Brook Lab

Brook Lab in the Valley: A Yosemite Weekend

Sun, 05 Apr 2026 01:00:00 -0700

by Martin Roland

Spring is a busy time in the Brook Lab, but with the snow finally melted we got the chance to go on a long awaited trip to Yosemite! Of course, it ended up being the busiest Friday possible to leave. Charlie passed his quals that afternoon (congratulations, Charlie!), and Gwen gave a talk on Henipavirus discovery and dynamics in Malagasy fruit bats at the Berkeley Virology Meeting, so by the time we actually got on the road the sun was long down.

We pulled into Yosemite around 11pm and the excitement was real, especially for the three of us visiting for the first time. Christian, a postdoc in the lab and head of Ekipa Fanihy in Madagascar, was happy to join for his second trip out to Yosemite. Cara and Benjamin opted for real camping under the open sky. The rest of us were very happy to settle into two of Yosemite’s heated cabins that Cara reserved for us — a welcome upgrade from what we’re used to while doing fieldwork in remote Madagascar.

Day One: Mist Trail and the Valley Floor

Saturday morning we hit the Mist Trail up to Vernal Fall. The waterfall was running hard with spring snowmelt. It was loud, powerful, and absolutely beautiful. It also lives up to its name: by the time we got close we were thoroughly soaked. Luckily, Monique reminded me to bring a rainjacket.

Pictured left to right: Gwen Kettenburg, Charlie Voirin, Cara Brook, Monique Ades, Martin Roland, Christian Ranaivoson.

After drying off and grabbing lunch, we spent the afternoon on the valley floor. Lower Yosemite Falls, the iconic Ahwahnee Hotel, and a lot of happy wandering. The cliffs in Yosemite are amazing — getting to see Half Dome, El Cap, and more all in person was special. We talked about how one of the cliff-dwelling fruit bats we study in Madagascar, Eidolon dupreanum, would absolutely love it here (minus the cold).

The day wrapped up with pizza at the Curry Village Pizza Deck, which was delicious and just what we needed after 12 miles of walking. Plenty of Common Ravens (Corvus corax) were perched nearby, ready to take any crumbs left behind by park visitors. Funnily enough, this relationship between human influence and raven foraging habits happened to be what Cara studied for her undergrad thesis at Stanford. Cara told us about her summer spent here studying these ravens, staying in the same cabins we were in on this trip!

Day Two: Sunrise, Mirror Lake, and the Sequoias

Sunday opened with the sunrise over the valley, which was worth every minute of the early alarm.

We followed that with a hike out to Mirror Lake. It was truly the stillest lake I’ve ever seen, offering a perfect reflection of the surrounding cliffs.

The famous photo spot had a long queue so I wasn’t able to get a good picture, but further down it was a bit quieter and still extremely scenic. Yosemite is busy this time of year so of course we weren’t going to get completely away from the crowds, but honestly it was really nice to see so many people taking advantage of natural resources and enjoying time outside.

We then made our way to Tuolumne Grove to see the giant sequoias. Standing among them is one of those experiences that’s hard to put into words — they’re just staggeringly tall and beautiful, and so long-lived that the feeling was similar to being next to a baobab tree in Madagascar.

Before heading back to Berkeley we grabbed ice cream in Groveland, which was the right call and a great way to close out the weekend. It was a wonderful trip and a great reminder of just how close we are to world class nature. It felt surreal to be back in the city so easily — being able to spend a weekend in a national park and be back in the lab by Monday is wild, and such a special perk of living in Berkeley.

Congrats again to Charlie and Gwen for making it a Friday worth celebrating before we even left, and a big thank you to Cara for organizing and taking us, and to Benjamin for joining us and bringing Luna along to spend the weekend with us!

Pictured left to right: Gwen Kettenburg, Charlie Voirin, Cara Brook, Monique Ades, Martin Roland, Christian Ranaivoson.

BONUS

Pictured: Luna, getting ready to take a nap after two days of adventuring in Yosemite.

