Microscopy: Resolution in Microscopy (Jeff Lichtman) iBiology Techniques 2024-10-11 | Microscopy: Resolution in Microscopy (Jeff Lichtman)
Next Generation Sequencing 2: Illumina NGS Sample Preparation - Eric Chow (UCSF) iBiology Techniques 2020-10-28 | ibiology.org/techniques/next-generation-sequencingNext generation sequencing allows DNA samples to be sequenced quickly and affordably. Learn how next gen sequencing works and get tips on preparing and running your samples. In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours! In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection. In his second talk, Chow discusses Illumina NGS Sample Preparation. He goes over DNA and RNA preparation, bead-based (Ampure or SPRI) cleanups, and sample quantification and quality control. And in two short how-to videos, Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.00:00 - Start00:36 - Review of next generation sequencing02:13 - DNA library preparation07:17 - RNA library preparation14:26 - Bead-based cleanups18:22 - Sample quantification and quality controlSpeaker Biography:Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.
Single Cell Sequencing - Eric Chow (UCSF) iBiology Techniques 2020-08-28 | ibiology.org/techniques/single-cell-sequencingDr. Eric Chow gives an overview of single cell sequencing, explains why this approach is useful, and talks through the leading methods.Single cell sequencing, as the name implies, allows researchers to examine the genomic information for individual cells. This provides an opportunity to examine cell-to-cell differences and identify cell subtypes, which provides insight into how specific cells function within and respond to their environment. Dr. Eric Chow begins his talk with an overview of single cell sequencing with a focus on RNA. He then goes on to outline the predominant approaches, including plate-based, microfluidic-based, and combinatorial indexing methods. He finishes by addressing approaches to single cell analysis that don’t rely on RNA, including methods that use DNA, proteins, and antibodies. He also reviews some of the benefits and limitations of analysis at the level of individual cells.0:00 Start0:31 Bulk vs. single cell analogy4:58 Plate-based SMART-seq7:08 DropSeq13:54 Combinatorial Indexing22:56 ConclusionsSpeaker Biography:Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.Credits: Karen Dell (iBiology): ProducerEric Kornblum (iBiology): Videographer & Video Editor
Bioimage Analysis - Christian Tischer (EMBL) iBiology Techniques 2019-09-25 | ibiology.org/techniques/introduction-to-bioimage-analysisDr. Christian Tischer walks us through the main concepts of a typical bioimage analysis workflow and explains how to quantitatively interpret the content of microscopy images. Microscopy is a key technology driving biological discovery. Nowadays, microscopy based scientific findings must be substantiated by quantitative image analysis. The discipline concerned with such quantification of biological microscopy images is called bioimage analysis. Dr. Christian Tischer walks us through the main concepts of a typical bioimage analysis workflow. He explains how to quantitatively interpret the content of microscopy images and how to automatically detect objects in images and derive object based measurements. He also emphasizes the importance of visual inspection and quality control of automated image analysis. Finally, he presents an overview of current bioimage analysis tools and communities.Speaker Biography:Christian Tischer studied physics in Heidelberg, followed by Ph.D. at the European Molecular Biology Laboratory (EMBL) with Dr. Philippe Bastiaens working on microscope development and signalling in mammalian cells. Subsequently, he did a postdoc with Dr. Marileen Dogertom at AMOLF in the Netherlands, where he worked on microtubule dynamics. From 2009 until 2018, he worked at EMBL's Advanced Light Microscopy Facility (ALMF) supporting scientists with both microscopy and image analysis. Since 2018, Christian’s focus shifted completely towards image analysis support and he is now running EMBL’s Centre for Bioimage Analysis (CBA).
Bioimage Analysis 1: The Basics: Getting Started (Anne Carpenter and Kevin Eliceiri) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Image Acquisition for Quantitative Analysis - Nico Stuurman (UCSF) iBiology Techniques 2019-09-25 | ibiology.org/techniques/image-acquisitionNico Stuurman provides an overview of the different tools, equipment, and software available to acquire an image of a biological sample, and the considerations one needs to take when using these tools. How do we visualize biological samples? In this talk, Dr. Nico Stuurman provides an overview of the different tools, equipment, and software available to acquire an image of a biological sample, and the considerations one needs to take when using these tools. This lecture will allow scientists to understand the principles behind image acquisition in order to improve and optimize the analysis of their sample. Speaker Biography:Nico Stuurman is a Research Specialist at the University of California, San Francisco, in the lab of Ron Vale. Nico combines his expertise in computer programming and microscopy to advance many projects including the Open Source software, Micro-Manager.
Bioimage Analysis 2: Pre-Processing (Kevin Eliceiri) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Bioimage Analysis 5: Measurement and Phenotype Classification (Anne Carpenter) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Bioimage Analysis 4: Tracking (Kevin Eliceiri) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Bioimage Analysis 3: Segmentation (Anne Carpenter) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Bioimage Analysis 6: Tips and Best Practices (Anne Carpenter and Kevin Eliceiri) iBiology Techniques 2019-09-25 | ibiology.org/techniques/bioimage-analysisIn this series of 6 videos, Dr. Anne Carpenter and Dr. Kevin Eliceiri provide an overview of bioimage analysis. Pre-processing is the first step that follows image acquisition and will prepare your image by reducing the signal-to-noise ratio, applying appropriate filters to the image, and color extraction. Once you perform pre-processing, you’re ready for segmentation, the process of identifying individual cells or structures within an image. If appropriate for your dataset, you can use tracking to be able to link objects in space and time and measure speed, directionality, and cell division. The last step of bioimage analysis is to analyze the data by measuring different features like the number of cells or biological structures, or their size, shape, intensity or texture. Carpenter and Eliceiri finalize this series by providing tips on best practices that will aid scientists in properly analyzing their data.Speaker Biographies:First Speaker: Anne Carpenter (Broad Institute)Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Second Speaker: Kevin Eliceiri (University of Wisconsin-Madison)Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
Multi-Dimensional Microscopy Datasets - Loic Royer (CZ Biohub) iBiology Techniques 2019-09-25 | ibiology.org/techniques/multi-dimensional-microscopy-datasetsModern microscopy produces large multi-dimensional datasets, which creates new challenges for data storage, processing and visualization. In this talk, Dr. Loic Royer uses a developing drosophila melanogaster embryo to explain how to solve some of the challenges produced by multi-dimensional microscopy datasets.Speaker Biography:Dr. Loic Royer is a Group Leader at the Chan Zuckerberg Biohub. Royer initially studied engineering and then obtained a master’s degree in artificial intelligence followed by a doctoral degree in bioinformatics from the Dresden University of Technology in Germany. He continued his scientific training as a postdoc in the laboratory of Dr. Gene Myers at HHMI’s Janelia Research Campus. He then joined the Max Planck Institute of Molecular Cell Biology and Genetics, where he developed novel technologies, including the first adaptive multi-view light-sheet microscope in collaboration with Dr. Philipp Keller. As a group leader at the Chan Zuckerberg Biohub, he continues to innovate and build new imaging machines.
