*Indicates a student co-author.
Bissett, Patrick G., Ian W. Eisenberg, Sunjae Shim, Jaimeli H. Rios, Henry M. Jones, McKenzie P. Hagen, Zeynep Enkavi, Jamie K. Li, Jeanette A. Mumford, David P. MacKinnon, Lisa A. Marsch and Russell A. Poldrack. “Cognitive tasks, anatomical MRI, and functional MRI data evaluating the construct of self-regulation.” Scientific Data, vol. 11, no. 1, 2024.
Abstract: We describe the following shared data from N = 103 healthy adults who completed a broad set of cognitive tasks, surveys, and neuroimaging measurements to examine the construct of self-regulation. The neuroimaging acquisition involved task-based fMRI, resting state fMRI, and structural MRI. Each subject completed the following ten tasks in the scanner across two 90-minute scanning sessions: attention network test (N), cued task switching, Columbia card task, dot pattern expectancy (DPX), delay discounting, simple and motor selective stop signal, Stroop, a towers task, and a set of survey questions. The dataset is shared openly through the OpenNeuro project, and the dataset is formatted according to the Brain Imaging Data Structure (BIDS) standard.
Arias-Ortiz, Ariane, Jaxine Wolfe, Scott D. Bridgham, Sara Knox, Gavin McNicol, Brian A. Needelman, Julie Shahan, Ellen J. Stuart-Haëntjens, Lisamarie Windham-Myers, Patty Y. Oikawa, Dennis D. Baldocchi, Joshua S. Caplan, Margaret Capooci, Kenneth M. Czapla, R. Kyle Derby, Heida L. Diefenderfer, Inke Forbrich, Gina Groseclose, Jason K. Keller, Cheryl Kelley, Amr E. Keshta, Helena S. Kleiner, Ken W. Krauss, Robert R. Lane, Sarah Mack, Serena Moseman-Valtierra, Thomas J. Mozdzer, Peter Mueller, Scott C. Neubauer, Genevieve Noyce, Karina V. R. Schäfer, Rebecca Sanders-DeMott, Charles A. Schutte, Rodrigo Vargas, Nathaniel B. Weston, Benjamin Wilson, J. Patrick Megonigal, and James R. Holmquist. “Methane fluxes in tidal marshes of the conterminous United States.” Global Change Biology, vol. 30, issue 9, September 2024.
Abstract: Methane (CH4) is a potent greenhouse gas (GHG) with atmospheric concentrations that have nearly tripled since pre-industrial times. Wetlands account for a large share of global CH4 emissions, yet the magnitude and factors controlling CH4 fluxes in tidal wetlands remain uncertain. We synthesized CH4 flux data from 100 chamber and 9 eddy covariance (EC) sites across tidal marshes in the conterminous United States to assess controlling factors and improve predictions of CH4 emissions. This effort included creating an open-source database of chamber-based GHG fluxes (https://doi.org/10.25573/serc.14227085). Annual fluxes across chamber and EC sites averaged 26 ± 53 g CH4 m−2 year−1, with a median of 3.9 g CH4 m−2 year−1, and only 25% of sites exceeding 18 g CH4 m−2 year−1. The highest fluxes were observed at fresh-oligohaline sites with daily maximum temperature normals (MATmax) above 25.6°C. These were followed by frequently inundated low and mid-fresh-oligohaline marshes with MATmax ≤25.6°C, and mesohaline sites with MATmax >19°C. Quantile regressions of paired chamber CH4 flux and porewater biogeochemistry revealed that the 90th percentile of fluxes fell below 5 ± 3 nmol m−2 s−1 at sulfate concentrations >4.7 ± 0.6 mM, porewater salinity >21 ± 2 psu, or surface water salinity >15 ± 3 psu. Across sites, salinity was the dominant predictor of annual CH4 fluxes, while within sites, temperature, gross primary productivity (GPP), and tidal height controlled variability at diel and seasonal scales. At the diel scale, GPP preceded temperature in importance for predicting CH4 flux changes, while the opposite was observed at the seasonal scale. Water levels influenced the timing and pathway of diel CH4 fluxes, with pulsed releases of stored CH4 at low to rising tide. This study provides data and methods to improve tidal marsh CH4 emission estimates, support blue carbon assessments, and refine national and global GHG inventories.
