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Snapshots of Life

The Synchronicity of Memory

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Credit: Zhou Y, et al. FASEB J, 2020

You may think that you’re looking at a telescopic heat-map of a distant planet, with clickable thumbnail images to the right featuring its unique topography. In fact, what you’re looking at is a small region of the brain that’s measured in micrometers and stands out as a fascinating frontier of discovery into the very origins of thought and cognition.

It’s a section of a mouse hippocampus, a multi-tasking region of the brain that’s central to memory formation. What makes the image on the left so interesting is it shows four individual neurons (numbered circles) helping to form a memory.

The table of images on the right shows in greater detail how the memory is formed. You see those same four neurons, their activity logged individually. Cooler colors—indigo to turquoise—indicate background or low neuronal activity; warmer colors—yellow to red—indicate high neuronal activity.

Now, take a closer look at the rows of the table that are labeled “Initial.” The four neurons have responded to an initial two-part training session: the sounding of a tone (gray-shaded columns) followed by a stimulus (red-shaded columns) less than a minute later. The neurons, while active (multi-colored pattern), don’t fire in unison or at the same activity levels. A memory has not yet been formed.

That’s not the case just below in the rows labeled “Trained.” After several rounds of reinforcing the one-two sequence, neurons fire together at comparable activity levels in response to the tone (gray) followed by the now-predictable stimulus (red). This process of firing in unison, called neuronal synchronization, encodes the memory. In fact, the four neurons even deactivate in unison after each prompt (unshaded columns).

These fascinating images are the first to show an association between neuronal burst synchronization and hippocampus-dependent memory formation. This discovery has broad implications, from improving memory to reconditioning the mental associations that underlie post-traumatic stress disorder (PTSD).

This research comes from a team led by the NIH-supported investigator Xuanmao Chen, University of New Hampshire, Durham. In the study, published in the FASEB Journal, Chen and colleagues used deep-brain imaging technology to shed new light on some old-fashioned classical conditioning: Pavlovian training [1].

Over a century ago, Ivan Pavlov conducted experiments that conditioned dogs to salivate at the sound of a bell that signaled their feeding time. This concept of “classical conditioning” is central to our understanding of how we humans form certain types of memories. A baby smiles at the sound of her mother’s voice. Stores play holiday music at the end of the year, hoping the positive childhood association puts shoppers in the mood to buy more gifts. Our phone plays a distinctive tone, and we immediately check our text messages. In each example, the association with an otherwise neutral stimulus is learned—and stored in the brain as a “declarative,” or explicit, memory.

The researchers wanted to see what happened in neural cells when mice learned a new association. They applied Pavlov’s learning paradigm, training mice over repeated sessions by pairing an audible tone and, about 30 seconds later, a brief, mild foot stimulus. Mice instinctively halt their activities, or freeze, in response to the foot stimulus. After a few tone-stimulus training sessions, the mice also began freezing after the tone was sounded. They had formed a conditioned response.

During these training sessions, Chen and his colleagues were able to take high-resolution, real-time images of the hippocampus. This allowed them to track the same four neurons over the course of the day—and watch as memory creation, in the form of neuronal synchronization, took place. Later, during recall experiments, the tone itself elicited both the behavioral change and the coordinated neuronal response—if with a bit less regularity. It’s something we humans experience whenever we forget a computer password!

The researchers went on to capture even more evidence. They showed that these neurons, which became part of the stored “engram,” or physical location of the memory, were already active even before they were synchronized. This finding contributes to recent work challenging the long-held paradigm that memory-eligible neurons “switch on” from a silent state to form a memory [2]. The researchers offered a new name for these active neurons: “primed,” as opposed to “silent.”

Chen and his colleagues continue studying the priming process and working out more of the underlying molecular details. They’re attempting to determine how the process is regulated and primed neurons become synchronized. And, of course, the big question: how does this translate into an actual memory in other living creatures? The next round of results should be memorable!


[1] Induction of activity synchronization among primed hippocampal neurons out of random dynamics is key for trace memory formation and retrieval. Zhou Y, Qiu L, Wang H, Chen X. FASEB J. 2020 Mar;34(3):3658–3676.

[2] Memory engrams: Recalling the past and imagining the future. Josselyn S, Tonegawa S. Science 2020 Jan 3;367(6473):eaaw4325.