Metadata in BioImaging - Jason Swedlow (U. Dundee) iBiology Techniques 2019-09-25 | ibiology.org/techniques/metadataJason Swedlow explains what constitutes image metadata, and provides examples on how to catalog, organize, analyze, and share the metadata of biological images.In order to understand an image of a biological sample and what it represents, one needs to understand its metadata. Metadata is the information behind the image that shows the experimental procedure, image acquisition settings, and the analysis performed on the data in order to obtain the represented image. Dr. Jason Swedlow explains what constitutes image metadata, and provides examples on how to catalog, organize, analyze, and share the metadata of biological images.Speaker Biography:Dr. Jason Swedlow is a professor at the University of Dundee in Scotland, and co-founder of the Open Microscopy Environment (OME) project. Swedlow obtained his bachelors in Chemistry from Brandeis University (1982), and completed his PhD in Biophysics at the University of California, San Francisco (1994). He continued his scientific training as a postdoctoral fellow in the lab of Dr. Tim Mitchison. In 1998, Swedlow joined the faculty at the University of Dundee where he studies the mechanisms and regulation of chromosome segregation during mitotic cell division. Swedlow is also involved in the development of software tools for accessing, processing, sharing and publishing large scientific image datasets. For his scientific contributions, Swedlow was named Fellow of the Royal Society of Edinburgh. Visit his lab website and learn more about Swedlow’s research:lifesci.dundee.ac.uk/people/jason-swedlow
iBiology Bioimage Analysis Course - Life cycle of an image data set iBiology Techniques 2019-09-09 | ibiology.org/online-biology-courses/bioimage-analysis-courseThis course is designed as a graduate student level introduction to bioimage analysis and will provide an overview of the practice and principles of microscopy digital image handling. This series follows the life cycle of an image data set, from acquisition to analysis. It teaches important concepts and best practices, and provides examples that will come in handy when scientists are designing their own experiments.
The Scientific Community Image Forum - Anne Carpenter and Kevin Eliceiri iBiology Techniques 2019-08-20 | ibiology.org/techniques/scientific-community-image-forumThe Scientific Community Image Forum is an online resource that helps scientists answer their bioimage analysis questions. In this talk, Dr. Anne Carpenter and Dr. Kevin Eliceiri encourage scientists to use the Scientific Community Image Forum when they have image analysis difficulties, and to familiarize themselves with the different tools that they can use to answer their questions.Speaker Biographies:Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
ImageJ - Kevin Eliceiri (U. Wisconsin) iBiology Techniques 2019-08-20 | ibiology.org/techniques/image-jIn this talk, Dr. Kevin Eliceiri provides an overview of ImageJ, explains how ImageJ has evolved through time, and demonstrates major functionalities of this open-source software. Since 1987, different versions of ImageJ have been used by scientists to analyze biological images. Speaker Biography:Dr. Kevin Eliceiri is an Associate Professor of Medical Physics and Biomedical Engineering and director of the Laboratory for Optical and Computational Instrumentation (LOCI) at the University of Wisconsin-Madison. Eliceiri completed his bachelor’s and doctoral degree in Biotechnology and Biomedical Engineering at the University of Wisconsin in Madison. In 2008, he founded LOCI and started his research group at the University of Wisconsin-Madison. His current research focuses on the development of novel optical imaging methods for investigating the role of the cellular microenvironment in disease, and the development of software for multidimensional image analysis.
CellProfiler - Anne Carpenter (Broad Institute) iBiology Techniques 2019-08-09 | ibiology.org/techniques/cellprofilerIn this talk, Dr. Anne Carpenter provides an overview of CellProfiler, a free, open-source software program for image analysis. CellProfiler helps scientists to identify and measure biological entities, process images, and export data for further analysis. Carpenter provides examples on how to use CellProfiler, and explains how CellProfiler can aid scientists in their bioimage analysis.Speaker Biography:Anne Carpenter is an Institute Scientist at the Broad Institute of MIT and Harvard. Carpenter completed her bachelor’s degree in biological sciences, and a doctoral degree in cell biology from the University of Illinois, Urbana-Champaign. She continued her scientific training as a postdoctoral fellow at the MIT/Whitehead Institute for Biomedical Research in the laboratory of Dr. David Sabatini and was co-mentored by Dr. Polina Golland of MIT’s Computer Science/Artificial Intelligence Laboratory. In 2017, Carpenter started her laboratory at the Broad Institute where she combines her background in cell biology, microscopy, and computational biology to develop methods extracting quantitative information from biological images.
Mass Cytometry Introduction - Susanne Heck (NIHR BRC) iBiology Techniques 2019-06-04 | ibiology.org/techniques/mass-cytometryHow does mass cytometry differ from other types of flow cytometry? When would you choose to use it? How does a mass cytometer work? Dr. Susanne Heck gives an overview of mass cytometry and answers all of these questions. Dr. Susanne Heck begins her talk by explaining why we might choose to use mass cytometry rather than other types of flow cytometry. Traditional flow cytometry is typically limited to the detection of about a dozen parameters in one sample due to overlap between the emission spectra of fluorochromes used to label antibodies. Mass cytometry, on the other hand, allows for the detection of up to 50 parameters in one sample because antibodies are labelled with metal isotopes and separated based on their mass. Heck goes on to explain which metal isotopes are typically used for mass cytometry and why, and she describes how a mass cytometer functions. She finishes by running through an example of using mass cytometry to perform functional phenotyping on human bone marrow cells.Speaker Biography:Dr. Susanne Heck received her PhD in molecular biology from the University of Bremen, Germany, in 1997. After a postdoc in molecular and cellular biology at Albert Einstein College in New York, Heck joined Cellular Genomics Inc., USA, to work on preclinical models for small molecule kinase inhibitors. In 2004, she moved to the Lindsey F. Kimball Research Centre to develop and run the Flow Cytometry Core of the New York Blood Centre. Heck was appointed as head of the NIHR BRC Flow Cytometry Core for Guys and St Thomas Hospital and King’s College London in 2009 and has established a successful human immune monitoring core of international reputation.
