The finding of natural quasicrystals is a tale of “crazy stubborn people or stubbornly crazy people,” said physicist and Princeton professor, Paul J. Steinhardt, who spoke at Duke University on October 10 regarding his role in their discovery.
Quasicrystals were once thought to be impossible, as crystals were the only stable form of matter. Crystals allow for periodic patterns of atoms while quasicrystals allow for an ordered, yet non-periodic pattern that results in rotational symmetry. Crystals only allow for two-, three-, four-, and six-fold symmetry and create the geographical shapes of squares/rectangles, triangles, hexagons, and rhombuses (Figure 1). However, quasicrystals allow for ten-fold symmetry with unlimited layers of quasicrystal patterns and various shapes. The penrose tiles (Figure 2) is an example of one-dimensional quasicrystal pattern, while the kitchen tiles of your home is an example of a traditional crystal pattern.
After the discovery of man-made quasicrystals from a fellow scientist, Steinhardt wanted to find quasicrystals in nature as opposed to laboratories. He began this by contacting museums with global mineral samples in case they contained undiscovered quasicrystals. This did not yield any results.
Luca Bindi, who then worked for the Museum of Natural History at the University of Florence in Italy, discovered that Steinhardt was searching for natural quasicrystal and wanted to join his endeavors. Bindi found the first interesting sample at the museum he worked in through the rare mineral, khatyrkite, from the Koryak Mountains of Chukotka, Russia. They analyzed the tip of this sample, the width was that of a strand of hair, and discovered the most perfect ten-fold, rotationally symmetric pattern of a quasicrystal from minerals in nature. Even more interesting was that the chemical compound of this quasicrystal, Al63Cu24Fe13, was the exact composition of quasicrystals created in a Japanese laboratory, now found in a rock.
Steinhardt then took these findings to Lincoln Hollister, a renowned geologist, for his expert opinion. Hollister proceeded to tell Steinhardt that this discovery is impossible as its chemical composition of metallic aluminum cannot be created in nature. Steinhardt wondered if this sample came from a meteorite, which was an “ignorant, stupid suggestion, but Lincoln didn’t know that,” Steinhardt said. Lincoln refers Steinhardt to Glenn Macpherson, an expert meteorologist, who further elaborated that metallic aluminum from meteorites is, once again, impossible.
Two renowned experts in their fields describing the impossibility of Steinhardt and Bindi’s hypotheses was not enough for them to quit. Their next step was to trace Bindi’s khatyrkite to obtain more samples. Firstly, they attempted to find Nico Koekkoek, a Dutch mineral collector who had sold innumerable mineral samples to various museums. Dead end. Then they wrote to museums globally regarding their khatyrkite samples and discovered four potential samples. All fakes. Yet another dead end. Next was to analyze the legitimate sample in St. Petersburg because any sample of a newly discovered mineral must be given to a museum. The uncooperative discoverer, Leonid Razin, had immigrated to Israel and refused to let anyone touch the sample. They had hit a dead end again.
Bindi relayed this story to his sister and her friend over dinner. The friend’s neighbor shared the same common last name as the Dutch mineral collector, so the friend decided to ask his neighbor if it was an unlikely connection. Miraculously, the neighbor was the widow of the Dutch mineral collector and, after much persuading, handed over her late-husband’s secret diary. The diary reveals a mineral smuggler named Tim from Romania whom he received the khatyrkite. They were unable to locate Tim until Koekkoek’s widow relented yet another secret diary, which revealed that Tim had received these minerals from ‘L. Razin.’ The same Leonid Razin who refused them to view the sample! Eventually, Steinhardt discovered that Leonid Razid had sent a man named Valery Kryachko on an expedition for platinum. While he did not find platinum, he gave his samples to Leonid Razin, which astoundingly contained the natural quasicrystals that Steinhardt had searched for decades. Kryachko was completely unaware of its journey and even provided the remaining sample, which Steinhardt and his team used for testing.
Steinhardt’s original “ignorant, stupid suggestion” proved remarkably accurate, as they discovered that a meteorite hit Chukotka and resulted in natural metallic aluminum.
Steinhardt and his dream team needed more samples of khatyrkite to conduct further research. Therefore, seven Russians, five Americans, one Italian, and a cat named Buck set forth the scientific Mission Impossible for natural quasicrystals. They came back with several million grains and after a few weeks, found a sample of clay layer that had not been touched in 10,000 years. This was the first quasicrystal to be declared a natural mineral. They ultimately discovered a total of nine quasicrystal samples, each from a different part of the meteorite.
Steinhardt and his team’s analysis of quasicrystals is still not over and his book, “The Second Kind of Impossible,” delves further into the outlandish details of the over 30 years of research. This extraordinary journey of passion and ambition allows for the thrilling hope for the future of scientific discovery.
As the world undergoes the great energy transition — from fossil fuels to alternative energy and batteries — rare earth metals are becoming more precious.
Open The Economist, Forbes, or Fortune, and you’ll see an article nearly every day on Lithium, Nickel, or Copper. For investors seeking to profit off of the transition, lithium seems like a sure bet. Dubbed “white gold” for electric vehicles, the lightweight metal plays a key role in the cathodes of all types of lithium-ion batteries that power electric vehicles (EVs). Although EVs produce fewer greenhouse gasses than gas- or diesel-powered vehicles, their batteries require more minerals, particularly lithium.
On Sept. 26, Duke’s campus welcomed the first in a series of discussions on climate and energy diplomacy focused on the challenges and opportunities of mining and development in South America’s Lithium Triangle. In a room crowded with curious undergraduate and graduate students alike, some lucky enough to have snagged a seat while others stood at the perimeters, three experts discussed the possible future of Bolivia as a major player in the global lithium market.
