256 Works

Data from: Developmental instability is genetically correlated with phenotypic plasticity, constraining heritability, and fitness

Stephen J. Tonsor, Tarek W. Elnaccash & Samuel M. Scheiner
Although adaptive plasticity would seem always to be favored by selection, it occurs less often than expected. This lack of ubiquity suggests that there must be trade-offs, costs, or limitations associated with plasticity. Yet, few costs have been found. We explore one type of limitation, a correlation between plasticity and developmental instability, and use quantitative genetic theory to show why one should expect a genetic correlation. We test that hypothesis using the Landsberg erecta ×...

Data from: Effect of IV glyburide on adjudicated edema endpoints in the GAMES-RP Trial

W. Taylor Kimberly, Matthew B. Bevers, Rüdiger Von Kummer, Andrew M. Demchuk, Javier M. Romero, Jordan J. Elm, Holly E. Hinson, Bradley J. Molyneaux, J. Marc Simard & Kevin Navin Sheth
Objective: In this secondary analysis of the GAMES-RP trial, we report the effect of IV glyburide on adjudicated, edema-related endpoints. Methods: Blinded adjudicators assigned designations for hemorrhagic transformation, neurological deterioration, malignant edema and edema-related death to patients from the GAMES-RP Phase II randomized controlled trial of IV glyburide for large hemispheric infarct. Rates of these endpoints were compared between treatment arms in the per-protocol sample. In those participants with malignant edema, the effects of treatment...

Data from: Genetic architecture of sexual dimorphism in a subdioecious plant with a proto-sex chromosome

Rachel B. Spigler, Kim S. Lewers & Tia-Lynn Ashman
The rise of sexual dimorphism is thought to coincide with the evolution of sex chromosomes. Yet because sex chromosomes in many species are ancient, we lack empirical evidence of the earliest stages of this transition. We use QTL analysis to examine the genetic architecture of sexual dimorphism in subdioecious octoploid Fragaria virginiana. We demonstrate that the region housing the male-function locus controls the majority of quantitative variation in proportion fruit set, confirming the existence of...

Data from: Monoamine abnormalities in the SAPAP3 knockout model of obsessive-compulsive disorder-related behaviour

Jesse Wood, Zoe LaPalombara & Susanne E. Ahmari
Obsessive-compulsive disorder (OCD) is a leading cause of illness-related disability, but the neuralmechanisms underlying OCDsymptoms are unclear. One potential mechanism of OCD pathology is monoamine dysregulation. Because of the difficulty of studying monoamine signalling in patients, animal models offer a viable alternative to understanding this aspect of OCD pathophysiology. We used HPLC to characterize post-mortem monoamine levels in lateral orbitofrontal cortex (OFC), medial OFC, medial prefrontal cortex and dorsal and ventral striatum of SAPAP-3 knockout...

Data from: Revisiting protein aggregation as pathogenic in sporadic Parkinson’s and Alzheimer’s diseases

Alberto J. Espay, Joaquin A. Vizcarra, Luca Marsili, Anthony E. Lang, David K. Simon, Aristide Merola, Keith A. Josephs, Alfonso Fasano, Francesca Morgante, Rodolfo Savica, J. Timothy Greenamyre, Franca Cambi, Tritia R. Yamasaki, Caroline M. Tanner, Ziv Gan-Or, Irene Litvan, Ignacio F. Mata, Cyrus P. Zabetian, Patrik Brundin, Hubert H. Fernandez, David G. Standaert, Marcelo A. Kauffman, Michael A. Schwarzschild, S. Pablo Sardi, Todd Sherer … & James B. Leverenz
The gold standard for a definitive diagnosis of Parkinson’s disease (PD) is the pathologic finding of aggregated alpha-synuclein into Lewy bodies and for Alzheimer’s disease (AD) aggregated amyloid into plaques and hyperphosphorylated tau into tangles. Implicit in this clinico-pathologic-based nosology is the assumption that pathological protein aggregation at autopsy reflect pathogenesis at disease onset. While these aggregates may in exceptional cases be on a causal pathway in humans (e.g., aggregated alpha-synuclein in SNCA gene multiplication...

