Fall 2020 -- Reengineering the Immune System

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Carolina Scientific

scıentıfic Fall 2020 | Volume 13 | Issue 1

Re-engineeringtheImmuneSystem —CAR T-CELLS PROMISING TREATMENT FOR CANCER— full story on page 26

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Work for Carolina Scientific!

Are you interested in communicating science to a broad audience?

Do you want to engage in thought-provoking investigations?

Does your passion for the sciences extend into the world of research?

Do you want to combine your creative talents with your fascination with the sciences?

Carolina Scientific is always looking for staff writers, designers, and illustrators!

If you are interested, please contact carolina.scientific@gmail.com Find us on facebook facebook.com/CarolinaScientific Follow us on twitter @UNCSci Check out our website carolinascientific.org

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Mission Statement:

Executive Board

Founded in Spring 2008, Carolina Scientific serves to educate undergraduates by focusing on the exciting innovations in science and current research that are taking place at UNC-Chapel Hill. Carolina Scientific strives to provide a way for students to discover and express their knowledge of new scientific advances, to encourage students to explore and report on the latest scientific research at UNC-Chapel Hill, and to educate and inform readers while promoting interest in science and research.

Letter from the Editors: Scientific research, at its most fundamental level, is an endeavor that allows us to ask questions about the world around us. This unrelenting process of posing questions and seeking answers can shed light on our place in the universe, help uncover the inner workings of our minds, and reveal insights that shape future innovations in technology and medicine. At Carolina, original and exciting questions are asked every day. How can we track wildlife in the aerial imaging and machine learning (p. 12) How do we utilize data from a global pandemic to enhance testing efficiency (p. 17)? How do we observe planets millions of light-years away (p.

38)? With this Fall 2020 edition of Carolina Scientific, we hope we inspire you to ask questions of your own. Enjoy!

- Andrew Se and Divya Narayanan

on the cover

UNC researchers are developing new and innovative strategies to apply cancer treatments to a range of liquid and solid cancer cells, such as the osteosarcoma cell pictured. Full story on page 26.

Contributors Staff Writers Kayla Blades Kylie Brown Henry Bryant Harris Davis Alisha Desai Abigail Dunnigan Kelly Fan Lasya Kambhampati Ryan Gomes Maya Groff Shanelle Jayawickreme Reva Kodre Sneha Makhijani Sophia Marcom Robert Rampani Alex Reulbach Joseph Schreder Jasmeet Singh Renna Voss Yue Yan Illustrators Ivonne Zhou Heidi Cao Hannah Kennedy Ivonne Zhou

Photo by Howard Vindin [CC BY-SA].

carolina_scientific@unc.edu carolinascientific.org facebook.com/CarolinaScientific @uncsci

Editors-in-Chief Andrew Se Divya Narayanan Managing Editor Megan Butler Design Editor Sarah (Yeajin) Kim Associate Editors Janie Oberhauser Maia Sichitiu Copy Editor Mehal Churiwal Treasurer Mehal Churiwal Faculty Advisor Gidi Shemer, Ph.D.

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Designers Heidi Cao Kelly Fan AJ Ferido Emma Kaeppler Ariana Reid Abigail Shuman Cassie Wan Olivia Wen Copy Staff Gillian Arleth Sara Barnate Julia Bay Elizabeth Bennett MaryAnn Bowyer Coleman Cheeley Elizabeth Coletti Emma Copenhaver Gargi Dixit AJ Ferido Evan Izzo Reva Kodre Nisha Lingam Jessie Ma Claire Nolan Aashita Rajput Alex Reulbach Krithika Senthil Stephen Thomas Sreya Upputuri

Carolina Scientific

contents

Environmental Science 6

Psychology & Neuroscience

3D Coral Imaging: Using a GoPro to Visualize Coral Reefs

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The Savvy Peoples of the Ecuadorian Amazon: Adapting to a Globalized Economy

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Alex Reulbach

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Renna Voss

up to a New Look at Solar 10 Warming Energy Maya Groff

Joseph Schreder

Medicine & Health

Unlocking the Secrets of Sleep

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Actively Reducing Inequality in the Classroom

Changing the Face of Early Cancer Detection

Using Bacterial Molecules to Kill Bacteria

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Time and THYME: The Search for Exoplanets

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Henry Bryant

What Makes Them Tick: The Fruit Fly’s Internal Gyrosope Harris Davis

Kayla Blades

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The Fungal Network: Syncytia are Integral to understanding Life Jasmeet Singh

Alisha Desai

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for A Cure: A Gene-Therapy 22 Hope Approach for Pitt-Hopkins Syndrome

Targeting Issues in AAV Vector Gene Therapy for Hemophilia Kelly Fan

Yue Yan

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Life Sciences

Shanelle Jayawickreme

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Sophia Marcom

Abigail Dunnigan

Covid-19 Testing Reaches New Heights with Pooled Testing Procedures Public Health Code of Ethics

Lasya Kambhampati

Physical Sciences

A “Turtle-y” New View

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Using Light to Control the Brain

Kylie Brown

to Life: Response Plans for 14 Keys Threatened Ecosystems

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Sneha Makhijani

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Robert Rampani

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Learning from Fruit Flies: How Memory Steers Action

The Secret Correlation between Cancer and Genetics Ryan Gomes

26 Re-engineering the Immune System Reva Kodre

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environmental science

3D Coral Imaging: Using a

GoPro to Visualize Coral Reefs

By Alex Reulbach Photo by Holobionics. [CC-BY-SA 4,0]

H

abitats across the world are quickly disappearing due to damaging human activities, and coral reefs are no exception. With coral reef disappearance accelerating at an alarming rate, scientists are working rapidly to understand the reasons these habitats are dying before it is too late. One method for studying coral reefs, used

by UNC-Chapel Hill marine ecologist Esteban Agudo and his team, has allowed scientists to quickly study coral reef ecosystems at a previously inconceivable level of detail. The method-structure from motion photogrammetryhas allowed Agudo and his team to further our understanding of coral reef habitats by making 3-dimensional (3D) Ph.D. student Esteban Agudo reconstructions of coral reefs and analyzing these structures for ecological trends.

Esteban Agudo, a marine ecologist and PhD student in the Department of Biology, lived in Venezuela before joining the Bruno Lab at UNC in 2019. Agudo’s research with his team in Venezuela focused on exploring the fish communities found within coral reefs in Archipelago de Los Roques National Park. During Agudo’s time working with his research team and his colleague Dr. Jose Cappelletto in Venezuela that he stumbled upon the process of 3D reconstruction that his current research relies upon. Be-

ing avid divers, Agudo and Cappelletto would frequently record their dives with a GoPro camera. On one of these trips, Agudo realized the potential his GoPro videos could have in studying the structure of coral reefs. As Agudo recalls, “At first we just started playing, just using a GoPro to take videos and finding the right software to use for 3-dimensional reconstruction. In that way we came up with pretty decent reconstructions of coral reef structure.”¹ As soon as they realized that this method of coral reef restoration was successful, they believed it could be utilized to solve problems in marine ecology.

To see if their method of 3D reconstruction could effectively be used to answer ecological questions, Aldo Croquer, Agudo’s former advisor and one of the team members, suggested that they start out on a small scale.

They wanted to know “how much coral reef fish are related to the structural complexity of a coral colony.”¹ Agudo relates structural complexity in coral reefs to the 3D framework that plants and trees create in a forest. In more structurally complex forests, different plants and trees create many nooks and crannies have many nooks and crannies that give refuge to the animals that inhabit the forest. The idea is very similar in coral reef habitats. “Coral reef fish are totally dependent on the refuge that they can find between the corals, rocks, and sponges you can find in a coral reef,” says Agudo.¹ More structurally complex corals have a greater number of holes, overhangs, and nooks that many reef fish depend on for shelter from predation. Agudo and his team hypothesized that as the structural complexity of a coral colony increased, the reef fish abundance and biodiversity would increase as well.

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environmental science

“One of the most important applications is coral reef monitoring. With this method of 3D reconstruction, you can have a more accurate picture of what is happening to coral reefs,” Agudo explained. ¹ With the health of coral reefs across the globe at an all-time low, coral reef monitoring is essential to understanding how coral reefs will respond to the ever-increasing threat of climate change. Agudo and his team believe that one of the main problems concerning coral reefs in the face of climate change is coral reef flattening. Agudo explains, “When coral dies, the structure

Figure 1. A. cervicornis colony (a) and 3D reconstruction created from the image (b, c)

To research this hypothesis, Agudo and his team headed north to Archipelago de Los Roques National, 100 miles off the coast of Venezuela Park. Once there, they used their GoPros to record 20 different coral colonies of the keystone coral species Acropora cervicornis and then created 3D reconstructions that modeled the coral colonies’ structural complexity.² Acropora cervicornis is a keystone species because it is essential to building the structural complexity of the coral reef that the other reef species rely upon. By comparing the structural complexity of the individual coral colonies to data collected about the fish communities via visual census, Agudo and his team were able to conclude that increased structural complexity of the coral colonies did indeed lead to higher fish abundance and biodiversity. The successful application of their method in an ecological experiment, while small in scale, demonstrated the effectiveness of using the GoPro to produce accurate 3D reconstructions.

Figure 2. Esteban collecting data on fish communities via visual census

“When coral dies, the structure of the reef starts falling apart. This is something that is called coral reef flattening. If coral reefs become flat, fish lose their refuge and are more likely to disappear.”

of the reef starts falling apart. The phenomenon is called coral reef flattening. If coral reefs become flat, fish lose their refuge and are more likely to disappear.”¹ Monitoring the structural complexity of coral reefs over time using Agudo’s 3D reconstruction method could help scientists determine if a coral reef is healthy or not.

While Agudo and his team have already discovered much about the relationship between structural coral reef complexity and fish communities, there is still more to explore. Agudo and his team’s next step is to see if the relationship they found between structural coral reef complexity and fish communities is consistent among different types of marine ecosystems. Agudo remarks, “It can be interesting to compare how much structural complexity different habitats have, and try to see how these relate to fish communities.”¹ Without a doubt, the answer to this question will be invaluable to our understanding of the relationship between habitats and fish community composition. Agudo and his team hope that their method of 3D reconstruction will be able to answer this question and many more in the coming years.

With their method scientifically verified, Agudo and his team returned to Los Roques National Park to implement their method on a much larger scale. Agudo and his team wanted to know if the relationship between structural complexity and fish communities they saw on the scale of individual coral colonies would be similar on a much larger, reef-wide scale. They repeated the same methods they had used in the small scale study, but recorded 50 meter transects of coral reef instead of just one small coral colony.³ What they discovered was that “structural complexity and the number of holes and the sizes of the holes in the reef actually explain fish abundance and fish biodiversity.”¹ Their important discovery demonstrated that their method of 3D reconstruction could be implemented to successfully recreate 3D structures of large swaths of coral reefs and in enough detail to answer important ecological questions.

Agudo and his team’s successful application of structure from motion photogrammetry to perform ecological experiments is just one way that this method can be used.

References

1. Interview with Esteban Agudo, Ph.D. student 10/16/20 2. E. Agudo-Adriani; J. Cappelletto; F. Cavada-Blanco; A. Croquer. PeerJ 2016, 4, eCollection 3. E. Agudo-Adriani; J. Cappelletto; F. Cavada-Blanco; A. Croquer. Frontiers in Marine Sciences 2019, 6, eCollection

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environmental science

The Sav v y Peoples of the Ecuadorian Amazon: Adapting to a Globalized Economy

By Renna Voss Figure 1. Ecuadorian Amazon Rainforest

Photo by Neil Palmer/CIAT. [CC-BY-SA 2.0]

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s a historical continuity, the success of colonialism is founded upon the displacement, exploitation, and even eradication of Indigenous populations. This concept is quite familiar to a highly colonized North America.

People often remember North American colonialism as a blip in history, forgetting about the Indigenous populations that still exist in their limited territory, adapting to their neocolonial surroundings while maintaining the strength of their own cultures. In the biodiverse Amazon Basin, oil and natural resource extraction constantly threaten the ecosystem and its already displaced inhabitants (Figure 1). Primarily, deforestation augments the effects of pollution, worsens erosion, and causes habitat loss for rainforest animals and plants. Indigenous peoples in the Amazon Basin respect their lands, preserving the biodiverse ecosystems and preventing further encroachments from exploitative economic bosses. One scholar who studies this phenomenon is Clark Gray, an associate Geography professor at the University of North Carolina at Chapel Hill and researcher in environment and population geography (Figure 2). He, along with fellow researcher Richard Bilsborrow, explores the relationship

between Indigenous groups who inhabit the Ecuadorian Amazon and their surrounding colonial market economies.

Their research can be found in their study entitled Stability and Change Within Indigenous Land Use in the Ecuadorian Amazon.š The resulting data collection suggests that the studied Indigenous groups generally adapt to growing global markets, but each Indigenous group adapts differently, and to its own extent.

This display of adaptation raises crucial questions regarding the future of these groups and their potential further adjustments. The existing environmental impacts of market economies on Indig-

Dr. Clark Gray

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enous lands also raise the question of whether colonial peoples have any responsibility to defend Indigenous lands from environment-degrading economic influence.

The study by Gray and Bilsborrow offers remarkably unique data because researchers conducted it over a tenyear time period. This was necessary for the examination of long-term changes in Indigenous land use in the Amazon Basin. This method of field research is conducive to the observation of gradual changes that impact underrepresented populations. Indigenous groups make up 20 percent of the population of Ecuador, but 90 percent of them live in the Andes while 10 percent live in the Amazon.² Thus, only 2 percent of the Ecuadorian population are Indigenous people residing in the Amazon. This relatively small, but valuable group of humans was seldom studied with long-term consideration prior to this research. In Dr. Gray’s study, 32 Indigenous communities, representing 5 ethnicities, participated in interview-style data collection in up to 22 households per community.

Interviewers used identical questionnaires in 2001 and 2012, asking heads of households about their land ownership,

Carolina Scientific agricultural production, demographics, and other related topics (Figure 3).¹ Clark Gray expresses that “collecting information directly from people” is “one of the great things about the population sciences and population geography,” as the intimate study method produces data that reflects the nuances of individual lives and viewpoints.² The results of his research reveal that although the environmental footprint of Indigenous agriculture remained consistent between 2001 and 2012, the groups adapted to surrounding market economic demands.

vironment. While Indigenous populations tend to remain more isolated from mainstream economies than colonial communities, they interact with their surrounding economies just enough for them to thrive under their circumstances.

Clark Gray points out the “different trajectories of […] urban adjacent Indigenous people and remote Indigenous people,” resulting in different levels of interaction with urban populations.² Considering the Shuar group’s heavy participation in land expansion for market demands, Gray refers to the urban-adjacent Shuar

Figure 2. The team of surveyors who conducted interviews in 2012 This means that the overall land area as “agricultural colonists.” Contrarily, the used by Indigenous groups kept its size, remotely located Cofàn and Waorani but the way each group used their land groups notably showed little change.¹ Inshifted as they found more opportunities digenous populations in the Ecuadorian in increasingly popular fields of agricul- Amazon are resilient when they choose tural production. to remain dissociated from colonial influOf course, changes in land owner- ence, but groups that choose to interact ship varied between specific Indigenous heavily with colonial economies prove communities. The Shuar group, for exam- to be adaptable and successful in maxiple, gained land area mizing their profits. On “We should support for their increased catthe topic of future entle ownership, whereas croachment by oil comthem, the Kichwa group lost panies and other large recognize their land area because of industries, Clark Gray independence, and their decreased cofrecognizes the disadfee production. The sivantage of handling be thankful for their multaneous decrease attempted incursions preservation of the in coffee cultivation under circumstances Amazon Basin. of poverty, geographic and increase in cacao cultivation was one of isolation, and social the most remarkable shifts in land use exclusion, but has utmost faith in these evident from the data. It corresponds select groups to advocate for themselves: directly to the shift in price for those “These communities are savvy, and they goods in Ecuadorian and global markets. will maneuver to extract the resources According to Clark Gray, the decrease in they want from oil companies [and] the coffee production is a result of a global government, and resist incursions that price decline, along with a plant disease they don’t want.”² and its detriment to a monoculture enClark Gray prioritizes the acknowl-

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environmental science edgement that Indigenous people in the Ecuadorian Amazon and their surrounding economies can work symbiotically.

