July/August 2020 The Scientist

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| WWW.THE-SCIENTIST.COM | WWW.THE-SCIENTIST.COM JULY/AUGUST MONTH 2018 2020

LIFE DURING A PANDEMIC UNDERSTANDING THE VIRUS IS JUST THE BEGINNING

ESTIMATING COVID-19 TRANSMISSIBILITY

PLUS

STEM-LIKE T CELLS AND IMMUNOTHERAPY

SOCIAL ISOLATION AND THE BRAIN BIOTECH AND PHARMA PIVOT TO STUDY COVID-19

Announcing The Scientist’s annual Top 10 Innovations Competition Submit your cutting-edge, life-science technology for consideration by a panel of expert judges. The winners will be the subject of a feature article in the December 2020 issue of The Scientist. • An “innovation” is defined as any product that life-science researchers use in a lab: machines, instruments, tools, cell lines, custom-made molecular probes and labels, software, apps, etc. • Products released on or after October 1, 2019 are eligible. • Entries accepted from May 1 to August 21, 2020. For further information, email: [email protected]

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JULY/AUGUST 2020

Contents

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THE SCIENTIST

THE-SCIENTIST.COM

VOLUME 34 NUMBER 07/08

Features

ON THE COVER: © GETTY IMAGES, ARTUR DEBAT

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32

40

Biology, sociology, and mathematics meet in a single statistic used to quantify the transmissibility of an infectious agent. The result is a shaky metric that policymakers are using to craft public health policies amidst the pandemic.

What a lack of socializing might mean for cognitive function

T cells with stem cell–like properties may be key to making immunotherapies work.

The Limits of R0

The Isolated Brain

BY CATHERINE OFFORD

Stemming the Tide of Cancer

BY DANIEL E. SPEISER AND WERNER HELD

BY KATARINA ZIMMER

07/08.2020 | T H E S C IE N T IST

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Department Contents 16

11

GUEST EDITORIAL

58

Dissecting the Pandemic

What we can and must do to make science more equitable

Although there is much yet to learn about COVID-19 and the global spread of the disease, some lessons have emerged.

BY JOSEPH GRAVES AND ERICH D. JARVIS

16

BY DEBORA MACKENZIE NOTEBOOK

Old Birds, New Tricks; More than Kisses; Bead Networking; Fly Forensics

23

MODUS OPERANDI

Modular Antiviral Antibodies

Using bacterial superglue, researchers create potent virus-neutralizing multimers.

46

READING FRAMES

Scientists and Racial Justice

60 FOUNDATIONS Multiple Causes, 1931 BY CATHERINE OFFORD IN EVERY ISSUE

10 13 59

CONTRIBUTORS SPEAKING OF SCIENCE THE GUIDE

BY RUTH WILLIAMS

LOUIS LEFEBVRE; © KELLY FINAN; MODIFIED FROM © ISTOCK.COM, MARK KOLPAKOV

46 THE LITERATURE How breastfeeding her children reduces a woman’s risk of diabetes; blood-borne microbial signatures for detecting cancer; fruit flies elucidate link between the Y chromosome and aging

48 PROFILE For the Greater Good

Through groundbreaking studies on dengue fever and efforts to build scientific infrastructure in Latin America, Eva Harris has bridged research with its benefits to society.

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CORRECTIONS:

In the June story “Old Enzymes Learn New Tricks,” a table erroneously described the role of a UUU sequence in the synthetase for lysine (LysRS) during HIV infection. The June profile of Noel Rose was updated to recognize the work of UK scientists Deborah Doniach and Ivan Roitt on autoimmunity and to clarify that in 1951 the University at Buffalo was not yet a State University of New York school. UB became affiliated with SUNY in 1962. The Scientist regrets the errors.

ANSWER

PUZZLE ON PAGE 13

BY DIANA KWON

51

SCIENTIST TO WATCH

Luis Alvarez: Bone Painter BY SHAWNA WILLIAMS

54 BIOBIZ Pandemic Pipelines

How biotech and pharma companies pivoted to COVID-19 research and development BY DIANA KWON

B N R E S E R U AGA R O WA T S D U Z E B R N G F OR E I O E D E N S

K P A RCH GR A O A K I N E S I E I T ON CUR V I A S COCC E I J N S I C U L A A I ME D I C I E A E

Q U A C K E R Y

B S D X

N A I N E E

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JULY/AUGUST 2020

Online Contents

THIS MONTH AT THE-SCIENTIST.COM: VIDEO

VIDEO

VIDEO

Blowing in the Wind

Peace and Cell Biology

Cure Against All Odds

Watch Critic at Large author and public health researcher Matthew Dacso wail on tenor saxophone during a 2010 concert with South African musician Ringo Madlingozi.

See profilee Eva Harris explain her early learning environment and how she sees the cell as a metaphor for human society in this HHMI biography.

Jean Macnamara, a pioneer in the treatment of polio patients and the subject of this issue’s Foundations, comes to life in the form of a Google Doodle to celebrate what would have been her 121st birthday.

AS ALWAYS, FIND BREAKING NEWS EVERY DAY ON OUR WEBSITE.

Coming in the September issue • When and how people populated South America • Genomic inquiries shed light on ancient hominin evolution in Africa.

• What is a scientist’s role in policymaking? AND MUCH MORE

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SPONSORED CONTENT

Unique Functional Multi-Omics from IsoPlexis Helps Accelerate Cancer Research

S

ingle-cell techniques have broadened our understanding of cellular heterogeneity, starkly highlighting the complexity of gene-, translation-, transcription-, and protein-level relationships within the

cell. These revelations stress the importance of employing multimodal -omics approaches for solving biological problems,1 especially for linking cellular functions to specific genotype or phenotype profiles. Acquiring and analyzing -omic profiles in individual cells is a technical challenge, and many current technologies encounter issues with sensitivity, noise, and throughput. IsoPlexis is uniquely positioned to offer deep functional multi-omic and full functional proteomic solutions through the fully automated IsoLight system, the advanced IsoSpeak informatics software suite, and a wide range of kits, panels, and products. Indeed, three of IsoPlexis’ core functional proteomic products, CodePlex Secretome, Single-Cell Secretome, and Single-Cell Intracellular Proteome, have been recently featured in studies published in Nature Communications. Whether probing extracellular, intracellular, or metabolomic markers, examining single cells or highly multiplexed population proteomics with small sample sizes, IsoPlexis provides solutions for researchers studying

simultaneously. The ability to rapidly analyze and screen secretomes

intracellular proteomic modulations, stem cell-related signaling, and innate

allowed scientists to better characterize what drives tumor cell migratory

and adaptive immune responses to pathogens and cancers.

behavior, as well as highlight new areas of investigation for reducing tumor cell metastatic capabilities.

Characterizing Cell Communication & How the Secretome Shapes Metastatic Behavior Cancer progresses from oncogenesis to tumor formation and growth

IsoPlexis’ Multi-Omic Functional Approach to Understanding the Mechanisms of Cancer Cell Drug Resistance

and culminates with metastasis and spread to secondary sites. However,

The knowledge gap surrounding cancer cell behavior extends to how

the mechanisms underlying cancer cell behavior during these processes

cancer cells rapidly develop tolerance and resistance to anti-cancer drugs.

are still largely uncharacterized. For example, cell migration resulting in

Researchers have some understanding of drug resistance mechanisms from

metastasis intertwines with proliferation, yet exactly how the two couple is

genetic, metabolic, and signaling standpoints. However, few detailed studies

unclear. With the assistance of IsoPlexis’ CodePlex Secretome technology,

have been conducted that account for functional cellular heterogeneity or

Hasini Jayatilaka from Denis Wirtz’s team at Johns Hopkins University

outline a cohesive temporal trajectory from sensitive to resistant states.

sought to clarify this relationship.

IsoPlexis’ Single-Cell Intracellular Proteome technology is starting to change

Secreted by tumor and non-tumor cells alike, cytokines collectively

that. Yapeng Su and colleagues at the California Institute of Technology

modulate both physiological and pathological responses within the tumor

recently reported in the journal Nature Communications3 that BRAFV600E mutant

microenvironment. Since cytokine secretion profiles (secretomes) are

melanoma cells use multiple trajectories to switch from a drug-responsive

affected by tumor properties, Jayatilaka et al. investigated the relationship

state to a drug-resistant state. IsoPlexis’ proteomic barcoding technology was

between cell density, cytokine secretion, and migratory behavior. In a study

used by Su et al. to analyze the levels of key proteins and metabolites within

published in Nature Communications,2 the authors outlined how cellular

individual cells at multiple timepoints. Mapping this data, the team created a

density positively correlated with motility and velocity in metastatic cancer

comprehensive picture of “the complex cell-state space” traveled by BRAFV600E

cells in 3D matrigels. The cause lay in a soluble factor as the phenomena

cells as they adopted drug resistant states, finding that the cells split into

could be reproduced in low-density cells by transferring conditioned media.

rapidly proliferating MITF-high and more invasive MITF-low subpopulations.

Jayatilaka et al. identified the specific factors involved by screening

Critically, IsoPlexis’ single-cell proteomic and metabolic analysis not

conditioned media. Probing 24 different molecules (including growth

only allowed Su et al. to characterize mechanisms for drug resistance,

factors such as FGF and VEGF, chemokines such as RANTES and MIP1α,

it also helped identify strategies to overcome this resistance. MITF-low

or pro-inflammatory cytokines such as IFNγ and TNFα) using IsoPlexis’

cells depended on NFκB signaling, while MITF-high cells were susceptible

highly multiplexed proteomic barcoding technology, the team found only

to inhibition of the glycolysis enzyme PKM2. Indeed, Su et al. found that

interleukins 6 (IL-6) and 8 (IL-8) to positively correlate with cell densities.

while cancer cell survival decreased upon either PKM2 or NFκB inhibition,

Using this knowledge as a base, Jayatilaka et al. further discovered that the

simultaneously inhibiting both pathways resulted in the greatest reduction

effects of IL-6 and IL-8 occurred only when both interleukins were active

in cell survival. 01 . 201 8 | T H E S C IE N T IST

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Evaluating and Improving Therapeutic Approaches with Single-Cell Proteomics

of the secreted cytokines. In a murine melanoma model, NKTR-214

Finally, IsoPlexis’ Single-Cell Secretome solution helps researchers

and a 1200-fold PSI in tumor-infiltrating lymphocytes compared to IL-2-

characterize how both host and cancer cells respond to potential treatments,

treated counterparts. The researchers observed similar responses in patient

administration with ACT resulted in a 21-fold PSI increase in CD8+ T cells

allowing them to augment and improve their approaches. In a study featured in

peripheral blood T and natural killer cells during a phase 1 clinical trial.

Nature Communications4 at the start of 2020, Giulia Parisi and her colleagues

This increase in polyfunctionality also correlated to increased expansion

from the University of California, Los Angeles outlined how NKTR-214, an

and persistence.

engineered IL-2 receptor agonist, boosted the efficacy and persistence of

IsoPlexis’ Functional Proteomics Fills the Gap Left by Genomics

adopted cell transfer (ACT) therapy. IL-2 is commonly administered during ACT therapy, as the cytokine

In light of cellular heterogeneity, the importance of ascertaining and predicting

supports the expansion and function of transferred T cells. However, IL-2 also

function on a single cell-level has never been more paramount. Highly

induces toxicity and immunosuppression, presenting potential problems for

multiplexed multimodal -omics techniques, exemplified by IsoPlexis’ deep

patients. Using IsoPlexis’ single-cell proteomics, Parisi et al. found that three

functional multi-omic and full functional single-cell proteomic solutions, offer

main T cell subpopulations within murine tumors following ACT: CD8+ T cells,

researchers the ability to characterize proteomic and metabolic signatures in

CD4+ T cells, and regulatory T cells (Tregs) displayed varied levels of response.

a truly functional context, while genomics is unable to identify direct function.

NKTR-214 treated mice showed increased expansion and persistence of the adoptively transferred cells, while the opposite was found in IL-2 treated mice. Since CD8+ T cells drive anti-tumor responses and Tregs control them, this trend offered an explanation for NKTR-214’s superior anti-cancer results. Parisi et al. also used IsoPlexis’ highly multiplexed single-cell proteomics to reveal that NKTR-214 treatment increased CD8+ T cell polyfunctionality. Polyfunctionality—the ability of an individual cell to secrete two or more cytokines—positively correlates with clinical response;5 it is commonly measured using the “polyfunctional strength index (PSI),” which is the percentage of polyfunctional cells in the sample multiplied by the intensities

IsoPlexis’ Functional Cytometry IsoPlexis’ unique omics allow complete functional phenotyping at single-cell resolution and ultra small sample volume characterization.

References 1. Method of the Year 2019: Single-cell multimodal omics. Nat Methods, 17:1, 2020. 2. H. Jayatilaka et al., “Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration,” Nat Commun, 8:15584, 2017. 3. Y. Su et al., “Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line” Nat Commun, 11:2345, 2020. 4. G. Parisi et al., “Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist,” Nat Commun, 11:660, 2020. 5. J. Rossi et al., “Preinfusion polyfunctional anti-CD19 chimeric antigen receptor T cells are associated with clinical outcomes in NHL,” Blood, 132(8):804-14, 2018.

ISOPLEXIS’ MULTI-OMIC PRODU CTS: Functional Phenotype SC Secretome 1

Functional Phenotype SC Intracellular Proteome SC Metabolome

Ultra Small Sample CodePlex Secretome

2

3 1

Published In

Published In

Published In

Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist

Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line

Synergistic IL-6 and IL-8 paracrine signalling pathway infers a strategy to inhibit tumour cell migration

Parisi G, et al. Persistence of adoptively transferred T cells with a kinetically engineered IL-2 receptor agonist, Nature Communications, 2020

Su Y,et al. Multi-omic single-cell snapshots reveal multiple independent trajectories to drug tolerance in a melanoma cell line, Nature Communications, 2020

Jayatilaka H, et al. Synergistic IL-6 and IL-8 Paracrine Signalling Pathway Infers a Strategy to Inhibit Tumour Cell Migration., Nature Communications, 8, 15584., 2017

nature communications

2 3

For Research Use Only. Not for Use in Diagnostic Procedures.

nature communications

nature communications

isoplexis.c om

JULY/AUGUST 2020

As a medical student at the University of Zurich in the 1980s, Daniel Speiser was intrigued by how the immune system responds to infection, transplantation, and cancer, he recalls. After graduating, he trained in clinical medicine and experimental immunology. In the ensuing three decades, he has investigated the use of patient’s immune cells to fight cancer, and performed clinical trials testing novel cancer immunotherapies. One of his proudest research accomplishments, Speiser says, came in the 1990s, when he helped work out the mechanisms of how T cells destroy leukemia cells in patients treated with bone marrow from a donor. His findings led to more effective matching of patients and donors. The success of such transplants—which allow patients to generate immune cells that fight their leukemia—was “the first demonstration in the clinic that the immune system can control cancer highly effectively, and that was really fantastic to see,” he says. Leveraging the immune system against cancer has since become the basis of immunotherapy, which Speiser, now a professor at the University of Lausanne, seeks to improve with his more recent work on stem cell–like T cells and their practical importance in improving cancer therapies. In his research, Speiser’s colleague Werner Held has focused on the body’s response to pathogens, and particularly what happens in infections, such as HIV and hepatitis C virus, that cannot be controlled by the immune response. The immune system normally clears an infection and develops memory that enables it to more efficiently wipe out the pathogen if it encounters it again. In persistent infections, T cells have reduced activity, a phenomenon known as exhaustion, yet persist long-term. “One open question in the field of exhaustion was whether there was something like a memory in a chronic infection,” Held says. He and his colleagues were the first to discover a subpopulation of exhausted T cells with stem cell–like properties that continue to produce new cells programmed to fight a particular pathogen and thus sustain the immune response over time. He and Speiser, longtime colleagues at the Ludwig Institute for Cancer Research and then at the University of Lausanne, teamed up for the first time to find that stem-like T cells are also present in tumors. They describe their work and how it could be used to improve immunotherapy in their feature story, “Stemming the Tide of Cancer,” on page 40.

Father and son Cliff and Matthew Dacso are seeking to understand the reach of the COVID-19 pandemic by zeroing in on its disproportionate effect on vulnerable communities such as people of color, incarcerated populations, and residents of nursing homes. This unevenness of COVID-19, and of other diseases, is especially prevalent in the US, one of the countries hardest hit by the pandemic. “I work in Houston, Texas, where more than 20 percent of children do not have payment capability for healthcare,” says Cliff, a professor of molecular and cellular biology and medicine at Baylor College of Medicine. “It’s an enormously impoverished state with regard to healthcare, and in the shadow of the world’s largest medical center, there are medical needs unmet.” The Dacsos, along with coauthor Kara McArthur—who are all affiliated with the nonprofit Institute for Collaboration in Health—write on page 14 about how “allostatic load,” which describes the economic, environmental, social, and other stressors that compromise biology, likely contributes to the COVID-19 pandemic’s oversized effect on underserved communities. “If you can really show the profound—not just social—influence, but the biological impact of these high-stress environments, there’s the potential to look at it as” a problem that can be ameliorated through social and political change as well as by applying therapeutic, preventive, and diagnostic advances, says Matthew, who is a physician and researcher at the University of Texas Medical Branch in Galveston. “With enough information about the biological facts, you’re able to start looking at the political interventions almost in the same way you’d look at a vaccine.” While studying the basic biology of SARS-CoV-2 and how and why COVID-19 is spreading is paramount, the Dacsos say, looking at all the factors that contribute to the pandemic and its uneven impact, especially among people of color, might also help academic scientists branch out and forge connections with their surrounding communities. “Part of the benefit of addressing this from the biological basis is that it will force us all to engage with communities of color and disadvantaged populations, and it will get scientists out of the academic setting and hopefully into the community and bridge some of those gaps and create alliances that never existed before,” says Matthew. “Maybe that’s a bit of a pipe dream, but if we did it well and we did it right, that’s what would happen.” 1 0 T H E SC I EN T I ST | the-scientist.com

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Contributors

GUEST EDITORIAL

Scientists and Racial Justice What we can and must do to make science more equitable BY JOSEPH GRAVES AND ERICH D. JARVIS

Editor’s note: This essay was published as an open letter on the-scientist.com on June 19, and as of June 29, it had been endorsed by more than 180 signatories.

© ISTOCK.COM, LJUBAPHOTO

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he unjust killings of George Floyd, Breonna Taylor, and Ahmaud Arbery, amplified by the health disparities of the COVID-19 pandemic and the ethnic disparities of the political climate, have shined a spotlight on historical and ongoing institutional racism in America. Many professional scientific organizations, such as the American Association for the Advancement of Science, March for Science, the Society for the Study of Evolution, the Society for Neuroscience, and Sigma Xi have published statements opposing it. But statements have little impact unless actions result from them. Determining the most effective actions requires understanding the concept of institutional racism. Institutional racism means that established structures within a society are infused with racial/racist ideology and practices. This includes the “enterprise” of science, which can be separated from the “method” of science. The scientific method is an objective means to better understand nature, whereas the scientific enterprise is a reflection of society’s values and decides whose interests are represented in the formulation of research questions and directions. American history shows that science, like other enterprises, has been mainly directed towards fulfilling the interests of persons of European descent: “whites.” This has resulted in the historical and ongoing underrepresentation of blacks in the sciences. Other racially subordinated minorities (RSMs) face these issues (e.g., brown and red people*). Here we describe the timeline of racial subordination in America in the context of the growth of modern science and the research university. De jure segregation was still in place when African American scientists began to enter historically white research universities in noticeable numbers in the mid-20th century. Ironically, many of these institutions owed their start directly to profits generated by the slave trade. The majority of those in the first wave of black scientists, however, received their undergraduate degrees at historically black universities—institutions that were not founded from black perspectives or agendas, but rather more as social palliatives to help maintain America’s system for separation of the races and white supremacy.

* This commentary uses color-scheme language throughout to describe racial/ethnic groups. This is because most readers are not used to thinking about the social definitions of race and the various anthropological titles and arbitrary euphemisms associated with them. Thus, we use the principle of parallelism for racial/ethnic terms, privileging no group over the others.