Cara wins Pew Biomedical Scholars fellowship!

Tue, 12 Aug 2025 01:00:00 -0700

The prestigious Pew Biomedical Scholars program announced the induction of 22 new faculty fellows today in its 2026 class. This national cohort included two Assistant Professors at UC Berkeley, one of whom was Cara. The Brook lab will use the support to design and implement anti-henipavirus vaccines in wild Madagascar fruit bats, with the aim to eradicate future zoonotic viruses in the wildlife population prior to human emergence. Read more about the fellowship from the UC Berkeley College of Letters and Science or on the Pew announcement page.

We are grateful for the support!

Brook lab moves to UC Berkeley!

Thu, 31 Jul 2025 01:00:00 -0700

by Cara Brook

After four truly wonderful years in the Department of Ecology and Evolution at the University of Chicago, the Brook Lab has moved to the Department of Integrative Biology at UC Berkeley.

While there are many things we will miss about Chicago and our amazing former department, we are excited to have arrived to the Golden State and looking forward to the scientific adventures ahead!

Stay tuned for future updates from California!

BatID 2025 at UChicago!

Sat, 12 Jul 2025 01:00:00 -0700

by Cara Brook

From July 9-11, 2025, the Brook lab hosted the Fourth International Symposium on the Infectious Diseases of Bats (BatID 2025) at the University of Chicago.

Over 140 people attended, representing 9 countries and 24 states. Plenary Speakers Dr. Liliana Davalos from Stony Brook University, Dr. Benhur Lee from Icahn School of Medicine at Mount Sinai, Dr. Daniel Streicker from the University of Glasgow, Dr. Simon Anthony from UC Davis, and Dr. Tigga Kingston from Texas Tech University led off five fascinating sessions focused, respectively, on ‘Bat immunology and within-host dynamics’, ‘Bat pathogen evolution’, ‘Bat pathogen persistence & transmission dynamics’, ‘Bat pathogen discovery’, and ‘Reconciling bat infectious diseases and conservation’.

I owe a huge thanks to co-organizers, Dr. Arinjay Banerjee from VIDO, University of Saskatchewan; Dr. Hannah Frank from Tulane University; Dr. Stephanie Seifert from Washington State University; and Dr. Daniel Becker from the University of Oklahoma.

With support from the NSF IOS Division, we were able to fund 17 students to attend with travel awards from all over the world. Please see the meeting webpage for more information.

We look forward to the next BatID, to be held tentatively in the summer of 2027.

A Day in the Life of a Field Project Manager

Tue, 21 Jan 2025 00:00:00 -0800

by Katherine McFerrin

Hi, I’m Katherine and I was a field project manager for Ekipa Fanihy (Team Fruit Bat) in 2023 and 2024. Here’s what a day in the field was like at my favorite field site, Analambotaka. I loved Analambotaka because it’s home to the Madagascar flying fox (Pteropus rufus)! As the largest bats in Madagascar, adult flying foxes have a 3-4 ft wingspan and lots of fluffy orange and black fur. They’re tree roosting bats as opposed to the other 2 species of Malagasy fruit bats the Brook Lab studies, which are both cave roosting. The second reason I enjoyed working at Analambotaka was the people. We worked with an extremely kind family, the Rabetsy family, and a field assistant named Patrick who loves Malagasy music. At Analambotaka, the days were long and the pace of work was slow, much slower than at sites with cave roosting bats, where catches were more guaranteed. There was time to be still and appreciate the people, the place and the bats.

At Analambotaka, we rise with the sun, well, really before the sun. My alarm goes off at 4:30 am and I open my tent to the still dark sky, the moon casting soft light on the pine and eucalyptus trees. I make my way to our kitchen tent and start a small fire as I wait for the others: Martin (my field partner and co-field project manager), Santino and Angelo (PhD students), Rova (MS student), Miora (technician), Dada Betsy (the father in the Rabetsy family), Nirina (Dada Betsy’s son), and Patrick. By 4:45 am we’re walking up the dirt road to check the bat nets. It’s mostly silent as we walk off our sleepiness. The sun peeks out, covering everything in a peach-colored wash, and the morning mist settles into the valley. It’s a routine we’ve become all too familiar with, but I still try to notice every sunrise.

