YSM Issue 93.1

yalescientific

MARCH 2020 VOL. 93 NO. 1 | $6.99

12

AN UNSUNG HERO

COCKTAIL SHRIMP

7

OR COMMA SHRIMP?

HOW DNA

18

TRAVELS

FROM THE ARCHIVES...

22

YSM APRIL 1970, P. 21

SCIENCE VS.

31

THE APOCALYPSE


T A B L E O F

VOL. 93 ISSUE NO. 1

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

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15

18

20

22

An Unsung Hero

Christina Hijiya

COVER ARTICLE: When discussing immune responses to infection, researchers rarely consider

the role of the nervous system. Yale researchers have discovered a new link between the

immune system and intestinal neurons that is important in combatting infection.

Printing Skin

Matt Spero

Researchers at Yale University’s Department of Biomedical Engineering recently developed a vascularized

multilayered skin substitute which inoculates with immunodeficient mice when implanted.

How DNA Travels

Britt Bistis

Over thirty years of research on the enzyme RAG1-RAG2 recombinase culminates in characterization

of its evolutionary precursor. This provides insight into how the recombinase function evolved.

How Sun Damage Really Causes Cancer

Catherine Zheng

Researchers have long sought to figure out the causes behind different kinds of cancer in order

to better treat them. A group of researchers at Yale recently found a correlation between UV

radiation, the genetic damage it causes, and the possible effects it may have on skin cancer.

From the Archives

Book reviews published in an issue of the Yale Scientific from April 1970.

2 Yale Scientific Magazine March 2020 www.yalescientific.org


C O N T E N T S

4

6

23

30

32

34

Q&A

NEWS

FEATURE

SPECIALS

PROFILES

SCIENCE IN

THE SPOTLIGHT

How Does Sugar Affect Caffeine? • Anmei Little

What Was Mars’s Atmosphere Like? • Athena Stenor

Snowballing into a New Age • Nancy Lin

Our Real Carbon Footprint • Jerry Ruvalcaba

The Evolution of Sex • Tiger Zhang

Cocktail Shrimp or Comma Shrimp? • James Han

War on Anxiety • Beatriz Horta

Explaining Evolution • Katie Schlick

Put Down Your Drink • Cindy Kuang

Pregnancy and Cancer • Gonna Nwakudu

Uranium—A Promising Catalyst • Sydney Hirsch

Of Mice and Running Wheels • Alice Huang

The Microbial Clock • Siena Cizdziel

From Cold to Hot Tumors • Viola Kyoung A Lee

The Future of Data Storage is Hidden in Plain Sight • Nicholas Archambault

Counterpoint: Revisiting the Effects of Ocean Acidification

on Coral Reef Fish • Christopher Poston

Science vs. The Apocalypse: Robot Takeover • Leslie Gonzalez

Undergraduate: Maddy Bender (TD ‘20) • Stephanie Hu

Alumni Lauren Abendshien (BS ‘06, LAW ‘12) • Raquel Sequeira

The Story Collider • Nithyashri Baskaran

Infinite Powers • Yu Jun Shen

www.yalescientific.org

March 2020

Yale Scientific Magazine

3


A

HOW DOES SUGAR

AFFECT CAFFEINE?

By Anmei Little

Most undergraduates love the sleep-fighting powers

of coffee. For those of us who can’t take it black, sugar

is a must. However, recent research from Ilan Shumilin,

Christoph Allolio, and Daniel Harries at the Hebrew

University of Jerusalem may make you question if adding sugar

affects how coffee’s caffeine interacts with your body.

Caffeine is a hydrophobic—water-repelling—drug, so its

molecules clump together in water, like penguins huddling

together to avoid the cold. Compounds

&WHAT

called hydrotropes can

WAS MARS’S

reduce clumping by surrounding the drug molecules. As the

drug molecules spread out, they often function more efficiently. ATMOSPHERE LIKE?

Harries and colleagues noticed that sugar, originally thought to By Athena Stenor

function as a bitter taste-masker of caffeine, actually has a far more

unique effect. According to their findings, sugars increase the Over billions of

water solubility and concentration of single caffeine molecules, years, Mars transformed

while decreasing that of caffeine oligomers—multiple caffeine from a wet planet with a thick

molecules joined together. This preferential interaction defines

what is called a selective hydrotrope. “[Drug] aggregates don’t

have the right physiological impact that you would want them

to have. By adding a hydrotrope that is selective, you can pick

out the species that really does the job,” Harries said.

It is difficult to determine whether this alters how our bodies

respond to coffee. The effectiveness of caffeine monomers

compared to that of oligomers is not yet quantified.

Additionally, the sugar itself has energy-boosting effects

that have to be considered. Regardless of its end effect,

Qthe next time you sip on a latte, reflect on all the

interesting interactions taking place in your cup. ■

atmosphere to one characterized by

dry, cold terrain and a thin atmosphere.

One of NASA’s longstanding goals is to

understand how this happened. In a recent

paper in Science, NASA researchers working

on the Mars Atmosphere and Volatile Evolution

Mission (MAVEN) revealed that they did something

rare: they collected two missions’ worth of data on

Mars’s atmosphere for the price of one.

MAVEN was intended as a mission to collect data on

the current composition of Mars’s upper atmosphere

and characterize the escape of particles into space. By

repurposing the spacecraft’s mass spectrometer, which

separates particles by mass, NASA scientists were also able to

take comprehensive wind measurements, mapping the global

circulation patterns in the upper atmosphere of a planet

besides Earth for the very first time. They observed that

Mars’s circulation patterns were less complex than Earth’s,

with winds closely following the land surfaces below them.

The new global circulation data can also improve existing

models, an achievement made all the more groundbreaking

“because we got [the information] for free,” said Mehdi

Benna, the scientist who first suggested repurposing the

spectrometer.

Every NASA space mission is a feat of coordination.

Over several years, scientists, engineers, accountants,

and countless other professionals collaborate to

bring humanity one step closer to unfurling the

secrets of the cosmos. “I’m more in admiration

of the people who put the mission together

than anything else,” he said. Benna believes

that ultimately, MAVEN will serve as

a reminder of the magnitude of

human ingenuity. ■

4 Yale Scientific Magazine March 2020 www.yalescientific.org


The Editor-in-Chief Speaks

A NEW DECADE

With this issue, the Yale Scientific Magazine steps into a new decade. Through the

first and second World Wars, economic crises, and other epoch-making events, the

Yale Scientific has remained steadfast in its mission to feature scientific advancements,

especially those made at Yale, in an accessible way. We occupy the unique intersection

between research, education, and communication on campus, which is an important

one given Yale’s world-class status as both a research and liberal arts institution.

Our cover article this issue by Christina Hijiya reports on the key role of our enteric

(intestinal) nervous system in maintaining our immune defenses. This discovery

resulted from a collaboration between neurologists and immunologists, and testifies

both to nature’s complexity and to the value of cross-specialization research. More

than ever, our articles reflect how science at Yale has become integrated across fields

of study. For instance, the new Yale Science Building is designed to harbor a breadth

of disciplines under one roof; many research institutes on West Campus combine

expertise from varied disciplines to tackle important problems.

On the other hand, the overarching objective of science can sometimes be lost in

the minutiae of equations, graphs, and code. Many articles in this issue showcase

science that is relevant to our lives: how UV damage causes cancer on a molecular

level (p. 20), how exercise is related to lower risk for atherosclerosis (p. 24), a new way

to understand the evolution of sex (p. 7), and, for you coffee lovers, how adding sugar

into your coffee affects the way caffeine works (p. 4).

Science is also a human endeavor. We have as much to learn from the end results as

from the process of scientific discovery—the obstacles, detours, and eureka moments.

To this end, our new quarterly Meet the Profs! webinar series, in collaboration with

the Yale Science and Engineering Association and the Yale Alumni Association,

features researchers each issue with opportunities for live audience questions. To

make our content more accessible, we also maintain a strong online presence, with

exclusive content on our website and the Scope, the YSM’s blog that addresses the

implications of current events from interdisciplinary scientific perspectives, whether

it be the recent Australian wildfires or the COVID-19 outbreak.

As we begin this volume of YSM, we want to acknowledge the mentorship of the

previous masthead and everyone who has worked on the Yale Scientific. We are very

grateful for our strong partnership with the Yale Science and Engineering Association,

a stalwart supporter of our work to communicate science beyond campus, particularly

with alumni. Finally, thank you for reading the Yale Scientific. We look forward to

sharing with you the scientific advancements that will define the next decade.

ABOUT THE ART

Marcus Sak, Editor-in-Chief

Inspired by the enteric nervous

system’s synergy with immunological

cells to combat infection, this

cover depicts a vibrant spread of

the iconographic cells and tissues

battling disease. This process is

both fascinating and dramatic,

emphasizing the hallmark of

biology: a deep interconnectedness

between systems.

Sophia Zhao, Cover Artist

MASTHEAD

March 2020 VOL. 93 NO. 1

EDITORIAL BOARD

Editor-in-Chief

Managing Editors

News Editor

Features Editor

Articles Editor

Online Editors

Copy Editors

Scope Editors

PRODUCTION & DESIGN

Production Manager

Layout Editor

Art Editor

Cover Artist

Photography Editor

Webmasters

Social Media Coordinator

BUSINESS

Publisher

Operations Manager

Advertising Managers

OUTREACH

Synapse Presidents

Synapse Vice President

Outreach Coordinators

STAFF

Selma Abouneameh

Nicholas Archambault

Nithyashri Baskaran

Britt Bistis

Ashwin Chetty

Mila Colizza

Mehana Daftary

Chelsea Fang

Maya Geradi

Leslie Gonzalez

James Han

Christina Hijiya

Sydney Hirsch

Beatriz Horta

ADVISORY BOARD

Priyamvada Natarajan

Sandy Chang

Kurt Zilm, Chair

Fred Volkmar

Stanley Eisenstat

James Duncan

Stephen Stearns

Jakub Szefer

Werner Wolf

John Wettlaufer

William Summers

Scott Strobel

Robert Bazell

Craig Crews

Ayaska Fernando

Robert Cordova

Stephanie Hu

Alice Huang

Cindy Kuang

Viola (Kyoung A) Lee

Nancy Lin

Zihao Lin

Anmei Little

Medha Majety

Kiran Masroor

Adriana Maciel Metal

Tai Michaels

Gonna Nwakudu

Christopher Poston

Jerry Ruvalcaba

Marcus Sak

Kelly Farley

Anna Sun

Xiaoying Zheng

Hannah Ro

James Han

Tiffany Liao

Maria Fernanda Pacheco

Nithyashri Baskaran

Serena Thaw-Poon

Lorenzo Arvanitis

Brett Jennings

Antalique Tran

Julia Zheng

Ellie Gabriel

Sophia Zhao

Kate Kelly

Siena Cizdziel

Matt Tu

Megan He

Sebastian Tsai

Jenny Tan

Stephanie Hu

Cynthia Lin

Michelle Barsukov

Katherine Dai

Chelsea Wang

Nadean Alnajjar

Blake Bridge

Raquel Sequeira

Yu Jun Shen

Anasthasia Shilov

Matt Spero

Katrina Starbird

Audrey Steinkamp

Athena Stenor

Eva Syth

Saijel Verma

Georgia Woscoboinik

Tiger Zhang

Catherine Zheng

Astronomy

Biological and Biomedical Sciences

Chemistry

Child Study Center

Computer Science

Diagnostic Radiology

Ecology & Evolutionary Biology

Electrical Engineering

Emeritus

Geology & Geophysics

History of Science, Medicine, & Public Health

Molecular Biophysics & Biochemistry

Molecular, Cellular, & Developmental Biology

Molecular, Cellular, & Developmental Biology

Undergraduate Admissions

Yale Science & Engineering Association

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

Scientific Publications, Inc. Third class postage paid in New Haven, CT

06520. Non-profit postage permit number 01106 paid for May 19, 1927

under the act of August 1912. ISN:0091-287. We reserve the right to edit

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to edit letters before publication. Please send questions and comments to

yalescientific@yale.edu. Special thanks to Yale STC.


SNOWBALLING

INTO A NEW AGE

OUR REAL

CARBON

FOOTPRINT

IMAGE COURTESY OF ELLI E GABRIEL

IMAGE COURTESY OF ELLIE GABRIEL

HOW THE MELTWATER PUMP MAY

HAVE CONTRIBUTED TO EVOLUTION

BY NANCY LIN

How was earth able to sustain life during a major ice age known

as Snowball Earth? During that period, the planet was covered with

ice sheets for millions of years. This phenomenon resulted in ocean

anoxia, a phenomenon characterized by a lack of oxygen and an

increase in carbon dioxide. Oceanic anoxic events threaten the

survival of organisms that depend on oxygen to make energy in

cellular respiration.

Yale researchers Dan Asael and Noah J. Planavsky, with a

cohort of other scientists, discovered that oases beneath ice

sheets may have played a role in the preservation of life during

the ice age. The scientists discovered a pattern of iron formation

deposits in Sturtian glaciation, the first and longest Cryogenian

ice age. This is significant because iron formations indicate that

there was oxygen present in glaciomarine habitats throughout

that ice age, meaning it was possible that aerobic eukaryotes

lived in these environments. In this study, thin sections of iron

formations were polished and analyzed using light microscopy

and scanning electron microscopy. This petrographic analysis of

rocks allowed researchers to study the chemical compositions of

the minerals to monitor the evolution of chemical weathering. The

study concluded the existence of a glacial oxygen pump, which

transferred atmospheric oxygen from oxic subglacial meltwater to

anoxic oceans throughout the Sturtian glaciation. This allows us

to understand how organisms were able to survive in such harsh

climates. It also sheds light on the importance of the meltwater

oxygen pump in how we understand the evolution of life. ■

CONSIDERING THE ENVIRONMENT

IMPACT OF CAPITAL CONSUMPTION

BY JERRY RUVALCABA

It has become increasingly clear that greenhouse gas

emissions are contributing to an unsustainable future. In the

United States, environmentally extended input/output analysis

(EEIO) has been used to track environmental footprints, but

this method has its limitations. Yale PhD candidates Peter

Berrill, Reed Miller, and their research team have produced an

extension to the existing EEIO model for the US, facilitating a

more comprehensive analysis. In the current analysis model,

the environmental cost of long-term capital assets used to

produce certain goods are neglected, underestimating the

true environmental impact. To address this, the researchers

incorporated these neglected capital assets, drawing on data

from multiple government sources. Their new modified version

is called environmental life-cycle assessment. “It’s not physical

process data that is used, but rather economic transactions

between sectors in a given year,” Berrill said. Their analysis

reveals the importance of capital assets to environmental

footprints, and identifies which sectors are most affected. For

instance, housing, federal defense, state and local services, as

well as personal transport fuels were found to have the largest

overall footprints related to capital consumption. In the future,

their approach and data could be utilized to enable more

accurate calculations of footprints, and better estimation of

the impacts due to government regulations. This new model

could drastically shift the way in which environmental action is

taken, and serve as the catalyst for a cleaner future. ■

6 Yale Scientific Magazine March 2020 www.yalescientific.org


THE EVOLUTION

OF SEX

COCKTAIL SHRIMP

OR COMMA

SHRIMP?