In the early 1970s, acknowledging that there was a great disparity between the percentage of RSMs in the US workforce (13 percent) and their representation in science careers (2 percent), the scientific community began to intervene. Federal science funding agencies spent ~$1.5 billion on RSM-focused STEM programs from 1972 to 1992, in what were then called affirmative action programs, including the National Institutes of Health’s Minority Biomedical Research Support and Minority Access to Research Careers (MARC) programs, from which one of us (E.D.J.) directly benefited. Although well-intentioned and producing some individual success stories, these programs did not achieve broader success in diversifying the scientific work force. Problems included insufficient oversight and assessment, poor commitment from leading faculty, inconsistent funding, lack of comprehension of behavioral/psychological impacts on student learning, recruitment of many unprepared students, and insufficient attention to the entire K–12-through-university pipeline. The oversight/assessment issue has been largely solved, and progress has been made in other arenas. But more work is needed. Helping to stymie this progress, in the 1990s the US Supreme Court made it harder to demonstrate that discrimination against racial minorities was taking place, and more difficult to demonstrate that affirmative action poli07/08 . 2020 | T H E S C IE N T IST 1 1

GUEST EDITORIAL cies were not harming white Americans. Ideological justifications for “race-blindness” in admissions and lawsuits claiming supposed “reverse discrimination” followed. While most of these complaints came against professional law and medical school programs, they affected other government programs in STEM. It is notable that MARC now stands for Maximizing Access to Research Careers. Colorblind racism and implicit bias continue to influence science careers. Colorblind racism argues that non-racial factors such as economics, naturally occurring phenomena, and the cultural attitudes of RSMs are the main cause of their social subordination. Closely aligned to colorblind racism is implicit bias. This occurs when an individual has a preference for (or aversion to) specific groups of people. This often results from ascribing stereotypes to a group without conscious knowledge of doing so. It has been argued that implicit bias plays a significant role in hindering RSMs’ success in science. In 2015, data indicated that from 1985 to 2013, RSMs were 10 to 22 percent less likely to receive a Research Award 01 (R01) grant from the NIH. This report ignited a firestorm of controversy, especially since there is still little data available to address whether this resulted from the implicit bias of reviewers or other factors. If one asks RSM researchers, most will agree from their experience that implicit bias against them has either harmed their career or made it more difficult. One 2019 study presented data that seemingly countered that perception. Researchers reviewed a sample of R01 grant applications using a well-established implicit bias testing experimental protocol and found no evidence of racial bias, but did find gender bias. However, the “ethnic name” methods of this experiment can be questioned. For example, the use of supposed “black-sounding” names—“Darnell,” “LaToya”—may not be fully capturing the means by which RSM researchers are discriminated against. Clearly more studies are required before we can accurately assess whether this force is currently working against RSM success in the science community. Another recent study demonstrated ongoing disparities in NIH R01 awards and linked this to the practice of combining criterion scores into impact scores that disadvantaged black applicants. Some fields are making progress towards improving diversity and inclusion in the scientific community over the last two decades. This progress has been slow, but noticeable. As noted, E.D.J. received important help from such diversity programs, but this assistance was necessary to counter the obstacles he faced in science as an African American. As reported by one of us (J.G.), the outstanding results of the BEACON (Bio/computational Evolution in Action CONsortium) Center for the Study of Evolution in Action, a National Science Foundation Science and Technology Center, are directly tied to the executive committee’s intentional mission to address diversity and inclusion. BEACON’s leadership team included three RSMs and four women in a group of 13 individuals. Progress has also come in the form of organizations such as the National Research Mentoring Network, the Annual Biomedical Research Conference for 1 2 T H E SC I EN T I ST | the-scientist.com

If one asks RSM researchers, most will agree from their experience that implicit bias against them has either harmed their career or made it more difficult.

Minority Students, the Black Women in Computational Biology Network, and the coalescence of groups united by social media, such as #BlackInSTEM. Changing the demography of the scientific community may also allow us to transform the enterprise of science. Specifically, there is a crucial need to address how racial/racist ideology persists within our research programs. Examples of how racist ideology influences the biomedical and behavioral sciences are well studied but probably less known. Other cases of racial bias are beginning to emerge in other disciplines, such as computer science, where one would have hardly thought this was possible. There is now a growing literature revealing how racial bias inherent in data training sets used in artificial intelligence (AI) can introduce racial bias in AI’s outcomes. The killing of George Floyd has revealed a deep and recalcitrant racism within American society. It permeates all of our institutions. The demography of science still lags behind the representation of RSMs in society. We would be naive to think that racial/racist ideology is not playing a role in maintaining this injustice. This raises the question: What can people of good will do about this? Some of the answers are obvious, such as taking a stand against societal assaults on the wellbeing of RSM communities. However, others may not be so obvious, such as examining the practices within your own institution that may still harbor implicit bias against RSMs; rethinking the notion that a colorblind approach is the best way to train students and treat colleagues; deeply listening to and learning from your colleagues from RSM communities; and examining your own work and practice for any implicit racial bias. Certainly, scientists alone cannot transform societies mired in racism, but we can and must do our part to help. g Joseph Graves is a professor of biological sciences at North Carolina A&T State University and a fellow of the American Association for the Advancement of Science. Erich D. Jarvis is a professor in the Laboratory of Neurogenetics of Language at the Rockefeller University and an investigator at the Howard Hughes Medical Institute. They are both members of The Scientist’s editorial advisory board. You can find them on twitter @gravesjl55 and @erichjarvis. If you would like to sign this open letter, please email Editor in Chief Bob Grant ([email protected]) to add your name and affiliation to a list of signatories that appears on the-scientist.com.

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INVESTIGATIONAL NEW DRUG (IND) APPLICATION • The sponsor company submits the IND. They describe the manufacturing and testing processes and the proposed study, and summarize preclinical laboratory reports.

• Researchers use tissue culture or cell culture and animal testing to broadly assess the safety and immunogenicity of the candidate vaccine.

PHASE 1 • This first attempt to assess the candidate vaccine in humans involves a small group of adults, usually between 20-80 subjects. • Researchers assess the safety of the candidate vaccine and determine the type and extent of immune response that the vaccine provokes in humans.

S M A L L- S C A L E C L I N I C A L T R I A

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PHASE 1,2,3 CLINICAL TRIALS • Safety / dose selection / efficacy

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VACCINE ATEGIES 2-3 YEARS

researchers are racing to develop one for COVID-19 within a much shorter timeframe due to the seriousness of the pandemic. To win this race, researchers must develop a vaccine that does not cause additional health problems, that provides long-term protection to prevent re-emergence of the virus in years to come, and that protects older people who may mount a weaker immune response. Several types of vaccines are currently in development, including deactivated viral vaccines, viral vector vaccines, RNA and DNA vaccines, and protein-based vaccines. Much work remains, but the number of agencies, pharmaceutical companies, and governments working on a potential COVID-19 vaccine is encouraging.

2-4 YEARS

PHASE 2 / PROOF OF CONCEPT

PHASE 3

• A larger group of several hundred individuals participates in Phase 2 testing. Some of the participants may belong to groups at risk of acquiring the disease. • The goals of Phase 2 testing are to study the candidate vaccine’s safety, immunogenicity, proposed doses, schedule of immunizations, and method of delivery.

A L S M AT E R I A L

It typically takes 5-20 years to develop a vaccine, but

• Successful Phase 2 candidate vaccines move on to larger trials involving thousands to tens of thousands of people. • Vaccine safety, efficacy, and dose are confirmed.

BIOLOGICS LICENSE APPLICATION (BLA) TO THE FDA • Identity, purity, impurity, potency and quantity are demonstrated by analytical testing. • Analytical testing includes chromatography, electrophoresis, immunological assays, microbial analysis, and various stability tests.

POST-MARKETING SURVEILLANCE • Various surveillance schemes including Phase 4 trials, the Vaccine Adverse Event Reporting System, and the Vaccine Safety Datalink are used to monitor vaccine safety post-licensure.

• The FDA will inspect the factory where the vaccine will be made and, if satisfied, approve the labeling of the vaccine.

M A N U F A C T U R I N G S C A L E - U P, V A L I D AT I O N

Normally, vaccine development is a lengthy and expensive process, and failure rates are high. However, for COVID-19, a “pandemic paradigm” is necessary, with multiple overlapping steps.

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1+ YEARS

LARGE-SCALE MANUFACTURING

Multiple Targets, Multiple Efforts Since detecting SARS-CoV-2 in late 2019, numerous groups began working towards potential vaccines. By mid-2020, more than 100 vaccine projects were in development, with several supported by the nonprofit Coalition for Epidemic Preparedness Innovations (CEPI). By early June 2020, there were at least 10 candidate vaccines undergoing clinical evaluation, and at least nine in Phase 1 or 2 human trials.

Virus Vaccines • Scientists make weakened viruses by introducing mutations to viral RNA. • Inactivated viruses become non-infectious following treatment with chemicals or heat.

Vaccine candidates in human trials as of late May 2020: • Sinovac, inactivated vaccine, Phase 1 • Sinopharm Group, inactivated vaccine, Phase 1/2

Weakened virus

Inactive virus

Nucleic Acid Vaccines • Composed of DNA or RNA encoding viral proteins, such as the spike (S) or membrane (M) proteins. • RNA is often encased in lipids so that it can enter cells.

Vaccine candidates in human trials as of late May 2020: • Inovio Pharmaceuticals, DNA vaccine, Phase 1 • Moderna/NIAID, RNA vaccine, Phase 1/2 • BioNTech/Pfizer, RNA vaccine, Phase 1/2

Coronavirus gene

DNA or RNA

Viral Vector Vaccines • Scientists weaken viruses such as measles or adenovirus and then modify them to carry genetic information for SARS-CoV-2 proteins.

Coronavirus gene

• These viral vectors may replicate or be modified to make them incapable of replicating.

Viral gene

Vaccine candidates in human trials as of late May 2020: • CanSino Biologicals, nonreplicating vector (two different vaccines), Phases 1 and 2 • University of Oxford/AstraZeneca, nonreplicating vector, Phase 1/2 • Shenzhen Geno-Immune Medical Institute, nonreplicating vector, Phase 1/2

Coronavirus gene Viral gene (some inactive)

Protein Vaccines • Protein subunits, such as S proteins or M proteins, or portions of subunits are mixed with adjuvants for injection.

Viral proteins

• Empty viral shells lacking genetic information provoke a strong immune response, but are difficult to manufacture.

Viral shells

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QUOTES

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—Kishana Taylor, a virologist at the University of California, Davis, talking to Nature about her experience as a Black scientist (June 22)

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MODIFIED FROM WIKIPEDIA, KEITHTYLER

BY EMILY COX AND HENRY RATHVON

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1. Calf of a glacier 2. Physician treating brain and spinal trauma 3. Sea monster of Scandinavian lore 4. Pertaining to speech sounds 5. Bad 20-Across practiced by frauds 7. Digestive fluid in the stomach (2 wds.) 11. Pharyngeal tissues that may swell 14. Seed for openers? 15. Homopterous insects with loud tymbals 18. Planetary tally from 1930 until 2006

Lab activity Lawn-damaging larva Culture medium in a Petri dish Study of body language James who wrote The Double Helix Like the horns of an ibex Relatives of the extinct quagga Bone below the sacrum Using scientific methods, as in crime-solving 17. Partner to a radius 19. Presumably aseptic spot of lore 20. The healing arts

My biggest pet peeve is when white colleagues, who do research for a living, ask me for advice on how to be an ally without having done any research. It’s not hard to find journal articles that detail the impact of diversity, equity and inclusivity initiatives.

Amid loud (and justifiable!) calls to protect and elevate the role of science, too many scientists and scientific organizations are eerily silent on the issues of racism and social justice—issues that are embedded into the history and practice of science. —500 Women Scientists leadership, writing in Scientific American on the need to address institutional racism in science (June 6)

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07/08 . 2020 | T H E S C IE N T IST 1 3

CRITIC AT LARGE

COVID-19 Along Color Lines People of color in the US have been disproportionately affected by COVID-19. Here’s what this outbreak can teach us about the biology of this inequity. BY MATTHEW DACSO, KARA MCARTHUR, AND CLIFFORD DACSO

1 4 T H E SC I EN T I ST | the-scientist.com

1993, allostatic load seeks to quantify the physiological effects of chronic stress. As the body attempts to maintain homeostasis in a stressful situation, its neuroendocrine system releases elevated levels of certain hormones. Over time, these fluctuating and heightened cellular-level biochemical responses damage immune, cardiovascular, and other systems. External stressors can come from degraded and inhospitable environments, pervasive violence, or constrained resources. Major life events such as illness and the death of a loved one contribute to allostatic load, as does personal trauma, both physical and psychological. Contrary to the old saw, “What doesn’t kill you makes you stronger,” the additive effect of social, economic, environmental, and disease stressors promotes vulnerability to disease and dysfunction. High allostatic load scores are consistently associated with increased all-cause mortality in adults. Individuals from lower-income communities, with higher allostatic

loads, can reasonably be expected to have an impaired immune response to novel pathogens such as SARS-CoV-2. Research has suggested that a number of biochemical processes, and even the physiology of organs, can change as a consequence of socioeconomic stress. Animal models have homed in on specific features of biology responsive to persistent physical, psychological, and social stress, from the hippocampus in the brain to neuroendocrine and immune systems, and these provide insight into how socioeconomic status, as represented by increased allostatic load, can reverberate into susceptibility to infection among people. For example, researchers studying rodents, pigs, and nonhuman primates consistently observe an immune defect resulting from persistent stress. Scientists have also reported defects in T cell functions and cytokine responses when animals’ normal social relationships are perturbed (See “The Isolated Brain” on page 32). Nonhuman primates consistently show markers

© ISTOCK.COM, LYUBOV IVANOVA

T

he COVID-19 pandemic has probed and exposed gaping fissures in the global healthcare landscape. There have been dramatic failures in the capacity to care for the affected, in the ability to diagnose, in prevention, and in intervention. Among the many astounding observations about the pandemic and the world’s response to it has been the consistent differential effect of SARS-CoV-2 on different communities and populations. In the United States, COVID-19 has been more widespread and injurious among people of color, particularly among African American and Latinx people. Epidemiologists made this observation soon after the virus’s introduction to the country, and the pattern has held up in metropolitan areas as diverse as Houston, New York City, and Seattle. Reports ascribe the difference to the higher prevalence of underlying disease such as diabetes, hypertension, and heart disease in these populations. That comfortable explanation, while true on its surface, does not go far enough to explain the disproportionate rates of infection. Research inspired by epidemiologist Michael Marmot’s pioneering Whitehall studies of British civil servants from the 1960s and 1980s have consistently demonstrated a clear relationship between socioeconomic status and health outcomes, independent of other risk factors, such as chronic disease or smoking. Thus, while the presence of chronic disease in disadvantaged populations is part of the reason for COVID-19’s unequal effect, other biological factors are likely also at play. “Allostatic load” is a useful construct to describe the cumulative effect of stressors affecting human biology. Introduced and developed by neuroendocrinologist  Bruce McEwen and physiological psychologist Eliot Stellar in

of enhanced inflammation when under persistent social stress. At a neurohumoral level in several experimental models, persistent stress is associated with elevations in glucocorticoids and catecholamines that can modulate immune function. Likewise, very similar findings from human studies support this biological response to social stress. Some studies have even linked environmental exposures and health disparities with epigenetic modification, such as DNA methylation. At the cellular level, stress is reflected in responses that lead to stress of the endoplasmic reticulum, which in turn causes cell senescence and regulated cell death. This phenomenon can have distant, pernicious effects on physiological function. Science is developing an understanding of how social and environmental stressors exert a significant and interconnected effect on both animal and human populations. These cumulative factors can lead to increased susceptibility to infection. In

sum, social factors such as discrimination, lack of access to healthcare, and economic inequality increase allostatic load, in turn providing a convincing argument for a biological contribution to increased susceptibility to infection and worse outcomes among underresourced populations. Of course the higher prevalence of chronic non-communicable diseases contributes to higher COVID-19 rates and worse outcomes in people of color, but the presence of chronic disease alone is not sufficient to explain the disparity. Furthermore, as allostatic load is a linking factor in the prevalence of underlying disease in disadvantaged populations, the explanation for why people of color have increased susceptibility to the ravages of SARS-CoV-2 may be just as much related to the effect that social inequality has on biology as to the biology of chronic disease itself. Emerging infectious threats thus propagate a cycle of vulnerability, due in large

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part to the complex interactions between epigenetics and the social determinants of health. A strong and humane public health strategy will take into account the entire life course and intergenerational issues, as well as directly contributing ecological and etiological factors. Failing to understand these propulsive factors in pandemics will condemn us to repeat this sad episode. g Matthew Dacso (@DrMattDacso) is a general internist and a professor in the department of internal medicine at University of Texas Medical Branch in Galveston and is Director of Academic Partnerships for the university’s Center for Global and Community Health. Clifford Dacso (@cdacso), Matthew’s father, is a professor at the Baylor College of Medicine in Houston, Texas, and is the scientific advisor of the Institute for Collaboration in Health in Houston. Kara McArthur is executive director of the Institute for Collaboration in Health.

NEWS AND ANALYSIS

Old Birds, New Tricks

G

iven the opportunity, some birds can be surprisingly inventive when gathering food. Ornithologists have spotted green herons (Butorides virescens) using bread to lure fish, ravens (Corvus corax) dropping nuts on roads for passing cars to crack, and Barbados bullfinches (Loxigilla barbadensis) taking and pecking open sugar packets from restaurants. One group of birdwatchers even caught rufous treepies (Dendrocitta vagabunda) stealing burning candles from a Hindu temple, only to extinguish the flames and consume the cotton-and-butter wick.

1 6 T H E SC I EN T I ST | the-scientist.com

Many ecologists suspect that these unusual behaviors are more than just curiosities—they could be part of a pattern that explains why some species survive while others go extinct. An idea known as the cognitive buffer hypothesis, introduced in the early 1990s, posits that animals capable of coming up with new behaviors are better able to respond to environmental change. According to this idea, bird species that have larger brains and are thus more capable of innovating new foraging techniques have an above-average chance of finding a way to survive if their native forest habitat is disturbed by development of agricultural land or suburbs, for example. The hypothesis is subject to a few caveats, though. One is that “species that have bigger brains also develop more

JULY/AUGUST 2020

AVIAN INNOVATION: A Carib grackle

(Quiscalus lugubris) dunks dry pet food in a puddle to soften it.

slowly and reproduce more slowly,” says Trevor Fristoe, an evolutionary biologist at the University of Konstanz in Germany. The large brains that enable some birds to adapt to change could therefore also make it harder for them to recover from a population decline. As a result, Fristoe notes, “we really don’t know [whether] big brains are going to help birds cope with all the ways that humans are changing the planet.” Wondering whether innovative behavior could help birds avoid extinction was what motivated Louis Lefebvre 25 years ago to start keeping tabs on unusual bird

LOUIS LEFEBVRE

Notebook

SWEET IDEA: A bullfinch (Loxigilla barbadensis)

LOUIS LEFEBVRE

makes off with a sugar packet from a restaurant in Barbados.

behavior. Every time an ornithologist described a bird species trying a new food or using a novel foraging technique, Lefebvre, an animal behavior researcher at McGill University in Montreal, recorded the innovation. After more than two decades of monitoring such reports from around the world, the innovation database covered more than 10,000 bird species and documented more than 3,800 behavioral innovations. These include great cormorants (Phalacrocorax carbo) in New Zealand following ferries to catch fish disturbed by the boats’ wake and Carib grackles (Quiscalus lugubris) stealing dry cat food left on porches and softening it by dipping the pellets in puddles. The database also lists innovations that Lefebvre calls a bit more “boring.” For example, if a bird known to eat nine types of seed was observed eating a tenth type of seed, that was registered as a new behavior. Lefebvre and his former graduate student, Simon Ducatez, now a postdoc at the Ecological and Forestry Applications Research Centre in Barcelona, used the dataset to test whether birds’ propensity for innovation correlated with their risk of extinction, as measured by the International Union for Conservation of Nature (IUCN) Red List. The team’s analysis also controlled for variation in generation time and other key differences among the birds in their database, as well as for the fact that ornithologists are more likely to spot innovations for species that are widespread and more frequently observed. After accounting for all these factors, Ducatez and Lefebvre found that species that had demonstrated at least one behavioral innovation were generally at a lower risk of extinction than species that had never been observed to innovate at all (Nat Ecol Evol, 4:788–93, 2020). Moreover, species with three or more documented innovations were more likely to have increasing populations than species with just one or

two new behaviors. “Population declines seem to be happening in species that do not frequently show changes in their feeding behaviors,” says Lefebvre.

Ecologists suspect that these unusual behaviors are more than just curiosities—they could be part of a pattern that explains why some species survive while others go extinct.