Data from: Selection for collective aggressiveness favors social susceptibility in social spiders

Jonathan N. Pruitt, Colin M. Wright, James L. L. Lichtenstein, Gregory T. Chism, Brendan L. McEwen, Ambika Kamath & Noa Pinter-Wollman
Particularly socially influential individuals are present in many groups, but it is unclear whether their emergence is determined by their social influence versus the social susceptibility of others. The social spider Stegodyphus dumicola shows regional variation in apparent leader-follower dynamics. We use this variation to evaluate the relative contributions of leader social influence versus follower social susceptibility in driving this social order. Using chimeric colonies that combine potential leaders and followers, we discover that leader-follower...

Data from: Phylogeny meets ecotoxicology: evolutionary patterns of sensitivity to a common insecticide

John I. Hammond, Devin K. Jones, Patrick R. Stephens & Rick A. Relyea
Pesticides commonly occur in aquatic systems and pose a substantial challenge to the conservation of many taxa. Ecotoxicology has traditionally met this challenge by focusing on short-term, single-species tests and conducting risk assessments based on the most sensitive species tested. Rarely have ecotoxicology data been examined from an evolutionary perspective and to our knowledge there has never been a phylogenetic analysis of sensitivity, despite the fact that doing so would provide insights into patterns of...

Data from: Animal personality in a foundation species drives community divergence and collapse in the wild

Jonathan N. Pruitt & Andreas P. Modlmeier
1. Despite thousands of papers on the topic, precious few of the studies on animal personality have considered the role of personality in shaping community-level processes. Here, we test the effect of individual variation on the long-term trajectories of biological communities, from initiation to their demise. The spider Anelosimus studiosus builds webs that serve as habitat for >50 species of spider, which together construct a species-rich silken reef. This species also exhibits a temporally consistent...

Data from: Clinal variation in seed traits influencing life cycle timing in Arabidopsis thaliana.

Alicia Montesinos-Navarro, F. Xavier Picó & Stephen J. Tonsor
Early life history transitions are crucial determining lifetime survival and fecundity. Adaptive evolution in early life history traits involves a complex interplay between the developing plant and its current and future environments. We examined the plant’s earliest life history traits, dissecting an integrated suite of pre-germination processes: primary dormancy, thermal induction of secondary dormancy, and seasonal germination response. We examined genetic variation in the three processes, genetic correlations among the processes, and the scaling of...

Data from: Associative learning of flowers by generalist bumble bees can be mediated by microbes on the petals

Avery L. Russell & Tia-Lynn Ashman
Communication is often vital to the maintenance of mutualisms. In plant-pollinator mutualisms, plants signal pollinators via floral displays, composed of olfactory, visual, and other plant-derived cues. While plants are understood to be associated with microbes, only recently has the role of microbial (yeast and bacteria) inhabitants of flowers as intermediaries of plant-pollinator communication been recognized. Animals frequently use microbial cues to find resources, yet no study has examined whether microbes directly mediate learned and innate...

Data from: Using a continuum model to decipher the mechanics of embryonic tissue spreading from time-lapse image sequences: an approximate Bayesian computation approach

Tracy L. Stepien, Holley E. Lynch, Shirley X. Yancey, Laura Dempsey & Lance A. Davidson
Advanced imaging techniques generate large datasets that are capable of describing the structure and kinematics of tissue spreading in embryonic development, wound healing, and the progression of many diseases. Information in these datasets can be integrated with mathematical models to infer important biomechanical properties of the system. Standard computational tools for estimating relevant parameters rely on methods such as gradient descent and typically identify a single set of optimal parameters for a single experiment. These...

Data from: Who shares? Who doesn’t? Factors associated with openly archiving raw research data

Heather A. Piwowar
Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn’t, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets...

