DNA barcoding identifies the plants a person has eaten

Reliable technique should improve clinical trials, nutrition studies and historical research

Peer-Reviewed Publication

DUKE UNIVERSITY

 

IMAGE: DNA BARCODING CAN NOW BE USED TO IDENTIFY WHAT PLANTS A PERSON HAS EATEN, AND IN WHAT RELATIVE AMOUNTS. THE TECHNIQUE SHOULD IMPROVE CLINICAL TRIALS AND NUTRITION STUDIES. (IMAGE, LAWRENCE A. DAVID) view more 

CREDIT: LAWRENCE A. DAVID, DUKE UNIVERSITY

DURHAM, N.C. – What people say they’ve eaten and what they’ve actually eaten are often two very different lists of foods. But a new technique using DNA barcoding to identify the plant matter in human feces may get at the truth, improving clinical trials, nutrition studies and more.

Building on earlier studies that attempted to compare DNA found in feces with reported diets, researchers in the lab of Lawrence David, an associate professor of molecular genetics and microbiology in the Duke School of Medicine, have developed a genetic marker for plant-based foods that can be retrieved from poop.

“We can go back after the fact and detect what foods were eaten,” said Brianna Petrone, PhD, an MD/PhD student who led the project.

The marker is a region of DNA plants use to power chloroplasts, the organelle that converts sunlight into sugars. Every plant has this genomic region, called trnL-P6, but it varies slightly from species to species. In a series of experiments, they tested the marker on more than 1,000 fecal samples from 324 study participants across five different studies, about twenty of whom had high-quality records of their diet.

In findings appearing June 27 in the Proceedings of the National Academy of Sciences, the researchers show that these DNA markers can indicate not only what was consumed, but the relative amounts of certain food species, and that the diversity of plant DNA found in feces varies according to a person’s diet, age, and household income.

David’s lab relied on a reference database of dietary plants that contains markers for 468 species typically eaten by Americans to connect versions of trnL-P6 detected in poop to specific plant sources. After some tweaking, their barcode was able to distinguish 83 percent of all major crop families.

Petrone said the subset of crop families that could not currently be detected tended to be consumed in other parts of the world. The lab is now working to add  crops such as pearl millet and pili nuts to their database.

They also haven’t tracked meat intake yet, though the technology is capable of that as well, David said. “That relative ratio of plant to animal intake is probably one of the most important nutritional factors we might look at.”

The scientists first tried the marker out on fecal samples from four individuals in a weight loss intervention where they knew exactly what study participants had been fed a day or two before. Knowing the patients had been given a dish called mushroom wild rice pilaf for example, they looked for the markers of its components: wild rice, white rice, portobello mushrooms, onion, pecans, thyme, parsley and sage.

In this and a second intervention group, they found that barcoding could not only identify the plants, it also could identify relative amounts consumed for some kinds of plants. “When big portions of grains or berries were recorded in the meal, we also saw more trnL from those plants in stool,” Petrone said.

Then they looked at samples from 60 adults who had taken part in two studies of fiber supplementation and kept track of what they were eating with surveys. The number of plants detected by trnL was in good agreement with dietary diversity and quality estimated from participants’ survey responses.

Next, they applied the barcoding to a study 246 adolescents with and without obesity with diverse racial, ethnic, and socioeconomic backgrounds. There was only a minimal record of diet in this cohort.

“Dietary data collection was challenging because some traditional surveys are 140 pages long and take up to an hour to fill out, families are busy, and a child might not be able to fill it out alone,” David said. “But because they had banked stool, we were able reanalyze those samples and then gather information about diet that could be used to better understand health and lifestyle patterns between kids. What really struck me was that we could recapitulate things that were known as well get new insights that might not have been as obvious.”

They found 111 different markers from 46 plant families and 72 species in the adolescents’ diet. Four kinds of plants were eaten by more than two thirds of subjects: wheat, found in 96 percent of participants, chocolate (88%), corn (87%)  and the potato family (71%), a group of closely related plants that includes potato and tomatillo.

David said the barcode isn’t able to distinguish individual members of the cabbage family – the brassica – such as broccoli, Brussels sprouts, kale, and cauliflower, which are closely related.

Still, the large adolescent cohort showed that dietary variety was greater for the higher-income study participants. The older the adolescents were however, the lower their intake of fruits, vegetables and whole grain foods, potentially because of a known pattern of older children eating with their families less often.

David said the barcode is readily able to identify the diversity of plants found in a sample as a proxy for dietary diversity, a known marker of nutrient adequacy and better heart health.

David said that in each of these cohorts, the genomic analyses had been carried out on samples that had been collected years in the past, so the technique opens up the possibility of reconstructing dietary data for studies that have already been finished.

