While breakthrough infections have increased with the emergence of the delta and omicron variants, the vaccines remain quite effective at preventing hospitalizations and deaths. The success of the new technology has led scientists to try to figure out why mRNA vaccines are so effective and whether the protection they provide is likely to endure as new variants arise.

A new study from researchers at Washington University School of Medicine in St. Louis and St. Jude Children’s Research Hospital shines light on the quality of the immune response triggered by mRNA vaccines. The study shows that the Pfizer vaccine strongly and persistently activates a kind of helper immune cell that assists antibody-producing cells in creating large amounts of increasingly powerful antibodies, and also drives the development of some kinds of immune memory. Known as T follicular helper cells, these cells last for up to six months after vaccination, helping the body crank out better and better antibodies. Once the helper cells decline, long-lived antibody-producing cells and memory B cells help to provide protection against severe disease and death, the researchers said.

Further, many of the T follicular helper cells are activated by a part of the virus that doesn’t seem to pick up mutations, even in the highly mutated omicron variant. The findings, published online Dec. 22, 2021, in the journal Cell, help explain why the Pfizer vaccine elicits such high levels of neutralizing antibodies and suggests that vaccination may help many people continue producing potent antibodies even as the virus changes.

“The longer the T follicular helper cells provide help, the better the antibodies are and the more likely you are to have a good memory response,” said co-corresponding author Philip Mudd, MD, PhD, an assistant professor of emergency medicine at Washington University. “In this study, we found that these T follicular helper cell responses just keep going and going. And what’s more, some of them are responding to one part of the virus’s spike protein that has very little variation in it. With the variants, especially delta and now omicron, we’ve been seeing some breakthrough infections, but the vaccines have held up very nicely in terms of preventing severe disease and death. I think this strong T follicular helper response is part of the reason why the mRNA vaccines continue to be so protective.”

The first antibodies produced in response to an infection or vaccination tend not to be very good. B cells need to go through a kind of boot camp in so-called germinal centers in the lymph nodes before they can produce really powerful antibodies. T follicular helper cells are the drill sergeants of these boot camps. The helper cells provide instruction to the antibody-producing cells on making ever more potent antibodies and encourage those with the best antibodies to multiply and, in some cases, turn into long-lived antibody-producing cells or memory B cells. The longer the germinal centers last, the better and stronger the antibody response.

Earlier this year, Ali Ellebedy, PhD, an associate professor of pathology & immunology, of medicine and of molecular microbiology at Washington University, reported that, nearly four months after people had received the first dose of the Pfizer vaccine, they still had germinal centers in their lymph nodes that were churning out immune cells directed against SARS-CoV-2, the virus that causes COVID-19.

In this latest study, Mudd and co-corresponding authors Ellebedy and Paul Thomas, PhD, of St. Jude, aimed to understand the role of T follicular helper cells in producing such a strong germinal center response. The research team also included co-first authors Anastasia Minervina, PhD, and Mikhail Pogorelyy, PhD, postdoctoral researchers who work with Thomas at St. Jude, and others.

The researchers recruited 15 volunteers who each received two doses of the Pfizer vaccine three weeks apart. The volunteers underwent a procedure to extract germinal centers from their lymph nodes 21 days after the first dose, just before the second dose; then at days 28, 35, 60, 110 and 200 after the initial dose. None of the volunteers had been infected with SARS-CoV-2 at the start of the study. The researchers obtained T follicular helper cells from the lymph nodes and analyzed them.

The researchers now are studying what happens after a booster dose and whether changes to T follicular helper cells could explain why people with compromised immune systems, such as those with HIV infection, do not mount a strong antibody response.

The device, published Dec. 23 in the journal Nature Nanotechnology, could enable scientists to gain more detailed insights into heart disorders and diseases such as arrhythmia (abnormal heart rhythm), heart attack and cardiac fibrosis (stiffening or thickening of heart tissue).

“Studying how an electrical signal propagates between different cells is important to understand the mechanism of cell function and disease,” said first author Yue Gu, who recently received his Ph.D. in materials science and engineering at UC San Diego. “Irregularities in this signal can be a sign of arrhythmia, for example. If the signal cannot propagate correctly from one part of the heart to another, then some part of the heart cannot receive the signal so it cannot contract.”

“With this device, we can zoom in to the cellular level and get a very high resolution picture of what’s going on in the heart; we can see which cells are malfunctioning, which parts are not synchronized with the others, and pinpoint where the signal is weak,” said senior author Sheng Xu, a professor of nanoengineering at the UC San Diego Jacobs School of Engineering. “This information could be used to help inform clinicians and enable them to make better diagnoses.”

