iBiology Videos: Recent Episodes
iBiology
iBiology Videos features iBioSeminars, Famous Discovery Talks, Conversations in Science, Background to Breakthrough, and plenty of other great science videos. iBiology is a non-profit organization that provides free video content by the world’s leading scientists that show the process of science and the wonders of discovery. Learn more about us at www.ibiology.org
The fat layer in our skin has the ability to expand and shrink. Yet, the regulatory mechanisms for skin fat growth and shrinking are not well understood. In this Share Your Research Talk, Edriss Yousuf describes his thesis research on the regulation of skin fat. He discovered a non-immune function of regulatory T cells and showed that they can induce autophagy in skin fat cells to decrease their lipid droplet size. These findings have implications for scarring and scleroderma, disorders which are typically associated with reduced skin fat abundance.
Dirt is anything but dumb. Inside soil lives a community of microbes that play an important role in everything from the environment to agriculture. In this Share Your Research talk, Dr. Julia Nepper describes her postdoctoral research to model and understand the microbial community inside the rhizosphere, the soil adjacent to plant roots. Dr. Nepper performed a series of experiments to understand how three key microbial species interact with one another to support each other’s growth and survival. These findings indicate that the soil microbiome is greater than the sum of its parts, and underscores the importance of modeling complex species
In this session, you will learn how to thoughtfully choose your next job opportunity and successfully negotiate with both your current research advisor and prospective one. You will learn how to strategically apply your negotiation skills as you navigate the process of securing a job offer; deciding which job opportunity is a good fit; and transitioning out of your PhD lab to begin a new chapter in your career. You will also learn how to execute each step with intention, clarity, and confidence.
In this session, you will learn how to thoughtfully choose your next job opportunity and successfully negotiate with both your current research advisor and prospective one. You will learn how to strategically apply your negotiation skills as you navigate the process of securing a job offer; deciding which job opportunity is a good fit; and transitioning out of your PhD lab to begin a new chapter in your career. You will also learn how to execute each step with intention, clarity, and confidence.
In this session, you will learn how to thoughtfully choose your next job opportunity and successfully negotiate with both your current research advisor and prospective one. You will learn how to strategically apply your negotiation skills as you navigate the process of securing a job offer; deciding which job opportunity is a good fit; and transitioning out of your PhD lab to begin a new chapter in your career. You will also learn how to execute each step with intention, clarity, and confidence.
After receiving an invitation to interview from your prospective postdoc lab you need to develop an interview game plan. Your ultimate goal is to demonstrate why you are a good fit for the position. A postdoc interview usually includes meeting and talking with the principal investigator and members of your prospective lab. In this session, you will learn how to strategically highlight your strengths during the interview process and prepare a postdoc job talk that is relevant to your audience and outlines how you will contribute as a scholar and potential colleague.
After receiving an invitation to interview from your prospective postdoc lab you need to develop an interview game plan. Your ultimate goal is to demonstrate why you are a good fit for the position. A postdoc interview usually includes meeting and talking with the principal investigator and members of your prospective lab. In this session, you will learn how to strategically highlight your strengths during the interview process and prepare a postdoc job talk that is relevant to your audience and outlines how you will contribute as a scholar and potential colleague.
When you apply for postdocs and other types of jobs, you typically need to submit a curriculum vitae and a cover letter as part of your application package. This session will teach you strategies to assemble an effective application package geared towards getting the position that you want.
As you start thinking about doing a postdoc, there are a few key questions you need to consider. What type of position will allow you to build the profile needed to be competitive for your ideal career? What skills, knowledge, experiences, and type of environment will support your success and productivity? Knowing this will help you prioritize what to look for in a postdoc and begin scouting for opportunities that fit your goals. This session will help you organize your postdoc search and leverage your mentoring network to find postdoc opportunities that match your career goals.
As you start thinking about doing a postdoc, there are a few key questions you need to consider. What type of position will allow you to build the profile needed to be competitive for your ideal career? What skills, knowledge, experiences, and type of environment will support your success and productivity? Knowing this will help you prioritize what to look for in a postdoc and begin scouting for opportunities that fit your goals. This session will help you organize your postdoc search and leverage your mentoring network to find postdoc opportunities that match your career goals.
The third video is a recording of a panel discussion moderated by SCL producer Rosa Veguilla on February 3, 2022. In this conversation, we asked the speakers follow-up questions about whether we can and should use CRISPR in the natural forest to combat climate change, and if so, what that might look like.
Coral reefs are truly magnificent ecosystems that support an abundance of marine life, and they are under threat. As climate change warms the oceans, corals become stressed by the heat and struggle to survive. Can modern genetic tools, like CRISPR-Cas9, help save them? Some scientists say it is our responsibility to make sure corals adapt to climate change.
Hearing loss, caused by the death of hair cells in the inner ear, is the third most common public health issue in the United States. Currently, there are no therapeutic strategies to restore hearing. In her thesis research, Dr. Amrita A. Iyer investigated the possibility of regenerating functional hair cells by reprogramming non-hair cells of the mouse inner ear. She found that overexpression of a single transcription factor, ATOH1, can successfully reprogram non-sensory cells into hair cells with typical characteristics in neonatal mice. However, a combination of three transcription factors - ATOH1, GFI1, and POU4F3 - was required to reprogram inner hair cells in 1-week old mice. Her findings provide a window into the developmental and gene expression requirements for regeneration of inner ear hair cells in mammals, and may inform future therapeutic strategies for hearing loss in humans.
Dr. Tshaka Cunningham received his PhD in molecular biology from Rockefeller University and completed postdoctoral training at the Institut Pasteur in Paris. He is the co-founder and CSO of Polaris Genomics, a precision behavioral health company. Dr. Cunningham is a leading advocate for diversity and representation in genomics and is Executive Director of the Faith-Based Genetic Research Institute.
The National Cancer Act was signed into law in 1971, declaring a “War on Cancer.” While cancer deaths have declined remarkably since then due to major advances in therapies, we are still far from eliminating cancer altogether. In her Share Your Research talk, Christina Cho discusses how we could make further progress in our fight against cancer by learning more about the tumor microenvironment and the role of the immune system on tumor growth. Her work focuses on the complicated functions associated with cancer-associated fibroblasts, which can both help and harm cancer cells.
More than 200 million people are infected with schistosomes, aquatic parasites that cycle between snails and humans, and cause the human disease schistosomiasis. Risk of contracting this disease is expected to rise in the coming years due to climate change, agricultural expansion, and population growth. In her Share Your Research Talk, Dr. Karena Nguyen provides an overview of the schistosome life cycle, including the points at which interventions can disrupt this cycle in order to reduce disease transmission. She then goes on to discuss her work modeling the impact of these interventions.
Intestinal villi are finger-like projections that line the small intestine, increasing surface area to help with absorption of nutrients. Injuries to the intestinal villi can cause a range of health problems, and can even be life-threatening. In this Share Your Research Talk, physician-scientist trainee Takahiro Ohara discusses his research on the molecular and cellular processes that drive recovery of intestinal villi. He describes the fetal-like state that cells on damaged villi take on, and how adaptive differentiation of these cells leads to proper villus recovery.
When we think of what makes two species distinct, we often think of their ability (or inability) to produce viable offspring. But is there anything we can learn from inviable offspring? In this Share Your Research talk, Maiko Kitaoka discusses her work on closely related Xenopus frogs. She reveals how examining hybridization between these species at the cellular level can provide insight into only the mechanisms that restrict cell division and development, but also broader patterns of how new species are able to evolve.
Unlike most animals, plants don’t have the option to run away when something is trying to eat them. Instead, they develop all kinds of chemical and structural defenses. But these defenses can be energetically costly, and plants’ ability to defend themselves can change over time and with the environment. In her Share Your Research Talk, Dr. Mia Howard discusses how soil microbes can influence defensive traits in goldenrod (Solidago altissima) at various stages of succession. Her work reveals that microbial communities from late succession soils can increase plant resistance to herbivory, and may even make plants less vulnerable to pests.
Exercise is like medicine for the mind and body, particularly in aging adults. Regular physical activity not only provides physiological benefits, it also reduces the risk of dementia, Alzheimer’s, and other declines in mental function associated with aging. In his Share Your Research Talk, Brandon Yates provides an overview how proper hydration during exercise can help maximize the health benefits associated with exercise. He also discusses why this is particularly important in older adults, who are often chronically dehydrated.
Saving The American Chestnut: A Case Study, we explore more deeply the complicated question of using biotechnology to make forests more resistant to climate change. We look to the story of the American Chestnut as an example of how scientists are trying to bring a once-abundant tree back from near extinction through genetic engineering. We also consider the budding genome-editing technology CRISPR Cas-9 as a more precise tool with great promise but also great uncertainty. Can we do it and should we do it?
Some people harbor deleterious mutations in disease-relevant genes, yet they are completely healthy. How are scientists trying to understand these so-called ‘genetic superheros’? In this Share Your Research talk, Dr. Mohamed El-Brolosy describes his thesis research in the model organism zebrafish. Dr. El-Brolosy found that genetic compensation to deleterious mutations relies on degradation of the mutant mRNA, which triggers upregulation of compensatory genes in a homology-dependent manner. These findings can inform strategies to better understand and treat genetic diseases, many of which have limited therapeutic options.
Solid tumors, such as those in the brain, can be deadly when they expand or spread to other parts of the body. Before they spread, tumors send out molecular messages within small membranous structures known as extracellular vesicles (EVs). The proteins and small non-coding RNAs inside EVs can help tumors evade the immune system and seed new sites of growth. In this Share Your Research talk, Dr. Luz Cumba García describes her thesis research on extracellular vesicles released by aggressive brain cancers called glioblastoma. Dr. Cumba García’s work helps scientists understand the EV profiles of different glioma subtypes, as well as how the messages inside EVs help them shut off the immune system.
In order to succeed in kindergarten and beyond, children must develop language skills within their home reading environment. This environment is often influenced by the reading ability of a child’s caregivers. In this Share Your Research talk, Dr. Paige Greenwood describes her doctoral research on the association between maternal reading ability and the development of the language brain network in children. Her work showed that lower maternal reading fluency is associated with higher language network connectivity to brain regions involved in cognitive control and semantics in children. These data suggest that if there is lower frequency or quality of engagement in the home reading environment, children’s brains may overcompensate to meet their language development needs.
Chronic liver diseases affect millions of people worldwide. By understanding how liver disease progresses, we may be able to identify new therapies that can protect the liver. Dr. Chrystelle Vilfranc studied the role of BRUCE, a protein that is known to be important in several cellular processes in our bodies, in liver disease. She found that the absence of BRUCE in mouse livers led to accelerated liver disease and higher rates of liver cancer when combined with a liver damaging compound. Furthermore, hepatocellular carcinomas that develop in the absence of BRUCE in the liver appear to have increased β-catenin activity. Loss of BRUCE may be a marker of early liver disease in humans, and rescuing BRUCE expression or activity may help stop or reverse disease in the liver.
Is it possible to define life using math? Dr. Alyssa Adams’s research seeks to answer precisely this question. In their Share Your Research talk, Dr. Adams introduces the concept of open-ended evolution, and describes how they have developed mathematical models to help us understand how biological systems can innovate within a changing environment. These studies could help us to identify living systems beyond our planet that may be vastly different from those we recognize on Earth!
What does a redwood forest look like, and sound like, in the wake of a devastating fire? See a forest in a new way in this new cinematic short from the Science Communication Lab. Walk through a fire-ravaged redwood forest with experts Beatrix Jiménez, a Land Stewardship Associate at the Sempervirens Fund, Ian Bornarth, a Bay Area-based photographer documenting post-fire recovery, and Alex Jones, the UC Santa Cruz Campus Natural Reserve Manager. Their observations make visible the forces of destruction and regrowth throughout the redwoods ecosystem.
Bat species are numerous and diverse, and are found in nearly every corner of the globe. Therefore, they serve as a valuable system to study the evolution of mammalian traits. Dr. Alexa Sadier collected field and museum samples from over 50 species of bats to ask how color vision evolved in this unique group of mammals. By looking at gene expression at multiple levels - DNA, RNA, and protein - Sadier determined that different bat species have color vision capabilities adapted to their diets, and UV vision has been lost independently in multiple species through regulation of all levels of gene expression. By “catching” evolution in action, Sadier’s research has revealed important insights into the mechanisms of evolution through trait loss.
Dr. Alex Moore provides an introduction to coastal wetlands, including the functional role they play in our world, as well as the many ways that these ecosystems are used for economic and recreational activities. Dr. Moore discusses the traditional approach to restoring coastal wetlands, and the ways that these efforts can fall short of restoring functional capacity in coastal salt marshes. Incorporating consumer interactions into restoration efforts may provide an opportunity to further improve wetland restoration. Moore finishes with a brief overview of work currently underway in coastal mangroves, another important wetland ecosystem.
Trees are magnificent organisms that have evolved very slowly over millions of years, making it hard for them to adapt to rapid changes in the environment. With climate change imminent, scientists estimate up to 25% of US forests will decline over the next three decades. In this film, four researchers ponder the question ”What can we do to help forests adapt to our changing planet?” The answer is, of course, not so straightforward, and leaves us thinking more deeply about the future of forest landscapes and how we can make them more resilient.
Nayak describes research she has done on methanogenic archaea – microorganisms that produce the potent greenhouse gas methane. One species of methanogens, Methanosarcina acetivorans, has unique chemical modifications on the enzyme it uses to produce methane. Dr. Nayak describes how she used CRISPR/Cas9 genome editing to determine that these modifications are used to protect M. acetivorans from environmental stress to ensure that the organism can support its metabolic needs in a changing environment.
Educational science videos are commonly used in undergraduate biology instruction, but what do we know about the student perspective on them? In this paper discussion and live Q&A, Dr. Laci Gerhart-Barley and Dr. Brittany Anderton present findings from their open-access paper “Engaging students through online video homework assignments: A case study in a large-enrollment ecology and evolution course.” Undergraduate biology educators will find a wealth of useful information on how to effectively implement science videos in homework assignments, develop assessment questions, and use the content in educational science videos to promote student engagement and learning of the process of science.
Synthetic cells can be used to teach us about the basic principles of life and evolution, and they hold promise for a range of applications including biomaterials and drug development. Dr. Kate Adamala narrates an introduction to this exciting field.
Meningioma is the most common intracranial tumor, with limited treatment options. In order to identify new therapies for meningioma, it is important to understand their underlying biology. In this Share Your Research talk, Dr. Abrar Choudhury describes his thesis research, which began by looking at DNA methylation patterns to better understand gene regulation in meningioma, leading him to identify the cell cycle proteins CDK4 and CDK6 as therapeutic targets.
Mentors shape our careers by guiding us through difficult decisions. But, how do you find a good mentor? In this series, Dr. Joanne Kamens advocates for the use of Peer Mentoring Groups as a method to provide and receive valuable mentoring opportunities. While working towards a common goal, group mentorship allows for an organic development of valuable experiences and accountability for your personal growth as you create a circle of mentors that will help throughout your career.
How do you go about forming a Peer Mentoring Group? In her second video, Kamens explains the logistics of forming a Peer Mentoring Group. First, you need to find 5-6 peers that share a similar problem. As you prepare to meet, you need to set the ground rules and provide structure to your meetings (e.g., provide agenda, assign a leader per meeting, decide on topics of interest, and provide curricula).
As Kamens explains, the commitment of the members is crucial for the success of the Peer Mentoring Group. In her third talk, Kamens overviews what are mentorship best practices while running a Peer Mentorship Group. From setting concrete content and activities to set up goals, these best practices will allow you to create an environment that will help you get feedback and find opportunities to grow.
Life on Earth evolved once - this means that all biological systems on our planet are rooted in the same fundamental framework. This framework is extremely complex and we have yet to fully understand the processes inside each living cell. One way of understanding complex systems is to break them down into simpler parts. This is the principle of engineering the synthetic cell: to use our current knowledge of biology for building a living cell with the least amount of parts and complexity. Synthetic cells can be used to teach us about the basic principles of life and evolution, and they hold promise for a range of applications including biomaterials and drug development. Dr. Kate Adamala narrates an introduction to this exciting field.
Gregor Mendel’s experiments with pea plants laid the foundation for our understanding of genetic inheritance. In this video, Shirley Tilghman tells the story of Mendel’s studies and how his data led to an understanding of how the information within genes is passed from generation to generation.
Rodolphe Barrangou studies beneficial microbes, focusing on the occurrence and diversity of lactic acid bacteria in fermented foods and as probiotics. Using functional genomics, he has focused on uncovering the genetic basis for health-promoting traits, including the ability to uptake and catabolize non-digestible carbohydrates. He spent 9 years at Danisco-DuPont, characterizing probiotics and starter cultures, and established the functional role of CRISPR-Cas as adaptive immune systems in bacteria. At NC State, he continues to study the molecular basis for their mechanism of action, as well as developing and applying CRISPR-based technologies for genotyping, building immunity and genome editing.
