New tech aims to make the ocean healthier for marine life
A defunct drydock basin arched by a rusting 19th century steel bridge seems an incongruous place to conduct state-of-the-art climate science. But this placid and protected sliver of water connecting Brooklyn’s Navy Yard to the East River was just right for Garrett Boudinot to float a small dock topped with water carbon-sensing gear. And while his system right now looks like a trio of plastic boxes wired up together, it aims to mediate the growing ocean acidification problem, caused by overabundance of dissolved carbon dioxide.
Boudinot, a biogeochemist and founder of a carbon-management startup called Vycarb, is honing his method for measuring CO2 levels in water, as well as (at least temporarily) correcting their negative effects. It’s a challenge that’s been occupying numerous climate scientists as the ocean heats up, and as states like New York recognize that reducing emissions won’t be enough to reach their climate goals; they’ll have to figure out how to remove carbon, too.
To date, though, methods for measuring CO2 in water at scale have been either intensely expensive, requiring fancy sensors that pump CO2 through membranes; or prohibitively complicated, involving a series of lab-based analyses. And that’s led to a bottleneck in efforts to remove carbon as well.
But recently, Boudinot cracked part of the code for measurement and mitigation, at least on a small scale. While the rest of the industry sorts out larger intricacies like getting ocean carbon markets up and running and driving carbon removal at billion-ton scale in centralized infrastructure, his decentralized method could have important, more immediate implications.
Specifically, for shellfish hatcheries, which grow seafood for human consumption and for coastal restoration projects. Some of these incubators for oysters and clams and scallops are already feeling the negative effects of excess carbon in water, and Vycarb’s tech could improve outcomes for the larval- and juvenile-stage mollusks they’re raising. “We’re learning from these folks about what their needs are, so that we’re developing our system as a solution that’s relevant,” Boudinot says.
Ocean acidification can wreak havoc on developing shellfish, inhibiting their shells from growing and leading to mass die-offs.
Ocean waters naturally absorb CO2 gas from the atmosphere. When CO2 accumulates faster than nature can dissipate it, it reacts with H2O molecules, forming carbonic acid, H2CO3, which makes the water column more acidic. On the West Coast, acidification occurs when deep, carbon dioxide-rich waters upwell onto the coast. This can wreak havoc on developing shellfish, inhibiting their shells from growing and leading to mass die-offs; this happened, disastrously, at Pacific Northwest oyster hatcheries in 2007.
This type of acidification will eventually come for the East Coast, too, says Ryan Wallace, assistant professor and graduate director of environmental studies and sciences at Long Island’s Adelphi University, who studies acidification. But at the moment, East Coast acidification has other sources: agricultural runoff, usually in the form of nitrogen, and human and animal waste entering coastal areas. These excess nutrient loads cause algae to grow, which isn’t a problem in and of itself, Wallace says; but when algae die, they’re consumed by bacteria, whose respiration in turn bumps up CO2 levels in water.
“Unfortunately, this is occurring at the bottom [of the water column], where shellfish organisms live and grow,” Wallace says. Acidification on the East Coast is minutely localized, occurring closest to where nutrients are being released, as well as seasonally; at least one local shellfish farm, on Fishers Island in the Long Island Sound, has contended with its effects.
The second Vycarb pilot, ready to be installed at the East Hampton shellfish hatchery.
Courtesy of Vycarb
Besides CO2, ocean water contains two other forms of dissolved carbon — carbonate (CO3-) and bicarbonate (HCO3) — at all times, at differing levels. At low pH (acidic), CO2 prevails; at medium pH, HCO3 is the dominant form; at higher pH, CO3 dominates. Boudinot’s invention is the first real-time measurement for all three, he says. From the dock at the Navy Yard, his pilot system uses carefully calibrated but low-cost sensors to gauge the water’s pH and its corresponding levels of CO2. When it detects elevated levels of the greenhouse gas, the system mitigates it on the spot. It does this by adding a bicarbonate powder that’s a byproduct of agricultural limestone mining in nearby Pennsylvania. Because the bicarbonate powder is alkaline, it increases the water pH and reduces the acidity. “We drive a chemical reaction to increase the pH to convert greenhouse gas- and acid-causing CO2 into bicarbonate, which is HCO3,” Boudinot says. “And HCO3 is what shellfish and fish and lots of marine life prefers over CO2.”
