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Finding Better Ways to Image the Retina

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Two light microscopy fields of the retina showing small blue dots (rods) surrounding larger yellow dots (cones)
Credit: Johnny Tam, National Eye Institute, NIH

Every day, all around the world, eye care professionals are busy performing dilated eye exams. By looking through a patient’s widened pupil, they can view the retina—the postage stamp-sized tissue lining the back of the inner eye—and look for irregularities that may signal the development of vision loss.

The great news is that, thanks to research, retinal imaging just keeps getting better and better. The images above, which show the same cells viewed with two different microscopic techniques, provide good examples of how tweaking existing approaches can significantly improve our ability to visualize the retina’s two types of light-sensitive neurons: rod and cone cells.

Specifically, these images show an area of the outer retina, which is the part of the tissue that’s observed during a dilated eye exam. Thanks to colorization and other techniques, a viewer can readily distinguish between the light-sensing, color-detecting cone cells (orange) and the much smaller, lowlight-sensing rod cells (blue).

These high-res images come from Johnny Tam, a researcher with NIH’s National Eye Institute. Working with Alfredo Dubra, Stanford University, Palo Alto, CA, Tam and his team figured out how to limit light distortion of the rod cells. The key was illuminating the eye using less light, provided as a halo instead of the usual solid, circular beam.

But the researchers’ solution hit a temporary snag when the halo reflected from the rods and cones created another undesirable ring of light. To block it out, Tam’s team introduced a tiny pinhole, called a sub-Airy disk. Along with use of adaptive optics technology [1] to correct for other distortions of light, the scientists were excited to see such a clear view of individual rods and cones. They published their findings recently in the journal Optica [2]

The resolution produced using these techniques is so much improved (33 percent better than with current methods) that it’s even possible to visualize the tiny inner segments of both rods and cones. In the cones, for example, these inner segments help direct light coming into the eye to other, photosensitive parts that absorb single photons of light. The light is then converted into electrical signals that stream to the brain’s visual centers in the occipital cortex, which makes it possible for us to experience vision.

Tam and team are currently working with physician-scientists in the NIH Clinical Center to image the retinas of people with a variety of retinal diseases, including age-related macular degeneration (AMD), a leading cause of vision loss in older adults. These research studies are ongoing, but offer hopeful possibilities for safe and non-intrusive monitoring of individual rods and cones over time, as well as across disease types. That’s obviously good news for patients. Plus it will help scientists understand how a rod or cone cell stops working, as well as more precisely test the effects of gene therapy and other experimental treatments aimed at restoring vision.


[1] Noninvasive imaging of the human rod photoreceptor mosaic using a confocal adaptive optics scanning ophthalmoscope. Dubra A, Sulai Y, Norris JL, Cooper RF, Dubis AM, Williams DR, Carroll J. Biomed Opt Express. 2011 Jul 1;2(7):1864-76.

[1] In-vivo sub-diffraction adaptive optics imaging of photoreceptors in the human eye with annular pupil illumination and sub-Airy detection. Rongwen L, Aguilera N, Liu T, Liu J, Giannini JP, Li J, Bower AJ, Dubra A, Tam J. Optica 2021 8, 333-343.


Get a Dilated Eye Exam (National Eye Institute/NIH)

How the Eyes Work (NEI)

Eye Health Data and Statistics (NEI)

Tam Lab (NEI)

Dubra Lab (Stanford University, Palo Alto, CA)

NIH Support: National Eye Institute

On-the-Spot Gene Readouts Offer Clues to How Cells Work

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Credit: MIT and Harvard Medical School, Cambridge, MA

Just as two companies can merge to expand their capabilities, two technologies can become more powerful when integrated into one. That’s why researchers recently merged two breakthrough technologies into one super powerful new method called ExSeq. The two-in-one technology enables researchers for the first time to study an intact tissue sample and track genetic activity on the spot within a cell’s tiniest recesses, or microenvironments—areas that have been largely out of reach until now.

ExSeq, which is described in a paper in the journal Science [1], will unleash many new experimental applications. Beyond enabling more precise analysis of the basic building blocks of life, these applications include analyzing tumor biopsies more comprehensively and even unlocking mysteries of how the brain works. The latter use is on display in this colorful cross-section of a mouse’s hippocampus, a region of the brain involved in the memory of facts and events.

Here you can see in precise and unprecedented detail the areas where genes are activated (magenta) in the brain’s neurons (green). In this particular example, the genes are working within subregions of the hippocampus called the CA1 and dentate gyrus regions (white, bottom and top left).

