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3D Animation Captures Viral Infection in Action

Posted on by Lawrence Tabak, D.D.S., Ph.D.

With the summer holiday season now in full swing, the blog will also swing into its annual August series. For most of the month, I will share with you just a small sampling of the colorful videos and snapshots of life captured in a select few of the hundreds of NIH-supported research labs around the country.

To get us started, let’s turn to the study of viruses. Researchers now can generate vast amounts of data relatively quickly on a virus of interest. But data are often displayed as numbers or two-dimensional digital images on a computer screen. For most virologists, it’s extremely helpful to see a virus and its data streaming in three dimensions. To do so, they turn to a technological tool that we all know so well: animation.

This research animation features the chikungunya virus, a sometimes debilitating, mosquito-borne pathogen transmitted mainly in developing countries in Africa, Asia and the Americas. The animation illustrates large amounts of research data to show how the chikungunya virus infects our cells and uses its specialized machinery to release its genetic material into the cell and seed future infections. Let’s take a look. 

In the opening seconds, you see how receptor binding glycoproteins (light blue), which are proteins with a carbohydrate attached on the viral surface, dock with protein receptors (yellow) on a host cell. At five seconds, the virus is drawn inside the cell. The change in the color of the chikungunya particle shows that it’s coated in a vesicle, which helps the virus make its way unhindered through the cytoplasm. 

At 10 seconds, the virus then enters an endosome, ubiquitous bubble-like compartments that transport material from outside the cell into the cytosol, the fluid part of the cytoplasm. Once inside the endosome, the acidic environment makes other glycoproteins (red, blue, yellow) on the viral surface change shape and become more flexible and dynamic. These glycoproteins serve as machinery that enables them to reach out and grab onto the surrounding endosome membrane, which ultimately will be fused with the virus’s own membrane.

As more of those fusion glycoproteins grab on, fold back on themselves, and form into hairpin-like shapes, they pull the membranes together. The animation illustrates not only the changes in protein organization, but the resulting effects on the integrity of the membrane structures as this dynamic process proceeds. At 53 seconds, the viral protein shell, or capsid (green), which contains the virus’ genetic instructions, is released back out into the cell where it will ultimately go on to make more virus.

This remarkable animation comes from Margot Riggi and Janet Iwasa, experts in visualizing biology at the University of Utah’s Animation Lab, Salt Lake City. Their data source was researcher Kelly Lee, University of Washington, Seattle, who collaborated closely with Riggi and Iwasa on this project. The final product was considered so outstanding that it took the top prize for short videos in the 2022 BioArt Awards competition, sponsored by the Federation of American Societies for Experimental Biology (FASEB).

The Lee lab uses various research methods to understand the specific shape-shifting changes that chikungunya and other viruses perform as they invade and infect cells. One of the lab’s key visual tools is cryo-electron microscopy (Cryo-EM), specifically cryo-electron tomography (cryo-ET). Cryto-ET enables complex 3D structures, including the intermediate state of biological reactions, to be captured and imaged in remarkably fine detail.

In a study in the journal Nature Communications [1] last year, Lee’s team used cryo-ET to reveal how the chikungunya virus invades and delivers its genetic cargo into human cells to initiate a new infection. While Lee’s cryo-ET data revealed stages of the virus entry process and fine structural details of changes to the virus as it enters a cell and starts an infection, it still represented a series of snapshots with missing steps in between. So, Lee’s lab teamed up with The Animation Lab to help beautifully fill in the gaps.

Visualizing chikungunya and similar viruses in action not only makes for informative animations, it helps researchers discover better potential targets to intervene in this process. This basic research continues to make progress, and so do ongoing efforts to develop a chikungunya vaccine [2] and specific treatments that would help give millions of people relief from the aches, pains, and rashes associated with this still-untreatable infection.


[1] Visualization of conformational changes and membrane remodeling leading to genome delivery by viral class-II fusion machinery. Mangala Prasad V, Blijleven JS, Smit JM, Lee KK. Nat Commun. 2022 Aug 15;13(1):4772. doi: 10.1038/s41467-022-32431-9. PMID: 35970990; PMCID: PMC9378758.

[2] Experimental chikungunya vaccine is safe and well-tolerated in early trial, National Institute of Allergy and Infectious Diseases news release, April 27, 2020.


