bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing the response of small RNA populations to allopolyploidy using resynthesized Brassica napus allotetraploids
Authors: Palacios Paulina Martinez , Jacquemot Marie-Pierre , Tapie Marion , Rousselet Agnès , Diop Mamoudou , Remoue Carine , Falque Matthieu , Lloyd Andrew , Jenczewski Eric , Lassalle Gilles , Chevre Anne-Marie , Lelandais Christine , Crespi Martin , Brabant Philippe , Joets Johann , Alix Karine 
Published: October 2018

AbstractAllopolyploidy, combining interspecific hybridization with whole genome duplication, has had significant impact on plant evolution. Its evolutionary success is related to the rapid and profound genome reorganizations that allow neo-allopolyploids to form and adapt. Nevertheless, how neo-allopolyploid genomes adapt to regulate their expression remains poorly understood. The hypothesis of a major role for small non-coding RNAs (sRNAs) in mediating the transcriptional response of neo-allopolyploid genomes has progressively emerged. Generally, 21-nt sRNAs mediate post-transcriptional gene silencing (PTGS) by mRNA cleavage whereas 24-nt sRNAs repress transcription (transcriptional gene silencing, TGS) through epigenetic modifications. Here, we characterize the global response of sRNAs to allopolyploidy in Brassica, using three independently resynthesized B. napus allotetraploids surveyed at two different generations in comparison with their diploid progenitors. Our results suggest an immediate but transient response of specific sRNA populations to allopolyploidy. These sRNA populations mainly target non-coding components of the genome but also target the transcriptional regulation of genes involved in response to stresses and in metabolism; this suggests a broad role in adapting to allopolyploidy. We finally identify the early accumulation of both 21- and 24-nt sRNAs involved in regulating the same targets, supporting a PTGS-to-TGS shift at the first stages of the neo-allopolyploid formation. We propose that reorganization of sRNA production is an early response to allopolyploidy in order to control the transcriptional reactivation of various non-coding elements and stress-related genes, thus ensuring genome stability during the first steps of neo-allopolyploid formation.
Distinct neural mechanisms and temporal constraints govern a cascade of audiotactile interactions
Authors: Zumer Johanna M. , White Thomas P. , Noppeney Uta 
Published: October 2018

AbstractAsynchrony is a critical cue informing the brain whether sensory signals are caused by a common source and should be integrated or segregated. It is unclear how the brain binds audiotactile signals into behavioural benefits depending on their asynchrony. Participants actively responded (psychophysics) or passively attended (electroencephalogrpahy) to noise bursts, ‘taps-to-the-face’, and their audiotactile (AT) combinations at seven audiotactile asynchronies: 0, ±20, ±70, and ±500ms. Observers were faster at detecting AT than unisensory stimuli, maximally for synchronous stimulation and declining within a ≤70ms temporal integration window. We observed AT interactions for (1) near-synchronous stimuli within a ≤20ms temporal integration window for evoked response potentials (ERPs) at 110ms and ∼400ms, (2) specifically ±70ms asynchronies, across the P200 ERP and theta-band inter-trial coherence (ITC) and power at ∼200ms, with a frontocentral topography, and (3) beta-band power across several asynchronies. Our results suggest that early AT interactions for ERP and theta-band ITC and power mediate behavioural response facilitation within a ≤70ms temporal integration window, but beta-band power reflects AT interactions that are less relevant for behaviour. This diversity of temporal profiles and constraints demonstrates how audiotactile integration unfolds in a cascade of interactions to generate behavioural benefits.
Molecularly distinct models of zebrafishMyc-induced B cell leukemia
Authors: Borga Chiara , Foster Clay A. , Iyer Sowmya , Garcia Sara P. , Langenau David M. , Frazer J. Kimble 
Published: October 2018

