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- Creator:
- Kharbush, Jenan, Rahman, Raisha, and Pearson, Ann
- Description:
- Amino acids are the primary nitrogen-containing compounds in cells, participating in various metabolic processes such as protein synthesis and degradation into other nitrogenous compounds. Compound-specific nitrogen isotope analysis of amino acids in environmental samples can provide insight into nitrogen sources, cycling, and tropic modifications in ecosystems. However, we lack comprehensive understanding of N utilization patterns in microorganisms, which are the site of nitrogen assimilation in biological systems, due to the varied and complex mechanisms by which microbes can acquire and metabolize nitrogen-containing compounds. δ15N measurements for free intracellular amino acids and protein-bound amino acids for environmentally-relevant microbial groups may aid in untangling the biochemical processes involved in amino acid metabolism performed by these microbial communities. Here, we report intracellular amino acid δ15N values for R. palustris, a metabolically versatile anoxygenic phototrophic bacterium.
- Keyword:
- amino acids, nitrogen stable isotope analysis, compound-specific isotope analysis, and batch culture
- Discipline:
- Science
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- Creator:
- Crowell, Hayley L . , Curlis, John David, Weller, Hannah I., and Davis Rabosky, Alison R.
- Description:
- Ultraviolet (UV) wavelengths invisible to humans are primarily studied in the context of reproduction and social signaling. This narrow focus can arise from bias in taxa studied, which are often brightly colored in human-visible wavelengths. Our research describes undocumented UV color patterns across 110 diverse species of Western Hemisphere snakes and tests the hypothesized roles of reproduction versus predator avoidance in the evolution of UV coloration. Phylogenetically-informed tests of life stage, sex, and habitat showed unexpected support for the predator defense hypothesis, with pronounced differences in snake conspicuousness explained by UV coloration. UV reflectance was not predictable from any aspect of visible color pattern, suggesting high potential for transformative discoveries in other “cryptically-colored” lineages across the tree of life.
- Keyword:
- color, ecology, evolution, predators, snakes, and ultraviolet
- Citation to related publication:
- Crowell, H. L., Curlis, J. D., Weller, H. I., & Davis Rabosky, A. R. (2024). Ecological drivers of ultraviolet colour evolution in snakes. Nature Communications, 15(1), 5213. http://doi.org/10.1038/s41467-024-49506-4
- Discipline:
- Science
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Jordan pterosaur CT scans & 3D models
User Collection
- Creator:
- Wilson Mantilla, Jeffrey A.
- Description:
- This collection includes computed tomography (CT) scans and 3D models of humeral remains from two Late Cretaceous pterosaurs from Jordan: Inabtanin alarabia (YUPC-INAB-6-001–010) and Arambourgiania philadelphiae (YUPC-RUSEIFA-1). Both specimens are accessioned to Yarmouk University, in the Hashemite Kingdom of Jordan. For inquiries about access, please contact Jeff Wilson Mantilla ( wilsonja@umich.edu) or Iyad Zalmout ( izalmout@ksu.edu.sa). Casts of selected elements of Inabtanin and Arambourgiania are available at the University of Michigan Museum of Paleontology. and The Jordanian pterosaurs were described in: Rosenbach, K. L., D. M. Goodvin, M. G. Albshysh, H. A. Azzam, A. A. Smadi, H. A. Mustafa, I. S. A. Zalmout, and J. A. Wilson Mantilla. [in press] New pterosaur remains from the Late Cretaceous of Afro-Arabia provide insight into flight capacity of large pterosaurs. Journal of Vertebrate Paleontology.
- Keyword:
- Jordan pterosaur cretaceous vertebrate gondwana afro-arabia paleontology
- Discipline:
- Science
5Works -
- Creator:
- Nagesan, Ramon S, Crowell, Hayley L, Kolmann, Matthew, and Davis Rabosky, Alison R
- Description:
- The datasets associated with this deposit are micro-CT data. These data were generated to be better understand how diffusion iodine contrast enhanced (diceCT) CT scanning can differ amongst major groups of vertebrates. This study stained fish, mammals, reptiles, and amphibians with either H20-Lugol's iodine or Ethylic-Lugol's iodine and measured the differences in the resulting stained soft tissue contrast levels and iodine uptake.
