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Brain plasticity and phantom limbs: Does amputation rewire the sense of touch?

Tue, 02/14/2017 - 12:51

Bensmaia hand brain

In October 2015, 28-year-old Nathan Copeland used a robotic prosthetic arm to give President Obama a fist bump at a scientific conference in Pittsburgh. Copeland, who was paralyzed from the chest down in a car accident in 2004, also showed the President how he could “feel” with the hand, which sent realistic sensory feedback through electrodes implanted in his brain.

It was a feat of engineering and neuroscience by a team of researchers from the University of Pittsburgh and Sliman Bensmaia, associate professor of organismal biology and anatomy at the University of Chicago—and a feat that was made possible by the resilience of the sensory parts of the brain.

Bensmaia has spent years researching how the nervous system interprets sensory feedback as we touch or grasp objects, move our limbs and run our fingers along textured surfaces. He believes that the best way to restore the sense of touch in patients like Copeland is to use a “biomimetic” approach that mimics the natural, intact nervous system. By studying how the brain normally encodes and responds to sensory information, scientists can reproduce those signals through a prosthetic limb connected directly to the brain.

This approach assumes that the part of the brain responsible for processing the sense of touch, the somatosensory cortex, is relatively stable—i.e., that if someone loses a limb or becomes paralyzed, the somatosensory cortex is still there, intact and ready to respond to stimulation. But Bensmaia says that every time he gives a presentation about his prosthetics research, someone invariably challenges him with a different idea—that after amputation, the brain reorganizes and uses that part of the somatosensory cortex for something else.

This notion was popularized by a series of famous studies in the 1990s by V.S. Ramachandran at the University of California, San Diego. Three amputees reported that when they were touched on the face, they felt sensations that corresponded to their missing, or “phantom” hand. This curious phenomenon was taken as direct evidence for brain reorganization–once input to the brain territory of the (now missing) hand is lost, this territory is claimed by the face.


In some studies, amputees reported that when they were touched on the face, they felt sensations that corresponded to their missing hand (A). But in others, different locations evoked the missing limb (B).

Ramachandran went on to become a popular scientific speaker and author of several books, most notably Phantoms in the Brain in 1998. His ideas added to a broader school of thought on the brain’s “plasticity,” or ability to change and accommodate for learning new skills or responding to trauma like losing a limb. This supposed malleability is what troubled Bensmaia.

“If the somatosensory cortex were so labile, then the biomimetic approach wouldn’t work,” he said. “Instead, the design of the neural interface would depend on the idiosyncratic neural representations of each individual, rather than based on general principles of organization, which we work to uncover.”

In response, he teamed up with Tamar Makin, an associate professor at the University of Oxford, United Kingdom, and an expert on the brains of amputees, to write a paper that challenges the notion of massive reorganization of sensory representations in the brain after amputation. Based on a reexamination of the existing literature and on their own work, Makin and Bensmaia argue that while other parts of the brain may indeed be plastic, the somatosensory cortex for processing the sense of touch is relatively stable.

“Previous researchers studying amputees focused on representations of body parts that are not directly affected by the amputation, such as the face, to study brain plasticity,” Makin said, but she thinks this is just one piece of the puzzle.

“Amputees ubiquitously report very vivid sensations of their missing hand, called ‘phantom sensations’. In my research, we take advantage of this remarkable phenomenon to study the persistent representation of the missing hand,” she said.

For instance, the body parts that are thought to benefit from the brain resources previously devoted to the missing hand do not gain any functionality by having access to that additional sensory processing power. In experiments, the skin surfaces of the face that trigger these sensations are no more sensitive to touch than before amputation.

University of Pittsburgh researchers perform a sensory test on a blindfolded Nathan Copeland who demonstrates his ability to feel by correctly identifying different fingers through a mind-controlled robotic arm. (Credit: UPMC/Pitt Health Sciences Media Relations)

Second, as in Bensmaia’s research, both amputees and paralyzed patients like Copeland reported realistic, natural-feeling sensations in their missing or otherwise insensate arm when stimulated through residual nerves or directly in the brain. This suggests that the portions of the brain responsible for that arm are still there, ready and waiting for sensory input from the arm.

“Even if they haven’t had an arm for 10 years, the way they report it is not as a phantom or vague sensation of the arm. They would describe it as, ‘My arm is still present. I can’t see it. I know it’s not really there, but it feels like it’s there,’” Bensmaia said.

Instead of the somatosensory cortex reorganizing and creating a new representation of the face, Bensmaia and Makin point to research showing that new nervous system circuits develop in the brain stem. After loss of input from the hand following amputation, parts of the brain stem that used to carry signals from the arm form new connections to neighboring areas, which can result in receiving input from a new source, like the face. However, the hand sensations generated by touching the face result from echoes of this new input, reverberating through the hand portion of the somatosensory cortex.

Bensmaia acknowledges that much of the brain is plastic of course, but suggests that we should have a more nuanced view of plasticity than is often taken for granted in the public imagination.

“You can learn how to play guitar, for example, even as an adult, so that implies that the motor parts of your brain can learn and are plastic,” he said. “And right next to these motor regions, you have somatosensory regions that are relatively fixed, at least in their coarse organization. This region carries the ground truth of what your body is doing at any time.”

Tagged: artificial touch, Biological Sciences, Brain, brain plasticity, neuroprosthetics, Neuroscience, prosthetics, Sliman Bensmaia, somatosensory cortex, touch
UPMC Pitt BCI Demonstration

National Academy of Sciences Honors Prof. Bernard Roizman for microbiology research

Mon, 02/13/2017 - 10:52

Bernard Roizman

Bernard Roizman holding a model of the herpes simplex virus, 1978 (University of Chicago Library / Chicago Maroon)

Bernard Roizman, ScD, the Joseph Regenstein Distinguished Service Professor of Virology, has been awarded the 2017 Selman A. Waksman Award in Microbiology for his pivotal research on how herpes viruses replicate and cause disease.

Supported by the Waksman Foundation for Microbiology, the National Academy of Sciences gives the award biannually to recognize a major advance in the field of microbiology. The honor is accompanied by a $20,000 prize.

“I am deeply honored to be a recipient of an award bearing Selman Waksman’s name,” Roizman said. “His research laid the foundations for discoveries of potent antibiotics, and over the course of half a century his pioneering research saved billions of lives. He continues to be an inspiration for scientists involved in research to curb the spread of infectious agents.”

Over the past five decades, Roizman’s contributions to the scientific understanding of herpes viruses have helped to improve human health. His research first identified viral herpes genes and proteins, as well as the structure of viral DNA, and defined the principles of herpes simplex virus gene regulation. He also constructed the first recombinant virus specifically targeted to malignant cells.

Using biochemistry, novel genetic strategies and cell biology, Roizman’s ongoing research focuses on how the herpes simplex virus, which has fewer than 100 genes, can take over a much more complex human cell, which contains more than 20,000 genes. This led to the first engineered virus, which has been used to study and target lethal tumors in humans.

Roizman’s role as a mentor has extended his research beyond his lab, with dozens of graduate student and postdoctoral fellows energizing the field of virology in premier universities in the United States, Europe, and Asia.

A member of the University faculty since 1965, Roizman was elected as a member of the National Academy of Sciences in 1979 and to the National Academy of Medicine in 2001. He is a Foreign Associate of the Chinese Academy of Engineering and the recipient of honorary degrees in the United States, France, Italy, and Spain. He will be honored in a ceremony on Sunday, April 30, during the National Academy of Sciences’ 154th annual meeting.

Tagged: Bernard Roizman, Biological Sciences, herpes, Microbiology, National Academy of Sciences, Selman Waksman Award, viruses

UChicago startups focus on microbiome medicine

Wed, 02/01/2017 - 10:39
Jack Gilbert

Prof. Jack Gilbert co-founded Gusto Global to better understand microorganisms inside humans and harness them to treat disease. (Photo: Andrew Collings)

Two startup companies founded by UChicago faculty are leveraging the microbiome to develop new medications that could prevent food allergies, stop infections, and treat disease.

