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Men with HPV are 20 times more likely to be reinfected after one year

Tue, 12/05/2017 - 11:00
hpv

Human papilloma virus (Image by Jean-Yves Sgro, virology.wisc.edu/virusworld)

A new analysis of genital human papillomavirus (HPV) in men shows that infection with one HPV type strongly increases the risk of reinfection with the same type. In fact, men who are infected with the type responsible for most HPV-related cancers are 20 times more likely to be reinfected within one year. This increased risk suggests that infection confers no natural immunity against HPV, as is often the case with other viruses.

The study, published December 5 in the Proceedings of the National Academy of Sciences, highlights the importance of vaccination for preventing the spread of HPV in young men before they become sexually active. Vaccination could potentially prevent reinfection in older men who have already contracted the virus.

“Vaccinating boys before HPV exposure could be a highly effective way to reduce the burden of HPV infection. Vaccinating men who have already been infected might also be effective,” said Sylvia Ranjeva, a PhD student in the University of Chicago Department of Ecology and Evolution and the Pritzker School of Medicine, who led the study.

HPV is the most common sexually transmitted infection. Approximately 40 percent of women and 45 percent of men in the United States are infected, and it is a major cause of genital warts and cancers of the genitals, mouth and throat. There are more than 200 genetically-distinct HPV types; vaccines protect against four to nine of the most common, disease-causing types.

Ranjeva and her UChicago colleagues, including Greg Dwyer, PhD, professor of ecology and evolution and Sarah Cobey, PhD, assistant professor of ecology and evolution, wanted to understand what allowed so many different types of HPV to coexist. They analyzed data regarding the spread of the disease from the HPV in Men study, which tracked more than 4,000 unvaccinated men from three cities in Florida, Mexico and Brazil over five years from 2005 to 2009.

Usually, diversity of so many types of viruses happens as they compete to evolve different ways to evade the immune defenses of hosts. The new analysis showed no evidence of such competition among HPV types, however. Instead, the diversity of HPV types may stem from recurring infections of particular types within individuals. While relatively few people are infected with any one type, the high overall HPV prevalence occurs because nearly half the adult population carries at least one type of genital HPV. The high risk of reinfection may be due to either auto-inoculation, spreading the infection by repeated contact between different sites on the body, or reactivation of a latent virus.

The results also show that men who are infected once with HPV16, the type responsible for most HPV-related cancers, are at 20 times higher risk of reinfection after one year, and 14 times higher after two years. The researchers saw the same effect in both men who are sexually active and celibate, suggesting that they are not reacquiring the virus from another sexual partner.

“That’s what makes this a biologically significant result,” Ranjeva said. “The best thing we can do is prevent the initial infection by vaccinating boys before sexual contact. However, if the increased risk of reinfection is due to auto-inoculation, then another effective strategy may be to vaccinate previously infected men as well.”

The study, “Recurring infection with ecologically distinct human papillomavirus (HPV) types explains high prevalence and diversity,” was supported by the National Institutes of Health. Additional authors include Edward Baskerville from the University of Chicago; Vanja Dukic and Anna Giuliano from the H. Lee Moffitt Cancer Center; Luisa Villa from Universidade de Sao Paulo, Brazil; and Eduardo Lazcano-Ponce from Instituto Nacional de Salud Publica, Cuernavaca, Mexico.

Researchers receive $500,000 grant to study the “microbiome of death”

Fri, 11/17/2017 - 11:55
Jack Gilbert

Jack Gilbert (Photo: Andrew Collings)

Bacteria surround us everywhere we go. They inhabit every corner of our world, from the places we work and live to the insides of our own bodies. They play an enormous role in our health and well-being, from the development of disease and allergies to how we respond to medicine—and they have the final say in death as well.

Jack Gilbert, faculty director of the Microbiome Center at the University of Chicago, and Gulnaz Javan, a forensic scientist from Alabama State University, received a two-year, $532,000 grant from the National Institute of Justice to study the thanatomicrobiome, or “microbiome of death.” The term was coined by Javan to describe the collection of microbes from internal organs collected during criminal casework. The project will develop tools to help determine the time and cause of death by identifying patterns of bacterial growth in a corpse’s internal organs after death.