IMAGE COURTESY OF ANMEI LITTLE

IMAGE COURTESY OF AUDREY STEINKAMP

EXPLAINING SAME-SEX

BEHAVIOR IN ANIMALS

BY TIGER ZHANG

Ever heard of damselflies engaging in same-sex behavior? It

turns out many different animals, from birds to mammals to

even insects, display same-sex behavior (SSB). However, since

SSB reduces the production of viable offspring, the behavior

is viewed as an evolutionary anomaly, raising important

questions about why SSB has persisted as a behavioral trait.

The most common perspective assumes that in animals,

different-sex behavior (DSB) was the baseline from which SSB

evolved, and that SSB has special evolutionary benefits that cause

it to be maintained. However, a recent study conducted at the Yale

School of Forestry and Environmental Studies (FES) reveals several

flaws in this model. Julia Monk, a graduate student at Yale FES and

one of the article’s key contributors, notes that “when evolutionary

biologists see a trait that’s widespread across evolutionary lineages,

we at least consider the idea that the trait is ancestral—so why

haven’t people considered that hypothesis for SSB?”

Monk and co-authors propose a shift in perspective, where

SSB and DSB evolved from a common ancestor that did not

distinguish the sex of its partners. “Compelling evidence suggests

the last common ancestor of sexually reproducing animals was

hermaphroditic, which, if true, would support our hypothesis,”

Monk said. In this regard, the SSB is not an anomaly, but an

important yet oft-misunderstood behavior with ancient origins.

Understanding the evolution of sex, “requires us to interrogate

assumptions that are perhaps colored by personal and cultural

perspectives,” Monk said. ■

WHAT ANCIENT SHRIMP CAN

TEACH US ABOUT EVOLUTION

BY JAMES HAN

Imagine mindlessly digging into the ground and suddenly

finding a fossil of a never-before-seen species. For some, such an

experience is merely a dream, but for Javier Luque, a postdoctoral

fellow at Yale’s Department of Geology and Geophysics, finding

such a fossil changed the direction of his career.

Though Luque knew he wanted to be a paleontologist since

elementary school, his love for fossils was solidified when

he unearthed a layer of sediment rich with a diverse range

of fossils while working on an undergraduate final project.

From the moment he laid eyes on the sediment, Luque knew

he wanted to devote his career to studying these crustaceans.

After joining the Smithsonian Tropical Research Institute as an

intern to conduct research full-time, Luque dived into the mysteries

of the fossils. In an article recently published in Proceedings of the

Royal Society, Luque describes a new, ancient cumacean, a type of

marine crustacean called Eobodotria muisca preserved in the rock.

While these cumaceans—sometimes called comma shrimp—may

not seem like much, Luque’s fossils are the first unambiguous fossils

of this group, and their ancient morphology is strikingly similar

that of the modern comma shrimp, bridging an evolutionary

gap of over 165 million years. Comparing such invariant species

to more volatile ones, such as the chimera crabs, described in a

previous Science Advances article, expands our understanding of

the diversity of evolutionary processes, especially in the tropics.

Luque plans to describe other exceptionally preserved species

also embedded in these rocks, and ultimately hopes to connect all

their stories to better understand the narrative of life. ■

www.yalescientific.org

March 2020

Yale Scientific Magazine

7


NEWS

Psychiatry

WAR ON

ANXIETY

Veterans’ Genomes

Used to Discover

Anxiety Genes

BY BEATRIZ HORTA

PHOTOGRAPH COURTESY OF MICHELLE BARSUKOV

Ever felt anxious before a test or important presentation? Maybe

it’s genetic. Researchers at the Yale School of Medicine and UC San

Diego partnered with the Department of Veterans Affairs to study

the genetic underpinnings of anxiety. The Million Veteran Program

(MVP) is a nationwide study by the US Department of Veterans

Affairs that collected varied biological data on US veterans to form

one of the world’s largest biobanks. Joel Gelernter and Daniel Levy,

from the Yale School of Medicine, made use of this large genetic

sample to understand the possible genetic causes for anxiety and

its coincidence with other syndromes, such as depression, PTSD,

and neuroticism.

Through a technique called a genome-wide association study

(GWAS), Gelernter and his team tested associations between

genetic markers and the traits of interest in around 200,000

participants from the MVP. GWAS was a revolutionary technique

that allowed the researchers to uncover biology without the need

for model organisms, such as mice. “What we hope to do is get at

new biology to understand the disorder and where it comes from,”

Gelernter said. GWAS looks at the difference in gene variation

between people who are affected and unaffected by the disorder,

and indicates the genetic markers that could be associated with it.

An association by GWAS suggests, but does not prove, a relation

to higher risk for the trait. In any case, this study is the largest

GWAS of anxiety traits ever conducted. For a sample size of this

magnitude, data collection and testing is challenging.

After testing over four million markers, they found several of

interest and continued further tests. The study found five genomewide

significant markers for European Americans and one for

African Americans. “During post-GWAS analyses, we were able to

dig deeply into the biology of the trait,” Gelernter said. They found

a gene locus that could also indicate vulnerability to other mental

disorders besides anxiety. This provides a possible explanation

for the coincidence with other symptoms. “When investigating

our GWAS results in the context of other samples, we were able

to replicate our findings, which is encouraging for future studies,”

Gelernter said. Comparing data from other studies which applied

GWAS to a smaller sample, the team was able to correlate many of

the markers they found. They were also hopeful that the estrogen

receptor gene, which they had specifically identified, would reveal

more about the nature of the syndrome. “We do not understand how

the estrogen receptor gene is involved in the development of anxiety

yet,” Gelernter said, “but it may help explain why anxiety disorders

are about twice as common in [biological] females as in males.”

The researchers have started thinking about improvements to the

study. “Even though the MVP sample has excellent representation

from non-European groups, we still have the most subjects [of]

European ancestry. Additionally, the MVP sample, like the veteran

population from which it is drawn, is mostly male,” Gelernter

said. He hopes that as the MVP sample increases, there will

be enough new subjects from different ancestry groups to be

able to draw specific conclusions from each group. This would

allow them to analyze in greater depth why some genetic risk

markers are significant only in African Americans or European

American subjects, explore different ethnic backgrounds that are

underrepresented in the sample, and dive deeper into the “clear sex

difference” in the development of anxiety disorder. Much is left to

be discovered regarding the different variations of genetic sources

for the disorder, but this will only be possible with greater absolute

numbers of subjects from each population group.

Gelernter is hopeful that in future studies, scientists will be able

to thoroughly examine the biology of the markers they found and

understand how they may cause anxiety or its co-occurring diseases.

Similar to the estrogen receptor gene, the researchers currently

know which gene loci are responsible for anxiety disorders,

but have not yet elucidated their mechanisms. Furthermore,

only about a third of individuals with anxiety disorders actually

receive treatment, which is one reason why more accessible and

effective pharmacotherapy development is so important. The study

could also lead to improved treatments by helping identify target

molecules for medicine. It points in a promising direction for the

treatment of anxiety, depression, PTSD and other syndromes,

eventually relying on more effective psychopharmacology. ■

8 Yale Scientific Magazine March 2020 www.yalescientific.org


Geology & Geophysics

NEWS

EXPLAINING

EXTINCTION

What Happened

Sixty-Six Million

Years Ago

IMAGE COURTESY OF FLICKR

BY KATIE SCHLICK

Geologists have long debated the primary driver of the mass

extinction which occurred more than sixty-six million years

ago. Until recently, the discussion had consistently bounced

between two dominant hypotheses: extraterrestrial impacts or

severe volcanic activity in the Deccan Province of India. New

research has presented a solid empirical case for the former—

the massive asteroid impact—as the definitive key motivator for

this fifth and most recent extinction event.

Doubt has remained for some time as to the precise

“mechanism” for mass ecosystem extinction. “This debate over

the driver of this K-Pg mass extinction is long-running and

contentious, and a lot of it focuses on the timing of the events

relative to the extinction,” said Sophie Westacott, Yale PhD

candidate for Geology and Geophysics. Scientists had agreed

that a massive meteorite made impact approximately sixty-six

million years ago at the Cretaceous-Paleogene (known as K-Pg)

boundary, as identified through a geological record in crust

and rock. The site is located under Mexico’s Yucatán Peninsula

near the town of Chicxulub and has been identified as the

crater that killed off all of the dinosaurs (except the birds) and

seventy-six percent of all species on Earth. According to the

study, the geological record holds signs of the crater’s impact,

including large tsunamis, earthquake-driven gravity flows,

and molten ejecta fallout, all of which would have contributed

to that terrestrial extinction. Still, it was previously unknown

what precise effect this impact had on marine life. Scientists

had found it plausible that oceanic organisms had already been

dying off prior to the Chicxulub impact event due to increased

volcanism in the presence of the Deccan volcanic traps.

Published last October in the Proceedings of the National

Academy of the Sciences, the groundbreaking study was coauthored

by fourteen researchers from institutions around the

United States—six with Yale affiliations—and Europe. This

collaboration allowed the researchers to pool resources and

technologies and ultimately undertake a suite of innovative

isotope and Earth system modeling methodologies. “The

paper uses empirical records from geochemical proxies

alongside computer models of the carbon cycle to help piece

together the cause of the mass extinction at the end of the

Cretaceous,” said Sofia Menemenlis (YC ’20), a major in

Geology and Geophysics. This combination of methods helped

the researchers empirically confirm and model the extinction

scenario and marine life recovery post-extinction.

The timing of ocean acidification processes, explored through

geochemistry, is key to understanding the extent of the effect that

the Chicxulub crater and underlying volcanism had in causing

the fifth extinction. The researchers’ first method, referred to

scientifically as a boron isotopic-pH proxy, was used on oceanic

foraminifera preserved at the K-Pg boundary to understand

the response of the marine world to the impact event. “Boron

isotopes are proxies that can tell us about the pH at the ocean’s

surface, which becomes more acidic as atmospheric carbon

dioxide increases,” Menemenlis said. The study measured boron

preserved in the marine creatures. After analyzing the samples

in a variety of temporal and geographical spaces, the researchers

did not find signs of ocean acidification until post-impact.

Instead, their results show that the ocean’s pH was primarily

“stable” at the end of the Cretaceous period and therefore likely

unaffected by volcanism. They suggest a rapid acidification

that led to near-immediate marine extinction directly after the

Chicxulub asteroid impact at the K-Pg. The GENIE, or Grid

Enable Earth System, model was used to visualize other changes

of the carbon cycle on pH levels. “The evidence for impact has

piled up in recent years, and there has been quite a bit that has

come out over the last few months—in fact, Science named

the collected evidence as one of its ‘breakthroughs of the year,’

calling it a ‘super-year’ for K-Pg work,” Westacott said. Together,

this recent research has unearthed a concrete truth explaining

the last extinction event this world has seen, sixty-six million

years later. The findings raise important questions about today’s

acidifying oceans and how marine life will manage in a sixth

anthropogenic extinction. ■

www.yalescientific.org

March 2020

Yale Scientific Magazine

9


NEWS

Psychiatry

PUT DOWN

YOUR DRINK

Investigating the Role of the

Kappa Opioid Receptor behind

Intense Alcohol Cravings

BY CINDY KUANG

Throughout history, alcohol has been enjoyed as a source of personal

relaxation, a delightful accompaniment to meals, and a social lubricant.

What happens when your preoccupation with alcohol becomes so intense

that it inhibits your daily activities, reaching “chronic disease” level?

The options are limited; only three pharmacotherapies are approved

by the US Food and Drug Administration for the treatment of alcohol

use disorder (AUD): disulfiram, acamprosate, and naltrexone. Of these,

naltrexone is the mildest: effective but without the harsh and nauseous

side-effects of disulfiram. However, naltrexone’s efficacy varies greatly

from person to person, and as a result, physicians hesitate to prescribe

naltrexone, doing so only thirteen percent of the time.

At Yale School of Medicine, Professor Evan D. Morris and

his team are collaborating with Professor Suchitra Krishnan-

Sarin’s team to investigate possible ways to moderate naltrexone

treatment such that higher therapeutic efficacy is achieved.

“How can we identify people where it will or won’t work?” asks

Bart de Laat, as associate research scientist at the Morris lab.

Normally, when we drink alcohol, our brain releases endorphins

and dynorphins, naturally produced proteins that then bind to opioid

receptors, producing the feelings of pleasure that are commonly

associated with intoxication. Naltrexone is a nonselective opioid

receptor antagonist, meaning it mimics the molecular structure of

these proteins and competes with them for binding to each of the

three opioid receptor subtypes: mu, delta, and kappa. By interrupting

the pathway in this way, naltrexone can decrease the pleasure

and rewarding effect of alcohol that promotes heavy drinking in

individuals. However, recent research suggests that the kappa

opioid receptor (KOR) plays a larger role in naltrexone’s effect than

previously thought. The lab hypothesized that KOR availability could

modify the effect of naltrexone, as well as feelings of cravings.

In this study, forty-eight non-treatment seeking heavy drinkers were

recruited to participate in two alcohol drinking paradigms (ADPs)

designed by Dr. Krishnan-Sarin and her team: one before naltrexone

administration and one after seven to eight days of naltrexone.

Subjects first consumed a priming alcohol drink, were monitored

for fifty minutes, then engaged in three self-administration periods.

Participants were offered a choice between consuming up to four of

PHOTOGRAPH COURTESY OF GRACE MACDONALD

their favorite mixed alcoholic drinks or receiving three dollars for

each drink declined. Afterwards, they were monitored overnight at the

Hospital Research Unit and discharged the next morning. Participants

received progressively stronger doses of naltrexone throughout the

next six days before finally repeating the ADP setup. By introducing

a small monetary reward each time that they declined a drink,

researchers set up what de Laat describes as a “dynamic changing of

relative value.” De Laat studies participants’ behaviors: “How high is

your craving? How high is your motivation? At what point is your

motivation for three dollars higher than your craving?” Their results

show that participants by-and-large reported lower levels of craving

and accepted fewer drinks in the second ADP post-naltrexone.

