44 Works

Novel synthetic 3’-untranslated regions for controlling transgene expression in transgenic Aedes aegypti mosquitoes

Keun Chae, Collin Valentin, Emma Jakes, Kevin M Myles & Zach N Adelman
Transgenic technology for mosquitoes is now more than two decades old, and a wide array of control sequences have been described for regulating gene expression in various life stages or specific tissues. Despite this, comparatively little attention has been paid to the development and validation of other transgene-regulating elements, especially 3ʹ-untranslated regions (3ʹUTRs). As a consequence, the same regulatory sequences are often used multiple times in a single transgene array, potentially leading to instability of...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

Data from: Plant functional types broadly describe water use strategies in the Caatinga, a seasonally dry tropical forest in northeast Brazil

Cynthia Wright, André Lima, Eduardo Souza, Jason West & Bradford Wilcox
In seasonally dry tropical forests, plant functional type can be classified as deciduous low wood density, deciduous high wood density, or evergreen high wood density species. While deciduousness is often associated with drought-avoidance and low wood density is often associated with tissue water storage, the degree to which these functional types may correspond to diverging and unique water use strategies has not been extensively tested. We examined (1) tolerance to water stress, measured by pre-dawn...

MCMC output files for: Quantitative characterization of population-wide tissue- and metabolite-specific variability in perchloroethylene toxicokinetics in male mice

Chimeddulam Dalaijamts, Joseph Cichocki, Yu-Syuan Luo, Ivan Rusyn & Weihsueh Chiu
Quantification of inter-individual variability is a continuing challenge in risk assessment, particularly for compounds with complex metabolism and multi-organ toxicity. Toxicokinetic variability for perchloroethylene (perc) was previously characterized across three mouse strains and in one mouse strain with various degrees of liver steatosis. To further characterize the role of genetic variability in toxicokinetics of perc, we applied Bayesian population physiologically-based pharmacokinetic (PBPK) modeling to the data on perc and metabolites in blood/plasma and tissues of...

Dataset from: Ardipithecus hand provides evidence that humans and chimpanzees evolved from an ancestor with suspensory adaptations

Thomas Cody Prang, Kristen Ramirez, Mark Grabowski & Scott Williams
The morphology and positional behavior of the last common ancestor of humans and chimpanzees are critical for understanding the evolution of bipedalism. Early 20th century anatomical research supported the view that humans evolved from a suspensory ancestor bearing some resemblance to apes. However, the hand of the 4.4 million-year-old hominin Ardipithecus ramidus, purportedly provides evidence that the hominin hand was derived from a more generalized form. Here we use morphometric and phylogenetic comparative methods to...

Investigating cooccurrence patterns and dynamics for many imperfectly detected species, using a log-linear modelling parameterisation

Darryl MacKenzie, Jason Lombardi & Michael Tewes
Patterns in, and the underlying dynamics of, species cooccurrence is of interest in many ecological applications. Unaccounted for, imperfect detection of the species can lead to misleading inferences about the nature and magnitude of any interaction. A range of different parameterisations have been published that could be used with the same fundamental modelling framework that accounts for imperfect detection, although each parameterisation has different advantages and disadvantages. We propose a parameterisation based on log-linear modelling...

A narrow window for geographic cline analysis using genomic data: effects of age, drift, and migration on error rates

Gaston Jofre & Gil Rosenthal
The use of genomic and phenotypic data to scan for outliers is a mainstay for studies of hybridization and speciation. Geographic cline analysis of natural hybrid zones is widely used to identify putative signatures of selection by detecting deviations from baseline patterns of introgression. As with other outlier-based approaches, demographic histories can make neutral regions appear to be under selection and vice versa. In this study, we use a forward-time individual-based simulation approach to evaluate...