Jennifer Doudna and Emmanuelle Charpentier won the 2020 Nobel Prize in Chemistry for their development of a powerful gene editing tool known as the CRISPR-Cas9 system. In this short film, Doudna, Charpentier, and Martin Jinek, who was a post-doc at the time in Doudna’s lab, describe how their famous collaboration happened and share the story behind the influential experiments that led to their discovery.
Parasitic plants are important in natural ecosystems and in agriculture. Parasitism is a successful life strategy that has convergently evolved in all kingdoms of life.
Do students learn more with clickers and peer-discussion?
Bill Wood (University of Colorado, Boulder) describes the Knight et al. study, which looks at student learning gains in an active learning classroom that utilizes clicker questions and peer-discussion, similar to a think-pair-share.
Think-Pair-Share is an active learning technique that can be used in small or large enrollment courses to engage students and encourage them to practice scientific thinking skills. In think-pair-share, students think about their answer to a question, pair with a partner to debate their choice, and then share their answers with the class. In this video showing examples of think-pair-share in action, Kimberly Tanner (San Francisco State University) shares her experience using this method in classrooms of all sizes.
Clickers are Audience Response Systems that enable instructors to ask a multiple-choice question, poll students for an answer, and display the aggregated results to the class. In this video showing examples of active learning classroom models, Bill Wood (University of Colorado Boulder) describes how clickers can be used effectively to engage students.
How can one shift from a teacher-centered to a student-centered classroom model? What are the benefits of active learning for students and instructors?
What are the issues with traditional undergraduate biology education? What is the role of an educator in a 21st century college classroom? What is missing in the way we currently teach science in college?
We have an online Q&A (hosted on January 6th, 2021) discussing the benefits and limitations of preprints from the perspective of early-career scientists. Panelists included Jessica Polka, Elizabeth Silva (Associate Dean of Graduate Programs at UCSF and former editor at PLoS), and Kate Carbone (an industry postdoc).
Course Directors A. Malcolm Campbell, Kimberly Tanner, and Bill Wood talk about the reasons why we need to reform undergraduate biology education and why they got involved in the Scientific teaching Series project.
Dr. Harold Varmus talks to Dan Rather about his journey from literature major to scientist, and from the discovery of oncogenes to creating PLoS. Varmus reflects on his time as a researcher, as Director of the NIH, and on the importance of open communication in science. He ends by emphasizing why good science communication is important to engage more people in conversations about science.
How should we consider a journey through a career in science? How should we think of the future of science training? Few have given these kinds of questions more thought than Shirley Tilghman, a leading genetics researcher at Princeton University who also became president of that prestigious institution. In this far-reaching interview, Dr. Tilghman tells Dan Rather about her own path in science and how we need to rethink how we train and inspire budding scientists in a challenging career environment. This interview was filmed in 2013.
This video is a collaboration between the Lasker Foundation and iBiology.
Secretary Shultz has been addressing global crises inside and outside of government for decades. He now has his attention firmly focused on concerns over climate change and renewable energy. In a candid and provocative conversation, he explains to veteran journalist Dan Rather why this has become his cause and why he thinks his fellow Republicans need to take it seriously or risk being “mugged by reality.” Secretary Shultz is not looking to point fingers but instead create a framework by which elected leaders across the political spectrum can come together and work on solutions. Funding for this video was provided by the Carnegie Foundation.
Paul Nurse and Dan Rather have both spent their lives looking at the world and how it works, albeit from very different perspectives. Now the Nobel Prize winning geneticist and esteemed journalist come together for a frank and thoughtful conversation on the state of science and its role in society. Topics include climate change, GMOs, science education, how research spurs economic development, and Dr. Nurse’s own remarkably inspiring and surprising personal history. Funding for this interview was provided by the Lasker Foundation.
Eric Kandel won the Nobel Prize in Physiology or Medicine in 2000 for his work on the nervous system. Here, he discusses the mind, the brain, and his journey into a life of science.
This interview was filmed in 2008 for a series on the mind and the brain. This video is a collaboration between the Lasker Foundation and iBiology.
There are many challenges when it comes to addressing the destructive effects of climate change, and few people are better suited to address these challenges than Chris Field. A world-renowned researcher, Dr. Field understands the nuances and implications of the science. And as a gifted and trusted communicator who has the ear of the world’s diplomats, he can explain the urgency of action to policy makers and the general public. In this wide-ranging and thoughtful interview with Dan Rather, Dr. Field calmly but firmly explains what we know about climate change, what the stakes are, and what can be done about it.
How can instructors get started with active learning? What simple and effective active learning methods can easily be implemented in a course? Hear from instructors about their experience and see classroom demonstrations using think-pair-share and clickers.
Compare different pedagogical approaches and undergraduate biology classrooms. Reflect on how your teaching fits within the spectrum of educational models.
In the last few years, the term CRISPR has exploded on the global scene, and with it UC Berkeley professor Jennifer Doudna, one of the pioneers in the field, has emerged into the spotlight. From magazine covers, to news broadcasts, to social media, CRISPR is the rare scientific breakthrough that has captivated the interest of the general public. But what is CRISPR really? What are its implications now and into the future? What profound ethical questions are raised by this ability to so precisely and easily edit the genome? In a candid and far-ranging conversation with Dan Rather, Doudna leads viewers through a nuanced and captivating view of this new technology. And along the way she shares her own improbable journey into science and her lessons for others – especially young women – who want to follow in her footsteps.
Funding for this interview was provided by the Lasker Foundation.
The Dalai Lama has always had a keen interest in science. In this interview from 2008, Dan Rather and His Holiness talk science and what we can learn from the practice of meditation.
This interview was filmed in 2008 for a series on the mind and the brain. This video is a collaboration between the Lasker Foundation and iBiology.
Daniel Colón-Ramos began his life in science by being fascinated as a young boy by the unique environment of his native Puerto Rico. But in formal schooling, he found the excitement of discovery too often absent. Now a respected researcher at Yale University, Dr. Colón-Ramos keeps his boyhood enthusiasm for the awe and wonder of the natural world. He is eager to encourage scientific exploration and share his infectious spirit with his students and the larger world, as he does in this inspiring conversation with Dan Rather.
Jennifer Doudna tells the story of how studying the way bacteria fight viral infection turned into a genomic engineering technology that has transformed molecular biology research. In 2013, Doudna and her colleagues developed the CRISPR-Cas9 gene expression system that, when introduced into animal cells, makes site-specific changes to intact genomes. CRISPR-Cas9 is more precise, more efficient, and less expensive than other genome editing tools and, as a result, has facilitated a wide range of studies that were previously unachievable.
Since 1987, different versions of ImageJ have been used by scientists to analyze biological images. In 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.
The 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.
In this series, 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.
In this series, 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.
In this series, 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.
In this series, 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.
In this series, 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.
In this series, 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.
In 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.
Modern 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.
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.
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.
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 using a light microscope, 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.
Just a few months after Tysabri was approved for MS treatment, two patients developed progressive multifocal leukoencephalopathy (PML), a fatal or seriously debilitating disease. In his second talk, Yednock describes the response of medical and regulatory groups and researchers to this discovery and its impact on the treatment of MS patients with Natalizumab/Tysabri.
Yednock relates the discovery and development, over 15 years, of the drug Tysabri, an alpha4 integrin antibody, as a treatment for multiple sclerosis.
In the first of his two talks, Ted Yednock begins with an overview of multiple sclerosis. He describes how, in MS, immune cells are able to transverse the wall of blood vessels and infiltrate the brain and central nervous system resulting in damage to the myelin surrounding neurons. Yednock and his colleagues hypothesized that by blocking the infiltration of immune cells into the brain, the progression of the disease might be slowed. They went on to identify alpha4 integrin as the molecule that mediates adhesion of immune cells to the blood vessel wall, and they found that an alpha4 integrin antibody (Natalizumab or Tysabri) could block infiltration of the blood cells into the brain in a animal model of MS. Yednock then details the clinical development of Tysabri through to its approval by the FDA in 2004.
Robert Bhisitkul and Tejal Desai describe how treatment for retinal diseases leading to vision loss, such as age related macular degeneration, may be much improved by efforts to develop implantable devices for drug delivery.
Age related macular degeneration (AMD) is one of several retinal diseases that can lead to vision loss and, ultimately, blindness. Dr. Bhisitkul explains that the class of anti-VEGF biologic drugs (Lucentis, Avastin, Eylea) can treat AMD, however, ongoing, monthly injections into the eye are required for the drugs to be fully effective. There are a number of drawbacks to this treatment regime, many of which could be mitigated by the development of a drug delivery device for implantation in the eye. Dr. Desai describes the work done in her lab to develop an injectable, biocompatible and biodegradable device that has the right release kinetics to successfully deliver needed drugs to the retina of patients with AMD.
Drug discovery for diseases of the nervous system is difficult. Although mouse models are helpful to study many human diseases, they have serious limitations for understanding neurological and psychiatric disease. Dolmetsch describes a method developed by his group to produce induced pluripotent stem cell-derived neurons from patients. Using these iPSC neurons, they can identify molecular defects associated with a neurodevelopmental disease and then identify medicines to treat those diseases.
MS begins as a disease of intermittent episodes with recovery in between. With time, however, MS changes to a progressive disease with increasing disability. In her talk, Dr. Stadelmann explains that studies of MS brain lesions have identified specific changes that occur with disease progression. For example, chronic MS lesions contain many fewer oligodendrocytes than do early lesions. Since oligodendrocytes produce the myelin sheath that surrounds axons, drugs that stimulate the migration and establishment of oligodendrocytes in lesions may increase axonal remyelination and improve the prognosis of MS patients. Stadelmann also explains that brain lesions can be caused by conditions other than MS, such as neuromyelitis optica. Improved studies will help to correctly diagnose and treat these distinct diseases.
Multiple sclerosis (MS) is a debilitating autoimmune disease in which immune cells infiltrate the central nervous system and attack the myelin sheath surrounding axons. Dr. Simons explains that myelin is necessary for signal conduction by nerve cells and for the metabolic support of axons. Demyelination results in axonal loss and formation of lesions in the brain. A small percentage of MS lesions are capable of remyelination following steps similar to axonal myelination during normal development. Since lesion remyelination correlates with reduced neurodegeneration, Simons and his colleagues strive to understand why remyelination occurs in only a small number of MS patients and to identify drugs that may promote it.
In his third lecture, Gadek outlines Lifitegrast clinical trials, from Phase 1 to Phase 3, and presents evidence of Lifitegrast’s safety profile in normal individuals as well as the efficacy of the drug in treating dry eye syndrome. Lifitegrast’s story shows the different layers of drug development and the steps that companies go through to take a drug from the laboratory to the patient’s bedside and ultimately to the market.
In his second lecture, Gadek reviews the molecular mechanism of dry eye syndrome, focusing on the role of inflammation and T-cells in this disorder. By analyzing clinical trial data from other drugs developed to treat dry eye, Gadek and colleagues confirmed the importance of LFA-1 as a possible target. LFA-1 is a surface protein on T-cells that binds to ICAM-1 on antigen presenting cells, T-cells, and epithelial cells and causes inflammation. Gadek and his colleagues developed Lifitegrast, a small molecule that serves as an ICAM-1 mimetic. By binding to LFA-1 on T-cells, Lifitegrast inhibits the binding of ICAM-1 and therefore inhibits the inflammation associated with dry eye syndrome.
Using the company he co-founded, SARcode, as an example, Dr. Tom Gadek tells us how one converts a novel idea into a successful company. He walks us through the discovery of Lifitegrast to treat dry eye syndrome, the founding of SARcode in 2006, and the subsequent clinical trials. In his first talk, Gadek highlights the financial challenges a company faces during its development and stresses the importance of presenting the company as a valuable investment to venture capital groups. While describing the process of developing a company, Gadek offers three main points of advice: surround yourself with people that work well with you, get good lawyers, and always do quality science and publish your results.
About half of the cells in an adult heart are cardiac myocytes, or muscle cells, and about half are cardiac fibroblasts or support cells. Following a heart attack, muscle is lost and fibroblasts form scar tissue. In his second talk, Srivastava asks whether our understanding of embryonic heart development can be used to reprogram fibroblasts to myocytes to repair damaged adult hearts. His lab showed that introducing the genes for 3 transcription factors important for embryonic cardiac development resulted in an increase in the number of myocytes in a mouse heart after an induced heart attack. Similar results were obtained in vivo in pigs and in vitro in human cells suggesting that in vivo cellular reprogramming by gene therapy has broad implications for organ regeneration.
During embryogenesis, the heart needs to form a specific three-dimensional shape or a child will be born with a defective heart. Srivastava and his colleagues hope that by better understanding the molecular pathways involved in normal heart development, it will possible to improve treatments for both congenital and adult onset heart disease. In his first talk, Srivastava describes studies from his lab and others which use animal models and induced pluripotent stem cells to elucidate many of the gene networks that determine cardiac cell fate. iPS cells have been particularly important for identifying a mutation in the human transcription factor GATA4. By understanding the importance of GATA4 during heart development, it has been possible to develop a model that explains how cardiac specific genes can be activated while genes for other cell types are repressed.
By studying families with sleep/wake disorders, Fu and Ptáček have shown that mutations that cause changes in the phosphorylation or acylation of the PER2 protein are responsible for regulating circadian rhythms.
In Part 2 of the talk, Dr. Fu explains that studies of families with sleep disorders have shown that post-translational modifications of the PER2 protein are involved in regulating circadian rhythms. Casein kinase 1 phosphorylates PER2 and mutations in either CK1 or specific serine residues in PER2 result in an advanced sleep phase phenotype. O-GlcNAcylation of PER2 also participates in regulating circadian rhythms because O-GlcNAcylation blocks the sites usually phosphorylated by CK1.
By studying families with sleep/wake disorders, Fu and Ptáček have shown that mutations that cause changes in the phosphorylation or acylation of the PER2 protein are responsible for regulating circadian rhythms.
Ptáček introduces the circadian clock and its relationship to sleep. He describes different sleep-wake behaviors including people who go to sleep and awaken exceptionally early or late. By studying families with an advanced sleep phase (ASP) phenotype, he and his colleagues showed that these individuals had a shortened circadian period. Further studies of families with similar sleep-wake behaviors have identified a number of mutations responsible for circadian rhythm regulation.
In the second video, Dr. Duncan explains that the inner segment of photoreceptor cells, where proteins are made, and the outer segment, where light is transduced into a chemical signal, are joined by connecting cilia. Mutations in proteins that localize to the connecting cilia can lead to photoreceptor cell death and vision loss. In a number of syndromic diseases, such as Bardet-Biedl Syndrome, retinal degeneration is just one of several symptoms all of which are caused by mutations in cilia throughout the body. By identifying specific gene mutations causing retinal degeneration, Duncan hopes that better treatments for patients with these syndromes will be developed.
Cilia and flagella are complex, but highly conserved, structures found on most cells of the human body. Mutations in proteins localized to cilia can cause a collection of human diseases including renal failure and retinal degeneration. Dr. Marshall begins with an overview of the complex internal structure of cilia and flagella and the machinery, called intraflagellar transport (IFT), required to build and maintain these structures. Mutations in motile cilia were known to cause several human diseases but it wasn’t until scientists began studying IFT in the green algae Chlamydomonas, that the key role of non-motile cilia in human health and development was recognized. Marshall describes how mutations in cilia and basal bodies can cause human diseases as different as renal failure and retinal degeneration.
In the second lecture, Dr. Matthew State overviews the hunt for genes associated with autism and explains how studying de-novo rare mutations in the germline has advanced the understanding of the genetics of autism spectrum disorder (ASD). Studying a cohort of families with one affected individual and one unaffected sibling, they were able to map multiple genes involved in ASD. Because of the complexity of the developing brain, the same gene could act upon different regions of the brain at different times during development. Therefore, after identifying genes associated with ASD, they characterized the region and time during development where these genes are expressed and more likely to have an effect that is associated with ASD.
In the first lecture, Dr. Bryan King introduces the autism spectrum disorder (ASD) and defines the clinical criteria that characterizes ASD. Although there is no universal drug that is used to treat ASD, there are multiple medications used in the setting of autism. King outlines the different drugs used to treat the core behavioral features of autism as well as psychiatric disorders associated with autism (e.g. ADHD and anxiety), and discusses the challenges and problems with designing clinical trials to study drugs to treat ASD, specifically with the heterogeneity of the ASD population.
Asthma is a heterogeneous disease with varying degrees of airway inflammation and variable response to treatment with inhaled corticosteroids. Woodruff and Arron describe experiments to develop a biomarker to detect asthma subtypes and determine which patients are likely to benefit from anti-inflammatory treatments.
In the second lecture, Joe Arron reiterates the fact that asthma patients present with varying degrees of airway inflammation. Characterizing this heterogeneity objectively and consistently can be challenging. Arron describes how he and Woodruff, together with their collaborators, were able to determine that the serum level of a protein called periostin was a candidate predictive diagnostic biomarker for patients who might benefit from novel anti-inflammatory drugs including an IL13 inhibitor and an IgE inhibitor. Periostin is currently one of the biomarkers used to select patients for enrollment in clinical trials for two drugs candidates under development by Genentech.