Previous work by Gilbert in 2016 showed how bacteria can help pinpoint the time and place of death, but he and Javan also want to see how stress on the body at the time of death leaves a unique signature on microbiota in the organs. The team will work with cadavers from national morgues in Montgomery, Ala., and Pensacola, Fla., plus an international morgue in Tampere, Finland, the largest morgue in that country. They will also explore relationships with morgues in Italy to increase the size and diversity of human corpses and organs that can be studied.

“The aim of this study is to determine whether we can calculate the time of death based on the bacteria that have escaped their normal body habitats and invaded internal organs” Gilbert said. “Once the body dies, the immune system fails and your microbiome is set free – we can track how the microbes migrate by examining the organs of hundreds of bodies.”

The team also hopes to determine if the microbial signature of the organs has any predictive ability when it comes to determining how the individual died.

“We have samples from natural deaths through murders, and we expect to be able to find a signature of how the person died based on the specific bacteria that colonize the organs first,” Gilbert said.

The study will run from January 2018 through December 2019.


Tagged: Biological Sciences, crime investigation, death, decomposition, forensics, Jack Gilbert, Microbiology, microbiome

How a “flipped” gene helped butterflies evolve mimicry

Tue, 11/07/2017 - 11:00
swallowtail butterflies

Several different swallowtail butterfly variations showing mimicry and polymorphism, or different forms of the same species. In the center, a female Papilio polytes that mimics another species that is toxic to predators. (Credit: Matt Wood)

Female swallowtail butterflies do something a lot of butterflies do to survive: they mimic wing patterns, shapes and colors of other species that are toxic to predators. Some – but not all – swallowtail species have evolved several different forms of this trait. But what kind of genetic changes led to these various disguises, and why would some species maintain an undisguised form when mimicry provides an obvious evolutionary advantage?

In a new study published this week in Nature Communications, scientists from the University of Chicago analyze genetic data from a group of swallowtail species to find out when and how mimicry first evolved, and what has been driving those changes since then. It’s a story that started around two million years ago, but instead of steady, progressive changes, one chance genetic switch helped create the first swallowtail mimics. And it has stuck around ever since.

“In butterflies with one color pattern, we have a gene in a normal orientation on the chromosome. In the butterflies with the unusual, alternate color pattern, that gene was spliced out, flipped, and then spliced back into the chromosome at some point,” said Marcus Kronforst, PhD, associate professor of ecology and evolution at UChicago and the senior author of the study.

“That flip, or inversion, keeps the two genes from recombining if those two different kinds of butterflies mate, so they’ve kept both copies of the gene over evolutionary time, since they split from their common ancestor two million years ago,” Kronforst said.

For a long time, scientists thought that butterfly mimicry was controlled by “supergenes,” groups of several tightly linked genes that were always inherited as a group. In a 2014 study, Kronforst and his colleagues showed what appears to be a supergene is actually a single gene called doublesex that controls the different color patterns and shapes we see in female swallowtails.

The doublesex gene was already well-known for its role in differentiating between sexes, but in females the inverted, or flipped, version also dictates wing patterns. It can still be thought of as a supergene because it controls the entire, complex process of wing patterning, but in this case, it is just the single gene.

In the new study, led by postdoctoral fellow Wei Zhang, PhD, the team analyzed whole-genome sequence data form Papilio polytes, the Asian swallowtail butterfly, and several similar species to see how they are related to each other, and how their copies of doublesex compare. Using these data, the team compared some alternative explanations for the origins of mimicry and identified key factors that have maintained different forms of mimicry long-term.

