157 Works

N-Glycosylation effects on T cell receptor kinetics

Zachary Rollins, Bradley Harris, Steven George & Roland Faller
This methodology is an atomic-level investigation of the physiochemical effects of glycosylation on TCR dissociation kinetics. The force-dependent bond lifetime and bond strength of the DMF5 T Cell Receptor (TCR) to the MART1 peptide-Major Histocompatibility Complexes (pMHCs) were simulated using Steered Molecular Dynamics. N-glycsoylated and aglycosylated configurations were compared in triplicate. This data set contains atomic structure of the TCR and pMHC (.gro files), atomic interactions between the TCR and pMHC (hmap & cmap .csv...

Transgenerational plasticity and the capacity to adapt to low salinity in the eastern oyster, Crassostrea virginica

Joanna Griffiths, Kevin Johnson, Kyle Sirovy, Mark Yeats, Francis Pan, Jerome La Peyre & Morgan Kelly
Salinity conditions in oyster breeding grounds in the Gulf of Mexico are expected to drastically change due to increased precipitation from climate change and anthropogenic changes to local hydrology. We determined the capacity of the eastern oyster, Crassostrea virginica, to adapt via standing genetic variation or acclimate through transgenerational plasticity. We outplanted oysters to either a low or medium salinity site in Louisiana for two years. We then crossed adult parents using a North Carolina...

Cave-adapted evolution in the North American Amblyopsid fishes inferred using phylogenomics and geometric morphometrics

Pamela Hart, Matthew Niemiller, Edward Burress, Jonathan Armbruster, William Ludt & Prosanta Chakrabarty
Cave adaptation has evolved repeatedly across the Tree of Life, famously leading to pigmentation and eye degeneration and loss, yet its macroevolutionary implications remain poorly understood. We use the North American amblyopsid fishes, a family spanning a wide degree of cave adaptation, to examine the impact of cave specialization on the modes and tempo of evolution. We reconstruct evolutionary relationships using ultraconserved element loci, estimate the ancestral histories of eye-state, and examine the impact of...

Dispersal of nectar microbes in California flowering communities

Rachel Vannette, Griffin Hall, Ivan Munkres, Marshall McMunn, Douglas Perry & Tobias Mueller
Variation in dispersal ability among taxa affects community assembly and biodiversity maintenance within metacommunities. Although fungi and bacteria frequently coexist, their relative dispersal abilities are poorly understood. Nectar-inhabiting microbial communities affect plant reproduction and pollinator behavior, and are excellent models for studying dispersal of bacteria and fungi in a metacommunity framework. Here, we assay dispersal ability of common nectar bacteria and fungi in an insect-based dispersal experiment. We then compare these results to the incidence...

Data from: Rare instances of haploid inducer DNA in potato dihaploids and ploidy-dependent genome instability

Kirk Amundson
In cultivated tetraploid potato, reduction to diploidy (dihaploidy) allows hybridization to diploid germplasm, introgression breeding, and may facilitate the production of inbreds. Pollination with haploid inducers yields maternal dihaploids, as well as triploid and tetraploid hybrids. It is not known if dihaploids result from parthenogenesis, entailing development of embryos from unfertilized eggs, or genome elimination, entailing missegregation and loss of paternal chromosomes. A sign of genome elimination is the occasional persistence of haploid inducer DNA...

Optical maps refine the bread wheat Triticum aestivum cv Chinese Spring genome assembly

Tingting Zhu, Le Wang, Hélène Rimbert, Juan Rodriguez, Karin Deal, Romain De Oliveira, Frédéric Choulet, Gabriel Keeble-Gagnère, Josquin Tibbits, Jane Rogers, Kellye Eversole, Rudi Appels, Yong Gu, Martin Mascher, Jan Dvorak, Ming-Cheng Luo, Juan C. Rodriguez, Karin R. Deal, Gabriel Keeble‐Gagnère, Yong Q. Gu & Ming‐Cheng Luo
This dataset contains a single whole-genome optical map file (.CMAP) for bread wheat (Triticum aestivum) cv Chinese Spring (CS). The methods for constructing this optical map and the properties of this map are described below. The definition of the CMAP format is documented in https://bionanogenomics.com/wp-content/uploads/2017/03/30039-CMAP-File-Format-Specification-Sheet.pdf. The extracted ultra-high-molecular weight DNA molecules of CS were labeled with the DLE-1 enzyme (Bionano Genomics, San Diego, CA, USA) and were then stained with the Bionano PrepTM DLS Kit...