ClostraBio, started by Cathryn Nagler, PhD, the Bunning Food Allergy Professor, and Jeffrey Hubbell, the Barry L. MacLean Professor of Molecular Engineering Innovation and Enterprise, is working to develop microbiome-based treatments for food allergies.

In 2014 Nagler and her team discovered that the presence of Clostridia, a common class of gut bacteria, protects against food allergies by acting as a barrier that prevents the trigger foods from entering the bloodstream and sparking an allergic reaction. Nagler’s group also identified the differences between the bacteria in the guts of healthy infants and those who were allergic to cow’s milk in 2015, and has created mouse models that mimic the human microbiome by transferring bacteria from infants into mice.

ClostraBio will use these special mice and controlled UChicago lab environments, such as the Gnotobiotic Mouse Facility, to test their potential treatments.

A second startup, Gusto Global, launched by Jack Gilbert, PhD, faculty director of the Microbiome Center, and John Alverdy, MD,  the Sarah and Harold Lincoln Thompson Professor of Surgery and executive vice chair of the Department of Surgery, is using computer models to predict how the trillions of bacteria in the body interact with each other and influence health. The company’s proprietary platform uses databases from human studies to run thousands of simulations to bolster the research and development of microbiome-based drugs.

Both companies have been supported by the Polsky Center for Entrepreneurship and Innovation, which provides resources for UChicago researchers to help commercialize their work.

Tagged: Biological Sciences, Cathryn Nagler, Food Allergies, Gastroenterology, Jack Gilbert, John Alverdy, microbiome, Surgery

Regulating “gasotransmitters” could improve care for sleep apnea

Mon, 01/23/2017 - 14:00

NP mice 1

Unbalanced signaling by two molecules that regulate breathing leads to sleep apnea in mice and rats, researchers report in the Jan. 23, 2017, Proceedings of the National Academy of Sciences. They show, working with rodents, that injection of a substance that reduces production of one of those signals, hydrogen sulfide, can prevent apneas. This approach has the potential to help people suffering from multiple forms of sleep-disordered breathing.

Apnea, the periodic cessation of breathing during sleep, is a major health problem. It affects more than 10 million people in the United States, often disrupting their sleep hundreds of times each night. This profoundly fragmented sleep causes daytime drowsiness, curtails academic achievement and professional productivity, and is a common cause of motor-vehicle or on-the-job accidents. It can lead to life-threatening health issues, including hypertension and stroke.

Current apnea treatments, such as the use of continuous positive airway pressure (C-PAP) while sleeping, are difficult for many patients to maintain and provide only limited benefits.


Nanduri Prabhakar, PhD

“We believe we have found an approach that could significantly improve the clinical management of sleep apneas by restoring the balance between two key gasotransmitters in the blood – carbon monoxide and hydrogen sulfide,” said Nanduri Prabhakar, PhD, the Harold Hines Jr. Professor of Medicine and Director of the Institute for Integrative Physiology and Center for Systems Biology of O2 at the University of Chicago.

Prabhakar and colleagues from the University of Chicago, the Illinois Institute of Technology, Beth Israel Deaconess Medical Center (Boston), and Johns Hopkins University (Baltimore), focused on the carotid bodies, a tiny cluster of cells embedded in the left and right carotid arteries, which pass through the neck.

The carotid bodies are the primary organ for sensing oxygen and carbon dioxide levels in arterial blood. Glomus cells in the carotid bodies produce the enzymes heme oxygenase 2 (HO-2), which generates carbon monoxide (CO) when oxygen levels are appropriate, and cystathionine-γ-lyase (CSE), which generates hydrogen sulfide (H2S) when oxygen levels dip.

During normal breathing during sleep, CO prevents the production of H2S by inhibiting CSE. When apnea begins and oxygen levels drop, however, CSE produces H2S, which stimulates the carotid bodies to increase breathing, heart rate and blood pressure. This leads to a sudden awakening.

carotidPrabhakar and colleagues tested two ways to manipulate this system by modulating the enzymes, CSE and HO-2, involved in CB signaling. When they gave a CSE inhibitor, L-propargyl glycine (L-PAG) by injection or by mouth to mice lacking HO-2 or rats predisposed to heightened CB activity – it reduced the frequency of apnea, underscoring the role of H2S in triggering apnea.

The response to L-PAG was “rapid, reversible, and did not result in overt toxicity within the dose range tested,” the investigators wrote. Conversely, administering CORM3 – a compound that releases carbon monoxide gas – to HO-2 deficient mice, restored normal breathing within 10 minutes. Notably, L-PAG reduced the number of both obstructive and central apneas in a dose-dependent and reversible manner.

The findings “demonstrate the salutary effects of blocking CSE during apnea and point to a potential therapeutic strategy for human sleep apnea,” according to the authors. “Our results suggest that pharmacologic targeting of the CB with a CSE inhibitor, such as L-PAG, might prevent apneas.”

These observations “provide proof-of-concept for the therapeutic potential of CSE inhibitors,” the authors wrote, but the doses of L-PAG required to normalize breathing were relatively high. More studies are needed to develop and test more potent CSE inhibitors.

“Nonetheless,” they conclude, “pharmacologic modulation of the CB chemoreflex by an inhibitor of H2S synthesis, as shown in the present study, has the potential to significantly improve the clinical management of sleep apnea.”

The study, “Gasotransmitters in Sleep Apnea: Complementary Roles of CO and H2S,” was funded by the National Institutes of Health’s Heart, Lung and Blood Institute. Additional authors were Ying-Jie Peng, Xiuli Zhang, Anna Gridina, Irina Chupikova, Gene Kim, Jayasri Nanduri and Ganesh Kumar of UChicago; David L. McCormick of IIT; Robert Thomas and Thomas Scammel of Beth Israel Deaconess; and Gregg Semenz, Chirag Vasavda and Solomon Snyder of Johns Hopkins University.

Tagged: Biological Sciences, Nanduri Prabhakar, Sleep, sleep apnea

How the chemical signals that shape animal bodies evolve

Thu, 01/19/2017 - 10:29

Representative images of Megaselia embryos with labeled RNA probes for tissue-type specific gene expression. Mab-eve is expressed in embryonic cells, Mab-doc in both amnion and serosa, and Mab-zen in serosa alone. Note the gradual repression of Mab-eve, first in the serosa and then also in the amnion. (Image: Chun Wai Kwan.)

The question of how the enormous range of animal diversity that surrounds us came to exist has fascinated scientists for centuries. Since the 1930s, Charles Darwin’s theory of evolution by natural selection has been broadly accepted as the process that shapes new species. Many people, myself included, usually imagine natural selection only during an organism’s adult lifetime – say, one finch’s beak might have superior digging power, allowing it to outcompete its fellow finches and pass on this trait to the next generation. However, an entire field of science studies evolution by examining variations in embryonic development between species, an area of work known as evolutionary developmental biology.

Two UChicago researchers in this field, Urs Schmidt-Ott, associate professor of Organismal Biology and Anatomy, and Chun Wai Kwan, a graduate student in the Schmidt-Ott lab, along with their colleagues Edwin L. Ferguson, professor of Molecular Genetics and Cell Biology, and postdoctoral scholar Jackie Gavin-Smyth (a former graduate student in the Ferguson lab), have provided evidence for a novel evolutionary mechanism during development in a study recently published in eLife.

As an embryo develops, chemical signals determine how distinct tissues form over time and space. Bone Morphogenetic Proteins (BMPs), found in organisms from fruit flies to humans, belong to a class of signaling molecules known as morphogens, essential factors in directing the arrangement of tissue types as an embryo grows. By comparing the distribution of BMP signaling during the development of two different fly species, Schmidt-Ott and his team have identified the BMP gradient as a target for evolution.

Urs Schmidt-Ott, PhD, professor of organismal biology and anatomy

During development, the fly embryo’s cells spit out BMPs into the extracellular space, where they diffuse around the embryo. Cells lining the back, or dorsal, region of the embryo carry receptors that bind the BMPs, which in turn sets off chemical signals within the cells that drive tissue specification. Generally, the intensity of BMP signaling follows a gradient pattern: most intense at the dorsal region and decreasing in magnitude in cells spread further to the sides. In Drosophila melanogaster, the fruit fly commonly used as a model organism, cells experiencing high BMP signaling early in development become an extraembryonic tissue called amnioserosa, which plays important roles in protecting the embryo and directing the movement of tissue in late developmental stages.