Asthma is a heterogeneous disease with varying degrees of airway inflammation and variable response to treatment with inhaled corticosteroids. Woodruff and Arron describe experiments to develop a biomarker to detect asthma subtypes and determine which patients are likely to benefit from anti-inflammatory treatments.
In the first of these lectures, Prescott Woodruff explains that while asthma may be episodic in nature, it is a chronic disorder characterized by airway hypersensitivity and bronchial inflammation. Although asthma is a heterogeneous disease, treatment is typically based upon clinical severity rather than the underlying molecular phenotype. Woodruff describes how he and Dr. Arron and their colleagues were able to distinguish two distinct groups of asthma patients, one of with higher levels of T helper 2 cytokines and one with lower levels, by measuring specific gene expression patterns. Patients with different levels of Th2 cytokines responded differently to inhaled steroid treatment. This finding suggests that developing biomarkers that could indicate whether patients were Th2-high or low would help guide anti-inflammatory treatment.
Acute respiratory distress syndrome is a life threatening condition with few effective treatment options. Preliminary studies using mesenchymal stem cells, or stromal cells, to treat ARDS have shown promise with decreased levels of bacteria in the lungs, reduced pulmonary edema and improved oxygenation. In Part 1, Dr. Calfee begins by explaining that acute respiratory distress syndrome (ARDS) is pulmonary edema, or fluid in the lungs, not due to heart failure. It is a condition that affects 200,000 people/year in the USA with a 30-40% mortality rate. During ARDS, there are many cellular changes with complex pathophysiology making it extremely difficult to treat. Currently, patients are treated by ventilation with low tidal volume and fluid conservative therapy as many pharmacological interventions have failed. Mesenchymal stem cells (MSC), however, may hold promise as a treatment.
In Part 2, Dr. Matthay provides the rationale behind treating ARDS patients with MSC. Initial studies in a mouse model of ARDS, showed that treatment with MSCs increased levels of anti-inflammatory cytokines and antimicrobial peptides in the lung, and increased phagocytosis of bacteria by monocytes. Further studies in ex vivo perfused human lungs and in sheep with severe lung injury showed that treatment with MSCs improved oxygenation and reduced pulmonary edema. An NIH/NHLBI supported phase 1 clinical trial for safety has been completed and a randomized, blinded phase 2 trial has now been initiated to test the safety and efficacy of MSC treatment in human patients with ARDS.
Manu Prakash always yearned to know the why and the how of things. As a boy in India, he spent endless hours playing outside with animals and making flammable artifacts in an abandoned lab in the basement of his home. Having the chance to explore his surroundings with open-ended curiosity, he learned to find the sublime in the mundane. Today, as a world-renowned researcher and inventor at Stanford University, he continues to be inspired by these childhood lessons, and is creating low-cost tools to empower people around the globe to go on their own journey of science and discovery.
Rebecca Calisi Rodríguez’s research on pigeons, like her life, is one of charting an original path. Her experiences as a Mexican-Italian-American woman, professor, artist and mother have provided her with fascinating and unusual perspectives to study the biology of parental behavior. And in so doing, she is redefining what it means to be a scientist.
There is ample evidence that race can be a major factor in health outcomes. But racial and ethnic minorities are underrepresented in clinical and biomedical research. In this series, Dr. Esteban Burchard talks about the consequences of this underrepresentation and what does it mean for equity in research and medicine. He also explains how race is used by your doctor to make critical decisions about your health, and discusses what happens if you don’t fit neatly in one racial box, and how does this impact the medical treatment. Finally, Burchard discusses how scientific breakthroughs often come when problems are approached from different perspectives, and the importance of improving diversity and inclusion in science.
There is ample evidence that race can be a major factor in health outcomes. But racial and ethnic minorities are underrepresented in clinical and biomedical research. In this series, Dr. Esteban Burchard talks about the consequences of this underrepresentation and what does it mean for equity in research and medicine. He also explains how race is used by your doctor to make critical decisions about your health, and discusses what happens if you don’t fit neatly in one racial box, and how does this impact the medical treatment. Finally, Burchard discusses how scientific breakthroughs often come when problems are approached from different perspectives, and the importance of improving diversity and inclusion in science.
There is ample evidence that race can be a major factor in health outcomes. But racial and ethnic minorities are underrepresented in clinical and biomedical research. In this series, Dr. Esteban Burchard talks about the consequences of this underrepresentation and what does it mean for equity in research and medicine. He also explains how race is used by your doctor to make critical decisions about your health, and discusses what happens if you don’t fit neatly in one racial box, and how does this impact the medical treatment. Finally, Burchard discusses how scientific breakthroughs often come when problems are approached from different perspectives, and the importance of improving diversity and inclusion in science.
In her third lecture, Zoghbi explores possible therapies for MECP2 disorders. First, using Deep Brain Stimulation (DBS), Zoghbi’s team together with collaborator Dr. Jianrong Tang were able to rescue learning and memory deficits, enhance neurogenesis, correct abnormal neural network activity, and improve MeCP2-linked gene expression changes in a mouse model of Rett Syndrome. Then, she discusses two approaches to normalize the MeCP2 protein in MECP2 duplication mice: by deleting the duplicated MECP2 gene in the genome, or by decreasing MECP2 mRNA levels using antisense-oligonucleotides. Even though these two approaches seem to rescue developmental issues caused by MECP2 duplication, titrating MeCP2 levels is required in order to avoid Rett-like symptoms caused by lowering the protein too much.
In her second lecture, Zoghbi explains how MeCP2 molecularly modulates neuronal function. Their studies uncovered a critical link between cytosine methylation, MeCP2, and the methylating enzyme Dnmt3a, in Rett Syndrome. They hypothesized that MeCP2 partially causes Rett-Syndrome symptoms by failure of reading methylated DNA marked by Dnmt3 and indeed showed that Dnmt3-dependent mCH plays a central role in Rett pathogenesis.
Dr. Huda Zoghbi’s work has provided insight into Autism Spectrum Disorders (ASD) by focusing on Rett Syndrome, a postnatal progressive neurological disorder. By studying the genetics of Rett Syndrome, her group made the seminal discovery of X-linked Methyl CpG-binding protein 2 (MECP2) as the gene that causes Rett Syndrome. Zoghbi’s group showed that the severity of the disease was highly dependent on the amount of functional MeCP2 protein expressed. Females, who carry one normal and mutant MECP2 allele typically suffer from Rett syndrome, but the amount of functional protein is influenced by X-chromosome inactivation, and girls with more cells expressing normal allele have milder features. Surprisingly, they also showed that duplications spanning MECP2 can cause a Rett-like progressive neurological disease, highlighting the importance of MeCP2 levels for neural functions. Zoghbi describes how these findings have spurred new research into how MeCP2 affects postnatal development and brain function.
Witkin provides a historical perspective on how working at Cold Spring Harbor (CSH) shaped her scientific career and led to the discovery of the SOS DNA damage response in bacteria. At CSH she worked with the pioneers of bacterial genetics, at a time when there was a major discovery every other week. As a PhD student Witkin observed that some bacteria were able to survive high doses of UV radiation. She speculated that these bacteria may have a mechanism to repair DNA making them UV resistant. These revolutionary ideas gave birth to the discovery that cells have a mechanism to repair DNA damage, the SOS response.
Dr. Chris Voigt explains that, for 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 genetic circuits, and the DNA can be synthesized and inserted into a cell. Voigt’s lab has successfully built and tested genetic circuits in many cell types to make many products.
Vale explains how doing science often follows a winding path with unexpected, sometimes wonderful surprises, and uses his own story to illustrate his point. When Vale was a graduate student, he initially hoped to show that myosin was involved in axonal transport, but ended up discovering a new molecule which he called kinesin.
As the COVID-19 pandemic escalated in the beginning of 2020, there was a need for the rapid dissemination of scientific information to understand everything from how the virus spreads, to how it affects the human body, to how the disease can be treated and prevented. Jessica Polka, Executive Director of ASAPbio, explains that, for this reason, the pandemic has inspired an increasing number of scientists to post their research papers on preprint servers. Publishing papers in traditional journals with formal peer review can take a lot of time. Posting manuscripts on preprint servers, on the other hand, can happen quite fast. But, considering that preprints do not undergo formal peer review before they are posted, is this prudent? Dr. Polka talks about how preprints experience their own crowd-sourced, informal peer review process through public commentary on social media and other venues by scientists and other experts, and this discourse can actually improve the quality of the paper over time. A major caveat of preprints is the potential for the media and the public, who may not be aware of the provisional nature of preprints, to disseminate erroneous or inaccurate information, and so, this requires proper education and training on what preprints are and how to interpret them.
Dr. Jan van der Meer begins by giving an introduction to synthetic biology. Through this introduction to synthetic biology, 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. For example, a simple system of a bacterial cell, which glows in the presence of arsenic, can be used to test drinking water in Bangladesh for high levels of arsenic.
In the cytoplasm of cells, thousands of tightly packed molecules and structures execute the numerous processes necessary to maintain life. Although there are many ways to study cellular processes, one of the simplest ways to understand the different parts of a cell is to visualize them. Dr. Sven Truckenbrodt sought to better understand the machinery of the neuronal synapse using fluorescence microscopy, yet he was limited by the physical properties of light. To circumvent the 250-nm resolution limit imposed by the photophysics of light waves, Truckenbrodt developed X10 expansion microscopy, based on the original concept of expansion microscopy invented in the Boyden lab. By uniformly expanding the volume of tissue by a thousand-fold using synthetic polymers (the same as those found in baby diapers!), this approach increases the distance between closely packed proteins, allowing them to be visualized with fluorescence microscopy. Truckenbrodt shares the story of the first time he used X10 expansion microscopy to clearly image synaptic vesicles, after studying them for years as a neuroscientist! He describes how he used X10 microscopy to characterize the precise localization of synaptic and cytoskeletal proteins that previously could not be visualized in detail. Truckenbrodt ends his talk by sharing how the X10 approach has been used by other research groups and encourages his viewers to consider applying this method in their own research to make new discoveries.
In his last lecture, Singer continues the story of the life and death of RNA. His lab has developed several more fluorescence microscopy techniques that let them study, in real time, the translation and degradation of mRNA. These techniques allow them to track when and where translation begins, how quickly a ribosome binds to a mRNA once it has reached its destination, how long the ribosome stays bound and how rapidly it adds amino acids to a growing protein chain. In addition, these techniques can be used to unveil the dynamics of RNA degradation. In an interesting twist, it turns out that for mRNAs that must be degraded during the cell cycle, their fate is decided at the time of their birth.
To understand the relationship between RNA localization and translation, it is necessary to visualize the movement of the RNA in real time. In his second lecture, Singer explains how his lab found an ingenious way to label RNAs in live cells and follow their movement. In the nucleus, RNA moves by diffusion and stochastically finds a nuclear pore to exit. In the cytoplasm, however, it is a different story. RNA, in a translationally repressed state, undergoes directed movement along the cytoskeleton. Once it reaches its destination, translation is activated. Singer’s lab showed that neuronal stimulation leads to ß-actin mRNA localization to dendritic spines, followed by translation, and stabilization of the synapse; events that are crucial for memory and learning.
In this series of lectures, Dr. Robert Singer explains how it is possible to follow a single mRNA molecule from its birth to its death. Singer begins by explaining that cell cultures are heterogeneous and analyzing single cells provides spatial and temporal information not available from bulk analysis. He outlines how his lab developed techniques such as fluorescence in situ hybridization (FISH) that have allowed them to measure gene expression in single cells. Using these techniques, they discovered that some RNAs localize to specific areas in the cell and RNA localization is linked to its regulation and function. For example, ß-actin mRNA localization to the leading edge of fibroblasts aids in cell motility. Singer’s lab identified “zip code” regions in mRNAs that are responsible for regulating mRNA localization.
In his second talk he reviews makeup of the plant cell wall and how hemicellulose, cellulose, and lignin can be broken down for use in aviation biofuel production. He describes the Joint BioEnergy Institute (JBEI) approach to maximize carbon efficiency at every step in the production of biofuels, from developing and feedstocks, deconstructing biomass, and use of microbes and enzymes to generate target intermediates for fuels. A major part of optimizing this process is the development of a one-pot process, in which conversion of biomass to fuel can be achieved in a single chamber.
Biofuels have been around for decades, but interest in them has grown considerably in recent years due to climate change. While they have the potential to provide a sustainable and renewable way to power our transportation systems, Dr. Blake Simmons points out that in order to become a viable replacement for fossil fuels, biofuels must also be efficient and affordable at global scales. In his first talk, he provides an overview of the advantages of using biofuels and walks through the biochemical processes required in order to convert biomass into usable fuels. He also discusses the ideal properties for advanced biofuels, the projected markets for these fuels in the coming years, and some of the key challenges associated with optimization of advanced biofuel production.
There are many career options open to PhD scientists, however it can be difficult to determine which career is right for you. In a series of talks, Dr. Alexandra Schnoes describes how internships for graduate students and postdocs might be a good way to explore careers and help make an informed career decision. She discusses the benefits of internships and how a graduate student or postdoc might go on one. She covers the basics of finding and applying for internships. She also talks about the process of talking to your advisor about going on an internship, and how to get the most out of your internship experience when you are on it.
There are many career options open to PhD scientists, however it can be difficult to determine which career is right for you. In a series of talks, Dr. Alexandra Schnoes describes how internships for graduate students and postdocs might be a good way to explore careers and help make an informed career decision. She discusses the benefits of internships and how a graduate student or postdoc might go on one. She covers the basics of finding and applying for internships. She also talks about the process of talking to your advisor about going on an internship, and how to get the most out of your internship experience when you are on it.
In his Part 3, Rutter emphasizes the challenge of mitochondrial protein synthesis. How do the components of the electron transport chain (ETC) assemble in the right stoichiometry at the right time? Rutter introduces the LYR family of proteins, which aid assembly of ETC components. LYR proteins interact with a common binding partner, the acyl carrier protein (ACP), via a unique fatty acyl moiety on ACP. Rutter’s group showed that ACP acylation is necessary for assembly of the ETC and activation of oxidative phosphorylation.
In Part 2 of his talk, Rutter describes his group’s work to unravel the relationship between the activity of the Mitochondrial Pyruvate Carrier (MPC) and the behavior of numerous cell types, including cancer and stem cells. His group found that forced expression of the MPC in multiple stem cell models led to reduced “stemness” and proliferative capacity, and that MPC inhibition could promote organoid formation in culture and tumor formation in vivo. These data indicate an important link between mitochondria, metabolism, and cell behavior.
Mitochondria are integral to the metabolism of eukaryotic cells, yet many of their properties are not fully understood. In Part 1 of this iBioSeminar, Dr. Jared Rutter lays out the foundational knowledge of mitochondrial structure and origin, and shares what is currently known about mitochondrial roles in metabolism, protein homeostasis, and signaling. He ends by highlighting a focus of his research group: to unravel the functions of uncharacterized mitochondrial proteins.
Part 2: Rooney-Varga discusses the need for integrating climate change into biology education and why it can be difficult to understand and teach. She explains that introducing simulation-based role-playing games to students is an effective and fun way to teach how decisions and actions taken today will impact climate change in the future.
Part 1: Rooney-Varga explains that a holistic, systems thinking approach is necessary to understand human-caused climate change. Systems thinking concepts that are critical to climate change science include the accumulation of atmospheric stocks of greenhouse gases, feedback processes that amplify or dampen the impacts of climate change, abrupt nonlinear change, and the delayed impacts of today’s actions, such as emissions today that will influence the climate for millennia.
This is the story behind the discovery of polynucleotide hybridization. In the early 1950s, the double helix structure of DNA had just been published, however, the structure of RNA was still unknown. Alexander Rich and his colleagues were investigating this question without much success until Rich combined polyadenylic acid and polyuridylic acid and, to his amazement, saw the diffraction pattern of a double helix. He realized that the base pairs had undergone hybridization to form a double stranded RNA structure. In the intervening 60 years, hybridization has become the foundation of much of modern biotechnology.
Many animals are able to regenerate following injury, some better than others. Dr. Reddien uses Planaria as a model system to investigate the cellular and molecular mechanisms that drive regeneration. RNAi makes it possible to inhibit specific genes in Planaria and follow the effects on protein expression and regeneration. Using this methodology, Reddien’s lab identified the notum gene as a regulator of the wnt signaling pathway for determining appropriate head or tail regeneration.
In his second talk, Peters presents evidence that cohesin is indeed necessary for genomic DNA to fold into loops. Long range DNA interactions such as loops can be detected using a technique called Hi-C. Using Hi-C, Peters shows that depleting cohesin removes DNA loops, while depleting the proteins that remove cohesin from DNA, results in bigger DNA loops. In addition, CTCF appears to recognize specific sequences that define the base of the loops. Incorporating all of this data, Peters describes a model in which DNA is extruded by cohesin to form a loop and the boundaries of the loop are determined by CTCF. Peters explains that many questions about the mechanism of DNA loop extrusion and its importance in cells remain to be answered.
