Polarity proteins shape efficient “breathing” pores in grasses

Peer-Reviewed Publication

UNIVERSITY OF BERN

 

IMAGE: ONE OF THE TWO “COMPASS PROTEINS” (POLAR, IN PINK) ORIENTS THE FUTURE CELL DIVISION. IN GREY ARE CELL OUTLINES ON THE DEVELOPING LEAF. view more 

CREDIT: © COURTESY OF MICHAEL T. RAISSIG

Grasses have "respiratory pores" (called stomata) that open and close to regulate the uptake of carbon dioxide for photosynthesis on the one hand and water loss through transpiration on the other. Unlike many other plants, stomata in grasses form lateral "helper cells". Thanks to these cells, the stomata of grasses can open and close more quickly, which optimizes plant-atmosphere gas exchange and thus saves water.

For the current study, Prof. Dr. Michael Raissig, Dr. Heike Lindner and co-author Roxane Spiegelhalder from the Institute of Plant Sciences (IPS) at the University of Bern investigated the development of helper cells in the grass Brachypodium distachyon. They discovered two proteins that accumulate on opposite sides of a cell, acting like a "compass” to ensure the correct development of helper cells in grasses. The research results were published in the journal eLife.

A cell compass for the development of helper cells

Helper cells are formed by unequal, asymmetric cell division. In this process, a cell divides into a small cell, the helper cell, and a larger neighboring cell. For this division to occur in the correct ratio and orientation, the cell needs landmarks. These landmarks act as points of orientation and are given by so-called polarity proteins, which accumulate on opposite sides of the cell and can thus define, for example, left and right or top and bottom. In this study, the Bern researchers discovered two polarity proteins that accumulate on two opposite sides. "In a sense, the two proteins act as a cellular compass and control the orientation of cell division and the development of helper cells. We found that helper cells do not form properly when one of these proteins is missing. This negatively influences the efficient and water-saving gas exchange of the grass," explains project leader Michael Raissig.

Plant respiratory pores and climate change

"I am always fascinated that the lack of a cell compass in a single cell type can affect the gas exchange dynamics and efficiency of the entire plant," says Michael Raissig. He says this is particularly relevant in light of climate change, which causes longer drought period and excessive heat. Grasses play a central role in human food security; cereals such as corn, rice and wheat are all grasses and together provide more than half of the calories consumed by humans. "Therefore, it is of utmost importance to understand how plants “breathe” and how and why grasses form more efficient “breathing” pores," adds Raissig.

While this study focuses mainly on developmental biology, these findings could nonetheless be relevant to improving agricultural crops. "Stomata are the cellular gatekeepers between the leaf and the environment and are the first to respond to changes in climate," says PhD student and co-author Roxane Spiegelhalder. Therefore, she says, it is imperative to understand how and why grasses form the most efficient "gatekeepers" in order to "breathe" in a more water-efficient manner. How and whether these findings can be transferred to other crops, however, requires further research, Spiegelhalder concludes.

A grass “breathing pore” consists of two central, dumbbell-shaped guard cells and two lateral helper cells. (IMAGE)

UNIVERSITY OF BERN

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A grass “breathing pore” consists of two central, dumbbell-shaped guard cells and two lateral helper cells.

The wild model grass Brachypodium distachyon.

CREDIT

© Courtesy of Michael T. Raissig

Publication Zhang D, Spiegelhalder RP, Abrash EB, Nunes TDG, Prados IH, Ximena Anleu Gil M, Jesenofsky B, Lindner H, Bergmann DC, Raissig MT. 2022. Opposite polarity programs regulate asymmetric subsidiary cell divisions in grasses. eLife, Dezember 2022 DOI: 10.7554/eLife.79913

 

The Institute of Plant Sciences The Institute of Plant Sciences at the University of Bern is dedicated to understanding how plants function, grow and develop. Basic research at the Institute spans many areas, from physiology to ecology, from molecules and cells to whole plants and vegetation. Michael Raissig's Stomatal Biology / Plant Genetics & Development department explores the cellular, developmental and physiological aspects of stomata in grasses and other plants. Read more

 

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JOURNAL

eLife

DOI

10.7554/eLife.79913 

SUBJECT OF RESEARCH

Cells

ARTICLE TITLE

Opposite polarity programs regulate asymmetric subsidiary cell divisions in grasses

ARTICLE PUBLICATION DATE

20-Dec-2022

People sleep the least from early 30s to early 50s

Peer reviewed | experimental study | people

Peer-Reviewed Publication

UNIVERSITY COLLEGE LONDON

People sleep less in mid-adulthood than they do in early and late adulthood, finds a new study led by UCL, University of East Anglia and University of Lyon researchers.