The authors think the new methodology should be a boon for all sorts of studies of human nutrition. “We are limited in how we can track our diets, or participate in nutrition research or improve our own health, because of the current techniques by which diet is tracked,” David said. “Now we can use genomics to help gather data on what people eat around the world, regardless of differences in age, literacy, culture, or health status.”

The team anticipates extending the technique to studies of disease across the globe, as well as monitoring food biodiversity in settings facing climate instability or ecological distress.

Funding for this work came from the National Institute of Diabetes and Digestive and Kidney Diseases (grants 5R24DK110492-05 and 5R01DK116187-05), the Burroughs Wellcome Fund Pathogenesis of Infectious Disease Award, the Duke Microbiome Center, the Springer Nature Limited Global Grant for Gut Health, the Chan Zuckerberg Initiative, the Triangle Center for Evolutionary Medicine, the Integrative Bioinformatics for Investigating and Engineering Microbiomes Graduate Student Fellowship, and the Ruth L. Kirschstein National Research Service Award to the Duke Medical Scientist Training Program. This work used a high-performance computing facility partially supported by grants from the North Carolina Biotechnology Center (2016-IDG-1013 and 2020-IIG-2109).

CITATION: “Diversity of Plant DNA in Stool is Linked to Dietary Quality, Age and Household Income,” Brianna L. Petrone, Ammara Aqeel, Sharon Jiang, Heather K. Durand, Eric P. Dallow, Jessica R. McCann, Holly K. Dressman, Zhengzheng Hu, Christine B. Tenekjian, William S. Yancy, Jr., Pao-Hwa Lin, Julia J. Scialla, Patrick C. Seed, John F. Rawls, Sarah C. Armstrong, June Stevens, Lawrence A. David. PNAS, June 27, 2023.

DOI: 10.1073/pnas.2304441120

Online: https://www.pnas.org/cgi/doi/10.1073/pnas.2304441120

DNA Barcoding can now be used to identify what plants a person has eaten, and in what relative amounts. The technique should improve clinical trials and nutrition studies. (Image, Lawrence A. David)

CAPTION

DNA Barcoding can now be used to identify what plants a person has eaten, and in what relative amounts. The technique should improve clinical trials and nutrition studies. (Image, Lawrence A. David)

CREDIT

Lawrence A. David, Duke University

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JOURNAL

Proceedings of the National Academy of Sciences

DOI

10.1073/pnas.2304441120 

METHOD OF RESEARCH

Observational study

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Diversity of Plant DNA in Stool is Linked to Dietary Quality, Age and Household Income

ARTICLE PUBLICATION DATE

27-Jun-2023

Illinois study reveals genetic secrets of America's favorite snack

Peer-Reviewed Publication

UNIVERSITY OF ILLINOIS COLLEGE OF AGRICULTURAL, CONSUMER AND ENVIRONMENTAL SCIENCES

 

IMAGE: MULTIPLE TYPES OF POPCORN ILLUSTRATE SOME OF THE GENOMIC DIVERSITY FOUND IN A UNIVERSITY OF ILLINOIS STUDY. THE RESULTS COULD FACILITATE FUTURE BREEDING EFFORTS TO CREATE YUMMIER AND EASIER-TO-GROW VERSIONS OF AMERICA'S FAVORITE SNACK. view more 

CREDIT: MADSEN SULLIVAN, UNIVERSITY OF ILLINOIS

URBANA, Ill. – In its simplest form, popcorn is pretty uncomplicated. Most supermarket varieties offer the choice of two kernel colors, yellow or white, and two kernel shapes, pointed or pearl. When popped, the flake typically expands into one of two shapes: mushroom or butterfly. But there’s more to popcorn than meets the eye. New research from the University of Illinois Urbana-Champaign reveals a wealth of untapped diversity lurking in popcorn’s genetic code.

Analyzing 320 publicly available popcorn lines, crop sciences researchers found variation at more than 308,000 locations across the genome. This diversity may or may not translate into more popcorn variety for consumers, but some of the differences could be important for improving the agronomic performance of the crop.

“This could be helpful if popcorn companies wanted to bring in material to diversify their germplasm, which is super important for things like disease resistance and herbicide tolerance. More work has to be done to identify traits of interest, but this dataset opens up those possibilities,” says study co-author Tony Studer, associate professor and popcorn breeder in the Department of Crop Sciences, part of the College of Agricultural, Consumer and Environmental Sciences at Illinois.

Studer’s team documented the genetic differences in a process known as genotyping by sequencing, which narrows the focus of genetic sequencing efforts to the most information-packed parts of the genome. Differences, or polymorphisms, among corn lines occurred at the level of single nucleotides, the building blocks of DNA.