The market is not a threat itself. Gray’s research results shift the crucial questions regarding colonial responsibility to address the future of market influence on Indigenous peoples and encroachment on their precious lands. Gray asserts that “the question [...] is not how to defend them against the market. It’s more like, ‘How do we help them live the lives that they want to live while also protecting the forest?’”² The provision of healthcare and educational resources, Gray claims, are the clearest solutions. Perhaps the Ecuadorian Amazon’s Indigenous folks should receive benefits from the government who reaps economic benefits from their agriculture, and hopefully the global economy can switch to renewable energy sources that prevent invasion of precious rainforests and Indigenous lands. The Indigenous groups in this region are surely marginalized. They face poverty and isolation from resources, hardships on their own that also augment struggles against attempted incursions from oil companies While negotiations with companies who desire land and resource access can yield benefits for Indigenous landowners, they require effort beyond daily obligations, stress that is unique to these groups.

Although these Indigenous groups face extra hardships, they manage, by no means relying on aid from colonial people. “I want to avoid the perception that they’re […] passive victims…” says Gray as he concludes his interview.² While colonial communities should provide more medical and educational resources for the marginalized Indigenous communities that protect Ecuadorian forests, no saviorism is necessary because these communities defend themselves, their cultures, and their lands. The savvy folks who protect the Ecuadorian Amazon will not go away or assimilate; that is no concern. We should support them, recognize their independence, and be thankful for their preservation of the Amazon Basin.

References 1. Gray C, Bilsborrow R. Stability and change within Indigenous land use in the Ecuadorian Amazon. Global Environmental Change. 2020;63:102116. doi:10.1016/j.gloenvcha.2020.102116 2. Interview with Clark Gray, Ph.D. 09/16/2020

environmental science

Warming up to a New Look at Solar Energy

by Robert Rampani Photo by Roy Bury. [CC0 1.0]

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lipping on a light switch. Charging a cell phone.

Driving to Starbucks.

For most of us, especially in the routine-filled world of virtual learning, our everyday actions with power consumption are barely an afterthought. There seem to be so many more pressing issues than a potential energy crisis – after all, is that not for the smartest minds of our generation to worry about? Such apathy towards the world’s tremendous consumption of energy is one of the many reasons the production and use of fossil fuels are so rampant across many parts of the globe. While the ramifications of such use go without saying, continued use of fossil fuels and the limits of those resources has created, albeit gradually, one of the greatest problems science has to face in the twenty-first century.

Dr. Gerald Meyer, a Professor of Chemistry at UNCChapel Hill, remembers sitting with his father in a long, tedious line for gasoline during the OPEC oil crisis of the 1970s when the apathy of the reliance on petroleum was turned on its head.

Dr. Gerald Meyer, PhD. The strong depen-

dence on the limited supply of fossil fuels, especially gasoline, was increasingly apparent during the peak days of the scare. From that moment forward, Dr. Meyer has dedicated much of his life’s work to discovering novel, renewable ways to meet the energy requirements of the world through his research in inorganic chemistry.

According to Dr. Meyer, the limited supply of fos-

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Figure 1. Hubbert’s Peak, showing peak oil production during the 2020s. Image courtesy of WikiCommons.

sil fuels should not be news to anyone – including large energy-producing corporations.2 In the 1950s, M. King Hubbert, a groundbreaking geologist who worked for the Shell Oil Company, developed what is now known

Carolina Scientific as Hubbert’s Peak: an approximation of oil production on a worldwide scale (Figure 1).2 While the approximation has not always been accurate, its data does represent a hard truth. Hubbert’s peak predicts that, while petroleum reserves will last longer than many activists suggest, they will eventually decline until wells dry up.2 Therefore, the next 100-200 years of remaining supply give researchers, including a new research partnership headed by Dr. Meyer, vital time to discover and employ innovative research methods to develop new renewable energy technology.

While growing in public favor and implementation, current renewable technology is far from dominating the energy marketplace.

Many avenues exist, including hydroelectric dams, generating power from the tides and ocean currents, digging geothermal wells, and the vast breadth of wind power, especially across the flat Midwest and coastlines of the United States. Still, none come close in possible energy production to meet the world’s needs other than solar energy. A simple walk outside during the hot months of the Carolina summer makes it clear that the problem is not a lack of abundance of solar energy striking the Earth; the problem is the storage of the power.1 The question of storage is where Dr. Meyer’s passion for research and development in renewable energy comes in.

The newly formed Center for Hybrid Approaches in Solar Energy to Liquid Fuels, or CHASE, is an exciting, collaborative effort between UNC-CH, North Carolina State University, Yale University, the University of Pennsylvania, Emory University, and the United States Department of Energy’s Brookhaven National Laboratory on Long Island.

Their goal, while complex and beyond the scope of many undergraduate chemistry classes, is to use the power of the sun to create liquid fuels to store solar energy in a more efficient way than traditional battery technology.

Chemical bonds can “store” solar energy through transferring that radiation into Gibbs free energy, which can be transformed through various chemical reactions.

By the principles of thermodynamics, everything wants to be at the lowest energy state, including atoms that bond together to form molecules. When creating a bond, atoms lower their individual energies and – through reactions completed later on with that molecule – that energy in the bond can be expressed in a variety of ways.

CHASE hopes to use simple and abundant molecules, like CO2 and H2O, to achieve its goals.

The concepts of energy storage may sound simple enough, but CHASE and Dr. Meyer are heading quickly into uncharted territory. “Storage” in chemical bonds pro-

environmental science

Figure 2. CHASE Scientists: A Collaborative Effort

vides large amounts of energy in a compact and highly efficient way, but manipulating molecules and attempting to understand the complex reactions of the quantum world can be hard to grasp and even harder to control.

The basic principles of chemical reactions are being pushed to their limits to react CO2, notoriously stable and pesky to use, to bond carbon atoms to each other. The carbons could build up to common molecules used for energy production such as ethanol, butanol, and – in an ideal world – other molecules that make up gasoline and natural gas. 1 Dr. Meyer hopes he, along with 30 scientists from the various institutions enrolled in the program across the country (Figure 2), can make significant breakthroughs over the next few years. Those goals include demonstrating that once-theoretical concepts are possible, which has caught the attention of the United States Department of Energy and has secured $40 million in funding for CHASE. Dr. Meyer implores students and faculty of UNC to investigate the data and come to their own conclusions about greenhouse gas emission and climate change. He urges those of the next generation to take a hard look at the world’s situation and strive for the eventual dominance of renewable energy. “These huge problems will be solved one person at a time through slow and steady research,” he admitted. It will require each of us to make incremental advancements that impact the world for the better.1 The task is now ours, and it is up to us to ensure the Earth is available, in all its beauty and splendor, for generations to come.

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References

1.Interview with Gerald Meyer, Ph.D. 09/08/20.

2.Hubbert, M. King; Shell Development Company Exploration and Production Division 1956, 59

environmental science

A “Turtle-y” New View

By Maya Groff

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lmost every month, thousands of olive ridley sea turtles flood the shores of Ostional, Costa Rica, covering the soft, cool sand with their olive colored shells. The turtles travel from all stretches of the ocean and swarm onto the shore for a nesting event called the arribada. Despite the arribada’s grandeur, olive ridley sea turtles, and five other participating species, are listed on the International Union for Conservation of Nature Red List of Threatened Species, primarily as a result of human behavior. This categorization indicates that the sea turtles will become endangered without adequate protection measures. The gravity of many species’ situation highlights the importance of collecting sea turtle population data in order to ensure their survival.

With the development of aerial imaging, scientists have recently enlisted unmanned aerial vehicles, or drones, in their efforts to track sea turtles. However, the images captured by

Olive ridley sea turtle quantified using machine learning technology.

Photo by C Watts [CC-BY-2.0]

drones require tedious analysis in order to determine the number of turtles in each shot. UNC Chapel Hill Professor of Biology Kenneth Lohmann hopes to apply machine-learning technology to expedite this analysis process. His team Figure 1. Drone image showing the presence of olive ridley sea turtles. Image courtesty of Dr. Lohmann

Dr. Kenneth Lohmann utilizes a technique known as convolutional neural networks to analyze photographs taken by drones flown above the ocean during mass sea turtle nesting events.

To develop this technique, Dr. Lohmann and his team conducted

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twenty drone imaging flights. Then, they utilized a selection of the resulting data to train the convolutional neural network. During this training process, a series drone images were uploaded to the network and the team “taught” it to determine which displayed turtles, and which did not. Another set of images could then be analyzed using the trained convolutional neural network to count the number of olive ridley sea turtles present during the arribada.

However, the fact that sea turtles are in constant motion poses a significant challenge. As Dr. Lohmann says, “there are complications because you

Carolina Scientific catch the turtles in different positions – as they’re swimming, they move their flippers down, or you can catch the turtles with their flippers tucked in close.” 1 Therefore, the convolutional neural network must be trained to recognize that a single turtle may exist in a range of different orientations.

To address this issue, convolutional neural networks were trained using image samples of turtles in a variety of positions, allowing the technology to account for the movement of each turtle and determine their presence at a specific moment.

Despite this challenge, Dr. Lohmann’s study found that convolutional neural networks represent a successful method for analyzing drone imagery of olive ridley sea turtles. He comments, “It was very exciting to see that these problems can be overcome — we can create technology with a good counting system in which the numbers look pretty similar to what we get if we painstakingly go through and count the turtles in the images.” 1 The use of convolutional neural networks drastically reduces the time and brainpower required to analyze aerial photographs of marine wildlife; it also improves counting accuracy. Machine learning technology positively identified 8-9% more turtles than human analysis, demonstrating a more accurate and reliable determination of sea turtle density. 2 In regard to future development of image processing technology, Dr. Lohmann says, “the dream version is to send your drone out over the water to collect the video, and

environmental science

Figure 3. Drone used to collect aerial images of olive ridley sea turtles.

Image courtesy of Dr. Lohmann

your machine vision system would automatically analyze all of those for you,” allowing for immediate detection of animal density in an area. 1 The greater significance of Dr. Lohmann’s study lies in the potential for such technology to be implemented for the protection of a wide

“The greater significance of Dr. Lohmann’s study lies in the potential for such technology to be implemented for the protection of a wide range of endangered species.”

range of endangered species. The ability to quickly and easily collect wildlife population data allows for the identification and limitation of harmful human actions in order to protect those species.

Most behavior that negatively impacts olive ridley sea turtles occurs along the shore, including intentional capture of turtles for their skin and meat as well as accidental ensnarement of turtles during fishing. Shrimp fishing, Figure 2. Arribada, mass nesting event of olive for example, often results ridley sea turtles. Photo by Wikimedia Commons. in inadvertent capture and

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killing of many turtles during highdensity nesting periods. Therefore, regularly scanning for sea turtle density near the Costa Rican coast could assist locals in the enforcement of protective measures and the limitation of harmful activities during periods of time in which large gatherings of turtles are present. Similar shifts in human behavior would have a huge impact on the protection of this species.

The development of machine learning technology capable of processing images has the potential to be of tremendous benefit to not only olive ridley sea turtles, but also to other at-risk wildlife in all environments around the world. Machine learning lends us a heightened awareness of species density and position, which allows for the protection of some of the world’s most vulnerable inhabitants. However, the responsibility does not fall solely on technological advancements like the methods developed by Dr. Lohmann’s team. It is up to the rest of the world to implement his research alongside a commitment to protect endangered species.

References 1. Interview with Kenneth Lohmann, PhD. 9/18/20 2. Gray, P; Fleishman, A; Klein, D; McKown, M; Bézy, V; Lohmann, K; Johnston, D. Methods Ecol and Evol.

2018, 10, 345-355.

environmental science

Keys to Life: Response Plans

For Threatened Ecosystems

By Joseph Schreder Image courtesy of Wikimedia Commons

W

hat if you knew the best way to respond to the stresses of your everyday life? Your life would be more successful and productive. The stakes are even higher for the environment. If we could develop the most advantageous response plan to things such as hurricanes, wildfires, and extensive pollution, the organisms that keep our planet rich with biodiversity would be protected. Food webs show the relationships of all organisms within an ecosystem and can display the consequences of changes to the environment. Currently, research is being done by Dr. F. Joel Fodrie of the University of North Carolina Institute of Marine Sciences to better understand these webs, which will allow scientists to formulate the optimal response to environmental stress.

One of the most prominent examples of an environmental stressor in the United States was 2010’s Deepwater Horizon oil spill, in which 5 million barrels of crude oil leaked into the Gulf of Mexico. The 5 million barrels of oil spread to over 100 kilometers of shoreline, with the marshes of Louisiana absorbing the brunt of the damage. Dr. Fodrie studies coastal biological oceanography with a focus on both trophic interactions in estuarine communities and the connectivity of marine populations and ecosystems. He conducted a study of the food webs in the Gulf of Mexico, and how they were affected by the tragic Deepwater Horizon oil spill.1 Disastrous accidents like this rarely occur, so as a marine scientist, Fodrie was interested in the possible effects that oil would have on the salt marsh ecosystem.2 To better understand the implications of the spill on local ecosystems, Dr. Fodrie began the study by constructing a model of the salt marsh food web located on the coast of Louisiana with a focus on one of the most heavily polluted areas: the Barataria Bay region. A food web is essentially a series of interdependent food chains, so there are many

Figure 1. Oil Spill Area. Image courtesy of BBC News.

links between organisms. For the purposes of the study, links were only established if organisms were directly observed in a predator-prey relationship, whether observed on site, experimentally, or through analysis of stomach contents.

Data from over 120 studies was analyzed to accurately represent the food web. Overall, the web has 52 organisms with a total of 376 links between them.3 To produce an accurate food web, Dr. Fodrie needed to understand which species were the most sensitive to oil.

He determined this by analyzing 37 different studies that documented the impacts of the oil spill on the populations of the 52 species in the food web. These pieces of literature were either published papers or field-based studies relevant to the effects of oil on the organisms. The purpose of this analysis was to create a baseline of oil sensitivity to compare to the results gathered by Fodrie and his team. If no studies existed for a particular species, the team used data from the

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Carolina Scientific

Dr. Joel Fodrie in the salt marsh

effects of other oil spills or that of laboratory experiments.

From the publications, every species involved was given an oil sensitivity index score. If no effect was observed or that species sustained a population increase, a 0 was recorded.

Taxa that were minimally affected by the oil and recovered quickly received a 1 and taxa that experienced slow recoveries were given a score of 2. These results were then utilized to determine the consequences that each species’ resilience to oil has on the complex food web of the salt marsh ecosystem.

This was broken into four categories: critically sensitive, critically resilient, sensitive with few food web effects, and uncertain consequences for the food web.3 Critically sensitive taxa were denoted by species that received high oil sensitivity indexes and were depended on by other species in the ecosystem. This impairs the food web, as organisms such as gulls and terns are killed by the oiling, destabilizing the ecosystem. Wading birds such as herons, egrets, and ibises were also categorized as critically sensitive.

Additionally, bottlenose dolphins and terrestrial plants were categorized as critically sensitive, as they perform versatile functions in the salt marshes.

