778 Works

Homologous chromosomes undergo sequential quasi-stable interactions during meiotic prophase

Trent Newman
The pairing of homologous chromosomes in meiosis I is essential for sexual reproduction and is mediated, in part, by the formation and repair of Spo11-induced DNA double strand breaks (DSBs). In budding yeast, each cell receives 150-200 DSBs, yet only a fraction go on to form crossover products. How and why the cell initially coordinates so many interactions along each chromosome is not well understood. Using a fluorescent reporter-operator system (FROS), we measure the kinetics...

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...

Effect of Drought Stress on the Genetic Architecture of Photosynthate Allocation and Remobilization in Pods of Common Bean (Phaseolus vulgaris L.), a Key Species for Food Security

Paul Gepts, Jorge Carlos Berny Mier Y Teran, Enéas R. Konzen, Antonia Palkovic, Siu M. Tsai, Idupulapati M. Rao & Stephen Beebe
Background: Common bean is the most important staple grain legume for direct human consumption and nutrition. It complements major sources of carbohydrates, including cereals, root crop, or plantain, as a source of dietary proteins. It is also a significant source of vitamins and minerals like iron and zinc. To fully play its nutritional role, however, its robustness against stresses needs to be strengthened. Foremost among these is drought, which commonly affects its productivity and seed...

Data deposition for Complex electrophysiological remodeling in postinfarction ischemic heart failure

Bence Hegyi & Ye Chen-Izu
Heart failure (HF) following myocardial infarction (MI) is associated with high incidence of cardiac arrhythmias. Development of therapeutic strategy requires detailed understanding of electrophysiological remodeling. However, changes of ionic currents in ischemic HF remain incompletely understood, especially in translational large animal models. Here, we systematically measure the major ionic currents in ventricular myocytes from the infarct border and remote zones in a porcine model of post-MI HF. We recorded eight ionic currents during the cell’s...


Raquel Peixoto, Phillipe Rosado, Deborah Leite, Gustavo Duarte, Ricardo Chaloub, Guillaume Jospin, Jonathan Eisen, David Bourne, Ulisses Da Rocha, João Saraiva & Francisco Dini-Andreote
Although the early coral reef-bleaching warning system (NOAA/USA) is established, there is no feasible treatment that can minimize temperature bleaching and/or disease impacts on corals in the field. Here, we present the first attempts to extrapolate the widespread and well-established use of bacterial consortia to protect or improve health in other organisms (e.g., humans and plants) to corals. Manipulation of the coral-associated microbiome was facilitated through addition of a consortium of native (isolated from Pocillopora...

Data for analysis of snowmelt timing as a determinant of inflow mixing in Lake Tahoe

Derek Roberts, Shohei Watanabe & S. Geoffrey Schladow
This dataset includes data files pertinent to the manuscript, "Snowmelting timing as a determinant of inflow mixing," accepted for publication in Water Resources Research in January 2018. Included data were used for an analysis of relative stream-lake conditions as they pertain to winter climate conditions and the subsequent mixing of snowmelt inflows into the lake. Included with each of the six files listed below is a [FILENAME]_Reference.txt file with details on data collection, curation, and...

Evolution of SSR diversity from wild types to U.S. advanced cultivars in the Andean and Mesoamerican domestications of common bean (Phaseolus vulgaris)

Paul Gepts
Progress in common bean breeding requires the exploitation of genetic variation among market classes, races and gene pools. The present study was conducted to determine the amount of genetic variation and the degree of relatedness among 192 selected common bean advanced cultivars using 58 simple-sequence-repeat markers (SSR) evenly distributed along the 11 linkage groups of the Phaseolus reference map. All the lines belonged to commercial seed type classes that are widely grown in the USA...

Temperature-Dependent Dynamics of Molecular Dopant in Conjugated Polymer

Jun Li, Tucker Murrey, Souleymane Diallo & Adam Moule
Understanding the nature of dopant dynamics in the solid state is critical for improving the longevity and stability of organic electronic devices and for optimizing the dopinginduced solubility control (DISC) patterning method. In this work, we use quasi-elastic neutron scattering (QENS) to study the dynamics of the soluble p-type molecular dopant tetrafluoromethyloxycarbonyltricyanoquinodimethane (F4MCTCNQ) in the semiconductive polymer poly(3-hexylthiophene-2,5-diyl) (P3HT). Specifically, fast dynamics (ps−ns) of the dopant, such as the methyl and the methoxycarbonyl group rotations,...

Supporting data for the manuscript: Observations and modeling of the surface seiches of Lake Tahoe, USA

Derek Roberts, S. Geoffrey Schladow & Alexander Forrest
This data set was created to make the data associated with the manuscript Observations and modeling of the surface seiches of Lake Tahoe, USA, accepted for publication in Aquatic Sciences, publically available per journal convention. The publication abstract is shown below: A rich array of spatially complex surface seiche modes exists in lakes. While the amplitude of these oscillations is often small, knowledge of their spatio-temporal characteristics is valuable for understanding when they might be...