Both Ducatez and Lefebvre emphasize that specific innovative behaviors are less important for extinction risk than birds’ capacity to innovate. “It’s not because one specific heron is using bait to catch fish that it’s going to fare better in the face of environmental changes,” Ducatez explains. “It’s the ability to develop new and complex behaviors that would help if it is facing changes in its environment.” The team found that the relationship between innovation and species survival was driven mainly by data on birds endangered by habitat destruction. Innovativeness was not significantly associated with extinction risk among species that were instead threatened by poaching or invasive species. Just because a species has the propensity to develop new foraging behaviors, Ducatez

notes, does not mean that it can also evade new competitors, hunters, or predators. Sahas Barve, an avian evolutionary ecologist at the Smithsonian Museum of Natural History, cautions that Lefebvre’s database considers innovations at the individual level, rather than the species level. To confirm the link between birds’ innovative capacity and reduced extinction risk, “the next step,” says Barve, is to determine whether “many individuals within those species are innovative.” Still, Barve was supportive of Ducatez and Lefebvre’s conclusion that the capacity to innovate plays a significant role in the resilience of many bird species to environmental change. The team’s findings also offer a glimpse of the potential future of ornithology. “Maybe in 100 years we’ll be left with crows and herons,” Lefebvre jokes. “Some birds are going to make it through whatever we throw at them.” —Michael Graw

More than Kisses In April, a scruffy pug named Winston started coughing and wouldn’t touch his chow—a clear sign the pup wasn’t feeling well. Three of the four humans in his family in Chapel Hill, North Carolina had come down with COVID-19, and they were concerned he’d caught it too. 07/08 . 2020 | T H E S C IE N T IST 1 7

Later testing showed the pug didn’t, in fact, have a SARS-CoV-2 infection. But a handful of other household pets have tested positive for the virus in the last few months, a cue for scientists to take a serious look at whether our canine and feline companions could transmit the virus to one another or to humans. There’s no evidence so far that they can. However, SARS-CoV-2 is not the only infectious agent that scientists worry our furry friends might share with us. Researchers have also been studying whether multidrug-resistant organisms— and the genes they use to resist death by antimicrobial drugs—are transferred from pets to humans. There have been cases of infection of humans by pet food, at least: in 2019, for example, more than 150 people in 34 states were sickened with multidrug-resistant Salmonella after handling contaminated pig-ear pet treats. Other research has also shown pet food to be a source of antibiotic-resistant bacteria. These findings led Ana Raquel Freitas and Luísa Peixe of the Research Unit on Applied Molecular Biosciences, a col1 8 T H E SC I EN T I ST | the-scientist.com

laboration of the University of Porto and NOVA University of Lisbon in Portugal, to ask whether or not dog food, specifically raw dog food, played host to antibiotic-resistant Enterococcus faecium, a bacterium that has been causing a growing number of infections worldwide. “For many years, we have known that humans share some lineages, some antibioticresistant lineages of Enterococcus with dogs,” Freitas tells The Scientist. “We don’t know the origin of transmission, and we thought, ‘Why not test the food?’” Between September and November last year, Freitas and Peixe gathered samples of dog food from eight supermarkets and a veterinary clinic in Porto. The researchers collected a total of 46 samples: 22 wet foods, 15 dry foods, and 9 raw-frozen foods, which are growing in popularity despite questions about their safety. Swabbing each sample on an agar plate, the team cultured any bacteria living in the food, then treated the plates with various antibiotics. All nine of the raw food samples tested positive for multidrug-resistant enterococci, while only one of the wet food

and none of the dry food samples had lineages resistant to antibiotics. “What we saw in the raw foods was surprising,” Freitas says. The team had expected those foods to have more bacteria because, unlike dry foods, they aren’t sterilized, “but the type and amount of bacteria in the samples was unexpected.” (The team had planned to present these early findings at the European Congress of Clinical Microbiology and Infectious Diseases in April, but the conference was canceled due to the COVID-19 pandemic.) Preliminary analysis of the data suggests that some of the bacterial strains identified in the raw foods have signatures of mobile genetic elements that promote antibiotic resistance, and some of those same signatures have been detected in people hospitalized for bacterial infections, Peixe notes, an important finding to follow up on. Another recent observational study from an independent team in Portugal supports Freitas and Peixe’s results. In their study, Constança Pomba of the University of Lisbon and colleagues analyzed fecal samples

ANDRZEJ KRAUZE

NOTEBOOK

YUCHAO ZHAO, UNIVERSITY OF MICHIGAN MUSEUM OF ANTHROPOLOGICAL ARCHAEOLOGY/JOHN KLAUSMEYER

of more than 100 humans and 84 of their companion animals. The great majority of the humans and animals tested positive for nonpathogenic strains of E. coli; most didn’t show signs of a bacterial infection. Digging deeper, the team identified evidence of genes resistant to colistin, a last-resort treatment to kill multidrug-resistant bacteria, in the fecal samples of two healthy humans and one dog that all lived in different households. Researchers should be aware of the risk that already multidrug-resistant bacteria could acquire a genetic defense against colistin if they pick up these genes while in humans or pets, the authors say. Overall, however, evidence is weak that large quantities of antibiotic-resistant bacteria or resistance genes are actually being transferred to humans from pets, at least at levels great enough to make us sick. Some studies have found that if it happens at all, it’s likely very rare. For example, Carolin Hackmann of the Charité-University Hospital in Berlin and colleagues have so far taken nasal and rectal swabs from 1,500 hospital patients and from several dozen of those patients’ pets, and in only two cases were pet and owner colonized with the same strain of multidrug-resistant organism. “We were surprised that the rate of pet-owner pairs who shared the same [strain] was so small,” Hackmann writes in an email to The Scientist. She adds that “it is too early to draw any final conclusions,” but based on the data she does have, owning a pet doesn’t appear to significantly raise the risk of pets and humans swapping multidrug-resistant bacteria.

The beads are often the last of many incarnations of an ostrich egg, explains Brian Stewart, an archaeologist at the University of Michigan. After finding an egg, the San—presumably like ancient human ancestors—carefully drill a hole in it and drain the white and yolk to be eaten. Then they wash out the shell, which makes a handy water flask. When the canteen eventually breaks, people reduce the fragments down to a standard size, drill a hole in the middle of each, string them together, and then shape the fragments into rounded beads. The beads can then be strung together to make jewelry or sewn onto clothing for decoration. Ethnographers have found that the San often exchange the beads, sometimes with people who live 200 or more kilometers away, to help cement social connections.

Ostrich eggshell beads have also been found in other parts of Africa and in north Asia, places where, in general, people no longer make and trade them. Many have been discovered in rock shelter sites in Lesotho, a small, mountainous country that lies far to the southeast of the Kalahari, completely surrounded by South Africa. These beads were found in archeological layers that range in age from a few hundred years old to tens of thousands of years old, according to work by Stewart and others. It’s not known whether ostriches lived in Lesotho at the time the beads were made, Stewart notes, but it’s unlikely they did. “They really shouldn’t be up there in terms of their ecological preferTIMELESS STYLE: Ostrich eggshell beads,

such as these specimens found in Lesotho, may have been exchanged as gifts among Stone Age humans.

—Ashley Yeager

Bead Networking If you’re looking for an accessory that never goes out of fashion, you can probably do no better than ostrich eggshell beads. The oldest known examples of these tiny, Cheerio-like decorations, found in rock shelters in Tanzania, have been dated to around 50,000 years ago, while similar creations are still made by San hunter-gatherers in Southern Africa’s Kalahari Desert today. 07/08 . 2020 | T H E S C IE N T IST 1 9

NOTEBOOK

ences,” he says. “And certainly they’re not up there today.” So archeologists have long wondered whether the beads were “brought in or exchanged in from other areas. But they were never able to really test that.” Stewart and his colleagues recently saw their chance to do such a test using strontium isotope analysis, which uses the ratio of strontium isotopes in a sample to trace organisms back to the geological environments where they originated. Lesotho is particularly well-suited to such an analysis because of its mountainous terrain surrounded by land that steadily decreases in elevation, with different types of rock—each with its own strontium ratio—dominating the surface at different levels. Because the ratios of strontium isotopes in eggshell and other animal remains reflect those of the rock and soil where they originated, researchers would be able to use this method to pinpoint where the beads came from.

There was a logistical hurdle the researchers would need to overcome, however: the group would need a large set of biological reference samples from multiple locations to create a strontium isotope map against which to compare the beads’ ratios. Assembling such a collection seemed like a Herculean task, but mulling over the problem, Stewart realized that such a collection already existed, albeit scattered across the back rooms of small natural history museums around South Africa. “They have these nice collections of small mammals . . . and they know exactly where they were taken from,” he says. “And, because they’re small mammals, they actually live in quite small, circumscribed territories.” Comparing the isotope ratios from the animals’ teeth with those of eggshell beads from two Lesotho rock shelters, the group found that none had strontium signatures that matched the local

The oldest bead the team analyzed dates to about 33,000 years ago.

geological strata, confirming that the beads didn’t come from local eggshells (PNAS, 117:6453–62, 2020). Instead, “pretty much all of them came from no closer than 100 kilometers away . . . and about 20 percent of the beads came from further than about 200 or 250 or so kilometers away,” Stewart says. Of those, a smaller subset came from at least 300 kilometers away—but possibly much more, he adds. Determining the provenance of that well-traveled subset will require more work. The oldest bead the team analyzed dates to about 33,000 years ago, and it happens to belong to the farthest-away subset. Combined with the climatic dif-

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ferences between verdant Lesotho and drylands to the west, and with what’s known about how the eggshell beads are exchanged today, the study’s results suggest the beads factored into savvy relationship-building, Stewart says. They “probably represent risk-hedging bets, or network[ing] attempts . . . on the part of desert hunter-gatherers who are trying to make . . . links with people that live up in the mountains where you’ve got more stable supplies of fresh water [and] of animals,” he says. How the beads physically got there is another question. One possibility, Stewart says, is that they traveled through a series of exchanges among desert groups who lived tens of kilometers apart. Ancient as some of them are, Lesotho’s ostrich beads are likely part of an older tradition of far-flung groups using goods to build social networks, perhaps as a way to ensure that they would receive help in tough times. “I think that gift exchange . . . is likely to have a much earlier origin,” Lyn Wadley, an archaeologist at the University of the Witwatersrand in Johannesburg, who was not involved in the study, writes in an email to The Scientist. Before ostrich shell beads came into fashion, “it may have operated through, for example, the early exchange of decorated eggshell flasks and marine shell beads.” Likewise, Stewart suspects that the small, uniform, mass-producible beads weren’t part of the first networking attempts, but represent “the end result of a longer process of evolution and becoming really flexible to difficult environments.” While Wadley thinks the isotope evidence the authors present for the beads’ far-flung origins is compelling, she adds that the results don’t rule out an alternative explanation: that, rather than being gifted, the beads were brought to Lesotho during long-distance seasonal migrations. Steven Kuhn, an anthropologist at the University of Arizona who was not involved in the research, also thinks it’s possible that the beads were transported long distances as personal possessions rather than gifts. But the authors’ explanation seems more plausible in light of

what’s known about modern huntergatherers, he adds. Anthropologists have suspected that Homo sapiens long used a relationship-building strategy like the one laid out in the study to boost their chances of survival, he says. Eggshell beads are compelling evidence for gift exchange, he notes, because they would have been easy for people to make locally if desired—even Lesotho residents probably wouldn’t have had to travel far to gather ostrich eggs from nearby deserts—so there was no other practical reason to exchange them with people from far away. He compares the behavior to today’s custom of businesses giving away calendars, pens, or fruit baskets. “Nobody really needs another calendar,” he says. “It’s more about establishing a relationship.” —Shawna Williams

Fly Forensics The six cadavers all wore the same clothes: red t-shirts, plaid boxers, and cargo shorts. They’d been shot in the head and then stuffed into the trunks of old, beat-up cars or deposited in densely shaded spots of forest in Maple Ridge, British Columbia. All died on July 24, 2007. Graduate student Stacey Malainey of Simon Fraser University checked on the six pigs, which served as proxies for human homicide victims, twice a week from the day they were killed, for nearly a month. When it comes to murder, cadavers are most commonly found dumped in the bushes or the forest. “But there are a remarkable number that are concealed, and particularly concealed in vehicles—in old, junker vehicles,” says forensic entomologist Gail Anderson, Malainey’s supervisor at Simon Fraser. Having worked with the police for more than 25 years, Anderson has seen her share of bodies left to decompose in the trunks of cars. Using her understanding of insect development on cadavers, she’s able to roughly estimate the minimum amount of time each victim has been dead—a crucial piece of information for corroborating alibis and other details in a criminal investigation.

Researchers typically use insects to calculate “what we call a ToC, or time of colonization,” says Lauren Weidner, a forensic entomologist at Arizona State University who was not involved in Anderson’s work. “We’re trying to figure out how long [the insects have] been there, so we can help determine how long a body has been there.” While there’s been a lot of research on how insects colonize bodies left outside, forensic entomologists have often wondered what happens when a body is confined or concealed. In a series of studies, Anderson and others have shown that pig cadavers decompose differently when wrapped in sheets or stashed in buildings versus just being dumped outside (J Med Entomol, 53:67–75, 2016); even zipped suitcases change the way insects inhabit the carcasses stuffed inside (Forensic Sci Int, 239:62–72, 2014). In the new study, Anderson and Malainey wanted to determine how long it would take for insects to get inside cars and colonize dead bodies.

People think they can get rid of a lot of evidence setting fire to things, and of course, they don’t. —Gail Anderson, Simon Fraser University

Every few days that summer, Malainey went to photograph the pigs, record their decomposition rate, and collect insect samples. However, she couldn’t just pop the trunk; that would risk giving insects easy access to the cadavers. So on each visit, she draped a huge piece of plastic around the rear end of the car, taping it to the rear windows and spreading it out like a train of a wedding dress. Then, she’d duck under the plastic and pull it down to ensure it touched the ground the entire time she had the trunk open. After she’d braved the stench of putrefaction to collect her data, she’d slip out from under the plastic train, then remove it, and roll it up. “We were very careful,” Anderson says. 07/08 . 2020 | T H E S C IE N T IST 2 1

NOTEBOOK

On the third day, the pigs left outside were bloated and covered in fly eggs and early stage larvae, mainly of blue bottle flies (Calliphora vomitoria and C. latifrons) and blow flies (Lucilia illustris). The pigs in the car trunks were bloated, but only one of the three had eggs, specifically from the blow fly Phormia regina. By day six, the pigs outside had larvae that were further along in development and moved as masses of maggots, while the pigs in the trunks were now all colonized by insect larvae in earlier stages of development. About a week later, the temperature inside the exposed dead pigs started to rise, as the maggots decomposed the dead flesh. Inside two of the cars, however, the pigs had already been reduced to mere skeletons, with pupae—the developmental stage between larva and adult insect—scattered throughout the trunk and car, with some even nestled into the front driver’s side floor carpet. The temperature of the car plus the pig was warmer than a pig sitting outside, allowing any hatching insects to grow faster and consume dead tissues more quickly than those in pigs dumped outside. On any given day, the temperature inside the cars was 10–25 ˚C higher than 22 T H E SC I EN T I ST | the-scientist.com

the ambient outdoor temperature, which peaked at about 25 ˚C. On the last day Malainey visited the pigs, day 28 of the experiment, the two skeletonized, car-stored pigs were infested with thousands of live and dead blow flies, while only one exposed pig showed evidence that adult flies had emerged (PLOS ONE, 15:e0231207, 2020). However, in the third car, which had the highest recorded temperatures, the pig was still intact and bloated, with far fewer larvae and no maggot masses—an oddity in the observations at the time. Overall, the work supports existing hypotheses on how stashing a cadaver inside a car affects insect colonization, says Daniel Martín-Vega of the University of Alcalá in Madrid. Car trunks lengthen the time to colonization, because they cause a delay in female blow flies accessing a body to lay eggs. But cadavers in cars can become warmer than those in open air, quickening the rate at which female blow flies’ larvae consume the cadaver, he writes in an email to The Scientist. The study provides “reference data for eventual cases taking place in similar scenarios.” And, it suggests that certain species of flies—P. regina and Proto-

phormia terraenovae in the study—might stick around until they find a way to colonize cars while others look for an easier place to lay eggs, Weidner notes. After the month of observations, Anderson and Malainey still weren’t finished with the cars: next, they lit them on fire. “That’s another common [scenario] you hear all the time: somebody dumping the car, then setting fire to it,” Anderson says. “People think they can get rid of a lot of evidence setting fire to things, and of course, they don’t.” From the burnt-out cars, the team recovered flies in advanced stages of development, all of which could help estimate time of colonization. They also discovered that the car in which the pig had been mysteriously preserved didn’t burn as well as the others (Forensic Sci Int, 306:110033, 2020). It turns out that the vehicle had a steel firewall between the passenger compartment and the trunk, which delayed decomposition of the pig in the first experiment and allowed the team to retrieve even more insect remains than from the other cars after the fire, Anderson says. But firewall or not, she adds, “there’s an awful lot of evidence left behind.” —Ashley Yeager

GAIL ANDERSON

LASTING EVIDENCE: Researchers who loaded car trunks with pig carcasses and set the vehicles on fire still found abundant entomological evidence that could help estimate when the body was placed there.

MODUS OPERANDI

Modular Antiviral Antibodies Using bacterial superglue, researchers create potent virus-neutralizing multimers. BY RUTH WILLIAMS

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inter the llama grabbed headlines recently for her part in generating a special type of anti-SARS-CoV-2 antibody. But in fact, any camelid has what it takes to create such valuable proteins, known as single-domain antibodies (sdAbs). These tiny proteins, which only sharks and camelids (llamas, camels, and related species) are known to make, differ from the antibodies found in humans and other animals in that they’re encoded by just one gene instead of two. This makes them far easier for geneticists to work with in the lab, says virologist Paul Wichgers Schreur of Wageningen University in the Netherlands. Indeed, sdAbs (also known as nanobodies, or VHHs) are being developed for a variety of applications and disease treatments, including antiviral therapies. The idea is that infected patients would be given sdAbs to bind and neutralize the virus, slowing its spread in the body. To achieve effective virus neutralization, sdAbs tend to be combined into multimers to improve binding—as soon as one sdAb releases a target, another sdAb is close by to immediately grab hold of it. Such multimers, which are composed of either multiple copies of the same sdAB or a mixture of different ones, are typically genetically engineered— requiring them to be cloned in bacteria or yeast. But “if you want to search for the best combination” of sdAbs for binding the virus, says Wichgers Schreur, “you have to clone all the options,” which can be tedious and tricky.

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MIX AND MATCH: To make multimeric antibody complexes to fight a pathogen, llamas are inoculated with a

virus of interest  1 . Researchers collect DNA from antibody-making cells in the llama’s blood and amplify it to produce single-domain antibodies (sdAbs)  2 . This collection of sdAbs is screened to find those with a strong virus-binding ability  3 , and those antibodies are then tagged with bacterial superglue peptides (superglues are peptide-protein partners that form irreversible bonds)  4 . By mixing the glue-tagged sdAbs with scaffolds containing the glue partner proteins, researchers can combine their desired sdAbs into multimers  5 , and then screen them to find the ones that best neutralize the virus  6.

Wichgers Schreur’s team opted for a faster method: sticking various sdAbs from llamas together with bacterial superglue— a technique developed by other groups for forming irreversible bonds between special bacterial peptides and their partner proteins. The team used a variety of available peptideprotein pairs, including SpyTag-SpyCatcher and SnoopTag-SnoopCatcher. One of the team’s test targets was Rift Valley fever virus (RVFV), which primarily affects ruminants but can be transmitted to humans, and for which there is no vaccine. They isolated sdAbs from llamas inoculated with RVFV, tagged the sdAbs with superglue peptides, then mixed different combinations of tagged sdABs together with scaffold

proteins containing the corresponding catcher sequences. The team tested these combinations in vitro to find one with potent RVFV-neutralizing ability, then turned to traditional genetic engineering to rebuild it. This enabled the researchers to modify the multimer to be more stable and less immunogenic than the original glued-together version. Infected mice treated with the multimer had reduced mortality compared with untreated mice. While the work focused on RVFV, “[the] technologies can easily be transferred to the current COVID-19 research” or work on other viral diseases, says Edward Dolk, the CEO of a company called QVQ that develops sdABs but was not involved in the research. (eLife, 9:e52716, 2020) g

© MELANIE LEE

AT A GLANCE MULTIMERIZATION OF sdAbs

HOW IT WORKS

ADVANTAGES

DISADVANTAGES

THERAPEUTIC USE

Genetic fusion

Multiple individual sdAb coding sequences are fused with linker sequences to create a multimer-encoding sequence that is cloned into an expression vector in bacteria or yeast.

Based on a well-established technique that can be applied in most molecular biology laboratories

Each combination of sdAbs to be tested needs to be individually cloned. Production yields of these multimers are frequently low.

Yes, in clinical trials. Can be applied to patients directly and can be designed to minimize immunogenicity

Bacterial superglue

Each individual sdAb is tagged with one of a series of glue peptides. These then couple to scaffold proteins containing corresponding catcher domains to form a variety of multimers.

Reserachers can assemble and test combinations of sdAbs rapidly. Production of individual building blocks is generally efficient.

Technique not yet optimal. Coupling not always 100 percent. Bacterial superglue proteins are immunogenic.

Not directly. The selected multimer should be reformatted into a human antibody–like molecule.

