841 Works

RNA sequencing of sorted conducting airway epithelial cells from FGF9-overexpressing and control mouse lungs at 1 day post-infection with IAV

Bradley Hiller
Influenza A virus (IAV) preferentially infects conducting airway and alveolar epithelial cells in the lung. The outcome of these infections is impacted by the host response, including the production of various cytokines, chemokines, and growth factors. Fibroblast growth factor-9 (FGF9) is required for lung development, can display antiviral activity in vitro, and is upregulated in asymptomatic patients during early IAV infection. We therefore hypothesized that FGF9 would protect the lungs from respiratory virus infection and...

Evolution in response to climate in the native and introduced ranges of a globally distributed plant

Simon Innes, James Santangelo, Nicholas Kooyers, Kenneth Olsen & Marc Johnson
The extent to which species can adapt to spatiotemporal climatic variation in their native and introduced ranges remains unresolved. To address this, we examined how clines in cyanogenesis (HCN production—an antiherbivore defense associated with decreased tolerance to freezing) have shifted in response to climatic variation in space and time over a 60-year period in both the native and introduced ranges of Trifolium repens. HCN production is a polymorphic trait controlled by variation at two Mendelian...

Data from: Climate change is associated with increased allocation to potential outcrossing in a common mixed mating species

Matthew Austin, Piper Cole, Kenneth Olsen & Adam Smith
Premise: The balance between cross- and self-fertilization is driven by the environment. Yet no long-term study has documented whether anthropogenic climate change is affecting reproductive strategy allocation in species with mixed mating systems. Here, we test whether the common blue violet (Viola sororia; Violaceae) has altered relative allocation to the production of potentially outcrossing flowers as the climate has changed across the 20th century. Methods: Using herbarium records spanning 1875 to 2015 from the central...

Phylogeographic and phenotypic outcomes of brown anole colonization across the Caribbean provide insight into the beginning stages of an adaptive radiation

Jason J. Kolbe, Richard E. Glor, Marta López‐Darias, C. Verónica Gómez Pourroy, Alexis S. Harrison, Kevin De Queiroz, Liam J. Revell, Jonathan B. Losos & Robert Graham Reynolds
Some of the most important insights into the ecological and evolutionary processes of diversification and speciation have come from studies of island adaptive radiations, yet relatively little research has examined how these radiations initiate. We suggest that Anolis sagrei is a candidate for understanding the origins of the Caribbean Anolis adaptive radiation and how a colonizing anole species begins to undergo allopatric diversification, phenotypic divergence and, potentially, speciation. We undertook a genomic and morphological analysis...

A new method to reconstruct quantitative food webs and nutrient flows from isotope tracer addition experiments

Andres Lopez-Sepulcre, Matthieu Bruneaux, Sarah Michelle Collins, Rana El-Sabaawi, Alexander S Flecker & Steven A Thomas
Understanding how nutrients flow through food webs is central in ecosystem ecology. Tracer addition experiments are powerful tools to reconstruct nutrient flows by adding an isotopically enriched element into an ecosystem, and tracking its fate through time. Historically, the design and analysis of tracer studies have varied widely, ranging from descriptive studies to modeling approaches of varying complexity. Increasingly, isotope tracer data is being used being used to compare ecosystems and analyze experimental manipulations. Currently,...

Untangling the importance of niche breadth and niche position as drivers of tree species abundance and occupancy across biogeographic regions

Dilys M. Vela Díaz, Cecilia Blundo, Leslie Cayola, Alfredo F. Fuentes, Lucio R. Malizia & Jonathan A. Myers
Aim: Ecological niches shape species commonness and rarity, yet the relative importance of different niche mechanisms within and across ecosystems remains unresolved. We tested the influence of niche breadth (range of environmental conditions where species occur) and niche position (marginality of a species’ environmental distribution relative to the mean environmental conditions of a region) on tree-species abundance and occupancy across three biogeographic regions. Location: Argentinian Andes; Bolivian Amazon; Missouri Ozarks. Time period: 2002–2010. Major taxa...

Aboveground carbon stocks and dynamics in Andean forests

Alvaro Duque, Miguel Peña, Francisco Cuesta, Sebastián González-Caro, Peter Kennedy, Oliver Phillips, Marco Calderón, Cecilia Blundo, Julieta Carilla, Leslie Cayola, William Farfán-Ríos, Alfredo Fuentes, Ricardo Grau, Jürgen Homeier, María I. Loza-Rivera, Jonathan A. Myers, Oriana Osinaga-Acosta, Manuel Peralvo, Esteban Pinto, Sassan Saatchi, Miles Silman, J. Sebastián Tello, Andrea Terán-Valdez & Kenneth J. Feeley
This dataset (Andean_AGB.xlsx) has the data employed in the paper entitled Old-growth Andean forests as globally important carbon sinks and future carbon refuges. The data was compiled as the results of the work of several research teams spread out across the Andean region. The information available here has data about aboveground carbon stocks and dynamics and the main explanatory variables, such as climate and symbiotic root associations.

Data From: TERRA-REF, An open reference data set from high resolution genomics, phenomics, and imaging sensors

David LeBauer, Burnette Maxwell, Jeffrey Demieville, Noah Fahlgren, Andrew French, Roman Garnett, Zhenbin Hu, Kimberly Huynh, Rob Kooper, Zongyang Li, Maitiniyazi Maimaitijiang, Jerome Mao, Todd Mockler, Geoffrey Morris, Maria Newcomb, Michael Ottman, Philip Ozersky, Sidike Paheding, Duke Pauli, Robert Pless, Wei Qin, Kristina Riemer, Gareth Rohde, William Rooney, Vasit Sagan … & Charles Zender
The ARPA-E funded TERRA-REF project is generating open-access reference datasets for the study of plant sensing, genomics, and phenomics. Sensor data were generated by a field scanner sensing platform that captures color, thermal, hyperspectral, and active flourescence imagery as well as three dimensional structure and associated environmental measurements. This dataset is provided alongside data collected using traditional field methods in order to support calibration and validation of algorithms used to extract plot level phenotypes from...

