Better pollen barcoding breaking down barriers to plant identification

"We're interested in pulling pollen off of bees, sequencing that pollen, and figuring out what the bees have been eating," says Emory biologist Berry Brosi. "We can start to construct networks between plants and pollinator species."

By Carol Clark

Pollen goes back about 491.2 million years, to the Devonian Period. Analysis of its traces have long been used to help solve mysteries related to the history of plants on Earth — from dating rocks for oil exploration to understanding the cultural practices of ancient peoples and investigating past habitats.

Now pollen analysis is poised to play an increasing role in solving modern-day mysteries, aided by gene-sequence libraries and advances in DNA barcoding, or the use of DNA to identify species. DNA metabarcoding enables the analysis of multi-species samples, if those species are contained in a gene-sequence reference library.

The Berry Brosi lab in Emory’s Department of Environmental Sciences recently expanded this gene-sequence library, adding a database for the rbcL gene to the already developed ITS2-gene library to improve the accuracy of plant species identification.

“We’re interested in pulling pollen off of bees, sequencing that pollen, and figuring out what the bees have been eating,” says Brosi, whose lab studies both managed honeybees and wild bees. “We can start to construct networks between plants and pollinator species.”

While Brosi is focused on bee research, pollen analysis contains temporal and spatial signatures that have the long-range potential for a broad range of applications, including forensic investigations. Examples include pinpointing the origin of an illicit drug, testing whether the marketing labels on products such as honey and olive oil match their actual geographic provenance, and determining whether the body of a murder victim had been moved.

The journal Applications in Plant Sciences published the work on the new rbcL library, and the database is publicly available.

“We chose rcbL because the length of the gene is readily applied to modern high-throughput sequencing methods,” says Karen Bell, who led the work as an Emory post-doctoral fellow.

The new rbcL library contains sequences from more than 38,400 plant species, adding to the ITS2 library of sequences from more than 72,000 species. After combining the two markers, the Brosi lab demonstrated that it could identify eight of nine plant species in a mixture, compared to only six species-level identifications based on ITS2 alone.

“Now you can simultaneously run a single analysis for both markers on the same sample,” Brosi says. “It’s a streamlined process that reduces false positives and false negatives coming back from the bioinformatics pipeline.”

If a plant species is not included in the reference library, however, it cannot be identified by DNA barcoding, so more sequences from the estimated 450,000 species of flowering plants must be added to make the pollen databases more comprehensive.

The Brosi lab tweaked the DNA metabarcoding bioinformatics pipeline to make it capable of using additional DNA barcodes once their databases have been developed. “The more genetic markers available,” Bell says, “the greater the chance of genetic identification.”

As the cost of genome sequencing comes down, researchers won’t be restricted to scanning the barcodes of small fragments of DNA either: “At some point in the future,” Bell says, “we’ll be doing DNA barcoding using whole plant genomes. The laboratory technology is available, but currently we don’t have enough complete plant genomes to make the databases.”

Another problem that the Brosi lab is working on is the fact that pollen samples are almost always mixed, and the current analytical methods are not quantitative. “We don’t know what the proportion of any species of pollen is within a sample,” Brosi says. “We’re currently trying to disentangle that problem.”

The Botanical Society of America contributed to this report. 

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For Emory students, 'a lifestyle approach to health'

First-year student Jessie Brightman participates in a class discussion in Health 200. Emory's peer-taught Health 1,2, 3 Program opens avenues for students to have stewardship of their own health. Emory Photo/Video

By April Hunt
Emory Report

If you’re going to change the way that college students talk about health, the first step is for students to do the talking.

It didn’t take long for Michelle Lampl to realize that. As director of Emory’s Center for the Study of Human Health, Lampl saw the success in a pilot “health partner” initiative conducted at the Center for Health Discovery and Well-Being, and turned it into the Human Health 1,2,3 Program for Emory College undergraduates.

The peer-taught program draws on the principles of predictive health and opens avenues for students to have stewardship of their own health. And, because Health 100 is required for every first-year Emory College student, the success of that foundational course has helped bolster student understanding of health.

