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WORKSHOPS Workshop Session I Sunday, June 24, 2012
16:15 - 17:30
Workshop 1 Microbial Single Cell Approaches to Cytomics, Transcriptomics and Proteomics Susann Müller, Helmholtz-Centre for Environmental Reserach Leipzig-Halle, Germany
Frank Schmidt, Ernst-Moritz-Arndt-University of Greifswald, Germany
New methods for single cell analysis show improved possibilities not only for the in depth analysis of individual cells but also to investigate what is happening in microbial populations and communities. Flow cytometry is a powerful technology to investigate and describe the dynamics of the cells in populations or communities. Completed by other techniques it extends the understanding of structure and function relationships by investigating phylogenetic, genomic, transcriptomic and proteomic levels at the scale of the single microorganism or that of sub-communities. The new information collected helps to better understand the functioning of the cells and their intra- or inter-relationships. The concept of cytomics has recently arisen and has given birth to a novel discipline in biology, considering not only higher organismic levels, but also microbes. The goal of this workshop is to discuss how the cytomic approach and the level of its resolution will contribute to reveal basic principles of microbial ecosystems or to interpret even simpler systems like pure cultures as are used in microbial (white) biotechnology. Potential applications will also be addressed. Workshop 2 Flow Cytometry in Reproductive Biology Anna Petrunkina, University of Cambridge, UK Detlef Rath, Federal Research Institute for Animal Health, Germany Richard Grenfell, Cancer Research UK, UK Heiko Henning, University of Veterinary Medicine Hanover, Foundation, Germany In this workshop, a range of topics related to applications of flow cytometry in reproductive biology will be discussed, especially with respect to X- and Y-sperm sorting, current and future research focuses, and publishing standards. Recent attempts to adapt flow cytometric applications and new technologies to the field of reproductive research will be described, in particular those relevant to artificial insemination, semen storage and assisted reproduction (e.g. ImageStream). Can we find practical and viable solutions to already known problems (such as technical sophistication of the instrumentation, lack of targeted education services and shortage of close proximity core facilities), that restrict field-wide application of flow cytometry both in reproductive science and industry?
Workshop 3 Innovation and Standardization of 8-Color Leukemia/Lymphoma Immunophenotyping: The Contribution of the EuroFlow Group Alberto Orfao, University of Salamanca, Spain Tomas Kalina, CLIP Pediatric Hospital, Czech Republic Jacques van Dongen, Erasmus Medical Center Rotterdam, Netherlands In recent years, the EuroFlow group has developed new tools that fit into a new strategy aimed at full standardization of leukaemia/lymphoma immunophenotyping. In this workshop, the most relevant developments and achievements of such process will be presented which involve: 1) standadization of instrument settings and calibration, sample processing and data acquisition across different clinical flow cytometry laboratories; 2) building antibody panels for leukaemia/lymphoma immunophenotyping, and; 3) software-guided analysis of multiparameter flow cytometry (leukaemia/lymphoma) data
Workshop 4 Writing, Publishing and Reviewing: Advice and tips from Cytometry A Attilla Tarnock, University of Leipzig, Germany Henning Ulrich, Universidade de São Paulo, Brazil
