Friday Five: "Cyclic breathing" can increase well-being, Stanford scientists find
In this week's Friday Five, breathing this way may cut down on anxiety, a fasting regimen that could make you sick, this type of job makes men more virile, 3D printed hearts could save your life, and the role of metformin in preventing dementia.
The Friday Five covers five stories in research that you may have missed this week. There are plenty of controversies and troubling ethical issues in science – and we get into many of them in our online magazine – but this news roundup focuses on scientific creativity and progress to give you a therapeutic dose of inspiration headed into the weekend.
Here are the promising studies covered in this week's Friday Five, featuring interviews with Dr. David Spiegel, associate chair of psychiatry and behavioral sciences at Stanford, and Dr. Filip Swirski, professor of medicine and cardiology at the Icahn School of Medicine at Mount Sinai.
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Here are the promising studies covered in this week's Friday Five, featuring interviews with Dr. David Spiegel, associate chair of psychiatry and behavioral sciences at Stanford, and Dr. Filip Swirski, professor of medicine and cardiology at the Icahn School of Medicine at Mount Sinai.
- Breathing this way cuts down on anxiety*
- Could your fasting regimen make you sick?
- This type of job makes men more virile
- 3D printed hearts could save your life
- Yet another potential benefit of metformin
* This video with Dr. Andrew Huberman of Stanford shows exactly how to do the breathing practice.
This podcast originally aired on March 3, 2023.
The latest tools, like whole genome sequencing, are allowing food outbreaks to be identified and stopped more quickly.
With the pandemic at the forefront of everyone's minds, many people have wondered if food could be a source of coronavirus transmission. Luckily, that "seems unlikely," according to the CDC, but foodborne illnesses do still sicken a whopping 48 million people per year.
Whole genome sequencing is like "going from an eight-bit image—maybe like what you would see in Minecraft—to a high definition image."
In normal times, when there isn't a historic global health crisis infecting millions and affecting the lives of billions, foodborne outbreaks are real and frightening, potentially deadly, and can cause widespread fear of particular foods. Think of Romaine lettuce spreading E. coli last year— an outbreak that infected more than 500 people and killed eight—or peanut butter spreading salmonella in 2008, which infected 167 people.
The technologies available to detect and prevent the next foodborne disease outbreak have improved greatly over the past 30-plus years, particularly during the past decade, and better, more nimble technologies are being developed, according to experts in government, academia, and private industry. The key to advancing detection of harmful foodborne pathogens, they say, is increasing speed and portability of detection, and the precision of that detection.
Getting to Rapid Results
Researchers at Purdue University have recently developed a lateral flow assay that, with the help of a laser, can detect toxins and pathogenic E. coli. Lateral flow assays are cheap and easy to use; a good example is a home pregnancy test. You place a liquid or liquefied sample on a piece of paper designed to detect a single substance and soon after you get the results in the form of a colored line: yes or no.
"They're a great portable tool for us for food contaminant detection," says Carmen Gondhalekar, a fifth-year biomedical engineering graduate student at Purdue. "But one of the areas where paper-based lateral flow assays could use improvement is in multiplexing capability and their sensitivity."
J. Paul Robinson, a professor in Purdue's Colleges of Veterinary Medicine and Engineering, and Gondhalekar's advisor, agrees. "One of the fundamental problems that we have in detection is that it is hard to identify pathogens in complex samples," he says.
When it comes to foodborne disease outbreaks, you don't always know what substance you're looking for, so an assay made to detect only a single substance isn't always effective. The goal of the project at Purdue is to make assays that can detect multiple substances at once.
These assays would be more complex than a pregnancy test. As detailed in Gondhalekar's recent paper, a laser pulse helps create a spectral signal from the sample on the assay paper, and the spectral signal is then used to determine if any unique wavelengths associated with one of several toxins or pathogens are present in the sample. Though the handheld technology has yet to be built, the idea is that the results would be given on the spot. So someone in the field trying to track the source of a Salmonella infection could, for instance, put a suspected lettuce sample on the assay and see if it has the pathogen on it.
"What our technology is designed to do is to give you a rapid assessment of the sample," says Robinson. "The goal here is speed."
Seeing the Pathogen in "High-Def"
"One in six Americans will get a foodborne illness every year," according to Dr. Heather Carleton, a microbiologist at the Centers for Disease Control and Prevention's Enteric Diseases Laboratory Branch. But not every foodborne outbreak makes the news. In 2017 alone, the CDC monitored between 18 and 37 foodborne poison clusters per week and investigated 200 multi-state clusters. Hardboiled eggs, ground beef, chopped salad kits, raw oysters, frozen tuna, and pre-cut melon are just a taste of the foods that were investigated last year for different strains of listeria, salmonella, and E. coli.
