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Immune Macrophages Use Their Own ‘Morse Code’

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Credit: Hoffmann Lab, UCLA

In the language of Morse code, the letter “S” is three short sounds and the letter “O” is three longer sounds. Put them together in the right order and you have a cry for help: S.O.S. Now an NIH-funded team of researchers has cracked a comparable code that specialized immune cells called macrophages use to signal and respond to a threat.

In fact, by “listening in” on thousands of macrophages over time, one by one, the researchers have identified not just a lone distress signal, or “word,” but a vocabulary of six words. Their studies show that macrophages use these six words at different times to launch an appropriate response. What’s more, they have evidence that autoimmune conditions can arise when immune cells misuse certain words in this vocabulary. This bad communication can cause them incorrectly to attack substances produced by the immune system itself as if they were a foreign invaders.

The findings, published recently in the journal Immunity, come from a University of California, Los Angeles (UCLA) team led by Alexander Hoffmann and Adewunmi Adelaja. As an example of this language of immunity, the video above shows in both frames many immune macrophages (blue and red). You may need to watch the video four times to see what’s happening (I did). Each time you run the video, focus on one of the highlighted cells (outlined in white or green), and note how its nuclear signal intensity varies over time. That signal intensity is plotted in the rectangular box at the bottom.

The macrophages come from a mouse engineered in such a way that cells throughout its body light up to reveal the internal dynamics of an important immune signaling protein called nuclear NFκB. With the cells illuminated, the researchers could watch, or “listen in,” on this important immune signal within hundreds of individual macrophages over time to attempt to recognize and begin to interpret potentially meaningful patterns.

On the left side, macrophages are responding to an immune activating molecule called TNF. On the right, they’re responding to a bacterial toxin called LPS. While the researchers could listen to hundreds of cells at once, in the video they’ve randomly selected two cells (outlined in white or green) on each side to focus on in this example.

As shown in the box in the lower portion of each frame, the cells didn’t respond in precisely the same way to the same threat, just like two people might pronounce the same word slightly differently. But their responses nevertheless show distinct and recognizable patterns. Each of those distinct patterns could be decomposed into six code words. Together these six code words serve as a previously unrecognized immune language!

Overall, the researchers analyzed how more than 12,000 macrophage cells communicated in response to 27 different immune threats. Based on the possible arrangement of temporal nuclear NFκB dynamics, they then generated a list of more than 900 pattern features that could be potential “code words.”

Using an algorithm developed decades ago for the telecommunications industry, they then monitored which of the potential words showed up reliably when macrophages responded to a particular threatening stimulus, such as a bacterial or viral toxin. This narrowed their list to six specific features, or “words,” that correlated with a particular response.

To confirm that these pattern features contained meaning, the team turned to machine learning. If they taught a computer just those six words, they asked, could it distinguish the external threats to which the computerized cells were responding? The answer was yes.

But what if the computer had five words available, instead of six? The researchers found that the computer made more mistakes in recognizing the stimulus, leading the team to conclude that all six words are indeed needed for reliable cellular communication.

To begin to explore the implications of their findings for understanding autoimmune diseases, the researchers conducted similar studies in macrophages from a mouse model of Sjögren’s syndrome, a systemic condition in which the immune system often misguidedly attacks cells that produce saliva and tears. When they listened in on these cells, they found that they used two of the six words incorrectly. As a result, they activated the wrong responses, causing the body to mistakenly perceive a serious threat and attack itself.

While previous studies have proposed that immune cells employ a language, this is the first to identify words in that language, and to show what can happen when those words are misused. Now that researchers have a list of words, the next step is to figure out their precise definitions and interpretations [2] and, ultimately, how their misuse may be corrected to treat immunological diseases.


[1] Six distinct NFκB signaling codons convey discrete information to distinguish stimuli and enable appropriate macrophage responses. Adelaja A, Taylor B, Sheu KM, Liu Y, Luecke S, Hoffmann A. Immunity. 2021 May 11;54(5):916-930.e7.