The device consists of a 3D array of microscopic field effect transistors, or FETs, that are shaped like sharp pointed tips. These tiny FETs pierce through cell membranes without damaging them and are sensitive enough to detect electrical signals — even very weak ones — directly inside the cells. To evade being seen as a foreign substance and remain inside the cells for long periods of time, the FETs are coated in a phospholipid bilayer. The FETs can monitor signals from multiple cells at the same time. They can even monitor signals at two different sites inside the same cell.

“That’s what makes this device unique,” said Gu. “It can have two FET sensors penetrate inside one cell — with minimal invasiveness — and allow us to see which way a signal propagates and how fast it goes. This detailed information about signal transportation within a single cell has so far been unknown.”

To build the device, the team first fabricated the FETs as 2D shapes, and then bonded select spots of these shapes onto a pre-stretched elastomer sheet. The researchers then loosened the elastomer sheet, causing the device to buckle and the FETs to fold into a 3D structure so that they can penetrate inside cells.

“It’s like a pop-up book,” said Gu. “It starts out as a 2D structure, and with compressive force it pops up at some portions and becomes a 3D structure.”

The team tested the device on heart muscle cell cultures and on cardiac tissues that were engineered in the lab. The experiments involved placing either the cell culture or tissue on top of the device and then monitoring the electrical signals that the FET sensors picked up. By seeing which sensors detected a signal first and then measuring the times it took for other sensors to detect the signal, the team could determine which way the signal traveled and its speed. The researchers were able to do this for signals traveling between neighboring cells, and for the first time, for signals traveling within a single heart muscle cell.

What makes this even more exciting, said Xu, is that this is the first time that scientists have been able to measure intracellular signals in 3D tissue constructs. “So far, only extracellular signals, meaning signals that are outside of the cell membrane, have been measured in these types of tissues. Now, we can actually pick up signals inside the cells that are embedded in the 3D tissue or organoid,” he said.

The team’s experiments led to an interesting observation: signals inside individual heart cells travel almost five times faster than signals between multiple heart cells. Studying these kinds of details could reveal insights on heart abnormalities at the cellular level, said Gu. “Say you’re measuring the signal speed in one cell, and the signal speed between two cells. If there’s a very big difference between these two speeds — that is, if the intercellular speed is much, much smaller than the intracellular speed — then it’s likely that something is wrong at the junction between the cells, possibly due to fibrosis,” he explained.

Biologists could also use this device to study signal transportation between different organelles in a cell, added Gu. A device like this could also be used for testing new drugs and seeing how they affect heart cells and tissues.

The device would also be useful for studying electrical activity inside neurons. This is a direction that the team is looking to explore next. Down the line, the researchers plan to use their device to record electrical activity in real biological tissue in vivo. Xu envisions an implantable device that can be placed on the surface of a beating heart or on the surface of the cortex. But the device is still far from that stage. To get there, the researchers have more work to do including fine-tuning the layout of the FET sensors, optimizing the FET array size and materials, and integrating AI-assisted signal processing algorithms into the device.

Paper: “Three-dimensional transistor arrays for intra- and inter-cellular recording.” Co-authors include Chunfeng Wang, Namheon Kim, Jingxin Zhang, Tsui Min Wang, Jennifer Stowe, Jing Mu, Muyang Lin, Weixin Li, Chonghe Wang, Hua Gong, Yimu Chen, Yusheng Lei, Hongjie Hu, Yang Li, Lin Zhang, Zhenlong Huang, Pooja Banik, Liangfang Zhang and Andrew D. McCulloch, UC San Diego; Rohollah Nasiri, Samad Ahadian and Ali Khademhosseini, Terasaki Institute for Biomedical Innovation; Jinfeng Li and Peter J. Burke, UC Irvine; Leo Huan-Hsuan Hsu, Xiaochuan Dai and Xiaocheng Jiang, Tufts University; Zheyuan Liu, Massachusetts Institute of Technology; and Xingcai Zhang, Harvard University.

This work was supported by the National Institutes of Health (1 R35 GM138250 01).

Their findings were published in the Federation of European Biochemical Societies journal on October 26.

Being allergic to dogs is a common malady and one that is growing worldwide. Over the years, scientists have been able to identify seven different dog allergens — molecules or molecular structures that bind to an antibody and produce an unusually strong immune response that would normally be harmless.

These seven are named Canis familiaris allergens 1 to 7 (Can f 1-7). But while there are seven, just one, Can f 1, is responsible for the majority (50-75 percent) of reactions in people allergic to dogs. It is found in dogs’ tongue tissue, salivary glands, and their skin.

Researchers have yet to identify Can f 1’s IgE epitopes — those specific parts of the antigens that are recognized by the immune system and stimulate or ‘determine’ an immune response (which is why epitopes are also called antigen determinants). More specifically, epitopes are short amino acid sequences making up part of a protein that induces the immune response.