Even with the extensive research and data, some questions are left unanswered. While blue crabs were ranked as the single most crucial species to the existence of the food web, their moderate sensitivity to oil and unclear population response makes it extremely difficult to pinpoint the consequences of the oil spill. The number of adult blue crabs in the Gulf of Mexico following the oil spill remained unchanged. The abundance of blue crabs in the early stages of life decreased, but studies were not able to conclude that it was a definite result of the Deepwater Horizon oil spill.3 The research provides considerable progress for understanding the higher-level trophic interactions in salt marsh food webs. However, the Gulf of Mexico is teeming with biodiversity, so studying the effects of an oil spill on all of the species involved in the ecosystem and food web is

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exceptionally challenging. The team was unable to come up with oil sensitivity index scores for a few salt marsh species, including reptiles and omnivorous terrestrial mammals.

Reptiles included snakes, alligators, and terrapins. The land mammals that the team was unable to study were coyotes and raccoons. Researchers like Fodrie normally repeat experiments over and over to confirm results, but Fodrie acknowledged the fortuitous aspect of his study. As the oil spill occurred “emergency room science” was conducted, and “everyone scrambled to collect data that would soon disappear”.2 According to Dr. Fodrie, the constructed model of the Gulf of Mexico salt marsh food web in relation to the relative oil sensitivity will allow scientists to predict responses to future oil spills in areas similar to that of the Deepwater Horizon oil spill. His study provides a valuable template for future research on trophic interactions, whether they be in salt marshes or completely different ecosystems. The framework for evaluating the role of each individual species in the food web as they respond to environmental stressors will facilitate more studies in the future. This method provides scientists with the data they need to properly respond to environmental stressors capable of decimating entire ecosystems anywhere in the world. When scientists know what the effects of an environmental stressor will be before it occurs, they can determine the best possible response plan to help ecosystems recover based on important species and their resistance.

Figure 2. Oil Sensitivity to Food Web Importance Matrix.

Image courtesy of ESA Journals.

References

1. F. Joel Fodrie. UNC Marine Sciences. https://marine.unc. edu/people/faculty/f-joel-fodrie/ (accessed February 3, 2020).

2. Interview with F. Joel Fodrie, Ph.D. 01/30/2020.

3. Able, K; Christian, R; Fodrie, J; Jensen, O; Johnson J; López-Duarte, P; Martin, C; McCan, M; Olin, J; Polito, M; Roberts, B; Ziegler, S. Key taxa in food web responses to stressors: the Deepwater Horizon oil spill. 2017, eCollection

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medicine & health

Covid-19 Testing Reaches New Heights with Pooled Testing Procedures

Image by HFCM Communicate. [CC-BY-SA 4.0]

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By Shanelle Jayawickreme

ave you been tested for Covid-19? As I anxiously awaited to take my test, deep down I wondered if I was being exposed to the virus at that very minute, standing in a long line. Sitting in my chair, part of me knew only a thin layer of disinfectant spray served as the barrier between my germs and those of the people who preceded me. Luckily, I ended up testing negative. This is not the case for the group of people who test positive, or the even larger population affected by limited access to resources and funding for testing and treatment sites in their area.

The COVID-19 outbreak has dominated the lives of U.S. citizens well into 2020, leaving many struggling to find stability in a period of overwhelming uncertainty. Although the coronavirus pandemic has been present for over seven months, the public constantly Dr. Daniel Westreich craves more information on how to better handle this situation. With increasing demand and a limited supply of testing resources, it is imperative that new solutions and strategies are publicized for the greater good.

UNC-Chapel Hill researchers Daniel Westreich and Michael G. Hudgens from the department of Epidemiology and the department of Biostatistics, respectively, in collaboration with Christopher D. Pilcher from the University of California San Francisco, have proposed a solution for upscaling COVID testing. “Pooled testing of a virus is an efficient way to move the testing agenda forward,” allowing for higher productivity and proper utilization of resources when compared to individual testing methods already in place.1 Pooled testing is a procedure that has been used for many decades by scientists and involves combining individ-

ual swab samples into one big pool before testing for the virus. In the case that the test comes back negative, the scientists save a large quantity of testing materials by only using one set for the entire cohort. If instead the pooled sample yields a positive result, then each individual sample within the pool is retested in order to identify those responsible for the positive result. This process can also involve an intermediary stage, in which the total group assay is split into smaller and smaller groups until the positive tests are located. In this manner, testing resources are conserved while still allowing the scientists to observe the results of each sample.

Figure 1. Pooled Testing Procedures. Image courtesy of Jean-Etienne Minh-Duy Poirrier [CC BY-SA 2.0]

Westreich began by producing a model that illustrated the distribution of the window for SARS-CoV-2 detection, which predicts changes in viral concentration from the first day to the last day of infection. This proved difficult to consolidate into a mean projection due to the fluctuating nature of the virus.2 Westreich explains, “there is a gap between when you’re infected with the virus, and when your body starts to produce measurable responses to the virus.”1 In that gap, one can be very infectious to others. Vi-

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Carolina Scientific ral loads, the measured quantities of the virus, increase and decrease significantly throughout the duration of an infection. For example, someone may pick up a large viral load that diminishes before it is able to duplicate. In order to create a viral detection model, Westreich, Pilcher, and Hudgens set the default detection window at 14 days and generated an equation for estimating peak viral load, rate of viral increase, and the slope of viral decay.

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that, for pooled testing methods in particular, efficiency is high where the virus prevalence is low. In other words, in a population likely to have a high density of negative cases, pooled testing methods allow for minimal retesting, since there are fewer positive cases. Low risk areas such as healthcare facilities and large clinical studies can benefit from such a strategy. Smaller sample pools, on the other hand, prove better suited for high-risk populations.2 Westreich wants these findings to be communicated transparently so that people can “make the tradeoffs between gains in efficiency and losses in detection due to the dilution of samples.”1 To top it off, Westreich, Pilcher, and Hudgens also created a free online calculator to help labs make decisions regarding how to conduct their pooled testing.2

Figure 2. Model for Window of Detection. Image courtesy of “Group Testing for Severe Acute Respiratory Syndrome– Coronavirus 2 to Enable Rapid Scale-up of Testing and RealTime Surveillance of Incidence”

Using their model, Westreich, Pilcher, and Hudgens predicted a detection window for group testing and compared it with the detection window for widely used individual testing. In particular, they wanted to determine how well the sensitivity of group testing compares to individual testing, and if group testing results in a significant dilution of each sample.2 The methods in which this model was meant to be used are similar to those once utilized in group testing software for HIV. Both take into account diagnostic sensitivity, or a measure of how accurately the test diagnoses a patient, and analytic sensitivity, or the test’s accuracy in identifying positive results.

Westreich, Pilcher, and Hudgens identified a tradeoff: large pool size allowed high output but lowered analytic sensitivity, while smaller pool sizes exhibited high analytic sensitivity at a slower rate.2 Their model illustrated that pool sizes greater than 25 people tend to reduce analytic sensitivity, so they set the upper limit at 25 samples. Each pooling strategy presents unique benefits and shortcomings, but such methods generally allow for 2-20 times the number of specimens to be processed using the same number of tests as are currently used. Their study investigated both two-stage and three-stage pooling. Both versions include the large-scale pool test and individual test (when necessary). The three-stage also includes an intermediary test.

Such methods improved average time to results, sensitivity, expected number of screenings, and Positive Predictive Values (PPV, the proportion of test results that are positive).2 Westreich and Hudgens ultimately detailed a wide range of methods to improve COVID-19 testing. They found

Figure 3. Efficiency for Various Pool Sizes. Image courtesy of “Group Testing for Severe Acute Respiratory Syndrome– Coronavirus 2 to Enable Rapid Scale-up of Testing and Real-Time Surveillance of Incidence”

Although SARS-Cov-2 represents a good candidate for pooled testing methods, a degree of analytic sensitivity can and will likely be sacrificed due to a lack of proper resources. However, the effects can be lessened with the implementation of pooled testing, as it requires less resources per assay. Looking ahead, serological antibody tests seem to optimize the diagnostic sensitivity of pool testing. Westreich, Pilcher and Hudgens recommend that large-scale laboratories begin implementing group testing methods in order to maximize use of the physical tests.2 Westreich hopes that his pool testing models will “help people with the rapid and massive scale up of testing.”1 Furthermore, he shares that the state of North Carolina is currently funding the expansion of their web calculator, and Westreich and Hudgens have launched a number of ongoing projects to ultimately make COVID-19 testing methods even more efficient.1

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References

1. Interview with Daniel Westreich, Ph.D. September 7th, 2020.

2. Pilcher, Christopher D.; Westreich, Daniel; Hudgens, Michael G.; The Journal of Infectious Diseases 2020, 222, 903–909.

medicine & health

Public Health Code of Ethics

By Kayla Blades

Photo by Edward Jenner. [CC0]

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he public health system in the United States is responsible for research and education that informs the decisions made regarding the population health of the entire country. Why do we trust the public health system? How do they provide the most unbiased information in a biased environment? What determines the principles by which such an important field abides?

How do we fight the inequities faced in this field? Historically, the United States has seen cases of a lack of effectiveness of the public health system and the use of the public health system to abuse the disenfranchised.

Instances such as forced sterilization in the U.S., the AIDS epidemic, and the Tuskegee study reveal a transgression pattern in the public health field.

Dr. James Thomas is an Associate Professor in the Department of Epidemiology at the University of North Carolina at Chapel Hill.

During his epidemiologic research in the 1990s into Dr. James Thomas the syphilis epidemic in

Eastern North Carolina, the unethical aspects of the public health field became evident when he witnessed multiple instances of racism and social inequality. In response to the inequities he witnessed in the public health field, Dr. Thomas developed a research interest in health ethics and began studying ethics, philosophy, and theology. Dr. Thomas worked in conjunction with other scholars to establish A Code of Ethics for Public Health to combat these forces in hopes that it would lead to change and restructuring of the public health field. This code is not an institutionalized code that someone can violate, but rather it provides clarity on the purpose and values of public health. The public health ethics code was widely adopted by the American Public Health Association, and Dr. Thomas is now a resource for other institutions regarding the role of ethics in the public health field – specifically concerning epidemics and pandemics. Dr. James Thomas discusses how “a code of ethics is fundamentally about preserving humanity and humanizing people” and can be utilized to prevent such events and further develop and establish the public health field.1 Public health ethics addresses a power imbalance between individuals’ interests with the overall wellbeing of the community. In the United States, attempts to resolve this imbalance often occur in government

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as they hold a responsibility for the welfare of the population, balancing the individual’s rights and autonomy with collective safety. A Code of Ethics for Public Health predominately focuses on addressing issues of the public field in the United States. It is not entirely applicable to other countries since circumstances and cultural differences often result in different priorities and approaches when it comes to addressing the various issues of the public health field.

Twelve main principles inform the ethical code and establish equity through different modes. The central idea running Figure 1 : Meeting about Ebola in Accra, Ghana. Courtesy of Dr. Thomas. throughout this code of ethics is scenario has different characteristics and factors that the value of equity in the public health field and individuals’ willingness to make sacrifices in make it difficult to anticipate ethical issues that will arise pursuit of equity.1 Public health is a community-focused in a public health emergency. Scholars must adjust and discipline that includes all areas of the community, adapt their thinking to compensate for the deviation including the disenfranchised – advocating and from original conjecture. In the case of COVID-19, there working so that public health includes programs and was a lack of understanding of the essential role of resources accessible to all is a key foundation of this service workers in keeping us in a functioning state. code. Establishing policies that are respectful of all There was also the discussion of redistribution based communities and encompasses all values, beliefs, and upon want and predicted needs of the communities.1 The public health field has been increasingly cultures is essential to this idea of equity.

A fundamental principle to the code of ethics valued by the public as globalization and the internet is transparency and public health institutions’ allow for greater information exchange about the responsibility to keep the public informed. Transparency overall health of the population and the urgent and not only allows the public to make educated decisions vital issues this field addresses. Dr. Thomas hopes that about the community, but it also builds trust. Trust by bringing ethical issues essential for public health to between the population and public health institutions the forefront of discussion, it will help prepare us for is essential to promoting cooperation.1 Understanding the next public health emergency. He aspires to adapt the interdependence of people is fundamental in public the public health code of ethics to create a standard health, especially in the wake of globalization in where of public health planning in the workplace to address the interconnectedness of society promptly puts many issues specific to their environment. Importantly, Dr. Thomas hopes to prevent the scramble to adapt to public health issues on a global scale.

Our awareness of ethical issues in public health emergent public health situations that people in the is under constant revision as scholars learn more U.S. are experiencing now with COVID-19. information to adapt to continually emerging public health issues in society. As a consultant to many institutions, Dr. Thomas has the opportunity to see the application of this ethical code and revise it to better References encompass a wide range of scenarios. In relation to 1. Interview with James Thomas, MPH, Ph.D. epidemics and COVID-19, anticipating the need to 09/08/2020 rethink who is essential or reexamine the allocation of 2. Thomas JC, Sage M, Dillenberg J, Guillory VJ. A scarce resources are just a few examples of the vast array code of ethics for public health. Am J Public Health. of issues this code must encompass. Each public health 2002;92(7):1057-1059. doi:10.2105/ajph.92.7.1057

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medicine and health

Changing the Face of Early Cancer Detection: Better detection of PTMs could help cancer diagnostics By: Alisha Desai

Image Courtesy of Pexels.

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he survival rate for individuals diagnosed with melanoma at the earliest stage of detection is 99 percent. This survival rate drops to a daunting 25 percent when the cancer is detected after spreading further throughout the body.1 Early detection could determine survival for the hundreds of thousands of individuals that get diagnosed with skin cancer every year. The field of epigenetics has played a significant role in establishing methods of early cancer diagnostics and UNC-Chapel Hill’s Dr. Marcey Waters is one of the scientists pioneering this groundbreaking research.

Epigenetics is the study of changes in an organism caused by modified gene expression. Gene expression describes the process of “turning [a gene] on or off.” . Every cell in the human body, whether it is in the liver or the eye, contains an set of genetic material. However, only specific genes are turned on in certain cells allowing the liver and the eye to have vastly different functions. The field of epigenetics is new; in fact, researchers have only begun examining modified gene expressions within the past twenty years. Nevertheless, it has quickly become clear that gene expression can cause severe diseases such as cancer; learning about these modifications and being able to reverse them could have significant effects

in the diagnostics and healthcare industry.

Dr. Marcey Waters specifically studies how methylation regulates gene expression.

Methylation is the addition of a methyl group, CH3, to a compound. CH3 is a small organic molecule that is very prevalent in Figure 1: Image depicts DNA the body. When asked wrapped around histones, and then unwrapped, displaying the what drew Dr. Waters to bonds which hold DNA together. this field of research, she stated, “It’s remarkable that doing something as small as adding a methyl group on the right nitrogen can turn on a protein-protein interaction that controls gene expression.”2 Dr. Waters is particularly examining the methylation of lysine in histones, a type of protein in DNA. Lysine is one of the amino acids that makes up these histones. Dr. Waters is investigating lysine methylations by applying various biological and organic techniques. The lab is taking two approaches to research these methylations: studying the proteins involved in methylation and using organic

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Carolina Scientific chemistry to mimic the proteins. A solid foundation of understanding these methylations has emerged over the past decade. In the future, the lab will focus on engineering protein inhibitors. These inhibitors will regulate gene expression on the histones.

Principles of organic chemistry are being applied to develop smaller molecules that are able to bind to the compounds of interest. Finding compounds with good binding affinity and selectivity has also been a major focus for the lab.

Typically, antibodies, proteins used by the immune system, sense the lysine methylations.

