Tag Archives: Washington University in St. Louis (WUSTL)

World’s smallest disco party features nanoscale disco ball

I haven’t featured one of these ‘fun’ (world’s smallest xxx) announcements in a long time. An August 14, 2024 news item on phys.org announces the world’s smallest disco party and a step towards exploring quantum gravity, Note: Links have been removed,

Physicists at Purdue [Purdue University, Indiana, US] are throwing the world’s smallest disco party. The disco ball itself is a fluorescent nanodiamond, which they have levitated and spun at incredibly high speeds. The fluorescent diamond emits and scatters multicolor lights in different directions as it rotates. The party continues as they study the effects of fast rotation on the spin qubits within their system and are able to observe the Berry phase.

The team, led by Tongcang Li, professor of Physics and Astronomy and Electrical and Computer Engineering at Purdue University, published their results in Nature Communications. Reviewers of the publication described this work as “arguably a groundbreaking moment for the study of rotating quantum systems and levitodynamics” and “a new milestone for the levitated optomechanics community.”

This graph illustrates a diamond particle levitated above a surface ion trap. The fluorescent diamond nanoparticle is driven to rotate at a high speed (up to 1.2 billion rpm) by alternating voltages applied to the four corner electrodes. This rapid rotation induces a phase in the nitrogen-vacancy electron spins inside the diamond. The diagram in the top left corner depicts the atomic structure of a nitrogen-vacancy spin defect inside the diamond. Graphic provided by Kunhong Shen.

An August 13, 2024 Purdue University news release (also on EurekAlert but published August 14, 2024) by Cheryl Pierce, which originated the news item, explains what makes this work so exciting (!), Note: Links have been removed,

“Imagine tiny diamonds floating in an empty space or vacuum. Inside these diamonds, there are spin qubits that scientists can use to make precise measurements and explore the mysterious relationship between quantum mechanics and gravity,” explains Li, who is also a member of the Purdue Quantum Science and Engineering Institute.  “In the past, experiments with these floating diamonds had trouble in preventing their loss in vacuum and reading out the spin qubits. However, in our work, we successfully levitated a diamond in a high vacuum using a special ion trap. For the first time, we could observe and control the behavior of the spin qubits inside the levitated diamond in high vacuum.”

The team made the diamonds rotate incredibly fast—up to 1.2 billion times per minute! By doing this, they were able to observe how the rotation affected the spin qubits in a unique way known as the Berry phase.

“This breakthrough helps us better understand and study the fascinating world of quantum physics,” he says.

The fluorescent nanodiamonds, with an average diameter of about 750 nm, were produced through high-pressure, high-temperature synthesis. These diamonds were irradiated with high-energy electrons to create nitrogen-vacancy color centers, which host electron spin qubits. When illuminated by a green laser, they emitted red light, which was used to read out their electron spin states. An additional infrared laser was shone at the levitated nanodiamond to monitor its rotation. Like a disco ball, as the nanodiamond rotated, the direction of the scattered infrared light changed, carrying the rotation information of the nanodiamond.

The authors of this paper were mostly from Purdue University and are members of Li’s research group: Yuanbin Jin (postdoc), Kunhong Shen (PhD student), Xingyu Gao (PhD student) and Peng Ju (recent PhD graduate). Li, Jin, Shen, and Ju conceived and designed the project and Jin and Shen built the setup. Jin subsequently performed measurements and calculations and the team collectively discussed the results. Two non-Purdue authors are Alejandro Grine, principal member of technical staff at Sandia National Laboratories, and Chong Zu, assistant professor at Washington University in St. Louis. Li’s team discussed the experiment results with Grine and Zu who provided suggestions for improvement of the experiment and manuscript.

“For the design of our integrated surface ion trap,” explains Jin, “we used a commercial software, COMSOL Multiphysics, to perform 3D simulations. We calculate the trapping position and the microwave transmittance using different parameters to optimize the design. We added extra electrodes to conveniently control the motion of a levitated diamond. And for fabrication, the surface ion trap is fabricated on a sapphire wafer using photolithography. A 300-nm-thick gold layer is deposited on the sapphire wafer to create the electrodes of the surface ion trap.”

So which way are the diamonds spinning and can they be speed or direction manipulated? Shen says yes, they can adjust the spin direction and levitation.

“We can adjust the driving voltage to change the spinning direction,” he explains. “The levitated diamond can rotate around the z-axis (which is perpendicular to the surface of the ion trap), shown in the schematic, either clockwise or counterclockwise, depending on our driving signal. If we don’t apply the driving signal, the diamond will spin omnidirectionally, like a ball of yarn.”

Levitated nanodiamonds with embedded spin qubits have been proposed for precision measurements and creating large quantum superpositions to test the limit of quantum mechanics and the quantum nature of gravity.

“General relativity and quantum mechanics are two of the most important scientific breakthroughs in the 20th century. However, we still do not know how gravity might be quantized,” says Li. “Achieving the ability to study quantum gravity experimentally would be a tremendous breakthrough. In addition, rotating diamonds with embedded spin qubits provide a platform to study the coupling between mechanical motion and quantum spins.”

This discovery could have a ripple effect in industrial applications. Li says that levitated micro and nano-scale particles in vacuum can serve as excellent accelerometers and electric field sensors. For example, the US Air Force Research Laboratory (AFRL) are using optically-levitated nanoparticles to develop solutions for critical problems in navigation and communication.