Popcorn populations

Having identified hundreds of thousands of differences, the team could then group corn lines by patterns of single nucleotide polymorphisms (SNPs), allowing the researchers to make inferences about relatedness. According to the analysis, North American popcorns fall into two groups: One primarily composed of yellow pearl types, with white pointed and Latin American types falling into a second group.

“Grouping popcorn based on genetic similarities allows us to look at the diversity present in each group and better predict the performance of crosses between lines. In addition, if a gene is found to improve performance, knowing its group membership will help breeders incorporate it into their program, something I hope popcorn companies will take advantage of to improve their products both on the consumer side and the grower side,” says Madsen Sullivan, doctoral student in crop sciences and the study’s first author.

The results showed a high level of inbreeding among yellow pearl popcorns. That means lower genetic diversity and greater relatedness among that group. Although this has resulted in better popping traits, material from the other group will likely contain versions of genes that could be useful but are not present in the yellow pearl popcorns.

The analysis also provides a starting point from which to uncover popcorn’s long history of movement across North America and the world. Studer says the first people to consume corn likely ate it popped, not buttered on the cob. He’s working to trace popcorn’s early origins in a follow-up study.

Demystifying popcorn’s herbicide tolerance

With popcorn’s genetic code spelled out, the researchers were eager to tackle a longstanding mystery related to herbicide application labels. Nicosulfuron has been killing weeds in cornfields since the early 1990s, but it’s only labeled for yellow-kerneled hybrids; farmers are specifically warned against using it on white-kerneled popcorn.  

“That was a red flag to me, because kernel color should have nothing to do with herbicide sensitivity,” says co-author Marty Williams, USDA-ARS ecologist and affiliate professor of crop sciences at Illinois. “Kernel color is controlled by genes in a completely different part of the genome.”

Williams worked with Studer’s team to test 294 popcorn genotypes from both populations, the yellow pearl group and the white pointed and Latin American group; incidentally, neither group is exclusively yellow or white, despite their names. The researchers applied nicosulfuron to the test group as well as sensitive and tolerant popcorn and sweet corn hybrids as controls.

While nicosulfuron did injure more white-kerneled popcorns, the effect had nothing to do with kernel color itself. Instead, nicosulfuron sensitivity correlated with genetic heritage and population structure. The pointed and Latin American types were more sensitive than yellow pearls. In dent corn, nicosulfuron is detoxified by a gene known as nsf1. The researchers immediately looked for the same gene in popcorn, assuming it would be active in the tolerant genotypes.

“We expected nsf1 to come up in popcorn, but instead we found a whole different set of genes that seemed to relate to nicosulfuron tolerance,” Studer says. “That opens up the possibility of an alternate mechanism for herbicide tolerance in popcorn, and we’re planning to follow up on that.”

Next steps

Williams recommends popcorn breeders use this research to improve tolerance to nicosulfuron, and perhaps other herbicides, in their existing and new cultivars.  Then herbicide labels ultimately could be updated to reflect tolerance throughout the crop, regardless of kernel color.

Could the results of the genome study improve popcorn’s agronomic traits? Studer says it will take more work to screen the dataset for desirable traits, but eventually elite popcorn lines could be developed and marketed by popcorn companies.

The study, “Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response,” is published in Crop Science [DOI: 10.1002/csc2.21039]. Madsen Sullivan, Marty Williams, and Tony Studer are authors. The research received funding from the University of Illinois, and Sullivan was supported by a fellowship from the Illinois Corn Growers Association.

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JOURNAL

Crop Science

ARTICLE TITLE

Genetic diversity of North American popcorn germplasm and the effect of population structure on nicosulfuron response

 DICKENSIAN PHOBIA

Bias in health care: study highlights discrimination toward children with disabilities

Peer-Reviewed Publication

UNIVERSITY OF UTAH HEALTH

Children with disabilities, and their families, may face discrimination in in the hospitals and clinics they visit for their health care, according to a new study led by researchers at University of Utah Health. These attitudes may lead to substandard medical treatment, which could contribute to poor health outcomes, say the study’s authors.

“They mistreated her and treated her like a robot. Every single time a nurse walked in the room, they treated her like she was not even there,” said one mother who was interviewed about her child’s health care encounters.

The findings, published in the journal Pediatrics, are based on 30 in-depth interviews with family caregivers living in 15 states in the U.S. The children they looked after had medically complex conditions, with most needing health care more than 20 times each year. While the study did not measure how common it is for clinicians to show bias against children with disability, it exposes a serious problem that needs to be addressed, says lead author Stefanie Ames, M.D., a critical care physician at U of U Health.

“Our goal was to validate families’ experiences and bring awareness to the issue,” Ames says. She and the study’s senior author, Nancy Murphy, M.D., are faculty in the Department of Pediatrics at the Spencer Fox Eccles School of Medicine at the University of Utah. “Recognizing the problem is the first step.”

