Bates College

Cellular lipids shape health and disease through specific protein interactions, yet lipid-protein networks remain poorly defined. Despite rapid advances in functional lipid probes, the field still lacks a practical, dedicated protocol for conducting lipid-protein interaction studies. We describe detailed methods for determining lipid interactomes from cells using multifunctionalized lipid derivatives. We provide protocols that detail 1) how to treat cells with lipid derivatives and perform photochemistry to obtain lipid-protein conjugates; 2) how to perform click chemistry with a fluorophore and observe lipid-protein conjugates by in-gel fluorescence; 3) how to perform click chemistry with azide beads and prepare lipid-protein conjugates for proteomic analysis. We provide context on important parameters for each step and include guidelines for controls, as well as suggestions for troubleshooting based on common problems encountered during the preparation of this protocol. This protocol enables mapping lipid interactomes across diverse biological systems. The entire workflow from cell treatment to complete proteomic sample preparation requires ∼15 hours over four days, depending on the type of experimental readout (in-gel fluorescence or proteomics), and the usage of pause points. Practitioners are expected to be familiar with standard biochemical techniques, such as sterile sample handling and tissue culture and gel electrophoresis. Additional skills are needed for mass spectrometric analysis, and collaboration with a proteomics core facility is recommended. The described procedures uniquely enable the identification of the protein interactors (the interactome) of select lipid species, providing for a major shift in the characterization of the biological roles of lipids in cellular systems.

Mapping the extents and terminations of surface ruptures is essential for a better seismic hazard assessment, as these factors indicate the magnitude and location of future earthquakes. The Himalayas and its active Himalayan Frontal Thrust (HFT) plate boundary, have experienced numerous damaging earthquakes in both recent and medieval times. The variability of the associated surface ruptures and the extent of the medieval earthquakes remain poorly understood. This study aims to improve the understanding of rupture extents and behavior along the ~ 650 km Central Seismic Gap (CSG) segment by analyzing paleoseismic trench data from sixteen previously published trenches, including new excavations during this study at Teliwara and Goujani. Evidence from Goujani suggests a penultimate event between calAD1437 and calAD1576 and Most Recent Earthquake (MRE) between calAD1662 and AD1894 with a minimum cumulative slip of at least 7 m. The Teliwara site reveals evidence of MRE occurring between calAD1665 and calAD1956 with a cumulative slip of 12.3 m. Integrating these findings with data from other paleoseismic sites allows for a detailed reconstruction of rupture patterns and timing along the CSG segment. Analysis of age probability density functions (PDFs) indicate three significant events: Earthquake 1 dated between calAD1320 and calAD1412, likely ruptured 259–360 km of the HFT. Earthquake 2, dated between calAD1437 and calAD1576, appears to have ruptured 490 km with rupture termination near the Faizabad Ridge, suggesting it was an asperity confined rupture. Earthquake 3 occurred between calAD1748 and calAD1894. These events correspond temporally to the 1344, 1505, and 1803 historical earthquakes, or to unrecorded events of similar age. Estimated moment magnitudes (Mw) for Earthquakes 1 and 2 are approximately 8.3–8.5 and 8.7, respectively. These findings suggest that the CSG segment has experienced large ruptures influenced by structural asperities.

BackgroundThe treatment of cholangiocarcinoma (CCA) continues to face numerous clinical challenges, including the prediction of sensitivity to immunotherapy and the development of preoperative diagnostic models.MethodsIn this study, we aimed to address these challenges by collecting bile samples from CCA patients for metabolomic and microbiomic analyses. We also performed immunofluorescence (IF) staining on tissue formalin-fixed, paraffin-embedded (FFPE) blocks to assess the expression of relevant biomarkers. Additionally, we followed up with patients to analyze prognostic indicators based on their survival times. Using advanced machine learning techniques, specifically LASSO regression, we constructed a predictive model to determine the effectiveness of programmed cell death protein 1 (PD-1) inhibitors in treating CCA. The model integrates bile metabolomic data with an Immune Hot-Cold Index (IHC Index) derived from IF results, providing a comprehensive metric of the patient’s immune environment.ResultsOur findings revealed significant differences in metabolomic profiles between CCA patients and those with non-malignant liver diseases, as well as between patients with different genetic mutations. The IHC Index successfully differentiated between immune “hot” and “cold” states, correlating strongly with patient responses to immunotherapy. Furthermore, in one CCA patient, the model’s predictions were validated, demonstrating high accuracy and clinical relevance.ConclusionOur predictive model offers a robust tool for assessing the sensitivity of CCA patients to PD-1 inhibitors, potentially guiding personalized treatment strategies. Additionally, the integration of bile metabolomics with IF data provides a promising approach for developing preoperative diagnostic models, enhancing early detection and treatment planning for CCA.