It has been known for many years that the protein cohesin is necessary to join sister chromatids together before they are segregated during mitosis. Electron micrographs have shown that cohesin subunits form a ring complex which is thought to encircle the DNA keeping the chromatids together. When they need to separate during anaphase, the cohesin complex is removed by another set of proteins. In his first talk, Dr. Peters explains how observations that he and others made suggested that cohesin may have additional roles in the cell. For instance, cohesin is initially loaded onto chromosome arms at discrete sites and in much larger amounts than is needed for chromatid cohesion. Cohesin also was shown to co-localize on chromosomes with a DNA binding protein called CTCF. CTCF is known to regulate transcription by forming DNA loops. Peters explains that, taken together, these observations hinted at a role for cohesin and CTCF in folding DNA into loops to allow efficient packing of very large eukaryotic genomes into small cell nuclei, and regulating functions such as gene expression.
In his third talk, Patel explores the function of additional Hox genes in the development of crustacean body plans. Using CRISPR-Cas9 genome editing, his laboratory has characterized the expression and function of six of the nine Hox genes in Parhyale, and describes the combinatorial role of Ubx, abdA, and AbdB in the development of specialized appendages in this species, and how changes in the regulation of abdA is responsible for several morphological transitions during crustacean evolution.
In the second lecture, Patel describes the work of his lab to expand the studies of Hox gene function to other arthropods. Patel describes the development of specialized body parts in crustaceans, and describes the transition between feeding to locomotor appendages. Using the beach hopper, Parhyale, his laboratory, in collaboration with the laboratory of Michalis Averof, showed that Ubx controls the boundary and transition between feeding and locomotor appendages during development.
Homeotic (Hox) genes are transcription factors that dictate the development and compartmentalization (regionalization) of body parts in animals along the anterior-posterior (head to tail) axis. Using various insects and crustaceans, Dr. Nipam Patel studies how alterations in the expression of Hox genes could explain the evolution of specialized body parts in arthropods. Patel describes the spatially restricted patterns of Hox gene expression, explains the effects of Hox gene deletions, and how these phenotypes help us understand the manner in which Hox genes act to control the insect body plan. Taking a closer look at the pattern of the Hox gene Ultrabithorax (Ubx) in different insects, Patel summarizes the discovery that what drives changes in the number of wings during insect evolution is the not changes in the expression pattern of Ubx, but the regulation of its downstream gene targets.
Dr. Vivek Mutalik highlights current challenges in synthetic biology and explains some of the solutions being implemented to address them. 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 the development of standardized parts with predictable behaviors, robust methods of biocontainment and software that allows data sharing and visualization.
In her second seminar, Parast explains the different models to study human placental development in-vitro. Scientists can derive induced pluripotent stem cells (iPSCs) from umbilical cord cells. Parast’s laboratory first differentiates the iPSCs into trophoblasts cells which can then generate the different cells found in the placenta. Her laboratory uses these placental cells to study developmental complications by comparing cells derived from normal pregnancies to cells derived from non-normal pregnancies (e.g. patients born from mothers with pre-eclampsia).
Dr. Mana Parast provides an introduction to placental development, the organ that every mammalian embryo needs for proper growth and development. The placenta derives from trophoblasts, embryonic cells located in the outermost layer of the embryo. Pre-eclampsia and other maternal factors can hinder placental development and therefore affect the development of the fetus. A better understanding on how defects associated with pregnancy disorders affect placental development could lead to novel therapeutics in the future.
What is the consequence of obesity in human health? Physically, obesity can result in lower mobility and sleeping disorders. But, in humans, the link between obesity and metabolic diseases isn’t straightforward. For example, not everyone that’s obese becomes insulin resistant. As O’Rahilly explains, the probability of an obese individual to have a metabolic disease is linked to the capacity of adipose tissue to store the extra fat. Mutations that decrease fat storage in adipose tissue increase the chance of metabolic diseases, like insulin resistance, even when the person is not obese.
Easy access to nutrients has contributed to the increase in obesity in the human population. But, what is obesity and why isn’t everybody fat? Dr. Stephen O’Rahilly provides a biomedical perspective of obesity, and evaluates which genes could potentially shift the balance towards obesity. As he explains, one becomes obese when the balance between energy intake and energy spent is shifted. Surprisingly, mutations that lead to obesity in humans aren’t in genes involved in metabolism and energy storage, but failure in satiety signals in the brain that result in people eating too much. The excess of energy intake over energy expenditure leads to obesity.
The severity of malarial disease is influenced by interactions between the parasite, the host and environmental factors. In her third talk, Mota explains how her lab used a mouse model to study the impact of host nutritional status on disease severity. When they compared infections in calorically restricted (CR) mice and freely fed mice, they found less reproduction of the malaria parasite and a lower parasite load in CR mice. This suggested that Plasmodium are able to sense and respond to host nutritional status. Mota describes how her lab identified a key Plasmodium kinase, KIN, that seems to regulate parasite response to nutrient availability and may provide a target for antimalarial drugs.
In Part 2, Mota goes into more depth about the liver stage of malaria infection. She reminds us that when Plasmodium parasites are transferred by a mosquito bite, they first travel to the liver. Once inside of a hepatocyte, a single malaria parasite will replicate and give rise to over 10,000 new parasites that go on to infect red blood cells and cause disease. For many years, this stage was called the silent stage as it was thought that malaria parasites were not detected by the host while in the liver. Mota tells us about data from her lab, and others, showing that the host innate immune response is, indeed, activated during hepatocyte infection. This immune response may play a role in modulating the host’s response to the blood-stage infection or future re-infection.
Malaria is currently responsible for about 500,000 deaths per year and is especially fatal to children under the age of 5 years. Two global eradication programs since 1950 have reduced the malaria burden significantly, however, progress has stalled in recent years. In her first talk, Dr. Maria Mota details the lifecycle of two malaria parasites, Plasmodium falciparum and P. vivax. The complex, multistage lifecycle makes it hard to diagnose and treat malaria. Mota explains that many attempts have been made to treat the disease with drugs but the malaria parasite very rapidly develops resistance. She describes how the recent development of drug combinations and a new vaccine, together with insecticide treated bed nets and improved early diagnosis, provide hope for better prevention and treatment of malaria in the future.
Almost every person in the world has been bitten by a blood feeding insect or arthropod, such as a mosquito or tick. Yet, most of us haven’t thought much about arthropod saliva. The molecules found in the saliva of blood feeders play a role in disease transmission and immune recognition. Therefore, it is important to better understand what makes up arthropod saliva. Dr. Mondragon-Shem begins her seminar by describing the phenomenon of red meat allergy, and how it was historically linked to tick bites. She then shares her research findings that confirm the presence of alpha-Gal sugar, the immunogenic molecule that leads to red meat allergy, in tick saliva. Her studies also identified protein candidates that are likely linked to alpha-Gal in tick saliva. Dr. Mondragon-Shem finishes her talk by describing how she has characterized the sugar molecules in the saliva of six species of blood feeding arthropods. This work has implications for better understanding disease transmission and immune recognition.
In 1953, Watson and Crick proposed a double-helical structure for DNA and suggested that it replicated in a semi-conservative manner. This method of replication was not universally accepted as correct, however. In this talk, Meselson recalls the events that led him to meet Frank Stahl and to plan and execute the now famous experiment proving that DNA does indeed undergo semi-conservative replication.
In her second talk, Lehmann focuses on the establishment of the dichotomy between somatic and germ line fate. She explains how Drosophila germ cells develop to become so different from the somatic cells that make up the rest of the embryo. Germ cell development depends solely on maternal transcripts from the egg, while development of the soma depends on new zygotic transcription. Lehmann describes how two different molecular strategies, precise spatially controlled protein degradation and complete interference with the mRNA transcriptional elongation process, are employed to prevent somatic differentiation, thus allowing germ cell specific gene expression to occur.
Very early in embryogenesis, germ cells, the cells that give rise to egg and sperm, are set aside from the somatic cells which give rise to the rest of the cells in our bodies. While germ cells are not necessary for survival of the individual, they are crucial for survival of the species. In her first talk, Dr. Ruth Lehmann explains that there are two mechanisms by which germ cells are specified in the early embryo; via germ plasm or via induction. Germ cells specified via either mechanism have in common the presence of germ granules; large, membraneless, ribo-nuclear particles. Interestingly, certain families of RNA regulatory proteins are conserved in germ granules across species. Lehmann describes work from her lab and others on the life cycle of germ granules in Drosophila, including how they are assembled, their interesting biophysical properties and how proteins and RNAs are organized within the granules.
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 of the dynamic cell behaviors that allow for proper growth and development of the embryo.
Corn is the backbone of the American food supply. Yet, about 10% of corn (equal to a field as big as the entire state of Florida!) is lost to disease and other types of crop stress each year. How can we make corn and other crops hardier so that we can grow more food, using less land and other resources? In her thesis research, Katie Murphy studies the synthesis of biochemicals produced by corn that help it survive stressful conditions such as drought and disease. She and her colleagues identified a new class of biochemicals called dolabralexins and showed that corn roots produce these molecules in response to drought and fungal infection, two common types of crop stress. She also determined that synthesis of dolabralexins and other terpenes influences the root microbiome of corn plants. Finally, Murphy’s work showed that dolabralexins have direct antifungal properties and identified the functional groups on dolabralexins that are necessary for this function. These findings may help scientists develop stress-resistant crops so that we are better equipped to feed a growing global population.
In his second talk, Kriegstein provides an overview of the use of cerebral organoids to study brain development and disease. Cerebral organoids are models that can be produced from induced pluripotent stem cells. Although organoids can contain the same broad categories of cell types found in the brain, organoids lack the structural, layer-like organization observed in the primary tissue. In addition, the gene expression profile is different between organoids and primary brain tissue. Nevertheless, although organoids do not reproduce all of the features of a developing human cortex, organoids can be a powerful model to study neuronal diseases and evolution, particularly when studying cells that cannot be found in animal models (e.g. oRG cells) or when scientists do not have access to primary brain tissue.
How do neurons develop to confer humans their unique brain functions? Dr. Arnold Kriegstein compares and contrasts the development of neurons from radial glial cells (RGCs) in mice and humans. In mice, RGCs give rise to most of the central nervous system’s neurons and glia and provide scaffolding for neurons to migrate. In contrast, human RGCs give rise to a unique set of cells, the outer subventricular zone radial glia (oRG) cells, which divide via mitotic somal translocation (MST). The oRG cells predominantly produce and guide the migration of the upper layer cortical neurons. Although rodents have oRG-like cells, these cells are more abundant in humans, and contribute to the large size of the human brain and possibly its unique function.
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.
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.
Scientists 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.
Matt Meselson and Frank Stahl were in their mid-20s when they performed what is now recognized as one of the most beautiful experiments in modern biology. In this short film, Matt and Frank share how they devised the groundbreaking experiment that proved semiconservative DNA replication, what it was like to see the results for the first time, and how it felt to be at the forefront of molecular biology research in the 1950s. This film celebrates a lifelong friendship, a shared love of science, and the serendipity that can lead to foundational discoveries about the living world.
In her third talk, Dr. Huber describes how a method known as RNA stable isotope probing (SIP) was used to characterize the metabolically active autotrophic microbes at an underwater vent at Axial Seamount. Dr. Huber’s group found that temperature influences the metabolic pathways, including the carbon fixation pathways, used by different organisms collected at the same vent. In addition, Dr. Huber’s group compared microbial activity across three vents and found that all three have different microbes that are active in a similar temperature environment. These findings suggest that subseafloor microbes prefer some environments over others and use different metabolic pathways in different environmental contexts.
In her second talk, Dr. Huber describes her research, which integrates microbiology, molecular biology, and ocean sciences approaches to characterize the microbial ecosystem below Axial Seamount, an underwater volcano off the coast of Oregon. Dr. Huber outlines how her group used environmental DNA and RNA sequencing techniques to analyze the crustal fluids (mix of ocean water & hydrothermal vent fluid) leaking from underneath the sea floor at three deep-sea vents. Her group determined that the metabolic potential of organisms was similar across vents (as indicated by DNA sequencing) but that there were larger differences in the “activity” of the microbes across vents (as indicated by mRNA profiling). Furthermore, Dr. Huber’s group identified vent-specific subseafloor microbial populations.
A mile or more below the surface of the ocean, microbes dominate the deep sea life. In this seminar, Dr. Julie Huber describes her research to better understand the microbial ecosystem in the rocky crust below the ocean floor. She begins the series by describing how reactions between seawater and the elements in ocean rocks enable chemosynthetic ecosystems to exist in the deep sea. She then introduces us to the tools scientists use to study microbial deep sea life below the ocean floor.
Hastings hypothesizes that luciferases, and thus bioluminescence, evolved as a mechanism to protect bacteria from oxidative damage as the Earth’s atmosphere became oxygenated 2.5 billion years ago.
In the late 1960s, Hastings was studying bioluminescence in the marine bacteria Vibrio fischeri. He and his post-doc, Kenneth Nealson, discovered that bacteria could communicate by secreting a small peptide. This allowed V. fischeri to sense the concentration of their fellow bacteria and, when the density reached a critical level, turn on bioluminescence. Hastings named this process autoinduction, also known as quorum sensing. Quorum sensing has since been shown to play a critical role in bacterial behaviors such as toxin production and biofilm formation.
In his second part, Hasson explores how the ability of the storyteller to be coupled to and shape the neural responses of listeners is used as a tool to share memories across brains. Furthermore, the studies reveal the tight connections between remembering and imagining and expose the ways by which the storyteller’s perspective shape the audience point of view.
How does your brain change with each story that you hear? How can storytelling shape your memories? In this talk, Dr. Uri Hasson explores how brain activity is shared between listeners of the same story, and how those shared neural responses are coupled to and shaped by the neural activity in the storyteller’s brain. In his studies, Hasson observed higher coupling between listener’s and storyteller’s neural activity as a function of the ability of the listener to understand the story. As Hasson explains, efficient communication occurs when the storyteller’s and listeners’ brain responses are coupled.
Dr. Leland Hartwell started his scientific career studying a fundamental question in biology: how do cells know that they have everything they need in order to divide. By studying the morphology of temperature sensitive mutants in yeast, Hartwell identified many of the key regulators of the cell cycle. In this conversation, Hartwell talks to Dr. Sue Biggins about his Nobel Prize winning discoveries and the experiments that led to his seminal findings.
In his second talk, Haber explains in greater detail the molecular steps that take place during the repair of a DNA double strand break. It turns out that the process of mating type switching in S. cerevisiae requires site-specific cutting and repair of a yeast chromosome and this is an excellent model for studying DNA DSB repair. Working in this system and using techniques such as Southern blots, PCR and chromatin immunoprecipitation, Haber’s group was able to identify the proteins and enzymatic steps in DNA repair.
Dr. Haber begins his talk by explaining that broken chromosomes frequently arise during the process of DNA replication. In healthy cells, these double strand breaks (DSBs) are repaired by homologous recombination, an orderly process that preserves the genome. If the homologous recombination machinery is impaired, DNA truncations, translocations, and deletions often occur, resulting in genome instability and cancer. All mechanisms of homologous recombination have one common principal; the broken ends of the DNA are repaired by base pairing with a sequence that is identical or nearly identical and acts as a template for repair enzymes. Haber explains the general principles of homologous recombination and its critical role in maintaining genome stability.
In his second presentation, Haas shares an example of how cryocrystallography has aided structure-based drug design.
In his postdoctoral studies, David Haas set out to reduce radiation damage to protein crystals during X-ray crystallography. In 1970, he published a paper on his invention of macromolecular cryocrystallography – freezing crystals to extend their lifetime in the X-ray beam. The widespread use of the synchrotron beginning in the 1970s made cryo-cooling essential, and today nearly all protein crystal structures deposited in the international Protein Data Bank use this method.
In her second talk, Glaunsinger explores gene expression control by viruses like Kaposi’s sarcoma herpesvirus (KSHV), a frequent cause of cancer in AIDS patients. KSHV stimulates degradation of mRNA by encoding a nuclease, SOX, which is able to target a broad set of mRNAs for degradation yet cleaves them at specific sites recognized by a combination of RNA sequence and structure. Glaunsinger then describes how widespread mRNA degradation by viral nucleases such as SOX causes redistribution of RNA binding proteins in the cell and restricts mRNA transcription by RNA polymerase II. Thus, alterations to the rate of mRNA decay can have ripple effects in the cell that influence upstream events in gene expression.
Dr. Britt Glaunsinger provides an overview of virology, and describes how the study of viruses has guided the understanding of many fundamental cellular processes, from gene expression to cancer. These insights arise from studying how viruses manipulate and hijack cellular machinery during infection and viral replication. Viruses can use the host machinery to their advantage, altering the gene expression landscape of the cell to create an environment favorable for the infection to progress. As Glaunsinger explains, one way viruses alter gene expression is by affecting the messenger RNA (mRNA) degradation process. By increasing decay of cellular messages, viruses can decrease competition for access to the translation machinery and dampen the expression of immune stimulatory elements that restrict viral replication.