Sleep duration declines in early adulthood until age 33, and then picks up again at age 53, according to the findings published in Nature Communications.

The study, involving 730,187 participants spread over 63 countries, revealed how sleep patterns change across the lifespan, and how they differ between countries.

Study participants were playing the Sea Hero Quest mobile game, a citizen science venture designed for neuroscience research, created by Deutsche Telekom in partnership with Alzheimer’s Research UK, UCL, UEA and game developers Glitchers. Designed to aid Alzheimer’s research by shedding light on differences in spatial navigational abilities, over four million people have played Sea Hero Quest, contributing to numerous studies across the project as a whole.

In addition to completing tasks testing navigational ability, anyone playing the game is asked to answer questions about demographic characteristics as well as other questions that can be useful to neuroscience research, such as on sleep patterns.

The researchers, led by Professor Hugo Spiers (UCL Psychology & Language Sciences) and Dr Antoine Coutrot (CNRS, University of Lyon) found that across the study sample, people sleep an average of 7.01 hours per night, with women sleeping 7.5 minutes longer than men on average. They found that the youngest participants in the sample (minimum age 19) slept the most, and sleep duration declined throughout people’s 20s and early 30s before plateauing until their early 50s and increasing again. The pattern, including the newly-identified key time points of age 33 when declining sleep plateaus and 53 for sleep to increase again, was the same for men and women, and across countries and education levels.

The researchers say the decline in sleep during mid-life may be due to demands of childcare and working life.

Professor Spiers said: “Previous studies have found associations between age and sleep duration, but ours is the first large study to identify these three distinct phases across the life course. We found that across the globe, people sleep less during mid-adulthood, but average sleep duration varies between regions and between countries.”

People who report sleeping the most are in Eastern European countries such as Albania, Slovakia, Romania and the Czech Republic, reporting 20-40 minutes extra sleep per night and the least in South East Asian countries including the Philippines, Malaysia and Indonesia. People in the United Kingdom reported sleeping slightly less than the average. People tended to sleep a bit less in countries closer to the equator.

The researchers found that navigational ability was unaffected by sleep duration for most of the sample, except for among older adults (aged 54-70) whose optimal sleep duration was seven hours, although they caution that the findings among older adults might be impacted by underlying health conditions.

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JOURNAL

Nature Communications

DOI

10.1038/s41467-022-34624-8 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Reported sleep duration reveals segmentation of the adult life-course into three phases

Predicting calving problems before insemination

Peer-Reviewed Publication

UNIVERSITY OF GRONINGEN

 

IMAGE: SCIENTIST USED ARTIFICIAL INTELLIGENCE TO CREATE A PREDICTIVE MODEL THAT IN THEORY COULD HALVE THE NUMBER OF CALVING PROBLEMS IN CATTLE. view more 

CREDIT: PXHERE.COM

A small percentage of cows will experience problems when calving and breeders would like to know which cows are at risk. Using the vast dataset of the Dutch cattle breeding company CRV, computer scientists at the University of Groningen used artificial intelligence to develop a predictive model that in theory could halve the number of calving problems. They published their results on 5 December in the journal Preventive Veterinary Medicine.

Cattle breeding is data science. Breeding firms provide semen from bulls and register the success of their offspring. Data on the milk yield of the cows and many other characteristics are collected and stored in a huge database, together with the genetic data from all the animals. This allows the companies to attribute an ‘estimated breeding value’ to the animals and find matches for optimal breeding.

Risk

One aspect of breeding is the birthing of calves. In about 3.3 percent of all cases, some kind of complication occurs during calving, which is referred to as dystocia. ‘This could range from the calf needing to be pulled to needing veterinary intervention,’ explains Ahmad Alsahaf. ‘There are models to predict the risk of dystocia, but these work with data that are only available after insemination. We wanted to produce a model that could predict the risk before insemination.’