We reach the first net within a 10 minutes walk. It is a tiered net hanging between two tall poles. The previous evenings we watched the sky for bats shortly after dark and set our net along their flight path from their roost to fruiting trees where they feed. This morning, when we spot bats suspended in the net above, we lower the net and work in groups of 2-3 to untangle the bats. It’s not an easy task, but a fun one. Patrick is our field assistant extraordinaire, having worked with the team for years, climbing trees and handling bats. Unintimidated by their razor sharp claws and teeth and strong movements, he quickly untangles the bat’s wings, the trickiest part. The fastest of us by far, Patrick makes it look like an art. Over the past several months, we’ve all gotten the hang of handling bats in the net and untangling them. There’s always something to help with from holding the neck or feet to untangling. As each bat is freed, we put them in a cloth bag that we’ll carry back to camp.

Next we check the gorge net, a net anchored to trees and spanning across the gorge in the flight path of the bats’ temporary roost. Our group splits to walk down each side of the valley. The hillside is covered in new shrubs, just recovering from a recent fire. We walk along the fire break, where vegetation was dug out to prevent fires from spreading beyond it. At the net spot, we can see the other side of the valley and a sea of mist in between. We yell and shout across the gorge to coordinate the ropes and pull in the net. We descend the uneven hillside carefully to avoid rolling ankles on the wet grass and shrub patches. Once we untangle the bats, we’re good to head back to camp.

We arrive to sounds of oil sizzling in a pan and logs being chopped. Mama Betsy, Dada Betsy’s wife, and her daughters are making breakfast. We hang the bat bags near the processing tents and get cleaned up. Mama Betsy makes eggs and rice, a delicious meal in the field, along with black coffee.

Then, we get to work. After lots of vial labeling and prepping the lab supplies, we put on the rest of our PPE. We each wear a tyvek suit, mask, and two layers of nitrile gloves. Then, we work in pairs with one person holding the bat and the other person processing (sampling). We take measurements, collect hair, wing punches, feces, urine, saliva, and ectoparasites, draw blood and insert PIT tags for future identification— all skills that we’ve learned through trial and error and guidance from Santino and Angelo. Eventually, these samples will be analyzed for viral presence and other markers of reproductive and immune health in our lab at Madagascar Biodiversity Center in Tana. After we take the samples, we give the bats sugar water to restore their energy (one of my favorite parts!) and then release them into a pine tree to fly away or rest until nightfall. Once we’ve released all the bats, we centrifuge the blood to collect sera (to look for viral antibodies) and red blood cell pellets (to PCR for bat malaria-like infections). Then, we store the samples, wash up and settle in for the rest of the day.

Aside from occasionally checking the nets for bats, the rest of the morning and afternoon is ours. We read books, catch up on sleep, walk around or play cards. Playing rummy is a favorite pastime of ours! This field mission, though, two of the Rabetsy daughters, Tanya and Monica, came to camp with us. So, I’ve been spending time with them! Upon Mama Betsy’s suggestion, I am teaching them English. They even bought notebooks and pens at the market in prep for my lessons. I type new words on my phone or spell them aloud and they jot down notes and draw pictures. The topic of these little lessons depends on which topics I feel like I have a solid grasp on to be able to explain in both English and Malagasy. This particular day we learn about foods and how to say that we like or dislike something. It turns into a frenzy of running around camp to ask everyone their favorite and least favorite foods and translating items at the kitchen tent. “Tiany indrindra ovy frite i Martin” (Martin likes fried potatoes the best). I love teaching the girls English and they teach me bits of Malagasy too. When I knew I would go to Madagascar back in 2023, I wanted to learn Malagasy, and during moments like this I am grateful I made language learning a part of my experience!

