Basecamp Research is using portable labs like this one to gather samples from ecosystems around the world.
Clark works for Basecamp Research, a biotech company headquartered in London, and his job is to collect samples from ecosystems around the world. By extracting DNA from soil, water, plants, microbes and other organisms, Basecamp is building an extensive database of the Earth’s proteins. While DNA itself isn’t a protein, the information stored in DNA is used to create proteins, so extracting, sequencing, and annotating DNA allows for the discovery of unique protein sequences.
Using what they’re finding in the middle of the Atlantic and beyond, Basecamp’s detailed database is constantly growing. The outputs could be essential for cleaning up the damage done by toxic chemicals and finding alternatives to these chemicals.
Catalysts for change
Proteins provide structure and function in all living organisms. Some of these functional proteins are enzymes, which quite literally make things happen.
“Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development. Biocatalysis is providing advantages, both to make more complex drugs and to be more sustainable, reducing the pollution and toxicity of conventional chemistry," says Ahir Pushpanath, who heads partnerships for Basecamp.
“Enzymes are perfectly evolved catalysts,” says Ahir Pushpanath, a partnerships lead at Basecamp. ”Enzymes are essentially just a polymer, and polymers are made up of amino acids, which are nature’s building blocks.” He suggests thinking about it like Legos — if you have a bunch of Lego pieces and use them to build a structure that performs a function, “that’s basically how an enzyme works. In nature, these monuments have evolved to do life’s chemistry. If we didn’t have enzymes, we wouldn’t be alive.”
In our own bodies, enzymes catalyze everything from vision to digesting food to regrowing muscles, and these same types of enzymes are necessary in the pharmaceutical, agrochemical and fine chemical industries. But industrial conditions differ from those inside our bodies. So, when scientists need certain chemical reactions to create a particular product or substance, they make their own catalysts in their labs — generally through the use of petroleum and heavy metals.
These petrochemicals are effective and cost-efficient, but they’re wasteful and often hazardous. With growing concerns around sustainability and long-term public health, it's essential to find alternative solutions to toxic chemicals. “Industrial chemistry is heavily polluting, especially the chemistry done in pharmaceutical drug development,” Pushpanath says.
Basecamp is trying to replace lab-created catalysts with enzymes found in the wild. This concept is called biocatalysis, and in theory, all scientists have to do is find the right enzymes for their specific need. Yet, historically, researchers have struggled to find enzymes to replace petrochemicals. When they can’t identify a suitable match, they turn to what Pushpanath describes as “long, iterative, resource-intensive, directed evolution” in the laboratory to coax a protein into industrial adaptation. But the latest scientific advances have enabled these discoveries in nature instead.
Marlon Clark, a research scientist at Basecamp Research, looks for novel biochemistries in the Azores.
Glen Gowers
Enzyme hunters
Whether it’s Clark and a colleague setting off on an expedition, or a local, on-the-ground partner gathering and processing samples, there’s a lot to be learned from each collection. “Microbial genomes contain complete sets of information that define an organism — much like how letters are a code allowing us to form words, sentences, pages, and books that contain complex but digestible knowledge,” Clark says. He thinks of the environmental samples as biological libraries, filled with thousands of species, strains, and sequence variants. “It’s our job to glean genetic information from these samples.”
“We can actually dream up new proteins using generative AI," Pushpanath says.
Basecamp researchers manage this feat by sequencing the DNA and then assembling the information into a comprehensible structure. “We’re building the ‘stories’ of the biota,” Clark says. The more varied the samples, the more valuable insights his team gains into the characteristics of different organisms and their interactions with the environment. Sequencing allows scientists to examine the order of nucleotides — the organic molecules that form DNA — to identify genetic makeups and find changes within genomes. The process used to be too expensive, but the cost of sequencing has dropped from $10,000 a decade ago to as low as $100. Notably, biocatalysis isn’t a new concept — there have been waves of interest in using natural enzymes in catalysis for over a century, Pushpanath says. “But the technology just wasn’t there to make it cost effective,” he explains. “Sequencing has been the biggest boon.”
AI is probably the second biggest boon.
