126 Works

Host Factor Experiment (ICL012-R)

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Purpose: To obtain samples from Calu-3 cells infected with A/Vietnam/1203-CIP048_RG4/2004 (H5N1). Details: Time Points = 0, 3, 7, 12, 18 and 24hrs post infection were taken for mutant virus while wild type virus was only tested at 7 and 24hrs post-infection; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock as rest of samples;...

Host Factor Experiment (IM007-P)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG4/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 and 10^4 PFU.

Host Factor Experiment (SCL006-P)

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Purpose: To obtain samples for transcriptional analysis and proteomics in triplicate using wild typeicSARS urbani and icSARS Bat SRBD mutant in 2B4 cells/sorted Calu3 cells with high ACE2 expression. Overview of Experiment: Time Points = 0, 7, 12, 24, 30, 36, 48, 54, 60 and 72 hrs post infection. (Note: there is no time point at 7 h for icSARS Bat SRBD.) Done in triplicate for both RNA and Protein. Triplicates are defined as 3...

Host Factor Experiment (ICL004-R)

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Purpose: To obtain samples from Calu-3 cells infected with A/Vietnam/1203/2004(H5N1) for both transcriptional and proteomics analyses. Details: Time Points = 0, 3, 7, 12, 18, and 24 h post infection; Done in triplicate for both RNA and Protein; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock as rest of samples; Culture medium (the...

Host Factor Experiment (ICL010-P)

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Purpose: To obtain samples from Calu-3 cells infected with A/Netherlands/602/2009 (H1N1) and A/CA/04/09 (H1N1) for transcriptional analysis and proteomics analysis for A/Netherlands/602/2009. For A/Netherlands/602/2009 and mock infected the time points are 0, 3, 7, 12, 18, 24, 30, 36 and 48 h post infection. For A/CA/04/09 the time points are 0,12, 24 and 48 h post infection.There are triplicate samples for all conditions for both transcriptional and proteomics analyses. Triplicates are defined as 3 different...

Host Factor Experiment (ICL011-P)

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Purpose: To obtain samples from Calu-3 cells infected with mutants A/Vietnam/1203-CIP048_RG2/2004 (H5N1) and A/Vietnam/1203-CIP048_RG3/2004 (H5N1). Details: Time Points = 0, 3, 7, 12, 18 and 24hrs post infection were taken for mutant viruses while wild type virus was only tested at 7 and 24hrs post-infection; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock...

Host Factor Experiment (ICL012-P)

&
Purpose: To obtain samples from Calu-3 cells infected with A/Vietnam/1203-CIP048_RG4/2004 (H5N1). Details: Time Points = 0, 3, 7, 12, 18 and 24hrs post infection were taken for mutant virus while wild type virus was only tested at 7 and 24hrs post-infection; Triplicates are defined as 3 different wells, plated at the same time using the same cell stock for all replicates; Time matched mocks done in triplicate from same cell stock as rest of samples;...

Host Factor Experiment (IM010-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203/2004 (H5N1) for transcriptional analyses. Details: Mouse strains = WT, IDO1 knock-out and Tnfrsf1b knock-out; Time Points = 2 and 6 days post-infection; 2-3 replicates for each mouse strain; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 1000 pfu.

Host Factor Experiment (SM007-R)

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Purpose: To obtain lung samples from Tnfrsf1a/1b knock out mutant mice infected with SARS MA15 virus for transcriptional analyses. Details: Time Points = days 2, 4 and 7 post-infection; 2-4 replicate mice for each condition; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^4 pfu.

Host Factor Experiment (CA04M001-P)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics. General Design: 20 week-old C57Bl6 mice; Three Doses = 1E3, 1E4, 1E5, 1E6 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Rapamycin rejuvenates oral health in aging mice

Kristopher Kerns
Periodontal disease is an age-associated disorder clinically defined by periodontal bone loss, inflammation of the specialized tissues that surround and support the tooth, and microbiome dysbiosis. Currently, there is no therapy for reversing periodontal disease, and treatment is generally restricted to preventive measures or tooth extraction. The FDA-approved drug rapamycin slows aging and extends lifespan in multiple organisms, including mice. Here we demonstrate that short-term treatment with rapamycin rejuvenates the aged oral cavity of elderly...