ExSeq is a joint effort from NIH grantees Ed Boyden, Massachusetts Institute of Technology (MIT), Cambridge, and George Church, Harvard Medical School, Boston. The new method combines a technology called tissue expansion with an in situ sequencing approach.

Tissue expansion swells the contents of tissue sections up to 100 times their normal size but retains their same physical structure [2]. It’s sort of like increasing the font size and line spacing on a hard-to-read document. It makes cellular details that were outside the resolution range of the light microscope suddenly accessible.

With the information inside cells now easier to see, the next step involves a technique called FISSEQ (fluorescent in situ sequencing), which generates readouts of thousands of mRNA molecules in cells [3]. FISSEQ works by detecting individual RNA molecules where they are inside cells and amplifying them into “nanoballs,” or rolled-up copies of themselves. Each nanoball can be read using standard sequencing methods and a fluorescence microscope.

Using the combined ExSeq approach, the team can analyze precisely where gene activity changes within tiny cellular microenvironments. Or, it can compile a more-comprehensive readout of gene activity within cells by analyzing as many gene readouts as detectable. When used in the hippocampus, this untargeted, “agnostic” approach led to some surprises—revealing unusual forms of RNA and, by association, genes for proteins not previously linked with communication between neurons.

Like many technology developments, the scientists envision that ExSeq can be used in many ways, including for more precise analysis of tumor biopsies. To illustrate this point, the researchers analyzed breast cancer metastases, which are cells from breast tumors that have spread to other areas in the body. Metastases contain many different cell types, including cancer cells and immune cells.

Using ExSeq, Boyden and Church learned that these distinct cell types can behave differently depending on where they are inside a tumor. They discovered, for example, that immune B cells near tumor cells expressed certain inflammatory genes at a higher level than immune B cells that were further away. Precise information about a tumor’s composition and activity may lead to development of more targeted approaches to attack it.

Many discoveries come on the heels of transformative new technologies. ExSeq shines a much brighter light on the world of the very small. And that should help us better understand how different parts of cells work together, as well as how cells work with each other in the brain, in cancer, and throughout the body.


[1] Expansion sequencing: Spatially precise in situ transcriptomics in intact biological systems. Alon S, Goodwin DR, Sinha A, Wassie AT, et al. Science. 2021 Jan 29;37:eaax2656.

[2] Expansion microscopy. Chen F, Tillberg PW, Boyden ES. Science. 2015;347:543-548.

[3]. Highly multiplexed subcellular RNA sequencing in situ. Lee JH, Daugharthy ER, Scheiman J, Kalhor R, et al. Science. 2014;343:1360-1363.


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

Synthetic Neurobiology Group (Massachusetts Institute of Technology, Cambridge)

George Church (Harvard Medical School, Boston)

NIH Support: National Human Genome Research Institute; National Cancer Institute; National Institute of Biomedical Imaging and Bioengineering; National Institute of Mental Health; National Institute of Neurological Disorders and Stroke

Large Study Reveals Prevalence, Health Benefits of Brown Fat

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Brown Fat
Credit: Andreas G. Wibmer and Heiko Schöder. Memorial Sloan Kettering Cancer Center, New York

It’s pretty easy to spot differences between the two people on these positron emission tomography (PET) scans. In the scan of the male individual on the left, you see lots of small, dark spots around the neck and shoulders. But you can’t see any on the female on the right. What’s the explanation? Is this a sex difference? No! Brown fat!

This energy-burning type of fat happens to show up as small, dark spots in the neck and shoulder area on PET scan studies. So, as these scans reveal, the individual on the left possesses an abundance of brown fat, while the person on the right has essentially none. This wide range of difference in abundance is true for both men and women.

Researchers’ interest in brown fat began to heat up (sorry about that!) more than a decade ago when it was discovered that certain adults have persistently high levels of brown fat. It’s long been known that babies have brown fat, but it had been thought this fat generally vanished as children grew up. It turns out that adults who hold onto their brown fat are less likely to be overweight than adults who do not. That’s because brown fat actually burns extra calories, instead of storing it in the way the more familiar white fat does.

But are people with more brown fat actually any healthier? After studying about 130,000 PET scans from more than 52,000 people, researchers led by Paul Cohen, The Rockefeller University Hospital, New York, NY, say that the answer is “yes” in certain key areas. In a recent study in the journal Nature Medicine, they found that people with detectable brown fat had a lower incidence of many cardiovascular and metabolic conditions, including type 2 diabetes, congestive heart failure, and high blood pressure.