Barney, Madison, Anya M. Hopple, Laura L. Gregory, Jason K. Keller, and Scott D. Bridgham. “Anaerobic oxidation of methane mitigates net methane production and responds to long-term experimental warming in a northern bog.” Soil Biology and Biochemistry, vol. 190, March 2024.
Abstract: Limited previous research indicates that anaerobic oxidation of methane (AOM) can be an important control over methane (CH4) emissions in freshwater wetlands. We examined the importance of AOM and its response to warming and elevated atmospheric carbon dioxide (CO2) in a whole-ecosystem climate change experiment in an ombrotrophic bog in northern Minnesota, USA. In the first experiment, we sampled plots seasonally and measured rates of net CH4 production or consumption with and without added porewater through the depth profile at in situ temperatures. Net CH4 production occurred in most samples with porewater addition, but net CH4 consumption occurred in most samples without porewater addition, despite being incubated under strictly anaerobic conditions. We hypothesized that these porewater-dependent results were due to the low solubility and initially low headspace concentrations of CH4, which together inhibited rates of AOM when porewater was added. In a second experiment, we directly measured rates of AOM and net CH4 production in the same plots and calculated gross CH4 production during a single sampling event. AOM and gross CH4 production rates were much higher in surface peat, and AOM responded more strongly to warming than CH4 production. Elevated CO2 had minimal effects on any measured process. AOM consumed over 50% of the CH4 produced in some samples, indicating that it is an important process in this bog. Surface soil samples with added porewater also had lower rates of AOM, corroborating the results of the first experiment. Overall, we show that AOM can be an important control over CH4 emissions and their response to climate change in peatlands. Also, laboratory incubations of net CH4 production represent the dual process of gross CH4 production and AOM, and incubation conditions that differentially affect these two processes can provide widely disparate results.
Keller, Jason, Co-Principal Investigator. “MONet Sampling in Coastal Sage Scrub Ecosystems at Primarily Undergraduate Institutions.” Pacific Northwest National Laboratory, Environmental Molecular Sciences Laboratory.
Abstract: Proposal was selected for in-kind support for molecular and genomic analysis of soil samples from the Bernard Field Station at the Environmental Molecular Sciences Laboratory. The California sage scrub (CSS) ecosystem historically dominated much of the coastal zone of the Pacific Southwest ecoregion. Agriculture and urban development have converted up to 90% of CSS ecosystems to alternative land uses, and, in Southern California, CSS remnants face increasing pressure from invasion by non-native vegetation, continued urbanization, and climate change, including changing fire frequency. Participation in the MONet soil program will expand long-term CSS research taking place at the Robert J. Bernard Biological Field Station (BFS). Specifically, we will sample soil from native CSS, non-native grassland, and non-native forbland communities. Past work has demonstrated that non-native grassland communities have reduced soil carbon and nitrogen concentrations, while non-native forbland communities generally have similar or higher soil carbon and nitrogen concentrations compared to CSS communities. These soil properties coincide with shifts in microbial assemblages and differences in, bacteria and fungi concentrations with microbes being elevated in nonnative grasslands and reduced in non-native forblands relative to CSS. We will also take advantage of CSS communities recovering from localized fire events in 2013 and 2017. Previous work suggests that fire has minimal direct effects on bacterial assemblages; however, these sites provide a unique opportunity to follow the impacts of plant recovery on soil and microbial properties in CSS ecosystems. The BFS supports faculty and undergraduate student research at the Claremont Colleges, including Claremont McKenna, Pomona, Pitzer, Scripps, and Harvey Mudd Colleges. Participation in the MONet soil program will expand teaching and mentorship opportunities at these primarily undergraduate institutions.