Brain Basics: Know Your Brain (National Institute of Neurological Disorders and Stroke/NIH)

Neuroanatomy, Hippocampus Fogwe LA, Reddy V, Mesfin FB. StatPearls Publishing (National Library of Medicine/NIH)

Xuanmao Chen (University of New Hampshire, Durham)

NIH Support: National Institute of Mental Health; National Institute on Aging; National Institute of General Medical Sciences

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

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)

Insulin-Producing Organoids Offer Hope for Treating Type 1 Diabetes

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Insulin-producing organoid
Caption: Human islet-like organoids express insulin (green). Credit: Salk Institute

For the 1 to 3 million Americans with type 1 diabetes, the immune system destroys insulin-producing beta cells of the pancreas that control the amount of glucose in the bloodstream. As a result, these individuals must monitor their blood glucose often and take replacement doses of insulin to keep it under control. Such constant attention, combined with a strict diet to control sugar intake, is challenging—especially for children.

For some people with type 1 diabetes, there is another option. They can be treated—maybe even cured—with a pancreatic islet cell transplant from an organ donor. These transplanted islet cells, which harbor the needed beta cells, can increase insulin production. But there’s a big catch: there aren’t nearly enough organs to go around, and people who receive a transplant must take lifelong medications to keep their immune system from rejecting the donated organ.

Now, NIH-funded scientists, led by Ronald Evans of the Salk Institute, La Jolla, CA, have devised a possible workaround: human islet-like organoids (HILOs) [1]. These tiny replicas of pancreatic tissue are created in the laboratory, and you can see them above secreting insulin (green) in a lab dish. Remarkably, some of these HILOs have been outfitted with a Harry Potter-esque invisibility cloak to enable them to evade immune attack when transplanted into mice.

Over several years, Doug Melton’s lab at Harvard University, Cambridge, MA, has worked steadily to coax induced pluripotent stem (iPS) cells, which are made from adult skin or blood cells, to form miniature islet-like cells in a lab dish [2]. My own lab at NIH has also been seeing steady progress in this effort, working with collaborators at the New York Stem Cell Foundation.

Although several years ago researchers could get beta cells to make insulin, they wouldn’t secrete the hormone efficiently when transplanted into a living mouse. About four years ago, the Evans lab found a possible solution by uncovering a genetic switch called ERR-gamma that when flipped, powered up the engineered beta cells to respond continuously to glucose and release insulin [3].

In the latest study, Evans and his team developed a method to program HILOs in the lab to resemble actual islets. They did it by growing the insulin-producing cells alongside each other in a gelatinous, three-dimensional chamber. There, the cells combined to form organoid structures resembling the shape and contour of the islet cells seen in an actual 3D human pancreas. After they are switched on with a special recipe of growth factors and hormones, these activated HILOs secrete insulin when exposed to glucose. When transplanted into a living mouse, this process appears to operate just like human beta cells work inside a human pancreas.

Another major advance was the invisibility cloak. The Salk team borrowed the idea from cancer immunotherapy and a type of drug called a checkpoint inhibitor. These drugs harness the body’s own immune T cells to attack cancer. They start with the recognition that T cells display a protein on their surface called PD-1. When T cells interact with other cells in the body, PD-1 binds to a protein on the surface of those cells called PD-L1. This protein tells the T cells not to attack. Checkpoint inhibitors work by blocking the interaction of PD-1 and PD-L1, freeing up immune cells to fight cancer.

Reversing this logic for the pancreas, the Salk team engineered HILOs to express PD-L1 on their surface as a sign to the immune system not to attack. The researchers then transplanted these HILOs into diabetic mice that received no immunosuppressive drugs, as would normally be the case to prevent rejection of these human cells. Not only did the transplanted HILOs produce insulin in response to glucose spikes, they spurred no immune response.

So far, HILOs transplants have been used to treat diabetes for more than 50 days in diabetic mice. More research will be needed to see whether the organoids can function for even longer periods of time.

Still, this is exciting news, and provides an excellent example of how advances in one area of science can provide new possibilities for others. In this case, these insights provide fresh hope for a day when children and adults with type 1 diabetes can live long, healthy lives without the need for frequent insulin injections.


[1] Immune-evasive human islet-like organoids ameliorate diabetes. [published online ahead of print, 2020 Aug 19]. Yoshihara E, O’Connor C, Gasser E, Wei Z, Oh TG, Tseng TW, Wang D, Cayabyab F, Dai Y, Yu RT, Liddle C, Atkins AR, Downes M, Evans RM. Nature. 2020 Aug 19. [Epub ahead of publication]

[2] Generation of Functional Human Pancreatic β Cells In Vitro. Pagliuca FW, Millman JR, Gürtler M, Segel M, Van Dervort A, Ryu JH, Peterson QP, Greiner D, Melton DA. Cell. 2014 Oct 9;159(2):428-39.

[3] ERRγ is required for the metabolic maturation of therapeutically functional glucose-responsive β cells. Yoshihara E, Wei Z, Lin CS, Fang S, Ahmadian M, Kida Y, Tseng T, Dai Y, Yu RT, Liddle C, Atkins AR, Downes M, Evans RM. Cell Metab. 2016 Apr 12; 23(4):622-634.