This de-acidifying “buffering” is something shellfish operations already do to water, usually by adding soda ash (NaHCO3), which is also alkaline. Some hatcheries add soda ash constantly, just in case; some wait till acidification causes significant problems. Generally, for an overly busy shellfish farmer to detect acidification takes time and effort. “We’re out there daily, taking a look at the pH and figuring out how much we need to dose it,” explains John “Barley” Dunne, director of the East Hampton Shellfish Hatchery on Long Island. “If this is an automatic system…that would be much less labor intensive — one less thing to monitor when we have so many other things we need to monitor.”
Across the Sound at the hatchery he runs, Dunne annually produces 30 million hard clams, 6 million oysters, and “if we’re lucky, some years we get a million bay scallops,” he says. These mollusks are destined for restoration projects around the town of East Hampton, where they’ll create habitat, filter water, and protect the coastline from sea level rise and storm surge. So far, Dunne’s hatchery has largely escaped the ill effects of acidification, although his bay scallops are having a finicky year and he’s checking to see if acidification might be part of the problem. But “I think it's important to have these solutions ready-at-hand for when the time comes,” he says. That’s why he’s hosting a second, 70-liter Vycarb pilot starting this summer on a dock adjacent to his East Hampton operation; it will amp up to a 50,000 liter-system in a few months.
If it can buffer water over a large area, absolutely this will benefit natural spawns. -- John “Barley” Dunne.
Boudinot hopes this new pilot will act as a proof of concept for hatcheries up and down the East Coast. The area from Maine to Nova Scotia is experiencing the worst of Atlantic acidification, due in part to increased Arctic meltwater combining with Gulf of St. Lawrence freshwater; that decreases saturation of calcium carbonate, making the water more acidic. Boudinot says his system should work to adjust low pH regardless of the cause or locale. The East Hampton system will eventually test and buffer-as-necessary the water that Dunne pumps from the Sound into 100-gallon land-based tanks where larvae grow for two weeks before being transferred to an in-Sound nursery to plump up.
Dunne says this could have positive effects — not only on his hatchery but on wild shellfish populations, too, reducing at least one stressor their larvae experience (others include increasing water temperatures and decreased oxygen levels). “If it can buffer water over a large area, absolutely this will [benefit] natural spawns,” he says.
No one believes the Vycarb model — even if it proves capable of functioning at much greater scale — is the sole solution to acidification in the ocean. Wallace says new water treatment plants in New York City, which reduce nitrogen released into coastal waters, are an important part of the equation. And “certainly, some green infrastructure would help,” says Boudinot, like restoring coastal and tidal wetlands to help filter nutrient runoff.
In the meantime, Boudinot continues to collect data in advance of amping up his own operations. Still unknown is the effect of releasing huge amounts of alkalinity into the ocean. Boudinot says a pH of 9 or higher can be too harsh for marine life, plus it can also trigger a release of CO2 from the water back into the atmosphere. For a third pilot, on Governor’s Island in New York Harbor, Vycarb will install yet another system from which Boudinot’s team will frequently sample to analyze some of those and other impacts. “Let's really make sure that we know what the results are,” he says. “Let's have data to show, because in this carbon world, things behave very differently out in the real world versus on paper.”
The Women of RNA: Two Award-Winners Share Why They Spent Their Careers Studying DNA's Lesser-Known Cousin
When Lynne Maquat, who leads the Center for RNA Biology at the University of Rochester, became interested in the ribonucleic acid molecule in the 1970s, she was definitely in the minority. The same was true for Joan Steitz, now professor of molecular biophysics and biochemistry at Yale University, who began to study RNA a decade earlier in the 1960s.
"My first RNA experiment was a failure, because we didn't understand how things worked," Steitz recalls. In her first undergraduate experiment, she unwittingly used a lab preparation that destroyed the RNA. "Unknowingly, our preparation contained enzymes that degraded our RNA."