Cohen, Dorrian G., Theresa M. Heidenreich, Jason W. Schorey, Jessica N. Ross, Daniel E. Hammers, Henry M. Vu, Thomas E. Moran, Christopher J. Winski, Peter V. Stuckey, Robbi L. Ross, Elizabeth Arsenault Yee, Felipe H. Santiago-Tirado, and Shaun W. Lee. “Minimal domain peptides derived from enterocins exhibit potent antifungal activity.” Frontiers in Fungal Biology, vol. 5, 2024.
Abstract: The antimicrobial peptide (AMP) circularized bacteriocin enterocin AS-48 produced by Enterococcus sp. exhibits broad-spectrum antibacterial activity via dimer insertion into the plasma membrane to form membrane pore structures, compromising membrane integrity and leading to bactericidal activity. A specific alpha-helical region of enterocin AS-48 has been shown to be responsible for the membrane-penetrating activity of the peptide. The canon syn-enterocin peptide library, generated using rational design techniques to have ninety-five synthetic peptide variants from the truncated, linearized, membrane-interacting domain of enterocin AS-48, was screened against three clinically relevant fungal strains: Cryptococcus neoformans, Candida albicans, and Candida auris for potential antifungal activity. Twelve peptides exhibited antifungal activity against C. neoformans, and two peptides exhibited activity against C. albicans. The fourteen active antifungal peptides were minimally cytotoxic to an immortalized human keratinocyte cell line (HaCats). Four select peptides were identified with minimum inhibitory concentrations (MICs) below 8 µM against C. neoformans. In 36-hour cell growth tests with these fungicidal peptides, fungicidal peptide no. 32 displayed inhibitory properties comparable to the leading antifungal medication fluconazole against C. neoformans. Screening of peptide no. 32 against a deletion library of C. neoformans mutants revealed that the mechanism of action of peptide no. 32 may relate to multivesicular bodies (MVBs) or polysaccharide capsule targeting. These findings importantly demonstrate that naturally derived AMPs produced by bacteria can be sourced, engineered, and modified to exhibit potent antifungal activity. Our results will contribute to the development of broad treatment alternatives to fungal infections and lend themselves to direct implications for possible treatment options for C. neoformans infections.
Flaherty Rebecca A., Shaun Lee, and Shannon D. Manning. “When Streptococci Seize the Opportunity: Identifying how Manipulation of Host Inflammatory Signaling Impacts Pathogenesis in Streptococcal Infections.” Frontiers in Cellular and Infection Microbiology, January 15, 2024.
Abstract: Many streptococcal pathogens such as Streptococcus pyogenes, Streptococcus agalactiae, and Streptococcus pneumoniae share the perplexing ability to live as relatively harmless human colonizers, while causing severe and potentially life-threatening illnesses in some cases. Severe diseases resulting from streptococcal infections are often marked by the induction of robust inflammatory responses in the infected host cells and surrounding tissues. The timing and type of inflammatory response can vary depending on factors such as pathovar type, which host cells are affected, and whether the host has certain genetic features or conditions that make them more susceptible to infection. In most cases, the activation of inflammatory signaling cascades benefits the host by alerting the immune system to the presence of microbial invaders. However, changes in the magnitude or type of inflammatory response can lead to pathogenic outcomes by causing extensive tissue damage at the primary infection site, promoting dissemination of the pathogen, and/or by triggering severe systemic outcomes such as septic shock. The articles in this Research Topic reveal the manifold complexities of streptococcal-host interactions using a variety of approaches. Two featured articles address regulation and production of bacterial virulence factors from the perspective of the invading pathogen.
Olesk, Johanna, Deborah Donahue, Jessica Ross, Conor Sheehan, Zach Bennett, Kevin Armknecht, Carlie Kudary, Juliane Hopf, Victoria A. Ploplis, Francis J. Castellino, Shaun W. Lee, and Prakash D. Nallathamby. “Antimicrobial peptide-conjugated phage-mimicking nanoparticles exhibit potent bactericidal action against Streptococcus pyogenes in murine wound infection models.” Nanoscale Advances, issue 4, 2024, pp. 1145-1162.