Type 1 Diabetes (National Institute of Diabetes and Digestive and Kidney Diseases/NIH)

Pancreatic Islet Transplantation (National Institute of Diabetes and Digestive and Kidney Diseases)

The Nobel Prize in Physiology or Medicine 2012” for Induced Pluripotent Stem Cells, The Nobel Prize news release, October 8, 2012.

Evans Lab (Salk Institute, La Jolla, CA)

NIH Support: National Institute of Diabetes and Digestive and Kidney Diseases; National Cancer Institute

Building a Better Bacterial Trap for Sepsis

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Credit: Kandace Gollomp, MD, The Children’s Hospital of Philadelphia, PA

Spiders spin webs to catch insects for dinner. It turns out certain human immune cells, called neutrophils, do something similar to trap bacteria in people who develop sepsis, an uncontrolled, systemic infection that poses a major challenge in hospitals.

When activated to catch sepsis-causing bacteria or other pathogens, neutrophils rupture and spew sticky, spider-like webs made of DNA and antibacterial proteins. Here in red you see one of these so-called neutrophil extracellular traps (NETs) that’s ensnared Staphylococcus aureus (green), a type of bacteria known for causing a range of illnesses from skin infections to pneumonia.

Yet this image, which comes from Kandace Gollomp and Mortimer Poncz at The Children’s Hospital of Philadelphia, is much more than a fascinating picture. It demonstrates a potentially promising new way to treat sepsis.

The researchers’ strategy involves adding a protein called platelet factor 4 (PF4), which is released by clot-forming blood platelets, to the NETs. PF4 readily binds to NETs and enhances their capture of bacteria. A modified antibody (white), which is a little hard to see, coats the PF4-bound NET above. This antibody makes the NETs even better at catching and holding onto bacteria. Other immune cells then come in to engulf and clean up the mess.

Until recently, most discussions about NETs assumed they were causing trouble, and therefore revolved around how to prevent or get rid of them while treating sepsis. But such strategies faced a major obstacle. By the time most people are diagnosed with sepsis, large swaths of these NETs have already been spun. In fact, destroying them might do more harm than good by releasing entrapped bacteria and other toxins into the bloodstream.

In a recent study published in the journal Blood, Gollomp’s team proposed flipping the script [1]. Rather than prevent or destroy NETs, why not modify them to work even better to fight sepsis? Their idea: Make NETs even stickier to catch more bacteria. This would lower the number of bacteria and help people recover from sepsis.

Gollomp recalled something lab member Anna Kowalska had noted earlier in unrelated mouse studies. She’d observed that high levels of PF4 were protective in mice with sepsis. Gollomp and her colleagues wondered if the PF4 might also be used to reinforce NETs. Sure enough, Gollomp’s studies showed that PF4 will bind to NETs, causing them to condense and resist break down.

Subsequent studies in mice and with human NETs cast in a synthetic blood vessel suggest that this approach might work. Treatment with PF4 greatly increased the number of bacteria captured by NETs. It also kept NETs intact and holding tightly onto their toxic contents. As a result, mice with sepsis fared better.

Of course, mice are not humans. More study is needed to see if the same strategy can help people with sepsis. For example, it will be important to determine if modified NETs are difficult for the human body to clear. Also, Gollomp thinks this approach might be explored for treating other types of bacterial infections.

Still, the group’s initial findings come as encouraging news for hospital staff and administrators. If all goes well, a future treatment based on this intriguing strategy may one day help to reduce the 270,000 sepsis-related deaths in the U.S. and its estimated more than $24 billion annual price tag for our nation’s hospitals [2, 3].


[1] Fc-modified HIT-like monoclonal antibody as a novel treatment for sepsis. Gollomp K, Sarkar A, Harikumar S, Seeholzer SH, Arepally GM, Hudock K, Rauova L, Kowalska MA, Poncz M. Blood. 2020 Mar 5;135(10):743-754.

[2] Sepsis, Data & Reports, Centers for Disease Control and Prevention, Feb. 14, 2020.

[3] National inpatient hospital costs: The most expensive conditions by payer, 2013: Statistical Brief #204. Torio CM, Moore BJ. Healthcare Cost and Utilization Project (HCUP) Statistical Briefs. Agency for Healthcare Research and Quality (US); 2016 May.


Sepsis (National Institute of General Medical Sciences/NIH)

Kandace Gollomp (The Children’s Hospital of Philadelphia, PA)

Mortimer Poncz (The Children’s Hospital of Philadelphia, PA)

NIH Support: National Heart, Lung, and Blood Institute

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