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- Creator:
- Teague, Seth, Yu, Zhiyuan, and Heemskerk, Idse
- Description:
- Images were collected as part of a project investigating the interpretation of BMP signaling dynamics by differentiating human pluripotent stem cells. Image files are in the proprietary Imaris (.ims) file format. MATLAB and Python code for image processing and quantification is provided with the data and at https://github.com/seth414/HeemskerkLabMethods. Processed data originally published in Teague et al., 2024 (see below).
- Keyword:
- cell tracking, human pluripotent stem cells, immunofluorescence, and signaling dynamics
- Citation to related publication:
- Teague, S., Primavera, G., Chen, B. et al. Time-integrated BMP signaling determines fate in a stem cell model for early human development. Nat Commun 15, 1471 (2024). https://doi.org/10.1038/s41467-024-45719-9
- Discipline:
- Health Sciences and Engineering
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- Creator:
- Savier Elise L
- Description:
- Visual information can have different meanings across species and the same visual stimulus can drive appetite or avoidance behavior. The superior colliculus, a visual center located in the midbrain has been involved in driving such behaviors. Within this structure, the wide-field-vertical cells (WFV), a conserved morphological cell-types, has been found in reptiles to highly visual mammals. Here we report our investigation of the connectivity of the WFV, their visual response properties and how these responses are modulated by locomotion in the laboratory mouse. We also address the molecular definition of these cells and attempt to reconcile recent molecular definitions acquired by single-cell and single-nucleus RNA sequencing of the SC with the NTSR1-Cre GN209 transgenic mouse line which was previously used to investigate WFV neurons. We use viral strategies to reveal WFV inputs and outputs and confirmed their unique response properties using in vivo two-photon imaging. Among the stimuli tested, WFV preferred looming and a small moving spot and displayed a bias for upward direction. When assessing the effect of locomotion, we found that only visual responses driven by a looming stimulus showed a significant change. We identified several inputs to the WFV as potential candidate for this modulation. These results suggest that WFV integrate information across multiple brain regions and are subject to behavioral modulation. Taken together, our results pave the way to elucidate the role of these neurons in visual behavior and allow us to interrogate the definition of cell-types in the light of new molecular definitions.
- Keyword:
- neuroscience, superior colliculus, calcium imaging, neuroanatomy, wide-field vertical cells
- Discipline:
- Science
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- Creator:
- Alofs, Karen, Schell, Justin, King, Katelyn, Thomer, Andrea, Wehrly, Kevin, and Lopez-Fernandez, Hernan
- Description:
- Archives at the Institute for Fisheries Research (IFR) hold records of thousands of lake surveys from the University of Michigan and Michigan Department of Natural Resources. The records contained in this dataset are jpeg images of the index card records from the IFR surveys. Images include the front of the card and when available, the back of a card. and Fish Collection Cards report the number of individuals of each species captured. The cards also record what gear (for example seine or gill net) was used for surveys, where fish were sampled in the lake, and when and for how long sampling occurred.
- Keyword:
- lake, fish, gill net , seine, trap net, electrofishing, survey , and abundance
- Citation to related publication:
- 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 and Erickson, Jim. "New crowdsourced project to digitize Michigan lake and fish records, looking for climate trends." University of Michigan School of Environment and Sustainability News. March 17, 2021. URL: https://seas.umich.edu/news/new-crowdsourced-project-digitize-michigan-lake-and-fish-records-looking-climate-trends
- Discipline:
- Science
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Collections, Heterogeneous data, and Next Generation Ecological Studies (CHANGES) - Michigan Lake Surveys
User Collection
- Creator:
- Zooniverse contributors, Alofs, Karen, Schell, Justin, King, Katelyn, Thomer, Andrea, Wehrly, Kevin, and Lopez-Fernandez, Hernan
- Description:
- Archives at the Institute for Fisheries Research (IFR) hold meticulous records of thousands of lake surveys from the University of Michigan and Michigan Department of Natural Resources. Starting more than a century ago, surveys have been used to understand how fish were distributed across the state, which lakes would support sportfishing, and how lakes should be managed. We can now use these records of lake conditions and fish abundance and growth to understand how climate change and other factors have impacted fish communities. and The records contained in this collection are digitized records from the IFR surveys stored as jpeg image files. This collection includes information on both lake factors (e.g. depth, nutrients, temperature) and fishes (e.g. species, catch, length). Scanned cards were organized by card type and each dataset in this collection is for a specific card type.
- Keyword:
- lakes, Michigan, fishes, and surveys
- Discipline:
- Science
26Works -
- Creator:
- Alofs, Karen, Schell, Justin, King, Katelyn , Thomer, Andrea, Wehrly, Kevin, and Lopez-Fernandez, Hernan
- Description:
- Archives at the Institute for Fisheries Research (IFR) hold records of thousands of lake surveys from the University of Michigan and Michigan Department of Natural Resources. The records contained in this dataset are jpeg images of the index card records from the IFR surveys. Images include the front of the card and when available, the back of a card. and Lake Summary cards include information about the lake location and its characteristics, such as lake depth, water chemistry, water color, and transparency (commonly measured as Secchi depth). There is information on surrounding characteristics such as its connectivity to other waterbodies, shoreline conditions, and surrounding land-use. This card also lists the fishes present in the lake and makes observations about fishing pressure, parasites, and reproduction.