However, in most insects, including many fly species, BMP signaling promotes the formation of two separate tissue types, the serosa and the amnion. These extraembryonic tissues fulfil functions similar to those of the amnioserosa, as well as mediating key elements of embryo immunity. In Megaselia abdita, a fly closely related to Drosophila, the serosa develops from the most dorsal region and the amnion from surrounding tissue. As Schmidt-Ott, Kwan, and their team demonstrate in the new paper, the BMP signaling gradient in Megaselia first becomes narrow and steep, and then broadens as development progresses. By observing and manipulating levels of tissue-specific genetic markers as well as the changing BMP gradient in Megaselia embryos, they found that a positive feedback loop in pre-amnion cells amplifies BMP signaling after the serosa has begun forming, widening the range of BMP signaling and thus determining amnion.

Timing as well as spatial distribution of BMP signaling is key for the formation of distinct tissue types. In Megaselia, early low-level BMP signaling activates genes in nested domains that mark, but do not specify, the two extraembryonic tissue types. Rather, target genes of the early BMP gradient function in a positive feedback loop, first concentrating BMP signaling in the prospective serosa and then– after serosa specification – in the prospective amnion. In Drosophila, with its single extraembryonic tissue, the BMP gradient also becomes narrow and steep in the process of amnioserosa specification, but fails to broaden thereafter.

These results suggest that at some point in its evolution, Drosophila lost the broadening of the BMP gradient. Rather than identifying a gene downstream of the BMP gradient that directly produces a trait that has changed between species, this study indicates that genes responsible for the spatiotemporal dynamics of the BMP gradient during development were targeted in evolution to alter tissue. In Kwan’s words, “we found that by changing the shape of the morphogen gradient, the morphology or tissue type in different species can also change. This is a different way of looking at how evolution can occur.”

The subtlety of the interplay between extracellular signals like BMP and the responding cells, and the implications in determining animal forms demonstrated by this work support a theory of body patterning proposed by Alan Turing, the famous mathematician, in the 1950s. A simple model of signaling in development posits that a field of cells responds to a static signaling gradient. In this model, evolutionary change of tissue types or the organization of the animal’s body plan would be mediated by changing the nature of the responding cells.

As Schmidt-Ott explains it, Turing instead imagined that pattern and form depend primarily on the form of the morphogen gradients. Turing envisioned multiple diffusing signaling molecules interacting with each other in a concentration-dependent manner, and thereby defining their respective gradient shapes. By modeling the diffusion and reactivity of morphogens mathematically, he illustrated how a stable pattern can emerge from random fluctuations. From Turing’s consideration of the importance of a dynamic signaling gradient in animal body plans, the potential for a change in a morphogen gradient to advance evolution naturally follows.

“What was interesting for us here is that it was the morphogens themselves that were driving the evolutionary process,” said Schmidt-Ott. “By changing the parameters by which they are distributed in time and space, you get different animal forms.”

Next, Kwan and Schmidt-Ott plan to examine a group of flies that have two tissue types, like Megaselia, but have a reversed morphology towards the end of development – the amnion tissue ends up on the ventral side, rather than the dorsal as in Megaselia. They plan to determine whether different signaling gradients play a role in determining the ultimate arrangement of tissues as well as specifying tissue types, and to determine the genetic elements involved. They plan to pursue this goal – once again – in close collaboration with the Ferguson laboratory to combine their work with new experimental with research in Drosophila.

Schmidt-Ott hopes that these results will inspire the consideration of signaling gradients as targets of evolution more broadly.

“We could imagine this being applicable to the neural tube of vertebrates or the eyespots on butterfly wings – the same principle in which morphogens control the evolution of the complexity of a trait through feedback loops,” he said. “As evolutionary targets, feedback loops would change the dynamic of these gradients and that would provide a mechanism for diversification of the trait in question.”

Kwan and Schmidt-Ott would like to acknowledge the contributions of the additional authors on the paper, Jackie Gavin-Smyth, a postdoctoral scientist in the Reinitz lab, and Edwin L. Ferguson, professor of Molecular Genetics and Cell Biology, whose work on body patterning in Drosophila provided insight into the signaling pathway that promotes formation of amnioserosa tissue.


Tagged: Biological Sciences, Chun Wai Kwan, developmental biology, Evolution, evolutionary biology, molecular biology, organismal biology, Urs Schmidt-Ott

Scientists engineer animals with ancient genes to test causes of evolution

Fri, 01/13/2017 - 10:00
A transgenic fruit fly

A transgenic fruit fly engineered to carry the alcohol dehydrogenase gene as it existed about 4 million years ago. Thousands of these “ancestralized” flies were bred and studied for their ability to metabolize alcohol and to survive on an alcohol-rich food source. (Photo: Kathleen Gordon)

Scientists at the University of Chicago have created the first genetically modified animals containing reconstructed ancient genes, which they used to test the evolutionary effects of genetic changes that happened in the deep past on the animals’ biology and fitness.

The research, published early online in Nature Ecology & Evolution on Jan. 13, is a major step forward for efforts to study the genetic basis of adaptation and evolution. The specific findings, involving the fruit fly’s ability to break down alcohol in rotting fruit, overturn a widely-held hypothesis about the molecular causes of one of evolutionary biology’s classic cases of adaptation.

“One of the major goals of modern evolutionary biology is to identify the genes that caused species to adapt to new environments, but it’s been hard to do that directly, because we’ve had no way to test the effects of ancient genes on animal biology,” said Mo Siddiq, a graduate student in the Department of Ecology and Evolution at the University of Chicago, one of the study’s lead scientists.

“We realized we could overcome this problem by combining two recently developed methods—statistical reconstruction of ancient gene sequences and engineering of transgenic animals,” he said.

Until recently, most studies of molecular adaptation have analyzed gene sequences to identify “signatures of selection”—patterns suggesting that a gene changed so quickly during its evolution that selection is likely to have been the cause.  The evidence from this approach is only circumstantial, however, because genes can evolve quickly for many reasons, such as chance, fluctuations in population size, or selection for functions unrelated to the environmental conditions to which the organism is thought to have adapted.

Joe Thornton, PhD

Siddiq and his advisor, Joe Thornton, PhD, professor of ecology and evolution and human genetics at the University of Chicago, wanted to directly test the effects of a gene’s evolution on adaptation.  Thornton has pioneered methods for reconstructing ancestral genes—statistically determining their sequences from large databases of present-day sequences, then synthesizing them and experimentally studying their molecular properties in the laboratory. This strategy has yielded major insights into the mechanisms by which biochemical functions evolve.

Thornton and Siddiq reasoned that by combining ancestral gene reconstruction with techniques for engineering transgenic animals, they could study how genetic changes that occurred in the deep past affected whole organisms–their development, physiology, and even their fitness.

“This strategy of engineering ‘ancestralized animals’ could be applied to many evolutionary questions,” Thornton said.  “For the first test case, we chose a classic example of adaptation–how fruit flies evolved the ability to survive the high alcohol concentrations found in rotting fruit.  We found that the accepted wisdom about the molecular causes of the flies’ evolution is simply wrong.”

The fruit fly Drosophila melanogaster is one of the most studied organisms in genetics and evolution.  In the wild, D. melanogaster lives in alcohol-rich rotting fruit, tolerating far higher alcohol concentrations than its closest relatives, which live on other food sources. Twenty-five years ago at the University of Chicago, biologists Martin Kreitman and John McDonald invented a new statistical method for finding signatures of selection, which remains to this day one of the most widely used methods in molecular evolution.  They demonstrated it on the alcohol dehydrogenase (Adh) gene—the gene for the enzyme that breaks down alcohol inside cells—from this group of flies.  Adh had a strong signature of selection, and it was already known that D. melanogaster flies break down alcohol faster than their relatives. So, the idea that the Adh enzyme was the cause of the fruit fly’s adaptation to ethanol became the first accepted case of a specific gene that mediated adaptive evolution of a species.

Drosophila melanogaster

In the wild, D. melanogaster lives in alcohol-rich rotting fruit, tolerating far higher alcohol concentrations than its closest relatives, which live on other food sources.