swallowtail butterflies

Several different swallowtail butterfly variations showing mimicry and polymorphism, or different forms of the same species. Row 1: A female and male Papilio protenor, the species that is closely related to Papilo polytes, the focal of the new study. In P. protenor, males and female look the same and they do not mimic. Row 2: Papilio ambrax, a species where males and females look different and the female is a mimic. In this species, there is no female polymorphism. The new study shows that its evolutionary ancestor was polymorphic, but females lost that train and only display the mimetic form. Row 3: Polymorphic Papilio polytes, (L-R) A mimetic female form (one of 3 mimetic forms in this species), a non-mimetic female, and the male. Row 4: A distantly related swallowtail, Pachliopta aristolochiae. This is the toxic species that the species in the new study mimic. (Credit: Matt Wood)

The most closely related species to the P. polytes group, called Papilio protenor, is spread across mainland Asia from India to Japan and did not develop mimicry—both males and females look alike. Other species that spread from the mainland to islands in the Philippines and Indonesia developed three or four distinct forms, a feature known as polymorphism. Still other swallowtail species spread further to Papua New Guinea and the northeast coast of Australia, but those females display only one disguised wing pattern.

The researchers compared the patterns they saw in the genome sequence data to some possible explanations for how these patterns of mimicry developed over time and geography. Did mimicry evolve independently in different species at different points in time? Did it evolve in one species, and then spread through cross-breeding or hybridization?

It appears that mimicry actually has a single ancient origin, when the doublesex gene flipped two million years ago. Since that initial inversion, Zhang and Kronforst did see signs of what’s known as balancing selection. When one type of butterfly becomes more common, predators realize they aren’t toxic and start to feed on them. This reduces the number of that particular butterfly, until another one becomes more common, and so on. Eventually this process balances out and preserves the relative number of each form.

They also saw that some butterfly populations have maintained multiple female forms for millions of years, while others lost the original, undisguised form. Historically, the smallest groups—e.g. the ones that spread the furthest to Australia—lost the polymorphism, allowing random genetic drift and natural selection to weed out the original form.

The researchers also looked at what maintained polymorphism over time. One cause could be sexual selection, that males prefer certain female color patterns over another. Previous research on mating behavior doesn’t back up that idea though. Another possibility is “crypsis,” or the idea that undisguised females blend into their natural surroundings better than the mimics. Kronforst and the team tested that hypothesis by comparing mimetic and non-mimetic females against a green forest background using models for predator (i.e. bird) vision. The non-mimetic, undisguised females actually don’t blend in to the background any more than mimics, so this idea is out too.

swallowtail butterflies

Several different swallowtail butterfly variations showing mimicry and polymorphism, or different forms of the same species. Row 1: A female and male Papilio protenor, the species that is closely related to Papilo polytes, the focal of the new study. In P. protenor, males and female look the same and they do not mimic. Row 2: Papilio ambrax, a species where males and females look different and the female is a mimic. In this species, there is no female polymorphism. The new study shows that its evolutionary ancestor was polymorphic, but females lost that train and only display the mimetic form. Row 3: Polymorphic Papilio polytes, (L-R) A mimetic female form (one of 3 mimetic forms in this species), a non-mimetic female, and the male. Row 4: A distantly related swallowtail, Pachliopta aristolochiae. This is the toxic species that the species in the new study mimic. (Credit: Matt Wood)

Those two findings, combined with the genomic sequence data, led the researchers to start thinking about another intriguing possibility. It could be that the genetic changes that led to mimicry in the first place also built in some long-term disadvantages. When the original doublesex gene inverted, it probably carried a bunch of other unrelated genetic material with it. Since the flipped doublesex gene can’t be recombined with its original version, the extra stuff has “hitchhiked” ever since—and it could have consequences. In fact, some research shows that female mimics don’t live as long as standard ones.

“We think a bunch of differences were accidentally captured when one copy of the gene flipped and became the mimetic copy. Because a lot of those changes are functional, they could be detrimental to health,” Kronforst said.

“The idea is that you have this hardwired disadvantage to mimicry. The standard females don’t have the protection of mimicry, but they also don’t have this inherent genetic cost and these two things offset one another” he said.

Now that they have unraveled some of the history behind the evolution of mimicry, Kronforst said his team wants to start looking for the specific genetic mutations on doublesex that cause different kinds of mimicry.