[2] NF-κB dynamics determine the stimulus specificity of epigenomic reprogramming in macrophages. Cheng QJ, Ohta S, Sheu KM, Spreafico R, Adelaja A, Taylor B, Hoffmann A. Science. 2021 Jun 18;372(6548):1349-1353.


Overview of the Immune System (National Institute of Allergy and Infectious Diseases/NIH)

Sjögren’s Syndrome (National Institute of Dental and Craniofacial Research/NIH)

Alexander Hoffmann (UCLA)

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

Learning from History: Fauci Donates Model to Smithsonian’s COVID-19 Collection

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Not too long after the global coronavirus disease 2019 (COVID-19) pandemic reached the United States, museum curators began collecting material to document the history of this devastating public health crisis and our nation’s response to it. To help tell this story, the Smithsonian Institution’s National Museum of American History recently scored a donation from my friend and colleague Dr. Anthony Fauci, Director of NIH’s National Institute of Allergy and Infectious Diseases.

Widely recognized for serving as a clear voice for science throughout the pandemic, Fauci gave the museum his much-used model of SARS-CoV-2, which is the coronavirus that causes COVID-19. This model, which is based on work conducted by NIH-supported electron microscopists and structural biologists, was 3D printed right here at NIH. By the way, I’m lucky enough to have one too.

Both of these models have “met” an amazing array of people—from presidents to congresspeople to journalists to average citizens—as part of our efforts to help folks understand SARS-CoV-2 and the crucial role of its surface spike proteins. As shown in this brief video, Fauci raised his model one last time and then, ever the public ambassador for science, turned his virtual donation into a memorable teaching moment. I recommend you take a minute or two to watch it.

The donation took place during a virtual ceremony in which the National Museum of American History awarded Fauci its prestigious Great Americans Medal. He received the award for his lifetime contributions to the nation’s ideals and for making a lasting impact on public health via his many philanthropic and humanitarian efforts. Fauci joined an impressive list of luminaries in receiving this honor, including former Secretaries of State Madeleine Albright and General Colin Powell; journalist Tom Brokaw; baseball great Cal Ripken Jr.; tennis star Billie Jean King; and musician Paul Simon. It’s a well-deserved honor for a physician-scientist who’s advised seven presidents on a range of domestic and global health issues, from HIV/AIDS to Ebola to COVID-19.

With Fauci’s model now enshrined as an official piece of U.S. history, the Smithsonian and other museums around the world are stepping up their efforts to gather additional artifacts related to COVID-19 and to chronicle its impacts on the health and economy of our nation. Hopefully, future generations will learn from this history so that humankind is not doomed to repeat it.

It is interesting to note that the National Museum of American History’s collection contains few artifacts from another tragic chapter in our nation’s past: the 1918 Influenza Pandemic. One reason this pandemic went largely undocumented is that, like so many of their fellow citizens, curators chose to overlook its devastating impacts and instead turn toward the future.

Multi-colored artificial flowers
An NIH staff member created these paper flowers from the stickers received over the past several months each time he was screened for COVID-19 at the NIH Clinical Center. Credit: Office of NIH History and Stetten Museum

Today, museum staffers across the country and around the world are stepping up to the challenge of documenting COVID-19’s history with great creativity, collecting all variety of masks, test kits, vaccine vials, and even a few ventilators. At the NIH’s main campus in Bethesda, MD, the Office of NIH History and Stetten Museum is busy preparing a small exhibit of scientific and clinical artifacts that could open as early as the summer of 2021. The museum is also collecting oral histories as part of its “Behind the Mask” project. So far, more than 50 interviews have been conducted with NIH staff, including a scientist who’s helping the hard-hit Navajo Nation during the pandemic; a Clinical Center nurse who’s treating patients with COVID-19, and a mental health professional who’s had to change expectations since the outbreak.

The pandemic isn’t over yet. All of us need to do our part by getting vaccinated against COVID-19 and taking other precautions to prevent the virus’s deadly spread. But won’t it great when—hopefully, one day soon—we can relegate this terrible pandemic to the museums and the history books!