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Biology, sociology, and mathematics meet in a single statistic used to quantify the transmissibility of an infectious agent. The result is a shaky metric that policymakers are using to craft public health policies amidst the pandemic. BY KATARINA ZIMMER

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n the evening of December 30, 2019, an email with the subject line “undiagnosed pneumonia – China (Hubei)” popped into Maia Majumder’s inbox. The notice, which the computational epidemiologist had received through ProMED, a global reporting system for infectious diseases, went on to describe Chinese news reports of patients pouring into hospitals in Wuhan presenting with an unexplained respiratory illness. It added: “Citizens need not panic.” 07/08 . 2020 | T H E S C IE N T IST 2 5

Majumder, a researcher at Harvard Medical School and Boston Children’s Hospital who had previously helped predict the spread of Saudi Arabia’s MERS epidemic of 2014 and the West African Ebola outbreak shortly thereafter, agreed with that statement—at that point, it wasn’t clear whether the culprit was an infectious pathogen capable of jumping from one person to the next. But when murmurs of possible humanto-human transmission started to circulate a few weeks later, she and her Harvard colleague Kenneth Mandl set out to calculate a metric—the pathogen’s basic reproductive number (R0)—that would hint whether it could cause an epidemic. Simply explained, R0 represents the average number of people infected by one infectious individual. If R0 is larger than 1, the number of infected people will likely increase exponentially, and an epidemic could ensue. If R0 is less than 1, the outbreak is likely to peter out on its own. R0 alone cannot definitively forecast an outbreak, but “it’s like an early warning system, in a lot of ways, for the possibility of an epidemic or pandemic,” Majumder says. To estimate R0 for the coronavirus now known to the world as SARS-CoV-2, Majumder and Mandl picked a simple mathematical model that can infer the R0 from the curve of rising case numbers as well as another metric that describes how quickly an infection spreads from one person to the next, based on previous studies of MERS, another coronavirus infection. On January 23, they published one of the first estimates for the R0 for SARS-CoV-2 infection: 2.5, significantly higher than estimates for MERS but relatively similar to another relative, SARS, which caused a deadly global epidemic in 2003.1 Within a week, five other research groups had produced their own R0 estimates, which all fell somewhere between 1.4 and 4, depending on the mathematical method they used and type of data they input.2 None were below 1. “It was a moment of realization for us where it was like, it definitely looks like we have something that can cause an epidemic on our hands, and this is probably not something that will just fizzle out on its own the way that we’ve seen with MERS outbreaks in the past,” Majumder recalls. Fast forward a month, and the world did have a pandemic on its hands. Modelers around the world scrambled to forecast the spread of SARS-CoV-2 and the COVID-19 disease it causes in their own countries and communities. Many epidemiologists were then and still are tasked by policymakers with answering urgent questions: How fast will it spread? How many hospital beds and ventilators will we need? When can we lift lockdowns and restart our economies again? Will we see a second wave? Will it be worse than the first? Getting good estimates for R0 is key to answering such questions with accuracy. But R0 is notoriously tricky to nail down. It depends not only on the biological characteristics of a virus—which are a mystery at the beginning of an outbreak— but also on understanding how often people come into contact with one another. Faced with uncertainty, modelers have 26 T H E SC I EN T I ST | the-scientist.com

to make assumptions about the factors that determine human movement, which can limit the precision of their models and the accuracy of the predictions they generate. “R0 is a metric that is, first of all, poorly measured. And secondly, it’s informing models that result in public health action,” says Juan B. Gutiérrez, a mathematician at the University of Texas at San Antonio. “If we get it wrong, the public health action will be misplaced.”

It’s extremely difficult at the beginning of an epidemic to get an accurate R0. —Nelly Yatich, epidemiologist in Nairobi, Kenya

Defining R0 With some notable exceptions, R0 forms a centerpiece in most disease forecasting models. The metric is often misconstrued as a fixed property of a pathogen, and it is indeed influenced by biological factors such as mode of transmission that stay more or less constant throughout an epidemic. But R0 also depends on how often people come into contact with one another, and that can differ drastically between countries, cities, or neighborhoods. For COVID-19, “it is unlikely that the R0 that has been calculated in China will be the same in the US or in Europe,” explains Constantine Siettos, a biomathematician at the University of Naples in Italy. How many people one infected individual infects can also change within localities as governments close essential businesses and issue shelter-in-place orders, or begin to reopen the economy. For that reason, epidemiologists typically distinguish between two forms of the reproductive number R: the basic reproductive number R0, which describes the initial spread of an infection in a completely susceptible population, and the effective reproductive number, Re, which captures transmission once a virus becomes more common and as public health measures are initiated. Re is typically much lower than R0. In the current pandemic, many policymakers are looking toward Re to gauge whether their policies reduce viral transmission, notes biomathematician Robert Smith? (the question mark is part of his name) of the University of Ottawa. “What you care about is, can we get the [Re] below one?” If the Re is even slightly above one—say around 1.1—then the outbreak could become too much for healthcare systems to handle, as German Chancellor Angela Merkel noted at a press conference in April. It was around this time that researchers at Germany’s Robert Koch Institute estimated that the nation’s Re for COVID-19 had dipped down to a safer value of 0.7, a finding that partly informed the government’s plan to begin relaxing lockdowns and reopening small businesses.

While the flexible, context-dependent nature of Re makes it useful to politicians, the same characteristic also makes it difficult to measure. Because the factors that influence Re are always in flux, epidemiologists estimate the metric from models that simulate a pathogen’s spread through a population, based on often incomplete data on known cases, hospitalizations, or deaths. Epidemiological models are also used to calculate the initial R0, and they vary in their complexity and in the way they calculate the two metrics. At one end of the spectrum are simple models that infer these metrics from case data and some other measures; Majumder and Mandl used a model of this nature. The most popular types of model, however, are susceptibleinfectious-recovered (SIR) models, which assign everyone in a population to one of several categories: susceptible, infectious, recovered, or depending on the disease, also “exposed but not yet infectious” or “dead.” Equations describe the rates at which people move from one category to another, relying on parameters such as the contact rate, the probability of transmission, and the duration over which someone is infectious. At the other end of the spectrum are “agent-based” models, an innovative, complex breed of model simulates the movement of individu-

als. For both agent-based and SIR models, R0 and Re can be derived from the models themselves. Once calculated, these metrics can also play a key role within the models to create predictions about the spread of a disease. The final result, R, is a metric that varies depending on the context, the model used and its underlying assumptions, as well as the quality of data it is built with. Especially in the early days of an epidemic, when information on the basic biological properties of a virus and its transmission is uncertain, estimates can be off the mark, notes Nelly Yatich, an epidemiologist based in Nairobi, Kenya. “It’s extremely difficult at the beginning of an epidemic to get [an accurate R0].”

Silent spreaders To estimate the biological parameters needed to determine R, such as the period over which an infected person can transmit a pathogen and the probability that she will do so, “we try to borrow information from similar viruses,” explains Sara Del Valle, a mathematical and computational epidemiologist at Los Alamos National Laboratory in New Mexico. To model Brazil’s Zika virus epidemic in 2015, for example, her team used data on the transmissibility of dengue. During the 2011

WHAT IS R? The reproductive number R describes the average number of individuals that a person infected with a particular pathogen infects. It depends on how that pathogen is transmitted as well as how often people come into contact with each other—factors that could vary depending on a pathogen’s strain and on the time and location of an outbreak. Scientists typically distinguish between R0, the basic reproductive number that describes disease transmission at the very beginning of an outbreak in a fully susceptible population, and Re, the effective reproductive number that describes transmission once measures such as social distancing or vaccination campaigns have been introduced. Re is typically much lower than R0. COVID-19 epidemic in Wuhan in early 2020 1.4–5.7 2014 MERS outbreak in Saudi Arabia 0.45–3.9 2014 Ebola outbreak in West Africa 1.5–2.5 2003 SARS epidemic in Hong Kong 1.7–3.6 1918 pandemic influenza outbreak in US and Europe THE SCIENTIST STAFF

2.2–2.9 Measles outbreaks in the UK and US in the 20th century 12–18

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MODELING AND R, THE REPRODUCTIVE NUMBER Researchers across the world have developed countless epidemiological models to project the future of the COVID-19 pandemic, and the effect of different public health policies on the spread of the causative virus, SARS-CoV-2. Most, but not all, models being used today give the two versions of R—R0 and Re—a central role. The basic reproductive number R0 describes the spread of a disease at the beginning of an outbreak, and Re, an “effective” version of the metric, describes spread later on. 

STATISTICAL MODELS Statistical techniques can predict the likely trajectory of an outbreak based on observed data. For example, an early iteration of a model developed by the University of Washington’s Institute of Health Metrics and Evaluation (IHME), which helped inform the White House’s response to the pandemic, works by characterizing the curve of death numbers in Wuhan and a number of European cities, and projecting those curves onto US data.

Case numbers

Time

Relationship with R: Such models don’t typically use R, but are sometimes used to make quick estimates for R. Performance: Statistical techniques can be useful for making very short-term predictions, but they do not capture the dynamics of disease transmission or changing contact rates between people due to social distancing measures. Likely for these reasons, early predictions of the IHME model were off. As of early May, IHME has been using a new “hybrid” model that uses both statistical and susceptibleinfectious-recovered (SIR) modeling techniques.

VARIOUS © ISTOCK.COM; THE SCIENTIST STAFF

H1N1 flu pandemic, they turned to data from influenza outbreaks in the 1960s. For COVID-19, Del Valle, like many other researchers, plugged in parameters documented for other coronaviruses, including MERS-CoV and SARS-CoV, to estimate R0. However, the transmission of SARS-CoV-2 turned out to be markedly different from that of these viruses, notes Jasmina Panovska-Griffiths, a mathematical modeler focusing on infectious diseases at University College London and Oxford University. For instance, while MERS and SARS patients typically shed coronaviruses while symptomatic, studies suggest that SARS-CoV-2 can be contagious even before patients know they’re sick.3,4 Such presymptomatic transmission means that the novel coronavirus’s infectious period is longer than that of SARS-CoV or MERS-CoV, throwing off early R0 estimates in Wuhan, which varied widely but tended to be lower than what some researchers now believe to be the case. “In fact, it seems like SARS-CoV-2 is more infectious than MERS and SARS, so [R] is likely higher for SARS-CoV-2 than originally estimated.” It’s even possible people who never show symptoms could play a role in spreading COVID-19. Asymptomatic transmission would also be in stark contrast to SARS and MERS, where asymptomatic carriers were relatively uncommon and were not thought to play a significant role in the outbreaks, notes Panovska-Griffiths. While early reports from China made little mention of possible asymptomatic individuals, studies elsewhere through March and April revealed significant numbers of individuals who tested positive for the virus but never developed so much as a cough. Around 43 percent of residents surveyed in the northeastern Italian town of Voʹ in February and March tested positive despite having no symptoms, and a recent review concluded that asymptomatic individuals could account for as many as 45 percent of infections. 5 What’s more, some contact tracing data hint that asymptomatic people can transmit the virus to others, although it’s still a mystery how often that occurs. The realization that large numbers of “silent spreaders” could exist undermines the predictions of epidemiological models in several ways. First, high numbers of undetected cases would shrink infection fatality rates. Asymptomatic carriers could also transform the trajectory of an outbreak by accelerating transmission. But if they’re present in massive numbers—which many scientists consider highly unlikely— and they become immune after infection, local epidemics could be over much sooner than expected if the virus runs out of susceptible people to infect. Finally, silent spreaders could change estimates of R0 or Re. However, it’s not the numbers of asymptomatic people capable of transmitting SARS-CoV-2 per se that influences R0—as long as their proportion stays constant in the population, estimates of R0 won’t necessarily change. Rather, what matters is how infectious people are. For instance, if infected people who are asymptomatic have shorter or longer infec-

Susceptible Infectious Recovered

AGENT-BASED MODELS Agent-based models simulate individuals—or “agents”— interacting in various social settings and can estimate the spread of disease as these agents come into contact with others. Such simulations are often based on activity surveys, census data, de-identified mobile phone location data, and information from public transportation or airlines.

Number of agents

Proportion of a population

SUSCEPTIBLE-INFECTIOUS-RECOVERED (SIR) MODELS SIR models subdivide populations into compartments such as “susceptible,” “infectious,” or “recovered,” and sometimes other compartments such as “exposed but not yet infectious,” “asymptomatic,” or “dead.” Data on cases, hospitalizations, or deaths can inform estimations of the sizes of those compartments, and equations describe the speed at which people move from one compartment to the next.

Susceptible Infectious Recovered

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Relationship with R: SIR models calculate R using several parameters, including the probability of infection, contact rate, and the period over which an individual is infectious. Once calculated, R helps determine how quickly susceptible people become infected, and thus shapes how fast a disease spreads across a population.

Relationship with R: Some researchers compute R separately and then plug it into their agent-based models, while others use these models to generate estimates of R and predict how R changes based on different interventions. In both cases, agentbased models typically calculate R per agent, unlike SIR-type models that calculate R over whole populations or demographics.

Performance: SIR-type models capture the fundamental dynamics of disease transmission and the effects of public health interventions, but they are often criticized for ignoring differences in contact rates across a population. More-refined SIR-type models, however, do account for varying contact rates, and some correctly predicted the fade-out of the SARS-CoV-2 outbreak in Wuhan earlier this year.

Performance: Several research groups prefer using agentbased models because they can simulate human behavior more accurately than SIR-type models and can predict how individuals’ decisions, such as staying at home, lead to collective or aggregate behavior, and thereby affect disease spread. However, such models require a lot of detailed data about human movement, and an enormous amount of computing power. 07/08 . 2020 | T H E S C IE N T IST 2 9

tious periods than symptomatic individuals, or if their pattern of shedding the virus differs, that could alter the populationwide R0, explains Sang Woo Park, a PhD student who models infectious disease at Princeton University.6 Their contact rates also matter. If asymptomatic people come into contact with more people than symptomatic individuals because they don’t think they’re sick and therefore don’t self-isolate, currently used R0 values will undershoot reality, notes Ben Althouse of the Institute for Disease Modeling in Washington State. “Estimates made early on did not take into account the possibly quite high level of asymptomatic individuals,” and therefore likely underestimate R0, he says. Some researchers, including Gutiérrez, argue that R0 values as high as 13 best explain the virus’ rapid spread across the world before governments instituted social distancing policies.7

All models are wrong, but some are useful. You just hope you’re in the useful category. —Benjamin Ridenhour, University of Idaho

Some clarity is starting to emerge from large-scale blood studies that scan for antibodies against SARS-CoV-2—telltale signs of a past infection—along with investigations into how infectious asymptomatic people are and for how long, Panovska-Griffiths notes. But problems with the accuracy of those tests will limit the value of the data they produce, and researchers will have to find new ways to account for those limitations in their models, Park adds. In the meantime, epidemiologists are reckoning with the uncertainty around SARS-CoV-2’s biological parameters by assuming a range of values rather than fixed numbers, says University of Idaho epidemiologist Benjamin Ridenhour, who is helping state officials predict the spread of the virus. He’s placing confidence intervals around every biological parameter in his model. His R0 could be anywhere from around 1.3 to 4, he says. “That way, obviously the chances that anything you model is exactly correct are zero, but hopefully you can capture it in that range somewhere.”

Super spreading How many people one person comes into contact with can differ dramatically depending on their activities and the populations and structures of their towns and cities. It’s particularly important to account for this variation in the early days of an outbreak, when some infected people, often called “super spreaders,” transmit a disease to an exceptional number of others. While it’s possible that some people might have some phenotype that causes them to shed more virus than others, super spreading 30 T H E SC I EN T I ST | the-scientist.com

usually arises from the fact that some infected people come into contact with a lot of others, such as those living or working in elderly care homes and passengers and crew aboard cruise ships. Althouse says he prefers to talk about super-spreading “events” rather than individuals. Research suggests that super-spreading episodes are in fact a normal feature of infectious disease outbreaks.8 Previous coronavirus epidemics were notorious for such events and some preprint studies are beginning to suggest that SARSCoV-2 is no exception. Because people responsible for super spreading events have an exceptionally high individual R, they can inflate estimates of R0—the mean of a population—early in an outbreak.9,10 This variation makes it impossible to project the overall spread of disease just from R0 alone, notes Stockholm University mathematician Pieter Trapman. As the numbers of infected people grow over the course of an outbreak, the relative effect of individual outliers dwindles. But infected people still vary widely in how many others they infect, and capturing differences in contact rates remains important. Traditional SIR models are often criticized for not capturing that variation well, because they generally make the assumption that a population is evenly distributed, such that everyone’s R is the same. Majumder argues this is one reason why predictions from the US Centers for Disease Control and Prevention (CDC) drastically overshot actual numbers of Ebola cases in West Africa in 2014.11 The agency’s SIR-type model assumed even mixing within the populations of Sierra Leone and Liberia. As a result, they posited the same R0 for everyone, when in reality only a small proportion of sick people infected many others. Most people didn’t infect anyone else at all. The model forecast more than half a million cases by January 2015, but thankfully, the outbreak was brought under control before it hit 25,000. Not many SIR models make this assumption, however. Ridenhour’s SIR-type model, for instance, accounts for differing contact rates across a population. For instance, he subdivided Idaho’s inhabitants into separate age groups and used published estimates on how often people of different ages come into contact with their own and other age groups to assign different contact rates to each group. Other researchers have structured the populations that inhabit their SIR models—not only by variables affecting contact rates such as the population density of their area, but also by factors that could affect health outcomes such as rates of comorbidities and employment. Although they’re still imperfect measures of reality, “the models often fit the disease dynamics pretty well,” Ridenhour says. Other researchers have started to build entirely different, “agent-based” models. These are designed to simulate the movement of individuals, or “agents,” in a population, and thereby predict how often they come into contact with one another. At Los Alamos, Del Valle and her colleagues are using supercomputers to construct an agent-based model for

the US to understand how states can best relax lockdowns without risking a second wave of COVID-19. They’re using census data as well as other federal data describing the typical commutes of workers and transportation via planes and roads, and they’ll soon include location tracking data from mobile phone carriers for insights into when, where, and how people are traveling, according to Del Valle. With these considerations, “we have very detailed information about how [R] varies by county, by state, by age,” and with shelter-inplace restrictions. While SIR models are relatively simple and can produce results within hours, agent-based models can require an enormous amount of computing power to run, and detailed rules that characterize how agents can decide to move around and mix. If the decisions that agents make in one simulation don’t reflect reality, the whole model’s predictions may be off, explains Elizabeth Hunter, a computational modeler at the Technological University Dublin who is developing an agent-based model to understand the spread of the coronavirus in Ireland’s counties. That’s why she repeats her simulation more than 300 times, allowing agents to make different decisions with each iteration. In a model with more than 100,000 agents, this can take days, but in doing so, “you get that inherent stochasticity, which is what really happens in a real outbreak.” Hunter then averages the results of those model runs to create predictions. The choice of model to predict a virus’s spread ultimately comes down to preference. Some groups are employing both agent-based and SIR modeling techniques. Neither breed of model will produce completely accurate estimates for R0, Re, or any other prediction, Ridenhour notes. Despite unprecedented data sharing about the biology of SARS-CoV-2, uncertainties continue to pervade estimates of R0. Numerous groups are still producing different values for R0 and Re even in the same geographic regions, depending on the methods they’re using and the assumptions they’re making about the virus and the populations. R0 estimates in Wuhan range from 1.4 all the way up to 5.7, according to a recent retrospective analysis. 12 And despite modelers’ best efforts to simulate human social behavior, a single, average metric such as R ultimately says very little about how a disease is transmitted across a large population. Several modelers lament that some policymakers seem to be relying on estimates of Re to make decisions such as when to lift lockdowns and other social distancing measures. “Policies should not rely on Re alone due to uncertainty both in the actual cases in the total population, as well as in the assumptions of the mathematical . . . models that are used for its calculation,” the University of Naples’s Siettos explains in an email. These limitations have motivated some researchers, such as Althouse, to explore alternative metrics. In a preprint posted earlier this year, he and his colleagues propose that rather

than using a mean value alone to describe the spread of disease, modelers should include information about how R0 and Re vary across a population.13 This can be estimated through detailed contact tracing studies, he explains. Other alternatives to R0 and Re have been proposed over the years, but they’ve never managed to overtake R0 and Re in popularity. R0 and Re are well-known metrics, they’re easy to interpret biologically, and ultimately, it’s difficult to break conventions that have been in place for decades, Smith? writes to The Scientist in an email. “I think it’s that R0 is simply too embedded in the ‘culture.’ Being such an old concept, it’s very hard to switch everyone to the same agreed-upon alternative.” But an alternative may have its own flaws, and no model or single metric will ever be able to fully capture the complexity of disease spread or make perfectly accurate predictions about it, says Ridenhour. After all, “all models are wrong, but some are useful,” he notes, citing a popular aphorism. “You just hope you’re in the useful category.” g

References 1. M.S. Majumder, K.D. Mandl, “Early transmissibility assessment of a novel coronavirus in Wuhan, China,” SSRN, doi:10.2139/ssrn.3524675, 2020. 2. M.S. Majumder, K.D. Mandl, “Early in the epidemic: impact of preprints on global discourse about COVID-19 transmissibility,” The Lancet, 8:E627– 30, 2020. 3. A. Kimball et al., “Asymptomatic and presymptomatic SARS-CoV-2 infections in residents of a long-term care skilled nursing facility — King County, Washington, March 2020,” MMWR Morb Mortal Wkly Rep, 69:377–81, 2020. 4. X. He et al., “Temporal dynamics in viral shedding and transmissibility of COVID-19,” Nat Med, 26:672–75, 2020. 5. D.P. Oran, E.J. Topol, “Prevalence of asymptomatic SARS-CoV-2 infection,” Ann Intern Med, doi:10.7326/M20-3012, 2020. 6. S.W. Park et al., “The time scale of asymptomatic transmission affects estimates of epidemic potential in the COVID-19 outbreak,” Epidemics, 31:100392, 2020. 7. J.B. Aguilar et al., “Investigating the impact of asymptomatic carriers on COVID-19 transmission,” medRxiv, doi: 10.1101/2020.03.18.20037994, 2020. 8. J.O. Lloyd-Smith et al., “Superspreading and the effect of individual variation on disease emergence,” Nature, 438:355–59, 2005. 9. A. Endo et al., “Estimating the overdispersion in COVID-19 transmission using outbreak sizes outside China,” Wellcome Open Res, doi:10.12688/ wellcomeopenres.15842.1, 2020. 10. D. Adam et al., “Clustering and superspreading potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections in Hong Kong,” Research Square, doi:10.21203/rs.3.rs-29548/v1, 2020. 11. M.S. Majumder, “Modelling transmission heterogeneity for infectious disease outbreaks,” MIT Libraries, 2018. 12. S. Sanche et al., “High contagiousness and rapid spread of severe acute respiratory syndrome coronavirus 2,” Emerg Infect Dis, doi:10.3201/ eid2607.200282, 2020. 13. L. Hébert-Dufresne et al., “Beyond R0: Heterogeneity in secondary infections and probabilistic epidemic forecasting,” medRxiv, doi:10.1101/2020.02.10.200 21725, 2020.

