Fine particulates associated with childhood autism

Exposure to fine particulate air pollution during pregnancy through the first two years of a child’s life may be associated with an increased risk of the child developing autism spectrum disorder (ASD), a condition that affects one in 68 children, according to a Graduate School of Public Health investigation of children in southwestern Pennsylvania.

Said lead author Evelyn Talbott, epidemiology faculty member: “Autism spectrum disorders are lifelong conditions for which there is no cure and limited treatment options, so there is an urgent need to identify any risk factors that we could mitigate, such as pollution. Our findings reflect an association, but do not prove causality. Further investigation is needed to determine possible biological mechanisms for such an association.”

Talbott and her colleagues performed a population-based, case-control study of families with and without ASD living in six southwestern Pennsylvania counties. They obtained detailed information about where the mothers lived before, during and after pregnancy and, using a model developed by public health faculty member and study co-author Jane Clougherty, were able to estimate individual exposure to a type of air pollution called PM2.5.

This type of pollution refers to particles found in the air that are less than 2.5 micrometers in diameter, or 1/30th the average width of a human hair. PM2.5 includes dust, dirt, soot and smoke. Because of its small size, PM2.5 can reach deeply into the lungs and get into the blood stream. Southwestern Pennsylvania has consistently ranked among the nation’s worst regions for PM2.5 levels, according to data collected by the American Lung Association.

Autism spectrum disorders are a range of conditions characterized by social deficits and communication difficulties that typically become apparent early in childhood. Reported cases of ASD have risen nearly eight-fold in the last two decades. While previous studies have shown the increase to be partially due to changes in diagnostic practices and greater public awareness of autism, this does not fully explain the increased prevalence. Both genetic and environmental factors are believed to be responsible.

Talbott and her team interviewed the families of 211 children with ASD and 219 children without ASD born between 2005 and 2009. The families lived in Allegheny, Armstrong, Beaver, Butler, Washington and Westmoreland counties. Estimated average exposure to PM2.5 before, during and after pregnancy was compared between children with and without ASD.

Based on the child’s exposure to concentrations of PM2.5 during the mother’s pregnancy and the first two years of life, the researchers found that children who fell into higher exposure groups were at an approximate 1.5-fold greater risk of ASD after accounting for other factors associated with the child’s risk for ASD, such as the mother’s age, education and smoking during pregnancy. This risk estimate is in agreement with several other recent investigations of PM2.5 and autism.

A previous public health analysis of the study population revealed an association between ASD and increased levels of air toxics, including chromium and styrene. Studies by other institutions using different populations also have associated pollutants with ASD.

“Air pollution levels have been declining since the 1990s; however, we know that pockets of increased levels of air pollution remain throughout our region and other areas,” said Talbott. “Our study builds on previous work in other regions showing that pollution exposures may be involved in ASD. Going forward, I would like to see studies that explore the biological mechanisms that may underlie this association.”

The research was funded by The Heinz Endowments and published in Environmental Research.

Additional Pitt co-authors of this study were Vincent C. Arena, Judith R. Rager, Drew R. Michanowicz, Ravi K. Sharma and Shaina L. Stacy.

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Can psychosocial treatments help autistic adults?

A School of Social Work researcher has received a $3.2 million grant from the National Institute of Mental Health to determine whether nondrug psychosocial treatments can improve the quality of life for adults with autism spectrum disorder.

It will be the largest study ever conducted to assess whether cognitive enhancement therapy and enriched supportive therapy can help adults with a complex disorder that influences how a person behaves, learns, communicates and interacts with others.

The research program, called Perspectives, will take place at Pitt and will be led by Shaun Eack, David E. Epperson Associate Professor of Social Work and a faculty member in psychiatry, in collaboration with Nancy Minshew, faculty member in psychiatry and neurology in the School of Medicine and director of the Center for Excellence in Autism Research.

The study will include 100 participants, ages 16-40, who will be assigned randomly to one of two psychotherapies for up to 18 months.