Habitat transitions alter the adaptive landscape and shape phenotypic evolution in needlefishes (Belonidae)

Matthew Kolmann, Michael D. Burns, Justin Y. K. Ng, Nathan R. Lovjoy & Devin D. Bloom
Habitat occupancy can have a profound influence on macroevolutionary dynamics, and a switch in major habitat type may alter the evolutionary trajectory of a lineage. In this study we investigate how evolutionary transitions between marine and freshwater habitats affect macroevolutionary adaptive landscapes, using needlefishes (Belonidae) as a model system. We examined the evolution of body shape and size in marine and freshwater needlefishes and tested for phenotypic change in response to transitions between habitats. Using...

Activity niches outperform thermal physiological limits in predicting global ant distributions

Fengyi Guo, Benoit Guénard, Evan Economo, Curtis Deutsch & Timothy Bonebrake
Aim: Thermal physiology is commonly used in mechanistic models to predict species distributions and project distribution change. Such thermal constraints for ants are often measured under laboratory conditions as critical thermal limits (CTmax and CTmin), but have also been observed in the field as foraging thermal limits (FTmin and FTmax). Here we compared distribution projections based on ant physiological and behavioural thermal limits with their realized distributions to assess the validity of using ecophysiological models...

Data from: Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Charles Waters, Jeffrey Hard, David Fast, Curtis Knudsen, William Bosch & Kerry-Ann Naish
Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic-based estimates of inbreeding to investigate their relationship with eight adult traits in a captive-reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction-site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by...

Level and spatial pattern of overstory retention impose tradeoffs for regenerating and retained trees

Charles Halpern & Lauren Urgenson
Variable retention (VR) has been adopted globally as an alternative to more intensive forms of regeneration harvest. By retaining live trees within harvest units, VR seeks balance among the commodity, ecological, and aesthetic values of managed forests. Achieving these multiple, often competing objectives requires an understanding of how level and spatial pattern of retention shape the abundance, growth, and mortality of regenerating and retained trees. Using long-term (18-19 yr) data from a regional-scale VR experiment,...

Fluid-preserved fishes are one solution for assessing historical change in fish trophic level

Rachel Welicky, Terry Rolfe, Karrin Leazer, Katherine Pearson Masklenikov, Luke Tornabene, Gordon Holtgrieve & Chelsea Wood
There are few resources available for assessing historical change in fish trophic dynamics, but specimens held in natural history collections could serve as this resource. In contemporary trophic ecology studies, trophic and source information can be obtained from compound-specific stable nitrogen isotope analysis (CSIA-AA-N). Can this method yield reliable trophic information from chemically-altered fish specimens held in natural history collections? We tested whether CSIA-AA-N can be used on fluid-preserved specimens by experimentally subjecting specimens to...

Data from: Gut microbiome critically impacts PCB-induced changes in metabolic fingerprints and the hepatic transcriptome in mice

Joe Lim, Julia Cui, Xueshu Li, Hans-Joachim Lehmler, Dongfang Wang & Haiwei Gu
Polychlorinated biphenyls (PCBs) are ubiquitously detected in the environment and have been linked to metabolic diseases. The liver serves as a central hub for the metabolism of xenobiotics and endogenous metabolites. Gut dysbiosis is recognized as a critical regulator of disease susceptibility, however, little is known regarding how PCBs and gut microbiome interact to modulate the interface between xenobiotic and intermediary metabolism. We hypothesized that the gut microbiome regulates PCBs-mediated changes in the metabolic fingerprints...

Data from: Phosphorus limitation does not drive loss of bony lateral plates in freshwater stickleback (Gasterosteus aculeatus)

Sophie L. Archambeault, Daniel J. Durston, Alex Wan, Rana El-Sabaawi, Blake Matthews & Catherine L. Peichel
Connecting the selective forces that drive the evolution of phenotypes to their underlying genotypes is key to understanding adaptation, but such connections are rarely tested experimentally. Threespine stickleback (Gasterosteus aculeatus) are a powerful model for such tests because genotypes that underlie putatively adaptive traits have been identified. For example, a regulatory mutation in the Ectodysplasin (Eda) gene causes a reduction in the number of bony armor plates, which occurs rapidly and repeatedly when marine sticklebacks...