Vera Donnenberg, University of Pittsburgh, USA Mario Roederer, NIAID, NIH, USA Scientific journals require certain quality standards from manuscripts to be acceptable for further reviewing and publication. There are some very common reasons why a paper gets reviewed and accepted or rejected. This workshop aims to highlight all major aspects of manuscript writing, submission and communication with the reviewers, points out what can (and very often does) go wrong and how to do it right in order to improve your chances to get your paper published. Special emphasis will be taken to focus on the needs for a biomedical and technical oriented journal such as Cytometry Part A including MIFlowCyt and OMIP. Experts from the Cytometry Part A editorial board and from the publisher Wiley-Blackwell will contribute. Workshop 5 How do we Evaluate and Measure System Performance in Flow Cytometers? Andy Riddell, EMBL, Germany Gardner Rui, Instituto Gulbenkian Ciencia, Portugal Alexis Perez Gonzalez, EMBL, Germany Lola Martinez, CNIO, Spain Telma Lopes, Instituto Gulbenkian Ciencia, Portugal Understanding the performance of an instrument is key in supplying a core service or in justifying purchasing new equipment. For a core facility service or an individual scientist, it is the capability of a particular instrument that dictates what assays can be run on it. We need some way in which to assess and compare instrument performance between each other and in different assays. Core facilities have an experienced staff base that is very capable of making such decisions, but this knowledge is often not formalised or exchanged. We would like to stimulate a discussion on how to measure a system’s performance and what metrics we think are important. One of the key approaches to these questions is to build and develop a tool set that allows us to allocate meaningful numbers to the system we are investigating. There are established tools such as Q,B and S when measuring the instrument’s sensitivity and in the case of sorting performance, we have Purity, Recovery and Yield. We would like to stimulate a discussion about what are the pros and cons of these approaches to gain a better understanding of when and how to apply them. Workshop Session II Monday, June 25, 2012
16:15 - 17:30
Workshop 6 Analysis of Cell-Derived Microvesicles John Nolan, La Jolla Bioengineering Institute, USA François Mullier, Université Catholique de Louvain, France Philippe Poncelet, Biocytex, France Françoise Dignat-George, University of Pharmacie of Marseille, France Mammalian cells release small membrane vesicles that can carry biological molecules and signals to exert biological effects at a distance. These membrane vesicles have been implicated in a wide range of physiological function, but their very small size makes them a challenge to analyze. Flow cytometry is distinguished by its ability to measure multiple targets on individual particles, but the small size and dim signals from most microvesicles challenges the sensitivity limits of flow cytometry. Because of the potential importance of microvesicles as diagnostic or prognostic markers, there is significant interest in standardizing sample preparation and measurement approaches for cell-derived microvesicles. These efforts above have led to several important insights that will help standardize microvesicle measurements using the current generation of commercial flow cytometers. However, they also highlight the need for new, more sensitive methods for measuring cell-derived vesicles. This workshop will introduce these issues via short presentations, with ample time provided for discussion. Workshop 7 10-Color Flow Cytometry in Myelodysplastic Syndromes and Acute Myeloid Leukemia Wolfgang Kern, MLL, Germany Marie-Christine Bene, Nancy-Université, France Anna Porwit, Toronto General Hospital, Canada Multiparameter flow cytometry (MFC) is a standard diagnostic procedure in acute myeloid leukemia (AML) and is increasingly used in myelodysplastic syndromes (MDS). This workshop will cover the general concepts of MFC in AML and MDS as well as presentation of detailed data on its application in cases with MDS/AML and non-MDS cytopenias. Flow cytometry findings will be related to morphology and cytogenetics. Data from an oligo-centric validation study using a 10-color panel and applying standardized analysis procedures will be demonstrated and discussed. Topics covered will include a) design of a 10-color antibody panel, b) standardization of instrument setup, c) sample preparation and data acquisition, d) description of MDS-specific aberrant antigen expression in different cell lineages, e) diagnostic significance of different aberrancies, f) clinical value of flow cytometry in the context of morphology and genetics in MDS g) differences between MDS and AML. Workshop 8 High Capacity (Contect, Throughput, Correlation) Flow Cytometry