- Keyword:
- Zoology
- Discipline:
- Science
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- Creator:
- Hutson, Abby , Fujisaki-Manome, Ayumi, and Glassman, Ryan
- Description:
- The data herein resulted from a study documenting the characteristics of extratropical cyclones that pass through the Great Lakes Region (GLR) and how the cyclones are trending with time. All scripts used to create these data can be found in the Github repository https://github.com/abkenyon/GLStormTrends_2024. storm_track_slp_xxxx.npz - Structured numpy files containing all storm tracks identified over one cold season, regardless of whether the storm encountered the GLR, with the file name indicating the year on which the season ended. storm_composite_xxxx-xxxx.nc - NetCDF files containing one seasonal cyclone composite with different atmospheric variables. A composite is storm-centered, and covers a 20 degree square area.
- Keyword:
- Extratropical Cyclones, Climate Trends, Great Lakes Climate
- Citation to related publication:
- Hutson A, Fujisaki-Manome A, Glassman R.: Historical Trends in Cold-Season Mid-Latitude Cyclones. Geophysical Research Letters. In press..
- Discipline:
- Science
-
- Creator:
- Sosa Alfaro, Victor, Palomino, Hannah, Liu, Sophia, Lemuh Njimoh, Cybele, and Lehnert, Nicolai
- Description:
- Pharmaceutical synthesis has been a driving force behind advancements in the field of biocatalysis. In this paper, we report the further optimization of the heme protein YfeX for regio- and stereoselective carbene transfer reactions using mutagenesis to explore the role of important amino acids in the active site for catalysis. In this way, we identified YfeX variants that are efficient and selective carbene transferases towards primary and secondary amines, olefins, and indoles. Molecular Dynamic simulations reveal that mutations within the secondary coordination sphere induce distinct alterations in the conformation and electrostatic properties within the active site. These changes, in turn, affect substrate positioning both within the active site and at its entrance, which explains the distinct and sometimes surprising variations in selectivity observed experimentally between select YfeX variants. Our results show that the I230A single variant identified here is one of the most active N-H insertion catalysts known, producing >90% yields in only 1 hour (typical reaction times in the literature are 8 – 24 hours). On the other hand, the R232A variant catalyzes the C-H insertion of unprotected indole in 21% yield. The capacity to selectively act on unprotected indole offers a cost-effective, environmentally-friendly approach for late-stage functionalization of indoles and similar precursors in pharmaceuticals. In addition, YfeX is an efficient and fast biocatalyst that shows no structural degradation or heme loss during turnover, underscoring YfeX’s robustness as a viable biocatalyst for both industrial and academic applications.
- Keyword:
- Biocatalysis, Heme proteins, Carbene transfer reactions, Peroxidases , N-H insertion, Cyclopropanation, and Molecular dynamics
- Citation to related publication:
- Sosa Alfaro, Victor; Palomino, Hannah; Liu, Sophia; Lemuh Njimoh, Cybele; Lehnert, Nicolai, "Combined Experimental and Molecular Dynamics Approach Towards a Rational Design of the YfeX Biocatalyst for Enhanced Carbene Transferase Reactivity", Catalysis Science & Technology 2024, 14, DOI: 10.1039/D3CY01489D
- Discipline:
- Science
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- Creator:
- Shin, Satbyeol and Gronewold, Andrew D.
- Description:
- - Temporal coverage: 1/1/1941 to 12/31/2020 - Spatial coverage: Entire Great Lakes basin - Output format: The original modeling outputs are provided at a 1 km/daily resolution in NetCDF format. There are two kinds of modeling outputs, which are land surface modeling outputs (LDASOUT) and hydrological modeling outputs (CHRTOUT). The author recommend using the netCDF Operators (NCO) program for data processing. For visualization and plotting, the author recommend using software like MATLAB, Python or R.