“At Purdue University, we have state-of-the-art facilities for our research in levitated optomechanics,” says Li. “We have two specialized, home-built systems dedicated to this area of study. Additionally, we have access to the shared facilities at the Birck Nanotechnology Center, which enables us to fabricate and characterize the integrated surface ion trap on campus. We are also fortunate to have talented students and postdocs capable of conducting cutting-edge research. Furthermore, my group has been working in this field for ten years, and our extensive experience has allowed us to make rapid progress.”

Quantum research is one of four key pillars of the Purdue Computes initiative, which emphasizes the university’s extensive technological and computational environment.

This research was supported by the National Science Foundation (grant number PHY-2110591), the Office of Naval Research (grant number N00014-18-1-2371), and the Gordon and Betty Moore Foundation (grant DOI 10.37807/gbmf12259). The project is also partially supported by the Laboratory Directed Research and Development program at Sandia National Laboratories.

Here’s a link to and a citation for the paper,

Quantum control and Berry phase of electron spins in rotating levitated diamonds in high vacuum by Yuanbin Jin, Kunhong Shen, Peng Ju, Xingyu Gao, Chong Zu, Alejandro J. Grine & Tongcang Li. Nature Communications volume 15, Article number: 5063 (2024) DOI: https://doi.org/10.1038/s41467-024-49175-3 Published online: 13 June 2024

This paper is open access.

Fashion, sustainability, and the protein threads that bind textiles and cosmetics

I’m starting with a somewhat enthusiastic overview of the role synthetic biology is playing in the world of clothing and cosmetics in The Scientist and following it up with some stories about fish leather, no synthetic biology involved but all of these stories are about sustainability and fashion and, in one case, cosmetics.

Fashionable synthetic biology

Meenakshi Prabhune’s June 14, 2024 article in The Scientist, in addition to the overview, provides information that explains how some of the work on textiles and leather is being used in the production of cosmetics. She starts with a little history/mythology and then launches into the synthetic biology efforts to produce silk and leather suitable for consumer use, Note: Links have been removed,

Once upon a time, circa 2700 BC in China, empress Xi Ling Shi was enjoying her afternoon tea under a mulberry tree, when a silkworm cocoon fell from the tree into her tea. She noticed that on contact with the hot beverage, the cocoon unraveled into a long silky thread. This happy accident inspired her to acquire these threads in abundance and fashion them into an elegant fabric. 

So goes the legend, according to the writings of Confucius, about the discovery of silk and the development of sericulture in ancient China. Although archaeological evidence from Chinese ruins dates the presence of silk to 8500 years ago, hinting that the royal discovery story was spun just like the silk fabric, one part of the legend rings true.1 The Chinese royals played a pivotal role in popularizing silk as a symbol of status and wealth. By 130 BC, emperors in the Ancient Civilizations across the world desired to be clad in silken garments, paving the Silk Road that opened trade routes from China to the West. 

While silk maintained its high-society status over the next thousands of years, the demand for easy-to-use materials grew among mass consumers. In the early 20th century, textile developers applied their new-found technological prowess to make synthetic materials: petrochemical-based polymer blended textiles with improved durability, strength, and convenience. 

In their quest to make silk powerful again, not by status but rather by thread strength, scientists turned to an arachnoid. Dragline silk, the thread by which the spider hangs itself from the web, is one of the strongest fibers; its tensile strength—a measure of how much a polymer deforms when strained—is almost thrice that of silkworm silk.2 

Beyond durable fashion garments, tough silk fibers are coveted in parachutes, military protective gear, and automobile safety belts, among other applications, so scientists are keen to pull on these threads. While traditional silk production relies on sericulture, arachnophobes can relax: spider farms are not a thing.

“Spiders make very little silk and are quite territorial. So, the only way to do it is to make microbes that make the protein,” said David Breslauer, cofounder and chief technology officer at Bolt Threads, a bio apparel company. 

For decades, researchers have coaxed microbes into churning their metabolites in large fermentation tanks, which they have harvested to solve dire crises in many areas. For instance, when pharmaceuticals struggled to meet the growing demand for insulin through the traditional methods of extraction from animal pancreas, researchers at Genentech sought the aid of E. coli to generate recombinant insulin for mass production in 1978.3  [emphases mine]

Prabhune’s June 14, 2024 article notes some difficulties with spider silk, Note: Links have been removed,

… researchers soon realized that producing spider silk in microbes was no easy feat. The spider silk protein, spidroin, is larger than 300 kDa in size—a huge jump from the small 6 kDa recombinant insulin. Bulky proteins impose a heavy metabolic load on the microbes and their production yield tanks. Also, spidroin consists of repeating regions of glycine and alanine amino acids that impart strength and elasticity to the material, but the host microbes struggle with protein folding and overexpression of the corresponding tRNA molecules.4  

… researchers had gotten close, but they hadn’t been able to synthesize the full spidroin protein. Since the molecular weight of the silk protein correlates with the strength of the silk thread, Zhang [Fuzhong Zhang, a synthetic biologist at Washington University in St. Louis] was determined to produce the entire protein to mimic the silk’s natural properties.5

To achieve this goal without pushing the metabolic limits of the bacteria, Zhang and his team literally broke down the problem. In 2018, they devised a recombinant spidroin by constructing two protein halves with split inteins—peptides known to catalyze ligation between proteins while splicing out their own residues—tagged at their ends. They synthesized the halves in separate E. coli cultures, mixed the two cultures, and ligated the proteins to yielded a recombinant spidroin of 556 kDa—a size that was previously considered unobtainable.6 The resulting silk fiber made from these recombinant spidroins matched the mechanical properties of natural spider silk fiber.