AbstractZebrafish models of T cell acute lymphoblastic leukemia (T-ALL) have been studied for over a decade, but curiously, robust zebrafish B cell ALL (B-ALL) models had not been described. Recently, our laboratories reported two seemingly closely-related models of zebrafish B-ALL. In these genetic lines, the primary difference is expression of either murine or human transgenic c-MYC, each controlled by the zebrafishrag2promoter. Here, we compare ALL gene expression in both models. Surprisingly, we find that B-ALL arise in different B cell lineages, withighm+vs.ighz+B-ALL driven by murineMycvs. humanMYC, respectively. Moreover, these B-ALL types exhibit signatures of distinct molecular pathways, further unexpected dissimilarity. Thus, despite sharing analogous genetic makeup, the ALL types in each model are markedly different, proving subtle genetic changes can profoundly impact model organism phenotypes. Investigating the mechanistic differences between mouse and human c-MYC in these contexts may reveal key functional aspects governing MYC-driven oncogenesis in human malignancies.
Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
Authors: Grady Keara L , Sorensen Jackson W. , Stopnisek Nejc , Guittar John , Shade Ashley 
Published: October 2018

AbstractPerennial grasses are promising feedstocks for biofuel production, and there is potential to leverage their native microbiomes to increase their productivity and resilience to environmental stress. Here, we characterize the 16S rRNA gene diversity and seasonal assembly of bacterial and archaeal microbiomes of two perennial cellulosic feedstocks, switchgrass (Panicum virgatum L.) and miscanthus (Miscanthus × giganteus). We sampled leaves and soil every three weeks from pre-emergence through senescence for two consecutive switchgrass growing seasons and one miscanthus season, and identified core leaf taxa based on abundance and occupancy. Virtually all leaf taxa are also detected in soil; source-sink modeling shows non-random, ecological filtering by the leaf, suggesting that soil is important reservoir of phyllosphere diversity. Core leaf taxa include early, mid, and late season groups that were consistent across years and crops. This consistency in leaf microbiome dynamics and core members is promising for microbiome manipulation or management to support biofuel crop production.
On Parameter Interpretability of Phenomenological-Based Semiphysical Models
Authors: Lema-Perez Laura , Muñoz-Tamayo Rafael , Garcia-Tirado Jose , Alvarez Hernan 
Published: October 2018

AbstractEmpirical and phenomenological based models are used to represent biological and physiological processes. Phenomenological models are derived from the knowledge of the mechanisms that underlie the behaviour of the system under study, while empirical models are derived from analysis of data to quantify relationships between variables of interest. For studying biological systems, the phenomenological modeling approach offers the great advantage of having a structure with variables and parameters with physical meaning that enhance the interpretability of the model and its further used for decision making. The interpretability property of models, however, remains a vague concept. In this study, we tackled the interpretability property for parameters of phenomenological-based models. To our knowledge, this property has not been deeply discussed, perhaps by the implicit assumption that interpretability is inherent to the phenomenological-based models. We propose a conceptual framework to address the parameter interpretability and its implications for parameter identifiability. We use as battle horse a simple but relevant model representing the enzymatic degradation ofβ–casein by aLactococcus lactisbacterium.
Conformational states control Lck switching between free and confined diffusion modes in T cells
Authors: Hilzenrat Geva , Pandžić Elvis , Yang Zhengmin , Nieves Daniel J. , Goyette Jesse , Rossy Jérémie , Gaus Katharina 
Published: October 2018

AbstractT cell receptor (TCR) phosphorylation by Lck is an essential step in T cell activation. It is known the conformational states of Lck control enzymatic activity; however, the underlying principles of how Lck finds its substrate in the plasma membrane remain elusive. Here, single-particle tracking is paired with photoactivatable localization microscopy (sptPALM) to observe the diffusive modes of Lck in the plasma membrane. Individual Lck molecules switched between free and confined diffusion in resting and stimulated T cells. Conformational state, but not partitioning into membrane domains, caused Lck confinement as open conformation Lck was more confined than closed. Further confinement of kinase-dead versions of Lck suggests that Lck interacts with open active Lck to cause confinement, irrespectively of kinase activity. Our data supports a model that confined diffusion of open Lck results in high local phosphorylation rates and closed Lck diffuses freely to enable wide-range scanning of the plasma membrane.
A genome-wide analysis of adhesion inCaulobacter crescentusidentifies new regulatory and biosynthetic components for holdfast assembly
Authors: Hershey David M. , Fiebig Aretha , Crosson Sean 
Published: October 2018