However, antibodies are expensive and creating them is a lengthy process which involves injecting rabbits with a compound and waiting for the rabbit’s body to create the proper antibodies. In addition, antibodies are very large and therefore have difficulty differentiating between smaller changes to the histone. Therefore, since methylations are very minor changes, the antibodies could have trouble detecting them. Dr. Waters also noted, “there are all these commercially available antibodies that have a large fraction of false positives and false negatives… they fail 25% of the time.”2 This posed an important question for the research group: is there a way we can use the existing reader proteins as sensors? The immediate answer was yes, but not nearly as well.

Reader proteins have the natural selectivity to bind to methylated amino acids like lysine, and they are much cheaper and easier to make using typical biochemical tools. However, they are thought to have a much lower binding affinity compared to antibodies. Antibodies bind to methylated lysine one to ten thousand times tighter than reader proteins. Therefore, in order to use reader proteins as binding sensors, Dr. Waters and her team had to engineer them in a way to allow for a higher binding affinity. They have found success with engineering these reader proteins by introducing three mutations. These mutations enhanced the

Figure 2: Illustration demonstrates the improved efficiency of engineered reader protein compared to the selected antibody.

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protein’s binding ability twenty-five-fold.

The Waters Lab have been pioneers in this niche of epigenetics.

Many other researchers have used reader proteins to look for methylations, but Dr. Waters was one of the first to engineer the reader proteins to Dr. Marcey Waters, PhD enhance their binding ability thereby increasing their efficiency. When compared to a sample antibody, the newly engineered reader protein had a greater binding ability. In the past, the Waters Lab has focused specifically on creating engineered reader proteins for a particular lysine methylation; however, they are now hoping to apply this method to enhance detections of various other lysine methylations. This research is particularly important as it pertains to cancer diagnostics and treatment. When discussing potential applications of her research, Dr Waters stated, “anything that controls gene expression, if it is not regulated, will lead to disease. Cancer is one of the main diseases associated with methylations or lack of methylations.”2 Many studies have proven a link between deregulation of methylations and increases in certain types of cancer including melanoma.3 Increased methylations on various histones can contribute to an increased production of melanoma cells. In the future, Dr. Waters’ research will create more efficient detection methods for histone methylations that will be utilized in order to detect cancer sooner. This new method of detection could drastically increase patients’ odds of surviving cancer.

References

1. American Cancer Society. “Survival Rates for Melanoma Skin Cancer”. https://www.cancer.org/ cancer/melanoma-skin-cancer/detection-diagnosisstaging/survival-rates-for-melanoma-skin-cancer-bystage.html 2. Interview with Marcey Waters, PhD. 09/11/20.

3. Azevedo, H., Pessoa, G.C., de Luna Vitorino, F.N. et al. Gene co-expression and histone modification signatures are associated with melanoma progression, epithelial-to-mesenchymal transition, and metastasis. Clin Epigenet 12, 127 (2020). https://doi. org/10.1186/s13148-020-00910-9

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medicine & health

Hope for a Cure: A Gene Therapy Approach for Pitt-Hopkins Syndrome

By Yue Yan

Image by Marta D. [CC-BY-4.0]

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ror most people, reciting the ABC’s and 123’s is a very simple task. For most people, their faces are just an average of their parents’ faces and nothing more. However, many men, women, and children in the world find learning even the simplest of concepts to be a challenge. For many men, women, and children, their entire lives were changed the moment they were born. These individuals all have one thing in common: Pitt-Hopkins Syndrome, a form of autism that causes breathing problems, epilepsy, developmental/intellectual delays, and facial deformities.

It can lead to social isolation and, in extreme cases, can even be fatal. Consequently, many researchers around the world are trying to understand this condition better to possibly treat or even cure it. One such researcher is Sally Kim. Sally Kim is a Ph.D. student working in Dr. Ben Philpot’s lab at UNCChapel Hill. Under Dr. Philpot, her study focuses on developing a gene therapy approach for Pitt-Hopkins Syndrome.

Pitt-Hopkins Syndrome is an extremely rare but Sally Kim, Ph.D student very serious genetic and

neurodevelopmental disorder. It is caused by a mutation in the chromosome 18 gene Tcf4, which creates a protein when expressed. Symptoms of this disorder include epilepsy, trouble breathing, developmental delay, digestive issues, impaired speech, and distinctive facial features (Figure 1). Since Pitt-Hopkins Syndrome is rare, it is not well-understood, so researchers like Sally Kim are working hard to better understand it.

Figure 1. A photo of the facial features caused by PittHopkins Syndrome. Image courtesy of Wikimedia.

To start, the researchers first identified which cells expressed the protein. By doing so, they would be able to locate in which cells Pitt-Hopkins Syn-

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Carolina Scientific drome patients are missing the fully-functional gene.

They also wanted to determine when Pitt-Hopkins Syndrome should be treated: the disease changes as affected individuals grow older.

The researchers discovered all of this information by developing a green fluorescent protein reporter mouse. The green fluorescent protein only glows if the gene of interest (in this case, Tcf4) is also expressed, to better see which cells were expressing the Tcf4 gene. They then used this protein reporter on the brains of mice of varying ages to see where in the brain Tcf4 is expressed.

As a result, Sally Kim and the other researchers found out that protein expression was prominent in the parts of the brain that focus on processing the senses and memory. They also discovered that the non-electrical cells focused on maintaining and supporting the nervous system also have prominent levels of the protein. However, their research is still ongoing. Sally Kim and her colleagues plan on using a group of mice with a Tcf4 mutation, causing lowered levels of the protein, and then bringing the protein to normal levels at different ages. Afterwards, they will perform a behavioral assessment to see how effective the treatment was at different ages to determine when it is best to treat Pitt-Hopkins Syndrome.

Sally Kim hopes to use this information to develop a treatment for Pitt-Hopkins with gene therapy (Figure 2). She describes gene therapy as “using a vi-

rus particle...think of this virus as a delivery truck… and then we’re going to add a genetic material into the truck and then we’re going to put this entire virus into the human system.”1 By researching which cells and parts of the brain express these genes, Sally Kim hopes to be able to develop a virus that only targets places where the protein is needed. She goes on to mention that because Pitt-Hopkins “develops early in life...we don’t know whether all the phenotypes (symptoms) can be treated.”1 Due to this uncertainty, and the fact that Pitt-Hopkins is a rare and understudied disorder, Kim predicts that it will take about 5-10 years before a treatment can be developed. Working under Dr. Philpot, Sally Kim has discovered which cells are affected by the mutated Tcf4 gene in individuals with Pitt-Hopkins Syndrome through the use of mice.

Their research has the potential to develop a gene therapy treatment that targets the correct cells and discover exactly when doctors should treat patients with the disorder. By using these findings, Sally Kim hopes to contribute to developing a treatment soon to ease the worries of the parents of those affected.

With this hope, Sally Kim and the many others researching Pitt-Hopkins continue to do their part to try and give those affected a normal life. They hope that one day, their parents can finally rest easily, knowing that their child’s life is no longer in constant danger. They dream that those kids can grow up and fulfill their goals, just like everyone else. Perhaps one day, their hopes and dreams can come true. Although, there is still a long way to go before they can without a doubt save the lives of the many men, women, and children that have been affected by Pitt-Hopkins Syndrome.

References

1. Interview with Sally Kim. 09/15/20

Figure 2. An illustration of how gene therapy works. Image courtesy of Sebastian Kaulitzki

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medicine & health

The Secret Correlation between Cancer and Genetics

By Ryan Gomes Image by Ruslan Kalendar. [CC-BY-SA 4.0]

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NA – the foundational component of sequences in our bodies that helps us live and be unique from one another.

This important structure in every single living organism holds many secrets that tell us about our past ancestral generations and our futures as well. Scientists are constantly trying to uncover these secrets and discover new information that will help improve the quality of human life. Dr. Federico Innocenti is an associate professor in the Division of Pharmacotherapy and Experimental Therapeutics of the UNC Eshelman’s School of Pharmacy. He uncovers secrets of our DNA and genetics that will be able to help treat future patients suffering with cancer, particularly cancers in the gastrointestinal regions of the body.

Throughout his research, Dr. Innocenti observed how certain sequences of DNA might influence survival rates from gastrointestinal tumors and how those sequences might affect how our bodies

Dr. Federico Innocenti

respond to chemotherapies.

The particular chemotherapy in Dr. Innocenti’s lab is a widely known drug called irinotecan, or CPT-11. Irinotecan inhibits the topoisomerase, a crucial enzyme that is needed for DNA replication. Cancer cells progress and spread through the body via DNA replication.

When inhibiting topoisomerase, DNA replication of cancer cells cannot proceed, therefore preventing further progress of the tumors. Irinotecan is used to treat many types of cancers within patients, including metastatic colorectal cancer, the second most lethal form.

Although irinotecan has a reputation to be very efficient and beneficial, studies show that roughly more than 30% of cancer patients who have taken irinotecan to treat their cancer, experienced a worse state of health.⁴ This is largely due to the dosage of irinotecan that doctors prescribe for patients. A higher dosage than necessary for the patient can result in CPT-11-induced toxicity that can cause severe neutropenia. Neutropenia is a reduction in blood counts of neutrophils, a type of white blood cell that helps the body defend against pathogens. Initially, scientists theorized that the link between the amount of dosage and patient health was related to certain factors such as the demographics of the patient like their gender and age, but research has shown that data does not reflect this.⁴ In order to understand and gain more informa-

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tion about the correlation between the dosage of irinotecan and the patient’s health, Dr. Innocenti’s lab has looked into the genetic makeup of cancer patients.

In order to look into this, the Innocenti lab investigated a certain gene inside the human body called the UGT1A1

Figure 1. This figure above shows how much Irinotecan is necessary in each genotype (the top) in order to get similar SN-38 results (the bottom). It is seen that a patient with *1/*1 genotype needs much more irinotecan dosage in order to maintain similar SN-38 levels compared to the other 2 genotypes. Reprinted with permission. © (2014) American Society of Clinical Oncology. All rights reserved.

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“Learning more about the genetic makeup in humans would not only allow new treatments to be developed to help with different forms of cancer.” gene and measured its common variation, called UGT1A1*28. The UGT1A1*28 gene helps in maintaining adequate levels of SN-38, the by-product formed when irinotecan is metabolized and processed in the body. SN-38 is the main component of the chemotherapy drug that helps in preventing the functionality of the topoisomerase in cancer cells, which helps in blocking further progress of the tumor. When looking into the UGT1A1*28 gene, the researchers found that there were three different forms of the gene and every person has one of those versions of the gene in their DNA.2 The three different forms are: *1/*1, *1/*28, and *28/*28.2 *1 and *28 are examples of alleles, which are variations of the gene that can be combined together in various ways to create what is called the genotype. Since this gene is hereditary and passed down from our biological parents, we all have two alleles or variations of the gene, one from each parent (either alleles *1 or *28), that come together to create one of the three combinations. Depending on the combination, a certain individual with cancer will react differently to a particular dose of irinotecan.

In order to test this, Dr. Innocenti designed a clinical trial with a handful of cancer patients that had either the *1/*1 genotype, the *1/*28 genotype, or the *28/*28 genotype. Based on their genotype, cancer patients were given a specific dosage of irinotecan every three weeks. While monitoring the patients’ health conditions during the three-week period, Dr. Innocenti observed whether or not the cancer patients had a negative reaction to the dosage and were at risk of severe neutropenia. The patients with *1/*1 and *1/*28 genotypes started off with intaking 700 mg of irinotecan every three weeks while the patients with the *28/*28 genotype began with 500 mg of irinotecan.2 Patients with *28/*28 genotype started with a smaller dosage

amount because “*28/*28 would likely tolerate less irinotecan than the other genotypes and it would not have been ethical to treat all patients at the same dose of irinotecan.”3 As the patients were monitored, the dosage of irinotecan was slowly adjusted to meet the amount that they would be able to tolerate in their bodies. After making proper adjustments to the dosage of irinotecan for the cancer patients, Dr. Innocenti observed that every genotype had a preferred amount of irinotecan that the patient could tolerate in their bodies. Patients with the *1/*1 genotype could intake 850 milligrams but not more than 1,000 milligrams. Those who had the *1/*28 genotype could have 700 milligrams of irinotecan but not any more than 850 milligrams. Lastly, cancer patients with the *28/*28 genotype had by far the lowest level of tolerance to the dosage of irinotecan, being able to take 400 milligrams of irinotecan but no more than 500 milligrams. The results of this experiment can be seen in figure 1 above. This helps to shows that across the three different genotypes, *1/*1, *1/*28, and *28/*28, patients are equally exposed to SN-38, but patients with the *28/*28 genotype need less amount of irinotecan than the patients with the other two genotypes.

Although this seems beneficial, further studies have indicated that patients with the *28/*28 genotype are more susceptible to neutropenia since their tolerance levels to irinotecan are so low.1 With further observations, the Innocenti lab were able to conclude that the UGT1A1*28 variation has a significant effect on the amount of irinotecan dosage that cancer patients can intake, providing lower chances of side effects while preserving antitumor potential.2 Dr. Innocenti’s research has helped to demonstrate that although there might be a particular treatment that is found for cancers in the body, the specific amount of treatment that is given to the patient is a very crucial aspect that needs to be considered. Not everyone will be able to take the same amount of dosage and Dr. Innocenti’s research has provided more information about how the genetic makeup of an individual can influence the amount of chemotherapy

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required for it to have an effect towards treating cancer without risk of side effects. Even though this research is very important, Dr. Innocenti realizes that there is still much to learn about the secrets hidden in our DNA that can help in developing the treatments for different forms of cancer: “the direction I foresee going in towards [the future] is the understanding of how all of these genetic mutations behave with tumors and whether these mutations can open the door to new drugs that can be given to patients.”3 Learning more about the genetic makeup in humans would not only allow new treatments to be developed to help with different forms of cancer, it would also allow doctors to prescribe certain amounts of treatment needed for maximum efficacy and minimum risk of side effects.

Figure 2. This figure shows that irinotecan metabolizes in the body into SN-38

References

1. Dean L. Irinotecan Therapy and UGT1A1 Genotype. 2015 May 27 [Updated 2018 Apr 4]. In: Pratt VM, McLeod HL, Rubinstein WS, et al., editors. Medical Genetics Summaries [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2012-. Available from: https:// www.ncbi.nlm.nih.gov/books/ NBK294473/ 2. Innocenti F, Schilsky RL, Ramírez J, et al. Dose-finding and pharmacokinetic study to optimize the dosing of irinotecan according to the UGT1A1 genotype of patients with cancer. J Clin Oncol. 2014;32(22):23282334. doi:10.1200/JCO.2014.55.2307 3. Interview with Federico Innocenti, M. D., Ph. D. 9/11/2020 4. Karas S, Etheridge AS, Tsakalozou E, et al. Optimal Sampling Strategies for Irinotecan (CPT-11) and its Active Metabolite (SN-38) in Cancer Patients. AAPS J. 2020;22(3):59.

Published 2020 Mar 17. doi:10.1208/ s12248-020-0429-4

medicine & health

Re-engineering the Immune System By. Reva Kodre

Figure 1. : Image of cross-section of a human breast cancer with cancerous regions.

O

ur immune system is an army of soldiers, armed with proteins that tag and alert killer cells to attack a foreign body or antigen. The B lymphocytes (Bcells) in our immune system are the military intelligence system of our body—trigger the production of Y-shaped proteins called antibody that lock onto specific antigens such as bacteria. After latching onto a certain antigen, the antibodies signal the T lymphocytes (T-cells) to destroy the tagged antigens or infected cells.1 Antibodies seems like a foolproof plan of defending our bodies from getting sick, but an issue arises when the immune system is unable to proDr. Gianpietro Dotti, M.D. duce enough antibodies to defend itself. The issue becomes even worse if the B-cells have transformed into malignant cells, unable to fulfill its task of protecting the body. The progression would result in something that is more daunting: cancer. To help with the loss of defenses, UNC-Chapel Hill Lineberger Comprehensive Center’s Dr. Gianpietro Dotti, M.D. has been actively involved in novel types of treatment in cancer immunotherapy clinical trials, specifically the re-engineering of immune cells.

