*Indicates a student co-author.
Huang, J., Sehgal, V., Alvarez, L. V., Brocca, L., Cai, S., Cheng, R., ... and Fisher, J. B. “Remotely Sensed High-Resolution Soil Moisture and Evapotranspiration: Bridging the Gap Between Science and Society.” Water Resources Research, vol. 61, issue 5, May 2025.
Abstract: This paper reviews the current state of high-resolution remotely sensed soil moisture (SM) and evapotranspiration (ET) products and modeling, and the coupling relationship between SM and ET. SM downscaling approaches for satellite passive microwave products leverage advances in artificial intelligence and high-resolution remote sensing using visible, near-infrared, thermal-infrared, and synthetic aperture radar sensors. Remotely sensed ET continues to advance in spatiotemporal resolutions from MODIS to ECOSTRESS to Hydrosat and beyond. These advances enable a new understanding of bio-geo-physical controls and coupled feedback mechanisms between SM and ET reflecting the land cover and land use at field scale (3-30 m, daily). Still, the state-of-the-science products have their challenges and limitations, which we detail across data, retrieval algorithms, and applications. We describe the roles of these data in advancing 10 application areas: drought assessment, food security, precision agriculture, soil salinization, wildfire modeling, dust monitoring, flood forecasting, urban water, energy, and ecosystem management, ecohydrology, and biodiversity conservation. We discuss that future scientific advancement should focus on developing open-access, high-resolution (3-30 m), sub-daily SM and ET products, enabling the evaluation of hydrological processes at finer scales and revolutionizing the societal applications in data-limited regions of the world, especially the Global South for socio-economic development.
Ho, Emily K., Rebecca P. Kim-Yip, Alison G. Simpkins, Payam E. Farahani, Harrison R. Oatman, Eszter Posfai, Stanislav Y. Shvartsman, and Jared E. Toettcher. “In vivo measurements of receptor tyrosine kinase activity reveal feedback regulation of a developmental gradient.” Cell Reports, vol. 44, issue 7, July 22, 2025.
Abstract: A lack of tools for detecting receptor activity in vivo has limited our ability to fully explore receptor-level control of developmental patterning. Here, we extend phospho-tyrosine tag (pYtag) biosensors to visualize endogenous receptor tyrosine kinase (RTK) activity in Drosophila. We build biosensors for three RTKs that function across developmental stages and tissues. By characterizing Torso::pYtag during embryonic terminal patterning, we find that Torso activity differs from downstream extracellular signal-regulated kinase (ERK) activity in two surprising ways: Torso activity is narrowly restricted to the poles but produces a broader gradient of ERK and decreases over developmental time, while ERK activity is sustained, an effect mediated by ERK pathway-dependent negative feedback. Our results suggest that a narrow domain of Torso activity, tuned in amplitude by negative feedback, locally activates signaling effectors, which diffuse through the syncytial embryo to form the ERK gradient. Altogether, the results of this work highlight the usefulness of pYtags for investigating receptor-level regulation of developmental patterning.
Rush, J.E., E.S. Kane, J. Keller, J.C. Bowen, C.A. Zalman, E.S. Eurskirchen, K.H. Wyatt, A.R. Rober, and E.S. Hinckley. “Direct and indirect effects of water-table levels on redox-active organic matter reduction in an Alaskan rich fen.” Journal of Geophysical Research: Biogeosciences, vol. 130, issue 11, November 2025.
Abstract: Redox-active organic matter (RAOM) reduction is an important control on methane production in northern peatlands, but it is unclear how global climate change will affect RAOM reduction. We investigated the effects of water-table levels on RAOM reduction by leveraging a long-term water-table manipulation experiment in an Alaskan fen, which includes Lowered and Raised treatment plots relative to a Control. Common substrate peat was incubated in each plot during one summer of experimental manipulation and another summer of site-wide flooding. During experimental manipulation, common substrate RAOM was more reduced in the Raised plot than the Lowered plot at both 10-20 cm (19.1 ± 0.8 vs. 0.7 ± 0.3 mmol e- d-1 dw peat, p = 0.003) and 30-40 cm (18.0 ± 0.5 vs. 3.6 ± 1.2 mmol e- g-1 dw peat, p = 0.011). During site-wide flooding, differences in common substrate RAOM persisted with greater RAOM reduction in the Raised plot than both Control and Lowered plots (p < 0.05) and greater methane production from Raised plot common substrate. A comparison of the chemical composition of Raised and Control peat during an anaerobic laboratory incubation showed that the compounds removed during microbial processing differed between plots with a higher double bond equivalence to carbon ratio for the Raised plot (0.54 ± 0.13) compared to the Control plot (0.44 ± 0.17). Together, these field and laboratory results suggest that long-term increases in water-table levels can have complex effects on RAOM beyond oxygen availability with the potential to impact methane production from northern peatlands.
