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Domestication during restoration: Unintentional selection during eight generations of wild seed propagation reduces herkogamy, dichogamy, and heterozygosity in the Clarkia pulchella. The authors grew Clarkia pulchella plants from a native seed farm and from the wild populations that served as a source population for the cultivated population. The farm population had been cultivated for eight generations. We measured traits that could affect inbreeding - the loss of herkogamy and dichogamy
(2024-08-29) Etterson, Julie; Fliehr, Paige; Pizza, Riley; Gross, Briana; jetterso@d.umn.edu; Etterson, Julie; Etterson & Gross labs, University of Minnesota Duluth
Seed production on native seed farms has increased to meet the rising demand for plant material for restoration. However, few studies have tested whether cultivation of wild populations imposes selection and elicits evolutionary change that aligns with process of crop domestication, and those that have report mixed results. Here we show that eight generations of propagation resulted in floral and genomic change in Clarkia pulchella Pursh (Onagraceae) compared to the wild source populations. Both herkogamy and dichogamy i.e., the physical and temporal separation of male and female flower parts, respectively) were significantly decreased between cultivated and wild populations. To determine if these changes resulted in the loss of heterozygosity and overall levels of genetic diversity, we examined >6,500 SNPs derived from RAD-seq data from 46 wild and 47 farmed samples. We show that mean and median heterozygosity of the farmed samples was 81.7% and 61.9% less than that of the wild samples, respectively. This was strongly driven by a loss of alleles, resulting in more than double the number of SNPs with a heterozygosity of zero. This reduction in genetic diversity was significant whether the farmed samples were compared to the pooled wild samples or to a single population. This suggests cultivation of wild populations may be having similar effects to the early stages of crop domestication. We discuss these results in the context of native seed farming and measures that can retain the genetic integrity of wild population during the process of seed increase for restoration. (Genomic data stored in GenBank)
Descriptive evaluation of a camera-based dairy cattle lameness detection technology
(2024-08-29) Cramer, Gerard; Swartz, Drew; Shepley, Elise; Burchard, Javier; Gaddis, Kristen; swart205@umn.edu; Swartz, Drew; Cramer Foot Health Lab
Lameness in dairy cattle is a clinical sign of impaired locomotion, mainly caused by painful foot lesions, compromising the US dairy industry's economic, environmental, and social sustainability goals. Combining technology and on farm data may be a more precise and less labor-intensive lameness detection tool, particularly for early detection. The objective of this observational study was to describe the association between average weekly autonomous camera-based (AUTO) locomotion scores and hoof trimming (HT) data. The AUTO data were collected from 3 farms from April 2022 to March 2023. Historical farm HT data were collected from March 2016 to March 2023 and used to determine cow lesion history and date of HT event. The HT events were categorized as a regular HT (TRIM; n = 2290) or a HT with a lesion recorded (LESION; n = 670). Events with LESION were sub-categorized based on lesion category: digital dermatitis (DD; n = 276), sole ulcer (SU; n = 79), white line disease (WLD; n = 141), and other (n = 174). The data also contained the leg of the LESION, classified as front left (FL; n = 54), front right (FR; n = 146), rear left (RL; n = 281), or rear right (RR; n = 183) leg with 6 events missing the leg. Cows' HT histories were classified as follows: cows with no previous recorded instance of any lesion were classified as TRIM0 (n = 1554). The first instance of any hoof lesion was classified as LESION1 (n = 238). This classification was retained until a subsequent TRIM occurred - recorded as TRIM1 (n = 632). The next unique instance of any lesion following a TRIM1 was classified as LESION2 (n = 86). Any LESION events occurring after LESION1 or LESION2 without a subsequent TRIM were considered a hoof lesion recurrence and classified as LESIONRE1 (n = 164) and LESIONRE2 (n = 22), respectively. TRIM events after LESION2 or LESION2RE (n = 104) or LESION events after LESIONRE1 or LESIONRE2 were classified as LESION_OTHER (n = 160). The AUTO scores from −28 to −1 days prior to the HT event were summarized into weekly scores and included if cows had at least 1 observation per week in the 4 weeks before the event. For all weeks, LESION cows had a higher median AUTO score than TRIM cows. Cows with TRIM0 had the lowest and most consistent median weekly score compared to LESION and other TRIM classifications. Before HT cows with TRIM0 and TRIM1, both had median score increases of 1 across the 4 weeks, while the LESION categories had an increase of 4 to 8. Scores increased with each subsequent LESION event compared to the previous LESION event. Cows with SU lesions had the highest median score across the 4 weeks, WLD had the largest score increase, and DD had the lowest median score and score increase. When grouping a LESION event by leg the hoof lesion was found on, the AUTO scores for four groups displayed comparable median values. Due to the difference between TRIM and LESION events, this technology shows potential for the early detection of hoof lesions.