In the meantime, Mamabetsy is preparing to make mofo akondro (bananas, dipped in batter and deep fried), probably my favorite food in Madagascar! After our English lesson, Monica and I, along with Nata, our field driver, join in and help cook mofo akondro in the afternoon.

Around sunset, we walk out to check the nets again. This time the girls want to join. For every bat we find, we untangle it and drop it into a bag and shuttle them all back to camp. Then we feed the bats sugar water and a banana to tide them over until the morning when we will process them. Then, it’s dinner. Similar to lunch, dinner is rice with a main dish (“loaka”). This time it’s a mountain of rice and potatoes, green beans and carrots. After dinner, some people go to bed and some of us stay up for a little while longer. Patrick and Nirina make a bonfire. We talk, listen to Malagasy music and maybe even dance a little. Then, it’s time for bed and we’ll do it all over again for the next 10 days or so.

After leaving Madagascar, I miss the simple routine and the small joys of the field— the sunrise over a sea of fog, the bright orange fur of Pteropus rufus, English lessons with the girls, afternoon card games, music around the fire, and Mama Betsy’s mofo akondro (if we’re lucky). Until next time, Madagascar. “Mandra piona, Madagasikara”

Cara speaks at ASM Microbe 2024!

Wed, 03 Jul 2024 01:00:00 -0700

Cara spoke at ASM Microbe as an invited ‘Track Hub’ speaker this year, and they wrote this fantastic summary of the talk: How Studying Bat Viruses Can Help Prevent Zoonotic Disease .

Coding for Conservation program concludes first round of funding. Watch our summary video!

Thu, 20 Jun 2024 01:00:00 -0700

Post-baccalaureate PREP scholar, Mars Woodward, made this inspiring video summarizing the first year of our Coding for Conservation outreach program. Watch here:

And be inspired!

Cara goes on camera with Vox Science to talk bat physiology and its consequences for viral infection!

Fri, 24 Nov 2023 00:00:00 -0800

Cara went on camera with Vox: “Science Explained!” to talk about bat physiology and its consequences for viral infection! Watch the short video here:

Emily publishes first application of VirScan technology to identify virus exposures in bats

Sun, 01 Oct 2023 01:00:00 -0700

by Emily Ruhs

What if we could apply technology designed for human viral surveillance to other mammals known to host a variety of highly pathogenic viruses? In a recent paper published by the Brook lab in Frontiers in Public Health, we do just that!

PhIP-Seq, or Phage-Immunoprecipitation Sequencing, uses recently advanced biomedical technology – broadly, multiplexed genomic sequencing - to identify antiviral antibody-specific binding to peptides displayed on bacteriophages. PhIP-Seq technology has previously been used to comprehensively profile human serum samples for antibodies to the VirScan peptidome, a peptide library representing over 200 viruses that constitute the complete known human virome (see here).

In this recent paper, we applied the original VirScan library to ~80 Pteropus alecto bats, collected from Queensland, Australia in 2015. P. alecto is a large, nectarivorous and frugivorous bat native to Australia, Papua New Guinea, and Indonesia. Pteropus alecto has been previously identified as a reservoir for zoonotic Australian bat lyssavirus (see here) and Hendra henipavirus (see here and here ). First, we asked whether this human-focused library could adequately profile antiviral antibodies to this bat host.

We identified preliminary evidence of prior viral exposure to 57 specific viral genera, 41 subfamilies, and 33 different families. These included putative evidence of prior exposure to multiple viral genera in P. alecto serum that represent the first record of association between these viruses and this bat host: alphatorquevirus, alphavirus, betapapillomavirus, betapolyomavirus, circovirus, deltavirus, erythroparvovirus, hepacivirus, hepatovirus, husavirus, lymphocryptovirus, mammarenavirus, metapneumovirus, mulluscipoxvirus, norovirus, orthohepadnavirus, orthohepevirus, orthopoxvirus, orthoneumovirus, parapoxvirus, parechovirus, pegivirus, phlebovirus, picobirnavirus, roseolovirus, rotavirus, rubivirus, salivirus, sapovirus, seadornavirus, spumavirus, and vesiculovirus. On average, P. alecto had a mean of 3.69 viral genera antibodies identified per individual – which compares to an average of 10 viral genera antibodies per human host (here). Particularly, this VirScan assay successfully differentiated between past exposures to the closely related bat virus genera, ebolavirus and marburgvirus, and even distinguished Hendra/Nipah virus exposure from other peptides within the bat-infecting henipavirus genus. However, we were sometimes unable to serologically distinguish exposures among subfamilies, likely in large part because certain viruses (e.g., picornaviruses) included in the VirScan library are entirely human in origin.