Bridgham, Scott D., Jeffrey R. White, Rachel M. Wilson, Jason K. Keller, and Jeffrey P. Chanton. “Methane transport pathways and oxidation in a Minnesota bog.” Journal of Geophysical Research: Biogeosciences, vol. 130, issue 12, December 2025.
Abstract: Despite the widely recognized importance of wetland CH4 emissions as a climate change feedback, simultaneous measurements of CH4 transport pathways and oxidation in a wetland are rare. Thus, these critical components of many CH4 models are poorly parameterized because of the lack of appropriate data. We measured plant CH4 transport and diffusion on two sampling dates in a Minnesota, USA, bog where a whole-ecosystem manipulation experiment of temperature and atmospheric CO2 (SPRUCE) is occurring. We also used stable-isotope methods to estimate CH4 oxidation rates. Plant CH4 transport was high in graminoids and, especially, the forb Maianthemum trifolium early in the growing season, while CH4 emissions from the trees Picea mariana and Larix laricina were minimal. Diffusive transport and CH4 oxidation rates were uniformly low. A prior study found low rates of episodic, large bubble CH4 ebullition in this bog. Despite large variation in plant and whole-plot CH4 emissions, a substantial fraction of whole-plot CH4 emissions could not be accounted for using a mass balance approach, which may be attributable to microbubble release from peat, although this requires further investigation. We compare our measured rates to two CH4 models that have been developed and tested at SPRUCE, both of which overestimate plant and diffusive CH4 transport in S1 Bog relative to our results. We emphasize the importance of enabling CH4 models to incorporate plant-mediated CH4 transport that is species-dependent and allowing plant species to dynamically change in response to climate change.
Price, Eric, Pranav C. Khandelwal, Daneil I. Rubenstein, and Aamir Ahmad. “A framework for fast, large-scale, semi-automatic inference of animal behaviour from monocular videos.” Methods in Ecology and Evolution, vol. 16, issue 9, pp. 1966-1982, September 2025.
Abstract:
- An automatic, quick, accurate and scalable method for animal behaviour inference using only videos of animals offers unprecedented opportunities to understand complex biological phenomena and answer challenging ecological questions. The advent of sophisticated machine learning techniques now allows the development and implementation of such a method. However, apart from developing a network model that infers animal behaviour from video inputs, the key challenge is to obtain sufficient labelled (annotated) data to successfully train that network—a laborious task that needs to be repeated for every species and/or animal system.
- In this work, we propose solutions for both problems, (i) a novel methodology for rapidly generating large amounts of annotated data of animals from videos and (ii) using it to reliably train deep neural network models to infer the different behavioural states of every animal in each frame of the video.
- Our method's workflow is bootstrapped with a relatively small amount of manually labelled video frames. We develop and implement this novel method by building upon the open-source tool Smarter-Labelme, leveraging deep convolutional neural networks for visual detection and tracking in combination with our behaviour inference model to quickly produce large amounts of reliable training data.
- We demonstrate the effectiveness of our method on aerial videos of plains and Grévy's Zebras (Equus quagga and Equus grevyi). We fully open-source the code (source code available at: https://github.com/robot-perception-group/Animal-Behaviour-Inference-Framework and archived at https://doi.org/10.5281/zenodo.15834944; Price et al., 2025) of our method as well as provide large amounts of accurately annotated video datasets (data available at: https://doi.org/10.18419/DARUS-5162; Ahmad, 2025; alternative link to data: https://keeper.mpdl.mpg.de/d/a9822e000aff4b5391e1/) of zebra behaviour using our method. A video abstract of this paper is available.
Schulz, Andrew K., Mrudul Chellapurath, Pranav C. Khandelwal, Seyed Reza Rezaei, Stefan Merker, and Ardian Jusufi. “Scaly-tail organ enhances static stability during Pel’s scaly-tailed flying squirrels’ arboreal locomotion.” Journal of the Royal Society Interface, vol. 22, issue 227, June 1, 2025.
Abstract: Scaly-tailed squirrels (Anomaluridae) are one of the least studied mammalian families. Their name is due to a peculiar and unique scaly-tail organ extruding from the caudal vertebra that has been predicted to help reduce skidding. This study investigates the function of the scaly-tail organ found in Anomalurus pelii, investigating its potential role in enhancing arboreal locomotion. As these animals glide from tree to tree in a habitat abundant with smooth-bark trees, we hypothesize that the scaly-tail organ assists with friction enhancement in their native smooth-bark habitat. Through a combination of analyses using mathematical and physical models for experimental validation, we explore whether the scaly-tail organ could improve the sliding and pitching stability during perching. Our experimental results showed that the scaly-tail organ can act as a skid-reduction mechanism by enhancing substrate engagement on intermediate roughness substrates by 58%. Mathematical models showed the scaly-tail organ enhances static pitch stability by acting as an additional support point. Our model showed that the scaly-tailed squirrel can reach up to 82.5° inclination without claw force; however, without scales, it reduces to 79.6°. Overall, this research highlights the functional significance of scaly-tail organs in adaptations in scaly-tailed flying squirrels and contributes to our understanding of their locomotion strategies and environmental stresses. Our study also provides insights into innovative locomotion mechanisms for robots operating in arboreal environments.