Professor Avner Vengosh of the Nicholas School
Duke Distinguished Professor Avner Vengosh, Nicholas Chair of Environmental Quality in the Nicholas School of the Environment, began by highlighting the staggering EV growth in 2020-2022: Sales of electric cars have more than tripled in three years, from around 4% of new car sales in 2020 to 14% in 2022. That number is expected to rise to 29.50% in 2028. Speaking of the critical element to EV production, lithium, Vengosh said frankly, “we don’t have enough.”
Lithium is mined from two major sources, Vengosh explained. The first is from hard-rock pegmatite, where lithium is extracted through a series of chemical processes. Most of these deposits are found in Australia, the world’s biggest source. The second is from lithium-rich brines, typically found in Argentina, Bolivia, and Chile, also known as the “Lithium Triangle.” These brine deposits are typically found in underground reservoirs beneath salt flats or saltwater lakes. The Salar de Uyuni in Bolivia is the world’s largest salt lake, and the largest lithium source in the world. It stretches more than 4,050 square miles and attracts tourists with its reflective, mirror-like surface.
Mountains surrounding the Uyuni salt flat during sunrise, (Diego Delso)
A group of Duke students led by a PhD candidate pursuing research on Bolivian lithium development recently traveled to Bolivia to understand different aspects of lithium mining. They asked questions including:
How renewable is the lithium brine?
Are there other critical raw minerals in the lithium-rich brines?
What are the potential environmental effects of lithium extraction?
What is the water footprint of the lithium extraction process?
Is water becoming a limiting factor for lithium production?
The Duke team conducted a study with the natural brine in the Salar, taking samples of deep brines, evaporation ponds, salts from evaporation ponds, wastewaters, and the lithium carbonate. Vengosh said that “we can see some inconsistency in the chemistry of the water that is flowing into the chemistry of the brine.”
This indicates that there is a more complex geological process in the formation of the brine than the simple flow of water into the lake. The team also confirmed the high purity of the lithium carbonate product and that there are no impurities in the material. Additionally, the Duke team found that the wastewater chemistry produced after lithium carbonate production is not different from that of the original brines. Thus, there are no limitations for recycling the water back to the Salar system.
After Vengosh shared the findings of the Duke research team, Kathryn Ledebur, director of the Andean Information Network (AIN) in Cochabamba, Bolivia and Dr. Scott MacDonald, chief economist at Smith’s Research & Gradings and a Caribbean Policy Consortium Fellow, discussed Bolivia’s lithium policy. With the largest untapped lithium deposits in the world, Bolivia has constructed a pilot plan for their lithium production, but Ledebur highlighted that the biggest hurdle is scaling. Additionally, with a unique prior-consultation system in place between the central government and 36 ethnic and indigenous groups in Bolivia, natural resources are a key topic of concern and grassroots action. Ledebur said, “I don’t see that issue changing any time soon.”
Another hurdle is that Bolivian law requires that the extraction process is controlled by the state (the state must own 51%). Foreign investors have been hesitant to work with the central government, which nationalized lithium in 2008 despite, critics said, lacking much of the necessary technology and expertise.
Maxwell Radwin, a writer for Mongabay, writes, “Evo Morales, the former socialist president who served from 2006 to 2019, nationalized the industry, promising that foreign interests wouldn’t plunder Bolivia’s natural resources as they had in the past. Instead, he said, lithium would propel the country to the status of a world power. Morales didn’t just want to export lithium, though; he wanted to produce batteries and cars for export. This complicated deals with potential investors from France, Japan, Russia and South Korea, none of which came to fruition because, among other things, they were required to take on YLB (the state-owned lithium company) as an equal partner.”
Ledebur said, “At this point in time, the Bolivian government has signed three contracts… and I think things will fall into place.”
Naysayers say that the Bolivian government hasn’t done anything to take advantage of the massive market sitting beneath their Salars and that grassroot consultations don’t work. Ledebur said, “I don’t think that it’s perfect, but it’s happening.”
Duke students will return to Bolivia with professor Vengosh next year to conduct more research on the lithium extraction process. Then, they’ll be able to see the effects of this ‘happening’ first-hand.
What are the trials and tribulations one can expect? And conversely, what are the highlights? To answer these questions, Duke Research & Innovation Week kicked off with a panel discussion on Monday, January 23.
The panel
Moderated by George A. Truskey, Ph.D, the Associate Vice President for Research & Innovation and a professor in the Department of Biomedical Engineering, the panelists included…
Claudia K. Gunsch, Ph.D., a professor in the Departments of Civil & Environmental Engineering, Biomedical Engineering, and Environmental Science & Policy. Dr. Gunsch is the director of the NSF Engineering Research Center for Microbiome Engineering (PreMiEr) and is also the Associate Dean for Duke Engineering Research & Infrastructure.
Dr. Claudia Gunsch
Yiran Chen, Ph.D., a professor in the Department of Electrical & Computer Engineering. Dr. Chen is the director of the NSF AI Institute for Edge Computing (Athena).
Dr. Yiran Chen
Stephen Craig, Ph.D., a professor in the Department of Chemistry. Dr. Craig is the director of the Center for the Chemistry of Molecularly Optimized Networks (MONET).
Dr. Stephen Craig
The centers
As the panelists joked, a catchy acronym for a research center is almost an unspoken requirement. Case in point: PreMiEr, Athena, and MONET were the centers discussed on Monday. As evidenced by the diversity of research explored by the three centers, large externally-funded centers run the gamut of academic fields.
PreMiEr, which is led by Gunsch, is looking to answer the question of microbiome acquisition. Globally, inflammatory diseases are connected to the microbiome, and studies suggest that our built environment is the problem, given that Americans spend on average less than 8% of time outdoors. It’s atypical for an Engineering Research Center (ERC) to be concentrated in one state but uniquely, PreMieR is. The center is a joint venture between Duke University, North Carolina A&T State University, North Carolina State University, the University of North Carolina – Chapel Hill and the University of North Carolina – Charlotte.