Participants also received two positron emission tomography (PET)

scans, one before naltrexone and one two hours after the last naltrexone

dose. Researchers injected a radioactive tracer that was designed to

attach to the endorphin associated with the KOR. By monitoring the

radioactive signal given off by the brain, they could quantify how many

kappa receptors were present and available throughout various brain

regions. Important findings arise from comparing the two PET scans:

“In the beginning you injected the tracer and it could just happily bind to

every receptor it finds—now it can’t because there is a lot of naltrexone

bound to the receptors, so it kind of has to look for a longer time, or it

doesn’t find a free spot at all,” de Laat said. With fewer kappa receptors

available, the radioactive signal coming from the brain decreases. The

larger this decrease is, the more effective naltrexone was in this individual.

Ultimately, researchers discovered a negative association between KOR

availability and efficacy of naltrexone. A greater reduction in drinking

was observed in individuals who had lower KOR availability, whereas

individuals with high levels of KOR throughout the brain received less

optimal results from naltrexone. This implicates KOR availability as a

crucial factor in continued craving after naltrexone therapy.

How can these results be utilized to predict naltrexone efficacy

in certain individuals on a large-scale? “With this information

you try to tease apart groups, or individuals, and that is the first

step to personalize medicine,” de Laat said. Correlating high or

low occupancy of KOR with efficacy of naltrexone paves way to

developing improved treatments for alcoholism. ■

10 Yale Scientific Magazine March 2020 www.yalescientific.org


Biomedical Engineering

NEWS

PREGNANCY

AND CANCER

The Evolutionary Link between

Embryo Implantation and

Tumor Growth

BY GONNA NWAKUDU

IMAGE COURTESY OF PEXELS.COM

When evolutionary biologist Günter Wagner was still a

child in Vienna, he watched a documentary on the Lipizzaner

horses used in his city’s famous horse-riding academy. As

he later learned, these horses were prone to developing

skin cancers similar to those found in humans. Unlike their

human counterparts, the Lipizzaner horses rarely died

from their cancers, instead living long lives with chronic

yet nonfatal disease. Wagner was fascinated by this breed’s

remarkable resistance to malignant cancers, and nearly fifty

years later, these performance horses would build the basis

for his research comparing cancer to pregnancy.

Leading a team of scientists funded by an National Institutes

of Health center grant, Wagner and systems biologist Andre

Levchenko sought to identify the relationship between the

method of embryo implantation within a species and the

relative vulnerability of that species to malignant cancers.

In placental mammals, embryos adheres to the uterine

walls in two major ways. For some species, such as dogs

and humans, the placenta embeds itself deep within the

uterus. For others, such as cows and horses, the placenta

remains on the surface of the uterus and is prevented from

moving deeper in the maternal tissue. Clinical data on

various mammals revealed a similar split when it comes to

cancer. While dogs and humans are more likely to have their

cancers spread throughout the body, cows and horses have

a lower likelihood of initial invasion and thus malignancy.

From their preliminary research, the team hypothesized

that hoofed animals may have developed through evolution

a method to both resist invasive embryo implantation and

limit the spread of cancer. “I started to make the connection

to this old memory about… Lipizzaner horses,” Wagner

said, “and I thought, maybe there’s a connection between the

ability of mothers to keep the placenta out and the ability of

the [species] to minimize the invasion of cancer cells.”

The team acquired samples of human and cow stroma, a

type of supportive tissue prevalent in the skin and the uteri

of both species. The scientists isolated the stromal tissues

www.yalescientific.org

in a culture with trophoblasts, the part of the embryo that

develops into the placenta, and melanoma cells, both known

for their invasive properties. Using the technique pioneered

by the Levchenko group, they found that, on average, bovine

tissue was more resistant invasion by the trophoblasts as well

as cancerous cells, compared to human tissue. To further

test the innate properties of the cow stroma, they sequenced

the RNA of the bovine and human tissue samples. The team

noticed that the cow cells showed a lower expression of genes

regulating the interactions between stroma and cancer cells,

allowing cows to better resist the spread of cancer. When

the same genes were turned off in another sample of human

stroma, the tissue was also able to resist melanoma invasion.

This led the team to believe the cow stroma evolved a

mechanism to better defend themselves against invasive cells.

Wagner and Levchenko aspire to change the public

perception of cancer and how to treat it. “I think there’s sort

of a split in the thinking about cancers,” Wagner said. “The

mainstream way that people think about the cancer is that

you want to target the cancer and… eliminate it or to kill it,

which, by its very nature, also breeds resistance.” As of now,

chemotherapy remains one of the most popular treatment

options for cancer. However, cancer cells may become

resistant to chemotherapy due to their rapid rate of mutation,

which means that patients thought to be in remission could

eventually return to a state of illness. The research led by

Wagner and Levchenko offers an alternative to treating

cancer, focusing more on managing cancer cells rather

than eradicating them. “In a way, this strategy is similar to

the recent revolutionary successes of immunotherapy, also

relying on immune cells in the organism,” Levchenko said,

“in this case the stromal cells can perhaps generate the key

to anti-cancer defense, as seen in other species.” As Wagner

puts it, “It’s a little bit less straightforward than just ‘Let’s kill

them all.’ But I think [ours] might be the more intelligent

strategy in the long run.” The research team is already one

step closer to developing better cancer management plans. ■

March 2020

Yale Scientific Magazine

11


AN

UNSUNG

How the

Enteric Nervous System

Fights Infection

BY CHRISTINA HIJIYA

PHOTOGRAPH COURTSEY OF WIKIPEDIA

A color-enhanced scanning electron micrograph

showing Salmonella Typhimurium (red) invading

cultured human cells.


When we think about infection, we think

about microscopic drama: the immune

system as the sole guardians of our bodies;

white blood cells as staunch defenders

against pathogenic invaders. However,

while B cells hunt for antigen-presenting

cells and phagocytes swallow bacteria

whole, there has been a hidden accomplice

in our bodies’ defense from infection: the

nerves that line our intestines.

In contrast to the bacteria-destroying

immune system, the intestines harbor

the peaceful presence of commensal

microflora, friendly gut bacteria that

help the body digest food and produce

vitamins. However, the amicable

existence of the gut microbiota survives

in delicate balance with the ruthless

elimination of pathogenic microbes. This

complex equilibrium relies on signaling

between cells in the immune system and

intestinal cells that form the mucosal

barrier, which segregates gut bacteria

from immune cells to avoid unnecessary

immune responses. Until now, scientists

have thought that these two cell types

were the lone ringleaders in the synthesis

of bactericidal proteins and molecules

that ward off threatening infections.

Earlier this month, scientists at the

Yale School of Medicine, in collaboration

with researchers at Harvard Medical

School, discovered that neurons in the

intestinal nervous system play a crucial

role in governing immune response in the

intestines. Moreover, they observed that

this antimicrobial function of intestinal

neurons was non-redundant, potentially

revealing another key player in the

struggle against infections of the intestine.

What is the Enteric Nervous System?

There are a variety of different cell types

in the intestine. Epithelial cells form the

border on the inside of your intestine

where food passes through, while outside

intestinal tissue contains immune cells that

detect and target bacteria. Until now, the

wide network of intestinal neurons, called

the enteric nervous system (ENS), was

often overlooked in gut immunity research.

“There are actually more neurons in your

intestine than in your brain, so it’s very

neuron-dense,” said Abigail Jarret, first

author of the paper and a PhD candidate

in Immunobiology at the Yale University

School of Medicine. The ENS has even

been described as a “second brain,” able to

operate autonomously and communicate

with the central nervous system to maintain

the delicate homeostasis in the intestine.

The brain-gut axis, referring to the

bidirectional link between the central

nervous system and the ENS, has recently

become a point of conversation in the

scientific community. Because of this,

scientists have also begun to explore how

the nervous system might influence the

immune response to infection.

“Up until maybe five years ago...

we [made] these beautiful plots of the

intestines, and we only put epithelial cells

there as a reference for the structure,

and ... everything else was immune cells

and empty space,” said Esen Sefik, a

postdoctoral fellow at the Yale School of

Medicine and a co-author of the paper.

But the community started to become

interested in that empty space. Over time,

scientific interest in the intestine grew

from epithelial cells to other cell types, and

more recently, cells in the nervous system.

This study stemmed from an interest in

understanding the relationship between

epithelial cells—the first line of defense

against infection by bacteria in the gut

microbiota—and neurons in the ENS.

Single Cytokine, Substantial Significance

Hirschsprung disease is a birth defect

characterized by missing nerves in the

intestine. A characteristic complication

of this disease is inflammative overgrowth

of the microbiota, which indicates a

profound relationship between the

ENS and the mucosal barrier. Taken

with studies reporting that the ENS

contributes to intestinal inflammation,

responds to pathogenic infection, and

triggers effects on bactericidal protein

secretions by epithelial cells, the authors

of the study were inspired to investigate

the role of the ENS in regulating mucosal

barrier immunity in the intestine.

In immune cells, cytokines act as

chemical messengers that cells use to talk to

each other, in order to regulate the immune

response. An especially important cytokine

in the separation of the gut microbiota

from the immune system is Interleukin-18

(IL-18), which helps to recruit other cells

to clear bacterial infection. Around thirty

years ago, scientists genetically modified

the first mouse that completely lacked

Chemical Biology

the ability to produce IL-18. When they

infected it with intestinal salmonella, it

died. Many years later, a version of the

mouse was created that lacked IL-18 only

in specific cells, allowing researchers to

further study the role of different cell types

in the immune response.

“I think people become very interested

in the function of a single cytokine or a

single molecule because as biologists, we

want to understand why we evolved to

have it,” Jarret said. “Why is lacking one

thing making these mice so sick? When

we had the ability to delete this gene in

specific cell populations, we could start

to understand the contribution of that

molecule from different cell sources.”

Secretion and Deletion

FOCUS

To further understand how different

sources of IL-18 contribute to protection

against infection, the researchers tested

mouse strains that lacked IL-18 in different

cell populations. They infected each strain

with Salmonella typhimurium, a bacterium

that targets the intestine, typically acquired

through contaminated water or food.

When mice could not produce IL-18 in

their epithelial and immune cells, they were

not susceptible to salmonella infection.

Surprisingly, when IL-18 was deleted from

intestinal neurons alone, mice displayed

symptoms associated with salmonella

infection. This helped the researchers

determine that neuronal IL-18 is essential

for preventing bacterial infection in a way

that epithelial and immune cells cannot.

Next, the researchers sought to

determine how IL-18 protected mice

from bacterial infection. The researchers

used RNA sequencing (RNA-Seq) to

understand whether unique cellular

signaling events were present in neuronal

IL-18-deficient mice compared to mice

that lacked the cytokine in other cell

types. Using RNA-Seq, the researchers

could determine the presence and

quantity of RNA in intestinal tissue

samples to analyze differences in gene

expression between different IL-18-

deficient mice strains. RNA-Seq revealed

that in mice lacking IL-18 secretion from

neurons, the expression of bactericidal

and antimicrobial genes that produce

proteins vital to the immune response

were exclusively reduced, rendering the

mice susceptible to salmonella infection.

www.yalescientific.org

March 2020

Yale Scientific Magazine

13


FOCUS

Chemical Biology

These proteins are called antimicrobial

proteins (AMPs), which constitute a

major arm of the innate immune system.

AMPs form holes in bacterial membrane,

which kills bacteria.

“So, IL-18 produced by neurons in the

intestine was instructing epithelial cells to

make these antimicrobial proteins,” Jarret

said, “and if you got rid of this IL-18, this

communication was no longer occurring,

and the mice didn’t have efficient

production of antimicrobial proteins and

became susceptible to infection.” Through

their experimentation with IL-18, the

researchers had described a novel pathway

of communication between neurons in

the intestine and epithelial cells.

Coexisting with Hostile Neighbors

The unearthing of this obscure

communicative route calls for a plethora

of further research. “Molecularly, we don’t

know how the IL-18 is being produced...

we’re really interested in what’s inducing

the IL-18 from neurons, and we think

it’s going to be something produced by

bacteria in our microbiota,” Jarret said.

Currently, there is scientific interest in what

molecules the microbiota produces and

how they can act as signals to other cells in

the intestine. She hopes that the study will

help people remember that considering

these non-classical immune cell subtypes

is still important in understanding the

immune response. “I think that’s really in

vogue right now,” Jarret said.

The findings of the study also provide novel

insights into diseases of the intestine. For

example, a number of disorders can induce

neuron death in the ENS, causing overgrowth

of bacteria or an imbalance in the number

or kinds of bacteria in the gut, leading to

impairment of the microbiota. This study

uncovers connections between neuronal

IL-18 secretion and the mucosal barrier’s

meticulously cultivated separation between

the immune system and gut microbiota.

“It could be really important in

maintaining that boundary and allowing us

to coexist with them,” Jarret said. Intestinal

diseases such as irritable bowel syndrome

and small intestinal bacteria overgrowth

can cause inflammation due to gut bacteria

migrating too close to epithelial cells.

ABOUT THE AUTHOR

This induces common symptoms such as

diarrhea, weight loss, and abdominal pain.

“It’s possible that in those circumstances,

if we could figure out a way to induce IL-

18 production in neurons that maybe

[we could increase] antimicrobial protein

production to help create space between

ourselves and bacteria,” Jarret said.

The study may also open new doors

to tackle antibiotic-resistant strains of

salmonella and other food-borne infections.

The rapid emergence of resistant bacteria has

been called one of the biggest threats to global

health by the WHO. Evolution of antibiotic

resistance in foodborne pathogens makes

infections from S. Typhimurium and E. coli

impossible to treat, adding to the 400,000

deaths worldwide caused by foodborne

disease each year. “[The study] might open up

new avenues of controlling these infections

rather than looking for an antibiotic that they

can get resistant to,” Sefik said.

Above all, the study reminds us of the

value in thinking more broadly about

the immune system and considering how

different systems are interacting within

the body. The unexpected findings of

the study demonstrate a relationship in

human physiology scientists have rarely

thought about before. Sefik emphasizes

the importance of partnerships between

different specializations in biological

research. “I love the collaborative aspect of

this [study]. I think that neuroscientists and

immunologists should start collaborating

more. It’s happening, but really only at

places like Yale,” Sefik said. Through such

interdisciplinary work, the scientific

community may finally be able to elucidate

modes of biological communication, like

those between the ENS and the immune

response, that could enable the treatment

of complex human disease. ■

ART BY ANASTHASIA SHILOV

CHRISTINA HIJIYA

CHRISTINA HIJIYA is a sophomore MCDB and HSHM major in Davenport College. In addition to

writing for YSM, she is a member of WORD: Performance Poetry at Yale, volunteers at HAVEN Free

Clinic, and teaches for Community Health Educators.

THE AUTHOR WOULD LIKE TO THANK Abigail Jarret and Esen Sefim for their time and thoughtful

comments about their research.

FURTHER READING

Flayer, Carmen H. and Caroline L. Sokol. 2020. “Nerves of Steel: How the Gut Nervous System Promotes

a Strong Barrier.” Cell 180 (1): 15-17. doi: 10.1016/j.cell.2019.12.021.