At the heart of the CDC investigations is PulseNet, a national network of laboratories that uses DNA fingerprinting to detect outbreaks at local and regional levels. This is how it works: When a patient gets sick—with symptoms like vomiting and fever, for instance—they will go to a hospital or clinic for treatment. Since we're talking about foodborne illnesses, a clinician will likely take a stool sample from the patient and send it off to a laboratory to see if there is a foodborne pathogen, like salmonella, E. Coli, or another one. If it does contain a potentially harmful pathogen, then a bacterial isolate of that identified sample is sent to a regional public health lab so that whole genome sequencing can be performed.
Whole genome sequencing can differentiate "virtually all" strains of foodborne pathogens, no matter the species, according to the FDA.
Whole genome sequencing is a method for reading the entire genome of a bacterial isolate (or from any organism, for that matter). Instead of working with a couple dozen data points, now you're working with millions of base pairs. Carleton likes to describe it as "going from an eight-bit image—maybe like what you would see in Minecraft—to a high definition image," she says. "It's really an evolution of how we detect foodborne illnesses and identify outbreaks."
If the bacterial isolate matches another in the CDC's database, this means there could be a potential outbreak and an investigation may be started, with the goal of tracking the pathogen to its source.
Whole genome sequencing has been a relatively recent shift in foodborne disease detection. For more than 20 years, the standard technique for analyzing pathogens in foodborne disease outbreaks was pulsed-field gel electrophoresis. This method creates a DNA fingerprint for each sample in the form of a pattern of about 15-30 "bands," with each band representing a piece of DNA. Researchers like Carleton can use this fingerprint to see if two samples are from the same bacteria. The problem is that 15-30 bands are not enough to differentiate all isolates. Some isolates whose bands look very similar may actually come from different sources and some whose bands look different may be from the same source. But if you can see the entire DNA fingerprint, then you don't have that issue. That's where whole genome sequencing comes in.
Although the PulseNet team had piloted whole genome sequencing as early as 2013, it wasn't until July of last year that the transition to using whole genome sequencing for all pathogens was complete. Though whole genome sequencing requires far more computing power to generate, analyze, and compare those millions of data points, the payoff is huge.
Stopping Outbreaks Sooner
The U.S. Food and Drug Administration (FDA) acquired their first whole genome sequencers in 2008, according to Dr. Eric Brown, the Director of the Division of Microbiology in the FDA's Office of Regulatory Science. Since then, through their GenomeTrakr program, a network of more than 60 domestic and international labs, the FDA has sequenced and publicly shared more than 400,000 isolates. "The impact of what whole genome sequencing could do to resolve a foodborne outbreak event was no less impactful than when NASA turned on the Hubble Telescope for the first time," says Brown.
Whole genome sequencing has helped identify strains of Salmonella that prior methods were unable to differentiate. In fact, whole genome sequencing can differentiate "virtually all" strains of foodborne pathogens, no matter the species, according to the FDA. This means it takes fewer clinical cases—fewer sick people—to detect and end an outbreak.
And perhaps the largest benefit of whole genome sequencing is that these detailed sequences—the millions of base pairs—can imply geographic location. The genomic information of bacterial strains can be different depending on the area of the country, helping these public health agencies eventually track the source of outbreaks—a restaurant, a farm, a food-processing center.
Coming Soon: "Lab in a Backpack"
Now that whole genome sequencing has become the go-to technology of choice for analyzing foodborne pathogens, the next step is making the process nimbler and more portable. Putting "the lab in a backpack," as Brown says.
The CDC's Carleton agrees. "Right now, the sequencer we use is a fairly big box that weighs about 60 pounds," she says. "We can't take it into the field."
A company called Oxford Nanopore Technologies is developing handheld sequencers. Their devices are meant to "enable the sequencing of anything by anyone anywhere," according to Dan Turner, the VP of Applications at Oxford Nanopore.
"The sooner that we can see linkages…the sooner the FDA gets in action to mitigate the problem and put in some kind of preventative control."
"Right now, sequencing is very much something that is done by people in white coats in laboratories that are set up for that purpose," says Turner. Oxford Nanopore would like to create a new, democratized paradigm.
The FDA is currently testing these types of portable sequencers. "We're very excited about it. We've done some pilots, to be able to do that sequencing in the field. To actually do it at a pond, at a river, at a canal. To do it on site right there," says Brown. "This, of course, is huge because it means we can have real-time sequencing capability to stay in step with an actual laboratory investigation in the field."