Digital Roman Carthage - Version I
(2024-08-26) Saladin, Christopher; saladin@rowan.edu; Saladin, Christopher
The Digital Roman Carthage project maps the archaeological history of the Roman colony at Carthage from its foundation in the late 1st century BCE to its destruction and abandonment in the late 7th century CE. The data presented here was gathered from nearly two centuries worth of archaeological excavations to reflect the most up to date consensus on each of Carthage's many Roman era features. This version of the project was created as a companion to the dissertation, "Resurrecting Carthage" (Chris Saladin, University of Minnesota, 2023). https://hdl.handle.net/11299/259650 The data can be downloaded here as ZIP file of map shapefiles, viewed in a table format in the dissertation, or viewed in the linked ArcGIS web application.
Stable potassium isotope analyses of seafloor hydrothermal vent fluids from Lost City Hydrothermal Field
(2024-08-26) Evans, Guy; Zheng, Xinyuan; Sosiri, Charin; xyzheng@umn.edu; Zheng, Xinyuan; University of Minnesota Zheng Isotope Geochemistry Lab
Stable isotope analyses of seafloor hydrothermal vent fluids from the Lost City Hydrothermal Field, collected in 2008.
Data for Utilizing a degradation prediction pathway system to understand how a novel methacrylate derivative polymer with flipped external ester groups retains physico-mechanical properties following esterase exposure
(2024-08-22) Kumar, Dhiraj; Ghose, Debarati; Mutreja, Isha; Bolskar, Robert; Aparicio, Conrado; Jones, Robert S; rsjones@umn.edu; Jones, Robert S; B-A-M Lab
The region of failure for current methacrylates (i.e. derivatives of acrylates) are ester bond linkages that hydrolyze in the presence of salivary and bacterial esterases that break the polymer network backbone. This effect decreases the mechanical properties of methacrylate-based materials. The ethylene glycol dimethacrylate (EGDMA) or novel ethylene glycol ethyl methacrylate (EGEMA) discs were prepared using 40μL of the curing mixture containing photo/co-initiators for 40second in a PTFE mold at 1000mW/cm2. The degree of conversion was used as a quality control measure for the prepared disks, followed by physical, mechanical, and chemical characterization of discs properties before and after cholesterol esterase treatment. After 9 weeks of standardized cholesterol esterase (CEase) exposure, EGDMA discs showed exponential loss of material (p=0.0296), strength (p=0.0014) and increased water sorption (p=0.0002) compared to EGEMA discs. We integrated a degradation prediction pathway system to LC/MS and GC/MS analyses to elucidate the degradation by-products of both EGEMA and EGDMA polymers. GC/MS analysis demonstrated that the esterase catalysis was directed to central polymer backbone breakage, producing ethylene glycol, for EGDMA, and to side chain breakage, producing ethanol, for EGEMA. The flipped external ester group linkage design is attributed to EGEMA showing higher resistance to esterase biodegradation and changes in mechanical and physical properties than EGDMA. EGEMA is a potential substitute for common macromer diluents, such as EGDMA, based on its resistance to biodegradation effects. This work inspires the flipped external group design to be applied to analogs of current larger, hydrophobic strength bearing macromers used in future dental material formulations. The data in this record supports the figures in the related manuscript.