14 Yale Scientific Magazine March 2020 www.yalescientific.org


PRINTING SKIN

PRINTING SKIN

PRINTING SKIN

Biomedical Engineering

FOCUS

Biological tissue is extraordinarily

complex and diverse. Human skin, for

example, guards the muscles, bones,

and internal organs, protects the body

from pathogens, and prevents water

loss. Furthermore, skin is composed

of a variety of cell types, varies in

thickness throughout your body, and is

vascularized, or houses blood vessels.

Developing new biomedical devices to

promote regeneration and healing of

our skin tissue is one of the forefronts of

current medical research.

IMAGE COURTESY OF WIKIMEDIA COMMONS

A vascular graft, an example of a tissue

engineered construct.

The Growth of Tissue Engineering

No matter your interests, you’ve

likely encountered tissue engineering

in one form or another. Cell culturing,

nanofibers, computer aided design, and

bioartificial organs are all used in the

field known as “regenerative medicine,”

a term used synonymously with tissue

engineering. According to the National

Science Foundation, the origins of

tissue engineering

can be traced back

to the late twentieth

century. Since then, the

field has experienced

unprecedented growth,

the volume of research

in the area growing

throughout the 1990’s and

early twenty-first century.

At Yale University, the bulk of

tissue engineering research has emerged

from the biomedical engineering

department, founded in 2003 by W.

Mark Saltzman, Goizueta Foundation

Professor of Biomedical and Chemical

Engineering. Saltzman, in collaboration

with Jordan Pober, Bayer Professor of

Translational Medicine and Professor of

Immunobiology, and Pankaj Karande,

Professor of Chemical and Biological

Engineering at the Rensselaer Polytechnic

Institute (RPI), recently published a paper

in Tissue Engineering in which they

developed vascularized skin graft utilizing

human cells and 3D printing.

On the nature of this longstanding

collaboration, Saltzman said, “We wanted to

take [Pober’s] expertise on endothelial cells

and my expertise on making materials and

combine them to try and find new ways to

make vascular networks in living animals.

That collaboration has been going on for

fifteen years, and we’ve had a lot of success.

This is a start of something new, [and] I

think it will take advantage of everything

we’ve learned and push it in directions that

will become clinically useful.”

by matt spero • art by m il a

The primary author of the paper, Tânia

Baltazar, a Postdoctoral Associate in the

Pober laboratory, studied biology as an

undergraduate and went on to receive a

master’s degree in biotechnology and a

PhD in cell therapy and regenerative

medicine in Lisbon, Portugal.

“Tissue engineering is

very application

driven. You

develop a

c o

product, and

you can see the

impact on the lives

of patients,” Baltazar

said, on why she chose

to pursue the field. “I

wanted to work on a

project that would allow

me to focus on regenerative medicine.”

This project was supported by the

strong collaboration between the two

research groups, as immunology and

engineering came together to form a

single product greater than the sum of its

parts. Though Saltzman studied chemical

engineering as an undergraduate student,

he was not interested in ‘traditional’

chemical engineering careers, such as the

petroleum industry. Instead, he chose to

enroll in a program at MIT and Harvard

Medical School that combined medical

school training with engineering. “There

weren’t a lot of formal programs in

biomedical engineering at the time, but it

gave me a way to use these tools to solve

l i z z a

generating multilayered vascularized human skin grafts

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March 2020

Yale Scientific Magazine

15


FOCUS

Biomedical Engineering

PHOTOGRAPH COURTESY OF YIMING ZHANG

People featured are Professor Jordan Pober (left) and postdoc researcher Tânia Baltazar (right).

Also featured between the two is the 3D bioprinter used for their research in this article.

medical problems. It was a transformative

experience,” Saltzman said.

Different Cells with Different Needs

This study, which tackles the longstanding

problems of designing and

implementing skin replacements for the

treatment of cutaneous ulcers, originated

as a collaboration between RPI and Yale,

with a focus on in vivo studies within

living organisms. The project began

by considering why nonnative skin

replacements, which do not come from

the same individual, often fail to engraft

within their hosts. This is tied to the lack

of blood vessel connections—known as

vascularization—between the skin and

the implant. In other words, our body

takes too long to perfuse the grafted

skin with blood. Without of nutrients

and oxygen, the implanted skin sloughs

off. Adding a pre-vascularized bed into

the graft accelerates the process of blood

perfusion and enhances graft survival.

“This is a project where you have

to combine four different cell types

to construct a tissue, and each has

very different needs,” Baltazar said.

Tissue engineering skin substitutes

do exist, but tend to function simply

as “expensive bandages.” That is to

say, while they protect wounds, they

do not integrate and eventually lose

their adhesive properties, because they

cannot become vascularized like real

skin. One example of this kind of skin

graft is Apligraf TM . Another alternative

to using tissue engineered constructs

includes autologous grafting, a process

by which a patch of skin is removed

from elsewhere on the subject’s body

and placed over the wound. Considering

many patients suffering from cutaneous

ulcers also suffer from diabetes, this

method may result in a second injury the

patient’s body is unable to heal.

“There were several hurdles in this

project, some of which have been

solved, others that have only been

partially solved,” Saltzman said. While

Baltazar was working on the project

as a visiting scholar at RPI, one of the

greatest challenges was the logistics of

tissue storage and transport from RPI to

Yale, where it would be implanted into

the animal models. As they worked to

develop the vascularized grafts, they often

found that the constructs would contract

following their implantation. “We had

to consider the biophysics, making

changes in how we produce the implants

to minimize this effect,” Saltzman said.

Luckily, surgical techniques improved as

the project progressed. The research team

moved from in vitro experimentation

to implanting the grafts into mice,

solving this issue with a combination of

physiology and surgical techniques.

Bioprinting Skin Grafts

Utilizing 3D bioprinting technologies,

the team successfully produced a

skin graft that was both multilayered

and vascularized, culminating in two

3D bioprinted vascularized skin grafts . . . [have] the

potential to become an ‘off-the-shelf’ clinical product.

16 Yale Scientific Magazine March 2020 www.yalescientific.org


Biomedical Engineering

FOCUS

bioinks. The first dermal layer combines

human foreskin dermal fibroblasts,

which are the cells responsible for

synthesizing structural proteins such

as collagen, as well as endothelial

(skin) cells and placental pericytes,

cells which wrap around vascularized

endothelium, to form the dermal layer.

The second epidermal layer contains

human foreskin keratinocytes, cells

which produce keratin, which typically

composes hair, skin and nails. These

keratinocytes form a barrier, protecting

the vascularized tissue. Keratin itself is

particularly resistant to scratching and

tearing. After implanting these tissue

constructs into immunodeficient mice,

the micro vessels of the mouse inoculate

with the implant and fully perfuse after

about a month, ‘fusing’ the tissues from

the graft and mouse.

IMAGE COURTESY OF WIKIMEDIA COMMONS

Transmission electron microscope image of a

red blood cell within a capillary.

This process is carried out through

a relatively new technology known

as bioprinting. Various forms of

bioprinting, including inkjet and laser

assisted printing, can be used to better

replicate the minutiae of human skin,

such as the capillaries. Inkjet printers

are primarily used in large-scale

products, while laser assisted printing is

expensive and used for higher resolution

projects. Bioprinting can be thought

of as 3D printing using biomaterials,

where structures are formed layerby-layer

through the deposition of

bioinks—substances comprised of a

variety of living cell types. These bioinks

can mimic the extracellular matrix,

have the unique capability to be printed

as a filament, and can be produced at

relatively mild conditions.

Off-the-Shelf Product

Finding solutions to the issue of skin

ulcers is a crucial scientific endeavor,

with more than seven million Americans

suffering from the condition each year.

Many of these cases result from venous

stasis and diabetes, with patients often

lacking the ability to efficiently heal their

wounds. According to the researchers,

while the generation and implementation

of 3D bioprinted vascularized skin grafts

has yet to be fully realized, it has the

potential to become an ‘off-the-shelf ’

clinical product with wide availability to

the public.

To this end, the produced grafts must

be compatible with the host immune

systems. One method by which the

research team has worked to eliminate

immune responses to ‘non-self ’ antigens

from members of the same species is

the implementation of CRIPSR/Cas9

gene editing. Within human endothelial

cells, a gene codes for the expression of

the human leukocyte antigen, or HLA,

protein, which plays a critical role in

the regulation of the human immune

system. The research team has shown

it is possible to delete this section of

the genome within their skin grafts,

potentially leading to implants which

would altogether avoid host rejection.

“One of the challenges is compatibility:

ABOUT THE AUTHOR

PHOTOGRAPH COURTESY OF YIMING ZHANG

Close-up photograph of a CELLINK 3D printer.

is this skin graft going to be rejected

when we implant it into a patient.

We are trying to make a universal

immuno-evasive vascularized skin graft,

something you could have available as

an off-the-shelf product,” Baltazar said.

Saltzman, whose background is in

chemical engineering, is particularly

excited by the potential integration of

drug delivery systems into printed skin

grafts and has already worked alongside

Prober to publish works covering the

delivery of drugs such as VEGF, or

vascular endothelial growth factor.

“This 3D printing technique allows us

to apply drug delivery technologies, but

in a much more sophisticated way. We

can make gradients of delivery systems,

deliver the drugs in different patterns,

and I think that is going to be a very

powerful part of the approach worth

exploring,” Saltzman said. ■

MATT SPERO

MATT SPERO is a junior in Morse College pursuing the simultaneous B.S./M.S. degree in

Biomedical Engineering. In addition to writing for the YSM, he is the president of both Yale

Biomedical Engineering Society & Taps at Yale and is a researcher in the Human Nature Lab.

THE AUTHOR WOULD LIKE TO THANK Tânia Baltazar and W. Mark Saltzman for their time

and enthusiasm.

FURTHER READING

Baltazar, T., Merola, J., Catarino, C., Xie, C., Kirkiles-Smith, N., Lee, V., … Karande, P. (2019). Three

Dimensional Bioprinting of a Vascularized and Perfusable Skin Graft Using Human Keratinocytes,

Fibroblasts, Pericytes, and Endothelial Cells. Tissue Engineering. Advanced online publication.

www.yalescientific.org

March 2020

Yale Scientific Magazine

17


FOCUS

Molecular Biology

HOW DNA TRAVELS

30 YEARS OF EVOLUTIONARY GENETICS RESEARCH BY BRITT BISTIS

In the era of high-resolution imaging

and advanced computer modeling,

scientists can see a protein’s composition

in great detail and gain extensive

information about its properties and

function. However, these images are only

transient snapshots of the protein. To

better understand protein structure and

function, scientists have more recently

developed powerful experimental and

analytical tools can be applied to deduce a

protein’s provenance and fill in the rest of

the story. One such success story has been

reported by the Schatz Lab at the Yale

School of Medicine, which used cuttingedge

imaging technology to characterize

a Transib transposase protein to elucidate

the evolutionary story of a critical enzyme

in the vertebrate adaptive immune system.

DNA Recombination and Adaptive Immunity

David Schatz, Chair of Immunobiology

and Professor of Immunobiology and

Molecular Biophysics and Biochemistry at

Yale, pioneered his line of research in the

late 1980s as a graduate student at MIT

studying V(D)J recombination, a specific

type of DNA recombination event that

only occurs in developing B and T cells,

and is an integral part of the adaptive

immune system. “Antibody genes and T

cell receptor genes are in a disassembled

nonfunctional state in the germ line

chromosomes. Specifically, these genes

are broken up into small pieces of DNA

called V, D, and J and need to be brought

together by cutting and recombining the

chromosome,” Schatz said. Although the

existence of this type of recombination

was widely accepted in the 1980s, the

nature of the biomolecules carrying out

this process remained elusive.

To discover the genes responsible for

the recombination, Schatz took cells and

transferred large segments of chromosomal

DNA into them to see which combination

of DNAs would yield the recombination

reaction. After extensive experimentation,

Schatz discovered two genes: RAG1 and

RAG2, which together encode the RAG1-

RAG2 recombinase, an enzyme that

facilitates the cutting of the V, D, and J

DNA segments in V(D)J recombination.

“It was a major advancement for the field,”

Schatz said. “Once they were isolated, they

provided the critical tools for studying the

reaction and its regulation.”

18 Yale Scientific Magazine March 2020 www.yalescientific.org


Molecular Biology

FOCUS

In Vitro but not In Vivo

In 1998, Schatz and his research team

made a surprising discovery: recombinant

RAG1-RAG2 recombinase was able to

perform transposition of its encoding

genes in vitro. This immediately raised the

question: if this transposition reaction can

occur in a test tube, does it also occur in

the human body? It doesn’t, the lab quickly

discovered, and Schatz and his team spent

the next twenty years trying to learn

why. However, this discovery supported

another theory that is now well-accepted:

the precursors of these recombination

activating genes (RAG) were transposons,

which Schatz describes to be “rather selfish

genetic elements,” whose main functions

are to encode the machinery necessary for

replicating and translocating themselves.

By studying the structure of Transib,

a RAG1-like transposase that the lab

used as a proxy for how predecessors of

the RAG1-RAG2 recombinase, the lab

hoped to characterize the evolutionary

predecessor of the recombinase, and

discover how contemporary recombinase

evolved to inhibit their transposase activity

in vivo. Transib transposition and V(D)

J recombination begin in a similar fashion

to RAG1-RAG2 recombination. Either end

of a terminal inverted repeated (TIR), a

pattern of nucleotide bases which defines

the transposon region, is nicked and

excised. While in classic cut-and-paste

transposition the Transib transposase

facilitates the integration of the excised

fragment into another region of the

genome, in V(D)J recombination facilitated

by RAG1-RAG2 recombinase, the two ends

of the excised DNA fragment are ligated

together and form a circular piece of DNA.

Transib Transposition Snapshots

Chang Liu of the Schatz lab and Yang

Yang used X-ray crystallography and

cryo-electron microscopy, high-resolution

imaging techniques, to either crystallize

protein and associated DNA or to freeze

it to cryogenic temperatures, respectively,

before imaging using electron microscopy

techniques. The research team imaged at

multiple stages in the Transib transposition

reaction. Through this series of high

resolution “snapshots,” the lab was able to

piece together a highly dynamic 3D model

of this transposition reaction with a level of

detail and accuracy that has not been done

for any other such reaction before this point.

Binding of the transposase Transib to

its TIR DNA sequence causes the protein

to adopt a conformation that resembles

a butterfly with its wings extended with

the DNA in the position of the butterfly’s

antennas. The ‘wings’ of the enzyme fold

inward as the DNA is cleaved, after which

the wings then re-open. With this clear

understanding of the Transib transposition

mechanism, Schatz, Liu, and Yang were then

able to compare their proxy for the precursor

for the RAG1 subunit, which contains the

active site of the enzyme complex and the

DNA recognition sequence, of RAG1-RAG2

recombinase. Through this comparison

between the two mechanisms provided,

relevant information as to the evolution of

the recombinase can be discovered.