PreMiEr – not to be confused with the English Premier League
Dr. Chen’s Athena is the first funded AI institute for edge computing. Edge computing is all about improving a computer’s ability to process data faster and at greater volumes by processing data closer to where it’s being generated. AI is a relatively new branch of research, but it is growing in prevalence and in funding. In 2020, 7 institutes looking at AI were funded by the National Science Foundation (NSF), with total funding equaling 140 million. By 2021, 11 institutes were funded at 220 million – including Athena. All of these institutes span over 48 U.S states.
Athena, or the Greek goddess of wisdom, is a fitting name for a research center
MONET is innovating in polymer chemistry with Stephen Craig leading. Conceptualizing polymers as operating in a network, the center aims to connect the behaviors of a single chemical molecule in that network to the behavior of the network as a whole. The goal of the center is to transform polymer and materials chemistry by “developing the knowledge and methods to enable molecular-level, chemical control of polymer network properties for the betterment of humankind.” The center has nine partner institutions in the U.S and one internationally.
MONET, like French painter Claude Monet
Key takeaways
Research that matters
Dr. Gunsch talked at length about how PreMiEr aspires to pursue convergent research. She describes this as identifying a large, societal challenge, then determining what individual fields can “converge” to solve the problem.
Because these centers aspire to solve large, societal problems, market research and industry involvement is common and often required in the form of an industry advisory group. At PreMiEr, the advisory group performs market analyses to assess the relevance and importance of their research. Dr. Chen also remarked that there is an advisory group at Athena, and in addition to academic institutions the center also boasts collaborators in the form of companies like Microsoft, Motorola, and AT&T.
Dr. Chen presenting on Athena’s partner institutions at Monday’s talk.
Commonalities in structure
Most research centers, like PreMiEr, Athena, and MONET, organize their work around pillars or “thrusts.” This can help to make research goals understandable to a lay audience but also clarifies the purpose of these centers to the NSF, other funding bodies, host and collaborating institutions, and the researchers themselves.
How exactly these goals are organized and presented is up to the center in question. For example, MONET conceptualizes its vision into three fronts – “fundamental chemical advances,” “conceptual advances,” and “technological advances.”
At Athena, the research is organized into four “thrusts” – “AI for Edge Computing,” “AI-Powered Computer Systems,” “AI-Powered Networking Systems,” and “AI-Enabled Services and Applications.”
Meanwhile, at PreMiEr, the three “thrusts” have a more procedural slant. The first “thrust” is “Measure,” involving the development of tracking tools and the exploration of microbial “dark matter.” Then there’s “Modify,” or the modification of target delivery methods based on measurements. Finally, “Modeling” involves predictive microbiome monitoring to generate models that can help analyze built environment microbiomes.
A center is about the people
“Collaborators who change what you can do are a gift. Collaborators who change how you think are a blessing.”
Dr. stephen craig
All three panelists emphasized that their centers would be nowhere without the people that make the work possible. But of course, humans complicate every equation, and when working with a team, it is important to anticipate and address tensions that may arise.
Dr. Craig spoke to the fact that successful people are also busy people, so what may be one person’s highest priority may not necessarily be another person’s priority. This makes it important to assemble a team of researchers that are united in a common vision. But, if you choose wisely, it’s worth it. As Dr. Craig quipped on one of his slides, “Collaborators who change what you can do are a gift. Collaborators who change how you think are a blessing.”
In academia, there is a loud push for diversity, and research centers are no exception. Dr. Chen spoke about Athena’s goals to continue to increase their proportions of female and underrepresented minority (URM) researchers. At PreMiEr, comprised of 42 scholars, the ratio of non-URM to URM researchers is 83-17, and the ratio of male to female researchers is approximately 50-50.
In conclusion, cutting-edge research is often equal parts thrilling and mundane, as the realities of applying for funding, organizing manpower, pushing through failures, and working out tensions with others sets in. But the opportunity to receive funding in order to start and run an externally-funded center is the chance to put together some of the brightest minds to solve some of the most pressing problems the world faces. And this imperative is summarized well by the words of Dr. Craig: “Remember: if you get it, you have to do it!”
It’s not enough to just publish a great scientific paper.
Somebody else has to think it’s great too and include the work in the references at the end of their paper, the citations. The more citations a paper gets, presumably the more important and influential it is. That’s how science works — you know, the whole standing-on-the-shoulders-of-giants thing.
So it always comes as a chest swelling affirmation for Dukies when we read all those Duke names on the annual list of Most Cited Scientists, compiled by the folks at Clarivate.
This year is another great haul for our thought-leaders. Duke has 30 scientists among the nearly 7,000 authors on the global list, meaning their work is among the top 1 percent of citations by scientific field and year, according to Clarivate’s Web of Science citation index.
As befits Duke’s culture of mixing and matching the sciences in bold new ways, most of the highly cited are from “cross-field” work.
Duke’s Most Cited Are:
Biology and Biochemistry
Charles A. Gersbach
Robert J. Lefkowitz
Clinical Medicine
Scott Antonia
Christopher Bull Granger
Pamela S. Douglas
Adrian F. Hernandez
Manesh R. Patel
Eric D. Peterson
Cross-Field
Chris Beyrer
Stefano Curtarolo
Renate Houts
Tony Jun Huang
Ru-Rong Ji
Jie Liu
Jason Locasale
Edward A. Miao
David B. Mitzi
Christopher B. Newgard
John F. Rawls
Drew T. Shindell
Pratiksha I. Thakore
Mark R. Wiesner
Microbiology
Barton F. Haynes
Neuroscience and Behavior
Quinn T. Ostrom
Pharmacology and Toxicology
Evan D. Kharasch
Plant and Animal Science
Xinnian Dong
Sheng Yang He
Psychiatry and Psychology
Avshalom Caspi
William E. Copeland
E. Jane Costello
Terrie E. Moffitt
Social Sciences
Michael J. Pencina
John W. Williams
Congratulations, one and all! You’ve done us proud again.