Creating a patient-centered report card for solid organ transplant candidates
(2024-08-15) Israni, Ajay K.; Bruin, Marilyn; Chu, Sauman; McKinney, Warren T.; Schaffhausen, Cory; Schladt, David; wmckinney@hhrinstitute.org; McKinney, Warren
Choosing a transplant center that will accept a particular candidate can be difficult and challenging for patients with end-stage organ failure. As transplant centers have varying levels of expertise, interests, and outcomes of solid organ transplant, patient health-related characteristics influence the variation in candidates centers will accept. Most transplant candidates undergo waitlist work-ups as outpatients and many undergo transplant at centers not closest to their homes. Some are listed at more than one center. Several studies suggest that patients have a choice of centers. The PI, as Deputy Director of the Scientific Registry of Transplant Recipients (SRTR), provides comparative information to the public about each solid organ transplant center in the United States. The risk adjusted outcomes, in the report cards, account for the transplant recipient's health-related characteristics, donor characteristics and transplant related factors. Many transplant centers provide a print-out of this SRTR report card to their candidates to comply with Centers for Medicare & Medicaid rules. Unfortunately, in their current format, the report cards are not designed for transplant candidates, many of whom may have low health literacy and numeracy. The proposed work aims to develop and evaluate a patient-centered website and printouts of the SRTR report cards that will effectively communicate comparative information to transplant candidates about their alternatives when choosing transplant centers. We will develop a novel tool to allow candidates to tailor the report cards to their clinical profiles based on their health-related characteristics and to communicate information on alternative transplant centers that perform transplants in patients like them. The website will also allow patients to self-refer to centers. Here, we provide copies of the interview / focus group guide as well as examples of the demographic / clinical questionnaires completed by study participants. We are releasing these materials to allow for greater insight into the study and to enhance reproducibility.
Data for Combining photocontrolled-cationic and anionic-group transfer polymerizations using a universal mediator: enabling access to two- and three-Mechanism block copolymers
(2024-08-15) Hosford, Brandon M; Ramos, William; Lamb, Jessica R; jrlamb@umn.edu; Lamb, Jessica R; Lamb Research Group
An ongoing challenge in polymer chemistry is accessing diverse block copolymers from multiple polymerization mechanisms and monomer classes. One strategy to accomplish this goal without intermediate compatibilization steps is the use of universal mediators. Thiocarbonyl thio (TCT) functional groups are well-known mediators to combine radical with either cationic or anionic polymerization, but a sequential cationic-anionic universal mediator system has never been reported. Herein, we report a TCT universal mediator that can sequentially perform photocontrolled cationic polymerization and thioacyl anionic group transfer polymerization to access poly(ethyl vinyl ether)-block-poly(thiirane) polymers for the first time. Thermal analyses of these block copolymers provide evidence of microphase separation. The success of this system, along with the established compatibility of radical polymerization, enabled us to further chain extend the cationic-anionic diblock using radical polymerization of N-isopropylacrylamide. The resulting terpolymer represents the first example of a triblock made from three different monomer classes incorporated via three different mechanisms without any end-group modification steps. The development of this simple, sequential synthesis using a universal mediator approach opens up new possibilities by providing facile access to diverse block copolymers of vinyl ethers, thiiranes, and acrylamides.
Genetic Analysis of Wild and Cultivated Populations of Northern Wild Rice (Zizania palustris L.) Reveal Insights into Gene Flow and Domestication
(2024-08-08) McGilp, Lillian; Haas, Matthew W; Shao, Mingqin; Millas, Reneth; Castell-Miller, Claudia; Kern, Anthony J; Shannon, Laura M; Kimball, Jennifer A; jkimball@umn.edu; Kimball, Jennifer, A.; University of Minnesota Cultivated Wild Rice Research Lab
Data for Equilibrium Phase Behavior of Gyroid-Forming Diblock Polymer Thin Films
(2024-08-08) Magruder, Benjamin; Ellison, Christopher; Dorfman, Kevin; dorfman@umn.edu; Dorfman, Kevin; Dorfman Research Group
The dataset contains the results of thin-film self-consistent field theory calculations for the double-gyroid phase and other related phases in AB diblock polymers. All results used to construct the figures in the referenced manuscript are included in this dataset, along with many of the scripts used to perform the analysis in the manuscript. To reduce the size of the dataset, we opted to include only the first and last field file in each parameter sweep, though we kept the corresponding summary file at every state point in every sweep, and included all necessary input files to regenerate the data if desired. The PSCF software package (C++ version) was used to generate this dataset (https://github.com/dmorse/pscfpp).