Siddiq and Thornton realized that this hypothesis could be tested directly using the new technologies.  Siddiq first inferred the sequences of ancient Adh genes from just before and just after D. melanogaster evolved its ethanol tolerance, some two to four million years ago. He synthesized these genes biochemically, expressed them, and used biochemical methods to measure their ability to break down alcohol in a test tube.  The results were surprising:  the genetic changes that occurred during the evolution of D. melanogaster had no detectable effect on the protein’s function.

Working with collaborators David Loehlin at the University of Wisconsin and Kristi Montooth at the University of Nebraska, Siddiq then created and characterized transgenic flies containing the reconstructed ancestral forms of Adh.  They bred thousands of these “ancestralized” flies, tested how quickly they could break down alcohol, and how well the larvae and adult flies survived when raised on food with high alcohol content.  Surprisingly, the transgenic flies carrying the more recent Adh were no better at metabolizing alcohol than flies carrying the more ancient form of Adh.  Even more strikingly, they were no better able to grow or survive on increasing alcohol concentrations. Thus, none of the predictions of the classic version of the story were fulfilled. There is no doubt that D. melanogaster did adapt to high-alcohol food sources during its evolution, but not because of changes in the Adh enzyme.

“The Adh story was accepted because the ecology, physiology, and the statistical signature of selection all pointed in the same direction. But three lines of circumstantial evidence don’t make an airtight case,” Thornton said. “That’s why we wanted to test the hypothesis directly, now that we finally have the means to do so.”

Siddiq and Thornton hope that the strategy of making ancestralized transgenics will become the gold standard in the field to decisively determine the historical changes in genes to their changes on organisms’ biology and fitness.

For his part, Kreitman, who is still a professor of ecology and evolution at UChicago, has been supportive of the new research, helping advise Siddiq on the project and sharing his vast knowledge about molecular evolution and Drosophila genetics.

“From the beginning, Marty was excited about our experiments, and he was just as supportive when our results overturned well-known conclusions based on his past work,” Siddiq said. “I think that’s extremely inspiring.”

The study, “Experimental test and refutation of a classic case of molecular adaptation in Drosophila melanogaster,” was supported by the National Science Foundation, the National Institutes of Health, the Howard Hughes Medical Institute, and the Life Sciences Research Foundation.

Tagged: Biological Sciences, ecology and evolution, Evolution, fruit flies, Genetics, Joe Thornton, Mo Siddiq

Universal flu vaccines could offer key benefits over seasonal shots

Thu, 01/05/2017 - 10:30

20131105_Flu drill_0674

Universal vaccines that protect against multiple strains of influenza (flu) virus at once could offer substantial advantages over conventional seasonal flu vaccines, when deployed on a large scale in the human population, according to research published in PLOS Computational Biology. The new study from the University Chicago, Princeton University and Imperial College London demonstrates potential effects of new vaccines that target multiple flu strains using mathematical modeling.

Current flu vaccines provide good protection, but only if they are well matched against a specific flu strain. Flu-causing viruses are continually evolving and cause annual epidemics. Scientists must update vaccines regularly to provide protection against whichever seasonal strains pose the greatest health risk. To keep from updating the vaccines every year, researchers are now working to develop universal vaccines that could protect against multiple flu strains instead.

According to the Centers for Disease Control, it is not possible to predict with certainty if the vaccine will be a good match for circulating viruses. The vaccine is made to protect against the flu viruses that research and surveillance indicate will be most common. However, experts pick which viruses to include in the vaccine many months in advance in order for vaccine to be produced on time.

In addition, every few decades a new virus emerges in the human population that causes a global pandemic, and the current flu vaccines cannot be used to protect the population against the next pandemic virus.

“There are certain proteins that are shared across a wide range of flu viruses. Only now with recent advances in biotechnology has it been possible to develop vaccines targeting these ‘conserved antigens’,” said UChicago graduate student Rahul Subramanian, the lead author of the study.

These universal flu vaccines currently being developed in the laboratory could protect against a broad range of seasonal flu viruses without having to be updated, as well as protecting against pandemic flu strains.

Research on universal flu vaccines has mostly focused on their potential effects in individual patients. To better understand their effects at the population level, Subramanian and colleagues mathematically modeled the interactions between vaccination, flu transmission and flu virus evolution.

“We asked the question – How would a universal flu vaccination program compare against a similar program using only current flu vaccines?” said Subramanian. “We wanted to know how would each compare in their ability to control seasonal flu, reduce the pace of flu evolution, and protect against the next influenza pandemic.”

The model revealed that deployment of universal vaccines across large populations could reduce flu transmission more effectively than conventional flu vaccines. It could also slow the evolution of new strains of flu virus and bolster the immunity of a population, allowing protection against the emergence of dangerous pandemic strains.

“New flu vaccines could, for the first time, maintain their effectiveness in the face of viral evolution,” said Subramanian. “In doing so they could transform the way we manage flu in future.”

However, when conventional vaccines are well matched against circulating flu strains they are highly effective at blocking infection and are likely to continue to play an important role. Strategic decisions about their deployment, alongside novel vaccines, could be guided by anticipated population impact, as well as their effectiveness in individuals.

“Our work suggests an optimal approach may be to strategically use universal vaccines alongside conventional vaccines to protect the health at-risk groups while promoting immune defense of the whole population,” said Subramanian.

Additional authors include Andrea Graham and Bryan Grenfell from Princeton University, and Nimalan Arinaminpathy from Imperial College London. This work was supported by: Health Grand Challenges Program, Center for Health and Wellbeing, Princeton University; Bob and Cathy Solomon Undergraduate Research Fund, Princeton Environmental Institute, Princeton University, and MRC Centre for Outbreak Analysis and Modeling.

Tagged: Biological Sciences, computational modeling, flu vaccine, health, Infectious Disease, influenza, mathematics, Rahul Subramanian, universal vaccine, vaccines

280 million-year-old fossil reveals origins of chimaeroid fishes

Wed, 01/04/2017 - 12:00

High-definition CT scans of the fossilized skull of a 280 million-year-old fish reveal the origin of chimaeras, a group of cartilaginous fish related to sharks. Analysis of the brain case of Dwykaselachus oosthuizeni, a shark-like fossil from South Africa, shows telltale structures of the brain, major cranial nerves, nostrils and inner ear belonging to modern-day chimaeras.

This discovery, published early online in Nature on Jan. 4, allows scientists to firmly anchor chimaeroids—the last major surviving vertebrate group to be properly situated on the tree of life—in evolutionary history, and sheds light on the early development of these fish as they diverged from their deep, shared ancestry with sharks.

“Chimaeroids belong somewhere close to the sharks and rays, but there’s always been uncertainty when you search deeper in time for their evolutionary branching point,” said Michael Coates, PhD, professor of organismal biology and anatomy at the University of Chicago, who led the study.

“Chimaeras are unusual throughout the long span of their fossil record,” Coates said. “Because of this, it’s been difficult to understand how they got to be the way they are in the first place. This discovery sheds new light not only on the early evolution of shark-like fishes, but also on jawed vertebrates as a whole.”


vertebrate family tree

Chimaeras include about 50 living species, known in various parts of the world as ratfish, rabbit fish, ghost sharks, St. Joseph sharks or elephant sharks. They represent one of four fundamental divisions of modern vertebrate biodiversity. With large eyes and tooth plates adapted for grinding prey, these deep-water dwelling fish are far from the bloodthirsty killer sharks of Hollywood.

For more than 100 years, they have fascinated biologists. “There are few of the marine animals that on account of structure and relationships to other forms living and extinct have as great interest for zoologists and palaeontologists as the Chimaeroids,” wrote Harvard naturalist Samuel Garman in 1904. More than a century later, the relationship between chimaeras, the earliest sharks, and other early jawed fishes in the fossil record continues to puzzle paleontologists.

Chimaeras—named for their similarities to a mythical creature described by Homer as “lion-fronted and snake behind, a goat in the middle”—are unusual. Their anatomy comprises features reminiscent of sharks, ray-finned fishes and tetrapods, and their form is shaped by hardened bits of cartilage rather than bone. Because they are found in deep water, they were long considered rare. But as scientists gained the technology to explore more of the ocean, they are now known to be widespread, but their numbers remain uncertain.