Abstract: Streptococcus pyogenes is a causative agent for strep throat, impetigo, and more invasive diseases. The main reason for the treatment failure of streptococcal infections is increased antibiotic resistance. In recent years, infectious diseases caused by pyogenic streptococci resistant to multiple antibiotics have been rising with a significant impact on public health and the veterinary industry. The development of antibiotic resistance and the resulting emergence of multidrug-resistant bacteria have become primary threats to the public health system, commonly leading to nosocomial infections. Many researchers have turned their focus to developing alternative classes of antibacterial agent based on various nanomaterials. We have developed an antibiotic-free nanoparticle system inspired by naturally occurring bacteriophages to fight antibiotic-resistant bacteria. Our phage-mimicking nanoparticles (PhaNPs) display structural mimicry of protein-turret distribution on the head structure of bacteriophages. By mimicking phages, we can take advantage of their evolutionary constant shape and high antibacterial activity while avoiding the immune reactions of the human body experienced by biologically derived phages. We describe the synthesis of hierarchically arranged core–shell nanoparticles, with a silica core conjugated with silver-coated gold nanospheres to which we have chemisorbed the synthetic antimicrobial peptide Syn-71 on the PhaNPs surface, and increased the rapidity of the antibacterial activity of the nanoparticles (PhaNP@Syn71). The antibacterial effect of the PhaNP@Syn71 was tested in vitro and in vivo in mouse wound infection models. In vitro, results showed a dose-dependent complete inhibition of bacterial growth (>99.99%). Cytocompatibility testing on HaCaT human skin keratinocytes showed minimal cytotoxicity of PhaNP@Syn71, being comparable to the vehicle cytotoxicity levels even at higher concentrations, thus proving that our design is biocompatible with human cells. There was a minimum cutoff dosage above which there was no evolution of resistance after prolonged exposure to sub-MIC dosages of PhaNP@Syn71. Application of PhaNP@Syn71 to a mouse wound infection model exhibited high biocompatibility in vivo while showing immediate stabilization of the wound size, and infection free wound healing. Our results suggest the robust utility of antimicrobial peptide-conjugated phage-mimicking nanoparticles as a highly effective antibacterial system that can combat bacterial infections consistently while avoiding the emergence of resistant bacterial strains.
Brodley, Carla, Valerie Barr, Elsa Gunter, Mark Guzdial, Ran Libeskind-Hadas, and Bill Manaris. “ACM 2023: CS + X---Challenges and Opportunities in Developing Interdisciplinary-Computing Curricula.” Association for Computing Machinery (ACM) Inroads, vol. 15, issue 3, September 2024, pp. 42-50.
Abstract: Interdisciplinary undergraduate computing curricula are of growing interest to students, institutions of higher learning, and employers, and range from single interdisciplinary courses to full majors. Interdisciplinary introductory CS+X courses and majors are often particularly attractive and compelling to students from groups that are traditionally underrepresented in STEM. CS+X programs provide students with a combination of complementary skills that allow them to engage with some of the most important problems to society and are also highly desirable to employers. In this article, we survey the range of types of CS+X programs and give recommendations for engaging with the opportunities and challenges in developing such programs.
Libeskind-Hadas, Ran. “Pairwise Distances and the Problem of Multiple Optima.” Journal of Computational Biology, vol. 31, no. 7, 2024.
Abstract: Discrete optimization problems arise in many biological contexts and, in many cases, we seek to make inferences from the optimal solutions. However, the number of optimal solutions is frequently very large and making inferences from any single solution may result in conclusions that are not supported by other optimal solutions. We describe a general approach for efficiently (polynomial time) and exactly (without sampling) computing statistics on the space of optimal solutions. These statistics provide insights into the space of optimal solutions that can be used to support the use of a single optimum (e.g., when the optimal solutions are similar) or justify the need for selecting multiple optima (e.g., when the solution space is large and diverse) from which to make inferences. We demonstrate this approach on two well-known problems and identify the properties of these problems that make them amenable to this method.