Cancer generally develops when there is an abnormality in a specific gene that causes a type of cell in the

Image Courtesy of Nazanin Rohani.

body to grow rapidly and possibly metastasize, in which the abnormal cells spread to a different region of the body.

As the director of the Cancer Cellular Immunotherapy program at UNC, Dr. Dotti is focused on Chimeric antigen receptor (CAR) T-cell therapy, which uses gene modified Tcells to create a targeted attack on cancer cells. CARs have been more commonly used to attack leukemia, or blood cancers, which typically begins with early forms of white blood cells, but it can originate from other types of blood cells as well (Figure 2).1 There are many different types of leukemia, but it is Acute Lymphoblastic Leukemia (ALL)

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Figure 2. Anatomy of the bone. Image Courtesy of Terese Winslow [CDR755927].

Carolina Scientific that targets lymphocytes specifically. ALL is common in young patients and can be fatal within a few months if not treated properly.1 Normally, the bone marrow would produce blood stem cells that eventually mature to become either myeloid or lymphoid stem cells and the lymphoid stems cells would then develop into infection-fighting cells.1 However, it is difficult for the immune system to defend itself when the cancer originates in the infectionfighting cells themselves.

CAR T-cell therapy involves taking T-cells from a patient diagnosed with cancer and are genetically engineering them in the laboratory to include special receptors on their surface, at which point the cells are classified as CAR T-cells.2 By changing the mechanism of the T-cells and converting them into CAR T-cells, they are now more capable of binding to and attacking the cancer cells (Figure 3).

Because these T-cells are taken directly from the patients, this type of treatment is personalized to the specific type of cancer present in their body, making the attack direct

Figure 3. Diagram of CAR T-cell Therapy Treatment.

Image Courtesy of Terese Winslow CDR774647].

and specific. One of the most common issues with cancer treatments is that the drug itself might negatively affect normal cells and have a toxic effect on the body. However, CARs are able to attack specific types of antigens that are present in higher levels on cancerous cells compared to normal cells. For example, with B-cell malignancies, it is becoming increasingly more common to target the CD19 antigen that is prevalent on surface of some blood cancer cells.2 In the case of childhood ALL, CD19 CAR T-cells can be used to treat relapsed ALL, along with chemotherapy.2 After observing remarkable regression of blood cancers after using CAR T-cell therapy, scientists like Dr. Gianpietro Dotti hope to apply this mode of therapy to solid, tissue-like tumors as well. The primary challenge with attacking solid tumors is the difficulty for CAR T-cells to reach the small, focused sites of the cancer while also avoiding the healthy cells that surround it (Figure 1). The

medicine & health

challenge for solid tumors is different from those of liquid cancers like leukemia, where the infused CAR T-cells are more likely to bump into the cancerous cells that are able to travel freely in the blood and target them. The concern is similar with chemotherapy, which Dr. Dotti explains, “when we do chemotherapy, we don’t kill all the tumor, we kill also a lot of normal cells—you lose your hair.”3 However, Dr. Dotti and his colleagues at UNC Lineberger have developed strategies to allow CAR T-cells to regulate their activity to effectively kill the lymphoma tumor cells without triggering harsh side effects. Dr. Dotti’s team has found that a molecule called LCK is able to increase the activity of a CAR T-cell that responds to the 4-1BB protein signal.4 The LCK molecule enhances the activity of the modified T-cells and thus results in a better tumor-targeted attack.

In order to decrease the activity of the CAR T-cells, they have found a new “safety switch” called SHP1 that binds to the CAR T-cells and reduces their activity without killing them.4 SHP1 allows the genetically engineered T-cells to slow down their attack on tumor cells and continue to grow and expand, while avoiding any side effects that may occur.4 There are still many obstacles with CAR T-cell treatments for solid tumors such as pancreatic cancer and ovarian cancer, but Dr. Dotti remains optimistic for future breakthroughs.

As these newer and more innovative models of treatment are discovered, researchers at UNC Lineberger hope to see progress towards creating safe treatments to alleviate the toxic effects of cancer. Although this process may take years of rotating through lab experiments and clinical trials, it is necessary to promote the patient’s safety first. Dr. Dotti expresses that CAR T-cell therapy may never be the one true cure for cancer, but when combined with chemotherapy and other forms of immunotherapy, it can dramatically reduce the size of the tumor, which is a huge step closer to the ultimate goal of healing the patient. As Dr. Dotti states, “with every single patient that will come in, you have step one, step two, step three, and hopefully after step three, we’re done.”3

References

1. PDQ® Pediatric Treatment Editorial Board. PDQ Childhood Acute Lymphoblastic Leukemia Treatment. Bethesda, MD: National Cancer Institute. Updated July 13, 2019. Available at: https://www.cancer.gov/types/leukemia/patient/child-all-treatment-pdq.

Accessed Sept. 13, 2020. [PMID: 26389385] 2. Dotti, G., Gottschalk, S., Savoldo, B., & Brenner, M. K. (2013).

Design and development of therapies using chimeric antigen receptor-expressing T cells. Immunological Reviews, 257(1), 107126. doi:10.1111/imr.12131 3. Interview with Gianpietro Dotti, M.D. 09/11/2020.

4. Sun, C., Shou, P., Du, H., Hirabayashi, K., Chen, Y., Herring, L. E., . . . Dotti, G. (2020). THEMIS-SHP1 Recruitment by 4-1BB Tunes LCK-Mediated Priming of Chimeric Antigen Receptor-Redirected T Cells. Cancer Cell, 37(2). doi:10.1016/j.ccell.2019.12.014

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psychology& neuroscience

Learning from Fruit Flies: How Memory Steers Action

By Sneha Makhijani

Image by Howard Vindin. [CC-BY-SA 4.0]

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he fruit fly has created quite a buzz in the world of neuroscience and learning. Similar to the way humans are now conditioned to hear a notification and pick up their phone, animals show different behavioral responses to the same sensory input, depending on past experiences and current contexts.

Learning is a permanent change in behavior that results from experience. One of the earliest learning techniques is classical conditioning, a learning process in which a neutral, unconditioned stimulus is paired with a conditioned response to naturally evoke a response. While the initial experiments were first done on dogs, the field of neuroscience is slowly understanding how synaptic plasticity, a change that occurs at the junctions of different neurons, and memory is steering this learning response.

UNC-Chapel Hill’s Dr. Toshihide Hige is one of the scientists doing pioneering research on the neurophysiology and learning behavior in the fruit fly – Drosophila melanogaster.

The brain enables flexibility to change its structure through mechanisms at the levels of synaptic plasticity, neural circuit, and behavior, where the neural circuit is a population of neurons that carry out a specific function. Dr. Hige first got involved in synaptic physiology during his PhD research. Using electrophysiology in mammalian systems, he studied the neural circuit basis of behavior in animals. As Dr. Hige progressed in his research, he started to use Drosophila melanogaster as a model organism. Although Dr. Toshihide Hige, PhD fruit flies have about 100,000 neu-

rons, which is 1000 times fewer than that of mice, some of the important circuit motifs remain conserved across all animals, both in sensory circuits and higher-order brain areas. Circuit motifs are connectivity patterns between specific cell types across different species and brain areas. Simpler model organisms, such as Drosophila melanogaster, have small brains but exhibit a wide range of sophisticated, adaptive behaviors. Fruit flies make for an easier reading of the neural circuit and they offer a larger selection of which circuit brain area to use, with fewer pathways of each of the brain circuits. Genetic tools can label specific neuron types in every area of the brain, and such tools can also manipulate neuronal activity and address its molecular basis. Furthermore, the whole-brain connectome data is readily available and allows for an easier link between synaptic plasticity and behavior by understanding Drosophila neural circuits.

Whole-brain connectome data is essentially a comprehensive map of the various neural connections in the brain that act as a wiring diagram of an organism’s nervous system.

There is a pair of structures in the brain of insects called Corpora Pedunculate, or mushroom bodies. The structures are

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Figure 1. Circuit diagram of the Drosophila mushroom body

Carolina Scientific known to play important roles in olfactory learning – that is, learning due to the sense of smell – and memory. The neurons that form the mushroom bodies are called Kenyon cells. In the Drosophila melanogaster there are about 2,000 Kenyon cells in each of the brain hemispheres.

The mushrooms bodies are what store different memories, which can be repetitive, aversive, short, or long. The different regions of the mushroom body, which are nicely segregated, deal with specific types of memory, and, when running an experiment, the memory type and its storage can be chosen.

The Kenyon cells in the mushroom bodies integrate information from the separate regions and are responsible for synthesizing different memories and relating them to decision making.

One of the strengths of using Drosophila is the ease of studying the genetics and neuronal circuit. Accordingly, the synaptic plasticity can be separated into the different regions of the brain. Ultimately, the mushroom bodies have a cascade of events that pave the way for a motor response. The mechanism is useful because it allows researchers to artificially induce memory or plasticity and observe how it affects downstream neurons.

Associative learning techniques such as that of classical conditioning use a molecule called dopamine as the main neurotransmitter in the brain circuit. For instance, synaptic depression, which is a decrease in the postsynaptic responses after repeated stimulation of a synapse, can be induced by dopamine activation in flies. Dopamine neurons in the brain project to different neuron bodies which are present in sensory pathways.

Dr. Hige’s lab studies the olfactory pathways, some of which act

psychology & neuroscience

sponse in the neuron, based on the behavioral response. Upon dopamine stimulation, a decrease in the synaptic impulse can be observed.

Using the olfactory sensory system, olfactory learning takes place. First, a particular odor is used to establish the behavior – the neutral stimulus. Then, the fly is given an immediate aversive response, such as a shock, which is the unconditioned stimulus. The unconditioned response will be the fly trying to avoid the shock. After a few trials of conditioning, the odor eventually becomes the conditioned stimulus so that whenever the fly detects the odor, it automatically anticipates and tries to avoid the shock. Thus, the smell of the odor becomes associated with the aversive shock and the fly learns to avoid both the shock and the odor. The behavior of the fly constitutes olfactory learning. Classical conditioning could also be done with a positive reinforcement and an odor. A positive reinforcement would be if something like a treat is given to the fly when a particular behavior is o b -

Figure 3. A tethered fly walking on a treadmill ball served with a specific odor. In order to test if the flies have learned the classical conditioning behavior aversive to the shock, they are put on a treadmill ball and their reaction to the odor is observed. The response is recorded via electrodes as the flies are tethered to the treadmill balls when they move towards or away from the smell.

Through this research, Dr. Hige hopes to visualize the neuronal changes that underlie learning by tracking the neural circuit of Drosophila melanogaster from the sensory input to the motor output. By studying this behavioral output, a precise circuit of the learning process that takes place in a fly’s brain can be obtained while integrating the sensory input to the behavioral output. Although humans have far more complex neural and behavioral circuits than flies’, this can be extrapolated to further research of the neuronal circuits in humans. Dr. Hige’s research can not only help us better understand how flies are engaged in learning behaviors, but also how it can be translated to neuronal activity and learning in humans.

Figure 2. Long-term depression in the mushroom body downstream to the mushroom bodies. Based on how quickly the effects are seen in the downstream neurons of the circuit and when the synaptic transmission is induced, the transmission can affect downstream neurons’ behavior. The Hige lab is studying this mechanism to identify the co-transmitter which works with dopamine to induce depression in these neuronal bodies.

One technique to study the synaptic depression in flies is by using Positron Emission Tomography (PET) scans. In this experiment, the flies are dissected alive after which an electrode is inserted in them. An odor is then applied to test the olfactory re-

References

1. Interview with Dr. Toshihide Hige, Ph.D. 09/20/20.

2. Hige, T., Aso, Y., Rubin, G.M., and Turner, G.C. Plasticitydriven individualization of olfactory coding in mushroom body output neurons. Nature. 2015, 526, 258-262.

3. Hige, T. What can tiny mushrooms in fruit flies tell us about learning and memory? Neurosci. Res.2017, 129, 8-16.

4. Takemura, S-Y., Aso, Y., Hige, T., et al. A connectome of a learning and memory center in the adult Drosophila brain.

Elife. 2017

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psychology & neuroscience

Using Light to Control the Brain

By Lasya Kambhampati

Image ZEISS Microscopy. [CC BY-2.0]

I

magine a pendulum swinging back and forth on a string.

Your job is to poke it in just the right way so that it stops moving. However, you are given no other information about the movement of the pendulum. You would end up just poking around in the dark, hoping that somehow you will be able to nudge in just the right direction with the right amount of force. This is the analogy that Dr. Andrea Giovannucci, an assistant professor in the Joint UNC-NCSU Department of Biomedical Engineering, uses to describe the current field of neuro-engineering. Scientists are sending signals to neurons (brain cells) hoping that one will eventually cause the reaction they are investigating.

At the moment, a prominent approach for artificially connecting with the brain is through the implantation of a chip, such as the NeuraLink technology created by Elon Musk. This chip can then be used to get input from sensory neurons (“read”) and send output to nerves (“write”). However, there are multiple issues with this idea – the implanted needles would corrode, and the chip cannot Dr. Andrea Giovannucci be maintained for long periods.

Furthermore, it is difficult to precisely modulate neurons to achieve the desired result. Chips do have positive aspects; for example, the signals to and from the chip can be decoded in real time, which is essential for effective prosthetics.

Dr. Giovannucci’s research aims to turn on the light so

that we can accurately and precisely poke specific neurons to elicit a particular reaction. He became interested in this particular topic when he realized that by combining his previous experience with algorithms, artificial intelligence (AI), and prosthetics, he could develop algorithms that would control neuroprosthetics. Instead of using a chip to control neural signals, he elected to use light (holography) to stimulate neurons. Although it is important to mention that, currently the technology is unable to read and modulate brain activity within 30 milliseconds, which is essential to have an effective dialog between input and output. Dr. Giovannucci describes the current relay time as “asking you a question and getting a response 20 minutes later.”1 To do this, two important changes need to be made to the brain’s physiology. Using a genome changing mechanism, the brain can express a gene that encodes a fluorescent protein (Figure 1). This protein activates when the neuron fires, signaling neuronal activity and allowing scientists to “read” the brain’s current state. Past literature has shown that this is possible and effective in the brains of mice and primates. In addition, there needs to be a gene that allows light to change the activity of the neuron. This allows researchers to shine a particular wavelength of light on a neuron and either activate it or suppress its activity. After completing these two Figure 1. Neurons labeled with fluorescent proteins modifications, an optical-

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psychology & neuroscience

can repeatedly perform skilled movements. Past attempts at this have failed, but Dr. Giovannucci believes it was due to the lack of precise activation and suppression of neurons.

Therefore, the results were unreliable, unskilled movements.

With the new information and algorithm, the results should be reproducible. To conduct this experiment, the researchers place a panel of clear glass on top of the brain of the mice and use light to stimulate neurons in the motor cortex (an area of the brain necessary for voluntary movement).3,2 See Figures 2 and 3 for more information.

Dr. Giovannucci is also planning for the future. He hopes to create a system that can estimate the internal dynamics

Figure 2. Light is used to stimulate neurons based neural prosthesis can be controlled through light firing on to the brain. However, this technology is years away from becoming a reality; we have the infrastructure but not the computational ability.