Evolution of RAG1 and Transib

Structurally, RAG1 and Transib

transposase are highly similar. The most

notable differences between the two

enzymes arise as a consequence of the

respective presence or absence of RAG2.

For instance, RAG1 possesses extra

motifs that are the binding site for the

RAG2 peptide. During formation of the

enzyme-DNA complex, the RAG1-RAG2

recombinase experiences less drastic

rotations of its chains than the Transib

enzyme as RAG2 interacts with the DNA,

forming stabilizing associations. RAG2

subsequently stabilizes the clamped

conformation of the enzyme about the

DNA, whereas Transib requires other

factors to facilitate the same effect. Further,

unlike the RAG1-RAG2 recombinase,

Transib interacts with the ends of excised

DNA, prohibiting the DNA from ligating

to itself as in RAG1-RAG2 recombinase

mediated V(D)J recombination.

The most significant difference between

the two enzymes is that Transib has a

critical target site-interaction loop that

is missing in the recombinase due to

the presence of the RAG2 subunit that

renders this loop obsolete. This and other

findings have led to the hypothesis that,

at some point in evolutionary history, a

Transib-like transposon gained the RAG2

gene, which would eventually developed

into the first RAG1-RAG2 transposon.

Twenty years after the discovery of

the transposition properties of RAG

recombinase in vitro, Schatz and his

research team pinpointed key amino

acids and protein domains whose loss

or gain drives the lack of transposition

of RAG recombinase in cells using

this concept of evolutionary genetics.

Schatz has dedicated his thirty-year

career to researching the mechanism

of V(D)J recombination and the RAG

recombinase. “We can now, in a detailed

molecular and structural manner, tell

the story of the evolutionary trajectory

of the RAG system to the present day.

While there are still some gaps in the

narrative, there is a sense of satisfaction

in having taken it this far,” Schatz said. ■

A R T B Y A N M E I L I T T L E

ABOUT THE AUTHOR

BRITT BISTIS

BRITT BISTIS is a junior majoring in Molecular Biophysics and Biochemistry. She works

in the Noonan lab working to characterize how mutations in high-confidence autism risk

genes alter the developmental trajectory of the brain and the regulatory mechanisms

through which this may occur. Outside of the lab, she can be found doing volunteer work in

programs for special needs students and science outreach programs or horseback riding.

THE AUTHOR WOULD LIKE TO THANK Professor David Schatz for his time and commitment

to his research.

Liu, C., Yang, Y., & Schatz, D. G. (2019). Structures of a RAG-like transposase during cutand-paste

transposition. Nature, 575, 540-544.

Huang, S., Tao, X., Yuan, S., Zhang, Y., Li, P., Beilinson, H. A., … Xu, A. (2016). Discovery of an

Active RAG Transposon Illuminates the Origins of V(D)J Recombination. Cell, 166, 102-14.

Carmona, L. M., Fugmann, S.D., & Schatz, D.G. (2016). Collaboration of RAG2 with RAG1-like

proteins during the evolution of V(D)J recombination. Genes & Development, 30, 909-17.

www.yalescientific.org

March 2020

Yale Scientific Magazine

19


FOCUS

Genetics

HOW SUN DAMAGE

BY CATHERINE

ZHENG

REALLY CAUSES CANCER

Cancer has been one of the hottest topics

in biomedical research in the past decades. In

lieu of a cure, researchers have been looking

for ways to treat or prevent it. Whilst cancers

can occur due to genetic factors, many of are

in fact caused by lifestyle-related factors. For

example, you’ve probably heard that things

like smoking and alcohol consumption

are common causes of cancer, and that

UV radiation from the sun can cause skin

cancer. This is because these environmental

factors either cause mutations or increase

the proliferation of cells, which increases the

probability of mutation.

PHOTOGRAPH COURTESY OF CRYSTAL XU

UV Radiation and DNA Mutation

A group of researchers at the Yale School

of Medicine have been looking into the

mechanism underlying how UV radiation

causes cancer. The effect of UV radiation

starts with a photon, a particle of energy,

striking the DNA. Of the four nucleotides that

comprise DNA, two of them, cytosine and

thymine, are known as pyrimidines. When

the photon hits two adjacent pyrimidines,

also known as a dipyrimidine or a PyPy site,

the pyrimidines join together, creating a

cyclobutane pyrimidine dimer (CPD).

Although UV radiation results in other

DNA damage as well, CPDs are the main

UV photoproducts and play the biggest role

in cancer. Some CPDs are cancer-causing

mutations in skin cells that activate or

inactivate signaling pathways. Starting from

one damaged cell, the process of DNA and

cell replication lead to the copying of DNA

containing CPDs, proliferating the mutant cell

to a group of abnormal clones. Unregulated

dividing cells a hallmark of cancer.

Mapping UV Hot Spots

Douglas Brash, one of the researchers

working on this project, was initially interested

in how DNA damage leads to cancer. After

looking into UV radiation, he decided to

explore whether there are specific parts of the

genome that are more correlated to disease

due to locally greater damage induction or

slower repair. Specifically, the group decided

to delve into mapping the genome for CPDs

and search for specific places most associated

with cancer as caused by UV radiation.

CPDs due to sun exposure usually occur

about once every ten thousand bases of

DNA, and occur in different places in each

cell. In mapping the genome, the group

found that there were certain spots, called

CPD hyperhotspots, that were approximately

a hundred times more likely than other

spots to be affected by UV radiation. These

hyperhotspots differed between cell types. In

addition, a lot of these hotspots were found

in promoters of genes as well, rather than just

the structural genes.

Six Years, Two Methods

Alejandro Garcia Ruiz exposing water to UV light in lieu of DNA from cells.

In total, the group’s development of

methods and research to make this discovery

took a lengthy six years. Eventually, they

came up with two methods that could be

used to understand the genome and analyze

the consequences in the overall scheme of

20 Yale Scientific Magazine March 2020 www.yalescientific.org


THE EFFECT OF UV RADIATION ON CANCER-CAUSING DNA MUTATIONS

UV radiation and cancer. The first step to

their analysis involves a method known as

adductSeq, which involves converting the

DNA damage caused by UV radiation into

something that can be understood by a highthroughput

DNA sequencing machine.

In adductSeq, a nick is first made in the

DNA right next to where the DNA damage

occurs (usually a CPD), using an enzyme

that’s normally involved in repairing the

damage. Then, a short segment of DNA,

called a linker, is ligated to the nick to tag

the CPD site to mark where the damage

occurred. Thus, the DNA can be sequenced

and analyzed for CPDs and other DNA

damage. The amount of damage is quantified

by counting the number of times the same

site appears in the experiment.

The next step to understanding the outcome

of DNA damage is the actual analysis of the

genome that has been sequenced. This is

done using a method called freqSeq, which

analyzes the data from the high-throughput

DNA sequencing machine and assesses its

validity. This is important because, when a

whole genome is being read and mapped,

there are often stochastic variations in

genome coverage and differences in DNA

loading and sequencing quality between

experiments. In addition, the reference

genome used for mapping the experiment’s

DNA fragments contains errors due to several

genome locations having been assigned

the same location. Since the experiment is

looking for CPDs (which are rare outliers

rather than consensus sequences), analyzing

the statistics behind the experiments is

incredibly important to quantifying the CPDs

in the genome and therefore to successfully

understanding the effects of UV radiation

and locating CPD hotspots.

Predicting Skin Cancer Risk

With these techniques, the researchers

were able to study the genome that resulted

from UV radiation and locate hyperhotspots.

One might expect that mutations are likely

to occur at these sites, and indeed mutations

occur there in melanoma skin cancers. In

addition, they found that, even in the absence

of UV, melanocytes also presented a certain

degree of lesions or DNA damage. This

is because, when melanin is synthesized,

highly reactive unpaired electrons known as

radicals are produced. These radicals often

create apurinic sites, sites at which a purine

(adenine or guanine) has been cleaved off

the DNA, leaving no base at all. The CPD

hotspots were distributed across genes and

gene-rich chromosomes. In addition, CPDs

were most commonly found at places where

certain transcription factors bind, which

corresponds to the effects CPDs have on

signaling pathways that make cells clone

more rapidly.

The ideal end goal of identifying cancer risk

factors and their effects on DNA is to develop

methods to predict cancer risk and prevent

cancer development. With skin cancer, for

example, Brash believes that, with the methods

outlined in their paper, the researchers could

determine someone’s risk of getting skin cancer

based on their previous sun exposure. Ideally,

this technology would ideally allow a family

physician to tell a patient that they ought to

be monitored by a dermatologist. This would

allow for better prevention methods, ranging

from simple things like applying sunscreen

to curative surgery. Skin cancers

start with early lesions which

can be cured, even for

melanoma, so catching them

early would allow doctors to

remove them, preventing the

cancer from spreading in the

first place.

More Mutations Moving Forward

While this research was primarily

done on fibroblasts and melanocytes,

the researchers who worked on this paper are

looking to apply the same concepts and methods

ABOUT THE AUTHOR

Genetics

to study different types of cells. Currently,

research is being done on keratinocytes and

whether the same patterns exist in those cells.

Being able to look at all the different types

of cells and map out the different spots for

DNA damage will further allow scientists to

understand the effect of UV radiation and other

factors on cells and cancer development.

Further research is also being done on rare

mutations, which are the end result of DNA

damage. Combined with the knowledge we

now have on the effect of UV radiation on

DNA, additional research on mutations could

lead to a conclusion about major risk factors of

cancer. This would further aid in the search for

more knowledge about the disease and ways to

prevent and treat it. ■

A R T B Y A N A S T H A S I A S H I L O V

CATHERINE ZHENG

CATHERINE ZHENG is a first-year student in Pauli Murray interested in studying either chemical

or biomedical engineering.

THE AUTHOR WOULD LIKE TO THANK Dr. Douglas Brash for discussing his research with her.

FOCUS

FURTHER READING

Mo, X., Preston, S., and Raza Zaidi, M. (2019). Chapter One - Macroenvironment-genemicroenvironment

interactions in ultraviolet radiation-induced melanomagenesis. Advances in

Cancer Research, 144, 1-54. doi: 10.1016/bs.acr.2019.03.008

Brash, D.E. (2015). Preprocancer: Normal skin harbors cancer-causing mutations. Science,

348(6237), 867-868. doi: 10.1126/science.aac4435

www.yalescientific.org

March 2020

Yale Scientific Magazine

21


FOCUS From the Archives: Yale Scientific Magazine, 44(7), 21

22 Yale Scientific Magazine March 2020 www.yalescientific.org


URANIUM —

A PROMISING CATALYST

Chemistry

FEATURE

THE HYDROGENATION OF

ETHENE TO ETHANE

BY SYDNEY HIRSCH

In chemical processes, catalysts are molecules that increase the rate

of a reaction. At the end of the reaction, the catalyst is replenished,

an important property that allows it to be used in a much smaller

amount than the reactants. Some of the most common catalysts in

organometallic chemistry are complexes of transition metals and

alkenes—carbon compounds containing one or more double bonds.

A team of scientists at the University of Sussex recently discovered

one such transition metal–alkene complex, specifically a uranium-

pentalene complex that catalyzes the hydrogenation (breaking of the

double bond) of ethene (C2H4) to ethane (C2H6). In the reaction of

this uranium(III) complex with ethene, the researchers observed the

formation of an intermediate ethene-bridged diuranium complex.

In this complex, ethene binds as a ligand to the uranium portion in

two places, and the oxidation state of uranium increases from +3 to

+4. The scientists were encouraged to investigate this phenomenon

further after noting that the intermediate complex reacted readily

with hydrogen gas to produce ethane. This means that uranium

could serve as a catalyst to convert ethene to ethane, a fundamental

but elusive reaction that, if done efficiently on an industrial scale,

could revolutionize how we make molecules.

“Uranium in the oxidation state +3 is known to be strongly

reducing for polar molecules such as carbon monoxide,” said Richard

Layfield, one of the researchers in the study. This means that uranium

in this form tends to give electrons to other molecules. However, due

to ethene’s low polarity, the researchers assumed that it would be a

poor acceptor of these electrons. To show that the uranium complex

did indeed fully convert ethene to ethane, they performed additional

characterization procedures to confirm the formation of ethane.

Natural bond orbital analysis, which looks at bonding orbitals with

the greatest electron density, confirmed the formal double reduction

of ethene, showing that the uranium-carbon bonding orbitals were

strongly polarized towards the carbon. The researchers were able

to determine that the C–C bonds of the ligand had lengthened

from 1.332 Angstroms, consistent with a double bond, to 1.497

Angstroms, consistent with a single bond. Therefore, it seemed as if

the alkene had been transformed into an alkane.

The scientists at Sussex first observed the formation of uranium

complex through nuclear magnetic resonance (NMR) spectroscopy,

which analyzes the components of mixtures. It does so by applying

an external magnetic field and recording the frequencies emitted

by the excited electrons; these various recorded emissions yield a

spectrum for analysis. The team observed features reminiscent of a

dinitrogen-bridged uranium complex, and from there predicted the

www.yalescientific.org

IMAGE COURTESY OF WIKIMEDIA COMMONS

Extracted uranium complex.

presence of the complex. After confirming the molecular structure

of the complex, the researchers ensured with solution NMR that the

solid-state structure did not change in solution. “When you have a

picture from the diffraction measurement, it is easy to be tempted

into thinking that the molecules look the same when you dissolve

them in solvent,” Layfield said. “Our chemical reactivity takes place

in solution, so if you make a reactivity prediction in solution based on

a solid-state structure you should gather evidence that the structure

is not significantly different in the two different environments.”

After a comprehensive analysis, the scientists were able to confirm

that this complex is a suitable catalyst for the formation of ethane

from ethene. Their research represents the first use of a uranium

catalyst for alkene-alkane conversion. The conversion of alkenes

into alkanes opens the door to the possibility of upgrading simple

molecules into valuable petrochemicals used as energy sources; for

instance, ethene specifically is often used in the making of plastics.

Also, depleted uranium is generally a feared element, stored in

expensive facilities, and only used for military or aircraft purposes.

According to Layfield, however, their discovery may allow for its

application in synthetic chemistry, slightly enabling the scaling-up

of uranium based-catalysts. ■

A piece of reduced uranium metal.