Our next objective was to understand how viral exposures covary with age and body condition in these P. alecto bats. Using records from age cementum analysis (for more information see here!) and mass : forearm residuals – essentially a body-mass index “BMI” for bats – we separated out the top viral genera and explored patterns across age and mass residuals.

We found that total peptide hits and the number of viral exposures slightly increased with age, which makes logical sense because as animals get older there are more opportunities to get exposed to new pathogens – more time being vulnerable! We also saw that the greater the number of viral exposures, the more likely P. alecto were to have low mass residuals, meaning that they were potentially in worse condition. These results suggest either some subtle negative effects of continued or repeated viral infection on bat health over time, or a heightened susceptibility to viral exposure in individuals with poor nutritional status – which is intriguing given that bats are thought to not suffer health consequences with viral infection.

As we are all aware, bats have recently been the focus of attention due to the COVID-19 pandemic and other implicated bat-hosted viruses; therefore, broad serological surveillance aimed at elucidating the viruses that bats host are of great public and scientific interest. VirScan offers a promising alternative for future wildlife surveillance efforts, combining the broad historical outlook of serology—by which to identify both current and past infections—with the broad, multi-pathogen approach of meta-genomic next generation sequencing. While we show here that the original VirScan library does a pretty good job at identifying antibodies to human-viruses in bats, future applications of this platform in bat systems should aim to develop a bat-focused peptide library, which can effectively distinguish between multiple exposures to closely-related bat viruses or bat virus strains in a single viral genus.

Currently, we are working on developing this bat-focused library in conjunction with the Grainger Bioinformatics Center at the Field Museum of Natural History (Chicago, Illinois). Keep a look out for new developments!

New paper offers a mechanism for the extreme virulence of bat virus zoonoses!

Sat, 09 Sep 2023 01:00:00 -0700

By Cara Brook

In a paper the Brook lab published in PNAS in 2022, we compiled data from the literature to demonstrate that bat-borne viral zoonoses result in higher case fatality rates following spillover to humans than do viruses derived from any other known mammal- or bird host. These highly virulent bat zoonoses include Ebola and Marbugh filoviruses, Hendra and Nipah henipaviruses, and SARS and MERS coronaviruses. In our new paper, out this week in PLoS Biology, we offer a mechanistic explanation for the extraordinary virulence of bat virus zoonoses.

Our paper presents a theoretical model that seeks to mechanistically recapture the virulence of zoonotic viruses in two key steps: first allowing a virus to evolve over long timescales in its reservoir host, then second, to spillover on shorter timescales in a human host while still maintaining traits (specifically its growth rate) optimized on its original reservoir.

In our first analysis, we focus on virus adaption in the reservoir host, using a nested, within-host and population-level model and a technique known as ‘adaptive dynamics’ to derive a mathematical expression that demonstrates how a virus’s evolutionarily optimal growth rate–which we call r^*–should reflect the diverse life history traits and physiologies of its reservoir. The optimal r^* balances the benefits of enhanced between-host transmission and the costs of elevated virulence for the host that both result from higher virus growth rates. Faster-reproducing viruses generate higher virus densities in their hosts to facilitate transmission to new hosts–but these high virus densities can also cause direct pathology (disease) or elicit inflammatory immunopathological responses in their hosts. In disease ecology, this paradox is known as the ‘transmission-virulence tradeoff’.