Vu, Henry M., Thomas E. Moran, Zhong Liang, Yun-Juan Bao, Paulina G. Carles, Jessica C. Keane, Madelyn G. Cerney, Caitlyn N. Dahnke, Ana L. Flores-Mireles, Victoria A. Ploplis, Francis J. Castellino, and Shaun W. Lee. “Group A Streptococcus remains viable inside fibrin clots and gains access to human plasminogen for subsequent fibrinolysis and dissemination.” Microbiology Spectrum, vol. 13, issue 2, February 2025.
Abstract: Group A Streptococcus (GAS) is a major human pathogen that causes several invasive diseases including necrotizing fasciitis. The host coagulation cascade initiates fibrin clots to sequester bacteria to prevent dissemination into deeper tissues. GAS, especially skin-tropic bacterial strains, utilize specific virulence factors, plasminogen binding M-protein (PAM) and streptokinase (SK), to manipulate hemostasis and activate plasminogen to cause fibrinolysis and fibrin clot escape. A major unresolved question regards the temporal dynamics of how GAS enmeshed in a fibrin clot can access plasminogen for clot dissolution and eventual dissemination. Here, we reveal through live imaging studies that GAS trapped inside a fibrin clot can remain viable in a latent state, until access to plasminogen activates fibrinolysis and dissemination. RNA-sequencing (RNA-seq) analysis shows marked changes in the wild-type (WT)-GAS transcriptome from the time bacteria were enmeshed inside the clot (4 h) to when dissemination was initiated (8 h). To gain a more fully realized model of how GAS trapped in fibrin clots can disseminate in the blood system, we utilized a novel 3D endothelial microfluidic device to demonstrate that GAS is fully capable of fibrinolysis in an endothelial environment, revealing a major underappreciated route by which GAS may cause more invasive outcomes. Our findings reveal for the first time that GAS can engage a latent, growth-suspended phase whereby physical structures such as fibrin clots that immobilize an invading pathogen allow bacteria to remain viable until sufficient access to plasminogen allows it to initiate fibrinolysis and escape into surrounding blood system and tissues.
Weinman, Jerod, Principal Investigator, with co-PIs Tracy Camp, Ran Libeskind-Hadas, Lisa Meeden, and Michael Wollowski. “NAIRR Pilot Expansion: FA2: Capacity and Community for 4-year Institutions.” National Science Foundation, April 2025 - September 2026, $299,762.
Abstract: Grinnell College in collaboration with the Computing Research Association, Claremont McKenna College, Swarthmore College, and Rose-Hulman Institute of Technology will engage faculty from four-year institutions to increase Artificial Intelligence (AI) education capacity and utilize shared resources in the National AI Research Resource (NAIRR) Pilot. Expanding access to AI education is critical to preparing a next-generation workforce. This project addresses challenges in expanding AI education by fostering a community of practice and supporting faculty at these institutions through a series of virtual roundtable discussions and an in-person workshop. As part of a broader national effort spanning different types of institutions of higher education, this initiative seeks to expand the NAIRR Pilot community by equipping educators with the tools and knowledge needed to bring AI learning experiences into classrooms nationwide.
The project has four primary goals: (1) facilitate increased instructional capacity and develop a sustainable community of practice among faculty at four-year institutions who are implementing AI courses or modules into undergraduate curricula; (2) establish a shared understanding of best practices for AI education relevant to four-year institutions; (3) improve faculty confidence at 4-year institutions in using NAIRR Pilot resources for AI instruction; and (4) develop strategies for integrating AI content into undergraduate courses, particularly where computational resources are limited. The virtual roundtable discussions will bring educators together in small groups to identify challenges and barriers to increasing AI education capacity and effectively utilizing NAIRR Pilot resources. Insights gathered from these discussions will shape the agenda for an in-person workshop, where participants will further explore these challenges, opportunities, and available resources. The workshop will culminate in a publicly available report outlining best practices, example implementations, and recommendations for leveraging NAIRR Pilot resources in AI education. By combining virtual and in-person engagement, the project fosters collaboration, enhances accessibility, and supports faculty in expanding AI education at four-year institutions.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
Tran, Suong, Kat Usavage, Lila P. Halbers, Claire Choplick, Grace Helton, Brenden Young, Jennifer A. Prescher, and Colin M. Rathbun. “Semisynthetic, multicolor probes for bioluminescence imaging.” ACS Omega, vol 10, issue 49, December 2025.