Coral reefs are a vital global ecosystem: despite comprising only 1% of the world’s oceans, they support more than 25% of marine life. In addition to supporting ocean life, coral reefs also support the survival of humans by providing habitat for fish and other seafood and protecting coastlines from erosion. Corals are complex organisms that rely on a symbiotic relationship between the coral animal, zooxanthellae algae, and microbes. To date, the role of the coral microbiome in coral health and disease hasn’t been extensively studied. In this Young Scientist Seminar, Maite Ghazaleh Bucher describes her thesis research at the University of Georgia in which she characterized the microbial communities of sick and healthy corals colocalized in the Florida Keys Reef during a disease outbreak in summer 2017. Using genetic analyses, Bucher found that the coral microbiome is relatively uniform in healthy corals, even among different coral species. In contrast, she found that the microbiomes of diseased corals are dissimilar, even among corals affected by the same disease. These data support an “Anna Karenina” hypothesis for the coral microbiome. In the second stage of her research, Bucher determined that the microbial communities of apparently healthy coral tissue on diseased corals exhibited an imbalance between “healthy” and “unhealthy” microbes. This finding could lead to a quantitative way to monitor the health of corals based on their microbial signatures. Bucher ends her talk with a call to action: we all have the power to reduce our impact on the planet, so that vital ecosystems like coral reefs can be protected. What can you do to support the survival of corals?
Squamous cell carcinomas (SCCs) are commonly occurring, dangerous cancers that may originate from skin stem cells. By developing methods to identify the stem cells that will lead to cancer, Fuchs’ lab has been able to study how these cells differ from normal skin stem cells. They found that the gene expression profile in normal versus cancer stem cells is very different and is likely the result of differences in the cancer stem cell niche. The tumor microenvironment may include immune cells and greater proximity to TGF-beta secreting blood vessels. Fuchs’ lab showed that cancer stem cells exposed to TGF-beta had increased expression of proteins in the glutathione metabolism pathway; the same pathway which is involved in the breakdown of chemotherapy drugs. Further studies in SCC patients, showed a strong correlation between increased mRNA levels for glutathione pathway proteins and decreased survival. These results suggest that drugs which block TGF-beta activity, in combination with other chemotherapeutics, may be an effective therapy for some SCC.
In her second talk, Fuchs focuses primarily on studies of adult skin stem cells. Adult stem cells have the ability to make more stem cells and to generate the cells of a differentiated tissue. Skin stem cells can replenish the epidermis and make hair follicle cells. Skin grown in culture from just a few skin stem cells can be used to treat burn patients or replace damaged corneal epithelium. Stem cells reside in specific niches or microenvironments and signals from the niche determine whether a stem cell is going to be quiescent or make tissue. Fuchs’ lab has studied hair follicle stem cells for many years and has identified the signals that activate hair follicle stem cells as well as the specific set of transcription factors that are upregulated in the activated stem cells. They have shown that many of the genes turned on during stem cell activation are regulated by super enhancers which sense the niche environment.
Dr. Fuchs begins her talk with a brief history of stem cells including the discovery in the 1970s that adult skin stem cells could be cultured in vitro indefinitely. This early work provided the foundation for later advances in embryonic stem cell (ESC) culture. ESCs are special because they can generate all the different tissues of the body, thus providing great potential for use in regenerative medicine. The use of ESCs is controversial, however, so scientists have developed ways of generating pluripotent stem cells that do not use embryonic tissue. Fuchs reviews methods such as nuclear transfer and the generation of induced pluripotent stem cells (iPSCs) by reprogramming adult somatic cells. Cells generated by these methods may be used for drug and therapy screening and they may provide treatments for human diseases such as macular degeneration, Parkinson’s and other degenerative diseases.
A horrific fungal disease called White Nose Syndrome began to cause massive mortality of small brown bats in the Northeastern United States in 2006. Dr. Frick explains that she and her colleagues used historical data from bat censuses and recent mortality data to model possible outcomes for bat populations in this region. Sadly, their data indicate almost certain regional extinction for the bats unless this disease can be stopped. This work was done in Dr. Thomas Kunz’s lab at Boston University. Dr. Frick is currently an Assistant Adjunct Professor of Ecology and Evolutionary Biology at the University of California, Santa Cruz.
This talk is a supplement to the annotated primary literature paper found in the American Association for the Advancement of Science’s (AAAS) Science in the Classroom Project.
A horrific fungal disease called White Nose Syndrome began to cause massive mortality of small brown bats in the Northeastern United States in 2006. Dr. Frick explains that she and her colleagues used historical data from bat censuses and recent mortality data to model possible outcomes for bat populations in this region. Sadly, their data indicate almost certain regional extinction for the bats unless this disease can be stopped. This work was done in Dr. Thomas Kunz’s lab at Boston University. Dr. Frick is currently an Assistant Adjunct Professor of Ecology and Evolutionary Biology at the University of California, Santa Cruz.
In their final talk, Walther and Farese explain how proteins are targeted specifically to the surface of lipid droplets. This has functional consequences since proteins at the surface of lipid droplets govern lipid droplet growth and hydrolysis, and some of these proteins are associated with diseases. Farese and Walther end their talk by describing a number of diseases or physiological conditions that are now recognized as resulting from mutations in genes encoding proteins involved in lipid droplet formation.
In Part 2, Walther and Farese explain in more depth how lipid droplets form in cells in an organized manner. Triglycerides and other neutral lipids are made in the ER membrane. They accumulate in localized regions of the membrane that grow towards the cytosol and eventually bud off into lipid droplets. Farese and Walther describe experiments from their lab and others that have identified a protein complex in the ER membrane called LDAF1/Seipin that regulates where triglycerides localize and grow into mature lipid droplets.
All life requires metabolic energy but energy supplies and demands change over time. For this reason, organisms have developed ways to store energy, predominantly as fat. Neutral lipids are packaged into lipid droplets, small organelles found in most eukaryotic cells and in some prokaryotes. Lipid droplets play a critical role in an organism’s physiology; too many lipid droplets can result in obesity and too few in metabolic disease. In their first video, Drs. Farese and Walther introduce us to lipid droplets and explain their importance in cellular biology.
DNA synthesis that occurs during repair is much less accurate than normal DNA replication. Using the yeast mating type switching system, Haber’s lab identified base pair substitutions, frame shifts and other mutations that occur when the newly synthesized strand dissociates from the template strand during homologous recombination. Interestingly, Haber found that sometimes the newly synthesized strand will “jump” to a related but divergent template, even on another chromosome, and then jump back to complete the repair. Further experiments showed that this happens because the repair polymerase falls off the template with a very high frequency. Understanding why this occurs may help us to decipher the complex chromosomal rearrangements associated with certain human diseases.
Esvelt’s second talk focuses on strategies to allow for the safe implementation of localized gene drive technologies that do not spread indefinitely. Daisy drive systems are made up of multiple elements connected like a daisy chain such that each causes the next to be preferentially inherited. They are designed to be self-exhausting by losing elements with each generation, thereby limiting spread. This technique has multiple applications such as removing an invasive species from one area without impacting the same species in its native habitat. Esvelt explains that daisy-drive stability might be tested in a species such as C. elegans where hundreds of generations can be grown in a short period of time. His lab is also developing technologies to reverse any unwanted genetic changes that might be introduced via gene drive. Once again, Esvelt emphasizes the importance of community input into any gene alteration projects. Although it does not currently involve gene drive, he uses the “Mice Against Ticks” project that seeks to prevent tick-borne diseases on the islands of Nantucket and Martha’s Vineyard as an example.
Evolution has selected wild organisms to be extremely well adapted to their environment. Because most genetic changes introduced by humans divert the resources of the organism to benefit humans, such mutations are typically eliminated by natural selection in the ancestral habitat. In his first talk, Dr. Kevin Esvelt explains how self-propagating CRISPR-based gene drives can be used to spread genetic alterations through wild populations, potentially impacting all organisms of the target species. Gene drives could be used to benefit public health, the environment, agriculture, and animal well-being. However, real-world use may incur ecological risks, and even research involving self-propagating gene drive systems may risk public trust in science and governance given the possibility of accidental spread. Esvelt explains how to minimize risk and discusses the importance of engaging communities in planning any projects which may affect them.
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 for bioremediation, 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.
When an infectious disease outbreak happens, medical workers and public health officials mobilize, but there are also teams of researchers that snap into action. Dr. Tracey Goldstein and Dr. Koen Van Rompay are both actively involved in different initiatives to find answers surrounding the COVID-19 epidemic. They talk about the process of studying coronaviruses and other infectious diseases, the steps taken once an outbreak hits, and the ways in which this process could change for the better. The changing world we live in makes predicting outbreaks a challenge, but each one teaches us something new about how to understand and to respond to the next.
In his third talk, Clevers describes how organoids can guide our understanding of disease progression in cancer. In addition, using Cystic Fibrosis and cancer as examples, Clevers shows how organoids can be used to predict therapeutic outcome in patients.
In his second talk, Clevers shows how one can apply what we have learned from developing gut organoids to generate mini-organs for other epithelial tissues, like liver and lung. Clevers shows that these organoids have a similar expression profile as well as structural characteristics to those observed in real tissue. In addition, he shows how this technique can be used to generate non-mammalian organoids, like the development of venom gland organoids from snake venom gland tissue. As Clevers explains, such organoids can be used to discover possible novel therapeutics, including new anti-venom serum.
In his first talk, Dr. Hans Clevers provides a historical perspective on the discovery of adult stem cells in the gut. They identified a Wnt-dependent, rapid proliferating population of cells at the bottom of the crypt which seemed to be important for generating all epithelial cells in crypts and villi, and they hypothesized that these were gut stem cells. By using the Lgr5 gene as a marker, the Clevers’ lab confirmed that these long-lived cells were indeed the gut stem cells by showing that they were able to generate all of the cell types of the gut epithelium throughout life. Clevers characterizes the gut stem cells and its progenitors, and explains how his lab developed a technique to grow from a single stem cell an organoid or mini-organ, a structure that recapitulates the normal structure of the gut.
All general anesthetics act in the brain stem region to induce slow brain oscillations. Brown shares EEG spectrograms that clearly show that the brain response to anesthesia varies with age. Younger brains show strong oscillations while those of older brains show weaker oscillations. Interestingly, not all brains “age” at the same rate. By using EEG spectrogram to visualize brain dynamics, anesthesiologists can optimize drug dosage for individual patients. Brown closes his talk by presenting recent research suggesting that it may be possible to “turn the brain back on” after general anesthesia as a way to speed patient recovery.
What happens to your brain when you are under general anesthesia? Dr. Emery Brown explains that under general anesthesia your brain is not turned off but is very dynamic. Electrical oscillations in the brain can be recorded using an electroencephalogram (EEG). Brown shows how oscillations induced by anesthesia interfere with normal communication between different regions of the brain. By following oscillations of different frequencies, it is possible to monitor and adjust a patient’s level of unconsciousness under anesthesia.
In her third talk, Braybrook switches gears and highlights work from her lab on cell walls found in brown algae (seaweed). Although seaweed cell walls have much in common with plant cell walls, they do have some differences. Seaweed cell walls contain much less cellulose than plants, in fact, most of the wall is made of the gel matrix material, alginate. Braybrook’s lab studies the Fucus seaweed embryo to learn how changes in the rigidity or fluidity of the gel matrix impacts cell expansion patterns during development.
For a plant seedling to grow upwards and out of the soil so it can begin to photosynthesize, it must grow more in length than in width. Growth that occurs in one direction more than in another is called anisotropic growth. How do cells do this? In plants such as Arabidopsis, almost all of the initial increase in plant length or height is due to anisotropic growth of cells rather than cell division. In her second talk, Braybrook explains how her lab is using this system to study the role of cell wall components in determining anisotropic growth.
Cell walls are found throughout the tree of life (even in some animals!) and in most cases they serve similar functions of strengthening and protecting cells. Dr. Braybrook’s research focuses on cell walls found in multicellular organisms such as plants and brown algae. In her first talk, Braybrook explains that cell walls are made of cellulose which forms long strong fibers, a gel matrix such as pectin or alginate in which the cellulose is embedded, and cross-links such as hemicellulose or lignin that provide strength and hold the wall together. By improving our understanding of cell wall structure and biology, Braybrook’s research may help facilitate our use of plants and seaweed for biofuels and other products.
Dr. J. Michael Bishop tells us the story of his Nobel Prize-winning discovery of cellular proto-oncogenes. Bishop was studying how the Rous Sarcoma Virus (RSV) causes cancer in chickens by expressing the viral protein called Src. Together with Dr. Harold Varmus, Bishop discovered that the chicken genome normally expresses a homolog of the viral Src protein that they called cellular-Src (c-Src). This finding led them to the remarkable conclusion that RSV had incorporated a mutated oncogene version of the normal chicken c-Src protein, and, provided the first evidence that mutations in our own genes can be linked to cancer development.
In his second talk, Dr. Benfey dives even further into the cellular differentiation pathway of plant roots. He provides an explanation of the signaling pathway that activates positive feedback and feed-forward loops that impact the organization of cells as the root develops. He also covers how roots function as they spread through soil and how a chemical compound his lab identified can help roots grow through saline soil.
In his first talk, Philip Benfey gives an overview of root genetics and his work to identify genes that are involved in the process that takes a stem cell to a differentiated tissue. He explains how mutant Arabidopsis plants with shorter roots helped his lab understand how specific genes are expressed in plant roots, and how these genes affect root function. He reveals how a protein encoded by a gene called SHORTROOT moves from the vascular tissue to the endodermis to induce expression of another gene called SCARECROW. This whole complex is the on-off switch that causes certain root cells to divide and differentiate properly. Benfey also talks about how these genes can be used to change cell identity.
In Part 2 of his talk, DeBose-Boyd introduces a rare genetic disorder known as Schnyder Corneal Dystrophy (SCD). SCD is characterized by accumulation of cholesterol in the corneas of affected individuals, indicating that the genetic defect in SCD may affect cholesterol synthesis. Mutations in the UBIAD1 gene cause SCD – therefore, DeBose-Boyd’s lab sought to understand the role of UBIAD1 in regulation of cholesterol metabolism. They found that UBIAD1 acts as a sensor for levels of the metabolite GGpp, which enhances sterol-mediated ERAD of HMG CoA reductase. In the presence of GGpp, UBIAD1 releases HMG CoA reductase, leading to its proteasomal degradation. DeBose-Boyd’s lab also discovered a fascinating spatial regulation of UBIAD1, whereby binding of UBIAD1 to GGpp causes UBIAD1 to accumulate in the Golgi apparatus and away from HMG CoA reductase in the ER. Finally, his group found that the SCD-associated mutation N102S in UBIAD1 inhibits the interaction between UBIAD1 and GGpp, such that mutant UBIAD1 is unable to translocate from the ER to the Golgi in the presence of high GGpp.
Regulation of cholesterol synthesis is very important: cholesterol is a component of cell membranes and a precursor of steroid hormones and bile acids, yet high levels of cholesterol can be toxic to cells and can contribute to heart disease. Cells in our body obtain cholesterol one of two ways – by taking it up from the bloodstream (via low-density lipoprotein or LDL) or by synthesizing it intracellularly. In Part 1 of his iBioSeminar, Dr. Russell DeBose-Boyd provides an overview of cholesterol regulation with a focus on HMG CoA reductase, the rate-limiting enzyme of cholesterol synthesis. He describes how the effects of statins, drugs prescribed to lower LDL in the blood, are blunted due to the disruption of feedback control of HMG CoA reductase. In the presence of sterols, HMG CoA reductase protein stability is decreased. This sterol-accelerated degradation of HMG CoA reductase is dependent on the enzyme’s membrane domain in a process known as ER-associated degradation (ERAD). DeBose-Boyd describes his lab’s contributions to a model of HMG CoA reductase ERAD in which polyubiquitination of the enzyme in response to sterols is mediated by two proteins, Insig-1 and Insig-2, leading to its ERAD by the 26S proteasome.
Have you ever tried to catch a flying fly only to be frustrated by their ability to evade your efforts? Then you know that many insects are extremely agile fliers. In his three talks, Dr. Michael Dickinson uses aerodynamics, muscle physiology, and neuroscience to explain how flies fly.
In Part 1, Dickinson focuses on lift. How do insects generate the aerodynamic forces necessary to stay in the air? Dickinson explains that by studying high speed videos of flies in flight, it is possible to determine the motion of the wing at each moment in time and, from that information, determine the forces that the insect is generating during an entire wing stroke. Early studies of this type calculated that insects did not generate enough force to keep them in the air! So how do flies fly? To answer this question, Dickinson and colleagues built a large scale robotic model of an insect wing moving through a viscous solution. Video tape of these models showed that the wing can form a large vortex at its leading edge. This vortex augments the forces generated by the insect and provides enough lift to keep the insect in flight. By changing the angle of attack of the wing, the fly can change the size of the leading edge vortex and how much lift is produced.
In Part 3, Dickinson discusses how insects control flight. Insects have many sensors on their bodies and wings that detect odors, the polarization of light, body rotation, air movement, and more. All of this sensory information is taken in and integrated by the insect’s brain. The brain then regulates muscle function to perform the behaviors needed for the fly to survive in its natural environment. Dickinson and his colleagues have built “arenas” in which a fly can be tethered and visual cues can be used to make the fly think it is flying in a specific direction with a certain speed, or being attacked by a predator. Using high speed video, it is possible to measure the flies response to these visual cues. Amazingly, within 20 milliseconds of detecting a predator, a fly can integrate its response so that it completely changes flight direction and flies away from the perceived predator.
