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Janet Iwasa (Harvard): Animating Cell Biology

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Janet Iwasa (Harvard): Animating Cell Biology



Janet Iwasa recalls the animation that first led her to realize how much more information can be included in an animation compared to a static image. She explains that animations can provide a visualization of a hypothesis and bring together structural data, protein-protein interactions and dynamic information in a process that often helps researchers refine their models.

Inner Life of a Cell | Protein Packing

Harvard University and XVIVO come together again to add to the growing series of scientific animations for BioVisions -- Harvard's multimedia lab in the department of Molecular and Cellular Biology. 'Protein Packing' strives to more accurately depict the molecular chaos in each and every cell, with proteins jittering around in what may seem like random motion. Proteins occupy roughly 40% of the cytoplasm, creating an environment that risks unintentional interaction and aggregation. Via diffusion and motor protein transport, these molecules are directed to sites where they are needed.

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Janet Iwasa: How animations can help scientists test a hypothesis

3D animation can bring scientific hypotheses to life. Molecular biologist (and TED Fellow) Janet Iwasa introduces a new open-source animation software designed just for scientists.

TEDTalks is a daily video podcast of the best talks and performances from the TED Conference, where the world's leading thinkers and doers give the talk of their lives in 18 minutes (or less). Look for talks on Technology, Entertainment and Design -- plus science, business, global issues, the arts and much more.
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A Protocell Forming from Fatty Acids

The work by Janet Iwasa is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 United States License.
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Janet Iwasa: Animating HIV

Why animate HIV?

Molecular biologist and animator Janet Iwasa hopes that illustrating the entire life cycle of HIV will push researchers closer to a cure.

Janet Iwasa got her PhD in Molecular Biology at the University of California, San Francisco and is now a Research Assistant Professor at the Univeristy of Utah. She's also an award-winning animator and illustrator who brings biological research to life in her amazing animations. Not satisfied to do all the animating herself, Janet has also developed a sreamlined animation application that can be used by other biologists to share their research with the world.

Like Janet Iwasa's profile? Visit The Secret Life of Scientists and Engineers online and on Facebook.
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The Secret Life of Scientists and Engineers is an Emmy-nominated web video series and site from the makers of the acclaimed science series, PBS's NOVA. Each episode profiles one of today's leading scientists, and shows what happens when the lab coats come off. Secret Life is produced by Seftel Productions, Inc.

Janet Iwasa: Biologists with Movies in Their Heads

Janet Iwasa animates other biologists' ideas and research and creates a beautiful and useful way to communicate about the molecular world.

Janet Iwasa got her PhD in Molecular Biology at the University of California, San Francisco and is now a Research Assistant Professor at the Univeristy of Utah. She's also an award-winning animator and illustrator who brings biological research to life in her amazing animations. Not satisfied to do all the animating herself, Janet has also developed a sreamlined animation application that can be used by other biologists to share their research with the world.

Like Janet Iwasa's profile? Visit The Secret Life of Scientists and Engineers online and on Facebook.
Web:
Facebook:

The Secret Life of Scientists and Engineers is an Emmy-nominated web video series and site from the makers of the acclaimed science series, PBS's NOVA. Each episode profiles one of today's leading scientists, and shows what happens when the lab coats come off. Secret Life is produced by Seftel Productions, Inc.
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Interview with a Scientist: Janet Iwasa, Molecular Animator

Janet Iwasa discusses the process of creating detailed animations that convey the latest thinking of how biological molecules interact.

National Institute of General Medical Sciences

HIV Replication 3D Medical Animation

It is a very excellent animation which explains the hiv replication very clearly.
For free download of this video please visit my webpage

And other 3D animation videos visit

Regards,
Dr.Rufus

The Lyrics of this video is here

Targeting HIV replication

The replication of HIV 1 is a multi-stage process.

Each step is crucial to successful replication and is therefore a potential target of antiretroviral drugs.

Step one is the infection of a suitable host-cell, such as a CD4-positive T-lymphocyte.

Entry of HIV into the cell requires the presence of certain receptors on the cell surface, CD4 -- receptors and co-receptors such as CCR5 or CXCR4.

These receptors interact with protein-complexes, which are embedded in the viral envelope.

These complexes are composed of two glycoproteins:

an extracellular gp 120 and
a transmembrane gp 41

When HIV approaches the target cell gp120 binds to the CD4-receptors. This process is termed attachment.

It promotes further binding to a co-receptor. Co-receptor binding results in a conformational change in gp120.

