YSM Issue 96.2

Yale Scientific 

THE NATION’S OLDEST COLLEGE SCIENCE PUBLICATION • ESTABLISHED IN 1894 

MAY 2023 

VOL. 96 NO. 2 • $6.99 

FATAL 

ATTRACTION 22 

TRACKING CARBON’S 

UNDERWATER DIVE 12 

IT’S IN OUR BONES 14 

16 

ACNE-BIOTICS 

ANIMALS AGAINST 

19 

RISING TIDES

TABLE OF 

VOL. 96 ISSUE NO. 2 

COVER 

22 

A R T 

I C L E 

Fatal Attraction 

Cindy Mei 

Tsetse flies are responsible for spreading a deadly disease that leads to agricultural and medical 

devastation in Africa. The Carlson lab at Yale and their collaborators have identified a pheromone 

produced by the fly that may be able to attract and halt the activity of the flies, which holds great 

potential to control the tsetse fly population. 

12 Tracking Carbon's Underwater Dive 

Tori Sodeinde 

Many marine animals form calcium carbonate shells that deposit minerals onto the surface of the 

Earth, but billions of years ago, before these biotic carbonate sources evolved, what were the most 

important contributing sources to the precipitation of carbonate? New geological isotope data 

challenges previous ideas about the ancient history of the marine carbonate factory. 

14 It's in Our Bones 

Evelyn Jiang 

Researchers at Yale have uncovered a key molecular link between bone marrow aging and the 

development of atherosclerosis—which causes heart attacks, strokes, and other cardiovascular 

complications, which are collectively the leading cause of death worldwide. Their findings offer 

new hope for the treatment and prevention of the disease. 

16 Acne-Biotics 

Crystal Liu 

Yale structural biologists determined the structure of a promising acne-fighting antibiotic, sarecycline, 

in complex with the ribosome of C. acnes, the bacterium largely responsible for acne. Read about 

sarecycline’s mechanism, why it can be more effective than other antibiotics, and other discoveries 

about the C. acnes ribosome. 

19 Animals Against Rising Tides 

Abigail Jolteus 

Global warming is causing sea levels to rise rapidly, which imposes stress on coastal ecosystems. Researchers 

at the Yale School of Environment and the University of Florida have investigated the impact of mussels 

on salt marshes, which could help provide more insight into how to help mitigate the effects of sea level 

rise —one of the most urgent climate threats today. 

2 Yale Scientific Magazine May 2023 www.yalescientific.org

CONTENTS 

More articles online at www.yalescientific.org & https://medium.com/the-scope-yale-scientific-magazines-online-blog 

4 

6 

25 

34 

Q&A 

NEWS 

FEATURES 

SPECIALS 

What is the World's Most Efficient Form of Urination? • Victor Nguyen 

Who were the First Cowboys in the World? • Jamie Seu 

The Changing Language of Our Changing Climate • Pratiksha Bhattacharyya 

Saving Birds on Yale's Campus • Mia Gawith 

A New Approach Against an Old Foe • Johnny Yue 

Taking a Peek at Pandora's Cluster • Ignacio Ruiz-Sanchez 

Sink or Swim • Lea Papa 

Using Machine Learning to Produce Metallic Glass • Maya Khurana 

A Dynamic Duo Fighting Against Brain Cancer • Casey McGuire 

The Carbon Footprint of Care • Jessica Le 

Wooden Corkscrew Robots Plant Seeds • Madeleine Popofsky 

Your Unique Fingerprint • Elisa Howard 

The Impossible Star • Elizabeth Watson 

Cyborg Zebrafish • Nathan Mu 

How Ancient Humans Escaped the Ice Age • Matthew Blair 

Plant-Animal Hybrids • Samantha Liu 

Undergraduate Profile: Charnice Hoegnifioh (YC '24) • Emily Shang 

Alumni Profile: Amymarie Bartholomew (YC '13) • William Archacki 

Science in the Spotlight: Measure for Measure • Henry Chen 

Science in the Spotlight: the Darkness Manifesto • Faith Pena 

Counterpoint: Quantum Cryptography • Matthew Dobre 

Perimeter • Sophia Zhao 

www.yalescientific.org 

May 2023 Yale Scientific Magazine 3

WHO WERE THE 

FIRST COWBOYS IN 

THE WORLD? 

& 

WHAT IS THE WORLD'S 

MOST EFFICIENT 

FORM OF URINATION? 

By Victor Nguyen 

Has inspiration ever hit you while you were on the toilet? For 

scientists studying the potty period of the glassy-winged 

sharpshooter, a half-inch-long insect in the Cicadellidae 

family, a revelation between physics and biology was born. Known to be 

serious agricultural pests, sharpshooters relieve themselves by forming 

small droplets of urine at their anal styluses, which are appendages 

involved in excretion. Eventually, the droplets grow to a diameter of 

0.725 millimeters, and the anal styluses launches the particulates 

repeatedly, accelerating up to forty times the force of gravity. 

Sharpshooters developed this bathroom behavior due to their waterheavy 

diets. The leafhoppers feed on plant xylem sap, which has a small 

nutrient-to-liquid ratio. As a result, they drink up to three hundred 

times their body weight. A closer analysis of this phenomenon, 

published by researchers at Georgia Tech in Nature Communications, 

showed that sharpshooters developed this biological mechanism to 

conserve energy given their small size and energy output. 

The sharpshooter’s urinary facilities mark a notable discovery because 

they are the first observation of superpropulsion in a biological system, 

a phenomenon in which a projectile moves faster than the launcher 

that propelled it. Applications of the sharpshooter’s mechanisms have 

a future in electronics. Researchers investigating the sharpshooters 

foresee how the insect’s energy-efficient solution can be used to remove 

solvents in micro-manufacturing or to eliminate water from complex 

surfaces. This intersection of the physical and biological sciences sets 

a precedent for finding unorthodox answers. Wherever and whenever 

inspiration or the need to relieve strikes, innovation may soon follow. ■ 

By Jamie Seu 

Stirrups. Leather boots. The Wild West. Cowboys have been 

a subject of fascination for centuries, appearing in every 

aspect of American pop culture from cliché Halloween 

costumes to Hollywood blockbusters. However, the modern 

perception of these equestrian cavaliers encapsulates only a 

minuscule piece of the long, intertwining history of humans 

and horses—a history that, according to recent archaeological 

findings, could date back over five thousand years. 

While evidence of equine domestication has been welldocumented 

throughout history, proof of ridership and determination 

of the practice’s exact origins have been difficult to establish. In a 

paper published in Science Advances, a team of researchers from 

Finland, Romania, Bulgaria, Hungary, and New York analyzed over 

two hundred skeletal remains to unravel these mysteries. They found 

the earliest bioanthropological evidence of horseback riding to date 

in the skeletons of five Yamnaya individuals, a people noted for their 

expansion across Eurasia during the Early Bronze Age in the third 

millennium BC. Each skeleton was analyzed according to six specific 

criteria indicative of “horsemanship syndrome.” The five skeletons 

displayed at least four of the six traits, including wear on the pelvis 

and femur, stress-induced vertebral degeneration, and alterations in 

certain bone shapes and sizes. 

The use of horses as a mode of transportation marked a dramatic 

transition in societal evolution, dictating patterns of migration and 

facilitating trade between previously isolated locations. So while the 

first cowboys were not quite the gun-toting, saloon-loving buckaroos 

we make them out to be, they—and their speedy, four-legged sidekicks 

—may have been some of the most influential figures in history. ■ 


The Editor-in-Chief Speaks 

THROUGH THE LOOKING GLASS 

This summer, I had the immense privilege of interviewing Dr. Vivek Murthy, 

the 19th and 21st U.S. Surgeon General and an alumnus of the Yale School 

of Medicine. When asked about the role of science journalism in our society, 

Dr. Murthy told me, “There could not be a time in my life where I think we have 

needed science journalists more to be there for us explaining what people need to 

know in a world where we’re awash in misinformation.” 

Indeed, with the polarization of online forums and social media platforms, 

conspiracy theories are spreading like never before, while the public’s distrust in the 

notion of ‘experts’ has rapidly grown. How, then, can we bridge the chasm that has 

emerged between science and society? 

There is no simple or straightforward answer, but as Dr. Murthy emphasized, 

science journalism plays a pivotal role in connecting the two. While I would 

typically use this space to tell you about the articles in this issue, I found it would 

be fitting to re-examine the mission of the Yale Scientific itself. At its core, our 

work strives to highlight the relevance of recent innovations in our daily lives, 

spark scientific interest in youth, help communities make informed decisions, and 

build public trust in science. We aim to present scientific, medical, and engineering 

discoveries to a general audience—no matter their background—in an accessible 

and unbiased manner. 

Recently, we’ve had the privilege of poring through the archives from the YSM 

offices in Welch Hall on Old Campus and in 305 Crown St. Flipping through the 

yellowing pages of our hand-bound volumes from the 19th century and learning 

about the history of the Yale School of Medicine, the Sheffield Scientific School, 

and the Yale Scientific Magazine itself has revealed that while a lot has changed, 

our central mission has remained steadfast. In fact, it has only been reaffirmed as 

science has become the center of attention in debates surrounding deeply divisive 

issues, ethical concerns, and public policy controversies. At YSM, we will continue 

to question the assumed, communicate the abstract, and weave distinctly human 

stories around technical scientific developments. 

I am honored and humbled to continue the Yale Scientific’s long legacy of 

science journalism alongside our incredible masthead, student contributors, and 

community partners. With you, our readers, let’s embark on the formidable quest 

to which we aspire at the Yale Scientific—to maintain objectivity without the loss of 

nuance, present technicality without the loss of perspective, and highlight science 

without the loss of humanity. 

About the Art 

Alex Dong, Editor-in-Chief 

Researchers have identified a 

pheromone that may influence the 

behavior of flies that spread disease 

in Africa. This cover illustration 

depicts two Tsetse flies with 

pheromones, represented as glowing 

particles, between them. 

Catherine Kwon, Cover Artist 

MASTHEAD 

May 2023 VOL. 96 NO. 2 

EDITORIAL BOARD 

Editor-in-Chief 

Managing Editors 

News Editor 

Features Editor 

Special Sections Editor 

Articles Editor 

Online Editors 

Copy Editors 

Scope Editors 

PRODUCTION & DESIGN 

Production Manager 

Layout Editors 

Art Editor 

Cover Artist 

Photography Editor 

BUSINESS 

Publisher 

Operations Managers 

Subscriptions Manager 

Outreach Manager 

OUTREACH 

Synapse Presidents 

Synapse Vice President 

Synapse Outreach Coordinators 

Synapse Events Coordinator 

WEB 

Web Managers 

Head of Social Media Team 

Social Media Coordinators 

STAFF 

Sanya Abbasey 

Luna Aguilar 

Ricardo Ahumada 

William Archacki 

Dinesh Bojja 

Risha Chakraborty 

Kelly Chen 

Leah Dayan 

Steven Dong 

Chris Esneault 

Erin Foley 

Mia Gawith 

Simona Hausleitner 

Tamasen Hayward 

Katherine He 

Miriam Huerta 

Sofia Jacobson 

Jenna Kim 

Catherine Kwon 

Charlotte Leakey 

Ximena Levya Peralta 

Yurou Liu 

Samantha Liu 

Helena Lyng-Olsen 

Kaley Mafong 

Georgio Maroun 

Cindy Mei 

Lee Ngatia Muita 

Lea Papa 

Hiren Parekh 

Himani Pattisam 

Emily Poag 

Madeleine Popofsky 

Tony Potchernikov 

Zara Ranglin 

Yusuf Rasheed 

Alex Roseman 

Ilora Roy 

Ignacio Ruiz-Sanchez 

Noora Said 

Alex Dong 

Madison Houck 

Sophia Li 

Sophia Burick 

Anavi Uppal 

Hannah Han 

Kayla Yup 

Krishna Dasari 

Mia Gawith 

Will Archacki 

Matthew Blair 

Jamie Seu 

Samantha Liu 

Anya Razmi 

Malia Kuo 

Ann-Marie Abunyewa 

Sydney Scott 

Kara Tao 

Catherine Kwon 

Jenny Wong 

Lucas Loman 

Dinara Bolat 

Tori Sodeinde 

Georgio Maroun 

Yusuf Rasheed 

Hannah Barsouk 

Sofia Jacobson 

Jessica Le 

Kaley Mafong 

Lawrence Zhao 

Anjali Dhanekula 

Abigail Jolteus 

Emily Shang 

Elizabeth Watson 

Keya Bajaj 

Eunsoo Hyun 

Jamie Seu 

Kiera Suh 

Yamato Takabe 

Joey Tan 

Kara Tao 

Connie Tian 

Van Anh Tran 

Sheel Trivedi 

Robin Tsai 

Sherry Wang 

Elise Wilkins 

Aiden Wright 

Elizabeth Wu 

Nathan Wu 

Johnny Yue 

Iffat Zarif 

Hanwen Zhang 

Lawrence Zhao 

Celina Zhao 

Matthew Zoerb 

The Yale Scientific Magazine (YSM) is published four times a year by Yale 

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Special thanks to Yale Science and Engineering Association.

NEWS 

Environmental Studies / Sustainability 

THE CHANGING 

LANGUAGE OF OUR 

CHANGING CLIMATE 

HOW WORD CHOICE AFFECTS 

CLIMATE CHANGE PERCEPTION 

BY PRATIKSHA BHATTACHARYYA 

FREE AS A BIRD 

SAVING BIRDS ON 

YALE’S CAMPUS 

BY MIA GAWITH 

IMAGE COURTESY OF FLICKR 

IMAGE COURTESY OF PXFUEL 

Researchers from the Yale Program on Climate Change 

Communication (YPCCC) are using a novel method to 

measure public opinion on climate change—studying how 

people react to different phrases used to describe emissions of 

carbon dioxide and methane. “Over the last few decades, there 

has been an increased interest in the terms ‘carbon emissions’ 

and ‘greenhouse gasses,’” said Matthew Goldberg, an author of 

the study and associate research scientist at the YPCCC. The 

team asked study participants questions about climate change, 

which were identical between participants apart from the specific 

phrase used to describe carbon emissions—either “greenhouse 

gas emissions,” “carbon emissions,” or “carbon pollution.” 

Then, the team tracked differences in responses based on 

the phrases used. “We were interested in getting a holistic 

perspective of these terms,” Goldberg said. A key finding was 

that different reactions to these phrases revealed more about the 

general associations that participants held with each term. For 

example, the phrases “carbon pollution” and “carbon emissions” 

evoked more negative reactions and correlated with a greater 

understanding of the environmental harms of climate change 

than the phrase “greenhouse gas emissions.” 

These insights are crucial for policymakers and 

environmentalists who want to effectively communicate the 

urgency of addressing climate change. By paying attention to how 

people react to the different words used to describe these crucial 

issues, we can gain insight into how we can best emphasize the 

need for action. Experts can tailor messaging to better resonate 

with their audience by being cognizant of widely held associations 

with key scientific phrases in their communication. ■ 

We all recognize the signs: the sickening thud on a 

window, the flutter of feathers hitting the ground, 

and the stomach-churning dread of peeking outside. 

As one of the top causes of bird deaths, bird-window collisions 

kill almost one billion birds per year. However, a new project 

at Yale University seeks to challenge this reality: the Yale Bird- 

Friendly Building Initiative, a collaboration between Yale Law 

School’s Law, Ethics and Animals Program, the Yale Peabody 

Museum of Natural History, the Yale Offices of Sustainability 

and Facilities, and the American Bird Conservancy. 

Launched in the spring of 2022, the Initiative aims to 

mitigate bird-window collisions and adopt bird-friendly 

designs on Yale’s campus and beyond. The Initiative records 

the location, time, and cause of all reported bird deaths, 

preserving the bodies for future research. “If I find a dead bird 

or someone else brings it to me, I want to preserve it because 

it gives them a second life in a way, because they become 

imminently useful,” said Kristoff Zyskowski, collections 

manager at the Yale Peabody Museum. The Initiative found 

that designs with highly reflective, transparent glass and 

nearby trees create a deadly optical illusion, luring birds to 

their death. 

“Our ultimate goal, in my view, is for Yale to be the gold 

standard of what it looks like to be a bird-friendly campus,” 

said Viveca Morris, executive director of the Law, Ethics, and 

Animals Program. Future developments involve retrofitting 

Yale buildings and implementing new design regulations on 

campus and beyond. By saving countless birds, this project 

sets its sights on a new vision of wildlife sustainability. ■ 


Physiology / Astronomy 

NEWS 

A NEW APPROACH 

TO AN OLD FOE 

INNOVATION IN AORTIC 

ANEURYSM SURGERY 

BY JOHNNY YUE 

TAKING A PEEK 

AT PANDORA’S 

CLUSTER 

LOOKING UP AT SPACE WITH 

THE JAMES WEBB SPACE 

TELESCOPE 

BY IGNACIO RUIZ-SANCHEZ 

IMAGE COURTESY OF NAIEM NASSIRI 

IMAGE COURTESY OF PIXABAY 

Thoracoabdominal aneurysms (TAAAs) occur when the 

aorta—the artery carrying blood from the heart to the rest of 

the body—balloons and weakens, which can lead to internal 

bleeding. Up until the past few years, TAAA surgery required 

highly invasive procedures with high chances of debilitating side 

effects, including paraplegia, or lower body paralysis. 