Risheh, Ali, Alles Rebel, Paul S. Nerenberg, and Negin Forouzesh. “Calculation of protein-ligand binding entropies using a rule-based molecular fingerprint.” Biophysical Journal, vol. 123, issue 17, September 2024, pp. 2839-2848.
Abstract: The use of fast in silico prediction methods for protein-ligand binding free energies holds significant promise for the initial phases of drug development. Numerous traditional physics-based models (e.g., implicit solvent models), however, tend to either neglect or heavily approximate entropic contributions to binding due to their computational complexity. Consequently, such methods often yield imprecise assessments of binding strength. Machine learning models provide accurate predictions and can often outperform physics-based models. They, however, are often prone to overfitting, and the interpretation of their results can be difficult. Physics-guided machine learning models combine the consistency of physics-based models with the accuracy of modern data-driven algorithms. This work integrates physics-based model conformational entropies into a graph convolutional network. We introduce a new neural network architecture (a rule-based graph convolutional network) that generates molecular fingerprints according to predefined rules specifically optimized for binding free energy calculations. Our results on 100 small host-guest systems demonstrate significant improvements in convergence and preventing overfitting. We additionally demonstrate the transferability of our proposed hybrid model by training it on the aforementioned host-guest systems and then testing it on six unrelated protein-ligand systems. Our new model shows little difference in training set accuracy compared to a previous model but an order-of-magnitude improvement in test set accuracy. Finally, we show how the results of our hybrid model can be interpreted in a straightforward fashion.
Nerenberg, Paul, Principal Investigator. “Track 1 Acquisition of a High-Performance Computing Cluster for Interdisciplinary Research at the Claremont Colleges.” NSF MRI Consortium, 2024-2027, $918,485.
Abstract: This MRI award will enable Claremont McKenna College (CMC) and Harvey Mudd College (CMC) to acquire a high-performance computing (HPC) cluster. Both CMC and HMC are primarily undergraduate institutions that place a strong emphasis on the engagement of students in research. This HPC cluster will be used by faculty and undergraduate students to perform research in a diverse set of disciplines spanning the natural sciences, mathematics, and economics. These research experiences will be transformative for the students by training them in state-of-the-art computational techniques that are widely employed in both academia and industry. The principal investigators will organize an annual multidisciplinary HPC research symposium, enhance existing courses involving computation, and enable the participation of high school students from underrepresented backgrounds in summer research. The joint CMC-HMC HPC cluster will contain a balanced mix of CPU and GPU resources, as well as large-memory nodes, that will support the research programs of ten faculty members at the two colleges. The heterogeneous hardware configuration of the HPC cluster will allow these faculty to develop and employ a variety of computational models in disciplines ranging from the natural sciences to mathematics to economics. Examples of the research projects that will be furthered by this cluster include the development of effective thermodynamic theories and efficient simulations to study solvent-solute interactions, fast ultra-sensitive algorithms and space-efficient representations for homology detection in large microbiome datasets, mathematical models for opinion dynamics using non-convex optimization methods, and machine learning and simulation techniques for constructing econometric models to assess the stability of financial institutions. Collectively, these projects will advance knowledge in both applied and theoretical areas of multiple disciplines, provide new models and software tools for their respective scholarly communities, and train and engage a new generation of undergraduate students in computational science.
Sternes, Phillip C., Lars Schmitz, and Timothy E. Higham. “The rise of pelagic sharks and adaptive evolution of pectoral fin morphology during the Cretaceous.” Current Biology, vol. 34, issue 12, June 2024, pp. 2764-2772.
