208 Works

Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

Christiane Bouchier, Jean-Emmanuel Hugonnet, Michel Arthur, Dominique Mengin-Lecreulx, Yves Brun, Michael Van Nieuwenhze, Louis B Rice, Alejandro Monton, Tanneke Den Blaauwen, Etienne Carbonnelle, Carole Veckerlé & Kuyek Tu
The target of β-lactam antibiotics is the D,D-transpeptidase activity of penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by L,D-transpeptidases were first detected in Escherichia coli more than four decades ago, however no phenotype has previously been associated with their synthesis. Here we show that production of the L,D-transpeptidase YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by RelA lead to full...

Data from: Resolving the evolutionary relationships of molluscs with phylogenomic tools

Stephen A. Smith, Casey W. Dunn, Nerida G. Wilson, Freya E. Goetz, Caitlin Feehery, Sónia C. S. Andrade, Greg W. Rouse & Gonzalo Giribet
Molluscs (snails, octopuses, clams, and relatives) have great body plan disparity, and among animals only arthropods surpass them in species number. This diversity has made Mollusca one of the best-studied groups of animals, yet their evolutionary relationships remain poorly resolved. Open questions have important implications for the origin of Mollusca and morphological evolution within the group. These include whether the shell-less vermiform aplacophoran molluscs diverged prior to the origin of the shelled molluscs (Conchifera), or...

Data from: Age‐dependent leaf physiology and consequences for crown‐scale carbon uptake during the dry season in an Amazon evergreen forest

Loren P. Albert, Jin Wu, Neill Prohaska, Plinio Barbosa De Camargo, Travis E. Huxman, Edgard S. Tribuzy, Valeriy Y. Ivanov, Rafael S. Oliveira, Sabrina Garcia, Marielle N. Smith, Raimundo Cosme Oliveira Junior, Natalia Restrepo-Coupe, Rodrigo Da Silva, Scott C. Stark, Giordane A. Martins, Deliane V. Penha & Scott R. Saleska
* Satellite and tower-based metrics of forest-scale photosynthesis generally increase with dry season progression across central Amazônia, but the underlying mechanisms lack consensus. * We conducted demographic surveys of leaf age composition, and measured age-dependence of leaf physiology in broadleaf canopy trees of abundant species at a central eastern Amazon site. Using a novel leaf-to-branch scaling approach, we used this data to independently test the much-debated hypothesis—arising from satellite and tower-based observations—that leaf phenology could...

Data from: Phenological and fitness responses to climate warming depend upon genotype and competitive neighborhood in Arabidopsis thaliana

Mark A. Taylor, Martha D. Cooper & Johanna Schmitt
1. Increasing temperatures during climate change are known to alter the phenology across diverse plant taxa, but the evolutionary outcomes of these shifts are poorly understood. Moreover, plant temperature-sensing pathways are known to interact with competition-sensing pathways, yet there remains little experimental evidence for how genotypes varying in temperature responsiveness react to warming in realistic competitive settings. 2. We compared flowering time and fitness responses to warming and competition for two near isogenic lines (NILs)...

Data from: The role of ontogeny in physiological tolerance: decreasing hydrostatic pressure tolerance with development in the northern stone crab Lithodes maja

Catriona Munro, James P. Morris, Alastair Brown, Chris Hauton & Sven Thatje
Extant deep-sea invertebrate fauna represent both ancient and recent invasions from shallow-water habitats. Hydrostatic pressure may present a significant physiological challenge to organisms seeking to colonize deeper waters or migrate ontogenetically. Pressure may be a key factor contributing to bottlenecks in the radiation of taxa and potentially drive speciation. Here, we assess shifts in the tolerance of hydrostatic pressure through early ontogeny of the northern stone crab Lithodes maja, which occupies a depth range of...

Data from: Structure and composition of altered riparian forests in an agricultural Amazonian landscape

R. Chelsea Nagy, Stephen Porder, Christopher Neill, Paulo Brando, Raimundo Mota Quintino & Sebastiâo Aviz Do Nascimento
Deforestation and fragmentation influence the microclimate, vegetation structure, and composition of remaining patches of tropical forest. In the southern Amazon, at the frontier of cropland expansion, forests are converted and fragmented in a pattern that leaves standing riparian forests whose dimensions are mandated by the Brazilian National Forest Code. These altered riparian forests share many characteristics of well-studied upland forest fragments, but differ because they remain connected to larger areas of forest downstream, and because...

Data from: Heterochrony in the evolution of Trinidadian guppy offspring size: maturation along a uniform ontogenetic trajectory

Terry R. Dial, David N. Reznick & Elizabeth L. Brainerd
The size and maturity of Trinidadian guppy (Poecilia reticulata) offspring vary among populations adapted to environments of differential predation. Guppy offspring born to low-predation, high-competition environments are larger and more mature than their high-predation ancestors. Here we ask: what specific changes in developmental or birth timing occur to produce the larger, more mature neonates? We collected specimens across the perinatal window of development from five populations and quantified musculoskeletal maturation. We found that all populations...

Data from: Different clades and traits yield similar grassland functional responses

Elisabeth J. Forrestel, Michael J. Donoghue, Erika J. Edwards, Walter Jetz, Justin C. O. Du Toit & Melinda D. Smith
Plant functional traits are viewed as key to predicting important ecosystem and community properties across resource gradients within and among biogeographic regions. Vegetation dynamics and ecosystem processes, such as aboveground net primary productivity (ANPP), are increasingly being modeled as a function of the quantitative traits of species, which are used as proxies for photosynthetic rates, and nutrient and water-use efficiency. These approaches rely on an assumption that a certain trait value consistently confers a specific...