Source Data for \"Block copolymers beneath the surface: measuring and molding complex morphology at the sub-domain scale\"

Abhiram Reddy, Edwin Thomas & Greg Grason

Data for \"The Oligocene-Miocene Guadalope-Matarranya Fan, Spain, as an Analog for Long-Lived, Ridge-Bearing Megafans on Mars\"

Alistair T Hayden, Michael P Lamb, Paul Myrow, David C Mohrig, Rebecca M E Williams, Jose Luis Cuevas Martínez, Benjamin T Cardenas, Clyde P Findlay, Ryan C Ewing & Brandon J McElroy
This data repository contains three spreadsheets of data referenced in the manuscript: - Ridge caprock dimensions - Stratigraphic data - Dimensions of unexhumed channel belts Article abstract: Numerous sedimentary fans on Mars have been studied to better understand the early martian hydrological system. Of particular interest is to estimate the duration of fluvial activity from alluvial fan size by dividing deposit volume by bankfull sediment flux. However, such a calculation requires an intermittency factor—a parameter...

Endemic plants of the Indian peninsular savannas

Ashish Nerlekar, Alok Chorghe, Jagdish Dalavi, Raja Kullayiswamy, Subbiah Karuppusamy, Vignesh Kamath, Ritesh Pokar, Ganesan Rengaian, Milind Sardesai & Sharad Kambale
Biodiversity of tropical grasslands and savannas (tropical grassy biomes; TGBs) remains poorly documented compared to tropical forests. This is in part due to the misplaced notion of TGBs being anthropogenic forest derivatives that support negligible biodiversity and endemism. For the Indian savannas, the legacy of colonial forestry has led to their misinterpretation as anthropogenic wastelands of low conservation value. One key assumption underlying the devaluation of Indian savannas against Indian forests is the presumed absence...

Ecosystem sulfur accumulation following woody encroachment drives a more open S-cycle in a subtropical savanna

Yong Zhou, Ayumi Hyodo & Thomas Boutton
Globally widespread woody encroachment into grass-dominated ecosystems has substantial consequences for carbon (C), nitrogen (N), and phosphorus (P) cycles. Despite its significance as an essential macronutrient, however, little is known regarding potential changes in the sulfur (S) cycle. We quantified S concentrations, stoichiometric relationships, and δ34S values in the plant-soil environment to investigate landscape-scale changes in the S cycle following grassland-to-woodland transitions in a subtropical savanna. Plant tissues of woody species had significantly higher S...

Natural variation in colony inbreeding does not influence susceptibility to a fungal pathogen in a termite

Pierre Andre Eyer, Carlos Aguero, Pierre-André Eyer, Jason Martin, Mark Bulmer & Edward Vargo
Reduced genetic diversity through inbreeding can negatively affect pathogen resistance. This relationship becomes more complicated in social species, such as social insects, since the chance of disease transmission increases with the frequency of interactions among individuals. However, social insects may benefit from social immunity, whereby individual physiological defenses may be bolstered by collective-level immune responses, such as grooming or sharing of antimicrobial substance through trophallaxis. We set out to determine whether differences in genetic diversity...

Comparative analysis of phenotypic plasticity sheds light on the evolution and molecular underpinnings of locust phase polyphenism

Hojun Song, Bert Foquet & Adrian Castellanos
Locusts exhibit one of nature’s most spectacular examples of complex phenotypic plasticity, in which changes in density cause solitary and cryptic individuals to transform into gregarious and conspicuous locusts forming large migrating swarms. We investigated how these coordinated alternative phenotypes might have evolved by studying the Central American locust and three closely related non-swarming grasshoppers in a comparative framework. By experimentally isolating and crowding during nymphal development, we induced density-dependent phenotypic plasticity and quantified the...