This allows gp41 to unfold and insert its hydrophobic terminus into the cell membrane.

Gp 41 then folds back on itself.

This draws the virus towards the cell and facilitates the fusion of their membranes.

The viral nucleocapsid enters the host cell and breaks open releasing two viral RNA-strands and 3 essential replication enzymes:

Integrase, Protease and Reverse Transcriptase.

Reverse Transcriptase begins the reverse transcription of viral RNA.

It has two catalytic domains:

The Ribonuclease-H active site

And the polymerase active site

Here single stranded viral RNA is transcribed into an RNA-DNA double helix. Ribonuclease- H breaks down the RNA.

The polymerase then completes the remaining DNA-strand to form a DNA -- double helix.

Now Integrase goes into action.

It cleaves a dinucleotide from each 3-prime end of the DNA creating two sticky ends.

Integrase then transfers the DNA into the cell nucleus and facilitates its integration into the host cell genome.

The host cell genome now contains the genetic information of HIV.

Activation of the cell induces transcription of proviral DNA into messenger RNA.

The viral messenger RNA migrates into the cytoplasm where building blocks for a new virus are synthesised.

Some of them have to be processed by the viral protease.

Protease cleaves longer proteins into smaller core proteins.

This step is crucial to create an infectious virus.

Two viral RNA-strands and the replication enzymes then come together and core proteins assemble around them forming the capsid.

This immature particle leaves the cell acquiring a new envelope of host and viral proteins.

The virus matures and becomes ready to infect other cells.

HIV replicates billions of times per day destroying the hosts` immune cells and eventually causing disease progression.

Drugs which interfere with the key steps of viral replication can stop this fatal process.

Entry into the host cell can be blocked by fusion inhibitors for example.

Inhibition of reverse transcriptase by nucleoside inhibitors or by non-nucleoside Reverse Transcriptase- inhibitors is part of standard antiretroviral regimens.

The action of Integrase can be blocked.

Protease inhibitors are also part of standard antiretroviral therapy.

Each blocked step in viral replication is a step towards better control of HIV disease.


Script, Storyboard, Art Direction by: Frank Schauder, MD
Animation: MACKEVISION
Publicity: Dr.Rufus Rajadurai.MD.,D.DiaDENS.,

Clathrin Mediated Endocytosis by Janet Iwasa and Tom Kirchhausen 2012

Molecular movie representing the assembly of a clathrin coated pit, its dynamin-based budding to form a coated vesicle and the removal of the coat mediated by the uncoating Hsc70/auxilin dependent reaction. It also shows the first five seconds when the coat starts to form. The simulation is based on high resolution snapshots obtained by x-ray crystalography and cryo-electron microscopy and time-series from single molecule/single object high resolution fluorescence microscopy. This 2012 rendition was created by Janet Iwasa and Tom Kirchhausen. Feel free to download and use for teaching purposes.
Tom Kirchhausen, Harvard Medical School.

Harvard Cell Animation mp4

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Janet Iwasa: Science Goes Hollywood

How do you make an animated film about proteins as visually interesting as a Lord of the Rings mob?

Molecular biologist Janet Iwasa told us how she went to Hollywood, learned the tricks of the trade, and now retools them to make the molecular world jump off the screen in her films.

Janet Iwasa got her PhD in Molecular Biology at the University of California, San Francisco and is now a Research Assistant Professor at the Univeristy of Utah. She's also an award-winning animator and illustrator who brings biological research to life in her amazing animations. Not satisfied to do all the animating herself, Janet has also developed a sreamlined animation application that can be used by other biologists to share their research with the world.

Like Janet Iwasa's profile? Visit The Secret Life of Scientists and Engineers online and on Facebook.
Web:
Facebook:

The Secret Life of Scientists and Engineers is an Emmy-nominated web video series and site from the makers of the acclaimed science series, PBS's NOVA. Each episode profiles one of today's leading scientists, and shows what happens when the lab coats come off. Secret Life is produced by Seftel Productions, Inc.