Advancing Treatment for Pancreatitis: A Prospective Observational Study of TPIAT (POST Study). Protocol, Manual of Procedures, and Case Report Forms
(2024-08-08) Bellin, Melena; post@umn.edu; POST, Staff Members; University of Minnesota Division of Pediatric Endocrinology and Division of Biostatistics and Health Data Science
This "dataset" contains supplemental materials only: the final version of the POST Study's protocol, Manual of Procedures (MOP), and Case Report Forms (CRFs), for reference generally and specifically for the public-use datasets, which will be made available after the primary publications appear. Please contact POST study staff at post@umn.edu to request access to the actual data.
Data supporting Motility directs Pseudomonas aeruginosa towards surfaces and enhances biofilm formation
(2024-08-08) Wei, Guanju; Yang, Judy Q; judyyang@umn.edu; Yang, Judy Q; University of Minnesota, Saint Anthony Falls Laboratory
This dataset contains all the angles and trajectories for both motile and non-motile Pseudomonas aeruginosa cells. In the manuscript, we demonstrated that the cell motility can enhance biofilm formation and utilized the orientation angle and trajectory data to support this conclusion.
Cell-culture Data Pipeline Python package (CDPpy) for processing and analyzing cell culture datasets
(2024-08-05) Lu, Yen-An; Fukae, Yudai; Hu, Wei-Shou; Zhang, Qi; qizh@umn.edu; Zhang, Qi; University of Minnesota Decision Discovery and Optimization Lab; University of Minnesota Cellular Engineering Lab
CDPpy (Cell-culture Data Pipeline Python package) is an open-source library designed for the analysis of fed-batch cell culture data from multiple experiments and cell lines. The package features the functions of a data processing pipeline and visualization toolbox. The processing pipeline reads raw data from Excel files following a fixed template, derives variables such as cumulative substrate consumption and various specific rates, and exports the processed dataset into an Excel file. The specific rates show changing cellular activities over time in culture, providing insights for process optimization. The visualization toolbox enables users to analyze process profiles across experimental runs and cell lines, aiding in future experimental design. In this repository, we include the source code for the package, an instruction for package setup, and a Jupyter notebook that provides step-by-step guidelines for data processing and visualization using an example dataset. The updated version will be announced in the GitHub repository: https://github.com/ddolab/CDPpy in the future.
Data for Wavelength Dependence of Plasmon-Induced Vibrational Energy Transfer in Fluorophore–Plasmonic Systems
(2024-08-01) Christenson, Gerrit N; Yu, Ziwei; Frontiera, Renee R; rrf@umn.edu; Frontiera, Renee R; Materials Research Science & Engineering Center
Understanding, predicting, and controlling plasmon–molecule energy transfer are important for improvements to plasmonic photocatalysis and photothermal therapies. Here, we use continuous wave surface-enhanced anti-Stokes and Stokes Raman spectroscopy to quantify the vibrational kinetic energy, equivalent to a molecular temperature under a Boltzmann approximation, of Raman-active vibrational modes of molecules at plasmonic interfaces. In previous work from our group, we observed an anomalous steady-state reduction in vibrational kinetic energies in benzenethiols absorbed onto the surface of gold nanoparticles. To further explore this effect, here, we quantify the wavelength dependence of vibrational energy in plasmon–fluorophore systems, where molecules can undergo electronic transitions with resonant excitation. We used three excitation wavelengths and three molecules with varying electronic resonance energies. We observe wavelength-dependent vibrational energy distributions, which we attribute to competing effects of on-resonance heating and off-resonance decrease in the population ratio. This work thus quantifies the resonance wavelength dependence of vibrational energy in plasmon molecular systems and helps to suggest future applications of tailored systems with controllable energy transfer pathways.
Snow properties, trajectories, and turbulence data collected during field deployments from 2022 to 2023 at Eolos research station
(2024-07-29) Li, Jiaqi; Guala, Michele; Hong, Jiarong; li001334@umn.edu; Li, Jiaqi
The data contains the three-dimensional trajectories, snow particle properties, and raw meteorological data of four datasets (with dominant snow types, including aggregates, dendrites, graupels, and needles). The datasets are collected during three deployments, on April 7th, 2022, December 19th, 2022, and January 2nd, 2023, at the Eolos Wind Research Field Station in Rosemount, MN.