While synthesizing the high molecular weight protein validated their technical prowess and strategy, Zhang knew that the yield with this approach was going to be unavoidably low. “It was not even enough to make a simple shirt,” he said.

Zhang and his team did solve the problem of getting a higher yield but that led to another problem, from Prabhune’s June 14, 2024 article,

Breslauer echoed the importance of this step. He recalled how scaling up was the biggest challenge when he and his cofounder Dan Widmaier, chief executive officer at Bolt Threads, first set up shop in 2009. The duo met during their graduate studies. Breslauer, a material science student at the University of California, Berkeley, was fascinated by spider silk and sought help for synthesizing the protein in microbes. Luckily, he met Widmaier, a synthetic biology graduate student who was optimizing systems to study complex proteins.

When their collaboration to produce recombinant spider silk proteins in yeast yielded promising results, the duo decided to challenge the status quo in the textile industry by commercially producing bio-silk apparel, and Bolt Threads was born. The market transition, however, was not as smooth as the threads they produced. 

“There was so little innovation in the textile space, and brands were really eager to talk about innovation. It felt like there was demand there. Turns out, the desire for storytelling outweighed the desire for actual innovation with those brands,” Breslauer said. “We didn’t realize how adverse [sic] people were going to be to the idea because it was so unfamiliar.”

Prabhune’s June 14, 2024 article also covers leather and cosmetics, Note: Links have been removed,

David Williamson, a chemist and the chief operations officer at Modern Meadow and his team wanted to separate themselves from the herd. In their quest for sustainable alternatives, they went back to the basic biology and chemistry of the material. As leather is made from animal skin, it is rich in collagen, a structural protein abundant in the extracellular matrix of connective tissues. If the team could produce this primary component protein at scale, they would be able to process it into leather downstream. 

In about 2017, Williamson and his team developed a fermentation-based approach to produce collagen from yeast. While they achieved scalable production, there was one small hiccup. The protein properties of collagen alone did not yield the mechanical properties they needed for their leather-like material. 

The team went to the drawing board and analyzed the amino acid residues that contributed to collagen’s characteristics to look for a substitute protein. They found an alternative that had the desirable functional elements of collagen but was also sustainable and cost effective for industrial scale up: soy protein isolate. While tinkering with their recipes, they found the perfect combination for material strength by mixing in a bio-based polyurethane polymer with the protein to yield a refined bioalloy called Bio-VERA. 

As natural textiles are derived from animal skin, hair, or proteins, it is no surprise that many synthetic biologists in the textile space have also found a niche in cosmetics. Even as the Modern Meadow team transitioned away from their protein fermentation strategies to innovate Bio-VERA, they realized that they could still apply their expertise in skincare. While leathery is not an adjective one desires to associate with skin, collagen is an integral component in both. “When our bodies make collagen and build our extracellular matrices, one of the first proteins that they deposit is type three collagen. So, you can think of type three collagen almost like the structure or scaffold of a building,” explained Williamson.

To cater to the increasing demand for solutions to achieve younger looking skin, Williamson and his team engineered a recombinant collagen type three protein containing part of the protein sequence that is rich in binding domains for fibroblast interactions.9,10  “After you expose the extracellular matrix to this protein, it stimulates the fibroblasts to make more type three collagen. That type three collagen lays down type one collagen and elastin and fibronectin in a way that actually helps to turn back time, so to speak, to increase the ratio of type three collagen relative to type one collagen,” Williamson said. 

The Modern Meadow team are not the only ones to weave their textile strands into cosmetic applications. When Artur Cavaco-Paulo, a biological engineer at the University of Minho [Portugal], was studying wool fibers, he was struck by their structural similarities to human hair. “We decided that it would be a really good idea to transfer some of the knowledge that we had in wool textiles to human hair,” said Cavaco-Paulo. Particularly, he was interested in investigating solutions to fix hair strands damaged by highly alkaline chemical products. 

Over the next few years, Cavaco-Paulo developed […] shortlisted peptides into the K18 peptide product, which is now part of a commercially available leave-in conditioner. Cavaco-Paulo serves as the chief scientific officer at the biotech company K18. 

Although he started his career with textile research, Cavaco-Paulo favors the cosmetics sector with regards to returns on research and technology investment. “The personal care market is much more accustomed to innovation and has a much better and more fluid pipeline on innovation,” seconded Breslauer. “Whereas, [in] apparel, you really have to twist arms to get people to work with your material.” Bolt Threads ventured into the personal care space when Breslauer and his team serendipitously stumbled upon an alternative use for one of their textile proteins. 

While it’s not mentioned in Prabhune’s June 14, 2024 article, sustainability is mentioned on two of the company websites,

Bolt Threads

Bolt Threads is a material solutions company. With nature as our inspiration, we invent cutting-edge materials for the fashion and beauty industries to put us on a path toward a more sustainable future.

Through innovative collaborations with world-class brands and supply chain partners, we are on a mission to create way better materials for a way better world. Join us.

Modern Meadow

Modern Meadow is a climate-tech pioneer creating the future of materials through innovations in biology and material science.

​Our bio-materials technology platform with nature-inspired protein solutions delivers better performance, sustainability, scalability, and cost while reducing reliance on petrochemical and animal-based inputs.​

K18 has not adopted a ‘sustainability’ approach to marketing its hair care products.