COVID-19 Research (NIH)

Video: National Museum of American History Presents The Great Americans Medal to Anthony S. Fauci (Smithsonian Institution, Washington, D.C.)

National Museum of American History (Smithsonian)

The Office of NIH History and Stetten Museum (NIH)

Using R2D2 to Understand RNA Folding

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If you love learning more about biology at a fundamental level, I have a great video for you! It simulates the 3D folding of RNA. RNA is a single stranded molecule, but it is still capable of forming internal loops that can be stabilized by base pairing, just like its famously double-stranded parent, DNA. Understanding more about RNA folding may be valuable in many different areas of biomedical research, including developing ways to help people with RNA-related diseases, such as certain cancers and neuromuscular disorders, and designing better mRNA vaccines against infectious disease threats (like COVID-19).

Because RNA folding starts even while an RNA is still being made in the cell, the process has proven hugely challenging to follow closely. An innovative solution, shown in this video, comes from the labs of NIH grantees Julius Lucks, Northwestern University, Evanston, IL, and Alan Chen, State University of New York at Albany. The team, led by graduate student Angela Yu and including several diehard Star Wars fans, realized that to visualize RNA folding they needed a technology platform that, like a Star Wars droid, is able to “see” things that others can’t. So, they created R2D2, which is short for Reconstructing RNA Dynamics from Data.

What’s so groundbreaking about the R2D2 approach, which was published recently in Molecular Cell, is that it combines experimental data on RNA folding at the nucleotide level with predictive algorithms at the atomic level to simulate RNA folding in ultra-slow motion [1]. While other computer simulations have been available for decades, they have lacked much-needed experimental data of this complex folding process to confirm their mathematical modeling.

As a gene is transcribed into RNA one building block, or nucleotide, at a time, the elongating RNA strand folds immediately before the whole molecule is fully assembled. But such folding can create a problem: the new strand can tie itself up into a knot-like structure that’s incompatible with the shape it needs to function in a cell.

To slip this knot, the cell has evolved immediate corrective pathways, or countermoves. In this R2D2 video, you can see one countermove called a toehold-mediated strand displacement. In this example, the maneuver is performed by an ancient molecule called a single recognition particle (SRP) RNA. Though SRP RNAs are found in all forms of life, this one comes from the bacterium Escherichia coli and is made up of 114 nucleotides.

The colors in this video highlight different domains of the RNA molecule, all at different stages in the folding process. Some (orange, turquoise) have already folded properly, while another domain (dark purple) is temporarily knotted. For this knotted domain to slip its knot, about 5 seconds into the video, another newly forming region (fuchsia) wiggles down to gain a “toehold.” About 9 seconds in, the temporarily knotted domain untangles and unwinds, and, finally, at about 23 seconds, the strand starts to get reconfigured into the shape it needs to do its job in the cell.

Why would evolution favor such a seemingly inefficient folding process? Well, it might not be inefficient as it first appears. In fact, as Chen noted, some nanotechnologists previously invented toehold displacement as a design principle for generating synthetic DNA and RNA circuits. Little did they know that nature may have scooped them many millennia ago!


[1] Computationally reconstructing cotranscriptional RNA folding from experimental data reveals rearrangement of non-naïve folding intermediates. Yu AM, Gasper PM Cheng L, Chen AA, Lucks JB, et. al. Molecular Cell 8, 1-14. 18 February 2021.


Ribonucleic Acid (RNA) (National Human Genome Research Institute/NIH)

Chen Lab (State University of New York at Albany)

Lucks Laboratory (Northwestern University, Evanston IL)

NIH Support: National Institute of General Medical Sciences; Common Fund

See the Human Cardiovascular System in a Whole New Way

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Watch this brief video and you might guess you’re seeing an animated line drawing, gradually revealing a delicate take on a familiar system: the internal structures of the human body. But this movie doesn’t capture the work of a talented sketch artist. It was created using the first 3D, full-body imaging device using positron emission tomography (PET).

