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Contents ON THE COVER: MODIFIED FROM © SHUTTERSTOCK.COM, GOLBA
SUMMER 2022 | WWW.THE-SCIENTIST.COM | VOL. 36, ISSUE 2

28 Features

37

© ISTOCK.COM, DESIGN CELLS; MODIFIED FROM © ISTOCK.COM, VIKI, YODIYIM; MODIFIED FROM © ISTOCK.COM, FEDRELENA; 44 54
COMPOSITE FROM: © ISTOCK.COM, HOMUNKULUS28; © ALAMY.COM, MARK GARLICK, SCIENCE PHOTO LIBRARY
28 37 44 54

A Virus’s SLiM Pickings Schizophrenia and Whispers of the Past The First Americans
Only recently appreciated as The concept of epigenetic New techniques have shown
critical components of cellular the Immune System inheritance has long been that people reached the
functions, unstructured Several lines of evidence controversial. Some research- New World far earlier than the
stretches of amino acids suggest that targeting the ers hope that new data on long-standing estimate
called SLiMs are key to viral- body’s defense pathways cross-generational effects of of 13,000 years ago, but sci-
host interactions. might help treat a subset of environmental exposures will entists still debate exactly
people with the psychiatric help settle the debate. when humans arrived on
BY CONCHITA FRAGUAS disorder. But many open the continent—and how.
questions remain. BY CATHERINE OFFORD
BRINGAS AND JAKOB NILSSON BY EMMA YASINSKI
BY DIANA KWON

SUMMER 2022 | THE SCIENTIST 3



Department Contents

COMPOSITE FROM: © ISTOCK.COM, KSENIA ZVEZDINA, TETIANA LAZUNOVA; © IKUMI KAYAMA, STUDIO KAYAMA; YUCAIPA HISTORICAL SOCIETY 13 8 FROM THE EDITOR 71 THE LITERATURE
67 Salmonella takes on cancer; distracted
90 Once More Unto the Breach brains are better at parsing unfamil-
Notes from my first in-person iar languages; SARS-CoV-2 can spread
mega-conference in two years via cell-to-cell transmission; genes are
BY BOB GRANT involved in the migratory behavior of
endangered caribou; ancestral bacteria
11 SPEAKING OF SCIENCE may have invaded early eukaryotic cells.

CRITICS AT LARGE 75 CAREERS

13 Big Science in the Age of COVID Making Peace with the Press
The pandemic has complicated large There are many benefits to com-
international research collaborations. municating science to the media,
But the tough situation has also yielded but talking with journalists doesn’t
valuable insights. always go smoothly.

BY SADYE PAEZ, GIULIO FORMENTI, BY KATARINA ZIMMER
AND ERICH D. JARVIS

15 Is Open Access Worth the Cost? 80 BIO BUSINESS
As we continue to transition out of
the print era of scientific publishing, Skin Deep
funders and institutions are paying Researchers are revealing the com-
a steep price to have trustworthy plexity of the microbial community
publishers certify research outcomes. living on the body—and paving the
way for new microbiome-targeting
BY JINGSHAN S. DU treatments for acne and other
dermatological conditions.
19 NOTEBOOKS BY BIANCA NOGRADY
Dwarf mongooses shun bullies to
manage conflict; researchers debate READING FRAMES
whether insect wings evolved from
legs or from the body wall; fish may 83 The Ape-Man of Flores
be a lot more vocal than previously Do members of Homo floresiensis still
thought; scientists explore the func- inhabit the Indonesian island where
tion of mouse sperm hooks. their fossils helped identify a new
human species fewer than 20 years ago?
SCIENTISTS TO WATCH
63 Ana Marija Jakšić: Shaping Fly Brains BY GREGORY FORTH

BY CHLOE TENN 85 The Dawn of Song
Listen to the sound of the land’s
65 Giannina Descalzi: Chronic Pain first known singer.

Detective BY DAVID GEORGE HASKELL
BY NATALIA MESA
FOUNDATIONS
67 MODUS OPERANDI
87 Universe 25, 1968–1973
CRACKing the Neural Code
A new technique reveals cells’ precise BY ANNIE MELCHOR
locations and functions in the brain. Its
developers have already used it to iden- 90 The Spider Lady, Circa 1939
tify a previously unknown neuron type.
BY DAN ROBITZSKI BY NATALIA MESA

SUMMER 2022 | THE SCIENTIST 5

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6 6 TSTHDEI GSECSITEN| TthISeT-s|ctiheen-tsisctie.cnotmist.com

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FROM THE EDITOR

Once More Unto the Breach

Notes from my first in-person mega-conference in two years

BY BOB GRANT ity added a new dimension to my apprehension. Sure, since the ANDRZEJ KRAUZE
pandemic’s start, I had travelled on public transit, had attended
With January’s Omicron wave behind us, giant research some less-than-full-capacity, open-air affairs such as sporting
organizations have again decided to hold their annual events, and had indulged in outdoor dining experiences with fel-
conferences in person. I started writing this dispatch low humans. But nothing like willfully entering a yawing inside
from the bowels of the immense Ernest N. Morial Convention space where thousands of other people would be showing up
Center in downtown New Orleans in mid-April. I was there, with intent on interaction.
more than 14,000 attendees involved in the enterprise of cancer
science, to attend the annual meeting of the American Associa- Apparently, I was not the only one harboring such feel-
tion for Cancer Research. The AACR and similarly sized groups ings. At the meeting, an AACR spokesperson shared with
have held their massive meetings virtually for the past two years me an estimate that more than 14,000 people were in physi-
as the pandemic engulfed the world, shuttering labs and scuttling cal attendance at this year’s conference. AACR counts more
events around the globe. than 50,000 members in its ranks, and prior to the pandemic,
its annual conferences were typically attended by more than
This year, the AACR jumped back into the fray and invited 30,000 people. International travel difficulties, widespread
its sizeable community into a common space to share, collabo- weather delays in domestic travel, and at least one case that I
rate, and network. Over the years, I’ve been to several AACR learned of where a presenter contracted COVID-19 just prior
conferences and meetings of other large, professional organi- to the meeting likely contributed to curtailing the number of
zations to cover the proceedings, speak with researchers, and conference-goers this year.
keep tabs on the latest discoveries in various fields. I’ve always
enjoyed the feeling of camaraderie and celebration. There is a As I boarded my flight to New Orleans, I noticed a smat-
certain buzz that even I, as someone who writes about the work tering of students shoving poster transport tubes into overhead
rather than actively participating in it, can access as it circu- compartments, and it became more real that this was actually
lates among people who are focused on a collective mission to happening. Upon landing at Louis Armstrong Airport, that
understand some aspect of biology, often to stamp out disease. realness intensified. I soon stood in a blocks-long line for a taxi,
This year, though, heading back into one of these mega-con- knowing that many of these vehicles would be ferrying my fel-
ferences—after such a tumultuous period in world history and low AACR attendees to their accommodations.
such a long break from those feelings of community and shared
purpose—felt different. The in-person conference required that attendees provide
proof of COVID-19 vaccination, evidence I was only too happy to
Being able to see and hear and feel the
presence of fellow humans who share
passions and pursuits . . . is something
that is hard to replicate, no matter how
innovative the virtual platform.

The thought of tiptoeing back into the world of face-to-face
meetings stirred a certain anxiety in me. It wasn’t just the vague
fear of contracting COVID-19 and potentially infecting vulner-
able people in my life. I’d learned to live with that feeling as a
constant companion over the past two years. Travelling to AACR
and leaping headlong back into the world of personal interac-
tion after living more than 24 months with a screen between
me and essentially anyone I spoke with in a professional capac-

8 THE SCIENTIST | the-scientist.com

supply as I finalized my registration for the meeting. And when homes using modern technology to connect outside the boundar-
I arrived at the conference center for the first time the morning ies of physical interaction. One certainly can’t complain, as there
after arriving in New Orleans, I was pleased that the greeters are still many people in communities across the globe who aren’t
who checked my credentials also asked to see the QR code that privileged enough to have access to such tools. And the pandemic
was generated when I had uploaded photos of my vaccination has exacted a much more sobering toll from millions of people.
card prior to travelling to the conference. I was also heartened But I must say that being able to see and hear and feel the pres-
to see that most of the people that I saw at the meeting on that ence of fellow humans who share passions and pursuits, such as
first day were wearing masks. understanding biology and trying to treat the ills that befall too
many people, is something that is hard to replicate, no matter
The anxiety that I had felt in the lead-up to the AACR meet- how innovative the virtual platform.
ing continued to dissipate as I attended symposia and lectures
at the meeting and navigated the halls, observing the appar- I sincerely hope that the future, with COVID-19 and perhaps
ent happiness that pervaded the gathering. Long-Zooming other pathogens as persistent threats, will feature more such
colleagues greeted each other, hopeful neophytes approached interactions and that we humans will find ways to assemble in
established figures, and practitioners reveled in sharing the spirit of peace and discovery despite the forces that conspire
insights and discoveries directly with past, present, and future to separate us. g
collaborators. Even though this year’s meeting attracted only
about half the normal number of attendees, the buzz at this Editor-in-Chief
long awaited in-person version of the conference seemed to [email protected]
exceed that of its prepandemic iterations. The assembled crowd
appeared to feel enhanced joy at being able to shake hands,
applaud well-delivered presentations, and partake in a coffee
and an intimate conversation.

Scientists and science journalists alike have made do for the
past two years, collaborating in and covering research from our

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QUOTES

Speaking of Science

Specifically, we hypothesize that
Mucorales-rich cow excrement, given
its use in multiple Indian rituals and
practices, especially during the pan-
demic, probably played a key role in
India’s CAM epidemic. We also posit
that the dispersal of fungal spores
most likely occurs through fumes gen-
erated from the burning of Mucorales-
rich biomass, such as cow dung
and crop stubble.

—Jessy Skaria et al., in a recently published mBio paper that identified the ritual use
of cow dung as a key contributor to a rash of infections with black fungus linked to
COVID-19 cases, or what’s known as COVID-19–associated mucormycosis (CAM),

in India last year (March 31)

© ISTOCK.COM, PHOTOMAN I feel as though there’s no more poignant signal Time is not on our side. The disease has
that you don’t care about trainees than to prioritize had a two-week head start and we are now
protecting and vindicating this one individual over playing catch-up.
our mental health and physical safety.
—The World Health Organization’s regional director for Africa, Matshidiso Moet,
—Julia Derk, a postdoc in neurobiology at the University of Colorado’s Anschutz announcing the agency’s declaration of an Ebola outbreak in the Democratic
Medical Center, speaking to The Scientist about the fact that cell signaling
researcher David Sabatini, who recently resigned from or was fired by three Republic of Congo, four months after the last one ended (April 24)
institutions following allegations of sexual misconduct, was being considered
for a faculty position at NYU Grossman School of Medicine, where Derk recently This case highlights the potential of the
Omicron variant to evade the previous immu-
completed her PhD (April 29) nity acquired either from a natural infection
with other variants or from vaccines.
False, distorted, and preposterous allega-
tions about me have intensified in the press —Gemma Recio of Institut Català de la Salut in Spain, speaking at the
and on social media in the wake of reports European Congress of Clinical Microbiology & Infectious Diseases in late
last week that New York University Langone April about the case of a 31-year-old healthcare worker who was infected
Health was considering hiring me. I under- with SARS-CoV-2 twice—first with the Delta variant and then with
stand the enormous pressure this has placed
on NYU Langone Health and do not want Omicron—within three weeks (February 22)
to distract from its important mission.

—David Sabatini announcing through a public relations firm that he was
withdrawing his name from consideration for the position at NYU Grossman

School of Medicine (May 3)

SUMMER 2022 | THE SCIENTIST 11

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CRITIC AT LARGE

Big Science in the Age of COVID

The pandemic has complicated large international research collaborations.
But the tough situation has also yielded valuable insights.