Saxicolous lichens (lichens that grow on stones) from the Namib Desert, and finger lichen, Dactylina arctica (bottom left insert), common in the Arctic, on display in Dr. Jolanta Miadlikowska’s office. The orange color on some of the lichen comes from metabolites, or secondary chemicals produced by different lichen species. The finger lichen is hollow.
Lichens are everywhere—grayish-green patches on tree bark on the Duke campus, rough orange crusts on desert rocks, even in the Antarctic tundra. They are “pioneer species,” often the first living things to return to barren, desolate places after an extreme disturbance like a lava flow. They can withstand extreme conditions and survive where nearly nothing else can. But what exactly are lichens, and why does Duke have 160,000 of them in little envelopes? I reached out to Dr. Jolanta Miadlikowska and Dr. Scott LaGreca, two lichen researchers at Duke, to learn more.
Dr. Jolanta Miadlikowska looking at lichen specimens under a dissecting microscope. The pale, stringy lichen on the brown bag is whiteworm lichen (Thamnolia vermicularis), used to make “snow tea” in parts of China.
According to Miadlikowska, a senior researcher, lab manager, and lichenologist in the Lutzoni Lab (and one of the Instructors B for the Bio201 Gateway course) at Duke, lichens are “obligate symbiotic associations,” meaning they are composed of two or more organisms that need each other. All lichens represent a symbiotic relationship between a fungus (the “mycobiont”) and either an alga or a cyanobacterium or both (the “photobiont”). They aren’t just cohabiting; they rely on each other for survival. The mycobiont builds the thallus, which gives lichen its structure. The photobiont, on the other hand, isn’t visible—but it is important: it provides “food” for the lichen and can sometimes affect the lichen’s color. The name of a lichen species refers to its fungal partner, whereas the photobiont has its own name.
Lichen viewed through a dissecting microscope. The black speckles visible on some of the orange lichen lobes are a “lichenicolous” fungus that can grow on top of lichen. There are also “endolichenic fungi… very complex fungal communities that live inside lichen,” Miadlikowska says. “We don’t see them, but they are there. And they are very interesting.”
Unlike plants, fungi can’t perform photosynthesis, so they have to find other ways to feed themselves. Many fungi, like mushrooms and bread mold, are saprotrophs, meaning they get nutrients from organic matter in their environment. (The word “saprotroph” comes from Greek and literally means “rotten nourishment.”) But the fungi in lichens, Miadlikowska says, “found another way of getting the sugar—because it’s all about the sugar—by associating with an organism that can do photosynthesis.” More often than not, that organism is a type of green algae, but it can also be a photosynthetic bacterium (cyanobacteria, also called blue-green algae). It is still unclear how the mycobiont finds the matching photobiont if both partners are not dispersed together. Maybe the fungal spores (very small fungal reproductive unit) “will just sit and wait” until the right photobiont partner comes along. (How romantic.) Some mycobionts are specialists that “can only associate with a few or a single partner—a ‘species’ of Nostoc [a cyanobacterium; we still don’t know how many species of symbiotic and free-living Nostoc are out there and how to recognize them], for example,” but many are generalists with more flexible preferences.
Two species of foliose (leaf-like) lichens from the genus Peltigera. In the species on the left (P. canina), the only photobiont is a cyanobacterium from the genus Nostoc, making it an example of bi-membered symbiosis. In the species on the right (P.aphthosa), on the other hand, the primary photobiont is a green alga (which is why the thallus is so green when wet). In this case, Nostoc is a secondary photobiont contained only in the cephalodia—the dark, wart-like structures on the surface. With two photobionts plus the mycobiont, this is an example of tri-membered symbiosis.
Lichens are classified based on their overall thallus shape. They can be foliose (leaf-like), fruticose (shrubby), or crustose (forming a crust on rocks or other surfaces). Lichens that grow on trees are epiphytic, while those that live on rocks are saxicolous; lichens that live on top of mosses are muscicolous, and ground-dwelling lichens are terricolous. Much of Miadlikowska’s research is on a group of cyanolichens (lichens with cyanobacteria partners) from the genus Peltigera. She works on the systematics and evolution of this group using morphology-, anatomy-, and chemistry-based methods and molecular phylogenetic tools. She is also part of a team exploring biodiversity, ecological rules, and biogeographical patterns in cryptic fungal communities associated with lichens and plants (endolichenic and endophytic fungi). She has been involved in multiple ongoing NSF-funded projects and also helping graduate students Ian, Carlos, Shannon, and Diego in their dissertation research. She spent last summer collecting lichens with Carlos and Shannon and collaborators in Alberta, Canada and Alaska. If you walk in the sub basement of the Bio Sciences building where Bio201 and Bio202 labs are located, check out the amazing photos of lichens (taken by Thomas Barlow, former Duke undergraduate) displayed along the walls! Notice Peltigera species, including some new to science, described by the Duke lichen team.
Lichens have value beyond the realm of research, too. “In traditional medicine, lichens have a lot of use,” Miadlikowska says. Aside from medicinal uses, they have also been used to dye fabric and kill wolves. Some are edible. Miadlikowska herself has eaten them several times. She had salad in China that was made with leafy lichens (the taste, she says, came mostly from soy sauce and rice vinegar, but “the texture was coming from the lichen.”). In Quebec, she drank tea made with native plants and lichens, and in Scandinavia, she tried candied Cetraria islandica lichen (she mostly tasted the sugar and a bit of bitterness, but once again, the lichen’s texture was apparent).
In today’s changing world, lichens have another use as well, as “bioindicators to monitor the quality of the air.” Most lichens can’t tolerate air pollution, which is why “in big cities… when you look at the trees, there are almost no lichens. The bark is just naked.” Lichen-covered trees, then, can be a very good sign, though the type of lichen matters, too. “The most sensitive lichens are the shrubby ones… like Usnea,” Miadlikowska says. Some lichens, on the other hand, “are able to survive in anthropogenic places, and they just take over.” Even on “artificial substrates like concrete, you often see lichens.” Along with being very sensitive to poor air quality, lichens also accumulate pollutants, which makes them useful for monitoring deposition of metals and radioactive materials in the environment.