Dickinson’s second talk focuses on power. Small insect wings must beat very rapidly – much more quickly than can be controlled by the release and uptake of Ca2+ that typically regulates muscle contraction. Instead flies use two sets of stretch activated power muscles. The contraction of downstroke muscles stretches and stimulates upstroke muscles, and vice versa, allowing the insect to beat its wings very quickly. In addition to power muscles, insects have tiny steering muscles that connect directly to the wing and regulate wing deviation during the wing stroke. With a combination of high speed video and electrical recording, Dickinson demonstrates how these tiny muscles can change wing position and allow a fly to undergo its amazing aerial acrobatics.
In her second talk, Churchland outlines her group’s studies of the relationship between decision-making and action. She notes that in addition to methods to track neural activity, high-resolution videos of the decision-making process in mice provide valuable movement data. Using labeled calcium to visualize neural activity across the dorsal cortex, Churchland’s group finds that maps of the visual world are represented up to six times in each mouse brain! The Churchland group also found that neural activity appeared to be the same across novice and expert decision-makers. They developed a mathematical model to predict the influence of numerous variables on neural activity and found that movement-related variables accounted for a greater proportion of the variance in neural activity than decision-related variables. Specifically, spontaneous (non-instructed) movements had the greatest predicted influence on neural activity. They then validated their results at the single-neuron level using two-photon microscopy. Dr. Churchland ends her talk by highlighting a significant remaining question: what are the neural differences between novice and expert decision-makers?
How do brains make decisions? In this seminar, Dr. Anne Churchland tells us why understanding decision-making is important, and outlines common approaches to study decision-making in the lab using a variety of mammals. She describes findings that suggest accurate decision-making results from a combination of visual and auditory stimuli in both humans and rats, and tells of the discovery of an explore-exploit tradeoff that allows rats to respond optimally to changing environments. Dr. Churchland then outlines the major methods for tracking neural activity in the brain and shows how they have been used to determine that many brain areas are active during decision-making. She ends her talk with an overview of new directions in the field.
Christofferson also works on characterizing understudied arboviruses like Bunyamwera, Batai, and Ngari, all of which are orthobunyaviruses. First, in the laboratory, her lab studied the growth of these Orthobunyaviruses in-vitro and investigated a mouse model to determine the cross-reactivity of these viruses. In addition, in collaboration with scientists in Rwanda, Christofferson investigated whether Bunyamwera, Batai and Ngari circulated in the country, and caused disease in cattle. As Christofferson explains, a better understanding of the prevalence of viruses that affects the cattle may alleviate misdiagnosis and allows us to follow the possible emergence of newly detected viruses.
In her second talk, Christofferson uses the Aedes aegypti-Zika system to explain how mosquito-life traits can be used to understand the process of vector competence. Zika is an arbovirus that is transmitted to humans via the Aedes aegypti mosquito. Christofferson measures how much time it takes for a mosquito to become infectious after its initial exposure (extrinsic incubation period) in order to understand how mosquito age interacts with the viral fitness measure of vector competence. This is done in the context of a commonly used mathematical framework, vectorial capacity.
In this talk, Dr. Rebecca Christofferson provides an overview of arboviruses, arthropod-borne viruses, like dengue. Arthropods, such as mosquitoes, act as vectors to transmit diseases to vertebrates, including humans. Christofferson studies arthropod-virus-vertebrate interactions and how environmental factors affect disease transmission. For example, she explains how environmental factors, like changes in temperature and drought, affect the intrinsic ability of a vector to transmit a pathogen (vector competence).
In his Part 3, Chang reminds us that every lncRNA gene has its own set of DNA regulatory elements, such as enhancers and promoters. These regulatory elements can confer functionality to lncRNA genes. Chang shares the research story of a mysterious lncRNA known as PVT1, which is frequently co-amplified with the proto-oncogene MYC in human cancers. His group found that PVT1 promoter activity is inversely correlated with MYC expression – when one is up, the other is down. Finally, Chang shows that the PVT1 and MYC promoters compete for four enhancers located within the PVT1 gene locus.
In his Part 2, Chang introduces long noncoding RNAs, or lncRNAs. As their name suggests, lncRNAs are not translated into proteins, and initially their functions were poorly understood. Chang’s group has developed technologies to better understand the function of lncRNAs. For example, his lab characterized the protein partners that interact with Xist, a canonical lncRNA that mediates X chromosome inactivation. They found that the protein Spen is necessary for X chromosome silencing. Interestingly, Spen has likely been co-opted by mammalian cells to inactivate the X chromosome via viral mimicry.
In Part 1 of this series, Dr. Howard Chang introduces epigenomics, the study of DNA regulatory mechanisms that determine which genes are turned on or off in cells at specific times. The epigenome integrates signals from the environment to modify expression of the DNA blueprint inherited from an individual’s parents. Chang’s lab has pioneered techniques to map the landscape of chromatin, the complex of DNA, RNA and protein that organizes the genome and regulates gene expression. One example is ATAC, the Assay of Transposase Accessible Chromatin, which uses a bacterial transposase to mark open chromatin and identify genes that are likely turned “on”.
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.
Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.
Chow gives advice on purifying DNA samples using magnetic beads and on determining the quality of your nucleic acid sample using an Agilent Bioanalyzer.
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.
Course Directors A. Malcolm Campbell, Kimberly Tanner, and Bill Wood talk about the reasons why we need to reform undergraduate biology education and why they got involved in the Scientific teaching Series project.
Katherine Thompson-Peer examines neuronal regeneration, focusing on the ability of dendrites to regrow after injury.
Tanaka expands on her work on signaling in axolotl limb regeneration. She explains how her lab used the technique of expression cloning to identify several factors required to trigger the cell migration and proliferation required for regeneration. Tanaka was also curious about what signals differentiate a wound from an amputation. It was known that regeneration required the presence of nerves as well as the interaction of anterior and posterior limb tissue. Tanaka’s lab was able to show that the expression of the signaling molecules SHH, on the posterior side, and FGF8, on the anterior side, of an amputated limb were enough to sustain regeneration. Identification of these signaling molecules has advanced our understanding of limb regeneration in vertebrates.
Among four limbed animals, salamanders are the champions of regeneration. They can regenerate an amputated leg or tail, as well as various internal organs. In her first talk, Elly Tanaka explains that axolotl limb regeneration is an excellent system to study the cellular and molecular mechanisms of limb regeneration in vertebrates. Tanaka and her colleagues have shown that the regenerating limb has positional memory. For example, an amputated hind limb with regenerate a hind limb and not a forearm. They also have identified the key signaling molecules involved in determining positional identity.
Sykes provides an overview of xenotransplantation, the use of organs or grafts from other (non-human) species. She outlines the challenges encountered with cross-species transplantation, and how scientist have been able to overcome these difficulties. Sykes and other laboratories are exploring the use of miniature pigs for xenotransplantations to humans. Sykes shows the outcome of xenotransplantations performed between different species (e.g. rat to mouse or pig to baboon), and what scientists have learned from these results.
Dr. Megan Sykes provides an introduction to the field of organ transplantation and discusses the immunological responses associated with this procedure. Rejection is a major limitation to the success of transplantation. Sykes explains what causes rejection episodes in different types of transplantation, and outlines what we can do to prevent this from happening.
As Sykes explains, the Holy grail of transplantation is tolerance, the long-term graft acceptance without the long-term use of immunosuppressants. Sykes and collaborators developed a hematopoietic cell transplantation and mixed chimerism technique that proved to induce true tolerance in humans. They showed that transient mixed chimerism, the co-existence of donor and recipient hematopoietic elements, was detected in patients where tolerance was observed. Sykes reviews the clinical trial results and explains the experimental techniques used to study the molecular features that predict tolerance and low rates of organ rejection in patients.
Spudich describes the technological and experimental advances of the last ~50 years that have allowed researchers to understand muscle contraction in molecular detail. The development of an in vitro assay let Spudich and his colleagues determine which domain of the myosin molecule (which is very large) is necessary for movement. A laser trap assay allowed them to measure the size of the “step” taken by a myosin molecule moving along actin, as well as the force generated by a single myosin molecule. The solution of a crystal structure for myosin also provided key information about its mechanism of action. These results, together with early enzymatic analysis, have led to a detailed molecular model for the chemo-mechanical cycle of myosin.
Spudich recounts his first foray into muscle research as a postdoc in Hugh Huxley’s lab. He wanted to understand how Ca2+ regulated muscle contraction via the troponin/tropomyosin complex. Using electron micrographs and diffraction analysis to investigate where tropomyosin filaments lie along actin filaments, Spudich showed that tropomyosin filaments block the myosin-binding sites on actin. When muscle is stimulated, Ca2+ is released from intracellular stores and binds to troponin causing tropomyosin to move. This allows myosin to bind to actin and the muscle to contract. These finding led Spudich and Huxley to propose a steric blocking mechanism for regulation of muscle contraction. Recent technological improvements have confirmed this model and filled in important details.
Spudich focuses on current studies in his lab to understand how mutations in cardiac myosin cause human hypertrophic cardiomyopathy (HCM). This is a disease characterized by a hyper-contractile heart and is the most common cause of sudden cardiac arrest in people under 35 years old. Based on insight from a dream, Spudich realized that many of the mutations associated with HCM are in a region of the myosin molecule (the myosin mesa) that may regulate the availability of myosin heads to bind to actin and thus, regulate muscle contraction. Spudich’s lab is now working to determine the importance of the myosin mesa in regulating cardiac contractility and, in particular, its role in HCM.
Dr. Spudich begins his talks with a clear overview of muscle biology. Muscles are made of many cells and each cell contains many contractile units called sarcomeres. Sarcomeres are made of parallel filaments of two different proteins, actin and myosin. The filaments slide relative to each other and cause the sarcomere, and in turn the muscle, to contract. Spudich recounts the breakthroughs that led muscle biologists to propose this sliding filament model (~1950). By 1969, experiments using electron microscopy, a relatively new technology at the time, and X-ray diffraction, had advanced the model to explain how the “swing” of individual myosin molecules along actin filaments could power muscle contraction.
Seydoux explains how the PAR domains reorganize other proteins in the cytoplasm of the one-cell embryo and creates a body axis. MEX-5 is an RNA-binding protein that localizes to the anterior side of the embryo, forming a concentration gradient in the cytoplasm. Excitingly, her lab discovered that the MEX-5 gradient is caused entirely by the difference in diffusion rates between two MEX-5 species! The shift between the two species is controlled by PAR-1-mediated phosphorylation. This simple mechanism explains how a protein can become localized to a particular area of the cell without directed transport.
During development, how do embryos distinguish their posterior (tail) versus anterior (head)? Dr. Geraldine Seydoux’s lab uses the small worm C.elegans as a simple model to study this question. In her first video, she introduces how the sperm divides the egg into distinct anterior and posterior domains shortly after fertilization to create the body axis. Her lab discovered that the sperm introduces microtubules that reorganizes the distribution of a network of polarity regulators, called PAR proteins. The PAR proteins segregate into two non-overlapping domains that define the anterior and posterior axis of the worm.
Schekman outlines exosome biogenesis. Exosomes are extracellular vesicles released by the cell, and in contrast to intracellular vesicles, exosomes contain small molecules of RNA. Schekman’s laboratory characterized the RNAs contained in exosomes and showed the importance of Ybx1 protein for the recruitment of certain miRNAs into exosomes.
Schiller discusses the high efficacy of HPV vaccine, which is exceptionally good at producing neutralizing antibodies and also benefits from the low mutation rate of HPV. Coming to a better understanding of the efficacy of the HPV vaccine will provide evidence to support single-dose vaccination and aids in the development of new vaccines.
Human Papillomavirus (HPV) causes 5% of all cancers worldwide, and the first vaccine against HPV was approved in 2006. In this seminar, Dr. John Schiller provides an overview of HPV virus and infection, compares the three FDA approved vaccines against HPV, and explains the endpoints used in the clinical trials to prove vaccine efficacy. After a decade of using the vaccine, retrospective studies now allow us to evaluate the possibility of using single-dose vaccination, which could lead to an increase in the general use of the vaccine (implementation), and improve HPV-related cancer prevention.
Dr. Randy Schekman overviews the secretory pathway and reviews historical experiments that shaped our molecular understanding of this pathway. The journey begins at the endoplasmic reticulum (ER), where proteins that engage the secretory pathway get translated. The mRNA of these proteins codes for a signal sequence that serves as a “tag” to bring the mRNA-ribosome-newly-synthesized protein to the ER for continued translation and movement of the new secretory protein across the ER membrane into the interior or lumen of the organelle. Vesicles transport the recently translated proteins to the Golgi Apparatus, where they get “packaged” and sent to their final destination.
Schekman explains how his laboratory used baker’s yeast to uncover major proteins involved in the secretory pathway, and describes proteins involved in budding, vesicle trafficking, and vesicle fusion. Schekman also presents data from his laboratory that helped to identify the ER channel through which proteins enter the secretory pathway. These series of experiments show how, step by step, scientific knowledge evolves, uncovering the fundamental mechanisms to better understand human disease.
Ramakrishnan’s laboratory has studied the molecular pathogenesis of TB using the power of forward genetics in the zebrafish. They discovered that mutations in LTA4H, a key enzyme in the eicosanoid pathway that alters the levels of the cytokine tumor necrosis factor (TNF), affect tuberculosis pathogenesis by regulating the inflammatory response. This work showed that a balance of TNF is required for good TB prognosis, and neither high nor low inflammation was favorable. Correspondingly, they showed that genetic variation in LTA4H in humans helps explain patterns of TB meningitis survival when patients were exposed to a treatment that suppresses the inflammatory response.
In this seminar, Dr. Lalita Ramakrishnan gives an introduction to tuberculosis (TB) pathogenesis, and gives an overview of Mycobacterium tuberculosis’ life cycle. She explains how the TB bacteria gain entry into the host by using specific lipids to avoid microbicidal macrophages and recruit growth-permissive ones. Once inside the macrophage, the bacteria use multiple virulence genes to survive intracellularly. In particular, Ramakrishnan discusses bacterial efflux pumps that, in addition to promoting intracellular survival, also induce tolerance to multiple antibiotics. Most individuals have effective counterstrategies so that they are able to clear TB infection by a combination of innate and adaptive immunity. Yet scientists have not been able to understand these defense strategies enough to harness them and create an effective vaccine against TB.
After the TB bacteria infect macrophages, a complex structure called a granuloma develops. Different immune cells arrive at the granuloma to surround the bacterial infection and fight the disease. In her second lecture, Ramakrishnan explains how her laboratory used a zebrafish model of TB to study the involvement of granulomas in TB progression. Although granulomas were thought to constrain infection, her laboratory showed that the bacteria hijack the granulomas to spread the disease. For example, Ramakrishnan showed that TB bacteria promote the recruitment of new macrophages to the granuloma that engulf dying infected macrophages to expand infection.
Pringle explains how one can use a “reverse ecology” approach to describe and characterize different organisms and their habitats, by studying their genes. Her laboratory used this approach to study the origins of the Bay Area Amanita phalloides. Although Amanita phalloides was thought to be an invasive species, historical records were mostly descriptive and hard to use as concrete evidence of the species’ biogeography. Using genetic information, the Pringle laboratory was able to definitively prove that early samples identified as Amanita phalloides in the US are distinct from the European species. They also used molecular data to document the symbiotic associations between Amanitaphalloides and plants, proving the efficacy of these approaches to study species that are hard to grow in the lab.
Pringle provides an overview of convergent interactions, defined as the independent emergence of multi-species interactions with similar physiological or ecological functions. For example, multiple plant lineages have independently evolved interactions with fungi in order to exchange resources and form what are known as mycorrhizal symbioses. To further understand how convergent interactions are formed, the Pringle laboratory studied the evolution of plants that have “pitcher”-like structures as well as the mycorrhizal symbiosis in the Amanita genus.
Although people usually relate fungi with diseases, Dr. Anne Pringle provides an overview of the vastly diverse and complex world of fungi, and provides examples of the beneficial roles that fungi have on Earth. For example, although some fungi have been associated with devastating infections that threaten harvests every year, other fungi are mutualists needed for the healthy development of plants and animals.
How is butterfly color created? In this lecture, Aaron Pomerantz takes us on a journey through the Amazon rainforest, where interesting observations about butterfly color and patterns lead him to use imaging and genetics to decode butterfly color.
This talk is part of the Young Scientist Seminars, a video series produced that features young scientists giving talks about their research and discoveries.
Ploegh describes how his lab takes advantage of the unique properties of antibodies from the Camelidae family (alpacas, llamas, camels, etc). In addition to traditional antibodies, these animals naturally make small, heavy-chain only antibodies (nanobodies). These molecules can be isolated, amplified in bacteria, and engineered for new applications. As well as using nanobodies to target viruses and inflammasomes, Ploegh explains how his lab uses labelled nanobodies for non-invasive, live imaging of cancer tumors in mice. These technologies have exciting implications in basic and biomedical studies.