Epitopes bind to a specific antigen receptor on the surface of immune system antibodies, B cells, or T Cells, much like how the shape of a jigsaw puzzle piece fits the specific shape of another puzzle piece. (The part of the receptor that binds to the epitope is in turn called a paratope). Antibodies, also known as immunoglobulin, come in five different classes or isotypes: IgA (for immunoglobulin A), IgD, IgE, IgG, or IgM. The IgE isotype (only found in mammals) plays a key role in allergies and allergic diseases. There is also an IgE epitope that is the puzzle piece that fits the IgE isotype’s paratope.

In recent years, there has been extensive effort at developing epitope-focused vaccines — in this case, a vaccine against dog allergies.

“We want to be able to present small doses of these epitopes to the immune system to train it to deal with them, similar to the principle behind any vaccine,” said Takashi Inui, a specialist in allergy research, professor at Osaka Prefecture University and a lead author of the study. “But we can’t do this without first identifying the Can f 1’s IgE epitope.”

So the researchers used X-ray crystallography (in which the diffraction of x-rays through a material is analyzed to identify its ‘crystal’ structure) to determine the structure of the Can f 1 protein as a whole — the first time this had ever been done.

They found that the protein’s folding pattern is at first glance extremely similar to three other Can f allergens. However, the locations of surface electrical charges were quite different, which in turn suggest a series of ‘residues’ that are good candidates for the IgE epitope.

Using this basic data, further experimental work needs to be performed to narrow the candidates down, but the findings suggest the development of a hypoallergenic vaccine against Can f 1 — a dog-allergy vaccine — is within our grasp.

The production of a ‘hypoallergenic vaccine’ by use of such epitopes would not just be a world-first with respect to dog allergies but is rare with respect to any allergic reaction. If the researchers’ work is indeed used to develop a dog allergy vaccine, the principles behind it could be used much more widely against various allergies.

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Materials provided by Osaka Prefecture University. Note: Content may be edited for style and length.

“Iodine, the same chemical added as a nutrient to table salt, is eating up ozone in dusty air high in the atmosphere,” said Rainer Volkamer, a CIRES Fellow and professor of chemistry at CU Boulder. Volkamer led the team that made precision atmospheric measurements by aircraft over the eastern Pacific Ocean several years ago. The new finding, he said, has implications for not only air quality, but climate, too — iodine chemistry can make greenhouse gases stick around longer and should give us pause to re-think geoengineering schemes involving dust.

“Our understanding of the iodine cycle is incomplete,” Volkamer said. “There are land-based sources and chemistry we didn’t know about, which we must now consider.”

Atmospheric researchers have long been interested in the observation that dusty layers of air are often very low in the air pollutant ozone, which, when concentrated, can damage people’s lungs and even crops. It seemed that some kind of dust-surface chemistry was eating up ozone, but no one had been able to show that happening in laboratory experiments. Others have speculated about this, but there’s been a lot of doubt, said Volkamer. By contrast, lab experiments have long shown that a gaseous form of iodine can gobble up ozone — but there were only hints of a connection between dust and iodine.

There were other tantalizing hints about the process in a dataset from 2012, from a series of aircraft flights offshore Chile and Costa Rica. Dust seen blowing offshore from South America had striking levels of gaseous iodine. Volkamer handed the data to then-CU Boulder graduate student Theodore Koenig, lead author on this study. Koenig describes those data as one in a set of blurry photographs shared by atmospheric chemists around the world. In one image, for example, “iodine seemed to correlate with dust … but not absolutely clearly,” he said. Everywhere, dust seemed to destroy ozone, but why? “Iodine and ozone clearly connect, but there weren’t any ‘photos’ of both with dust,” said Koenig, who is now an air pollution researcher at Peking University in China.

The data from TORERO (the “Tropical Ocean Troposphere Exchange of Reactive Halogens and Oxygenated Hydrocarbons,” a field campaign funded by the National Science Foundation) captured those three characters together, finally, in one image he said, and it was clear that where desert dust contained significant levels of iodine — like dust from the Atacama and Sechura deserts in Chile and Peru — the iodine was quickly transformed into a gaseous form and ozone dropped to very low levels. But how did that dust-based iodine transform? “The mechanism still remains elusive,” Volkamer said. “That’s future work.”

So the picture is another blurry one, Koenig said, but still, the science is sharper than it was. “I have more questions at the end of the project than at the start,” he said. “But they’re better, more specific questions.”

They’re also very important, for anyone interested in the future of the atmosphere, Volkamer said. Iodine’s reactions in the atmosphere are known to play a role in reducing levels of OH, for example, which can increase the lifetime of methane and other greenhouse gases. Perhaps more importantly, various geoengineering ideas involve injecting dust particles high into Earth’s atmosphere, to reflect incoming solar radiation. There, in the stratosphere, ozone is not a pollutant; rather, it forms a critical “ozone layer” that helps shield the planet from incoming radiation.