At the time, scientists pursuing genetic research tended to focus on DNA, or deoxyribonucleic acid — and for good reason. It was clear that the enigmatic double-helix ribbon held the answers to organisms' heredity, genetic traits, development, growth and aging. If scientists could decipher the secrets of DNA and understand how its genetic instructions translate into the body's functions in health and disease, they could develop treatments for all kinds of diseases. On the contrary, the prevailing dogma of the time viewed RNA as merely a helper that passively carried out DNA's genetic instructions for protein-making — so it received much less attention.
But Maquat and Steitz weren't interested in heredity. They studied biochemistry and biophysics, so they wanted to understand how RNA functioned on the molecular level — how it carried instructions, catalyzed reactions, and helped build protein bonds, among other things.
"I'm a mechanistic biochemist, so I like to know how things happen," Maquat says. "Once you understand the mechanism, you can think of how to solve problems." And so the quest to understand how RNA does its job became the focus of both women's careers.
"People can now appreciate why some of us studied RNA for such a long time."
Half a century later, in 2021, their RNA work has earned two prestigious recognitions only months from each other. In February, they received the Wolf Prize in Medicine, followed by the Warren Alpert Foundation Prize in May, awarded to scientists whose achievements led to prevention, cure or treatments of human diseases.
It was the development of the COVID-19 vaccines that made RNA a household name. Made by Moderna and Pfizer, the vaccines use the RNA molecule to deliver genetic instructions for making SARS-CoV-2's characteristic spike protein in our cells. The presence of this foreign-looking protein triggers the immune system to attack and remember the pathogen. As the vaccines reached the finish line, RNA took center stage, and it was Maquat's and Steitz's research that helped reveal how these molecular cogwheels drive many biological functions within cells.
If you think of a cell as a kingdom, the DNA plays the role of a queen. Like a monarch in a palace, DNA nestles inside the cell's nucleus issuing instructions needed for the cell to function. But no queen can successfully govern without her court, her messengers, and her soldiers, as well as other players that make her kingdom work. That's what RNAs do — they act as the DNA's vassals. They carry instructions for protein assembly, catalyze reactions and supervise many other processes to make sure the cellular kingdom performs as it should.
There are a myriad of these RNA vassals in our cells, and each type has its own specific task. There are messenger RNAs that deliver genetic instructions for protein synthesis from DNA to ribosomes, the cells' protein-making factories. There are ribosomal RNAs that help stitch together amino acids to make proteins. There are transfer RNAs that can bring amino acids to this protein synthesis machine, keeping it going. Then there are circular RNAs that act as sponges, absorbing proteins to help regulate the activity of genes. And that's only the tip of the iceberg when it comes to RNA diversity, researchers say.
"We know what the most abundant and important RNAs are doing," says Steitz. "But there are thousands of different ones, and we still don't have a full knowledge of them."
Critical to RNA's proper functioning is a process called splicing, in which a precursor mRNA is transformed into mature, fully-functional mRNA — a phenomenon that Steitz's work helped elucidate. The splicing process, which takes place in cellular assembly lines, involves removing extra RNA sequences and stringing the remaining RNA pieces together. Steitz found that tiny RNA particles called snRNPs are crucial to this process. They act as handy helpers, finding and removing errant genetic material from the mRNA molecules.
A dysfunctional RNA assembly line leads to diseases, including many cancers. For instance, Steitz found that people with Lupus — an autoimmune disorder — have antibodies that mistakenly attack the little snRNP helpers. She also discovered that when snRNPs don't do their job properly, they can cause what scientists call mis-splicing, producing defective mRNAs.
Fortunately, cells have a built-in quality-control process that can spot and correct these mistakes, which is what Maquat studied in her work. In 1981, she discovered a molecular quality-control system that spots and destroys such incorrectly assembled mRNA. With the cryptic name "nonsense-mediated mRNA decay" or NMD, this process is vital to the health and wellbeing of a cellular kingdom in humans — because splicing mistakes happen far more often than one would imagine.
"We estimate that about a third of our mRNA are mistakes," Maquat says. "And nonsense-mediated mRNA decay cleans up these mistakes." When this quality-control system malfunctions, defective mRNA forge faulty proteins, which mess up the cellular machinery and cause disease, including various forms of cancer.
