144 Works

Data from: Predicting allosteric mutants that increase activity of a major antibiotic resistance enzyme

Malgorzata J. Latallo, George A. Cortina, Salem Faham, Robert K. Nakamoto & Peter Kasson
The CTX-M family of beta lactamases mediate broad-spectrum antibiotic resistance and present in the majority of drug-resistant gram-negative bacteria infections worldwide. Allosteric mutations that increase catalytic rates of these drug resistance enzymes have been identified in clinical isolates but are challenging to predict prospectively. We have used molecular dynamics simulations to predict allosteric mutants increasing CTX-M9 drug resistance, experimentally testing top mutants using multiple antibiotics. Purified enzymes show an increase in catalytic rate and efficiency,...

Data from: Characterization of transcriptomes from sexual and asexual lineages of a New Zealand snail (Potamopyrgus antipodarum)

Peter R. Wilton, Daniel B. Sloan, John M. Logsdon, Harshavardhan Doddapaneni, Maurine Neiman &
Understanding the evolution and maintenance of sexual reproduction is one of the central challenges of evolutionary biology, yet we know very little about how sex influences molecular evolution. The New Zealand freshwater snail Potamopyrgus antipodarum is ideally suited to address this knowledge gap because obligately sexual individuals often coexist with multiple independently derived obligately asexual lineages. This unusual situation allows direct comparisons both between sexual and asexual P. antipodarum and across populations that differ in...

Data from: Range‐wide population genetic structure of the Caribbean marine angiosperm Thalassia testudinum

Kor-Jent Van Dijk, Eric Bricker, Brigitta Ine Van Tussenbroek & Michelle Waycott
Many marine species have widespread geographic ranges derived from their evolutionary and ecological history particularly their modes of dispersal. Seagrass (marine angiosperm) species have ranges that are unusually widespread, which is not unexpected following recent reviews of reproductive strategies demonstrating the potential for long distance dispersal combined with longevity through clonality. An exemplar of these dual biological features is turtlegrass (Thalassia testudinum) which is an ecologically important species throughout the tropical Atlantic region. Turtlegrass has...

Data from: Climate affects the outbreaks of a forest defoliator indirectly through its tree hosts

Kyle Haynes, Andrew Liebhold, Jonathan Lefcheck, Randall Morin & Guiming Wang
Spatial variation in climate is known to affect the survival and reproduction of herbivorous forest insects and tree-species compositions, but the importance of indirect effects of climate on outbreaks of forest insects through its effects on forest composition is unclear. This data was compiled to examine the direct and indirect effects of climate, water capacity of the soil, host tree density, and non-host density on the spatial extent of Lymantria dispar outbreaks in the Eastern...

Data from: Rapid genetic and morphologic divergence between captive and wild populations of the endangered Leon Springs pupfish, Cyprinodon bovinus

Andrew Black, Heidi A. Seears, Christoper M. Hollenbeck, Paul B. Samollow, Andrew N. Black & Christopher M. Hollenbeck
The Leon Springs pupfish (Cyprinodon bovinus) is an endangered species currently restricted to a single desert spring and a separate captive habitat in southwestern North America. Following establishment of the captive population from wild stock in 1976, the wild population has undergone natural population size fluctuations, intentional culling to purge genetic contamination from an invasive congener (Cyprinodon variegatus) and augmentation/replacement of wild fish from the captive stock. A severe population decline following the most recent...

Data from: The timing of molecular and morphological changes underlying reproductive transitions in wild tomatoes (Solanum sect. Lycopersicon)

Stacey L. Vosters, Cathleen P. Jewell, Natasha A. Sherman, Frances Einterz, Benjamin K. Blackman & Leonie C. Moyle
Molecular mechanisms underlying the transition from genetic self-incompatibility to self-compatibility are well documented, but the evolution of other reproductive trait changes that accompany shifts in reproductive strategy (mating system) remain comparatively poorly understood. A notable exception is the transition from exserted styles to styles with recessed positions relative to the anthers in wild tomatoes (Solanum Section Lycopersicon). This phenotypic change has been previously attributed to specific mutation in the promoter of a gene that influences...