March 2020

IMAGE COURTESY OF THE AMES LABORATORY, USDOE

Yale Scientific Magazine

23


FEATURE

Systems Biology

OF MICE AND RUNNING WHEELS

physical activity mediates the risk for atherosclerosis

BY ALICE HUANG

Most would consider it common knowledge that exercise

enhances physical health and that an active lifestyle reduces risk

of heart disease. However, few have been able to demonstrate, on a

cellular level, the mechanisms of this relationship between exercise

and heart health. This curious ambiguity led Matthias Nahrendorf

and his research group at Massachusetts General Hospital

and Harvard University in pursuit of answers. Nahrendorf ’s

group, which studies the interaction between the immune and

cardiovascular systems and their subsequent connection to

cardiovascular diseases (CVDs), demonstrated that reduced

production of inflammatory cytokines and leukocytes is the link

between voluntary exercise and improved cardiovascular health.

According to David Rohde, a postdoctoral researcher in

Nahrendorf ’s lab, and Vanessa Frodermann, a lead author of

this publication, researchers who used mice in previous studies

targeting the effects of physical exercise on heart health often

found increased leukocyte production. In order to convince

the mice to exercise, the scientists subjected mice to high-stress

scenarios, such as forcing them to run with electric shocks for

long periods of time. Such stressful and high intensity practices

may have wiped out any beneficial effects of exercise.

Therefore, the Nahrendorf study emphasizes voluntary

exercise. “We put running wheels into cages, and the mice

run about seven to eight miles each day,” Rohde said. Because

this behavior is, surprisingly, voluntary—due to the natural

tendency of the mice to run in the wild—they do not experience

the detrimental side effects of stress, and the Nahrendorf lab

was able to collect concrete evidence that physical activity

indeed decreases the production of inflammatory leukocytes.

When researchers compared the proliferation of cells between

exercising and sedentary mice, they discovered that voluntary

exercise promotes hematopoietic stem and progenitor cell (HSPC)

quiescence. HSPCs are stem cells that normally differentiate

into blood cells. In exercising mice, HSPCs proliferated less

and showed a decreased rate of leukocyte—a type of white

blood cell—production. Additionally, these mice exhibited

reduced body fat, which resulted in lower adipose expression

of the hormone leptin. The bone marrow of the exercising mice

expressed higher levels of genes that promote HSPC quiescence

and retention. To further investigate this correlation between

leptin and HSPC quiescence, researchers elevated the levels

of leptin in exercising mice to those in sedentary mice and

observed an increase in inflammatory leukocytes and a decline

in quiescence gene expression. In contrast, neutralizing the

leptin hormone resulted in decreased production of blood cells.

The study found that voluntary exercise not only decreased the

risk of CVD in exercising mice during the period of daily exercise,

but also induced changes that lasted weeks after the running wheels

were withdrawn. These epigenetic changes are a type of DNA

ART BY ANTALIQUE TRAN

modification that affects the activity of genes. Researchers proved

the existence of these epigenetics changes by transplanting LSK cells

(cell population derived from HSPCs) into irradiated sedentary

mice, which resulted in 1.8-fold more circulating leukocytes than

transplants with the same cells obtained from exercising mice.

This indication that exercise has longer-lasting effects on HSPC

differentiation than leptin was attributed to the discovery of

reduced DNA accessibility at certain promoter regions associated

with transcription and stem cell proliferation in exercising mice.

Because these regions also control the cell cycle, nucleosome

organization and mRNA processing, these mice maintained these

benefits of exercise for up to six weeks after cessation of exercise.

After studying mice, the researchers then examined the

association between exercise and plasma leptin levels or

white blood cell counts in more than five thousand study

participants. Blood levels of leptin and leukocyte numbers

were lowest in participants who exercised either four to six

times or two to five hours a week, with less exercise time

resulting in suboptimal effects and more time resulting in

potentially harmful effects on overworked muscles.

In the long run, this study may enable a new

pharmacological approach to improve heart health.

Considering the pathway and mechanisms the researchers

uncovered, the researchers hope to develop a drug that mimics the

effects of exercise, an especially encouraging prospect for older

patients and those who are unable to adhere to physically active

lifestyles. The complexity of this project lies in the specificity of

targeting the discovered mechanism. “While we have figured

out the main mechanism, it is much more difficult to target that

mechanism,” Rohde said. “Any target has to be very specific, so

we are now in the process of screening different cell types.”

Despite advances in medicine, cases of atherosclerosis

are steadily rising. This global

epidemic is exacerbated by

increasingly unhealthy

diets and lifestyles. In

such a context, the

development of

a drug that can

confer the benefits

of exercise

could contribute

significantly to

improving global

health. ■

24 Yale Scientific Magazine March 2020 www.yalescientific.org


THE

Ecology

FEATURE

MICROBIAL CL CK

DIVERSE AIRBORNE MICROBIOTA FOLLOW A DIEL CYCLE

BY SIENA CIZDZIEL

An aerial view of the gardens of Singapore.

IMAGE COURTESY OF PIXABAY

The world is teeming with microorganisms in the soil, water,

and even air. However, the study of the atmospheric microbial

ecosystem has long been outshone by research into the Earth’s

diverse terrestrial, aquatic, and human microbiomes. At the

Singapore Center for Environmental Life Sciences Engineering

at Nanyang Technological University, researchers discovered an

ecosystem of microorganisms in Singapore’s tropical air that rivals

the diversity and complexity of the Earth’s other ecosystems.

The next-generation sequencing (NGS) revolution, which

began in 2005, demonstrated the ease of directly sequencing

DNA from the environment without the need for cloning or

growing it in a lab. Stephan Schuster, a professor at Nanyang

Technological University, was an early pioneer of nextgeneration

sequencing at Pennsylvania State University. “With

next-generation sequencing, it suddenly became possible to

produce genomic data so cheaply and so quickly that you could

do...projects that were unthinkable before,” Schuster said.

Before NGS, scientists could only sequence the DNA of a

miniscule fraction of the microbial world that could be cultivated

in a laboratory. NGS opened up the microbial world for study by

allowing direct DNA sequencing from the environment, but the

atmosphere was still out of reach. Only with an industry-sized

air sampler, massive amounts of air, and months of analysis

could scientists attempt to analyze the genome of a single cell in

the atmosphere. To increase efficiency and reduce unintended

bacteria growth on biomass filters, Schuster and his colleagues

developed an approach that could reduce the air sampling time

from months to days, and ultimately to fifteen minutes. In this

study, the researchers took air samples every two hours for five

days in a row—this was a frequency and precision of sampling

that had never before been possible. They called their new

approach the “ultra-low biomass pipeline.”

After analyzing 795 metagenomes from the atmosphere, the

scientists discovered something incredible. During each 24-

hour period, the atmosphere cycled through numerous different

species and numbers of microorganisms. Microbe communities

remained stable over weeks and months, but during the span of

a day, they fluctuated significantly. Schuster and his colleagues

found that they could isolate a microbial community and predict

with strong accuracy the exact time of day the sample had been

taken. The differences in microbial communities changed even

more drastically between day and night. “If you want to put

your finger on the pulse, the heart rate, of the planet, you can

do this by sequencing the organisms that are in the air. This

rhythm—the pulse—that’s the diel cycle,” Schuster said.

Researchers found that microbial communities responded

to environmental factors as well, including carbon dioxide,

temperature, and humidity levels. Schuster believes that these

communities could have applications as biological sensors; for

example, researchers could find carbon dioxide levels in the past

through microbial archives in sediments and geological layers.

The temporal study of the atmosphere was just the first

step. Schuster is now in the process of studying the variation

of microbial communities with more breadth and depth: how

will microbial communities change over different climates and

atmospheric levels? “Whatever work has been done over the

two decades in the ocean in trying to find out how the marine

microbial systems are organized, we are doing the same for

the air. Because of the throughput in technology and the level

of automation, we can do this much faster than what has been

done in the ocean,” Schuster said.

This potential for efficient data collection and analysis has

exciting implications, particularly for respiratory health. For

instance, concentrations of mold in buildings prevalent with

sick building syndrome can be more accurately examined and

quantified. Air quality standards for industrial law can begin to

encompass the biological content of air (e.g. microorganisms

and bioaerosols) in addition to its physical and chemical

characteristics. Currently, the researchers are working with

infectious disease hospitals in China to monitor the spread

of the airborne coronavirus pathogen. Monitoring the safety

of the air in hospitals or isolation wards is vital to keeping

medical personnel safe from the disease.

All in all, examining the living organisms in our atmosphere

is crucial to maintaining healthy and breathable air. “You have

a choice not to drink water, you have a choice not to eat, but

you do not have a choice to breathe,” Schuster said. ■

www.yalescientific.org

March 2020

Yale Scientific Magazine

25

W


FEATURE

Cancer Biology

BY VIOLA KYOUNG A LEE

FROM COLD

T

The ability to harness the body’s

immune system to fight cancer has

transformed medicine in recent years. A

new study from the Zloza research group

at the The State University of New Jersey

suggests that we may be able to use the

flu vaccine to improve patient outcomes

in cancer, potentially saving millions

of lives and tremendously reducing the

financial burden of cancer patients.

Oncologists call a tumor “cold” when

there are very few immune cells infiltrating

the tumor, and “hot” when the tumor

is characterized by significant immune

cell infiltration. Cancer patients whose

treatment regimens are unsuccessful

often have cold tumors. Even with novel

therapies such as immune checkpoint

inhibitors that allow immune cells to

engage in antitumor activity, patients with

cold tumors simply do not have enough

immune cells at the tumor site for the

checkpoint inhibitors to make tangible

impacts. Because immune cells’ migration

to the tumor site is highly correlated with

the patient’s clinical outcomes, developing

an effective method to induce immune cell

migration to the tumor site is absolutely

critical to the advancement of immunooncology

therapies.

Another challenge of cancer

immunotherapy is its affordability.

Current estimates of immuno-oncology

drug costs are about $270,000 per

patient, an expense that is burdensome—

if not unaffordable—for many patients.

The possibility of injecting the fifteendollar

seasonal flu vaccine to transform

“cold” tumors unresponsive to treatment

regimens to “hot” tumors could

transform both the accessibility and

efficacy of cancer therapy. Vaccination

is an old idea in medicine, dating

back to over a hundred years ago, but

using FDA-approved vaccines against

pathogens has never been suggested as a

method for enhancing the body’s ability

to fight cancer, until now.

When Andrew Zloza, the principal

investigator of this study, was a

postdoctoral associate in Chicago

studying tumor immunology, he

recognized an increasing number of

epidemiological studies showing that

patients with an HIV infection developed

more cancers and had less favorable

outcomes. This was happening even when

the patients were treated for HIV and

their immune system was able to prevent

AIDS-defining infections. Hypothesizing

that there was some connection between

the immune system having to fight foreign

pathogens and cancer at the same time,

Zloza and his group began investigating

the interference of foreign infections with

the body’s ability to fight tumors.

“When the body has two things to

fight, the immune system sends most of

its resources to fight the greater danger,”

Zloza said. “And when there is an infection

like HIV or influenza in a cancer patient,

the immune system appears to see the

infection as a greater danger than the

tumor.” This results in fewer immune

cells infiltrating the patient’s tumor, and a

greater number sent to fight the infection

elsewhere in the body. The researchers

wondered how the body would respond

if the infection was at the same site of the

tumor. According to their hypothesis, the

immune cells might migrate to the tumor

to fight the infection. This might serve as

a way to draw the attention of the immune

system to a cancer patient’s tumor.

Zloza’s group tried injecting live influenza

virus in the tumors of mice with melanoma.

But it didn’t work—live influenza virus

injections did not induce immune cells

to migrate to the tumor site or cause the

tumor to shrink. So, what had gone wrong?

It turns out that live viruses are limited

to specific sites of infection. Because the

live influenza virus infects the lungs, but

not the skin, the injection of live influenza

virus to tumors of the skin of mice was not

going to infect the tumor, and thus could

not induce immune cells to migrate to

the tumor. Instead, the researchers came

up with a new approach: to inactivate the

influenza virus with heat or chemicals, then

combating

cancer

26 Yale Scientific Magazine March 2020 www.yalescientific.org


Cancer Biology

FEATURE

O

HOT TUMORS

ART BY SOPHIA ZHAO

with the flu vaccine

www.yalescientific.org

introduce the inactivated influenza viral

components to the tumor. This approach

could circumvent the problem of having to

infect the skin tumor with live influenza.

The easiest way to obtain large quantities of

inactivated influenza virus that is cheap and

commercially available was the seasonal flu

vaccine, a concoction of inactivated strains

of influenza virus. They set out to test their

hypothesis that the tumor site-directed

injection of the flu vaccine could stimulate

antitumor activity of immune cells.

Zloza’s group used two types of

commercially available mouse cancer

models—melanoma and breast cancer—

in addition to generating their own

mouse model where immune cells and

tumor tissue from the same patient

were transplanted into a mouse that

does not have an immune system of its

own. They call this model AIR-PDX,

or autologous immune reconstituted

patient-derived xenograft. The AIR-

PDX model, according to Zloza,

allowed the researchers to model the

patient’s immune system in these mice

as accurately as possible, especially

compared to observing the mouse’s

immune cells’ response to mouse tumors.

“The PDX mouse models are as close as

we can get to modeling human immune

cells’ response to human tumors. We

were essentially recreating the patient’s

immune system in these mice,” he said.

Following the injection of the flu vaccine,

the researchers evaluated the efficacy of their

method by measuring immune cell infiltration

at the tumor site as well as tumor size. “We

evaluated immune cell infiltration using flow

cytometry. We would take a biopsy of the

tumor, then dissociate the tumor into single

cells, stain with antibodies against different

immune cell proteins to visualize how many

immune cells were infiltrating the tumor, as

well as which specific subtypes of immune

cells were there,” Zloza said. They obtained

a very exciting finding—after injecting the

flu vaccine at the tumor site, previously ‘cold’

tumors went from having no immune cell

infiltration to being highly infiltrated.

After verifying that the flu shot was

in fact responsible for the antitumor

immune response, Zloza’s group

then injected the flu shot in mice

in conjunction with an antitumor

immunotherapy, expecting that the

antitumor effect would be further

enhanced. In mice with intratumoral

injection of the flu vaccine, they

administered an immune checkpoint

inhibitor—a class of therapeutics that

reverses tumoral suppression of the

immune system by releasing the breaks

on the immune system put in place by

the tumor. As expected, the addition

of the immune checkpoint inhibitor

increased the antitumor response and

caused more tumor shrinkage.

Interestingly, in mice with multiple

tumors, injecting the flu vaccine at one of

the tumor sites appeared to result in tumor

shrinkage in other tumors that were not

injected. This suggested that artificially

targeting one tumor apparently directed

the immune system to all the tumors. Even

better, the injection of the flu vaccine at the

tumor site also protected the mice against

live lung influenza infections, exerting a

dual protective function combating both

influenza and tumor progression.

“If you can put a needle into something

to take something out, like a biopsy, for

example, then you can also put a needle

into something to put something in, say to

inject the flu vaccine. Any tumor that can

be biopsied can be injected with the flu

vaccine, which makes this a highly feasible

treatment option for patients,” Zloza said.