“We can actually dream up new proteins using generative AI,” Pushpanath says, which means that biocataylsis now has real potential to scale.
Glen Gowers, the co-founder of Basecamp, compares the company’s AI approach to that of social networks and streaming services. Consider how these platforms suggest connecting with the friends of your friends, or how watching one comedy film from the 1990s leads to a suggestion of three more.
“They’re thinking about data as networks of relationships as opposed to lists of items,” says Gowers. “By doing the same, we’re able to link the metadata of the proteins — by their relationships to each other, the environments in which they’re found, the way those proteins might look similar in sequence and structure, their surrounding genome context — really, this just comes down to creating a searchable network of proteins.”
On an Azores island, this volcanic opening may harbor organisms that can help scientists identify enzymes for biocatalysis to replace toxic chemicals.
Emma Bolton
Uwe Bornscheuer, professor at the Institute of Biochemistry at the University of Greifswald, and co-founder of Enzymicals, another biocatalysis company, says that the development of machine learning is a critical component of this work. “It’s a very hot topic, because the challenge in protein engineering is to predict which mutation at which position in the protein will make an enzyme suitable for certain applications,” Bornscheuer explains. These predictions are difficult for humans to make at all, let alone quickly. “It is clear that machine learning is a key technology.”
Benefiting from nature’s bounty
Biodiversity commonly refers to plants and animals, but the term extends to all life, including microbial life, and some regions of the world are more biodiverse than others. Building relationships with global partners is another key element to Basecamp’s success. Doing so in accordance with the access and benefit sharing principles set forth by the Nagoya Protocol — an international agreement that seeks to ensure the benefits of using genetic resources are distributed in a fair and equitable way — is part of the company's ethos. “There's a lot of potential for us, and there’s a lot of potential for our partners to have exactly the same impact in building and discovering commercially relevant proteins and biochemistries from nature,” Clark says.
Bornscheuer points out that Basecamp is not the first company of its kind. A former San Diego company called Diversa went public in 2000 with similar work. “At that time, the Nagoya Protocol was not around, but Diversa also wanted to ensure that if a certain enzyme or microorganism from Costa Rica, for example, were used in an industrial process, then people in Costa Rica would somehow profit from this.”
An eventual merger turned Diversa into Verenium Corporation, which is now a part of the chemical producer BASF, but it laid important groundwork for modern companies like Basecamp to continue to scale with today’s technologies.
“To collect natural diversity is the key to identifying new catalysts for use in new applications,” Bornscheuer says. “Natural diversity is immense, and over the past 20 years we have gained the advantages that sequencing is no longer a cost or time factor.”
This has allowed Basecamp to rapidly grow its database, outperforming Universal Protein Resource or UniProt, which is the public repository of protein sequences most commonly used by researchers. Basecamp’s database is three times larger, totaling about 900 million sequences. (UniProt isn’t compliant with the Nagoya Protocol, because, as a public database, it doesn’t provide traceability of protein sequences. Some scientists, however, argue that Nagoya compliance hinders progress.)
“Eventually, this work will reduce chemical processes. We’ll have cleaner processes, more sustainable processes," says Uwe Bornscheuer, a professor at the University of Greifswald.
With so much information available, Basecamp’s AI has been trained on “the true dictionary of protein sequence life,” Pushpanath says, which makes it possible to design sequences for particular applications. “Through deep learning approaches, we’re able to find protein sequences directly from our database, without the need for further laboratory-directed evolution.”
Recently, a major chemical company was searching for a specific transaminase — an enzyme that catalyzes a transfer of amino groups. “They had already spent a year-and-a-half and nearly two million dollars to evolve a public-database enzyme, and still had not reached their goal,” Pushpanath says. “We used our AI approaches on our novel database to yield 10 candidates within a week, which, when validated by the client, achieved the desired target even better than their best-evolved candidate.”
Basecamp’s other huge potential is in bioremediation, where natural enzymes can help to undo the damage caused by toxic chemicals. “Biocatalysis impacts both sides,” says Gowers. “It reduces the usage of chemicals to make products, and at the same time, where contamination sites do exist from chemical spills, enzymes are also there to kind of mop those up.”