Endovascular Debranched Aortic Repair (EDAR), a new 

surgical technique performed at Yale, was first invented by 

Patrick Kelly of Sanford Health in South Dakota. Vascular 

surgeon Naiem Nassiri learned about the technology under 

Kelly’s guidance. “I built six prototypes on my breakfast table, and 

some took up to six hours to build,” Nassiri said. Together with 

Prashanth Vallabhajosyula, director of Yale’s Aortic Institute, the 

medical duo has implemented EDAR to treat the weakened aorta 

in a minimally-invasive manner. “TAAA surgery used to involve 

patients getting their entire chest, abdomen, and diaphragm split 

open, and the procedures were attached to high morbidity and 

mortality,” Vallabhajosyula said. 

But EDAR simply involves a stent that is inserted into the 

body through two small penetrations made in the groin using 

a needle. The stent, compressed in a tube, is delivered through 

blood vessels to the aorta. “We’ve done about sixteen cases and 

haven’t encountered any paraplegia cases (patient paralysis),” 

Vallabhajosyula said. 

EDAR shows tremendous promise to treat TAAAs. “What is 

wonderful about this platform is that at any time, you can decide to 

stop the operation and bring the patient back at a later date,” Nassiri 

said. “This minimizes the harm for the patient.” With the surgeons’ 

expertise, TAAA patients now have new hope for better outcomes. ■ 

The black background of outer space is studded with 

white bursts of light—some are sharp lines, while others 

are surrounded by a white hazy glow. In the foreground 

sits a star from our own galaxy, shining among a giant group 

of galaxies located four billion light years away from Earth: 

Pandora’s Cluster. After the launch of NASA’s James Webb 

Space Telescope, we’ve been fortunate to witness images from 

the distant corners of our universe, but these are the first, 

detailed images of Pandora itself. 

Scientists have been monitoring this galaxy cluster for over 

a decade, utilizing the most advanced technology available, 

mainly the Hubble Space Telescope, to get a glimpse of 

Pandora. However, none have achieved as much as the Webb 

Telescope to capture stellar pictures of the cluster, unveiling 

never-before-seen details. The new images were a tireless effort 

by the Ultradeep NIRSpec and NIRCam ObserVations before 

the Epoch of Reionization (UNCOVER) program, whose team 

of astronomers included several Yale scientists. The team 

captured thirty hours of data using Webb’s Near-Infrared 

Camera (NIRcam), with wavelengths capable of detecting the 

earliest stars in the process of formation and nearby galaxy 

populations. What’s even more exciting is that the telescope 

captured Pandora as a megacluster, meaning the combined 

mass of the four galaxies creates a powerful gravitational lens 

to expose other very large distant galaxies in the early Universe. 

While strikingly beautiful, these images are not just potential 

dorm-room posters or lock screens—this achievement could 

ultimately help us discover other hidden galaxies, further 

unraveling the mysteries of our Universe. ■ 



FOCUS 

Ecology & Evolutionary Biology 

SINK OR 

SWIM 

Climate change 

impacting fish 

evolution 

BY LEA PAPA 

PHOTOGRAPHY COURTESY OF PAUL-ALEXANDER LEJAS 

When we think about global warming, many of us 

imagine melting ice caps or mass extinction events, 

undoing the work done by millions of years of 

evolution. But could climate change also threaten the forward 

progress of evolution? A recent study investigating the role of 

changes in water depth in the rapid speciation, or formation 

of new species, of fish in polar latitudes strongly suggests that 

yes, global warming can affect evolution’s progress. The study 

specifically points to the potential negative impact of warming 

waters on the ability of fish to rapidly speciate and, therefore, 

further their evolution. 

Published by Yale researchers Sarah Friedman and Martha Muñoz, 

the paper addresses the relationship between the remarkably rapid 

speciation rates of fish in polar latitudes and the ability of those 

fish species to move through the “depth gradient”—the intervals of 

water depth populated by different species in a body of water. 

Friedman was prompted to explore this idea after reading a 

paper that revealed that despite the higher biodiversity among 

fish in tropical regions, fish in the polar regions show faster rates 

of speciation. This discovery was both utterly surprising and 

intriguing to Friedman, who worked with Muñoz—an assistant 

professor of Ecology and Evolutionary Biology at Yale—to pursue 

research that could probe this finding. “When you look at the 

global scale, you’re going to see more species in the tropics,” 

Friedman said. “But what they found was that speciation rates are 

actually fastest towards the poles, which is [a] really interesting 

and counterintuitive result.” 

After intensive research into the prior literature on this 

phenomenon, Friedman hypothesized that shifting water depth 

may be the mechanism for rapid fish speciation in polar latitudes. 

Deep waters allow fish to move across the depth gradient, isolating 

fish groups from each other. This separation promotes more rapid 

speciation than in shallow, lower latitudes, where fish are more 

likely to interact and reproduce, thus slowing speciation. 

To investigate their hypothesis, the researchers used phylogeny, 

a common evolutionary biology technique that visualizes the 

ancestry and genetic relationships between different groups 

through the creation and analysis of phylogenetic trees. Because 

of limitations caused by the COVID-19 pandemic, Friedman 

and Muñoz analyzed existing data on fish evolution in this metaanalytic 

approach to reach their conclusions about biodiversity 

and speciation rates in polar-region fish. 

By the end of their extensive research, the team’s findings 

supported their hypothesis. “I think it was really reassuring to 

find what I hypothesized to be true,” Friedman said. “Those clades 

that are rapidly speciating are also those ones that are moving 

across the depth gradient pretty rapidly as well.” The relationship 

between rapid speciation rates and the ability to traverse a wider 

depth gradient explained the surprising speciation rates in the 

polar latitudes. 

Friedman and Muñoz also consider other findings from their 

study to be particularly intriguing, including one that suggested 

a pipeline of biodiversity exchange across latitudes, particularly 

from polar to tropical latitudes. “In fact, what we discovered is that 

speciation is faster at the poles, reflecting greater depth transitions, 

and that diversity is later transported to the tropics, so the polar 

regions are actually supplying species to the tropics,” Muñoz said. 

What could these findings mean for biodiversity and speciation 

in the era of extreme climate change and warming waters? 

According to Dr. Friedman, the effects will be disastrous. Because 

of the constant cold of the poles, there is little difference in water 

temperature throughout the depth gradient, meaning that the fish 

species through the gradient in the poles are similarly adapted 

for temperature, which contributes to how easily polar fish move 

between shallow and deep water. “As temperatures, and especially 

those surface temperatures, start warming up due to global 

warming, it’s going to increase the barriers to moving along that 

gradient,” Friedman said. 

Could global warming stall evolution? According to the 

researchers, this may be an extreme conclusion. Nevertheless, 

their research opens our eyes to a previously unknown harm of 

climate change, re-emphasizing the need for meaningful action. ■ 


Computer Science 

FOCUS 

TEACHING 

MACHINE 

LEARNING 

PHOTOGRAPHY COURTESY OF PAUL-ALEXANDER LEJAS 

Machine learning is often thought of as the silver bullet 

for solving puzzles in science. With enough data in 

any given subject, a model with impressive predictive 

properties can be created to produce an abundance of helpful 

information. But sometimes, machine learning isn’t perfect. In their 

recent paper, Guannan Liu and his colleagues at the Schroers Lab 

at Yale explore the limitations of machine learning models and how 

we can incorporate human learning into new models to strengthen 

their predictive power. 

Liu, a Ph.D. candidate in Mechanical Engineering and Materials 

Science, has spent most of his time at Yale studying machine learning 

and its ability to solve complex materials science problems. The 

study of glass-forming ability is a canonical example of one of these 

problems. It is quantified by the minimum cooling rate required to 

prevent the formation of undesired crystalline structures, resulting 

in a glass with an amorphous atomic structure. Studying glassforming 

ability by performing hands-on experiments in the lab 

can be tedious, and this is where machine learning comes in to 

potentially accelerate the process. “Simply put, machine learning is 

trying to make inferences from data, and maybe predict something 

from [that] data,” Liu said. 

But there’s a catch—previous machine learning models designed 

to predict the glass-forming ability of metallic glasses have fallen 

short of providing useful insights on the subject. Metallic glasses 

are alloys, which are made by combining two or more elements. 

“You have to have meaningful features that describe the particular 

alloy after the mixing of elements,” Liu said. Liu contextualized this 

idea by offering an example. “For atomic size, it’s not the average 

[element size] that matters but the difference in size,” Liu said. 

“This allows space to be filled as much as possible, favorable for 

glass formation.” Models that lack such information and instead 

arbitrarily use statistical functions to construct features do not truly 

capture the essence of the alloy’s glass-forming ability. 

The other issue with the previous machine learning model for 

the glass-forming ability of alloys was its limited capacity to make 

new predictions. “[In] the previous model, usually the task was 

interpolation—the model was only predicting things that were 


Improving a machine learning 

model to better predict 

metallic glass formation 

BY MAYA KHURANA 

similar to the dataset,” Liu said. In other words, the model could not 

make any predictions for new and unfamiliar data—it could only 

work inside the bounds of the dataset. 

To rectify these errors, Liu and his team worked on a new machine 

learning model: one that incorporated scientific insights from 

human learning. “Our model used extrapolation, [or] prediction 

into unknown space,” Liu said. This way, they were able to align their 

machine learning model with the reality that they have observed in 

the lab. Take, for instance, the property of atomic size again. Larger 

differences in size result in better glass-forming ability because the 

atoms are able to pack in more tightly. It is properties such as these 

that Liu and his team were better able to account for in their model, 

and their approach worked. “We found that our model was actually 

very successful in predicting glass-forming ability,” Liu said. 

Unlike its predecessors, this model was much better at 

extrapolation. “Our model can predict alloys that are more distinct 

from the training set,” Liu said. “We concluded that physical insights 

are really needed [to develop effective machine learning models].” 

This project is far from the end of Liu’s work with machine 

learning for materials science. He has three main goals moving 

forward. “The first is to use machine learning to test [our] current 

understanding of complex material science problems,” Liu said. It 

can be hard to quantify the efficacy of foundational rules within 

material science, so Liu plans to use machine learning to evaluate 

these guiding principles. Secondly, Liu strives to combine machine 

learning and high-throughput fabrication methods to discover 

new metallic glasses. 

Finally, Liu will investigate the contexts in which machine 

learning can be helpful. His goal is to determine what kinds of 

problems it can help solve and what circumstances limit its utility. 

“[We want to] have a viewpoint that can be meaningful for the 

community as to what machine learning is useful for [versus] 

situations where machine learning would be hard to use,” Liu said. 

This research will ensure that machine learning models are taking 

all possible human insights into account while making inferences 

from data. Clearly, machine learning can be an extremely valuable 

tool if it is wielded skillfully. ■ 


FOCUS 

Biomedical Engineering 

A DYNAMIC 

DUO 

Combining two 

technologies to fight 

brain cancer 

BY CASEY MCGUIRE 

PHOTOGRAPHY COURTESY OF YAZHE WANG 

It’s a diagnosis that strikes fear in the hearts of patients and their 

loved ones: glioblastoma, a type of brain cancer that is notoriously 

aggressive and difficult to treat. However, hope may be on the 

horizon, as researchers from Yale and the University of Connecticut 

(UConn) have developed a groundbreaking new therapeutic approach 

for those battling this devastating disease. The treatment loads tiny 

particles called nanoparticles, developed by Professor Mark Saltzman’s 

lab at Yale, with proteins that target the tumor cells, designed by 

Professor Raman Bahal and his team at UConn. Currently, the best 

treatment for glioblastoma is the removal of the bulk of the tumor 

during surgery, followed by radiation and chemotherapy. However, the 

median survival is only fifteen months. This new treatment combines 

two cutting-edge technologies, nanoparticles and peptide nucleic 

acids, to tackle this lethal disease and provide hope for future patients. 

Nanoparticles are particles that can infiltrate cells due to their small 

size. Saltzman’s lab has extensively researched nanoparticles as a vehicle 

to deliver drugs to specific areas of the human body. The polymerbased 

nanoparticle developed by his team can penetrate the brain 

and reach the tumor cells. Saltzman underlined the importance of the 

nanoparticles remaining at the tumor site and continuing to deliver 

the drug over time. “You can only administer the therapy after surgery 

directly into the brain and you cannot re-administer, but we want the 

therapy to last a long time,” Saltzman said. “We designed nanoparticles 

with certain properties to allow for this behavior.” The particles have 

an affinity for tumor cells due to their bioadhesive coating, and they 

will stick around to slowly release the drug inside the cells. 

The drugs encapsulated in the nanoparticles were designed 

by Bahal, who was a postdoctoral researcher and collaborator of 

Saltzman’s at Yale before moving to UConn. Bahal’s team developed 

peptide nucleic acids, or PNAs, to be loaded inside the nanoparticles. 

These proteins are synthetically constructed to be complementary 

to a certain sequence of microRNA, or short strands of RNA that 

regulate gene expression in cells. The tumor cells of glioblastomas 

overexpress certain microRNAs, leading to more tumor growth 

and decreased patient survival. Past studies suggest that two of 

these upregulated microRNAs, miR-10b and miR-21, are the most 

significant in glioblastomas. These microRNAs have been shown 

to exacerbate tumor growth and invasion, while decreasing the 

effectiveness of Temozolomide, the type of chemotherapy typically 

used for glioblastomas. The researchers loaded a mixture of the PNAs 

against miR-10b and miR-21 into the nanoparticles. 

After surgery, this treatment can be administered directly into 

the brain to target the remaining cancerous cells. Therefore, this 

treatment would be an addition to the current standard of care. 

During mouse trials, this therapy improved survival and also 

enhanced the efficacy of the chemotherapy. “The results are very 

promising, and I think there is an opportunity here,” Saltzman said. 

He described how the researchers are striving to move towards more 

extensive safety testing and eventually clinical trials. 

Glioblastomas account for just a fraction of cancer patients. In 

2022, brain and other nervous system cancers added up to 1.3 

percent of cancer cases in the United States, and 14.5 percent of 

these nervous system tumors were glioblastomas. Despite this 

seemingly low percentage, Saltzman has researched drug delivery 

systems for glioblastomas for around thirty-five years and defends 

its importance as a focus of research. “It’s rare, but not as rare as you 

would think,” Saltzman said. Even though his results were published 

in early February in Science Advances, he still receives one or two 

emails a day from people searching for new treatments for a family 

member suffering from a glioblastoma. Saltzman’s driving force for 

his glioblastoma research and this project is the hope it provides 

for patients. “I’ve become fascinated with this challenge and want 

to do something that really helps people,” Saltzman said. “Along the 

way, I have met a lot of individuals with glioblastoma. They are not 

alive anymore and that has had a huge impact on me. It feels more 

like a mission now than just an interesting project to work on.” 

Saltzman’s nanoparticles loaded with PNAs present a novel 

and precise approach to address the currently inadequate 

landscape of therapeutic options for glioblastoma. When 

integrated into the standard of care, this dynamic duo has the 

potential to improve survival rates, finally giving glioblastoma 

patients a fighting chance. ■ 


Environmental Science 

FOCUS 

THE CARBON 

FOOTPRINT 

OF CARE 

The unexpected 

environmental impacts 

of prostate biopsies 

BY JESSICA LE 

IMAGE COURTESY OF WIKIMEDIA COMMONS 

When someone is planning to get a prostate biopsy— 

the main diagnostic test for prostate cancer—the 

environmental impact of their impending procedure 

is not usually at the forefront of their mind. However, a Yale-led 

study by Associate Professor of Urology Michael Leapman did just 

that: the team examined the environmental impacts of common 

screening methods like prostate magnetic resonance imaging 

(MRI) and prostate cancer procedures, estimating that a single 

transrectal prostate biopsy has the same CO 2 emissions as a roundtrip 

flight from New York to San Francisco. 

On a global scale, healthcare systems are a major source of 

pollution and constitute over four percent of global CO 2 emissions. 

Although the environmental impacts of medical procedures 

are not currently considered when making medical decisions, 

Leapman urges for a change in attitude within the medical industry 

to prioritize environmental stewardship that aligns with patient 

interest without compromising patient care. “Carbon impact comes 

into question when we have excessive medical care,” Leapman said. 

Unnecessary over-screening is a common occurrence, and 

invasive procedures such as prostate biopsies actually have the 

potential to harm certain patients. As early as fifty years old, men are 

advised to consider undergoing a biopsy screening to catch prostate 

cancer in its early stages. Overall, these procedures are shown to 

reduce death rates; however, for patients who are over seventy or 

have existing comorbidities, this invasive diagnostic procedure 

would risk unwarranted side effects, major hospitalization, or even 

death. This form of medical care is often considered low-value and 

may harm both the planet and the patient. 

“The story is more than just the carbon footprint of one 

procedure. It is also about making better healthcare decisions that 

equip patients and physicians with more reliable information for 

who might need what intervention,” Leapman said. Approximately 

one million prostate biopsies are performed per year in the United 

States alone, with more than half of the patients evaluated found to 

not have prostate cancer at all. His research found that performing 

one hundred thousand fewer biopsies would avoid over eight 


million kilograms of CO 2 emission, the equivalent of burning 1.1 

million gallons of gasoline (larger procedures, such as surgeries, 

may easily account for more than ten times that amount). 

However, this issue addresses a broader problem facing healthcare 

management. Leapman noted that physicians are not proactive in 

considering the economic burden, much less the environmental 

burden, of expensive procedures. Introducing carbon footprint 

as a price to be considered when making important medical 

decisions should be implemented in a holistic conversation around 

when exactly to prescribe medical treatment. This ensures that the 

patient understands the broader benefits and risks of undergoing 

an expensive procedure, encouraging physicians and patients to be 

more considerate of both economic and environmental costs. 