Alsahaf now works as a postdoctoral researcher at the Department of Biomedical Sciences of Cells & Systems of the University Medical Center Groningen, but he has worked on a predictive model for dystocia during his PhD project at the Intelligent Systems research group at the Bernoulli Institute for Mathematics, Computer Science and Artificial Intelligence at the University of Groningen in The Netherlands.

Challenges

‘We were asked to create this model for the cattle breeding company CRV and they gave us a large dataset comprising information on cows and bulls,’ says Alsahaf. ‘We first used a machine-learning system to analyse the data and create a provisional model. Then, we checked if the most important risk factors made sense. They did and, therefore, we proceeded to build a full model.’

There were two main challenges: the first was to clean up and compile the available data. The second was that only 3.3 percent of pregnant cows experience dystocia. ‘This meant that there was a huge imbalance in our dataset,’ explains Alsahaf. To solve this, he created a large number of subsets with balanced data and aggregated those to train the predictive model. ‘Subsequently, we tested this model on a subset of the data that was not used for training and studied the results.’ It turned out that the model performed significantly better than chance.

‘A colleague of ours calculated that, under ideal circumstances, our model could roughly halve the risk of dystocia. But this requires an ideal combination of bull and cow, which is not always possible.’ Nevertheless, the model can help farmers and the breeding company to assess the risk of a particular mating before insemination. ‘This is important since, so far, all other models require information gathered after insemination, which means you are not really preventing complications.’

Reference: Ahmad Alsahaf, Radu Gheorghe, André M. Hidalgo, Nicolai Petkov and George Azzopardi: Pre-insemination prediction of dystocia in dairy cattle. Preventive Veterinary Medicine, 5 December 2022

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JOURNAL

Preventive Veterinary Medicine

DOI

10.1016/j.prevetmed.2022.105812 

METHOD OF RESEARCH

Computational simulation/modeling

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Pre-insemination prediction of dystocia in dairy cattle

A type of simple, DIY air filter can be an effective way to filter out indoor air pollutants

A study from researchers at Brown University and Silent Spring Institute found that inexpensive, easy-to-assemble Corsi-Rosenthal boxes can help reduce exposure to indoor air pollutants

Peer-Reviewed Publication

BROWN UNIVERSITY

 

IMAGE: A STUDY FROM RESEARCHERS AT BROWN UNIVERSITY AND SILENT SPRING INSTITUTE FOUND THAT INEXPENSIVE, EASY-TO-ASSEMBLE CORSI-ROSENTHAL BOXES CAN HELP REDUCE EXPOSURE TO INDOOR AIR POLLUTANTS. (PHOTOS: KEN ZIRKEL) view more 

CREDIT: PHOTO: KEN ZIRKEL

PROVIDENCE, R.I. [Brown University] — A team of researchers from Brown University's School of Public Health, Brown’s School of Engineering and Silent Spring Institute found that simple air filtration devices called Corsi-Rosenthal boxes are effective at reducing indoor air pollutants.

The study, which analyzed the effectiveness of Corsi-Rosenthal boxes installed at the School of Public Health to help prevent the spread of COVID-19, is the first peer-reviewed study of the efficacy of the boxes on indoor pollutants, according to the authors.

Lowering indoor air concentrations of commonly-found chemicals known to pose a risk to human health is a way to improve occupant health, according to lead author Joseph Braun, an associate professor of epidemiology at Brown.

“The findings show that an inexpensive, easy-to-construct air filter can protect against illness caused not only by viruses but also by chemical pollutants,” Braun said. “This type of highly-accessible public health intervention can empower community groups to take steps to improve their air quality and therefore, their health.”

Corsi-Rosenthal boxes, or cubes, can be constructed from materials found at hardware stores: four MERV-13 filters, duct tape, a 20-inch box fan and a cardboard box. As part of a school-wide project, boxes were assembled by students and campus community members and installed in the School of Public Health as well as other buildings on the Brown University campus.

To assess the cubes’ efficacy at removing chemicals from the air, Braun and his team compared a room’s concentrations of semi-volatile organic compounds before and during the box’s operation.

The results, published in Environmental Science & Technology, showed that Corsi-Rosenthal boxes significantly decreased the concentrations of several PFAS and phthalates in 17 rooms at the School of Public Health during the period they were used (February to March 2022). PFAS, a type of synthetic chemical found in a range of products including cleaners, textiles and wire insulation, decreased by 40% to 60%; phthalates, commonly found in building materials and personal care products, were reduced by 30% to 60%.