Data from: Automation and evaluation of the SOWH test with SOWHAT

Samuel H. Church, Joseph F. Ryan & Casey W. Dunn
The Swofford–Olsen–Waddell–Hillis (SOWH) test evaluates statistical support for incongruent phylogenetic topologies. It is commonly applied to determine if the maximum likelihood tree in a phylogenetic analysis is significantly different than an alternative hypothesis. The SOWH test compares the observed difference in log-likelihood between two topologies to a null distribution of differences in log-likelihood generated by parametric resampling. The test is a well-established phylogenetic method for topology testing, but it is sensitive to model misspecification, it...

Data from: Effects of fertilizer on inorganic soil N in East Africa maize systems: vertical distributions and temporal dynamics

Katherine L. Tully, Jonathan Hickman, Madeline McKenna, Christopher Neill & Cheryl A. Palm
Fertilizer applications are poised to increase across sub-Saharan Africa (SSA), but the fate of added nitrogen (N) is largely unknown. We measured vertical distributions and temporal variations of soil inorganic N following fertilizer application in two maize (Zea mays L.)-growing regions of contrasting soil type. Fertilizer trials were established on a clayey soil in Yala, Kenya, and on a sandy soil in Tumbi, Tanzania, with application rates of 0–200 kg N/ha/yr. Soil profiles were collected...

Spacetimes, A New Vision for Islamic Pasts and Futures

Shahzad Bashir

A Woman’s Voice, A New Vision for Islamic Pasts and Futures

Shahzad Bashir

Reading the Stars, A New Vision for Islamic Pasts and Futures

Shahzad Bashir

Pigmentation biosynthesis influences the microbiome associated with sea urchins

Gary Wessel, Masato Kiyomoto, Adam Reitzel & Tyler Carrier
Organisms living on the seafloor are subject to encrustations by a wide variety of animal, plants, and microbes. Sea urchins, however, thwart this covering. Despite having a sophisticated immune system, there is no clear mechanism that allows sea urchins to remain clean. Here, by using CRISPR/Cas9, we test the hypothesis that pigmentation biosynthesis in sea urchin spines influences their interactions with microbes in vivo. We have three primary findings. First, the microbiome of sea urchin...

At a Heightened Level of Intensity: A Discussion of the Philosophy and Politics of Language in John Cayley’s Digital Poetics

John Cayley & Scott Rettberg
A conversation at a heightened level of intensity, ranging from the aleatory tradition of Emmett Williams, Jackson Mac Low, and John Cage, through post-Poundian poetry and its Chinese influences, kinetic poetry or programmable media where the poem itself is performing, not just the poet. Attention is also given to the Internet as these two literary artists knew it for a very brief moment, before Google and Facebook, circa 2004, ¨figured out that everybody needed an...

Seeking Coherence in a COVID-19 Context: The Maltese Islands During the Pandemic

Maximilian Bonnici, Isabelle Bonnici, Brett Miller, Jack Victory, Parth Panchal & Nathan Williams

Data from: Comparing forest structure and biodiversity on private and public land: secondary tropical dry forests in Costa Rica

Moana McClellan, Rebecca Montgomery, Kristen Nelson & Justin Becknell
Secondary forests constitute a substantial proportion of tropical forestlands. These forests occur on both public and private lands and different underlying environmental variables and management regimes may affect post‐abandonment successional processes and resultant forest structure and biodiversity. We examined whether differences in ownership led to differences in forest structure, tree diversity, and tree species composition across a gradient of soil fertility and forest age. We collected soil samples and surveyed all trees in 82 public...

Data from: Measuring couple relationship quality in a rural African population: validation of a couple functionality assessment tool in Malawi

Allison Ruark, Rachel Chase, John Hembling, Valerie Rhoe Davis, Paul Clayton Perrin & Dorothy Brewster-Lee
Available data suggest that individual and family well-being are linked to the quality of women’s and men’s couple relationships, but few tools exist to assess couple relationship functioning in low and middle-income countries. In response to this gap, Catholic Relief Services has developed a Couple Functionality Assessment Tool (CFAT) to capture valid and reliable data on various domains of relationship quality. This tool is designed to be used by interventions which aim to improve couple...

Data from: Both morph- and species-dependent asymmetries affect reproductive barriers between heterostylous species

Barbara Keller, Jurriaan M. De Vos, Alexander N. Schmidt-Lebuhn, James D. Thomson & Elena Conti
The interaction between floral traits and reproductive isolation is crucial to explaining the extraordinary diversity of angiosperms. Heterostyly, a complex floral polymorphism that optimizes outcrossing, evolved repeatedly and has been shown to accelerate diversification in primroses, yet its potential influence on isolating mechanisms remains unexplored. Furthermore, the relative contribution of pre- versus postmating barriers to reproductive isolation is still debated. No experimental study has yet evaluated the possible effects of heterostyly on pre- and postmating...

Data from: Fossils matter: improved estimates of divergence times in Pinus reveal older diversification

Bianca Saladin, Andrew B. Leslie, Rafael O. Wueest, Glenn Litsios, Elena Conti, Nicolas Salamin & Niklaus E. Zimmermann
Background: The taxonomy of pines (genus Pinus) is widely accepted and a robust gene tree based on entire plastome sequences exists. However, there is a large discrepancy in estimated divergence times of major pine clades among existing studies, mainly due to differences in fossil placement and dating methods used. We currently lack a dated molecular phylogeny that makes use of the rich pine fossil record, and this study is the first to estimate the divergence...

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