BY SADYE PAEZ, GIULIO FORMENTI, AND ERICH D. JARVIS

COMPOSITE FROM: © ISTOCK.COM, KSENIA ZVEZDINA, TETIANA LAZUNOVA Large-scale international research programs require signifi- Some of the key planning challenges
cant project management and operational infrastructure. brought about by the pandemic also
They face different complications than do projects under- gave rise to unexpected opportunities.
taken by individual labs. These differences have been amplified
by the COVID-19 pandemic. Our lab at the Rockefeller Univer- ing our understanding of SARS-CoV-2 and the development of
sity has been a lead and participant in one of these sprawling much-needed vaccines, but also reducing the scope of available
research programs as one of the main hubs of the Vertebrate financial resources for basic science projects.
Genomes Project (VGP), a global effort to sequence high-qual-
ity reference genomes of all ~70,000 living vertebrate species. Other significant hurdles for large-scale basic science proj-
(One of us, Jarvis, is the chair of the VGP.) The consortium had ects were phased reopenings as the pandemic fluctuated and the
been generating a mountain of genomic data every week since impact of that emotional roller coaster on morale for an increas-
the VGP started in 2017. But production of new data nearly came ingly disengaged workforce. Keeping the VGP and other consor-
to a halt for several months as the pandemic took hold of the tia functioning required additional strategic planning to miti-
world in 2020. gate or prevent the negative impacts of these circumstances on
The VGP is also part of an even larger scientific program, the project’s goals. We designed contingency plans, with consid-
the Earth Biogenome Project. The initiative endeavors to obtain
reference genomes for each of the named ~1.5 million living
eukaryotic species on Earth. This mission is daunting because
of the number of species, complexity of the genome assembly
process, technological logistics, and coordination of more than
5,000 scientists in more than 100 countries. The fact that no
single country has more than 10 percent of those ~1.5 million
known animal, plant, and microorganism species makes global
coordination in the best of times both urgent and complicated. 
At the onset of the pandemic in early 2020, researchers,
like many other people, transitioned to working from home
because of the closure of laboratories, a shift that caused innu-
merable sociocultural challenges and scientific disadvantages.
Many aspects of genome sequencing became impossible, such
as preparing samples at wet-lab benches or venturing into the
field to collect new samples. Problems with shipping and per-
mitting, which often result in additional time to clear customs,
also halted or slowed the generation of new data. These delays
can cause deterioration of samples, making them useless for
sequencing. Transport postponements also affected the deliv-
ery of consumables or reagents and backlogged installations of
additional instrumentation. For the VGP, we estimated that this
constellation of problems accounted for an 80 percent decrease
in new data generation from March to August 2020.
Even once labs began reopening in late 2020, many researchers
had pivoted to COVID-19–specific projects and were operating
at limited capacity to maintain social distancing. Additionally, a
significant amount of public and private funding was prioritized
toward COVID-19 and related biomedical research, accelerat-

SUMMER 2022 | THE SCIENTIST 13

CRITIC AT LARGE

The pandemic highlighted that we are bakeoffs, in which all the leading available technologies were © ISTOCK.COM, TETIANA LAZUNOVA
undeniably and intimately interconnected applied to one sample to obtain the highest automated assembly
as a planet and as scientists. possible to date. The T2T and VGP consortia efforts also helped
advance the mission of the Human Pangenome Reference Con-
eration for each team member’s physical, emotional, and men- sortium, which aims to produce high-quality human genomes
tal health as well as for their roles outside the lab, particularly of hundreds of individuals representing human world diversity
as parents or caregivers. We found that there was a need to con- to form a panhuman reference genome. 
tinually adjust to the changing pandemic policies, which differed
not only across countries, but also within countries, across insti- Another silver lining of the past two years was that the
tutions and even between individual laboratories.   increased adoption of virtual conferencing technologies during
the pandemic gave rise to a more inclusive and internationally
Some of the key planning challenges brought about by the diverse genomics community. Most ongoing planning meet-
pandemic also gave rise to unexpected opportunities, however. ings and yearly conferences, such as our Biodiversity Genom-
Computational scientists, who focus on the design, implemen- ics annual meeting, moved online, where we made attendance
tation, and use of mathematical models to solve scientific prob- free, allowing participation by researchers who would not have
lems, further increased their contributions to the VGP, while had the resources to travel for an in-person conference. 
many wet-lab scientists transitioned to bioinformatic activities,
which can be easily done from home. Many of these researchers The number of collaborations also increased, boosting the
focused on further developing the methods and software tools exchange of results and ideas. New biodiversity genomics con-
to better analyze the large, complex genomic datasets that were sortia even emerged during the pandemic, such as the Euro-
accessible even with labs temporarily shuttered.  pean Reference Genome Atlas spearheaded by VGP members,
to some extent as a result of enhanced international interactions
Others focused on data that had already been collected and among scientists. Expanded efforts to democratize education
made many new discoveries. For example, the telomere-to- and access to the VGP assembly methods via a free web system
telomere (T2T) genome consortium, an international group with further increased the number of scientists involved in these proj-
the goal of generating an error-free, gapless, complete human ects. These positive outcomes do come with their own suite of
genome, greatly benefited from the contributions of scientists caveats. Access to computers, genome technologies, internet,
who suddenly became available during the pandemic to redi- and cloud-based storage systems remains inequitable, further
rect their work toward the completion of the human genome. calling attention to the need for capacity building in under-
In this context, scientists engaged in activities such as assembly served areas and populations of the world. 

As the world emerges from the acute pandemic phase,
we researchers progressively resume our individual scientific
endeavors. These endeavors, like many large-scale interna-
tional projects, are sure to be changed by the past two years
of shared experience. The pandemic highlighted that we are
undeniably and intimately interconnected as a planet and as
scientists. As we continue to transition, managing large-scale
projects now will require an evolution of our thinking and
actions. This evolution includes building strategies to main-
tain the unintended opportunities that grew out of the pan-
demic, while recapturing the benefits of in-person activities
and collaborations. g

Sadye Paez is a biomechanist and physiotherapist studying
the neurobiology of dance as a senior research associate in
the Laboratory of Neurogenetics of Language at the Rocke-
feller University and as a fellow in New York University’s
Center for Ballet and the Arts. She is the program director for
the Vertebrate Genomes Project (VGP) at Rockefeller. Giulio
Formenti is a biologist and the Bioinformatics Lead at Rock-
efeller’s Vertebrate Genome Lab. In addition to heading the
Laboratory of Neurogenetics of Language, Erich D. Jarvis is
a professor, chair of the VGP, and investigator of the Howard
Hughes Medical Institute. Jarvis also serves on The Scientist’s
editorial advisory board.

14 THE SCIENTIST | the-scientist.com

CRITIC AT LARGE

Is Open Access Worth the Cost?

As we continue to transition out of the print era of scientific publishing, funders and
institutions are paying a steep price to have trustworthy publishers certify research outcomes.

BY JINGSHAN S. DU

© ISTOCK.COM, JINDU SAVALIYA On January 11, 2022, the journal Nature Neuroscience Email
announced its article processing charge for open-access
papers in 2022. Despite being unchanged from the pre- ******
vious year when open-access (OA) became available for the first
time in all Nature Springer family journals, a tweet about the sub- What researchers are paying for is a certification
stantial fees of €9,500/US $11,390/£8,290 immediately triggered service—the credibility lent to research when
more than 400 replies, 2,300 retweets, and of course, memes, most it is published in a peer-reviewed journal.
of which conveyed a single sentiment: “How dare you charge so
much!” This was not the first time scientists protested such steep the amount a publisher spends on development and marketing var-
OA publishing fees, and it likely won’t be the last. ies each year, a linear correlation is evident on a five-year scale. (See
graph on next page.) This analysis shows that OA journals positioned
There is a massive range of journal article processing charges and running on a level similar to eLife’s can at least be self-sustain-
(APCs), typically ranging from around $1,000 to more than ing with an APC at somewhere between $2,700 and $4,700 if they
$10,000. Just five years ago, an APC of approximately $5,000 publish around 2,000 articles per year. Large OA publishers that
charged by Cell was considered outrageously high by some and made fee breakdowns publicly available, such as Frontiers (which
raised questions about how these fees were justified. (See “Opin- published approximately 85,000 articles across 139 journals in 2021)
ion: Understanding and Coping With Rising Publication Costs,” and MDPI (which published about 240,000 articles in 386 journals
The Scientist, September 2017.) Much has happened in the OA that same year), typically charge an APC within this range or lower.
marketplace since then. With the European Commission–backed (Full disclosure: I am a guest associate editor at Frontiers in Chem-
Plan S, which mandates OA publishing for research funded by istry, which charges and APC of $2,950.)
participating public agencies, going into effect last year, major
scholarly publishers introduced OA options to existing journals, When we turn our attention back to high-end titles such as the
created a mirror journal that was completely OA, or both. Under Nature Springer research journals, which each typically publish
a Transformative Agreement, a subscription-based journal must fewer than 200 articles per year, the linear model estimates a per-
gradually increase its share of OA papers and meet specific cri- article cost range of $7,400 to $9,400. Albeit calculated based
teria annually. These hybrid journals, though, are usually expen-
sive to publish in.

The million-dollar question is: Are these extremely high APCs
reasonable? Because many types of running costs, such as staff
wages, scale with the volume of the journal, it is not difficult to
grasp that the average cost per article depends on the number of
annual publications. A journal that publishes fewer articles needs
to charge a higher APC to maintain the same profit margin.

Let’s look at the journal eLife, the only journal published by eLife
Sciences Publications, a nonprofit organization that still relies on
funding agencies to a significant extent to keep revenues and expen-
ditures balanced and thus may be treated as a fair reference model
for analyzing publication costs that are not primarily fueled by APCs.
eLife was a no-cost-to-publish OA journal when it was launched in
2012, but five years later, it imposed an APC of $2,500, which was
further increased to $3000 in April 2021 (though authors may
request a waiver). During 2015–2020, the number of articles pub-
lished in eLife and the associated expenses steadily increased. By
dividing expenditures by the annual number of articles, we can esti-
mate how the cost per article scales with journal volume. Although

SUMMER 2022 | THE SCIENTIST 15

CRITIC AT LARGE

SCALABLE COSTS: Annual publishing volume, expenditure, and novelty and quality requirements associated with the brand
average costs to publish an article in the nonprofit OA journal name. Likewise, readers tend to choose references carrying a
eLife from 2015–2020. Inflation adjustment to the 2022 level was trustworthy reputation so they do not have to verify every con-
calculated based on the UK CPI data. clusion on their own benchtop.

