neighborhoods alter in various disease states.   These shapes and neighborhoods are altered during immune surveillance and “imprinted” during, and after, pathogen attack, traumatic injury, or auto-immune disease.  Hierarchies of functionally defined trans-cellular modules are observed that can be used for mechanistic and clinical insights in cancer and immune therapies.

    Yury Goltsev

    Stanford University

    More information coming!

  • SLAS2018 Innovation Award Finalist: Pharos – A Torch to Use in Your Journey In the Dark Genome

    Contains 1 Component(s) Recorded On: 02/07/2018

    Given the heterogeneous set of data types available for individual targets, it is useful to quantify how much and what types of data is available for a target. We describe the development of knowledge profiles and a Knowledge Availability Score (KAS), both derived from the Harmonizome, which is a resource that has characterized data availability across different data sources and types in a uniform manner.

    It is well known that a relatively small set of protein targets receive the bulk of research attention and thus funding. However, there are potential (druggable) opportunities in the remaining under-studied and un-studied proteins. To address this the NIH initiated the "Illuminating the Druggable Genome" program to characterize the dark regions of the druggable genome. As part of this program, a Knowledge Management Center (KMC) was created to aggregate and integrate heterogeneous data sources and data types creating a centralized location for information about all protein targets identified as part of the druggable genome. Since then the KMC has expanded to consider the entire human proteome. In this presentation, we describe Pharos, the user interface for the KMC knowledgebase. We provide an overview of the data sources and types made available via Pharos and then describe the architecture of the system and its integration with KMC & external resources. In particular we highlight the rich search facilities that enable a user to drill down to relevant subsets of data but also support the notion of "serendipitous search".  Given the heterogeneous set of data types available for individual targets, it is useful to quantify how much and what types of data is available for a target. We describe the development of knowledge profiles and a Knowledge Availability Score (KAS), both derived from the Harmonizome, which is a resource that has characterized data availability across different data sources and types in a uniform manner. We then highlight how the KAS is concordant with knowledge trends characterized by traditional metrics such as publications and grants.  We discuss the use of the KAS in the Pharos interface and an example of prioritizing understudied targets by computing the similarity of their knowledge availability profiles with that of well-studied targets.

    Rajarshi Guha

    NIH

    Rajarshi Guha is Group Leader (Research Informatics) in the Division of Pre-Clinical Innovation at NCATS. With over 10 years of experience in handling, analysing and visualizing chemical information, he brings a diverse range of skills and experience to his current role at NCATS. He is involved in small molecule development projects in a variety of therapeutic areas including rare cancers and infectious diseases. He is also involved in software and algorithm development in the areas of cheminformatics methods and large scale infrastructure projects including Pharos (http://pharos.nih.gov/) BARD (http://bard.nih.gov/). His research interests focus on methodology development to analyze and visualize chemical biology data sets, with specific focus on techniques to link chemical structure information to molecular, bibliographic, genomic and clinical covariates.   He has held multiple leadership roles in the American Chemical Society’s Division of Chemical Information and is currently a co-Editor in Chief of the Journal of Cheminformatics.

  • The Ig Nobel Prizes: The Fine Line Between Sound and Silly Science

    Contains 1 Component(s) Recorded On: 02/07/2018

    The Ig Nobel Prizes are renowned as a spoof alternative to the Nobel Prizes. The annual Ig Nobel awards ceremony is a celebration of curious, imaginative studies that make people laugh. Yet while studies of cats behaving like liquids or frogs levitating inside of a magnet might have you chortling, its founder Marc Abrahams has an equally important purpose in mind for the Prizes: to get you to think.

    The Ig Nobel Prizes are renowned as a spoof alternative to the Nobel Prizes. The annual Ig Nobel awards ceremony is a celebration of curious, imaginative studies that make people laugh. Yet while studies of cats behaving like liquids or frogs levitating inside of a magnet might have you chortling, its founder Marc Abrahams has an equally important purpose in mind for the Prizes: to get you to think. Once something becomes generally understood and accepted, then it comes to be seen as serious and important. Almost everybody either forgets or doesn’t become aware that this thing started out as something that everyone else regarded as nuts! Any scientific discovery seems like such an easy thing after it has been discovered, and it almost never was. Your understanding of a study might change – drastically – if you spend time looking at its details!