The device is called an EXPLORER (EXtreme Performance LOng axial REsearch scanneR) total-body PET scanner. By pairing this scanner with an advanced method for reconstructing images from vast quantities of data, the researchers can make movies.

For this movie in particular, the researchers injected small amounts of a short-lived radioactive tracer—an essential component of all PET scans—into the lower leg of a study volunteer. They then sat back as the scanner captured images of the tracer moving up the leg and into the body, where it enters the heart. The tracer moves through the heart’s right ventricle to the lungs, back through the left ventricle, and up to the brain. Keep watching, and, near the 30-second mark, you will see in closer focus a haunting capture of the beating heart.

This groundbreaking scanner was developed and tested by Jinyi Qi, Simon Cherry, Ramsey Badawi, and their colleagues at the University of California, Davis [1]. As the NIH-funded researchers reported recently in Proceedings of the National Academy of Sciences, their new scanner can capture dynamic changes in the body that take place in a tenth of a second [2]. That’s faster than the blink of an eye!

This movie is composed of frames captured at 0.1-second intervals. It highlights a feature that makes this scanner so unique: its ability to visualize the whole body at once. Other medical imaging methods, including MRI, CT, and traditional PET scans, can be used to capture beautiful images of the heart or the brain, for example. But they can’t show what’s happening in the heart and brain at the same time.

The ability to capture the dynamics of radioactive tracers in multiple organs at once opens a new window into human biology. For example, the EXPLORER system makes it possible to measure inflammation that occurs in many parts of the body after a heart attack, as well as to study interactions between the brain and gut in Parkinson’s disease and other disorders.

EXPLORER also offers other advantages. It’s extra sensitive, which enables it to capture images other scanners would miss—and with a lower dose of radiation. It’s also much faster than a regular PET scanner, making it especially useful for imaging wiggly kids. And it expands the realm of research possibilities for PET imaging studies. For instance, researchers might repeatedly image a person with arthritis over time to observe changes that may be related to treatments or exercise.

Currently, the UC Davis team is working with colleagues at the University of California, San Francisco to use EXPLORER to enhance our understanding of HIV infection. Their preliminary findings show that the scanner makes it easier to capture where the human immunodeficiency virus (HIV), the cause of AIDS, is lurking in the body by picking up on signals too weak to be seen on traditional PET scans.

While the research potential for this scanner is clearly vast, it also holds promise for clinical use. In fact, a commercial version of the scanner, called uEXPLORER, has been approved by the FDA and is in use at UC Davis [3]. The researchers have found that its improved sensitivity makes it much easier to detect cancers in patients who are obese and, therefore, harder to image well using traditional PET scanners.

As soon as the COVID-19 outbreak subsides enough to allow clinical research to resume, the researchers say they’ll begin recruiting patients with cancer into a clinical study designed to compare traditional PET and EXPLORER scans directly.

As these researchers, and other researchers around the world, begin to put this new scanner to use, we can look forward to seeing many more remarkable movies like this one. Imagine what they will reveal!


[1] First human imaging studies with the EXPLORER total-body PET scanner. Badawi RD, Shi H, Hu P, Chen S, Xu T, Price PM, Ding Y, Spencer BA, Nardo L, Liu W, Bao J, Jones T, Li H, Cherry SR. J Nucl Med. 2019 Mar;60(3):299-303.

[2] Subsecond total-body imaging using ultrasensitive positron emission tomography. Zhang X, Cherry SR, Xie Z, Shi H, Badawi RD, Qi J. Proc Natl Acad Sci U S A. 2020 Feb 4;117(5):2265-2267.

[3] “United Imaging Healthcare uEXPLORER Total-body Scanner Cleared by FDA, Available in U.S. Early 2019.” Cision PR Newswire. January 22, 2019.