$6,000 Publishing cost per article Things are slightly different in computer science, mathe-
$5,500 Total cost per article matics, and theoretical physics, where openly sharing preprints,
$5,000 source code, and data is a common practice. In these fields, audi-
$4,500 800 1,000 1,200 1,400 1,600 1,800 2,000 ences can usually verify and build upon the results published by
$4,000 Number of articles published per year others via standardized toolsets: programs should run in the
$3,500 same way on any computer, and derivations should follow the
$3,000 same norms in a chosen theoretical framework. Consequently,
$2,500 there is less need for a third-party authority, such as a pricey
$2,000 high-profile journal, to certify the quality of a study. Computer
scientists’ discontent with commercial journals eventually led
0 to a boycott of the journal Nature Machine Intelligence, which
was founded in 2018.
on a nonprofit operation model, these astonishing numbers DATA FROM: ELIFE SCIENCES PUBLICATIONS
are comparable to estimates made more than nine years ago. The subscription model was inherited from the paper media
Indeed, the controversial APC rates unveiled at the beginning era when communicating knowledge was expensive, and read-
of this year now seem reasonable. A high rejection rate in these ers chose to pay for what they could read. In this internet age,
journals further increases their running costs. Keep in mind that the ongoing evolution to OA publishing is more compatible
these journals are not only for-profit, but all the editors are full- with the needs of both authors and funding agencies, at least
time employees rather than academics who work with journals in experimental sciences. Under this new model, grant money
for little or no compensation. is now used to certify and publish resulting studies in a jour-
nal, whether it be society-run or commercial, meaning that
But there is still an unaddressed question. As customers—the funders and employers, not readers, are responsible for the
scientists who author papers to flesh out the corpus of the OA lit- cost of evaluating research.
erature—what are we buying from the publishers?
Before the transformation fully concludes, journals will still
To come up with an answer, I asked myself why I still seek court allegations of “double-dipping,” that is, receiving money
to publish findings in journals at all, even though file sharing is from both the libraries and authors when OA and paywalled
absurdly easy in this day and age. I can post my manuscripts on articles coexist in an issue. Several publishers have responded by
a WordPress blog or Reddit with a few clicks or choose a more either reducing the subscription fee or providing discounted or
formal path by leaving them on arXiv or other preprint servers fully waived APCs to institutional subscribers. However, estab-
without ever submitting a manuscript to a journal. Either way, lishing a fee model that satisfies all parties remains a challenge.
there is no publishing cost or paywall at all. There is more need now than ever for high-quality certification
and validation services provided by publishers. Funders and insti-
What researchers are paying for is a certification service— tutions must recognize the urgency of shifting resources from sub-
the credibility lent to research when it is published in a peer- scription to publication, and play an active role in negotiation
reviewed journal. This was not financially clear in the pay-to-read with publishers on fees and benefits.
era, but such services are backed by a collection of key components,
including the journal’s branding/reputation, the editorial and Most importantly, resources should only be allocated to
review services, and broader multimedia promotion. In partic- publishers that offer exemplary service and value in the mar-
ular, studies in life or physical sciences are usually not easily ket. And please don’t forget that scientists’ voices make a dif-
reproducible by peers without considerable human resources ference in decision-making processes, even at large, well-estab-
and money. Therefore, rather than seeking post-publication lished publishers and funders. By urging grant providers and
judgment (which, of course, is emerging but still far from main- institutions to allocate sufficient budgets toward publication
stream), most researchers want to get a stamp of approval from and providing feedback on each publisher’s service quality, we
a recognized journal to certify that their manuscript meets the will be able to navigate this pay-to-publish landscape as a cohe-
sive research ecosystem. g

Jingshan S. Du is a Washington Research Foundation Postdoctoral
Fellow at Pacific Northwest National Laboratory. He is an Early
Career Editorial Advisory Board member of ACS Biomaterials Sci-
ence & Engineering and Guest Associate Editor of OA journal Fron-
tiers in Chemistry.

16 THE SCIENTIST | the-scientist.com

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Notebook SUMMER 2022

SHANNON WILD Mongoose tion of free-living animals on Sorabi Rock WATCHFUL EYES: Dwarf mongooses (Helogale
Manners Lodge Reserve in South Africa. The proj- parvula) pay attention to conflicts among other
ect was initiated in 2011 by Julie Kern, members of their groups, a study suggests.
Agrowl from the aggressor, fol- then a master’s student at the university,
lowed by a hip-slam. High-pitched and has led to a number of findings about of various relatives and unrelated immi-
squeals of surrender as the loser how mongooses manage within-group grants. Though not as well-known as some
retreats. This is what a disagreement relationships, most recently as they relate of Africa’s iconic wildlife, dwarf mon-
between two dwarf mongooses (Helogale to food-based disagreements. In addition gooses have proved amenable to up-close
parvula) looks and sounds like. It’s usu- to shedding light on how friendships and observation, says behavioral ecologist
ally instigated by a dominant mongoose disputes are handled within mongoose Andrew Radford, Kern’s graduate advi-
that wants to steal prey from a subordi- society, results from the project could sor at Bristol. Indeed, the animals in the
nate, and it’s not uncommon, even in this have implications for scientists’ under- Dwarf Mongoose Research Project—now
highly cooperative species. standing of social animals more broadly, comprising eight groups—are habituated
say researchers. to the presence of researchers. Kern and
Researchers from the University of her colleagues have used elongated paint-
Bristol have been studying this and other Africa’s smallest carnivore—about brushes to individually mark the study
social behaviors in dwarf mongooses for the size of a 500 ml bottle when stand- animals with harmless blonde hair dye,
years as part of the Dwarf Mongoose ing upright—dwarf mongooses live in Radford notes. They’ve even trained some
Research Project, a long-term investiga- groups (sometimes called “businesses”)
of between 5 and 30 individuals, a mix

SUMMER 2022 | THE SCIENTIST 19

NOTEBOOK

of the mongooses to climb onto balance a specific subordinate out of its meals. Faye Thompson, a behavioral ecologist
scales to weigh themselves in exchange The track was played to the mongooses as at the University of Exeter who was not
for a piece of hard-boiled egg. they foraged over the course of an after- involved in the study, notes that a strength
noon, so that group members heard what of this research is the combination of
While they’re habituated to humans, sounded like repeated conflicts between natural observations and experimental
these animals are still in the wild and these two out-of-sight individuals. approaches. “This shows that these types of
going about their natural behaviors, says vocalizations provide rich social informa-
Radford, now the principal investigator of There did not appear to be any change tion to group members and that aggressive
the Dwarf Mongoose Research Project. He in behavior by the mongooses immedi- interactions can affect the social behavior
says the duration of the project has allowed ately after hearing the squabbles, says of the whole group,” she writes in an email
Kern, himself, and their colleagues to run Radford. But the researchers found that, from her field site in Uganda.
field experiments that might otherwise in the evening, mongooses that heard the
Although conflict management strat-
Group members heard what sounded like repeated conflicts egies are known to have evolved in many
between two out-of-sight individuals. social animals, little research had exam-
ined what happens beyond the immediate
be impossible. “The dwarf mongooses are simulated conflict reduced their grooming aftermath of a falling-out, says Radford.
this wonderful, tractable study system for of the perceived aggressor while grooming
big questions about cooperation and con- one another more than usual. The results, “This study adds a new perspective,”
flict and how those get mediated by vocal- published last November, suggest that says Bonaventura Majolo, a professor of
izations,” he says, adding that they are also mongooses not only tracked the behav- social evolution in the University of Lincoln’s
“amazingly cute and charismatic.” ior of their groupmates during the after- School of Psychology. Majolo, who was not
noon through their chatter, they acted on involved in the mongoose research, says the
A few years ago, Kern and Radford used that information later in the day by shun- study adds to a growing body of work sug-
audio playbacks to study how mongooses ning the bully (eLife, 10:e69196, 2021). The gesting that bystanders are also affected by
perceive groupmates’ actions, specifically researchers also saw hints that the simu- conflicts. “The results show that conflict
when it comes to an individual taking on lated victim received slightly more groom- has cascading effects on a number of indi-
more than their fair share of work. Groups ing than usual, although Radford says that viduals, not just those involved in the fight
of mongooses move around their terri- a larger sample size will be necessary to or the genetic relatives or friends of the for-
tory during the day, digging and foraging tease out the significance of these results. mer opponents,” he says. “Conflicts may have
for invertebrates and other prey, explains
Radford. Because they are vulnerable to a GROUP MEMBERS: Study coauthor Amy Morris-
number of predators, one mongoose often Drake with a dwarf mongoose in South Africa
serves as sentinel, foregoing eating so it can
monitor the surroundings, and announc- MARTIN AVELING
ing that it’s on watch with what is known
as a watchman’s song. In their experiment,
the researchers played recordings of songs
from specific dwarf mongooses to make
it seem like those individuals were doing
additional sentinel work and found that
those individuals were rewarded later that
day with extra grooming by their group-
mates (PNAS, 115:6255–260, 2018).

These findings inspired Radford’s
then–PhD student Amy Morris-Drake
to ask whether there might also be social
consequences for mongooses who weren’t
so well-behaved. Using recorded growls
and squeals, Morris-Drake, Kern, and
Radford crafted a recording simulating
one of the dominant mongooses bullying

20 THE SCIENTIST | the-scientist.com

SOCIAL TIME: Dwarf mongooses socialize as the
day comes to an end.

significant and long-term effects on how
social interactions are shaped in groups.”

Radford says that while it’s difficult
to extrapolate the findings to other spe-
cies, his gut tells him that other animals
may also keep tabs on bullies and dole out
punishment later. “There is no reason to
think that dwarf mongooses are unique
in this capacity,” he says. Majolo agrees,
saying that studies such as this one have
implications for understanding the socio-
ecological factors driving conflict and the
consequences for bullying in social ani-
mals more generally. “These studies on
animals are important for understanding
social evolution and in particular for mak-
ing inferences about human evolution,” he
says. “I believe the more we study other
species, the more we see that similarities
are more common than differences.”

—Mary Bates

SHANNON WILD What’s in a Wing 2016, and Bruce was working in Nipam produced somewhat ambiguous findings.
Patel’s lab at the University of California, Although Bruce hadn’t expected to have
For more than a century, research- Berkeley, with a little shrimp-like critter much more luck, her analyses using the
ers have argued over the evolution- called Parhyale hawaiensis, often used lab’s new CRISPR techniques were sup-
ary origin of insect wings. Although in developmental and genetics research. porting the idea that insects’ and crus-
many hypotheses have been proposed, She’d set out to determine how the seven taceans’ legs actually were homologous
biologists typically support one of two segments of each of the crustacean’s 14 if you simply counted segments from the
competing ideas: that wings evolved as an locomotory legs matched up with the leg tips in toward the body.
outgrowth from the tergum, a part of the six segments that make up each of an
body wall on an insect’s back, or that they insect’s six legs, to figure out which seg- But, Bruce wondered, what had hap-
originated in the pleura, the insect’s sides, pened to insects’ seventh leg segment—
which are themselves generally thought to What had happ­ ened the one that made up the top part of the
be derived from ancestral leg segments. to insects’ seventh leg leg in Parhyale, and was presumably
“[T]hese two schools of  thought have segment? present in a common ancestor of crus-
been in an intellectual battle for decades,” taceans and insects? And, for that mat-
Miami University evolutionary biologist ments were homologous to which. Other ter, what about the eighth leg segment
Yoshi Tomoyasu tells The Scientist in an researchers had previously attempted to found in some arthropods—and pre-
email. He calls the origin of wings “one of use gene expression assays to align the sumably in a common ancestor of the
the major mysteries in biology.” leg segments of the four major arthropod entire clade—but which neither Parhyale
When PhD student Heather Bruce groups (arachnids, crustaceans, insects, nor insects seem to have? Using genetic
began a last-minute thesis project on and millipedes and centipedes) and had knockouts and gene expression imag-
crustacean leg segments, she had no idea ing, Bruce found that Parhyale’s sev-
that she was wading into this compli- enth leg segment, the one closest to its
cated and long-standing debate. It was body, was in fact homologous to insect
pleura, while the eighth leg segment of
ancestral arthropods matched part of

SUMMER 2022 | THE SCIENTIST 21

NOTEBOOK

the tergum of both Parhyale and insects. outgrowth in Parhyale called the tergal new work, the team gathered further evi-
The data supported an old hypothesis plate (Nat Ecol Evol, 4:1703–12, 2020). In dence, this time in Parhyale. Using the
that ancestral crustacean leg segments other words, Bruce’s study supported the same CRISPR techniques as Bruce—which
had, over millions of years of evolution, idea that insect wings had evolved as out- Clark-Hachtel learned when she visited
become incorporated into the body wall growths of the tergum. the Patel lab at UC Berkeley—Tomoyasu
in insects and some other arthropods. and Clark-Hachtel knocked out vestigial
Century-old debates don’t get resolved and other genes associated with insect
Realizing that the project might reveal in a day, of course, and in the same issue wing development, and observed impaired
insights into the insect wing debate, of Nature Ecology & Evolution where development not only of the crustacean ter-
Bruce used fluorescent tags to visualize Bruce and Patel published these results, gal plate but also of the lobed outgrowths
the expression of vestigial, a gene asso- Tomoyasu and PhD student Courtney on the crustacean’s seventh leg segment—
ciated with wing development, in Par- Clark-Hachtel put forward data that the bit that appears to be homologous to
hyale and red flour beetles (Tribolium pointed to a different conclusion—namely, insect pleura. Expression data backed up
castaneum). She saw swipes of fluores- that wings evolved as outgrowths of both the idea that a gene network similar to the
cence in this incorporated eighth leg seg- tergal and pleural tissues. Tomoyasu’s one involved in insect wing development
ment area in both animals, suggesting that group had already published experiments “operates both in the crustacean terga and
this chunk of tissue was the evolutionary in red flour beetles to support this idea, in the proximal leg segments, suggesting
source of wings in insects, as well as of an called the dual-origin hypothesis. In the that . . . both of these tissues qualify as
potential crustacean wing homologues,”
they wrote in the paper (Nat Ecol Evol, ANDRZEJ KRAUZE
4:1694–702, 2020).