Data from: Expiratory aerosol particle escape from surgical masks due to imperfect sealing

Christopher Cappa, Sima Asadi, Anthony Wexler, Santiago Barreda & Nicole Bouvier
The dataset provided here is associated with the work "Expiratory aerosol particle escape from surgical masks due to imperfect sealing," by Cappa et al, currently available as a preprint at https://doi.org/10.21203/rs.3.rs-142138/v1. This includes measurements made of the influence of surgical masks and leakage flows out the mask sides on the emission of micron-scale aerosols from various expiratory activities (coughing, speaking). The dataset provided here includes *.txt files exported from an Aerodynamic Particle Sizer that contain...

Genetic diversity and population structure in Vitis species illustrate phylogeographic patterns in eastern North America

Jean-Pierre Peros, Peter Cousins, Amandine Launay, Philippe Cubry, Andrew Walker, Emilce Prado, Elisa Peressotti, Sabine Wiedemann-Merdinoglu, Valérie Laucou, Didier Merdinoglu, Patrice This, Jean-Michel Boursiquot & Agnès Doligez
Geographical distribution and diversity of current plant species have been strongly shaped by climatic oscillations during the Quaternary. Analyzing the resulting divergence among species and differentiation within species is crucial to understand the evolution of taxa like the Vitis genus, which provides very useful genetic resources for grapevine improvement and might reveal original recolonization patterns due to growth habit and dispersal mode. Here, we studied the genetic structure in natural populations of three species from...

Semi-artificial datasets as a resource for validation of bioinformatics pipelines for plant virus detection

Lucie Tamisier, Annelies Haegeman, Yoika Foucart, Nicolas Fouillien, Maher Al Rwahnih, Nihal Buzkan, Thierry Candresse, Michela Chiumenti, Kris De Jonghe, Marie Lefebvre, Paolo Margaria, Jean Sébastien Reynard, Kristian Stevens, Denis Kutnjak & Sébastien Massart
In the last decade, High-Throughput Sequencing (HTS) has revolutionized biology and medicine. This technology allows the sequencing of huge amount of DNA and RNA fragments at a very low price. In medicine, HTS tests for disease diagnostics are already brought into routine practice. However, the adoption in plant health diagnostics is still limited. One of the main bottlenecks is the lack of expertise and consensus on the standardization of the data analysis. The Plant Health...

Controls of chlorophyll fluorescence spectra vary among leaves in a boreal forest and over a spring recovery of photosynthesis

Paulina Rajewicz, Chao Zhang, Jon Atherton, Shari Van Wittenberghe, Anu Riikonen, Troy Magney, Beatriz Fernandez-Marin, Jose Ignacio Garcia Plazaola & Albert Porcar-Castell
Chlorophyll fluorescence can be used to track to seasonal dynamics of photosynthesis in boreal forests. However, the relationship between chlorophyll fluorescence and photosynthesis is affected by biochemical and morphological factors, which vary across time and space as a function of light environment, species, and environmental conditions. We investigated how various factors, and their spatio-temporal dynamics during spring recovery of photosynthesis in a boreal forest, affect spatio-temporal variation in chlorophyll fluorescence spectra. The factors under consideration...

Age affects strain-rate dependence of the mechanical properties of kelp tissue

Nicholas Burnett & M.A.R. Koehl
Premise: The resistance of macroalgae to hydrodynamic forces imposed by ambient water motion depends in part on the mechanical properties of their tissues. In wave-swept habitats, tissues are stretched (strained) at different rates as hydrodynamic forces constantly change. Kelp have tissues of different ages, and mechanical properties of kelp tissue change with age. However, the effects of age on the strain-rate dependence of the mechanical behavior of kelp tissues is unknown. Methods: Using the kelp...

Pierce's disease vector transmission-preference experiment on PdR1 resistant grapevines

Adam Zeilinger, Dylan Beal, Anne Sicard, Christopher Wallis, M. Andrew Walker & Rodrigo Almeida
Host defense against vector-borne plant pathogens is a critical component of integrated disease management. However, theory predicts that traits that confer tolerance or partial resistance can, under certain ecological conditions, enhance the spread of pathogens and spillover to more susceptible populations or cultivars. A key component driving such epidemic risk appears to be variation in host selection behavior of vectors based on infection status of the host. While recent theory has further emphasized the importance...