Studies to explore the health benefits of brown fat have been challenging to do. That’s because brown fat only shows up on PET scans, which measure how much glucose various tissues consume, an indication of their metabolic activity. What’s more, PET scans are quite costly and involve radiation exposure. So, researchers have been reluctant to ask healthy people to undergo a PET scan just to look at brown fat. But a solution occurred to the study’s first author Tobias Becher, who was aware that thousands of patients at nearby Memorial Sloan Kettering Cancer Center were undergoing PET scans each year as part of routine evaluation and care. In fact, cancer doctors often make note of brown fat on PET scans, if only to make sure it’s not mistaken for cancer.

So, the Cohen lab teamed up with Memorial Sloan Kettering Cancer Center radiologists Heiko Schöder and Andreas G. Wibmer to review many thousands of PET scans for the presence of brown fat. And they found it in about one of 10 people.

Next, they looked for health differences between the 10 percent of people with brown fat and the 90 percent who lack it. The differences turned out be striking. Type 2 diabetes was about half as prevalent in folks with detectable brown fat compared to those without. Individuals with brown fat also were less likely to have high cholesterol, high blood pressure, congestive heart failure, and coronary artery disease.

The findings suggest that brown fat may even help to offset the negative health effects of obesity. The researchers found that obese people with brown fat had a health profile that otherwise appeared more similar to individuals who weren’t obese. In fact, the benefits of brown fat were more pronounced in individuals who were overweight or obese than they were in people of normal weight.

Still, the researchers note that people with cancer might tend to show differences in brown fat compared to healthy adults. There’s some evidence also that prevalence may vary across cancer types and stages. The researchers took those variables into account in their studies. It’s also known that women are more likely to have brown fat than men and that the amount of brown fat tends to decline with age. What’s not yet well understood is whether differences in brown fat exist among people of different racial and ethnic backgrounds, and whether specific genetic factors are involved.

So, plenty of questions remain! Researchers not only want to figure out why some adults have so much more brown fat than others, they want to explore whether brown fat produces hormones that may add to its calorie-burning benefits. The hope is that these and other discoveries could eventually lead to new strategies for treating obesity, diabetes, and other metabolic conditions.


[1] Brown adipose tissue is associated with cardiometabolic health. Becher T, Palanisamy S, Kramer DJ, Eljalby M, Marx SJ, Wibmer AG, Butler SD, Jiang CS, Vaughan R, Schöder H, Mark A, Cohen P. Nat Med. 2021 Jan;27(1):58-65.


Paul Cohen (The Rockefeller University, New York, NY)

Heiko Schöder (Memorial Sloan Kettering Cancer Center, NY)

Andreas Wibmer (Memorial Sloan Kettering Cancer Center, NY)

NIH Support: National Center for Advancing Translational Sciences

What A Year It Was for Science Advances!

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Science Breakthroughs of the Year 2020

At the close of every year, editors and writers at the journal Science review the progress that’s been made in all fields of science—from anthropology to zoology—to select the biggest advance of the past 12 months. In most cases, this Breakthrough of the Year is as tough to predict as the Oscar for Best Picture. Not in 2020. In a year filled with a multitude of challenges posed by the emergence of the deadly coronavirus disease 2019 (COVID-2019), the breakthrough was the development of the first vaccines to protect against this pandemic that’s already claimed the lives of more than 360,000 Americans.

In keeping with its annual tradition, Science also selected nine runner-up breakthroughs. This impressive list includes at least three areas that involved efforts supported by NIH: therapeutic applications of gene editing, basic research understanding HIV, and scientists speaking up for diversity. Here’s a quick rundown of all the pioneering advances in biomedical research, both NIH and non-NIH funded:

Shots of Hope. A lot of things happened in 2020 that were unprecedented. At the top of the list was the rapid development of COVID-19 vaccines. Public and private researchers accomplished in 10 months what normally takes about 8 years to produce two vaccines for public use, with more on the way in 2021. In my more than 25 years at NIH, I’ve never encountered such a willingness among researchers to set aside their other concerns and gather around the same table to get the job done fast, safely, and efficiently for the world.

It’s also pretty amazing that the first two conditionally approved vaccines from Pfizer and Moderna were found to be more than 90 percent effective at protecting people from infection with SARS-CoV-2, the coronavirus that causes COVID-19. Both are innovative messenger RNA (mRNA) vaccines, a new approach to vaccination.

For this type of vaccine, the centerpiece is a small, non-infectious snippet of mRNA that encodes the instructions to make the spike protein that crowns the outer surface of SARS-CoV-2. When the mRNA is injected into a shoulder muscle, cells there will follow the encoded instructions and temporarily make copies of this signature viral protein. As the immune system detects these copies, it spurs the production of antibodies and helps the body remember how to fend off SARS-CoV-2 should the real thing be encountered.