- Keyword:
- lake, fishes, depth, land use, temperature, thermocline, fishing pressure, and Secchi depth
- Citation to related publication:
- Erickson, Jim. "New crowdsourced project to digitize Michigan lake and fish records, looking for climate trends." University of Michigan School of Environment and Sustainability News. March 17, 2021. URL: https://seas.umich.edu/news/new-crowdsourced-project-digitize-michigan-lake-and-fish-records-looking-climate-trends
- Discipline:
- Science
-
- Creator:
- Alofs, Karen, Schell, Justin, King, Katelyn, Thomer, Andrea, Wehrly, Kevin, and Lopez-Fernandez, Hernan
- Description:
- Archives at the Institute for Fisheries Research (IFR) hold records of thousands of lake surveys from the University of Michigan and Michigan Department of Natural Resources. The records contained in this dataset are jpeg images of the index card records from the IFR surveys. Images include the front of the card and when available, the back of a card. and Fish Growth Cards report information on the age and length of fishes captured in lake surveys. The age of a fish was determined by counting annual rings on hard structures including scales, spines and otoliths (fish ear bones).
- Keyword:
- Lake, fish , length, age, and growth
- Citation to related publication:
- Erickson, Jim. "New crowdsourced project to digitize Michigan lake and fish records, looking for climate trends." University of Michigan School of Environment and Sustainability News. March 17, 2021. URL: https://seas.umich.edu/news/new-crowdsourced-project-digitize-michigan-lake-and-fish-records-looking-climate-trends
- Discipline:
- Science
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- Creator:
- Wittkopp, Patricia J and Massey, Jonathan H
- Description:
- Data provided in this record were collected in the course of studying the genetic basis of differences in wing pigmentation and wing display between Drosophila elegans and Drosophila gunungcola.
- Citation to related publication:
- Massey, J. H., Rice, G. R., Firdaus, A. S., Chen, C.-Y., Yeh, S.-D., Stern, D. L., & Wittkopp, P. J. (2020). Co-evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution, 74(6), 1098–1111. https://doi.org/10.1111/evo.13990
- Discipline:
- Science
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- Creator:
- Moore, Talia Y., Danforth, Shannon M., Larson, Joanna G., and Davis Rabosky, Alison R.
- Description:
- Warning signals in chemically defended organisms are critical components of predator-prey interactions, often requiring multiple coordinated display components for a signal to be effective. When threatened by a predator, venomous coral snakes (genus Micrurus) display a vigorous, non-locomotory thrashing behaviour that has been only qualitatively described. Given the high-contrast and often colourful banding patterns of these snakes, this thrashing display is hypothesized to be a key component of a complex aposematic signal under strong stabilizing selection across species in a mimicry system. By experimentally testing snake response across simulated predator cues, we analysed variation in the presence and expression of a thrashing display across five species of South American coral snakes. Although the major features of the thrash display were conserved across species, we found significant variation in the propensity to perform a display at all, the duration of thrashing, and the curvature of snake bodies that was mediated by predator cue type, snake body size, and species identity. We also found an interaction between curve magnitude and body location that clearly shows which parts of the display vary most across individuals and species. Our results suggest that contrary to the assumption in the literature that all species and individuals perform the same display, a high degree of variation persists in thrashing behaviour exhibited by Micrurus coral snakes despite presumably strong selection to converge on a common signal. This quantitative behavioural characterization presents a new framework for analysing the non-locomotory motions displayed by snakes in a broader ecological context, especially for signalling systems with complex interaction across multiple modalities.
- Keyword:
- aposematism, biomechanics, coral snake mimicry, curvature, Elapidae, non-locomotory motion, Peruvian Amazon, and snake behaviour
- Citation to related publication:
- Moore, T. Y., Danforth, S. M., Larson, J. G., & Davis Rabosky, A. R. (2020). A Quantitative Analysis of Micrurus Coral Snakes Reveals Unexpected Variation in Stereotyped Anti-Predator Displays Within a Mimicry System. Integrative Organismal Biology, 2(1). https://doi.org/10.1093/iob/obaa006
- Discipline:
- Science
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- Creator:
- Ridley, Aaron and Cnossen, Ingrid
- Description:
- These are modeling results of the thermospheric and ionospheric response to the solar eclipse of August 21, 2017. The results are discussed in a research paper published in the Journal of Geophysical Research (doi: 10.1029/2018JA026402) .
- Citation to related publication:
- Cnossen, I., Ridley, A. J., Goncharenko, L. P., and Harding, B. J.. ( 2019), The response of the ionosphere‐thermosphere system to the August 21, 2017 solar eclipse. J. Geophys. Res. Space Physics, 124. https://doi.org/10.1029/2018JA026402
- Discipline:
- Science
-
- Creator:
- Burgin, Tucker and Mayes, Heather B.
- Description:
- This project aimed to discover and analyze the molecular mechanism of synthesis of two particular fucosylated oligosaccharide products in a mutant enzyme, Thermatoga maratima Alpha-L-Fucosidase D224G, whose wild type performs the opposite reaction (cleavage of fucosyl glycosidic bonds). Discovery of the mechanism was performed using an unbiased simulations method known as aimless shooting, whereas analysis of the mechanism in terms of the energy profile was performed using a separate method known as equilibrium path sampling. The data here concerns the latter method. and The contents of the atesa_master.zip are the ATESA GitHub project. A Python program for automating transition path sampling with aimless shooting using Amber. https://github.com/team-mayes/atesa
- Keyword:
- Equilibrium Path Sampling, Transition Path Sampling, Enzymatic Mechanism, and GH29
- Citation to related publication:
- Burgin, T., & Mayes, H. B. (2019). Mechanism of oligosaccharide synthesis via a mutant GH29 fucosidase. Reaction Chemistry & Engineering, 4(2), 402–409. https://doi.org/10.1039/C8RE00240A
- Discipline:
- Engineering