PFAS and phthalates have been linked to various health problems, including asthma, reduced vaccine response, decreased birth weight, altered brain development in children, altered metabolism and some cancers, said Braun, who studies the effect of these chemicals on human health. They are also considered to be endocrine-disrupting chemicals that may mimic or interfere with the body’s hormones. What’s more, PFAS have been associated with reduced vaccine response in children and also may increase the severity of and susceptibility to COVID-19 in adults.

“The reduction of PFAS and phthalate levels is a wonderful co-benefit to the Corsi-Rosenthal boxes,” said study co-author Robin Dodson, a research scientist at Silent Spring Institute and expert in chemical exposures in the indoor environment.. “These boxes are accessible, easy to make and relatively inexpensive, and they’re currently being used in universities and homes across the country.”

“The Corsi-Rosenthal box was designed to be a simple, cost-effective tool to promote accessible and effective air cleaning during the COVID-19 pandemic; the fact that the boxes are also effective at filtering out air pollutants is a fantastic discovery,” said Richard Corsi, one of the inventors of the boxes and dean of the College of Engineering at the University of California, Davis. “I am thrilled that researchers at Brown University and Silent Spring Institute have identified a significant co-benefit of the boxes with respect to reduced exposure to two harmful classes of indoor pollutants: PFAS and phthalates.

The sentiment was echoed by Jim Rosenthal, Corsi’s collaborator and CEO of Air Relief Technologies, the company that manufactures the MERV-13 filters used in Corsi-Rosenthal Boxes.

“This interesting research showing that the air filters not only reduce particles carrying the SARS-CoV-2 virus but also reduce other indoor air pollutants could be very significant as we continue to work to create cleaner and safer indoor air," Rosenthal said.

The researchers also found that the Corsi-Rosenthal boxes increase sound levels by an average of 5 decibels during the day and 10 decibels at night, which could be considered distracting in certain settings, such as classrooms. However, Braun said, the health benefits of the box likely outweigh the audio side effects.

“The box filters do make some noise,” Braun said. “But you can construct them quickly for about $100 per unit, with materials from the hardware store. They are not only highly effective but also scalable.”

Brown study authors include Kate Manz and Kurt Pennell from the School of Engineering, and Jamie Liu, Shaunessey Burks and Richa Gairola from the School of Public Health. This research was supported by the National Science Foundation and the National Institute of Environmental Health Sciences.

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JOURNAL

Environmental Science & Technology

DOI

10.1021/acs.est.2c05169 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Using Corsi-Rosenthal Boxes to Mitigate COVID-19 Transmission Also Reduce Indoor Air Concentrations of PFAS and Phthalates?

ARTICLE PUBLICATION DATE

23-Dec-2022

COI STATEMENT

Competing financial interests: Joseph Braun was financially compensated for his services as an expert witness for plaintiffs in litigation related to PFAS-contaminated drinking water.

Mired in silence

Health of Southern California’s farmworkers needs to be a priority, says UC Riverside study

Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - RIVERSIDE

 

IMAGE: ANN CHENEY (SECOND FROM LEFT) IS SEEN HERE WITH PROMOTORAS, SPANISH-SPEAKING COMMUNITY HEALTH WORKERS. view more 

CREDIT: UC RIVERSIDE.

RIVERSIDE, Calif. -- A University of California, Riverside, study performed in the Eastern Coachella Valley, one of California’s top agricultural production regions, has found that farmworkers there lack information and the means to advocate for improved public health even when they are aware of being exposed to health risks stemming from working and living in rural farmlands.

About 76% of the 2.4 million farmworkers in the United States are immigrants, most of whom are from Mexico. In Inland Southern California, where the Eastern Coachella Valley, or EVC, is located, not much research has been done on Latinx farmworkers’ health concerns and barriers to care.

“Agricultural production demands in the U.S. impose a heavy burden on Latinx immigrant farmworkers, which shapes their health and informs their decisions about their living conditions,” said Ann Cheney, an associate professor of social medicine, population, and public health in the School of Medicine and lead author of the study that appears in the International Journal of Environmental Research and Public Health. “The health of these workers and their families should be a national priority.”