“If we can find ways to piece through all the differences that we see, we should be able to narrow it down to something much more discrete than all the differences we see now,” he said.

The study, “Tracing the origin and evolution of supergene mimicry in butterflies,” was supported by University of Chicago Neubauer research funds, a Pew Biomedical Scholars Fellowship, the National Science Foundation and the National Institutes of Health. Additional authors include Erica Westerman from the University of Arkansas, along with Eyal Nitzany and Stephanie Palmer from the University of Chicago.


Tagged: Biological Sciences, butterflies, Evolution, Genetics, insects, Marcus Kronforst, mimicry

Mapping the microbiome of… everything

Wed, 11/01/2017 - 13:00
earth-microbiome-egg-swab

Swabbing bird eggshells from Spain (photo credit: Juan M. Peralta-Sánchez).

In the Earth Microbiome Project, an extensive global team co-led by researchers at University of California San Diego, Pacific Northwest National Laboratory, University of Chicago and Argonne National Laboratory collected more than 27,000 samples from numerous, diverse environments around the globe. They analyzed the unique collections of microbes — the microbiomes — living in each sample to generate the first reference database of bacteria colonizing the planet. Thanks to newly standardized protocols, original analytical methods and open data-sharing, the project will continue to grow and improve as new data are added.

The paper describing this effort, published November 1 in Nature, was co-authored by more than 300 researchers at more than 160 institutions worldwide.

The Earth Microbiome Project was founded in 2010 by Rob Knight, PhD, professor and director of the Center for Microbiome Innovation at UC San Diego; Jack Gilbert, PhD, professor and faculty director of The Microbiome Center at University of Chicago and group leader in Microbial Ecology at Argonne National Laboratory; Rick Stevens, PhD, associate laboratory director at Argonne National Laboratory and professor and senior fellow at University of Chicago; and Janet Jansson, PhD, chief scientist for biology and laboratory fellow at Pacific Northwest National Laboratory. Knight, Gilbert and Jansson are also co-senior authors of the Nature paper and Stevens is a co-author.

“The potential applications for this database and the types of research questions we can now ask are almost limitless,” Knight said. “Here’s just one example — we can now identify what kind of environment a sample came from in more than 90 percent of cases, just by knowing its microbiome, or the types and relative quantities of microbes living in it. That could be useful forensic information at a crime scene… think ‘CSI.’”

earth-microbiome-monkeys

Trachypithecus francoisi adult female and infant, a colobine monkey from China, whose fecal microbiome was sampled for this study (photo credit: Kefeng Niu).

The goal of the Earth Microbiome Project is to sample as many of the Earth’s microbial communities as possible in order to advance scientific understanding of microbes and their relationships with their environments, including plants, animals and humans. This task requires the help of scientists from all over the globe. So far the project has spanned seven continents and 43 countries, from the Arctic to the Antarctic, and more than 500 researchers have contributed to the sample and data collection. Project members are using this information as part of approximately 100 studies, half of which have been published in peer-reviewed journals.

“Microbes are everywhere,” said first author Luke Thompson, PhD, who took on the role of project manager while a postdoctoral researcher in Knight’s lab and is currently a research associate at the National Oceanic and Atmospheric Administration (NOAA). “Yet prior to this massive undertaking, changes in microbial community composition were identified mainly by focusing on one sample type, one region at a time. This made it difficult to identify patterns across environments and geography to infer generalized principles.”

earth-microbiome-antarctica

Researcher sampling the southernmost geothermal soils on the planet at the summit of Mt Erebus, Ross Island, Antarctica (photo credit: S. Craig Cary, Univ. of Waikato, New Zealand).

Project members analyze bacterial diversity among various environments, geographies and chemistries by sequencing the 16S rRNA gene, a genetic marker specific for bacteria and their relatives, archaea. The 16S rRNA sequences serve as “barcodes” to identify different types of bacteria, allowing researchers to track them across samples from around the world. Earth Microbiome Project researchers also used a new method to remove sequencing errors in the data, allowing them to get a more accurate picture of the number of unique sequences in the microbiomes.