Imaging Flow Cytometry: A Brief Overview - Andrew Filby (Newcastle U.) iBiology Techniques 2019-04-23 | ibiology.org/techniques/imaging-flow-cytometryIn this talk, Dr. Andrew Filby provides an overview of imaging flow cytometry, a powerful technique used to measure the phenotype of cells using image-based metrics. Compared with traditional flow cytometry, imaging flow cytometry increases the number of parameters one can measure by providing morphological and spatial information in a high-throughput, controlled manner. Filby explains how the imaging flow cytometer works and describes the benefits of using this technique to better answer biological questions, as well as giving us a glimpse into the future of this exciting field.Speaker Biography:Dr. Andrew Filby is the Director of the flow cytometry core facility at Newcastle University in the UK. He received his bachelor’s degree in biochemistry from the University of Huddersfield, and his Ph.D. in molecular and cellular immunology from the National Institute for Medical Research (NIMR) in Mill Hill, London. Filby joined the laboratory of Dr. George Kassiotis at the NIMR where he continued his post-doctoral training. After his post doc, he joined the London Research Institute as the deputy head of the cytometry core facility. Filby continues to innovate and develop new cytometric applications in his current position at Newcastle University.
Next Generation Sequencing 3: Purifying DNA Samples with Magnetic Beads - Eric Chow (UCSF) iBiology Techniques 2019-04-03 | ibiology.org/techniques/next-generation-sequencingNext generation sequencing allows DNA samples to be sequenced quickly and affordably. Learn how next gen sequencing works and get tips on preparing and running your samples. In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours! In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection. In two short how-to videos, Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.Speaker Biography:Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.
Next Generation Sequencing 4: Checking Nucleic Acids with an Agilent BioAnalyzer - Eric Chow (UCSF) iBiology Techniques 2019-04-03 | ibiology.org/techniques/next-generation-sequencingNext generation sequencing allows DNA samples to be sequenced quickly and affordably. Learn how next gen sequencing works and get tips on preparing and running your samples. In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours! In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection. In two short how-to videos, Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.Speaker Biography:Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.
Next Generation Sequencing 1: Overview - Eric Chow (UCSF) iBiology Techniques 2019-04-03 | ibiology.org/techniques/next-generation-sequencingNext generation sequencing allows DNA samples to be sequenced quickly and affordably. Learn how next gen sequencing works and get tips on preparing and running your samples. In the past decade there has been an amazing change in the efficiency of DNA sequencing. Using traditional Sanger sequencing, the human genome project took 20 years and cost $3 billion. Current next generation sequencing methods allow a human genome to be sequenced for $1000, in 48 hours! In this talk, Eric Chow explains the chemistry behind next generation sequencing, and describes how the next gen sequencers detect and display results. The most commonly used Illumina sequencers are image based and detect the addition of fluorescently labelled nucleotides. Chow also describes two different next generation sequencing technologies which provide benefits such as much longer reads but with downsides such as higher error rates. Chow finishes the talk with some insights into medical applications of next gen sequencing such as much less invasive prenatal testing or cancer detection. In two short how-to videos, Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.Speaker Biography:Eric Chow is an assistant professor in the Department of Biochemistry and Biophysics and the Director of the Center for Advanced Technology (CAT) at the University of California, San Francisco. The CAT provides resources for UCSF labs wishing to use next generation sequencing techniques and Chow’s research program strives to develop new applications for NGS in pathogen diagnostics. Chow received his BA in molecular biology from the University of California, Berkeley and his PhD in biochemistry from UCSF.
Visual Communication in Biology 2: Animating Molecular Biology, Part I - Janet Iwasa (U. Utah) iBiology Techniques 2019-03-13 | ibiology.org/techniques/visual-communication-biologyScientists commonly use visual representation of data to show their results and ideas. In this seminar, Dr. Janet Iwasa provides an introduction to the field of molecular animation, and walks us through the process of using visualization tools to communicate scientific information. In her first video, Iwasa summarizes the common types of visualizations used in biology, explains the steps you should take to create a model figure, and summarizes key elements you should consider when creating your figures and models.In her second and third videos, Iwasa provides an overview of the animation process. She shows different software that can be used to create molecular models (e.g. UCSF chimera), and illustrates the process of creating an animation and finalizing the video using software like Maya and Adobe After Effects. These videos will familiarize you with the process of creating an animation and show best practice techniques when using visual communication in biology.Speaker Biography:While completing her PhD in cell biology at the University of California, San Francisco, Janet Iwasa began taking classes in animation. She honed her skills as a molecular animator during her post-doctoral fellowship and she has since joined forces with researchers to make animations of various biological processes. Iwasa joined the faculty at Harvard Medical School in 2008 and is currently at the University of Utah School of Medicine.Learn more about Iwasa’s work here:https://medicine.utah.edu/faculty/mddetail.php?facultyID=u0863544and here:https://animationlab.utah.edu
Visual Communication in Biology 1: Introduction - Janet Iwasa (U. Utah) iBiology Techniques 2019-03-13 | ibiology.org/techniques/visual-communication-biologyScientists commonly use visual representation of data to show their results and ideas. In this seminar, Dr. Janet Iwasa provides an introduction to the field of molecular animation, and walks us through the process of using visualization tools to communicate scientific information. In her first video, Iwasa summarizes the common types of visualizations used in biology, explains the steps you should take to create a model figure, and summarizes key elements you should consider when creating your figures and models.In her second and third videos, Iwasa provides an overview of the animation process. She shows different software that can be used to create molecular models (e.g. UCSF chimera), and illustrates the process of creating an animation and finalizing the video using software like Maya and Adobe After Effects. These videos will familiarize you with the process of creating an animation and show best practice techniques when using visual communication in biology.Speaker Biography:While completing her PhD in cell biology at the University of California, San Francisco, Janet Iwasa began taking classes in animation. She honed her skills as a molecular animator during her post-doctoral fellowship and she has since joined forces with researchers to make animations of various biological processes. Iwasa joined the faculty at Harvard Medical School in 2008 and is currently at the University of Utah School of Medicine.Learn more about Iwasa’s work here:https://medicine.utah.edu/faculty/mddetail.php?facultyID=u0863544and here:https://animationlab.utah.edu