Abstract: The emergence and subsequent evolution of pectoral fins is a key point in vertebrate evolution, as pectoral fins are dominant control surfaces for locomotion in extant fishes. However, major gaps remain in our understanding of the diversity and evolution of pectoral fins among cartilaginous fishes (Chondrichthyes), a group with an evolutionary history spanning over 400 million years with current selachians (modern sharks) appearing about 200 million years ago. Modern sharks are a charismatic group of vertebrates often thought to be predators roaming the open ocean and coastal areas, but most extant species occupy the seafloor. Here we use an integrative approach to understand what facilitated the expansion to the pelagic realm and what morphological changes accompanied this shift. On the basis of comparative analyses in the framework of a time-calibrated molecular phylogeny, we show that modern sharks expanded to the pelagic realm no later than the Early Cretaceous (Barremian). The pattern of pectoral fin aspect ratios across selachians is congruent with adaptive evolution, and we identify an increase of the subclade disparity of aspect ratio at a time when sea surface temperatures were at their highest. The expansion to open ocean habitats likely involved extended bouts of sustained fast swimming, which led to the selection for efficient movement via higher aspect ratio pectoral fins. Swimming performance was likely enhanced in pelagic sharks during this time due to the elevated temperatures in the sea, highlighting that shark evolution has been greatly impacted by climate change.
Smith, Nathan D., Nicole Klein, P. Martin Sander, and Lars Schmitz. “A new pseudosuchian from the Favret Formation of Nevada reveals that archosauriforms occupied coastal regions globally during the Middle Triassic.” Biology Letters, vol. 20, issue 7, July 2024.
Abstract: Recent studies suggest that both stem- and crown-group Archosauria encompassed high ecological diversity during their initial Triassic radiation. We describe a new pseudosuchian archosaur, Benggwigwishingasuchus eremicarminis gen. et sp. nov., from the Anisian (Middle Triassic) Fossil Hill Member of the Favret Formation (Nevada, USA), a pelagic setting in the eastern Panthalassan Ocean characterized by the presence of abundant ammonoids and large-bodied ichthyosaurs. Coupled with archosauriforms from the eastern and western Tethys Ocean, Benggwigwishingasuchus reveals that pseudosuchians were also components of Panthalassan ocean coastal settings, establishing that the group occupied these habitats globally during the Middle Triassic. However, Benggwigwishingasuchus, Qianosuchus, and Ticinosuchus (two other pseudosuchians known from marine sediments) are not recovered in a monophyletic group, demonstrating that a nearshore marine lifestyle occurred widely across Archosauriformes during this time. Benggwigwishingasuchus is recovered as part of an expanded Poposauroidea, including several taxa (e.g. Mandasuchus, Mambawakalae) from the Middle Triassic Manda Beds of Tanzania among its basally branching members. This implies a greater undiscovered diversity of poposauroids during the Early Triassic, and supports that the group, and pseudosuchians more broadly, diversified rapidly following the End-Permian mass extinction.
AGU Editorial Network, “Challenges facing scientific publishing in the field of Earth and space sciences.” AGU Advances, vol. 5, issue 4, August 2024.
Abstract: The scientific publishing landscape is evolving rapidly. This evolution is driven by a confluence of internal and external forces, including the growth of metrics-based evaluation of scientists; an increasing volume of manuscripts combined with expectations for rapid review and publication; an increasing number of journals, including for-profit Open Access publications; and the adoption of preprint servers across a growing range of disciplines. Many of these forces are contributing to personal anxiety and fatigue for authors, reviewers, and editors. Collectively, they are placing substantial stress on scientific publishing, which is a foundational pillar of the scientific enterprise. As editors of American Geophysical Union journals and books, we remain confident in the fundamental foundations of scientific publishing, but we are concerned about the impact of these increasing stressors. By affirming and investing in editorial values, respecting scientific integrity and credibility, and committing to accessibility, transparency, and accountability, we can fortify the foundations of the scientific enterprise during a time of rapid change.
McMahon, Teagan, Diana Thatcher, Branwen Williams, Alan Wanamaker, Brittany Jellison, Heidi Franklin, Katherine Guay, Nina M. Whitney, Joseph A. Stewart, and Michèle LaVigne. “Contrasting responses of commercially important Northwest Atlantic bivalve species to ocean acidification and temperature conditions.” PLOS Climate, vol. 3, number 11, 2024.