    Marc Abrahams

    Co-founder/Editer, Annals of Improbable Research

    Marc Abrahams writes about research that makes people LAUGH, then THINK. Marc founded Ig Nobel Prize Ceremony in 1991, and serves as its Master of Ceremonies. He co-founded and edits the magazine Annals of Improbable Research (AIR), hosts the Improbable Research weekly podcast (distributed by CBS), and wrote This is Improbable, The Ig Nobel Prizes, and other books. He edits and writes much of the web site and blog www.improbable.com, and the monthly newsletter mini-AIR.

  • SLAS2018 Innovation Award Finalist: An Ultra High-Throughput 3D Assay Platform for Evaluating T-cell-Mediated Tumor Killing

    Contains 1 Component(s) Recorded On: 02/06/2018

    We have developed a novel microphysiological 3D assay that quantitates T-cell-mediated killing of 3D colorectal cancer tumor spheroids using a new 1536-well spheroid plate. This assay incorporates CD3-stimulated primary patient T-cells in culture with colorectal cancer tumor spheroids and enables parallel assessment of spheroid size and viability as well as T-cell penetration into the 3D spheroid structure.

    3-dimensional cellular assay platforms are increasingly recognized as robust surrogates for mimicking in vivo disease pathology. In particular, the multicellular spheroid model has been widely utilized in exploratory drug discovery campaigns. However, these complex 3D cell models have previously been restricted to low- or medium-throughput formats due to the technical logistics of forming spheroids in a 1536-well microtiter plate. We have developed a novel microphysiological 3D assay that quantitates T-cell-mediated killing of 3D colorectal cancer tumor spheroids using a new 1536-well spheroid plate. This assay incorporates CD3-stimulated primary patient T-cells in culture with colorectal cancer tumor spheroids and enables parallel assessment of spheroid size and viability as well as T-cell penetration into the 3D spheroid structure. Using this assay platform we screened a library of annotated compounds for spheroid viability and discovered several small molecule candidates that synergize with CD3 stimulation and enhance T-cell-mediated tumor spheroid killing. This phenotypic 3D cell model represents a robust organotypic ultra-HTS platform that can greatly enhance immuno-oncology drug discovery programs.

    Shane Horman

    GNF

    Dr. Shane Horman runs the Advanced Assay group at the Genomics Institute of the Novartis Research Foundation (GNF) in San Diego, California. He received his Ph.D. from King’s College-London in molecular genetics and was a postdoc at the University of Pennsylvania-School of Medicine and then at Cincinnati Children’s Hospital Medical Center investigating mouse models of human leukemias. Dr. Horman’s Advanced Assay group at GNF is dedicated to the development and implementation of complex and 3D high content screening platforms that may better reflect in vivo patient biology for early stage drug discovery. Dr. Horman has published numerous papers on high content 3D screening platforms and regularly presents at phenotypic drug discovery conferences. 

  • SLAS2018 Innovation Award Finalist: Microfluidic Siphoning Array (MSA) – A Novel Scalable Digital PCR Integrated Platform

    Contains 1 Component(s) Recorded On: 02/06/2018

    We have developed the patented Microfluidic Siphoning Array (MSA) Technology where bulk qPCR reagents can be partitioned into “lollipops”, a novel injection molded microfluidic device coupled with a semi-permeable thin film.

    Digital PCR offers compelling advantages over the current gold standard qPCR with the ability to: 1) detect rare events (high sensitivity); 2) be less prone to inhibition (high specificity); 3) quantify nucleic acids in an absolute manner without a standard-curve (high precision). However, widespread adoption has not occurred despite the proven advantages of dPCR over qPCR as existing dPCR platforms are capital intensive, cost prohibitive, have workflows with many steps and are not easily accessible to automation.