CB201 - Cellular Biology course at Harvard Medical School

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Clathrin mediated endocytosis - cell proccess.flv

Clathrin-mediated endocytosis This animation shows the process of clathrin-mediated endocytosis of transferrin receptors, focusing on the assembly and disassembly of the clathrin cage. A single triskelion, which is approximately 100nm across at its widest point. Iron-bound transferrin is bound to its receptor on the exterior cell membrane. The transferrin receptor in turn binds to adaptor proteins in the interior of the cell, triggering the formation of a clathrin cage around the bound transferrin receptors. Soon after the vesicle has budded off the membrane, clathrin cage disassembly begins. Disassembly is mediated by HSC70, and its cofactor auxilin. The animation takes place in real time, as clathrin cages have been observed to assemble in ~ 1 minute and disassemble in a few seconds after budding from the membrane. Endocytosis is the process by which cells are able to internalize membrane and extracellular materials through the formation of a vesicle. The process of membrane budding to form a vesicle is generally mediated by a protein coat, which acts both as a means to deform the membrane and to concentrate specific types of proteins inside the nascent vesicle. Clathrin is a coat protein that has been shown to function in receptor-mediated endocytosis events at the plasma membrane. Celldance 2008, 1st Place Video.

Image contributed by Janet Iwasa (Harvard Medical School); Tomas Kirchhausen (Harvard Medical School)

Cellular Biology

Animation Director | What I do & how much I make | Part 1 | Khan Academy

Lisa talks about her role as an animation director for TED-Ed and as a freelance animator, including key responsibilities and compensation. This video is part of a new series on Khan Academy covering the responsibilities, requirements, and financial aspects of careers.

Careers and Personal Finance on Khan Academy: Are you wondering how to land your dream job? How to pay off student loans? What’s the best way to negotiate your salary? Finding answers to questions like these can be hard, but we’re here to help. We ask real people in real jobs how they make it all work in our new video series about careers and personal finance, brought to you with support from Bank of America. Check out the videos on Better Money Habits, Bank of America's financial literacy website:

About Khan Academy: Khan Academy is a nonprofit with a mission to provide a free, world-class education for anyone, anywhere. We believe learners of all ages should have unlimited access to free educational content they can master at their own pace. We use intelligent software, deep data analytics and intuitive user interfaces to help students and teachers around the world. Our resources cover preschool through early college education, including math, biology, chemistry, physics, economics, finance, history, grammar and more. We offer free personalized SAT test prep in partnership with the test developer, the College Board. Khan Academy has been translated into dozens of languages, and 100 million people use our platform worldwide every year. More free lessons at KhanAcademy.org

And remember, you can learn anything. For free. For everyone. Forever. #YouCanLearnAnything

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Rob Phillips (Cal Tech): A Vision for Quantitative Biology



Rob Phillips is Professor of Applied Physics and Bioengineering at The California Institute of Technology. His research focuses on understanding the physical basis of biological phenomena. Phillips is a co-author of the recently published textbook Physical Biology of the Cell. Prior to the privilege of a life in science, he spent seven years of travel, self-study and work as an electrician.

Dr. Steven Gygi from the Harvard Medical School on the use of genomic technologies for proteomics

Steven Gygi, Ph.D., Associate Professor of Cell Biology, Harvard Medical School, discusses applying strategies for genomic technologies toward the field of proteomics.

Cell Biology: How Do Cells Make Decisions?

The UCSF community honored J. Michael Bishop's 11-year tenure as chancellor of UCSF with an all-day symposium addressing vexing biomedical issues at the Mission Bay campus on June 7. The event focused on four topics: malaria, cell biology, cancer and neurosciences.

As chancellor, Bishop, MD, a Nobel laureate, led UCSF through one of its most expansive periods of growth and achievement, including development of the Mission Bay campus.

In this segment of the symposium, titled Cell Biology: How Do Cells Make Decisions?, the moderator is Marc Kirschner, PhD, John Franklin Enders University Professor of Systems Biology, Department of Systems Biology, Harvard University; the speaker is Richard Losick, PhD, Maria Moors Cabot Professor of Biology, Department of Molecular and Cellular Biology, Harvard University; and panelists are Hana El Samad, assistant professor, Biochemistry & Biophysics, UC Berkeley/UCSF Graduate Group in Bioengineering; and Jonathan Weissman, PhD, professor of Cellular and Molecular Pharmacology and of Biochemistry and Biophysics at UCSF.

Matthew Meselson (Harvard): The Semi-Conservative Replication of DNA



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.

Molecular Motor Struts Like Drunken Sailor

Molecular motors, built from proteins, are a kind of transport service that keep us functioning by trafficking essential chemical packages throughout the cell. To understand how molecular motors work, some researchers are creating animations. Here, each leg of a molecular motor called dynein moves as it progresses along a cellular structure called a microtubule. New data—collected by a team led by Samara Reck-Peterson and published online Jan. 8, 2012, in Nature Structural & Molecular Biology—suggest that dynein's walk is even stranger than the one modeled.

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