Within this first release of data, the Earth Microbiome Project team identified around 300,000 unique microbial 16S rRNA sequences, almost 90 percent of which don’t have exact matches in pre-existing databases.

Pre-existing 16S rRNA sequence are limited because they were not designed to allow researchers to add data in a way that’s useful for the future. Project co-author Jon Sanders, PhD, a postdoctoral researcher in Knight’s lab compares the difference between these other databases and the Earth Microbiome Project to the difference between a phone book and Facebook. “Before, you had to write in to get your sequence listed, and the listing would contain very little information about where the sequence came from or what other sequences it was found with,” he said. “Now, we have a framework that supports all that additional context, and which can grow organically to support new kinds of questions and insights.”

earth-microbiome-puerto-rico

Hiking through the rain forest of Puerto Rico to sample soils with students (photo credit: Krista McGuire)

“There are large swathes of microbial diversity left to catalogue. And yet we’ve ‘recaptured’ about half of all known bacterial sequences,” Gilbert said.  “With this information, patterns in the distribution of the Earth’s microbes are already emerging.”

According to Gilbert, one of the most surprising observations is that unique 16S sequences are far more specific to individual environments than are the typical units of species used by scientists. The diversity of environments sampled by the Earth Microbiome Project helps demonstrate just how much local environment shapes the microbiome. For example, the skin microbiomes of cetaceans (whales and dolphins) and fish are more similar to each other than they are to the water they swim in; conversely, the salt in saltwater microbiomes makes them distinct from freshwater, but they are still more similar to each other than to aquatic animal skin. Overall, the microbiomes of a host, such as a human or animal, were quite distinct from free-living microbiomes, such as those found in water and soil. For example, the free-living microbiomes were far more diverse, in general, than host-associated microbiomes.

“These global ecological patterns offer just a glimpse of what is possible with coordinated and cumulative sampling,” Jansson said. “More sampling is needed to account for factors such as latitude and elevation, and to track environmental changes over time. The Earth Microbiome Project provides both a resource for the exploration of myriad questions, and a starting point for the guided acquisition of new data to answer them.”

EMP-infographic

Story provided by the University of California San Diego

For more about the Earth Microbiome Project, visit http://earthmicrobiome.org and follow @earthmicrobiome on Twitter. For the complete list of co-authors and institutions participating in the Earth Microbiome Project, view the full paper at Nature.

The project was funded, in part, by the John Templeton Foundation, W. M. Keck Foundation, Argonne National Laboratory, Australian Research Council, and Extreme Science and Engineering Discovery Environment, which is supported by National Science Foundation (ACI-1053575).

Data collected and analyzed in the Earth Microbiome Project have already been used in many studies of:


Tagged: Biological Sciences, earth microbiome project, ecology, ecology and evolution, environment, Jack Gilbert, Microbiology, microbiome

Flu forecasting tool uses evolution to make earlier predictions

Wed, 10/25/2017 - 13:00

Flu shot

Each year, public health officials monitor the spread of influenza to identify which flu strains need to go into that year’s vaccines and where outbreaks will occur. But it can be difficult to predict how bad a particular flu season will be until people actually start getting sick.

A new flu forecasting tool built by scientists at the University of Chicago aims to make better predictions by combining data about how the virus spreads with an estimate of how much the current virus evolved compared to recent years. Using historical data as a test, the new model accurately predicted the total number of cases for each season in the U.S. from 2002 to 2016, and produced an accurate, real-time prediction for the 2016-17 season before it started last year.

The researchers say the new model, described this week in Science Translational Medicine, can be used to complement existing forecasting tools that track flu outbreaks in real time by providing an early warning before the season starts.

“Combining information about the evolution of the virus with epidemiological data will generate disease forecasts before the season begins, significantly earlier than what is currently possible,” said Mercedes Pascual, PhD, professor of ecology and evolution at UChicago and senior author of the study. “You could imagine using our model to make an early prediction about overall severity of the season, and then use other methods to forecast the timing of the outbreak once it begins.”