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What a lack of socializing might mean for cognitive function

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BY CATHERINE OFFORD

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aisy Fancourt was at her home in Surrey in southeast England when the UK government formally announced a nationwide lockdown. Speaking in a televised address on March 23, UK Prime Minister Boris Johnson laid out a suite of measures designed to curb the spread of COVID-19, including closing public spaces and requiring people to stay home except for exercise and essential tasks. For Fancourt, an epidemiologist at University College London (UCL), the announcement meant more than just a change to her daily life. It was the starting gun for a huge study, weeks in the planning, that would investigate the effects of enforced isolation and other pandemic-associated changes on the British public. In more normal times, Fancourt and her colleagues study how social factors such as isolation influence mental and physical health. Before Johnson’s late-March announcement, the team had been watching as Italy, and subsequently other countries in Europe, began closing down public spaces and enforcing restrictions on people’s movements. They realized it wouldn’t be long before the UK followed suit. “We felt we had to start immediately collecting data,” Fancourt says. She and her colleagues rapidly laid the groundwork for a study that would track some of the effects of lockdown in real time. Between March 24 and the middle of June, the study had recruited more than 70,000 participants to fill out weekly online surveys, and in some cases answer questions in telephone interviews, about wellbeing, mental health, and coping strategies. This project and others like it underway in Australia, the United States, and elsewhere aim to complement a broader literature on how changes in people’s interactions with those around them influence their biology. Even before COVID-19 began its global spread, millions of people were already what researchers consider to be socially isolated—separated from society, with few personal relationships and little communication with the outside world. According to European Union statistics, more than 7 percent of residents say they meet up with friends or relatives less than once a year. Surveys in the UK, meanwhile, show that half a million people over the age of 60 usually spend every day alone. These figures are concerning to public health experts, because scientific research has revealed a link between social isolation—along with negative emotions such as loneliness that often accompany it—and poor health. “We are seeing a really growing body of evidence,” says Fancourt, “that’s showing how isolation and loneliness are linked in with incidence of different types of disease [and] with premature mortality.” Alongside myriad connections to poor physical health, including obesity and cardiovascular problems, a range of possible effects on the human brain have now been documented: Social isolation is associated with increased risk of cognitive decline and dementia, as well as mental health consequences such as depression and anxiety.

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It’ll be years before researchers understand whether and how measures enacted during the pandemic play into any of these risks. The sort of isolation people are experiencing right now is unprecedented, and is compounded with other pressures, such as fear of disease and financial strain. But now more than ever, it’s important to study the effects of social isolation, and potential means to mitigate it, says Stephanie Cacioppo, a social neuroscientist and cognitive psychologist at the University of Chicago. “We’re a social species,” she says. “We really need others to survive.”

Lonely connections In 1972, French adventurer and scientist Michel Siffre famously shut himself in a cave in Texas for more than six months—what still clocks in as one of the longest self-isolation experiments in history. Meticulously documenting the effects on his mind over those 205 days, Siffre wrote that he could “barely string thoughts” together after a couple months. By the five-month mark, he was reportedly so desperate for company that he tried (unsuccessfully) to befriend a mouse. This kind of experiment, and less extreme isolation periods such as those experienced by spaceship crews or scientists working in remote Antarctic research stations, has offered glimpses of some of the cognitive and mental effects of sensory and social deprivation. People routinely report confusion, changes in personality, and episodes of anxiety and depression. A crueler version of those experiments is continually underway in prisons across the world. In the US alone, tens of thousands of incarcerated people are in long-term solitary confinement, with devastating and lasting effects on cognitive and mental health. (See “Extreme Isolation” on page 39.)

We’re a social species. We really need others to survive. —Stephanie Cacioppo, University of Chicago

For most of human society, however, social isolation acts in more insidious ways than these “experiments” capture, often disproportionately affecting vulnerable members of the population, such as the elderly, and with effects accumulating slowly such that they may go unnoticed for many years, if not decades. The effects of this subtler sort of social isolation, which some health researchers and psychologists have already described as a public health risk, are better observed in longer-term studies that look for links between a person’s social connections and how the mind functions. Many studies have found that chronic social isolation is indeed associated with cognitive decline, and that isolation often precedes decline by several years. One 2013 study, for

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example, measured cognitive function at two time points in a cohort of more than 6,000 older individuals taking part in the English Longitudinal Study of Ageing (ELSA). 1 People who reported having fewer social contacts and activities at the beginning of the study, researchers found, showed greater decline in cognitive function, as measured by verbal fluency and memory recall tasks, after four years. More-recent studies have added weight to the association. A 2019 study of more than 11,000 people taking part in ELSA found that men who reported higher-than-average social isolation and women who reported increasing social isolation both experienced above-average decline in memory function within two years of being surveyed.2 However, the results don’t demonstrate that isolation causes deterioration in brain function, cautions ELSA director Andrew Steptoe, a UCL psychologist and epidemiologist who collaborates with Fancourt; it’s also possible that cognitive decline encourages some people to socialize less. Indeed, the relationship between isolation and cognitive health isn’t entirely clear-cut. A recent meta-analysis of more than 50 studies, carried out by clinical psychologist Linda Clare and colleagues at the University of Exeter, found that while there was reasonably good evidence for an association between social isolation and cognitive decline later in life, the relationship wasn’t as strong as that reported for cognitive decline and some other lifestyle factors such as educational attainment.3 “We have to acknowledge that there are lots of different measures used and different studies and different ways of approaching this,” says Clare, whose work focuses on ways to help dementia patients and their caregivers in the UK. Different studies assess social isolation and cognition differently, and not all research takes into account potential confounding factors such as isolated people’s frequency of leisure activities, or their participation in voluntary or paid work. Despite all the variability, Clare says, “we did see that there is a reasonably robust association between more engagement in social activity and better cognitive function in later life.” To add to the challenges in understanding these complex relationships, there’s sometimes confusion in the scientific literature about the distinction between objective and subjective measures of isolation, notes Cacioppo. “We know that there’s a difference between being physically isolated and emotionally isolated,” she says. Not everyone with limited social connections feels lonely, and some people with lots of social connections do. Cacioppo adds that while some people might choose solitude without suffering particularly adverse effects, loneliness is an inherently negative emotion, and when experienced for long periods, is often associated with depressive symptoms. “Loneliness is a discrepancy between what you want and what you have” in your relationships, she says. A number of studies have tried to parse these subtleties by measuring social isolation and loneliness in parallel, partly aided by a metric known as the University of California, Los

Angeles (UCLA) loneliness scale. This scale, developed by UCLA researchers in the 1970s, uses a list of statements to evaluate how connected people feel, in contrast to measures of social isolation, which rely on more-objective measures of social network size or the frequency of contacts with other people. One recent longitudinal study in England found that social isolation and loneliness were each associated with poorer physical and mental health, and the strongest association was seen in the group of people who reported both conditions.4 A three-year study of adults in Spain published in 2019, meanwhile, found that loneliness and social isolation were independently associated with cognitive decline.5 Other work has found effects for only one of the two measures: Studies in the Netherlands and the UK, for example, have found that loneliness, but not social isolation, was predictive of the onset of dementia.6,7 In contrast to these findings, a preprint published on bioRxiv a few months ago reported that social isolation, but not loneliness, was associated with elevated dementia risk among more than 150,000 adults in the UK when genetic risk factors for dementia were taken into account.8 “It’s quite a varied picture,” says Steptoe. “One sometimes finds different patterns.”

Physical manifestations By the time the nine-person crew of the Antarctic research station Neumayer III emerged from their 14-month stay a couple of years ago, they’d endured winter temperatures of -50 °C, drastic changes in natural light, and prolonged lack 07/08 . 2020 | T H E S C IE N T IST 3 5

of contact with the outside world. The effects on their brains, it turned out, were substantial. Structural MRI performed by neuroscientists at the Max Planck Institute for Human Development before and after the trip showed anatomical changes to the dentate gyrus, a region of the brain that feeds information into the hippocampus and is associated with learning and memory; the crew members’ dentate gyruses had shrunk by an average of around 7 percent. 9 The crew members also had reduced blood levels of brain-derived neurotrophic factor (BDNF), a protein involved in stress regulation and memory, and they performed worse on tests of spatial awareness and attention than they had before they left. The participants in this study were contending with more than just social isolation during their expedition, making it hard to know whether the observed brain changes are linked to lack of social contact as opposed to circadian disruption or some other aspect of their experience. But researchers studying social isolation and loneliness in the general population are also beginning to document differences in brain

structure that could help reveal biological mechanisms at play. (See illustration below.) Sandra Düzel, a neurobiologist at the same Max Planck Institute (though not a collaborator on the Antarctic study), recently set out to study such differences in more than 300 people participating in a longitudinal project called the Berlin Aging Study. Using MRI to map the volume of the brain’s various regions, Düzel and her colleagues found that, regardless of their level of social contact, people who scored high on the UCLA loneliness scale tended to have smaller gray matter volumes in a handful of regions.10 Those areas included the hippocampus and the amygdala, known for its role in emotion processing. The findings don’t demonstrate that loneliness causes shrinkage of these brain structures, Düzel writes in an email to The Scientist, but the researchers are considering both a lack of social stimulation and loneliness-induced stress as possible contributing factors. Recent research in mice, which, like humans, are social organisms, supports a role for social interaction in maintaining normal brain structure and function, and hints at possible molecular mechanisms. One 2018 study, for example,

THE ISOLATED BRAIN Studies of animals and people experiencing isolation have identified several brain structures that appear to be affected by a lack of social interaction. Although these studies can’t identify causal relationships—and don’t always agree with one another—they shine a light on some of the mechanisms by which physical isolation, or feelings of loneliness, could impair brain function and cognition.

HIPPOCAMPUS: People and other animals experiencing isolation may have smallerthan-normal hippocampi and reduced concentrations of brain-derived neurotrophic factor (BDNF), both features associated with impaired learning and memory. Some studies indicate that levels of the stress hormone cortisol, which affects and is regulated by the hippocampus, are higher in isolated animals.

AMYGDALA: About a decade ago, researchers found a correlation between the size of a person’s social network and the volume of their amygdalae, two almond-shaped brain areas associated with processing emotion. More-recent evidence suggests the amygdalae are smaller in people who are lonely.

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PREFRONTAL CORTEX: In some studies, people who are lonely have been found to have reduced brain volumes in the prefrontal cortex, a region important in decision making and social behavior, although other research suggests this relationship might be mediated by personality factors. Rodents that have been isolated from their conspecifics show dysregulated signaling in the prefrontal cortex.

investigated the effects of social isolation on mice’s ability to recognize other individuals—something researchers assess by recording how long mice spend interacting with one another, as an unfamiliar mouse normally elicits more interest than a familiar one. Adult mice that had been kept in isolation for up to a week were worse at discriminating familiar and unfamiliar mice, the researchers found. Returning mice to enclosures containing their colony mates restored their recognition abilities, as did inhibiting a small signaling protein known as Rac1, which has been linked to memory problems in Alzheimer’s disease. Activating Rac1 in mice that had not been isolated caused the animals to show the same forgetfulness exhibited by isolated individuals. 11

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Surveys already suggest that many people have felt increasing loneliness since the pandemic began. While distinguishing between loneliness and social isolation is impossible in animal studies, these kind of manipulative experiments offer a unique insight into effects of isolation on the brain, says Moriel Zelikowsky, a neuroscientist at the University of Utah School of Medicine. Mouse work she carried out while a postdoc at Caltech, for example, revealed a previously unknown role for Tac2, a signaling neuropeptide implicated in diverse cognitive functions, in mediating the behavioral effects of isolation.12 The peptide was highly expressed across broad regions of the brain in mice that had been housed alone for several weeks, the team found, but not in controls kept with two other mice, nor in rodents isolated for just 24 hours. Mice that had spent weeks by themselves also displayed aggression—a typical behavioral effect of isolation—but that behavior was inhibited by a drug that blocks the protein receptor that Tac2 normally binds to. The findings suggest that Tac2 may be involved in regulating some of the effects of longterm isolation, rather than immediate stress induced by separation from companions, Zelikowsky notes. She adds, however, that there’s still a lot about the neuropeptide the team doesn’t know, including how it may interact with hormones involved in the stress response and whether it functions the same way in humans. One area where animal studies and observational research in humans may be starting to align is the link between isolation and inflammation—a response that can have negative effects on cognitive function as well as on other processes throughout the body. For example, more than a decade of animal work has shown increased circulation of inflammatory signaling molecules such as interleukin-6 in isolated mice, and a recent meta-

analysis of more than two dozen human-focused papers on the topic noted that studies of people experiencing loneliness consistently reported increased blood concentrations of this same cytokine. The meta-analysis also found that social isolation was primarily linked to higher levels for C-reactive protein (CRP) and fibrinogen, two molecules involved in inflammatory responses in mice and humans.13 Fancourt, a coauthor of one of the studies included in that meta-analysis, says that the picture starting to emerge from this line of research is that social isolation and loneliness have distinct but closely related effects on inflammatory responses. Her study found that social isolation was associated with higher levels of CRP and fibrinogen, while loneliness was associated with lower insulin-like growth factor-1, a molecule that helps inhibit inflammation.14 “Both isolation and loneliness were linked to inflammation,” she says, “but while social isolation was linked to inflammatory markers themselves, for loneliness it was related to a pathway that involved how much those inflammatory responses are allowed to happen, or are inhibited from happening.” Like research on any potential health risk, studies of social isolation still struggle to connect the dots between observations and concrete biological outcomes. Human studies can only reveal correlations, and experimental animal research “can show you that pathways can work in principle, but it doesn’t show they operate like that” in practice, says Steptoe. Nevertheless, research so far has helped to flesh out neuroscientists’ understanding of the sorts of factors involved in 07/08 . 2020 | T H E S C IE N T IST 37

Social intervention In recognition of the potential risks of social isolation, whether they be related to brain health or to other, less direct risks of living alone, many countries and health organizations have funded outreach campaigns to improve connections between people most likely to be (or to feel) isolated and the rest of the community. Cohousing organizations in the US and elsewhere, meanwhile, aim to foster social engagement with shared living spaces, although their ability to reduce loneliness has yet to be evaluated. Where changes in a person’s social life or living arrangement aren’t possible or are unlikely to improve the situation, some researchers argue that pharmacological treatments could help—at least temporarily. Cacioppo and her late husband John, a pioneer in the study of loneliness and social neuroscience, proposed a few years ago that allopregnanolone, a steroid involved in regulation of BDNF as well as various emotional and behavioral responses to stress, might help alleviate loneliness in humans.15 Since 2017, Cacioppo’s team has been working with lonely patients to test a closely related molecule, pregnanolone, although the work has had to be put on hold because of the pandemic. Zelikowsky notes that osanetant, the drug that she and her colleagues used to block Tac2 receptors in their mouse experi-

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ments, may also have promise as a therapeutic for people experiencing chronic isolation. The drug was originally developed in the 1990s by France-based pharmaceutical company SanofiSynthélabo (now Sanofi) as a treatment for schizophrenia, but was discontinued due to lack of efficacy, she says, adding she doesn’t know of clinical work currently underway to investigate its potential for people experiencing isolation or loneliness.

If we’re all putting in lots of extra effort to speak to people, are we able to offset some of the negative effects of isolation? —Daisy Fancourt, University College London

Other researchers, meanwhile, are focusing on behavioral interventions that may help reduce the risk of cognitive decline and other effects associated with social isolation. Fancourt and Steptoe, for example, have shown that boosting cognitive engagement, regardless of a person’s social engagement, may have a protective effect. One recent study found that people who more frequently visited museums, galleries, or exhibitions or attended theater performances, concerts, or operas were less likely to show decreases in memory recall and verbal skills within the next decade.16 (The relationship didn’t hold for visits to the cinema.) A 2019 study by the same researchers suggests that engaging in these kinds of cultural activities is associated with a lower risk of dementia.17 It’s this kind of area in which research from the ongoing pandemic might also really contribute, says Fancourt. During the crisis, millions of people have found themselves isolated without choosing to be that way, and surveys already suggest that many people—particularly women, according to one recent study in the UK—have felt increasing loneliness since the pandemic began. While some people may appreciate the chance to be alone, others have found new ways to stay connected with their social network—behaviors that could provide critical information about how different people cope with the effects of being physically separated from society. For example, Fancourt says, “if we’re all putting in lots of extra effort to speak to people, have Skype calls, Zoom calls, message people, are we able to offset some of the negative effects of isolation?” From a research perspective, she adds, it’s an unprecedented opportunity to ask new questions about how a lack of traditional social contact influences human biology. “It might really change the way we think about concepts like loneliness and isolation,” Fancourt says, “and mean that we might actu-

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responses to social isolation—and, perhaps more importantly, has inspired several efforts to mitigate the problems that such isolation may cause.

ally start to define and research them differently based on what this very unusual natural experiment teaches us.” g

References 1. A. Shankar et al., “Social isolation and loneliness: Relationships with cognitive function during 4 years of follow-up in the English Longitudinal Study of Ageing,” Psychosom Med, 75:161–70, 2013. 2. S. Read et al., “Social isolation and memory decline in later-life,” J Gerontol B Psychol Sci Soc Sci, 75:367–76, 2019. 3. I.E.M. Evans et al., “Social isolation and cognitive function in later life: A systematic review and meta-analysis,” J Alzheimers Dis, 70:S119–44, 2019. 4. K.J. Smith, C. Victor, “Typologies of loneliness, living alone and social isolation, and their associations with physical and mental health,” Ageing Soc, 39:1709–30, 2019. 5. E. Lara et al., “Are loneliness and social isolation associated with cognitive decline?,” Int J Geriatr Psychiatry, 34:1613–22, 2019. 6. T.J. Holwerda et al., “Feelings of loneliness, but not social isolation, predict dementia onset: Results from the Amsterdam Study of the Elderly (AMSTEL),” J Neurol Neurosurg Psychiatry, 85:135–42, 2014. 7. S.B. Rafnsson et al., “Loneliness, social integration, and incident dementia over 6 years: Prospective findings from the English Longitudinal Study of Ageing,” J Gerontol B Psychol Sci Soc Sci, 75:114–24, 2020. 8. M. Elovainio et al., “Association of social isolation, loneliness, and genetic risk with incidence of dementia: UK Biobank cohort study,” medRxiv, doi:10.1101/ 2020.02.25.20027177, 2020. 9. A.C. Stahn et al., “Brain changes in response to long Antarctic expeditions,” N Engl J Med, 381:2273–75, 2019. 10. S. Düzel et al., “Structural brain correlates of loneliness among older adults,” Sci Rep, 9:13569, 2019. 11. Y. Liu et al., “Social isolation induces Rac1-dependent forgetting of social memory,” Cell Rep, 25:P288–95.E3, 2018. 12. M. Zelikowsky et al., “The neuropeptide Tac2 controls a distributed brain state induced by chronic social isolation stress,” Cell, 173:1265–79.E19, 2018. 13. K.J. Smith et al., “The association between loneliness, social isolation and inflammation: A systematic review and meta-analysis,” Neurosci Biobehav Rev, 112:519–41, 2020. 14. E. Walker et al., “Social engagement and loneliness are differentially associated with neuro-immune markers in older age: Time-varying

associations from the English Longitudinal Study of Ageing,” Brain Behav Immun, 82:224–29, 2019. 15. S. Cacioppo, J.T. Cacioppo, “Why may allopregnanolone help alleviate loneliness?” Med Hypotheses, 85:947–52, 2015. 16. D. Fancourt, A. Steptoe, “Cultural engagement predicts changes in cognitive function in older adults over a 10 year period: findings from the English Longitudinal Study of Ageing,” Sci Rep, 8:10226, 2018. 17. D. Fancourt et al., “Community engagement and dementia risk: time-to-event analyses from a national cohort study,” J Epidemiol Community Health, 74:71–77, 2019.