After a 2014 study detailing their extremely slow-evolving genomes was published in Nature, interest in chimaeras blossomed. Of all living vertebrates with jaws, chimaeras seemed to offer the best promise of finding an archive of information about conditions close to the last common ancestor of humans and a Great White.

Like sharks, also reliant on cartilage, chimaeras rarely fossilize. The few known early chimaera fossils closely resemble their living descendants. Until now, the chimaeroid evolutionary record consisted mostly of isolated specimens of their characteristic hyper-mineralized tooth plates.

Rock nodule containing the Dwyka fossil Rock nodule containing the Dwyka fossil Rock nodule containing the Dwyka fossil Rock nodule containing the Dwyka fossil Roy Oosthuizen

The Dwykaselachus fossil resolves this issue. It was originally discovered by amateur paleontologist and farmer Roy Oosthuizen when he split open a nodule of rock on his farm in South Africa in the 1980s. An initial description named it based on material visible at the broken surface of the nodule. It was carefully archived in the South African Museum in Cape Town, where its splendor awaited technology able to unwrap its long-shrouded secrets.

In 2013, when the University of the Witwatersrand Evolutionary Studies Institute obtained a micro CT scanner, Dr. Robert Gess, a South African Centre of Excellence in Palaeosciences partner and co-author of this study, began scanning Devonian shark fossils while he was based at the Rhodes University Geology Department. Coates encouraged him to investigate Dwykaselachus.

Reconstruction of Dwykaselachus oosthuizeni

Reconstruction of Dwykaselachus oosthuizeni (Image: Kristen Tietjen)

At the surface, Dwykaselachus appeared to be a symmoriid shark, a bizarre group of 300+ million-year-old sharks, known for their unusual dorsal fin spines, some resembling boom-like prongs and others surreal ironing boards.

CT scans showed that the Dwykaselachus skull was remarkably intact, one of a very few that had not been crushed during fossilization. The scans also provide an unprecedented view of the interior of the brain case.

“When I saw it for the first time, I was stunned,” Coates said. “The specimen is remarkable.”

The images, one reviewer commented, are “almost dripping with data.”

They show a series of telltale anatomical structures that mark the specimen as an early chimaera, not a shark. The braincase preserves details about the brain shape, the paths of major cranial nerves and the anatomy of the inner ear. All of which indicate that Dwyka belongs to modern-day chimaeras. The scans reveal clues about how these fish began to diverge from their common ancestry with sharks.

A large extinction of vertebrates at the end of the Devonian period, about 360 million years ago, gave rise to an explosion of cartilaginous fishes. Instead of what became modern-day sharks, Coates said, revelations from this study indicate that “much of this new biodiversity was, instead, early chimaeras.”

“We can now say that the first radiation of cartilaginous fishes after the end Devonian extinction was chimaeras, in abundance.” Coates said. “It’s the inverse of what we’ve got today, where sharks are far more common.”

The study, “A symmoriiform chondrichthyan braincase and the origin of chimaeroid fishes,” was supported by the National Science Foundation, the National Research Foundation (NRF) / Department of Science and Technology South African Centre of Excellence in Palaeosciences, and the NRF African Origins Programme. Additional authors include John Finarelli from the University College Dublin, Ireland, and Katharine Criswell and Kristen Tietjen from the University of Chicago.

Tagged: Biological Sciences, chimaeras, Evolution, fossils, Michael Coates, paleontology, sharks
Dwykaselachus oosthuizeni CT scan

Silicon nanowires put electronics inside your cells

Thu, 12/22/2016 - 10:13
Ramya Parameswaran

UChicago MD/PhD student Ramya Parameswaran at the controls of the chemical vapor deposition system that manufactures silicon nanowires that can be internalized inside the body’s cells

Humans have long dreamed of melding electronics and machines with the body, but this usually trends toward the realm of science fiction: computer chips in the brain, bionic sight, robotic limbs and the like. We’re a long way from this cyborg future, but research on electronic interfaces with the body that can diagnose and treat disease is already underway, and they’re a lot smaller than you think.

Bozhi Tian, PhD

Bozhi Tian, PhD

In a paper published Friday, December 16, in the journal Science Advances, scientists from the University of Chicago describe how silicon nanowires, microscopic snippets of the same material used for computer chips, can be embedded inside individual cells. Once inside, the nanowires can be stimulated to take measurements, manipulate internal components of the cell, or deliver drugs and genetic therapies.

“You can treat it as a non-genetic, synthetic biology platform,” said Bozhi Tian, PhD, assistant professor of chemistry and senior author of the new study. “Traditionally in biology we use genetic engineering and modify genetic parts. Now we can use silicon parts, and silicon can be internalized. You can target those silicon parts to specific parts of the cell and modulate that behavior with light.”

In the new study, Tian and his team show how cells consume or internalize the nanowires through phagocytosis, the same process they use to engulf and ingest nutrients and other particles in their environment. The nanowires are simply added to cell media, the liquid solution the cells live in, the same way you might administer a drug, and the cells take it from there. Eventually, the goal would be to inject them into the bloodstream or package them into a pill.

nanowire internalization

After first coming into contact with the nanowire, the cell membrane extends along the entire length, engulfing the particle. This results in either complete or partial encapsulation of the SiNW into the cell.

Once inside, the nanowires can interact directly with individual parts of the cell, organelles like the mitochondria, nucleus and cytoskeletal filaments. Researchers can then stimulate the nanowires with light to see how individual components of the cell respond, or even change the behavior of the cell. They can last up to two weeks inside the cell before biodegrading.

Currently, the standard technology for recording and measuring electrical stimulation in a cell, called patch clamp, measures these signals across the entire cell membrane. This gives readings on cell behavior as a whole, but the nanowires would allow much more precise, targeted investigation of the cell.

Ramya Parameswaran

Ramya Parameswaran, study co-author

Seeing how individual parts of a cell respond to stimulation could give researchers insight into how medical treatments that use electrical stimulation work at a more detailed level. For instance, deep brain stimulation helps treat tremors from movement disorders like Parkinson’s disease by sending electrical signals to areas of the brain. Doctors know it works at the level of tissues and brain structures, but seeing how individual components of nerve cells react to these signals could help fine tune and improve the treatment.

The experiments in the study used umbilical vascular endothelial cells, which make up blood vessel linings in the umbilical cord. These cells readily took up the nanowires, but others, like cardiac muscle cells, did not. Knowing that some cells consume the wires and some don’t could also prove useful in experimental settings and give researchers more ways to target specific cell types.

Tian and his team manufactures the nanowires in their lab with a chemical vapor deposition system that grows the silicon structures to different specifications. They can adjust size, shape, and electrical properties as needed, or even add defects on purpose for testing. They can also make wires with porous surfaces that could deliver drugs or genetic material to the cells. The process gives them a variety of ways to manipulate the properties of the nanowires for research.

John Zimmerman

John Zimmerman, study lead author

“The studies here are really fundamental to understand how exactly these materials interact with cellular systems,” said Ramya Parameswaran, a MD/PhD student in Tian’s lab and co-author on the study. “The studies we did in this paper help us understand how certain cells internalize these nanowires so we can use them for many applications.”

Research on silicon nanowire-based cellular interfaces has been underway for less than 10 years, so there is still much to learn about their potential for research and treatment. But Tian and his team see the technology as a potential alternative to more permanent genetic methods.

“If you can put in an electronic device that’s transient, it’s much more similar to a traditional drug model where you put something in the body and it goes away over time,” said John Zimmerman, lead author of the study, a PhD recently graduated from Tian’s lab and now at Harvard as a postdoctoral scholar. “We like that aspect of the nanowires because it allows us to have a more transient synthetic biology, rather than a permanent genetic modification.”