It also can’t be understated that both mRNA vaccines—one developed by Pfizer and the other by Moderna in conjunction with NIH’s National Institute of Allergy and Infectious Diseases—were rigorously evaluated in clinical trials. Detailed data were posted online and discussed in all-day meetings of an FDA Advisory Committee, open to the public. In fact, given the high stakes, the level of review probably was more scientifically rigorous than ever.

First CRISPR Cures: One of the most promising areas of research now underway involves gene editing. These tools, still relatively new, hold the potential to fix gene misspellings—and potentially cure—a wide range of genetic diseases that were once to be out of reach. Much of the research focus has centered on CRISPR/Cas9. This highly precise gene-editing system relies on guide RNA molecules to direct a scissor-like Cas9 enzyme to just the right spot in the genome to cut out or correct a disease-causing misspelling.

In late 2020, a team of researchers in the United States and Europe succeeded for the first time in using CRISPR to treat 10 people with sickle cell disease and transfusion-dependent beta thalassemia. As published in the New England Journal of Medicine, several months after this non-heritable treatment, all patients no longer needed frequent blood transfusions and are living pain free [1].

The researchers tested a one-time treatment in which they removed bone marrow from each patient, modified the blood-forming hematopoietic stem cells outside the body using CRISPR, and then reinfused them into the body. To prepare for receiving the corrected cells, patients were given toxic bone marrow ablation therapy, in order to make room for the corrected cells. The result: the modified stem cells were reprogrammed to switch back to making ample amounts of a healthy form of hemoglobin that their bodies produced in the womb. While the treatment is still risky, complex, and prohibitively expensive, this work is an impressive start for more breakthroughs to come using gene editing technologies. NIH, including its Somatic Cell Genome Editing program, continues to push the technology to accelerate progress and make gene editing cures for many disorders simpler and less toxic.

Scientists Speak Up for Diversity: The year 2020 will be remembered not only for COVID-19, but also for the very public and inescapable evidence of the persistence of racial discrimination in the United States. Triggered by the killing of George Floyd and other similar events, Americans were forced to come to grips with the fact that our society does not provide equal opportunity and justice for all. And that applies to the scientific community as well.

Science thrives in safe, diverse, and inclusive research environments. It suffers when racism and bigotry find a home to stifle diversity—and community for all—in the sciences. For the nation’s leading science institutions, there is a place and a calling to encourage diversity in the scientific workplace and provide the resources to let it flourish to everyone’s benefit.

For those of us at NIH, last year’s peaceful protests and hashtags were noticed and taken to heart. That’s one of the many reasons why we will continue to strengthen our commitment to building a culturally diverse, inclusive workplace. For example, we have established the NIH Equity Committee. It allows for the systematic tracking and evaluation of diversity and inclusion metrics for the intramural research program for each NIH institute and center. There is also the recently founded Distinguished Scholars Program, which aims to increase the diversity of tenure track investigators at NIH. Recently, NIH also announced that it will provide support to institutions to recruit diverse groups or “cohorts” of early-stage research faculty and prepare them to thrive as NIH-funded researchers.

AI Disentangles Protein Folding: Proteins, which are the workhorses of the cell, are made up of long, interconnected strings of amino acids that fold into a wide variety of 3D shapes. Understanding the precise shape of a protein facilitates efforts to figure out its function, its potential role in a disease, and even how to target it with therapies. To gain such understanding, researchers often try to predict a protein’s precise 3D chemical structure using basic principles of physics—including quantum mechanics. But while nature does this in real time zillions of times a day, computational approaches have not been able to do this—until now.

Of the roughly 170,000 proteins mapped so far, most have had their structures deciphered using powerful imaging techniques such as x-ray crystallography and cryo–electron microscopy (cryo-EM). But researchers estimate that there are at least 200 million proteins in nature, and, as amazing as these imaging techniques are, they are laborious, and it can take many months or years to solve 3D structure of a single protein. So, a breakthrough certainly was needed!

In 2020, researchers with the company Deep Mind, London, developed an artificial intelligence (AI) program that rapidly predicts most protein structures as accurately as x-ray crystallography and cryo-EM can map them [2]. The AI program, called AlphaFold, predicts a protein’s structure by computationally modeling the amino acid interactions that govern its 3D shape.

