Kraus, B. Frances; Gao, Lan; Hill, K. W.; Bitter, M.; Efthimion, P. C.; Hollinger, R.; Wang, Shoujun; Song, Huanyu; Nedbailo, R.; Rocca, J. J.; Mancini, R. C.; MacDonald, M. J.; Beatty, C. B.; Shepherd, R.
Hill, K. W.; Gao, L.; Kraus, B. F.; Bitter, M.; Efthimion, P. C.; Pablant, N. A.; Schneider, M. B.; Thorn, D. B.; Chen, H.; Kauffman, R. L.; Liedahl, D. A.; MacDonald, M. J.; MacPhee, A. J.; Scott, H. A.; Stoupin, S.; Doron, R.; Stambulchik, E.; Maron, Y.; Lahmann, B.
Bourrianne, Philippe; Chidzik, Stanley; Cohen, Daniel; Elmer, Peter; Hallowell, Thomas; Kilbaugh, Todd J.; Lange, David; Leifer, Andrew M.; Marlow, Daniel R.; Meyers, Peter D.; Normand, Edna; Nunes, Janine; Oh, Myungchul; Page, Lyman; Periera, Talmo; Pivarski, Jim; Schreiner, Henry; Stone, Howard A.; Tank, David W.; Thiberge, Stephan; Tully, Christopher
Abstract:
The detailed information on the design and construction of the Princeton Open Ventilation Monitor device and software are contained in this data repository. This information consists of the electrical design files, mechanical design files, bill of materials, human subject recording and analysis code, and a copy of the code repository for operating the patient monitors and central station.
This entry contains video files and tabular data associated with the PhD dissertation titled: The Evolution and Regulation of Morphological Complexity in the Vibrios.
Severe acute respiratory coronavirus 2 (SARS-CoV-2), the causative agent of COVID-19, is of zoonotic origin. Evolutionary analyses assessing whether coronaviruses similar to SARS-CoV-2 infected ancestral species of modern-day animal hosts could be useful in identifying additional reservoirs of potentially dangerous coronaviruses. We reasoned that if a clade of species has been repeatedly exposed to a virus, then their proteins relevant for viral entry may exhibit adaptations that affect host susceptibility or response. We perform comparative analyses across the mammalian phylogeny of angiotensin-converting enzyme 2 (ACE2), the cellular receptor for SARS-CoV-2, in order to uncover evidence for selection acting at its binding interface with the SARS-CoV-2 spike protein. We uncover that in rodents there is evidence for adaptive amino acid substitutions at positions comprising the ACE2-spike interaction interface, whereas the variation within ACE2 proteins in primates and some other mammalian clades is not consistent with evolutionary adaptations. We also analyze aminopeptidase N (APN), the receptor for the human coronavirus 229E, a virus that causes the common cold, and find evidence for adaptation in primates. Altogether, our results suggest that the rodent and primate lineages may have had ancient exposures to viruses similar to SARS-CoV-2 and HCoV-229E, respectively. Included in this repository are the instructions and corresponding code required to build the dataset and run the analysis in the manuscript.