Scientists' newfound appreciation of RNA opens door to many novel treatments.
Now that the first RNA-based shots were approved, the same principle can be used for create vaccines for other diseases, the two RNA researchers say. Moreover, the molecule has an even greater potential — it can serve as a therapeutic target for other disorders. For example, Spinraza, a groundbreaking drug approved in 2016 for spinal muscular atrophy, uses small snippets of synthetic genetic material that bind to the RNA, helping fix splicing errors. "People can now appreciate why some of us studied RNA for such a long time," says Maquat.
Steitz is thrilled that the entire field of RNA research is enjoying the limelight. "I'm delighted because the prize is more of a recognition of the field than just our work," she says. "This is a more general acknowledgment of how basic research can have a remarkable impact on human health."
Lina Zeldovich has written about science, medicine and technology for Popular Science, Smithsonian, National Geographic, Scientific American, Reader’s Digest, the New York Times and other major national and international publications. A Columbia J-School alumna, she has won several awards for her stories, including the ASJA Crisis Coverage Award for Covid reporting, and has been a contributing editor at Nautilus Magazine. In 2021, Zeldovich released her first book, The Other Dark Matter, published by the University of Chicago Press, about the science and business of turning waste into wealth and health. You can find her on http://linazeldovich.com/ and @linazeldovich.
In 2010, a 67-year-old former executive assistant for a Fortune 500 company was diagnosed with mild cognitive impairment. By 2014, her doctors confirmed she had Alzheimer's disease.
As her disease progressed, she continued to live independently but wasn't able to drive anymore. Today, she can manage most of her everyday tasks, but her two daughters are considering a live-in caregiver. Despite her condition, the woman may represent a beacon of hope for the approximately 44 million people worldwide living with Alzheimer's disease. The now 74-year-old is among a small cadre of Alzheimer's patients who have undergone an experimental ultrasound procedure aimed at slowing cognitive decline.
In November 2020, Elisa Konofagou, a professor of biomedical engineering and director of the Ultrasound and Elasticity Imaging Laboratory at Columbia University, and her team used ultrasound to noninvasively open the woman's blood-brain barrier. This barrier is a highly selective membrane of cells that prevents toxins and pathogens from entering the brain while allowing vital nutrients to pass through. This regulatory function means the blood-brain barrier filters out most drugs, making treating Alzheimer's and other brain diseases a challenge.
Ultrasound uses high-frequency sound waves to produce live images from the inside of the human body. But scientists think it could also be used to boost the effectiveness of Alzheimer's drugs, or potentially even improve brain function in dementia patients without the use of drugs.
The procedure, which involves a portable ultrasound system, is the culmination of 17 years of lab work. As part of a small clinical trial, scientists positioned a sensor transmitting ultrasound waves on top of the woman's head while she sat in a chair. The sensor sends ultrasound pulses throughout the target region. Meanwhile, investigators intravenously infused microbubbles into the woman to boost the effects of the ultrasound. Three days after the procedure, scientists scanned her brain so that they could measure the effects of the treatments. Five months later, they took more images of her brain to see if the effects of the treatment lasted.
Promising Signs
After the first brain scan, Konofagou and her team found that amyloid-beta, the protein that clumps together in the brains of Alzheimer's patients and disrupts cell function, had declined by 14%. At the woman's second scan, amyloid levels were still lower than before the experimental treatment, but only by 10% this time. Konofagou thinks repeat ultrasound treatments given early on in the development of Alzheimer's may have the best chance at keeping amyloid plaques at bay.
This reduction in amyloid appeared to halt the woman's cognitive decline, at least temporarily. Following the ultrasound treatment, the woman took a 30-point test used to measure cognitive impairment in Alzheimer's. Her score — 22, indicating mild cognitive impairment — remained the same as before the intervention. Konofagou says this was actually a good sign.
"Typically, every six months an Alzheimer's patient scores two to three points lower, so this is highly encouraging," she says.
Konofagou speculates that the results might have been even more impressive had they applied the ultrasound on a larger section of the brain at a higher frequency. The selected site was just 4 cubic centimeters. Current safety protocols set by the U.S. Food and Drug Administration stipulate that investigators conducting such trials only treat one brain region with the lowest pressure possible.