"The timeliness of this information is critical," says Marc Allard, a senior biomedical research officer and Brown's colleague at the FDA. "The sooner that we can see linkages…the sooner the FDA gets in action to mitigate the problem and put in some kind of preventative control."
At the moment, the world is rightly focused on COVID-19. But as the danger of one virus subsides, it's only a matter of time before another pathogen strikes. Hopefully, with new and advancing technology like whole genome sequencing, we can stop the next deadly outbreak before it really gets going.
What Will Make the Public Trust a COVID-19 Vaccine?
A successful deployment of an eventual vaccine will mean grappling with ongoing cultural tensions.
With a brighter future hanging on the hopes of an approved COVID-19 vaccine, is it possible to win over the minds of fearful citizens who challenge the value or safety of vaccination?
Globally, nine COVID-19 vaccines so far are being tested for safety in early phase human clinical trials.
It's a decades-old practice. With a dose injected into the arm of a healthy patient, doctors aim to prevent illness with a vaccine shot designed to trigger a person's immune system to fight serious infection without getting the disease.
This week, in fact, the U.S. frontrunner vaccine candidate, developed by Moderna, safely produced an immune response in the first eight healthy volunteers, the company announced. A large efficacy trial is planned to start in July. But if positive signals for safety and efficacy result from that trial, will that be enough to convince the public to broadly embrace a new vaccine?
"Throughout the history of vaccines there has always been a small vocal minority who don't believe vaccines work or don't trust the science," says sociologist and researcher Jennifer Reich, a professor at the University of Colorado in Denver and author of Calling the Shots: Why Parents Reject Vaccines.
Research indicates that only about 2 percent of the population say vaccines aren't necessary under any circumstance. Remarkably, a quarter to one third of American parents delay or reject the shots, not because they are anti-vaccine, but because they disapprove of the recommended timing or administration, says Reich.
Additionally, addressing distrust about how they come to market is key when talking to parents, workers or anyone targeted for a new vaccine, she says.
"When I talk to parents about why they reject vaccines for their kids, a lot of them say that they don't fully trust the process by which vaccines are regulated and tested," says Reich. "They don't trust that vaccine manufacturers -- which are for-profit companies -- are looking out for public health."
Balancing Act
Globally, nine COVID-19 vaccine candidates so far are being tested for safety in early phase human clinical trials and more than 100 are under development as scientists hustle to curtail the disease. Creating a new vaccine at a record pace requires a delicate balance of benefit and risk, says vaccinology expert Dr. Kathryn Edwards, professor of pediatrics in the division of infectious diseases at Vanderbilt University School of Medicine in Nashville, Tenn.
"We take safety very seriously," says Dr. Edwards. "We don't want something bad to happen, but we also realize that we have a terrible outbreak and we have a lot of people dying. We want to figure out how we can stop this."
In the U.S., all vaccine clinical trials have a data safety board of experts who monitor results for adverse reactions and red flags that should halt a study, notes Dr. Edwards. Any candidate that succeeds through safety and efficacy trials still requires review and approval by the Food and Drug Administration before a public launch.
Community vs. Individual
A major challenge to the deployment of a safe and effective coronavirus vaccine goes beyond the technical realm. A persistent all-out anti-vaccine sentiment has found a home and growing community on social media where conspiracies thrive. Main tenets of the movement are that vaccines are ineffective, unsafe and cause autism, despite abundant scientific evidence to the contrary.
Best-case scenario, more than one successful vaccine ascends with competing methods to achieve the same goal of preventing or lessening the severity of the COVID-19 virus.
In fact, widespread use of vaccines is considered by the U.S. Centers of Disease Control and Prevention to be one of the greatest public health achievements of the 20th Century. The World Health Organization estimates that between two million to three million deaths are avoided each year through immunization campaigns that employ vaccination to control life-threatening infectious diseases.
Most people reluctant to give their children vaccines, however, don't oppose them for everyone, but believe that they are a personal choice, says Reich.
"They think that vaccines are one strategy in personal health optimization, but they shouldn't be mandated for participation in any part of civil society," she says.
Vaccine hesitancy, like the teeter totter of social distancing acceptance, reflects the push and pull of individual versus community values, says Reich.
"A lot of people are saying, 'I take personal responsibility for my own health and I don't want a city or a county or state telling me what I should and shouldn't do,'" says Reich. "Then we also see calls for collective responsibility that says 'It's not your personal choice. This is about helping health systems function. This is about making sure vulnerable people are protected.'"