Each year, four influenza strains circulate in the human population: H3N2, H1N1, and two B variants. These viruses spread seasonally each year because of a phenomenon known as antigenic drift. They evolve just enough to evade human immune systems, but not enough to develop into completely new versions of the virus.

If the virus changed a lot, more people get sick because they haven’t been exposed to that particular variation. But most flu forecasting models don’t factor in this change. Instead, they are based on mathematical calculations of how quickly the virus is spreading—and these projections can’t be made until the current season is already underway.

Factoring in evolution

For the new model, Pascual and Xiangjun Du, PhD, a postdoctoral fellow at UChicago who led the study, analyzed genetic sequences from previous years of the H3N2 virus. They then compared them to early samples of the current virus that were collected before the season started each year. This allowed them to create an evolutionary index for the current virus, or a measure of how much it changed. Adding this crucial piece of information to the new model generates an early estimate of the overall severity of the coming flu season, because they can make a projection as soon as current year’s variation of the virus starts to emerge in the spring and summer.

“Every two or three years, there is a big genetic change in the virus, which can make many more people sick,” Du said. “Without factoring evolution into the model, you cannot capture these peaks in the number of cases.”

The model was built with historical data about the H3N2 virus, although it could be adapted for other strains of flu. The researchers tested its accuracy by seeing how well it predicted past seasons from 2002-2016, including years that weren’t used to initially calibrate the tool (the final five from 2011-2016). It generated accurate estimates of the overall number of cases in the U.S. for each year, and produced an accurate forecast for the 2016-17 season before it started last fall.

So, what’s in store for this flu season?

“That’s the million-dollar question,” Pascual said. “Our analysis for this year showed that the virus is already changing in a significant way. We predict an outbreak that is above average but moderate, not severe, because last year was such a bad season.”

The study, “Evolution-informed forecasting of seasonal influenza A (H3N2),” was supported by the University of Chicago. Additional authors include Aaron A. King and Robert J. Woods from the University of Michigan, who were supported by the National Institutes of Health, the National Institute of General Medical Sciences and the National Institute of Allergy and Infectious Diseases.


Tagged: Biological Sciences, epidemiology, Flu, influenza, Mercedes Pascual, public health, vaccination, Xiangjun Du

What soot-covered, hundred-year-old birds can tell us about saving the environment

Mon, 10/09/2017 - 14:00
horned-larks-10

Horned Larks collected in Illinois between 1904 and 1916 (left) and California and British Columbia between 1903 and 1922 (right). (Photo: Carl Fuldner and Shane DuBay)

Horned Larks are cute songbirds with white bellies and yellow chins—at least, now they are. One hundred years ago, at the height of urban smoke pollution in the United States, their pale feathers were stained dark gray by soot in the atmosphere.

A new paper in the Proceedings of the National Academy of Sciences shows that the discoloration of these birds in museum collections can be used to trace the amount of black carbon in the air over time and measure the effects of environmental policy on pollution.

“The soot on these birds’ feathers allowed us to trace the amount of black carbon in the air over time,” said study author Shane DuBay, a graduate student in the Committee on Evolutionary Biology at the University of Chicago and The Field Museum. “We found that the air at the turn of the century was even more polluted than scientists previously thought.

DuBay and study co-author Carl Fuldner, a graduate student in the Department of Art History at UChicago, analyzed more than a thousand birds collected over the last 135 years to determine and quantify the effects of soot in the air over cities in the Rust Belt.

“If you look at Chicago today, the skies are blue. But when you look at pictures of Beijing and Dehli, you get a sense for what U.S. cities like Chicago and Pittsburgh were once like,” DuBay said. “Using museum collections, we were able to reconstruct that history.”

red-headed-woodpeckers-field-museum

Red-headed Woodpeckers from the specimen collection at The Field Museum, Chicago. (Photo: Carl Fuldner and Shane DuBay)

Flying air filters

Ornithologists at The Field Museum have long known that bird specimens in the collection from the early 1900s were visibly darker than expected, and atmospheric soot was the suspect.