The Columbia trial is aided by microbubble technology. During the procedure, investigators infused tiny, gas-filled spheres into the woman's veins to enhance the ultrasound reflection of the sound waves.
The big promise of ultrasound is that it could eventually make drugs for Alzheimer's obsolete.
"Ultrasound with microbubbles wakes up immune cells that go on to discard amyloid-beta," Konofagou says. "In this way, we can recover the function of brain neurons, which are destroyed by Alzheimer's in a sort of domino effect." What's more, a drug delivered alongside ultrasound can penetrate the brain at a dose up to 10 times higher.
Costas Arvanitis, an assistant professor at Georgia Institute of Technology who studies ultrasonic biophysics and isn't involved in the Columbia trial, is excited about the research. "First, by applying ultrasound you can make larger drugs — picture an antibody — available to the brain," he says. Then, you can use ultrasound to improve the therapeutic index, or the ratio of the effectiveness of a drug versus the ratio of adverse effects. "Some drugs might be effective but because we have to provide them in high doses to see significant responses they tend to come with side effects. By improving locally the concentration of a drug, you open up the possibility to reduce the dose."
The Columbia trial will enroll just six patients and is designed to test the feasibility and safety of the approach, not its efficacy. Still, Arvantis is hopeful about the potential benefits of the technique. "The technology has already been demonstrated to be safe, its components are now tuned to the needs of this specific application, and it's safe to say it's only a matter of time before we are able to develop personalized treatments," he says.
Konofagou and her colleagues recently presented their findings at the 20th Annual International Symposium for Therapeutic Ultrasound and intend to publish them in a scientific journal later this year. They plan to recruit more participants for larger trials, which will determine how effective the therapy is at improving memory and brain function in Alzheimer's patients. They're also in talks with pharmaceutical companies about ways to use their therapeutic approach to improve current drugs or even "create new drugs," says Konofagou.
A New Treatment Approach
On June 7, the FDA approved the first Alzheimer's disease drug in nearly two decades. Aducanumab, a drug developed by Biogen, is an antibody designed to target and reduce amyloid plaques. The drug has already sparked immense enthusiasm — and controversy. Proponents say the drug is a much-needed start in the fight against the disease, but others argue that the drug doesn't substantially improve cognition. They say the approval could open the door to the FDA greenlighting more Alzheimer's drugs that don't have a clear benefit, giving false hope to both patients and their families.
Konofagou's ultrasound approach could potentially boost the effects of drugs like aducanumab. "Our technique can be seamlessly combined with aducanumab in early Alzheimer's, where it has shown the most promise, to further enhance both its amyloid load reduction and further reduce cognitive deficits while using exactly the same drug regimen otherwise," she says. For the Columbia team, the goal is to use ultrasound to maximize the effects of aducanumab, as they've done with other drugs in animal studies.
But Konofagou's approach could transcend drug controversies, and even drugs altogether. The big promise of ultrasound is that it could eventually make drugs for Alzheimer's obsolete.
"There are already indications that the immune system is alerted each time ultrasound is exerted on the brain or when the brain barrier is being penetrated and gets activated, which on its own may have sufficient therapeutic effects," says Konofagou. Her team is now working with psychiatrists in hopes of using brain stimulation to treat patients with depression.
The potential to modulate the brain without drugs is huge and untapped, says Kim Butts Pauly, a professor of radiology, electrical engineering and bioengineering at Stanford University, who's not involved in the Columbia study. But she admits that scientists don't know how to fully control ultrasound in the brain yet. "We're only at the starting point of getting the tools to understand and harness how ultrasound microbubbles stimulate an immune response in the brain."
Meanwhile, the 74-year-old woman who received the ultrasound treatment last year, goes on about her life, having "both good days and bad days," her youngest daughter says. COVID-19's isolation took a toll on her, but both she and her daughters remain grateful for the opportunity to participate in the ultrasound trial.
"My mother wants to help, if not for herself, then for those who will follow her," the daughter says. She hopes her mother will be able to join the next phase of the trial, which will involve a drug in conjunction with the ultrasound treatment. "This may be the combination where the magic will happen," her daughter says.