Dr. Scott LaGreca with some of the 160,000 lichen specimens in Duke’s herbarium.
LaGreca, like Miadlikoska, is a lichenologist. His research primarily concerns systematics, evolution and chemistry of the genus Ramalina. He’s particularly interested in “species-level relationships.” While he specializes in lichens now, LaGreca was a botany major in college. He’d always been interested in plants, in part because they’re so different from animals—a whole different “way of being,” as he puts it. He used to take himself on botany walks in high school, and he never lost his passion for learning the names of different species. “Everything has a name,” he says. “Everything out there has a name.” Those names aren’t always well-known. “Some people are plant-blind, as they call it…. They don’t know maples from oaks.” In college he also became interested in other organisms traditionally studied by botanists—like fungi. When he took a class on fungi, he became intrigued by lichens he saw on field trips. His professor was more interested in mushrooms, but LaGreca wanted to learn more, so he specialized in lichens during grad school at Duke, and now lichens are central to his job. He researches them, offers help with identification to other scientists, and is the collections manager for the lichens in the W.L. and C.F. Culberson Lichen Herbarium—all 160,000 of them.
The Duke Herbarium was founded in 1921 by Dr. Hugo Blomquist. It contains more than 825,000 specimens of vascular and nonvascular plants, algae, fungi, and, of course, lichens. Some of those specimens are “type” specimens, meaning they represent species new to science. A type specimen essentially becomes the prototype for its species and “the ultimate arbiter of whether something is species X or not.” But how are lichens identified, anyway?
Lichenologists can consider morphology, habitat, and other traits, but thanks to Dr. Chicita Culberson, who was a chemist and adjunct professor at Duke before her retirement, they have another crucial tool available as well. Culbertson created a game-changing technique to identify lichens using their chemicals, or metabolites, which are often species-specific and thus diagnostic for identification purposes. That technique, still used over fifty years later, is a form of thin-layer chromatography. The process, as LaGreca explains, involves putting extracts from lichen specimens—both the specimens you’re trying to identify and “controls,” or known samples of probable species matches—on silica-backed glass plates. The plates are then immersed in solvents, and the chemicals in the lichens travel up the paper. After the plates have dried, you can look at them under UV light to see if any spots are fluorescing. Then you spray the plates with acid and “bake it for a couple hours.” By the end of the process, the spots of lichen chemicals should be visible even without UV light. If a lichen sample has traveled the same distance up the paper as the control specimen, and if it has a similar color, it’s a match. If not, you can repeat the process with other possible matches until you establish your specimen’s chemistry and, from there, its identity. Culberson’s method helped standardize lichen identification. Her husband also worked with lichens and was a director of the Duke Gardens.
Thin-layer chromatography plates in Dr. LaGreca’s office. The technique, created by Dr. Chicita Culberson, helps scientists identify lichens by comparing their chemical composition to samples of known identity. Each plate was spotted with extracts from different lichen specimens, and then each was immersed in a different solvent, after which the chemicals in the extracts travel up the plate . Each lichen chemical travels a characteristic distance (called the “Rf value”) in each solvent. Here, the sample in column 1 on the rightmost panel matches the control sample in column 2 in terms of distance traveled up the page, indicating that they’re the same species. The sample in column 4, on the other hand, didn’t travel as far as the one in column 5 and has a different color. Therefore, those chemicals (and species) do not match.
LaGreca shows me a workroom devoted to organisms that are cryptogamic, a word meaning “hidden gametes, or hidden sex.” It’s a catch-all term for non-flowering organisms that “zoologists didn’t want to study,” like non-flowering plants, algae, and fungi. It’s here that new lichen samples are processed. The walls of the workroom are adorned with brightly colored lichen posters, plus an ominous sign warning that “Unattended children will be given an espresso and a free puppy.” Tucked away on a shelf, hiding between binders of official-looking documents, is a thin science fiction novel called “Trouble with Lichen” by John Wyndham.
The Culberson Lichen Herbarium itself is a large room lined with rows of cabinets filled with stacks upon stacks of folders and boxes of meticulously organized lichen samples. A few shelves are devoted to lichen-themed books with titles like Lichens De France and Natural History of the Danish Lichens.
Each lichen specimen is stored in an archival (acid-free) paper packet, with a label that says who collected it, where, and on what date. (“They’re very forgiving,” says LaGreca. “You can put them in a paper bag in the field, and then prepare the specimen and its label years later.”) Each voucher is “a record of a particular species growing in a particular place at a particular time.” Information about each specimen is also uploaded to an online database, which makes Duke’s collection widely accessible. Sometimes, scientists from other institutions find themselves in need of physical specimens. They’re in luck, because Duke’s lichen collection is “like a library.” The herbarium fields loan requests and trades samples with herbaria at museums and universities across the globe. (“It’s kind of like exchanging Christmas presents,” says LaGreca. “The herbarium community is a very generous community.”)
Duke’s lichen collection functions like a library in some ways, loaning specimens to other scientists and trading specimens with institutions around the world.
Meticulous records of species, whether in databases of lichens or birds or “pickled fish,” are invaluable. They’re useful for investigating trends over time, like tracking the spread of invasive species or changes in species’ geographic distributions due to climate change. For example, some lichen species that were historically recorded on high peaks in North Carolina and elsewhere are “no longer there” thanks to global warming—mountain summits aren’t as cold as they used to be. Similarly, Henry David Thoreau collected flowering plants at Walden Pond more than 150 years ago, and his samples are still providing valuable information. By comparing them to present-day plants in the same location, scientists can see that flowering times have shifted earlier due to global warming. So why does Duke have tens of thousands of dried lichen samples? “It comes down to the reproducibility of science,” LaGreca says. “A big part of the scientific method is being able to reproduce another researcher’s results by following their methodology. By depositing voucher specimens generated from research projects in herbaria like ours, future workers can verify the results” of such research projects. For example, scientists at other institutions will sometimes borrow Duke’s herbarium specimens to verify that “the species identification is what the label says it is.” Online databases and physical species collections like the herbarium at Duke aren’t just useful for scientists today. They’re preserving data that will still be valuable hundreds of years from now.