Abstract: Bioluminescence imaging is a sensitive and noninvasive technique for monitoring molecular and cellular processes in living systems. NanoLuc is one of the brightest and most widely used luciferase enzymes; however, the native blue emission of NanoLuc limits its applications due to poor sample penetration. NanoBiT, a split luciferase reporter derived from NanoLuc, consists of two subunits: LgBiT and HiBiT. Herein, we leverage bioluminescence resonance energy transfer (BRET) to red-shift the emission of NanoBiT by chemically labeling the N-terminus of HiBiT with fluorescent probes. Upon association of HiBiT and LgBiT, the appended fluorophores emit red-shifted light. When LgBiT is genetically encoded on the surface of mammalian cells, each probe produces unique emission profiles that can be distinguished by spectral phasor analysis microscopy. Moreover, by conjugating HiBiT peptides to fluorescent quantum dots, we extended BRET emission into the near-infrared. This modular system allows easy synthesis, rapid color switching, and tunable emission across the visible to near-infrared spectrum, providing a versatile platform for multicolor bioluminescence imaging.
Rathbun, Colin M., Principal Investigator. “Collaborative Research: Discovering enzymatic pathways to break carbon fluorine bonds in perfluorinated carboxylic acids.” National Science Foundation, November 2025, $150,000.
Abstract: Fluorinated organics, like perfluoroalkyl carboxylic acids (PFCAs), are common industrial additives which persist in the environment and have limited, expensive, and energy-intensive destruction technologies. So far, efforts to degrade PFCAs enzymatically have stalled, due to strong C-F bonds and a lack of evolutionary pressure to reward their destruction. As a result, PFCAs and other per- and polyfluoroalkyl substances (PFAS) are increasingly found to contaminate environmental media and require removal. Therefore, there is a critical need for new techniques to identify and enhance enzymatic defluorination mechanisms. In the absence of such knowledge, PFAS destruction will remain elusive, and PFAS-laden waste streams will continue to accumulate.
We propose a new approach to discover and improve enzymatic defluorination, positing that proper evolutionary incentive and high-throughput screening techniques can create and discover biocatalysts that degrade perfluorinated carbon chains. We will use a genetic circuit that links growth with defluorination and use this method to engineer known defluorinases to degrade new substrates. Initial work in our labs has already shown this technique can detect competent defluorinating enzymes. The successful completion of this project would establish new pathways for defluorination of perfluorinated carbon chains, opening the door for further enzymatic defluorination research and sustainable water treatment options.
Walker, Nia S., Hayley Luke*, Spencer Miller, Darienne Kealoha*, Carlo Caruso, Erika C. Johnston, Elena M. Mujica*, Joshua R. Hancock, and Crawford Drury. “Thermal tolerance is associated with enhanced growth and recovery in the reef-building coral Montipora capitata.” Marine Ecology Progress Series, vol. 773, November 2025, pp. 17-28.
Abstract: Relationships between ecologically important traits are increasingly important for the future of coral reefs, which are declining globally due to a variety of stressors. Corals that resist and recover from bleaching will be selected under future climates, which may negatively or positively impact a range of associated traits that are important for the structure and function of contemporary and future reefs. We investigated growth under ambient conditions, bleaching tolerance, and recovery in a model population of 60 Montipora capitata colonies harboring diverse symbiont communities. Specifically, we determined percent change in surface area and buoyant weight over a 3-mo ambient period, degree heating weeks required to reach a 30% decline in photochemical efficiency (Fv/Fm) in a 2-wk heat stress assay (27-32°C), Fv/Fm rebound over 80 d, and baseline Durusdinium and Cladocopium spp. communities in all genotypes. We observed higher trait variance among Durusdinium-dominated corals, highlighting the interaction between host and symbiont. Durusdinium-dominated corals displayed higher thermal tolerance and stress-induced mortality than Cladocopium-dominated corals, but there was no association between symbiont community and coral thermal stress recovery or growth. Thermal tolerance was also positively correlated with recovery after equivalent stress, and corals with moderate to high tolerance exhibited the highest surface area change. These results demonstrate limited tradeoffs associated with thermal tolerance in M. capitata and suggest that thermally tolerant corals in this model system can effectively recover from stress and maintain moderate-to-high growth rates under ambient conditions, providing insight into the adaptive capacity of thermally tolerant corals in the Anthropocene.
Tortorelli, Giada, Sabrina L Rosset, Clarisse E. S. Sullivan, Sarah Woo, Erika C. Johnston, Nia Symone Walker, Joshua R. Hancock, Carlo Caruso, Alyssa C. Varela, Kira Hughes, Christian Martin, Robert A. Quinn, and Crawford Drury. “Heat-induced stress modulates cell surface glycans and membrane lipids of coral symbionts.” The ISME Journal, vol. 19, issue 1, January 2025.