    We have developed the patented Microfluidic Siphoning Array (MSA) Technology where bulk qPCR reagents can be partitioned into “lollipops”, a novel injection molded microfluidic device coupled with a semi-permeable thin film. The key advantages of the MSA include (a) Open source chemistry, which allows direct assay translation from qPCR to dPCR without tailored reagent formulations. (b) Experiment-to-experiment reproducibility with high fidelity microstructures with fixed number and known volume partitions insensitive to liquid handling errors. (c) Low cost due to a highly scalable manufacturing process (d) No cross talk with physically isolated partitions. The prototype device utilizes a standard format, making it compatible with automated liquid handlers. There are 8 units per prototype device, and 5,000 partitions per unit (1 μL total assay volume), with the model to create “application-specific” dPCR consumables balancing between throughput and sensitivity. To enable walkaway dPCR workflow with the MSA device, an instrument integrating pneumatic control, thermal cycling, and optical imaging was developed. An Image J pipeline was used to subtract background, extract fluorescent intensities from each lollipop, and converting them into scattered plot before applying Poisson statistics for absolute quantification. An HIV viral load assay and a Copy Number Variation (CNV) analysis assay were demonstrated with the prototype platform and achieved equal performance to the current market leader. An additional benefit of this platform is that real-time imaging of each partition during the thermal cycling process can be monitored, minimizing false positives, and enabling digital high-resolution melt analysis (dHRMA) to further improve multiplexing capability.

    In summary, the advantages enabled by this platform include lowering both the workflow and cost barriers of digital PCR without compromising the performance in precision, and sensitivity. The real-time imaging capability allows background subtraction to minimize false positives, as well as digital melt analysis to improve multiplexity. We envision a scalable and automatable digital PCR platform which can easily be integrated to research laboratories, and extend to the clinic.

    Paul Hung

    COMBiNATi Inc

    Paul Hung has 11 years of experience developing life science research tools using microfluidic technology. After receiving his PhD from UC Berkeley in 2005, he has successfully grown CellASIC Corporation, which he co-founded in 2006, to self-sufficiency with the commercialization of the ONIX live cell imaging platform, and sold to MillporeSigma (then EMD Millipore) in 2012. After the acquisition, he worked as a senior R&D manager to gain more knowledge in systematic product development in a large corporate. He founded COMBiNATi in 2016 to continue driving the vision of disrupting the life science industry with microfluidic technology, one consumable at a time. 

  • Designed diversity and bioannotated compound libraries for obtaining maximal value from screens in induced pluripotent stem cell-derived cells and other complex biological systems

    Contains 1 Component(s) Recorded On: 02/06/2018

    ​As part of the current resurgence in phenotypic screening, early stage assay systems are becoming increasingly complex in an attempt to better model the disease state and therefore improve translation to the clinic. One downside to this complexity is that it substantially reduces the throughput of such systems, and it is generally not feasible to screen millions of molecules in them as would be common in a more traditional HTS campaign.

    As part of the current resurgence in phenotypic screening, early stage assay systems are becoming increasingly complex in an attempt to better model the disease state and therefore improve translation to the clinic. One downside to this complexity is that it substantially reduces the throughput of such systems, and it is generally not feasible to screen millions of molecules in them as would be common in a more traditional HTS campaign. In response to this constraint we have developed two focused compound collections for use in phenotypic screening projects. The first is a bioannotated or chemogenomic library containing molecules with well-characterised pharmacology, intended for use in repurposing and knowledge-driven target deconvolution approaches. The second is a diverse phenotypic library that attempts to maximise chemical and pharmacological diversity within a compact set of 20,000 compounds, intended as a representative sample of our regular HTS collection. In this presentation the design, construction and annotation of these libraries will be outlined. Some examples of our experiences with screening them in drug discovery projects will then be discussed. Finally, analysis of the extent to which these first generation collections have fulfilled their design criteria to date will be presented, and directions of future enhancements reviewed.

