In a paper published in Science today, an international team of scientists present a detailed blueprint of how plants construct phloem cells — the tissue responsible for transporting and accumulating sugars and starch in the parts of the plant that we harvest (seeds, fruits and storage tubers) to feed much of the world.

This pivotal research reveals how global signals in root meristems coordinate distinct maturation phases of the phloem tissue.

Phloem is a highly specialised vascular tissue that forms an interconnected network of continuous strands throughout a plant’s body. It transports sugars, nutrients and a range of signalling molecules between leaves, roots, flowers and fruits.

As a result, phloem is central to plant function. Understanding how the phloem network is initiated and develops is important for future applications in agriculture, forestry and biotechnology as it could reveal how to better transport this sugar energy to where it is needed.

How do plants build a sugar lane in a multi-lane highway?

Plant roots continue to grow throughout a plant’s life. This phenomenon, known as indeterminate growth, means roots continually elongate as they add new tissues to the tip of the root — like constructing a never-ending highway. A continuous file of specialised phloem cells running the length of roots (analogous to a lane on a highway) delivers the primary nutrient, sucrose, to the parts of the plant where it is needed for growth. To fulfil this vital role, phloem tissue must develop and mature rapidly so it can supply sugars to surrounding tissues — akin to building a service lane that needs to be completed in the first stage of constructing a multi-lane highway.

The problem that has long puzzled plant scientists is how a single instructive gradient of proteins are able to stage the construction phases across all the different specialised cell files (highway lanes) that are present in roots. How does one cell type read the same gradient as its neighbours, but interprets it differently to stage its own specialised development is a question that plant scientists have been working to resolve.

Over the past 15 years, researchers in Yrjö Helariutta’s teams at the University of Cambridge and University of Helsinkihave uncovered the central role of cell-to-cell communication and complex feedback-mechanisms involved in vascular patterning. This new research, undertaken with collaborators at New York University and North Carolina State University, reveals how this single lane of phloem cells is constructed independently of surrounding cells.

The Sainsbury/Helsinki group dissected each step in the construction of the phloem cell file (the sugar transport lane) in the model plant Arabidopsis thaliana using single-cell RNA-seq and live imaging. Their work showed how the proteins that control the broad maturation gradient of the root interact with the genetic machinery that specifically controls phloem development.

This is one mechanism that appears to help the phloem cell file to fast-track maturation using its own machinery to interpret the maturation cues. Dr Pawel Roszak, co-first-author of the study and researcher at the Sainsbury Laboratory Cambridge University (SLCU), explains: “We have shown how global signals in the root meristem interact with the cell type specific factors to determine distinct phases of phloem development at the cellular resolution. Using cell sorting followed by deep, high-resolution single-cell sequencing of the underlying gene regulatory network revealed a “seesaw” mechanism of reciprocal genetic repression that triggers rapid developmental transitions.”

The group also showed how phloem development is staged over time, with early genetic programs inhibiting late genetic programs and vice versa — just as the road asphalt-laying work crews’ hand over construction to lane painters in the latter stages of highway construction. In addition, they showed how early phloem regulators instructed specific genes to split the phloem cells into two different subtypes — like the construction of a fork in the road leading to two separate destinations.

Co-leader of the work, Professor Yrjö Helariutta, said his teams’ reconstruction of the steps from birth to terminal differentiation of protophloem in the Arabidopsis root exposed the steps. Helariutta said: “Broad maturation gradients interfacing with cell-type specific transcriptional regulators to stage cellular differentiation is required for phloem development.”

“By combining single-cell transcriptomics with live imaging, here we have mapped the cellular events from the birth of the phloem cell to its terminal differentiation into phloem sieve element cells. This allowed us to uncover genetic mechanisms that coordinate cellular maturation and connect the timing of the genetic cascade to broadly expressed master regulators of meristem maturation. The precise timing of developmental mechanisms was critical for proper phloem development, with apparent “fail safe” mechanisms to ensure transitions.”

The researchers plan to further explore the evolution of these mechanisms and whether these steps are replicated in other regions of plants and other plant species.