Abstract: The susceptibility of corals to environmental stress is determined by complex interactions between host genetic variation and the Symbiodiniaceae family community. We exposed genotypes of Montipora capitata hosting primarily Cladocopium or Durusdinium symbionts to ambient conditions and an 8-day heat stress. Symbionts’ cell surface glycan composition differed between genera and was significantly affected by temperature and oxidative stress. The metabolic profile of coral holobionts was primarily shaped by symbionts identity, but was also strongly responsive to oxidative stress. At peak temperature stress, betaine lipids in Cladocopium were remodeled to more closely resemble the abundance and saturation state of Durusdinium symbionts, which paralleled a larger metabolic shift in Cladocopium. Exploring how Symbiodiniaceae members regulate stress and host-symbiont affinity helps identify the traits contributing to coral resilience under climate change.
Greenspan, Kyle*, Branwen Williams, Heather Williams, Stefan Rahimi, Alex Hall, and Lei Huang. “Preparing for Uncertain Water Futures: An Analysis of Intrannual Snowpack Processes in the Southern Sierra Nevada Under Climate Change.” Geophysical Research Letters, vol. 52, issue 15, August 2025.
Abstract: In this paper, we seek to understand how useful the Western United States Dynamically Downscaled Data set (WUS-D3) is to water managers in California, as well as how climate change will impact the state's water resources. We analyze intrannual snowpack water storage skill of this data set over the southern Sierra Nevada, and project future changes in timing and magnitude of snowpack water storage over this region. We find that WUS-D3 downscaled climate models are skillful at capturing peak SWE timing, but overestimate peak SWE and melt date. The model ensemble projects diminished peak SWE and earlier, shorter snowmelt seasons. Further improvements in intrannual skill of these data would be useful to water managers. Altered timing and magnitude of southern Sierra snowpack water storage will have impacts in that region and throughout California, indicating that we must accelerate climate change adaptation planning.
Williams, Branwen, Sarah Barnes*, Mary Knaak*, Ellen R. M. Druffel, Matt McCarthy, Genevieve Pugsley, Natasha Vokhshoori, Jerome Fiechter, Peter Etnoyer, and Chris Caldow.“ Proteinaceous corals reveal heterogeneity in shifting southern California oceanographic regimes.” Marine Environmental Research, vol. 204, 106954, February 2025.
Abstract: The Southern California Bight is an ecologically important region for many local and migratory fauna. We combine bulk and compound-specific amino acid stable isotope measurements in the skeletons of proteinaceous octocorals with new regional ocean modeling system model output to explore biogeochemical changes at two locations within the Bight – Santa Cruz Basin and Santa Barbara Channel. Separated by the Channel Islands, these sites display distinct oceanographic regimes. Corals from the southeastern Santa Cruz Basin display lower bulk δ13C and higher bulk δ15N values than those in the northern Santa Barbara Channel. Amino acid isotope analyses indicate that the higher δ15N values in Santa Cruz Basin reflect both higher δ15N of baseline primary production and nitrate and higher trophic positions of the sinking particles that comprise the coral's diet. These findings suggest low nitrate concentrations, more complete nitrate utilization, lower productivity, and a longer planktonic food web. A 50-year time series of coral skeleton δ15N bulk values increases with time, consistent with sediment cores that capture an increase in the δ15NNO3 advected into the central Bight. In contrast, the Santa Barbara Channel corals display decadal-scale fluctuations, likely driven by interdecadal fluctuations in upwelling and nitrate supply. These findings agree with physical-biogeochemical model simulations showing greater sensitivity of upwelled surface nitrate concentrations to ocean climate variability in the Santa Barbara Channel. The importance of nutrient availability on ecosystem structure is emphasized using compound specific amino acid analysis, in a way that may be overlooked in bulk isotope palaeoceanographic records.
Stewart, Joseph A., Branwen Williams, Michèle LaVigne, Alan D. Wanamaker, Aaron L. Strong, Brittany Jellison, Nina M. Whitney, Diana L. Thatcher, Laura F. Robinson, Jochen Halfar and Walter Adey. “Delayed onset of ocean acidification in the Gulf of Maine.” Scientific Reports, vol. 15, number 2039, January 2025.
Abstract: The Gulf of Maine holds significant ecological and economic value for fisheries and communities in north-eastern North America. However, there is apprehension regarding its vulnerability to the effects of increasing atmospheric CO2. Substantial recent warming and the inflow of low alkalinity waters into the Gulf of Maine have raised concerns about the impact of ocean acidification on resident marine calcifiers (e.g. oysters, clams, mussels). With limited seawater pH records, the natural variability and drivers of pH in this region remain unclear. To address this, we present coastal water pH proxy records using boron isotope (δ11B) measurements in long-lived, annually banded, crustose coralline algae (1920-2018 CE). These records indicate seawater pH was low (~7.9) for much of the last century. Contrary to expectation, we also find that pH has increased (+ 0.2 pH units) over the past 40 years, despite concurrent rising atmospheric CO2. This increase is attributed to an increased input of high alkalinity waters derived from the Gulf Stream. This delayed onset of ocean acidification is cause for concern. Once ocean circulation-driven buffering effects reach their limit, seawater pH decline may occur swiftly. This would profoundly harm shellfisheries and the broader Gulf of Maine ecosystem.