Data from: The genetic architecture of novel trophic specialists: higher effect sizes are associated with exceptional oral jaw diversification in a pupfish adaptive radiation

Christopher H. Martin, Priscilla A. Erickson & Craig T. Miller
The genetic architecture of adaptation is fundamental to understanding the mechanisms and constraints governing diversification. However, most case studies focus on loss of complex traits or parallel speciation in similar environments. It is still unclear how the genetic architecture of these local adaptive processes compares to the architecture of evolutionary transitions contributing to morphological and ecological novelty. Here we identify quantitative trait loci (QTL) between two trophic specialists in an excellent case study for examining...

Data from: Aging in an herbaceous plant: increases in mortality and decreases in physiology and seed mass

Brandie M. Quarles & Deborah Ann Roach
1. Little is known about plant age-dependent trait expression and how environmental conditions might affect aging in the wild. This study evaluates age variation in multiple traits of a short-lived perennial herb using a manipulative field experimental design. 2. Two different-aged cohorts were followed in a field plot for over a year to evaluate trait expression in response to a competition treatment and seasonal stress. Traits measured included size, mortality, reproduction, and physiology, including photosynthetic...

Data from: Performance of TaqMan Array Card to detect TB drug resistance on direct specimens

Sayera Banu, Suporn Pholwat, Suporn Foongladda, Rattapha Chinli, Duangjai Boonlert, Sara Sabrina Ferdous, S.M. Mazidur Rahman, Arfatur Rahman, Shahriar Ahmed & Eric R. Houpt
Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between...

Data from: Correlation between sequence divergence and polymorphism reveals similar evolutionary mechanisms acting across multiple timescales in a rapidly evolving plastid genome

Karen B. Barnard-Kubow, Daniel B. Sloan & Laura F. Galloway
Background: Although the plastid genome is highly conserved across most angiosperms, multiple lineages have increased rates of structural rearrangement and nucleotide substitution. These lineages exhibit an excess of nonsynonymous substitutions (i.e., elevated dN/dS ratios) in similar subsets of plastid genes, suggesting that similar mechanisms may be leading to relaxed and/or positive selection on these genes. However, little is known regarding whether these mechanisms continue to shape sequence diversity at the intraspecific level. Results: We examined...

Data from: Ret and Etv4 promote directed movements of progenitor cells during renal branching morphogenesis

Paul Riccio, Cristina Cebrian, Hui Zong, Simon Hippenmeyer & Frank Costantini
Branching morphogenesis of the epithelial ureteric bud forms the renal collecting duct system and is critical for normal nephron number, while low nephron number is implicated in hypertension and renal disease. Ureteric bud growth and branching requires GDNF signaling from the surrounding mesenchyme to cells at the ureteric bud tips, via the Ret receptor tyrosine kinase and coreceptor Gfrα1; Ret signaling up-regulates transcription factors Etv4 and Etv5, which are also critical for branching. Despite extensive...

C. Elegans meiotic spindles

Stefanie Redemann
The female meiotic spindles of most animals are acentrosomal and undergo striking morphological changes while transitioning from metaphase to anaphase. The ultra-structure of acentrosomal spindles, and how changes to this structure correlate with such dramatic spindle rearrangements remains largely unknown. To address this, we applied light microscopy, large-scale electron tomography and mathematical modeling of female meiotic C. elegans spindles undergoing the transition from metaphase to anaphase. Combining these approaches, we find that meiotic spindles are...

Data for: Variation in reproductive isolation across a species range

Karen Barnard-Kubow & Laura Galloway
Reproductive isolation is often variable within species, a phenomenon that while largely ignored by speciation studies, can be leveraged to gain insight into the potential mechanisms driving the evolution of genetic incompatibilities. We used experimental greenhouse crosses to characterize patterns of reproductive isolation among three divergent genetic lineages of Campanulastrum americanum that occur in close geographic proximity in the Appalachian Mountains. Substantial, asymmetrical reproductive isolation for survival due to cytonuclear incompatibility was found among the...