Data from: Eutrophication and predation risk interact to affect sexual trait expression and mating success

Rickey Duane Cothran, Andy R Stiff, Punidan D Jeyasingh & Rick A Relyea
Sexual traits are especially sensitive to low food resources. Other environmental parameters (e.g., predation) should also affect sexual trait expression by favoring investment in viability traits rather than sexual traits. We know surprisingly little about how predators alter investment in sexual traits, or how predator and resource environments interact to affect sexual trait investment. We explored how increasing phosphorous (P) availability, at a level mimicking cultural eutrophication, affects the development of sexual, non-sexual, and viability...

Competition for pollination and isolation from mates differentially impact four stages of pollination in a model grassland perennial

Lea K. Richardson, M. Kate Gallagher, Tracie E. Hayes, Amanda S. Gallinat, Gretel Kiefer, Kristen Manion, Miriam Jenkins, Greg Diersen & Stuart Wagenius
1. Species that persist in small populations isolated by habitat destruction may experience reproductive failure. Self-incompatible plants face dual threats of mate-limitation and competition with co-flowering plants for pollination services. Such competition may lower pollinator visitation, increase heterospecific pollen transfer, and reduce the likelihood that a visit results in successful pollination. 2. To understand how isolation from mates and competition with co-flowering species contribute to reproductive failure in fragmented habitat, we conducted an observational study...

Pollinators mediate floral microbial diversity and network under agrochemical disturbance

Na Wei, Avery Russell, Abigail Jarrett & Tia-Lynn Ashman
How pollinators mediate microbiome assembly in the anthosphere is a major unresolved question of theoretical and applied importance in the face of anthropogenic disturbance. We addressed this question by linking visitation of diverse pollinator functional groups (bees, wasps, flies, butterflies, beetles, true bugs and other taxa) to the key properties of floral microbiome (microbial α- and β-diversity and microbial network) under agrochemical disturbance, using a field experiment of bactericide and fungicide treatments on cultivated strawberries...

Interferon beta drives intestinal regeneration after radiation

Jian Yu & Brian Leibowitz
The cGAS-STING cytosolic DNA sensing pathway is critical for host defense. Here, we report that cGAS-STING–dependent type 1 interferon (IFN) response drives intestinal regeneration and animal recovery from radiation injury. STING deficiency has no effect on radiation-induced DNA damage or crypt apoptosis but abrogates epithelial IFN beta production, local inflammation, innate transcriptional response, and subsequent crypt regeneration. cGAS KO, IFNAR1 KO, or CCR2 KO also abrogates radiation-induced acute crypt inflammation and regeneration. Impaired intestinal regeneration...

Targeting Myc-driven stress vulnerability in mutant KRAS colorectal cancer (Ruan et al.)

Jian Yu & Hang Ruan
Mutant KRAS is a key driver in colorectal cancer (CRC) and promotes Myc translation and Myc-dependent stress adaptation and proliferation. Here, we report that the combination of two FDA-approved drugs Bortezomib and Everolimus (RAD001) (BR) is highly efficacious against mutant KRAS CRC cells. Mechanistically, the combination, not single agent, rapidly depletes Myc protein, not mRNA, and leads to GCN2- and p-eIF2a-dependent cell death through the activation of extrinsic and intrinsic apoptotic pathways. Cell death is...

Revisiting the origin of octoploid strawberry

Aaron Liston, Na Wei, Jacob Tennessen, Jumin Li, Ming Dong & Ashman Tia-Lynn
The cultivated strawberry (Fragaria ×ananassa) is an octoploid, and the identity of its four subgenomes has long been a mystery. In their recent strawberry genome publication, Edger et al. present a novel hypothesis: each subgenome originated from a different extant diploid progenitor, and the hexaploid species Fragaria moschata was a direct ancestor. We reanalyzed the four octoploid subgenomes in a phylogenomic context and our results support only two extant diploids progenitors; we also found no...