The first, cognitive enhancement therapy, will involve about three and a half hours a week of computer exercises in attention, memory and problem solving, along with small-group sessions in which the participant learns how to act appropriately in social situations by learning to read nonverbal cues, understanding another person’s perspective and other aspects of successful social interaction.

The second, enriched supportive therapy, will take place for about an hour a week and is a one-on-one therapy to help adults learn about their condition, manage their emotions and stress, improve their social skills and cope with everyday problems.

Said Eack: “The evidence base for treatment for adults with autism is almost nonexistent. This study will establish whether cognitive enhancement therapy and enriched supportive therapy are effective for treating autism, which is essential for making more treatments available in the community for adults.

“Ultimately, we hope the study will establish an evidence base for both cognitive enhancement therapy and enriched supportive therapy and also will tell us about the comparative benefits of both interventions in adults, about which we know very little.”

The research team will collect neuroimaging data as well as data from interviews with clinicians and family members to assess if the therapies are working.

It is Eack’s hope that the therapies also eventually can be made available to children who have autism spectrum disorder who will continue to need help as they grow into adulthood. His earlier work revealed that cognitive enhancement therapy was very successful in patients with schizophrenia.

“Social work has a long history of developing psychosocial interventions for people with disabilities,” he added. “And we are working closely with Pitt’s experts in the Department of Psychiatry. This work could not be done without interdisciplinary collaborations.”

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Jumping spider sees the spectrum

The Habronattus pyrrithrix jumping spider is about a half-centimeter long and has superb visual acuity. It also can see in full color through the use of a red filter in its two primary eyes, according to research done in the Dietrich School of Arts and Sciences.

Said Nathan Morehouse, faculty member in biological sciences: “The eyes of jumping spiders could not be more different from those of butterflies or birds, and yet all three tune their color sensitivities using pigments that filter light. It’s actually a pretty clever, simple solution with a big payoff.”

The payoff, for the male of the species, is that he gets to mate. Male Habronattus are quite colorful and use their vibrant appearance to attract a female. Scientists knew that some Habronattus pyrrithrix could see green and ultraviolet light through two of their eight eyes. It was assumed that they also could see reds and oranges — what would be the evolutionary benefit for males having red and orange coloration otherwise? But scientists had yet to figure out how the spiders could see ruby hues.

In his recent study, Morehouse and colleagues found that the arachnids have red filters that sit in front of cells in their eyes that normally detect green light. The effect is similar to the gels placed in front of theater lights to get different colors on a stage.

The research on this “spectral filtering” was published in Current Biology. It had never before been described in any spider, although similar strategies are known in birds, butterflies and mantis shrimp. That makes this visual strategy a remarkable example of evolutionary convergence.

The spiders may have “true” color vision, but that’s not to say they see the world in quite the way we do. The similarity lies in the fact that both this spider and humans have three color channels: Jumping spiders have ultraviolet, green and red channels, whereas people have blue, green and red channels. The difference is that humans have three different, distinct color receptors rather than making use of a filter to perceive certain hues.

Said Daniel Zurek, a postdoctoral researcher in Morehouse’s lab: “One fascinating thing about the trichromatic area in these spiders’ retinas is that it is very restricted in field of view, which means they’d have to scan scenes ‘line by line’ to accumulate color information.”

With the new findings in hand, the researchers say they are about to go spider hunting in Arizona in search of other species in this diverse Habronattus group. They hope to explore the role that color vision may have played in generating the diversity of these spiders over evolutionary time.

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Gene mutations cause some male infertility

Some cases of male infertility are due to mutations in the maternal X chromosome that prevent development of viable sperm, according to a study led by researchers at the School of Medicine and the Magee-Womens Research Institute (MWRI). The study was published online in the New England Journal of Medicine.