© ISTOCK.COM, MARIA ZAMCHY

EXTREME ISOLATION Every year in the US, tens of thousands of incarcerated people spend weeks or months at a time alone in small windowless cells, deprived of sensory stimuli and separated from other people. Surveys of people who have experienced this form of extreme isolation point to a range of negative cognitive consequences, including difficulties thinking or remembering information, obsessive thinking, and hallucinations and other psychotic symptoms, as well as longer-term mental illness risks, and increased incidence of suicide. Research on these effects of solitary confinement isn’t new; in the 19th century, observers of incarcerated people began attributing high rates of psychotic illnesses to having been housed alone and deprived of sensory stimulation, while work carried out in the last few decades in countries including Canada, Norway, South Africa, and Switzerland have drawn similar conclusions. Animal studies that try to mimic the conditions of solitary confinement, meanwhile, indicate numerous potential biological effects on the brain. Studies of mice, for example, show that the stress induced by prolonged isolation can cause changes in brain structure, including reduced hippocampal volume, plus changes in the expression of genes associated with neuroplasticity and chemical signaling. Neuroscientists face an uphill battle in using this research in legal settings for people who have experienced solitary confinement. Many US courts have rejected evidence of psychological pain on the grounds that, unlike a diagnosed mental illness or physiological harm, it is insufficient evidence of “cruel and unusual punishment,” and therefore doesn’t count as a violation of the US Constitution. Neurobiological research based on animal studies, meanwhile, has been rejected on the grounds that animal-based studies cannot be extrapolated to humans. That said, a landmark settlement between incarcerated people and the governor of California in 2015 was decided partly on the basis on neuroscientific evidence and resulted in the end of indeterminate solitary confinement in the state’s prisons.

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© SCIENCE SOURCE, KEITH CHAMBERS

Stemming the Tide of Cancer T cells with stem cell–like properties may be key to making immunotherapies work. BY DANIEL E. SPEISER AND WERNER HELD

CREDIT LINE

T

umors are relatively easy to treat if they stay put, but cancer cells become more deadly when they disseminate to distant parts of the body. Surgery and local irradiation are not well suited for treating cancers that have spread and formed metastases at multiple body locations, and most types of meta-

static cancer become progressively resistant to treatment with chemotherapeutic drugs or small molecule inhibitors that aim to block tumor growth. The development of immunotherapy, a treatment that does not act directly on the tumor but rather stimulates the immune system to more

effectively defend the whole body, has improved prognoses for some types of metastatic cancer. About 50 years ago, researchers found that one component of the immune system, CD8 + T cells, have the remarkable potential to detect and kill cancer cells. Groundbreaking research on melanoma, an aggressive 07/08 . 2020 | T H E S C IE N T IST 41

type of skin cancer, and later on cancers of breast, prostate, ovaries, and colon have shown that patient survival was significantly extended when tumors harbored a high abundance of CD8+ T cells. 1 These studies provided compelling evidence that CD8 + T cells are in principle able to protect against cancer. Researchers established that CD8+ T cells isolated from tumors and cultured in vitro for several days to weeks could specifically detect and kill cancer cells. But a decade ago, we found that these cells targeted cancer relatively poorly when tested immediately after their isolation from tumors.2 This indicated that, while tumor-reactive CD8+ T cells manage to get into tumors, the tumor environment somehow prevents the cells from efficiently killing tumor cells. Then, an unusual feature of tumorspecific CD8+ T cells offered a clue to the reason for that waning effectiveness. The immune cells expressed receptors known as checkpoints that decreased, rather than improved, the capacity of CD8 + T cells to kill tumor cells. The importance of such cell-surface receptors in dampening the function of T cells was first recognized separately by Tasuku Honjo and James Allison in the 1990s. Their pioneering work, for which they were awarded the Nobel Prize in Physiology or Medicine in 2018, led to the development of antibodies that prevented inhibitory receptors, such as programmed death 1 (PD-1), from engaging their binding partners present on other cells. This tweak improved the function of CD8+ T cells in vitro. Blocking inhibitory receptors has revolutionized the treatment of several cancers, including melanoma and certain types of lung, bladder, kidney, intestinal, and gynecological cancers. Metastatic melanoma, which formerly was untreatable, can now be cured in a significant fraction of patients thanks to these immunotherapies. When the inhibitory PD-1 receptor is blocked by treatment with antibodies, CD8 + T cells present in the tumor increase expression of the cytotoxic granzyme B protein, a hallmark 4 2 T H E SC I EN T I ST | the-scientist.com

of killer cells, and start to multiply; this is often associated with tumor shrinkage and therapy success. 3 However, PD-1 expressing CD8+ T cells present in tumors were thought to be “exhausted” and unable to divide. It was thus difficult for immunologists to understand the full cellular and molecular basis for the CD8+ T cell expansion in response to checkpoint blockade. It was also unclear why the therapy was effective for some patients but not others.

Science often does not follow a linear path, and important new insights frequently derive from studying seemingly unrelated problems. For example, exhausted CD8+ T cells were first described in chronic viral infections more than 20 years ago. More recently, detailed analyses of virus-fighting T cells by us4 and by Rafi Ahmed’s group at Emory University5 revealed that there are at least two distinct types of CD8+ T cells. A rare cell type does not engage directly with infected cells but

CHECKPOINT INHIBITORS AND STEM-LIKE T CELLS The body’s defense system against infection also fights tumors, generating tumor resident stem-like T cells and killer T cells that express inhibitory receptors such as PD-1. When PD-1 binds to PD-L1 or PD-L2 on tumor cells or other cells, T cell functions are subdued. Checkpoint blockade treatments interrupt this interaction. This allows stem–like T cells to proliferate and to produce new killer T cells that can now kill tumor cells.

LYMPH NODE

TUMOR

Dendritic cell Stem-like T cell

Antigen (from tumor) Antigen receptor

PD-1

Naive T cell

Part of the body’s natural defense system against cancer involves dendritic cells taking up tumor-derived proteins and presenting them to antigen naive CD8+ T cells present in lymph nodes. The stimulated T cells can then migrate to the tumor.

While tumor-reactive CD8+ T cells manage to get into tumors, the tumor environment somehow prevents the cells from efficiently killing tumor cells. rather sustains the CD8+ T cell response to infection by renewing itself and by dividing to form the more common type of CD8+ T cells that has the potential to kill virus-infected cells.

These findings raised the possibility that a similar division of labor among CD8+ T cells exists in tumors, and that this plays a role in the mechanisms of tumor immunotherapy.

Stem-like T cell

Tumors harbor stem cell–like CD8+ T cells that express PD-1 Two recent papers, one by us6 and one from Nick Haining’s group at Harvard Medical School,7 used mouse models to look for different types of PD-1 expressing CD8+ T cells in tumors and found that there are indeed two main subsets of cells: one that produces granzyme B, a hallmark of cellkilling CD8+ T cells, and one that does not make granzyme B but instead expresses T cell factor 1 (TCF1), a transcription factor

Treatment with checkpoint blockade immunotherapies, such as antibodies to PD-1, can prevent the interaction of PD-1 with PD-L1/2. This enables stem-like T cells to proliferate and produce more killer T cells that can now kill cancer cells.

Active killer T cell Deactivated killer T cell Antibody

PD-1

Immune checkpoint blockade

Immune checkpoint PD-L1

PD-L1

© LUCY READING-IKKANDA

Cancer cell Dying cancer cell No cancer cell death

In the tumor, chronic activation yields stem–like T cells and killer T cells that express inhibitory receptors such as PD-1. The binding of PD-1 to PD-L1 or PD-L2 ligands on tumor cells deactivates killer T cells and prevents the killing of cancer cells.

Stem-like T cell proliferates

needed for CD8+ T cell memory formation, as we had shown 10 years earlier.8 The granzyme B+ cells did not make TCF1; these subsets were not overlapping. We wondered whether it is the nonkiller, TCF1-expressing subset of cells that multiplies in response to PD-1 blockade. (See illustration on page 42.) In additional mouse experiments, we showed that the presence of PD-1+ TCF1+

CD8+ T cells was essential to increasing the abundance of T cells during checkpoint blockade immunotherapy and to controlling tumors.6 As PD-1+ TCF1+ CD8+ T cells expanded, most of the offspring cells transitioned from one subtype to the other: TCF1 expression fell off, limiting the cells’ capacity to divide, while granzyme B expression increased and the cells gained the potential to kill cancer

cells. Some of the offspring maintained TCF1 expression, however, ensuring they maintained the potential for continued multiplication and killer cell production. These capacities of a subset of tumorresident PD-1+ CD8+ T cells—to multiply, differentiate, and self-renew—mirror those of memory CD8+ T cells and tissuespecific stem cells. The tumor environment therefore contains stem cell–like

ADOPTIVE CELL THERAPY AND STEM CELL–LIKE T CELLS In patients with metastatic disease, tumor tissue can be surgically removed and immune cells extracted from it. The T cells, which include both cells that can fight the tumor and cells that cannot, are cultured with specific growth factors to increase their numbers and restore the functionality of cells that have become exhausted and thus less effective. This T cell mixture is then reinfused into the patient, with the aim of increasing the number of functional cells that can kill tumor cells and that will persist in the patient. The number of stem-like CD8+ T cells— which sustain the production of killer CD8+ T cells—that make it back into the patient is currently unclear. But the importance of these cells to sustain tumor-fighting in response to checkpoint blockade raises the possibility that the conditions used to expand cells for infusion can be further optimized to favor higher proportions of stem-like CD8+ T cells.

 2 The T cells, which include both cells that can fight the tumor (killer T cells) and cells that cannot, are cultured with specific growth factors to increase their numbers.

Optimal culture population (homogeneous) Current culture capability (heterogeneous)

The cultured T cells are infused into the patient with the aim of increasing the number of tumor-fighting T cells that the patient can produce.

Other T cells

 3 Killer T cells Stem-like T cells

 1

Stem-like T cells help sustain tumorfighting in response to checkpoint blockade in two ways: they can differentiate into killer T cells that can kill cancer cells and also proliferate into more stem cells. This raises the possibility that the conditions used to expand cells for infusion should be further optimized to favor higher proportions of stem-like T cells. 4 4 T H E SC I EN T I ST | the-scientist.com

Tumor

Infused cells © LUCY READING-IKKANDA

In patients with metastatic disease, immune cells (T cells) can be extracted from tumor tissue.

(in short, “stem-like”) CD8+ T cells whose presence is necessary for the expansion of tumor-specific CD8+ T cells in response to checkpoint blockade in cases where the immunotherapy successfully induces tumor control in a preclinical animal model.6 Similar stem-like CD8+ T cells were found in protein-stained, microscopically analyzed sections of human melanoma and lung cancer biopsies, and through gene expression analysis of single CD8+ T cells from these tumors.6,7,9

Predicting and improving the efficacy of immunotherapy The overall response rates of cancer patients treated with antibodies to PD-1 remain relatively low. Even in the case of metastatic melanoma, which has the highest response rate of any cancer type, a considerable fraction of patients does not benefit from this or other checkpoint blockade immunotherapies. Other patients show initial tumor shrinkage, but the effect is transient. It is vital to be able to predict which patients will respond, not only to avoid useless treatments and reduce side effects, but also to more rapidly offer patients alternative options. Unfortunately, current markers used to predict immunotherapy’s success, including the number of somatic mutations in the tumor, the presence on the tumor of ligands that bind PD-1, and the abundance of T cells in the tumor, are rather poor predictors of clinical outcome in individual patients. The importance of stem-like CD8+ T cells to controlling tumors in mice treated with checkpoint blockade therapy raises the question of whether the presence of these cells accurately predicts treatment response in humans. The jury is still out on this point. Stem-like TCF1 + PD-1 + CD8+ T cells have been found in the melanoma and lung cancer tissue of patients who subsequently responded to immunotherapy as well as of those who did not,7 indicating that the mere presence of stem-like CD8+ T cells does not guarantee treatment response. More patients will have to be analyzed to see whether the

It is likely that current immunotherapy approaches do not fully unleash the functional potential of stemlike CD8+ T cells. cells’ abundance and/or function is different in responders and non-responders. Such predictive biomarkers would allow us to identify those patients who could benefit from the therapeutic potential of checkpoint blockade. Such insights might also help boost the efficacy of other types of immunotherapy. Adoptive T cell therapy, for example, involves isolating lymphocytes, including CD8 + T cells, from resected tumors; culturing the T cells in laboratory incubators to restore their function and expand them; and then reinfusing them into the patient. (See illustration on page 44.) It seems likely that the initial isolates used in adoptive T cell therapy contain variable numbers of stemlike PD-1 + CD8 + T cells, and that the long-term persistence and efficacy of the reinfused cells depends on the presence of CD8+ T cells with stem-like properties. These are two predictions that can be tested now that scientists have identified the hallmarks of these stem-like cells. It is also essential to determine how culture conditions used in adoptive therapy affect stem-like cells. Indeed, the abundance and quality of stem-like CD8+ T cells obtained with current cell amplification procedures is unclear. Optimizations could include growth factors that favor the expansion of stem-like CD8+ T cells or limit the generation of killer CD8+ T cells, as the latter cells’ multiplication capacity and persistence is limited. We expect that improving the stem cell properties of the infused cells would improve the therapeutic efficacy and durability of adoptive cell therapy. It is likely that current immunotherapy approaches do not fully unleash the functional potential of stem-like CD8 + T cells. A better understanding of these cells should improve immunotherapy for cancer patients. Going

back to research the behavior of these immune cells in the context of infection may again help to gain critical insights. Besides infection and cancer, the discovery of stem-like T cells may be relevant in other situations where chronic T cell stimulation arises, such as autoimmune disease and transplantation. Daniel E. Speiser and Werner Held are professors in the Department of Oncology at the University of Lausanne in Switzerland.

References 1. C.G. Clemente et al., “Prognostic value of tumor infiltrating lymphocytes in the vertical growth phase of primary cutaneous melanoma,” Cancer, 77:1303–10, 1996. 2. L. Baitsch et al., “Exhaustion of tumor-specific CD8+ T cells in metastases from melanoma patients,” J Clin Invest, 121:2350–60, 2011. 3. P.C. Tumeh et al., “PD-1 blockade induces responses by inhibiting adaptive immune resistance,” Nature, 515:568–71, 2014. 4. D.T. Utzschneider et al., “T cell factor 1-expressing memory-like CD8+ T cells sustain the immune response to chronic viral infections,” Immunity, 45:415–27, 2016. 5. S.J. Im et al., “Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy.” Nature, 537:417–21, 2016. 6. I. Siddiqui et al., “Intratumoral Tcf1+ PD-1+ CD8+ T cells with stem-like properties promote tumor control in response to vaccination and checkpoint blockade immunotherapy,” Immunity, 50:195–211.e10, 2019. 7. B.C. Miller et al., “Subsets of exhausted CD8+ T cells differentially mediate tumor control and respond to checkpoint blockade,” Nat Immunol, 20:326–36, 2019. 8. G. Jeannet et al., “Essential role of the Wnt pathway effector Tcf-1 for the establishment of functional CD8 T cell memory,” PNAS, 107:9777– 82, 2010. 9. D.S. Thommen et al., “A transcriptionally and functionally distinct PD-1+ CD8+ T cell pool with predictive potential in non-small-cell lung cancer treated with PD-1 blockade,” Nat Med, 24:994–1004, 2018.

07/08 . 2020 | T H E S C IE N T IST 4 5

EDITOR’S CHOICE PAPERS

The Literature Pituitary gland

DISEASE & MEDICINE

THE PAPER

J. Moon et al., “Lactation improves pancreatic β cell mass and function through serotonin production,” Sci Transl Med, 12:eaay0455, 2020. When a woman becomes pregnant, her risk of type 2 diabetes increases for the rest of her life, perhaps because of her growing weight and rising insulin resistance. But if she breastfeeds, epidemiological studies have shown that the uptick in risk shrinks or disappears. The mechanisms underlying this lactation perk have been unclear, but Michael German, a biologist at the University of California, San Francisco, hypothesized that the pancreas’s beta cells are involved. “For long-term protection over decades, you have to fundamentally change some part of the mechanism that controls blood sugar,” says German. “The best way to do that is by affecting the beta cell, because it makes the insulin.” Insulin helps glucose enter the body’s cells from the blood. But in type 2 diabetes, cells become insulin resistant and thus less able to absorb enough glucose, forcing the pancreas to make more insulin until it can’t keep up and blood sugar rises. In a new study, German and Hail Kim of the Korea Advanced Institute of Science and Technology collaborated with another group in Korea that had recruited pregnant women with impaired glucose tolerance or full-blown gestational diabetes. About half of the women breastfed their babies, and half did not (the study was not randomized). Two months after delivery, lactating and non-lactating mothers had comparable blood glucose concentrations after a glucose tolerance test (though fasting glucose was lower in lactating women), but three and a half years after delivery, women who 4 6 T H E SC I EN T I ST | the-scientist.com

Prolactin

β cells

Serotonin

Pancreas

Free radical

Insulin

UPPING PRODUCTION: Lactation stimulates cells in the pituitary gland to produce the hormone prolactin

 1 , which, in mice, binds to beta cells in the pancreas  2 . This leads to a signaling cascade that increases the cell’s production of serotonin  3 . Serotonin binds to a separate receptor on the beta cells, stimulating them to proliferate and produce more insulin  4 , and also serves as an antioxidant that protects cells

from free radicals. Researchers propose that these mechanisms explain why women who breastfeed their children have reduced long-term risk of developing type 2 diabetes.

had breastfed their babies had significantly lower blood glucose concentrations after the test, and, most importantly, better beta cell function than those who did not—something that had not been shown before. German and Kim had previously demonstrated that beta cells can make serotonin; immunofluorescence now showed that serotonin concentrations within beta cells were 200-fold higher in lactating mice than in non-lactating mice. Through a series of knockout experiments in the animals, the team surmised that prolactin, the hormone produced when humans or mice make milk, binds to beta cells and triggers a signaling cascade that results in serotonin production, which then spurs beta cell proliferation and insulin production. In addition, the researchers found that serotonin in lactating mice acts as an antioxidant, helping keep beta cells healthy. Erica Gunderson, an epidemiologist at Kaiser Permanente Division of Research in

Northern California who runs a large epidemiological study on pregnancy, lactation, and risk of type 2 diabetes, has a few concerns about the study’s human data. Differences in gestational diabetes rates and treatment between the lactation and no lactation groups, as well as the length and intensity of breastfeeding, were not reported, she says, and all these play a major role in type 2 diabetes risk. She adds that “there can be reverse confounding involved, with the diabetes risk factors causing reduced ability to breastfeed, rather than lactation protecting against diabetes.” German says that the two groups had similar baseline characteristics and there was no difference in their glucose tolerance tests during pregnancy. Despite her reservations, Gunderson says, “I think it’s a very interesting study that provides some new data on [changes in] beta cell function connected with lactation [in humans] that we did not have previously.” —Rachael Moeller Gorman

© KELLY FINAN

A Breastfeeding Superpower

LEORE GELLER AND RAVID STRAUSSMAN, WEIZMANN INSTITUTE OF SCIENCE, ISRAEL; © ISTOCK.COM, ROB_LAN

ROOM AND BOARD: DNA and RNA from bacteria that live inside human tumors, such as these Serratia marcescens bacteria (green) in human pancreatic cancer cells, could serve as blood-borne biomarkers.

A FLY’S Y: Male Drosophila live shorter lives than females, possibly because

MICROBIOLOGY

GENETICS & GENOMICS

Microbial Signs of Cancer

The Y of Aging

THE PAPER

THE PAPER

G.D. Poore et al., “Microbiome analyses of blood and tissues suggest cancer diagnostic approach,” Nature, 579:567–74, 2020.

E.J. Brown et al., “The Y chromosome may contribute to sex-specific ageing in Drosophila,” Nat Ecol Evol, 4:853–62, 2020.

When Greg Poore was a freshman in college, he lost his grandmother to pancreatic cancer. “She . . . essentially had 33 days from diagnosis to death,” he recalls. “No one could explain why they hadn’t detected the cancer before.” Three years later, in 2016, as an MD/PhD student in Rob Knight’s lab at the University of California, San Diego, Poore began investigating microbial inhabitants of tumors—and eventually, whether he could find traces of those microbes in the blood that might be used to diagnose patients earlier. Poore and his colleagues used machine learning to mine microbial genome and transcriptome information from a database of blood and tissue samples from more than 10,000 cancer patients as well as data the team collected on healthy controls. There were indeed distinct microbial mixes in the cancerous versus healthy tissue of individuals with cancer, the researchers found, and in the blood of healthy people compared with those with cancer. In addition, the machine learning models were able to distinguish cancers of various types—and for some cancers, different stages—using microbial DNA and RNA in tumors and DNA in the blood. The data were taken at a single point in time for each patient and don’t establish cause and effect, says Poore, but the microbial signatures could have diagnostic value. He, Knight, and another coauthor, Sandrine MillerMontgomery, have founded a startup, Micronoma, that aims to develop a liquid biopsy based on microbial sequences in the blood. The study “builds upon findings of numerous reports over the past decade demonstrating that solid tumors are not sterile sites as once thought,” says Susan Bullman, who studies links between cancer and the microbiome at Fred Hutchinson Cancer Research Center in Seattle and was not involved in the study. But to be translated into a clinical diagnostic tool, she adds, the results will first need to be replicated with more samples, this time collected using protocols designed to avoid microbial contamination. —Shawna Williams

The Y chromosome is chock-full of “selfish” genetic elements, which can jump around causing mutations. But the Y chromosome’s densely packed DNA, called heterochromatin, keeps these elements in check. Because heterochromatin deteriorates as organisms age, University of California, Berkeley, evolutionary biologist Doris Bachtrog wondered what role that change played in how long individuals live. She and colleagues turned to Drosophila. As in mammals, males are XY and tend to live shorter lives than XX females. Quantifying the amount of heterochromatin in the genomes of young and old flies, Bachtrog’s team found that levels were well maintained in females as they aged. In old males, the amount of densely packed DNA was greatly reduced, especially across each fly’s Y chromosome, which also showed increased expression of selfish genetic elements. Next, the team created flies with abnormal numbers of Y chromosomes, including XXY females and XYY and X0 males. Sure enough, females carrying a Y chromosome and males with an extra Y did not live as long their wildtype counterparts. Expression of selfish genetic elements was also “dramatically increased” in the flies with added Ys, says Bachtrog. “As soon as we put another Y chromosome in the genome, flies died quicker.” In contrast, males without any Y chromosomes lived substantially longer than normal XY males. By providing a quantitative look at heterochromatin loss with age, as well as experimental evidence that higher levels of transposable element expression may reduce lifespan in flies, “the current paper is more definitive” than previous research, says Willis Li, a geneticist and cell biologist at the University of California, San Diego. He’s investigated loss of heterochromatin and Drosophila aging in the past and says Bachtrog’s paper is “a very nice study.” —Jef Akst

the Y chromosome loses heterochromatin that normally suppresses selfish genetic elements.