    Tim James

    Evotec

    With a background in computational chemistry and data analysis, my current focus within the Research Informatics group at Evotec is the area of chemical biology. This includes the design of compound libraries, the analysis of phenotypic screening results and integrating the output from various 'omics technologies.

  • Complex Tissue Biology and Throughput in a Microplate-Based Organ-on-a-Chip System

    Contains 1 Component(s) Recorded On: 02/06/2018

    In this presentation, I will focus on biological and technological aspects of both healthy and diseased tissue models in the OrganoPlate, including platform specific assays, such as a barrier integrity assay and neuronal network activity assays. I will present data demonstrating that 3D tissues cultured in the OrganoPlate are suitable for any-throughput drug efficacy and toxicity screening, trans-epithelial transport studies, and complex co-culture models in an in vivo-like microenvironment.

    The OrganoPlate is a microfluidic tissue culture platform, which enables high-throughput culture of microtissues in miniaturized organ models. In the OrganoPlate(1), extracellular matrix (ECM) gels can be freely patterned in microchambers through the use of phaseguide technology. Phaseguides (capillary pressure barriers) define barrier-free channels in microchambers that can be used for ECM deposition or medium perfusion. The microfluidic channel dimensions not only allow solid tissue and barrier formation, but also perfused tubular epithelial vessel structures can be grown. We have developed a range of multi-cellular organ- and tissue models for drug efficacy and toxicity studies, including blood vessels, brain, gut(2), and kidney.

    In this presentation, I will focus on biological and technological aspects of both healthy and diseased tissue models in the OrganoPlate, including platform specific assays, such as a barrier integrity assay and neuronal network activity assays. I will present data demonstrating that 3D tissues cultured in the OrganoPlate are suitable for any-throughput drug efficacy and toxicity screening, trans-epithelial transport studies, and complex co-culture models in an in vivo-like microenvironment.

    References:
    1. S. J. Trietsch, G. D. Israëls, J. Joore, T. Hankemeier, and P. Vulto, “Microfluidic titer plate for stratified 3D cell culture.,” Lab Chip, vol. 13, no. 18, pp. 3548–54, Sep. 2013
    2. S. J. Trietsch, E. Naumovska, D. Kurek, M. C. Setyawati, M. K. Vormann, K. J. Wilschut, H. L. Lanz, A. Nicholas, C. P. Ng, J. Joore, S. Kustermann, A. Roth, T. Hankemeier, A. Moisan, P. Vulto, “Membrane-free culture and real-time barrier integrity assessment of perfused intestinal epithelium tubes.”, Nature Communications, 2017 accepted

    Jos Joore

    MIMETAS - the Organ-on-a-Chip Company

    Jos Joore is co-founder and Managing Director of MIMETAS. He is a biotech entrepreneur, co-founder of four companies with over 17 years of executive level biotech experience in a variety of companies including Pepscan, Skyline Diagnostics, Kreatech and Westburg. During his ten-year research career, he worked as a postdoctoral researcher at the Hubrecht Institute (Utrecht) and King's College (London). He holds a cum laude Masters degree in business marketing (MBM), a Ph.D. in developmental biology and a Masters degree in biology.

  • Lab Automation Drones for Mobile Manipulation in High Throughput Systems

    Contains 1 Component(s) Recorded On: 02/06/2018

    In lab automation, there is a wide range of robots. Robots are employed to accelerate sample handling, such as in high throughput screening (HTS), manipulators and transfer lines rapidly manipulate micro-plates amongst numerous test stations. The net result is that a typical HTS system can handle over 500,000 samples a week. In the age of big data, higher throughput means faster pharmaceutical development and hence quicker patent registrations and earlier market penetration.