Bruce Edwards, University of New Mexico, USA Susan R. Watson, XOMA LLC, USA In this workshop we are soliciting input from industrial and academic laboratories that have experience with high throughput flow cytometry, now designated as high capacity flow cytometry because it combines both high content and throughput. Topics of interest include: assay development and validation, techniques and tricks for efficient sample and plate preparation, perspectives on the role of high capacity flow cytometry in high content screening and systems biology, recent developments in hardware and software, favorite equipment excluding the flow cytometer/sampling platform, and future needs and trends. Workshop 9 Grace Chojnowski, Queensland Institute of Medical Research, Australia Howard Shapiro, Shapiro Laboratories, USA Simon Apte, Queensland Institute of Medical Research, Australia Brian Grimberg, Case Western Reserve University, USA Thomas Hänscheid, Faculdade de Medicina de Lisboa, Portugal Workshop 10 Computational Methods for Learning from Cell Images Gustavo Rohde, Carnegie Mellon University, USA Jean Christophe Olivo-Marin, Institut Pasteur, France Robert F. Murphy, Carnegie Mellon University, USA Christian Conrad, DKFZ/Bioquant, USA Novel microscopy imaging techniques have enabled the acquisition of cellular and sub-cellular information with unprecedented accuracy and specificity. The development of computational methods for extracting information related to the organization of cells, sub-cellular structures, organelles, protein and molecule distributions from the large image databases that are now being created is a fundamental step in enabling a better understanding of cellular and subcellular processes. Spurred both by the need arising from the ability to acquire specific and high-throughput data as well as recent advances in computational power, this area of engineering and scientific research has undergone substantial growth in the past couple of decades. The aim of the workshop is to offer an overview of state of the art methods and technologies that are available to scientists wishing to optimize information acquisition from microscope systems. Presentations on topics such as methods for building and estimating models of cellular and subcellular organization from images, real-time decision making during image acquisition, and analyzing differences in cell and organelle morphology between different classes of cells (e.g. normal vs. diseased, control vs. experiment), will be given by experts in the field. Discussion will be focused on highlighting current capabilities and limitations of different methods, as well as current and future challenges. Workshop Session III Wednesday, June 27, 2012
15:45 - 17:00
Workshop 11 Cytometry Challenges and Opportunities for Regenerative Medicine Laura Teodori, ENEA, Italy Vera Donnenberg, University of Pittsburgh, USA Anne Plant, NIST, USA Tissue engineering, regenerative medicine and stem cell biology are fields for which cytometry has great potential impact. The recent advancements in this area together with the new biomaterials discoveries is opening up the possibility of a tissue factory that may offer new treatment alternatives for organ replacement or repair of deteriorated organs and represent a major challenge for the treatment of otherwise incurable diseases. However, despite the enormous hope for these new therapies, many failures are preventing these approaches from reaching the clinic. Basic biological mechanisms are not well understood, and there is a growing realization that a lack of procedural and regulatory standards is creating huge translational challenges. Stem cell biologists lack clear definitions for cell types and have few consensus protocols for handling and characterizing them. Both flow and imaging cytometry can be critical tools for evaluating biomarkers, identifying subpopulations, and providing quantitative molecular data that can be used for characterization of cellular therapy products and prediction of biological fate. Rigorous cytometry methods can help move this field from creativity to engineering. The time is right to address these measurement and standards challenges, because many cell-based therapy organizations are highly engaged in thinking about the measurement and standardization priorities.