The chemical vapor deposition system for manufacturing silicon nanowires

The chemical vapor deposition system for manufacturing silicon nanowires

Tagged: biochemistry, Biological Sciences, Bozhi Tian, chemistry, electrophysiology, John Zimmerman, molecular biology, Nanotechnology, Ramya Parameswaran, silicon nanowires

Video on UChicago octopus research wins Emmy

Tue, 12/13/2016 - 10:38

A feature video produced by UChicago Creative’s Anthony Penta has won a 2016 Chicago/Midwest Region Emmy for Outstanding Achievement for Informational/Instructional Programming. The segment looks at the work of Cliff Ragsdale, PhD, professor of neurobiology, and graduate students Carrie Albertin and Yan Wang as they study one of the weirdest and most amazing creatures on the planet.

In 2015, Ragsdale and his team sequenced the genome of the California two-spot octopus (Octopus bimaculoides), the first cephalopod ever to be fully sequenced. They found striking differences from other invertebrates, including a dramatic expansion of a gene family involved in nervous system development that was once thought to be unique to vertebrates. At the time, Ragsdale said, “The late British zoologist Martin Wells said the octopus is an alien. In this sense, then, our paper describes the first sequenced genome from an alien.”

 Judit Pungor  Judit Pungor/Nature. Octopus bimaculoides, one of the species being studied by the CephSeq Consortium

UChicago Creative is part of UChicago’s Communications office, serving as an on-campus multimedia and creative agency. The award-winning video was one of their Producer Pilot Projects, which allows staff producers to explore creative work outside of their day-to-day client assignments.


Tagged: Biological Sciences, Carrie Albertin, cephalopods, Clifton Ragsdale, Genetics, genome sequencing, neurobiology, octopus

How ants evolve different ways of defending themselves

Mon, 12/05/2016 - 12:24

Ant photos by Alex Wild

Did an ant sting you? Did it run away from you? Did an entire ant colony swarm in large numbers to defend its nest from you? If so, then you have witnessed firsthand the importance of defensive traits in ants.

Ants use a remarkable array of defenses to repel or avoid attackers, ranging from painful stings to the recruitment of a soldier caste. But despite this variety of traits, very little work has addressed the role of defensive traits in ant evolution or ecology.

I have been investigating the evolution of ant defenses for my Ph.D. dissertation in evolutionary biology, under the guidance of Corrie Moreau, my PhD advisor at the University of Chicago and the Field Museum of Natural History. In the first chapter, which was recently published in the journal Evolution, I asked two primary questions: Do defensive traits promote the evolution of increased species diversity in ants, and do these defensive traits exhibit an evolutionary trade-off?


Benjamin Blanchard

But what is an “evolutionary trade-off”? Different scientists may give you slightly different answers, but in my paper, I define an “evolutionary trade-off” as a negative correlation across species between different traits that serve similar functions. For example, I hypothesized that the presence of a chemical sting may “trade-off” with sharp spines on the exoskeleton. Both spines and a sting typically serve defensive functions, so using both traits may be redundant and therefore a waste of energy. Thus, over evolutionary time, it is possible that species usually evolve either spines or a sting, but not both.

To conduct my study, I first compiled a large trait database for all 326 currently identified ant genera, and included five traits that often serve defensive functions: Large colony size, large eye size, worker polymorphism (i.e. having a “worker” caste and a “soldier” caste), exoskeletal spines, and chemical sting. I also reconstructed a new, expanded phylogeny (“tree of life”) for the ants. This took quite a long time, but with these data, I could address my questions.

Using various statistical analyses, I found that several defensive traits are very important in ant evolution. In particular, spines, large eyes, and large colony size all promote increases in species diversity in ants. Furthermore, the chemical sting appears to exhibit an evolutionary trade-off with all of the other defensive traits I investigated, possibly due to the high cost of a sting with its chemicals and complicated structure.

Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild Ant photos by Alex Wild

The mechanisms for the patterns I detect are still uncertain though, due to surprisingly little work on defensive traits in ants. My results show that studies of these important traits are likely to be an exciting avenue of research, because such work will help us understand the causes of widespread ecological success in one of the most dominant and conspicuous group of insects on Earth.

So, the next time you see an ant defend itself by using a sting or swarming in large numbers, you’re not just witnessing a split decision. They may be traits that have driven the evolution of these little insects over the course of millions of years.

Tagged: ants, Biological Sciences, ecology and evolution, Evolution, evolutionary biology

European epidemics left a genetic legacy in Native Americans

Tue, 11/29/2016 - 09:45
A Tsimshian shaman tending to a sick boy

A Tsimshian shaman tending to a sick boy, 1910 (Image: Canadian Museum of History)

European conquest of North America had a devastating effect on its indigenous people. Warfare, forced migration and the resulting social upheaval decimated the populations of Native Americans, but perhaps nothing had a greater impact than the spread of diseases like smallpox.

Scientists have long wondered whether Native Americans were susceptible to European-borne diseases simply because they hadn’t been exposed, or if they were somehow more susceptible to pathogens carried by invaders. A new analysis of DNA from Canadian First Nations individuals suggests that genetic adaptions were at least part of the explanation. The study, published earlier this month in Nature Communications, shows big differences in immune system genes before and after European contact, suggesting that while these people had been well adapted to their environment before colonization, those who survived the epidemics rapidly developed immune system adaptations to protect against the new threats.

John Lindo, a postdoctoral scholar in human genetics at the University of Chicago, led a team that analyzed exome data—the subset of DNA that encodes protein needed for biological functions—from communities in the Prince Rupert Harbor region of British Columbia, Canada. This included 25 ancient samples, some more than 6,000 years old, taken from archaeological sites and 25 living individuals from modern Coast Tsimshian communities in the same area.

John Lindo, PhD

John Lindo, PhD

Lindo and the team first used the DNA to confirm oral histories and archaeological records showing that the modern individuals were indeed from the same ancestral population as the ancient samples. They then modeled the population history of the groups, and identified a 57 percent population decline about 175 years ago—corresponding with historical records of large smallpox epidemics.

When they scanned the samples for signs of positive selection—widespread, high frequencies of gene variants that indicate some genetic advantage—one gene stood out. One variant of HLA-DQA1, a gene directly involved in the immune system, was present in nearly 100 percent of the ancient individuals but only 36 percent of the modern ones. Instead, a different variant took its place in a span of about 150 years.

“It looks like an immune gene was selected for in the ancient population, which suggested that there were pathogens that could’ve existed when they first came into the Americas or particularly that region,” Lindo said.

But did that version of the gene make the ancient Tsimshian people more vulnerable to smallpox?

“You can’t say that,” Lindo said. “They were adapted to something else it seems, and then they quickly readapted to provide some sort of resistance potentially to the survivors of these pathogens.”

Lindo said the rapid shift from one gene variant to another in such a short amount of time is astonishing in human genetic terms.

“We wouldn’t have been able to detect it by using modern DNA alone,” he said. “But in adding the ancient DNA component, we’re seeing evolution happen essentially in humans for one of the first times. We’ve actually seen this shift happen in terms of genes, and can now correlate it to epidemics.”

More coverage:
Tagged: Biological Sciences, epidemiology, Genetics, human genetics, John Lindo, Native Americans, population genetics

Paint by number: Understanding how color patterns arise in nature using science and art

Mon, 11/21/2016 - 14:18

Erick Bayala inspects a butterfly inside a butterfly habitat in the University of Chicago Greenhouse

Erick Bayala once had a professor tell him he had a problem – he was a good artist and a good scientist, so he had to choose between them. “Well, I didn’t think I had to choose,” said Bayala.

“Many people have the idea that art and science are two things that will never mix,” said Bayala, a graduate student in the Department of Organismal Biology and Anatomy at the University of Chicago. “A lot of the first greatest scientists were also really good artists and the reason why we still learn about their science today is because of their art back then.”

While working on organisms that were unfamiliar to most people, Bayala would draw schematics to explain his research. Some of his professors suggested that he think about scientific illustration as a career possibility after graduate school.

“Some people think that scientific illustration died a long time ago because now people can just take pictures,” said Bayala. “The role of a scientific illustrator is to not only draw an image of what they see, but to take the knowledge of something and convert it into an image that people can relate to.”

Bayala uses scientific illustration to compile his data into representative images that can help people understand his research.

“Scientific illustrators have to know both the science and the art behind an image,” said Bayala.