    In lab automation, there is a wide range of robots. Robots are employed to accelerate sample handling, such as in high throughput screening (HTS), manipulators and transfer lines rapidly manipulate micro-plates amongst numerous test stations. The net result is that a typical HTS system can handle over 500,000 samples a week.  In the age of big data, higher throughput means faster pharmaceutical development and hence quicker patent registrations and earlier market penetration. HTS systems are often custom-tailored to maximize throughput with many high- precision 6-DOF robot manipulators. Such robots employ parallel jaw grippers to gently and precisely position and orient micro-plates. However, once configured, they are not easily changed. This is important because as new tests emerge, older HTS systems cannot easily perform them. The National Institutes of Health (NIH) in the United States are looking at the potential of lab automation drones to add flexibility to existing HTS systems. The notion has merit; aerial manipulation research is an active area. High degree of freedom (DOF) robots with dexterous arms has been addressed in transformative applications such as material handling, disaster response, and personal assistance. And micro-plates are relatively easy to robotically lift and orient. Issues like ground effect, limited battery life, and obstacle avoidance are indeed relevant to lab automation but also remain open research topics. The critical gap in a lab automation drone appears to be the lack of aerial manipulation arms and grippers. Recently, several configuration systems including single DOF aerial grasping, non-redundant and fully redundant articulated aerial manipulation, have been explored to create manipulation systems. But all the arms in aerial manipulation are serial; a motor in each joint results in a heavy arm. To the author’s best knowledge, the author’s lab has been the first to introduce a parallel-mechanism arm for aerial manipulation. The previous work concluded its higher degree of precision and lower toque impact on the drone’s stability versus serial manipulators. In this work, the authors present a design of a 6-DOF parallel mechanism arm with a sensorized parallel jaw gripper. The test-and-evaluation approach and results are given.

    Dongbin Kim

    University of Nevada, Las Vegas

    Dongbin Kim has completed his B.S. in aircraft systems engineering from Korea Aerospace University, S. Korea in 2016. He is currently studying PhD in Mechanical Engineering in University of Nevada in Las Vegas. He serves as lab manager in Drones and Autonomous Systems Lab.

  • Integrating Environmentally Friendly Tactics into a High-Throughput Screening Setting

    Contains 1 Component(s) Recorded On: 02/06/2018

    Throughout everyday life there are many considerations and practices in place when it comes to recycling, minimizing waste, cleaner energy and reuse to cut down on the impact to our planet’s ecosystem, with millions of individuals around the world making the choice to conserve keeping these principles in mind.

    Throughout everyday life there are many considerations and practices in place when it comes to recycling, minimizing waste, cleaner energy and reuse to cut down on the impact to our planet’s ecosystem, with millions of individuals around the world making the choice to conserve keeping these principles in mind.  However, this mindset and conscientiousness to conserve is not on the radar when it comes to the world of high-throughput screening and science in general, where the term ‘consumable’ is ubiquitous and pipette tips, petri dishes, microplates, solvents and an extensive list of materials are disposed of after one use every day, with most of this waste needing to be handled as chemical or biohazardous, further increasing the negative environmental impact.  Luckily this mentality is changing, with the availability of new technologies and the use of experimental data proving its effectiveness NCATS has been able to implement and adopt several methods into many aspects of their high-throughput screening processes which are friendlier to our environment than the traditional equivalents.  In many cases these eco conscious practices yield higher quality, cleaner data as well as even eliminating the need for automated assays having to be repeated by catching detrimental issues in real time.  Here the focus will be about the integration of equipment onto peripheral devices of the robotic screening platforms, processes and supporting modular operations with the overall goal of conservation.  Not only will the use of these concepts be demonstrated but more importantly the successful adaptation will be shown with supporting data.  Spanning the last 7 years NCATS has not only been mindful but has been continuously advancing and developing tactics in order to minimize waste without sacrificing high quality data.  This ultimately proves that science including high-throughput screening specifically can evolve to incorporate environmentally friendly techniques while continuously advancing the field.