Stable social groups foster conformity and among-group differences

Marcus Michelangeli, Amelia Munson & Andrew Sih
The social niche hypothesis theorizes that repeated social interactions between group members is an important mechanism for generating consistent individual differences in behaviour. However, such frequent interactions also have the potential to mask or suppress behavioural differences if individuals conform towards a group behavioural norm (i.e. the social conformity) by either synchronizing their behaviour or shifting their behaviour towards that of influential group members. Both of these predictions hinge on the notion that social feedback...

Scaling up experimental stress responses of grass invasion to predictions of continental-level range suitability

Bo Zhang, Yingdan Yuan, Lele Shu, Edwin Grosholz, Yuxi Guo, James Cuda, Jinchi Zhang, Lu Zhai & Jiangxiao Qiu
Understanding how the biological invasion is driven by environmental factors will improve model prediction and advance early detection, especially in the context of accelerating anthropogenic ecological changes. Although a large body of studies has examined how favorable environments promote biological invasions, a more comprehensive and mechanistic understanding of invasive species response to unfavorable/stressful conditions is still developing. Grass invasion has been problematic across the globe; in particular, C4 grass invaders, with high drought tolerance, adaptations...

Data and analysis scripts for: Asymmetrical reproductive barriers in sympatric Jewelflowers: are floral isolation, genetic incompatibilities, and floral trait displacement connected?

Kyle Christie
Floral visitors influence reproductive interactions among sympatric plant species, either by facilitating assortative mating and contributing to reproductive isolation, or by promoting heterospecific pollen transfer, potentially leading to reproductive interference or hybridization. We assessed preference and constancy of floral visitors on two co-occurring Jewelflowers (Streptanthus breweri and S. hesperidis, Brassicaceae) using field arrays, and quantified two floral rewards potentially important to foraging choice – pollen production and nectar sugar concentration – in a greenhouse common...

Scaling up experimental stress responses of grass invasion to predictions of continental-level range suitability

Bo Zhang
Understanding how the biological invasion is driven by environmental factors will improve model prediction and advance early detection, especially in the context of accelerating anthropogenic ecological changes. Although a large body of studies has examined how favorable environments promote biological invasions, a more comprehensive and mechanistic understanding of invasive species response to unfavorable/stressful conditions is still developing. Grass invasion has been problematic across the globe; in particular, C4 grass invaders, with high drought tolerance, adaptations...

Fighting for curb space: Micro-simulation

Miguel Jaller, Caroline Rodier, Michael Zhang, Huachao Lin & Kathryn Lewis
This study conducted a comprehensive literature review on several topics related to curb space management, discussing various users (e.g., pedestrians, bicycles, transit, taxis, and commercial freight vehicles), summarizing different experiences, and focusing the discussion on Complete Street strategies. Moreover, the authors reviewed the academic literature on curbside and parking data collection, and simulation and optimization techniques. Considering a case study around the downtown area in San Francisco, the authors evaluated the performance of the system...

Retention of green leaves not brown leaves increases spring cynipid diversity on large valley oaks

Vincent Pan, Adam Pepi, Jake Goidell & Richard Karban
Plants can retain either physiologically active green leaves or inactive brown leaves over winter. Research has suggested that leaf retention incurs a cost due to higher herbivore load in the following year; however, no distinction has, thus, far been made between retention of green and brown leaves. We surveyed the over-winter retention of physiologically active green and inactive brown leaves of valley oaks (Quercus lobata) and examined their relationship with the diversity and density of...

CNS isotope values in eye lenses for juvenile and adult Chinook Salmon

Miranda Bell Tilcock, Carson Jeffres, Andrew Rypel, Ted Sommer, Jacob Katz, George Whitman & Rachel Johnson
Tracking habitat use and dietary shifts in migratory species is vital to conservation and management. Yet conventional animal tracking often precludes tracking small juveniles at critical life-stages where recruitment bottlenecks often manifest. Stable isotope analysis (SIA) in consecutive laminae in eye lenses, a protein-rich depositional tissue, has emerged as a promising tool in fishes to develop long-term interpretive records of dietary histories using a single archival tissue. Currently, studies using fisheye lenses to study SIA...

The timing of herbivory: early-season herbivory affects plant size and late-season herbivory affects seed production

Nick Rasmussen & Louie Yang
Phenological shifts in timing of species interactions have the potential to change size-structured species interactions, but relatively few studies have used experimental manipulations to examine the season-long effects of phenological mismatches in multiple development contexts. While previous experimental studies have examined how phenological mismatches in plant-herbivore interactions can affect both plants and their herbivores, less is known about their effects on subsequent plant-pollinator interactions. Here, we conducted an experiment to determine how shifts in the...