Sustainability without synthetic biology: fish leather

In a January 3, 2022 posting I featured fish leather/skin in a story about the “Futures exhibition/festival” held at the Smithsonian Institute from November 20, 2021 to July 6, 2022.

Before getting to Futures, here’s a brief excerpt from a June 11, 2021 Smithsonian Magazine exhibition preview article by Gia Yetikyel about one of the contributors, Elisa Palomino-Perez (Note: A link has been removed),

Elisa Palomino-Perez sheepishly admits to believing she was a mermaid as a child. Growing up in Cuenca, Spain in the 1970s and ‘80s, she practiced synchronized swimming and was deeply fascinated with fish. Now, the designer’s love for shiny fish scales and majestic oceans has evolved into an empowering mission, to challenge today’s fashion industry to be more sustainable, by using fish skin as a material.

Luxury fashion is no stranger to the artist, who has worked with designers like Christian Dior, John Galliano and Moschino in her 30-year career. For five seasons in the early 2000s, Palomino-Perez had her own fashion brand, inspired by Asian culture and full of color and embroidery. It was while heading a studio for Galliano in 2002 that she first encountered fish leather: a material made when the skin of tuna, cod, carp, catfish, salmon, sturgeon, tilapia or pirarucu gets stretched, dried and tanned.

The history of using fish leather in fashion is a bit murky. The material does not preserve well in the archeological record, and it’s been often overlooked as a “poor person’s” material due to the abundance of fish as a resource. But Indigenous groups living on coasts and rivers from Alaska to Scandinavia to Asia have used fish leather for centuries. Icelandic fishing traditions can even be traced back to the ninth century. While assimilation policies, like banning native fishing rights, forced Indigenous groups to change their lifestyle, the use of fish skin is seeing a resurgence. Its rise in popularity in the world of sustainable fashion has led to an overdue reclamation of tradition for Indigenous peoples.

Brendan Jones provides an update of sorts in his Alaska-forward take in his February 22, 2024 article “Fish Leather Is Incredibly Strong and Beautiful. Can Makers ‘Scale Up’? Meet artisans in Alaska and BC who are sustaining, and advancing, an ancient art.” for The Tyee,

Fish leather artist June Pardue began her journey into the craft not knowing where to start. Which was a problem, considering that she had been given the job of demonstrating for tourists how to tan fish skin at the Alaska Native Heritage Center in Anchorage. “I couldn’t find anyone to teach me,” Pardue said with a laugh.

“One day a guy from Mississippi noticed me fumbling around. He kindly waited until everyone had left. Then he said, ‘Do you want me to share my grandpappy’s recipe for tanning snake skins?’”

His cocktail of alcohol and glycerin allowed her to soften the skins — as tourists looked on — for future use in clothing and bags. This worked fine until she began to grow uncomfortable dumping toxins down the drain. Now she uses plant-based tannins like those found in willow branches after the season’s first snowmelt. She harvests the branches gingerly, allowing the trees to survive for the next generation of fish tanners.

Pardue, who teaches at the University of Alaska, was born on Kodiak Island, off the southern coast of the state, in Old Harbor village. Alutiiq and Iñupiaq, she was raised in Akhiok, population about 50, and Old Harbor.

Following her bumpy start at the heritage center, Pardue has since gone on to become one of Alaska’s and Canada’s most celebrated instructors and practitioners in the field of fish leather, lighting the way for others in Alaska and Canada.

Among the people Pardue has advised is CEO and founder of 7 Leagues tannery Tasha Nathanson, who is based in Vancouver. She met with Pardue to share her idea of creating a business built on making fish leather into boots and other items for a large customer base.

Before making her move to open a business, Nathanson spent a year running the numbers, she said. In 2022, the global fish leather market was valued at US$36.22 million. As fish tanneries open their doors and fashion houses take notice, the number is expected to grow 16 per cent annually, topping $100 million by 2030.

“Salmon certainly don’t come to mind when you think of tanning, but people are catching on,” said Judith Lehmann, a Sitka-based expert in fish leather, who took Pardue’s class. (The Tyee reached Lehmann in Panama, where she was experimenting with skins of bonito and mahi mahi.)

Growing numbers of buyers are willing to pay for not only the beauty but also the remarkable durability fish leather can offer. California-based eco-fashion designer Hailey Harmon’s company Aitch Aitch sells the Amelia, a teal backpack made of panelled salmon leather, for $795.

One company in France has started to collect fish skins from restaurants — material that would otherwise end up in trash cans — to make luxury watch bands and accessories. Designers like Prada, Louis Vuitton and Christian Dior have incorporated fish leather into their lines. Even Nike introduced running shoes made of perch skin.

Whether they know it or not, today’s trendsetters are rooted in ancient history. “People have been working with fish skins for thousands of years,” Pardue said. “Ireland, Iceland, Norway, China, Japan — it’s an age-old practice.”

“On a molecular level, fibres in fish leather are cross-hatched, as opposed to cow leather, which is just parallel,” Nathanson explained. “So, pound for pound, this leather is stronger, which is great for shoes. And it’s more available, and eco-conscious. It’s a win across the board.”

Jones’s February 22, 2024 article has some wonderful embedded pictures and Beth Timmins’s May 1, 2019 article for the BBC (British Broadcasting Corporation), while a little dated, offers more information about the international scene.

Synthetic biology is a scientific practice that I find disconcerting at times. That said, I’m glad to see more work on sustainable products however they are derived. On that note I have a couple of recent stories:

  • “Three century long development of a scientific idea: body armor made from silk” is the title of my July 11, 2024 posting
  • “Grown from bacteria: plastic-free vegan leather that dyes itself” is the title of my June 26, 2024 posting

Enjoy!