    Carleen Klumpp-Thomas

    NIH/NCATS

    Carleen Klumpp-Thomas currently leads the Automation Group at the National Center for Advancing Translational Sciences (NIH/NCATS) in Rockville MD. Carleen manages and runs all of the automated screening platforms for NCATS Research Services Section (RSS). RSS’ multi-disciplinary capabilities enables the ongoing operation of all of NCATS’ research activities. These automated platforms perform a wide variety of experiment types ranging from biochemical, cell based, RNAi and other existing and novel assay technologies. Carleen’s automation and engineering expertise has been critical for projects ranging from cancer to Ebola to Parkinson’s disease.  The advanced instrumentation, protocols and methods are necessary to keep NCATS at the leading edge of scientific research and Carleen manages these requirements with ease, all while staying in constant communication with all researchers. Carleen earned her B.S. degree in Bioengineering from Syracuse University and her M.S. in Biomedical Engineering from NYU Tandon School of Engineering.

  • An Acoustic Microfluidic Device for Hematopoietic Stem Cell Enrichment from Whole Blood

    Contains 1 Component(s) Recorded On: 02/06/2018

    Here, we present a system that continuously separates HSCs from both healthy and diseased whole blood using acoustically-mediated separation in a plastic microfluidic device. We and others have previously demonstrated acoustic separation of bacteria, beads, and liposomes from blood cells, but this is the first report showing enrichment of HSCs directly from patient samples.

    Emerging cell therapies require efficient methods for purification of target cells prior to subsequent processing. In the case of stem cell-based therapies large numbers of hematopoietic stem cells (HSCs) must be collected and purified from patient peripheral blood; a challenging task because even after mobilization, the concentration of HSCs in the collected product is typically less than 1% of all cells. Existing processing techniques, such as density gradient centrifugation and subsequent magnetic separation, achieve some of the requirements, however, they often provide low yield, are costly, time-consuming, and labor intensive. Acoustic separation has emerged as a versatile technology for flow-through liquid handling and particle manipulation. The technique relies upon differences in the size, density, and compressibility of various blood components in order to achieve rapid label-free discrimination between target and off-target cells.

    Here, we present a system that continuously separates HSCs from both healthy and diseased whole blood using acoustically-mediated separation in a plastic microfluidic device. We and others have previously demonstrated acoustic separation of bacteria, beads, and liposomes from blood cells, but this is the first report showing enrichment of HSCs directly from patient samples. In addition, because our microchannel is constructed entirely of polystyrene, it is suitable for scale-up to clinically relevant processing rates, with the potential for flow rates approaching 100 ml/hr. Our device consists of a microchannel mounted on a piezoelectric actuator and a temperature-controlled stage. The actuator excites an acoustic standing wave within the fluid cavity, transverse to the flow direction. This standing wave exerts a force on blood cells which drives them toward the centerline of the flow. Larger and denser cells experience a larger force compared to smaller and less dense cells, and are more strongly focused. At the downstream end of the channel, a trifurcating outlet allows for the separation of strongly focused cells (e.g., red blood cells and neutrophils) from those that are weakly focused  (e.g., HSCs and lymphocytes). In this work the system is tuned to enable the separation and collection of HSCs.

    We achieve enrichment of the HSC population (CD34+ as % total white blood cells) from 9% to 22%, a factor of 2.4x, starting from unpurified whole patient blood. This enrichment was achieved in a single pass through the device with HSC recovery of 40% and reduction of the red blood cell concentration by 62%. These figures can be improved by multiple passes through the system and by device optimization. Our results demonstrate that we are able to efficiently and specifically purify HSCs from whole blood in a continuous flow-through device. In addition, our device is fabricated from low-cost components and is straightforward to operate, giving it the potential for future use in sample purification for cell therapy.

    Charles Lissandrello

    Draper

    Charles Lissandrello is a Senior Member of the Technical Staff in the Nano Structured Materials group at Draper. He received his Ph.D. in Mechanical Engineering at Boston University in 2015, where he conducted research with Kamil Ekinci on the transition from hydrodynamic to kinetic gas behavior in fluid systems far from equilibrium. At Draper, he has worked with a team of collaborators to develop novel microfluidic devices for biological sample processing.