Additional references for: Brain arteriovenous malformations: a review of natural history, pathobiology, and interventions

Jason Sheehan & Ching-Jen Chen
Brain arteriovenous malformations (AVMs) are anomalous direct shunts between cerebral arteries and veins that convalesce into a vascular nidus. The treatment strategies for AVMs are challenging and variable. Intracranial hemorrhage and seizures comprise the most common presentations of AVMs. However, incidental AVMs are being diagnosed with increasing frequency due to widespread use of noninvasive neuroimaging. The balance between the estimated cumulative lifetime hemorrhage risk versus the risk of intervention is often the major determinant for...

Floral spectral reflectance data for: Floral color properties of serpentine seep assemblages depend on community size and species richness

Kathryn LeCroy, Gerardo Arceo-Gómez, Matthew Koski, Nathan Morehouse & Tia-Lynn Ashman
Functional traits, particularly those that impact fitness, can shape the ecological and evolutionary relationships among coexisting species of the same trophic level. Thus, examining these traits and properties of their distributions (underdispersion, overdispersion) within communities can provide insights into key ecological interactions (e.g., competition, facilitation) involved in community assembly. For instance, the distribution of floral colors in a community may reflect pollinator-mediated interactions between sympatric plant species, and the phylogenetic distribution of color can inform...

Data from: Analyzing negative feedback using a synthetic gene network expressed in the Drosophila melanogaster embryo

Ashley Jermusyk, Nicholas P. Murphy & Gregory Reeves
Background: A complex network of gene interactions controls gene regulation throughout development and the life of the organisms. Insights can be made into these processes by studying the functional interactions (or “motifs”) which make up these networks. Results: We sought to understand the functionality of one of these network motifs, negative feedback, in a multi-cellular system. This was accomplished using a synthetic network expressed in the Drosophila melanogaster embryo using the yeast proteins Gal4 (a...

Data from: Response to joint selection on germination and flowering phenology depends on the direction of selection

Laura F. Galloway, Ray H.B. Watson, Holly R. Prendeville & Ray H. B. Watson
Background and Aims. Flowering and germination time are components of phenology, a complex phenotype that incorporates a number of traits. In natural populations, selection is likely to occur on multiple components of phenology at once. However, we have little knowledge of how joint selection on several phenological traits influences evolutionary response. Methods. We conducted one generation of artificial selection for all combinations of early and late germination and flowering on replicated lines within two independent...

Data from: The genetic architecture of local adaptation and reproductive isolation in sympatry within the Mimulus guttatus species complex

Kathleen G. Ferris, Laryssa L. Barnett, Benjamin K. Blackman & John H. Willis
The genetic architecture of local adaptation has been of central interest to evolutionary biologists since the modern synthesis. In addition to classic theory on the effect size of adaptive mutations by Fisher, Kimura and Orr, recent theory addresses the genetic architecture of local adaptation in the face of ongoing gene flow. This theory predicts that with substantial gene flow between populations local adaptation should proceed primarily through mutations of large effect or tightly linked clusters...

Data from: Historical contingency in a multigene family facilitates adaptive evolution of toxin resistance

Joel McGlothlin, Megan Kobiela, Chris R. Feldman, Todd A. Castoe, Shana L. Geffeney, Charles T. Hanifin, Gabriela Toledo, Freek J. Vonk, Michael K. Richardson, , Michael Pfrender &
Novel adaptations must originate and function within an already established genome [ 1 ]. As a result, the ability of a species to adapt to new environmental challenges is predicted to be highly contingent on the evolutionary history of its lineage [ 2–6 ]. Despite a growing appreciation of the importance of historical contingency in the adaptive evolution of single proteins [ 7–11 ], we know surprisingly little about its role in shaping complex adaptations...