Butterflies are used as model organisms to understand how color patterns develop in nature

As a scientist-artist Bayala was interested in pursuing biological questions related to color patterns of animals for his graduate work.

“Color patterns completely appealed to my artistic eye. I wanted to understand how these pieces of art in nature are formed,” said Bayala.

Bayala’s research in the lab of Marcus Kronforst, PhD, assistant professor in the Department of Ecology and Evolution, focuses on how color patterns are encoded during the development of an organism and how these complex processes are regulated.

“One thing we see a lot in nature is how animals have stripes, circles, and all of these beautiful color patterns, but we don’t really know how during development they acquire all of that information to produce the pattern.”

Bayala uses butterfly species as model organisms to understand how color patterns, which are important for reproduction, camouflage, and survival, are established and how they evolve. He wants to understand what happens during development that allows a particular color to be in a particular location.

“Butterflies have magnificent and diverse color patterns,” said Bayala. “I want to know how in development tweaking these mechanisms of establishing the colors can allow for much of the diversity we see in the animal world.”

Tagged: Biological Sciences, butterflies, developmental biology, Erick Bayala, evolutionary biology, Marcus Kronforst, Scientific Illustration

Four University of Chicago faculty named AAAS Fellows

Mon, 11/21/2016 - 10:00

Four University of Chicago scientists representing the Biological Sciences Division have been named as Fellows of the American Association for the Advancement of Sciences (AAAS). Fellows are elected by AAAS members for their scientifically or socially distinguished efforts to advance science or its applications. They are among 391 newly elected AAAS Fellows this year.

The 2016 University of Chicago AAAS Fellows are:

Geoffrey Greene, PhD

Geoffrey Greene, PhD

Geoffrey Greene, PhD, the Virginia and D. K. Ludwig Professor and Chair of the Ben May Department for Cancer Research

For distinguished contributions to the field of steroid hormone action and breast cancer, particularly for the development of estrogen and progesterone receptor antibodies.

Zhe-Xi Luo, PhD

Zhe-Xi Luo, PhD

Zhe-Xi Luo, PhD, Professor in Organismal Biology and Anatomy

For outstanding descriptions of mammals from Jurassic and Cretaceous strata of China, and for documenting the diversity, ecology and relationships of early mammals

Clifton Ragsdale, PhD

Clifton Ragsdale, PhD

Clifton Ragsdale, PhD, Associate Professor in Neurobiology and Organismal Biology and Anatomy

For exceptionally insightful experimental observations on the evolution and development of the brain.

Jonathan Staley, PhD

Jonathan Staley, PhD

Jonathan Staley, PhD, Professor in Molecular Genetics and Cell Biology

For distinguished contributions to the RNA splicing field, particularly conformational rearrangements, maintenance of fidelity and active site of the spliceosome, a highly dynamic RNA-protein machine.

The AAAS is the world’s largest general scientific society and publisher of the journal Science as well as several other journals and EurekAlert, the premier science news wire service. AAAS was founded in 1848 and includes nearly 250 affiliated societies and academies of science, serving 10 million individuals. The tradition of AAAS Fellows began in 1874.

The non-profit AAAS is open to all and fulfills its mission to “advance science and serve society” through initiatives in science policy, international programs, science education, public engagement, and more.

This year’s AAAS Fellows will be formally announced in the AAAS News & Notes section of Science on Nov. 25, 2016. New fellows will also be honored on Feb. 18, 2017, at the AAAS Annual meeting in Boston, Mass.

Tagged: AAAS, AAAS Fellows, Biological Sciences, Cancer, Clifton Ragsdale, Geoffrey Greene, Jonathan Staley, molecular genetics, neurobiology, organismal biology and anatomy, paleontology, Zhe-Xi Luo

Beyond the Gut: Unlocking the Secrets of the Microbiome

Wed, 11/16/2016 - 10:31


Alzheimer’s disease researcher Myles Minter, PhD, still sounds a little surprised while describing the improbable group of researchers he is collaborating with these days — not just neuroscientists but also colleagues from fields as disparate as gastroenterology and marine biology.

Minter and his advisor, Sangram Sisodia, PhD, the Thomas Reynolds Sr. Family Professor of Neurosciences, wanted to take their Alzheimer’s research in an unexpected direction, exploring the link between bacteria in the digestive system and brain health. The resulting study, published in July in Scientific Reports, broke new ground. It showed that a long-term course of antibiotics in mice weakened some of the telltale symptoms of Alzheimer’s disease in the brain, while at the same time producing marked changes in the makeup of their gut bacteria.

“I’ve been working with marine biologists who go deep-sea diving and take samples,” said Minter, a postdoctoral scholar in neurobiology, shaking his head. “Yes, previously I definitely would laugh at it, but once you put ideas together from different fields that largely have been believed to be segregated from one another, the possibilities are really amazing.”

This research marks one of the first collaborations coming out of the Microbiome Center, a joint effort by the University of Chicago, the Marine Biological Laboratory (MBL) and Argonne National Laboratory to support scientists at all three institutions who are developing new applications and tools to understand and harness the capabilities of microbial systems across different fields.

The term “microbiome” is shorthand for the vast and still largely unexplored world of bacteria, viruses, fungi and other microorganisms that inhabit every corner of the planet. To put it simply, they’re everywhere. They’re in the air, water and soil. Commensal bacteria live side by side with our own cells on our skin, in our mouths and along our airways. The bacteria that live in us also colonize all the surfaces we interact with, including our homes, offices and hospitals. Perhaps most important to human health, microbes in the gut constitute what some researchers consider a separate organ that shapes our metabolism, susceptibility to allergies and even responses to medical treatments.

Scientists in fields as diverse as microbiology, physics, chemistry and medicine are just beginning to understand how these ecosystems of microbes interact with each other and influence their environments. Until recently, researchers largely worked within their own disciplines, but as new technologies such as large-scale genetic sequencing and analysis have become more accessible and the momentum behind microbiome research builds, so have the opportunities for scientific serendipity.

Jack Gilbert, PhD, faculty director of the Microbiome Center

Jack Gilbert, PhD, faculty director of the Microbiome Center

“We’re starting to find that we have a unique ability—through the microbiome—to control how environments work and maybe even use the bacteria as a method of tracking those environmental changes,” said Jack Gilbert, PhD, faculty director of the Microbiome Center, as he and a group of like-minded scientists called for a concerted national effort to coordinate microbiome research across disciplines in the fall of 2015. “So we’re at a point now where if we coordinate our activities as a community, we can go after the really big questions.”

The scientists’ call to action eventually resulted in the White House Office of Science and Technology Policy launching its National Microbiome Initiative in May 2016 to bring together public and private entities to coordinate and fund microbiome research. The new Microbiome Center is one of the first models of how research institutions can leverage existing affiliations and pool intellectual horsepower across disparate fields.

Gilbert’s collection of titles speaks to the scope and ambition of the center: group leader in microbial ecology at Argonne, senior fellow at MBL, and his most unlikely appointment, professor of surgery at UChicago. He started his career as an entomologist studying butterflies before becoming a microbial ecologist (and is a fellow of the Field Museum). His work on the Hospital Microbiome Project, in which he and his team tracked the development of the microbial ecosystem in the University of Chicago Medicine’s new Center for Care and Discovery as it opened in 2013, led to a collaboration with John Alverdy, MD, the Sara and Harold Lincoln Thompson Professor of Surgery, who is working to prevent infections after surgery.

“It’s really bizarre. But here I am sitting in my office in the Department of Surgery, so I guess it is real,” Gilbert said. “I’ve been in environmental microbial ecology my entire life, and then suddenly over the last five years I’ve started to apply the same approaches to explore the human body as an ecosystem.”

So far, much of the attention on microbiome research, understandably, has centered on the digestive system and its contribution to conditions like inflammatory bowel disease or the onset of food allergies. But researchers across UChicago are already turning up evidence of the microbiome’s effects in new, unexpected places.

Read more about these unexpected collaborations, published previously on Science Life:

The “second brain”

Minter and Sisodia are exploring new territory in how the gut influences brain health. They teamed with microbiome researchers to study what effect, if any, changing the bacteria in the digestive system could have on symptoms of Alzheimer’s disease.