AbstractDue to their intimate physical interactions with the environment, surface polysaccharides are critical determinants of fitness for bacteria.Caulobacter crescentusproduces a specialized structure at one of its cell poles called the holdfast that enables attachment to surfaces. Previous studies have shown that the holdfast is a carbohydrate-based material and identified a number of genes required for holdfast development. However, incomplete information about its chemical structure, biosynthetic genes and regulatory principles has limited progress in understanding the mechanism of holdfast synthesis. We have leveraged the adhesive properties of the holdfast to perform a saturating screen for genes affecting attachment to cheesecloth over a multi-day time course. Using similarities in the temporal profiles of mutants in a transposon library, we defined discrete clusters of genes with related effects on cheesecloth colonization. Holdfast synthesis, flagellar motility, type IV pilus assembly and smooth lipopolysaccharide (SLPS) production represented key classes of adhesion determinants. Examining these clusters in detail allowed us to predict and experimentally define the functions of multiple uncharacterized genes in both the holdfast and SLPS pathways. In addition, we showed that the pilus and flagellum control holdfast synthesis separately by modulating the holdfast inhibitorhfiA.This study defines a set of genes contributing to adhesion that includes newly discovered genes required for holdfast biosynthesis and attachment. Our data provide evidence that the holdfast contains a complex polysaccharide with at least four monosaccharides in the repeating unit and underscore the central role of cell polarity in mediating attachment ofC. crescentusto surfaces.ImportanceBacteria routinely encounter biotic and abiotic materials in their surrounding environments, and they often enlist specific behavioral programs to colonize these materials. Adhesion is an early step in colonizing a surface.Caulobacter crescentusproduces a structure called the holdfast, which allows this organism to attach to and colonize surfaces. To understand how the holdfast is produced, we performed a genome-wide search for genes that contribute to adhesion by selecting for mutants that could not attach to cheesecloth. We discovered complex interactions between genes that mediate surface contact and genes that contribute to holdfast development. Our genetic selection identified what likely represents a comprehensive set of genes required to generate a holdfast, laying the groundwork for a detailed characterization of the enzymes that build this specialized adhesin.
Local and landscape drivers of aquatic-to-terrestrial subsidies in riparian ecosystems: a worldwide meta-analysis
Authors: Lafage D. , Bergman E. , Eckstein R. L. , Österling M. , Sadler J.P. , Piccolo JJ 
Published: October 2018

AbstractCross-boundary fluxes of organisms and matter, termed “subsidies”, are now recognized to be reciprocal and of roughly equal importance for both aquatic and terrestrial systems, even if terrestrial input to aquatic ecosystems has received most attention. The magnitude of aquatic to terrestrial subsidies is well documented, but the drivers behind these subsidies and their utilization by terrestrial consumers are characteristically local scale studies, limiting the inferences that can be drawn for broader geographic scales. We therefore built and analyzed a database of stable isotope data extracted from 21 studies worldwide, to identify both landscape and local scale variables that may affect the diet of terrestrial predators in riparian ecosystems. Our meta-analysis revealed a greater magnitude of aquatic-to-terrestrial subsidies (> 50%) than previously reported, albeit with large geographic and inter-annual variations. We demonstrated a large effect of landscape-scale factors on aquatic-to-terrestrial subsidies, particularly anthropogenic land use and tree cover. Local human population was the only relevant factor at the local scale. We also found that studies on landscape-scale and anthropogenic land use effects on aquatic-to-terrestrial subsidies are currently strongly under-represented in the ecological literature. Such studies are needed to improve our understanding of how land use and environmental change might influence future patterns of biodiversity and ecosystem function.
Whole genome sequencing Mycobacterium tuberculosis directly from sputum identifies more genetic diversity than sequencing from culture
Authors: Nimmo Camus , Shaw Liam P. , Doyle Ronan , Williams Rachel , Brien Kayleen , Burgess Carrie , Breuer Judith , Balloux Francois , Pym Alexander S. 
Published: October 2018