Everything in our world is made from materials, meaning life is enabled by material development and efficiency. In today’s society, from constant technological revolution to the global pandemic, life as we know it is always evolving. But as the world around us evolves, the materials around us also need to evolve to keep up with current demands. But how? As a part of Duke University’s annual Research Week on Feb. 3, researchers from a multitude of practices offered their wisdom and research.
Moderated by Dr. Catherine L. Brinson, Ph.D., the panel hosted three Duke Scholars and their research on ‘Materials for a Changing World’. “The development of new materials can really be key in solving some of the more critical challenges of our time,” Brinson maintained.
Dr. David Beratan explaining his research on bio-machines and their material efficiency.
The first scholar to present was R.J Reynolds distinguished professor of chemistry, Dr. David N Beratan, Ph.D. His research concerns the transition from soft, wet, and tiny research machines to more durable, long-term research machines in the science field. “The machines of biology tend to be stochastic and floppy rather than deterministic and hard,” Beratan began. “They’re messy and there are lots of moving parts. They’re intrinsically noisy and error-prone, etc…They’re very different from the kinds of things you see under the hood of your car, and we’d really like to understand how they work and what lessons we might derive from them for our world.” His complex research and research group have aided in bridging the gap in knowledge regarding the transition of biological functional machines to synthetic ones.
Dr.Rubinstein presenting his research on materials at Duke’s Pratt School of Engineering in 2019.
The panel continued with Aleksandar S. Vesic Distinguished Professor in mechanical engineering, Dr. Michael Rubinstein, Ph.D. His research involves the development of self-healing materials across multiple spectrums. “What you want to think about is materials that can heal themselves,” he stated. “If there’s a crack or a failure in a material, we would like the material to heal itself without external perturbation involvement. So it could be done by the other diffusion of molecules across some physical approaches, or by a chemical approach where you have bonds that were broken to the form.” His research on this possibility has made strides in the scientific field, especially in a time of such ecological stress and demand for materials.
Dr. Segura talking with Dr. Brinson on her research involving self-healing materials.
The panel concluded with biomedical engineering professor Dr. Tatiana Segura, Ph.D. Segura talked about work they are doing at their lab regarding materials that can be used to heal the human body after damage or injury. She began by mentioning that “we are a materials lab and that’s what we’re interested in designing. So what are we inspired by? Well, we are really inspired by the ability of our body to heal.” At her lab, a primary motivation is healing disabilities after a stroke. “Sometimes you have something that you deal with for a long time no matter how your body healed. And that inspires us to consider how do we actually engage this process with materials to make it go better and actually make our body heal in a way that we can promote repair and regeneration.” Understanding this process is a complex one, she explained, but one that she believes is crucial in understanding the design of the material.
‘Materials for a Changing World’ was yet another extremely powerful speaker series offered this year during Duke Research Week. Our world is changing, and our materials need to keep up. With the help of these experts, material innovation has a bright future.
Cypress swamp, eastern North Carolina. Photo by Steve Anderson, Duke
DURHAM, N.C. — The Albemarle-Pamlico Peninsula covers more than 2,000 square miles on the North Carolina coastal plain, a vast expanse of forested swamps and tea-colored creeks. Many people would probably avoid this place, whose dense thickets of cane and shrubs and waterlogged soils can slow a hike to a crawl.
“It’s hard fieldwork,” says Duke researcher Steve Anderson. “It gets really dense and scratchy. That, plus the heat and humidity mixed with the smell of sulfur and the ticks and the poison ivy; it just kind of adds up.”
But to Anderson and colleagues from Duke and North Carolina State University, these bottomlands are more than impenetrable marsh and muck and mosquitoes. They’re also a barometer of change.
Researchers surveying plants in Alligator River National Wildlife Refuge in 2016. Photo by Mathew Stillwagon, North Carolina State University
Most of the area they study lies a mere two to three feet above sea level, which exposes it to surges of ocean water — 400 times saltier than freshwater — driven inland by storms and rising seas. The salt deposits left behind when these waters recede build up year after year, until eventually they become too much for some plants to cope with.
Trudging in hip waders through stunted shrubs and rotting tree stumps, Anderson snaps a picture with his phone of a carpet of partridge berry trailing along the forest floor. In some parts of the peninsula, he says, the soils are becoming so salty that plants like these can no longer reproduce or are dying off entirely.
Along the North Carolina coast, understory plants such as this partridge berry (left) are quickly ceding ground to species such as this bigleaf marsh-elder (right) as the soils become too salty for them to thrive. Credit: Steve Anderson
In a recent study the team, led by professors Justin Wright and Emily Bernhardt of Duke, and Marcelo Ardón of NC State, surveyed some 112 understory plants in the region, making note of where they were found and how abundant they were in relation to salt levels in the soil.
The researchers identified a ‘tipping point,’ around 265 parts per million sodium, where even tiny changes in salinity can set off disproportionately large changes in the plants that live there.
Above this critical threshold, the makeup of the marsh floor suddenly shifts, as plants such as wax myrtle, swamp bay and pennywort are taken over by rushes, reeds and other plants that can better tolerate salty soils.
Certain dwindling plants could be an early warning sign that salt is poisoning inland waters, researchers say. Credit: Steve Anderson
The hope is that monitoring indicator species like these could help researchers spot the early warning signs of salt stress, Anderson says.
This research was supported by grants from the National Science Foundation (DEB1713435, DEB 1713502, and Coastal SEES Collaborative Research Award Grant No. 1426802).