Squirrel observations in St. Louis: a story of bias in citizen science data

Squirrels and other members of the family Sciuridae. Credit: Chicoutimi (montage) Karakal AndiW National Park Service en:User:Markus Krötzsch The Lilac Breasted Roller Nico Conradie from Centurion, South Africa Hans Hillewaert Sylvouille National Park Service – Own work from Wikipedia/CC by 3.0 licence

A March 5, 2024 news item on phys.org introduces a story about squirrels, bias, and citizen science,

When biologist Elizabeth Carlen pulled up in her 2007 Subaru for her first look around St. Louis, she was already checking for the squirrels. Arriving as a newcomer from New York City, Carlen had scrolled through maps and lists of recent sightings in a digital application called iNaturalist. This app is a popular tool for reporting and sharing sightings of animals and plants.

People often start using apps like iNaturalist and eBird when they get interested in a contributory science project (also sometimes called a citizen science project). Armed with cellphones equipped with cameras and GPS, app-wielding volunteers can submit geolocated data that iNaturalist then translates into user-friendly maps. Collectively, these observations have provided scientists and community members greater insight into the biodiversity of their local environment and helped scientists understand trends in climate change, adaptation and species distribution.

But right away, Carlen ran into problems with the iNaturalist data in St. Louis.

A March 5, 2024 Washington University in St. Louis news release (also on EurekAlert) by Talia Ogliore, which originated the news item, describes the bias problem and the research it inspired, Note: Links have been removed,

“According to the app, Eastern gray squirrels tended to be mostly spotted in the south part of the city,” said Carlen, a postdoctoral fellow with the Living Earth Collaborative at Washington University in St. Louis. “That seemed weird to me, especially because the trees, or canopy cover, tended to be pretty even across the city.

“I wondered what was going on. Were there really no squirrels in the northern part of the city?” Carlen said. A cursory drive through a few parks and back alleys north of Delmar Boulevard told her otherwise: squirrels galore.

Carlen took to X, formerly Twitter, for advice. “Squirrels are abundant in the northern part of the city, but there are no recorded observations,” she mused. Carlen asked if others had experienced similar issues with iNaturalist data in their own backyards.

Many people responded, voicing their concerns and affirming Carlen’s experience. The maps on iNaturalist seemed clear, but they did not reflect the way squirrels were actually distributed across St. Louis. Instead, Carlen was looking at biased data.

Previous research has highlighted biases in data reported to contributory science platforms, but little work has articulated how these biases arise.

Carlen reached out to the scientists who responded to her Twitter post to brainstorm some ideas. They put together a framework that illustrates how social and ecological factors combine to create bias in contributory data. In a new paper published in People & Nature, Carlen and her co-authors shared this framework and offered some recommendations to help address the problems.

The scientists described four kinds of “filters” that can bias the reported species pool in contributory science projects:

* Participation filter. Participation reflects who is reporting the data, including where those people are located and the areas they have access to. This filter also may reflect whether individuals in a community are aware of an effort to collect data, or if they have the means and motivation to collect it.

* Detectability filter. An animal’s biology and behavior can impact whether people record it. For example, people are less likely to report sightings of owls or other nocturnal species.

* Sampling filter. People might be more willing to report animals they see when they are recreating (i.e. hanging out in a park), but not what they see while they’re commuting.

* Preference filter. People tend to ignore or filter out pests, nuisance species and uncharismatic or “boring” species. (“There’s not a lot of people photographing rats and putting them on iNaturalist — or pigeons, for that matter,” Carlen said.)

In the paper, Carlen and her team applied their framework to data recorded in St. Louis as a case study. They showed that eBird and iNaturalist observations are concentrated in the southern part of the city, where more white people live. Uneven participation in St. Louis is likely a consequence of variables, such as race, income, and/or contemporary politics, which differ between northern and southern parts of the city, the authors wrote. The other filters of detectability, sampling and preference also likely influence species reporting in St. Louis.

Biased and unrepresentative data is not just a problem for urban ecologists, even if they are the ones who are most likely to notice it, Carlen said. City planners, environmental consultants and local nonprofits all sometimes use contributory science data in their work.

“We need to be very conscious about how we’re using this data and how we’re interpreting where animals are,” Carlen said.

Carlen shared several recommendations for researchers and institutions that want to improve contributory science efforts and help reduce bias. Basic steps include considering cultural relevance when designing a project, conducting proactive outreach with diverse stakeholders and translating project materials into multiple languages.

Data and conclusions drawn from contributory projects should be made publicly available, communicated in accessible formats and made relevant to participants and community members.

“It’s important that we work with communities to understand what their needs are — and then build a better partnership,” Carlen said. “We can’t just show residents the app and tell them that they need to use it, because that ignores the underlying problem that our society is still segregated and not everyone has the resources to participate.

“We need to build relationships with the community and understand what they want to know about the wildlife in their neighborhood,” Carlen said. “Then we can design projects that address those questions, provide resources and actively empower community members to contribute to data collection.”

Here’s a link to and a citation for the paper,

A framework for contextualizing social-ecological biases in contributory science data by Elizabeth J. Carlen, Cesar O. Estien, Tal Caspi, Deja Perkins, Benjamin R. Goldstein, Samantha E. S. Kreling, Yasmine Hentati, Tyus D. Williams, Lauren A. Stanton, Simone Des Roches, Rebecca F. Johnson, Alison N. Young, Caren B. Cooper, Christopher J. Schell. People & Nature Volume 6, Issue 2 April 2024 Pages 377-390 DI: https://doi.org/10.1002/pan3.10592 First published: 03 March 2024

This paper is open access.