Abstract: Modern calcifying marine organisms face numerous environmental stressors, including overfishing, deoxygenation, increasing ocean temperatures, and ocean acidification (OA). Coastal marine settings are predicted to become warmer and more acidic in coming decades, heightening the risks of extreme events such as marine heat waves. Given these threats, it is important to understand the vulnerabilities of marine organisms that construct their shells from calcium carbonate, which are particularly susceptible to warming and decreasing pH levels. To investigate the response of four commercially relevant bivalve species to OA and differing temperatures, juvenile Mercenaria mercenaria (hard shell clams), juvenile Mya arenaria (soft shell clams), adult and juvenile Arctica islandica (ocean quahog), and juvenile Placopecten magellanicus (Atlantic sea scallops) were grown in varying pH and temperature conditions. Species were exposed to four controlled pH conditions (7.4, 7.6, 7.8, and ambient/8.0) and three controlled temperature conditions (6, 9, and 12°C) for 20.5 weeks and then shell growth and coloration were analyzed. This research marks the first direct comparison of these species’ biological responses to both temperature and OA conditions within the same experiment. The four species exhibited varying responses to temperature and OA conditions. Mortality rates were not significantly associated with pH or temperature conditions for any of the species studied. Growth (measured as change in maximum shell height) was observed to be higher in warmer tanks for all species and was not significantly impacted by pH. Two groups (juvenile M. arenaria and juvenile M. mercenaria) exhibited lightening in the color of their shells at lower pH levels at all temperatures, attributed to a loss of shell periostracum. The variable responses of the studied bivalve species, despite belonging to the same phylogenetic class and geographic region, highlights the need for further study into implications for health and management of bivalves in the face of variable stressors.
Williams, Branwen, Diane M. Thompson, Anne L. Cohen, and Hannah Mandell. “Constraining Uncertainties in Marine Calcifier Oxygen Isotope Values (δ18Ο) Across Latitudes and Kingdoms Using a Proxy System Modeling Framework.” Paleoceanography and Paleoclimatology, vol. 39, issue 12, December 2024.
Abstract: Paleoceanographic proxy archives encode information about the marine environment, which can yield key insights into past climate variability. In particular, marine calcifiers' stable oxygen isotopic composition (δ18Ο) tells us about seawater temperature and oxygen isotope composition. Here, we use a proxy system model (PSM) framework to systematically evaluate the drivers of skeletal/shell δ18Ο in three taxa of fast-growing marine calcifiers (crustose coralline algae, bivalves, and sclerosponges) from disparate locations, including high latitudes and deeper waters. We evaluate the impact of the quality of environmental data, the recording season in which the calcifier might document the environmental variability, and the importance of uncertainties on the PSM. Whereas the overall PSM-modeled δ18Οpseudocarb captured the measured δ18Ο well at some locations, local environmental variability derived from a reanalysis product and chronological uncertainties limit the ability to effectively model δ18Ο at other locations. Using the PSM approach we highlight the complexity of interpreting δ18Ο as seawater temperature and oxygen isotope composition in these remote locations.
Flöter, Sebastian, Gavin Lee Foster, Andrea Grottoli, Peter Swart, Branwen Williams, and Gert Wörheide. “Hidden from plain sight: Sclerosponges as environmental archives of ocean conditions from the surface to the mesophotic zone.” Past Global Changes Magazine, vol. 32, issue 1, pp. 44-45.
Abstract: Sclerosponges dwell in an underexplored region of reefs. Their massive basal skeleton offers an opportunity as a unique, but underappreciated, paleoenvironmental archive. Here, we give an overview of the paleoclimate potential of sclerosponges and highlight current and future research areas.
Pugazhendhi, Abinaya Sindu, Craig J. Neal, Khoa Minh Ta, Marco Molinari, Udit Kumar, Fei Wei, Elayaraja Kolanthai, Andrew Ady, Christina Drake, Megan Hughes, Shibu Yooseph, Sudipta Seal, Melanie J. Coathup, “A neoteric antibacterial ceria-silver nanozyme for abiotic surfaces.” Biomaterials, vol. 307, 2024.
