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- Creator:
- Howard, Cecilia M., Sheldon, Nathan D., Loveall, Zachary, Keating, Katarina A., Hong, Jungpyo, Smith, Selena Y., and Passey, Benjamin H.
- Description:
- This study uses an array of stratigraphic, morphological, and geochemical tools to investigate lateral and temporal variability in environmental records preserved by microbialites during a global hothouse environment. It also inverts tools for reconstructing environmental conditions to elucidate ancient microbial processes. Key Points: - The Green River Basin, WY, USA preserves lacustrine microbialites deposited during the Early Eocene Climatic Optimum, a period of high CO2 and temperatures - Morphological and geochemical analyses of these microbialites preserve variable local, regional, and global environmental conditions - Measurements of environmental conditions can be inverted to understand ancient microbial processes, which could be used to inform modeling of microbial influences on carbon cycling and Abstract: The Green River Basin, WY, USA, contains extensive lacustrine microbialite beds that formed during the hothouse Early Eocene Climatic Optimum (53–49 Ma). The records of biological, chemical, and physical processes preserved in these microbialites can inform our understanding of terrestrial conditions in this warm climate, but separating the competing signals of local, regional and global changes is difficult. Studies focusing on individual localities may miss spatial drivers of differences in microbialites. In this study, we used stratigraphic, morphological, and geochemical techniques to study microbialites deposited in the Green River Basin across three million years spanning the peak of the EECO, including samples from two beds covering 13–25 km of lateral extent. These samples cover a broad set of lake conditions as well as local differences such as spring deposits. We found that these microbialites preserved a mixture of conditions such as global hothouse temperatures, regional shifts in lake level, and local variability from sediment and water sources. Morphological and elemental variability were driven primarily by local and regional conditions such as stream, spring, and clastic inputs and water depth. Isotopic data preserved these local and regional changes as well as evidence of global hothouse conditions. Comparison of past [CO2] estimates to reconstructions using organic and inorganic carbon isotopes with clumped isotope-derived temperatures provides evidence for low to moderate microbial growth rates in these microbialite building communities, demonstrating that environmental tools can be inverted to better understand ancient microbial processes. A diverse toolkit was necessary to isolate the individual controls on microbialite records, and comparing across both space and time enabled us to identify local drivers that lead to significant differences from the expected regional signal.
- Keyword:
- Geosciences, Paleoclimate, Microbialite, Stromatolite, Eocene, Paleolake, and Green River Basin
- Citation to related publication:
- Howard, C.M. (2025). Unraveling Records of Time and Environment in Microbial Ecosystems from the Archean to Today (Ph.D. Dissertation). University of Michigan. and Howard, C.M., et al. (in prep). Disentangling Morphological and Chemical Records of Climate, Hydrology, and Diagenesis in Microbialites from the Eocene Green River Basin, WY, USA.
- Discipline:
- Science
-
- Creator:
- Phillips, Chrystian D, DeFazio, R. Anthony, and Moenter, Suzanne M.
- Description:
- Supplemental tables containing the statistical analysis for the manuscript "Sex and time of day alter the interactions between hypothalamic glia and the neural circuits controlling reproduction"
- Discipline:
- Science
-
- Creator:
- Raymond, Matt, Elvati, Paolo, Saldinger, Jacob C, Lin, Jonathan, Shi, Xuetao, and Violi, Angela
- Description:
- Nanoparticles (NPs) formed in nonthermal plasmas (NTPs) can have unique properties and applications. However, modeling their growth in these environments presents significant challenges due to the non-equilibrium nature of NTPs, making them computationally expensive to describe. In this work, we address the challenges associated with accelerating the estimation of parameters needed for these models. Specifically, we explore how different machine learning models can be tailored to improve prediction outcomes. We apply these methods to reactive classical molecular dynamics data, which capture the processes associated with colliding silane fragments in NTPs. These reactions exemplify processes where qualitative trends are clear, but their quantification is challenging, hard to generalize, and requires time-consuming simulations. Our results demonstrate that good prediction performance can be achieved when appropriate loss functions are implemented and correct invariances are imposed. While the diversity of molecules used in the training set is critical for accurate prediction, our findings indicate that only a fraction (15-25%) of the energy and temperature sampling is required to achieve high levels of accuracy. This suggests a substantial reduction in computational effort is possible for similar systems.