Chikungunya Virus (Centers for Disease Control and Prevention, Atlanta)

Global Arbovirus Initiative (World Health Organization, Geneva, Switzerland)

The Animation Lab (University of Utah, Salt Lake City)

Video: Janet Iwasa (TED Speaker)

Lee Lab (University of Washington, Seattle)

BioArt Awards (Federation of American Societies for Experimental Biology, Rockville, MD)

NIH Support: National Institute of General Medical Sciences; National Institute of Allergy and Infectious Diseases

A Nose for Science

Posted on by Dr. Francis Collins

Mouse Nasal Cavity
Credit: Lu Yang, David Ornitz, and Sung-Ho Huh, Washington University School of Medicine, St. Louis; University of Nebraska Medical Center, Omaha

Our nose does a lot more than take in oxygen, smell, and sometimes sniffle. This complex organ also helps us taste and, as many of us notice during spring allergy season when our noses get stuffy, it even provides some important anatomic features to enable us to speak clearly.

This colorful, almost psychedelic image shows the entire olfactory epithelium, or “smell center,” (green) inside the nasal cavity of a newborn mouse. The olfactory epithelium drapes over the interior walls of the nasal cavity and its curvy bony parts (red). Every cell in the nose contains DNA (blue).

The olfactory epithelium detects odorant molecules in the air, providing a sense of smell. In humans, the nose has about 400 types of scent receptors, and they can detect at least 1 trillion different odors [1].

But this is more than just a cool image captured by graduate student Lu Yang, who works with David Ornitz at Washington University School of Medicine, St. Louis. The two discovered a new type of progenitor cell, called a FEP cell, that has the capacity to generate the entire smell center [2]. Progenitor cells are made by stem cells. But they are capable of multiplying and producing various cells of a particular lineage that serve as the workforce for specialized tissues, such as the olfactory epithelium.

Yang and Ornitz also discovered that the FEP cells crank out a molecule, called FGF20, that controls the growth of the bony parts in the nasal cavity. This seems to regulate the size of the olfactory system, which has fascinating implications for understanding how many mammals possess a keener sense of smell than humans.

But it turns out that FGF20 does a lot more than control smell. While working in Ornitz’s lab as a postdoc, Sung-Ho Huh, now an assistant professor at the University of Nebraska Medical Center, Omaha, discovered that FGF20 helps form the cochlea [3]. This inner-ear region allows us to hear, and mice born without FGF20 are deaf. Other studies show that FGF20 is important for development of the kidney, teeth, mammary gland, and of specific types of hair [4-7]. Clearly, this indicates multi-tasking can be a key feature of a protein, not a trivial glitch.

The image was one of the winners in the 2018 BioArt Scientific Image & Video Competition, sponsored by the Federation of American Societies for Experimental Biology (FASEB). Its vibrant colors help to show the basics of smell, and remind us that every scientific picture tells a story.


[1] Humans can discriminate more than 1 trillion olfactory stimuli. Bushdid C1, Magnasco MO, Vosshall LB, Keller A. Science. 2014 Mar 21;343(6177):1370-1372.

[2] FGF20-Expressing, Wnt-Responsive Olfactory Epithelial Progenitors Regulate Underlying Turbinate Growth to Optimize Surface Area. Yang LM, Huh SH, Ornitz DM. Dev Cell. 2018;46(5):564-580.

[3] Differentiation of the lateral compartment of the cochlea requires a temporally restricted FGF20 signal. Huh SH, Jones J, Warchol ME, Ornitz DM. PLoS Biol. 2012;10(1):e1001231.

[4] FGF9 and FGF20 maintain the stemness of nephron progenitors in mice and man. Barak H, Huh SH, Chen S, Jeanpierre C, Martinovic J, Parisot M, Bole-Feysot C, Nitschke P, Salomon R, Antignac C, Ornitz DM, Kopan R. Dev. Cell. 2012;22(6):1191-1207

[5] Ectodysplasin target gene Fgf20 regulates mammary bud growth and ductal invasion and branching during puberty. Elo T, Lindfors PH, Lan Q, Voutilainen M, Trela E, Ohlsson C, Huh SH, Ornitz DM, Poutanen M, Howard BA, Mikkola ML. Sci Rep. 2017;7(1):5049

[6] Ectodysplasin regulates activator-inhibitor balance in murine tooth development through Fgf20 signaling. D Haara O, Harjunmaa E, Lindfors PH, Huh SH, Fliniaux I, Aberg T, Jernvall J, Ornitz DM, Mikkola ML, Thesleff I. Development. 2012;139(17):3189-3199.