Abstract: Community-associated and hospital-acquired infections caused by bacteria continue to yield major global challenges to human health. Bacterial contamination on abiotic surfaces is largely spread via high-touch surfaces and contemporary standard disinfection practices show limited efficacy, resulting in unsatisfactory therapeutic outcomes. New strategies that offer non-specific and broad protection are urgently needed. Herein, we report our novel ceria-silver nanozyme engineered at a molar ratio of 5:1 and with a higher trivalent (Ce3+) surface fraction. Our results reveal potent levels of surface catalytic activity on both wet and dry surfaces, with rapid, and complete eradication of Pseudomonas aeruginosa, Staphylococcus aureus, and methicillin resistant S. aureus, in both planktonic and biofilm form. Preferential electrostatic adherence of anionic bacteria to the cationic nanozyme surface leads to a catastrophic loss in both aerobic and anaerobic respiration, DNA damage, osmodysregulation, and finally, programmed bacterial lysis. Our data reveal several unique mechanistic avenues of synergistic ceria-Ag efficacy. Ag potentially increases the presence of Ce3+ sites at the ceria-Ag interface, thereby facilitating the formation of harmful H2O2, followed by likely permeation across the cell wall. Further, a weakened Ag-induced Ce–O bond may drive electron transfer from the Ec band to O2, thereby further facilitating the selective reduction of O2 toward H2O2 formation. Ag destabilizes the surface adsorption of molecular H2O2, potentially leading to higher concentrations of free H2O2 adjacent to bacteria. To this end, our results show that H2O2 and/or NO/NO2−/NO3− are the key liberators of antibacterial activity, with a limited immediate role being offered by nanozyme-induced ROS including O2•- and OH•, and likely other light-activated radicals. A mini-pilot proof-of-concept study performed in a pediatric dental clinic setting confirms residual, and continual nanozyme antibacterial efficacy over a 28-day period. These findings open a new approach to alleviate infections caused by bacteria for use on high-touch hard surfaces.
Yooseph, Shibu, Co-Principal Investigator. “Track 1 Acquisition of a High-Performance Computing Cluster for Interdisciplinary Research at the Claremont Colleges.” NSF MRI Consortium, 2024-2027, $918,485.
Abstract: This MRI award will enable Claremont McKenna College (CMC) and Harvey Mudd College (CMC) to acquire a high-performance computing (HPC) cluster. Both CMC and HMC are primarily undergraduate institutions that place a strong emphasis on the engagement of students in research. This HPC cluster will be used by faculty and undergraduate students to perform research in a diverse set of disciplines spanning the natural sciences, mathematics, and economics. These research experiences will be transformative for the students by training them in state-of-the-art computational techniques that are widely employed in both academia and industry. The principal investigators will organize an annual multidisciplinary HPC research symposium, enhance existing courses involving computation, and enable the participation of high school students from underrepresented backgrounds in summer research. The joint CMC-HMC HPC cluster will contain a balanced mix of CPU and GPU resources, as well as large-memory nodes, that will support the research programs of ten faculty members at the two colleges. The heterogeneous hardware configuration of the HPC cluster will allow these faculty to develop and employ a variety of computational models in disciplines ranging from the natural sciences to mathematics to economics. Examples of the research projects that will be furthered by this cluster include the development of effective thermodynamic theories and efficient simulations to study solvent-solute interactions, fast ultra-sensitive algorithms and space-efficient representations for homology detection in large microbiome datasets, mathematical models for opinion dynamics using non-convex optimization methods, and machine learning and simulation techniques for constructing econometric models to assess the stability of financial institutions. Collectively, these projects will advance knowledge in both applied and theoretical areas of multiple disciplines, provide new models and software tools for their respective scholarly communities, and train and engage a new generation of undergraduate students in computational science.