An aerodynamic perspective on hurricane-induced selection on Anolis lizards

Shamil Debaere, Colin Donihue, Anthony Herrel & Sam Van Wassenbergh
Studies have demonstrated that hurricanes can drive selection in Neotropical anoles. In a recent study it was shown that post-hurricane survivors showed increased toepad areas, and surprisingly, shorter femurs. One potential explanation for the reduction in femur length is that increased drag on individuals with longer femurs causes them to be blown off their perch. Consequently, lizards with shorter femora might survive better in hurricanes. To gain insight into the form-function relationships of drag-reduction in...

Scripts for analyzing Paspalum vaginatum GBS data

David Goad
Seashore paspalum (Paspalum vaginatum Swartz) is a halophytic turfgrass and emerging genomic model system for the study of salt tolerance in cereals and other grasses. Despite recent interest and an increase in available tools, little is known about the diversity present in wild populations of P. vaginatum and its close relative P. distichum. Variation in ploidy, clonal propagation, hybridization, and subgenome composition appear to occur in the wild and may interact to influence geographic patterns...

Filtered SNPs for wild Paspalum vaginatum and Paspalum distichum

David Goad
Filtered SNP calls in .ped format from "Hybridization, polyploidy and clonality influence geographic patterns of diversity and salt tolerance in the model halophyte seashore paspalum (Paspalum vaginatum)". We used GBS to genotype 218 P. vaginatum and P. distichum accessions collected from the US Gulf and Atlantic coasts plus available USDA germplasm. We confirm that P. vaginatum and P. distichum are genetically distinct and that the coarse-textured ecotype of P. vaginatum is composed of hybrids between...

Gene expression profiles compared in environmental and malnutrition enteropathy in Zambian children and adults

Paul Kelly, Mubanga Chama, Beatrice Amadi, Kanta Chandwe, Ellen Besa, Kanekwa Zyambo, Phillip I. Tarr, Nurmohammad Shaikh, I Malick Ndao, Chad Storer & Richard Head
Background: Environmental enteropathy (EE) contributes to growth failure in millions of children worldwide, but its relationship to clinical malnutrition has not been elucidated. We used RNA sequencing to compare duodenal biopsies from adults and children with EE, and from children with severe acute malnutrition (SAM), to define key features of these malnutrition-related enteropathies. Methods: RNA was extracted and sequenced from biopsies of children with SAM in hospital (n=27), children with non-responsive stunting in the community...

Mental Health Service Use Of Youth Leaving Foster Care (Voyages) 2001-2003

Curtis McMillen, Lionel Scott & Wendy Fran Auslander
The study was funded to explore the changes in mental health service use as older youth leave the foster care system. The data, however, examine many parameters of the lives of older youth in the foster care system, from their perspective. Four-hundred six youth in the Missouri foster care system were interviewed in person near their 17th birthday. They were re-interviewed when possible every three months until their 19th birthday. Eighty percent of the youth...

Data from: Rapid evolution of an adaptive cyanogenesis cline in introduced North American white clover (Trifolium repens L.)

Nicholas J. Kooyers & Kenneth M. Olsen
White clover is polymorphic for cyanogenesis (HCN production after tissue damage), and this herbivore defense polymorphism has served as a classic model for studying adaptive variation. The cyanogenic phenotype requires two interacting biochemical components; the presence/absence of each component is controlled by a simple Mendelian gene (Ac/ac and Li/li). Climate-associated cyanogenesis clines occur in both native (Eurasian) and introduced populations worldwide, with cyanogenic plants predominating in warmer locations. Moreover, previous studies have suggested that epistatic...

Data from: Ancestral polyploidy in seed plants and angiosperms

Yuannian Jiao, Norman J. Wickett, Ayyampalayam Saravanaraj, André S. Chanderbali, Lena Landherr, Paula E. Ralph, Lynn P. Tomsho, Yi Hu, Haiying Liang, Pamela S. Sotis, Douglas E. Soltis, Sandra W. Clifton, Scott E. Schlarbaum, Stephan C. Schuster, Hong Ma, Jim Leebens-Mack & Claude W. DePamphilis
Whole-genome duplication (WGD), or polyploidy, followed by gene loss and diploidization has long been recognized as an important evolutionary force in animals, fungi and other organisms1, 2, 3, especially plants. The success of angiosperms has been attributed, in part, to innovations associated with gene or whole-genome duplications4, 5, 6, but evidence for proposed ancient genome duplications pre-dating the divergence of monocots and eudicots remains equivocal in analyses of conserved gene order. Here we use comprehensive...

Data from: Molecular evolution of shattering loci in U.S. weedy rice

Carrie Thurber, Michael Reagon, Briana Gross, Kenneth Olsen, Yulin Jia & Ana Caicedo
Cultivated rice fields worldwide are plagued with weedy rice, a conspecific weed of cultivated rice (Oryza sativa L.). The persistence of weedy rice has been attributed, in part, to its ability to shatter (disperse) seed prior to crop harvesting. In the United States, separately evolved weedy rice groups have been shown to share genomic identity with exotic domesticated cultivars. Here, we investigate the shattering phenotype in a collection of U.S. weedy rice accessions, as well...

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