CITATION: “Salinity Thresholds for Understory Plants in Coastal Wetlands,” Anderson, S. M., E. A. Ury, P. J. Taillie, E. A. Ungberg, C. E. Moorman, B. Poulter, M. Ardón, E. S. Bernhardt, and J. P. Wright. Plant Ecology, Nov. 24, 2021. DOI: 10.1007/s11258-021-01209-2.
Salt is poisoning the soils past a point of no return for some marsh plants; one team is trying to pinpoint the early warning signs. By Steve Anderson.
In 2011, Dr. Jennifer Doudna began studying an enzyme called Cas9. Little did she know, in 2020 she would go on to win the Nobel Prize in Chemistry along with Emmanuelle Charpentier for discovering the powerful gene-editing tool, CRISPR-Cas9. Today, Doudna is a decorated researcher, the Li Ka Shing Chancellors Chair, a Professor in the Department of Chemistry and Molecular as well as Cell Biology at the University of California Berkeley, and the founder of the Innovative Genomics Institute.
Doudna was also this year’s speaker for the MEDx Distinguished Lecture in October where she delivered presented on “CRISPR: Rewriting DNA and the Future of Humanity.”
“CRISPR is a system that originated in bacteria as an adaptive immune system” Doudna explained.
Dr. Jennifer Doudna holding the Nobel Prize in Chemistry
When bacterial cells are infected by viruses those viruses inject their genetic material into the cell. This discovery, a couple decades ago, was the first indication that there may be ways to apply bacteria’s ability to acquire genetic information from viruses.
CRISPR itself was discovered in 1987 and stands for “Clustered Regularly Interspaced Short Palindromic Repeats.” Doudna was initially studying RNA when she discovered Cas-9, a bacterial RNA-guided endonuclease and one of the enzymes produced by the CRISPR system. In 2012, Doudna and her colleagues found that Cas9 used base pairing to locate and splice target DNAs when combined with a guide RNA.
Essentially, they designed guide RNA to target specific cells. If those cells had a CRISPR system encoded in their genome, the cell is able to make an RNA copy of the CRISPR locus. Those RNA molecules are then processed into units that each include a sequence derived from a virus and then assemble with proteins. This RNA protein then looks for DNA sequences that match the sequence in the RNA guide. Once a match occurs, Cas9 is able to bind to and cut the DNA, leading to the destruction of the viral genome. The cutting of DNA then triggers DNA repair allowing gene editing to occur.
“This system has been harnessed as a technology for genome editing because of the ability of these proteins, these CRISPR Cas-p proteins, to be programmed by RNA molecules to cut any desired DNA sequence,” Doudna said.
CRISPR-cas9 is also being applied in many clinical settings. In fact, when the COVID-19 pandemic hit, Doudna along with several colleagues organized a five-lab consortium including the labs of Dan Fletcher, Patrick Hsu, Melanie Ott, and David Savage. The focus was on developing the Cas13 system to detect COVID-19. Cas13 is a class of proteins, that are RNA guided, RNA targeting, CRISPR enzymes. This research was initially done by one of Doudna’s former graduate students, Alexandra East-Seletsky. They discovered that if the reporter RNA is is paired with enzymes that have a quenched fluorophore pair on the ends, when the target is activated, the reporter is cleaved and a fluorescent signal is released.
One study out of the Melanie Ott group demonstrated that Cas13 can be used to detect viral RNA. They are hoping to apply this as a point-of-care diagnostic by using a detector as well as a microfluidic chip which would allow for the conduction of these chemical reactions in much smaller volumes that can then be read out by a laser. Currently, the detection limit is similar to what one can get with a PCR reaction however it is significantly easier to run.
Graphical Abstract of Cas13 Research by the Melanie Ott lab
“And this is again, not fantasy, we’ve actually had just fabricated devices that will be sitting on a benchtop, and are able to use fabricated chips that will allow us to run the Cas13 chemistry with either nasal swab samples or saliva samples for detection of the virus,” Doudna added.
Another exciting development is the use of genome editing in somatic cells. This involves making changes in the cells of an individual as opposed to the germline. One example is sickle cell disease which is caused by a single base pair defect in a gene. Soon, clinicians will be able to target and correct this defect at the source of the mutation alleviating people from this devastating illness. Currently, there are multiple ongoing clinical trials including one at the Innovative Genomics Institute run by Doudna. In fact, one patient, Victoria Gray, has already been treated for her sickle cell disease using CRISPR.
Victoria Gray being treated for Sickle Cell Anemia Meredith Rizzo/NPR
“The results of these trials are incredibly exciting and encouraging to all of us in the field, with the knowledge that this technology is being deployed to have a positive impact on patient’s lives,” Doudna said.
Another important advancement was made last summer involving the use of CRISPR-based therapy to treat ATR, a rare genetic disease that primarily affects the liver. This is also the first time CRISPR molecules will be delivered in vivo.
In just 10 years CRISPR-cas9 has gone from an exciting discovery to being applied in several medical and agricultural settings.
“This powerful technology enables scientists to change DNA with precision only dreamed of a few years ago,” said MEDx director Geoffrey Ginsburg, a Professor of Medicine at Duke. “Labs worldwide have redirected the course of research programs to incorporate this new tool, creating a CRISPR revolution with huge implications across biology and medicine.”
Examples of further CRISPR-Cas9 research can also be found in the Charles Gersbach lab here at Duke.
Tiffany Yen, a Duke junior majoring in chemistry, grew up in the sunny suburbs of Los Angeles, never too far from the coastline. She’s always loved being outside, especially in California where there is no shortage of trails to hike and beaches to go to. Friends know her as a Patagonia aficionado, going so far as to buy her a book profiling the company’s business model for her birthday. In fact, from Yen, I learned that every Patagonia store gives out city-specific stickers, so if you feel so inclined, you can collect them (as Yen obviously does). All this is to say: Tiffany Yen has always been interested in sustainability.
“I never understood why what we do has to come at the cost of the planet,” Yen said, in discussing how her years in school learning about climate change fueled her passion for sustainable science. “The environment is so important. Without it, we wouldn’t be here.”