- Keyword:
- machine learning, molecular dynamics, nanoparticle, nonthermal plasma, silane, and sticking coefficient
- Citation to related publication:
- Raymond, M., Elvati, P., Saldinger, J. C., Lin, J., Shi, X., & Violi, A. (2025). Machine learning models for Si nanoparticle growth in nonthermal plasma. Plasma Sources Science and Technology. https://doi.org/10.1088/1361-6595/adbae1 and https://arxiv.org/abs/2501.00003
- Discipline:
- Science
-
- Creator:
- Wang, Danhao and Mi, Zetian
- Description:
- Wurtzite ferroelectrics possess transformative potential for next-generation microelectronics. A comprehensive understanding of their ferroelectric properties and domain energetics is crucial for tailoring their ferroelectric characteristics and exploiting their functional properties in practical devices. Despite burgeoning interest, the exact configurations, and electronic structures of domain walls in wurtzite ferroelectrics remain elusive. In this work, we elucidate the atomic configurations and electronic properties of electric-field-induced domain walls in ferroelectric ScGaN. By combining transmission electron microscopy and theoretical calculations, a novel charged domain wall with a buckled two-dimensional hexagonal phase is revealed. Density functional theory calculations confirm that such domain wall structures further give rise to unprecedented mid-gap states within the forbidden band. Quantitative analysis unveils a universal charge-compensation mechanism stabilizing antipolar domain walls in ferroelectric materials, wherein the polarization discontinuity at the 180º domain wall is compensated by the unbonded valence electrons. Furthermore, the reconfigurable conductivity of these domain walls is experimentally demonstrated, showcasing their potential for ultra-scaled device applications. Our findings represent a pivotal advancement in understanding the structural and electronic properties of wurtzite ferroelectric domain walls and lay the groundwork for fundamental physics studies and device applications.
- Keyword:
- Charged domain walls, Scanning transmission electron microscopy, and Density functional theory calculations
- Discipline:
- Science
-
- Creator:
- Brinkmeier, Michelle L, Wang, Su Qing, Pittman, Hannah, Cheung, Leonard Y, and Prasov, Lev
- Description:
- MYRF is a gene that regulates the development and function of the retinal pigmented epithelium (RPE), which play an important role in maintaining photoreceptor structure and function. Mutations in patients have been implicated in eye size disorders, particularly causing a small, but structurally normal eye. We have utilized a molecular technique, single cell RNA sequencing, to investigate how loss of Myrf specifically in the RPE in a mouse model impacts downstream gene expression at three developmental timepoints and used this information to define the role of Myrf in development. Our work identified key cytoskeletal structural genes specific to the RPE, Ermn and Upk3b, and a gene important for the cell survival, Sox10, as critical targets of Myrf. In addition, we have identified and confirmed that the TGFbeta signaling pathway is dysregulated when Myrf is lost during development. This pathway is particularly relevant in RPE health and eye growth. Our electron microscopy and histologic analyses also confirm a defect in RPE structure and function. We place MYRF within a hierarchy of genes involved in RPE development and introduce novel candidate genes for further study as retinal degeneration and nanophthalmos candidate genes.