Data for Chain and Structural Dynamics in Melts of Sphere-Forming Diblock Copolymers
(2024-07-22) Chawla, Anshul; Bates, Frank S; Dorfman, Kevin D; Morse, David C; dorfman@umn.edu; Dorfman, Kevin D; Dorfman Research Group
Processed simulation data appearing in the related manuscript
Observations of wolves eating berries in the Greater Voyageurs Ecosystem
(2024-07-18) Evavold, Isabella; Gable, Thomas D; Homkes, Austin T; Bump, Joseph K; gable079@umn.edu; Gable, Thomas; University of Minnesota Voyageurs Wolf Project
Wolves are opportunistic generalists that can respond quickly to new and unique food sources. Wolves in some ecosystems will consume berries and other fruits when they are abundant and available, however many aspects of this behavior remain unknown. In the Greater Voyageurs Ecosystem (GVE), Minnesota, USA, wolves consistently consume berries, particularly blueberries, when they are available. We deployed remote cameras in blueberry patches to record wolves foraging on berries over several years. We captured footage of wolves of all age-classes, social statuses, and sex foraging on blueberries alone or with other wolves. Our observations indicate berry consumption by wolves is a widespread behavior in the GVE and likely similar southern boreal ecosystems. We hope our work spurs researchers across wolf range to examine whether berry consumption by wolves is a widespread and ubiquitous behavior for wolves.
The evolution of freezing tolerance in oaks
(2024-07-18) Fontes, Clarissa; Hoerner, Frank; Hipp, Andrew; Meireles, Jose Eduardo; Cavender-Bares, Jeannine; cavender@umn.edu; Cavender-Bares, Jeannine
Freezing tolerance is a critical factor controlling the broad-scale distribution of organisms. Freezing temperatures result in intra- and extracellular ice crystal formation, which can cause physical damage and cellular dehydration, resulting in losses of xylem function. Yet, how rapidly plants can adapt to changing climate and whether there are trade-offs between freezing tolerance and growth remain poorly understood. We grew 48 species of Quercus (oaks) from five sections of the genus under temperate and tropical growth conditions and measured their stem freezing tolerance and growth rate. We found significant differences among species in their freezing tolerance and their capacity to cold acclimate. Species from colder regions have higher freezing tolerance and slower growth rates than species from warmer climates. Nevertheless, a direct evolutionary trade-off did not emerge because deciduousness rather than freezing tolerance appears to constrain growth rates. Deciduous species have consistently slower growth rates than evergreen species regardless of climatic niche but vary markedly in freezing tolerance in step with the broad climatic range they span. In contrast, evergreen species occur only in warm climates and have low freezing tolerance. Species from colder regions also have higher acclimation potential than species from warmer areas, indicating that cold-climate species have evolved higher capacity to acclimate to seasonal fluctuations in climate, while warm-climate species have constraints to surviving in colder climates. Freezing tolerance in the oaks is relatively close to its optimal evolutionary state (r=0.77), however, the phylogenetic half-life is 8.9 Myr (ca. 17% of the crown age of the genus). Consequently, despite a high level of adaptation to the climates in which species occur, evolution towards optimal freezing tolerance has a considerable lag time.