“Emory is a leader in the paradigm shift in the science of health,” Lampl says. “Medicine is defined by disease. We focus on health. Our program is about changing the culture.”

Launched in 2012, human health is an interdisciplinary degree that has exploded in demand, from four majors its first year to 250 now. It has also attracted the notice of peer schools and beyond for its innovative approach that connects the liberal arts focus of Emory College with the groundbreaking research in public and global health sciences happening across the university.

Health 1,2,3 offers undergraduates the sort of education often reserved for graduate students: a framework to understand not only the science needed in health-related careers, but also the physical, mental and spiritual components of health.

Here’s how it works: All first-year students must take Health 100, which includes the study of timely health topics, such as getting enough sleep, and training for each student to set specific goals. 

Students who find Health 100 informative can enroll in Health 200, where they get training on the science of health and how to lead peers in discussions. Health 300 is the course where trained students become peer health partners for Health 100, overseeing the course with faculty supervision. 

“The way I describe it is, this is a lifestyle approach to health,” says Dylan Hurley, a first-year student who enrolled in Health 200 this spring.

“This is an integration of science and discussion, to make the concepts come to life,” Hurley adds. “That’s what makes it so essential.”

Read the whole article in Emory Report.

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The Peeps experiments: Science that never goes stale

It’s that time of year again: The sugary, squishy, neon-bright baby chicks and bunnies known as Peeps have reappeared and people are inexplicably eating them. Vox wrote a roundup of some of the best cultural phenomena concerning Peeps over the years. It included an excerpt from a classic Emory Report story from 1999, describing how Emory researchers Gary Falcon and James Zimring “performed perhaps the most exhaustive Peeps testing in human history," exploring the candies’ durability in the face of a variety of substances:

“To test Peep solubility, they began with simple tap water, then moved on to boiling water, then to acetone, sulfuric acid and sodium hydroxide, but were left dumbfounded by Peeps' apparent invulnerability to each.

“Then they tried Phenol, a protein-dissolving solvent lethal to humans in amounts as small as a single gram. Peeps proved mortal to such a substance — well, almost. One hour after plunging an unfortunate Peep into its grisly demise, all that remained in the beaker was a pair of brown carnauba wax eyes floating in a purple Phenol soup.”

Emory’s groundbreaking Peeps research lives on at peepresearch.org, including details of an investigation of the effects of smoking and alcohol on Peeps health and the medical miracle of separating quintuplet Peep siblings, conjoined at birth.

Small world, big impact: The Emory Global Health Institute

The Emory Global Health Institute helped fund a program in Haiti for those suffering from depression in communities ravaged by natural disaster and conflict. This photo, near the town of Hinche, was taken by Emory medical student Jesse Rappaport, one of the 2016 winners of the EGHI Global Health Student Photography Contest.

By Sylvia Wrobel
Emory Magazine 

The little boy died at home, without medical attention, before his fifth birthday. It happens to as many as one in five children in poor African and South Asian countries. The boy was deeply mourned, but never counted. His death was not noted in any registry. Except for a fever, no one had any idea why he died—information that might have been lifesaving for family members, or helped health officials recognize and address a widespread problem, or been the earliest indication of a smoldering epidemic.

In 2015, when the Bill and Melinda Gates Foundation wanted to learn why so many die young, they turned to the Emory Global Health Institute (EGHI) to lead the Child Health and Mortality Prevention and Surveillance Network (CHAMPS), designed to help high-child-mortality countries strengthen their capability to collect, analyze, interpret, and share data. Innovative methods include training local teams to visit families soon after a child dies,gathering information on symptoms and, with permission, taking small needle tissue biopsies, which when examined with specialized tools developed at the US Centers for Disease Control and Prevention (CDC) can identify the specific organisms causing illness and death.

“While we would think we have a pretty good idea of why children are dying—respiratory disease, enteric infections, fevers, and sepsis from different microorganisms—we don’t know those specific causes,” says Jeffrey Koplan, former director of the CDC and now Emory Vice President for Global Health and EGHI’s founding director. “There are a lot of different things that can cause respiratory failure. A lot of illnesses can lead to gastroenteritis and then death. The objective of this grant is to identify the specific causes of death so that we can develop programs to address them and save lives.”