Leapman emphasizes that global climate change directly 

influences public health. “Healthcare providers are not doing a 

good job if what we are doing hurts the community and our world,” 

Leapman said. However, the movement towards environmentally 

friendly healthcare is not easy and faces many barriers to 

progress. Leapman’s study found that energy expenditure is the 

largest contributor to the overall carbon footprint calculation 

(approximately forty percent). In general, hospitals require an 

immense amount of resources and energy. However, they work 

within a very thin financial margin for extra expenses, making 

it difficult for individual practitioners and hospitals to prioritize 

advocating for greener energy sources. “Federal regulation and 

oversight may need to come in if our overall goal is to improve 

public health,” Leapman said. “We need to make some hard 

decisions about the resources we allocate to ensure we are being 

good stewards of the environment.” 

Leapman hopes that generating more data to clearly illustrate the 

environmental impact of healthcare will help increase awareness 

and target areas of excessive medical care. By doing so, necessary 

modifications can be made to decrease superfluous resource 

use. Then, doctors can make better decisions when choosing 

appropriate patients to undergo certain procedures, in the interest 

of both the patient and the planet. ■ 


FOCUS 

Geochemistry 

TRACKING CARBON’S 

UNDERWATER 

DIVE 

ART BY LUNA AGUILAR 

Clearing up the history of the 

marine carbonate cycle 

BY TORI SODEINDE 

Carbon: it’s in the atmosphere, the 

oceans, the solid Earth, and even in us. 

This element is found all throughout 

Earth’s environment and exists in numerous 

chemical forms. One form of carbon, calcium 

carbonate (the major component of limestone 

and chalk), is the main form in which carbon 

in the ocean and atmosphere is returned 

to the earth. The precipitation pathways of 

carbonate minerals in the ocean are referred 

to as the marine carbonate factory and greatly 

influences abiotic and biotic geochemistry, 

including ocean acidity. 

Despite its important role in ocean 

chemistry, there has been little consensus 

on how the marine carbonate factory has 

changed throughout Earth’s history. It is 

challenging to 

find wellpreserved 

and reliable markers for its status 

over billions of years. However, Lidya Tarhan, 

an assistant professor of earth and planetary 

sciences, and Jiyuan Wang, an Agouron 

postdoctoral fellow in Tarhan’s research 

group, along with colleagues from Yale’s 

Department of Earth and Planetary Sciences, 

Northwestern University and University of 

Miami, recently developed a novel technique 

to trace the history of the marine carbonate 

factory. By measuring the ratios of different 

isotopes (atoms of the same element with 

different masses) of strontium within 

carbonate samples, they uncovered a more 

definitive history of carbonate precipitation 

and mineral saturation states from the ancient 

Precambrian to the recent Phanerozoic 

Eon, and published their findings in Nature. 

During the Precambrian, contrary to previous 

conjecture, a major proportion of carbonate 

was buried in the deep sea through abiotic 

processes, rather than in the shallow marine 

environment like reefs that dominate most of 

the Phanerozoic marine carbonate factory. 

The Marine Carbonate Cycle 

The marine carbonate factory is one piece 

of a bigger puzzle, the carbon cycle, which 

encompasses the cycling of carbon through 

nature. The carbon cycle can be divided into 

short-term and long-term cycles. The shortterm 

carbon cycle involves living organisms. 

Photosynthesizers, largely phytoplankton 

and algae, absorb carbon dioxide into their 

cells and use it to generate carbohydrates 

through photosynthesis. The carbohydrates 

can be broken down later to provide energy, 

releasing carbon dioxide back into the ocean 

and atmosphere. 

In the long-term carbon cycle, rain 

combines with atmospheric carbon dioxide 

to form carbonic acid, which falls to the earth 

and slowly dissolves bodies of rock. This 

releases ions, including calcium, that are then 

carried through rivers to the ocean, where they 

combine with dissolved carbonate ions to form 

calcium carbonate, a solid in water. This process 

is called carbonate precipitation and can occur 

abiotically (without living organisms). 

However, many marine organisms also use 

calcium and carbonate ions to build their 

shells. When they die, these shells and other 

sediments form rock, sequestering carbon 

within the ocean floor and the geologic 

record. Some bacteria can also facilitate 

precipitation of calcium carbonate in their 

surroundings—for instance, by taking up 


Geochemistry 

FOCUS 

carbon dioxide during photosynthesis. 

Regardless of the route, precipitation of 

dissolved carbonate into solid calcium 

carbonate incorporates other ions including 

strontium, an alkaline earth metal. This study 

exploited the incorporation of strontium into 

carbonate precipitates to gain insight into the 

history of the marine carbonate cycle. 

Strontium in the Marine Carbonate 

Factory's History 

The metal strontium has multiple stable 

isotopes, including strontium-88 and 

strontium-86. When carbonate precipitation 

occurs in the ocean, it incorporates trace 

amounts of strontium, but the two isotopes 

are incorporated at different ratios depending 

on environmental conditions. Strontium-88, 

the heavier isotope, is incorporated into 

carbonate minerals less often than the lighter 

strontium-86, but higher saturation of 

carbonates in the ocean leads to both faster 

precipitation and an even lower strontium-88 

to strontium-86 ratio (δ 88/86 Sr) in carbonates. 

The ratio of these strontium isotopes in 

carbonates, in particular, is a novel proxy 

for the history of the marine carbonate 

cycle because this signature is tied closely to 

precipitation rates, rather than—like many 

other isotope systems—seawater temperature 

or the type of carbonate mineral in which 

strontium is incorporated. Thus, strontium 

stable isotope ratios can serve as a marker 

for changes in the marine carbonate factory, 

specifically the rate of carbonate precipitation 

which, in turn, reflects marine carbonate 

saturation state at the time of precipitation. 

However, using stable isotope measurements 

has not previously been possible due to 

technical limitations. Luckily, with the 

resources of the Yale Metal Geochemistry 

Center, the researchers were able to develop 

a novel method using mass spectrometry to 

measure stable strontium isotope ratios with 

five-decimal place precision, according to 

Wang. “[Our work] opened the door toward 

using the stable strontium isotope proxy to 

reconstruct long-term records in Earth's 

history—and will, we hope, allow us and others 

to tackle new and exciting questions down the 

road,” Tarhan said. 

Unexpected Sources of Carbonate 

Precipitation 

While shallow regions of the ocean like 

reefs and carbonate platforms are commonly 


thought of as hotspots for carbon deposition, 

which is true today, Tarhan and Wang found 

an unexpected phenomenon during the 

Precambrian, the interval preceding the 

explosion of organisms that created calcium 

carbonate shells around 540 million years 

ago. They found evidence of an unforeseen 

level of abiotic contribution to the marine 

carbonate cycle in deep ocean waters 

during this time. “A major part of carbonate 

was buried outside of the shallow marine 

environment during Earth’s early history, 

which is radically different than previously 

envisaged,” Wang said. 

When tracing the ratios of strontium 

isotopes in carbonate samples formed in 

shallow seafloor sediments, the researchers 

found a marked decrease in δ 88/86 Sr 

values during the transition between the 

Precambrian era and the Phanerozoic era (the 

interval in which biomineralizing animals 

caused skeletal carbonates to become a large 

contributor to the marine carbonate factory). 

This decrease implies slower precipitation 

and a lower carbonate saturation state in 

Phanerozoic relative to Precambrian oceans, 

which is consistent with the increase in 

precipitation due to calcifying animals in the 

Phanerozoic period. 

Additionally, the Precambrian δ 88/86 Sr 

record also suggests the unexpected presence 

of a large, non-skeletal carbonate sink within 

the Precambrian deep ocean—one formed 

as a result of the activities of bacteria living 

in seafloor sediments devoid of oxygen. This 

condition was likely characteristic of much 

of the Precambrian deep seafloor, leading to 

carbonate precipitation in the spaces between 

grains of previously deposited sediment. 

It is difficult to directly confirm the ancient 

history of the deep oceans, as the constant 

shifting of Earth’s tectonic plates leads to 

subduction, plates layering over each other on 

the deep seafloor, which would have contained 

this missing piece of the Precambrian 

ABOUT THE AUTHOR 

carbonate record. “The deep oceans have been 

something of a 'black box' for much of Earth's 

history, due to the continual loss of deep-sea 

sediments with seafloor subduction,” Tarhan 

said. However, this study has unveiled an 

aspect of this murky history. “The deep sea, 

among other muddy stretches of the ancient 

seafloor, may have been an important locus of 

carbonate sediment accumulation prior to the 

emergence of any carbonate-biomineralizing 

organisms, and this was the baseline state 

until biomineralizing animals evolved in the 

shallow oceans approximately 540 million 

years ago,” Tarhan said. 

Looking into the Future 

This new research challenges past 

assumptions about the main players in the 

marine carbonate factory and helps fill in the 

history of oceanic geochemistry prior to the 

evolution of marine calcifying animals. This 

research could also be used to predict the 

future. As humans continue to pump carbon 

dioxide into the atmosphere, the increased 

emissions alter the natural carbon cycle. 

While this study focused on Earth’s ancient 

history, the mechanisms underlying the 

carbon cycle remain the same, so clarifying 

the mechanism of past changes can help us 

extrapolate how human actions may now 

affect the carbon cycle. 

Tarhan’s lab is currently trying to 

quantify the behavior of strontium isotopes 

as it relates to changing seawater carbonate 

chemistry under ongoing climate change. 

“The discoveries in this study enable us 

to better understand how carbon cycled 

among Earth’s different layers and how 

Earth maintained its habitability under 

different levels of CO 2 ,” Wang said. “This 

is crucial information that can be used to 

perceive and predict the behaviors of our 

Earth and oceans [during] contemporary 

climate change.” ■ 

TORI SODEINDE 

TORI SODEINDE is a sophomore MCDB major in Ezra Stiles College. In addition to writing for YSM, she 

is involved in telomere biology research, Danceworks, and the Downtown Evening Soup Kitchen. 

THE AUTHOR WOULD LIKE TO THANK Dr. Lidya Tarhan and Dr. Jiuyuan Wang for their time and 

enthusiasm about their research. 

REFERENCES: 

Wang, J., Tarhan, L.G., Jacobson, A.D. et al. The evolution of the marine carbonate factory. Nature 615, 

265–269 (2023). https://doi.org/10.1038/s41586-022-05654-5 


FOCUS 

Medicine 

IT'S IN OUR 

BON 

E S 

THE LINK BETWEEN AGING 

AND ATHEROSCLEROSIS 

BY EVELYN JIANG | ART BY GIA GABRAL 

They lurk in your arteries, plaques that 

build up like hidden time bombs. 

These tiny fatty deposits can slowly yet 

steadily narrow your blood vessels, causing 

potentially life-threatening complications. 

Atherosclerosis, as it’s medically known, 

is a complex and often silent disease. 

Despite its lack of obvious warning 

signs, atherosclerosis is the leading 

cause of heart attacks, strokes, and other 

cardiovascular complications, which are 

collectively the leading cause of death 

worldwide. The deadly disease has earned 

itself the nickname the ‘silent killer’ and its 

prevalence has made it a central focus in 

cardiovascular research. 

Aging is the biggest risk factor for 

developing atherosclerosis, but the 

reasons for this observation have been 

a longstanding mystery for scientists. A 

team of researchers in the Greif Lab at 

the Yale School of Medicine has recently 

uncovered a crucial link between bone 

marrow aging and atherosclerosis that may 

offer part of the answer. By examining the 

role of bone marrow cells in the clonality 

of smooth muscle cells, the researchers 

pinpointed key molecular mechanisms 

that contribute to atherosclerosis. 

Born From Bone Marrow 

Smooth muscle is a type of muscle found 

in the walls of many organs and tissues in the 

body. It is called ‘smooth’ because smooth 

muscle cells (SMCs) lack the striations or 

visible bands characteristic of skeletal and 

cardiac muscle cells. SMCs have a spindleshaped 

appearance and are not under 

voluntary control like skeletal muscle 

cells. Instead, they are controlled by the 

autonomic nervous system and hormones. 

SMCs are responsible for maintaining the 

structural integrity of the arterial wall, but 

research has shown that only a select few 

SMCs also play a significant role in the 

development of atherosclerosis. 

When a plaque begins to form, 

macrophages—a type of white blood cell— 

are the first to arrive on the scene. They engulf 

oxidized low-density lipoprotein and form 

foam cells that, over time, accumulate to form 

fatty streaks and eventually develop into fullfledged 

plaques. Macrophages also release 

pro-inflammatory cytokines, chemicals that 

attract more immune cells, that contribute 

to plaque growth. Later on, rare SMCs arrive 

and initially attach themselves to the surface 

or cap of the plaque, proliferate robustly, and 

migrate to cover this fibrous cap. Some of the 

SMCs then dive into the core of the plaque. 

The cap stabilizes the plaque, protecting it 

from rupturing; if the cap becomes weak and 

ruptures, the contents of the plaque core are 

exposed to the bloodstream, triggering the 

formation of a clot. “When a clot blocks the 

artery, then blood can’t get beyond it, and the 

tissue that’s beyond it doesn’t get oxygen,” 

said Daniel Greif, professor of cardiology at 

the Yale School of Medicine and principal 

investigator. “That’s what causes the vast 

majority of heart attacks and strokes.” 

Even though up to seventy percent of cells 

in advanced plaques originate from SMCs, 

they originate from only one or a couple 

of SMCs that enter the plaque. In younger 

mice that are prone to atherosclerosis, the 

SMCs that contribute to plaque formation 

are clonally related, or monoclonal, meaning 

they originate from a single cell that entered 

the plaque. However, with aging, the number 

of monoclonal plaques decreases, and 

there is an increase in polyclonal plaques, 

where multiple SMCs contribute to plaque 

formation. Polyclonality creates a more 

genetically diverse and perhaps unstable 

population of cells that can lead to aggressive 

plaque formation, thereby increasing both 

the size of the plaque and the risk of rupture. 

How Does Age Impact Clonality? 

To study the connection between SMC 

clonality and aging, the research team 


Medicine 

FOCUS 

PHOTOGRAPH COURTESY OF THOMAS R. SHARKEY. 

Atherosclerosis is a disease in which plaque builds up inside the arteries, leading to a narrowing and hardening 

of the arteries, which can restrict blood flow. 

compared atherosclerotic plaques of aged 

and young mice. The mice carried the 

ROSA26R-Rainbow (Rb) Cre reporter, 

which is used to label cells with different 

fluorescent colors, allowing the researchers 

to track the clonal expansion of cells. 

Sections of aortas from the mice were 

stained and imaged for Rb colors, and 

analysis revealed that aged mice had larger 

plaques with increased SMC polyclonality 

and lipid content, implying an increased 

risk of plaque rupture. 

The researchers then transplanted bone 

marrow from aged mice into young mice 

genetically engineered to be prone to 

atherosclerosis to see if aged bone marrow 

was sufficient to induce polyclonality. 

They found that the mice that received 

the aged bone marrow transplant 

developed greater plaque buildup in their 

arteries and that their plaques exhibited 

increased SMC polyclonality. They also 

found that when liquid from cultures of 

macrophages of aged mice was incubated 

with aortic SMCs from young mice, 

SMC proliferation increased by about 

threefold, compared to incubation with 

the liquid from macrophage cultures of 

young mice. These results suggest that 

the age of the bone marrow, specifically 

the age of macrophages, is a key factor in 

determining the recruitment and clonality 

of SMC-derived plaque cells. 

The Molecular Mechanisms 

The researchers next sought to explain 

the molecular mechanisms underlying 

aging’s observed effect on how SMCs were 

recruited and expanded in the plaque. To do 

so, they isolated monocytes—precursors to 

macrophages—from a blood draw of young 

and aged humans and from the bone marrow 

of young and aged mice, then performed 

RNA and protein analysis on them. They 

found that a gene called integrin β3—which 

is essential for blood clot formation— 

was downregulated in aged monocytes. 

Decreased integrin β3 levels in mice were 

found to contribute to atherosclerosis. 

Single-cell RNA sequencing of bone 

marrow cells from mice with or without 

integrin β3 revealed that the absence of 


integrin β3 leads to the upregulation of 

pro-inflammatory tumor necrosis factor α 

(TNFα) signaling pathways, and inhibition 

of TNFα led to a reduction of over fifty 

percent of SMC-derived plaque cells. It 

also promoted monoclonality, suggesting 

that integrin β3 deficiency promotes 

atherosclerotic plaque development by 

inducing inflammation through the TNFα 

signaling pathway. This inflammation 

further damages the artery walls, triggering 

the recruitment of more macrophages to 

the site and therefore the formation of more 

fatty streaks. Inflammatory molecules can 

also stimulate the proliferation of SMCs 

and weaken fibrous caps of plaques, making 

them more likely to burst. 

The researchers also showed that 

overexpression of integrin β3 in the bone 

marrow of aged mice led to predominantly 

monoclonal SMC populations and reduced 

the amount of plaque buildup within 

arteries. By increasing the levels of integrin 

β3, the researchers were able to prevent 

the recruitment and expansion of multiple 

SMC progenitors into the plaque, resulting 

in a reduced risk of plaque rupture. 

The study was led by Inamul Kabir, an 

associate research scientist in the Greif Lab. 

"It is gratifying to uncover the molecular 

mechanism of atherosclerotic disease 

progression at the cellular level during aging, 

thus informing potential novel therapy,” 

Kabir said. The team’s research revealed 

the previously unknown mechanisms 

of how aged macrophages induce SMC 

polyclonality and the development of fatty 

plaques in the arteries. This breakthrough 

marks the start of a long journey toward 

effective treatments for atherosclerosis. 