How does our immune system protect us against all of the infectious agents and foreign substances we encounter? Much of the answer lies in antibody diversity. In his first talk, Dr. Hidde Ploegh explains how B cells shuffle their genetic material such that regions of the immunoglobulin protein are rearranged. This generates the antibody diversity needed to recognize an almost infinite number of antigens. Interactions of B cells with T helper cells results in the formation of structurally distinct classes of immunoglobulins, further increasing antibody diversity. T killer cells are primed to attack infectious agents when immunoglobulins on their surface recognize antigens presented by the major histocompatibility complex (MHC). Ploegh explains that by subverting the MHC pathway, viruses and cancer cells can evade the immune system.
Dr. Helen Piwnica-Worms provides a historical perspective on cell cycle regulation and outlines important experiments in frogs, clams, and yeast that revealed crucial mediators of the cell cycle. Scientists observed that there were factors that allowed cell cycle progression, while there were other factors that prevented the cell from going backward. Using these model organisms, scientists were able to characterize the activation of the inducer of mitosis, the M-Phase promoting factor, which is a heterodimer between cyclin-dependent kinase (Cdc2/Cdk1) and cyclin B.
Piwnica-Worms explains how scientists have used their understanding of the cell cycle regulation to generate targeted cancer therapies. The cell has proteins that serve as cell cycle checkpoints, which allows the cell to respond appropriately to DNA damage. Although not all of the checkpoints are functional in a cancer cell, these cells still need the checkpoint proteins to respond to DNA damage. Piwnica-Worms’ laboratory studies the use of combining DNA damage agents with checkpoint inhibitors to selectively kill cancer cells. Her laboratory developed a patient-derived xenograft mouse model to study Triple Negative Breast Cancer (TNBC), and predict how the genotype of the tumor affects treatment.
Dr. Shiv Pillai provides a historical perspective on the current model of how the immune system works. Scientists observed that the body produces molecules (antibodies) that recognize the entry of foreign particles (antigens). He outlines the different models of the structure and functions of antibodies and explains the process by which antibody diversity is generated during B cell development (VDJ recombination). B cell development also involves two checkpoints to ensure the generation of functional antibodies and prevent the recognition of self-structures.
Pillai explains how earlier in his career he discovered that two surrogate light chains bind to the heavy chain in pre-B cells to create the pre-B cell receptor (pre-BCR). He showed that binding of the surrogate chains facilitates the formation of the pre-BCR that is needed for B cell development. Pillai demonstrated that the pre-BCR signals through Bruton Tyrosine Kinase (Btk). Patients with non-functional Btk manifest signs of immunodeficiency and deficiency of B-cells in the blood, which shows the importance of pre-BCR signaling for proper B-cell development.
Pillai explains IgG4-Related Disease (IgG4-RD), a chronic inflammatory condition characterized by elevated numbers of T cells and IgG4 secreting plasma cells in the affected tissue. Using tissue samples from patients with the disease, his laboratory isolated and characterized the CD4+ T cells associated with IgG4-RD. Furthermore, he explains how the crosstalk between these CD4+ T cells and B cells is important for IgG4-RD development, and showed that depletion of B cells improves the outcome of the disease.
Before 1977, all life on Earth was classified into two groups: single-celled microorganisms and complex cellular life such as fungi, plants, and animals. A seminal discovery in 1977 rewrote the tree of life and introduced a whole new domain of organisms known as the archaea - mysterious microbes that are genetically distinct from bacteria. Fast forward to the 21st century, and again new discoveries about archaea are leading scientists to reshape the tree of life and rewrite the evolutionary history of complex organisms. Dr. Dipti Nayak introduces the fascinating organisms known as archaea and explains how they are helping scientists answer the question Where do we come from?.
What if we could understand the human cell in such detail that we could paint an accurate representation of a cell’s molecular organization? In this lecture, Dr. Manuel Leonetti outlines the different genome-wide approaches that scientists are using to build a complete map of the human cellular architecture. Understanding protein networks and localization could aid our quest to understand human biology and disease.
Dr. Ruslan Medzhitov provides an overview of the field of inflammation and outlines its role in pathology and homeostasis. Medzhitov explains how Inflammation is generated when pathogens, allergens, or other perturbations are recognized by sensor cells that then release inflammatory mediators (cytokines and chemokines) to activate effector cells. Inflammation is then followed by a resolution phase that brings the system back to homeostasis.
Why do we experience fatigue and loss of appetite, as well as other symptoms when we get ill? Sometimes what we associate with a pathogenic response and illness is the effect of inflammation. In his second talk, Medzhitov outlines the symptoms that we often feel when we get sick, like the lack of appetite (anorexia), and unveils the molecular mechanisms that explain why we have evolved this way. In addition, he compares and contrasts how anorexia affects the outcome of bacterial and viral infections.
Knoblich describes experiments in his lab to develop 3 dimensional brain organoids from human pluripotent stem cells. While studying the development of rodent brains has proved extremely useful, there are some important developmental differences that require human tissue for investigation. In addition, some diseases such as microcephaly cannot be modeled in mice. Knoblich and his colleagues have developed cerebral organoids that mimic early human brain development and can be used to model neurodevelopmental disorders. They have also been able to generate separate organoids from various regions of the human brain and then fuse them and follow the migration of live neurons between these parts, opening the path to many more studies of neuronal development.
Dr. Knoblich begins his talk by explaining the key role that asymmetric cell division plays in development of the human brain. During mammalian brain development, neuronal progenitor cells initially divide symmetrically to increase their numbers. Later they divide asymmetrically to produce one progenitor cell and one (or two) cells which will terminally differentiate to become neurons. What determines which daughter cell will become which? Working in Drosophila, Knoblich and others elucidated a signaling pathway in which Par proteins are asymmetrically localized before cell division. This recruits a complex of proteins which defines the orientation of the mitotic spindle and causes the localization of Numb protein at one pole of the cell. Upon cell division, only one daughter cell will inherit Numb protein and this ultimately will determine the fate of the daughter cells. Interestingly, this signaling pathway is conserved from insects to mammals, however, Knoblich found an important difference that may explain why humans have many more cortical neurons than mice.
Since little is known about the Toxoplasma gondii genome, in his second iBiology seminar, Lourido explains how his lab developed CRISPR tools to study apicomplexan biology. His lab designed a strain of T. gondii constitutively expressing Cas9 that can be used in conjunction with guide libraries to identify biologically significant genes. Lourido explains how his lab used this system to identify genes encoding proteins necessary for apicomplexan invasion. These include a claudin-like protein, that they are calling CLAMP, that is conserved across apicomplexa and is necessary for invasion by both toxoplasma and the parasites that cause malaria.
In a peer-discussion, do well-prepared students simply tell other students the answer?
Bill Wood (University of Colorado Boulder) describes the Smith et al. study, which examines whether students who change their mind as a result of peer-discussion have actually learned the concepts being tested.
Michael Alley has been teaching scientists and engineers how to design presentation slides and deliver effective scientific talks for over three decades. In this three-part lecture, you will learn (a) how to design your PowerPoint or Keynote slides, (b) how to organize your talk, and (c) how to confidently deliver your research seminar. This series will help trainees and research scientists alike improve their presentation skills.
Michael Alley has been teaching scientists and engineers how to design presentation slides and deliver effective scientific talks for over three decades. In this three-part lecture, you will learn (a) how to design your PowerPoint or Keynote slides, (b) how to organize your talk, and (c) how to confidently deliver your research seminar. This series will help trainees and research scientists alike improve their presentation skills.
Michael Alley has been teaching scientists and engineers how to design presentation slides and deliver effective scientific talks for over three decades. In this three-part lecture, you will learn (a) how to design your PowerPoint or Keynote slides, (b) how to organize your talk, and (c) how to confidently deliver your research seminar. This series will help trainees and research scientists alike improve their presentation skills.
Proteins such as signaling molecules, catalytic enzymes, and membrane transporters are not static but are in a state of constant motion for function. In her first talk, Dorothee Kern explains how she uses techniques such as nuclear magnetic resonance (NMR), X ray crystallography, single molecule FRET and computational simulations to visualize rapid protein dynamics. Kern walks us through the basics of these techniques and explains how they can provide structural and energetic information about a protein and how it functions in the cell.
Gleevec (Imatinib) is a very effective drug for treating chronic myelogenous leukemia. It acts by binding to and inhibiting the signaling molecule Abl kinase with extreme specificity. Abl kinase is very closely related to Src kinase, and, in fact, the drug binding pocket for Gleevec is almost identical between the two proteins. Interestingly, however, Gleevec binds to Abl 3000 fold more tightly than it does to Src. Why? In her second talk, Kern answers this question. Her lab used NMR, and the techniques she described in Part 1, to show that the protein dynamics of Abl and Src are dramatically different when Gleevec is bound. In a clever experiment in which they synthesized proteins that were likely evolutionary ancestors of Src and Abl, Kern’s lab was able to show how changes in amino acids throughout the kinases determined the differential binding affinity of Gleevec for Abl kinase over Src kinase. Experiments such as these demonstrate the importance of understanding protein dynamics at the atomic level of the whole protein, not just the drug binding site, when designing new drugs.
Ion channels are crucial for proper neuronal communication and cellular homeostasis. But, how do ion channels perform their work? In this seminar, Dr. Lily Jan defines the physiological role of potassium channels in the generation of an action potential and regulation of excitability in neurons. She outlines the role of voltage-gated and inward-rectifier potassium channels and provides evidence of the evolutionary importance of these proteins.
Jan characterizes the Calcium-Activated Chloride Channels (CaCC) in the TMEM16 family of transmembrane proteins with unknown functions and explains experiments from her lab that aided in the understanding of the molecular role of these channels. As she explains, one family member, TMEM16A, is typically expressed in peripheral cells and is involved in the rhythmical contraction of smooth muscles in the gastrointestinal tract. On the other hand, the TMEM16B CaCC is expressed in multiple brain regions as well as sensory neurons, like photoreceptors, and they have an inhibitory role in these cells.
A dendrite is a tree-like structure in neurons, which receives the incoming signal from adjacent neurons or from sensory stimuli. Dr. Yuh-Nung Jan is interested in understanding the molecular underpinnings that drive dendrite morphogenesis. His laboratory uses the fruit fly larvae as a model organism to study the development of dendritic arborization (da) neurons. Using these neurons, Jan and others have shown that the combinatorial expression of different transcription factors, such as Cut, as well as the interactions between dendrites and between dendrites and epithelial cells is what drives dendrite morphogenesis. In addition, Jan explains the role of Dscam isoforms in the regulation of dendrite-dendrite interactions for proper dendrite patterning.
Jan explains how dendrite morphology relates to the function of neurons. For example, class IV da neurons are photoreceptors and their dendrites form a regular array in the fruit fly larvae to enable the avoidance of noxious signals, like light. On the other hand, class III da neurons are mechanosensors, and they use no mechanoreceptor potential C (NompC) protein to detect gentle touch. Jan and collaborators showed that NompC works by tethering ankyrin repeats to microtubules, providing evidence for the first time that this type of gating mechanosensor mechanism is possible.
What mechanisms do plants have to fight pathogens? In this seminar, Dr. Sheng-Yang He explores plant-pathogen interactions and provides an overview of a plant’s basic immunological responses. As He explains, plants have “resistant” genes, which trigger the immune response after pathogenic infections (effector-triggered immunity). Also, plants immune system can be activated by the recognition of general patterns in pathogens (pattern-triggered immunity). Understanding these interactions could aid in the prevention of disease in plants, which would be beneficial to the agricultural industry and global food security.
He provides evidence on the effect of environmental factors (e.g. humidity) in the development of disease in plants. In order to understand disease susceptibility, He’s laboratory studies the interaction that Arabidopsis has with the bacteria Pseudomonas syringae. He’s laboratory showed that an increase in temperature and humidity increase bacterial disease severity. By genetically creating a plant that is altered in its immune system and water homeostasis, they were able to define the minimal factors that bacteria need to infect the plant.
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.
Microglia are the primary immune cells in the central nervous system. In the brain, they play central roles in proper development and function, as well as dysfunction and disease. In her first talk, Dr. Beth Stevens provides an overview of the many ways microglia cells operate, and how they can both harm and protect the brain. Fairly recent advances in the study of microglia through imaging have allowed researchers to identify different microglia states and study their dynamic roles at different stages of development.
Dr. Stevens dives deeper into the mechanisms that allow microglia to shape the network of connections between neurons in the brain. She provides an introduction to the role of microglia in synaptic pruning, the process of eliminating extra synapses in healthy developing brains. She then goes on to explain how the reactivation of this process affects aging and diseased brains.
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.
The nucleosome is the central organizing structure of the eukaryotic genome. It consists of DNA wrapped around histone proteins. Dr. Karolin Luger shares her discovery of the three-dimensional structure of the nucleosome using X-ray crystallography, which provided a deeper understanding of chromatin organization.
When he was a graduate student, Dr. Ruslan Medzhitov read a theory written by Dr. Charles Janeway that foresaw the existence of a set of receptors that would directly detect pathogens and signal to T- and B-cells to generate an immune response (adaptive immunity). Medzhitov was determined to find such receptors! In this discovery talk, Dr. Ruslan Medzhitov provides a historical perspective that frames his involvement in the discovery of Toll-Like Receptors. By following the clue that NF-kB was involved in the immune response, he searched for receptors, like Toll, that had the capacity to activate NF-kB.
Apicomplexa are evolutionarily distinct eukaryotes that play an important role in human diseases such as toxoplasmosis and malaria. So how do scientists study their unique biology? Dr. Sebastian Lourido explains that his lab uses Toxoplasma gondii as a model to study the phylum Apicomplexa. In part one of his talk, he explains the complex life cycle of T. gondii and he describes the unique organelles found in apicomplexa and used to facilitate invasion, survival and replication inside host cells. He highlights research from his lab demonstrating the importance of calcium signaling for T. gondii invasion.
Ostrander explains that canine genetics can be used to understand disease susceptibility and cancer risk. By analyzing the pedigree of dogs, her laboratory identified a series of genes involved in the elevated cancer risk of particular dog breeds. Specifically, her laboratory studied invasive transitional cell carcinoma of the bladder, a disease for which breeds like Scottish Terriers have a high susceptibility. In human cases of this disease, the cause is unknown in 50% of patients. Ostrander’s laboratory identified genetic mutations that explain the elevated cancer risk in these dogs. This information may improve diagnosis and targeted therapy in dogs and humans.
Although all domestic dogs belong to the same species, different breeds display unique morphological traits and different disease susceptibility. Dr. Elaine Ostrander provides an overview of canine genetics, and explains how scientists are using genetics to decipher the molecular basis of different traits such as height and cancer risk.
Hegde explains that although the protein localization system usually operates accurately, it does sometimes fail. This can be due to genetic mutations, stress within an organelle, or just intrinsic inefficiencies that accompany any complex process. As a graduate student, Hegde used a cell-free in vitro system to study the translocation of prion protein into the ER. He found that a small amount of prion protein did not completely cross the ER membrane as expected, but remained in a transmembrane form. Worried that this was an artifact of the in vitro system, he designed experiments in mice to see what the effect of an increase in mislocalized, transmembrane prion protein would be. He found a striking result - even a small increase in the amount of transmembrane prion protein caused increased neurodegeneration in mice. It turns out that incomplete translocation is not unique to prion protein. Hegde tells us how, as an independent investigator, his lab went on to investigate why this happens and how the cell monitors and degrades proteins that are not properly localized.
Proteins that are secreted from the cell or localized to the plasma membrane need first to be translocated into the lumen of the ER or inserted into the ER membrane. Thousands of proteins, each with a unique signal sequence, move through this pathway. How does the protein translocation machinery recognize these diverse signals and correctly localize the protein? In his third talk, Hegde describes studies from his lab using cryo-electron microscopy to visualize the translocation machinery at different stages in the recognition and engagement of a secreted or membrane inserted protein. The structural information gleaned from these experiments helps to explain how the protein translocation machinery works with high fidelity even when it needs to recognize diverse signal sequences.
Cells are organized into many different compartments such as the cytosol, nucleus, endoplasmic reticulum (ER), and mitochondria. Almost all proteins are made in the cytosol, yet each cellular compartment requires a specific set of proteins. How does the cell regulate protein localization to be sure that proteins end up where they should? In his first lecture, Manu Hegde reviews the history of this field and highlights key experiments that have led to our current understanding of how protein localization occurs.
Richard Harland begins his talk by asking how a fertilized egg goes from a single cell to a complex, multicellular organism during vertebrate development. He explains that amphibians, and in particular Xenopus laevis, are an excellent system for addressing this question. For example, early experiments by Spemann and Mangold in newt embryos were the first to demonstrate the presence of an “organizer” region, and more recent studies in Xenopus have identified many signaling molecules that control embryogenesis. Throughout his talk, Harland shows stunning movies to illustrate the beauty and complexity of early frog development.
During gastrulation, cell movements result in a massive reorganization of the embryo from a simple spherical ball of cells, the blastula, into a multi-layered organism. In his second video, Harland simplifies this complex phase of frog development by breaking it down into 7 separate steps and describing the specific cell rearrangements associated with each step.