Getting there wasn’t easy. While a complete de novo calculation of protein structure still seemed out of reach, investigators reasoned that they could kick start the modeling if known structures were provided as a training set to the AI program. Utilizing a computer network built around 128 machine learning processors, the AlphaFold system was created by first focusing on the 170,000 proteins with known structures in a reiterative process called deep learning. The process, which is inspired by the way neural networks in the human brain process information, enables computers to look for patterns in large collections of data. In this case, AlphaFold learned to predict the underlying physical structure of a protein within a matter of days. This breakthrough has the potential to accelerate the fields of structural biology and protein research, fueling progress throughout the sciences.

How Elite Controllers Keep HIV at Bay: The term “elite controller” might make some people think of video game whizzes. But here, it refers to the less than 1 percent of people living with human immunodeficiency virus (HIV) who’ve somehow stayed healthy for years without taking antiretroviral drugs. In 2020, a team of NIH-supported researchers figured out why this is so.

In a study of 64 elite controllers, published in the journal Nature, the team discovered a link between their good health and where the virus has inserted itself in their genomes [3]. When a cell transcribes a gene where HIV has settled, this so-called “provirus,” can produce more virus to infect other cells. But if it settles in a part of a chromosome that rarely gets transcribed, sometimes called a gene desert, the provirus is stuck with no way to replicate. Although this discovery won’t cure HIV/AIDS, it points to a new direction for developing better treatment strategies.

In closing, 2020 presented more than its share of personal and social challenges. Among those challenges was a flood of misinformation about COVID-19 that confused and divided many communities and even families. That’s why the editors and writers at Science singled out “a second pandemic of misinformation” as its Breakdown of the Year. This divisiveness should concern all of us greatly, as COVID-19 cases continue to soar around the country and our healthcare gets stretched to the breaking point. I hope and pray that we will all find a way to come together, both in science and in society, as we move forward in 2021.


[1] CRISPR-Cas9 gene editing for sickle cell disease and β-thalassemia. Frangoul H et al. N Engl J Med. 2020 Dec 5.

[2] ‘The game has changed.’ AI triumphs at protein folding. Service RF. Science. 04 Dec 2020.

[3] Distinct viral reservoirs in individuals with spontaneous control of HIV-1. Jiang C et al. Nature. 2020 Sep;585(7824):261-267.


COVID-19 Research (NIH)

2020 Science Breakthrough of the Year (American Association for the Advancement of Science, Washington, D.C)

A Close-up of COVID-19 in Lung Cells

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SARS-CoV-2 infected lung cells
Credit: Ehre Lab, UNC School of Medicine

If you or a loved one have come down with SARS-CoV-2, the coronavirus responsible for COVID-19, you know it often takes hold in the respiratory system. This image offers a striking example of exactly what happens to cells in the human airway when this coronavirus infects them.

This colorized scanning electron microscope (SEM) image shows SARS-CoV-2-infected human lung cells (purple) covered in hair-like cilia (blue). Those cilia line the inner surface of the airways and help to clear mucus (yellow-green) containing dust and other debris from the lungs. Emerging from the surface of those infected airway cells are many thousands of coronavirus particles (red).

This dramatic image, published recently in the New England Journal of Medicine, comes from the lab of pediatric pulmonologist Camille Ehre, University of North Carolina at Chapel Hill. Ehre and team study mucus and how its properties change in cystic fibrosis, chronic obstructive pulmonary disease (COPD), and various other conditions that affect the lungs. These days, they’re also focusing their attention on SARS-CoV-2 and potentially new ways to block viral entry into cells of the human airway.

As part of that effort, she and her colleagues captured this snapshot of SARS-CoV-2 viruses exiting from lung cells in a lab dish. They first cultured cells from the lining of a human airway, then inoculated them with the virus. Ninety-six hours later, this is what they saw in greyscale. The vivid colors were added later by UNC medical student Cameron Morrison.

The image illustrates the astoundingly large number of viral particles that can be produced and released from infected human cells. Ehre notes that in a lab dish containing about a million human cells, they’ve witnessed the virus explode from about 1,000 particles to about 10 million in just a couple of days.

The dramatic increase in viral particles helps to explain how COVID-19 spreads so easily from the lungs to other parts of the body and—all too often—on to other individuals, especially in crowded, indoor places where people aren’t able to keep their distance. Hopefully, images like this one will help to inspire more of us this winter to avoid the crowds (especially indoors), wear masks, and wash our hands frequently.


[1] SARS-CoV-2 infection of airway cells. Ehre C. NEJM. 2020 Sep 3;383(10):969.


Coronavirus (COVID-19) (NIH)

Camille Ehre (University of North Carolina, Chapel Hill)

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