If iodine from dust was chemically transformed into an ozone-depleting form in the stratosphere, Volkamer said, “well, that’d not be good, as it could delay the recovery of the ozone layer. Let’s avoid adding anthropogenic iodine into the stratosphere!”

But how do cells fold themselves so precisely into such complicated configurations during development? What are the fundamental forces driving this process?

Now, researchers at Harvard Medical School have discovered a mechanical process by which sheets of cells morph into the delicate, looping semicircular canals of the inner ear.

Published Dec. 22 in Cell, the research, done in zebrafish, reveals that the process involves a combination of hyaluronic acid, produced by cells, that swells with water, and thin connectors between cells that direct the force of this swelling to shape the tissue.

Although conducted in zebrafish, the work reveals a basic mechanism for how tissues take on shapes — one that is likely to be conserved across vertebrates, the researchers say, and may also have implications for bioengineering.

A Model of Transparency

Study senior author Sean Megason, professor of systems biology in the Blavatnik Institute at HMS, and his team study how cells develop into complex, three-dimensional structures. To address this question, they turned to a classic — and ideal — model organism: zebrafish.

“They’re transparent, so we just stick them under a microscope and look at this entire process from a single cell to a larva that can swim and has all its parts,” explained study first author Akankshi Munjal, who conducted the research as a postdoctoral researcher at HMS and is now an assistant professor of cell biology at Duke University.

These parts include the semicircular canals, three fluid-filled tubes in the inner ear that are needed for balance and orienting in space. Little is known about how the semicircular canals form, in part because in many species they are obscured by the middle and outer ear. In zebrafish, however, the canals sit close to the surface, allowing researchers to watch them develop under a microscope.

“This was an exciting opportunity for us to look at how a three-dimensional organ forms from a simple sheet of cells,” Munjal said. “We could look at the inner ear in the embryo with complete accessibility.”

“The inner ear is a model for how cells work together to make complex structures that are needed for organisms to function,” Megason added. “We went into it thinking it was a beautiful structure, but not knowing what we would find.”

What they did find surprised them.

The conventional thinking is that the proteins actin and myosin act as tiny motors inside cells, pushing and pulling them in different directions to fold a tissue into a specific shape. However, the researchers discovered that zebrafish semicircular canals form through a markedly different process. During development, the cells produce hyaluronic acid, which is perhaps most well known as an antiwrinkle agent in beauty products. Once in the extracellular matrix the acid swells up, not unlike a diaper in a swimming pool. This swelling creates enough force to physically move nearby cells, but since the pressure is the same in all directions, the researchers wondered how the tissue ends up stretching in one direction and not another to form an elongated shape. The team found that this is accomplished by thin connectors between cells — dubbed cytocinches — that constrain the force.

“It’s like if you were to put a corset on a water balloon and deform it into an oblong structure,” Munjal said. This combination of swelling and cinching progressively shapes an initially flat sheet of cells into tubes.

“Our work shows a new way of doing things,” Megason said, adding that he hopes it will encourage people to consider additional mechanisms that may be involved in shaping tissues. “Cells have to use many different forces in order to accomplish what they need to, and time will tell exactly what the balance is between the molecular approaches of actin and myosin and the more physical approaches of pressure.”

Their discovery likely has broader implications, Megason and Munjal added.

The genes that control hyaluronic acid production in zebrafish semicircular canals are also present in the semicircular canals of mammals, suggesting that a similar process may be occurring. Moreover, hyaluronic acid is found in multiple parts of the human body, including skin and joints, indicating that it may play a role in shaping many tissues and organs — an avenue for future research.

If that does turn out to be the case, then studying the genes involved in hyaluronic acid production could help researchers understand congenital defects in organs where hyaluronic acid drives development.

“This is likely to be a widespread, conserved mechanism across species and organs,” Munjal said.

The mechanism could also be applied to bioengineering, where researchers are attempting to prod stem cells into forming buds, tubes, and other complicated shapes, with the ultimate goal of culturing organs in the lab.

Lab-grown organs are still a work in progress, Megason noted, but a key step will be parsing how organs form inside an organism. “We’re trying to dissect the steps of how a complex organ such as the inner ear is made in vivo, and then quantitatively understand those steps,” Megason said. “We hope this will set the foundational groundwork for having cells grow into whatever pattern and shape we want.”

This work was supported by the National Institutes of Health (R01DC015478), the Eunice Kennedy Shriver National Institute of Child Health and Human Development (K99HD098918), and a Human Frontier Science Program Long-Term Fellowship.