Nearly half of cases of male infertility not due to a physical obstruction are estimated to have genetic roots, and about 20 percent of infertile men have azoospermia, meaning they don’t make sperm, explained co-principal investigator Alexander Yatsenko, faculty member in obstetrics, gynecology and reproductive medicine and an MWRI investigator. He noted the only causes for infertility that have been identified are defects of sex chromosomes, such as the deletions of the Y (male) chromosome or duplication of the entire X (female) chromosome in Klinefelter syndrome.

Said Yatsenko: “Eight times out of 10, conventional genetic testing doesn’t reveal a chromosomal problem, so the cause is considered idiopathic or unknown. This study is among the first to describe specific gene mutations on the X chromosome that contribute to azoospermia and male infertility.”

First, the research team scanned the genomes of 15 men with azoospermia and found a deletion in part of the DNA coding of the testis-expressed gene 11 (TEX11) on the X chromosome, which men inherit from their mothers. The alteration caused meiotic arrest, meaning the precursor cells could not properly undergo meiosis, the cell division process that produces daughter cells with half the parental chromosomes for reproduction.

Then, they found similar TEX11 gene mutations and meiotic arrest in two out of 49 men diagnosed with idiopathic azoospermia from the Center for Fertility and Reproductive Endocrinology at Magee-Womens Hospital and the Institute of Human Genetics of the Polish Academy of Sciences in Poznan, Poland. Also, TEX11 gene errors were found in five out of 240 infertile men from the Center of Reproductive Medicine and Andrology in Münster, Germany.

Yatsenko noted that it might be possible for an older father, whose precursor sperm cells have a greater likelihood of acquiring a mutation, to pass along the genetic error to his daughter, which could make it impossible for her son to make viable sperm. Also, men without seminal sperm who undergo a procedure to have a few rare, viable sperm extracted from the testes to attempt conception with in vitro fertilization could unknowingly pass a TEX11 gene mutation to a daughter, making her a carrier.

“This research suggests screening for TEX11 gene mutations might be useful in cases of otherwise unexplained azoospermia,” Yatsenko said. “It might be possible to one day correct these problems with gene therapy and other interventions. More work must be done to identify other genetic causes of male infertility.”

The team included other authors from Pitt, the University of Münster and the Polish Academy of Sciences.

The project was funded by Pitt, the Eunice Kennedy Shriver National Institute of Child Health and Human Development, the Pennsylvania Department of Health, MWRI, the Polish National Science Centre and the German Research Foundation.

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Electrons “swing dance” in pairs

A research team led by Jeremy Levy, distinguished professor of physics and Pittsburgh Quantum Institute director, has discovered electrons that can “swing dance.” This unique electronic behavior could lead to new families of quantum devices.

Superconductors, materials that permit electrical current to flow without energy loss, form the basis for magnetic resonance imaging devices as well as emerging technologies such as quantum computers. At the heart of all superconductors is the bunching of electrons into pairs.

Levy has discovered a long-postulated phase in which electrons form pairs but do not reach a superconducting state. The discovery provides fundamental new insights into a mechanism that could one day be used to design a material that is superconducting at room temperature.

Such a breakthrough would radically transform an array of technologies such as high-speed trains, energy-efficient power transmission and computers that operate with negligible power requirements. The work, done in collaboration with researchers from the University of Wisconsin-Madison and the U.S. Naval Research Laboratory, was published in Nature.

One way to understand this novel state is to extend an analogy first articulated by J. Robert Schrieffer, who shared the 1972 Nobel Prize in Physics for the theory of superconductivity. In a superconductor, the motion of paired electrons is highly coordinated, similar to waltzing couples on a dance floor. In the “normal” or non-superconducting state, electrons move independently, bumping into one another occasionally and dissipating energy.

What the new research has identified is an in-between state where the electrons form pairs, but each pair moves independently. One may regard the electron pairs as “swing dancing,” where dancing pairs hold hands but do not move in any synchronized fashion.