Using life history data from the literature, we make predictions of the evolutionarily optimal virus growth rate (r^*) for 19 different mammalian orders. These r^* predictions vary across different mammal hosts because of variation in the extent to which higher r^* enhances transmission or casuses virulence for diverse host physiologies. We predict the evolution of particularly high r^* values for bat-evolved viruses as a result of a few unique features of bat physiology and immunity that minimize the pathology typically incurred by a high growth rate virus. In particular, several bat species are known to have perpetually primed antiviral immune systems (via constitutive expression of the antiviral cytokine, IFN-α), offering a resistance trait that elevates r^* in our model. In addition, bats also appear to be highly resilient to the immunopathological consequences of virus control by the immune system (chiefly inflammation), providing yet another parameter value in our model (‘tolerance of immunopathology’) which drives r^* predictions upwards. Critically, we scale this latter parameter as proportional to the residual of predicted lifepsan per body size, such that mammalian orders with longer lifespans than predicted for their body size have high values for the tolerance of immunopathology–and vice versa. As bats are the longest-lived mammals for their body size known, we model very high values for immunopathological tolerance in bats, thus elevating r^*.

The link between inflammation, longevity, and tolerance of virus infection rests on a body of recent work out Dr. Linfa Wang’s lab at Duke National University of Singapore, which demonstrates how bat longevity results from unique molecular mechanisms that mitigate inflammation–which are thought to have first evolved to dispel the extreme physiological stress that accrues with the highly metabolic activity of powered flight, itself unique to bats among all mammals. See here, here, and here for some relevant examples.

After evolving optimal virus growth rates for reservoir hosts, we next allow these reservoir-optimized viruses to “spillover” into secondary, human hosts. We assume that the first spillover infections in the human host should be acute, allowing limited opportunity for virus adaptation to the new host. Thus, we model human infections using immunological and physiological properties of the human host but with the same r^* virus growth rate previously optimized on the reservoir host. We also include a term for the ‘tolerance of direct virus pathology’ in the human host which we model as proportional to phylogenetic distance between reservoir host and human. This term is meant to embody any mismatch in immunity and physiology between reservoir and human not already captured in the optimal virus growth rate–which may result in further virulence in the spillover host.

From this, we are able to make predictions of the variation in virulence–here, mortality–caused by zoonotic viruses evolved in diverse reservoir host orders following spillover to human hosts. In most cases, the predicted virulence in humans mirrors the predicted r^* values, such that reservoir-optimized viruses with high r^* also cause high virulence in humans. For a subset (8) of reservoir orders, including bats, we can compare their predicted relative virulence in humans (from our nested model) against that previously presented in our 2022 paper. Our model does quite well in this regard–most notably recapturing the extreme virulence of bat virus zoonoses.

Intriguingly, our model also allows us to make spillover virulence predictions for viruses derived from reservoir orders from which zoonoses have yet to be demonstrated. For example, we predict that viruses evolved in the order Monotremata (echnidna and platypus) should evolved high growth rates likely to cause virulence in the event that they spilled over to humans. Importantly, our paper does not consider the probability of this zoonosis occurring–and given the large phylogenetic distance between humans and monotremes–such an event would be highly unlikely to begin with. Before getting too excited about these virulence forecasts, it’s important to note that we make predictions only at the very coarse, crude level of mammalian order–and base these predictions on extremely limited within-host immunological and physiological data available for comparison across mammals. In reality, we should expect virulence to vary greatly based on species-level differences in the life history and physiological traits modeled here.

All told, our paper is, essentially, a robust, quantitative hypothesis meant to stimulate further data collection at the in vitro scale that will facilitate more fine-scaled predictions and empirical tests of those predictions in the future. In previous work in bat cell tissue culture, we found some evidence of high virus growth rates evolving in bat immune systems. In upcoming work, we plan to use similar approaches to directly challenge and evaluate the predictions outlined here.

For further insights, read this fantastic primer summarizing our paper by Samuel Alizon!