Community matters

Marisa Alegre, MD, PhD, and her team are studying the role microbiota play in the body’s ability to accept transplanted skin and other organs. In a recent study, the researchers demonstrated that skin grafts in mice treated with antibiotics prior to transplantation survive longer.

An unexpected ally

Thomas Gajewski, MD, PhD, and his team produced one of the first studies to show how differences in the gut microbiome could impact the effectiveness of cancer treatment.

An ecosystem of research

To microbiologists, the idea that there is a vast world of microbes out there, living in just about any nook and cranny you can think of, isn’t all that earth-shattering.

“If there is a carbon source out there, there is an organism that’s going to gure out a way to make a living off it,” said Dionysios Antonopoulos, PhD, a microbial systems biologist at Argonne and assistant professor of medicine at UChicago. He started his career studying the microbiology of ruminant digestive systems — i.e., cow guts — and has since moved on to studying the broader ecosystems these microbes inhabit and the give and take with resources that makes those communities stable.

To him, the interesting leap is when scientists start to take what they’ve learned about those other systems, from cow guts to waterways to man-made buildings, and apply it to human health.

“We’re not really in complete control of our bodies; these millions and millions of other entities are influencing the way our bodies function,” he said. “It’s that sort of work that’s sort of captured the imagination.”

For Gilbert, the secret to maintaining that momentum lies in breaking down barriers between different disciplines to create an ecosystem of shared research, so that a postdoc studying Alzheimer’s disease — such as Minter — may find himself learning sampling techniques from a marine biologist.

“We want to be able to break down boundaries between disciplines and institutions so that they are essentially nonexistent,” Gilbert said. “Yes, individual institutes have their own research agendas. But when people talk about the Microbiome Center, they won’t say the Microbiome Center at UChicago or the Microbiome Center at Argonne. They will just say the Microbiome Center.”

This article was originally published in the Fall 2016 edition of Medicine on the Midway, our premier publication for friends, alumni and faculty of the University of Chicago Medicine, the University of Chicago Division of Biological Sciences and the Pritzker School of Medicine.

Tagged: Alzheimer's disease, Biological Sciences, Cancer, immunotherapy, Jack Gilbert, Maria-Luisa Alegre, Microbiology, microbiome, Myles Minter, neurology, Neuroscience, organ transplant, Sangram Sisodia, Thomas Gajewski, Transplant, transplant rejection

Neil Shubin, Down (Way) Under

Fri, 11/11/2016 - 09:00
Neil Shubin, PhD, with a fossil model of Tiktaalik roseae

Neil Shubin, PhD, with a fossil model of Tiktaalik roseae

Neil Shubin, the Robert Bensley Distinguished Service Professor at the University of Chicago, is a veteran of the Arctic, but this year he and five colleagues will spend their Christmas holiday and celebrate the New Year – in a quiet way – at the other end of the world, Antarctica.

They will be looking for fossils. It will be zero to 10 degrees, about a mile above sea level, high winds, limited shelter, at the margin of where a helicopter can travel. “It’s going to be physically hard,” he said, but he and colleagues are excited about “the adventure of it.”

Shubin, a paleontologist, is a member of the National Academy of Sciences, author of two popular science books: “Your Inner Fish,” named best book of 2008 by the National Academy of Sciences, and “The Universe Within: The Deep History of the Human Body” (2013).  He has discovered some of the most important creatures in the fossil record and uses their anatomy to explore hypotheses about anatomical transformations. His most famous discovery, the 375-million-year-old Tiktaalik roseae fossil, is a key transitional form between fish and land animals.

ScienceLife spoke with him about his pending adventure.

Where did the idea come from to work in Antarctica?

In the hunt for key fossils in the history of life we look for places in the world that have three things—rocks of the right age to answer the question we’re interested in, rocks of the right type to preserve high quality fossils, and rocks that are exposed on the surface. These criteria led us to the Canadian Arctic to find the fishapod, Tiktaalik, in 2004 in rocks about 375 million years old.

We wanted to push the search farther back in time. Those criteria led us to the Dry Valleys and nunataks (mountains that poke through the ice) of Antarctica. There, rocks about 10 million years older are exposed extremely well. The winds form a kind of rain shadow, creating one of the driest climates on Earth. These areas have rock exposed adjacent to the ice. So we’ll have lots of good Devonian Age rocks, from the right kind of ancient river and stream environments that are very well exposed. To top it off, other teams in the area have found fossils at several sites. So we’re walking into a very promising area.

Who else is on your team?

Ted Daeachler, my co-PI on this project has been my collaborator on the Tiktaalik project. Adam Maloof (Princeton) is a great field geologist who will help us study and map the rocks themselves. John Long (Flinders, Australia) is expert on Devonian fish and has visited some of these areas before. Tim Senden (Australian National University) is expert on imaging, and Sune Tamm is a professional mountaineer and ice-rescue expert.

Has anyone on your team been to Antarctica before?

Yes: Sune has been a mountaineer on a number of scientific expeditions and John has worked some of the sites before.

How long did it take to devise and organize this adventure?

We first had the idea to work here in 2004 and sent off a proposal to the NSF. We found Tiktaalik that year, so were committed to the North for about the next 10 years. It is too hard to do both North and South polar expeditions in the same year, so we deferred this one until we were satisfied that we’ve accomplished what we needed in the Arctic.

We applied to NSF Polar Programs (the home of the US Antarctic Program) a few years back and began planning in earnest only this past summer/fall. The organization part happened fast because it occurs with the assistance of the US Antarctic Program and their contractors at Lockheed. In the Arctic we had to bring our own food and gear. Here, it is provided for us.

Where specifically are you planning to go?

We’ll work about 60-80 miles out of McMurdo Station, on bedrock, not on ice.

Antarctica map


How will you get there and how do you travel once you arrive?

We travel from Chicago to Los Angeles to Christchurch, New Zealand. There, the NSF has a station that outfits expeditions with clothing and does some training. From Christchurch we take an Air Force plane, hopefully a jet, for the voyage to McMurdo Station. We’ll stay in McMurdo for five days to a week gearing up, planning menus and training. We’ll also do a reconnaissance flight of the areas to determine campsites. The sites are about an hour’s helicopter ride from McMurdo. We’ve planned on three camps.

How different is it from Ellesmere Island?

The fossils will be older in time. We should find all kinds of fish from sharks to bony fish that are close relatives of limbed creatures. That’s what drew us there: the possibility of finding early sharks and other kinds of fish that tell of the early evolution of very basic skeletal architectures.

It is at a higher altitude than Ellesmere, so the sites will be drier, colder, and more solar (if that is possible).

What special precautions do you have to make for a trip like this?

Each field team member has to pass a series of medical and dental tests to work down there.

I’m running the stairs in my high rise to train for the 1km hike up the rocks each day.

How scary is this?

The scariest thing is being away and missing the holidays with my loved ones.

What do you expect to find?

This period contains the early evolution of many groups of fish, including the branch of the evolutionary tree that led to us. So, we are likely to find a number of important creatures.

What do you intensely hope, but only marginally expect, to find?

A well-preserved early shark would be amazing. Because their skeletons are mostly cartilage, they tend not to fossilize well. But, we’ll see…

Antarctica mountains


How much of the continent is accessible and exposed, rather than being covered with thick ice?

About 98 percent of Antarctica is covered by a mile-thick sheet of ice. The Dry Valleys, however, are one of the world’s most extreme deserts, with extremely low humidity and surrounding mountains that block the flow of ice from nearby glaciers. The bedrock is extremely well preserved.

Does climate change open up untapped inland areas to explore?

It is hard to say whether climate change has affected the exposures on the nunataks.

Are there specific prehistoric periods you plan to focus on?

The Late Devonian, rocks about 385 million years old.

What would be your dream find? Anything comparable to Tiktaalik?

Yes. We’d love to find a cousin of Tiktaalik. It is highly possible something like that is lying there waiting for us.

What will this adventure cost, how unpredictable is that, and how is it being funded?

It is funded through NSF and, honestly, I’ve no idea how much the logistics cost. I’m imagining it is not insignificant.

Tagged: Antarctica, Biological Sciences, Evolution, fossils, Neil Shubin, paleontology, Tiktaalik roseae