The first theory to describe how electrons pair without forming a superconducting state was published by David M. Eagles in 1969. Lead author and research assistant professor in the Levy lab, Guanglei Cheng, described how the theory was proven right: “The breakthrough comes from the technological advancement to fabricate superconducting single-electron transistors at an oxide interface, a technology that allows us to count electrons and pairs one by one. And this is just the beginning. We now have a novel platform to study the fascinating electron-electron correlations at nanoscale dimensions.”

Levy and Cheng also worked with a research team led by Chang-Beom Eom at the University of Wisconsin-Madison and employed theoretical contributions from C. Stephen Hellberg at the U.S. Naval Research Laboratory.

The Air Force Office of Scientific Research and the National Science Foundation supported the research.

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Computer simulation replicated trauma outcomes

A computer simulation, or “in silico” model, of the body’s inflammatory response to traumatic injury accurately replicated known individual outcomes and predicted population results counter to expectations, according to a study recently published in Science Translational Medicine by a School of Medicine research team.

Traumatic injury is a major health care problem worldwide. Trauma induces acute inflammation in the body with the recruitment of many kinds of cells and molecular factors that are crucial for tissue survival, explained senior investigator Yoram Vodovotz, surgery faculty member and director of the Center for Inflammation and Regenerative Modeling at the School of Medicine. But if inappropriately sustained, the inflammatory response can compromise healthy tissues and organs.

Said Vodovotz: “Thanks to lifesaving surgery and extensive supportive care, most patients who require trauma care are now highly likely to survive. But along the way, they may experience a variety of complications, such as multiple organ failure, that are difficult to predict in initial assessment. Our current challenge is to identify which patients are vulnerable to certain problems so that we can better implement surveillance and prevention strategies and use resources more effectively.”

Building from a model developed for swine, the research team examined blood samples from 33 survivors of car or motorcycle accidents or falls for multiple markers of inflammation, including interleukin-6 (IL-6), and segregated the patients into one of three (low to high) categories of trauma severity. They were able to validate model predictions regarding hospital length of stay in a separate group of nearly 150 trauma patients. They then generated a set of 10,000 “virtual patients” with similar injuries and found the model could replicate outcomes in individuals, such as length of stay and degree of multi-organ dysfunction. Intriguingly, the in silico model also predicted a 3.5 percent death rate, comparable to published values and to the Pitt group’s own observations, even though the model did not include patients who didn’t survive their injuries.

The in silico model predicted that, on an individual basis, virtual patients who made more IL-6 in response to trauma were less likely to survive. But, as the model predicted, that was not true at the population level: Among nearly 100 real patients whose genetic predisposition to make greater or lower amounts of IL-6 had been determined, there was little difference in survival between high- and low-IL-6 producers.

“These findings demonstrate the limitations of extrapolating from single mechanisms to outcomes in individuals and populations, which is the typical paradigm used to identify potential treatments,” Vodovotz said. “Instead, dynamic computational models like ours that simulate multiple factors that interact with each other in complex diseases could be a more efficient and accurate way of predicting outcomes for both individuals and populations. Then we can pursue those avenues that have the greatest likelihood of success in clinical trials.”

Noted co-investigator Timothy Billiar, George Vance Foster Professor and Department of Surgery chair: “The potential impact of this work is high because clinical trials are difficult and expensive to carry out, and usually can test only a single dose of a drug. Determining the best dose, timing and biomarkers that would characterize patients likely to respond well to therapy is a major thrust of the pharmaceutical and biotechnology companies. This approach could help tailor treatments.”

The project was carried out by the Trauma Research Center, which is headed by Billiar, and included other researchers from Pitt, the McGowan Institute for Regenerative Medicine, Upstate Medical University in Syracuse, N.Y., and Immunetrics.

It was funded by the National Institutes of Health.

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Bacteriophage paper has 2,863 authors

Bacteriophages are viruses that infect and replicate within bacteria, and are the most abundant organisms on Earth. But we don’t know much about their genetic architecture.