So far, Basecamp's round-the-world sampling has covered 50 percent of the 14 major biomes, or regions of the planet that can be distinguished by their flora, fauna, and climate, as defined by the World Wildlife Fund. The other half remains to be catalogued — a key milestone for understanding our planet’s protein diversity, Pushpanath notes.
There’s still a long road ahead to fully replace petrochemicals with natural enzymes, but biocatalysis is on an upward trajectory. "Eventually, this work will reduce chemical processes,” Bornscheuer says. “We’ll have cleaner processes, more sustainable processes.”
This fall, Robert Reinhart of Boston University published a study finding that electrical stimulation can boost memory - and Reinhart was surprised to discover the effects lasted a full month.
Scientists believe brain circuits tend to uncouple as we age. Since brain neurons communicate by exchanging electrical impulses with each other, the breakdown of these links and associations could be what causes the “senior moment”—when you can’t remember the name of the movie you just watched.
In 2019, Boston University researchers led by Robert Reinhart, director of the Cognitive and Clinical Neuroscience Laboratory, showed that memory loss in healthy older adults is likely caused by these disconnected brain networks. When Reinhart and his team stimulated two key areas of the brain with mild electrical current, they were able to bring the brains of older adult subjects back into sync — enough so that their ability to remember small differences between two images matched that of much younger subjects for at least 50 minutes after the testing stopped.
Reinhart wowed the neuroscience community once again this fall. His newer study in Nature Neuroscience presented 150 healthy participants, ages 65 to 88, who were able to recall more words on a given list after 20 minutes of low-intensity electrical stimulation sessions over four consecutive days. This amounted to a 50 to 65 percent boost in their recall.
Even Reinhart was surprised to discover the enhanced performance of his subjects lasted a full month when they were tested again later. Those who benefited most were the participants who were the most forgetful at the start.
An older person participates in Robert Reinhart's research on brain stimulation.
Robert Reinhart
Reinhart’s subjects only suffered normal age-related memory deficits, but NIBS has great potential to help people with cognitive impairment and dementia, too, says Krista Lanctôt, the Bernick Chair of Geriatric Psychopharmacology at Sunnybrook Health Sciences Center in Toronto. Plus, “it is remarkably safe,” she says.
Lanctôt was the senior author on a meta-analysis of brain stimulation studies published last year on people with mild cognitive impairment or later stages of Alzheimer’s disease. The review concluded that magnetic stimulation to the brain significantly improved the research participants’ neuropsychiatric symptoms, such as apathy and depression. The stimulation also enhanced global cognition, which includes memory, attention, executive function and more.
This is the frontier of neuroscience.
The two main forms of NIBS – and many questions surrounding them
There are two types of NIBS. They differ based on whether electrical or magnetic stimulation is used to create the electric field, the type of device that delivers the electrical current and the strength of the current.
Transcranial Current Brain Stimulation (tES) is an umbrella term for a group of techniques using low-wattage electrical currents to manipulate activity in the brain. The current is delivered to the scalp or forehead via electrodes attached to a nylon elastic cap or rubber headband.
Variations include how the current is delivered—in an alternating pattern or in a constant, direct mode, for instance. Tweaking frequency, potency or target brain area can produce different effects as well. Reinhart’s 2022 study demonstrated that low or high frequencies and alternating currents were uniquely tied to either short-term or long-term memory improvements.
Sessions may be 20 minutes per day over the course of several days or two weeks. “[The subject] may feel a tingling, warming, poking or itching sensation,” says Reinhart, which typically goes away within a minute.
The other main approach to NIBS is Transcranial Magnetic Simulation (TMS). It involves the use of an electromagnetic coil that is held or placed against the forehead or scalp to activate nerve cells in the brain through short pulses. The stimulation is stronger than tES but similar to a magnetic resonance imaging (MRI) scan.
The subject may feel a slight knocking or tapping on the head during a 20-to-60-minute session. Scalp discomfort and headaches are reported by some; in very rare cases, a seizure can occur.
No head-to-head trials have been conducted yet to evaluate the differences and effectiveness between electrical and magnetic current stimulation, notes Lanctôt, who is also a professor of psychiatry and pharmacology at the University of Toronto. Although TMS was approved by the FDA in 2008 to treat major depression, both techniques are considered experimental for the purpose of cognitive enhancement.