Published today in Science, the study led by the University of Texas and the National Institutes of Health is a promising development in the fight against multiple types of cancer including melanoma, the most deadly form of skin cancer, the researchers said.

Nationwide, melanoma is the fifth-most common cancer. Roughly 100,000 new melanoma cases will be diagnosed in the United States in the coming year, and more than 7,000 of those patients are expected to die, according to the American Cancer Society.

One of the most aggressive cancers, melanoma kills by metastasizing, or spreading, to other organs such as the liver, lungs and brain.

The new study focuses on a therapeutic technique called immune checkpoint blockade, often referred to by its initials of ICB, which has revolutionized treatment of melanoma, and cancer in general.

ICB therapy relies on inhibitor drugs that block proteins called checkpoints that are produced by certain immune system cells — T cells, for example — and also by some cancer cells.

Checkpoints help prevent immune responses from being too strong, but sometimes that means keeping T cells from killing cancer cells. Thus, when the checkpoints are blocked, T cells can do a better job of killing cancer cells.

“ICB has been a game-changer in cancer therapy, and the influence of the gut microbiome on therapeutic response has been demonstrated in numerous studies, in preclinical models and also in research involving human cohorts,” Morgun said. “A person’s microbiome is shaped by a wide range of environmental factors including food and medications, while human genetics accounts for a much smaller proportion of the microbiome variation from person to person.”

The human gut microbiome is a complicated community of more than 10 trillion microbial cells from about 1,000 different bacterial species. It has remained unclear whether dietary fiber intake and the use of commercially available probiotics affect immunotherapy response in cancer patients, Morgun said.

Morgun and collaborators on this study looked at hundreds of melanoma patients, analyzing their gut microbiomes, dietary habits, use of probiotics, disease features and treatment outcomes. Most of the patients were being treated via ICB, typically a type known as anti-programmed cell death protein therapy, abbreviated to anti-PD-1.

A parallel study involving mice implanted with tumors was also part of the research.

In the human, observational cohort portion of the study, higher dietary fiber intake was associated with disease non-progression among patients on ICB; the most pronounced benefits were found in patients with strong dietary fiber intake and no probiotic use.

The mouse model generated similar results.

“We showed that dietary fiber and probiotic use, both known to impact the gut microbiome, are associated with differing ICB outcomes,” Morgun said. “From the human cohort results we can’t assign causality — there may have been other things going on with those patients that we didn’t measure in this study.”

But Morgun said the results in the mice support the idea that anti-tumor immunity is strongest with a high-fiber diet and no probiotics.

To help make sense of microbiome complexity, Morgun and Natalia Shulzhenko of Oregon State’s Carlson College of Veterinary Medicine earlier invented a computer modeling technique known as transkingdom network analysis.

The model, used in this latest work, integrates multiple types of “omics” data — metagenomic, metabolomic, lipidomic, proteomic, etc. — in determining how interactions among specific types of gut microbes help or hinder biological functions in the host. In this case, the microbial interactions involved how well the host responds to immune checkpoint blockade.

It’s important to note, Morgun said, that transkingdom network analysis in mice showed a family of bacteria, Ruminococcaceae, among the organisms increased by the high-fiber diet; the same bacteria were found in the current study involving humans and in previous, related research with people.

Double-blind, randomized dietary intervention studies will be critical for establishing whether a targeted, achievable diet change at the start of ICB therapy can improve patient outcomes, he said.

“And though the findings suggest that some commercially available probiotics may be harmful for patients on ICB, more research is needed to determine which probiotics could actually be beneficial,” Morgun said.

Leading the study were Jennifer Wargo, Lorenzo Cohen and Carrie Daniel of the University of Texas and Giorgio Trinchieri of the National Institutes of Health. Approximately 80 scientists took part in the research.

Funders included the NIH and the U.S. Department of State.

Previous research led by the U.S. Department of Agriculture had shown evidence of antibodies in wild deer. This study, published today (Dec. 23, 2021) in Nature, details the first report of active COVID-19 infection in white-tailed deer supported by the growth of viral isolates in the lab, indicating researchers had recovered viable samples of the SARS-CoV-2 virus and not only its genetic traces.