Harland introduces the signaling molecules responsible for specifying distinct tissues in the embryo. He explains how signaling effectors, such as beta-catenin and Nodal/PSmad2, become localized in the blastula by determinants set up in the egg, and how these signals induce the formation of the mesoderm layer. He also describes classic experiments from the 1990s showing that the organizer is necessary to pattern the mesoderm into tissues such as muscle and neural plate. Harland then focuses on experiments from his lab that identified the molecules expressed in the organizer that specify dorsal cell fate.
Diabetes is a devastating disease which takes an enormous toll on both human life and healthcare spending worldwide. Dr. Frances Ashcroft begins her talk by explaining that blood glucose must be controlled within narrow limits. In a healthy person, insulin is released from the pancreatic beta cells in response to a rise in blood sugar, which stimulates the uptake of glucose into muscle, liver and fat and so restores the blood glucose to its resting level. Diabetes occurs when the beta cells do not release enough insulin, resulting in chronically high blood sugar levels. There are several types of diabetes: type 1 occurs because the beta cells are damaged by autoimmune attack; type 2, the most common form, is usually due to a combination of insulin resistance and decreased insulin secretion and is exacerbated by obesity and age; monogenic diabetes results from a mutation in a single gene. Neonatal diabetes is a rare monogenic form of diabetes that presents at, or shortly after, birth. Ashcroft explains that in 1984, she and her colleagues found that the function of an ATP-sensitive potassium channel (KATP channel) in the plasma membrane of pancreatic beta cells is critical for linking increased blood glucose levels to insulin secretion. They postulated that a mutation that caused the KATP channel to be permanently open would impair insulin release. Twenty years later, these mutations were identified and shown to be the cause of neonatal diabetes.
The first video is a shortened version in which Dr. David Baltimore introduces the different types of viruses, and defines how viruses are classified depending on their genetic material. Using HIV as an example, Baltimore explains what constitutes an equilibrium versus a non-equilibrium virus, and shows how the discovery of the reverse transcriptase helped scientist understand viruses.
Cryo-Electron Microscopy (Cryo-EM) is a form of transmission electron microscopy in which a beam of electrons is transmitted through a frozen-hydrated sample, and is used to study the molecular structure of biological samples. In this lecture, Dr. Yifan Cheng overviews the principles of Cryo-EM, and describes how advances in this technique have allowed scientists to solve biological structures to atomic resolution.
For decades, a strange neurological disease has plagued snakes around the world. The snakes tie themselves into knots, exhibit strange behaviors, and eventually die. In this talk, Dr. Joseph DeRisi describes how using genome sequencing his lab uncovered the mysterious agent responsible for this disease, which turned out to be an ancient arenavirus.
TOR, the Target of Rapamycin, is now known to be a central controller of cell, tissue and organism growth and an important molecule in many human diseases including cancer, cardiac hypertrophy, diabetes and obesity. Michael Hall explains how the fortuitous decision, in 1991, to investigate the action of rapamycin in yeast led to the discovery of TOR.
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.
How does the brain translate sensory stimuli into a behavior? In his first iBiology talk, Dr. Florian Engert explains that larval zebrafish are an excellent model to tackle this question. Larval zebrafish are tiny, translucent, and genetically tractable vertebrates. By making transgenic fish with labelled neurons, it is possible to visualize neuronal activity in the entire brain of a living and awake fish. Engert introduces the virtual behavior simulators that his lab members use to trigger and measure neuronal activity in the fish.
Dr. Colón-Ramos describes his group’s finding of a previously-unknown metabolic subcompartment that powers synaptic function. His group observed that under conditions of energy stress, glycolytic proteins, which are normally diffusely distributed in cells, co-localize to a punctate structure adjacent to synapses. The local formation of these complexes is required for the synaptic vesicle cycle and synaptic function. The discoveries contribute to an unsolved question in neuroscience: how local, rapid and transient changes in energy demands are met at synapses to sustain their function. He frames his lab’s cell biological findings in the context of the long history of research of energy metabolism, drawing new lessons and discussing how the discoveries now provide new opportunities to examine the cell biology of metabolism at the neuronal synapse.
Colón-Ramos discusses how his group uses the approaches they have developed to reduce system’s level questions, like behavior, to cell biological questions at the synapse. He describes his lab’s discovery that two plasticity mechanisms—sensory adaptation and presynaptic plasticity—act within a single cell in C. elegans to encode thermosensory information and actuate a temperature-preference memory. The integration of these plasticity mechanisms result in a single-cell logic system that can both represent sensory stimuli and guide memory-based behavioral preference. These findings allow the Colón-Ramos group to directly link cell biological changes at the neuronal synapse with memory and behavior.
Engert describes work done with collaborators to develop a robust operant learning assay for larval zebrafish. Using this assay and techniques for measuring neuronal activity in tethered, awake fish, they are beginning to decipher what happens in a vertebrate brain while the animal is learning.
Neuronal activity can be triggered by either external stimuli or by stimuli that are a result of your own actions. In his second talk, Engert explains how his lab measured and compared neuronal activity in response to these two types of stimuli. Using a set up where larval zebra fish are immobilized with drugs, yet the neurons which innervate the muscles fire normally, they measured neuronal activity in response to visual stimuli. By moving a virtual landscape quickly or slowly they could mimic fast or slow swimming by the fish. Interestingly, they found that the fish would adjust its neuronal activity up or down so its perceived swim speed matched the movement of the virtual landscape or, in other words, so the external stimuli matched the expected result of its actions. Engert’s group mapped the neurons responsible for visual processing and locomotion, as well as those responsible for gain control up or down to match the fish’s swimming strength with the external stimuli.
Drubin describes how his lab began studying actin dynamics and endocytosis in yeast using two-color, real-time fluorescence and kymographs. These tools enabled his team to confirm that actin regulated clathrin-mediated endocytosis. They discovered that BAR and F-BAR proteins stabilized the process by acting as a scaffold for actin and facilitating invagination and fission of the cell membrane to develop vesicles.
Actin forms many cellular structures and regulates a variety of critical biological processes. Dr. David Drubin’s lab focuses on studying actin in the context of membrane trafficking. In his first iBiology seminar, Drubin recounts seminal research done using the intracellular pathogen Listeria that uncovered how the bacteria harnesses phagocytosis and actin polymerization to facilitate motility. These initial studies led to the discovery of key regulators of actin filament formation including Arp2/3 and N-WASP. Advances in yeast genetics, biochemistry and imaging then allowed Drubin and others to expand their studies to actin dynamics and endocytosis in yeast.
Drubin explains how he and his lab transferred their knowledge of endocytosis in yeast to determine how actin dynamics are harnessed to drive endocytic traffic in mammalian cells. In mammalian cells, his team observed the importance of actin-dynamin interactions in clathrin-dependent endocytosis. Interestingly, they found variability in endocytic site morphology and dynamics. Studies using stem cells suggested that this diversity in actin-mediated endocytosis is important for determining cell identity and development.
Drubin explains how endocytosis can be used as a system to dissect the mechanisms of actin dynamics in yeast. He focuses on his lab’s research on three key processes: actin disassembly, filament capping and Arp2/3 nucleation. By giving an overview of the importance of actin dynamics in regulating a single cell process, endocytosis, Drubin highlights the crucial role of actin assembly and disassembly in both yeast and mammalian cells.
A fundamental question in neuroscience is how synapses are assembled in living animals to produce behaviors and store memories. Dr. Daniel Colón-Ramos and his lab address these questions by studying the cell biology of the neuronal synapse. In the first part of his seminar series, he introduces approaches his group has pioneered and implemented to image and manipulate synapses in vivo and with single-cell resolution in the nematode C.elegans. He also discusses fundamental aspects of genetics, cell biology and neuroscience which are necessary for understanding his research program and, more generally, for understanding how scientists make use of model organisms to generate new knowledge.
Cheng shows how his laboratory has used Cryo-EM to study the atomic resolution of membrane proteins. It is challenging to use conventional methods to study membrane protein structure, given that the 3D structure of most membrane proteins is dependent on their interaction with the phospholipid bilayer. Cheng describes how his laboratory has overcome these challenges to successfully solve the protein structure of the TRPV1 ion channel in different conformations at atomic resolution. He describes the benefits of using of amphipols, lipid nanodiscs, and Fab-assisted approaches to facilitate structural studies.
Why do females fight? For over a century, biologists thought that female aggression was uncommon in the animal kingdom. In this lecture, Dr. Eleanor Bath dispels that notion and shows that female aggression in fruit flies increases after mating. More specifically, she shows that semen and a small protein in the male ejaculate lead to increased female aggression in Drosophila melanogaster.
What is the involvement of microRNAs in the inflammatory response? In this seminar, Dr. David Baltimore shows that the expression of three microRNAs (miR-132, miR-146, and miR-155) increase upon activation of the inflammatory pathway. Baltimore characterizes these microRNAs and shows how they are involved in the precise tuning of the inflammatory response.
Ashcroft expands on what is known about the KATP channel and its role in insulin secretion. It is an octomeric complex composed of 4 Kir6.2 subunits and 4 SUR1 subunits. ATP binds to both proteins, and changes in metabolically generated ATP couple metabolism to KATP channel activity. Functional studies showed that the KATP channel mutations found in neonatal diabetes impair the ability of ATP to close the channel and stimulate insulin release. This suggested that drugs that could directly close the KATP channel would stimulate insulin release and might be a good therapy for neonatal diabetes. Sulfonylurea drugs were already known to directly close the KATP channel and have been safely used to treat type 2 diabetes for many years. Based on this knowledge, many patients with neonatal diabetes have now switched from insulin injections to oral sulfonylurea drugs. This has resulted in much better glucose control. Ashcroft goes on to explain how insights from studying neonatal diabetes have also led to a better understanding of the impact of chronic hyperglycemia in type 2 diabetes.
Dr. Norma Andrews overviews the mechanisms of cellular plasma membrane repair. As she describes, a lesion is followed by a Ca2+-dependent movement of vesicles to the plasma membrane. By studying how the Trypanosoma cruzi parasite enters the cell, Andrews’ laboratory discovered that an increase of intracellular calcium was triggering lysosomal fusion to the plasma membrane. This unexpected observation allowed them to conclude that upon an injury to the plasma membrane, a Ca2+ influx induces lysosomal exocytosis mediated repair. This research demonstrates that lysosomes are not only responsible for the degradation of material that comes inside the cell through endocytosis, but also have an important role in plasma membrane repair.
Andrews further explains how Ca2+-dependent exocytosis of lysosomes aids membrane repair. Her laboratory showed that after lysosomal exocytosis, an injury to the plasma membrane would also trigger a Ca2+-dependent endocytosis that is required for the repair mechanism. Andrews laboratory showed that lysosomes release the enzyme acid sphingomyelinase (ASM) which induce the endocytosis required for plasma membrane repair.
Injecting adult stem cells into the bloodstream could help regenerate tissue damaged by heart attacks. For this to happen, circulating stem cells need to exit blood vessels and reach the damaged tissue. While scientists knew that circulating stem cells are able to exit the bloodstream, how they did it was a mystery. In this lecture, Tyler Allen describes angiopellosis, a new way for circulating stem cells exit blood vessels when injected into the blood for therapies.
This talk is part of the Young Scientist Seminars, a video series produced that features young scientists giving talks about their research and discoveries.
Many of us are used to seeing cartoons of cells with organelles shown as static, isolated structures.
Voeltz explains how her lab used a BioID strategy to identify some of the proteins found at membrane contact sites between the ER and endosomes; a difficult task given the transient nature of contact sites.
Eukaryotic cells have many different membrane-bound organelles with distinct functions and characteristic shapes. How does this happen? Dr. Tom Rapoport explains the important role of protein sorting in determining organelle shape and function.
The ER is a vast network that includes different domains with different functions. The rough ER is made of ribosome covered membrane sheets and is involved in protein translation.
Dan Littman discusses the opposing roles of Th17 cells. They protect mucosal surfaces from infection with bacteria and fungi, but they can also cause autoimmune inflammation.
Littman explains that different commensal microbes in our gut elicit different T cell responses - either pathogenic or non-pathogenic.
In mammals, sex is determined by a pair of unequal sex chromosomes. Genetically male mammals have an X and a Y chromosome while genetically female mammals have two X chromosomes. The X chromosome is many times larger than the Y chromosome. To compensate for this genetic inequality, female mammals undergo X chromosome inactivation in which one of the X chromosomes is randomly chosen to be silenced. X chromosome inactivation has been studied for over 50 years both because it is a physiologically important event and because it is an excellent model for studying epigenetic silencing of genes by long non-coding RNAs. In her first talk, Dr. Jeannie Lee gives an overview of the steps a cell must go through during X inactivation. These include “counting” the X chromosomes, deciding which X chromosome to inactivate, initiating the inactivation and spreading it across the chromosome, and finally maintaining inactivation of the same X chromosome for the rest of the life of the organism.
Lee elaborates on the early steps of X inactivation. Very early in development, cells “count” the number of X chromosomes and decide if one needs to be inactivated, and if so which one. There is a region of the X chromosome called the X inactivation center which is enriched in long non-coding RNAs (lncRNAs). Lee explains how she and others showed that by sensing the ratio of two specific lncRNAs the cell can determine how many X chromosomes are present. Further studies showed that two different lncRNAs are responsible for randomly determining which X chromosome will be inactivated. Finally, she discusses the hypothesis that the allelic choice mechanism depends on a transient chromosomal pairing event that occurs at the beginning of the dosage compensation process.
Lee describes how X inactivation is nucleated and spreads across the X chromosome. The Xist lncRNA is known to be necessary and sufficient for X inactivation. Lee describes experiments that identified the factors that tether Xist to the X chromosome and showed how Xist spreads to cover the entire X chromosome. She then goes on to explain that Xist blocks transcription in three ways: 1) Xist recruits factors that repress transcription via epigenetic modification such as histone methylation 2) Xist repels factors that open chromatin preparing it for transcription and 3) Xist changes the 3 dimensional organization of chromosomes. Lee ends with a model of our current understanding of the complex but critical process of X chromosome inactivation.
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.
The expansion of lungs for oxygen uptake is facilitated by lung surfactant. The groundbreaking discovery of this substance was made by Dr. John Clements. In this Discovery Talk, Clements details his scientific journey, touching on his early research, the resistance he encountered in the field, and the discovery of lung surfactant, which has saved millions of neonatal lives.
There are many processes and signals in cells that must be turned on and off, sometimes very quickly. How is this done? One important way is via post-translational modification of proteins such as phosphorylation or dephosphorylation. In her first talk, Dr. Anne Bertolotti introduces us to protein phosphatases, the enzymes that remove phosphate from proteins and work in opposition to protein kinases. She gives a brief history of the early experiments that showed that phosphatases are vital to regulating the stability, localization and interactions of many proteins. Bertolotti also describes more recent work demonstrating that protein phosphatases are split enzymes with a catalytic subunit and a subunit that determines substrate specificity. This selective subunit makes phosphatases exquisitely specific and attractive targets for drug development.
Bertolotti’s lab has had a long time interest in understanding protein folding and the role of misfolded proteins in neurodegenerative disease. In her second talk, Bertolotti explains how her lab found that selectively inhibiting the dephosphorylation of eIF2⍺, a translation initiation factor, led to a reduction in protein synthesis. Decreasing protein synthesis allowed cells to “catch up” with the degradation of misfolded proteins that may accumulate as a result of cell stress. Her lab went on to show that a selective small molecule phosphatase inhibitor had therapeutic effects in a mouse model of Charcot-Marie-Tooth disease; a disease that results from the accumulation of misfolded protein in the ER. This exciting result suggested that targeted inhibition of protein phosphatases may have therapeutic potential for neurodegenerative diseases.
Bertolotti describes a platform developed by her lab that has allowed them to rationally identify selective protein phosphatase inhibitors. Using this platform her lab identified a novel small molecule phosphatase inhibitor that blocks the accumulation of misfolded proteins in the cytosol or nucleus and showed the therapeutic effects of the molecule in a model of Huntington’s disease.
Brangwynne tells us about recent work in which his lab has used light to control phase separation behavior in cells. By linking IDRs from proteins that are known to phase separate to protein domains that weakly oligomerize in response to light, his lab has generated tools that are allowing them to investigate the role of phase separation in different cell processes in many cell types.
Brangwynne focuses on the formation of the nucleolus; one of several membrane-less bodies found in the nucleus. Brangwynne’s lab was able to show that assembly of the nucleolus also can be described by the physics of phase separation.
How do the tiny, crowded, constantly moving molecules inside of cells come together to form functional structures such as organelles? Dr. Cliff Brangwynne explains that many of the organelles we are familiar with, such as the nucleus and the Golgi apparatus, are membrane bound. However, some organelles, such as P granules and nuclear bodies, are not surrounded by a membrane.
Förster Resonance Energy Transfer (FRET) microscopy is a technique that allows monitoring of interactions between dyes that occur on the nanometer scale. This sensitivity to small changes in distance and orientation make it a popular technique for building biosensors. Here, Philippe Bastiaens describes the physics behind FRET and how FRET can be measured with a microscope.