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DaQuane Cherry was once the kid who wore a hoodie to hide skin flare-ups in school. Now he’s an artist and advocate helping others feel seen. He reflects on his psoriasis journey, the power of small joys, and why loving yourself first isn’t a cliché—it’s essential. Plus, a deep dive into the history of La Roche-Posay’s legendary spring. See omnystudio.com/listener for privacy information.…
المحتوى المقدم من iBiology. يتم تحميل جميع محتويات البودكاست بما في ذلك الحلقات والرسومات وأوصاف البودكاست وتقديمها مباشرة بواسطة iBiology أو شريك منصة البودكاست الخاص بهم. إذا كنت تعتقد أن شخصًا ما يستخدم عملك المحمي بحقوق الطبع والنشر دون إذنك، فيمكنك اتباع العملية الموضحة هنا https://ar.player.fm/legal.
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
المحتوى المقدم من iBiology. يتم تحميل جميع محتويات البودكاست بما في ذلك الحلقات والرسومات وأوصاف البودكاست وتقديمها مباشرة بواسطة iBiology أو شريك منصة البودكاست الخاص بهم. إذا كنت تعتقد أن شخصًا ما يستخدم عملك المحمي بحقوق الطبع والنشر دون إذنك، فيمكنك اتباع العملية الموضحة هنا https://ar.player.fm/legal.
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.…
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