07/08 . 2020 | T H E S C IE N T IST 47

PROFILE

For the Greater Good Through groundbreaking studies on dengue fever and efforts to build scientific infrastructure in Latin America, Eva Harris has bridged research with its benefits to society. BY DIANA KWON

4 8 T H E SC I EN T I ST | the-scientist.com

Harris has “really helped with the buildup of laboratory capacity in Nicaragua and in other countries. I think that’s just amazing work.”

VISIONS OF A BETTER WORLD Harris was born in New York City in 1965 to a pair of academics. Her mother, Naomi Sager, was a computational linguist at New York University. Her father, Zellig Harris, was an influential mathematician and linguist at the University of Pennsylvania whose ideas shaped those of his most famous trainee, the linguist Noam Chomsky. Although she spent most of her childhood and adolescent years in New York City, Harris spent summers in France with her parents. “I really grew up very French,” she says. “I practically spoke French before English.” In Paris, Harris’s parents were part of a social circle that would meet over meals to talk about politics and the state of the world. The group was diverse, Harris recalls, and included people in both white- and blue-collar jobs. “That was a very big part of my life—those people and the views of the society that I listened to, which were socialist and very much about a better future,” Harris says. “Hearing those animated discussions imbued me with a vision of the world that could be better than what’s out there now.” Once she became a teenager, Harris started to travel across Europe on her own. While enjoying the rich history and beauty that the continent had to offer, she developed a desire to give back. “I always felt that society was very lopsided. That there was this huge gap between the haves and the have-nots,” Harris says. “[My family] wasn’t rich, but we had a place in New York, I could travel, and I wasn’t going hungry. I wanted everyone to have the same opportunities.” That desire for equity motivated Harris to become politically active. Starting in high school, she joined protests in Washington, D.C., calling for nuclear disarmament and the end of US military activities in foreign countries such as Nicaragua, she says. “I was very upset about US intervention in Central America.” At the same time, Harris was drawn to science. In one of her high school biology classes, Harris caught her first glimpse of the cell and was blown away by the complex world held within the tiny unit. “I saw the cell in the body as the most beautiful metaphor for human society, because in a cell, all the elements work together for the good of the greater whole,” Harris says. “That was very inspiring to me. I had this vision of, well let’s just learn from ourselves, how to get along.”

UC BERKELEY

W

hen Eva Harris arrived in Nicaragua for the first time in March 1988, the poverty-stricken country was in the middle of the decade-long Contra War between its socialist government and US-backed right-wing rebel groups. Harris had traveled to Central America through a volunteer organization and was financing her own trip with money saved from working odd jobs during a gap year she took after graduating from Harvard University the previous spring. Coinciding with her arrival in Managua, the Nicaraguan government was devaluing the country’s currency—and the funds that were supposed to cover Harris’s months-long trip were suddenly stretched thin. “It was really a petrifying moment in my life,” she says. After wandering the streets of the country’s capital city searching for a place to stay, Harris eventually found one she could afford—a small, seedy room with a busted bed and broken lightbulbs. As she struggled to fall asleep in the sweltering heat of the Nicaraguan summer, she gripped photocopied pages of Molecular Biology of a Cell, a textbook she’d cherished as an undergraduate for its scientific richness and beautiful diagrams, and she reminded herself that she was there for a reason: to use her scientific expertise to help those in need. Through the volunteer organization, Harris was stationed at a manufacturing plant that was producing blood plasma to provide transfusions for Nicaraguan soldiers fighting on the front lines. The factory was having a problem with bacterial endotoxins in the plasma, and the kits that workers there used to detect the toxins were defective. Harris was tasked with finding a way to make the test kits work. One of the problems, she realized, was the quality of water used to carry out the test. Using ampules of sterile water, alcohol, cotton swabs, and tongs, Harris put together a makeshift apparatus that solved the problem. Her accommodations also improved when Irene Vallecillo, the chemical engineer who directed the plasma factory, invited Harris to stay with her instead. Harris ended up frequenting Vallecillo’s home for more than two decades as she continued to take regular trips to Nicaragua. “She’s become like my family,” Harris says. Since that first visit to Central America, Harris has returned multiple times a year to build scientific infrastructure and to conduct crucial studies on arthropod-borne pathogens such as mosquito-transmitted dengue, which is endemic to several Latin American countries. “She’s made a huge contribution to understanding the development of immunity to dengue,” says Aubree Gordon, an epidemiologist at the University of Michigan and one of Harris’s former students and longtime collaborators.

In 1983, Harris went off to Harvard University to study biochemical sciences. She spent the summers in labs in the US and Europe dabbling in a range of projects, from dissecting leeches for neurophysiology studies to examining mitochondria in yeast.

BRINGING HER SCIENCE TO LATIN AMERICA

CAREER TITLES AND AWARDS Professor, Division of Infectious Diseases, School of Public Health, UC Berkeley (2008–present) Director, Center for Global Public Health, School of Public Health, UC Berkeley (2007–present) President, Sustainable Sciences Institute, San Francisco, California (1998–present) Global Citizen Award, United Nations Association, East Bay Chapter, 2012 Pew Scholar, Pew Scholars Program in the Biomedical Sciences (2001–2005) MacArthur Fellowship, MacArthur Foundation (1997–2002)

Greatest Hits • Found that the dengue virus protein NS1 plays a key role in making blood vessels more permeable in patients with severe dengue fever. • Demonstrated that people who had been infected with one type of dengue were more likely to have severe reactions to an infection with another type, depending on their antibody levels, a phenomenon known as antibody-dependent enhancement. • Tracked the epidemiology of dengue outbreaks in Nicaragua through long-term assessments at hospitals and health centers and in the community.

After completing her undergraduate studies at Harvard, Harris was accepted to several PhD programs. But instead of immediately enrolling in graduate school, she decided to take a year off to work and travel. Nicaragua was her final stop, and of all the places she’d gone, it was the country she knew she’d return to. After she began her doctorate in the lab of Jeremy Thorner, a cell and molecular biologist at the University of California (UC), Berkeley, in the fall of 1988, Harris returned to Nicaragua every summer to bring laboratory equipment and to teach workshops on molecular biology techniques such as the polymerase chain reaction (PCR) to scientists and clinicians there. Before leaving on those trips, Harris would scour the halls of UC Berkeley’s science buildings for discarded equipment such as gel boxes, vortex mixers, pipette tips, and glassware. Along with a group of like-minded friends, she cleaned and repaired the items before taking them to Nicaragua. “People thought I was a little too lenient, letting her take off so many chunks of time throughout her graduate career,” Thorner says. “But she was so passionate about it. And she was so efficient during the time she was in the lab that I was happy to support her.” Once her doctoral dissertation was complete in 1993, Harris accepted a postdoctoral fellowship at Stanford University. Instead of going straight back to the lab, however, Harris took a year off from research to focus on her effort on scientific capacity–building projects. One year turned out not to be enough. Harris ended up transferring her postdoc to UC San Francisco (UCSF), where her advisor, Nina Agabian, a professor of global health science, allowed her to continue her work in Latin America. In addition to working in Nicaragua, Harris and other volunteers helped introduce molecular science expertise, technology, and resources to Ecuador, Bolivia, Cuba, and other countries. With Josefina Coloma, a researcher now at UC Berkeley’s School of Public Health, Harris led the Applied Molecular Biology/Appropriate Technology Transfer Program at UCSF. The initiative aimed to provide researchers in developing countries with resources to help them set up their own epidemiological and biomedical studies to combat infectious diseases. 07/08 . 2020 | T H E S C IE N T IST 49

PROFILE In one workshop, for example, Harris performed manual cycling—a cheap alternative to laboratory PCR—on samples of the disease-causing parasite Leishmania. When the bands of Leishmania DNA showed up on the gel, people were “elbowing their way to take a look,” Harris recalls. None of the attendees had ever worked with DNA before, so this method “just blew everyone’s mind,” Harris says, adding that many of the people who attended those courses are now the heads of science and health programs in several Latin American countries. Harris’s work earned her a MacArthur Foundation Fellowship in 1997, when she was an assistant adjunct professor at UCSF—a position she had been offered after completing her postdoc. The award provided funding to establish the Sustainable Sciences Institute (SSI), an organization designed to build research and public health resources in developing countries. As the years passed, however, Harris realized that she missed the lab. While racking her brain for ways to bridge her love of basic science with her passion for putting research into a social context, she realized that studying an infectious disease would be the best way forward. Not only were pathogens fascinating biologically, they would also provide the opportunity to deal with a much “broader picture,” Harris says, “because infectious diseases were deeply connected to various aspects of society, including socioeconomic status and politics.” To find the perfect pathogen to study, Harris went around to contacts in the health departments of various Latin American countries to ask which infectious disease was their top concern. One of the answers that came up time and time again was dengue fever.

DANCING AND DENGUE Harris started setting up her own lab to establish a research program on dengue in the late 1990s while she worked on her postdoc at UCSF. “We would meet in coffee shops in San Francisco, because the lab space was not ready,” recalls Michael Diamond, one of Harris’s first postdocs, who is now a virologist and immunologist at the Washington University School of Medicine in St. Louis. “She was clearly excited by the science and had a lot of interesting ideas.” After her lab was ready, Harris and her team got to work deciphering the molecular biology of the dengue virus, examining the structure and function of the pathogen and the features that contributed to its pathogenicity. Through years of meticulous work, her group demonstrated the critical role the viral protein NS1 plays in causing permeability in the lining of the blood vessels, a key feature of the severe form of dengue fever (Sci Trans Med, 7:304ra141, 2015). They are now working on further elucidating the mechanism of NS1induced vascular leak. She and her team also established a long-term study of children in Nicaragua, regularly collecting blood samples to monitor for dengue infections among families living in more than 4,000 households. The researchers aimed to better understand the spectrum of the disease, how it is transmitted, and the immune responses that patients mount. The results gave the researchers much-needed details about antibody-dependent enhancement (ADE), a phenomenon in which antibodies to a virus can lead to worse illness during a secondary 5 0 T H E SC I EN T I ST | the-scientist.com

infection. Dengue comes in four different types that carry unique surface molecules. Through their cohort study, Harris and her colleagues demonstrated that those who were infected with one type were more likely to have severe—and sometimes deadly—disease when infected with another. They have also found that ADE occurs in previously infected individuals who possess a specific range of antibody concentrations, a finding that has major implications for the development of vaccines (Science, 358:929–32, 2017). The cohort study, which is still ongoing, has also helped reveal important insights into the human immune system’s response to the Zika virus, which hit the Americas in 2015, and has challenged long-standing scientific hypotheses about antibody dynamics in response to dengue infection. “Everyone has thought that antibodies [to dengue] wane and then you get to a danger point,” where infection with another serotype can make you develop severe illness, she explains. “When we looked at 15 years of data, we found that antibodies are very stable after a first infection.” A key factor that determines whether someone will get sick after the second infection appears to be the level of antibodies developed after the first infection. Building on the results of the cohort study, Harris has spearheaded several ongoing projects. One is examining the unique features of an individual’s immune system that lead to different levels of innate immunity, and how that varies with factors such as environment, pathogen exposure, and age. Another project involves looking more closely at the adaptive immune response to dengue to help inform vaccine development. Through the years, Harris’s research has spanned virology, immunology, diagnostics, and epidemiology. Much of this work has been conducted in Latin America, where she also has ongoing scientific capacity–building efforts. Her work in those countries is currently stalled, however, as a result of the COVID-19 pandemic. Earlier this year, she was sheltering at home in San Francisco with her husband, a professor of US history and foreign policy at the City College of San Francisco, and her 19-yearold son, who is currently back at home from college. Because of the pandemic, Harris has temporarily pivoted her research, launching studies into the pathogenesis of COVID-19 and a longitudinal assessment of asymptomatic and past infections in 5,000 residents in the East Bay. Balancing many projects has some downsides. When things get really busy, “I’ll go to two to three hours of sleep a night, and I’ll burn out horribly,” Harris says. Even so, Harris somehow finds time for her favorite pastime: dance. Her love of music and movement is clear even over Zoom. While talking via the video conferencing service in May, she spontaneously busted out dance moves while describing her love for a wide range of musical genres, including hip-hop, salsa, and merengue. Dancing is what usually keeps her going through tough times—but the pandemic has made it difficult to enjoy that passion. “It’s hard not to be able to do that now,” Harris says. However, she adds, the upside is that she gets to spend more time with her son. “She’s the ‘dancing scientist,’” says Coloma, now the executive director of SSI. “That’s how she gets her energy.” g

SCIENTIST TO WATCH

Luis Alvarez: Bone Painter Founder, Theradaptive, Age: 45 BY SHAWNA WILLIAMS

COURTESY OF LUIS ALVAREZ

W

hen Luis Alvarez was about 11 years old, he accidentally lit a tree on fire while heating up pool chemicals. His interest in science persisted after that mishap, and he earned a master’s in chemical engineering from MIT in 1999. But it wasn’t until his service as a military intelligence officer in the US Army in Iraq that Alvarez realized he wanted to focus on developing treatments to spur tissue regeneration. “Many of the people I was serving with were having severe injuries and coming back to the States, [and] having delayed amputations [and] other complications that were all related to the inability of modern medicine to correct tissue defects or to regenerate tissues,” he says. When he returned from Iraq, he went back to MIT with the aim of finding ways to better treat such patients. Working with Linda Griffith of MIT’s biological engineering department and Richard Lee, a regenerative medicine researcher at Harvard University and Brigham and Women’s Hospital, Alvarez developed a technique to tether proteins to materials, and demonstrated it with a protein called epidermal growth factor (PLOS ONE, 10:e0129600, 2015). Cell culture experiments suggested that the surface-bound epidermal growth factor protected bone-building cells from inflammation in the damaged bone, allowing those cells to proliferate and drive healing in the area. After earning his PhD in 2009, Alvarez continued his military service, this time as an army scientist managing research and development programs, and eventually as an instructor at West Point, where he’d attended undergrad. He also founded a company called Theradaptive to further develop and commercialize paint-like bioactive coatings for implants, similar to ones he’d worked on at MIT. He retired from the military in 2017. In addition to his work at Theradaptive, Alvarez is a co-founder

of Elevian, a Harvard spinout developing therapies in stroke and age-associated neurological conditions. Theradaptive’s team has developed a method to coat orthopedic implants with other molecules that might improve healing, such as a variation of bone morphogenetic protein 2 (BMP2), which is already used clinically to promote bone regeneration after spine surgery and other bonerelated procedures. In work conducted with collaborators at Cleveland Clinic and presented at the 2020 Orthopedic Research Society Meeting, Alvarez and his colleagues found that goats treated for a 5-centimeter defect in a limb with a standard surgical procedure and an implant coated with Theradaptive’s BMP2 variant, called AMP2, exhibited complete healing in the bone, while those treated with the uncoated implant did not. The company hopes to begin clinical trials of AMP2 next year. The overarching idea is “that using that technology, you can modify any protein so that it sticks to an implant almost like a paint,” Alvarez says. “And it will remain on the implant so you don’t have any risk of it bleeding away or diffusing away.” Alvarez thinks the tethering approach will also be useful in other applications. He’s partnered with Colonel Leon Nesti, a former West Point classmate who is now a hand surgeon and researcher at Walter Reed National Military Medical Center, to evaluate AMP2 and to develop a separate therapy aimed at precision repair of hand bones. With many clinical drug delivery systems, “you essentially put a dose of a drug at one time point within the area of regeneration,” Nesti says, and “the initial concentration then very rapidly becomes metabolized or taken away from the site of injury.” Alvarez’s technology, in contrast, “allows the drug to stay at the site of regeneration for a much longer period of time, and be released in a much more controlled fashion,” he explains, “so its ultimate effectiveness is much greater.”

The fact that living tissues don’t currently integrate well with implanted materials is “one of the main hurdles in surgical treatment and replacement of tissue functions through foreign materials,” says Harald Ott, a surgeon and tissue engineering researcher at Massachusetts General Hospital. (Ott and Alvarez aren’t research collaborators, but Alvarez is on the scientific advisory board of a startup founded by Ott.) “I think improving that through changing the way cells interact with material is a very attractive proposition.” g

07/08 . 2020 | T H E S C IE N T IST 51

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Neuroinflammation plays a prominent role in the onset and progression of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, and amyotrophic lateral sclerosis. Exactly how neuroinflammation leads to neurodegeneration is unclear, but neuroinflammation is associated with altered CNS homeostasis, protein misfolding, and neuronal degradation. This webinar, brought to you by The Scientist and sponsored by PerkinElmer | Cisbio, will highlight the complex interactions between neuroinflammation and neurodegeneration, and will explain how scientists are securing a better understanding of this relationship.

MICHAEL HENEKA, MD, PhD Chair, Dept. of Neurodegenerative Disease and Geriatric Psychiatry/Neurology German Center for Neurodegenerative Disease (DZNE) University of Bonn Medical Center

ORIGINALLY AIRED THURSDAY, JUNE 4, 2020 WATCH NOW! the-scientist.com/neuroinflammation-and-neurodegeneration TOPICS COVERED

SHANE LIDDELOW, PhD

• Innate immunity in neurodegenerative disease

Neuroscience Institute Departments of Neuroscience & Physiology and Opthalmology NYU Grossman School of Medicine

• Incorporating functional assays to understand immune-glial interactions in both acute injury and chronic disease

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Wearable Technology for Disease Diagnostics: Looking Under the Hood

Many people wear or carry devices that monitor their steps, heart rate, and activity levels. Data collected from more-complex biosensors can associate deviations from normal patterns, even signaling disease states before the wearer feels sick. This multisponsored webinar by The Scientist will highlight advances in wearable devices that can monitor health data and the new modeling and data analysis tools that help researchers pull out meaningful information. The presentations will focus on the basics of materials, mechanics, and manufacturing for soft bioelectronics systems, and how wearable electronics can be applied for human healthcare, human-machine interfaces, and advanced therapeutics.

MICHAEL SNYDER, PhD Professor & Chair of Genetics Director, Stanford Center for Genomics & Personalized Medicine Stanford University

ORIGINALLY AIRED TUESDAY, MAY 26, 2020 WATCH NOW! the-scientist.com/wearable-technology-disease-diagnostics

WOONHONG YEO, PhD Assistant Professor George W. Woodruff School of Mechanical Engineering Wallace H. Coulter Department of Biomedical Engineering Institute for Electronics and Nanotechnology Parker H. Petit Institute for Bioengineering and Bioscience Flexible and Wearable Electronics Advanced Research Program Georgia Institute of Technology

TOPICS COVERED • The potential for using wearables to predict illness • Smart and connected soft bioelectronics for advancing human healthcare and human-machine interfaces

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CRISPR-based methods have opened new possibilities for scientists studying gene function. While CRISPR knockout is the most discussed tool, CRISPR activation (CRISPRa) is becoming the preferred method for gene activation and overexpression for gain-of-function studies. In this webinar sponsored by Horizon Discovery, Steve Smith from Horizon will discuss how harnessing the specificity of CRISPR to activate or overexpress a gene within its endogenous context adds a powerful alternative approach to studying pathway components that may go undetected by loss-of-function analyses. The consistency of the single-guide format associated with CRISPRa gene expression solves many of the challenges related to traditional vector-based approaches, including minimizing differences in expression and transfection due to transcript sizes.

ORIGINALLY AIRED WEDNESDAY, MAY 6, 2020 STEVE SMITH, PhD, MBA Product Manager, Gene Modulation Horizon Discovery

WATCH NOW! the-scientist.com/CRISPRa-GoF TOPICS COVERED • What is CRISPRa and how does it work? • Tools needed to perform CRISPRa gene activation • Experimental strategies for successful CRISPRa implementation • Examples of CRISPRa applications • CRISPRa for functional genomic screening

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SARS-CoV-2, the coronavirus behind the COVID-19 pandemic, has infected hundreds of thousands of people. In response, the scientific community sprang into action to uncover its sequence, structure, and potential biological mechanisms. This information helps guide public health policies as well as drug, vaccine, and diagnostic test development. In this webinar, Emily Troemel and David Wang will discuss the emergence of SARS-CoV-2, diagnostic tests, and possibilities for treatment.