Jordan, Charlotte*, Chisato Kamakura*, Jiyeon Kim*, Albert L. Park, Andrew Wald, Branwen Williams, and Diana Zhou* “Rural Futures: Prospective pathways for the Asian Rural Institute.” EnviroLab, Claremont Mckenna College, May 2025.
Moseley, Patience E., Elizabeth A.D. Hammocka, and Diana L. Williams.“ Oxytocin as a modulator of adaptive behavior: integrating ingestive and social mechanisms.” Physiology and Behavior, vol. 299, 114992, October 2025.
Abstract: Oxytocin (OXT) is synthesized in the hypothalamus and has well established roles in many physiological functions. OXT acts on G-protein-coupled receptors in the brain to influence a range of adaptive behaviors, including eating, social behavior and closely linked stress-related behaviors. The underlying mechanisms by which OXT influences these behaviors are still not well understood. Recent frameworks suggest that OXT may influence multiple adaptive behaviors at once to promote a contextually appropriate behavioral outcome. It is possible that this highly conserved neuropeptide subserves an evolutionary mechanism to promote behaviors that fulfill current homeostatic need and ultimately to promote survival. Here, we discuss the literature on OXT in ingestive behavior and consider overlapping mechanisms for OXT effects on social behavior. We highlight interactions between OXT and the hypothalamic melanocortin system and mesolimbic dopamine system as potential mechanisms for context-dependent behavioral selection. Finally, we suggest that OXT effects on behavior result at least in part from a positive shift in reward value of the stimuli that will fulfill the strongest homeostatic need at the time. Considering how these systems interact to influence behavior, particularly when multiple competing behavioral outcomes are possible, may facilitate the development of therapeutic targets across ingestive, social, and stress-related behaviors.
Keel, Pamela K., Lindsay P. Bodell, Jonathan Appelbaum, and Diana L. Williams. “Test of a biobehavioral model linking weight suppression to binge-eating severity via leptin and glucagon-like peptide 1 in bulimia nervosa and related syndromes in women.” Psychological Medicine, vol. 55, June 2025.
Abstract:
Background: Weight suppression represents the difference between highest and current body weight and predicts maintenance of bulimia nervosa and related syndromes (BN-S). This study tested a biobehavioral model of binge-eating severity in which greater weight suppression links to reduced leptin, which links to reduced glucagon-like peptide 1 (GLP-1) release, which links to both decreased reward satiation and increased reward valuation, which link, respectively, to excessive food intake and loss of control while eating - the defining features of DSM-5 binge-eating episodes.
Methods: Women (N = 399) who met DSM-5 criteria for bulimia nervosa or another eating disorder with binge eating (n = 321) or had no lifetime eating disorder symptoms (n = 78) participated in a multi-visit protocol, including structured clinical interviews, height, weight, weight history, percent body fat, fasting leptin, post-prandial GLP-1 response to a fixed meal, and self-report and behavioral assessments of food reward satiation (ad lib meal) and food and nonfood reward valuation (progressive ratio tasks).
Results: A structural equation model (SEM) demonstrated excellent fit to data with significant pathways from greater weight suppression to lower leptin, to blunted GLP-1 response, to lower reward satiation, to larger eating/binge-eating episode size, with significant indirect paths through leptin, GLP-1, and reward satiation. SEM with paths via reward valuation to loss of control eating demonstrated inadequate fit.
Conclusions: Findings specifically link reduced GLP-1 response to severity of binge-episode size and support weight history assessment in eating disorders, DSM-5 over ICD-11 criteria for binge eating, and may inform future clinical trials of GLP-1 agonists for BN-S.
Keel, Pamela K., Lindsay P. Bodell, Sarrah I. Ali, Austin Starkey, Jenna Trotta, J. Woody Luxama, Chloé Halfhide, Naomi G. Hill, Jonathan Appelbaum, and Diana L Williams. “Examining Weight Suppression, Leptin, Glucagon-like Peptide 1, and Reward-Related Constructs in Severity and Maintenance of Bulimic Syndromes: Protocol and Sample Characteristics for a Cross-sectional and Longitudinal Study.” JMIR Research Protocols, vol 14, April 2025.
Abstract:
Background: Bulimia nervosa and related syndromes (BN-S) characterized by binge eating vary considerably in illness severity and course. Using the Research Domain Criteria framework of the National Institute of Mental Health, we developed a model positing that the same set of physiological consequences of weight suppression (WS; defined as the difference between the highest and current adult body weight) contribute to binge-eating severity and maintenance by (1) increasing the drive or motivation to consume food (reward valuation effort [RVE]) and (2) decreasing the ability for food consumption to lead to a state of satiation or satisfaction (reward satiation).