Furthermore, we need more data on exactly which neurons to target to neurons to target to elicit particular motions, which is the focus of Dr. Giovannucci’s current experiments. He is working on a way of getting a readout of the brain’s current state and integrating algorithms that can modulate the firing or suppression of neurons in collaboration with Dr. Nicolas Pegard. Dr. Pegards’ algorithms use Deep learning – a type of machine learning based on neural networks – to analyze inputs and produce outputs. For example, if you were to input a starting “picture” of the brain at a certain point in time and a state of the brain that you want to reproduce, the algorithm would be able to output a pattern of light (hologram) that would target specific neurons that need to be activated or inactivated.

There are two experiments that Dr. Giovannucci would like to carry out using the above technology. The first would be to estimate the connectivity of a specific subset of neurons in areas of the brain related to motor function. Imagine you have a series of pendulums all swinging at different speeds but close enough that changing the motion of one of the pendulums will affect the others. If you only wanted to stop the motion of one of the pendulums, you would need to know how each pendulum is connected to the others so that you could poke it in exactly the right direction and with the correct force to achieve your goal. Researchers face a similar conundrum when it comes to modulating the synaptic activity of the neurons they are targeting. Neurons are all part of a network – changing the activity of only one neuron could affect the behavior of all the neurons that they are connected to. To provide data on the connectivity between the neurons, Dr. Giovannucci will read the status of the brain, modulate specific sets of neurons, measure the response in the surrounding neurons, and then use this data to estimate connectivity.

Once he has gathered this data on connectivity, Dr. Giovannucci also plans to try to stimulate neurons so that mice

Figure 3. A microscope is used to examine a mouse brain which has been labeled with a fluorescent protein

of the brain in terms of a specific set of variables – similar to equations used in physics to determine the movement of particles. With the combination of all of these experiments, there is a possibility of real-life applications, but there are still some obstacles that need to be overcome. Primarily, there are ethical and viability issues with using technology to implant new genetic material into the neurons of human patients along with health issues since these technologies can drastically reduce life span. Furthermore, light can only penetrate a short depth into the brain so it can only regulate the activity of surface-level neurons. Regardless, the therapeutic uses of the technology are boundless. There is literature that shows that seizures can be stopped by modulating activity in the cerebellum, which coordinates a variety of functions including motor activity, perception, and balance.2,4 Optogenetics, the science of using light to control neurons, could also be used to solve “underlying pathological states and recover cognitive functions.”1 One day, amputees could even control their prosthetics seamlessly, as if it were truly a part of their own body.

References 1. Interview with Andrea Giovannucci, Ph.D. 9/23/20.

2. Wnuk A.; Davis A.; Parks C.; et al. Movement. In Brain 3.

4.

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Facts, Edition 8; Society for Neuroscience: Washington DC, 2018; pp 26-32.

Heo C.; Park H.; Kim Y.; et al. Nature. 2016, 6.

Krook-Magnuson E.; Szabo G.; Armstrong C.; et al. eNeuro. 2014.

psychology & neuroscience

Unlocking the Secrets of Sleep

By Sophia Marcom

Image by Jose Luis Navarro [CC-BY-NC-SA 4.0]

T

he average person spends about one third of their life asleep, yet our knowledge of what actually happens during this time is still limited. Sleep is incredibly important for physical and mental health, but scientists do not fully understand what actually happens in the brain that allows one to wake up feeling refreshed and focused. As such, scientists all around the world are attempting to unlock the mystery of sleep. Some of the answers can be found right here at UNC-Chapel Hill in Dr. Graham Diering’s neuroscience lab. Dr. Diering and his team study sleep as it relates to neurodegenerative and neurodevelopmental diseases such as Alzheimer’s disease and Autism Spectrum Disorder respectively. The goal of their research is to develop a therapy to give individuals with sleep issues the benefits of a good night’s rest. However, in order to mimic the effects of a good night’s sleep, they must first identify what happens during sleep.

Dr. Graham Diering, an assistant professor in UNC’s department of Cell Biology and Physiology, started out his career at the University of British Columbia in the early 2000s. Though originally interested in physics, he gravitated towards Dr. Graham Diering, PhD biology throughout his undergraduate years and completed a PhD in biochemistry in 2011. During his PhD, he developed a strong interest in neuroscience and learned that studying the intricacies of

the brain could lead to significant medical advances. Following this interest, he worked as a postdoctoral researcher in a neuroscience lab at Johns Hopkins University from 2011 to 2017 before coming to UNC and starting his own lab.

Dr. Diering’s research is geared toward understanding sleep disruption as it relates to diseases. While sleep disruption is a part of many diseases, his research focuses on Alzheimer’s and Autism Spectrum Disorder specifically. Dr. Diering’s goal is to better the lives of individuals with these diseases by improving their ability to sleep. He believes that poor sleep quality is a causative factor in the progression of these diseases. As he stated in an interview, “The idea is to develop some kind of a therapy to target sleep. But I want to be clear that the kind of therapy I’m talking about is not some sedative that would just make you want to lie down.

I’m talking about some kind of therapy that would really give you the benefits of a good night’s sleep. A kind of a drug that’s based on detailed knowledge of what sleep is doing.”

1 The kind of medicine that Dr. Diering describes does not currently exist, so many people resort to sleeping pills that act as sedatives but are unable to mimic the benefits of natural sleep. With a deeper understanding of the basis of sleep’s restorative patterns, scientists could design revolutionarily effective medicines that would be useful in many types of diseases.

While working in the neuroscience lab at Johns Hopkins, Dr. Diering came across a phenomenon that has helped him better understand brain activity during sleep: homeostatic scaling, which is when neurons adapt their levels of activity in response to certain stimuli by either increasing or decreasing their synaptic connections. The synapse is a small gap separating neurons through which neurotrans-

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Carolina Scientific mitters pass on nerve impulses. The regulation of synaptic activity allows the brain to maintain stability and carry out the appropriate level of function despite changing external conditions. Homeostatic scaling was described over 20 years ago after being observed in in-vitro neurons, but labs all over the world are currently working to discover how and when it happens in-vivo. While scaling up activity in the brain in response to an injury or disruption is commonly observed in-vivo, scaling down is not as well understood. Dr. Diering came across the hypothesis that the scaling down of synaptic connections occurs during sleep, and through experimentation, he found that to be the case. The hypothesis is known as “The Synaptic Homeostasis HYpothesis (SHY) of Sleep.”2 It states that while humans are awake, synaptic connections are strengthened; when one is asleep, the strengthening is off-set by the weakening of synapses. Using SHY as a starting point, Dr. Diering’s work moved towards a focus on disease and sleep. He uses the idea of synaptic scaling as a basis for his understanding of the mechanisms and functions of sleep. According to Dr. Diering, one of the many purposes of sleep is to clear out all of the unimportant information humans take in during the day. He describes it as an “Etch A Sketch model,” saying “if you want to store new information on the next day, you have to shake all that stuff out and clean it away, and literally make new space to learn more things.”

He describes forgetting as an intentional and necessary process, rather than a passive and disadvantageous one. “We talk about the brain’s ability to remember and the brain’s ability to form memory, and it’s pretty great. But actually,

pyschology & neuroscience

symptoms.”1 With Alzheimer’s specifically, Dr. Diering hypothesized that sleep quality is the first to take a hit during onset. Knowing this information opens up the potential to deter or minimize more severe symptoms by starting therapies to target and prioritize quality sleep. The cause-effect relationship between sleep quality and cognitive and social behavior in autism is not well known, however, Dr. Diering hopes to discover whether an improvement in sleep quality can lead to the recovery of some positive behaviors. His lab uses a combination of in-vitro neuron models and invivo mouse models to conduct this research. As they move towards a disease focus, more specific mouse models are being used that either have Alzheimer’s-like degeneration or mimic the sleep disruption observed in autism. Mouse models provide in-vivo models of homeostatic scaling and demonstrate that scaling-down is an essential component of quality sleep.

Figure 2. Increasingly, researchers are recognizing sleep as one of the three “pillars” of health alongside nutrition and exercise. Image by Sarah Monroe

Figure 1. A diagram showing the weakening of synaptic connections during sleep, as explained by the SHY hypothesis

we’re much better at forgetting. And I would say that 95% of the information that we take in does not get turned into long term memory and it’s forgotten.”1 The understanding of sleep as a way to clear necessary brain space sheds a light on the dangerous consequences of sleep deprivation and helped Dr. Diering’s lab make the connection between sleep disruption and the onset or worsening of many diseases.

The research conducted by Dr. Diering goes in two major directions: one studying sleep at the end of life with Alzheimer’s disease and the other studying younger stages of life with autism. The diversity in his research shows that sleep is extremely important at all ages and can have drastic effects on quality of life. Dr. Diering started these research projects with the hypothesis that “sleep disruption is a core part of the disease that really does contribute to the other

Due to the abundance of research being conducted on sleep, there is controversy present in the field. Dr. Diering explained that disagreements between scientists arise from the complicated nature of sleep – many processes occur during sleep that serve multiple purposes. There are also discrepancies between research done on differing age groups. Although sleep is important at all ages, many hypotheses that address sleep in one age group contradict patterns observed in other age groups. Looking at sleep from a developmental angle will help scientists reconcile their disagreements. As Diering said, “it’s a complicated business, sleep, just like being awake is a complicated business.”1 There is no easy way to explain all of the functions of sleep, but understanding the process of scaling down can assist scientists in developing effective treatments to improve the lives of those suffering from a wide variety of diseases.

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References 1. Interview with Graham Diering, Ph.D. 4 September 2020.

2. Graham Diering. Diering Lab. http://dieringlab.web.unc. edu/research/ [accessed September 4, 2020]

psychology & neuroscience

Actively Reducing Inequality in the Classroom

By Kylie Brown Photo by Rosmarie Voegtli. [CC-BY-2.0]

A

diverse student body represents a significant part of the appeal of a college campus. People from all over the world gather at universities to interact and exchange ideas, experiences, and beliefs.

When such a variety of individuals are combined together in a classroom, one would expect each one of them to learn differently. Students come from different academic backgrounds, and some will grasp the material faster than their peers. Traditional teaching methods can exacerbate these differences, promoting inequality and negatively impacting select groups of students.

When students attend a typical college lecture, they receive information galore about the subject matter, but rarely receive any guidance about how to study for exams.

Research shows that a self-reguDr. Kelly Hogan lated approach to

learning, where material is learned in steady chunks instead of crammed the night before the exam, is the most effective method. However, not every student knows the correct way to study as when entering their first semester of college. Certain students enter higher education more prepared than others because of prior exposure to studying and note-taking skills. Essentially, they have been taught how learning works.2 Unfortunately, the combination of a lack of prior knowledge and systemic inequality can cause minority undergraduates to fall behind and earn failing grades. Students who earn a poor grade in an introductory course are highly unlikely to continue a major in that field, thus contributing to the underrepresentation of minorities in the STEM field.1 Dr. Kelly Hogan, a STEM Teaching Professor and the Associate Dean of Instructional Innovation for the College of Arts and Sciences at UNC Chapel Hill, leads an ongoing movement toward inclusive teaching. The movement strives to level the playing field and ensure students of all backgrounds have an equal opportunity to participate and succeed.1 Dr. Hogan’s research specifically focuses on implementing inclusive methods and getting the methods to “stick�.2 Her research demonstrates how simple alterations to teaching techniques can dramatically reduce inequity in the classroom.

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approach is to ensure that engagement with the material is not optional. Requiring students to practice both in class as well as afterward through weekly homework assignments levels the playing field.

Mandatory practice benefits the students who came into college unaware of the benefits of such reinforcement to the learning process while having no negative impact on the students with prior knowledge.2

Dr. Hogan’s research also suggests that the adoption of anonymous participation in the classroom could Figure 1. Dr. Kelly Hogan teaching during one of her introductory counteract barriers to enbiology courses. Photo by Travis Dove gaged learning. Anxiety pres ents a major barrier to learning. Therefore, students Ten years ago, a colleague presented Dr. Hogan with data that broke down the grades of her intro- who are introverted, share a minority opinion, and/ ductory biology course by demographics. The data or feel unwelcome in the college classroom are unshowed a dramatic racial discrepancy and “it was likely to interact with the class via public speaking. clear there was an achievement gap.”2 1 in 14 white Anonymous participation methods include swapstudents earned either a D or an F in the course, while ping notecards containing student responses and 1 in 7 Latino students earned grades in the same the use of technology, such as web-based polling, to range.1 However, a staggering 1 in 3 black students make student responses anonymous to to the class.3 Most recently, Dr. Hogan has been working to underreceived failing grades in the course.1 In order to mitigate the inequalities, Dr. Hogan stand the incentives that help institutions and faculty developed changes to the traditional teaching meth- overcome barriers to the implementation of inclusive ods used in large lecture halls. Universally effective learning practices in the classroom. Dr. Hogan hopes “to infuse this kind of inclusive mindset in everything we do in teaching.” 2 By making inclusivity a priority, “the combination of a lack of prior knowledge and systemic inequality can professors can more effectively cultivate an equal learning environment for the wide range of students cause minority undergraduates to fall found in a modern university.

behind and earn failing grades.”

learning requires a highly structured course. One way to create such structure is to break up long lectures with periods of silence.3 Asking students to sit quietly and think about a problem before turning to their neighbor to discuss allows individual students to form their own thoughts. Without this method, more outspoken students tend to share their ideas more often than quieter students, whose thoughts tend to go unvoiced or unconsidered. It can cause reserved students to feel overwhelmed and left behind.3 Another

References 1. Supiano, Beckie. Traditional Teaching May Deepen Inequality. Can a Different Approach Fix It? https://www.chronicle.com/article/traditionalteaching-may-deepen-inequality-can-a-differentapproach-fix-it/ Accessed September 10th, 2020.

2. Interview with Kelly Hogan. 2/25/20.

3. Sathy, Viji and Hogan, Kelly. How to Make Your Teaching More Inclusive. https://www.chronicle. com/article/how-to-make-your-teaching-moreinclusive/ Accessed September 10th, 2020.

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physical science

Using Bacterial Molecules to Kill Bacteria

Image by Sage Ross [CC-BY-SA 3.0]

T

By Henry Bryant

he discovery of the first antibiotic — Penicillin — in 1928 was one of the greatest accidents to have happened in the medical field. Being able to treat bacterial infections has saved millions of lives.

Now nearly 100 years after the discovery, medicine is faced with a new problem: antibiotic resistance. In the U.S. alone, over 2.8 million people get antibiotic-resistant infections, out of which 35,000 die every year.1 As antibiotics are used more frequently, the chance that antibiotic resistance develops increases. While reducing the overuse of antibiotics can significantly combat resistance, the resistance still has a low potential of occurring during each use. Antibiotic resistance occurs when all bacteria susceptible to an antibiotic are killed, leaving only naturally resistant bacteria. The resistant bacteria no longer have to compete for space and resources and therefore grow and multiply rapidly. The potential for antibiotic resistance does not mean that antibiotic use should be stopped to prevent resistance, but rather creates a perpetual need for new antibiotic discoveries.

Dr. Bo Li, an associate professor in the chemistry department at UNC-Chapel Hill, investigates three aspects related to antibiotic discovery: natural products, antibiotic modes of action, and virulence factors (Figure 1). Natural products are bioactive molecules that are made by a living organism. Specifically, Dr.

Li researches potential antibiotics that are produced naturally by bacteria. His research seeks to understand why bacteria themselves would make antibiotics.Although seemingly counterintuitive, antibiotics are quite effective in helping bacteria Dr. Bo Li, PhD. both survive and thrive in complex environments. Bacteria make antibiotics naturally to compete with other types of bacteria for the limited resources, and the bacteria have developed protections against the antibiotics they produce so that they are unharmed.