The next steps in advancing the flu

vaccine for oncology applications will

entail receiving approval and funding for

clinical trials. While clinical trials take

eight to ten years on average to receive FDA

approval for a treatment, the researchers

expect that receiving approval for this

application could be expedited. After all,

the flu vaccine is already FDA-approved,

and the objective is to simply repurpose it

for cancer patients. The goal, Zloza says, is

to get this to patients as soon as possible. ■

March 2020

Yale Scientific Magazine

27


FEATURE

Biotechnology

IS

THE HIDDEN FUTURE OF IN DATA PLAIN STORAGE SIGHT

of using DNA as a medium

for information storage within

inanimate objects.

The rapidly expanding field of

DNA data storage, dubbed “DNA-ofthings”

(DoT), has important implications

for industry, specifically digital storage. As

social reliance on digital systems mounts

rapidly, current storage architectures such

as hard drives are becoming constrained by

the physical limitations of their shapes and

sizes. DNA offers transformative advantages

as a storage medium with its capacity to

store data at unparalleled densities without

degrading, as well as its ability to adopt any

conceivable shape through DoT engineering.

If properly protected, DNA can withstand

both environmental and artificial stresses,

allowing information to potentially be

“cold-stored” for thousands of years. That

level of structural integrity combined with a

superior storage density of up to 455 exabytes

per gram, where one exabyte equals one

thousand petabytes. This value outstrips the

currently most advanced hard drive storage

method by 215 orders of magnitude, and

renders DoT an innovation that could define

the next decade of information technology.

Sequencing the genetic code of an object

BY NICHOLAS ARCHAMBAULT

ART BY ZIHAO LIN

A petabyte is the equivalent of 10 15

bytes of digital information, one billion

times larger than the standard megabyte

that composes common digital files

like an audio clip or high-resolution

picture. Approximately ten billion users’

photos that comprise Facebook’s storage

warehouses amount to 1.8 petabytes of

data. The entire Netflix library of raw

video content totals around 3.1 petabytes.

Imagine being able to carry petabytes

worth of information on a device that fits

in your pocket. Though it may sound farfetched,

compact portability of massive

amounts of data is closer to becoming a

reality than ever before, thanks to recent

work from the bioengineering lab of Robert

Grass at ETH Zurich. The researchers’

breakthrough paper, published last

December, demonstrates the first examples

Interest in DoT’s largely untapped potential

led Grass and his collaborator Yaniv Erlich,

Professor of Computer Science at Columbia

University and Chief Science Officer of the

online genealogy platform MyHeritage,

to test DNA’s stability as a vehicle for

information. “Erlich’s idea was to put not just

a trackable barcode but ‘real information’ into

materials—ideally something connected to

the object itself,” Grass said. They settled on

3D printing a Stanford bunny—a common

graphical quality test object—embedded

with its own blueprint.

First, the 45-kilobyte file detailing the

bunny’s creation was converted from

binary digital format to a DNA sequence.

28 Yale Scientific Magazine March 2020

www.yalescientific.org


Biotechnology

FEATURE

To protect it against the mechanical and

thermal stresses of being incorporated

into the polymer material that serves as

the “ink” of the 3D printer, the DNA was

encapsulated into silica nanoparticles

prior to mixing. The encoded polymer was

extruded into a filament compatible with

ordinary desktop 3D printers. Once the

bunny was printed, the researchers snipped

off ten milligrams of its ear—an amount

equal to 0.3 percent of total bodily mass—

in order to recover DNA and synthesize

another bunny. With the polymer dissolved

and silica beads cleaned, the encapsulated

dataset could be processed and the complete

digital file recovered. Using DNA from the

same ten milligrams of material, the team

generated and recovered perfect digital

files from five subsequent generations of

bunnies, including one that was stored for

nine months prior to re-synthesis.

The final generation of offspring was

subject to sequencing errors and the dropout

of over twenty percent of the original data,

but Grass explains that these types of errors

are already overcome by inserting backup

data in the initial phase of the DNA storage

process. Higher levels of redundancy allow

for more generations of error-free replicas.

“If you know that every generation loses two

percent of data then you add ten percent

redundancy at the beginning to allow for

five generations. That’s much easier than

trying to solve the problem down the road,”

Grass said. The key outcomes of the file’s

perfect recovery stand undiminished by the

errors, he added. The bunnies’ generational

synthesis provided support for the theoretical

possibility that lost portions of data can be

recovered with redundant DNA—a process

likened to solving a sudoku puzzle given

only limited information. The experiment

also required a miniscule amount of sample

material to recover the data necessary to

engineer subsequent generations. A sample

of such a small scale, essential to recreating

offspring products without impairing their

appearance or functionality, is only possible

due to DNA’s enormous storage capacity.

Inspired by their successful pilot, Erlich

urged the group to attempt a more ambitious

follow-up, embedding more data in a new

type of polymer. For the next experiment,

the group repeated the sequencing and

material infusion processes, this time

for a 1.4-megabyte YouTube video in a

transparent plexiglass polymer that would be

3D-printed into a lens. When mounted onto

a frame, the lens exhibited normal optical

properties, allowing an ordinary-looking,

functional pair of glasses to secretly contain

a DNA-encoded video message. Once again,

a mere ten milligrams taken from the frames

allowed for full recovery of the video file.

A revolutionary industrial force

Once it is polished, Grass and Erlich

envision DoT technology to broadly

impact the future of manufacturing on

both personalized and industrial scales.

This shared perspective arises from each

scientist’s industrial background—Erlich’s

as CSO of MyHeritage and Grass’ as CEO

of Turbobeads, a nanotechnology company

he founded ten years ago.

Their group devoted a significant portion

of its research to examining factors that

will influence DoT’s ability to become

a widespread and flexible solution to

the challenges of digital storage. This

included testing new types of polymers that

could serve as viable materials for DNA

storage, as well as discussing potential

DoT applications and their economic

challenges. Personalized items will likely

be the first industrial application. Dental

implants, for example, could be encoded

through DoT with information pertaining

to an individual’s unique implant design.

The problem, Grass said, would be the

high upfront cost of encoding an entire

blueprint. For every implant, a new set

of DNA would have to be synthesized at

around one thousand dollars per megabyte.

A more feasible general application could

arise in products with long lifetimes, such

as construction materials or other items

which would retain their own instructions

for replication when traditional data storage

methods may have been lost. According

to Grass, however, the most notable

impact will be in the mass-manufacturing

industry, in which the enormous initial cost

New ‘DNA-of-Things’ technology has the

power to transform our digitized world

IMAGE COURTESY OF ETH ZURICH/ROBERT GRASS

One lens of these glasses modeled by an assistant

researcher contains DNA encoding a video file.

of synthesizing the DNA for the first item

would be offset by the ability to regenerate

identical replicas with little material and no

added expense. The ten milligrams snipped

from each of the group’s test bunnies

theoretically yielded enough data to create

eighty quintillion (10 18 ) offspring within

five generations—without resynthesizing

the initial DNA even once.

Though the researchers’ work suggests

DNA could potentially store files of much

greater size, their focus is to think in terms of

an everyday budget rather than speculating

about the dizzying cost of encoding a vast

library of information. “At the moment,

one hundred kilobytes costs perhaps ten or

twenty dollars,” Grass said. “What can I do

with that? Right now, our products contain

zero or very little information. What if I

could put just ten kilobytes of information

into that item instead? That’s the first step.”

These preliminary steps have

already turned heads in industrial and

governmental sectors. Some companies

currently offer megabyte-scale personal

DNA sequencers, and the United States

Intelligence Advanced Research Projects

Activity recently committed fifty million

dollars toward DNA data storage research.

“We dream of a world where everyone

can do DNA sequencing,” Grass said. “I

see it as our job to give examples, even if

they’re still academic, which demonstrate

where we can get value out of this

technology. We have a proof of concept

that shows that it’s doable. Now the next

step is to show that we can build a case

where we can generate value.” The future,

it seems, is hidden in plain sight after all. ■

www.yalescientific.org

March 2020

Yale Scientific Magazine

29


REVISITING THE EFFECTS OF

OCEAN ACIDIFICATION ON

CORAL REEF FISH

COUNTERCOUNTER

BY

CHRISTOPHER

POSTON

POINT

POSTON

Affectionately termed the “rainforests of the sea,” coral reefs are among the most diverse ecosystems in existence.

If you have ever watched Finding Nemo or listened to an

aquarium guide, you know that coral reefs are the teeming

metropolises of the ocean. Despite accounting for less than one

percent of the seabed, they provide a home for a quarter of all

marine species. Ten years ago, conservationists and news outlets

alike were quick to sound the alarm when a series of high-profile

papers from 2009 to 2014 found that ocean acidification—caused

by increasing atmospheric carbon dioxide (CO 2

), with which

water reacts chemically to produce acid—was disrupting the

behavior and sensory mechanisms of coral reef fish. Among the

reported impairments were hearing, vision, olfaction, activity

levels, and even response to predator cues. However, when

a team of researchers from Australia, Canada, Norway, and

Sweden put these results to the test in a replication study, they

found the effects simply could not be reproduced. Their results,

published recently in Nature, have important implications for

how we understand coral reef health in the future.

In their comprehensive three-year examination, the team

took great pains to recreate the conditions of the original

studies. The species and life stages of the fish, as well as the

locations and seasons they were studied in, all matched those of

the earlier studies referenced. The researchers even employed

automated tracking software to minimize biased reporting and

made all of their raw data and code publicly available.

Perhaps the most surprising result reported in previous papers

was an extreme reversal of chemical cue preferences: earlier

studies alarmingly reported that fish exposed to elevated levels

of CO 2

chose to spend more than ninety percent of their time

in water containing predator cues. Across 560 individuals, the

replication study found no replicable effect in any species or

age group. It also demonstrated that exposure to high CO 2

did

not cause significant elevation in activity levels or changes in

behavioral lateralization—directional bias when making turns.

Suspecting that the lower sample sizes of the earlier studies

might explain their different results, the team even went a step

further with a bootstrapping simulation, a statistical analysis

technique in which they took thousands of subsets of their vast

dataset to simulate the smaller four-minute trials of the earlier

IMAGE COURTESY OF PIXABAY

studies. Out of ten thousand simulations, not one matched the

extreme results reported previously.

In retrospect, there were several red flags with the earlier

studies. Although the researchers used similar methods

and reported remarkably low variance, there were often

discrepancies between papers on the actual data. “I have never

seen such strong treatment effects and such reported consistency

in behavior… it is hard to believe,” said Josefin Sundin, one of

the study’s coauthors and behavioral ecologist of the Swedish

University of Agricultural Sciences.

The team’s original goal was quite different: “We wanted to

look at the physiology behind those reported effects,” Sundin said.

“But in order to do that you have to repeat the effects. If you fail

to replicate it, what do you do? Do you still try to publish?” These

questions relate to a perennial issue in the scientific community:

the unpopularity and lack of platform for negative, or null, results.

Because these findings are usually viewed as dull or unsurprising,

even high-quality studies with large sample sizes are often left

unpublished when they conclude a null effect. However, such

results are crucial for developing well-informed strategies moving

forward. “Mostly we are happy that such a high-impact journal was

willing to publish negative results and replications,” Sundin said.

Ultimately, these coral reef revelations underscore the need for

comprehensive and independent replication studies in the scientific

community, especially on issues of global importance. The negative

results of this study, for instance, will shift the way we approach

the essential task of coral reef protection. Reefs already face grave

threats from human activities such as habitat destruction, and

ocean acidification still wreaks devastation on them through coral

bleaching, which kills off essential energy-providing algae colonies.

Most current management strategies for ocean acidification prioritize

“natural refugia”—habitats more naturally resistant to stressors,

such as reefs with carbonate-rich deposits and CO 2

-dissolving

seagrass. The results of this study suggest that conservationists need

not worry about local fish species at those locations; in the bigger

picture, this study challenges well-accepted precedent, challenging

us to rethink and reassess how coral reefs and the species they harbor

are affected by environmental change. ■

30 Yale Scientific Magazine March 2020 www.yalescientific.org


VS.

SCIENCE

THE APOCALYPSE

ROBOT

TAKEOVER

BY LESLIE

GONZALEZ

L

IMAGE COURTESY OF WIKIMEDIA

ARMAR II, an anthropomorphic service robot developed by the Karlsruhe Institute of Technology, performs tasks such as power drilling and hammering in industrial environments.

In science fiction movies such as The Terminator and The

Matrix, robots develop such sophistication that they overpower

the humans who invented them. Amidst rapidly advancing robot

technology, such a scenario may seem less like a fictional trope

and more like a real possibility. How will humans interact with

our increasingly life-like robots? Using a game theory experiment

involving human-robot cooperation, University of Plymouth

scientist Debora Zanatto and her team endeavored to find out.

When we interact with other humans, we seek empathy and

feelings of positivity. By the rule of human-human interaction,

it is our instinct to reward others’ cooperation with cooperation

of our own, and to punish their selfishness with selfishness of

our own. Zanatto’s team set up a scenario to investigate the

implications of this concept for human-robot interactions.

Participants in the study engaged in an investment game in which

collaborating with a robotic teammate was essential to success. The

human and robot teammate each started the game with a set amount

of virtual money. Both were required to independently decide how

much of it to invest in a robot banker. Then, they were given the

opportunity to alter their respective choices after seeing the other’s

investments, with the human participant making their final choice

last. Invested money could be returned to each teammate with

profit, but the robot banker deducted money whenever the robot

and human investments differed by a substantial amount.

Three sets of factors varied. The robot banker adopted either a

“generous” condition, in which it returned fifty to eighty percent

of each investment to the players, or a “mean” condition, in

which it returned zero to thirty percent. The robot teammate was

programmed to adopt either a collaborative strategy, adapting its

investment to fit that of the human participant, or a fixed strategy,

acting regardless of the human’s choice. And finally, the robotic

teammate was either immobile and mute, or anthropomorphized

to look at the human participant, follow a verbal script, and point

to its investment choices on the screen. Each human participant

played two games with the same robot, which utilized the

collaborative strategy in one and the fixed strategy in the other.

It was found that when payoff was high—when the robot banker

was “generous”—participants were more likely to be cooperative with

a mute, collaborative robot, suggesting a preference for subservient

and less humanoid qualities when there was more to be gained.

However, when payoff was low and the robot banker was “mean,”

participants demonstrated higher cooperation with a collaborativestrategy

anthropomorphic robot partner, suggesting a preference

for empathy and anthropomorphism in times of difficulty.

“Everything was related to the criticality of the situation. When

the payoff was low, the participant had a tendency to cooperate

with the confederate showing more human-like behavior. On

the opposite, when the payoff was high, the participants couldn’t

care less about the confederate’s social skills—they even seemed

to prefer a robot that wore robotic features expected of nonhuman

agents,” Zanatto explained.

