Session 4: James Merrill: Life and Archive

2:45 p.m. — Session 4: James Merrill: Life and Archive An introduction to James Merrill resources in Washington University Special Collections. See http://omeka.wustl.edu/omeka/exhibits/show/merrill-life-archiv

Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary events leading to the diversification of this genus over the last 20 million years. Here, we show the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.Some computations were performed on Tirant III of the Spanish Supercomputing Network (“Servei d’Informàtica de la Universitat de València”) under the project BCV-2021-1-0001 granted to DP, while others were performed at the Wisconsin Energy Institute and the Center for High-Throughput Computing of the University of Wisconsin–Madison. During a portion of this project, DP was a researcher funded by the European Union’s Horizon 2020 research and innovation program Marie Sklodowska-Curie, grant agreement No. 747775, the Research Council of Norway (RCN) grant Nos. RCN 324253 and 274337, and the Generalitat Valenciana plan GenT grant No. CIDEGENT/2021/039. D.P. is a recipient of an Illumina Grant for Illumina Sequencing Saccharomyces strains in this study. Q.K.L. was supported by the National Science Foundation under Grant No. DGE-1256259 (Graduate Research Fellowship) and the Predoctoral Training Program in Genetics, funded by the National Institutes of Health (5T32GM007133). This material is based upon work supported in part by the Great Lakes Bioenergy Research Center, Office of Science, Office of Biological and Environmental Research under Award Numbers DE-SC0018409 and DE-FC02-07ER64494; the National Science Foundation under Grant Nos. DEB-1253634, DEB−1442148, and DEB-2110403; and the USDA National Institute of Food and Agriculture Hatch Project Number 1020204. C.T.H. is an H. I. Romnes Faculty Fellow, supported by the Office of the Vice Chancellor for Research and Graduate Education with funding from the Wisconsin Alumni Research Foundation. QMW was supported by the National Natural Science Foundation of China (NSFC) under Grant Nos. 31770018 and 31961133020. C.R.L. holds the Canada Research Chair in Cellular Systems and Synthetic Biology, and his research on wild yeast is supported by an NSERC Discovery Grant.Peer reviewe

BMQ

BMQ: Boston Medical Quarterly was published from 1950-1966 by the Boston University School of Medicine and the Massachusetts Memorial Hospitals

Hybridization and adaptive evolution of diverse Saccharomyces species for cellulosic biofuel production

Additional file 15. Summary of whole genome sequencing statistics

Increased temperature mitigates the effects of ocean acidification in calcified green algae (Halimeda spp.)

The singular and interactive effects of ocean acidification and temperature on the physiology of calcified green algae (Halimeda incrassata, H. opuntia, and H. simulans) were investigated in a fully factorial, 4-week mesocosm experiment. Individual aquaria replicated treatment combinations of two pH levels (7.6 and 8.0) and two temperatures (28 and 31 °C). Rates of photosynthesis, respiration, and calcification were measured for all species both prior to and after treatment exposure. Pre-treatment measurements revealed that H. incrassata displayed higher biomass-normalized rates of photosynthesis and calcification (by 55 and 81 %, respectively) relative to H. simulans and H. opuntia. Furthermore, prior to treatment exposure, photosynthesis was positively correlated to calcification, suggesting that the latter process may be controlled by photosynthetic activity in this group. After treatment exposure, net photosynthesis was unaltered by pH, yet significantly increased with elevated temperature by 58, 38, and 37 % for H. incrassata, H. simulans, and H. opuntia, respectively. Both pH and temperature influenced calcification, but in opposing directions. On average, calcification declined by 41 % in response to pH reduction, but increased by 49 % in response to elevated temperature. Within each pH treatment, elevated temperature increased calcification by 23 % (at pH 8.0) and 74 % (at pH 7.6). Interactions between pH, temperature, and/or species were not observed. This work demonstrates that, in contrast to prior studies, increased temperature may serve to enhance the metabolic performance (photosynthesis and calcification) of some marine calcifiers, despite elevated carbon dioxide concentrations. Thus, in certain cases, ocean warming may mitigate the negative effects of acidification

Responses of calcifying algae (Halimeda spp.) to ocean acidification implications for herbivores

Ocean acidification (OA) can alter the development and physiology of many marine organisms. In addition to calcified invertebrates, studies documenting the responses of calcareous algae are critical because of their prominent role in habitat structure and carbonate production within coastal environments. While many studies report physiological responses, few have examined how OA might ultimately alter interactions with generalist herbivores via shifts in algal chemistry. This study describes a series of experiments that examine the influence of OA on the growth and herbivore defensive compounds of calcareous green algae ( spp.). One experiment was conducted in an open, outdoor seawater system with , while the other was conducted in an indoor, closed system with and . Both experiments were conducted over similar ranges in pCO₂ (300 to 2400 μatm) and monitored shifts in calcification and herbivore defenses (calcium carbonate [CaCO₃] and terpenoid metabolite content). Feedings assays with common sea urchins ( and ) were further conducted to test the degree to which shifts in algal chemistry influence herbivore feeding preferences. Our results were variable among spp., highlighting that OA-induced shifts in chemical composition are species-specific. OA reduced the CaCO₃ content (% dry wt) of yet had no effect on or . Terpenoid metabolite concentrations were unaltered by pCO₂ for all species. Assays with sea urchins revealed that feeding significantly increased on diets of lower CaCO₃ and secondary metabolite content. Our work suggests that certain algal species may be relatively more susceptible to OA-induced shifts in chemical composition, and those shifts have the potential to weaken the efficacy of herbivore defenses. Future research on how OA influences marine plant–herbivore interactions will improve our broader understanding of how OA stands to alter community and ecosystem properties

Population Pharmacokinetics of Rifampin in Pulmonary Tuberculosis Patients, Including a Semimechanistic Model To Describe Variable Absorption ▿

This article describes the population pharmacokinetics of rifampin in South African pulmonary tuberculosis patients. Three datasets containing 2,913 rifampin plasma concentration-time data points, collected from 261 South African pulmonary tuberculosis patients aged 18 to 72 years and weighing 28.5 to 85.5 kg and receiving regular daily treatment that included administration of rifampin (450 to 600 mg) for at least 10 days, were pooled. A compartmental pharmacokinetic model was developed using nonlinear mixed-effects modeling. Variability in the shape of the absorption curve was described using a flexible transit compartment model, in which a delay in the onset of absorption and a gradually changing absorption rate were modeled as the passage of drug through a chain of hypothetical compartments, ultimately reaching the absorption compartment. A previously described implementation was extended to allow its application to multiple-dosing data. The typical population estimate of oral clearance was 19.2 liters·h−1, while the volume of distribution was estimated to be 53.2 liters. Interindividual variability was estimated to be 52.8% for clearance and 43.4% for volume of distribution. Interoccasional variability was estimated for CL/F (22.5%) and mean transit time during absorption (67.9%). The use of single-drug formulations was found to increase both the mean transit time (by 104%) and clearance (by 23.6%) relative to fixed-dose-combination use. A strong correlation between clearance and volume of distribution suggested substantial variability in bioavailability, which could have clinical implications, given the dependence of treatment effectiveness on exposure. The final model successfully described rifampin pharmacokinetics in the population studied and is suitable for simulation in this context