Within the study of natural product antibiotics, the Li Lab has two main objectives: to find out which natural products could potentially be used as antibiotics, then discover how the bacteria make these natural product molecules. The most common way to test a molecule for antibiotic properties is by testing its potential to prevent bacterial growth and then, measuring the minimum concentration of the molecule needed to prevent growth. Once a molecule has been identified as an antibiotic, the Li Lab uses a va-

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Carolina Scientific riety of advanced biochemical methods to determine how the molecule is produced. By discovering how the antibiotics are made, scientists can then refine the process to increase efficiency add to the overall understanding of bacteria and natural production mechanisms.

Once an antibiotic has been identified, the next goal of the Li Lab is to investigate how the antibiotic works to eliminate bacteria, called the “mode of ac-

Figure 1. Mode of action for the antibiotic Holomycin, which was discovered in Dr. Li’s lab.

tion.” There are five main ways that common antibiotics kill bacteria. The first is by disrupting the replication of DNA — the genetic material of all organisms — so that bacteria cannot divide and multiply. The second method is when antibiotics disrupt the production of proteins — the molecules that perform nearly all functions in a cell — so that the bacteria can no longer function. The third method is by inhibiting the transcription of DNA into RNA. RNA is an intermediate that converts the genetic information from DNA into functional proteins. The fourth and fifth ways operate by disrupting the cell wall or membrane of bacteria.

Both structures protect the cell and serve as gates to keep cell contents in and foreign material out. When either the cell membrane or cell wall are damaged, these gates can no longer perform their function and the cell will then die.2 Determining if an antibiotic operates via one of five methods is the initial step in discovering how it works. Dr. Li is researching antibiotics that have novel modes of action that do not fall into the five common categories which makes studying

physical science

the molecules even more difficult. For example, Dr. Li discovered an antibiotic, holomycin, which disrupts the use of metal ions in the cell (Figure 2). While such uncommon novel modes of action are more difficult to explore, their specificity gives the antibiotics the potential to overcome bacterial resistance to existing antibiotics. The information on mode of action is an important step to move antibiotics toward clinical use in humans and animals.

The final objective of Dr. Li and her lab is one that she has “on [her] mind a lot.”3 Her goal is to look at virulence factors, small molecules made by infectious bacteria, which can enable the bacteria to cause infections.

Virulence factors are the most unexplored of the three subject areas in Dr. Li’s lab, yet they are crucial in understanding how bacteria infect and avoid the host’s defenses. Small-molecule virulence factors also have the potential to one day be targeted in the treatment of bacterial infections. However, at this point, not enough is known to develop any clinical treatments.

Outside of her scientific research goals, Dr. Li trains a variety of science students at UNC for them to become “fearless problem-solvers.”3 She takes great joy in walking through the lab to interact with her students, regularly meeting with them to discuss their research, help them overcome any hurdles, and contribute her own vision. Dr. Li is very proud of her research and says it feels “invigorating” to share it with others — to be able to add a grain of sand to the beach of knowledge.

References

1. Biggest Threats and Data. 18 Jun. 2020, https://www.cdc. gov/DrugResistance/Biggest-Threats.html. Accessed 17 Sep. 2020.

2. Nonejuie, P.; Burkart, M., Pogliano, K., & Pogliano, J. Proceedings of the National Academy of Sciences, 2013.

Bacterial cytological profiling rapidly identifies the cellular pathways targeted by antibacterial molecules, 110(40), 1616916174. doi:10.1073/pnas.1311066110 3. Interview with Bo Li, Ph.D. 09/15/20.

Figure 2. Illustration of the flow of discovery of virulence factors from genome to bacterial impact.

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physical science

Time and THYME: The Search for Exoplanets

By Abigail Dunnigan

Image by Felix Mittermeier. [CC0]

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he unknown planet zips around its host star, undisturbed for millions of years. It continues to remain undisturbed, but for the first time we can see it. Dr. Andrew Mann and his team study these previously unknown planets, more specifically exoplanets found in telescope data from NASA’s Kepler, K2, and Transiting Exoplanet Survey Satellite (TESS) missions. Exoplanets are all planets outside of our solar system. Their goal is to look for planets in young star clusters, moving groups of stars (which move similarly through space), and star-formation regions. They hope that studying the statistical properties of stars at different ages will provide insight into planet evolution.

Dr. Mann is an Associate Professor within the Department of Physics and Astronomy at UNC-Chapel Hill. He is part of the group that leads the Zodiacal Exoplanets in Time (ZEIT) Survey, as well as the TESS Hunt for Young and Maturing Exoplanets (THYME). The ZEIT Survey identifies faint or low-mass stars from K2 observations, while THYME uses data collected from bright or high-mass stars from TESS observations. “Zeit” is the German term for “time”, a clever wordplay for these projects.1 While they use different data, both the ZEIT Survey and THYME have the same overall goals: to study how statistical properties of planets evolve, thus shedding light on planet evolution.

The primary tool for identifying exoplanets is through the transit method. Take a solar eclipse as an example. When

Figure 1. Image courtesy of the European Southern Observatory.

the moon passes in front of the sun, it undergoes what is called a transit.

While the moon is in transit, the areas on Earth in the path of the eclipse are darkened. This darknening occurs because the moon is blocking sunlight from reaching the Earth. The same principle applies as exoplanets far away from Earth pass in front of their host star. As the planet is in transit, it causes a small dip in the brightness of Dr. Andrew Mann the star. The amount of light detected at a given point in time is referred to as flux.

“The saying you go by is that you only know planets as well as their stars” Other characteristics of the transiting planet can be calculated based off of the change in flux, but only if you know the properties of the host star. “The saying you go by is that you only know planets as well as their stars,”1 says Dr. Mann. To be able to measure the radius of the planet, “the drop [in light] is proportional to the ratio of the planet size to the star size. So you actually only measure the planet size as well as you measure the star size.”1 Dr. Mann and his team are currently focusing on THYME, which uses data from NASA’s TESS mission.1 The satellite collects

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Carolina Scientific flux measurements of target stars every two minutes.2 To make sense of the data, they use statistical and computational methods to map it out into light curves. From there, they can determine properties of the host star and planets such as their radii, masses, and orbital periods. While many different analysis methods are used, light curves make it all happen. Each flux measurement is plotted as a function of time, and periodic dips in flux can be a sign of a transiting planet. However, that is not all that needs to be done. Stars are not static. Other factors, such as dark spots and flares, can cause either dips or spikes in the brightness of each star. In fact, the curves you see on a light curve (Figure 2) are most likely not the signals from the transiting planet.3 The star’s activity actually causes much more fluctuation in brightness than the planet does. In addition, younger planets usually orbit younger stars. Younger stars are more active, making it more challenging to find orbiting planets than if one was studying older stars. Despite this, younger stars are still a necessary component of studying planet evolution.

The question remains then for Dr. Mann’s team as to how does one go about finding planets with all of this “astrophysical noise.” The answer is not simply by making better telescopes.

More advanced telescopes would only measure the flux more precisely. The flux would not affect the brightness variations of the star, and the variation of the transiting planets would still be too small to detect just by looking at the light curve.1 A common mitigating technique that Dr. Mann and his team use is called the Notch Filter. It assumes that there is a transit in the light curve when there are small brightness variations because transiting planets slightly lower the brightness of the host star. To ensure that no transits are left out, a computer program uses an aggressive algorithm to run the data. This algorithm is more sensitive to flux changes. A downside to the Notch Filter is that because it uses such an aggressive algorithm, there is a lot of extra data that scientists like Dr. Mann have to sort out afterward. One way to discern between planets and “junk” data is to see if the variations in brightness occur periodically and obey orbital mechanics.1 The period of a planet is the amount of time it takes to travel one full rotation around its host star. Each transit Dr. Mann and his team view via satellite telescope happens once per period. The “notches,” or trapezoidal dips in the light curve, represent each transit that a planet takes (Figure 1).4

Figure 2. A closer look at the notch filter “dip” from planetary

transit.

One thing that benefits these projects is Dr. Mann’s research background. Prior to studying exoplanets in the ZEIT Survey and THYME, he primarily worked with stars. His background in studying stars aids in the search for exoplanets because he is more skilled in modeling host stars. In fact, the majority of re-

physical science

searchers in the ZEIT survey and THYME have a background in stellar astrophysics.1 By having a stronger understanding of stellar astrophysics, Dr. Mann is better equipped to deal with current uncertainties; for example, there is still much that is unknown about young stars, as the underlying physics behind them is tricky and complicated.

Dr. Mann is currently working on a paper connected to THYME. He and other researchers discovered two planets transiting a young, Sun-like star in the Ursa Major moving group.

The host star in this system is bright, making it easier to analyze planet properties.3 Figure 2 shows the notch filter “dips” as each planet makes a transit. The blue and yellow arrows indicate where each transit is occurring.3 Notice how the yellow and blue arrows occur over equal periods of time. The arrows indicate how long each rotation around the host star takes. Since there is more space between the blue arrows, the planet they represent has a longer period than the planet represented by the yellow arrows.

By using statistical and computational methods, Dr. Mann and his team were able to discover, characterize, and measure properties of the two exoplanets.

Figure 3. The light curve (top) indicates where each transit (bottom) is occurring.

Discoveries of exoplanets have already led to significant findings. For example, through his research, Dr. Mann has found that younger planets are statistically larger than their older counterparts. There are multiple theories for this, such as the hypothesis that younger planets are warmer and therefore expand in size.1 In the future, Dr. Mann intends on continuing with TESS to look for more young planets: “The big advantage of TESS is that the stars we find are statistically brighter. It’s better for this whole other regime of work we want to do called transmission spectroscopy.”1 Transmission spectroscopy goes further with studying the planets themselves, such as researching the atmospheres of these planets. THYME and the ZEIT survey have paved the way to conduct detailed studies of objects that are not even seen as specks in the night sky.

References 1. Interview with Andrew Mann, PhD. 09/10/20 2. TESS Mission. https://heasarc.gsfc.nasa.gov/docs/tess/ (accessed September 25th, 2020).

3. Mann, A., Johnson, M., Vanderburg, A., Kraus, A., Rizzuto, A., Wood, M., Bush, J., Rockliffe, K., Newton, E., Latham, D., et al. astro-ph 2020, arXiv:2005.00047v2.

4. Mann, A. https://andrewwmann.com/ (accessed September 25th, 2020).

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life science

What Makes Them Tick: The Fruit Fly’s Internal Gyroscope

By Harris Davis

Illustration by Hannah Kennedy

There’s something special about flying. Birds, reptiles, mammals, and insects have been flying for millions of years, and yet until very recently in our evolution, the physics of flying have eluded human beings. Animal flight mechanisms have fascinated biologists since Darwin, and have been studied in a diverse range of species. For the first time, neuroscientific research at UNC is revealing the role of otherwise poorly understood mechanisms of flight control in fruit flies.

The fruit fly (D. melanogaster) has long been of particular interest to researchers for a unique and deceptively simple aspect of its flight. A few centuries ago, a pair of tiny structures that twitch and vibrate during flight were discovered on the fly’s thorax. It was later found that the removal of these structures completely compromises the fly’s

Figure 1: (A) Map of haltere muscles, where hDVM is the power muscle. Steering muscles include basalares (hB1and hB2) and axillaries (hI1–hIII3). (B) Experimental setup of LED arena, which tracks wing motion and images muscle activity.

(C) amplitude and muscle activity in axillaries and basalares when visual field simulates rotation to the left (red) and right (blue).

ability to get off the ground.1 And unlike many insects—which have two sets of wings—flies have only one, along with a pair of these appendages that came to be known as halteres. Despite these observations, the function of halteres in flies has largely remained a mystery.

Approximately 80 years ago, however, it was proposed that halteres may function as a kind of biological gyroscope, maintaining the fly’s balance midair.3 This is one of the hypotheses that Dr. Brad Dickerson and his team have spent the last year exploring at UNC. When they began their work, the lab didn’t just want to verify the halteres’ function as a gyroscope; they wanted to know exactly how sensory input causes changes in muscle motion during flight.

Furthermore, they wanted to investigate the halteres’ potential role in the timing of wing motion.2 Because of the high speed at which the fruit fly beats its wings—200 to 250 times per second, the team knew that motor circuits commonly involved in timing the gaits of other animals were unlikely to control fruit fly wing strokes. Thus, the fly must have a faster, more reflexive way to control motor activity. First, Dr. Dickerson’s team explored the relationship between visual inputs that trigger neural signals to the haltere muscles. They then looked at how those signals in turn provide immediate feedback to the wing muscles to determine if neural information from the halteres to the wing muscles plays a significant role in controlling wing motion.

Figuring out which inputs trigger feedback is key to interpreting the function of any biological structure. To understand how halteres regulate flight, it is first necessary to consider the nerves that make them tick. Each of the halteres has one “power muscle” for generating force, and a group of “control muscles” for fine tuning the direction of that force.1,2

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Brad Dickerson Ph.D., Assistant Professor in UNC Biology Department and Kenan Honors Fellow

Each muscle is controlled by a single motor neuron. A “firing” of that neuron triggers a contraction of the corresponding muscle. These firings are triggered by physical input from sensors, which line the fly’s wings and halteres, and from visual input transmitted from the eyes to the brain.1 While this may seem relatively straightforward, the key to completely understanding how motor changes occur in response to stimuli has remained hidden in the difficult-to-analyze neural feedback mechanisms between halteres and wings. Past analyses of the motion of haltere muscles in response to stimuli have largely failed because the physical movement of the structures is so finely

Figure 2: Diagram of halteres on D. melanogaster.

Carolina Scientific

Figure 3I and 3J: Wingbeat amplitude (bottom) and muscle activity (top) in haltere (right) and wing (left). Note similarities in muscle activity during cardinal rotations.

tuned that changes are too small to be observable.1 Dr. Dickerson’s team, however, took a different approach, which did not attempt to see the motion of the halteres, per se. Instead, they analyzed fluctuations in the chemistry of motor neurons and the muscles they control, and their latest experiments have employed cutting-edge neural imaging technology to observe the activity of fly’s muscles during flight—down to the millisecond—in response to physical and visual stimuli.

One experiment the team conducted involved placing a fly in an LED arena and broadcasting images to that fly to create the illusion of motion, thereby providing a visual stimulus. The team tracked changes in the fly’s direction in response to visual stimuli, simultaneously observing activity in the motor neurons of the wings and halteres. When an action potential fires across a motor neuron, there is an influx of calcium ions by nearby muscle tissue. Using a fluorescent microscope, the lab was able to record these calcium spikes and dips, which correspond to motor neuron activity, and thus show changes to the motion of the haltere muscle. Imaging the axon terminals of the motor neuron instead of the haltere itself allowed Dickerson and his team to not only record these changes during flight, but to correlate them with specific shifts in the fly’s visual stimulus.

A caveat to this type of observation is that calcium fluctuations only show that something about the motion of the haltere is changing—they don’t tell you what. Hence the other advan-

tage of calcium imaging. The wing nerve of the fly is homologous to that of the haltere; it has the same kinds of sensory structures, and it sends similar sensory inputs to the brain. It can also be imaged in the same manner as the haltere, using calcium. While changes in haltere motion are difficult to observe physically, changes in the wing motion are not.

Thus, if physical changes in wing motion can be correlated with specific fluctuations in calcium activity in the muscles, the same fluctuations in the haltere muscles can be interpreted as similar motion changes.

The data were pretty hard to argue with. First, the Dickerson Lab found a clear correlation between the simulation of motion in the fly’s visual field and changes in wingbeat amplitude. Changes in the fly’s perceived cardinal directions resulted in haltere responses that would cause the fly to change its flight angle to correct the change. Second, the link between haltere feedback and wing motion was verified when activation of haltere muscles resulted in immediate, pronounced changes in wing steering.