Objective: Our funded project aimed to test concurrent associations among WS, physiological factors (leptin concentrations and postprandial glucagon-like peptide 1 [GLP-1] response), behavioral indicators of RVE (breakpoint on progressive ratio tasks) and reward satiation (ad-lib test meal intake), self-report of these core constructs, and binge-eating severity in BN-S (aim 1); test prospective associations to determine whether WS predicts BN-S maintenance in longitudinal models and whether posited mediators also predict BN-S maintenance (aim 2); and determine whether associations between WS and BN-S severity and maintenance are mediated by alterations in leptin levels, GLP-1 response, RVE, and reward satiation (aim 3).
Methods: We aimed to recruit a sample of 320 women with BN-S or noneating disorder controls, with BMI from 16 kg/m2 to 35 kg/m2, for our study. The study included diagnostic interviews; questionnaires; height, weight, and percentage of body fat measurements; weight history; fasting leptin level; postprandial GLP-1 and insulin responses to a fixed meal; and ad-lib meal and progressive ratio tasks to behaviorally measure reward satiation and RVE, respectively, at baseline, with at least 78.1% (250/320) of the participants providing data at 6- and 12-month follow-up visits. Data will be analyzed using structural equation models to test posited pathways.
Results: Data collection began in November 2016 and ended in April 2023, pausing in-person data collection from March 2020 to February 2021 due to the COVID-19 pandemic. Of 399 eligible women enrolled, 290 (72.7%) provided clinical, behavioral, and biological data at baseline, and 249 (62.4%) provided follow-up data. Measures demonstrated strong psychometric properties.
Conclusions: We seek to identify biobehavioral predictors to inform treatments that target key factors influencing the severity and course of binge eating. These data, supported solely through federal funding, can inform questions emerging from recent interest and controversy surrounding the use of GLP-1 agonists for binge eating.
Williams, Diana L. and Pamela K. Keel. “Neuroendocrine Function and Gut-Brain Axis in Eating Disorders.” The Handbook of the Neurobiology of Eating Disorders, edited by Christina E. Wierenga and Joanna E. Steinglass. Oxford University Press, 2025, pp. 42-69.
Abstract: The neuroendocrine factors that influence food intake are complex, and dysfunction in these systems may contribute to the development and/or maintenance of eating disorders. The brain integrates sensory, cognitive, and emotional variables with long-term endocrine signals of metabolic status and fuel storage, and short-term endocrine and paracrine signals related to the nutrient content of individual meals. This chapter focuses on those short-term signals involved in gut–brain communication. A number of peptides released by the gastrointestinal tract and the pancreas play an important role in interoception, the perception of internal physiological states including hunger and satiety. This chapter reviews evidence from humans as well as laboratory animal models, to address whether eating disorders involve impaired function of leptin, ghrelin, cholecystokinin, peptide tyrosine tyrosine, glucagon-like peptide 1, insulin, and amylin. The chapter also discusses limitations, clinical implications, and future directions for this area.
Alser, Mohammed, Mukul S. Bansal, Yury Khudyakov, Serghei Mangul, Ion I. Mandoiu, Marmar R. Moussa, Murray Patterson, Sanguthevar Rajasekaran, Pavel Skums, Shibu Yooseph, and Alexander Zelikovsky, eds. Computational Advances in Bio and Medical Sciences: 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers. Springer Nature, 2025.
Abstract: This volume contains the papers presented at ICCABS 2025, the 13th International Conference on Computational Advances in Bio and Medical Sciences, held on January 12-14, 2025 in Atlanta, Georgia, USA. ICCABS 2025 was hosted by the Department of Computer Science at Georgia State University with Alexander Zelikovsky from Georgia State University and Sanguthevar Rajasekaran from University of Connecticut as General Chairs, and Murray Patterson from Georgia State University and Shibu Yooseph from Claremont McKenna College as Program Committee Chairs. ICCABS has the goal of bringing together researchers, scientists, and students from academia, laboratories, and industry to discuss recent advances on computational techniques and applications in the areas of biology, medicine, and drug discovery.
Yooseph, Shibu. “Model Selection for Sparse Microbial Network Inference Using Variational Approximation.” Computational Advances in Bio and Medical Sciences: 13th International Conference, ICCABS 2025, Atlanta, GA, USA, January 12-14, 2025, Revised Selected Papers, 2025, pp. 103-129.
Abstract: Microbial communities are often composed of taxa from different taxonomic groups. The associations among the constituent members in a microbial community play an important role in determining the functional characteristics of the community, and these associations can be modeled using an edge weighted graph (microbial network). A microbial network is typically inferred from a sample-taxa matrix that is obtained by sequencing multiple biological samples and identifying the taxa abundance in each sample. Motivated by microbiome studies that involve a large number of samples collected across a range of study parameters, here we consider the computational problem of identifying the number of microbial networks underlying the observed sample-taxa abundance matrix. Specifically, we consider the problem of determining the number of sparse microbial networks in this setting. We use a mixture model framework to address this problem, and present formulations to model both count data and proportion data. We propose several variational approximation based algorithms that allow the incorporation of the sparsity constraint while estimating the number of components in the mixture model. We evaluate these algorithms on a large number of simulated datasets generated using a collection of different graph structures (band, hub, cluster, random, and scale-free).