Visual Communication in Biology 3: Animating Molecular Biology, Part II - Janet Iwasa (U. Utah) iBiology Techniques 2019-03-13 | ibiology.org/techniques/visual-communication-biologyScientists commonly use visual representation of data to show their results and ideas. In this seminar, Dr. Janet Iwasa provides an introduction to the field of molecular animation, and walks us through the process of using visualization tools to communicate scientific information. In her first video, Iwasa summarizes the common types of visualizations used in biology, explains the steps you should take to create a model figure, and summarizes key elements you should consider when creating your figures and models.In her second and third videos, Iwasa provides an overview of the animation process. She shows different software that can be used to create molecular models (e.g. UCSF chimera), and illustrates the process of creating an animation and finalizing the video using software like Maya and Adobe After Effects. These videos will familiarize you with the process of creating an animation and show best practice techniques when using visual communication in biology.Speaker Biography:While completing her PhD in cell biology at the University of California, San Francisco, Janet Iwasa began taking classes in animation. She honed her skills as a molecular animator during her post-doctoral fellowship and she has since joined forces with researchers to make animations of various biological processes. Iwasa joined the faculty at Harvard Medical School in 2008 and is currently at the University of Utah School of Medicine.Learn more about Iwasa’s work here:https://medicine.utah.edu/faculty/mddetail.php?facultyID=u0863544and here:https://animationlab.utah.edu
Single-Cell Imaging and Reconstructing Mouse Development - Philipp Keller (Janelia/HHMI) iBiology Techniques 2019-03-05 | ibiology.org/techniques/single-cell-imagingDr. Philipp Keller describes the adaptive light-sheet microscope that his lab developed to image and quantitatively reconstruct mouse embryogenesis from gastrulation through early organogenesis at the single-cell level. Talk Overview:To better understand how an entire embryo develops from a single cell, Dr. Philipp Keller and colleagues developed a technique to image and quantitatively reconstruct mouse embryogenesis from gastrulation through early organogenesis at the single-cell level. Keller’s lab developed an adaptive light-sheet microscope to follow the mouse embryo for 48 hours while it’s developing its germ layers (mesoderm, endoderm, and ectoderm), early tissues, and organs. By combining long-term high-resolution imaging, computational, and statistical analyses, they generated a dynamic fate map of the embryo. These open-access resources aid in the understanding on the dynamic cell behaviors that allow for proper growth and development of the embryo.Speaker Biography:Dr. Philipp Keller earned his Master of Science in Physics at the University of Karlsruhe and at the University of Heidelberg in 2005. He continued his graduate studies at the European Molecular Biology Laboratory (EMBL). After a short postdoc at EMBL, he joined the faculty at HHMI’s Janelia Research Campus in 2010. His lab uses advanced light-sheet microscopy and computational methods to quantitatively study neural development in fruit fly, zebrafish and mouse. To learn more about Keller’s research, visit his website:janelia.org/lab/keller-lab
FACS - Fluorescence Activated Cell Sorting - Steffen Schmitt (DKFZ) iBiology Techniques 2018-12-19 | ibiology.org/techniques/facsDr. Steffen Schmitt explains the principles of FACS and describes the basic components of a droplet cell sorter. He gives advice on optimizing the yield, purity, recovery time, and viability of isolated cells. FACS (fluorescence activated cell sorting) differs from conventional flow cytometry in that it allows for the physical separation, and subsequent collection, of single cells or cell populations. FACS is useful for applications such as establishing cell lines carrying a transgene, enriching for cells in a specific cell cycle phase, or studying the transcriptome or genome or proteome of a whole population on a single cell level. Dr. Steffen Schmitt explains the components and basic function of droplet-based cell sorters. He also provides strategies to optimize the key values in cell sorting (e.g. yield, purity, recovery time, and viability) depending on the downstream assay to be performed on the isolated cells.Speaker Biography:Dr. Steffen Schmitt studied biology at the Ruprecht-Karls-University of Heidelberg and completed his PhD in the Department of Cellular Immunology at the German Cancer Research Center (DKFZ). After a short post-doc, he established and led a flow cytometry core lab at the Natural Science and Medical Research Center (NMFZ) at Johannes Gutenberg University of Mainz. Since 2007, Schmitt has been head of the Flow Cytometry Unit of the Imaging and Cytometry Core Facility at the DKFZ in Heidelberg.
Flow Cytometry Introduction - Malte Paulsen (EMBL) iBiology Techniques 2018-12-11 | ibiology.org/techniques/introduction-to-flow-cytometryThis video provides an excellent introduction to flow cytometry. Dr. Malte Paulsen covers the basic principles of the technique including fluidics, optics and data display. Talk Overview:Dr. Malte Paulsen gives an introduction to flow cytometry with an excellent explanation of the basic principles governing the technique. He explains how fluid flow is used to focus a sample in a laser beam. Light from the laser is scattered by cells in the sample and the degree of scatter provides information about the cell’s optical density and other characteristics. In conventional flow cytometry, lasers are used primarily to excite fluorescent antibodies bound to specific cell types. A detector with different filters allows specific wavelengths to be dissected from the overall fluorescence. This signal can then be displayed in ways that provide the most information about the cell type of interest.Speaker Biography:Dr. Malte Paulsen has been Head of the Flow Cytometry Core Facility at EMBL since 2015. Prior to joining EMBL, Paulsen was Head of the flow cytometry facilities first at Institute for Molecular Biology (IMB) in Mainz, and later at the National Heart and Lung Institute, Imperial College, London. Paulsen received his PhD from the German Cancer Research Center and the University of Heidelberg in 2011.