[7] Fgf20 governs formation of primary and secondary dermal condensations in developing hair follicles. Huh SH, Närhi K, Lindfors PH, Häärä O, Yang L, Ornitz DM, Mikkola ML. Genes Dev. 2013;27(4):450-458.


Taste and Smell (National Institute on Deafness and Other Communication Disorders/NIH)

Ornitz Lab, (Washington University, St. Louis)

Huh Lab, (University of Nebraska Medical Center, Omaha)

BioArt Scientific Image & Video Competition, (Federation of American Societies for Experimental Biology, Bethesda, MD)

NIH Support: National Heart, Lung, and Blood Institute; National Institute of Neurological Disorders and Stroke; National Institute on Deafness and Other Communication Disorders

Snapshots of Life: A Colorful Look Inside the Retina

Posted on by Dr. Francis Collins

Mapping neurons in the retina

Credit: Amy Robinson, Alex Norton, William Silversmith, Jinseop Kim, Kisuk Lee, Aleks Zlasteski, Matt Green, Matthew Balkam, Rachel Prentki, Marissa Sorek, Celia David, Devon Jones, and Doug Bland, Massachusetts Institute of Technology, Cambridge, MA; Sebastian Seung, Princeton University, Princeton, NJ

This eerie scene might bring back memories of the computer-generated alien war machines from Steven Spielberg’s War of the Worlds thriller. But what you’re seeing is a computer-generated depiction of a quite different world—the world inside the retina, the light-sensitive tissue that lines the back of the eye. The stilt-legged “creatures” are actually ganglion nerve cells, and what appears to be their long “noses” are fibers that will eventually converge to form the optic nerve that relays visual signals to the brain. The dense, multi-colored mat near the bottom of the image is a region where the ganglia and other types of retinal cells interact to convey visual information.

What I find particularly interesting about this image is that it was produced through the joint efforts of people who played EyeWire, an internet crowdsourcing game developed in the lab of computational neuroscientist Sebastian Seung, now at Princeton University in New Jersey.  Seung and his colleagues created EyeWire using a series of high-resolution microscopic images of the mouse retina, which were digitized into 3D cubes containing dense skeins of branching nerve fibers. It’s at this point where the crowdsourcing came in. Online gamers—most of whom aren’t scientists— volunteered for a challenge that involved mapping the 3D structure of individual nerve cells within these 3D cubes. Players literally colored-in the interiors of the cells and progressively traced their long extensions across the image to distinguish them from their neighbors. Sounds easy, but the branches are exceedingly thin and difficult to follow.

Snapshots of Life: Lost Connections in Pompe Disease

Posted on by Dr. Francis Collins

Junctions between motor neurons (green) and muscle fibers (red)

Caption: Abnormal connections between leg muscle fibers (red) and nerves (green) in Pompe disease.
Credit: Darin J. Falk, A. Gary Todd, Robin Yoon, and Barry J. Byrne, University of Florida, Gainesville

Mistletoe? Holly? Not exactly. This seemingly festive image is a micrograph of nerve cells (green) and nerve-muscle junctions (red) in a mouse model of Pompe disease. Such images are helping researchers learn more about this rare form of muscular dystrophy, providing valuable clues in the ongoing search for better treatments and cures.

People with Pompe disease lack an enzyme that cells depend on to break down a stored sugar, known as glycogen, into smaller glucose molecules that can be readily used for energy. Without enough of this enzyme, called acid alpha-glucosidase (GAA), glycogen can accumulate destructively in the liver, heart, and skeletal muscles, making it increasingly difficult to walk, eat, and even breathe.

Snapshots of Life: Tracing the Fibers of Addiction

Posted on by Dr. Francis Collins

DTI fiber tracking image

Credit: John D. Olson, Paul W. Czoty Michelle Bell, Wake Forest School of Medicine, Winston-Salem, NC

This may look like a light-hearted piece of string art, but it’s actually part of a very serious effort to understand what happens to the brain when it’s strung out on drugs. The image, one of the winners of the Federation of American Societies for Experimental Biology’s 2013 BioArt competition, was created with an advanced form of magnetic resonance imaging called Diffusion Tensor Imaging (DTI).

DTI works by detecting the movement of water in the nerve cells of a living brain. By determining which direction water is flowing in axons, the long processes that convey signals to other neurons, researchers can figure out whether the neurons are stretching from the left to right side of the brain (red), top to bottom (blue), or front to back (green). This data is then used to construct a three-dimensional view of the brain and its connections.

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