Furthermore, a multi-part questionnaire assessing participant

perceptions of the credibility, trust, animacy, and likeability of the robot

teammates was given to participants after the two games. Participants

ranked the fixed-strategy anthropomorphic robot highest in each

category. This revealed two distinct conclusions of the study. Human

collaboration with robots depends on the challenge’s difficulty; we

always value robotic cooperativeness, but based on the scenario,

we differentially value either anthropomorphism or immobility.

Conversely, positive human perception of a robot, regardless of

scenario, favors anthropomorphism and behavior consistency.

Could this be a cause to fear future manipulation at the hands

of robots? Zanatto expresses a belief in the power of humanrobot

interactions to improve not only our lives, but also our

understanding of our behavior. Yet in some ways, she thinks that

it might seem that a pernicious robotic future is already here,

“Some will trust fake news and incorrect medical information on

the internet, but not a plastic robot, because the internet follows

our stereotypical view of non-human technology,” Zanatto said.

In any case, we should be cognizant of the power and problems

of anthropomorphic technology in other situations. “Robots are

programmed; they can break and cease to work. If we become

too trusting of the broken code and machine, we might follow its

incorrect suggestions. It is like the problem we face with human

interactions, following cues that lead us to trust someone we

should not,” Zanatto said. ■

www.yalescientific.org

March 2020

Yale Scientific Magazine

31


MADDIE BENDER (TD ’20)

BY STEPHANIE HU

COURTESY OF MICHELLE BARSUKOV

For Maddie Bender (TD ’20), it all started with

chess. Growing up, she was a competitive player of the

game, which takes place in a notoriously majoritymale

arena. Bender, however, never minded being the

only girl. Her willingness to stand out endured as she

grew older and became interested in STEM, another

male-dominated field. Rather than hold her back, her

unique position propelled her to pursue science even

more. “I felt like if I was comfortable in those spaces,

then I should do it, on behalf of all the other people

who would love to see a woman in that field,” Bender

recalled. Now an aspiring science journalist, Bender

has always loved to break molds.

In high school, Bender realized she was interested

in not only science, but also the humanities, taking

a variety of classes in both areas. She was never sure

how to combine these interests until her junior year

of high school. “I was listening to [the podcast]

Radiolab, the first of a two-part series on CRISPR-

Cas9 genome editing, and they had [science writer

and Yale professor] Carl Zimmer on to explain how

that gene editing works,” Bender said. “As I was

listening to him… I realized that I didn’t even know

someone could have that job of taking science and

explaining it to non-scientists.”

Inspired by that moment, Bender came to Yale

certain she wanted to pursue a combination of

biology and humanities, going as far as to create

a four-year plan her freshman year. She quickly

decided to double major in Ecology and Evolutionary

Biology and Classics. Her freshman counselor and

everyone else around her told her, “You’re not going

to stick to it.” As always, Bender was the exception.

Bender joined the Yale Daily News her freshman year,

and by sophomore year was editor of the Science and

Technology desk. She has honed her skills during various

internships, including a coveted one at CNN. Bender is

particularly proud of a feature she wrote for CNN about

technology overuse. “I had a very intense conversation

with a girl who was trying to take a step back from

technology and social media because she was aware of

how it was negatively affecting her life. I thought it was

really important to share her story,” Bender said.

UNDERGRAD

PROFILE

Bender has also grown her writing skills through

other publications. She previously interned at Wow

in the World, an NPR science podcast targeted toward

younger children. Today, she is an assistant editor at

Massive Science, a publication where scientists can

write about the topics they know best for a non-scientist

audience. And since August, she has published weekly

articles for Vice about fascinating topics that range

from evolution to climate change to gene editing.

Bender has also spent two years conducting

research on bacteria at the Sanchez lab, which

researches microbes on Yale’s West Campus. While

she loves the work she does, she does not view it

as a future career path. “I don’t think I could focus

on a very niche, minute topic for years and years.

It’s much more exciting to get to go in at the point

of discovery, when in reality the scientific process

is years and years of not necessarily exciting

discoveries,” Bender explained.

When asked about challenges in science journalism,

Bender acknowledges that, just like in her chessplaying

days, it can be difficult to fit in. “Being a

young-ish woman in a science-adjacent field, I

haven’t always felt taken seriously by people who

are established in the field,” she said. This feeling of

isolation is echoed, although to a lesser degree, in

her journalism community, “because I don’t plan on

going to journalism school and because I’ve only really

wanted to do science up until this point,” Bender said.

But, none of these challenges faze her. Bender is

currently pursuing a Master of Public Health degree

in the epidemiology of microbial diseases through

a prestigious five-year BS/MPH program at the

Yale School of Public Health. After graduating, she

is determined to go into science writing full time,

though she is unsure whether that will be as a fulltime

journalist or as a freelancer.

Despite all the challenges that come from constantly

pursuing the path less traveled, nothing will dim

Bender’s passion for science journalism. “I love the idea

of taking something so specialized it’s almost in another

language, something so jargon-y, and just translating it

so it can be accessible to anyone,” she said. ■

32 Yale Scientific Magazine March 2020 www.yalescientific.org


ALUMNI ALUMNI

PROFILE

Even on paper, Lauren Abendshien (BS ’06, LAW

’12) defies classification. Chemist-turned-patentlawyer,

national defense scientist, ballerina—any of

these technically accurate titles would be insufficient.

Abendshien has been bridging worlds her whole life:

finding the intersection of art and logic in her organic

chemistry problem sets, uniting fact and persuasion

in her legal briefs, reading her favorite science fiction

book, Isaac Asamov’s Prelude to Foundation, in French

and English. Now, in her job as a patent lawyer, she

considers herself an “interpreter” of science.

Though Abendshien intended to study biology when

she entered Yale as an undergraduate, she quickly fell

in love with chemistry. “Interestingly, it was organic

chemistry that really got me hooked,” Abendshien said.

“[The mechanisms] were almost artistic, but at the same

time very logical and mathematical.” It was not only the

material that drew Abendshien to chemistry, but also

the professors. She recalls physical chemistry professor

Patrick Vaccaro, under whom she conducted her thesis

research, as the best professor she has ever had. Not only

did he make quantum mechanics comprehensible and

approachable, but he also demonstrated immense care

for his students through the quality of his lectures. Ann

Valentine, a former professor of inorganic chemistry, was

another inspiring and caring mentor for Abendshien.

As much as she loved her professors and courses,

Abendshien realized that a research career was not for her.

“The laboratory existence felt lonely to me, and I wasn’t

sure that that would be something that I would enjoy

doing for the rest of my life,” she said. After graduating,

Abendshien worked at the FBI’s forensic science lab

making a database of automotive carpet fibers: tiny scraps

of evidence that investigators could use to narrow their

searches. Once again, though the work was enjoyable

and interesting—she once saw it referenced in an episode

of the TV show Bones—Abendshien still found the lab

environment somewhat isolating.

Abendshien then took a job as a chemical and

biological defense consultant at the Pentagon, where

she helped negotiate the international transport of

hazardous substances for research. This job required

her to bridge the communication divide between

COURTESY OF LAUREN ABENDSHIEN

scientists and lawyers. “It was like they were speaking

two completely different languages… and I really liked

talking to both,” she said. She found herself acting as

a “de-facto interpreter,” explaining the science and

its significance to lawyers, while helping scientists

understand the lawyers’ point of view. Excited by

this newly discovered intersection of science and law,

Abendshien returned to Yale for law school.

Now, Abendshien works as a patent attorney,

representing clients in infringement lawsuits. Intellectual

property law is the perfect fit for her interlocking

passions. While her cases are not always chemistryrelated,

they often involve immersion into some new area

of science—a new dialect for her interpretive toolbox.

“I’m always learning, and I love that,” said Abendshien.

“It feels like home, in a way.” Many of her current cases

deal with computer software, which has required a steep

learning curve for someone who “prefer[s] analog to

digital in many respects.” But her science background

prepared her well for tackling unfamiliar concepts. “As

a chemistry major, physics was not my strong suit, but I

had to get through it. Now, it seems less intimidating to

take those first steps,” she said.

Abendshien finds that the connection between

science and law goes deeper than the content of her

cases. Going into law school without a political science or

economics degree was intimidating at first, but she soon

discovered surprising similarities between the methods

of science and law. Both scientific writing and legal

writing have a logical sequence: set the stage, present the

data, make an argument for why the data supports your

hypothesis. And both research and arguments must

be communicated in a way that is “replicable”—one in

experimental method, the other in logical flow.

Looking back on her time as a science major at

Yale, Abendshien is grateful for the freedom she had

to explore other areas. “I came out with a healthy

balance of skills and interests. Even if didn’t put my

chemistry degree into direct use, I still had a wealth of

experiences to draw upon in whatever I chose to do,”

she said. She left having honed the skills of a future

interpreter—not simply learning a few languages, but

learning how to constantly learn more. ■

BY RAQUEL SEQUEIRA

LAUREN ABENDSHIEN (BS ’06, LAW ’12)

www.yalescientific.org

March 2020

Yale Scientific Magazine

33


THE STORY COLLIDER

BY NITHYASHRI BASKARAN

In a not-so-unusual scene at Benjamin Franklin College, whose dining hall often seats professors from nearby Science Hill, I meet three

scientists over lunch. Not once do I see their faces. Instead, their identities unravel through their voices, shuttled by my headphones. Within an

hour, I listen to three stories that transform my perspectives on love, longing, and loss.

Through weekly podcasts and live shows, The Story Collider exposes listeners to

true science stories that combat the traditional portrayal of science as exclusive.

“Storytelling is powerful to scientists because it takes science out of the abstract

and esoteric and draws the audience into the lived experiences of human beings,”

said Liz Neeley, executive director of the nonprofit.

Zoologist Devon Kodzis, the first scientist I listen to, begins by recounting

her botched attempt at attracting a kindergarten crush using the topi antelope

strategy, the first of many animal fact fiascos that thwart her romantic interests.

When she finally represses her references when conversing with a guy at a college

party, she is stunned to hear him gush over their shared favorite animal, the

giant Pacific octopus. “To many, scientists barely register as real people due to

caricatures in their minds that are dominated by ideas from fiction or popular

media,” Neeley said. But Kodzis’ endearing personality reveals that scientists,

shockingly, experience emotions as irrational as love.

Wetland scientist Lylianna Allala follows by recalling a phone call her mother

has with a classmate’s mother that mysteriously prevents Allala from collaborating

with the classmate on a solar system project. Twenty years later, she realizes the

partnership ended because her classmate’s white mother did not want her child to

be involved with a Mexican American family. “When people process information

relating to a politically polarized issue, data-based argumentation only reinforces

opposition,” Neeley said. Allala’s story—ultimately about how feeling unfit to be

a science partner deterred her pursuit of science—conveys disparities in STEM

representation more powerfully than numbers.

Attending surgeon Bhuvanesh Singh concludes the podcast by depicting a bond

with his patient, Alice. Blissful at having perfectly executed her operation, Singh

is devastated when she returns months later and neither physician precision nor

patient perseverance can cure the cancer. “Sometimes the criticism of storytelling

is that its rhetorical power comes from making people feel emotions instead of

think logically, but I believe that to be human is to have both those sides, and

the parts of me that respond to emotional stories do not somehow make me less

scientific,” Neeley said. From Alice, Singh realizes that healing comes less from

steeliness—of scalpel or state of mind—and more from emotional vulnerability that eases patients’ fears at their most difficult times.

Neeley tells me that story-listening has pushed her to appreciate the everyday stories around her. After listening to The Story Collider’s

podcasts, I can corroborate. As I leave the dining hall, I wonder how stories shape the passions, scientific and otherwise, of everyone I

pass. I wonder how they will shape mine. ■

PHOTOGRAPH COURTESY OF THE STORY COLLIDER

SCIENCE IN TH

34 Yale Scientific Magazine March 2020 www.yalescientific.org


INFINITE POWERS

BY YU JUN SHEN

Have you ever wondered how DreamWorks animators created Shrek? Or how we may measure the speed of light using cheese in a microwave?

Calculus holds the key. Whether you are a prospective STEM major or just hoping to pass your mandatory math class, Steven Strogatz will intrigue

you with his book Infinite Powers: How Calculus Reveals the Secrets of the Universe.

Infinite Powers has no complex formulae or rigorous proofs; rather it sketches out the

logic behind some of mathematics’ greatest breakthroughs by revealing the stories and

characters that led to their discovery.

Strogatz’s central theme is the pervasiveness of calculus. From classical examples in

physics, to modern applications in computer animation and biological systems, we rely

on calculus every day. It is for this reason that Strogatz loves calculus and “wanted to share

that love with a wider audience,” he says. “Many students never really see the point of it.”

Infinite Powers progresses chronologically, starting with the earliest forays into

the “infinite.” Sandwiching a circle between two increasingly many-sided polygons,

Archimedes approached the constant π. Modern physics emerged when Kepler and

Galileo scrutinized the problem of motion using mathematics. In subsequent pages,

more mathematicians appear—Descartes (the namesake of Cartesian coordinates),

Fermat (who explained how light travels to minimize time), and Newton (who

established classical mechanics). Strogatz carefully introduces, and then explains,

the concepts of derivatives and integrals. The history of the fundamental theorem of

calculus—the telescopic sum of many steps equals the difference between two boundary

points—is rarely known, even for readers who have tackled calculus in school.

A key strength of Infinite Powers is how it showcases the mathematicians’ varied

personalities. Strogatz describes Kepler and Galileo—who established the foundations

of modern astronomy and physics—as the mystic and rational heirs, respectively,

to Pythagoras and Archimedes. We glimpse Descartes’s disdain in 1638 of Fermat’s

work on calculating gradients: “I do not even want to name him, so that he will feel

less shame at the errors that I have found,” Descartes wrote. Similar rivalry appeared

between Newton and Leibniz, as British and continental European mathematicians

bickered over who developed calculus first.

Amidst this historically male-dominated field, Sophie Germain stands out as

a tenacious female mathematician who “wrapped herself in quilts and worked

by the light of stolen candles” to study mathematics, eventually solving a

difficult standing wave problem. These delightful stories bring to life the stale

portraits typically found in college textbooks. “[Calculus is] one of humanity’s

greatest collective achievements … and the story of how it was discovered and

developed is one of the greatest intellectual adventures of all time,” Strogatz explained.

As promised, Infinite Powers explains calculus for everyday readers. It is also a valuable addition for science and engineering majors given the

sheer breadth of applications covered. With any luck, you will find calculus less intimidating and obscure than before, and be inspired to dive

deeper into this magic that powers our modern world. ■

PHOTOGRAPH COURTESY OF PIXNIO

www.yalescientific.org

March 2020

E SPOTLIGHT

Yale Scientific Magazine

35


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