Nonetheless, these new findings represent a 

notable milestone in our understanding of 

the ‘silent killer.’ ■ 

EVELYN JIANG 

EVELYN JIANG is a first-year in Morse College interested in studying neuroscience. In addition 

to writing for the YSM, she works at Yale’s Alzheimer’s Disease Research Unit and plays with 

proteins at the Koleske Lab. 

THE AUTHOR WOULD LIKE TO THANK Daniel Greif and Inamul Kabir for their time and 

enthusiasm in sharing their research. 

REFERENCES: 

Kabir, I., Zhang, X., Dave, J.M. et al. The age of bone marrow dictates the clonality of smooth 

muscle-derived cells in atherosclerotic plaques. Nat Aging 3, 64–81 (2023). https://doi. 

org/10.1038/s43587-022-00342-5 



FOCUS 

Dermatology 

ACNE-BIOTICS 

Demystifying a promising 

acne-fighting antibiotic 

BY CRYSTAL LIU 

ART BY HANNAH HAN 


Dermatology 

FOCUS 

Bumps, whiteheads, rashes, scars: acne 

vulgaris is the most prevalent skin 

disease in the world, affecting the 

physical and mental health of 9.4 percent of 

the global population. This figure includes 

a whopping eighty-five percent of people 

between twelve and twenty-four years old. 

Cutibacterium acnes is the major cause 

of acne. It is a Gram-positive bacterium, 

meaning it has a thicker cell wall and causes 

different infections than Gram-negative 

bacteria. C. acnes coexists with healthy skin 

follicles and pores, but certain strains lead 

to acne and other complications, such as 

eye inflammation after tissue implantation. 

To treat these infections, dermatologists 

often prescribe a class of antibiotics called 

“tetracycline,” which include doxycycline, 

minocycline, and sarecycline. 

Tetracycline-class antibiotics are a group 

of medications used in the treatment of 

bacterial infectious diseases. They target 

the ribosome, an organelle that translates 

genetic information from RNA sequences 

into amino acid chains, which then fold into 

proteins. Tetracycline is a naturally-occurring 

antibiotic isolated from actinomycetes, a 

soil bacteria, and was approved by the FDA 

for medical use in 1954. Doxycycline and 

minocycline, termed second-generation 

tetracyclines, were approved in 1967 

and 1971, respectively, thanks to their 

improved stability and pharmacological 

efficacy. Almost half a century later, in 

2018, sarecycline was introduced as a thirdgeneration 

tetracycline-class antibiotic. 

While doxycycline and minocycline kill 

all types of bacteria—meaning they are 

broad-spectrum antibiotics—sarecycline has 

narrow-spectrum activity against only certain 

Gram-positive bacteria, including C. acnes. 

Christopher Bunick, associate professor 

of dermatology at the Yale School of 

Medicine, noticed the importance of this 

novel antibiotic and decided to look into 

its molecular mechanism. “Because of our 

expertise in protein synthesis, ribosome 

structure, and dermatology, we couldn’t 

resist taking on this project,” said Ivan 

Lomakin, an associate research scientist in 

the Bunick lab. Lomakin, Bunick, and their 

collaborators analyzed how sarecycline 

interacts with the C. acnes ribosome using 

cryogenic electron microscopy (cryo-EM), 

and published the results in Nucleic Acids 

Research. They discovered that sarecycline 

binds to the C. acnes ribosome at two 

different sites, which had not been observed 

in structures with other tetracyclines or 

model bacteria. They also discovered two 

novel ribosomal proteins and demonstrated 

their antimicrobial properties independent 

of the ribosomal complex. This study 

ultimately confirmed that sarecycline may 

be a more effective treatment option for C. 

acnes infections. 

Why Bind To Ribosomes? 

Since protein synthesis is an 

indispensable part of life, many antibiotics 

inhibit the activity of bacterial ribosomes, 

and sarecycline is no exception. As a 

complex—an assembly of multiple subunits 

that carry out a function together—the 

ribosome is made of ribosomal RNA 

(rRNA) associated with certain ribosomal 

proteins. Translation, the process it 

catalyzes, involves messenger RNAs 

(mRNAs) and transfer RNAs (tRNAs). The 

mRNA contains information ‘copied’ from 

the DNA that the ribosome must ‘read and 

translate.’ The tRNA contains nucleotides 

that recognize specific, three-base long 

mRNA sequences and the amino acid that 

corresponds to this sequence. The ribosome 

consists of large and small subunits, which 

are responsible for different steps of the 

process. The small subunit binds to the 

mRNA strand and identifies the correct 

tRNA molecule for every three bases within 

the decoding center. The large subunit then 

catalyzes the addition of the new amino 

acid to the growing polypeptide 

(protein) chain, which exits 

the ribosome through a 

structure called the nascent 

peptide exit tunnel (NPET). 

This process is how cells 

make proteins. 

Structural biologists have 

characterized the binding 

mechanisms of many antibiotics 

with ribosomes of model 

bacteria like E. coli and Thermus 

thermophilus. For first- and 

second-generation tetracyclines, 

all existent structures suggest that 

they bind to the decoding center 

of the small ribosomal subunit, 

inhibiting mRNA-tRNA interactions 

and slowing protein synthesis. The 

interaction patterns that Lomakin and 

colleagues characterized with cryo-EM 

agree with models of other tetracyclines. 

They show that the stacking of three 

hydrophobic layers stabilizes the binding of 

sarecycline in the decoding center of the C. 

acnes ribosome and inhibits tRNA arrival. 

Besides the canonical binding site, 

researchers were surprised to discover that 

sarecycline has a second binding site (SBS) 

on the C. acnes large ribosomal subunit, 

in the NPET. Here, sarecycline blocks 

the NPET and is thought to suppress the 

growth of the peptide chain. This binding 

site is specific to the C. acnes ribosome, 

as X-ray crystallography of sarecycline in 

complex with the Thermus thermophilus 

ribosome—also performed by the Bunick 

Lab—showed only the canonical binding 

site. Based on indirect experiments, 

researchers speculated that sarecycline 

could probably bind to both sites with 

similar affinities, and the sarecycline 

molecule in the SBS may assist with 

function in the canonical binding site. 

The paper compared this binding 

interaction with an antibiotic from 

another structural family, tetracenomycin 

X, which was recently shown to bind to 

the E. coli ribosome at a similar site. The 

team postulated that certain uridine bases 

were important in this interaction, and 

mutations from uridine to another base, 

cytosine, would confer resistance. However, 

Lomakin is not too worried about bacteria 

gaining sarecycline resistance, compared 

to other tetracyclines. “For sarecycline, 

we have an additional site on the large 

ribosomal subunit, encoded 

by a different gene than 

the small ribosomal 

subunit. The probability 

of simultaneously getting 

mutations on both of them 

is the multiplication 

of getting mutations 

on each, so it is very 

low,” Lomakin said. 



FOCUS 

Dermatology 

Potential Antimicrobial Properties 

Using cryo-EM, the researchers 

managed to capture the first highresolution 

structure of the C. acnes 

ribosome. They also examined the 

ribosomal proteins attached to the 

ribosomal RNA and explored how the C. 

acnes ribosome’s catalytic mechanisms 

could differ from other known bacterial 

models. This knowledge would help 

inform the future design of antibiotics 

against C. acnes. 

But of particular interest to the team 

were the bacterial small ribosomal subunit 

protein 22 (bS22) and the bacterial large 

ribosomal subunit protein 37 (bL37). 

These proteins are normally part of the 

ribosome and help synthesize proteins, 

but independent of the complex, they have 

displayed antimicrobial properties. C. 

acnes exists in normal skin, so researchers 

wonder if it helps defend the skin against 

other pathogenic bacteria. “From a 

dermatology perspective, we know C. acnes 

lives in our follicles and pilosebaceous units 

as a commensal organism—only certain 

strains of it are pathogenic for acne. We 

are trying to probe whether or not C. acnes 

has a natural defense mechanism against 

Staphylococcus aureus, which is a major 

pathogenic skin organism,” Bunick said. 

They discovered that the bS22 could inhibit 

the growth of E. coli and S. aureus while the 

bL37 only affected S. aureus but not E. coli. 

The next step down the antimicrobial 

properties path was to understand whether 

these proteins were present independent 

of the ribosome. Usually, ribosomal 

proteins form a complex with ribosomal 

RNAs to catalyze protein synthesis, but 

additional functions outside of ribosomes 

are possible. Bunick proposes that C. acnes 

may either secrete these peptides directly 

or release them when they die and lose 

their membranes. 

Sarecycline: The Better Acne-Biotic? 

Sarecycline was introduced in 2018 as a 

drug with higher specificity and fewer side 

effects than minocycline and doxycycline. 

However, primarily due to pricing issues, 

it only has about six percent of the 

prescription market for oral tetracycline 

in dermatology. To Bunick, sarecycline 

deserves more recognition. “At least to my 

knowledge, it is the only FDA-approved 

PHOTOGRAPHY BY EMILY POAG 

Dr. Christopher Bunick (left) and Dr. Ivan Lomakin (right) discussing a model of the ribosome. 

drug that targets two active centers of the 

ribosomes currently,” he said. 

The human gastrointestinal tract 

contains many beneficial Gram-negative 

bacteria. Since sarecycline is more specific 

to certain Gram-positive bacteria and 

spares Gram-negative bacteria, it causes 

fewer side effects in the gastrointestinal tract 

while effectively targeting Gram-positive 

C. acnes. Doxycycline is photosensitive, 

so certain users may experience rashes, 

itching, or severe sunburn, while 

sarecycline is not. Sarecycline is also 

less hydrophobic, meaning a decreased 

possibility of diffusing through the bloodbrain 

barrier and causing dizziness, vertigo, 

or tubular disturbance. 

The Bunick lab partners with Almirall, the 

pharmaceutical company that licenses and 


sells sarecycline in the United States. “Our 

laboratory [work] has been predominantly 

keratins, intermediate filaments, and the 

skin barrier for over a decade. But [learning 

about sarecycline] presented a unique 

opportunity as an entryway into a new area 

of research understanding the molecular 

mechanisms of dermatology drugs. 

Sometimes the science leads you to where 

you need to be,” Bunick said. He does 

not rule out the possibility of developing 

a fourth-generation tetracycline. This 

paper was the first to publish a C. acnes 

ribosomal structure. Given the new 

information about multiple active sites, it is 

possible to further optimize the structure 

of the antibiotic to achieve more precise 

treatment of the infection behind your 

bumps and whiteheads. ■ 

CRYSTAL LIU 

CRYSTAL LIU is a sophomore at Pierson College majoring in molecular, cellular and developmental 

biology. Besides writing for YSM, she is involved in the Irish Lab, Chinese Undergraduate Students 

at Yale, and Club Jump Rope. You can also find her trying out new restaurants and boba, playing 

IM volleyball, and listening to a lot of Mandopop and Cantopop songs. 

THE AUTHOR WOULD LIKE TO THANK Christopher Bunick and Ivan Lomakin for for their time 

and enthusiasm about their research. 

FURTHER READING: 

Lomakin, I. B., Devarkar, S. C., Patel, S., Grada, A., & Bunick, C. G. (2023). Sarecycline inhibits 

protein translation in Cutibacterium acnes 70S ribosome using a two-site mechanism. Nucleic 

Acids Research. https://doi.org/10.1093/nar/gkad103 

Batool, Z., Lomakin, I. B., Polikanov, Y. S., & Bunick, C. G. (2020). Sarecycline interferes with tRNA 

accommodation and tethers mRNA to the 70s ribosome. Proceedings of the National Academy of 

Sciences, 117(34), 20530–20537. https://doi.org/10.1073/pnas.2008671117 

Grada, A., Del Rosso, J. Q., Moore, A. Y., Stein Gold, L., Harper, J., Damiani, G., Shaw, K., Obagi, S., 

Salem, R. J., Tanaka, S. K., & Bunick, C. G. (2022). Reduced blood-brain barrier penetration of acne 

vulgaris antibiotic sarecycline compared to minocycline corresponds with lower lipophilicity. 

Frontiers in Medicine, 9. https://doi.org/10.3389/fmed.2022.1033980 


Ecology 

FOCUS 

ANIMALS 

AGAINST 

RISING 

TIDES 

BY ABIGAIL JOLTEUS 

ART BY LUNA AGUILAR 

How mussels flex to keep 

coastal ecosystems afloat 

Due to climate change, sea levels could rise twelve inches 

in the next three decades, equivalent to the measured 

rise seen over the last century. This rise stresses 

vegetated coastal ecosystems, which include mangroves, salt 

marshes, and seagrasses. Coastal ecosystems provide habitats 

for a wide variety of wildlife and protect both humans and 

animals from storms. They also stabilize the shoreline, filter 

nutrients, and store carbon dioxide from the atmosphere in 

the ground. “Coastal ecosystems are very near and dear to my 

heart,” said Sinéad Crotty, associate director of science at the 

Yale Carbon Containment Lab, said. 

In a recent paper published in Nature Communications, 

Crotty examined the direct and indirect effects of one 

unassuming invertebrae—mussels—on the persistence of 

vegetated coastal ecosystems. 

Even small changes in sea levels can substantially alter these 

ecosystems through coastal flooding, resulting in higher 

storm surges—the rise of seawater during a storm—and an 

influx of saltwater into freshwater habitats. Rising sea levels 


have prompted the increase in resources directed to vertical 

and horizontal accretion, a natural process that results in a 

change in the elevation of salt marshes. Accretion can indicate 

how well a salt marsh is persisting in spite of changes in sea 

level, and, according to Crotty, refers to how the marsh moves 

upwards to compensate for sea level rise. It can increase 

vertically or horizontally, in the landward direction of the 

boundary of the marsh. 

Studying accretion is particularly important because it helps 

prevent a phenomenon known as drowning, in which the 

vegetated area of a salt marsh is converted into an open water 

area. This originally looks like a small pond that eventually 

grows larger. As the salt marshes drown, the vital services 

that they provide, including habitation, storm buffering, and 

carbon storage, also disappear, destabilizing the wildlife around 

it.“We care deeply about accretion because for marshes to not 

drown, we need the rate of accretion to be greater than the rate 

of sea level rise,” said Hallie Fischman, a Ph.D. student at the 

University of Florida and an author of the paper. 


FOCUS 

Ecology 

Historically, studies on accretion 

focused on environmental factors, such 

as tidal range and sediment supply. The 

tidal range consists of the difference 

between the highest and lowest point 

of the tide, and sediment supply refers 

to the availability and transport of 

sediment. However, organisms can also 

shape their environment, which includes 

modifying accretion processes. This 

concept is known as faunal engineering. 

It refers to animals that provide habitats, 

nutrients, or some other alterations that 

allow other organisms, as Crotty put it, 

to ‘persist and thrive.’ 

Mussels: The Underdogs Of Coastal 

Ecosystems 

One of the most abundant faunal 

engineers present in salt marshes in 

the United States are Atlantic ribbed 

mussels. Mussels can be easy to miss in 

these vast ecosystems. Yet even though 

these organisms are tiny, their functions 

are vital—they can, either directly or 

indirectly, alter plant growth and improve 

water quality by removing organic 

matter and unwanted particles. These 

particles and organic matter are filtered 

by mussels, processed, and subsequently 

excreted. Therefore, mussels help with 

sediment deposition, the excretion of 

Atlantic ribbed mussels. 

It was a crazy idea that we could feed mussels 

orange chalk, they would poop it out, and 

we could follow it across the marsh. 

digested organic material. Mussels are 

also an important food source for many 

terrestrial and aquatic organisms. 

Researchers at the Yale Carbon 

Containment Lab and the University of 

Florida were interested in quantifying 

the effects of the Atlantic ribbed mussel 

on accretion in southeastern US salt 

marshes. They performed three field 

experiments to fulfill this objective. 

The first field experiment was to 

investigate whether the sediments 

deposited by mussels could supply 

marshes beyond the areas where the 

mussels were gathered. Where exactly 

was the sediment spreading? To answer 

this question, the researchers tagged 

biodeposits that were already on the 

mound. Then, the fluorescent chalk 

was mixed with already deposited 

biodeposits, and the researchers came 

PHOTOGRAPH COURTESY OF FLICKR 

back to trace the movement at night. 

“It was a crazy idea that we could feed 

mussels orange chalk, they would poop 

it out, and we could follow it across the 

marsh,” Fischman said. 

The researchers returned at night and 

used black light detection to trace the 

distribution of the fluorescently-tagged 

biodeposits. Blacklight, or ultraviolet 

(UV) light, is a tool commonly used to 

detect fluorescently-tagged materials. 

The maximum distance that fluorescent 

biodeposits traveled was measured in 

every direction. 

Interestingly, the team discovered 

that the biodeposits were quickly 

redistributed beyond the areas where 

mussels were present. To confirm 

these results, the researchers collected 

approximately ten mussels from each 

of their six mounds, brought them to 

the University of Georgia’s laboratory, 

and fed them a mixture of seawater and 

chalk, which resulted in the excretion of 

fluorescently-tagged biodeposits. After 

the previous fluorescent material was 

washed away, the researchers planted the 

mussels in the respective mounds and 

performed the study again, subsequently 

confirming their previous findings. 

One limitation of this experiment that 

the researchers hope will be addressed 

in future studies is that the dye in the 

biodeposits fluoresced for only the first 

twenty-four hours, so the study was 

performed on a limited time scale. 