“One attractive feature of tES is that it’s inexpensive—one-fifth the price of magnetic stimulation,” Reinhart notes.
Don’t confuse either of these procedures with the horrors of electroconvulsive therapy (ECT) in the 1950s and ‘60s. ECT is a more powerful, riskier procedure used only as a last resort in treating severe mental illness today.
Clinical studies on NIBS remain scarce. Standardized parameters and measures for testing have not been developed. The high heterogeneity among the many existing small NIBS studies makes it difficult to draw general conclusions. Few of the studies have been replicated and inconsistencies abound.
Scientists are still lacking so much fundamental knowledge about the brain and how it works, says Reinhart. “We don’t know how information is represented in the brain or how it’s carried forward in time. It’s more complex than physics.”
Lanctôt’s meta-analysis showed improvements in global cognition from delivering the magnetic form of the stimulation to people with Alzheimer’s, and this finding was replicated inan analysis in the Journal of Prevention of Alzheimer’s Disease this fall. Neither meta-analysis found clear evidence that applying the electrical currents, was helpful for Alzheimer’s subjects, but Lanctôt suggests this might be merely because the sample size for tES was smaller compared to the groups that received TMS.
At the same time, London neuroscientist Marco Sandrini, senior lecturer in psychology at the University of Roehampton, critically reviewed a series of studies on the effects of tES on episodic memory. Often declining with age, episodic memory relates to recalling a person’s own experiences from the past. Sandrini’s review concluded that delivering tES to the prefrontal or temporoparietal cortices of the brain might enhance episodic memory in older adults with Alzheimer’s disease and amnesiac mild cognitive impairment (the predementia phase of Alzheimer’s when people start to have symptoms).
Researchers readily tick off studies needed to explore, clarify and validate existing NIBS data. What is the optimal stimulus session frequency, spacing and duration? How intense should the stimulus be and where should it be targeted for what effect? How might genetics or degree of brain impairment affect responsiveness? Would adjunct medication or cognitive training boost positive results? Could administering the stimulus while someone sleeps expedite memory consolidation?
Using MRI or another brain scan along with computational modeling of the current flow, a clinician could create a treatment that is customized to each person’s brain.
While Sandrini’s review reported improvements induced by tES in the recall or recognition of words and images, there is no evidence it will translate into improvements in daily activities. This is another question that will require more research and testing, Sandrini notes.
Scientists are still lacking so much fundamental knowledge about the brain and how it works, says Reinhart. “We don’t know how information is represented in the brain or how it’s carried forward in time. It’s more complex than physics.”
Where the science is headed
Learning how to apply precision medicine to NIBS is the next focus in advancing this technology, says Shankar Tumati, a post-doctoral fellow working with Lanctôt.
There is great variability in each person’s brain anatomy—the thickness of the skull, the brain’s unique folds, the amount of cerebrospinal fluid. All of these structural differences impact how electrical or magnetic stimulation is distributed in the brain and ultimately the effects.
Using MRI or another brain scan along with computational modeling of the current flow, a clinician could create a treatment that is customized to each person’s brain, from where to put the electrodes to determining the exact dose and duration of stimulation needed to achieve lasting results, Sandrini says.
Above all, most neuroscientists say that largescale research studies over long periods of time are necessary to confirm the safety and durability of this therapy for the purpose of boosting memory. Short of that, there can be no FDA approval or medical regulation for this clinical use.
Lanctôt urges people to seek out clinical NIBS trials in their area if they want to see the science advance. “That is how we’ll find the answers,” she says, predicting it will be 5 to 10 years to develop each additional clinical application of NIBS. Ultimately, she predicts that reigning in Alzheimer’s disease and mild cognitive impairment will require a multi-pronged approach that includes lifestyle and medications, too.
Sandrini believes that scientific efforts should focus on preventing or delaying Alzheimer’s. “We need to start intervention earlier—as soon as people start to complain about forgetting things,” he says. “Changes in the brain start 10 years before [there is a problem]. Once Alzheimer’s develops, it is too late.”