EMILY TROEMEL, PhD Professor, Cell and Developmental Biology Division of Biological Sciences University of California San Diego

ORIGINALLY AIRED WEDNESDAY, JUNE 17, 2020 WATCH NOW! the-scientist.com/sars-cov-2-webinar TOPICS COVERED

DAVID WANG, PhD Professor, Departments of Molecular Microbiology and Pathology & Immunology Washington University School of Medicine in St. Louis

• The basic biology of SARS-CoV-2 and its potential host-pathogen interactions • The current state of the field in SARS-CoV-2 molecular biology research

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BIO BUSINESS

Pandemic Pipelines How biotech and pharma companies pivoted to COVID-19 research and development BY DIANA KWON

5 4 T H E SC I EN T I ST | the-scientist.com

platform,” which uses machine learning algorithms to design potential therapeutic molecules. Initially, the researchers focused on identifying inhibitors for a key SARS-CoV-2 protease based on the crystal structure of the enzyme. They’re now working with collaborators to synthesize these small molecules and test them against the virus in the lab.

What started out as an outbreak in China has now spread to almost every nation in the world, infected millions of people, and killed hundreds of thousands. To deal with the global threat, numerous pharmaceutical and biotech companies have adapted their pipelines to COVID-19 over the last few months. There are now close to 400 compounds

MODIFIED FROM © ISTOCK.COM, MARK KOLPAKOV

I

n mid-January, as cases of a mysterious illness climbed in China and began to appear in other parts of the world, Alex Zhavoronkov realized that this outbreak was becoming a major public health problem. As founder and chief executive officer of Insilico Medicine, a biotech startup based in Hong Kong—where measures to reduce the disease’s spread were already beginning to be put in place—he began to wonder what his company could do to help. Insilico had never tackled viral diseases before; the company’s focus was on noninfectious conditions such as cancer, immunological diseases, and fibrosis. But Zhavoronkov realized that Insilico’s approach, which applies artificial intelligence (AI) for rapid novel drug discovery, could help identify potential therapeutics to fight the virus we now know as SARS-CoV-2. Later that month, Zhavoronkov pitched the idea to his investors and colleagues. Some were concerned that pivoting to address the novel coronavirus might be a waste of resources. “They said, ‘Look, if you do this, we can’t spend too many resources, because it’s going to go away. It’s going to be like SARS,’” Zhavoronkov recalls. During the SARS epidemic of 2002–2003, a decade before he founded Insilico, there was a surge of interest in developing treatments and vaccines—but once the virus was contained, research interest and funding streams quickly dried up. Still, enough of the people he spoke with in January were convinced that this outbreak would be more serious, and they were willing to do something to help, even if it meant recouping costs later or not at all. (See sidebar, “Ensuring Global Access,” on page 57) Quickly, the team got to work on repurposing their “generative chemistry

being evaluated as treatments or vaccines in various preclinical studies or clinical trials and more than 700 diagnostic tests either commercially available or in development. The need for rapid solutions has brought companies together, and has pushed researchers to work at breakneck speeds—often while dealing with complications brought about by lockdowns and social distancing measures.

A shift in focus As the novel coronavirus spread around the globe, scientists at many pharmaceutical and biotech companies started to think about how to lend their expertise— either by identifying potential solutions within existing storehouses of compounds and technologies, or by applying research platforms and expertise to identify new ones. “I think everybody probably felt the urgent need to contribute,” says Dan Skovronsky, the chief scientific officer of the global pharmaceutical firm Eli Lilly. “The question that many pharmaceutical companies had, including us, was: Where are our skills, capabilities, and knowledge, and how do we best apply them?” For companies already focusing on virus-related diagnostics, treatments, and vaccines, the switch to COVID-19 was a natural one. Pfizer, for example, had been working on vaccines for various viral and bacterial infections long before COVID19 emerged. In March, Pfizer announced a collaboration with the German company BioNTech to develop a vaccine. Within a few months, they’d launched clinical trials of their vaccine candidates in Germany and the US. John Kelly, the CEO of Atomo Diagnostics, an Australian startup company that developed a rapid blood test for HIV, says that his team decided to make the shift after getting several queries from diagnostics companies about whether their platform could support a test for COVID-19. The main challenge, Kelly says, was the sheer quantity of tests that they were asking for. “The numbers that these companies were talking about were significantly beyond our existing volumes.”

For other companies, the shift to COVID-19 has meant delving into a new research area. Prior to the pandemic, for example, UK-based startup biotech Owlstone’s pipeline didn’t contain any virus-focused products. The company’s diagnostic tools, which are designed to identify specific chemical compounds in people’s breath, had been geared toward cancer detection and tracking the progression of conditions such as fatty liver disease. The pandemic got the team wondering whether SARS-CoV-2, which is transmitted through respiratory droplets, could be detected with their technology. “We very quickly put together a team with a range of different academic clinical partners, along with others interested in breath research,” says Billy Boyle, Owlstone’s CEO. Within a matter of weeks, they had designed a clinical trial to test the technique and obtained the necessary approval from the UK’s Health Research Authority. That study is currently underway.

Everyone, whether requested by the company priorities or just their own values, was willing to work endlessly around the clock. —Mikael Dolsten, Pfizer

Big pharmaceutical companies have also pivoted from their usual work. Before COVID-19 hit, therapeutics for infectious diseases had not been a focus for Lilly, says Skovronsky. But he and his colleagues realized there were certain areas—the development of therapeutic antibodies, for example—where their expertise could be applied to the pandemic. In March, Lilly joined with AbCellera, a biotech based in Vancouver, Canada. AbCellera already had a platform designed to rapidly develop medicines during pandemics, which it had established with a grant from the US Defense Advanced Research Projects Agency (DARPA). Scientists at AbCellera had

obtained a blood sample from a recovered COVID-19 patient, and after running the sample through its platform—which rapidly screened for potential therapeutic antibodies using a combination of techniques, including high-throughput imaging, genomics, and AI—had identified more than 500 potential therapeutic molecules. The two companies launched a Phase 1 clinical trial of one of those antibodies in June. “[AbCellera] told us that they had this blood and were embarking on this project and said, ‘Is this something that you guys are interested in?’” Skovronsky says. “It took us about as long as it took to read the email to make the decision.” Within about a week, the two companies had signed a deal, with the goal of starting clinical trials of a new therapeutic within four months.

Adapting and rearranging The launch of new COVID-19 projects has required companies to quickly mobilize staff and resources. As a result, people involved in those projects have been working longer-than-usual hours. “The pace that we’ve had to work to fight COVID-19 is different than our normal course of work,” Skovronsky says. “I have many teams that meet every day, seven days a week.” Mikael Dolsten, the chief scientific officer of Pfizer global R&D, says the same has been true at his company. “This was the one occasion where I felt everyone, whether requested by the company priorities or just their own values, was willing to work endlessly around the clock,” Dolsten says. “I think everyone is inspired by the call to action to have a vaccine or treatment as fast as possible.” Many of the staff working on COVID19 projects have been reshuffled from some of the hundreds of clinical trials that drug companies have been forced to put on hold due to the pandemic. In March, Lilly announced that the start of most new studies would be delayed and that new enrollment in ongoing studies would be halted. According to Skovronsky, many of the staff who would have been working on 07/08 . 2020 | T H E S C IE N T IST 5 5

BIO BUSINESS these trials were redeployed to work on the COVID-19 research instead. Other companies are shuffling staff around in a similar way. Owlstone’s Boyle says his company’s stalled trials freed some employees and resources to focus on COVID-19. “We’re trying to make sure that we can still deliver on those core programs,” he adds. “But [we’re] redeploying the resources into the specific areas of the COVID problem in the near term.” All of this has to happen alongside measures put in place to contain the virus’s spread—culling the number of staff in the lab, for example, and sending home people who could do their job virtually. “Most of our laboratories are operating at the reduced scale because of the need for social distancing,” says Dolsten. “[In the labs], we have prioritized people at work on COVID-19 and certain lifesaving new medicines that are very close to coming to the clinic.”

AUGUST 31 - SEPTEMBER 4, 2020

■ INTERACTIVE NETWORKING

We’re all asking ourselves: How do we continue to work this way, to bring this same sense of urgency and collaboration to other diseases? —Dan Skovronsky, Eli Lilly

Companies have had to be flexible in other ways as well. Insilico usually synthesizes its compounds in Wuhan, China, for example, so when the lockdown started in that city, that part of their work was put on hold. “We just started synthesis in March,” Zhavoronkov says, adding that, as the epicenter of the pandemic has shifted, they’ve been able to restart work in Wuhan. “I think a lot of people who were using biotech services from China, when China went into lockdown, they started shifting to Europe and the US. Now it’s the other way around.”

Collaborations ramp up The pandemic has brought together people from many sectors—academia, industry, and government. “One of the wonderful things that’s happened during COVID-19 is that people are working together more so than I’ve ever seen,” says Gary Wilcox, the CEO of Cocrystal Pharma, a company working with scientists at Kansas State University to develop novel antiviral compounds to treat COVID-19. “Scientists don’t always join together in one great big group for the benefit of mankind. But here, there’s been a remarkable sharing of information.” Some of these collaborations have been formalized as larger consortia made up of multiple companies, and in some cases also funding bodies and governmental agencies. “There’s been a really interesting pivot towards embracing open innovation and a willingness to team up with partners outside of

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the life science ecosystem,” says Angela Radcliffe, the research and development lead for life sciences at the consulting firm Capgemini. In March, several large pharmaceutical companies, including Eli Lilly, Novartis, Gilead, and AstraZeneca, formed a group called COVID R&D to share resources and expertise to try to accelerate the development of effective therapies and vaccines for COVID-19. That same month, the Bill & Melinda Gates Foundation, the Wellcome Trust, and Mastercard launched the COVID-19 Therapeutics Accelerator to bring researchers in industry and academia together to identify potential treatments. In April, the National Institutes of Health announced the launch of Accelerating COVID-19 Therapeutic Interventions and Vaccines (ACTIV), a partnership between federal researchers and 16 pharmaceutical companies to standardize the testing of therapeutics in both the lab and in clinical trials. “There are still some companies out there who prefer to work in a more insular fashion, and that’s fine. But most of us are working together,” Skovronsky says. “I think there’s more to come, because if we have a successful drug or drug antibody, we’re going to have to work together in manufacturing it.”

It is very tempting to profit from this, but I think for at least the very first steps, it is important to keep things open. —Alex Zhavoronkov, Insilico Medicine

Whether the accelerated rate of drug and diagnostics development or the heightened level of cooperation among different players in the business will last beyond the pandemic remains to be seen. Company leaders are thinking about how to apply the lessons being learned now to expedite the development of therapeutics for other conditions as well. “We’re all asking ourselves: How do we continue

to work this way, to bring this same sense of urgency and collaboration to bear against all the other diseases—Alzheimer’s disease and cancer and autoimmune diseases and diabetes—that we work on?”

Skovronsky says. “Because those patients need it also.” g Diana Kwon is a freelance science journalist based in Berlin, Germany.

ENSURING GLOBAL ACCESS As pharmaceutical and biotech companies rush to bring COVID-19 tests and therapeutics to the market, they have also faced increasing pressure from advocacy groups, humanitarian organizations, and investors to ensure that their products will be broadly available. Some advocates have urged governments to override patents and asked companies to commit their intellectual property to the public domain. A handful of companies have announced plans to promote access to their products. For example, the pharmaceutical company Johnson & Johnson has promised that its effort to develop a COVID-19 vaccine with hundreds of millions of dollars from the US government’s Biomedical Advanced Research and Development Authority (BARDA) will be a nonprofit endeavor—and that if and when a product is available, the company will work with health authorities to ensure global access. Meanwhile, the pharmaceutical company Gilead Sciences, in addition to committing to donating 1.5 million doses of its experimental antiviral therapy remdesivir to the US government, signed deals with generic pharmaceutical manufacturers in India and Pakistan to distribute the drug to 127 countries that “face significant obstacles to healthcare access.” Some companies are being more open with their intellectual property, too, at least at the early stages of research and development. Through initiatives such as the COVID-19 Therapeutics Accelerator, pharmaceutical companies including Eli Lilly have agreed to share proprietary libraries of molecular compounds for others to screen for potential COVID19 therapeutics. These collections are shared “without worrying about [intellectual property] protection,” says Dan Skovronsky, the chief scientific officer of Eli Lilly. Insilco Medicine, although not a member of the Accelerator, has also released the molecular structures identified through its platform without patent protection, says the company’s founder and CEO, Alex Zhavoronkov. “Of course, it is very tempting to profit from this, but I think for at least the very first steps, it is important to keep things open,” he says. “Later, once we see that something works, we might be able to recover something.” Still, many companies, including Gilead, are retaining patents on COVID-19-related products. “We want to do the right thing from a humanitarian standpoint,” says Cocrystal Pharma’s CEO Gary Wilcox. “But we also have to recognize our shareholders, and our shareholders expect us to have a return on their investment. That’s where patents come in.” In February, Cocrystal obtained an exclusive license to develop coronavirus drug candidates identified and patented by researchers at Kansas State University. Patenting is “just a part of good science,” says Pfizer Chief Scientific Officer Mikael Dolsten. “Without patents, this is not a sustainable ecosystem. Nobody would be able to afford to invest.”

READING FRAMES

Dissecting the Pandemic Although there is much yet to learn about COVID-19 and the global spread of the disease, some lessons have emerged. BY DEBORA MACKENZIE

T

here is still much science doesn’t know about COVID-19, and so it may seem the height of hubris to write a book about the pandemic now. But I just did—and in researching and writing COVID-19, I found we can largely answer several important questions already. How did the pandemic start? SARS-CoV-2 most likely jumped to people from bats—a virus already able to infect and replicate in human cells. Could we have stopped the pandemic? Our best chance would have been to stop it before it started: we could have done far more to prevent humans from catching viruses from bats. It can be done. Bats in the US carry rabies, for example, but human cases are vanishingly rare because, left to their own devices, the two rarely encounter each other. Scientists have been warning of a zoonotic pandemic for decades. And many caution that there will be more of them. Their reasons for concern have not changed with the COVID-19 pandemic. Those reasons include human population increases that mean more people are penetrating wild ecosystems, where they encounter new animal infections; poor systems for early detection and containment of disease; and a lack of vaccines, drugs, and diagnostic R&D for “emerging” diseases that do not yet constitute a sufficient market for such products. If we are to focus scientific attention on those problems, it might help to know what pathogens humanity may be up against. Virologist Dennis Carroll wants to find out. Until recently, Carroll ran emerging disease programs at the US Agency for International Development. These included a pathogen discovery program called PREDICT, which helped US and Chinese scientists identify and warn about the family of bat coronaviruses that includes SARS-CoV-2. He now runs the Global Virome Project (GVP), which aims to sequence and map viruses harbored by animals that belong to families we know can infect humans. The idea is that the

5 8 T H E SC I EN T I ST | the-scientist.com

GVP’s sequences will help in developing antiviral drugs, vaccines, and diagnostics before pandemics start. Meanwhile, the search itself will help reduce the risk of pathogen spillover by establishing enhanced local capacity to monitor viruses in zoonosis “hotspots,” most of which occur in less-developed, tropical countries. The cost of cataloging what Carroll calls “biological dark matter” will be about $3.7 billion over the next 10 years, but he told me that this is trivial compared to the cost of just this latest pandemic. GVP member Peter Daszak of the New York–based EcoHealth Alliance, a nonprofit research organization collaborating on the PREDICT project, agrees. “We should find our plagues before they find us,” Daszak told me. Critics of the GVP argue that while sequencing thousands of viruses would be great science, such an effort won’t prevent the next pandemic unless we also know what those viruses do. “No amount of gene sequencing can tell us when or where the next outbreak will appear,” Andrew Rambaut of Edinburgh University in the UK told me. Better, he noted, to track novel infections in people. Infectious diseases researcher Amesh Adalja of Johns Hopkins University agreed, noting that in 2013 virologists sequenced viruses similar to SARS-CoV that already possessed the ability to infect human airway cells, but that didn’t stop the COVID-19 pandemic. The real biological dark matter, he said, lies in many human infections, which clinicians tend to diagnose as “a cold” or “diarrhea,” with no effort to identify the pathogen. More precise tracking of which pathogens are actually infecting humans, he argues, might reveal impending trouble. Both sides agree that whether viruses are tracked in animals or people, such monitoring would be best accomplished by a global network of local researchers studying their own backyards. David Heymann of the London School of Hygiene and Tropical Medicine led the 2005 revision of the World Health Organiza-

Hachette Books, June 2020 tion’s International Health Regulations, which required countries to inform one another of outbreaks with the potential to spread internationally. The treaty’s requirement that rich countries help poor countries conduct their own disease monitoring is among its most important, he told me, but rich countries have neglected it. Meanwhile, no amount of viral tracking will help if there is still a gap between scientific warnings and government action. The discovery of hundreds of bat viruses similar to SARS-CoV in 2005, and the further finding that some were already primed to infect humans seven years ago, should have spurred a renewed focus on coronavirus drugs and vaccines. It did not. In the 1980s, scientists around the world organized to reach consensus positions on ozone depletion, then on climate change, which finally led to international treaties that aimed to address those global crises. We need such a scientific consensus now on viral threats, to present the risks to governments in a way that compels and directs action. Without that, it won’t matter whether we find our plagues before or after they have jumped to us: we still won’t be able to stop them. g Debora MacKenzie is a science journalist who has been covering emerging diseases for more than 30 years. Read an excerpt from COVID-19 at the-scientist.com. Follow her on Twitter @debmackenzie1.

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07/08.2020 | T H E S C IE N T IST 59

FOUNDATIONS

Multiple Causes, 1931 BY CATHERINE OFFORD

I

6 0 T H E SC I EN T I ST | the-scientist.com

SHARP FOCUS: “Quick-witted and

blunt in manner,” according to the Australian Dictionary of Biography, Jean Macnamara was a respected physician and scientist who won both admirers and critics for the way she argued her views on science and medicine. In a letter to her mother in 1932, she wrote, “my best chance of real happiness is to hitch onto some ideal . . . and go for it.”

Rockefeller Institute for Medical Research in New York City. Flexner had struggled to develop a polio vaccine several years earlier, and subsequently declared the task impossible. He maintained until his death in 1946 that there was only one kind of poliovirus, and his influence dissuaded many researchers from following up on Macnamara’s and Burnet’s work. But in 1949, Johns Hopkins University researchers conclusively demonstrated that there were, in fact, hundreds of strains of poliovirus, which fell into three types. Antibodies to one strain granted immunity against other strains in that type, they showed, but not against strains of another type. This finding was a critical foundation for the trivalent

vaccines developed in the 1950s to combat strains of all three types. By that time, Macnamara had adopted another high-profile cause: the use of myxoma virus against Australia’s economically devastating plagues of invasive rabbits. Despite the approach’s failure in trials during the 1930s, Macnamara lobbied to have researchers try it again. In the 1950s, it worked, killing millions of rabbits, although rabbit populations eventually developed genetic resistance to the virus. Macnamara’s determined nature often rankled other scientists. But she was also widely admired. In 1935, she was made Dame of the British Empire, and her funeral, following her death in 1968, was attended by many of her former polio patients. g

DAME JEAN MACNAMARA C. 1930 BY DONOVAN. COLLECTION: NATIONAL PORTRAIT GALLERY, AUSTRALIA

t was touch and go whether Jean Macnamara would be able to work at Melbourne’s Royal Children’s Hospital. When she sought employment there after graduating with a medical degree from the University of Melbourne in the early 1920s, hospital authorities were openly reluctant to hire a woman, telling Macnamara that there weren’t appropriate toilet facilities on the premises. Macnamara ended up getting the position, but it wouldn’t be the last time she faced resistance from the medical community. A few years later, a polio epidemic hit Melbourne. The disease, which had been on the rise since the late 1800s and had recently caused a devastating outbreak in New York City, was notorious for its effect on children, who, in severe cases, died or were left paralyzed. At the time, not much was known about polio other than that it was a viral disease, says Gareth Williams, an emeritus professor of medicine and dentistry at the University of Bristol and author of the 2013 book Paralysed with Fear: The Story of Polio. Early attempts to create a vaccine had failed and, confusingly, some people seemed to get polio more than once—a phenomenon that went against traditional ideas about immunity. Collaborating with a colleague, Macfarlane Burnet of the Walter and Eliza Hall Institute, Macnamara began studying blood serum from polio survivors. When the researchers tested this serum, as well as serum from polioinfected monkeys, against different samples of the virus, they found that not every serum sample neutralized every virus sample. The antibodies in the serum were specific to a particular version of the virus, the pair realized: there was more than one type of polio. The finding, published in 1931, was a breakthrough. “Until then, people assumed it was just one virus,” says Williams. However, the work was dismissed by Simon Flexner, then head of the

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