Despite these contrasting conclusions,
the researchers who spoke with The Scien-
tist agree that some sort of consensus
is growing. Bruce, who wrapped up her
PhD at UC Berkeley and moved with the
Patel lab to Marine Biological Laboratory
in Woods Hole, Massachusetts, says she
still thinks that the incorporated eighth
leg segment—the tergal piece—is the
primary and likely the sole contributor.
Tomoyasu says he agrees with the first
part—that the tergum “appears to be the
major source of insect wing tissue”—but
maintains that “there seem to be addi-
tional contributions from other tissues.”
He adds that he now suspects there may
be three distinct contributors. “At this
point, I think it is still elusive which of
these tissues contributed to the emer-
gence of the insect wing.”

University of Connecticut evolution-
ary biologist Elizabeth Jockusch, who
was not involved in either study but
who coauthored an accompanying per-
spective about the “duelling models,”
agrees that both papers provide con-
vincing evidence for the old hypothesis
that “chunks of the leg have essentially
become chunks of body wall.” But the
fundamental question remains: Did the
wings evolve from the tergal chunk or
the pleural chunk, or both?

22 THE SCIENTIST | the-scientist.com

PHOTOS BY HEATHER BRUCE, CURRENT BIOLOGY In December 2021, Jockusch and a HOMOLOGY HIGHLIGHTED: Red flour beetles “doesn’t favor either of those hypotheses
few other colleagues published a study of (Tribolium castaneum; top) and the crustacean about wings.” Rather, “what it says is we
milkweed bugs (Oncopeltus fasciatus) sug- Parhyale hawaiensis (bottom) show remarkable need other kinds of evidence.”
gesting that the story could be even more similarity in the expression of body patterning
complicated. Genes that researchers typ- genes (green) and of genes associated with wing Moreover, she adds, the origin of wings
ically use as signposts of wing develop- development in insects (magenta). is not the only facet of their evolution that’s
left unsettled. Hand in hand with the
ment, including vestigial, are expressed inquiry into wings’ evolutionary origins
in various projections, or outgrowths, is a lively discussion about their novelty—
of the insect body wall—not just in the whether they should be considered a com-
wings (Proc R Soc B, 288:20211808, 2021). pletely new structure or merely a modi-
“There’s these set of genes that people have fication of a homologous body part in an
thought of as wing genes and we think that ancestral animal. “I think that’s probably a
those ‘wing genes’ are probably more likely significant point of debate,” says Jockusch.
to be margin outgrowth genes,” says Jock- Evolutionary biologists have often argued
usch’s coauthor and former graduate stu- that wings are novel structures, but Bruce
dent Cera Fisher, now a postdoc at Cor- says she sees clear homology, and now sus-
nell University. The group has also found pects that true evolutionary novelty is even
“wing genes” at play in the development rarer than currently appreciated.
of elaborate helmets in treehoppers (fam-
ily Membracidae) (Nat Ecol Evol, 4:250– As for her introduction to these multi-
60, 2020). In terms of the tergum versus faceted debates about insect appendages
pleura debate, Jockusch says her work as the result of a last-minute change in her
thesis project, Bruce chuckles. “Luckily, it
actually was interesting.” —Jef Akst

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NOTEBOOK

© ISTOCK.COM, LAURENT OLIVIER Ocean Sounds the same neural circuits that govern SOCIAL SWIMMERS: Fish in the Haemulidae
vocalization in other vertebrates regulate family are known as grunts for the sounds they
Whales are famous for their sound production in fish. make by grinding their teeth.
songs, but fish are often
thought to be silent. Indeed, Aaron Rice of Cornell University got for they have no lungs, nor windpipe and
noise-making fish have historically been hooked on the idea of fish sound pro- pharynx; but they emit certain inarticu-
considered so unusual that whole fami- duction back in grad school in the early late sounds and squeaks.” Later studies
lies have been named for the sounds they 2000s. Scientists at the time knew that emerged sporadically in Europe during
produce. Fish like the Atlantic croaker some fish could and did make sounds, the Enlightenment. World War II proved
(Micropogonias undulatus), part of the Rice says, but little was known about pivotal, with the widespread use of sub-
drum family of fishes (Sciaenidae), make how or why they did it and the behavior marines exposing sailors to more under-
sound by vibrating specialized mus- was not appreciated as widespread. “As water sounds than ever before and helping
cles against their swim bladders. The a grad student, the idea of getting into a to advance hydrophone technology. From
grunts (family Haemulidae), meanwhile, field where there was so much to learn, 1950 to 1970, marine biologist Marie Fish
rub their pharyngeal teeth together, even at a basic discovery level, was excit- and engineer William Mowbray used
using their swim bladders as amplifiers. ing to me,” he tells The Scientist. hydrophones to listen to 220 species of
Although the sounds are produced by dif- fish, eventually compiling sound record-
ferent mechanisms, researchers charac- Although there aren’t many, reports of ings from 153 of them, including the had-
terize them all as vocalizations because fish sounds go back a long way. In his 4th-
century work Historia Animalium, Aris-
totle writes: “Fishes can produce no voice,

SUMMER 2022 | THE SCIENTIST 23

NOTEBOOK

dock (Melanogrammus aeglefinus), black NOT SO SILENT: Croakers (family Sciaenidae) Their analysis, published earlier this
drum (Pogonias cromis), and bluestriped vocalize by vibrating muscles against their year, suggests that two-thirds of all act-
grunt (Haemulon sciurus), among others. swim bladders. inopterygian species belong to families
that contain at least one sound-producing
These days, Rice says, hydrophones extant ray-finned fish families, which
are cheap and powerful, making number in the hundreds. fish, and that vocalization has indepen-
large-scale underwater dently evolved 33 times across
eavesdropping possible. Combing the literature, Rice and col- the clade (Ichthyol Her-
Still, most underwa- leagues turned up reams of accounts of act- petol, 110:1–12, 2022).
ter acoustic research inopterygian sound production. Combining That’s a lot more than
focuses on whales and this with analyses of fish morphology in some other taxa.
other cetaceans, and allowed the researchers to predict new Among terrestrial
many questions about fish candidates for sound production, based vertebrates, for exam-
vocalizations remain unanswered. on morphological characteristics in fish ple, research indicates that
While fish appear to use sound for the families and evolutionary relationships
same purposes that other vertebrates do— with known sound-producing fishes, vocalization has evolved just once in
typically to attract mates or chase away while bioinformatics approaches probed each of the six major clades.
competitors—it was unclear how common when and how often the phenomenon had
the phenomenon is. evolved in the clade. Vocalization therefore appears to be
both widespread and highly important
To find out, Rice recently set out to do in fish, says Rice. If it had arisen just
a large-scale survey of published research once, he explains, researchers might have
on sound production in ray-finned fishes, thought it was simply an evolutionary
or actinopterygians, which represent holdover from a common ancestor. The
more than half of all vertebrate species. fact that it evolved multiple times across
“Working with a [clade] with 34,000 spe- families and geographies suggests that it
cies is a massive undertaking,” he says. serves an important adaptive function for
So the researchers went with a family- many different kinds of fish in many dif-
level analysis, rather than a species-level ferent contexts.
one, relying on a recent phylogeny of
Washington State University neuro-
scientist Allison Coffin says the paper is ANDRZEJ KRAUZE; © ISTOCK.COM, PUNGEM
a “tour de force” and a “really comprehen-
sive evolutionary study.” She adds that it
fills a gap in existing research. Figura-
tively speaking, where many studies to
date have been an inch wide and a mile
deep, focusing on one or a few species,
this study is an inch deep and a mile wide,
she explains.

The study also suggests that research-
ers could study vocalization behaviors
in many more species than they have
until now, Coffin adds. Her research
is focused on fish hearing, and some
of her lab’s work has found that female
midshipman fish (genus Porichthys) are
better able to hear male calls thanks
to the growth of additional specialized
hair cells during the breeding season.
Fish in closely related genera don’t show
this trait, Coffin says. But after reading
Rice’s argument that sound production
itself evolved independently so many
times, she wonders: “Could seasonal
changes in sound reception have evolved
independently multiple times as well?”

24 THE SCIENTIST | the-scientist.com

HEIDI FISHER Kieran Cox, a postdoctoral fellow Peromyscus genus, which Hook studies, BETTER TOGETHER: Some researchers have
at Simon Fraser University in British but across almost all mice—which is why hypothesized that in species such as Peromyscus
Columbia, says the study provides a it’s so surprising that scientists don’t know maniculatus, hooks may help sperm aggregate
strong foundation for future work. Cox, what they’re for. and swim faster en masse than they could alone.
whose own work focuses on incorporat-
ing bioacoustics, particularly among fish, Despite their singular purpose—fer- be advantageous in more-promiscuous
into conservation efforts in marine eco- tilizing an egg—sperm are among the mouse species, in which females mate
systems off the coast of Canada, is work- most diverse cell types on Earth. “Some with multiple males in quick succession,
ing on a species-level analysis of sound have multiple hooks [while] some have with particularly hooky sperm gaining a
production in fish that he says builds on multiple heads. . . . They have this huge boost over sperm from other males.
the family-level work done by Rice and his amount of diversity of sizes and shapes,”
coauthors. Before the study by Rice and Fisher, an evolutionary biologist, tells But there was counterevidence, too.
his colleagues helped identify families The Scientist. “The question is, why?” The sperm from some mouse species don’t
likely to contain vocalizing fish, trying to She says that Hook, now a biologist aggregate. In fact, sperm aggregation is
categorize sound production at a species with the US Government Accountability rare. Evolutionary biologist Renée Firman
level was simply too big a job. “Sonifer- Office, was an excellent person to have of the University of Western Australia, for
ous fishes, to some extent in their current on the case—and not just because of her example, has surveyed the sperm morphol-
prevalence, are a needle in a haystack,” last name. ogy of various Australian mouse species,
he says. The Cornell team’s paper breaks including the sandy inland mouse (Pseu-
up a 34,000-strand haystack into many A clue about sperm hook function domys hermannsburgensis). In 2013, she
smaller ones. seemed to emerge about two decades ago, published a study detailing that these mice
when a study in wood mice reported that have “elaborate sperm hook complexes,”
The work should also be a reminder hooks help sperm lock together—either at Firman says, that contain three individual
of what Cox calls the single largest form their heads or head to tail—to form clus- hooks—but the sperm don’t clump together.
of unregulated pollution in the world’s ters or trains that swim faster than indi-
oceans: noise. He’s part of the team that vidual cells do. This speediness might
launched the open source FishSounds
website, a global inventory of fish sounds
and research. Human-made soundscapes
could have a big impact on fish behav-
ior, he says—for example, noise pollution
that keeps animals from hearing potential
mates could impact the reproductive suc-
cess of that population. If it turns out that
many species of fish are relying on noise
for mating or other behaviors, the rami-
fications could be substantial. “Fish that
produce noise aren’t doing so in isolation,”
Cox says. “They’re interacting with habi-
tat, other fish, other noises, [and] chang-
ing soundscapes.” —Connor Lynch

Hooked

If you look at a mouse sperm cell
through a microscope, as postdoctoral
researcher Kristin Hook did hundreds
of times while working in Heidi Fisher’s
lab at the University of Maryland, College
Park, you’ll likely see a striking, talon-like
hook curving from its head. These sperm
hooks are found not only in animals in the