Based on genomic sequencing of the samples collected between January and March 2021, researchers determined that variants infecting wild deer matched strains of the SARS-CoV-2 virus that had been prevalent in Ohio COVID-19 patients at the time. Sample collection occurred before the Delta variant was widespread, and that variant was not detected in these deer. The team is testing more samples to check for new variants as well as older variants, whose continued presence would suggest the virus can set up shop and survive in this species.

The fact that wild deer can become infected “leads toward the idea that we might actually have established a new maintenance host outside humans,” said Andrew Bowman, associate professor of veterinary preventive medicine at The Ohio State University and senior author of the paper.

“Based on evidence from other studies, we knew they were being exposed in the wild and that in the lab we could infect them and the virus could transmit from deer to deer. Here, we’re saying that in the wild, they are infected,” Bowman said. “And if they can maintain it, we have a new potential source of SARS-CoV-2 coming in to humans. That would mean that beyond tracking what’s in people, we’ll need to know what’s in the deer, too.

“It could complicate future mitigation and control plans for COVID-19.”

A lot of unknowns remain: how the deer got infected, whether they can infect humans and other species, how the virus behaves in the animals’ body, and whether it’s a transient or long-term infection.

The research team took nasal swabs from 360 white-tailed deer in nine northeast Ohio locations. Using PCR testing methods, the scientists detected genetic material from at least three different strains of the virus in 129 (35.8%) of the deer sampled.

The analysis showed that B.1.2 viruses dominant in Ohio in the early months of 2021 spilled over multiple times into deer populations in different locations.

“The working theory based on our sequences is that humans are giving it to deer, and apparently we gave it to them several times,” Bowman said. “We have evidence of six different viral introductions into those deer populations. It’s not that a single population got it once and it spread.”

Each site was sampled between one and three times, adding up to a total of 18 sample collection dates. Based on the findings, researchers estimated the prevalence of infection varied from 13.5% to 70% across the nine sites, with the highest prevalence observed in four sites that were surrounded by more densely populated neighborhoods.

White-tailed deer functioning as a viral reservoir of SARS-CoV-2 would likely result in one of two outcomes, Bowman said. The virus could mutate in deer, potentially facilitating transmission of new strains to other species, including humans, or the virus could survive in deer unmutated while it simultaneously continues to evolve in humans, and at some point when humans don’t have immunity to the strains infecting deer, those variants could come spilling back to humans.

How transmission happened initially in these deer, and how it could happen across species, are among the pending questions related to these findings. The research team speculated that white-tailed deer were infected through an environmental pathway — possibly by drinking contaminated water. Research has shown that the virus is shed in human stool and detectable in wastewater.

The white-tailed deer tested for this study were part of a population control initiative, so they are not a transmission threat.

Though there are an estimated 600,000 white-tailed deer in Ohio and 30 million in the United States, Bowman said this sampling focused on locations close to dense human populations and is not representative of all free-ranging deer.

This work was supported by the Ohio State Infectious Diseases Institute and the National Institute of Allergy and Infectious Diseases. In addition to USDA, NIAID, Ohio Wildlife Center and Cleveland Metroparks contributors, Ohio State co-authors include Vanessa Hale, Patricia Dennis, Dillon McBride, Jacqueline Nolting, Christopher Madden, Devra Huey, Margot Ehrlich, Jenessa Winston, Dubraska Diaz-Campos, Page Yaxley, Alexis McLaine, Risa Pesapane, Mark Flint, Jaylene Flint, Anastasia Vlasova, Scott Kenney, Qiuhong Wang, Linda Saif and Seth Faith.

Cell culture experiments showed that SARS-CoV-2, which causes COVID-19, limits the release of viral particles that can be inactivated by antibodies, instead staying tucked within cell walls and spreading between cells.

“It’s basically an underground form of transmission,” said lead author Shan-Lu Liu, a virology professor in the Department of Veterinary Biosciences at The Ohio State University and an investigator in the university’s Center for Retrovirus Research.