In the second field experiment, the 

researchers wanted to investigate the effects 

of cordgrass, also known as marsh grass, 

and mussels on sediment deposition at 

different marsh elevations. Seven different 

scenarios were tested in two zones in the 

state of Georgia for a month: the creekhead, 

where a narrow inlet called a tidal creek 


Ecology 

FOCUS 

to sediment deposition and vertical 

accretion in salt marshes. 

New Ideas For Mitigating Sea Level Rise 

A salt marsh in Georgia. 

enters onto the marsh, and the marsh 

platform, the main flat surface of the mark 

that extends landward. 

Cordgrass was found to have no 

significant effect on sediment deposition 

in both zones, which further highlights 

the importance of mussels. As for mussels, 

after performing statistical analysis, 

the researchers discovered a positive 

correlation between the number of mussels 

and increased sediment deposition. The 

implications of this study are limited by the 

size of the areas that were observed. 

In the third field experiment, to assess 

the potential effects of mussels on marsh 

accretion at the level of a creekshed, a 

smaller version of a watershed, researchers 

manipulated the presence and population 

size of mussels. Approximately two hundred 

thousand mussels were manually moved 

from one creekhead to another. A control 

creekhead side in the same marsh was also 

established. With the help of a tool called 

the Digital Elevation Model (DEM), the 

researchers were able to assess the elevation 

of the creekheads after three years. DEM 

was created using drone imagery, which 

was then filtered and edited to remove 

vegetation to focus on the sediment. The 

team discovered that the creek from which 

the mussels were removed decreased in 

elevation, but the creek to which mussels 

were added increased in elevation. Mussels 

were putting in the work. 

To further explore and validate the 

conclusions from their field experiments, 

the researchers used the Delft-3D- 

BIVALVES model, a digital tool to 

IMAGE COURTESY OF FLICKR 

create simulations, generating different 

scenarios that mimicked salt marshes in 

the region. This model determined that 

the highest sediment accretion was found 

on mussel aggregations using simulations 

based on the assumption that mussels 

filter the water column—which refers to 

the space between the surface and floor of 

a body of water. Mussels expel the filtered 

content and their feces on mounds, which 

facilitates a build-up of sediments that 

increases the elevation of the salt marsh. 

“While the manual labor and 

methodology development were at times 

challenging, I think ultimately this has 

been one of the most collaborative and 

gratifying scientific efforts that I have 

been a part of,” Crotty said. Each of 

these field experiments in addition to 

the simulation models contributed to 

the overall claim that mussels increase 

salt marsh accretion. The results suggest 

that mussels contribute significantly 


“The coolest takeaway of this study 

is that mussels increase salt marsh 

accretion, which means that mussels 

are important in helping marshes keep 

up with sea level rise,” Fischman said. 

Other researchers can use the insights 

provided by this study to direct their 

research projects on animals similar to 

mussels. Mussels may not, however, be 

the only animals that are contributing to 

the health of their ecosystems. 

Due to climate change, small animals 

are adapting their roles to their 

changing environment. Understanding 

the behavior of these animals can help 

guide future research on other types 

of terrestrial and marine ecosystems. 

“Relatively small animals are increasing 

in their relative importance and the roles 

that they play in response to the changes 

that climate change is implementing,” 

Crotty said. 

As for next steps, Fischman is interested 

in the effect of mussels on nitrogen 

cycling, which is a cycle of various 

processes in which nitrogen moves 

through living and non-living things in 

the environment. 

As climate change continues to worsen, 

an additional rise in sea levels is inevitable. 

Among its dangers are more frequent and 

intense floods, higher storm surges, and loss 

and alteration of coastal habitats. Future 

studies, including those on overlooked 

parts of an ecosystem, can hopefully help 

mitigate its harmful effects. ■ 

ABIGAIL JOLTEUS 

ABIGAIL JOLTEUS is a sophomore in Berkeley College studying Ecology and Evolutionary Biology. 

In addition to managing the website for YSM, she conducts research in the Konnikova Lab. 

THE AUTHOR WOULD LIKE TO THANK Sinéad Crotty and Hallie Fischman for their time and 

enthusiasm about their research. 


Jones, Clive G., et al. “Organisms as Ecosystem Engineers.” Ecosystem Management, 1994, pp. 130– 

47, https://doi.org/10.1007/978-1-4612-4018-1_14. 

FitzGerald, D. M. & Hughes, Z. Marsh Processes and Their Response to Climate Change and Sea- 

Level Rise. Annu. Rev. Earth Planet. Sci. 47, 481–517 (2019). 



FOCUS 

Public Health 

FATAL ATTRACTION 

Using fly pheromones against disease 

A natural tsetse fly odorant could 

help prevent African sleeping sickness 

BY CINDY MEI 

ART BY COURT JOHNSON 

From evoking long-forgotten memories through nostalgic scents to detecting 

imminent danger through noxious odors, smells hold undeniable power. 

Our sense of smell has served as a prime mechanism for survival since the 

beginning of time. Much of the work in the lab of John Carlson, a Yale professor 

of Molecular, Cellular, and Developmental Biology, is dedicated to studying the 

intricate mechanisms of Drosophila (fruit fly) olfaction: how do these insects detect 

and behave in the presence of volatile pheromones? An example of chemosensation, 

these pungent odorants—chemical compounds that have a smell—produced by 

organisms facilitate sexual attraction and mating by affecting behavior. The lab is 

interested in studying chemosensation as a method to control populations of insects 

that spread disease—such as the tsetse flies, insects that are responsible for spreading 

African trypanosomes, the causative agents of African sleeping sickness in Sub- 

Saharan regions. 


Public Health 

FOCUS 

In a paper published in Science earlier 

this year, a team of researchers conducted 

a study to find natural odorants that 

may control the behavior of tsetse flies. 

Led by Shimaa Ebrahim, a postdoctoral 

researcher in the Carlson lab, the project 

was conducted in collaboration with Hany 

Dweck, an associate scientist in the Carlson 

lab, and Brian Weiss, a senior research 

scientist at the Yale School of Public Health. 

“I fell in love with the [tsetse fly],” Ebrahim, 

who studies the courtship behavior of 

Drosophila, said. Weiss echoed Ebrahim’s 

fascination, pointing out behaviors unique 

to the tsetse flies, such as the live birth and 

nurturing of their young, in contrast to the 

majority of insects, which lay eggs. 

Importantly, tsetse flies feed exclusively 

on vertebrate blood, leading to the 

transmission of Trypanosoma brucei 

(trypanosomes), a classification of 

protozoan parasites that cause African 

sleeping sickness and nagana in humans 

and domesticated animals, respectively. 

These diseases have devastating effects: 

nagana is responsible for an average loss of 

4.5 billion dollars in resources every year 

in Africa. If left untreated, African sleeping 

sickness has a one hundred percent 

mortality rate. Unfortunately, access to 

treatment is not available everywhere. 

“Most of the drugs used to treat sleeping 

sickness are arsenic-based and horribly 

toxic. Very recently, there’s been some 

newly-developed medications, and they're 

much less toxic—but they’re much more 

expensive,” said Weiss, who studies tsetse 

flies and their associated microorganisms. 

To find alternative solutions, the 

researchers turned their attention to 

preventative measures. According to Weiss, 

the best solution to reduce fly populations is 

to use traps, as they are cheap and effective. 

However, not much is understood about 

the chemical signaling of tsetse flies, which 

may be key to luring the flies to traps. “If 

you want to control any insect that could 

cause disease or damage to any crop, you 

have to study their behavior to find the way 

to control this insect,” Ebrahim said. 

The Role Of Smell In Mating 

The researchers utilized the tsetse fly 

species Glossina morsitans. While Glossina 

fuscipes is the most abundant species in 

Kenya, they are difficult to rear in the 

insectary, according to Weiss. To examine 

possible odorants in sexual attraction, the 

researchers first studied tsetse fly mating 

behaviors. When paired together, G. 

morsitans males initiate mating with G. 

morsitans virgin females within seconds, 

and copulation continues on average for 

an hour. However, this reaction was not 

observed when G. morsitans males were 

paired with mated females, suggesting 

that there may be a difference in chemical 

signaling that results in the male’s 

behavioral responses. 

To determine whether differences 

in mating are driven by olfaction, 

pheromone extracts were obtained from 

the exoskeleton, also called the cuticle 

(the layer that covers the extracellular 

surface of the fly), of male and female 

flies that were soaked and gently shaken 

in hexane for ten minutes. Dummy tsetse 

flies made out of yarn were sprayed with 

these extracts and placed in a container 

with male G. morsitans, and a measure 

of attraction was determined by the 

percentage of males that initiated mating 

and stayed attached to the decoy flies for 

more than five minutes. However, the 

males were not attracted at all, suggesting 

that any odorants associated with mating 

are stored beyond the cuticles. 

After soaking another set of tsetse flies 

in hexane for twenty-four hours, it was 

observed that males were attracted sixty 

percent of the time to dummies sprayed 

with extracts from virgin females and 

twenty-seven percent of the time with 

extracts from mated females, with no 

response observed with male extracts. 

This observation indicates that there may 

be a difference in the composition of the 

extracts that made male flies more attracted 

to virgin than mated female G. morsitans. 

The longer soaking time may also explain 

why these compounds were not detected as 

potential pheromones in earlier research. 

The Discovery Of A Key Pheromone 

To determine if differences in compound 

composition were responsible for mating 

behaviors, the researchers obtained the 

chemical profile of the extractions via gas 

chromatography-mass spectrometry (GC- 

MS), which separates and detects different 

compounds. GC-MS identified three fatty 

acids and three fatty acid methyl esters that 

were not present in the ten-minute hexane 

immersion, which suggests the pheromones 

stored in internal glands may play a part in 

facilitating attraction. 

To test this hypothesis, the researchers 

repeated the previous experiment by 

spraying the dummy flies with each of 

these six compounds. They found that the 

male flies were strongly attracted to certain 

compounds that are present in higher 

levels in virgin females, such as methyl 

palmitoleate (MPO)—which attracted G. 

morsitans males eighty-seven percent of 

the time even when diluted—methyl oleate 

(MO), and methyl palmitate (MP). The 



FOCUS 

Public Health 

male fly stayed attached to the dummy for 

a prolonged period of time, suggesting that 

these compounds also act as arrestants— 

halting all motion—to prevent premature 

interruption of mating. Clearly, smell 

seemed to play a powerful role in mating! 

Next, the researchers sought to investigate 

cellular mechanisms that may facilitate 

the observed behavioral responses. 

Removing G. morsitans males’ antennae 

eliminated their attraction response, 

suggesting that the observed behavioral 

responses in mating are facilitated by scent. 

Furthermore, research has suggested that 

volatile odors are detected via the trichoid 

sensilla, a sensory organ located in the 

antenna of the fly. 

In a method called single-sensillum 

electrophysiology, the researchers 

obtained recordings of trichoid sensilla 

response to odors detected in the air 

by antenna. Initially, only MPO elicited 

excitatory responses from both sexes, but 

particularly from males. After reducing 

the distance from which the odor was 

delivered, activation in neurons was seen 

with MP, MO, and MPO, correlating 

with the behavioral results observed 

in earlier experiments. However, there 

was little to no response in olfactory 

neurons to these six compounds in G. 

fuscipes, another tsetse species that is 

the prominent vector of trypanosomes 

in east Africa. This finding suggested 

that these pheromones are specific to G. 

morsitans mating mechanisms. Indeed, 

it was found that G. morsitans males 

made no attempt to mate with untreated 

G. fuscipes females; however, when G. 

fuscipes females were sprayed with MPO, 

the males began to engage, suggesting 

that MPO may act as an 

aphrodisiac, a stimulant 

for sexual desire, for G. 

morsitans males. 

Could Infection Change 

Mating? 

The last study 

examined if these 

findings held for 

tsetse flies infected 

with trypanosomes, 

which is the 

ultimate target for 

traps to prevent 

the spread of African sleeping sickness. 

There were no changes in single-sensillum 

electrophysiology, meaning there was no 

change in neuronal response. However, 

there were significant behavioral changes 

observed in mating. 

When paired together, uninfected 

virgin female G. morsitans mated with 

infected and uninfected males at the same 

frequency. However, uninfected virgin 

male G. morsitans mated with uninfected 

females one hundred percent of the 

time over infected females, suggesting 

that there may be a compound that 

lowers the sexual receptivity of infected 

females and acts as a repellent against 

G. morsitans males. The group hopes to 

further study twenty-one compounds 

that were identified in GC-MS as specific 

to infected flies. “I'm interested to study 

if this compound is produced as a defense 

against the parasites,” Ebrahim said.“We 

don't know if those compounds were 

produced by the tsetse fly in response 

to an infection, or maybe they were 

produced by the parasites themselves,” 

Weiss said. 

Harnessing The Power Of Pheromones 

The results of the study suggest that 

MPO acts specifically as an attractant, 

aphrodisiac, and arrestant on G. morsitans 

males to activate circuits that mediate 

olfactory attraction, sexual desire, and the 

halting of movement, respectively. The 

usage of MPO in traps holds great promise 

from both an environmental and economic 

perspective. “Compounds from the fly itself 

[…] will be less toxic if we want to use it in 

the field compared to other compounds like 

DEET,” Ebrahim explained. These natural 


compounds are also much less expensive 

than DEET, which makes implementation 

of tsetse fly control more realistic in 

developing countries. 

In the future, the researchers hope to test 

MPO in Kenya with collaborators, who are 

currently using tsetse fly host odors such 

as cow urine as attractants. “If we combine 

MPO with natural host odors, it might 

increase the efficiency of control for a trap,” 

Ebrahim said. “A more specific odor might 

attract more flies and reduce the number 

of cases of infection by trypanosomes.” 

However, there are challenges 

validating field work with lab work, since 

the flies in the experiment are different 

from those found in a typical African 

savanna. In addition, in the real world, 

there are many fluctuating and uncertain 

factors, according to Ebrahim. Despite 

these challenges, the group remains 

undeterred, and their passion stays 

vibrant. “You will have to be optimistic 

and creative for the biggest experiments 

you design,” Ebrahim said. ■ 

CINDY MEI 

CINDY MEI is a sophomore in Grace Hopper studying neuroscience. In addition to writing for YSM, 

she serves as communications chair on Yale Math Competitions and volunteers with Yale DEMOS 

and Yale New Haven Hospital. She also conducts epilepsy and Tourette’s syndrome research at the 

Yale School of Medicine. 

THE AUTHOR WOULD LIKE TO THANK Shimaa Ebrahim, Brian Weiss, and John Carlson for their 

time and enthusiasm in answering questions and providing interactive insight about their research. 


Ebrahim, S.A.M., Dweck, H.K.M., Weiss, B.L., & Carlson, J.R. (2023). A volatile sex attractant of tsetse 

flies. Science, 379 (6633), doi: 10.1126/science.ade1877 


Environmental Engineering 

FEATURE 

SEEDING 

ROBOTS 

WOODEN CORKSCREW 

ROBOTS PLANT SEEDS 

BY MADELEINE POPOFSKY 

Look, up in the sky! It’s a bird! It’s a plane! It’s… hundreds of 

autonomous self-burying seed carriers? These small wooden 

contraptions are built with a unique design that lets them bury 

a seed into the ground after dropping from a great height. While 

unlikely to drop into your backyard, this new invention spearheaded 

by Lining Yao of Carnegie Mellon University and Teng Zhang of 

Syracuse University could change the face of reforestation via air. The 

design for these carriers is inspired by Erodium seeds and their natural 

dispersal mechanisms, and they are made using natural materials such 

as wood. The carriers provide a nature-based solution to our manmade 

problems regarding habitat loss, forest shrinkage, and even 

agricultural complications. 

Aerial seeding—scattering seeds by plane, drone, or helicopter— 

is an invaluable technique when it comes to wildland restoration, 

reforestation, and agriculture, especially for large swaths of hard-toaccess 

land. However, the scattered seeds often fail to penetrate the 

ground. This dramatically decreases their chances of germination, as 

they can get eaten by wildlife or swept away by harsh weather conditions. 

The device is closely modeled on the seeds of Erodium, a flowering 

plant that has seeds with a special design: a coiled body and single 

twisting tail that allows them to bury into the soil. “It’s very hard to 

reproduce the performance and also the biodegradable nature of the 

Erodium seeds,” Zhang said. 

After many rounds of testing, the final design has a twist: three 

tails instead of one. “These three points provide a stable contact 

between the structure and 

the soil,” Zhang said. 

Imagine a propeller 

with three blades 

circling each other 

on top—these are the 

three tails. In the center, 

where the three tails meet, 

a coil extends downward 

in a straight line—this is the coil 

body. At the end of the coil body lies the seed 

tip, where the seed is stored. In addition to the 

three tails, the other main innovation is the coil, 

which provides the mechanical force to allow the 

carriers to drill into the ground. The researchers 

treated the wood used to make the coil body 

with multiple rounds of chemical 

treatment and mechanical 

deformation in order to 

create its twisting shape. 

ART BY KARA TAO 


The carrier is rain-driven—another concept borrowed from 

Erodium seeds, which change shape depending on humidity. The 

wood cells in the coil swell during rainfall, with those on the inside 

swelling more than those on the outside, causing the coil to unwind 

and the seed to be drilled into the ground. As the coil dries, the 

cells on the inside shrink more than 

those on the outside, promoting 

another coiling mechanism in 

the opposite direction that 

further embeds the seed. 

The main challenges 

faced by the researchers 

included field tests that 

could be done best only in 

the spring, resulting in months of 

wait time until conditions were suitable, 

in addition to day-of weather concerns. 