Causes and Consequences of Bias

Analysis of interviews with caregivers identified six recurring reasons for, and consequences of, health care provider bias against children with disability and complex medical conditions.

Family caregivers perceived that the main drivers of discrimination were:

• A lack of knowledge of how to care for children with complex medical needs
• A lack of interest in providing health care or medical interventions based on a perception that the child may not be worthy of care  
• Negative assumptions based on the child’s disability and quality of life

The interviews revealed that family caregivers felt that discrimination resulted in:

• Limited accommodations, for example for wheelchairs, making it difficult for children and their families to access health care
• Clinicians not providing the same health care and medical treatments to children with disabilities as they would for those without disabilities
• Clinicians dehumanizing children with disability and treating them differently than they would typically developing children 

According to family caregivers, these attitudes, at times, impacted patient care. One said that a doctor recommended against treating her daughter’s cancer despite there being a high chance of success that the treatment would work. Another parent indicated that health care providers did not give her child adequate pain relievers before carrying out an uncomfortable medical procedure.

“My perception is that [clinicians] wanted to take care of the patients that didn’t have a severe, special need… They just seemed like they didn’t even care to treat [my daughter],” said one child’s mother.

Ames and Murphy say the experiences of these families reveal an urgent need for additional medical training in caring for people with disability. The research team will be carrying out additional studies to determine how common these attitudes are nationally and whether they ultimately impact the health of children with complex medical needs.

“I believe that all healthcare providers choose this line of work because of the common goal of helping those in need,” Murphy says. “Yet when providers lack the knowledge, experience or resources to render care, we tend to shy away from situations. This tends to happen without our awareness, and this research brings this issue into clear view.”

# # #

The project was supported by a grant from the University of Utah Health Equity Research Core in the Woman and Child Institute and the Children and Youth with Special Healthcare Needs National Research Network.

In addition to Ames and Murphy, the study’s co-authors are Rebecca Delaney, Claudia Delgado-Corcoran, Justin Alvey, and Melissa Watt from U of U Health and Amy Houtrow from University of Pittsburgh. The research published as “Perceived disability-based discrimination in healthcare for children with medical complexity.”

About University of Utah Health

University of Utah Health  provides leading-edge and compassionate care for a referral area that encompasses Idaho, Wyoming, Montana, and much of Nevada. A hub for health sciences research and education in the region, U of U Health has a $458 million research enterprise and trains the majority of Utah’s physicians, and more than 1,670 scientists and 1,460 health care providers at its Colleges of Health, Nursing, and Pharmacy and Schools of Dentistry and Medicine. With more than 20,000 employees, the system includes 12 community clinics and five hospitals. U of U Health is recognized nationally as a transformative health care system and provider of world-class care.

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JOURNAL

PEDIATRICS

DOI

10.1542/peds.2022-060975 

METHOD OF RESEARCH

Survey

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Perceived Disability-Based Discrimination in Health Care for Children With Medical Complexity

ARTICLE PUBLICATION DATE

26-Jun-2023

Fear of being exploited is stagnating our progress in science

Peer-Reviewed Publication

THE POLISH ASSOCIATION OF SOCIAL PSYCHOLOGY

 

IMAGE: RESEARCHERS IN LABORATORY view more 

CREDIT: RHODA BAER / NATIONAL CANCER INSTITUTE

Science is a collaborative effort. What we know today would have never been, had it not been generations of scientists reusing and building on the work of their predecessors.

However, in modern times, academia has become increasingly competitive and indeed rather hostile to the individual researchers. This is especially true for early-career researchers yet to secure tenure and build a name in their fields. Nowadays, scholars are left to compete with each other for citations of their published work, awards and funding. 

So, understandably, many scientists have grown unwilling to cooperate and help their peers by sharing their work. They would “hide” their raw data, despite having taken years-long efforts to collect. They would also conceal experiments that have failed or proved insignificant. All these practices would then result in different teams wasting precious time in running the same useless studies, rather than making further progress and contributing to the world’s knowledge.

In the meantime, recent years have witnessed a growing global push for open science: a movement standing for and celebrating an extensive set of good practices founded on transparency, collaboration and sharing.

This is why a German team of social psychologists from the LMU Munich and the University of Marburg ran a series of studies with scientists from across Europe and North America, in order to find what is driving researchers to withhold knowledge from their colleagues. Their results were recently published in the open-access peer-reviewed scholarly journal Social Psychological Bulletin.

“Knowledge hiding is problematic, not only for the private economy, but also in academia. One might say that knowledge hiding in the scientific domain is even more problematic because science should be all about acquiring, scrutinising, and disseminating knowledge,”

explain the authors of the study.