- Keyword:
- ERMN, MYRF, Hypopigmentation, TMEM98, SOX10, Retinal Pigment Epithelium (RPE), and Retinal degeneration
- Discipline:
- Science
-
- Creator:
- Kersten, Roland D, Ousley, D, Wang, Xiaofeng, Chigumba, Desnor N, Davis, Dulciana, Shafiq, Khadija, McDonough, Kali, Mydy, Lisa M, and Sexton, Jonathan Z
- Description:
- Moroidins are plant ribosomally synthesized and posttranslationally modified peptides (RiPPs) called burpitides biosynthesized from copper-dependent peptide cyclases. The bicyclic structure of moroidins contains (1) a stephanotic acid scaffold with a Leu-Cꞵ-Trp-indole-C6-crosslink and (2) a C-terminal ring formed by a Trp-indole-C2-His-imidazole-N1-crosslink. Moroidin is cytotoxic to H1437 non-small cell lung adenocarcinoma cells in vitro, underscoring the potential of stephanotic acid-type burpitides as anticancer lead structures and the importance of exploring diversification strategies to discover analogs with enhanced bioactivity. We mined the transcriptome of 7579 plant species from 498 plant families to identify moroidin analogs with novel second-ring structures and the cyclases responsible for their biosynthesis. A search of >27000 candidate burpitide cyclases reveals two stephanotic acid-type burpitides in plants with new second-ring crosslinks derived from posttranslational modification: Glechomanin from ground ivy (Glechoma hederacea) with a C-C-crosslink between a C-terminal tryptophan-indole-C6 and the β-carbon of a valine, and Mercurialin from annual mercury (Mercurialis annua) featuring a C-O-crosslink between a C-terminal tyrosine-phenol hydroxy and the β-carbon of a phenylalanine, respectively. Furthermore, our transcriptomics-guided burpitide genotyping enabled isolation of a moroidin analog from water chickweed (Stellaria aquatica), which exhibits a ten-fold higher in vitro cytotoxicity than moroidin and selective toxicity against H1437 lung adenocarcinoma cells. We demonstrate that plant transcriptome mining can expand the medicinal chemistry toolbox for chemical and biological exploration of burpitide lead structures.
- Keyword:
- RNA-seq, de novo transcriptome assembly, plant peptides, natural products, and RiPP
- Citation to related publication:
- in preparation
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:238369 (NOTOTRITON PICADOI) - Limbs. Raw Dataset includes 1601 TIF images (each 461 x 741 x 1 voxel at 0.01300206 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:238369 (NOTOTRITON PICADOI) - Limbs. Reconstructed Dataset includes 0.013002 TIF images (each 461 x 741 x 1 voxel at 0.013002 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, NOTOTRITON PICADOI, 1987030882, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987030882
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:194448 (PSEUDOTRITON RUBER) - Limbs. Raw Dataset includes 1601 TIF images (each 372 x 652 x 1 voxel at 0.03100344 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:194448 (PSEUDOTRITON RUBER) - Limbs. Reconstructed Dataset includes 0.031003 TIF images (each 372 x 652 x 1 voxel at 0.031003 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PSEUDOTRITON RUBER, 1987126336, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987126336
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Raw Dataset includes 1601 TIF images (each 642 x 2000 x 1 voxel at 0.02199678 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction., Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Reconstructed Dataset includes 0.021997 TIF images (each 642 x 2000 x 1 voxel at 0.021997 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction., and Scan of specimen ummz:herps:143736 (PSEUDOEURYCEA BELLII) - Limbs. Reconstructed Dataset includes 0.021997 TIF images (each 642 x 2000 x 1 voxel at 0.021997 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, PSEUDOEURYCEA BELLII, 1987206748, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987206748
- Discipline:
- Science
-
- Creator:
- University of Michigan Museum of Zoology
- Description:
- Scan of specimen ummz:herps:137395 (OEDIPINA POELZI) - Limbs. Raw Dataset includes 1601 TIF images (each 514 x 670 x 1 voxel at 0.02500204 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction. and Scan of specimen ummz:herps:137395 (OEDIPINA POELZI) - Limbs. Reconstructed Dataset includes 0.025002 TIF images (each 514 x 670 x 1 voxel at 0.025002 mm resolution, derived from 1601 scan projections), xtek and vgi files for volume reconstruction.
- Keyword:
- Animalia, Chordata, Amphibia, CAUDATA, PLETHODONTIDAE, OEDIPINA POELZI, 1987178002, computed tomography, X-ray, and 3D
- Citation to related publication:
- For more information on the original UMMZ specimen, see: https://www.gbif.org/occurrence/1987178002
- Discipline:
- Science