“SARS-CoV-2 can spread efficiently from cell to cell because there are essentially no blockers from the host immunity. Target cells become donor cells, and it just becomes a wave of spread, as the virus may not get out of the cells.”

Liu and colleagues found other revealing details about SARS-CoV-2: The spike protein on its surface alone enables cell-to-cell transmission, and yet the virus’s primary receptor on target cells — to which the spike binds — is not a necessary part of the cell-to-cell transmission operation. Additionally, they found that neutralizing antibodies are less effective against the virus when it spreads through cells.

The research was published Wednesday (Dec. 22, 2021) in the journal Proceedings of the National Academy of Sciences.

A major point of this study was comparing SARS-CoV-2 to the coronavirus behind the 2003 SARS outbreak, known as SARS-CoV. The findings help explain why while the first outbreak led to much higher fatality rates and lasted only eight months, we’re about to surpass the two-year mark of the current pandemic, with a majority of cases being asymptomatic, Liu said.

The comparison showed that the SARS-CoV that caused SARS in 2003 is more efficient than SARS-CoV-2 at what is called cell-free transmission, when freely floating viral particles infect target cells by binding to a receptor on their surface — but also remain vulnerable to antibodies produced by previous infection and vaccines. SARS-CoV-2, on the other hand, is more efficient at cell-to-cell transmission — which makes it harder to neutralize with antibodies.

The viruses’ differing efficiencies were first demonstrated in experiments using pseudoviruses — a non-infectious viral core decorated with both kinds of coronavirus spike proteins on the surface.

“The spike protein is necessary and sufficient for both SARS-CoV-2 and SARS-CoV cell-to-cell transmission because the only difference in these pseudoviruses were the spike proteins,” said Liu, also a program director of the Viruses and Emerging Pathogens Program in Ohio State’s Infectious Diseases Institute.

Looking more deeply into those differences, the researchers found that SARS-CoV-2 is also more capable than SARS-CoV at initiating fusion with a target cell membrane, another key step in the viral entry process. And that stronger fusion action was associated with the virus’s enhanced cell-to-cell transmission.

Paradoxically, too much cell membrane fusion leads to cell death and can actually interfere with cell-to-cell transmission, Liu also found.

The team then turned to the role of the ACE2 receptor, a protein on cell surfaces that acts as the gateway for entry of the virus that causes COVID-19. The researchers found, unexpectedly, that cells with no or low levels of ACE2 on their surfaces can be penetrated by the virus, enabling robust cell-to-cell transmission.

“There is no perfect correlation between SARS-CoV-2 infection and the level of ACE2,” Liu said. “ACE2 may be needed for initial infection, but once infection is established, the virus may not need ACE2 anymore because it can spread from cell to cell.”

Finally, in experiments testing blood samples from human COVID-19 patients against the authentic SARS-CoV-2 virus, researchers determined that the virus could evade an antibody response through cell-to-cell transmission, but that antibody neutralization of the virus in the cell-free transmission mode was effective.

“We were able to confirm cell-to-cell transmission is not sensitive to inhibition from antibodies from COVID patients or vaccinated individuals,” Liu said. “Cell-to-cell transmission’s resistance to antibody neutralization is probably something we should watch for as SARS-CoV-2 variants continue to emerge, including the most recent, Omicron. In this sense, developing effective antiviral drugs targeting other steps of viral infection is critical.”

There are still many unknowns, including the exact mechanism the virus uses to spread from cell to cell, how that may influence individuals’ responses to viral infection, and whether or not efficient cell-to-cell transmission contributes to the emergence and spread of new variants. Liu’s lab is planning additional studies using the authentic virus and human lung cells to further explore these questions.

This work was supported by grants from the National Institutes of Health and funds from an anonymous private donor to Ohio State.

Ohio State co-authors include Cong Zeng, Jack Evans, Tiffany King, Yi-Min Zheng, Eugene Oltz, Linda Saif and Mark Peeples, also a researcher at Nationwide Children’s Hospital. Sean Whelan of the Washington University School of Medicine also contributed.

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).