“If scientists were inclined to hide what they know from their peers, then accumulating scientific knowledge would be impossible and instead of maximising the collective effort of discovering the truth, science would merely produce unconnected, insular, and probably non-replicable single effects.”

According to their findings, a specific personality trait called “victim sensitivity” predicted knowledge hiding in science. Researchers with this personality trait are characterised by a latent fear of being exploited by others and, thus, are more suspicious about their colleagues.

The research team also tested whether reminding the participants about their identity as a “researcher” might help or hinder collaboration. Their motivation to observe the impact of this approach is linked to prior studies, which showed that people are inclined to favour those belonging to their own group.

Surprisingly, though, when participants in one of the studies got their sense of identity as “researchers” activated, they actually became more suspicious and ready to hide their knowledge. One explanation for this would be that being reminded of being a “researcher” activated an obstructive self-stereotype: a researcher is a highly ambitious person, but is cold, rather than caring and cooperative.

The good news, point out the authors of the study, is that - among the participants - the intention to hide knowledge was rather low.

However, the authors warn about a potential bias. It is likely that researchers who volunteered to take part in these studies were more cooperative to begin with. Additionally, it might be that in the context of self-reporting, the participants tried to present themselves as more likeable.

“We may need to change the stereotypical way we think about ourselves as researchers, in order to build trust and create a sharing environment among scientists,"

concludes the research team. 

“Identifying as a researcher should include being cooperative, other-oriented, and trustworthy: a social identity that stands for knowledge sharing – not knowledge hiding.”

Research article:

Altenmüller, M. S., Fligge, M., & Gollwitzer, M. (2023). Among Us: Fear of Exploitation, Suspiciousness, and Social Identity Predict Knowledge Hiding Among Researchers. Social Psychological Bulletin, 18, 1-22. https://doi.org/10.32872/spb.10011

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JOURNAL

Social Psychological Bulletin

DOI

10.32872/spb.10011 

ARTICLE TITLE

Among Us: Fear of Exploitation, Suspiciousness, and Social Identity Predict Knowledge Hiding Among Researchers

DECRIMINALIZE DRUGS

Easier access to opioid painkillers may reduce opioid-related deaths

Peer-Reviewed Publication

RUTGERS UNIVERSITY

Increasing access to prescription opioid painkillers may reduce opioid overdose deaths in the United States, according to a Rutgers study.

“When access to prescription opioids is heavily restricted, people will seek out opioids that are unregulated,” said Grant Victor, an assistant professor in the Rutgers School of Social Work and lead author of the study published in the Journal of Substance Use and Addiction Treatment. “The opposite may also be true; our findings suggest that restoring easier access to opioid pain medications may protect against fatal overdoses.”

America’s opioid crisis has evolved across several waves, with each increasingly fatal. Wave one, which began in the 1990s, was associated with overdose deaths because of the misuse of opioid medications.

A policy implemented during the initial wave was the creation of prescription drug monitoring programs (PDMPs), state-based initiatives that track controlled substance prescribing. While the policy made it more difficult to access prescription opioids and rates of prescribing did decrease, it had the unintended consequence of pushing people toward off-market opioids, raising the risk of accidental death, said Victor.

This led to wave two of the crisis, a surge in heroin-related deaths, beginning around 2010, followed by wave three (which started in 2013), fueled by synthetic opioids such as fentanyl.

To measure trends and sociodemographic disparities in access to buprenorphine – a common treatment for opioid use disorder – and opioid painkillers, the researchers examined toxicology data, death records, and available PDMPs from 2,682 accidental overdose deaths that occurred from 2016 to 2021 in Indianapolis, Indiana.

The researchers found fewer than half of all decedents (43.3 percent) had a PDMP record of any kind, meaning they didn’t even try to access prescription opioids. Of the 10.6 percent that had been prescribed buprenorphine, most (64.7 percent) were prescribed treatment more than 30 days prior to death, suggesting they were not actively seeking treatment.

Victor and collaborators also found racial disparities in buprenorphine and opioid prescription trends, with dispersal for Blacks significantly lower than whites (7.3 percent and 21.9 percent versus 92.7 percent and 77.7 percent, respectively).

“Buprenorphine uptake is associated with significantly reduced rates of nonfatal and fatal overdose,” the researchers wrote. “Despite these positive treatment outcomes, several barriers remain to the widespread uptake of [medications for opioid use disorder] in the United States,” such as stigma and cost.

“For these reasons, a lack of adequate buprenorphine prescribing, combined with reductions in the availability of opioid analgesics, have left individuals contending with [opioid use disorder] at an elevated risk of overdose,” they concluded.

Given these trends and past research, Victor said it is time to re-evaluate policies that make it nearly impossible to obtain opioid prescriptions, even for those with a legitimate need.