Supplementary figures for: Of traits and trees: probabilistic distances under continuous trait models for dissecting the interplay among phylogeny, model, and data

Richard Adams, Heath Blackmon & Michael DeGiorgio
Stochastic models of character trait evolution have become a cornerstone of evolutionary biology in an array of contexts. While probabilistic models have been used extensively for statistical inference, they have largely been ignored for the purpose of measuring distances between phylogeny-aware models. Recent contributions to the problem of phylogenetic distance computation have highlighted the importance of explicitly considering evolutionary model parameters and their impacts on molecular sequence data when quantifying dissimilarity between trees. By comparing...

Novel synthetic 3’-untranslated regions for controlling transgene expression in transgenic Aedes aegypti mosquitoes

Keun Chae, Collin Valentin, Emma Jakes, Kevin M Myles & Zach N Adelman
Transgenic technology for mosquitoes is now more than two decades old, and a wide array of control sequences have been described for regulating gene expression in various life stages or specific tissues. Despite this, comparatively little attention has been paid to the development and validation of other transgene-regulating elements, especially 3ʹ-untranslated regions (3ʹUTRs). As a consequence, the same regulatory sequences are often used multiple times in a single transgene array, potentially leading to instability of...

Millennial-scale change on a Caribbean reef system that experiences hypoxia

Blanca Figuerola, Ethan L. Grossman, Noelle Lucey, Nicole D. Leonard & Aaron O'Dea
Coastal hypoxia has become an increasingly acknowledged threat to coral reefs that is potentially intensifying because of increased input of anthropogenic nutrients. Almirante Bay (Caribbean Panama) is a semi-enclosed system that experiences hypoxia in deeper waters which occasionally expand into shallow coral reefs, suffocating most aerobic benthic life. To explore the long-term history of reefs in the bay we extracted reef matrix cores from two reefs that today experience contrasting patterns of oxygenation. We constructed...

Divergent patterns and spatial heterogeneity of soil nutrients in a complex and dynamic savanna landscape

Yong Zhou, Robert Taylor & Thomas Boutton
Many grassy ecosystems around the world are experiencing woody encroachment. These woody encroachers often cause nutrient enrichment in the plant-soil environment, potentially facilitating their growth and reproduction. However, studies of encroachment effects on nutrient distributions have been confined to a few major elements (e.g., N, and P) and limited in spatial extent. We analyzed 19 elements in dominant plants and in georeferenced soils across a subtropical savanna landscape experiencing woody encroachment to quantify their spatial...

Data from: Distinct colony boundaries and larval discrimination in polygyne red imported fire ants (Solenopsis invicta)

MacKenzie Kjeldgaard, Pierre-André Eyer, Collin McMichael, Alison Bockoven, Joanie King, Ayumi Hyodo, Thomas Boutton, Edward Vargo & Micky Eubanks
Evaluating the factors that promote invasive ant abundance is critical to assess their ecological impact and inform their management. Many invasive ant species show reduced nestmate recognition and an absence of boundaries between unrelated nests, which allow populations to achieve greater densities due to reduced intraspecific competition. We examined nestmate discrimination and colony boundaries in introduced populations of the red imported fire ant (Solenopsis invicta; hereafter, fire ant). Fire ants occur in two social forms:...

ISIMIP3b ocean input data

Matthias Büchner
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a consistent set of climate impact data across sectors and scales. It also provides a unique opportunity for considering interactions between climate change impacts across sectors through consistent scenarios.
The ISIMIP3b part of the third simulation round is dedicated to a quantification of climate-related risks at different levels of global warming and socio-economic change. ISIMIP3b group I simulations are based on historical...

Registration Year

  • 2021
    44

Resource Types

  • Dataset
    44

Affiliations

  • Texas A&M University
    44
  • Potsdam Institute for Climate Impact Research
    3
  • Queensland University of Technology
    3
  • Geophysical Fluid Dynamics Laboratory
    3
  • Zhejiang University
    2
  • Central South University
    2
  • Stanford University
    2
  • Third Affiliated Hospital of Guangzhou Medical University
    2
  • Chengdu University of Traditional Chinese Medicine
    2
  • Chinese University of Hong Kong
    2