Cleaning water with bacteria

There seems to be much interest in bacteria as collaborators as opposed to the old ‘enemy that must be destoyed’ concept. The latest collaborative effort was announced in a January 19,2019 news item on Nanowerk,

More than one in 10 people in the world lack basic drinking water access, and by 2025, half of the world’s population will be living in water-stressed areas, which is why access to clean water is one of the National Academy of Engineering’s Grand Challenges. Engineers at Washington University in St. Louis [WUSTL] have designed a novel membrane technology that purifies water while preventing biofouling, or buildup of bacteria and other harmful microorganisms that reduce the flow of water.

And they used bacteria to build such filtering membranes.

A January 17, 2019 WUSTL news release by Beth Miller, which originated the news item, provides more detail,

Srikanth Singamaneni, professor of mechanical engineering & materials science, and Young-Shin Jun, professor of energy, environmental & chemical engineering, and their teams blended their expertise to develop an ultrafiltration membrane using graphene oxide and bacterial nanocellulose that they found to be highly efficient, long-lasting and environmentally friendly. If their technique were to be scaled up to a large size, it could benefit many developing countries where clean water is scarce.


Biofouling accounts for nearly half of all membrane fouling and is highly challenging to eradicate completely. Singamaneni and Jun have been tackling this challenge together for nearly five years. They previously developed other membranes using gold nanostars, but wanted to design one that used less expensive materials.

Their new membrane begins with feeding Gluconacetobacter hansenii bacteria a sugary substance so that they form cellulose nanofibers when in water. The team then incorporated graphene oxide (GO) flakes into the bacterial nanocellulose while it was growing, essentially trapping GO in the membrane to make it stable and durable.

After GO is incorporated, the membrane is treated with base solution to kill Gluconacetobacter. During this process, the oxygen groups of GO are eliminated, making it reduced GO.  When the team shone sunlight onto the membrane, the reduced GO flakes immediately generated heat, which is dissipated into the surrounding water and bacteria nanocellulose.

Ironically, the membrane created from bacteria also can kill bacteria.
“If you want to purify water with microorganisms in it, the reduced graphene oxide in the membrane can absorb the sunlight, heat the membrane and kill the bacteria,” Singamaneni said.

Singamaneni and Jun and their team exposed the membrane to E. coli bacteria, then shone light on the membrane’s surface. After being irradiated with light for just 3 minutes, the E. coli bacteria died. The team determined that the membrane quickly heated to above the 70 degrees Celsius required to deteriorate the cell walls of E. coli bacteria.

While the bacteria are killed, the researchers had a pristine membrane with a high quality of nanocellulose fibers that was able to filter water twice as fast as commercially available ultrafiltration membranes under a high operating pressure.

When they did the same experiment on a membrane made from bacterial nanocellulose without the reduced GO, the E. coli bacteria stayed alive.

“This is like 3-D printing with microorganisms,” Jun said. “We can add whatever we like to the bacteria nanocellulose during its growth. We looked at it under different pH conditions similar to what we encounter in the environment, and these membranes are much more stable compared to membranes prepared by vacuum filtration or spin-coating of graphene oxide.”

While Singamaneni and Jun acknowledge that implementing this process in conventional reverse osmosis systems is taxing, they propose a spiral-wound module system, similar to a roll of towels. It could be equipped with LEDs or a type of nanogenerator that harnesses mechanical energy from the fluid flow to produce light and heat, which would reduce the overall cost.

Here’s a link to and a citation for the paper,

Photothermally Active Reduced Graphene Oxide/Bacterial Nanocellulose Composites as Biofouling-Resistant Ultrafiltration Membranes by Qisheng Jiang, Deoukchen Ghim, Sisi Cao, Sirimuvva Tadepalli, Keng-Ku Liu, Hyuna Kwon, Jingyi Luan, Yujia Min, Young-Shin Jun, and Srikanth Singamaneni. Environ. Sci. Technol., 2019, 53 (1), pp 412–421 DOI: 10.1021/acs.est.8b02772 Publication Date (Web): September 14, print Jan. 2, 2019.

Copyright © 2018 American Chemical Society

This paper is behind a paywall.

Quantum back action and devil’s play

I always appreciate a reference to James Clerk Maxwell’s demon thought experiment (you can find out about it in the Maxwell’s demon Wikipedia entry). This time it comes from physicist  Kater Murch in a July 23, 2018 Washington University in St. Louis (WUSTL) news release (published July 25, 2018 on EurekAlert) written by Brandie Jefferson (offering a good explanation of the thought experiment and more),

Thermodynamics is one of the most human of scientific enterprises, according to Kater Murch, associate professor of physics in Arts & Sciences at Washington University in St. Louis.

“It has to do with our fascination of fire and our laziness,” he said. “How can we get fire” — or heat — “to do work for us?”

Now, Murch and colleagues have taken that most human enterprise down to the intangible quantum scale — that of ultra low temperatures and microscopic systems — and discovered that, as in the macroscopic world, it is possible to use information to extract work.

There is a catch, though: Some information may be lost in the process.

“We’ve experimentally confirmed the connection between information in the classical case and the quantum case,” Murch said, “and we’re seeing this new effect of information loss.”

The results were published in the July 20 [2018] issue of Physical Review Letters.