SUMMER 2022 | THE SCIENTIST 25

NOTEBOOK

Peromyscus is a great system to test HELP OR HINDRANCE? A study of sperm hooks hooklessness is not representative of P. leu-
hypotheses about sperm hooks, says in Peromyscus leucopus finds that larger hooks copus as a whole.
Fisher. Closely related species in this genus hinder the sperm’s swimming.
vary in how promiscuous they are—some Firman says that the results are consis-
species are monogamous, while others only aggregation, but an individual sperm’s tent with her findings in Australian wild
have multiple mates—and only some spe- swimming. And, thanks to a lucky break, mice. “There’s no evidence [in the Cells
cies’ sperm group together, even though the pair was recently able to test this idea. study] to suggest that . . . the mouse hook
all of them have hooks. In one study, pub- A few months ago, as Hook was taking vid- has something to do with sperm compe-
lished online last fall, she, Hook, and PhD eos of a sample of Peromyscus leucopus tition,” she says. But Eduardo Roldan,
student David Webber found that sperm sperm in a petri dish to document their an evolutionary biologist at the Spanish
aggregations in polygamous Peromyscus size and speed, she noticed that the sperm’s National Research Council in Madrid,
mice swim faster than those in monoga- hooks were missing. She immediately ran says he still thinks there is a role for sperm
mous species, supporting the idea that next door to tell Fisher. Fisher was initially hooks in sperm competition in some spe-
aggregation has something to do with skeptical—it’s hard to see hooks on sperm cies. “My general . . . conclusion is that
sperm competition (Behav Ecol, 33:55– as they’re darting around in a petri dish, there may be differences between spe-
64, 2022). she tells The Scientist. But Fisher took a cies or between groups of species as to
look and saw, to her surprise, that the how the hook serves either to aggregate
To measure how sperm hooks influence sperm were indeed hookless. sperm or influence swimming patterns,
aggregation, Hook and Fisher recorded not only velocity but also the trajectory
videos of sperm from six species of Pero- Fisher told Hook to move quickly and of the sperm,” he says. Even though big-
myscus, analyzing how the hooks’ length, preserve the sperm, as well as every tis- ger hooks can prevent sperm from form-
width, and curvature affected the number sue in the mouse they came from, think- ing aggregates, for example, some cross-
of sperm in aggregates. The evidence sug- ing they might have stumbled on some- species studies show that, compared to
gested that there was an optimum hook size thing very rare. But just a few weeks later, males in less-promiscuous species, males in
for sperm clumping: while the structures Hook found another male with hookless more-promiscuous species produce sperm
were necessary for fast-moving sperm bun- sperm. Then another, and another. After with larger hooks that curve more tightly,
dles to form, bigger hooks prevented sperm they’d analyzed dozens of animals, the perhaps influencing swimming patterns.
from grouping effectively. But the research- researchers realized that about 1 in 10
ers also found that hook size showed no animals in their Peromyscus mouse col- Fisher says she thinks that, instead
correlation with species’ promiscuity, leav- ony don’t have hooks. of influencing aggregation or swimming
ing the link between hook size and sperm speed, sperm hooks might have “something
competition murky (Cells, 10:2279, 2021). to do with the female reproductive tract

One possibility, Hook and Fisher real- If you look at a mouse sperm cell through a microscope, you’ll
ized, was that hooks might influence not likely see a striking, talon-like hook curving from its head.

It was the perfect opportunity to test or interactions with the egg.” The sperm, KRISTIN HOOK
the hypothesis that hooks increase the Fisher says, could be using their hook to
speed of individual sperm, Fisher says. snag onto the sides of the female reproduc-
But after analyzing more than 30 ani- tive tract, staying there longer so as not to
mals, both with hooks and without, Hook expend too much energy as they swim up
found the opposite. “[The hook] seems to the tract and wait for fertilization. “Most of
slow them down as single cells, which is us in the field assume that [sperm] diver-
interesting,” Fisher says. “Why is it in most sity has come from . . . diverse mechanisms
sperm in most species if it inhibits sperm or modes of fertilization . . . or the coevolu-
velocity?” The hooks also didn’t seem nec- tion of sperm shape with different features
essary for a male to reproduce—mice with of the female reproductive tract,” she says.
hookless sperm were fertile, although they She adds that Hook’s studies help bring the
seemed to have lower sperm counts. Fisher field one step closer to linking the “form
says she suspects that the hookless sperm and function” of sperm, giving insight into
may have arisen spontaneously as a result why sperm have the diversity that they do.
of the mice being in captivity, and that
—Natalia Mesa

26 THE SCIENTIST | the-scientist.com

STREAMLINING
QPCR THROUGH
STANDARDIZATION

Quantitative real-time PCR (qPCR) is highly
popular, but this has led to a wide array of qPCR
protocols, reagents, cycle steps, analysis methods,
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workflows incorporate automation, is therefore vital
for qPCR data consistency, reproducibility,
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A VIRUS’S CREDIT LINE

Only recently appreciated as critical components of cellular
functions, unstructured stretches of amino acids called SLiMs
are key to viral-host interactions.
BY CONCHITA FRAGUAS BRINGAS AND JAKOB NILSSON

© ISTOCK.COM, DESIGN CELLS

28 THE SCIENTIST | the-scientist.com

CREDIT LINE

SUMMER 2022 | THE SCIENTIST 29

During an early COVID-19 lockdown in March 2020 in CoV-2’s nucleocapsid (N) protein, which packages the viral RNA
Copenhagen, Denmark, we, like many in the scientific and is critical for viral replication, and the human stress granule
community, turned our attention to SARS-CoV-2, the proteins G3BP1 and G3BP2. A cell forms stress granules upon
virus responsible for the world-changing disease. Things were sensing a stressor such as a virus. Alongside other functions, this
moving at a fast pace. Every day, countless papers were published causes the cell to stop protein production and minimize energy use,
with clues to how this virus invades our cells and wreaks havoc which can hamper viral functions, and viruses have evolved to dis-
in our bodies, with the hope of slowing its spread and helping rupt this and other defense mechanisms.
the infected.
Our team at the University of Copenhagen’s Novo Nordisk In this context, we showed that SARS-CoV-2’s N protein dis-
Foundation Center for Protein Research wanted to contribute to rupts stress granules by binding to G3BP proteins via a SLiM-
the global research effort by studying the interactions between based interaction that supports viral replication. Furthermore,
viral and host proteins. Specifically, we wanted to look for the role to exploit this SLiM-based interaction, we developed a strong
of a type of protein interaction that is relatively new to science, peptide inhibitor that significantly hampered viral proliferation
one that involves short stretches of amino acids known as SLiMs in cells. This exposes an attractive avenue to follow for antiviral
(short linear motifs). While the traditional structure-begets- drug development, focusing on these short and elusive motifs,
function mentality regarding protein interactions had largely shown to be critical components in viral-host interactions.
overlooked the unstructured protein regions and the short motifs
within them, the past few decades have challenged this view, as As we look back at the evolving field of protein interactions,
researchers have documented the importance of SLiMs in a wid- it’s exciting to consider just how recently the discovery of SLiMs
ening range of cellular functions. rests on the timeline. Protein regions that were once ignored,
grouped with others that lacked a defined structure, are now a
In the late 1990s, it became growing focus in protein research, providing a new lens through
clear that unstructured protein which to study cellular function and disease. Beyond the more
regions were not only abundant, traditional view that protein interactions are mainly mediated
they mediated important by well-structured, three-dimensional domains whose interac-
cellular functions. tions tend to be strong and long-lasting, we are coming to appre-
ciate the transient and complex nature of proteins and the sig-
What first drew our attention to SLiMs at the onset of the naling networks they build, the foundation of cellular biology as
COVID-19 pandemic was the increasing recognition that many we know it.
pathogens have evolved to “mimic” host SLiMs. With only a few
amino acid changes, viruses can become equipped to interact with Paradigm shift
key host proteins and thereby meddle in critical cellular functions There are more than 20,000 proteins encoded in the human
to promote viral proliferation or avoid detection by the immune genome, and if you look at any structure in the RCSB Protein
system. In fact, many SLiMs were first discovered in viruses Data Bank, you will likely find that one part is consistently
before they were described in non-viral proteins. missing—a region that researchers could not solve. This is com-
monly seen in protein regions that lack a three-dimensional
Together with our collaborators in Sweden and London, we structure. For decades, these cases were dismissed as excep-
developed a novel pipeline to discover SLiMs in viral-host inter- tions because the scientific community thought that a protein’s
actions.1 Our work revealed a specific interaction between SARS- distinct three-dimensional structure determined its function,
governing how it can interact with other proteins, like a key fit-
ting neatly into a lock.

This idea was first described by German chemist Emil Fischer
at the turn of the 20th century, and his hypotheses largely aligned
with the results of many researchers interrogating protein struc-
ture over the second half of the 20th century, determined with

30 THE SCIENTIST | the-scientist.com

SLiM BASICS

In the early days of studying protein behavior, researchers recognized that large, structured protein domains often interacted with each other in a
lock-and-key fashion, fitting together almost like puzzle pieces. Toward the end of the 20th century, however, the growing discovery of previously
overlooked unstructured regions suggested that there was more to the story. One type of protein interaction mediated by the unstructured pro-
teome involves short linear motifs (SLiMs), abundant stretches of up to 10 amino acids. Their interactions with other proteins are generally tran-
sient and weak, but SLiMs are nevertheless significant contributors to protein function and regulatory mechanisms in the cell.

Structured protein domains SLiMs

Approximately 50–200 amino acids, with several points of contact Just ~2–10 amino acids, with only 2–3 that act as core
binding determinants
Distinct three-dimensional structure Lack a three-dimensional structure
Strong and often long-lasting interactions, such as in protein complex formation Weak, transient interactions
Bind domains of other protein partners, interactions that often resemble a
lock-and-key mechanism Typically bind to a conserved pocket on a globular protein domain

SLiM

© SCOTT LEIGHTON the help of novel techniques such as X-ray crystallography and these posed a new challenge to protein biologists: How can we
nuclear magnetic resonance spectroscopy. But while these often study such unstructured proteins if there is no structure to solve?
strong interactions between well-structured protein regions Where do we start?
undoubtedly hold a critical place in biology, the focus on them
overlooked countless unstructured regions that exist in the pro- Turning to bioinformatics, researchers uncovered many
teome. That all changed in the late 1990s when it became clear interactions within disordered protein regions, with the major-
that these unstructured protein regions were not only abundant, ity of interactions taking place between short stretches of just
they mediated important cellular functions. 2 to 10 amino acids—SLiMs, a term coined in 2006 by a group
at the University College Dublin Conway Institute of Bio-
This shift in our thinking, coupled with new biochemical and molecular and Biomedical Sciences.2 Compared with other types of
computational tools, resulted in the recognition of a new class of interactions, these motifs bind weakly and transiently, often to con-
proteins that are unstructured, or intrinsically disordered. But served pockets on globular proteins. (See illustration on page 32.)

SUMMER 2022 | THE SCIENTIST 31

SLiMS IN SARS-COV-2 INFECTION

SARS-CoV-2 appears to take advantage of the host stress granule machinery deployed in response to viral infection to favor its prolif-
eration. Specifically, our work shows that its nucleocapsid (N) protein, responsible for encapsulating viral RNA and coordinating replica-
tion and other functions, contains a SLiM that competes with cellular proteins in binding with stress granule–forming proteins, namely
G3BP1 and G3BP2 (G3BPs). In doing so, the virus effectively promotes its proliferation while dampening the cell’s antiviral defenses.
Targeting these SLiM-mediated protein interactions may one day prove to be a feasible antiviral therapy approach.

Upon viral entry, stress NORMAL STRESS RESPONSE
granules assemble in the
cell’s cytoplasm In response to viral infection or other stress-
ors, cells form stress granules, membrane-
mRNA RNA-binding Stress less organelles that contain host mRNA, viral
proteins granule RNA, translation factors, and RNA-binding
proteins. These include G3BPs, which bind
Viral Cytoplasm to other stress granule proteins via an ΦxFG
RNA SLiM, where Φ represents a hydrophobic
Cellular proteins bind amino acid, x represents any residue, and F
G3BPs via ΦxFG SLiMs and G represent phenylalanine and glycine,
in stress granules respectively. This response causes cells to
limit their energy use and restrict protein
ΦxFG production. Because viruses need the cellular
machinery to produce their viral proteins and
proliferate, the stress response can hamper
this, with stress granules often associated
with an antiviral role.