“When you touch these birds, you get traces of soot on your hands. We’d wear white gloves while handling them, and the gloves would come away stained, like when you get ink on your fingertips reading a newspaper,” DuBay said, because the soot in the air clung to the birds like dust to a feather duster. “These birds were acting as air filters moving through the environment.”

Birds were also ideal candidates for the study because they molted and grew new sets of feathers every year, meaning that the soot on them had been accumulating only for the past year when they were collected. And there was an apparent trend: old birds were dirtier, and new birds were cleaner.

To measure the changes in sootiness over the years, the pair of researchers turned to a novel approach: photographing the birds and measuring the light reflected off of them. Fuldner, a photo historian who focuses on images of the environment, worked with DuBay to develop a method for analyzing the birds using photography.

Carl Fuldner and Shane DuBay talk about their work in a video from UChicago Arts

The birds photographed for the study, numbering over a thousand, were all from five species that bred in the Manufacturing Belt and have lots of white feathers that show off soot. The images, depicting the contrast between the soiled gray birds and the clean white ones, are dramatic.

“The photographs give the project a visceral dimension—you make a connection to the images,” Fuldner said.

The two researchers plotted the amount of light bouncing off the feathers according to the year the birds were collected. To make sense of their findings, they then delved into the social history of urban air pollution.

“The changes in the birds reflect efforts, first at the city level but eventually growing into a national movement, to address the smoke problem,” Fuldner said. “We are actually able to go back and see how effective certain policy approaches were.”

“We were surprised by the precision we were able to achieve,” DuBay said. “The soot on the birds closely tracks the use of coal over time. During the Great Depression, there’s a sharp drop in black carbon on the birds because coal consumption dropped—once we saw that, it clicked.”

The amount of soot on the birds rebounded around World War II, when wartime manufacturing drove up coal use. Then it dropped off quickly after the war, around when people in the Rust Belt began heating their homes with natural gas piped in from the West rather than with coal.

“The fact that the more recent birds are cleaner doesn’t mean we’re in the clear,” DuBay said. “While the U.S. releases far less black carbon into the atmosphere than we used to, we continue to pump less-conspicuous pollutants into our atmosphere—those pollutants just aren’t as visible as soot. Plus, many people around the world still experience soot-choked air in their cities.”

field-sparrrows

Field Sparrows collected in Joliet, Ill., in 1906 (top) and Chicago in 1996 (bottom). (Photo: Carl Fuldner and Shane DuBay)

Filling in a blank space in the historical record

Analysis of atmospheric black carbon might assist scientists studying climate change. “We know black carbon is a powerful agent of climate change, and at the turn of the century, black carbon levels were worse than previously thought,” DuBay said. “I hope that these results will help climate and atmospheric scientists better understand the effects of black carbon on climate.”

DuBay and Fuldner initially teamed up through a Graduate Collaboration Grant from the Arts, Science + Culture Initiative at UChicago, which encourages independent trans-disciplinary research between students in the arts and sciences. Both said that being able to apply their research beyond their respective fields of evolutionary biology and photographic history was both unexpected and rewarding.

“As a historian, one of the questions I always ask is, ‘What is the point of this research to the way we live now?’ In this case the answer quickly became clear,” Fuldner said. “Filling in a blank space in the historical record of something as large as air pollution in American cities, and being able to share that with atmospheric scientists who study the effects of black carbon on the climate, is extraordinary.”

“This study shows a tipping point when we moved away from burning dirty coal, and today, we’re at a similar pivotal moment with fossil fuels,” DuBay said. “In the middle of the 20th century, we made an investment in infrastructure and regulated fuel sources—hopefully, we can take that lesson and make a similar transition now to more sustainable, renewable energy sources that are more efficient and less harmful to our environment.”

DuBay notes that in addition to the environmental implications of the project, their work also shows the importance of museum collections like those they used from The Field Museum in Chicago, the Carnegie Museum of Natural History in Pittsburgh, and the University of Michigan Museum of Zoology in Ann Arbor.