“A big reason that we have such a problem with addiction in this country is because people can't access legitimate pain medication,” he said. “Our findings support a change in policy.”

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JOURNAL

Journal of Substance Use and Addiction Treatment

DOI

10.1016/j.josat.2023.209053 

METHOD OF RESEARCH

Data/statistical analysis

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Buprenorphine and opioid analgesics: Dispensation and discontinuity among accidental overdose fatalities in the Indianapolis metropolitan area, 2016–2021

ARTICLE PUBLICATION DATE

22-Jun-2023

Penn State researchers use ultrasound to control orientation of small particles

The demonstration has implications for drug delivery and bioprinting, according to scientists

Peer-Reviewed Publication

PENN STATE

 

IMAGE: PENN STATE BIOMEDICAL ENGINEERING GRADUATE STUDENT LEONARDO DOMINGUEZ RUBIO, LEFT, AND PENN STATE DOROTHY FOEHR HUCK AND J. LLOYD HUCK CHAIR PROFESSOR OF BIOMEDICAL ENGINEERING IGOR ARONSON ARE PART OF A TEAM THAT USED ULTRASOUND TECHNOLOGY AND A NOZZLE TO SEPARATE, CONTROL AND EJECT DIFFERENT PARTICLES BASED ON THEIR SHAPE AND VARIOUS PROPERTIES. view more 

CREDIT: PENN STATE COLLEGE OF ENGINEERING

UNIVERSITY PARK, Pa. — Acoustic waves may be able to control how particles sort themselves. While researchers have been able to separate particles based on their shape — for example, bacteria from other cells — for years, the ability to control their movement has remained a largely unsolved problem, until now. Using ultrasound technology and a nozzle, Penn State researchers have separated, controlled and ejected different particles based on their shape and various properties.  

They published their results in the journal Small.

“We engineered a microchannel nozzle and applied ultrasound energy to the system,” said corresponding author Igor Aronson, the Penn State Dorothy Foehr Huck and J. Lloyd Huck Chair Professor of Biomedical Engineering and professor of chemistry and of mathematics. “The nozzle plays two roles. It concentrates fluid flow, which is something other researchers have done. But in addition to that, the walls of the nozzle reflect the acoustic waves of the ultrasound energy.”

Aronson and his collaborators worked with tiny materials called nanorods, which are some of the most studied synthetic self-propelled particles, according to Aronson. Because they are a similar size and have a similar swimming speed to bacteria, Aronson said, many of the conclusions drawn from observing nanorods can be applied to bacteria movement. For this reason, they are often used as proof of concept for future separation tasks.

In this case, the nanorods were half platinum and half gold. The researchers placed the nanorods in a nozzle, shaped like a miniature syringe, and then added hydrogen peroxide. The hydrogen peroxide is decomposed — or burned — on the platinum half of each nanorod, forcing them to swim in an imitation of how bacteria behave. 

The researchers applied ultrasound to the nozzle, producing acoustic waves that, along with the flow of fluid, were able to separate the nanorod particles, aggregate them or extrude them from the nozzle. 

"The separation concept relies on the fact that nanorods and spherical particles have different responses to acoustic radiation and generated fluid flow,” Aronson said. “By controlling the nozzle shape and the frequency and amplitude of the acoustic radiation, we can coerce particles of different shapes and material properties to behave differently. This, especially, applies to active particles such as nanorods: They can swim autonomously, and their control is especially challenging.” 

This level of control in separating out particles had not been demonstrated previously, according to the researchers.

Aronson said this demonstration has implications for future technologies, including additive manufacturing, also known as 3D printing, and drug delivery.

“For 3D printing, the idea is you can add certain additives to the ink — for example, nanorods,” he said. “So now, we could separate nanorods from spherical particles to deposit only some in the printout, such as depositing polymers without nanorods and so on, all to change the property of the printout.”

Aronson said this principle also applies to printing living cells, known as bioprinting.

“Potential bioprinting applications may include designing acoustic nozzles for bio-inkjet-like printers,” he said. “By controlling the acoustic radiation in the nozzle, we can potentially extrude certain types of cells — for example, stem cells — and trap other types — for example, bacteria. It’s an additional control for bioprints.”

This capability could also be useful for separating bacteria from cells in targeted drug delivery, Aronson said. The researchers next plan to mix live bacteria and cells in a lab setting and then separate and control them. 

The paper’s other authors are Leonardo Dominguez Rubio, a graduate student in the Penn State Department of Biomedical Engineering; Ayusman Sen, the Verne M. Willaman Professor of Chemistry at Penn State; and Matthew Collins, who was a Penn State chemistry graduate student at the time of this work.

The U.S. Department of Energy supported this work.  

An image of the modeling depicts how the applied ultrasound orients nanorods in a microfluidic nozzle.