G3BP ΦxFG
ΦxFG

Nucleus

Restricted protein
production limits
viral proliferation

32 THE SCIENTIST | the-scientist.com

SARS-COV-2 INFECTION
In the case of SARS-CoV-2, we found in human cells that the N protein is able to bind G3BP proteins via an ΦxFG SLiM, pos-

sibly to localize viral replication to stress granules in early infection. As levels of the SARS-CoV-2 N protein increase in later
infection stages, N effectively displaces all cellular proteins from G3BPs and disrupts cytoplasmic stress granules. This ulti-
mately promotes viral proliferation and the dampening of antiviral defense mechanisms.

Early SARS-CoV-2 infection Late SARS-CoV-2 infection

SARS-CoV-2
enters the cell

High levels of N Virus proliferates
protein are reached
Stress granules
SARS-CoV-2 N Cellular proteins are disrupted
protein competitively are displaced
binds G3BP proteins and cannot
(G3BPs) and localizes bind G3BPs
to stress granules

ΦxFG

SARS-CoV-2 N

G3BP

© SCOTT LEIGHTON

ΦxFG G3BPi binds strongly to Viral TARGETING STRESS
G3BPs, displacing the proliferation GRANULE FORMATION
G3BP SARS-CoV-2 N protein
inhibited Based on these findings, we designed a pep-
G3BPi tide inhibitor containing ΦxFG-like SLiMs
that bound strongly to G3BPs, preventing the
binding of SARS-CoV-2 N protein in human
cells. This peptide (G3BPi) inhibited viral
proliferation in a monkey cell line commonly
used in SARS-CoV-2 studies, though the
specific downstream mechanisms remain
to be elucidated.

SUMMER 2022 | THE SCIENTIST 33

In the ’90s and into the early 2000s, investigations into G3BPs have been linked to innate immune signaling and
SLiMs linked these motifs to many important cellular func- are known effectors in the assembly of stress granules, dynamic
tions in higher eukaryotes, including protein localization, gene structures composed of proteins and RNA that form in response
expression, cell cycle control, and protein degradation via the to diverse cellular stresses such as viral infections. During the
proteasome. SLiMs work alongside structured protein domains stress granule response, cells will limit their energy expenditure
to ensure the maintenance of cellular signaling networks. Given and, among other functions, restrict protein production. Because
their importance, it isn’t surprising that SLiMs are often dysreg- viruses need cellular machinery to produce their viral proteins
ulated in diseases such as cancer. Ongoing computational efforts and proliferate, stress granules can hamper this co-option. But
aid in motif discovery and help to grow databases compiling viruses have evolved a counterattack.
unstructured proteins and their mounting numbers of known
interactions. A recent prediction estimates that the number of SLiMs offer a versatility that
SLiMs in the human proteome exceeds 100,000, and that num- structured protein domains
ber skyrockets to nearly a million when post-translational modi- cannot achieve alone, providing
fications are considered.3 a fast and simple way for new
protein interactions to arise.
Because they are so short, SLiMs can easily arise through muta-
tion. They thus offer a versatility that structured protein domains
cannot achieve alone, providing a fast and simple basis for new
protein interactions and thereby allow organisms to rapidly adapt
to their changing environment. This feature, however, also makes
these motifs easy targets for pathogens to tap into host biology.

Viral hijacking Various studies have described multiple viral proteins that can
Viral protein sequences that mimic cellular SLiMs interfere with recruit G3BP1/2 and other stress granule components to disrupt
a range of host processes, exploiting cellular transport machin- stress granule formation or facilitate viral replication. More-recent
ery, manipulating signaling pathways, and otherwise making work has revealed that the SARS-CoV-2 N protein interacts with
themselves at home. In 2018, for example, our group showed that the G3BP proteins and that this leads to the disruption of stress
the nucleoprotein of Ebola virus mimics a SLiM binding a host granules.7,8 These studies even pointed to the N protein’s amino-
phosphatase to facilitate viral transcription.4 And the LMP1 pro- terminal domain, where we found the G3BP-interacting SLiM, as
tein from the Epstein-Barr virus contains a SLiM that mimics a being central in this role. We thus suspected that this SLiM—a
motif in CD40—a protein involved in the activation of antigen- so-called ΦxFG SLiM, where Φ represents a hydrophobic amino
presenting cells—allowing the virus to interfere with the host’s acid, x represents any residue, and F and G represent phenylalanine
immune defense.5 and glycine, respectively—could help promote viral replication in
the face of a cellular stress response. (See illustration on page 32.)
Several years ago, our Uppsala University colleague Ylva
Ivarsson and her collaborators showed that proteomic peptide- We transfected cultured human cells with the SARS-CoV-2
phage display (ProP-PD), a technique useful for screening other N protein, either containing the ΦxFG motif or a mutated motif,
protein interactions, can help identify SLiM-based protein inter- and used live cell microscopy to image G3BP1 and thereby visu-
actions.6 In a nutshell, this approach involves a library of bacte- alize stress granule formation in response to an introduced
riophages that are engineered to display peptides in their exposed stressor, the compound arsenite. We found that stress gran-
coat protein. The phages are then presented to bait proteins, some ules were disrupted in cells expressing the N protein with an
of which will bind to the displayed peptides. Bound phages are intact ΦxFG but not with the SLiM-mutated N protein. We then
then sequenced to find out which peptide motifs interacted with infected monkey cells (commonly used in studies of SARS-CoV-2
which bait proteins. To apply this to SLiMs, researchers engi- and other viruses) with SARS-CoV-2 and examined the local-
neered phages to present unstructured protein regions. ization of G3BP1, the N protein, and viral RNA using immuno-
fluorescence. Intriguingly, when levels of SARS-CoV-2 N were
Using this technology, we and our collaborators designed a relatively low, we saw normal stress granule formation, with all
unique ProP-PD library, with phages displaying nearly 20,000 three molecules found clustered in the granules. But as infection
unstructured regions of more than a thousand viral proteins advanced and viral N protein levels increased, we could no longer
from 229 RNA viruses, including 23 coronaviruses. We presented detect any G3BP1 granules. This made us suspect that the viral
these to known globular domains from human proteins that had N protein is tapping into the stress granule machinery at early
been previously linked to viral-host interactions, uncovering a stages of infection, but once a threshold level of N viral protein
total of 117 SLiM-based human-coronavirus protein interactions.1 is reached, the stress granules are disrupted.
Turning our focus to SARS-CoV-2, we found that a peptide con-
taining an unstructured region of the viral N protein was bind- Still, the mechanism by which this all happens wasn’t clear.
ing a specific domain in the human proteins G3BP1 and G3BP2. We wondered which cellular proteins might be using this SLiM

34 THE SCIENTIST | the-scientist.com

to bind the G3BPs—that is, which cellular proteins was the viral Conchita Fraguas Bringas is a PhD fellow at the University of
SLiM mimicking? If we could learn more about the process in Copenhagen and a past member of Jakob Nilsson’s group at the
the absence of infection, perhaps we could obtain a clue about the university’s Novo Nordisk Foundation Center for Protein Research.
ΦxFG-mediated pathways the virus was tampering with. Nilsson, a biochemist and cell biologist, focuses on SLiMs in the
regulation of cellular signaling.
For this we prepared a second ProP-PD library, this time dis-
playing disordered protein regions of the human proteome, and References
used the conserved SLiM binding domain on G3BPs as bait. We
identified 72 peptides that bound these proteins, with most of 1. T. Kruse et al., “Large scale discovery of coronavirus-host factor protein
them containing an ΦxFG SLiM. Nineteen of these belonged to interaction motifs reveals SARS-CoV-2 specific mechanisms and
stress-granule associated proteins. Because the N protein is the vulnerabilities,” Nat Commun, 12:6761, 2021.
most abundant viral protein during infection, we hypothesized
that it could compete with these host proteins for binding to the 2. N.E. Davey et al., “SLiMDisc: Short, linear motif discovery, correcting for
G3BP proteins. Sure enough, quantitative mass spectrometry common evolutionary descent,” Nucleic Acids Res, 34:3546–54, 2006.
revealed this to be the case, with binding analyses confirming
that ΦxFG-containing host proteins are displaced by the SARS- 3. P. Tompa et al., “A million peptide motifs for the molecular biologist,” Mol
CoV-2 N peptide. Cell, 55:161–69, 2014.

We considered whether these ΦxFG-mediated interac- 4. T. Kruse et al., “The Ebola virus nucleoprotein recruits the host PP2A-B56
tions could be targeted for therapeutic applications and sought a phosphatase to activate transcriptional support activity of VP30,” Mol
high-affinity peptide that would prevent viral N protein–G3BP Cell, 69:136–45.e6, 2018.
interactions. Aided by previous research on G3BP binding to viral
proteins in another RNA virus,9 we engineered a G3BP inhibitor 5. O. Gires et al., “Latent membrane protein 1 of Epstein-Barr virus interacts
(G3BPi). The designed peptide inhibitor successfully prevented the with JAK3 and activates STAT proteins,” EMBO J, 18:3064–73, 1999.
N protein binding to G3BP1 in cultured human cells and potently
inhibited SARS-CoV-2 proliferation after 16 hours of infection.1 6. Y. Ivarsson et al., “Large-scale interaction profiling of PDZ domains
Excitingly, earlier this year a research group at the department through proteomic peptide-phage display using human and viral phage
of biochemistry at the University of California, Riverside, solved peptidomes,” PNAS, 111:2542–47, 2014.
the structure of G3BP1 bound to SARS-CoV-2 N, confirming that
this molecular interaction is largely mediated by the ΦxFG SLiM.10 7. J. Wang et al., “SARS-CoV-2 nucleocapsid protein undergoes liquid–liquid
The results revealed that the SLiM occupies a conserved pocket in phase separation into stress granules through its N-terminal intrinsically
G3BP1’s globular domain, validating our conclusions and shedding disordered region,” Cell Discov, 7:5, 2021.
light on our proposed binding mechanism. Furthermore, it serves
as a key example of a SLiM binding a conserved pocket on a globu- 8. L. Luo et al., “SARS-CoV-2 nucleocapsid protein phase separates with
lar protein domain, elucidating the nature of SLiM-based interac- G3BPs to disassemble stress granules and facilitate viral production,”
tions and highlighting their therapeutic potential. Sci Bull, 66:1194–204, 2021.

SLiMs are shaping up to be major regulatory motifs in cellular 9. T. Schulte et al., “Combined structural, biochemical and cellular evidence
biology, from stress granule formation to innate immune signal- demonstrates that both FGDF motifs in alphavirus nsP3 are required for
ing. In the context of infection, this raises questions about how efficient replication,” Open Biol, 6:160078, 2016.
a pathogen can rewire host protein networks to its own benefit.
Despite their abundance and functional importance, super-short 10. M. Biswal et al., “SARS-CoV-2 nucleocapsid protein targets a conserved surface
and quickly-evolving SLiMs are challenging to study. Traditional groove of the NTF2-like domain of G3BP1,” J Mol Biol, 434:167516, 2022.
biochemical methods and technologies such as mass spectrom-
etry screens tend to be biased toward stronger binding interac-
tions. And although computation can allow us to predict the exis-
tence of SLiMs, experimental validation is still needed.

These are exciting times, as we move forward holding a flash-
light in what seems to be a dark room filled with an overwhelm-
ing number of protein interactions that support life at the most
basic level. But with novel approaches such as ProP-PD, alongside
up-and-coming biochemical and computational tools, the field is
becoming equipped to fully explore the unstructured proteome.
Results from our group and others remind us to keep an open
mind regarding how proteins function, as it’s now abundantly
clear that structure cannot tell us the whole story. 