Tiffany Yen
Unsure of what she wanted to study at Duke and where she wanted to go post-graduation, she decided to take her two interests – sustainability and chemistry, particularly polymer chemistry – and see what she could do to combine them. She knew coming into college that she wanted to do research, so that landed her at the Becker Lab for Functional Materials.
The Becker Lab is a multidisciplinary organic materials lab focused on biomedical applications – specifically, things like adhesives and drug delivery. Yen works on improvements to intercranial pressure sensors. Traditionally, after head trauma, doctors need to measure the intercranial space to see if the brain is damaged. The sensor that is used is wired and tends to be a very invasive procedure – the probe is connected to a machine outside, and there’s a high risk of infection.
Collaborators at Northwestern developed a biodegradable wireless device that, after implantation, doesn’t require a secondary procedure to take out. The problem is that it degrades a little too fast – and so measurements can’t be taken. Yen, with her mentor, is working on building a film encapsulation to make it possible for the device to take good measurements.
Right now, they’re trying out azelaic acid instead of succinic acid. Azelaic acid has favorable anti-inflammatory properties and is commonly used in acne medications. It could also potentially increase the bioresorbability of the polymer. Their hope is that the film not only helps the body metabolize more of the polymer, but actually helps in healing.
Snapshots from Yen’s life at the lab
So why medical research? Yen explains that while her work may not seem obviously linked to sustainability, the push for finding materials that can degrade is extremely relevant. And while she’s not all that interested in medicine specifically, she likes things that are practical and applicable.
“When I did research in the past,” Yen said, “there wasn’t always an application. It sometimes was about synthesizing something, just for the sake of science.” And while there’s certainly value in strengthening science fundamentals, she admits that research in that vein doesn’t really appeal to her. “I want to work on things that I directly see adding value to society.”
After college, Yen sees herself going to graduate school and working towards a PhD in “some physical science related to chemistry.” Ultimately, her goal is to work at the interface of venture capital and scientific research, using her science background to find and fund promising innovations in sustainability. “There are so many incredible things being researched out there,” Yen says, “but the biggest problem in research is funding and commercializing.” She continues, “I think there are other people out there who can do better research than I can, so I want to go out there, find the stuff, and fund it.”
Yen has come to believe that just because she dedicated her time at Duke to science, it doesn’t mean she needs to stay in science forever. There’s value in scientific knowledge no matter where you go. And as businesses realize that public interest in sustainability is growing, she’s crossing her fingers that her skillset will poise her to be a valuable asset in seeking out new innovations.
Snapshots from Yen’s life at the lab
She said that when she came into college, she felt a pressure to pursue a more traditional path, like being pre-med. “I value stability, and I’m very risk-averse,” she laughs.
But when she asked herself what she’d be happiest doing, she knew it would be trying to save the planet in some way. But she clarifies: “At this point, I can’t save the planet. I think that’s a very far-fetched thing for one person to do.” Instead, “I’d rather try and maybe fail than not try at all.”
My name is Olivia Ares (she/her), and I’d like to provide the opportunity for you to get to know me better. In true blog post fashion, here are some quick facts at the outset:
Those close to me claim I have a “cardigan problem.” (By that, they mean that I own an obscene amount of cardigans. If you ask me, that sounds like the exact opposite of a problem.)
Pictured here is my green three-quarter sleeve cardigan with flower-shaped buttons, which provides a colorful accent.
You may be asking yourself what interest I could possibly have in being a research blogger, since I’m clearly destined for a future in comedy (or cardigan connoisseurship). And especially since, as you’ll soon learn, I’m not a science person.
Like a lot of people during our year of virtual school, I went through a lifetime of hobby phases in a matter of months. I started with baking, which only lasted until the bread flour ran out. I watched a lot of movies that I had always wanted to see (which often disappointed), and I rewatched a lot of movies I loved (which never disappointed). I tried learning the guitar, but I never practiced enough to build up the right callouses, so I never practiced at all. I discovered a love for puzzles and an utter lack of skill for them. I downloaded The Sims 4 on a free trial, spent months building a super cool house, then deleted the whole game.
My three favorite things in one picture: lavender cold brew, Taylor Swift, and my blue wool cardigan.
The only thing that’s stuck so far has been reading. In middle school, we used to stay up late with a flashlight under our covers to finish books, then abruptly lost all motivation somewhere between The Giver and The Scarlet Letter. I think we forgot along the way that there are no rules to reading; there’s no one to impress. There’s no one to sample your sourdough or judge your twangy, painful acoustic cover of “Three Blind Mice.” Reading is something you do purely for yourself.
Reading makes information and ideas universally accessible; it connects worlds using only ink on a page. There’s this myth that analytical minds are not creative minds and vice versa, and it alienates people: people who would bring such great perspectives to the table if they hadn’t been defined by a checklist of abilities. Reading is for everyone to find what they love and to love what they find (or hate it; one of the great things about doing things for yourself is that you can just quit whenever you want to).
Scientific research, on the other hand, is something produced for everyone. Humans exploring more and more about the world is something that affects all of us, despite the research being conducted only by a select few of us.
My black long-sleeve cardigan is a personal favorite, as it goes with pretty much everything.
Freshman year of high school, I finished chemistry with a B, which was a miracle considering I was rocking a D around November. I had to change my way of looking at the material; I couldn’t remember the makeup of an atom, but I could remember it if I thought about the stories of individuals who built off of each model in succession. I didn’t understand stoichiometry, but I did understand you have to balance equations just like weights on a scale or kids on a see-saw.
My point is: everyone sees things differently. Exclusivity in different fields is fabricated to make information and education elitist, and it is not reflective of individuals’ ability to understand the world. If you want to read about cool science stuff, you shouldn’t feel left out because you’re more of an art history person. If you want to read about cool art history stuff, you shouldn’t feel left out because you’re an aerospace engineer.
So I like to think that I can be that bridge for some people; at the very least, I can do it for myself.