This made sense given the similarities muscle activity between the wings and halteres.2 Not only does this relationship between feedback from the haltere muscles and wing movement support the hypothesis that halteres are involved in timing; the interlocked nature of the two systems also provides further evidence that halteres in flies evolved from a pair of hindwings present in their ancestors.1 For Dr. Dickerson, this validated countless hours of painstaking literature

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life science review, confirming in a matterof weeks a hypothesis that had taken years to generate. More broadly, these data are a major step in resolving a question about flight mechanisms that has persisted for centuries.

Evidence seldom comes together quite this neatly. Biology is messy. Stable physiology in living systems requires order, forcing organisms to grapple with the second law of thermodynamics.

Constantly shifting ecological pressures demand that populations adjust and readjust to their environments, often with but a handful of molecular accidents in their toolbox. This is the kind of chaos that biologists work to understand and interpret, and research is often fraught with strife, stubborn data, and dead ends. Every once in a while, however, a researcher will experience what Dr. Dickerson calls a “brief moment of extreme simplicity,” when the data just make sense.

The data the Dickerson Lab presented last year are not by any means an end to the study of the fruit fly’s flight mechanisms. However, they are representative of a large-scale paradigm shift in the way we think about neural timing systems. This shift opens the door to answering entirely new questions. If halteres are involved in wingbeat timing in flies, how do insects without halteres solve timing problems? How can we begin to explore the relationships between timing systems and motor systems in other animals? These data imply a certain elegance to the seemingly complex systems we have yet to understand. Still, the road to elegant solutions is paved with struggle and frustration, and every new question presents a new set of challenges to which scientists must adapt.

References

1. Interview with Brad Dickerson, Ph.D. 2. Bradley H. Dickerson, Alysha M. de Souza, Ainul Hudal, Michael H. Dickinson.

Current Biology. 2019, Volume 29, Issue 20, pp.

3517-3524. “Flies Regulate Wing Motion via Active Control of a Dual-Function Gyroscope.”

3. J.W.S. Pringle. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences. 1948, Volume 233, Issue 602, pp. 347384. “The gyroscopic mechanism of the halteres of Diptera.”

4. R. Thompson, M. Wehling, J. Evers, W. Dixon.

Journal of Comparative Physiology. 2008, Volume 195, pp. 99-112. “Body Rate Decoupling Using Haltere Mid-Stroke Measurements for Inertial Flight Stabilization in Diptera.”

life science

The Fungal Network Syncytia are integral to understanding life

By Jasmeet Singh

Image by USCDCP. [CC0]

I

magine this: You are walking through the forest when cells such as cancer and SARS-CoV-2 (the virus responsible you stumble upon a patch of toadstools. Even though for COVID-19), and more.1 you cannot hear them, these organisms chat with countYou may be asking, why cells? Dr. Gladfelter explains less other species via a web of branched out multinucle- that examining cells at the microscopic level is intuitive ated cells known as syncytia. By transmitting information for her. “There’s people that study elephants,” she says, to trees that appear far out of reach and communicating “and that’s their scale. And then there’s people who with bacterial colonies deep inside study galaxies. I like thinking about “By understanding the the soil, fungi effectively bridge the problems at the scale of a cell.” gaps between ecosystems. It is no biophysics of the processes Studying live fungi with fluorescent wonder they are thought of as “the inside these structural units, a microscopy provides one such Earth’s internet.”1 approach, as most fungi are giant Dr. Amy Gladfelter, a professor new world and perspective can fused cells that house many nuclei of cell biology at UNC-Chapel Hill, — and thus, many genomes — be unlocked.” bathed in the same cytoplasm. uses this example to illustrate the importance of her work with While it is not yet understood why fungal cells take fungal syncytia in an effort to on this form, their unusual structure fascinates researchers. understand cell organization. Fungi take on shapes ranging from branched to sporous, Her lab is conducting a multitude and the organelles inside their cells constantly perform of research projects at any given a myriad of actions. This may sound like chaos. However, moment, projects that span the Gladfelter lab is able to pry open cells, look at their human and environmental individual components, and understand this complex bodies. The applications of system in a simpler fashion. Thus, the inner workings of this research could provide fungal cells become ordered chaos as Dr. Gladfelter and the pathway to understanding her team investigate the cell’s governing rules and overall integral components of the organization.1 One mechanism that Dr. Gladfelter’s research has biosphere, neurodegenerative Dr. Amy Gladfelter diseases, the science of syncytial explored involves the ways in which cells create functionally

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Carolina Scientific

life science

While the Gladfelter lab and the greater science community are not yet certain of the reason cells adopt this form, it certainly holds significant relevance to their field. Alongside its very topical SARS-CoV-2 research, the Gladfelter lab is currently engaged in a project about a cell (the syncytiotrophoblast) that covers the entire placenta.

The syncytiotrophoblast provides a barrier between the mother and the fetus, secretes hormones, and controls a number of metabolic functions. Though captivating in its own right, its prospective relevance to women and children’s health is a significant development.

Figure 1. Syncytial cell under a microscope. Syncytia are unique because they are giant, multinucleated cells. Image courtesy of Wikimedia Commons

distinct areas. Proteins undergo phase separation in a manner similar to a water molecule changing from a liquid to a solid and vice versa. Contained in droplets defined as “condensates” inside the cells, proteins are part of a phenomenon which differs from the usual membraneenclosed, compartmentalized organelles. Also residing in the droplets are RNA (short for ribonucleic acid, which assumes a fundamental role in gene regulation and coding) and mRNA (messenger ribonucleic acid, which carries genetic information from the nucleus to proteingenerating complexes in the cytoplasm). By inspecting the RNA-binding protein (RBP) Whi3, another study in which Dr. Gladfelter is involved proposes the following: each condensate is kept separate due to components of the RNA that dictate the particular properties of the condensates formed by Whi3.1,2 These findings could be monumental in understanding how information is organized within these condensates.

Although the Gladfelter lab concentrates more on research at the cellular level, its applications could prove monumental. For example, an amalgamation of fungi, protein, and condensate data can be applied to neurodegenerative diseases. Droplet formation is part of normal cell function. When mutation and aging occur as a result of oxidative stress, however, toxic aggregates form in place of the droplets, and phase separation halts so that the condensates exist in a perpetually solid-like state.

The loss of the droplets’ dynamic properties characterizes neurodegeneration. This can be seen in a recent discovery which describes that “proteins linked to [amyotrophic lateral sclerosis (ALS)] form condensates, and mutations in these proteins can make the condensates more viscous than usual.”3 Condensates are also said to be linked with other neurodegenerative diseases such as Alzheimer’s and Huntington’s.

Additionally, cancer, SARS-CoV-2, HIV, and human orthopneumovirus all cause cells to become syncytial.

Figure 2. Fibrillarin is an example of an RNA-binding protein. These proteins bind to the RNA in cells and play an important role in the transcription, translation, and regulation of gene expression. Image courtesy of Wikimedia Commons

Dr. Gladfelter’s work with fungi and other syncytial cells takes on a level of complexity that causes it to be sometimes underappreciated. Of course, the applications of these studies are acknowledged for good reason: many people are primarily interested in large-scale ideas. But by understanding the biophysics of the processes inside these structural units, a new world and perspective can be unlocked. For researchers, this means more investment of time and money into investigating syncytial cells and gaining a steady grasp on how cells are organized. This knowledge could then be utilized in conceptualizing the inner structure of condensates, shedding more light on how neurodegenerative diseases work and possibly even precipitating the race for a cure. Just as the future of humanity lies in technology, it is also deeply rooted in fungi.

References

1. Interview with Amy Gladfelter, Ph.D. 09/11/20.

2. Langdon, E.M.; Qui, Yupeng; Niaki, A.G.; McLaughlin, G.A.; Weidmann, C.A.; Gerbich, T.M.; Smith, J.A.; Crutchley, J.M.; Termini, C.M.; Gladfelter A.S., et al. Science. 2018, 360, 922-927.

3. Bayer makes first move into condensates. Nat Biotechnol 38, 5 (2020). https://doi.org/10.1038/s41587-019-0386-6 (accessed September 16th, 2020).

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life science

H

Targeting Issues in AAV Vector Gene Therapy for Hemophilia

emophilia is a bleeding disorder affecting more than 1,125,000 people worldwide: three times higher than the previous estimate of 400,000.1 The disorder is caused by mutations of factor genes in hepatocyte cells of the liver, resulting in partial or total deficiencies of blood-clotting proteins. Physical symptoms range from severe bleeding after a major injury to spontaneous bleeding in muscles and blood build-up in joints, all of which limit the lifestyle and shorten the lifespan of those affected. Hemophilia currently has no cure. Treatments such as injecting clotting factor concentrates exist; however, such therapies require thousands of injections over a lifetime and cost an average of more than $270,000 annually. These factors only make it harder for hemophilia patients living in less industrialized nations or more rural areas to access adequate treatment.

Researchers around the world are currently exploring alternative treatment methods, namely gene therapies using non-viral naked DNA or viral vectors. Such experimental techniques use protective molecules or human-modified viruses to transport and introduce genes into target cells. The end result is the creation of necessary proteins that correct mutations and alleviate disease symptoms. Of the two methods, viral vectors are more popular for liver gene therapy.

At the University of North Carolina Gene Therapy Center, Dr. Chengwen Li and his team focus on the adeno-associated virus (AAV) for application in viral vector gene therapy. AAV has shown promising results in clinical trials for hemophilia, with patients’ blood-clotting factors increasing to therapeutic Illustration by Heidi Cao

By Kelly Fan levels for long periods of time. Furthermore, in theory, AAV gene therapy has the potential to cure hemophilia with one injection, since the correct genetic code would stay in the human body for autonomous protein creation. This improves upon current treatment options, which involve multiple expensive injections that only alleviate hemophilia symptoms.

Many of the AAV’s characteristics render it an attractive gene therapy vector. For example, the virus allows for long-term protein production in the cell, has the ability to infect a broad spectrum of cell types, invokes a relatively low but still present immune response, and lacks the ability to cause illness. 2 Despite its beneficial features, researchers like Dr. Li must continue to search for ways to modify the AAV genome in order to make it more suitable for effective disease treatment.

Dr. Li and his lab mainly investigate how to overcome the immune response against AAV vectors, developing new strategies to enhance AAV vector transduction and specifying AAV vector gene therapy for rare diseases like hemophilia. Their most recent research addresses all three necessary improve-

Dr. Chengwen Li

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Figure 1. AAV vector transduction pathway, starting with the vector entering the cell and ending with the therapeutic protein, like clotting factor protein for hemophilia.

ments to AAV gene therapy, with a focus on neutralizing antibodies called Nabs.

The fact that “over 90% of humans have already gotten an AAV infection” presents a significant problem for hemophilia-centered AAV gene therapy. 3 Around 50% of previously-infected people generate Nabs, which recognize and block AAV capsids (the outer coating surrounding the genome) from interacting with host cells. As a result, transduction cannot occur and AAV gene therapy would not show many, if any, beneficial effects for hemophilia patients in that 50%.

However, many varieties, or serotypes, of AAV exist. The various serotypes have different genetic material but similar protein structures with nuances impacting their interactions.

Carolina Scientific Certain AAV vector serotypes compared to others might better escape the Nabs produced by an individual patient. The basic theory provides the foundation for the directed evolution method.

Thus, Dr. Li and his team modified the AAV genome to change the capsid’s protein structures that interact with Nabs and cells—DNase enzymes cut DNA from different AAV serotypes into small pieces, which are recombined to form mutant AAVs. At first, the Li Lab randomized the process in order to create a library of different mutants. Then, they injected mutant AAV into chimeric mice with livers made up of human hepatocytes. 4 Dr. Li and his team used these humanized mice to address the problem that “results from animals cannot exactly represent what will work in humans.” Certain serotypes may show great transduction in mouse cells in lower dosages, but necessitate much higher dosages to show the same level of transduction in humans. 3 Using hepatocyte-humanized mice may allow for smoother transition of beneficial results from animal models to human clinical trials. Once mutant AAV vectors were extracted from the xenografted hepatocytes, the lab tested their transduction efficiency and resistance to Nab activity.

Dr. Li and other researchers identified Mutant AAV LP2-10 as the mutant capsid with the highest ability to escape Nabs and, accordingly, a better chance of transducing hepatocytes. Its capsid

life science

Nab activity through the methods of directed evolution and using chimeric mice.

With such positive results, more hemophilia patients who have Nabs could be recruited for clinical trials and treated Figure 3. Results of AAV neutralization for different AAV serotypes

by AAV gene and mutant. AAV mutant LP2-10 required the highest concentration of Nab in IVIG to have transduction abilities inhibited completely. therapy, since searchers can take inspiration from such their immune system would not react as strongly in an methods to develop more mutant AAV vectors able to travel to the brain, musattempt to eradicate AAV vectors.

The current major drawback to cles, and anywhere else in the body as AAV LP2-10 is that its transduction ef- well as deliver therapeutic genes.

A future where people from all ficiency in human hepatocytes is less than the best serotypes used to create over the world with hemophilia can fithe mutant AAV library, indicating a nally receive adequate treatments and direction of future study for Dr. Li and live more full lives is possible with conhis lab. The lab plans to use the mu- tinuous research and improvements in tant AAV LP2-10 as a “template to build AAV gene therapy. Furthermore, those upon,” rationally targeting places in its possibilities are not only limited to heDNA genome to modify so that its he- mophilia. Dr. Li suggests hopes that as patocyte transduction is high enough research on AAV gene therapy improves to have viable therapeutic effects on its effectiveness, “any disease in the fuhemophilia. Alternatively, the lab could ture could possibly be treated by gene also do another round of direct evolu- therapy.” 3 tion, creating a new mutant AAV library References with the inclusion of AAV LP2-10 to “mix 1.Iorio, A.; Stonebraker, J. S.; Chambost, H.; in its significant ability to escape Nabs.” 3 Makris, M.; Coffin, D.; Herr, C.; Germini, This may lead to the F.; Data and Demographics Committee creation of a better of the World Federation of Hemophilia. vector with a higher Establishing the Prevalence and Prevalence transduction effi- at Birth of Hemophilia in Males: A Meta-analytic Approach Using National ciency for hepato- Registries. Ann Intern Med 2019, 171(8), cytes.

540-546. https://www.acpjournals.org/doi/ The results full/10.7326/M19-1208 are not specific to 2.Li, C.; Samulski R.J. Engineering adenohemophilia.

Re- associated virus vectors for gene therapy. searchers can also Nat Rev Genet 2020, 21, 255–272. https://doi. org/10.1038/s41576-019-0205-4 apply Dr. Li’s find- 3.Interview with Chengwen Li, Ph.D. Figure 2. The left shows wild type AAV being inhibited by ings to other liver 09/11/2020 neutralizing antibodies once in the body. The right displays an diseases because 4.Pei, X.; Shao, W.; Xing, A.; Askew, C.; overview of the directed evolution process.

AAV LP2-10 widely Chen, X.; Cui, C.; Abajas, Y. L.; Gerber, surface structures can escape higher avoids Nabs in human bodily fluids. Ad- D. A.; Merricks, E. P.; Nichols, T. C.; et al. concentrations of Nabs than other se- ditionally, the methods of direct evo- Development of AAV Variants with Human Hepatocyte Tropism and Neutralizing rotypes and mutants.4 The outcomes lution, viral libraries, and humanized Antibody Escape Capacity. Mol Ther prove it is possible to isolate mutant mice have the potential to further gene Methods Clin Dev 2020, 18, 259–268.

AAV vectors with the ability to evade therapy research on more diseases. Re- https://doi.org/10.1016/j.omtm.2020.06.003

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