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- Creator:
- Stringer, Kathleen A.
- Description:
- These data were produced from the survival analysis of the pre-treatment metabolomics data generated from the Phase II clinical trial of L-carnitine treatment for septic shock (the RACE trial - see https://clinicaltrials.gov/ct2/show/NCT01665092). The results based on respective acetylcarnitine or valine concentration are presented (pdf). The csv files contain the at risk numbers from the Kaplan-Meier survival analysis. These findings described in our manuscript: Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. and All of the metabolomics data are available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org which is supported by NIH grant U2C-DK119886 and where it has been assigned Project ID (accession number ST001319). The data can be accessed directly via its Project DOIs: (DOI: http://dx.doi.org/10.21228/M8VX0Z).
- Keyword:
- sepsis, septic shock, survival, mortality, metabolomics, and pharmacometabolomics
- Citation to related publication:
- Puskarich, M. A., Jennaro, T. S., Gillies, C. E., Evans, C. R., Karnovsky, A., McHugh, C. E., Flott, T. L., Jones, A. E., Stringer, K. A., & Investigators, O. behalf of the R. T. (2021). Pharmacometabolomics Identifies Candidate Predictor Metabolites of an L-carnitine Treatment Mortality Benefit in Septic Shock. (Preprint) https://doi.org/10.1101/2021.01.28.21250687 and Puskarich MA, Jennaro TS, Gillies CE, et al; the RACE Trial Investigators. Pharmacometabolomics identifies candidate predictor metabolites of an L-carnitine treatment mortality benefit in septic shock. Clin Transl Sci. 2021; 14: 2288–2299. https://doi.org/10.1111/cts.13088
- Discipline:
- Health Sciences
- Creator:
- Ludlow, Andrew
- Description:
- Single molecule long read RNA/cDNA sequencing of TERT revealed 45 TERT mRNA variants including 13 known and 32 novel variants. Among the variants, TERT Delta 2-4, which lacks exons 2-4 but retains the original open reading frame, was selected for further study. Induced pluripotent stem cells and cancer cells express higher levels of TERT Delta 2-4 compared to primary human bronchial epithelial cells. Overexpression of TERT Delta 2-4 enhanced clonogenicity and resistance to cisplatin-induced apoptosis. Knockdown of endogenous TERT Delta 2-4 in Calu-6 cells reduced clonogenicity and resistance to cisplatin. Our results suggest that TERT Delta 2-4 enhances cancer cells’ resistance to intrinsic apoptosis. RNA sequencing following knockdown of Delta 2-4 TERT indicates that translation is downregulated and that mitochondrial related proteins are upregulated compared to controls.
- Keyword:
- TERT, Alternative splicing, Telomere, and Telomerase
- Citation to related publication:
- Kim, J.J., Ahn, A., Ying, J.Y. et al. Discovery and characterization of a novel telomerase alternative splicing isoform that protects lung cancer cells from chemotherapy induced cell death. Sci Rep 15, 6787 (2025). https://doi.org/10.1038/s41598-025-90639-3
- Discipline:
- Science
- Creator:
- Ludlow, Andrew and Kim, Jeongjin
- Description:
- Part of the regulation of telomerase activity includes the alternative splicing (AS) of the catalytic subunit telomerase reverse transcriptase (TERT). Although a therapeutic window for telomerase/TERT inhibition exists between cancer cells and somatic cells, stem cells express TERT and rely on telomerase activity for physiological replacement of cells. Therefore, identifying differences in TERT regulation between stem cells and cancer cells is essential for developing telomerase inhibition-based cancer therapies that reduce damage to stem cells. In this study, we measured TERT splice variant expression and telomerase activity in induced pluripotent stem cells (iPSCs), neural progenitor cells (NPCs), and non-small cell lung cancer cells (NSCLC, Calu-6 cells). We observed that a NOVA1-PTBP1-PTBP2 axis regulates TERT alternative splicing (AS) in iPSCs and their differentiation into NPCs. We also found that splice-switching of TERT, which regulates telomerase activity, is induced by different cell densities in stem cells but not cancer cells. Lastly, we identified cell type-specific splicing factors that regulate TERT AS. Overall, our findings represent an important step forward in understanding the regulation of TERT AS in stem cells and cancer cells. These data and subsequent studies may reveal a splicing factor(s) or their binding site(s) that could be targeted with small molecule drugs or antisense oligonucleotides, respectively, to reduce telomerase activity in cancer cells and promote durable cancer remissions.
- Keyword:
- Telomere, telomerase, TERT, alternative RNA splicing
- Citation to related publication:
- Kim JJ, Sayed ME, Ahn A, Slusher AL, Ying JY, et al. (2023) Dynamics of TERT regulation via alternative splicing in stem cells and cancer cells. PLOS ONE 18(8): e0289327. https://doi.org/10.1371/journal.pone.0289327
- Discipline:
- Science
- Creator:
- King, Katelyn B., Fujisaki-Manome, Ayumi, Brant, Cory, and Alofs, Karen
- Description:
- This collection includes raster layers (as a geodatabase) with ice metrics for each of the Great Lakes representing the historical time period of 1898-1960. One metric is spatial mean ice duration (the number of days per year when the lake was frozen) and the other is coefficient of variation of ice duration (variability across years).