Cheney and her team used a community-based participatory research approach. They conducted nine in-home meetings in 2017-2018, with the help of “promotoras,” Spanish-speaking community health workers, to gather information on the health concerns of rural residents of the EVC as well as the barriers they face in accessing healthcare services. The majority of the 82 participants in the study were Mexican immigrants, women, and low-income. Nearly 60% of participants worked in agriculture. Many resided close to farmlands and were regularly exposed to pesticides, chemicals, agricultural runoff, and mosquitoes.

In the interviews, participants discussed health concerns related to agricultural labor, such as heat-related illness, musculoskeletal ailments and injuries, skin disorders, respiratory illness, and trauma. They expressed their concerns about environmental exposures related to agriculture and the nearby Salton Sea, a land-locked highly saline lakebed, and offered solutions to improve the health of their communities.

Respiratory illness in the ECV is disproportionately high, affecting about 20% of children living along the Salton Sea. Study participants said they were aware of the negative effects of the Salton Sea on their health. 

“Farm work exposes laborers to heat, cold, and ultraviolet rays, increasing the risk to health,” Cheney said. “Farmworkers have more exposure to pesticides than non-agricultural workers, which can increase risk for skin disease, vision problems, and respiratory-associated illness.”

Cheney added that the kind of work the farmworkers do — picking of crops, heavy lifting, and standing or kneeling for long periods — can cause injuries and chronic pain. 

“The fast-paced, high-risk working environment can affect mental health,” she said. 

The study found many farmworkers stay quiet when it comes to unsafe workplace conditions and injuries because they fear losing their jobs. Many farmworkers lack health insurance and have little access to medical facilities, sick pay, and transportation. Most are not fluent English. Indeed, the situation of rural farmworkers has not changed significantly since the farm labor leader and civil rights activist Cesar Chavez brought attention in the 1960s to the poor living and working conditions endured by farm workers.

“Much of the lack of change is tied to structural level inequities produced by macro-level processes, neoliberal economic and political policies, that extend beyond what individuals or communities can do and reflect the values of governments,” Cheney said. “An example is NAFTA, the North American Free Trade Agreement of 1994. What we know is NAFTA compromised the financial stability of small-scale farms in Mexico, the primary occupation in many rural regions of Mexico. Some estimates suggest more than 3 million people involved in agricultural labor lost their jobs and their livelihood.”

Cheney explained that the EVC is home to a large population of Purépecha, an indigenous group from Michoacán Mexico. 

“Living in the valley and working in the fields, they make up an incredibly vulnerable community as many cannot speak Spanish or English,” she said. “They speak their native indigenous language of Purépecha and are undocumented. They choose farm labor because they don’t need language or technical skills to be pickers. This, though, is the lowest ranking position in agricultural labor and least paid.”

According to Cheney, structural level interventions — interventions that change the political and economic landscape — are needed to effect positive change in the lives of farm workers.

“We need to move away from neoliberal policies that privilege those already in positions of power, open the border between US and Mexico so that those crossing the border are not labelled as ‘illegal’ and have the opportunity to find stable employment, access educational and social opportunities for themselves and their families,” she said. “Such an approach also aligns with the thinking of NAFTA — open the borders for trade to eliminate tariffs. We, too, should open the border for human migration to eliminate inequities.”

Cheney was joined in the study by Tatiana Barrera and Katheryn Rodriguez of UCR; and Ana María Jaramillo López of the College of the Northern Border, Tijuana, Mexico.

The research was funded by the Research Program on Migration and Health.

The title of the research paper is “The Intersection of Workplace and Environment Exposure on Health in Latinx Farm Working Communities in Rural Inland Southern California.”

The University of California, Riverside is a doctoral research university, a living laboratory for groundbreaking exploration of issues critical to Inland Southern California, the state and communities around the world. Reflecting California's diverse culture, UCR's enrollment is more than 26,000 students. The campus opened a medical school in 2013 and has reached the heart of the Coachella Valley by way of the UCR Palm Desert Center. The campus has an annual impact of more than $2.7 billion on the U.S. economy. To learn more, visit www.ucr.edu.