The international team included Eric Lutz of the University of Stuttgart; J. J. Alonzo of the University of Erlangen-Nuremberg; Alessandro Romito of Lancaster University; and Mahdi Naghiloo, a Washington University graduate research assistant in physics.

That we can get energy from information on a macroscopic scale was most famously illustrated in a thought experiment known as Maxwell’s Demon. [emphasis mine] The “demon” presides over a box filled with molecules. The box is divided in half by a wall with a door. If the demon knows the speed and direction of all of the molecules, it can open the door when a fast-moving molecule is moving from the left half of the box to the right side, allowing it to pass. It can do the same for slow particles moving in the opposite direction, opening the door when a slow-moving molecule is approaching from the right, headed left. ­

After a while, all of the quickly-moving molecules are on the right side of the box. Faster motion corresponds to higher temperature. In this way, the demon has created a temperature imbalance, where one side of the box is hotter. That temperature imbalance can be turned into work — to push on a piston as in a steam engine, for instance. At first the thought experiment seemed to show that it was possible create a temperature difference without doing any work, and since temperature differences allow you to extract work, one could build a perpetual motion machine — a violation of the second law of thermodynamics.

“Eventually, scientists realized that there’s something about the information that the demon has about the molecules,” Murch said. “It has a physical quality like heat and work and energy.”

His team wanted to know if it would be possible to use information to extract work in this way on a quantum scale, too, but not by sorting fast and slow molecules. If a particle is in an excited state, they could extract work by moving it to a ground state. (If it was in a ground state, they wouldn’t do anything and wouldn’t expend any work).

But they wanted to know what would happen if the quantum particles were in an excited state and a ground state at the same time, analogous to being fast and slow at the same time. In quantum physics, this is known as a superposition.

“Can you get work from information about a superposition of energy states?” Murch asked. “That’s what we wanted to find out.”

There’s a problem, though. On a quantum scale, getting information about particles can be a bit … tricky.

“Every time you measure the system, it changes that system,” Murch said. And if they measured the particle to find out exactly what state it was in, it would revert to one of two states: excited, or ground.

This effect is called quantum backaction. To get around it, when looking at the system, researchers (who were the “demons”) didn’t take a long, hard look at their particle. Instead, they took what was called a “weak observation.” It still influenced the state of the superposition, but not enough to move it all the way to an excited state or a ground state; it was still in a superposition of energy states. This observation was enough, though, to allow the researchers track with fairly high accuracy, exactly what superposition the particle was in — and this is important, because the way the work is extracted from the particle depends on what superposition state it is in.

To get information, even using the weak observation method, the researchers still had to take a peek at the particle, which meant they needed light. So they sent some photons in, and observed the photons that came back.

“But the demon misses some photons,” Murch said. “It only gets about half. The other half are lost.” But — and this is the key — even though the researchers didn’t see the other half of the photons, those photons still interacted with the system, which means they still had an effect on it. The researchers had no way of knowing what that effect was.

They took a weak measurement and got some information, but because of quantum backaction, they might end up knowing less than they did before the measurement. On the balance, that’s negative information.

And that’s weird.

“Do the rules of thermodynamics for a macroscopic, classical world still apply when we talk about quantum superposition?” Murch asked. “We found that yes, they hold, except there’s this weird thing. The information can be negative.

“I think this research highlights how difficult it is to build a quantum computer,” Murch said.

“For a normal computer, it just gets hot and we need to cool it. In the quantum computer you are always at risk of losing information.”

Here’s a link to and a citation for the paper,

Information Gain and Loss for a Quantum Maxwell’s Demon by M. Naghiloo, J. J. Alonso, A. Romito, E. Lutz, and K. W. Murch. Phys. Rev. Lett. 121, 030604 (Vol. 121, Iss. 3 — 20 July 2018) DOI:https://doi.org/10.1103/PhysRevLett.121.030604 Published 17 July 2018

© 2018 American Physical Society

This paper is behind a paywall.

All-natural agrochemicals

Michael Berger in his May 4, 2018 Nanowerk Spotlight article highlights research into creating all natural agrochemicals,

Widespread use of synthetic agrochemicals in crop protection has led to serious concerns of environmental contamination and increased resistance in plant-based pathogenic microbes.

In an effort to develop bio-based and non-synthetic alternatives, nanobiotechnology researchers are looking to plants that possess natural antimicrobial properties.

Thymol, an essential oil component of thyme, is such a plant and known for its antimicrobial activity. However, it has low water solubility, which reduces its biological activity and limits its application through aqueous medium. In addition, thymol is physically and chemically unstable in the presence of oxygen, light and temperature, which drastically reduces its effectiveness.

Scientists in India have overcome these obstacles by preparing thymol nanoemulsions where thymol is converted into nanoscale droplets using a plant-based surfactant known as saponin (a glycoside of the Quillaja tree). Due to this encapsulation, thymol becomes physically and chemically stable in the aqueous medium (the emulsion remained stable for three months).

In their work, the researchers show that nanoscale thymol’s antibacterial and antifungal properties not only prevent plant disease but that it also enhances plant growth.

“It is exciting how nanoscale thymol is more active,” says Saharan [Dr. Vinod Saharan from the Nano Research Facility Lab, Department of Molecular Biology and Biotechnology, at Maharana Pratap University of Agriculture and Technology], who led this work in collaboration with Washington University in St. Louis and Haryana Agricultural University, Hisar. “We found that nanoscale droplets of thymol can easily pass through the surfaces of bacteria, fungi and plants and exhibit much faster and strong activity. In addition nanodroplets of thymol have a larger surface area, i.e. more molecules on the surface, so thymol becomes more active at the target sites.”