Data for Alkyl Substituted Polycaprolactone Poly(Urethane-Urea)s as Mechanically-Competitive and Chemically-Recyclable Materials
(2024-07-18) Pfau-Cloud, Michaela R; Batiste, Derek C; Kim, Hee Joong; Ellison, Christopher J; Hillmyer, Marc A; hillmyer@umn.edu; Hillmyer, Marc A; Hillmyer Group
We report the mechanical performance and chemical recycling advantages of implementing alkyl-substituted poly(ε-caprolactones) (PCLs) as soft segments in thermoplastic poly(urethane-urea) (TPUU) materials. Poly(4-methylcaprolactone) (P4MCL) and poly(4-propylcaprolactone) (P4PrCL) were prepared, reacted with isophorone diisocyanate, and chain-extended with water to form TPUUs. The resulting materials’ tensile properties were similar to or superior to a commercially available polyester thermoplastic poly(urethane), and had superior elastic recovery compared to a PCL analogue due to the non-crystalline nature of P4MCL and P4PrCL. Additionally, monomers were recovered from the TPUU materials in high yields via ring-closing depolymerization using a reactive distillation approach at elevated temperature and reduced pressure (240–260 °C, 25-140 mTorr) with zinc chloride (ZnCl2) as the catalyst. The thermodynamics of polymerization were estimated using Van’t Hoff analyses for 4MCL and 4PrCL; these results indicated that the propyl group in 4PrCL results in a lower practical ceiling temperature (Tc) for P4PrCL.
Data supporting Cell-free expression with a quartz crystal microbalance enables rapid, dynamic, and label-free characterization of membrane-interacting proteins
(2024-07-15) Khakimzhan, Aset; Izri, Ziane; Thompson, Seth; Dmytrenko, Oleg; Fischer, Patrick; Beisel, Chase; Noireaux, Vincent; noireaux@umn.edu; Noireaux, Vincent; Noireaux Lab
Integral and interacting membrane proteins (IIMPs) constitute a vast family of biomolecules that perform essential functions in all forms of life. However, characterizing their interactions with lipid bilayers remains limited due to challenges in purifying and reconstituting IIMPs in vitro or labeling IIMPs without disrupting their function in vivo. Here, we report cell-free transcription-translation in a quartz crystal microbalance with dissipation (TXTL-QCMD) to dynamically characterize interactions between diverse IIMPs and membranes without protein purification or labeling. As part of TXTL-QCMD, IIMPs are synthesized using cell-free transcription-translation (TXTL), and their interactions with supported lipid bilayers are measured using a quartz crystal microbalance with dissipation (QCMD). TXTL-QCMD reconstitutes known IIMP-membrane dependencies, including specific association with prokaryotic or eukaryotic membranes, and the multiple-IIMP dynamical pattern-forming association of the E. coli division-coordinating proteins MinCDE. Applying TXTL-QCMD to the recently discovered Zorya anti-phage system that is unamenable to labeling, we discovered that ZorA and ZorB integrate within the lipids found at the poles of bacteria while ZorE diffuses freely on the non-pole membrane. These efforts establish the potential of TXTL-QCMD to broadly characterize the large diversity of IIMPs.
Data for Chiral Optical Properties of Metasurfaces Comprised of Chiral Media: Effects of Geometric and Material Chirality
(2024-07-15) Ramamurthy, Maya; Cote, Bryan M; Ferry, Vivian E; veferry@umn.edu; Ferry, Vivian E; Department of Chemical Engineering and Materials Science, University of Minnesota
Chiral nanomaterials and metamaterials are the subject of intense recent interest, but the principles that govern their design can be challenging to identify. With the emergence of a host of new chiral molecules and nanocrystals, metamaterials can be created from materials that are intrinsically chiral, potentially enhancing chiroptical properties by combining geometrical and material factors. To take advantage of this, we first need to deconvolute the distinct and sometimes competing effects of geometric and material chirality on chiroptical properties. Here, we investigate the role of the meta-atom geometry, optical resonances, and chirality of the constituent medium on the optical chirality enhancement, circular dichroism (CD), g-factor, and relative transmission of LCP versus RCP light (∆T) in metasurfaces comprised of chiral material. We find that overlapping Mie-like resonances in nanodisk arrays lead to 6-fold CD enhancement compared to a uniform film. Our analysis also suggests that making the medium chiral does not necessarily increase CD or g-factor; enhancement in the CD and optical chirality depend on the magnitude of the Pasteur parameter as well as its real and imaginary components. As a demonstration of how geometric and material chirality can be combined to enhance chiroptical properties, we design a geometrically chiral meta-atom out of chiral media and observe over 9-fold enhancement in both CD and g-factor compared to a metasurface comprised of achiral material. This work systematically investigates different approaches to tailoring a chiral response from nanostructured arrays and provides design rules that can be broadly applied to metastructures comprised of chiral media.