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JOURNAL

International Journal of Environmental Research and Public Health

DOI

10.3390/ijerph191912940 

METHOD OF RESEARCH

Survey

SUBJECT OF RESEARCH

People

ARTICLE TITLE

The Intersection of Workplace and Environmental Exposure on Health in Latinx Farm Working Communities in Rural Inland Southern California

Universities, rich in data, struggle to capture its value, study finds

UCLA–MIT Press research finds pervasive lack of data infrastructure, strategy in U.S. higher ed

Peer-Reviewed Publication

THE MIT PRESS

Universities are literally awash in data. From administrative data offering information about students, faculty and staff, to research data on professors’ scholarly activities and even telemetric signals — the functional administrative data gathered remotely from wireless networks, security cameras and sensors in the course of daily operations — that data can be an invaluable resource.

But a new study by researchers at UCLA and the MIT Press, published Dec. 23 in the journal Science, finds that universities face significant challenges in capturing such data, and that they severely lag the private sector and government entities in using data to solve challenges and inform strategic planning.

“This new research shines a bright light on the ways in which universities are data rich and data poor — and sometimes intentionally data blind,” said Christine L. Borgman, distinguished research professor at the UCLA School of Education & Information Studies and one of the study’s authors. “They are struggling to capture and exploit the true value of their data resources and reluctant to initiate the conversations necessary to build consensus for data governance.”

The study, co-authored by Amy Brand, director and publisher of the MIT Press, is based on a dozen interviews with provosts, vice provosts, university librarians and other senior officials engaged in university data governance and management. The researchers found that although universities have made sporadic initiatives to integrate systems and reduce redundancies in academic data management, most still lack needed coordination and expertise.

The respondents expressed concerns about commercial control of their internal systems and continuing tensions about local capacity for data-informed planning. Many also said they felt handicapped by the lack of databases of record — centralized data repositories — and by the lack of coordinated information management strategies and administrators with data science training and skills.

The study also contends that universities have been slower than other economic sectors in creating senior positions such as chief data officers to coordinate data quality, strategy, governance and privacy matters.

“Our study sought to identify sources of these tensions along with innovative solutions adopted or under development within the academy,” Brand said. “We unexpectedly found a pervasive void of infrastructure thinking and a relatively limited set of data-informed planning successes.”

Almost all respondents said they wanted to be able to better integrate data among departments and schools within their institutions, and to make data from various sources work better when integrated with other data systems. For example, for university libraries to best serve student and faculty researchers, they might need to gather information about academic courses from the institution’s internal systems, and use or merge it with data from external parties such as publishers or public or private sector organizations.

University leaders said they could make better strategic decisions about hiring and curriculum if they had more comprehensive data on faculty research, prospective students, research funding, higher-education policy trends and competitive intelligence about other universities. But data that would help guide decision-making is often inaccessible because of data governance practices or friction among units, departments or schools within a university. And such data might be accessible but unexploited because of a lack of staff expertise.

The findings underscore the need for system and institutional leadership that encourages a broad view of data infrastructure and policies, senior-level personnel with the authority and budgets to help universities capture and use their data more effectively, and greater involvement by faculty and others who are involved in determining how data is used.

To address the issues raised by the research, the authors suggest that universities could expand investments in infrastructure that would improve access, integration and intelligence — the ability to gather, analyze and gain insight. Institutions could also bolster their data management capacity — training personnel and developing career paths for them, for example. Doing so, the authors write, would improve universities’ abilities to manage a range of data, and to mine data for strategic, policy, social, cultural and technical insights.

“Data-informed decision-making provides opportunities to promote transparent governance; advance fairness and equity for faculty, students, and staff; and save money,” the authors write. “We encourage university leaders to embrace more objective and transparent data-informed models for decision-making.”

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JOURNAL

Science

DOI

10.1126/science.add2734 

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Data blind: Universities lag in capturing and exploiting data

ARTICLE PUBLICATION DATE

23-Dec-2022

Designing with DNA

Software lets researchers create tiny rounded objects out of DNA. Here’s why that’s cool

Peer-Reviewed Publication

DUKE UNIVERSITY

 

IMAGE: NO BIGGER THAN A VIRUS, EACH OF THESE NANOSTRUCTURES WAS BUILT USING NEW SOFTWARE THAT LETS RESEARCHERS DESIGN OBJECTS OUT OF CONCENTRIC RINGS OF DNA. MODELS (TOP) SHOWN ALONGSIDE ELECTRON MICROSCOPE IMAGES OF THE ACTUAL OBJECTS (BOTTOM). view more 

CREDIT: COURTESY OF RAGHU PRADEEP NARAYANAN AND ABHAY PRASAD, YAN LAB, ARIZONA STATE UNIVERSITY.