Synthetic Biology: Realizing synthetic carbon dioxide fixation - Tobias Erb iBiology Techniques 2018-03-28 | ibiology.org/bioengineering/synthetic-carbon-dioxide-fixationTobias Erb outlines the principles of building synthetic metabolism using, as an example, work in his lab to engineer bacteria to undergo synthetic carbon dioxide fixation.Talk Overview:The conversion of atmospheric carbon dioxide (CO2) to biomass via photosynthesis is the foundation for all of our food and energy. Tobias Erb explains how his lab is working to design, build and optimize pathways for synthetic CO2 fixation. By combining enzymes from multiple organisms with “re-engineered” enzymes and optimizing the processes, Erb and his lab generated a synthetic cycle that fixes CO2 more energy efficiently than photosynthesis. In the future, they plan to test the system in artificial cells and to transplant it into bacteria and chloroplasts. The video exemplifies the general rules and principles of building synthetic metabolism.Speaker Biography:Tobias Erb studied biology and chemistry at the University of Freiburg and Ohio State University. He was a postdoctoral fellow at the University of Illinois before starting his own group at the Swiss Federal Institute of Technology (ETH) in Zurich, Switzerland. In 2014, Erb moved to the Max Planck Institute for Terrestrial Microbiology in Marburg, Germany where he became Director and Head of the Department of Biochemistry and Synthetic Metabolism in 2017. Erb’s lab studies the principles of natural metabolism with the aim of using this knowledge to build, from basics, novel synthetic metabolic processes. Erb is particularly interested in the enzymes and pathways of bacteria that capture and convert carbon dioxide. In 2015, Erb was named one of 12 up-and-coming-scientists by the American Chemical Society and in 2016 he received the Heinz-Maier-Leibniz prize of the German Research Foundation. Learn more about Erb’s research here: http://www.mpi-marburg.mpg.de/erb
Synthetic Biology: Engineering bacteria with CRISPR - David Bikard iBiology Techniques 2018-02-08 | ibiology.org/bioengineering/engineering-bacteria-crisprDavid Bikard’s talk focuses on engineering bacteria with CRISPR to combat microbial pathogens. He explains how CRISPR technologies could eliminate antibiotic resistance. Talk Overview:Dr. David Bikard’s lab focuses on engineering bacteria with CRISPR to combat microbial pathogens. In this video, he introduces the historical context for using CRISPR in bacteria and then delves into two CRISPR technologies being developed by his lab. Part of his lab is using CRISPR/Cas9 to eliminate antibiotic resistance in bacterial populations. His group is also optimizing a catalytically dead Cas9 (dCas9) to modulate levels of CRISPR-induced transcriptional repression and use it in pooled high throughput screens for gene function. Speaker Biography:Dr. David Bikard is the head of the Synthetic Biology Group at the Institut Pasteur in Paris, France. Originally trained in engineering at AgroParisTech, he later received his Masters and PhD from Paris Diderot University for his work with the Institut Pasteur on the intergron bacterial recombination system. He began working with CRISPR during his postdoctoral fellowship with Dr. Luciano Marraffini at Rockefeller University. His work led to him becoming the founder and CSO of the company Eligo Biosciences. In 2014, he returned to the Institut Pasteur as an Investigator in Microbiology. More information about David Bikard’s work can be found on his lab website: https://research.pasteur.fr/en/team/synthetic-biology/
Synthetic Biology: Cyborg-ization of bacteria for degradation of pollutants - Victor de Lorenzo iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/bioremediationIn this talk, Dr. Victor de Lorenzo discusses applications of bacteria as whole-cell catalysts for decontamination and bioremediation. Dr. de Lorenzo shows that many bacteria can use pollutants as carbon sources, allowing them to decontaminate dangerous chemicals in the environment. He highlights one example of engineering the bacterium Pseudomonas putida, using a set of standardized tools, to metabolize 1,3-dichloropropene under anaerobic conditions; this project resulted in both enhanced natural capabilities and introduced novel functions to P. putida.Speaker Biography:Although trained as a chemist, Víctor de Lorenzo is now a Professor of Molecular Environmental Microbiology at the Centro Nacional de Biotecnología-CSIC. His lab uses Pseudomonas putida to recreate and build circuits for the sake of new-to-nature biological activities that will have an environmental impact by interacting with chemical waste. Dr. de Lorenzo is a member of the EMBO Council, the American Academy of Microbiology (AAM) and the European Academy of Microbiology (EAM). He was the course director for the EMBO Synthetic Biology in Action Course and the EMBO/EMBL/iBiology online course in Synthetic Biology.
Synthetic Biology: Overview - Victor de Lorenzo iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/synthetic-biology-overviewThe European Molecular Biology Organization (EMBO)/iBiology synthetic biology course is a series of talks about synthetic biology, covering general principles, technical challenges, current research, and ethical issues in synthetic biology research. This course is based on the EMBO Synthetic Biology in Action Course, which was held at the European Molecular Biology Lab (EMBL) in Heidelberg, Germany over two weeks in June 2015. In addition to the faculty lectures, there are five videos created by the graduate student and post-doc course participants where they describe and demonstrate the lab portion of the course. Dr. Victor de Lorenzo (Centro Nacional de Biotecnología), Dr. Jacqueline Dreyer-Lamm (EMBL), Dr. Sarah Goodwin (iBiology), and Dr. Ron Vale (iBiology/UCSF/HHMI) were the course directors for this collaboration, and video production was care of the Photolab team at EMBL (Claudiu Grozea, Marietta Schupp, and Doros Panayi) and iBiology (Eric Kornblum). EMBO funded the production of this course.Speaker Biography:Although trained as a chemist, Víctor de Lorenzo is now a Professor of Molecular Environmental Microbiology at the Centro Nacional de Biotecnología-CSIC. His lab uses Pseudomonas putida to recreate and build circuits for the sake of new-to-nature biological activities that will have an environmental impact by interacting with chemical waste. Dr. de Lorenzo is a member of the EMBO Council, the American Academy of Microbiology (AAM) and the European Academy of Microbiology (EAM). He was the course director for the EMBO Synthetic Biology in Action Course and the EMBO/EMBL/iBiology online course in Synthetic Biology.