SUMMER 2022 | THE SCIENTIST 35

DIY CELLS: UNDERSTANDING
LIFE WITH A SYNTHETIC
MINIMAL CELL

In this episode, The Scientist’s Creative Services
Team spoke with John Glass, a professor and
leader of the synthetic biology and bioenergy
group at the J. Craig Venter Institute, about how
his team achieved this scientific milestone and its
significance for understanding life itself.
JOHN I. GLASS, PHD

Professor and Leader
Synthetic Biology

and Bioenergy Group
J. Craig Venter Institute

LISTEN HERE

viewonline.the-scientist.com/diy-cells-understanding-
life-with-a-synthetic-minimal-cell

36 THE SCIENTIST | the-scientist.com

CREDIT LINE Schizophrenia &
MODIFIED FROM © ISTOCK.COM, VIKI, YODIYIM the Immune System

Several lines of evidence suggest that targeting the body’s
defense pathways might help treat a subset of people with
the psychiatric disorder. But many open questions remain.

BY DIANA KWON

SUMMER 2022 | THE SCIENTIST 37

Susannah Cahalan was 24 years old when her world turned There were records of
upside down. influenza pandemics whereby
Cahalan was living a busy life as a news reporter at the people acutely affected
New York Post when she suddenly began experiencing sensitivity to with influenza acted in ways
light, numbness in her limbs, and an unsettling feeling that some- consistent with what we now
thing was not quite right in her body and her brain. One day at understand to be psychosis.
work, she found herself inexplicably going from crying hysterically
to skipping giddily down a hall. After a seizure landed her in the —Thomas Pollak, King’s College London
hospital, her condition rapidly worsened. She started having delu-
sions and hallucinations, believing that her father was a murderer, encephalitis was a game changer. Not only did it lead researchers
that she was being secretly recorded, and that she could age peo- to uncover more than a dozen other autoimmune diseases of
ple using her mind. In a matter of weeks, walking, speaking, and the brain, but the uncanny similarities between the psychotic
swallowing became difficult. She eventually became immobile and symptoms of autoimmune encephalitis and schizophrenia gen-
unresponsive, lying in her hospital bed in a catatonic state. erated a flurry of interest among scientists seeking an answer
to an age-old question: What role does the immune system
Despite her worsening condition, dozens of specialists play in schizophrenia?
from various fields—psychiatry, neurology, internal medicine—
couldn’t figure out what was wrong. Numerous blood tests and The neurological underpinnings of schizophrenia have long
brain scans failed to generate answers. To many who saw her, eluded scientists. In some instances, people diagnosed with
Cahalan’s condition looked indistinguishable from mental ill- schizophrenia were later found to have other ailments, includ-
nesses such as bipolar disorder or schizophrenia, in which peo- ing anti-NMDAR encephalitis. The majority of schizophrenia
ple can experience delusions and hallucinations that make it patients still await answers. Evidence from many lines of research,
difficult for them to distinguish what’s real and what’s not. It including epidemiology and genetics, point to the possibility that
wasn’t until a neurologist asked Cahalan to draw a clock that the in at least a subset of schizophrenia cases, the immune system is
problem became clear. Cahalan had drawn all the numbers on the culprit. Many research groups continue to hunt for clues, and
just one side of the clock face, indicating that there was a prob- as part of this search, several are assessing whether therapies that
lem in the functioning of one half of her brain. target the immune system might also benefit those with schizo-
phrenia and other psychiatric illnesses.
A brain biopsy confirmed what the doctor had suspected.
Cahalan had anti-NMDAR encephalitis, a rare autoimmune disease Some researchers remain skeptical that the immune system
in which the body produces antibodies that attack the NMDA recep- plays a meaningful part in mental illnesses that are not clear-cut
tor, a protein found throughout the brain. The condition had only cases of autoimmunity. But others are optimistic. “I’m hopeful
been discovered in the early 2000s, just a few years prior to Cahalan’s that this is a new era for schizophrenia research,” says Belinda
diagnosis, by neurologist Josep Dalmau, then at the University of Lennox, a professor of psychiatry at the University of Oxford
Pennsylvania.1 This diagnosis was much-needed good news for in the UK. “I think getting people excited and interested in the
sufferers of the mysterious condition—their disease was treatable. immune system in schizophrenia can only be for the benefit of
After receiving immunotherapy, Cahalan was able to fully recover. patients, because we’re so desperately in need of new treatments
and for a better understanding of the causes.”
Cases like Cahalan’s, which she details in her memoir Brain
on Fire, are rare. The estimated occurrence of anti-NMDAR
encephalitis is just 1.5 cases per 1 million people each year.
Despite the disease’s rarity, the discovery of anti-NMDAR

38 THE SCIENTIST | the-scientist.com

The infection connection in the blood of some patients, suggesting that exposure to the parasite
Following large outbreaks of influenza in the 1800s and 1900s, might trigger schizophrenia. And during the COVID-19 pandemic,
including the 1918 flu pandemic, physicians took note of an uptick cases of psychosis following a SARS-CoV-2 infection among people
in patients exhibiting mental disturbances, particularly delusions and with no history of mental illness have emerged all around the globe.
hallucinations. Such cases were so common that medical professionals
at the time even coined the term “psychoses of influenza” to describe Some data suggest that maternal exposure to infections may
this condition. “There were records of influenza pandemics whereby heighten the risk of offspring developing conditions such as
people acutely affected with influenza acted in ways consistent with schizophrenia. Numerous studies have found that children who
what we now understand to be psychosis,” says Thomas Pollak, a neuro- are born in the winter or spring—when infectious agents tend to
psychiatrist and clinical lecturer at King’s College London in the UK. circulate—are at a greater risk for schizophrenia and other men-
tal illnesses than those born during another season. There are
This type of infection-triggered psychosis was not unique to also reports of maternal influenza infections increasing the risk
influenza. Many other instances of psychiatric symptoms developing of psychosis, although this link has not been consistently found.
after encountering a pathogen have been documented through-
out history. Neurosyphilis, for example, occurs when the bacterium More-recent evidence has also emerged from large epidemio-
Treponema pallidum invades the central nervous system, causing logical studies in Scandinavia, where researchers have access to
psychosis and depression, among other schizophrenia-like symptoms. nationwide registries containing medical data and other personal
When the link with the syphilis-causing microbe was established, information. A series of studies using such data in Denmark from
some mental institutions reported that the symptoms in around a a group led by Michael Benros, a professor of immunopsychiatry
third of their patients could be attributed to the infectious disease. at the University of Copenhagen, revealed that as an individual’s
Other examples include Toxoplasma gondii, a parasite that com- number of infections increased, the subsequent risk of developing a
monly infects cats: anti-Toxoplasma antibodies have been observed schizophrenia spectrum disorder—a cluster of mental illnesses that
share similar features, including psychosis—increased in a dose-

AUTOIMMUNE UNDERPINNINGS OF PSYCHOSIS

One of the most well-known autoantibodies with targets in the brain is the anti-NMDAR antibody, which targets the
NMDA receptor (NMDAR) that is found on excitatory neurons in the brain. When present, this autoantibody prompts
neurons to engulf NMDARs and reduces these receptors’ numbers at the synapse. This dearth of NMDARs, in turn,
causes problems in synaptic transmission that underlie a range of neuropsychiatric symptoms such as hallucinations,
delusions, seizures, and movement abnormalities. Researchers have pinpointed more than two dozen other brain-targeting
antibodies, most of which are found in patients with autoimmune disease of the central nervous system. The role these
antibodies play in psychiatric illnesses such as schizophrenia is the subject of active investigation.

HEALTHY SYNAPSE ANTI-NMDAR DISEASE

NMDA Glutamate Anti-
receptor NMDAR
antibodies
© LISA CLARK
APRSIULM2M0E2R2 2| 0I S2S2U| ET H2 E| TSSC IDEINGTEIST 3 9

dependent manner. The researchers found that more severe infec- that you could remove antibodies from the brain relatively easily and
tions, such as those requiring hospitalization, led to a higher risk reverse a clinical presentation—treat people and actually quite often
of developing schizophrenia later in life. These assessments also completely get rid of the underlying problem.” For Lennox, what was
revealed that there was a higher prevalence of autoimmune dis- striking was how patients with autoimmune encephalitis would
eases among people with schizophrenia, and vice versa. often present symptoms nearly identical, at least in the early stages
of their illness, to those she was seeing with first-episode psycho-
Despite the centuries-old link between infections and psycho- sis—new-onset psychotic symptoms that, in some cases, mark the
sis, researchers’ interest in this connection waned until recently, beginning of schizophrenia. This got her thinking: What if the first-
according to Benros. One of the reasons for this, he explains, was episode patients also had antibodies? And could giving immune-
that many scientists believed the brain to be immune privileged, modulating treatments benefit these patients, too? “That was sort
with the blood-brain barrier keeping it safe from the collateral of the start of my research journey, and I thought it would be quick
damage sometimes caused by the body’s defensive maneuvers. and straightforward,” Lennox notes. “But of course, it hasn’t been.”
Over the last decade, however, several findings have overturned
this notion. Researchers have recognized that the blood-brain In the years since the discovery of anti-NMDAR enceph-
barrier can become leaky, compromising its ability to act as an alitis, scientists have discovered self-directed antibodies, or
impermeable shield, and that the brain possesses resident immune autoantibodies, against more than a dozen other neuronal pro-
cells, microglia, as well as its own lymphatic system, a network of teins. Like anti-NMDAR antibodies, many of these antibodies
vessels that shuttles immune cells around the body. Large-scale can cause confusion and hallucinations, among other neuro-
genomic studies in people with schizophrenia turned up genetic psychiatric symptoms. But as research groups, including Lennox’s,
sequences associated with major histocompatibility complex have begun looking more broadly for neuronal autoantibodies
(MHC) proteins, molecules on the surface of immune cells that in patients with first-episode psychosis, schizophrenia, or other
present pathogen-derived peptides, as key regions implicated in psychiatric disorders, they’ve generated highly variable results.
the illness.2,3
Researchers doing this work typically test a patient’s blood
“A lot of research—and particularly the discovery of anti-NMDAR for such antibodies, then conduct further lab experiments to see
antibodies—brought back the interest into this field,” Benros says. how strongly those antibodies bind to neuronal proteins such as
NMDAR. To diagnose an autoimmune encephalitis, clinicians use
I’m hopeful that this is a new a spinal tap to take cerebrospinal fluid (CSF), which unlike blood
era for schizophrenia research. is in direct contact with the brain. But spinal taps are not always
available—largely because they are not often conducted in psychiatric
—Belinda Lennox, University of Oxford clinics—so many researchers use blood as a proxy. One 2014 meta-
analysis by Pollak and his colleagues found that across seven stud-
Searching for signs ies with 1,441 patients, approximately 8 percent of people with first-
Though tantalizing, the many studies reporting a link between infec- episode psychosis had neuronal autoantibodies in their blood; the
tion and neuropsychiatric symptoms like psychosis merely illustrate an prevalence rates were mixed, however—some of the studies had
association, not a causative relationship, between the immune system found no antibodies at all.4 Researchers have also found such auto-
and schizophrenia. The discovery of anti-NMDAR encephalitis, how- antibodies in the blood of healthy people, raising the question of
ever, provided evidence that the body’s own antibodies could attack the whether the presence of these molecules has any clinical significance.5
brain and trigger symptoms that resembled those of schizophrenia.
Not only that, the findings fit nicely with one of the leading hypotheses Some, including Dalmau, now at the August Pi i Sunyer
of schizophrenia: that the illness is caused by problems in the synapses Biomedical Research Institute (IDIBAPS) in Spain, are uncon-
of glutamate neurons, where NMDA receptors are plentiful. vinced that antibodies against NMDAR or other neuronal targets
found in the blood are responsible for symptoms in primary psychi-
The “groundbreaking discovery” was finding antibodies aimed at atric disease—such antibodies must be found in the cerebrospinal
neuronal cell surface targets that caused a catastrophic but treatable fluid to definitively diagnose them with an autoimmune encephalitis,
brain illness, Lennox says. “That was the dramatic breakthrough, he says. According to Dalmau, many of these studies have been
plagued by methodological problems, such as mixing patients with
different disorders, a lack of control groups with healthy individu-
als, and an absence of confirmatory results using other methods. If
you look at the literature over the past 10 to 15 years for clinically
meaningful immune markers in people who only have a psychiatric
disorder, Dalmau says, “there is no evidence whatsoever.”