Metagenome-assembled genomes provide new insight into the microbial diversity of two thermal pools in Kamchatka, Russia

Cassandra Ettinger, Laetitia Wilkins, Guillaume Jospin & Jonathan Eisen
Culture-independent methods have contributed substantially to our understanding of global microbial diversity. Recently developed algorithms to construct whole genomes from environmental samples have further refined, corrected and revolutionized understanding of the tree of life. Here, we assembled draft metagenome-assembled genomes (MAGs) from environmental DNA extracted from two hot springs within an active volcanic ecosystem on the Kamchatka peninsula, Russia. This hydrothermal system has been intensively studied previously with regard to geochemistry, chemoautotrophy, microbial isolation, and...

Is the USDA core collection of common bean representative of genetic diversity of the species, as assessed by SNP diversity?

Paul Gepts, Saarah Kuzay & Paige Hamilton
Core collections are envisioned to be a representative subset of larger germplasm collections. They were introduced to facilitate the characterization and use of these germplasm collections. The common bean (Phaseolus vulgaris) core collection of the USDA Western Regional Plant Introduction Station was one of the first ones to be established in the early 1990s. Here, we evaluate the representativity of this common bean collection in light of the availability of a SNP platform and new...

Data from: Feline immunodeficiency virus in puma: estimation of force of infection reveals insights into transmission

Jennifer Reynolds, Scott Carver, Mark Cunningham, Ken Logan, Winston Vickers, Kevin Crooks, Sue VandeWoude & Meggan Craft
Determining parameters that govern pathogen transmission (such as the force of infection, FOI), and pathogen impacts on morbidity and mortality, is exceptionally challenging for wildlife. Vital parameters can vary, for example across host populations, between sexes and within an individual's lifetime. Feline immunodeficiency virus (FIV) is a lentivirus affecting domestic and wild cat species, forming species-specific viral--host associations. FIV infection is common in populations of puma (Puma concolor), yet uncertainty remains over transmission parameters and...

NCST Caltrans project on sensor data error estimation

Yueyue Fan & Saurabh Maheshwari
The aim of this script is to automate the process of directed network graph formation, i.e., creation of incidence matrix, node adjacency matrix, and map the sensors to appropriate links. The data used for creating the freeway network is obtained from open street maps, whereas, the data for sensors is obtained from PeMS. The results of the algorithm will later be fed to the network sensor error estimation algorithm, that quantifies the erroneous sensors using...

Habitats and fish communities at mesophotic depths in the Mexican Pacific

Jordan A. Hollarsmith, Georgina Ramirez-Ortiz, Tallulah Winquist, Manuel Velasco-Lozano, Katherine DuBois, Hector Bonilla, Kyle Neumann & Ted Grosholz
Aim: Mesophotic ecosystems, found at the limit of light penetration in the ocean, are rich in biodiversity and harbor unique ecological communities. However, they remain among the least studied habitat zones on earth due to high costs and technological limitations. Here, we characterize mesophotic communities in two marine reserves across a range of habitat types, depths, and temperatures using submersible technologies, with the goal of understanding the processes that structure these communities across biogeographic regions....

Data from: Detailed temporal mapping of global human modification from 1990 to 2017

David Theobald, Christina Kennedy, Bin Chen, James Oakleaf, Joe Kiesecker & Sharon Baruch-Mordo
Data on the extent, patterns, and trends of human land use are critically important to support global and national priorities for conservation and sustainable development. To inform these issues, we created a series of detailed global datasets for 1990, 2000, 2010, 2015, and 2017 to evaluate temporal and spatial trends of land use modification of terrestrial lands (excluding Antarctica). Our novel datasets are detailed (0.09 km2 resolution), temporally consistent (for 1990-2015), comprehensive (11 change stressors,...

Long-term evidence shows crop-rotation diversification increases agricultural resilience to adverse growing conditions in North America

Timothy Bowles, Maria Mooshammer, Yvonne Socolar, Franciso Calderón, Michel Cavigelli, Steve Culman, William Dean, Axel Garcia Y Garcia, Amélie Gaudin, W Scott Harkom, Michael Lehman, Shannon Osborne, G Philip Robertson, Jonathan Salerno, Marty Schmer, Jeffrey Strock, A Stuart Grandy & Craig Drury
A grand challenge facing humanity is how to produce food for a growing population in the face of a changing climate and environmental degradation. Though empirical evidence remains sparse, management strategies that increase environmental sustainability, like increasing agroecosystem diversity through crop rotations, may also increase resilience to weather extremes without sacrificing yields. We used multilevel regression analyses of long-term crop yield datasets across a continental precipitation gradient to assess how temporal crop diversification affects maize...

Interspecific competition slows range expansion and shapes range boundaries

Geoffrey Legault, Matthew Bitters, Alan Hastings & Brett Melbourne
Species expanding into new habitats as a result of climate change or human introductions will frequently encounter resident competitors. Theoretical models suggest that such interspecific competition can alter the speed of expansion and the shape of expanding range boundaries. However, competitive interactions are rarely considered when forecasting the success or speed of expansion, in part because there has been no direct experimental evidence that competition affects either expansion speed or boundary shape. Here we demonstrate...