Positron Emission Tomography (PET) (NIH Clinical Center)

EXPLORER Total-Body PET Scanner (University of California, Davis)

Cherry Lab (UC Davis)

Badawi Lab (UC Davis Medical Center, Sacramento)

NIH Support: National Cancer Institute; National Institute of Biomedical Imaging and Bioengineering; Common Fund

Finding Beauty in Cell Stress

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Most stressful situations that we experience in daily life aren’t ones that we’d choose to repeat. But the cellular stress response captured in this video is certainly worth repeating a few times, so you can track what happens when two cancer cells get hit with stressors.

In this movie of two highly stressed osteosarcoma cells, you first see the appearance of many droplet-like structures (green). This is followed by a second set of droplets (magenta) and, finally, the fusion of both types of droplets.

These droplets are composed of fluorescently labeled stress-response proteins, either G3BP or UBQLN2 (Ubiquilin-2). Each protein is undergoing a fascinating process, called phase separation, in which a non-membrane bound compartment of the cytoplasm emerges and constrains the motion of proteins within it. Subsequently, the proteins fuse with like proteins to form larger droplets, in much the same way that raindrops merge on a car’s windshield.

Julia Riley, an undergraduate student in the NIH-supported lab of Heidi Hehnly and lab of Carlos Castañeda, Syracuse University, NY, shot this movie using the sophisticated tools of fluorescence microscopy. It’s the next installment in our series featuring winners of the 2019 Green Fluorescent Protein Image and Video Contest, sponsored by the American Society for Cell Biology. The contest honors the discovery of green fluorescent protein (GFP), which—together with a rainbow of other fluorescent proteins—has enabled researchers to visualize proteins and their dynamic activities inside cells for the last 25 years.

Riley and colleagues suspect that, in this case, phase separation is a protective measure that allows proteins to wall themselves off from the rest of the cell during stressful conditions. In this way, the proteins can create new functional units within the cell. The researchers are working to learn much more about what this interesting behavior entails as a basic organizing principle in the cell and how it works.

Even more intriguing is that similar stress-responding proteins are commonly altered in people with the devastating neurologic condition known as amyotrophic lateral sclerosis (ALS). ALS is a group of rare neurological diseases that involve the progressive deterioration of neurons responsible for voluntary movements such as chewing, walking, and talking. There’s been the suggestion that these phase separation droplets may seed the formation of the larger protein aggregates that accumulate in the motor neurons of people with this debilitating and fatal condition.

Castañeda and Hehnly, working with J. Paul Taylor at St. Jude Children’s Research Hospital, Memphis, earlier reported that Ubiquilin-2 forms stress-induced droplets in multiple cell types [1]. More recently, they showed that mutations in Ubiquilin-2 have been linked to ALS changes in the way that the protein undergoes phase separation in a test tube [2].

While the proteins in this award-winning video aren’t mutant forms, Riley is now working on the sequel, featuring versions of the Ubiquilin-2 protein that you’d find in some people with ALS. She hopes to capture how those mutations might produce a different movie and what that might mean for understanding ALS.


[1] Ubiquitin Modulates Liquid-Liquid Phase Separation of UBQLN2 via Disruption of Multivalent Interactions. Dao TP, Kolaitis R-M, Kim HJ, O’Donovan K, Martyniak B, Colicino E, Hehnly H, Taylor JP, Castañeda CA. Molecular Cell. 2018 Mar 15;69(6):965-978.e6.

[2] ALS-Linked Mutations Affect UBQLN2 Oligomerization and Phase Separation in a Position- and Amino Acid-Dependent Manner. Dao TP, Martyniak B, Canning AJ, Lei Y, Colicino EG, Cosgrove MS, Hehnly H, Castañeda CA. Structure. 2019 Jun 4;27(6):937-951.e5.


Amyotrophic Lateral Sclerosis (ALS) (National Institute of Neurological Disorders and Stroke/NIH)

Castañeda Lab (Syracuse University, NY)

Hehnly Lab (Syracuse University)

Green Fluorescent Protein Image and Video Contest (American Society for Cell Biology, Bethesda, MD)

2008 Nobel Prize in Chemistry (Nobel Foundation, Stockholm, Sweden)

NIH Support: National Institute of General Medical Sciences

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