- Keyword:
- Hydrologic modeling, Overland precipitation, Air temperature, Evapotranspiration, Snow Water Equivalent, Runoff, Surface Soil moisture, St. Lawrence river, Great Lakes basin, Reanalysis data, WRF-Hydro, and ERA-5
- Discipline:
- Science
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- Creator:
- Fahim, Abigail T
- Description:
- The purpose of this research is to compare levels of unprenylated Rab proteins in CHM-/- iPSC-RPE cells with and without compactin. Compactin is a statin that inhibits prenyl synthesis and thereby reduces prenylation overall and has an unbiased inhibitory effect on all protein prenylation. So we expect that for Rabs that are already poorly prenylated at baseline in choroideremia RPE cells, compactin will have minimal effect. However, for Rabs that are efficiently prenylated at baseline, compactin should have a much greater effect. And then we used tandem mass tag spectrometry to compare the ratio of each unprenylated Rab in compactin-treated choroideremia cells vs untreated choroideremia cells. In the spreadsheet, "F8" refers to the CHM-/- iPSC-RPE cells and "WT" refers to the isogenic control iPSC-RPE cells. In the "Proteins only" tab, column M shows the ratio of each protein in "DMSO" (untreated) choroideremia cells compared to Compactin-treated choroideremia cells. Compactin-treated control cells are also included in other columns. Untreated control cells could not be used because prenylation is so efficient in these cells, there is almost no material available after doing the in vitro prenylation assay (i.e. almost no unprenylated proteins to biotinylate). The column descriptions can be found in the sheet titled "Explanations." In addition, AAs= number of amino acids in the protein, MW= molecular weight of the protein, and pI= isoelectric point. The software is set to report abundance values only when certain criteria are met (S/N of 6, unique peptide etc). A value is NOT reported when the data for a protein fall below these criteria and the cell is instead left blank.
- Keyword:
- choroideremia, retinal pigment epithelium, prenylation, and Rab protein
- Citation to related publication:
- Raeker, M.O., Perera, N.D., Karoukis, A.J., Chen, L., Feathers, K.L., Ali, R.R., Thompson, D.A., Fahim, A.T. Reduced retinal pigment epithelial autophagy due to loss of Rab12 prenylation in a human iPSC-RPE model of choroideremia. Cells, manuscript accepted, in press.
- Discipline:
- Health Sciences and Science
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- Creator:
- Yu, Chi-Lin
- Description:
- The study aims to describe how children worldwide progress through a sequence of theory of mind understandings in their development of insights into persons and minds. The focus is on the studies using Wellman and Liu's (2004) Theory of Mind Scale. A comprehensive search was run in PsycINFO, PsycArticles, Child Development & Adolescent Studies, Education Abstracts, Family & Society Studies Worldwide, and Social Sciences Abstracts. The dataset includes 91 studies using Wellman and Liu's (2004) Theory of Mind Scale.
- Keyword:
- meta-analysis, theory of mind, social cognitive development, culture, and conceptual sequences
- Discipline:
- Science
-
- Creator:
- Abdul Kareem, Tariq
- Description:
- The four specimens (GSI SR/YS/1, GSI SR/YS/2, GSI SR/YS/3, and GSI SR/YS/4) are identified as tail clubs that are attributed to the basal sauropod Kotasaurus yamanpalliensis. The specimens were collected by the Geological Survey of India Southern Region (GSI SR) and, in 2018, the specimens were studied as a collaboration between GSI SR and the University of Michigan Museum of Paleontology. The specimens are housed in the collections of the GSI SR (Hyderabad, India).
- Keyword:
- Paleontology, India, Sauropod, Dinosaurs, Tail club, and Jurassic
- Citation to related publication:
- Kareem, T. A., S. Chakraborty, and J. A. Wilson Mantilla. (in prep.) Sauropod tail clubs from the Kota Formation (Early to Middle Jurassic) of India and their implications for early sauropod evolution. Journal of Vertebrate Paleontology
- Discipline:
- Science