Disk-integrated observations of the Sun provide a unique vantage point to explore stellar activity and its effect on measured radial velocities. Here we report a new approach for disk-integrated solar spectroscopy and evaluate its capabilities for solar radial velocity measurements. Our approach is based on a near-infrared laser heterodyne radiometer (LHR) combined with an optical frequency comb calibration, and we show that this combination enables precision, disk-integrated solar spectroscopy with high spectral resolution (∼800,000), high signal-to-noise ratio (∼2600), and absolute frequency accuracy. We use the comb-calibrated LHR to record spectra of the solar Fe i 1565 nm transition over a 6-week period. We show that our measurements reach sub-meter-per-second radial velocity precision over a single day, and we use daily measurements of the absolute line center to assess the long-term stability of the comb-calibrated LHR approach. We use this long-duration data set to quantify the principal uncertainty sources that impact the measured radial velocities, and we discuss future modifications that can further improve this approach in studies of stellar variability and its impact on radial velocity measurements.

Newborn rats have a biphasic hypoxic ventilatory response (HVR) that typically matures during the second postnatal week. In contrast, neonatal rats reared in moderate hyperoxia exhibit a sustained increase in ventilation during the late-phase of the HVR by 3 days of age (P3), and this earlier-than-expected transition from a biphasic HVR to a sustained HVR is partially mediated through NMDA receptors (Bavis et al., Respir Physiol Neurobiol 191: 84-94, 2014). To determine whether non-NMDA glutamate receptors also contribute to this respiratory plasticity, newborn Sprague Dawley rats were exposed to 21% O 2 (Control) or 60% O 2 (Hyperoxia) until their HVR were measured by head-body plethysmography at P3-4. Systemic administration of the non-NMDA glutamate receptor antagonist NBQX (12.5 mg kg -1 , i.p.) caused rats from both treatment groups to adopt a slower, deeper breathing pattern with a modest reduction in baseline minute ventilation. As a result, baseline O 2 convection requirement was approximately 13% lower after NBQX. NBQX also attenuated the HVR measured during the first minute of acute hypoxia in both treatment groups, but it did not alter the overall shape of the HVR. Specifically, Hyperoxia rats exhibited a sustained increase in ventilation throughout the entire 15-minute exposure to 11% O 2 regardless of whether they received saline or NBQX injections, while Control rats exhibited a strongly biphasic HVR. Therefore, non-NMDA glutamate receptors do not appear to contribute to the expression of respiratory plasticity after chronic postnatal hyperoxia. However, contrary to prior reports, non-NMDA glutamate receptors have significant effects on normoxic ventilation and the acute HVR in neonatal rats. Supported by the Department of Biology at Bates College. This abstract was presented at the American Physiology Summit 2025 and is only available in HTML format. There is no downloadable file or PDF version. The Physiology editorial board was not involved in the peer review process.

Salt marshes are regarded as key blue carbon stocks with high rates of carbon sequestration due to tidal inundation. However, the impacts that rising sea levels and human development and alterations to salt marshes have on carbon stocks and organic matter deposition have yet to be fully understood. The Sprague River Marsh, in Phippsburg Maine, has been subject to many alterations through the last 400 years (ditching, the building of a tidal restriction and the dredging and redirection of the natural tidal channel).  This study analyzes the geochemical records (carbon density and sequestration, d13C, d15N, and C:N ratio) of 40 previously collected sediment cores and 3 new sediment cores, from the Sprague River Marsh. The carbon density data were used to identify areas of high carbon stocks within the upper meter of the marsh. The northernmost area of the Sprague Marsh had significantly higher carbon stocks than elsewhere. The stable isotope data were parsed into different time intervals (0-50, 50-100, 100-200, 200-300, 300-500, 500-1000, 1000-2000 YRS BP) based on an age model derived from 7 radiocarbon dates. Marsh surfaces were mapped using ArcGIS and Empirical Bayesian Kriging to identify areas and times where organic deposition was dominated by high salt marsh, upland plant input, or marine input. These marsh surface reconstructions illuminate shifts in organic matter deposition with changes in relative sea level rise (in agreement with Johnson et al., 2007), the dredging of the tidal channel, marsh evolution and colonization, and growth of the marsh prior to European Colonization. This detailed history of Sprague Marsh can be used to identify areas of high carbon content and the number of sediment cores needed to accurately reconstruct marsh history and analyze and predict carbon stocks.

In previous work, respondents overestimated the size of the US Black population, while underestimating the White population. In the present study, we examined perceptions of the racial composition of more specific locations within the US, comparing relatively rural and urban locations to one another. We expected that observers would see more rural places as having smaller Black populations, and larger White populations, compared to less rural places, but these perceived differences would exist independent of actual variation in racial makeup. In three samples, US residents judged 70 locations, estimating their racial demographics, rurality/urbanness, and desirability. Study 1 ( N = 241) tested an all-White sample; Study 2 tested a White subsample ( n = 246) and a Black subsample ( n = 263).As expected, more rural locations were judged as having larger White populations and smaller Black populations than less rural locations, beyond any actual differences in racial composition. These results support the conclusion that the mental images that Black and White respondents have of rural and urban America are characterized by stereotypes of their populations. Public Significance Statement Academic and public scholarship has assumed that the meaning of the idea of “rural” is racialized, such that places judged as rural are thought of as White, and places judged as urban are thought of as Black, beyond any actual racial differences among locations. The present data confirm the operation of such biases, demonstrating them among both Black and White observers. The data also speak to how observers estimate the size of Black and White populations in specific locations, supporting the following conclusion: people’s judgments of the racial composition of the residents of places are a product of multiple, not entirely consistent, processes.