A team of professional scholars and budding scientists — chiefly college freshmen — have joined forces under SEA-PHAGES (Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science), which is run jointly by Pitt and the Howard Hughes Medical Institute (HHMI), to study the little-known genetics of bacteriophages. In a new paper published in eLIFE, the authors show that phages do not form discrete populations as previously suggested but are rampantly exchanging genes with each other to generate a broad spectrum of genetic diversity, albeit with some types being more prevalent than others.

Of the paper’s nearly 3,000 authors, 2,664 were students from among 81 colleges and universities that participate in the SEA-PHAGES undergraduate science program, created by Pitt’s Graham Hatfull and colleagues and funded by HHMI. This paper is believed to have the second-highest number in history of authors on a scientific paper, trailing only that which described the discovery of the Higgs boson, which had more than 6,000 authors.

Forty of the authors on the phages paper are students at Pitt. This level of brainpower was crucial to the paper’s findings, said Hatfull, the Eberly Family Professor of Biotechnology in the Department of Biological Sciences within the Dietrich school and an HHMI Professor.

The numbers, Hatfull says, allowed the massive team to sequence a much larger number of complete genomes than those investigators who claimed phages are grouped into discrete groups. “It’s a matter of resolution,” with the SEA-PHAGES team looking at more than 600 individual phages. “Our team was able to look at more pixels. We have gained insights into the complexities of the phage population via this higher resolution view of this group of phages.”

The work illustrates “how little of the global phage population has been genomically sampled,” the paper said, and “with a near endless supply of diverse viruses readily accessible for isolation and analyses, large integrated research and education programs like SEA-PHAGES will continue to play substantial roles in defining the nature of the virosphere.”

In addition to making an important finding about the genetic nature of the bacteriophage population, Hatfull said SEA-PHAGES again has proven itself to be a valuable, widely implementable course-based research experience.

To date, SEA-PHAGES students nationwide have found thousands of new bacteriophages (all catalogued in Pitt’s Mycobacteriophage Database) and have been listed as co-authors of more than 10 scientific journal articles. The students get to name their own phages, which not only is fun but also gives students a sense of ownership over their contributions to phage research.

The course has proven to deeply engage students in STEM disciplines, and SEA-PHAGES “graduates” are more likely to continue in the sciences, one of the faster-growing fields in today’s global economy.

As a practical scientific matter, the discovery and genetic profiling of new bacteriophages is shedding light on what information their genes encode and what individual genes do, enabling a better understanding of their role in the environment (how they impact carbon turnover rates) and their role in bacterial pathogenesis (how bacteria make us ill).

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Genes altered with aid of light

Scientists have been manipulating genes for a while, but Alexander Deiters has found a way to control the process more precisely with light.

His research was published in the Journal of the American Chemical Society.

Since 2013, scientists have used a gene-editing tool called CRISPR/Cas9. The method employs a bacterially derived protein (Cas9) and a synthetic guide RNA to induce a double-strand break at a specific location in the genome. This enables excision of a gene, alteration of its function or introduction of desired mutations.

In practice, the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats of DNA base sequences) method has shown tremendous promise to enable researchers to treat cystic fibrosis and sickle cell anemia, create laboratory animals that mimic human disease and create a strain of wheat resistant to powdery mildew.

Deiters, a chemistry faculty member in the Dietrich school, and colleagues at the University of North Carolina-Chapel Hill have found a residue of lysine, an amino acid, in Cas9 that can be replaced with a light-activated analog.

The approach developed by Deiters generates a Cas9 protein that is functionally inactive, or “caged,” until the cage is removed through light exposure, activating the enzyme and thereby activating gene editing.

Said Deiters: “This method may allow people to engineer genes in cells or animals with better spatial and temporal control. Previously, if you wanted to knock out a gene, you had limited control over where and when it would happen. Engineering a light switch into Cas9 provides a more precise editing tool.”

The improved control over manipulation of genes, Deiters said, may help eliminate off-target effects and could potentially enable genetic studies with unprecedented resolution.

—Compiled by Marty Levine

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The University Times Research Notes column reports on funding awarded to Pitt researchers as well as findings arising from University research.

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