These same debates are likely to continue if a vaccine comes to market, she says.
Building Public Confidence
Reich offers solutions to address the conflict between embedded American norms and widespread embrace of an approved COVID-19 vaccine. Long-term goals: Stop blaming people when they get sick, treat illness as a community responsibility, make sick leave common for all workers, and improve public health systems.
"In the shorter run," says Reich, "health authorities and companies that might bring a vaccine to market need to work very hard to explain to the public why they should trust this vaccine and why they should use it."
The rush for a viable vaccine raises questions for consumers. To build public confidence, it's up to FDA reviewers, institutions and pharmaceutical companies to explain "what steps were skipped. What steps moved forward. How rigorous was safety testing. And to make that information clear to the public," says Reich.
Dr. Edwards says clinical trial timelines accelerated to test vaccines in humans make all the safeguards involved in the process that more compelling and important.
"There's no question we need a vaccine," she says. "But we also have to make sure that we don't harm people."
The Road Ahead
Think of manufacturing and distribution as key pitstops to keep the race for a vaccine on the road to the finish line. Both elements require substantial effort and consideration.
The speed of getting a vaccine to those who need it could hinge on the type of technology used to create it. Best-case scenario, more than one successful vaccine ascends with competing methods to achieve the same goal of preventing or lessening the severity of the COVID-19 virus.
Technological platforms fall into two basic camps, those that are proven and licensed for other viruses, and experimental approaches that may hold great promise but lack regulatory approval, says Maria Elena Bottazzi, co-director of Texas Children's Center for Vaccine Development at Baylor College of Medicine in Houston.
Moderna, for instance, employs an experimental technology called messenger RNA (mRNA) that has produced the encouraging early results in human safety trials, although some researchers criticized the company for not making the data public. The mRNA vaccine instructs cells to make copies of the key COVID-19 spike protein, with the goal of then triggering production of immune cells that can recognize and attack the virus if it ever invades the body.
"We were already seeing a lot of dissent around questions of individual freedoms and community responsibilities."
Scientists always look for ways to incorporate new technologies into drug development, says Bottazzi. On the other hand, the more basic and generic the technology, theoretically, the faster production could ramp up if a vaccine proves successful through all phases of clinical trials, she says.
"I don't want to develop a vaccine in my lab, but then I don't have anybody to hand it off to because my process is not suitable" for manufacturing or scalability, says Bottazzi.
Researchers at the Baylor lab hope to repurpose a shelved vaccine developed for the genetically similar SARS virus, with a strategy to leverage what is already known instead of "starting from scratch" to develop a COVID-19 vaccine. A recombinant protein technology similar to that used for an approved Hepatitis B vaccine lets scientists focus on identifying a suitable vaccine target without the added worry of a novel platform, says Bottazzi.
The Finish Line
If and when a COVID-19 vaccine is approved is anyone's guess. Announcing a plan to hasten vaccine development via a program dubbed Operation Warp Speed, President Trump said recently one could be available "hopefully" by the end of the year or early 2021.
Scientists urge caution, noting that safe vaccines can take 10 years or more to develop. If a rushed vaccine turns out to have safety and efficacy issues, that could add ammunition to the anti-vaccine lobby.
Emergence of a successful vaccine requires an "enormous effort" with many complex systems from the lab all the way to manufacturing enough capacity to handle a pandemic, says Bottazzi.
"At the same time, you're developing it, you're really carefully assessing its safety and ability to be effective," she says, so it's important "not to get discouraged" if it takes longer than a year or more.
To gauge if a vaccine works on a broad scale, it would have to be delivered into communities where the virus is active. There are examples in history of life-saving vaccines going first to people who could pay for them and not to those who needed them most, says Reich.
"Agencies are going to have to think about how those distribution decisions are going to be made and who is going to make them and that will go a certain way toward reassuring the public," says Reich.
A Gallup survey last year found that vaccine confidence, in general, remains high, with 86 percent of Americans believing that vaccines are safer than the diseases that they are designed to prevent. Still, recent news organization polls indicate that roughly 20 to 25 percent of Americans say they won't or are unlikely to get a COVID-19 vaccine if one becomes available.
Until the 1980s, every vaccine to hit the market was appreciated; a culture of questioning science didn't exist in the same way as today, notes Reich. Time passed and attitudes changed.
"We were already having robust arguments nationally about what counts as an expert, what's the role of the government in daily life," says Reich. "We were already seeing a lot of dissent around questions of individual freedoms and community responsibilities. COVID-19 did not create those conflicts, but they've definitely become more visible since we've moved into this pandemic."