CHAMPS is big: A $75 million investment for the first three years of a projected 20-year study, involving hundreds of partners at field sites and programmatic support from Emory, the CDC, and other Atlanta-based and international partners. But EGHI was created to serve as the mainframe for just such large-scale, long-term efforts—whether addressing high rates of maternal and childhood morbidity, understanding the spike of diabetes in developing nations, or increasing access to safe water.

Borders don’t mean much to infectious diseases, from shape-shifters like HIV and drug-resistant tuberculosis to sudden outbreaks like Ebola, SARS, or Zika. Chronic problems like diabetes and cardiovascular disease no longer belong primarily to richer, fatter nations but take an increasingly heavy toll on the economic stability, development, and even national security of developing nations, all with global impact.

Founded 10 years ago as the flagship program to expand Emory’s commitment to global health, EGHI is its own entity, university-wide, not part of any individual school. The organization is deliberately compact—a staff of ten, a cluster of offices, no big signs on the door. But its design—pragmatic, strategic, multidisciplinary, partner focused—gives it maximum flexibility in how to identify and tackle problems.

Read the whole article in Emory Magazine.

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How babies see faces: New fMRI methods open window into infants' minds

“We’ve provided the first neural evidence that our basic mechanisms for face and place recognition are in place in infancy and only a little weaker than that of adults,” says Emory psychologist Daniel Dilks.

By Carol Clark

The ancient philosophers Descartes, Aristotle and Plato are among those who have pondered variations on the question: How much of our brain and mind are we born with and how much comes from being in the world?

“It’s an age-old debate, and one that we’re still having because it’s one of the most difficult questions to answer,” says Emory psychologist Daniel Dilks. “You can’t do controlled experiments to fully test the question in humans because you would have to take away a person’s experiences.”

Modern-day techniques, such as functional magnetic resonance imaging, or fMRI, offer a window into neural activity. Subjects must remain perfectly still and alert during scanning, however, making it difficult to do experiments with very young children. As a result, most measurements of children’s neural activity only go back to age four, at the earliest.

Until now, that is. As a post-doctoral fellow at MIT, Dilks was part of a team that successfully scanned the brains of awake human infants using fMRI. The researchers wanted to learn whether infants used similar neural mechanisms as adults to visually distinguish specific types of input, such as faces and objects.

“Two thirds of the adult brain is involved in visual processing, so the origins of how we process visual stimuli is particularly important to understanding the brain and the mind,” Dilks says.

The researchers adapted fMRI technology to make it baby friendly. They built a special fMRI head coil – the receiving antenna of the scanner – that allows a subject to recline in what resembles an infant car seat. A mirror attached to the seat allows a baby to watch videos while in the scanner. The researchers also muffled the noise of the scanner.

Using this technology, and other modifications, they conducted fMRI experiments on babies just four to six months old. The babies watched movies of faces and places and other stimulus categories while in the scanner, as data was collected on their neural activity. Their responses were then compared to those of adults.

The results, published this year by Nature Communications, found that the visual cortex of the infants responded preferentially to the categories of faces and places, with a spatial organization similar to adults. The adult responses, however, were more sensitive.

“We’ve provided the first neural evidence that our basic mechanisms for face and place recognition are in place in infancy and only a little weaker than that of adults,” Dilks says.

The work adds to the growing evidence that babies do not come into the world as what the ancient philosophers referred to as tabular rasa, or blank slates.

“Thirty years ago, we thought that infants were basically little sponges, absorbing everything around them,” Dilks says. “We now know that babies are full of knowledge really early — and we’re learning that some of that knowledge is pretty complex. It’s a big paradigm shift.”

Dilks has brought the fMRI scanning technology for infants and children to Emory, where his lab will build on the research to learn more about the development of visual processing. One goal is to map the progression of the category-selective visual cortex from infancy to adulthood. In addition to adding to basic scientific knowledge, the research may one day have medical applications.

“We can’t fix most neurological problems right now, partly because we don’t know enough about the brain,” Dilks says. “By continuing to learn more about how the brain develops and functions normally, we may keep moving closer to being able to repair it when something goes wrong.”

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