Data from: Determinants of genetic structure in a nonequilibrium metapopulation of the plant Silene latifolia

Peter D. Fields & Douglas R. Taylor
Population genetic differentiation will be influenced by the demographic history of populations, opportunities for migration among neighboring demes and founder effects associated with repeated extinction and recolonization. In natural populations, these factors are expected to interact with each other and their magnitudes will vary depending on the spatial distribution and age structure of local demes. Although each of these effects has been individually identified as important in structuring genetic variance, their relative magnitude is seldom...

Data from: Evolutionary shifts in habitat aridity predict evaporative water loss across squamate reptiles

Christian L. Cox & Robert M. Cox
Aridity is an important determinant of species distributions, shaping both ecological and evolutionary diversity. Lizards and snakes are often abundant in deserts, suggesting a high potential for adaptation or acclimation to arid habitats. However, phylogenetic evidence indicates that squamate diversity in deserts may be more strongly tied to speciation within arid habitats than to convergent evolution following repeated colonization from mesic habitats. To assess the frequency of evolutionary transitions in habitat aridity while simultaneously testing...

Data from: microCT-based phenomics in the zebrafish skeleton reveals virtues of deep phenotyping in a distributed organ system

Matthew Hur, Charlotte A. Gistelinck, Philippe Huber, Jane Lee, Marjorie H. Thompson, Adrian T. Monstad-Rios, Claire J. Watson, Sarah K. McMenamin, Andy Willaert, David M. Parichy, Paul Coucke & Ronald Y. Kwon
Phenomics, which ideally involves in-depth phenotyping at the whole-organism scale, may enhance our functional understanding of genetic variation. Here, we demonstrate methods to profile hundreds of phenotypic measures comprised of morphological and densitometric traits at a large number of sites within the axial skeleton of adult zebrafish. We show the potential for vertebral patterns to confer heightened sensitivity, with similar specificity, in discriminating mutant populations compared to analyzing individual vertebrae in isolation. We identify phenotypes...

Data from: Toxicity and population structure of the Rough-Skinned Newt (Taricha granulosa) outside the range of an arms race with resistant predators

Michael T. J. Hague, Leleña A. Avila, Charles T. Hanifin, W. Andrew Snedden, Amber N. Stokes, , , Michael T.J. Hague & Edmund D. Brodie
Species interactions, and their fitness consequences, vary across the geographic range of a coevolutionary relationship. This spatial heterogeneity in reciprocal selection is predicted to generate a geographic mosaic of local adaptation, wherein coevolutionary traits are phenotypically variable from one location to the next. Under this framework, allopatric populations should lack variation in coevolutionary traits due to the absence of reciprocal selection. We examine phenotypic variation in tetrodotoxin (TTX) toxicity of the Rough-Skinned Newt (Taricha granulosa)...

Data from: An examination of fitness costs of glyphosate resistance in the common morning glory, Ipomoea purpurea

Catherine L. Debban, Sara Okum, Kathleen E. Pieper, Ariana Wilson & Regina S. Baucom
Fitness costs are frequently invoked to explain the presence of genetic variation underlying plant defense across many types of damaging agents. Despite the expectation that costs of resistance are prevalent, however, they have been difficult to detect in nature. To examine the potential that resistance confers a fitness cost, we examined the survival and fitness of genetic lines of the common morning glory, Ipomoea purpurea, that diverged in the level of resistance to the herbicide...

Data from: Systems analysis of adaptive responses to MAP Kinase pathway blockade in BRAF mutant melanoma

Brian J. Capaldo, Devin Roller, Mark J. Axelrod, Alex F. Koeppel, Emanuel F. Petricoin, Craig L. Slingluff, Michael J. Weber, Aaron J. Mackey, Daniel Gioeli & Stefan Bekiranov
Fifty percent of cutaneous melanomas are driven by activated BRAFV600E, but tumors treated with RAF inhibitors, even when they respond dramatically, rapidly adapt and develop resistance. Thus, there is a pressing need to identify the major mechanisms of intrinsic and adaptive resistance and develop drug combinations that target these resistance mechanisms. In a combinatorial drug screen on a panel of 12 treatment-naïve BRAFV600E mutant melanoma cell lines of varying levels of resistance to mitogen-activated protein...

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