Riccardi, Christopher, Yuqiu Wang, Shibu Yooseph, and Fengzhu Sun. “Bidirectional subsethood of shared marker profiles enables accurate virus classification.” Microbiome, vol 13, number 170, 2025.
Abstract:
Background: Due to the impact of viral metagenomic sequencing, the official virus taxonomy is updated several times a year, with labels being renamed even substantially across releases. While this helps reveal newer aspects on the classification of viruses, existing bioinformatic methods for classification struggle to stay in sync with this ever-improving resource.
Results: We developed a new computer program, named Virgo, that is able to correctly predict virus families from metagenomic data with an F1 score above 0.9 using a novel viral sequence similarity metric proposed in this work. Moreover, it ensures compatibility with any version of the official taxonomy of viruses.
Conclusions: Virgo is designed to easily incorporate newer releases of the official taxonomy, thus representing a valuable resource in the virology community while raising awareness to develop computational methods that evolve alongside manually curated resources.
Rathbun, Kimberly Paige, Mary Lou Sole, Shibu Yooseph, Rui Xie, Annette M. Bourgault, and Steven Talbert. “Oral Microbiome Changes During Hospitalization in Older Adults Not Receiving Mechanical Ventilation.” American Journal of Critical Care, vol. 34, issue 3, May 2025, pp. 208-217.
Abstract:
Background: Oral bacteria can be pathogenic and may change during hospitalization, potentially increasing risk for complications for older adults, including residents of skilled nursing facilities (SNFs).
Objectives: To compare the oral microbiome at hospital admission by prehospital residence (SNF vs home) in older adults not receiving mechanical ventilation and to assess changes in their oral microbiome during hospitalization.
Methods: This prospective, observational study included 46 hospitalized adults (≥65 years old) not receiving mechanical ventilation, enrolled within 72 hours of hospitalization (15 admitted from SNF, 31 from home). Oral health was assessed with the Oral Health Assessment Tool at baseline and days 3, 5, and 7. Genomic DNA was extracted from unstimulated oral saliva specimens for microbiome profiling using 16S ribosomal RNA sequencing. Taxonomic composition, relative abundance, α-diversity (Shannon Index), and β-diversity (Bray-Curtis dissimilarity) of bacterial communities were determined.
Results: Most patients were female (70%) and White (74%) or Hispanic (11%). Mean age was 78.7 years. More patients admitted from SNFs than from home had cognitive impairment (P < .001), delirium (P = .01), frailty (P < .001), and comorbidities (P = .04). Patients from SNFs had more oral bacteria associated with oral disease, lower α-diversity (P < .001), and higher β-diversity (P = .01). In the 28 study completers, α-diversity altered over time (P < .001). A significant interaction was found between groups after adjusting for covariates (P < .001).
Conclusions: Hospitalized older adults admitted from SNFs experience oral microbial and oral health disparities.
Thompson, A.R., B.J. Adams, I.D. Hogg, and S. Yooseph. “Evidence for Trace Gas Metabolism and Widespread Antibiotic Synthesis in an Abiotically Driven, Antarctic Soil Ecosystem.” Environmental Microbiology Reports, vol. 17, issue 6, December 2025.
Abstract: The McMurdo Dry Valleys (MDVs) of Antarctica are a uniquely pristine, low-biodiversity model system for understanding fundamental ecological phenomena, the impact of a warming climate on ecosystem functioning, community structure and composition and the dynamics of adaptation. Despite the scientific value of this system, we still know little about the functional ecology of its biota, especially the bacteria. Here, we analysed the bacterial taxonomic and functional diversity of 18 shotgun metagenomes using the VEBA metagenome processing pipeline. We recovered 701 medium-to-high quality metagenome-assembled genomes (MAGs) (≥ 50% completeness and contamination < 10%) and 201 high-quality MAGs (≥ 80% completeness and < 10% contamination), almost 50% more than found in similar sites previously. We found that: (1) community composition shifts along environmental gradients correlated with soil moisture, elevation and distance to the coast; (2) many MDV bacteria are capable of performing trace gas metabolism; (3) genes associated with antibiotic-mediated competitive interactions (e.g., antibiotic biosynthesis and antibiotic resistance genes) are widespread; and (4) MDV bacteria employ survival strategies common to bacteria in similarly extreme environments. This study provides novel insight into microbial survival strategies in extreme environments and lays the groundwork for a more comprehensive understanding of the autecology of MDV bacteria.