Ambiguity in medical concept normalization: An analysis of types and coverage in electronic health record datasets

Denis Newman-Griffis, Guy Divita, Bart Desmet, Ayah Zirikly, Carolyn Rosé & Eric Fosler-Lussier
Objective: Normalizing mentions of medical concepts to standardized vocabularies is a fundamental component of clinical text analysis. Ambiguity—words or phrases that may refer to different concepts—has been extensively researched as part of information extraction from biomedical literature, but less is known about the types and frequency of ambiguity in clinical text. This study characterizes the distribution and distinct types of ambiguity exhibited by benchmark clinical concept normalization datasets, in order to identify directions for advancing...

Using convolutional neural networks to efficiently extract immense phenological data from community science images

Rachel Reeb, Naeem Aziz, Samuel Lapp, Justin Kitzes, J. Mason Heberling & Sara Kuebbing
Community science image libraries offer a massive, but largely untapped, source of observational data for phenological research. The iNaturalist platform offers a particularly rich archive, containing more than 49 million verifiable, georeferenced, open access images, encompassing seven continents and over 278,000 species. A critical limitation preventing scientists from taking full advantage of this rich data source is labor. Each image must be manually inspected and categorized by phenophase, which is both time-intensive and costly. Consequently,...

Data from: The size, symmetry, and color saturation of a male guppy’s ornaments forecast his resistance to parasites

Jessica Stephenson, Martin Stevens, Jolyon Troscianko & Jukka Jokela
Sexually selected ornaments range from highly dynamic traits to those that are fixed during development and relatively static throughout sexual maturity. Ornaments along this continuum differ in the information they provide about the qualities of potential mates, such as their parasite resistance. Dynamic ornaments enable real-time assessment of the bearer’s condition: they can reflect an individual’s current infection status, or resistance to recent infections. Static ornaments, however, are not affected by recent infection but may...

Data from: Experimental demonstration of the importance of keystone communities for maintaining metacommunity biodiversity and ecosystem functioning

Xian Yang, Jiaqi Tan, Kevin Harry Sun & Lin Jiang
As local communities within a metacommunity may differ considerably in their contributions to biodiversity and ecosystem functioning, it has been suggested that conservation priority should be given to disproportionately important local communities (i.e., keystone communities). However, we know little about what characterizes a keystone community. Using laboratory protist microcosms as the model system, we examined how the environmental uniqueness and location of a local community affect its contributions to the metacommunities. We found that the...

Data from: Spatially-explicit depiction of a floral epiphytic bacterial community reveals role for environmental filtering within petals

Maria Rebolleda-Gomez, Rebecca Hayes, Kristen Butela, Leah F. Cabo, Nevin Cullen, Nancy Kaufmann, Steffani A. O'Neil & Tia-Lynn Ashman
The microbiome of flowers (anthosphere) is an understudied compartment of the plant microbiome. Within the flower, petals represent a heterogeneous environment for microbes in terms of resources and environmental stress. Yet little is known of drivers of structure and function of the epiphytic microbial community at the within-petal scale. We characterized the petal microbiome in two co-flowering plants that differ in pattern of ultraviolet (UV) absorption along their petals. Bacterial communities were similar between plant...

Recipient and donor characteristics govern the hierarchical structure of heterospecific pollen competition networks

Jose B. Lanuza, Ignasi Bartomeus, Tia-Lynn Ashman & Romina Rader
Pollinator sharing can have negative consequences for plant fitness with the arrival of foreign (i.e. heterospecific) pollen, yet responses are often variable among species. Plant traits and relatedness of donor and recipient species have been suggested to drive the variations in plant fitness, but how they shape the structure of pollen competition networks has been overlooked at the community level. To understand the importance of reproductive traits and relatedness on the impacts of heterospecific pollen...

Data from: Delimiting Species Using DNA and Morphological Variation and Discordant Species Limits in Spiny Lizards (Sceloporus)

John J. Wiens & Tonya A. Penkrot
Haplotype phylogenies based on DNA sequence data are increasingly being used to test traditional species-level taxonomies based on morphology. However, few studies have critically compared species limits based on morphological and DNA data, and the methods used to delimit species using either type of data are only rarely explained. In this paper, we review three approaches for species delimitation (tree-based with DNA data and tree-based and character-based with morphological data) and propose explicit protocols for...

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