“I hope this study exposes collections as a valuable resource to address present day environmental concerns,” he said. “This paper shows the ways that natural history collections can be used, underlining the value in collections and in continuing to build collections, to help us improve our understanding of human impacts on the natural world.”

Story provided by Kate Golembiewski at The Field Museum


Tagged: air pollution, Biological Sciences, birds, carbon emissions, Carl Fuldner, climate change, Field Museum, photography, pollution, Shane DuBay

UChicago scientists receive NIH Director’s high-risk research awards

Thu, 10/05/2017 - 12:01

20140605_5757University_7730

Three University of Chicago researchers received awards from the National Institutes of Health’s High-Risk, High-Reward Research program. Part of the NIH Common Fund, the program funded 86 awards to exceptionally creative scientists proposing to use highly innovative approaches to tackle major challenges in biomedical research. It supports high-risk ideas with high-impact potential, such as building imaging platforms to monitor genetic processes at a molecular level, identifying immune system proteins that can detect tumors, and creating new chemicals to target genetic factors that lead to disease.

The program accelerates scientific discovery by supporting high-risk research proposals that may not fare well in the traditional peer review process despite their potential to advance the field. Applicants of the program are encouraged to think outside-the-box and to pursue exciting, trailblazing ideas in any area of research relevant to the NIH mission.

“I continually point to this program as an example of the creative and revolutionary research NIH supports,” said NIH Director Francis S. Collins, MD, PhD. “The quality of the investigators and the impact their research has on the biomedical field is extraordinary.”

The NIH Common Fund supports a series of exceptionally high-impact programs that cross NIH Institutes and Centers. Common Fund programs pursue major opportunities and gaps in biomedical research that require trans-NIH collaboration to succeed.

The High-Risk, High-Reward Research program manages four awards. The three UChicago faculty members received the NIH Director’s New Innovator Award, established in 2007, which supports unusually innovative research from early career investigators who are within 10 years of their final degree or clinical residency and have not yet received a research project grant or equivalent NIH grant:

Jingyi Fei, PhDJingyi Fei, PhD

Project Title: Quantitative Imaging of Epitranscriptomic Regulation Mediated by RNA Modification

Jingyi Fei is an Assistant Professor in the Department of Biochemistry and Molecular Biology and the Institute for Biophysical Dynamics at The University of Chicago. Her research has been focused on RNA-mediated gene regulations, including trans-acting small regulatory RNAs in bacterial systems, and RNA internal modifications in eukaryotic systems, with the development and application of new imaging methods.

Seungmin Hwang, PhD

Seungmin Hwang, PhD

Project Title: Targeting by Autophagy Proteins for Anti-Tumor Immunity

Seungmin Hwang is an Assistant Professor in the Department of Pathology at the University of Chicago. The focus of his research group has been understanding the function of the ubiquitin-like conjugation system of the autophagy pathway in sensing and destroying the vacuole-like shelters of intracellular pathogens, expanding this research subject into antitumor immunity.

Raymond Moellering, PhDRaymond Moellering, PhD

Project Title: Targeting Transcription with Synthetic Biologics

Raymond Moellering is an Assistant Professor in the Department of Chemistry at the University of Chicago. He started his independent research program at UChicago in 2015, where his laboratory is focused on developing new chemical tools and technologies to study complexity and dynamics in the proteome, thus illuminating causal pathways in disease as well as novel therapeutic strategies to target them.

For 2017, NIH issued 12 Pioneer awards55 New Innovator awards8 Transformative Research awards, and 11 Early Independence awards. The 2017 awards total approximately $263 million, pending available funds, and represent contributions from the NIH Common Fund; National Institute of General Medical Sciences; National Institute of Mental Health; National Center for Complementary and Integrative Health; and National Institute of Dental and Craniofacial Research.

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Tagged: biochemistry, Biological Sciences, Cancer, chemistry, Genetics, Jingyi Fei, molecular biology, NIH, pathology, Ray Moellering, research funding, Seungmin Hwang