- Keyword:
- Great Lakes, Ice , Ice duration, Ice variability, Historical , Huron, Ontario, Erie, Michigan, and Superior
- Discipline:
- Science
- Creator:
- Bu, Xiangyun, Geng, Yihao, Yin, Siyuan, Luo, Liyan, Aubin, Cameron A., and Moore, Talia Y.
- Description:
- Suction is a useful strategy to grasp objects or anchor a body, especially when prolonged contact is desired. For passive suction cups, detachment requires manual delamination, which cannot occur autonomously. Active suction cups detach via equalizing pressure in the suction cavity with the surrounding environment, either by adding fluid (e.g., from a compressed air source) or reducing the cavity volume. While this detachment mechanism can be autonomous, it is inefficient, resulting in a net zero or loss of fluid. A more efficient detachment mechanism would enable multiple iterations of attachment and detachment without requiring additional fluid. To address this need, we designed a suction cup with a secondary release chamber embedded in the contact ring. The release chamber triggers delamination by deforming the shape of the contact ring. Through empirical testing, we found the optimal location and geometry of the release chamber. Our design allows for reliable detachment with a 5~mL decrease in release chamber volume, regardless of the adhesive suction force. Because the release chamber is a closed system, attachment and detachment results in net gain of fluid. Therefore, we propose a novel secondary benefit of adhesion via suction: harvesting fluid to power other pressure-driven soft robotic systems. and This ZIP archive includes CAD models for: The exploded view of the suction cup assembly and the molds of all suction cup configurations shown in Figure 4 of the paper: (b) Different release chamber locations (c) Different membrane thicknesses (d) Constant volume with varying release chamber areas (e) Constant area with varying release chamber heights (f) Constant height with varying release chamber areas
- Keyword:
- suction, adhesion, energy harvesting, and soft robotics
- Citation to related publication:
- Xiangyun Bu, Yihao Geng, Siyuan Yin, Liyan Luo, Cameron A. Aubin, Talia Y. Moore (2025) "Release Chamber Enables Suction Cup to Delaminate and Harvest Fluid" IEEE RoboSoft.
- Discipline:
- Engineering
- Creator:
- Howard, Cecilia M. and Sheldon, Nathan D.
- Description:
- This study uses a compilation of microbialite occurrences in the Archean and Paleoproterozoic from the literature to investigate how depositional environment changed across environmental shifts such as the Great Oxidation Event and the Huronian Glaciations. Key Points: - We compiled microbialite occurrences from the Archean and Paleoproterozoic with broad depositional environment information, which has not previously been incorporated in larger compilations of occurrences. - Tidal and other terrestrially-influenced settings comprise the majority of the early microbialite record, even across major environmental shifts and Abstract: Changes in microbialite abundance during the Archean and Paleoproterozoic have been attributed to a variety of environmental and biological factors. Past work looking at large-scale patterns of microbialite abundance generally assumes shallow marine deposition rather than incorporating specific settings, however, there is significant variance in conditions that might impact microbialite formation and preservation between marine, tidal, and terrestrial environments. We compiled microbialite occurrences from the Archean and Paleoproterozoic with integrated depositional environment information in order to assess how microbialite development and preservation changed across different settings. Microbially induced sedimentary structures formed a significant part of the record, but their identification primarily in conjunction with stromatolites rather than independently suggests that they may be undercounted. Broad trends in abundance were similar to previous compilations, but critically, we found that the majority of microbialites from this period formed in tidal environments. The proportion of terrestrially-influenced (including tidal) microbialites increased during periods of craton development in the Neoarchean and mid-Paleoproterozoic, with increases in marine microbialite abundance trailing. Tidal microbialite abundance also recovered more quickly than marine abundance following the Great Oxidation Event and Huronian Glaciations.
- Keyword:
- Microbialite, Stromatolite, Archean, Paleoproterozoic, Geosciences, and Tidal
- 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. and Sheldon, N.D. (in prep). Chapter 2 Microbialite Niches across the Archean and Paleoproterozoic.
- Discipline:
- Science
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Growth Analysis (GROW) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish growth cards document fish that were aged and measured during fish surveys. The data that were transcribed from these cards and included in this dataset (grow_data.csv) are for each fish species: the number of fish measured in each age group, and the minimum, maximum, and average length of the fish for each age group. The final growth dataset includes length-at-age information for 36 different species (grow_species_table). For a description of all fields of this data table see grow_datadictionary.