Evolution of the Greater Caucasus basement and formation of the Main Caucasus Thrust, Georgia

Dylan Vasey, Eric Cowgill, Sarah Roeske, Nathan Niemi, Tea Godoladze, Irakli Skhirtladze & Salome Gogoladze
Along the northern margin of the Arabia-Eurasia collision zone in the western Greater Caucasus, the Main Caucasus Thrust (MCT) juxtaposes Paleozoic crystalline basement to the north against Mesozoic metasedimentary and volcaniclastic rocks to the south. The MCT is commonly assumed to be the trace of an active plate-boundary scale structure that accommodates Arabia-Eurasia convergence, but field data supporting this interpretation are equivocal. Here we investigate the deformation history of the rocks juxtaposed across the MCT...

Channel types predictions for the South Fork Eel River basin

Hervé Guillon, Colin F. Byrne, Belize A. Lane, Samuel Sandoval Solis & Gregory B. Pasternack
Hydrologic and geomorphic classifications have gained traction in response to the increasing need for basin-wide water resources management. Regardless of the selected classification scheme, an open scientific challenge is how to extend information from limited field sites to classify tens of thousands to millions of channel reaches across a basin. To address this spatial scaling challenge, we leveraged machine learning to predict reach-scale geomorphic channel types using publicly available geospatial data.

Ecological rigidity and the hardness of selection in the wild

Denon Start
Hutchinson’s ecological theater and evolutionary play is a classical view of evolutionary ecology—ecology provides a template in which evolution occurs. An opposing view is that ecological and evolutionary changes are like two actors on a stage, intertwined by density- and frequency-dependence. These opposing views correspond to hard and soft selection respectively. While often presented as diametrically opposed, both types of selection can occur simultaneously, yet we largely lack knowledge of the relative importance of hard...

Effects of low-carbon energy adoption on airborne particulate matter concentrations with feedbacks to future climate over California

Anikender Kumar, Christina Zapata, Sonia Yeh, Chris Yang, Joan Ogden, Hsiang-He Lee, ShuHua Chen & Michael Kleeman
California plans to reduce emissions of long-lived greenhouse gases (GHGs) through adoption of new energy systems that will also lower concentrations of short-lived absorbing soot contained in airborne particulate matter (PM). Here we examine the direct and indirect effects of reduced PM concentrationsunder a low-carbon energy (GHG-Step) scenario on radiative forcing in California. Simulations were carried out using the source-oriented WRF/Chem (SOWC) model over California with 12 km spatial resolutionfor the year 2054. The avoided...

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...

Data from: Indirect genetic control of migration in a salmonid fish

Suzanne Kelson, Stephanie Carlson & Michael Miller
The paper titled "Indirect genetic control of migration in a salmonid fish" examines the genetic architecture of migration in a partially migratory salmonid fish, Oncorhynchus mykiss. We assess the shared genetic basis between early life growth and migration, and find a shared allelic basis on the Omy05 region of the genome. We then test if early life growth differs among resident/migratory genotype juvenile fish in streams in the South Fork Eel River watershed, in Northern...

The effectiveness of flower strips and hedgerows on pest control, pollination services and crop yield: a quantitative synthesis

Matthias Albrecht, David Kleijn, Neal Williams, Matthias Tschumi, Brett Blaauw, Riccardo Bommarco, Alistair Campbell, Matteo Dainese, Frank Drummond, Martin Entling, Dominik Ganser, Arjen De Groot, David Goulson, Heather Grab, Hannah Hamilton, Felix Herzog, Rufus Isaacs, Katja Jacot, Philippe Jeanneret, Mattias Jonsson, Eva Knop, Claire Kremen, Doug Landis, Greg Loeb, Lorenzo Marini … & Louis Sutter
Floral plantings are promoted to foster ecological intensification of agriculture through provisioning of ecosystem services. However, a comprehensive assessment of the effectiveness of different floral plantings, their characteristics and consequences for crop yield is lacking. Here we quantified the impacts of flower strips and hedgerows on pest control (18 studies) and pollination services (17 studies) in adjacent crops in North America, Europe and New Zealand. Flower strips, but not hedgerows, enhanced pest control services in...

Analytical Modeling Framework to Assess the Economic and Environmental Impacts of Residential Deliveries, and Evaluate Sustainable City Logistics Strategies

Anmol Pahwa & Miguel Jaller
In the last decade, e‐commerce has grown substantially, increasing business‐to‐business, business‐to‐consumer, and consumer‐to‐consumer transactions. As a result, there has been a continuous growth in last mile operations, especially deliveries to residential areas, bringing along externalities such as congestion, air and noise pollution, and energy consumption. This project aims to develop an analytical framework to model last mile operations based on continuous approximation techniques. The model will help estimate the economic and environmental impacts of residential...

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  • University of California, Davis
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