Pilar Martinez Martinez, a professor of neuroinflammation
in neuropsychiatric disorders at Maastricht University in the
Netherlands, also notes that based on her research, it appears that
people with autoimmune diseases such as anti-NMDAR encephalitis

40 THE SCIENTIST | the-scientist.com

usually show neurological symptoms such as seizures or movement Other groups have investigated immune system dysfunction by
abnormalities in addition to psychiatric symptoms such as halluci- focusingonmoleculessuchascytokines,which,unlikeantibodies,don’t
nations and delusions. “I think in the unlikely scenario that there have a specific target. Rather, they function as part of more-generic
are only psychiatric symptoms, these are very, very, very rare cases, immune responses like inflammation. Sophie Erhardt, a professor
which I have not been able to identify myself,” Martinez Martinez of experimental psychiatry at the Karolinska Institutet in Sweden,
says. However, she adds, “I do think that in the future we might be says that the benefit of targeting cytokines is that they provide a
able to identify other antibodies that may [cause] symptoms that “snapshot of what the immune activation is right now.” The down-
at the moment we cannot separate from [psychiatric disorders].” side, however, is that it’s not easy to interpret why, exactly, cytokines

CYTOKINE
CONTRIBUTIONS
TO PSYCHOSIS

Some researchers have found higher-than-normal levels of
cytokines, chemical messengers of the immune system, in people
with psychosis. The mechanism through which these molecules
might contribute to psychiatric symptoms remains an open
question, but at least two potential pathways have been proposed:
one in which cytokines act via connections with the peripheral

nervous system A and another in which the molecules enter
the brain by penetrating the blood-brain barrier B .

Cytokines Vagus nerve Immune cell

Immune Cytokines
cell

© LISA CLARK A NEURAL PATHWAY B HUMORAL PATHWAY

Cytokines in the body’s periphery may activate the vagus nerve, a large, Inflammation may cause the blood-brain
multi-branched cluster of neurons that carries signals from the brain to barrier to become “leaky” and allow immune
various organs and vice versa. This may, in turn, trigger immune cells cells and molecules such as cytokines to enter
and chemical messengers in the brain that alter neurotransmission. the surrounding brain tissue.

APRSIULM2M0E2R2 2| 0I S2S2U| ET H2 E| TSSC IDEINGTEIST 41

are elevated, Erhardt adds, as levels of these molecules can rise in that clinicians could use to help diagnose their patients when a
response to various insults, from sleep deprivation to infection. spinal tap is not an option.7 These suggestions were met with
some criticism, including from Martinez Martinez, who noted
The search continues, with researchers conducting experi- that there was no evidence that patients without autoantibodies
ments and analyses that could uncover more-robust evidence of in their CSF would benefit from immunotherapy. On top of that,
the immune system’s contributions to schizophrenia and other psy- Dalmau notes that his team attempted to validate these red flags
chiatric illnesses. Benros’s team, for example, is currently conduct- in a large cohort of patients with first episode psychosis and found
ing a large study in Denmark that is looking in the CSF, blood, and that those criteria were unable to identify individuals with anti-
microbiome for signs of immune dysfunction in patients with a new NMDAR encephalitis.8
diagnosis of a psychotic disorder that are not present in healthy
individuals. Currently, only about 1 percent of people with psychosis Pollak notes that a spinal tap should be sought whenever a
or other psychiatric symptoms have clear neuroimmunological patient has these red flags—and that there could be downsides
alterations detectable in the CSF. “We’re trying to see if we can to screening every single patient with psychosis for signs of auto-
broaden the percentage of people for whom we can say there’s a immunity, such as uncovering incidental findings that might lead
direct immune cause to psychiatric symptoms,” Benros says. to misdiagnoses. “De-diagnosing someone is a very difficult thing
to do,” Pollak says. “For whatever reason, we’re in this slightly
Seeking solutions unusual position, where psychiatric diagnoses are so stigmatized
Several clinical trials have tested whether various immunomodu- . . . that in some cases an inflammatory diagnosis feels more real.”
latory drugs can improve the symptoms of schizophrenia. In one Ultimately, he adds, “until investigation in psychiatry is given
recently published study, researchers reported that patients who parity with investigation of physical health problems, this is going
received methotrexate, a powerful immunosuppressive drug used to be an ongoing problem.” g
for chemotherapy, exhibited a slight reduction in symptoms such
as hallucinations and delusions compared to those who received References
a placebo.6 Most other trials, however, have found little or no clear 1. R. Vitaliani et al., “Paraneoplastic encephalitis, psychiatric symptoms, and
benefit or such treatments.
hypoventilation in ovarian teratoma,” Ann Neurol, 58:594–604, 2005.
The trouble with the studies that have been conducted to date, 2. Schizophrenia Working Group of the Psychiatric Genomics Consortium,
Lennox says, is that they did not select patients who show signs of
immune dysfunction. The immune system may only be involved in “Biological insights from 108 schizophrenia-associated genetic loci,” Nature,
a subset of patients with schizophrenia or other psychosis-related 511:421–27, 2014.
disorders, she explains, so it is unlikely that everyone with these 3. J.G. Pouget et al., “Genome-wide association studies suggest limited immune
conditions would see improvements on immune-suppressing gene enrichment in schizophrenia compared to 5 autoimmune diseases,”
drugs. To address this limitation, Lennox and her colleagues Schizophr Bull, 42:1176–84, 2016.
are conducting a double-blind, placebo-controlled trial to test 4. T.A. Pollak et al., “Prevalence of anti-N-methyl-d-aspartate (NMDA) receptor
whether an immunotherapy—intravenously injected antibodies antibodies in patients with schizophrenia and related psychoses: a systematic
from healthy donors combined with rituximab, an antibody cur- review and meta-analysis,” Psychol Med, 44:2475–87, 2014.
rently used to treat autoimmune diseases such as arthritis—can 5. L. Dahm et al., “Seroprevalence of autoantibodies against brain antigens in
benefit patients with psychosis who have detectable brain-targeting health and disease,” Ann Neurol, 76:82–94, 2014.
antibodies in their blood. 6. I.B. Chaudhry et al., “A randomised clinical trial of methotrexate points to
possible efficacy and adaptive immune dysfunction in psychosis,” Transl
For now, both skeptics and proponents of the idea that the Psychiatry, 10:415, 2020.
immune system may be involved in schizophrenia agree on at 7. T.A. Pollak et al., “Autoimmune psychosis: an international consensus on
least one thing: clinicians seeing patients with psychotic symp- an approach to the diagnosis and management of psychosis of suspected
toms need to more vigilant about identifying possible auto- autoimmune origin,” Lancet Psychiat, 7:93–108, 2020.
immune causes of their illness. Some, like Ludger Tebartz van 8. M. Guasp et al., “Clinical, neuroimmunologic, and CSF investigations in first
Elst, a professor and psychiatrist at the University of Freiberg and episode psychosis,” Neurology, 97:e61–75, 2021.
its associated hospital in Germany, are now administering spinal
taps to all patients with psychotic symptoms. In most countries,
however, such a practice is difficult to implement, Tebartz van Elst
notes, largely due to the fact that most psychiatrists don’t conduct
spinal taps. (Germany is unusual in that psychiatrists receive a
year of neurology training, and neurologists of psychiatry train-
ing, making the two practices much more closely intertwined than
in other parts of the world.)

For this reason, Tebartz von Elst, Pollak, and several of their
colleagues recently published a paper outlining several red flags

42 THE SCIENTIST | the-scientist.com

TSU TECHNIQUE TALKS

PURIFYING PLANT-BASED
ENDOGENOUS BIOMOLECULES

Nucleic acid isolation from plant tissues presents unique challenges. Commonly used
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In this Technique Talk, April Bauer will discuss negative chromatography-based
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MODIFIED FROM
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Whispers

of the Past
The concept of epigenetic inheritance has long been
controversial. Some researchers hope that new data on
cross-generational effects of environmental exposures
will help settle the debate.

BY CATHERINE OFFORD

A ndrea Baccarelli loves black and the environment. Over the last couple off the mark.” (See “Inheritance of Acquired MODIFIED FROM © ISTOCK.COM, FEDRELENA
truffles—the fungi, not the of decades, however, scientific and pub- Traits: From Lamarck to Now” on page 50.)
chocolates. His parents, he says, lic conversations about inheritance have
are also fond of the delicacy. His grappled with an apparently separate, Now, just a few years after that peak in
grandparents liked them, too, as non-genetic dimension of inheritance. interest, it’s become abundantly clear just
did his great-grandparents. Did how varied and complicated the different
he inherit the preference from previous The shift was driven by an explosion of theories of epigenetic inheritance are, and
generations through some biological interest in epigenetics—broadly, the study how many often-controversial hypotheses
mechanism? Or could this multigenera- of proteins and other factors beyond DNA they rest on. Critics have pointed out that,
tional appreciation for clumps of a sub- sequences that influence how genes are while there does appear to be evidence for
terranean fungus be related to the fact expressed. In the early 2000s and 2010s, as some sorts of epigenetic inheritance in plants
that all these people were constantly sur- researchers delved deeper into the molec- and non-human animals, it’s uncertain how
rounded by black truffles at the family ular mechanisms of gene regulation, other much the environment really affects the
home in Umbria, the northern Italian papers accumulated supposedly showing human epigenome—much of which is actu-
region that happens to be a global black that changes in DNA methylation, non- ally dictated by genome sequence—and to
truffle hotspot? coding RNAs, and other elements might what extent changes in the epigenome affect
offer a mechanism by which a person’s gene expression and human biology. What’s
This question of what’s passed down exposure to environmental factors—such as more, it’s now thought that much, although
from parent to child is complex and toxic chemicals, trauma, or, hypothetically, not all, of the mammalian epigenome gets
has often been socially and politically truffle-heavy diets—could have intergen- wiped out and reprogrammed twice per
charged, says Baccarelli, who now chairs erational (parent-to-child) and even trans- generation, once in a newly fertilized egg
the environmental health sciences depart- generational (grandparent-to-child and and again during the formation of egg and
ment at Columbia University’s Mailman beyond) effects on health and behavior. sperm cells, challenging the idea that epi-
School of Public Health (and who attri- genetic alterations could have a consistent
butes his truffle love to his childhood in The findings tapped into an old and influence from one generation to the next,
Umbria). The nuances of inheritance long-discredited idea—often associated let alone across multiple generations.
are perhaps most commonly framed as with the writings of Jean-Baptiste Lamarck
the age-old debate of nature versus nur- and Trofim Lysenko, among others—that Some researchers question whether
ture, the pervasive idea of a tug-of-war traits acquired within one’s lifetime can be evolutionary biology even needs an addi-
between deterministic genetic sequences inherited. As Oliver Rando of the Univer- tional inheritance mechanism, after
and changing environmental influences— sity of Massachusetts Medical School wrote genes, culture, and other existing factors
a dichotomy that scientists have long crit- in The Scientist at the height of the epigen- are taken into account, to explain the per-
icized as an oversimplification, given the etic inheritance boom in the mid-2010s, sistence of characteristics across multi-
complex interactions between genetics scientists were discovering that this out- ple generations. “Nah,” is the assessment
of-favor proposal “may not be completely of Bas Heijmans, a biomedical data sci-
entist at Leiden University Medical Cen-
ter (LUMC) who studies within-gener-
ation epigenetic changes in people who
endure famine and other environmental
conditions. “I think that epigenetic inher-
itance does not exist, according to what
seems logical, reasonable, and what data
we have.” The idea has lost its shine in the
public sphere, too; where books, maga-
zines, and news stories once hailed it as
revolutionary, they now ask whether it’s a
“lost cause,” a phenomenon for which evi-
dence has “crumbled.”

Despite this criticism, many research-
ers haven’t given up on the possibility that
one generation’s environment can influence
future generations via epigenetic mecha-
nisms. While there isn’t strong evidence for
these kind of effects happening on a large
scale in humans, particularly over two or

46 THE SCIENTIST | the-scientist.com