Synthetic Biology: Synthetic Biology and Escherichia coli - Steve Busby iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/regulation-of-bacterial-rna-polymeraseBusby gives an overview of the function and regulation of bacterial RNA polymerase. The distribution of RNA polymerase between genes is determined by interactions between RNA polymerase sigma factor, promoter sequences and activating or repressing transcription factors. By engineering additional activators into E. coli and changing where they bind to DNA, Busby and colleagues have been able to regulate the activity of polymerase on specific transcription units. Speaker Biography:Steve Busby is a Professor and Head of the School of Biosciences at the University of Birmingham, where his work focuses on understanding the mechanisms that control gene expression in bacteria. His lab has made fundamental contributions to the understanding of transcription factor activity and promoter recognition by RNA polymerase. Busby is a Fellow of the Royal Society.
Synthetic Biology: Synthetic Biology in a Societal Context - Emma Frow iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/scientists-society-synthetic-biology-societal-contextDr. Frow suggests that discussions of synthetic biology, both amongst scientists and between scientists and society, need to be reframed in a different context. Conversations need to focus on current, rather than future, experiments and anticipate realistic results rather than speculate about outcomes that are only likely in science fiction. Scientists need to listen to and address questions from the public rather than assume they know how they will react to a new technology such as synthetic biology. And finally, synthetic biology would benefit from governance by the many involved parties rather than regulations imposed by a few perceived experts. Speaker Biography:http://sbhse.engineering.asu.edu/emma-frow/http://www.stis.ed.ac.uk/people/honorary_fellows_and_visitors/frow_emmaEmma Frow is an assistant professor at Arizona State University in the School of Biological and Health Systems Engineering and the Consortium for Science, Policy and Outcomes. She received her PhD in biochemistry and cell signaling at Cambridge University and her MSc in Science and Technology Studies from the University of Edinburgh. Her current work focuses on setting standards in synthetic biology, the movement of ideas from engineering into biology, and objectivity in synthetic biology.
Synthetic Biology: Genetic Firewalls to Horizontal Gene Transfer - Group 2 iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/dna-repair-enzymesSynthetic biology can be used to create biofuels, therapeutics, biosensors, and bioremediation. This often involves introducing new DNA into an existing organism. However, at the same time, it is important to also develop genetic safeguards to ensure that this new DNA is not unwillingly transferred to another organism. One safeguard is to create an organism lacking key DNA repair enzymes (UNG and DUT) that are responsible for fixing misincorporated uracil in the genome. Therefore, this organism will accumulate uracil mutations in its genome, and if it mates with another organism the uracil mutated genome will be recognized as faulty and destroyed. The Synthetic Biology in action participants describe these different safeguarding mechanisms and how they created a host organism with UNG and DUT deletions. Speakers:Yu Heng Lau, Post-doctoral scholar at Harvard Medical SchoolRoberto Ferro, PhD student at the Technical University of DenmarkDario Neves, PhD student at RWTH Aachen UniversityJason Whitfield, PhD student at the Australian National University, Canberra
Synthetic Biology: Engineering a Bioplastic-Producing E. Coli Cell Factory - Group 1 iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/biodegradable-plasticMost plastic is derived from crude oil, causing bad environmental consequences from the oil extraction and plastic production processes and from the accumulation of the slowly degrading plastic in oceans and landfills. One solution to this problem is to create biodegradable plastics from biomass using bacteria. These bacteria can be engineered into plastic producers by synthetic biology tools. The Synthetic Biology in Action course participants tried this approach, and in this video they explain the experiments that led to the production of a biodegradable plastic.Speakers: Luis Carreira, PhD student at the Max Planck Institute for Terrestrial Microbiology Nico Claassens, PhD student at Wageningen UniversityValeriy Paramonov, PhD student at the Turku Centre for BiotechnologyCordelia Rampley, PhD, Postdoctoral Researcher at the University of Oxford
Synthetic Biology: High throughput synthetic biology and biosensors - Group 4 iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/biosensorsHumans are bad at detecting weak signals in the environment, for example sensing pollutants in the area or toxins in drinking water. Most instruments that have been developed to detect such signals are very expensive and cannot be used in day-to-day lives. Using synthetic biology, inexpensive and efficient biosensors can be created to detect weak signals and create a response that humans can detect, such as emitting light. Using engineering principles and robotics, the Synthetic Biology in Action participants describe the steps they used to optimize a biosensor to sense an environmental input and create the maximal response possible. Speakers:Angela Carvalho, PhD student at Evolva Lauri Reuter, PhD student at the VTT Technical Research Centre of FinlandClaudia Wehrspaun, PhD student at Oxford University
Synthetic Biology: (Re)-programming adhesion properties of bacteria - Group 3 iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/biofilmsMany bacteria express adhesion proteins that allow them to stick to surfaces and each other forming biofilms, which can cause problems such as gum disease and implant contamination. However, by manipulating the adhesion proteins that bacteria express, scientists can control what the bacteria interact with. For example, different strains of bacteria can be engineered to adhere to one another, which might be helpful if several different bacteria are needed in close proximity to break down an environmental contaminant. The participants in the Synthetic Biology in created a strain that had many of its own surface proteins and then introduced different adhesion genes to alter the adhesion properties of the bacteria so that desired traits were expressed on the cell surface.Speakers:Alex Fedorec, PhD student at the University College LondonEsteban Martinez Garcia (course instructor), scientist at the Centro Nacional de BiotecnologíaYong Lai, PhD student at the University of Hong KongDharmik Patel, PhD student at the Vellore Institute of Technology, India
Synthetic Biology: An Emerging Engineering Discipline - Timothy Lu iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/biological-circuitsIn his iBiology talk, Dr. Timothy Lu describes how biological circuits, using principles from engineering, can be used as digital (all or none) or analog (continuous spectrum) sensors, and can be programmed in a cell to ‘remember’ an input and pass this memory to the cell’s offspring after it divides. Dr. Lu gives several examples of biological circuits that his lab created that can allow a cell to sense the extracellular environment and give a readable output that can be maintained through subsequent cell divisions. In the future, these types of circuits can be developed as non-invasive diagnostics or therapeutics in humans. Dr. Lu ends his talk by discussing the open challenges facing this area of synthetic biology. Speaker Biography: Timothy Lu is an Associate Professor of Biological Engineering and Electrical Engineering and Computer Science at MIT. He is also affiliated with the Broad Institute of MIT and Harvard. Dr. Lu received his undergraduate and M.Eng. degrees from MIT in Electrical Engineering and Computer Science. He then obtained an M.D. from Harvard Medical School and a Ph.D. from the Harvard-MIT Health Sciences and Technology Medical Engineering and Medical Physics Program. His work in the Synthetic Biology Group focuses on the utilization of engineered biological circuits and cellular sensors to tackle infectious diseases and amyloid-associated conditions, and make advancements in diagnostics, therapeutics, and biotechnology. Lu has been awarded many prizes, including the Lemelson-MIT Student Prize, Grand Prize in the National Inventor Hall of Fame’s Collegiate Inventors Competition, and the Leon Redneck Memorial Prize. He was also listed as one of TR35 Top 35 Innovators Under 35 (MIT Technology Review), as a Kavli Fellow by the National Academy of Sciences, and a Siebel Scholar.