CREDIT

Provided by Igor Aronson

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JOURNAL

Small

DOI

10.1002/smll.202300028 

METHOD OF RESEARCH

Experimental study

SUBJECT OF RESEARCH

Not applicable

ARTICLE TITLE

Ultrasound Manipulation and Extrusion of Active Nanorods

The more stakeholders are included in policy planning, the better those policies protect them

Researchers pored over 108 groundwater management plans in California, finding those that incorporated stakeholder input offered greater protection from groundwater depletion

Peer-Reviewed Publication

UNIVERSITY OF CALIFORNIA - SANTA BARBARA

Having a seat at the table, and voices heard, makes a world of difference when it comes to natural resources. It sounds intuitive, but experts didn’t have enough data to prove it until now.

A team of researchers from across the country pored over 108 groundwater management plans in California to see how well they protect stakeholders like domestic well users, farmers and ecosystems. They found that the plans that incorporated stakeholder input offered greater protection from groundwater depletion. Unfortunately, only 9% of the sustainability plans integrated these users in a comprehensive manner.

The findings have broad implications for resource management, both in California and abroad. The authors published their independent analysis in Nature Communications. The data and findings from this study were shared with different stakeholders and organizations, who have used it to inform policy recommendations.

“It’s a big deal that we found empirical evidence that stakeholder integration leads to better protection,” said co-lead author Debra Perrone, an assistant professor in UC Santa Barbara’s Environmental Studies Program. “There are very few published papers that show this connection empirically.”

“I was pretty stunned,” added co-lead author Courtney Hammond Wagner, formerly a postdoctoral scholar at Stanford University and now at the U.S. Department of Agriculture. “I thought this was going to be a different paper.”

An ambitious aim

By 2014, more than a century of unregulated pumping in California had dried up wells, depleted aquifers and even sunk the ground level in many parts of the state. Meanwhile, the region was gripped by unprecedented drought. In dire straits, California passed the Sustainable Groundwater Management Act (SGMA), the first statewide effort to regulate groundwater resources.

Recognizing the complexity of the task at hand, the new legislation took a decentralized approach to groundwater management. The state tasked newly formed, local groundwater sustainability agencies with bringing their basins into balance within 20 years by reducing pumping or increasing groundwater recharge. Plans also needed to avoid undesirable results such as: 

• lowering groundwater levels; 
• losing groundwater storage; 
• seawater intrusion, 
• land subsidence; 
• deteriorating groundwater quality; 
• and losing streamflow.

If a local agency failed to meet the sustainability targets as set, the State Water Resources Control Board would step in to take the helm.

A bevy of groundwater sustainability plans have come out since SGMA was passed. But because planning is a local process, it wasn’t clear how the effort was adding up overall. To answer this question, co-lead authors Perrone, Wagner and Melissa Rohde worked in collaboration with a forum of NGOs tackling groundwater issues in California. Together, they evaluated how well the sustainability plans integrated and protected stakeholders.

Evaluating impact

The authors surveyed 108 management plans, encompassing more than 160,000 pages of text. They came up with a rubric to evaluate stakeholder integration across three groups: domestic users, agriculture and ecosystems. The authors looked at how informed stakeholders were, how much representation they had, and whether their water needs were integrated into the plans. Most importantly, they examined whether stakeholder input had an impact on the protection of wells and ecosystems in the final plan.

How well a plan protected various stakeholders depended on where it set the aquifer’s minimum thresholds, namely the lowest the water table can dip before potentially causing an undesirable result. Only wells deeper than the minimum threshold are protected by the management plan, and the same is true for plant roots in ecosystems. For the sake of caution, the authors also assumed that any well or ecosystem more than 1.5 miles away from a monitoring well was not protected.

Groundwater users and ecosystems are only protected by a management plan if their wells or roots extend below the minimum threshold the policy established for the underlying aquifer. Otherwise, their access to water can’t be guaranteed.

The study distills years of painstaking analysis. It took an entire summer to train the eight co-authors who combed through the lengthy technical documents, and another year and a half to actually go through the management plans.

“I was disappointed to see how many of the state’s wells and ecosystems are not being protected by SGMA,” said Rohde, an independent environmental consultant who worked at The Nature Conservancy during the study. A mere 9% of plans integrated all three stakeholder groups. The 108 management plans failed to protect 60% of agricultural wells, 63% of domestic wells and 91% of groundwater-dependent ecosystems. What’s more, 40% of the state’s wells and 87% of the state’s groundwater-dependent ecosystems are outside the basins regulated by SGMA.

These shortcomings were especially true for stakeholders with less political and economic power, like small farms and disadvantaged communities, terms that are defined by the state and federal governments. “Economically vulnerable groups were not only less integrated into the planning process, but they were also less protected,” Perrone said.