Here’s a link to and a citation for the paper,

Thymol nanoemulsion exhibits potential antibacterial activity against bacterial pustule disease and growth promotory effect on soybean by Sarita Kumari, R. V. Kumaraswamy, Ram Chandra Choudhary, S. S. Sharma, Ajay Pal, Ramesh Raliya, Pratim Biswas, & Vinod Saharan. Scientific Reportsvolume 8, Article number: 6650 (2018) doi:10.1038/s41598-018-24871-5 Published: 27 April 2018

This paper is open access.

Final note

There is a Canadian company which specialises in nanoscale products for the agricultural sector, Vive Crop Protection. I don’t believe they claim their products are ‘green’ but due to the smaller quantities needed of Vive Crop Protection’s products, the environmental impact is less than that of traditional agrochemicals.

Locusts inspire new aerosol-based nanoparticle drug delivery system

Getting medication directly to the brain is a worldwide medical research goal and it seems that a team of scientists at the Washington University at St. Louis (WUSTL) has taken a step forward to accomplishing the goal. From an April 12, 2017 news item on ScienceDaily,

Delivering life-saving drugs directly to the brain in a safe and effective way is a challenge for medical providers. One key reason: the blood-brain barrier, which protects the brain from tissue-specific drug delivery. Methods such as an injection or a pill aren’t as precise or immediate as doctors might prefer, and ensuring delivery right to the brain often requires invasive, risky techniques.

A team of engineers from Washington University in St. Louis has developed a new nanoparticle generation-delivery method that could someday vastly improve drug delivery to the brain, making it as simple as a sniff.

“This would be a nanoparticle nasal spray, and the delivery system could allow a therapeutic dose of medicine to reach the brain within 30 minutes to one hour,” said Ramesh Raliya, research scientist at the School of Engineering & Applied Science.

Caption: Engineers at Washington University have discovered a new technique that could change drug delivery to the brain. They were able to apply a nanoparticle aerosol spray to the antenna of locusts, then track the nanoparticles as they traveled through the olfactory nerves, crossed the blood-brain barrier and accumulated in the brain. This new, non-invasive approach could someday make drug delivery as simple as a sniff for patients with brain injuries or tumors.

Credit: Washington University in St. Louis

An April 12, 2017 WUSTL news release by Erika Ebsworth-Goold (also on EurekAlert), which originated the news item, describes the work in more detail,

“The blood-brain barrier protects the brain from foreign substances in the blood that may injure the brain,” Raliya said. “But when we need to deliver something there, getting through that barrier is difficult and invasive. Our non-invasive technique can deliver drugs via nanoparticles, so there’s less risk and better response times.”

The novel approach is based on aerosol science and engineering principles that allow the generation of monodisperse nanoparticles, which can deposit on upper regions of the nasal cavity via diffusion. Working with Assistant Vice Chancellor Pratim Biswas, chair of the Department of Energy, Environmental & Chemical Engineering and the Lucy & Stanley Lopata Professor, Raliya developed an aerosol consisting of gold nanoparticles of controlled size, shape and surface charge. The nanoparticles were tagged with fluorescent markers, allowing the researchers to track their movement.

Next, Raliya and biomedical engineering postdoctoral fellow Debajit Saha exposed locusts’ antennae to the aerosol, and observed the nanoparticles travel from the antennas up through the olfactory nerves. Due to their tiny size, the nanoparticles passed through the brain-blood barrier, reaching the brain and suffusing it in a matter of minutes.

The team tested the concept in locusts because the blood-brain barriers in the insects and humans have anatomical similarities, and the researchers consider going through the nasal regions to neural pathways as the optimal way to access the brain.

“The shortest and possibly the easiest path to the brain is through your nose,” said Barani Raman, associate professor of biomedical engineering. “Your nose, the olfactory bulb and then olfactory cortex: two relays and you’ve reached the cortex. The same is true for invertebrate olfactory circuitry, although the latter is a relatively simpler system, with supraesophageal ganglion instead of an olfactory bulb and cortex.”

To determine whether or not the foreign nanoparticles disrupted normal brain function, Saha examined the physiological response of olfactory neurons in the locusts before and after the nanoparticle delivery. Several hours after the nanoparticle uptake, no noticeable change in the electrophysiological responses was detected.

“This is only a beginning of a cool set of studies that can be performed to make nanoparticle-based drug delivery approaches more principled,” Raman said.

The next phase of research involves fusing the gold nanoparticles with various medicines, and using ultrasound to target a more precise dose to specific areas of the brain, which would be especially beneficial in brain-tumor cases.

“We want to drug target delivery within the brain using this non-invasive approach,” Raliya said.  “In the case of a brain tumor, we hope to use focused ultrasound so we can guide the particles to collect at that particular point.”

Here’s a link to and a citation for the paper,

Non-invasive aerosol delivery and transport of gold nanoparticles to the brain by Ramesh Raliya, Debajit Saha, Tandeep S. Chadha, Baranidharan Raman, & Pratim Biswas. Scientific Reports 7, Article number: 44718 (2017) doi:10.1038/srep44718 Published online: 16 March 2017

This paper is open access.

I featured another team working on delivering drugs directly to the brain via the olfactory system, except their nanoparticles were gelatin and they were testing stroke medication on rats, in my Sept. 24, 2014 posting.