Synthetic Biology: Building cell signaling networks - Wendell Lim iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/signaling-networksDr. Lim explains that many signaling proteins are built from simple modules arranged in different ways. Some modules are catalytic and transmit information (for instance kinase or phosphatase domains) while others are interaction modules that regulate information flow (for example protein-protein interaction domains). By rearranging these modules, LIm’s lab has reprogrammed signaling pathways to generate novel cell behavior. They are now working to use these techniques to develop cell based therapies. Speaker Biography:Wendell Lim is currently a Professor and Chair of the Department of Cellular and Molecular Pharmacology at University of California-San Francisco, director of the UCSF Center for Systems & Synthetic Biology, as well as an Investigator at Howard Hughes Medical Institute. He obtained his bachelor’s degree from Harvard University and his PhD from MIT. Today, Lim’s lab focuses on the molecular logic of signaling systems and understanding the underlying principles that govern the design, function, and evolution of cell-cell signaling.
Synthetic Biology: Engineering Microbes to Solve Global Challenges - Jay Keasling iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/engineering-microbesDr. Jay Keasling discusses the promise of biological systems to create carbon-neutral products for a range of applications, including fuels, chemicals and drugs. Dr. Keasling discusses the application of these principles to the development of a microbial platform for the synthesis of artemisinic acid, which has helped stabilize global supply of this anti-malarial drug. He also discusses additional applications of these techniques to fuel production, and discusses some of the current challenges and possible solutions facing the metabolic engineering community.Speaker Biography:Jay Keasling is a Professor of Chemical engineering and Bioengineering at the University of California, Berkeley, an Associate Laboratory Director for Biosciences at Lawrence Berkeley National Laboratory, and also chief executive officer of the Joint BioEnergy Institute (JBIE). He received his PhD in Bernhard Palsson’s lab at University of Michigan, and was a post-doc with Arthur Kornberg at Stanford University. The Keasling lab focuses on the bioengineering of microorganisms, to enhance biofuel extraction from plant biomass and improve environmental clean-up strategies. Of Dr. Keasling’s numerous honors, his most recent notable awards include the Heinz Award for Technology, the Economy and Employment (2012), the George Washington Carver Award (2013), and the ENI Renewable Energy Prize (2014). Dr Keasling was also elected a Fellow of the National Academy of Inventors in 2014.
Synthetic Biology: Technical Challenges in Synthetic Biology - Vivek Mutalik iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/challenges-in-synthetic-biologyIn this talk, Dr. Vivek Mutalik highlights current difficulties in the field of synthetic biology, and explains some of the approaches that are underway to improve the state-of-the-art in the field. Dr. Mutalik discusses some of the elements that make current approaches to synthetic biology unpredictable and expensive, and reviews possible ways to move the field forward, including standardized parts with predictable behaviors, robust methods of biocontainment and software that allows data sharing and visualization.Speaker Biography:Vivek Mutalik is a Staff scientist at the Environmental Genomics and Systems Biology Division and Biological Systems and Engineering Division at the Lawrence Berkeley National Laboratory; previously Dr. Mutalik was a team leader at the BIOFAB, the first biological design-build-test facility, which focuses on developing extensively tested standard biological parts to facilitate easier engineering of biology. Currently, his work focuses on developing a standardized genetic tools for industrially important microorganisms, a robust functional genomics platform and study of regulatory design principles in microbial stress responses.
Synthetic Biology: Synthetic Biology for Industrial Biotechnology - Group 5 iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/industrial-biotechnologySynthetic biology can be used to engineer metabolic pathways to create high value chemicals using model microorganisms such as yeast. During the Synthetic Biology in Action course, participants engineered yeast to produce beta-caretone. In this talk, they describe the steps they took to engineer an existing yeast pathway to produce the new chemical. These steps include modeling the metabolic pathway outputs, DNA design, amplification, and assembly, and analysis of the final result. Speakers:Joana Guedes, PhD student at i3S-Instituto de Investigação e Inovação em Saúde, IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto Portugal Nicolas Koutsoubelis, PhD student at the Max-Planck Institute for Terrestrial Microbiology and the Research Center for Synthetic Microbiology (SYNMIKRO), Marburg, GermanyGita Naseri, PhD student at the University of Potsdam Pavel Zach, PhD student at the University of West Bohemia
Synthetic Biology: Metabolic Engineering and Synthetic Biology of Yeast - Jens Nielsen iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/metabolic-engineeringDr. Jens Nielsen introduces the idea that cells can act as microbial factories for the sustainable production of diverse products. Dr. Nielsen explains that the goal of metabolic engineering is to alter a cell’s metabolism to produce a desired product. He gives examples of successful implementation of these concepts in yeast, including acetyl-CoA overproduction and synthesis of polyhydroxybutyrate (for biodegradable plastics), n-butanol (a biofuel) and resverotrol (a cancer and diabetes drug). He concludes by highlighting a project to improve the thermotolerance of yeast to facilitate industrial applications.Speaker Biography:Jens Nielsen received his PhD in Biochemical Engineering from the Danish Technical University. Currently, he is a professor and head of the Division of Systems and Synthetic Biology at Chalmers University of Technology in Gothenburg, Sweden. His research focuses on understanding metabolic processes in humans and microbes along with developing chemical and protein production pathways in yeast. He is a member of many organizations including: the Academy of Technical Sciences in Denmark, the National Academy of Engineering in USA, and the Royal Swedish Academy of Sciences.