Furthermore, the researchers created a simulation 

to test the device’s performance which proved difficult, 

considering friction and the many connections between 

the tails and coil body. 

The carriers have a few issues: they can be negatively 

affected by extreme weather conditions, the tip-coil connection 

can sometimes break, and the tails can tangle during release. The 

team aims to fix these issues as well as test other types of materials. 

The tested carriers were made of white oak, but other woods or 

materials could potentially be used with the design. A larger material 

library will enhance the feasibility of production in different regions. 

Additionally, the researchers are exploring other dimensions for the 

seed carriers that could improve their performance. 

Currently, the carriers are lovingly crafted by hand—which is 

not a production method that can continue long-term. The team 

is now focusing on producing on an industrial scale. “The cost [of 

production] is really about the time and the effort. The material 

cost is relatively cheap,” Zhang said. 

Yao, Zhang, and their team are currently seeking partners and 

stakeholders to expand their impact. “Responsive and functional 

structures that are powered by renewable energy could play a 

critical role in natural contexts, for ecological purposes such as 

restorations and environmental monitoring,” Yao said. 

When faced with a problem, sometimes the best inspiration is to 

look to nature. That has certainly proved to be the case with these 

self-drilling seed carriers. And in ten years’ time, maybe the future 

of our world’s forests will be saved by a swarm of plucky, threetailed 

robots falling from the sky. ■ 

May 2023 

Yale Scientific Magazine 

25

FEATURE 

Anatomy 

YOUR UNIQUE FINGERPRINT 

GENETIC AND NON-GENETIC DETERMINANTS OF 

FINGERPRINT PATTERN FORMATION 

BY ELISA HOWARD 

ART BY BREANNA BROWNSON 

Look at your hands. Look closely at the patterns drawn on 

the tips of your fingers. The fingerprint is present from 

birth, unchanging over the human lifespan, and unique 

to each and every individual. Even identical twins with the 

same genes exhibit distinct fingerprints. So, how does your 

fingerprint develop? And what factors contribute to the unique 

patterns that you see? 

Fingerprints exhibit three main pattern types: arches, loops, 

and whorls. Fingerprint ridges begin to form in the twelfth 

week of gestation, the period between conception and birth, 

and the organization of the fingerprint pattern is defined by 

week fourteen. However, little is known about the biological 

mechanisms underlying fingerprint variation. In a recent paper 

published in Cell, researchers at the University of Edinburgh 

and the Shanghai Institute of Nutrition and Health provide 

insight into the genetic foundations of fingerprint development. 

“We are interested in individual molecules and genes and how 

they work together to create structure and form,” said Denis 

Headon, a senior research fellow at the University of Edinburgh 

and an author of the study. 

Leading the project, Shanghai Institute researchers in the 

Laboratory of Dermatogenomics performed genome-wide 

association studies (GWAS) linking fingerprint pattern type 

with genetics. A GWAS is a research approach that correlates 

variation in observable traits with variation in the DNA. The 

Shanghai researchers conducted GWAS of several thousand Han 

Chinese individuals characterized for the three main fingerprint 

patterns. This GWAS method identified forty-three locations of 

genes associated with developing arches, loops, or whorls. 

The researchers then studied the functions of fingerprintassociated 

genes and the timing of their activity in development. 

“Interestingly, locations in the genome that correlate with 

fingerprint type are populated by genes involved in limb 

formation, rarely skin development,” Headon said. That is, genes 

involved in embryonic limb formation appear as the predominant 

factors determining heritable variation in fingerprint patterns. 

The researchers also found that many of the fingerprint-associated 

genes identified through GWAS are not even active in the skin 

when the fingerprint forms. Rather, the genes function early in 

development to set up the proportions and shapes of the fingertips. 

As development progresses, the genes switch off. These findings can 

be understood in the context of correlative work from the twentieth 

century, which argues that the shape of the finger strongly influences 

fingerprint 

patterns. Thus, 

it appears 

that limb 

development 

genes dictate the 

presence or absence 

of arches, loops, or 

whorls through their involvement in 

finger shape. 

However, the GWAS results 

only explain part of the variation 

in fingerprints across the human 

population because fingerprint type 

is not entirely heritable. For instance, 

identical twins have different fingerprints, 

and the fingerprints of the left and right hand are 

not mirror images. “The same genome running through the process 

of making a fingerprint at different times, for different fingers, 

for different individuals will come up with a slightly different 

outcome,” Headon said. Therefore, rather than simply focusing 

on genes, it is important to consider development as a process. 

“The genes inform, but then there is a process of development that 

interprets and gives an outcome in the anatomy,” Headon said. 

How can this study help explain the distinct fingerprints of 

identical twins? If one identical twin has all arches, then the 

other twin is more likely to have all arches than a random, 

unrelated member of the population. In other words, there is 

at least some genetic influence. “But genetic variation will go 

through a developmental process that has a certain amount 

of randomness to it,” Headon said. Simply knowing the list 

of genes active in a particular tissue provides an incomplete 

understanding of how that tissue develops. “You need to 

abstract a step from that and say, ‘what is the process through 

which these genes operate together to produce a particular 

outcome?’” Headon said. 

Look at your hands again. How might your fingerprints 

have formed? ■ 

26 

Yale Scientific Magazine 

May 2023 

www.yalescientific.org

FEATURE 

Materials Engineering 

Astrophysics 

FEATURE 

THE 

IMPOSSIBLE 

ART BY YUROU LIU 

STAR 

A NEWBORN STAR LIVING ON 

THE CUSP OF A BLACK HOLE 

BY ELIZABETH WATSON 

Most of the stars we see in the night sky are billions of 

years old, their light only just now reaching us from 

light-years away. But what lies beyond what we can see? 

The reach of the universe extends far beyond the stars that we’re 

able to observe with the naked eye. 

A team led by Florian Peißker, a postdoctoral researcher at the 

University of Cologne’s Institute of Astrophysics in Germany, 

recently discovered a newborn star named X3 whose existence 

defies all odds. Dubbed “the impossible star,” X3 is located over 

twenty-five thousand light-years away and is currently undergoing 

early stages of stellar formation in the vicinity of Sagittarius A*, the 

supermassive black hole at the heart of our galaxy. Star formation 

so close to a black hole was thought to be theoretically impossible, 

but X3 persists all the same. 

“I enjoy thinking about the opportunity to witness processes 

nobody else has seen before,” Peißker said. The paper, published in 

The Astrophysical Journal, is the product of two and a half years of 

work and explores how X3 was able to form in spite of Sagittarius A*. 

Star formation typically requires two conditions: relatively low 

temperatures and high gas density, neither of which holds true for 

the environments created by black holes. The area that Sagittarius A* 

occupies, known as the Galactic Center, is extremely hot and volatile. 

“This source should not exist in the first place because of the 

harsh environment of the supermassive black hole Sagittarius 

A*,” Peißker said. “The fact that we observe such a young object 

so close to Sgr A* implies that this is not the only [such object]. 

It furthermore shows that star formation can occur, although the 

classical criteria are not fulfilled.” 

Previous research in the field identified clumps of silicon 

monoxide (SiO) gas near Sagittarius A* that may have been dense 

enough to permit high-mass star formation. A study in 2014 

suggested that these clumps originated from the Circumnuclear 

Disk (CND), a ring of molecular gas that surrounds Sagittarius A*. 

It was proposed that some SiO clumps found within the CND either 

had high enough velocity gradients or had experienced a sufficient 

decrease in angular momentum to spiral closer to Sagittarius A* 


than would be otherwise possible. This process, called molecular 

cloud inspiraling, was thought to be part of what could foster 

stellar formation so close to a black hole. 

The team behind Peißker’s study sought to build upon this work. 

They compiled data on X3 spanning three decades from four 

different telescopes, including the Very Large Telescope in Chile, to 

better map out the X3 system and its surroundings. The team divided 

the X3 system into three components—designating the young stellar 

object as X3a and two neighboring thermal blobs as X3b and X3c— 

and collected data about nearby stars and gas clusters. The analysis 

helped the team confirm the star’s proximity to Sagittarius A* and 

better understand its origins by examining its characteristics. 

In addition to the accretion of the SiO gas clumps discussed in 

previous research, the team believes that rotating regions of dust 

and gas in the Galactic Center, called stellar disks, may also have 

been key to X3’s formation. The thickness of these disks would have 

been sufficient to lower the temperature within the region for star 

formation to be feasible, while simultaneously protecting the area 

from the black hole’s radiation. 

As they rotate, these stellar disks become dense enough to create 

massive gas clusters conducive to high-mass stellar formation. The 

team believes that one of these clusters, IRS 13, was instrumental 

to the formation of the X3 system. Based on the team’s data points, 

the timeline for this formation theory aligns with our current 

understanding of this region’s stellar history. 

Peißker was excited upon confirming X3’s proximity to Sagittarius 

A*, but joked that the process of discovery was far more prolonged 

than an ordinary surprise reaction. “For six months, I ran day-in and 

day-out simulations to fit the data points,” Peißker said. “Back then, 

my daughter demanded milk almost every three hours each night. 

So I woke up, gave baby milk to my daughter, and started simulations 

with the new parameters. I did this around the clock.” 

Peißker hopes to build upon this work in the future to learn 

more about how the mechanisms of stellar formation respond to 

unconventional situations, which could lay the groundwork for a 

richer understanding of star evolution and our universe at large. ■ 


FEATURE 

Bioelectronics 

CYBORG ZEBR AFISH 

BY NATHAN MU 

USING THE BODY TO GROW FLEXIBLE ELECTRODES 

The human body is a machine. At a 

fundamental level, it depends on 

electrical currents within cells and 

electrical signals between cells to function. 

So, in a sense, the body produces its own 

electricity. But what happens if this power 

gets unplugged? This is the problem that 

researchers have faced in trying to cure 

diseases such as Parkinson’s, Alzheimer’s, 

epilepsy, and depression. In the brain— 

where electrical signaling is paramount— 

any small "unplugging" can throw off the 

system of electrical currents and quickly 

lead to improper function. Without a way 

to fix an improper pattern of electrical 

signaling, that part of the brain will slowly 

lose its charge and fizzle out, leading to the 

visible symptoms of these diseases. 

A team led by organic bioelectronics 

researchers Xenofon Strakosas and 

Hanne Biesmans of Linköping University 

in Sweden may be on track to develop 

a viable solution to this problem. They 

have targeted this issue of restoring 

dysfunctional electrical pathways by 

harnessing the body’s chemistry to form 

an electrode, or electrical conductor 

that helps produce a current, within the 

IMAGE COURTESY OF UC SAN DIEGO 

Researchers have developed brain sensor implants 

that can detect electrical signals. 

brain. “The really cool thing about this 

electrode is that it is a soft polymer that 

forms in situ, or within the brain, unlike 

metal electrodes that are harsh and rigid, 

and require open skull surgery,” Biesmans 

said. Any implant in the human body 

that does not belong there runs the risk 

of causing inflammation and inducing an 

immune response that will try to fight the 

implant. Current standards for inducing 

artificial electrical currents in the brain, 

such as gold electrodes, are not optimal. 

Biesmans’ team’s primary goal was to 

develop a "softer" alternative that could be 

formed within the body. 

Their approach was to create a gel 

mixture that, once injected into the brain, 

could self-assemble into a polymer that was 

able to restore electrical activity. There’s a 

popular saying that "the answer you seek is 

within you," and that’s the advice that the 

researchers followed. Previous researchers 

at Stanford had used an outside solution— 

genetic modification—to produce soft 

electrodes. However, this pathway comes 

with its own problems when it comes to 

human application due to ethical concerns 

over modifying human DNA. “With our 

simple injectable gel, there’s no need for 

genetic modification. And in the long 

term, maybe there is also no more need for 

open skull surgeries,” Biesmans said. 

This gel cocktail concoction is composed 

of monomers, or building blocks, as well 

as enzymes that will be used to make the 

polymer electrode. The powerful part of 

this research is that it takes advantage of 

the enzymatic breakdown of two types 

of biological sugars found in the body to 

assemble these monomers into a polymer 

electrode. First, glucose or lactate— 

two types of sugars in the body—are 

converted into hydrogen peroxide by 

common enzymes known as oxidases. 

Next, hydrogen 

peroxide is used 

by horseradish 

peroxidase (HRP), 

a naturally 

occurring enzyme, 

to start the 

p o l y m e r i z a t i o n 

process. And that’s 

it—a simple, twostep 

process links 

together the monomer 

components from the 

injected gel to form a soft 

electrode directly in the body. 

But even the coolest products still 

need to be tested for quality, and that’s why 

Biesmans and her team came up with a set 

of seven criteria ranging from fluidity to 

biocompatibility and stability to assess the 

electrodes. The first test they ran assessed 

the effectiveness of their injected electrode 

gel on 0.6 percent agarose gels, which is a 

well-known model for simulating brain 

chemistry and conditions. “In the early 

stages of research, if you don’t know 

much, you don’t want to go straight to 

zebrafish or animal models because you 

don’t know what works yet,” Biesmans 

said. In this initial stage of testing, the 

researchers went through at least fifty to 

sixty different injectable electrode gels to 

find a few that were promising enough to 

continue working with. “Some gels were 

too thick and did not even make it into the 

agarose gels,” Biesmans said. 

The team then moved on to 

demonstrating the conductivity, 


Bioelectronics 

FEATURE 

stability, and biocompatibility of the 

gel and the formed electrode. It would 

have been ideal to test these long-term 

effects with zebrafish, but this was not 

possible. “Our ethical permits did not 

allow us to keep the zebrafish alive for 

more than three days, so we had to find 

a different way,” Biesmans said. Instead, 

the researchers used electrode arrays to 

test for electrical currents maintained by 

the electrode polymer. They also exposed 

the polymers to harsh sound energy and 

live cell conditions to ensure that the 

polymer would not degrade. Both tests 

showed excellent results and confirmed 

the stability of the gel. 

These tests showed that the gel performs 

well, but is it safe to use? This was the 

team’s next question and perhaps the 

trickiest because of the potency of glucose 

oxidase enzymes. These enzymes can 

quickly produce lots of hydrogen 

peroxide, which can kill cells at 

very high concentrations. “We 

had to find an optimal balance 

between lactate oxidase and 

HRP enzymes so that we could 

get rid of the hydrogen peroxide 

as fast as it was being produced,” 

Biesmans said. Finally, the team 

had a breakthrough and found 

that a twenty-seven to one ratio of 

HRP to lactate oxidase worked best. “We 

were finally able to tune the amount of 

hydrogen peroxide so that we are not 

creating more problems than we 

are fixing,” Biesmans said. 

The final hurdle for Biesmans 

and her team was to test 

their gel in two live models: 

zebrafish and medicinal 

leeches. In zebrafish, the 

gel was introduced in the 

tailfin first, followed by 

the brain and heart. 

The gel turns deep 

blue when successfully 

polymerized, and the team 

saw this beautiful color in all 

three locations. Their hard work 

had finally resulted in a working 

electrode, without noticeable 

side effects on the zebrafish. 


One of Biesmans’ favorite experiments 

was soaking zebrafish hearts in the gel 

cocktail. “I really like that the polymer 

formed around the arteries, where 

you find glucose and lactate. It’s not 

covering the entire heart. That was a nice 

demonstration of the specificity of this 

gel,” she said. 

Leeches were another nice proof 

of concept for demonstrating the 

effectiveness of this polymer electrode 

since they are easy to visualize. “Leeches 

have one central nerve, and if you stimulate 

the nerve, it will contract immediately. So, 

you get instant visual proof of whether 

your stimulation worked,” Biesmans said. 

A key finding from the leech model was 

that the polymer electrodes produced a 

gentler, tissue-friendly current as opposed 

to the stronger, harsher current produced 

by gold electrodes. 

Even with the success of this initial 

experiment, there is still much work to 

be done. Biesmans and her research team 

plan to further optimize the current gel, 

test new versions of gels with different 

monomer building blocks, and introduce 

their current gel in mice models. 

Biesmans is also working on trying to 

induce a similar gel-based polymerization 

in single cells, as opposed to tissues. 

“Overall, we are working 

on building up this 

toolbox of 

monomers and 

techniques for so many 

different applications,” Biesmans said. 

These applications include treating 

various diseases requiring electrical 

stimulation by forming polymer 

electrodes at many different sites with 

disparate properties. 

This is just the beginning of exploring 

electrical patterns in the brain. While 

this team focused on restoring electrical 

activity, there are also projects such as 

Elon Musk’s Neuralink program that seek 

to use machines to interpret the meaning 

of the brain’s electrical signals. Perhaps 

this research will lead us towards a future 

of not just cyborg zebrafish, but cyborg 

humans that fully utilize the brainmachine 

interface. This makes organic 

bioelectronics a highly interdisciplinary 

field, and for Biesmans, this has been one 

of her favorite aspects of the work. “It’s 

interesting and fun to work with all these 

collaborators from different disciplines 

together. So, let’s see where it brings me,” 

Biesmans said. ■ 

ART BY 

COURTNEY JOHNSON 


FEATURE 

Palaeogenomics 

BY MATTHEW BLAIR 

ART BY MALIA KUO 

VACATIONING IN SPAIN 

HOW ANCIENT HUMANS ESCAPED THE ICE AGE 

Genetic testing platforms like 

23andMe and Ancestry.com 

have been in the spotlight for 

many years now. These testing programs 

have grown immensely popular, with 

some people finding long-lost relatives 

or discovering that a historical figure is 

somewhere in their family tree. 