However, in the few cases where stakeholders were integrated into the planning process, management policies protected their interests rather well. “This suggests that if we can design our policies to more explicitly require stakeholder integration, we can likely get better outcomes for stakeholders,” Perrone explained.

“I did not think we would find a relationship between stakeholder integration and protection,” Wagner added, noting how many variables can affect a policy’s outcome: geography, climate, economics, demographics, etc. “And yet,” she said, “we still saw a strong indication that stakeholder integration was associated with better protection. That blew me away.”

Broad implications

SGMA was designed with adaptation in mind. Legislators knew it wouldn’t be perfect at first, so they built in opportunities to evaluate and improve. This study presents one such evaluation and offers the chance to correct course.

That said, the stakes are high. Farmers and communities are running out of water and ecosystems are in decline. So, if management plans aren’t protecting stakeholders, are they failing?

“SGMA is unfortunately not living up to its fullest intent, in the sense that a large majority of wells and ecosystems are not being protected by these groundwater sustainability plans,” Rohde said. “But, the results are also a reminder of how difficult it can be to fully engage diverse stakeholder groups with different needs and values, especially after a long legacy of groundwater depletion.”

“SGMA is a great example of how discretion is a double-edged sword,” Perrone added. “It offers a lot of flexibility, which is great for local control, but it’s at the cost of concrete guidance.”

“To correct course,” Rohde said, “state and local agencies need to be more intentional about ensuring that everyone is at the table and has the technical and financial resources to integrate their water needs into the plans.”

Sustainability policies are on the rise globally to address some of society’s tough challenges, such as climate change, biodiversity loss and natural resource depletion. “But in order to be successful, these plans must intentionally be inclusive of diverse stakeholder needs, especially those groups that have been disenfranchised or historically marginalized,” Rohde said.

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JOURNAL

Nature Communications

BU study unpacks how medical systems harm the intersex community

One of the first studies to highlight intersex peoples’ perspectives on their own medical care

Peer-Reviewed Publication

BOSTON UNIVERSITY SCHOOL OF MEDICINE

(Boston)— Intersex people’s (people whose sex characteristics do not fit within the strict binary categorizations of male or female) healthcare has received a lot of media attention recently, particularly with the uptick in anti-transgender legislation, which often also targets this community. Discrimination and mistreatment in social and medical settings, largely due to the stigma of not conforming to binary views of sex, results in many intersex individuals experiencing isolation, secrecy and shame, which can have a lasting impact on their mental health.

 

A new study from researchers at Boston University Chobanian & Avedisian School of Medicine highlights the need for a systemic shift in the way healthcare providers view intersex variations.

 

“This is a community that has been greatly harmed by the healthcare system and the false ideas that sex and gender exist as a strict binary. One such example is how many intersex infants and children are subject to non-consensual ‘normalizing’ genital surgeries, which have been shown to cause both physiological and psychological harm,” explains corresponding author Kimberly Zayhowski, MS, CGC, assistant professor of obstetrics and gynecology.

 

The researchers conducted and analyzed 15 interviews with members of the intersex community about their experiences with healthcare providers and perspectives on how their care could be improved. The study points to areas of healthcare where intersex people have experienced medical trauma and highlights the need for healthcare providers to use a trauma-informed approach. In their interviews, intersex people highlighted the need to normalize intersex variations and incorporate comprehensive teachings of intersex history and medical care into medical curricula to relieve the burden placed on patients to be their own medical experts and advocates.

 

According to the researchers, this study challenges the commonly held notion that sex exists as strictly male and female–an idea readily refuted by science but which is all too often defended through misrepresentation or misunderstanding of biology. The study also highlights the importance of bodily autonomy and trauma-informed care, which are frameworks that benefit everyone.

 

“This study has implications for the medical care of anyone with an intersex variation, also called variations of sex characteristics. Sometimes physicians will use the term ‘disorders of sex development’ (DSD) to describe intersex variations, but the intersex community has largely rejected this language because it is pathologizing,” says first author Darius Haghighat, MS, CGC, assistant professor of obstetrics and gynecology at the School.

 

The researchers believe that the study participants have been failed by a medical system that discriminated against, violated and misled them. “Systemic change is paramount to address these disparities, oppose abusive practices, and provide the care that the intersex community deserves,” adds Haghighat.

 

These findings appear online in the journal Social Science and Medicine.

 

Funding for this project was provided by Boston University’s Genetic Counseling Program. 

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DOI

10.1016/j.socscimed.2023.116047 

METHOD OF RESEARCH

Survey

SUBJECT OF RESEARCH

People

ARTICLE TITLE

Intersex People's perspectives on affirming healthcare practices: A qualitative study

ARTICLE PUBLICATION DATE

24-Jun-2023