Synthetic Biology: Production of Novel Antibiotics - Eriko Takano iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/development-of-new-antibioticsAntibiotic resistance is a growing problem worldwide. To address this problem, Eriko Takano and her colleagues are developing methods to produce novel antibiotics using a synthetic biology approach. By performing genome analysis on many microbes, they can identify genes encoding novel biosynthesis pathways that may produce antibiotics. These gene clusters can be transferred to pre-engineered bacterial hosts to optimize drug production. Takano’s lab has developed software systems to search for gene clusters, and model, analyze, optimize and debug antibiotic production. Speaker Biography:Eriko Takano is a Professor at the University of Manchester, where she is Co-Director of the Manchester Synthetic Biology Research Centre SYNBIOCHEM. Takano studied pharmacy at Kitasato University in Tokyo before moving to the UK and receiving her PhD in the School of Biological Sciences at the University of East Anglia and the John Innes Centre. She became an Assistant Professor at the University of Tübingen and then a Rosalind Franklin Fellow and Associate Professor at the University of Groningen. In 2012, she started at the University of Manchester. Her lab develops microbial synthetic biology tools and uses them to produce fine and specialty chemicals.
Synthetic Biology: Mechanistic Insights into Engineered Riboswitches - Beatrix Suess iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/riboswitchesRiboswitches are highly structured RNA elements that are located in the 5’ UTR of many bacterial mRNAs. Riboswitches bind ligands with high specificity. This causes a termination of transcription or the inhibition of translation initiation. Dr. Suess explains that it is possible to select for RNA aptamers that bind a specific ligand, such as tetracyline or neomycin, and engineer these into the 5’ region of a yeast mRNA allowing gene expression to be regulated by adding ligand. Suess discusses what makes an aptamer into a riboswitch. Speaker Biography:Beatrix Suess is a Professor at the Technical University, Darmstadt. She received her PhD from the University of Erlangen, Germany where she was also a post-doctoral fellow. Suess was also a research fellow at the University of Vienna, Austria and at Yale University, USA. Dr. Suess’s research focuses on the ability of RNA to operate as a regulator of activities within the cell. In particular, her work focuses on the use of riboswitches as regulatory devices in synthetic biology applications.
Synthetic Biology: Principles and Applications - Jan Roelof van der Meer iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/introduction-to-synthetic-biologyDr. van der Meer begins by giving a very nice outline of what synthetic biology is. He explains that DNA and protein “parts” can be put together to form biological circuits in a manner analogous to making electrical circuits from transformers, capacitors and the like. These circuits can be designed for many applications in health and agriculture etc. van der Meer concludes his talk by describing work from his lab to engineer biosensor bacteria that can measure toxic compounds in the environment. A simple system is presented of a bacterial cell which glows in the presence of arsenic, that has been used to test drinking water in Bangladesh for high levels of arsenic.Speaker Biography:Jan van der Meer is a professor at the University of Lausanne (Switzerland) in the Department of Fundamental Microbiology. Previous to his appointment in Lausanne, he worked as group leader at the Swiss Federal Institute for Aquatic Research (Eawag). Dr. van der Meer received his PhD from the Wageningen University and Research Centre, and completed postdoctoral work at the National Dairy Institute in Ede, The Netherlands. His research focuses on how bacteria respond and adapt to contaminated environments, and how these adaptations can be used for useful purposes, such as generating environmental reporters. One application, a bacterial biosensor for arsenic, was awarded the 2010 Erwin Schrödinger Prize.
Synthetic Biology: Programming Living Bacteria - Christopher Voigt iBiology Techniques 2016-01-05 | ibiology.org/bioengineering/genetic-circuitsFor synthetic biologists to engineer cells that can make complex chemicals or perform complex functions, they must be able to tell the cell which genes to turn on and at what time. To do this they build genetic circuits composed of a series of gates that respond to a specific input with a specific output. Voigt’s lab has developed a library of gates that can be interconnected, will function robustly and will not interfere with each other. In addition, they have developed software that lets users arrange the gates to form a circuit of their choice. The software provides DNA sequence encoding the circuit and the DNA can be synthesized and inserted into a cell. Voigt’s lab has successfully built and tested circuits in many cell types to make many products. Speaker Biography:Chris Voigt obtained his Bachelor's degree in chemical engineering from the University of Michigan and his PhD in biochemistry and biophysics from the California Institute of Technology. He was a postdoctoral researcher at the University of California, Berkeley and his first faculty position was at the University of California, San Francisco. In 2011, he joined the Department of Biological Engineering at the Massachusetts Institute of Technology as an associate professor. His lab is developing a programming language for cells to allow the regulation of complex cellular functions and their application to problems in biotechnology.
iBiology Engineering Life Flipped Course iBiology Techniques 2015-11-02 | http://www.ibiology.org/ibioeducation/taking-courses/engineering-life-flipped-course.htmlHow did life evolve? How can we understand the principles of biological systems to create new proteins, new chemicals, biological structures, cells and tissues? These topics are covered in this graduate level "flipped course" which combines online lectures from scientific leaders in the field with related scientific papers, along with a series of questions to prompt discussion. This course was designed by Drs. Ron Vale and James Fraser at UCSF for a flipped course with UCSF graduate students in Spring 2015. The students in the course created the discussion questions for the class period, and co-led the discussions with the faculty members. The students also each prepared teaching tools to go with each of the online lectures as the final project of the class. These teaching tools provide more review and discussion questions and answers on the seminars and paper, as well as notes on the seminar for Educators to be able to adapt for their own classrooms.
Mimicry and Conflict - Harmit Malik (FHCRC/HHMI) iBiology Techniques 2015-07-28 | Dr. Malik explains mimicry on the example of Amazon butterflies and why it results in evolutionary conflict.
PKR Evolution in Response to Viral Mimicry: Harmit Malik (FHCRC/HHMI) iBiology Techniques 2015-07-28 | PKR evolves in response to viral mimicry of the host eIF2α, a translation elongation factor, which PKR antagonizes when it senses viral RNA.