But for those living over forty thousand 

years ago, unfortunately, no such genetic 

testing was available. Those early humans 

lived without ever knowing their full 

genetic history. Some early humans 

perhaps wholly missed the opportunity to 

gloat that they were related—somewhere 

in their bloodline—to the first Homo 

sapiens to discover fire. 

Now, however, He Yu of Peking 

University in Beijing, China and her 

team of researchers have constructed a 

genetic narrative for these early humans. 

Their study is the most comprehensive 

examination of certain hunter-gatherer 

groups living in Europe around the Ice 

Age. It reveals important information 

about the mixing between different 

groups and their migratory patterns. 

This study shines a light on the genetic 

differences and similarities of different 

hunter-gatherer groups and focuses 

especially on how these groups survived 

the Last Glacial Maximum (LGM), which 

was the most intense period during the 

last Ice Age. 

The group’s study examined where 

hunter-gatherer groups migrated in 

order to evade the massive glaciers and 

blisteringly cold temperatures moving 

across the globe during the LGM, which 

lasted from twenty-five thousand to 

nineteen thousand years ago. The LGM is 

particularly interesting to study because 

researchers believe it created a large 

migration of hunter-gatherer groups. 

Prior studies have found that the LGM 

pushed hunter-gatherer groups to move 

into southern latitudes, specifically the 

Iberian peninsula and southern France, 

with some studies also suggesting that 

hunter-gatherers could have moved into 

the Italian peninsula, the Balkans, and 

the southeastern European Plain. 

It is impossible to determine where 

groups may have moved during the 

LGM without having a snapshot of their 

locations and genetic makeups before and 

after this period. As such, the study spans 

from thirty-five thousand to five thousand 

years ago, covering before, during, and 

after the LGM. “This paper focuses on 

where people traveled to find refuge and, 

after the LGM, expanded again to form 

the later population structure,” Yu said. 

Using mostly bones, teeth, and other 

materials that could contain genetic 

information, Yu and her research team 

created new genomic information for 

hunter-gatherer groups that are now 

extinct. It is easy to send in your saliva 

sample to a genetic testing company site, 

but researchers had to meticulously comb 

through paleogenomic data to construct 

a very large and complex family tree. In 

this paper, 356 ancient hunter-gatherer 

genomes were analyzed, 116 of which were 

newly reported by researchers across the 

globe in fourteen countries throughout 

western and central Eurasia. 

Once the researchers confirmed that 

these samples contained genetically viable 

information, they began the process of 

genetic testing. The first, most crucial, 

step in this process is to extract the 

DNA and sequence the genome. Often, 

however, sequencing the genome is the 

simplest part. “When we get the data, we 

have a lot to do with it. We first examine 

their genetic differentiation, trying to 

see what samples look more similar and 

which are more dissimilar. Specifically, 

we focus on the alleles and other genetic 

information that could be shared between 

some individuals and not others,” Yu 

said. Alleles are the genetic information 

that could potentially be shared between 

individuals—the genetic information that 

could contribute to physical traits like 

blue eyes or brown hair. This process of 

analyzing these alleles and other genetic 

information involves a great deal of 

high-level statistical analysis and other 

methods of biological comparison. 

This data analysis allows researchers 

to test specific hypotheses about the 

movement and mixing of hunter-gatherer 

groups. There are many different ideas 

about where a group could have gone 

and which other hunter-gatherers they 


Palaeogenomics 

FEATURE 

might have 

e n c o u n t e r e d 

along the way, but 

this method of data 

collection and analysis can 

quantitatively prove or disprove 

these conclusions. 

The researchers also considered a 

multitude of other factors, including 

the radiocarbon dates of the materials, 

so that they can pinpoint the age 

of the samples and discover other 

archaeological information. Simply, 

radiocarbon dating is the process by 

which researchers analyze the amount 

of radioactive carbon-14 left in a sample 

in order to measure its age. Further, 

cultural information about specific 

hunter-gather groups, such as knowledge 

about their mortuary practices or the 

types of weaponry they commonly used, 

allowed the researchers to make 

increasingly sound conclusions about the 

movements of certain hunter-gatherer 

groups and their possible relations to 

other groups. 

With this research, Yu and her team of 

researchers have established a genomic 

study of remarkable depth and breadth. 

By drawing on multitudes of biological 

and historical information, they created 

a firmly-rooted “family tree” for huntergatherer 

groups. 

When working with a data set that is so 

ancient, many challenges can arise. The 

majority of the time, the samples used 

usually come from bones or teeth. These 

physical samples last through the ages 

which makes them strong candidates 

for DNA extraction. In especially old 

samples, however, the DNA degenerates 

and is poorly preserved. “The samples 

that are reported, of course, are not the 

only samples that we have processed. 

There were various samples that did not 

produce enough DNA and some which 

had none at all, failing during the DNA 

extraction process,” Yu said. 

Even when a sample does 

produce enough DNA, that data 

must be observed with a critical eye. As 

these samples have often been studied by 

multiple parties and transported across 

the globe, the risk for contamination is 

high. “For many samples, we also had a 

hard time trying to detect and confirm if 

they are contaminated or not. Further, if 

samples were found to be contaminated, 

we then had to go through the process 

of separating the DNA of that specimen 

from its contaminants so that we could 

get real information,” Yu said. 

This study showed that huntergatherer 

groups flocked to western and 

southwestern Europe to escape the Ice 

Age. “It was always assumed that the 

Iberian Peninsula was a refuge during 

the Ice Age, but this is the first time we 

genetically confirmed that there is really a 

human population—with the same genetic 

ancestry found earlier in other regions of 

Europe—living in that area,” Yu said. This 

is a powerful confirmation that paints a 

clearer picture of the survival, migration, 

and mixing of hunter-gatherer groups. 

But researchers still have questions, 

especially about the importance of another 

region as a refuge during the Ice Age: the 

Italian Peninsula. In this region, there 

were massive genomic changes before 

and after the Ice Age, so researchers 

cannot make a succinct conclusion on 

whether or not it was a refuge based 

on DNA evidence alone. These 

regions saw a huge genomic 

turnover, with distinct genetic populations 

before and after the LGM. “Genetic 

information could help us to answer or 

confirm some points, but it alone cannot 

confirm them all. It is important in these 

sorts of studies to combine information 

from different sources and evidence from 

different disciplines,” Yu said. 

History itself is expansive, and trying to 

capture the movement of many different 

groups over tens of thousands of years is an 

exceedingly difficult task, but researchers 

like Yu and her team are embarking on this 

journey through time to reveal important 

information about how our earliest 

ancestors survived and how all of us are 

here today. As we move forward and learn 

more about our personal genomic histories 

through popular testing platforms, we can 

appreciate the work they are doing to 

capture the genomic ancestry of 

humans across the world. ■ 



FEATURE 

Immunology 

PLANT-ANIMAL 

HYBRIDS 

PROTECTING PLANTS 

WITH ANIMAL ANTIBODIES 

BY SAMANTHA LIU 

ART BY KARA TAO 

Plant-animal hybrids are here, and 

they are exactly what they sound 

like. In the Sainsbury Laboratory 

in Norwich, UK, wild tobacco plants have 

been engineered to produce "pikobodies," 

synthetic proteins that can recognize and 

attack pathogens expressing fluorescent 

proteins. These pikobodies are made 

by taking rice-derived receptors and 

swapping in antibody 

f r a g m e n t s 

originating 

from 

camelid mammals, specifically llamas and 

alpacas. In a proof-of-concept study— 

carried out by postdoctoral scientist Jiorgos 

Kourelis of the group headed by Sophien 

Kamoun—the team discovered that these 

pikobody-producing tobacco plants could 

successfully stave off viral invaders. 

This discovery arrives at a crucial 

moment: in the past year alone, wars, 

climate change, and trade routes in flux 

have ferried pathogens around the 

globe in dangerously unprecedented 

ways. Meanwhile, as a wheat 

blast devastates crop yields 

in Africa and Asia, 

and scientists 

sound 

alarm 

bells to food security worldwide, protection 

against plant diseases is more important 

than ever. 

While current mechanisms of disease 

resistance in agriculture are mostly 

chemical (think pesticides, fungicides, 

and a host of other -ides), with pikobodies, 

genetic treatments may replace our reliance 

on chemical treatments. “We can generate 

made-to-order resistance genes against 

virtually any pathogen,” Kourelis said. 

The idea is certainly an imaginative if 

not unbelievable one, almost like science 

fiction. But it didn’t originate out of the blue. 

Scientists have long been interested in the 

integrated domain (ID) of plant receptors, 

which is responsible for recognizing 

pathogen effectors and triggering an 

immune response. In one key study by 

French scientist Stella Cesari, engineering 

the ID of Pik-1—a receptor that normally 

attacks fungal invaders—could allow 

tobacco plants to gain specificity and bind 

new sequences. Ever since then, Kamoun 

has wondered if he could engineer Pik-1 to 

recognize other pathogens. 

The second piece of the puzzle— 

introducing the animal antibody—came 

four years ago, with Kourelis’ arrival at 

the lab. During a lab meeting, Kourelis 

proposed “A General Solution for Plant 

Pathology”—a title which, of course, caught 

the attention of everyone in the room. 

As Kourelis noted, one problem with 

plant immune defenses is that they lack 

mobile or specialized cells for attacking 


Immunology 

FEATURE 

viruses, unlike animals. Plants instead 

rely on nucleotide-binding, leucine-rich 

receptors (NLRs), which can recognize 

diverse pathogen components and 

activate the immune response. But NLRs 

are limited in what they can recognize— 

and their scope is hard-coded by DNA, 

which cannot evolve as fast as rapidlychanging 

viruses. 

In contrast, mammals can create and 

proliferate specific antibodies for virtually 

any virus they are exposed to. Not only do 

these antibodies target, mobilize, and kill 

viral particles, but the animal also retains 

them well after the infection, in case of 

future threats—the same principle which 

guides vaccines. “Basically, you could 

potentially build a disease resistance gene 

against any plant pathogen by exploiting 

the adaptive immune system of animals,” 

Kamoun said. 

Enter the llamas. Kourelis suggested 

taking camelid mammal nanobodies— 

the fragment of antibodies which actually 

binds to the pathogen—and fusing them 

to Pik-1. In this way, plants’ integrated 

domains could serve as a scaffold to trigger 

the immune response, while mammalian 

antibodies could let them recognize a host 

of other pathogens. 

To turn their concept into practice, 

Kourelis still needed a framework for 

where and how to engineer the receptors. 

His answer was bolstered by an earlier 

project by colleague and Ph.D. student 

Aleksandra-Ola Bialas, who investigated 

how the Pik-1 receptor arose fifty million 

years ago. Critically, by looking at the 

evolutionary origins of Pik-1, Bialas’s 

work helped delimit the boundaries of the 

domain that Kourelis was so interested in. 

“So fifty million years ago, nature 

actually did this engineering and 

integrated the domain into this [Pik- 

1] receptor,” Kamoun said. “And if you 

understand how nature has done it, you 

could repeat it in the lab. 

Even with Bialas’s contribution, the 

process to pare down potential candidates 

was arduous. It required iterations of 

revisiting basic science, tweaking existing 

combinations, and, at some point, sheer 

brute force, Kourelis recalled. “Sometimes 

we were like, ‘Let's drop in as many 

nanobodies as we can and see if some of 

them work,’” Kourelis said. “‘And then, if a 

Transgenic tobacco plants serve as the model organism for pikobody testing. 

few work, even if they don't work great, let's 

understand what's going on there.’” 

Eventually, he engineered eleven 

pikobody candidates to recognize 

fluorescent proteins. They were vetted 

for autoimmune responses and cell death 

responses until only four pikobodies 

remained. After introducing a live Potato 

virus X, which was engineered to express 

fluorescent proteins, two pikobodies were 

found to halt viral spread substantially. 

And if used together, these two pikobodies 

proved to be even more effective. 

Now, Kourelis and Kamoun are looking 

toward future applications for pikobodies. 

They are both enamored with the potential 

of “designer” domains, with each plant 

tailored with pikobodies against diseases 

that might threaten it. They even speculated 

that, with advanced artificial intelligence, 

computers may someday design the 

binding domains, circumventing the need 

for antibodies altogether. 

For Kourelis, one of the challenges lies 

in accounting for—and staying ahead 

of—pathogen evolution. As he looks to 

apply his model and develop a toolkit of 

new receptors, he hopes to identify target 

sequences that will be long-lasting. If they 

can pick target sequences that are unlikely 

to change, then the pathogen is less likely 

to evolve to resist that receptor. “Then 

IMAGE COURTESY OF PIXABAY 

again, I like to say, ‘Never bet against the 

pathogen,’” Kamoun said. 

In the book-lined office from which 

Kamoun and Kourelis take this Zoom 

interview, it is not difficult to envision 

them collaborating in a laboratory. 

Kourelis fields a question. Kamoun 

modifies Kourelis’s answer, then raises 

another point, which reminds Kourelis of 

another idea. Even as they talk to me, their 

conversation with each other never ceases. 

Their dialogue—revising, rephrasing, 

circling—reflects the cycles it took Kourelis 

to get to his top-performing pikobodies. 

But this is their process and, perhaps, 

the reason they are successful. Kourelis 

emphasized multiple times that they 

regard themselves as scientists first, and 

engineers second. No matter what sciencefiction 

universe plant-animal hybrids and 

pikobodies seem to resemble, for Kourelis 

and Kamoun, these ideas are firmly rooted 

in listening to what already exists—to 

plants, to other scientists, to each other— 

before they create something new. 

“There’s a more fundamental 

understanding in seeing how, in nature, 

these proteins have evolved, how these 

domain integrations have happened,” 

Kourelis said. “You have to understand 

before you can take the next step. You have 

to understand nature by making it.” ■ 



UNDERGRADUATE PROFILE 

CHARNICE HOEGNIFIOH 

YC ’24 

BY EMILY SHANG 

A 

double major in Classical Civilizations and Molecular 

Biophysics and Biochemistry, Charnice Hoegnifioh (BF ’24) 

is studying the science behind ancient makeup and skincare 

artifacts. Hoegnifioh was recently awarded the Edward A. Bouchet 

Fellowship and the $35,000 Beinecke Scholarship, which will support 

her academic research and post-graduate studies in the medical 

humanities, respectively. 

Hoegnifioh fell in love with biochemistry in 

high school. She especially enjoyed conducting 

experiments involving spectroscopy, the study of 

the emission and absorption of electromagnetic 

radiation by matter. After participating in 

the MIT Introduction to Technology, 

Engineering, and Science program 

in high school, she realized that she 

wanted to devote her undergraduate 

studies to biophysics. At the same 

time, she loved Latin, and her 

passion for Classics was cemented 

by a school trip to Greece. Ultimately, 

she found that “following her passion” 

at Yale meant loading up on five credits 

of Classical Civilization courses in her first 

year, while also researching ultrafast protein 

folding in the Davis Lab. She decided to pursue 

a double major and focus her time on honing her 

skills in these two areas. 

One of Hoegnifioh’s most recent classes applied spectroscopy and 

isotopic dating—the analysis of materials based on the decay rates of 

unstable elemental isotopes—to examine seals from the ancient Near 

East. Traditionally, these seals, which were ubiquitous in Mesopotamia 

and used for administrative and decorative purposes, were dated based 

on their iconography since their styles could be traced back in time. 

Hoegnifioh explained that studying the seals’ isotopic proportions can 

allow researchers to determine their geographical origins. “By looking 

at isotopic ratios of materials, you can differentiate whether a material 

or mineral came from Scandinavia or the Middle East,” Hoegnifioh said. 

As an Edward A. Bouchet Fellow, Hoegnifioh will study abroad in 

Germany, Greece, Italy, the United Kingdom, and France this summer 

and visit archaeological sites to research ancient cosmetic artifacts and 

their effects on healing. One artifact she’s particularly excited to see is an 

ointment tin from ancient Rome, excavated by the Museum of London 

twenty years ago, that still shows the preserved 

fingerprints of the original owner. Beyond 

the Museum of London, 

Hoegnifioh will go to the 

archeological museum in 

Frankfurt to view 

their exhibition 

of paint pots. “[Cosmetics] were posited as healing outward feminine 

flaws but also inward flaws in women. So I’ll be going to some healing 

sanctuaries and learning more about healing authority and what 

ingredients were thought [to have] curative properties,” Hoegnifioh said. 

Her work will culminate in her senior thesis, tentatively titled 

“Remedies for Roman Beauty: Curative Cosmetics during the 

Roman Empire.” Hoegnifioh’s interest in cosmetics 

began during her summer internship at Harvard, 

where she conducted a research project on the 

painful and poisonous aspects of beauty as 

a first-year student. Through her research, 

she learned that one of the most popular 

misconceptions about beauty routines 

in the classical world is that the ancient 

Romans unknowingly used lead 

within the cosmetic pigment. “It 

turns out that the Romans were 

actually aware that white lead 

was extremely toxic, as there was 

a treatise written that lead shouldn’t 

be used in pipes or buildings because it 

will lead to poisoning. But women were 

still being hurt, so I wanted to investigate 

why these societal standards were coming 

before women’s health,” Hoegnifioh said. 

Hoegnifioh cites multiple major influences in 

PHOTOGRAPHY BY HANNAH HAN 

her journey throughout Yale, the first being her 

Latin professor from her first year, Irene Peirano Garrison, who 

left Yale to teach at Harvard but remained her close confidant and 

advisor. Peirano Garrison advised Hoegnifioh to pursue a Ph.D. 

in the humanities and guided her through an ongoing graduate 

project on makeup in antiquity. “Her impact on my life is 

beyond words. I would not be where I am without her and 

her motivational presence in my life,” Hoegnifioh said. 