Environmental metadata for: 2019/2020 biomineral sampling of drainpipes from California public rest areas

Kahui Lim, Harold Leverenz, Cara Wademan, Samantha Barnum & Matthew Rolston
This environmental data set corresponds to a two part study. The first part details a multiple regression analysis of measured and categorical parameters that influence biomineral urease activity. Using an expanded version of the dateset used in the first part, a second and separate microbial ecology study focuses on the bacterial community structure related to both biomineral and liquid associated bacteria. The expanded data set includes liquid samples obtained from urine drainage systems. Part 1:...

Chromosome evolution and the genetic basis of agronomically important traits in greater yam

Jessen Bredeson, Jessica Lyons, Ibukun Oniyinde, Nneka Okereke, Olufisayo Kolade, Ikenna Nnabue, Nneka Okereke, Christian Nwadili, Eva Hribova, Matthew Parker, Jeremiah Nwogha, Shengqiang Shu, Joseph Carlson, Robert Kariba, Samuel Muthemba, Katarzyna Knop, Geoffrey Barton, Anna Sherwood, Antonio Lopez-Montes, Robert Asiedu, Ramni Jamnadass, Alice Muchugi, David Goodstein, Chiedozie Egesi, Jonathan Featherston … & Daniel Rokhsar
The nutrient-rich tubers of the greater yam, Dioscorea alata L., provide food and income security for millions of people around the world. Despite its global importance, however, greater yam remains an ‘orphan crop.’ Here we address this resource gap by presenting a highly contiguous chromosome-scale genome assembly of D. alata combined with a dense genetic map derived from African breeding populations. The genome sequence reveals an ancient allotetraploidization in the Dioscorea lineage, followed by extensive...

Reevaluating claims of ecological speciation in Halichoeres bivittatus

Dan Warren, Ron Eytan, Alex Dornburg, Teresa Iglesias, Matt Brandley, Peter Wainwright, Dan L. Warren, Ron I. Eytan, Teresa L. Iglesias, Matthew C. Brandley & Peter C. Wainwright
Allopatry has traditionally been viewed as the primary driver of speciation in marine taxa, but the geography of the marine environment and the larval dispersal capabilities of many marine organisms render this view somewhat questionable. In marine fishes, one of the earliest and most highly cited empirical examples of ecological speciation with gene flow is the slippery dick wrasse, Halichoeres bivittatus. Evidence for this cryptic or incipient speciation event was primarily in the form of...

Oxylipin Data set

K. M. Wagner, Jun Yang, Christophe Morisseau & Bruce D. Hammock
The soluble epoxide hydrolase (sEH) enzyme is a major regulator of bioactive lipids. The enzyme is highly expressed in liver and kidney and modulates levels of endogenous epoxy-fatty acids which have pleiotropic biological effects including limiting inflammation, neuroinflammation and hypertension. It has been hypothesized that inhibiting sEH has beneficial effects on limiting obesity and metabolic disease as well. There is a body of literature published on these effects, but typically only male subjects have been...

Data for: Freeze tolerance influenced forest cover and hydrology during the Pennsylvanian

William Matthaeus, Sophia I. Macarewich, Jon D. Richey, Jonathan P. Wilson, Jennifer C. McElwin, Isabel P. Montañez, William A. DiMichele, Michael T. Hren, Christopher J. Poulsen & Joseph D. White
Global forest cover affects the Earth system by altering surface mass and energy exchange. Physiology determines plant environmental limits and influences geographical vegetation distribution. Ancient plant physiology, therefore, likely affected vegetation-climate feedbacks. We combine climate modeling and ecosystem-process modeling to simulate arboreal vegetation in the late Paleozoic ice age. Using GENESIS V3 GCM simulations, varying pCO2, pO2, and ice extent for the Pennsylvanian, and fossil-derived leaf C:N, maximum stomatal conductance, and specific conductivity for several...

Registration Year

  • 2021

Resource Types

  • Dataset


  • University of California, Davis
  • Colorado State University
  • University of California, Berkeley
  • University of California, Riverside
  • National Research Institute for Agriculture, Food and Environment
  • The Nature Conservancy
  • Duke University
  • University of Georgia
  • University of Minnesota
  • San Diego State University