DURHAM, N.C. -- Marvel at the tiny nanoscale structures emerging from research labs at Duke University and Arizona State University, and it’s easy to imagine you’re browsing a catalog of the world’s smallest pottery.

A new paper reveals some of the teams’ creations: itty-bitty vases, bowls, and hollow spheres, one hidden inside the other, like housewares for a Russian nesting doll.

But instead of making them from wood or clay, the researchers designed these objects out of threadlike molecules of DNA, bent and folded into complex three-dimensional objects with nanometer precision.

These creations demonstrate the possibilities of a new open-source software program developed by Duke Ph.D. student Dan Fu with his adviser John Reif. Described December 23 in the journal Science Advances, the software lets users take drawings or digital models of rounded shapes and turn them into 3D structures made of DNA.

The DNA nanostructures were assembled and imaged by co-authors Raghu Pradeep Narayanan and Abhay Prasad in professor Hao Yan’s lab at Arizona State. Each tiny hollow object is no more than two millionths of an inch across. More than 50,000 of them could fit on the head of a pin.

But the researchers say these are more than mere nano-sculptures. The software could allow researchers to create tiny containers to deliver drugs, or molds for casting metal nanoparticles with specific shapes for solar cells, medical imaging and other applications.

To most people, DNA is the blueprint of life; the genetic instructions for all living things, from penguins to poplar trees. But to teams like Reif’s and Yan’s, DNA is more than a carrier of genetic information -- it’s source code and construction material.

There are four “letters,” or bases, in the genetic code of DNA, which pair up in a predictable way in our cells to form the rungs of the DNA ladder. It’s these strict base-pairing properties of DNA -- A with T, and C with G -- that the researchers have co-opted. By designing DNA strands with specific sequences, they can “program” the strands to piece themselves together into different shapes.

The method involves folding one or a few long pieces of single-stranded DNA, thousands of bases long, with help from a few hundred short DNA strands that bind to complementary sequences on the long strands and “staple” them in place.

Researchers have been experimenting with DNA as a construction material since the 1980s. The first 3D shapes were simple cubes, pyramids, soccer balls -- geometric shapes with coarse and blocky surfaces. But designing structures with curved surfaces more akin to those found in nature has been tricky. The team’s aim is to expand the range of shapes that are possible with this method.

To do that, Fu developed software called DNAxiS. The software relies on a way to build with DNA described in 2011 by Yan, who was a postdoc with Reif at Duke 20 years ago before joining the faculty at Arizona State. It works by coiling a long DNA double helix into concentric rings that stack on each other to form the contours of the object, like using coils of clay to make a pot. To make the structures stronger, the team also made it possible to reinforce them with additional layers for increased stability.

Fu shows off the variety of forms they can make: cones, gourds, clover leaf shapes. DNAxiS is the first software tool that lets users design such shapes automatically, using algorithms to determine where to place the short DNA “staples” to join the longer DNA rings together and hold the shape in place.

“If there are too few, or if they're in the wrong position, the structure won't form correctly,” Fu said. “Before our software, the curvature of the shapes made this an especially difficult problem.”

Given a model of a mushroom shape, for example, the computer spits out a list of DNA strands that would self-assemble into the right configuration. Once the strands are synthesized and mixed in a test tube, the rest takes care of itself: by heating and cooling the DNA mixture, within as little as 12 hours “it sort of magically folds up into the DNA nanostructure,” Reif said.

Practical applications of their DNA design software in the lab or clinic may still be years away, the researchers said. But “it's a big step forward in terms of automated design of novel three dimensional structures,” Reif said.

This research was supported by the National Science Foundation (1909848, 2113941, 2004250, 1931487).

CITATION: "Automated Design of 3D DNA Origami With Non-Rasterized 2D Curvature," Daniel Fu, Raghu Pradeep Narayanan, Abhay Prasad, Fei Zhang, Dewight Williams, John S. Schreck, Hao Yan, John Reif. Science Advances, Dec. 23, 2022. DOI: 10.1126/sciadv.ade4455

 

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JOURNAL

Science Advances

DOI

10.1126/sciadv.ade4455 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Automated Design of 3D DNA Origami With Non-Rasterized 2D Curvature