- Keyword:
- fish, lake, growth, length, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and Grabda, E.E., Flood, P.J., King, K.B.S., Breck, J.E., Wehrly, K.E., and Alofs, K.M. 2025. Mismatch between climate-based bioenergetics model of fish growth and long-term and regional-scale empirical data. Canadian Journal of Fisheries and Aquatic Sciences. 82: 1-15. https://doi.org/10.1139/cjfas-2024-0266
- Discipline:
- Science
- Creator:
- King, Katelyn , Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael , and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Lake Summary (SUMM) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Lake summary cards that we transcribed and curated include habitat information for a lake as well as observed fish species (summ_data.csv). These variables include anthropogenic lake characteristics such as fishing intensity, shoreline structures, and dams; lake morphometric characteristics like depth and area; as well as in situ measures of temperature, dissolved oxygen, and Secchi depth. Many of the characteristics were listed as a range, and therefore, have a column for minimum and maximum in the data file (e.g. temp_surface_min_c and temp_surface_max_c). In addition, the lake summary cards listed the fish species present, so the csv file includes columns with the fish species common name (summ_species_table) and corresponding values are either a ‘1’ representing presence of a species or ‘0’ representing absence. For a full description of all the fields of this data table see summ_datadictionary.
- Keyword:
- lake, fish, Secchi, temperature, nutrients, oxygen, shoreline, habitat, dams, lake depth, lake area, and fishing intensity
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review
- Discipline:
- Science
- Creator:
- King, Katelyn, Schell, Justin, Alofs, Karen, Thomer, Andrea, Wehrly, Kevin, Lenard, Michael, and Lopez-Fernandez, Hernan
- Description:
- Michigan lakes are an important resource, however, their ecosystems are declining and projected to continue to face further impacts under future land use and climate change. Understanding how lake ecosystems respond to environmental stressors and management actions is critical for identifying resilient lakes and developing adaptation strategies. However, the ability to manage lakes is hampered by a lack of historical information. Historical lake data in Michigan were originally archived as index cards at the Michigan Department of Natural Resources. All of the images of these cards are stored in this collection, Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys, and the images for this specific dataset are stored in the CHANGES Project- Fish Collection (FISHc) dataset. The CHANGES project used a crowd sourcing platform called Zooniverse to transcribe at least basic information (i.e. dates, collected by) from all of these cards. Some of the card types, such as the one in this dataset, were prioritized to transcribe to produce a usable (i.e. machine-readable, uniform, and standardized) historical dataset. and Fish collection card types include targeted and non-targeted fisheries surveys by the Department of Natural Resources and this information was transcribed and curated into a csv file (fishc_data.csv). These records include information on the gear types used, the area surveyed and the length and mesh size of nets fished. The number and common name of fish species caught were recorded as well and included in a species table (fishc_species_table). A description of all data fields can be found in the fishc_datadictionary.
- Keyword:
- lake , fish, gear, abundance, and Michigan
- Citation to related publication:
- King, K.B.S., Schell, J, Wehrly, K.E., Lenard, M., Singer, R., López-Fernández, H., Thomer, A.K., & Alofs, K.M. Community science helps digitize 78 years of fish and habitat data for thousands of lakes in Michigan, USA. under review and King, K.B.S, Giacomini, H.C., Wehrly, K., López-Fernández, H., Thomer, A.K., & Alofs, K.M. (2023). Using historical fish catch data to evaluate predicted changes in relative abundance in response to a warming climate. Ecography. 2023:8. https://doi.org/10.1111/ecog.06798
- Discipline:
- Science
- Creator:
- Sutton, Etienne, Snapp, Sieglinde, Morrone, Vicki, and Blesh, Jennifer
- Description:
- Cover crops support ecosystem services in agroecosystems, but their performance can be highly variable. Functional trait ecology provides a useful framework for understanding variation in cover crop performance across different growing conditions. However, trait variation within species remains understudied compared to variation between species. In a two-year experiment, we measured nine functional traits for three cover crop species across 13 fields on working farms that spanned a gradient of soil health. Each field contained three cover crop treatments: a functionally diverse mixture of cereal rye (Secale cereale), crimson clover (Trifolium incarnatum), and dwarf-essex rapeseed (Brassica napus), and rye and clover monocrops. We evaluated i) the magnitude and relative importance of intraspecific and interspecific trait variation; ii) which soil health indicators best explained trait variation; and iii) whether interspecific interactions in mixture induced trait plasticity. Despite strong trait contrasts between species, intraspecific trait variation comprised 50% of total trait variation, on average. Trait variation was best explained by particulate organic matter nitrogen (POM N), soil phosphorus, pH, and permanganate oxidizable carbon for clover; by POM N and soil phosphorus for rye; and by POM N for dwarf essex. Rye and clover also showed significant trait plasticity in mixture relative to monocrop treatments. Our study demonstrates that intraspecific and interspecific trait variation are equally important, and that examining trait variation within species can improve the ability to predict cover crop outcomes. This information can inform cropping system design in distinct contexts to promote success of component species and complementary ecosystem functions.
- Keyword:
- cover crop, functional trait, soil health, mixture, species interactions, and intraspecific trait variation
- Citation to related publication:
- Sutton, E., Snapp, S., Morrone, V., & Blesh, J. (2025). Cover crop functional trait plasticity in response to soil conditions and interspecific interactions. Plant and Soil. https://doi.org/10.1007/s11104-025-07471-x
- Discipline:
- Science