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- 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
-
Great Lakes Historical Ice Dynamics
User Collection
- 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
1Works -
- 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
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- 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
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- 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
-
- Creator:
- Quartey, Nii-Boi A and Liemohn, Michael W
- Description:
- This dataset contains results from the BATS-R-US multispecies MHD code simulating the solar wind interaction at Mars at the following orbital and solar cycle locations: solar maximum at perihelion, solar maximum at aphelion, solar minimum at perihelion, solar minimum at aphelion. These simulations contain results with and without the crustal magnetic fields and includes variables such as the magnetic field and ion density., 2025-02-25: The metadata in this dataset has been updated in response to reviewer comments during the journal review process. Additional Tecplot 360 EX file containing MAVEN multifluid MHD simulation data added. The multifluid MHD simulation result from this result is from the MAVEN simulation library. The simulation result is run for 25,000 iterations., and 2025-04-28: The following files have been replaced with the following as these files contain the nominal solar wind conditions: z_0_mhd_permax.plt -> permax_3d.plt z_0_mhd_aphmax.plt -> aphmax_3d.plt z_0_mhd_permin.plt -> permin_3d.plt z_0_mhd_aphmin.plt -> aphmin_3d.plt The following file has been removed as the slice can be extracted from permax_3d.plt: x_0_mhd_permax.plt
- Keyword:
- mars, magnetosphere, magnetotail, current sheet, asymmetry, multispecies, multifluid, MHD, and MAVEN
- Citation to related publication:
- https://doi.org/10.1029/2024JA033445
- Discipline:
- Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- Studies of fate patterning during development typically emphasize cell-cell communication via diffusible chemical signals. Recent experiments on stem cell colonies (see Xue et al. Nature Materials 2018), however, suggest that in some cases mechanical stresses, rather than secreted chemicals, enable long-ranged cell-cell interactions that specify positional information and pattern cell fates. The authors of this earlier publication reported a set of in vitro experiments in which uniformly supplied chemical media induced spatially patterned fates in cell colony in a disc geometry. They provided significant evidence that inter-cellular mechanical interactions, as well as mechanical interactions between cells and the substrate, play an important role in this in vitro differentiation process. As part of these experiments, they showed that the concentric width of the outer fate domain is approximately constant as the colony diameter is increased from 300 um to 800 um. In this subsequent publication, we propose a mathematical model for this fate patterning process and explore how the fate pattern depends on substrate stiffness. The experimental images of cell colonies, both for varying cell colony diameter (from Xue et al. Nature Materials 2018) and for varying substrate stiffness (data generated for the publication linked to these data), are provided here. Each example has an image for PAX3 signal (marker for outer fate domain; Paired box gene 3) and an image for DAPI signal (staining nuclei; 4′,6-diamidino-2-phenylindole).
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Science and Engineering
-
- Creator:
- Nunley, Hayden and Lubensky, David K
- Description:
- In a previous study (Xue et al. Nature Materials 2018), the authors showed that a key fate patterning event in vertebrate development can be reproduced in an in vitro stem cell culture. They further showed that this in vitro fate pattern seems to depend on mechanical signals rather than secreted chemical signals. In this follow-up study, a mathematical model of this process is proposed. The code in this deposit is for the simulation of this mathematical model in various cell layer geometries and substrate geometries. These geometries include a 1D cell layer, quasi-1D stripe geometry, disc geometry (all on a very thin substrate or a substrate composed of microposts) as well as a 1D cell layer on a finite-thickness substrate. Our model implies that the width of the outer fate domain varies non-monotonically with substrate stiffness, a prediction that we confirm experimentally.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, and Force sensing
- Citation to related publication:
- Nunley H, Xue X, Fu, J, Lubensky, DK. Generation of fate patterns via intercellular forces. BioRxiv 442205 [Preprint]. April 30, 2021 [cited 2025 Feb 20]. Available from: doi: https://doi.org/10.1101/2021.04.30.442205, Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9, Banerjee S, Marchetti MC. Substrate rigidity deforms and polarizes active gels. EPL (Europhysics Letters) 96, 28003 (2011). https://doi.org/10.1209/0295-5075/96/28003, Edwards CM, Schwarz US. Force Localization in Contracting Cell Layers, Physical Review Letters 107, 128101 (2011). https://doi.org/10.1103/PhysRevLett.107.128101, and Banerjee S, Marchetti MC. Contractile Stresses in Cohesive Cell Layers on Finite-Thickness Substrates, Physical Review Letters 109, 108101 (2012). https://doi.org/10.1103/PhysRevLett.109.108101
- Discipline:
- Engineering and Science
-
- Creator:
- Nunley, Hayden, Xue, Xufeng, Sun, Yubing, Resto-Irizarry, Agnes M, Yuan, Ye, Yong, Koh Meng Aw, Zheng, Yi, Weng, Shinuo, Shao, Yue, Lubensky, David K, Studer, Lorenz, and Fu, Jianping
- Description:
- In an earlier study (Xue et al. Nature Materials 2018), stem cells differentiated into one of two cell types, neural plate border (NPB) or neural plate (NP), in vitro. This previous study demonstrated that this differentiation is likely mechanics-guided. Part of this demonstration was measurements of the displacement of microposts under the cell layer as the cells differentiate. These measurements suggested that the NPB cells are more contractile than NP cells. In a follow-up study (linked to this dataset), we quantitatively analyzed these data to demonstrate even further that the NPB cells are mechanically different than the NP cells and that the post displacement profile is not explained by a model of a cell layer with uniform mechanical properties. This analysis motivated the mathematical model -- for this cell colony system -- that we proposed and analyzed.
- Keyword:
- Biomechanics, Cell communication, Cell mechanics, Developmental pattern formation, Force sensing, and Vertebrate development
- Citation to related publication:
- Hayden Nunley, Xufeng Xue, Jianping Fu, David K. Lubensky bioRxiv 2021.04.30.442205; doi: https://doi.org/10.1101/2021.04.30.442205 and Xue X, Sun Y, Resto-Irizarry A.M. et al. Mechanics-guided embryonic patterning of neuroectoderm tissue from human pluripotent stem cells. Nature Mater 17, 633–641 (2018). https://doi.org/10.1038/s41563-018-0082-9
- Discipline:
- Engineering and Science