She also cites Jessica Lamont, an assistant professor of 

Classics, and Milette Gaifman, the Andrew Downey 

Orrick Professor of Classics and History of Art, as 

other advisors who have guided her through her 

undergraduate studies. 

When asked what advice she would give to 

underclassmen, Hoegnifioh emphasized that double 

majoring in two disparate fields is achievable given 

proper preparation, and she hopes that no one is 

deterred because of the prerequisite courses. “Planning 

is key, but don’t hold yourself to super strict standards 

because things change. So allow yourself that flexibility,” 

Hoegnifioh said. “Remember that imposter 

syndrome is real, but you are talented, and if 

you’re at Yale, you definitely deserve to be here.” ■ 

34 Yale Scientific Magazine May 2023 

www.yalescientific.org

ALUMNI PROFILE 

AMYMARIE BARTHOLOMEW 

YC ’13 

BY WILLIAM ARCHACKI 

This June, graduates from Yale’s Class of 2013 will flock back to 

campus for their ten-year reunion. For Amymarie Bartholomew 

(YC ’13), the trip will be as simple as a walk down Science 

Hill from her new lab at Kline Chemistry Laboratory. Appointed an 

assistant professor in January of this year, Bartholomew now works 

in the chemistry department alongside many of the faculty members 

she had as teachers and mentors during her time as an undergraduate. 

Back and better than ever, Bartholomew is a doctorate-wielding 

chemist whose work focuses on synthesizing stimuli-responsive 

inorganic materials. The graduate-level course she teaches, “Molecular 

Materials,” reflects the aims of her research: to produce materials that 

change their physical, magnetic, and electrical properties in response 

to interactions at the molecular level. For instance, the absorption of 

light might change the way bonds form, or an increase in temperature 

might alter the way electrons behave in a magnetic field. 

Bartholomew thinks of her work as a search for new ways to apply 

these tiny molecular changes to the creation of useful materials. 

“I’ve always had a lot of ideas for things to synthesize and things to 

try, and I think in chemistry—as well as in 

other fields—it’s really about just trying 

things,” Bartholomew said. “Being 

able to see which of my ideas hold 

promise and which of them are able 

to move forward—I think that’s 

really exciting.” 

One project the lab group is 

working on seeks to use the 

molecule azobenzene to 

produce electricity from 

sunlight. For a long time, 

scientists have known 

that azobenzene can switch 

between two shapes: 

one that bends back 

on itself and one that is 

long and straight. When 

high-energy ultraviolet 

light strikes azobenzene 

crystals, they tend to 

flex and deform as their 

many constituent atoms 

switch between the two shapes. Bartholomew’s 

research is taking this behavior of azobenzene to 

new heights. By creating larger molecules that contain 

multiple azobenzene components bonded at special angles, 

Bartholomew and her collaborators have produced a 

material that rotates around a central axis when 

exposed to visible light. Under a microscope, 

crystals of this material appear to continuously 


PHOTOGRAPHY BY HANNAH HAN 

roll like long axles, performing the kind of mechanical work that 

can generate electricity. Bartholomew hopes that this single-step 

conversion from solar energy to mechanical work will provide a 

starting point for more efficient solar power. 

Bartholomew also focuses on the kinds of stimuli-responsive 

changes that could pave the way for new nanoscale electronics. 

Like the azobenzene complexes, most of Bartholomew’s materials 

are crystalline in structure. Not only does the ordered pattern of 

crystals make for useful physical properties, but it also provides 

chemists with an insight into how and why stimuli responses occur. 

“If you ever need to find me, I’m probably trying out crystals on the 

diffractometer in the crystal lab,” Bartholomew said. “I love being 

able to make something, crystallize it, and then use those crystals 

to determine the three-dimensional structure of what I’ve made.” 

The research that Bartholomew has carried out in her first months 

as a professor has largely taken place thanks to generous colleagues 

who have lent their research spaces to her. After all, it takes time 

to acquire all the equipment necessary to run a cutting-edge 

chemistry lab. Bartholomew’s own space is just a short 

walk from the lab of chemistry professor Nilay 

Hazari, where Bartholomew conducted research 

as an undergraduate. Bartholomew explained 

that Hazari acts as a model for her now that 

she has the responsibility of mentoring. 

Bartholomew also credited Professor 

Kurt Zilm, the instructor of 

her undergraduate physical 

chemistry class, for showing 

her how to teach chemistry. 

“I think pedagogically I 

definitely took a lot from 

that class—hopefully. 

You’ll have to ask the 

graduate students in my 

class now if that’s the case, 

but that’s the aim anyway,” 

Bartholomew said. 

Now with the classroom 

and the lab under her control, 

Bartholomew is putting her own 

creativity to the test. Fortunately, 

Bartholomew has an endless stream of fresh 

ideas in her niche of synthetic chemistry. “I 

sit at home and think of new things we should 

try to make, and I have to sketch them out at 

like ten p.m. and send myself a weird email 

with two sentences of an idea,” Bartholomew 

said. To handle the strange world of molecular 

materials, there may be no better approach. ■ 


MEASURE FOR MEASURE 

BY HENRY CHEN 

IMAGE COURTESY OF MEASURE FOR MEASURE 

SCIENCE 

How would you rank the following: Friends, The Office, and Modern 

IN 

Family? How do you—and other people—differentiate between your 

favorite shows, books, and podcasts? Is there a universally defined 

scale? What are some factors we use to compare? These are all questions that 

“Measure for Measure” seeks to explore. 

Run by the organization Ministry of Ideas and co-hosted by Liya Rechtman 

and Andrew Middleton, “Measure for Measure” is a limited podcast series 

that investigates a different form of measurement in our daily lives. The 

nine episodes, which range from nine to twenty-five minutes in length, are 

perfect to squeeze in during a walk between classes. The podcast covers topics 

spanning the Scoville spice scale, used to measure the pungency of chili 

peppers, to star “heartbeats,” which are pulses that cause a star to expand and 

contract, leading to variations in brightness. Most importantly, each episode 

tries to answer the overarching question: why has measurement been crucial 

throughout human history? 

For example, in episode two, Rechtman talks about how the Talmud, a central 

Judaic text, contains a number of references to measurements, like how much 

matzah to eat during Passover, that were based on the size of other foods, like 

olives. Because olive sizes have varied over the centuries, many Jewish people 

today have tried to update the medieval measurement to determine how much 

matzah to eat. The story of the olive is one of unity across time—how even 

though Jewish people are separated from their ancestors by thousands of years, 

they can still celebrate in the same way, following similar cultural guidelines. 

Importantly, each episode presents a narrative about using measurement as a 

way for us to (re)connect with the rest of the world—both past and present. 

As I made my way through the series, it became clear where each of the cohosts’ 

passions came into the episodes. Rechtman is a Jewish climate activist, 

while Middleton is a cartographer and ocean enthusiast. As a result, each episode 

was a science lesson infused with niche, thoroughly interesting historical and 

cultural facts—an engaging format that sparks questions about the intersection 

between the humanities and science. For instance, in episode three, we learn about 

the Mohs scale for categorizing the hardness of rocks and how it was created by 

the Habsburg Empire to distinguish itself from competing empires and increase 

national unity. These stories reinforce the idea that measurement isn’t restricted 

to the International System of Units we use in chemistry class. Instead, it extends 

far beyond, into almost every facet of human life. 

At the end of the nine episodes, I still haven’t found a definitive scale to rank 

podcasts, but I have learned the importance of tools for measurement in our lives 

and how they turn a continuous reality with infinite possibilities into discrete 

categories—and maybe that’s the point. For its combination of historical facts, 

scientific trivia, and broad cultural trends, I’m placing “Measure for Measure” 

in the category of “highly recommended.” ■ 

T 


THE DARKNESS MANIFESTO 

You’ve probably flown over a city at night and noticed the bright glow of 

lights staring back at you through the airplane window. As intriguing 

and surreal as it feels to see such a sight, these lights are disrupting 

the behavioral patterns and circadian rhythms of many organisms across 

the globe, from insects and bats to bioluminescent creatures and humans. In 

his newly released book, The Darkness Manifesto, Johan Eklöf describes the 

myriad consequences related to light pollution and urges readers to defend 

the darkness. 

The majority of nature’s activities, such as mating and pollination, occur 

at night because eighty percent of all organisms are nocturnal. Humans are 

diurnal organisms (active during the day) and, as a result, have resorted 

to artificial light to extend our activities into the night. Eklöf echoes the 

claims that we have entered a new era: the Anthropocene, in which humans 

have had a critical impact on the Earth’s ecosystems. In particular, he argues 

that man-made sources of light are disrupting Earth’s natural rhythms by 

generating light pollution. 

Eklöf devotes several chapters to describing the ways in which light 

pollution has thrown off the reproductive cycles of organisms across the 

planet. For instance, he claims that the pollination rate of some plants like 

apple trees has slowed down because moths, which serve as pollinators, get 

easily confused by artificial sources of illumination. For animals like our 

beloved friend Nemo, the consequences of light pollution are as severe as eggs 

failing to hatch since clownfish larvae rely on the darkness to signal when it 

is time to break free from their sacs. Without complete darkness at night, the 

behavioral patterns of organisms are becoming increasingly out of tune, and 

as a result, the ecosystems they inhabit are being destroyed. 

But it isn’t just plants and animals that are affected. We humans are facing 

serious consequences as well. Because humans aren’t nocturnal, we rely on 

our natural sleep cycles to rest. But true rest is difficult to achieve when we are 

using our phones too late into the night. Blue light from our phones tricks our 

brains into thinking it is still daytime, so we produce insufficient levels of our 

natural sleep hormone, melatonin, making it difficult to fall asleep. Similarly, 

Eklöf states that people who work night shifts are at a higher risk of hormonal 

cancers such as breast and prostate cancer. We can prevent a multitude of 

THE 

SPOTLIGHT 

serious health conditions by restoring our natural circadian rhythms and 

avoiding light at night. 

In his manifesto at the end of the novel, Eklöf calls upon readers to cherish 

and learn more about the darkness due to its importance in our behavioral 

patterns. Some countries, like France, are already moving towards decreased use 

of artificial light at night, and Eklöf hopes that more countries will follow suit. 

“The darkness is not the world of humans. We’re only visitors,” Eklöf reminds 

readers. It’s not too late to change our habits and start protecting the darkness. ■ 

BY FAITH PENA 

IMAGE COURTESY OF WALLPAPER FLARE 



COUNTERPOINT 

QUANTUM 

BY MATTHEW DOBRE 

CRYPTOGRAPHY 

Encrypting data in holograms composed of corkscrews of light 

In 1933, Nobel Prize-winning chemist Sir William 

Bragg said, “Light brings us the news of the 

Universe.” Though it would take decades before 

scientists better understood the properties of light, 

researchers today are devising ways to utilize this 

resource to store information by uniting information 

theory and quantum mechanics, a subfield of physics 

that governs the behavior of photons, or light particles. 

Among the general public, anything that includes the 

word “quantum” elicits a degree of awe. Even Einstein 

was troubled by one of the theoretical implications of 

quantum mechanics, which he called “spooky action 

at a distance.” Today, Einstein’s boogeyman is called 

entanglement. When two particles are entangled, their 

quantum states, which may include properties like 

geometric orientation, angular momentum, and energy, 

are inextricably linked. A change in the state of one 

particle will immediately affect its twin. For example, 

consider a pair of entangled mittens: one is given to a 

lab assistant named Bob, and the other to his partner, 

Alice. No attempt is made to observe either mitten. Bob 

is then sent to a neighboring solar system. Up to this 

point, nobody in the universe knows the handedness of 

either Alice’s or Bob’s mittens. In fact, by the postulates 

of quantum mechanics, their handedness will be 

indeterminate until they are observed. If this experiment 

was repeated many times, it would reveal that when 

Alice observes her mitten, she will have a right-handed 

mitten half the time, and a left-handed mitten the other 

half. Eerily, Bob’s mitten will instantaneously acquire 

the opposite handedness, even though he’s two million 

light years away from Alice. 

These same principles of entanglement have been 

used to send data over thin air. In 2015, a research 

team in Vienna transmitted information by changing 

the relative angular momentum, or “twistiness,” of 

entangled pairs of photons. In quantum mechanics, 

angular momentum can only take on certain values 

called discrete quantities, separated by a constant ‘step 

size’. These entangled particles stored information by 

acting analogously to computer bits, which can only 

have a value of zero or one. In the experiment, each twist 

served as an alternative channel of communication, 

enabling ultra-high-speed data transmission. 

A group of physicists from the Beijing Institute of 

Technology (BIT) recently expanded on this research 

to create an unprecedented storage system. Instead of 

transmitting information via distinct light channels, 

they stored several unique data sets at a time by creating 

holograms made of entangled photon pairs. Though 

holograms seem to be a quintessential element of 

science fiction, they already have applications in 

everyday life. Used as a security feature in credit 

cards, passports, and banknotes, holograms are stacks 

of slightly misaligned images that are difficult for a 

computer to read. The physicists generated holograms 

made of twisted, entangled photon pairs by using 

β-barium borate crystals to manipulate the relative 

angular momentum between the particles, creating 

corkscrew patterns of light that resemble rotini pasta. 

To prove their setup worked, the researchers encoded 

words in the holograms and used twisted light to 

reconstruct the data by measuring the coincidence 

between the particles’ angular momentums. 

By increasing the number and diversity of twists 

in a single hologram, the system securely encrypted 

information since the odds of guessing the degree and 

direction of the twisted light’s path became very low. For 

instance, seven distinct twists, which is a relatively small 

system, led to millions of potential combinations. 

Many quantum technologies are sensitive to noise. 

However, the researchers asserted that entanglement 

can diminish the effect of classical noise sources, which 

include mechanical vibrations and thermal fluctuations. 

Thus, the decrypted output was of a higher quality 

compared to other similar systems. 

This technology, however, is still in its infancy. 

Utilizing six forms of entangled light, the group was 

able to decode an image of the acronym “BIT” by 

measuring the orbital angular momentum states of the 

particles over the course of twenty minutes, which is far 

from practical. Fortunately, the group is optimistic that 

these difficulties can be overcome with improvements 

in quantum technology. Though holographic data 

storage is still in a nascent stage, today’s scientists 

are utilizing techniques that the founders of modern 

physics laid the groundwork for—but may not have 

even understood. ■ 


Wrought into a cycle, 

carbon schleps from one stop 

to the next. 

Perhaps I recall it 

swept along the atmosphere, or 

gathered by the ground. 

But in this primordial painting, 

lumbering green bacteria 

nose for warmth in the ocean, 

their cellular frames tousling the tides. 

Eventually, they dissolve 

like salt, and carbon stretches 

down to retire under the sand. And in 

this dizzying deepsea, the muddy 

seafloor, slumbering beneath 

carbon’s gray lines like a shutter 

over the dark, unsheathes 

the largest passage. 

Slate-streaked rocks from the byway 

pull open their pores. Quietly, 

I watch as carbon rolls out 

toward the surface. 

PERI 

A CARBON SEA SCENE 

POEM AND ART BY 

SOPHIA ZHAO 

Artist’s Statement 

I wanted to convey research’s brilliant 

ability to shift preconceived notions 

through my poem, “A Carbon Sea Scene,” 

which offers a window into the findings 

of Lidya Tarhan, Jiyuan Wang, and their 

colleagues recently published in Nature. 

Inspired by their stepwise discovery of an 

abiotic deep-sea carbon sink, I aimed to 

depict my own gradual understanding of 

their research by crafting a metaphoric 

“painting” representative of their study. 

To draw out the beauty of the authors’ 

breakthrough, I relied on a poetic 

structure that “streche[d] down” the 

page—much like how the carbon cycle 

transcends depth—to emphasize the rich 

information that the deepest waters hold. 

Phrases such as “tousling the tides” and 

“seafloor, slumbering” maintain a steady 

rhythm that crescendos with “pull open 

their pores”—the most pivotal moment 

of this poem, and ultimately, the research 

of Tarhan, Wang, and their colleagues 

(Tracking Carbon’s Underwater Dive, pg. 

12-13). ■ 

METER 



Interested in getting involved with 

Yale Scientific 

for writing, production, web, 

business or outreach? 

Learn more at 

yalescientific.org/get-involved 

YSEA's 2023 Awardees for 

Outstanding Academic Achievement 

Aliza Fisher 

BS Mechanical Engineering 

Charlie Loitman 


Bryan Regan 


Evan Lipton 

BS Engineering Sciences - Mechanical 

Class of 2023 

Katerina Kargioti 

BS Applied Physics 

Jennifer Giampalmo 


Saachi Grewal 


Cooper Newsom 


Yu Jun Shen 

BS Electrical Engineering (ABET) 

Tamar Geller 

BS Electrical Engineering and Computer Science 

Ahtena Stenor (F22) 

Engineering Sciences - Chemical 

Sam Karp 


Laiba Akhtar 


Emily Quisenberry 

Chemical Engineering 

Hoang Le 


Pablo Garcia 


Thomas Blum 

BS Biomedical Engineering 

Sophie Naud 

BS/MS Biomedical Engineering 

Grayson Wagner 

BS Biomedical Engineering & Mechanical Engineering 

Tanya Jomaa 

BS Engineering Sciences – Electrical 

Michal Gerasimiuk 

Computer Science 

Lachlan Keller 

Computer Science & English 

Jessica Pan 

Computer Science & Economics 

Aidan Evan 

Computer Science & Philosophy

YSM Issue 96.2

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