Data from - Ecological insights from three decades of animal movement tracking across a changing Arctic

Gil Bohrer, Sarah Davidson, Eliezer Gurarie, Scott LaPoint, Peter Mahoney, Emma Grier, Ophélie Couriot, Allicia Kelly, Bryan Bedrosian, Jerrold Belant, Travis Booms, Bridget Borg, Stan Boutin, Erica Craig, Tracy Davison, Robert Domenech, James Hodson, Kyle Joly, Nicholas Larter, A. David M. Latham, Stephen Lewis, Carol McIntyre, Tricia Miller, Kelsey Russell, Dale Seip … & Judy Williams
We provide here the data used in analysis of 3 test cases, presented in the manuscript "Ecological insights from three decades of animal movement tracking across a changing Arctic". We utilized the new Arctic Animal Movement Archive (AAMA), a growing collection of 201 standardized terrestrial and marine animal tracking studies from 1991–present. The AAMA supports public data discovery, preserves fundamental baseline data for the future, and facilitates efficient, collaborative data analysis. With three AAMA-based case...

Confronting sources of systematic error to resolve historically contentious relationships: a case study using gadiform fishes (Teleostei, Paracanthopterygii, Gadiformes)

Adela Roa-Varon, Rebecca Dikow, Giorgio Carnevale, Luke Tornabene, Carole Baldwin, Chenhong Li & Eric Hilton
Reliable estimation of phylogeny is central to avoid inaccuracy in downstream macroevolutionary inferences. However, limitations exist in the implementation of concatenated and summary coalescent approaches, and Bayesian and full coalescent inference methods may not yet be feasible for computation of phylogeny using complicated models and large datasets. Here, we explored methodological (e.g., optimality criteria, character sampling, model selection) and biological (e.g., heterotachy, branch length heterogeneity) sources of systematic error that can result in biased or...

Newick trees for \"Within-patient phylogenetic reconstruction reveals early events in Barrett's Esophagus\"

Mary Kuhner & Lucian Smith
Newick format within-patient phylogenetic trees for a Barrett's Esophagus WGS dataset

Host Factor Experiment (SM001-P)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; ThreeDoses = 1E2, 1E3,1E4 and 1E5 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Host Factor Experiment (SM019-R)

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Purpose: To obtain lung samples from Tnfrsf1b knock out mutant mice infected with SARS MA15 virus for transcriptional analyses. Details: Time Points = days 4 and 7 post-infection; 2-3 replicate mice for each condition; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^5 pfu.

Host Factor Experiment (IM007-R)

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Purpose: To obtain lung samples from C57BL6 mice infected with Vietnam/1203-CIP048_RG4/2004 (H5N1) for both transcriptional and proteomic analyses. Details: Time Points = 1, 2, 4 and 7 days post infection; 5 replicates for infected mice and triplicate mice for the mocks; Inoculation medium for mock infection was the same as the medium used for virus infection. Infection dose was 10^3 and 10^4 PFU.

Host Factor Experiment (IM001-P)

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Purpose: To look at the host response to different doses across 4 time points after infection. Samples were collected for both transcriptomics and proteomics.General Design: 20 week-old C57Bl6 mice; ThreeDoses = 1E2, 1E3, & 1E4 (PFU); Time points of 1, 2, 4 and 7 days; ~5 mice/time point for infections; 3 mice/timepoint for time matched mocks

Registration Year

  • 2020
    126

Resource Types

  • Dataset
    126

Affiliations

  • University of Washington
    126
  • University of Queensland
    3
  • Oregon State University
    3
  • University of California, Berkeley
    3
  • Smithsonian Institution
    3
  • Arizona State University
    3
  • University of California Los Angeles
    3
  • Bangor University
    2
  • Stanford University
    2
  • University of Pretoria
    2