The workshop has the intent to address the following major questions: 1) What are the main cytometry challenges for the standardized and reproducible isolation/production of stem or progenitor cells? 2) What are the main biomarker challenges for the standardized and reproducible differentiation of stem cells into progenitor cells, and of progenitor cells into differentiated cells or tissues? 3) What is the state of standardization of isolation and differentiation protocols for regenerative medicine? Which organizations are developing, coordinating these? What are the standardization initiatives worldwide? What efforts are related to cytometry? 4) What are the biggest cell analysis needs for regenerative medicine that should be brought to the attention of the cytometry technology development community? 5) What is the role of core facilities in promoting standardization in regenerative medicine? We would like to end the workshop with a document which will help this field to move forward and the engagement of cytometry community is critical at this regard. Workshop 12 How do Immune Cells Kill Tumor Cells and Can Flow Cytometry Aid in Predicting the Procedure? Tim Kute, Wake Forest School of Medicine, USA Sophia N. Karagiannis, Biomedical Research Center/NIHR, England Janos Szollosi, Department of Biophysics and Cell Biology, Hungary This is a 2nd in the series on the use of flow cytometry and other procedures to better understand the immune system. The first was given at ISAC in Baltimore last year. It is now clear that tailored treatment of cancer patients based on the characteristics of the tumor cell has made substantial gains. A prime example is the use of antibodies directed against antigens found on the tumor cells. In this workshop, there will be three invited speakers and there will be time for open discussion and presentations by any other individual. The invited speaker topics are "How does Trastuzumab (Herceptin) Work in Killing Tumor Cells?," "Trastuzumab Resistance - What is Going Wrong - It Should Work?" and "How do Immune Cells Kill Tumors - is it in the Kiss?" Workshop 13 Publishing MIFlowCyt Compliant Data to ISAC’s FlowRepository.org for Cytometry A and Other Journals Ryan Brinkman, British Columbia Cancer Agency/University of British Columbia, Canada Josef Spidlen, BC Cancer Angency, Canada
Attila Tarnok, University of Leipzig, Germany History has shown the profound need for scientific data to be easily available and accessible. To address this requirement for flow cytometry, ISAC has facilitated the development of FlowRepository.org - a public online resource where researches can deposit flow cytometry data so that these become easily available to others. FlowRepository.org was developed by extending and adapting Cytobank - an online tool for collaborative analysis of cytometric data. Flow cytometrists, researchers and clinicians preparing or publishing manuscripts can use FlowRepository to satisfy funder and/or publisher requirements for making their data available to the community. Researchers can use the repository to retrieve and further explore datasets of interest. The facilitators will demonstrate how to query FlowRepository, how to upload data, and how to annotate these with respect to the Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) - a standard adopted by ISAC and leading journals as criteria for recording and reporting information about flow cytometry. How the repository fits into the manuscript submission process works will also be illustrated, along with various practicality aspects, tips, and additional features of FlowRepository and Cytobank. Workshop 14 "Cytometry Needs You? But do You Need Cytometry?" - A Workshop for Young Cytometrists looking at Developing their Careers in Cytometry Rachael Walker, University of Cambridge, UK
Reiner Schulte, Cambridge Research Institute, UK Andy Filby, London Research Institute, UK
Are you new to cytometry? Been doing cytometry for a few years? Want a change in career? Want some help working in cytometry? We aim in this workshop to discuss issues that affect ‘developing’ ‘young’* cytometrists. There will be brief talks on the various cytometry-related career choices, which we hope will turn into a lively debate on whether you really want your boss’s job as a core manager or a different role in this dynamic field. We share experiences of working in industry, core-facilities and jobs associated with cytometry. The workshop aims to be interactive and we will be open to discuss any issue that arise such as how to set up a lab from scratch, running a core as a one (wo)man show, what you need to know to work in a core facility, what should be put on your CV to get you the dream job and how to deal with difficult customers. This workshop is aimed for young cytometrists and is being organised and run by young cytometrists. It is also aimed at technical staff, those new to cytometry and people interested in a career change. Workshop 15 Industrial Flow Cytometry: Perspectives, Challenges, and Directions Chris Groves, MedImmune, USA
Carol Oxford, UC Davis, USA Ruud Hulspas, Cytonome/ST, USA Bhargavi Rajan, MedImmune, USA Most all flow cytometry cores provide technical and scientific support, troubleshooting, training, data analysis, cell sorting services, and manage some version of a metric for instrument usage and scheduling. Flow cytometry core facilities in the biopharmaceutical industry are no different in this regard to their academic and clinical counterparts. However, by nature, the development of biopharmaceuticals presents additional challenges and some new methodologies applied differ dramatically to other settings. We plan to share our experiences in an informal and open forum. Specific topics are; cell sorter setup for the preservation of cell function, technical challenges when approaching ultra-sterile cell sorting, GxP cell sorting requirements and practices, and close encounters with regulatory body review of operations protocols. While not all of the presenters come from BioPharma the conceptual challenges are similar. We hope that our combined experiences will entertain as well as enlighten.
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