AbstractBackgroundRepeated culture reduces within-sample Mycobacterium tuberculosis genetic diversity due to selection of clones suited to growth in culture and/or random loss of lineages, but it is not known to what extent omitting the culture step altogether alters genetic diversity. We compared M. tuberculosis whole genome sequences generated from 33 paired clinical samples using two methods. In one method DNA was extracted directly from sputum then enriched with custom-designed SureSelect (Agilent) oligonucleotide baits and in the other it was extracted from mycobacterial growth indicator tube (MGIT) culture.ResultsDNA directly sequenced from sputum showed significantly more within-sample diversity than that from MGIT culture (median 5.0 vs 4.5 heterozygous alleles per sample, p=0.04). Resistance associated variants present as HAs occurred in four patients, and in two cases may provide a genotypic explanation for phenotypic resistance.ConclusionsCulture-free M. tuberculosis whole genome sequencing detects more within-sample diversity than a leading culture-based method and may allow detection of mycobacteria that are not actively replicating.
Live cell imaging of meiosis in Arabidopsis thaliana - a landmark system
Authors: Prusicki Maria Ada , Keizer Emma Mathilde , van Rosmalen Rik Peter , Komaki Shinichiro , Seifert Felix , Müller Katja , Wijnker Erik , Fleck Christian , Schnittger Arp 
Published: October 2018

AbstractMeiosis is essential for sexual reproduction and key to the generation of genetic diversity. To reveal the robustness of meiocyte differentiation and progression through meiosis, we have here established a live cell imaging setup to follow the dynamics of individual male meiocytes in Arabidopsis. Our method is based on the concomitant visualization of microtubules and a meiotic cohesion subunit that allowed following five cellular parameters: cell shape, nucleus position, nucleolus position, chromatin condensation and microtubule array. We find that the states of these parameters are not randomly associated and identify 11 states, referred to as landmarks, that occur much more frequently than closely related states, indicating that they are convergent points of meiotic progression. With this, the here-presented landmark system represents a novel method to analyze meiosis not only allowing a high-temporal dissection but also providing new criteria to evaluate mutants or environmental effects on meiosis.
Expectation and attention increase the integration of top-down and bottom-up signals in perception through different pathways
Authors: Gordon Noam , Tsuchiya Naotsugu , Koenig-Robert Roger , Hohwy Jakob 
Published: October 2018

AbstractPerception results from the integration of incoming sensory information with pre-existing information available in the brain. In this EEG (electroencephalography) study we utilised the Hierarchical Frequency Tagging method to examine how such integration is modulated by expectation and attention. Using intermodulation (IM) components as a measure of non-linear signal integration, we show in three different experiments that both expectation and attention enhance integration between top-down and bottom-up signals. Based on multispectral phase coherence, we present two direct physiological measures to demonstrate the distinct yet related mechanisms of expectation and attention. Specifically, our results link expectation to the modulation of prediction signals and the integration of top-down and bottom-up information at lower levels of the visual hierarchy. Meanwhile, they link attention to the propagation of ascending signals and the integration of information at higher levels of the visual hierarchy. These results are consistent with the predictive coding account of perception.
A Mathematical Model Relating Pitocin Use During Labor with Offspring Autism Development in Terms of Oxytocin Receptor Desensitization in the Fetal Brain
Authors: Gottlieb Mark M. 
Published: October 2018

ABSTRACTThis paper develops a mathematical model describing the potential buildup of high oxytocin concentrations in the maternal circulation during labor in terms of continuous Pitocin infusion rate, half-life and maternal weight. Oxytocin override of the degradation of oxytocin by placental oxytocinase is introduced to model the potential transfer of oxytocin from the maternal circulation across the placenta into the fetal circulation, and from there into the brain of the fetus. The desensitization unit D equal to 1.8E6 (pg-min)/ml is employed to establish a desensitization threshold, and by extension; a down-regulation threshold as a function of oxytocin override concentration and continuous Pitocin infusion time, that could be a factor in the subsequent development of autism among offspring. Epidemiological studies by Duke University (S.G. Gregory, 2013), Yale University (O. Weisman, 2015) and Harvard University (A.S. Oberg, 2016) are discussed regarding Pitocin use and offspring autism development for an explanation of the weak correlations they identified. The findings of the Harvard epidemiological study are re-interpreted regarding Pitocin use, and its conclusion questioned. Further evaluations of the findings of these three epidemiological studies are called for to incorporate medical information on quantity of Pitocin used, continuous Pitocin infusion rate, length of labor and maternal weight to determine if a correlation can be established with offspring autism development above an empirically determined desensitization threshold for Pitocin use. Suggestions for research are discussed, including an alternative to continuous Pitocin infusion, pulsatile infusion of Pitocin during labor induction, that may mitigate possible offspring autism development.HIGHLIGHTSBuildup of oxytocin (OT) in the maternal circulation mathematically modeled.Relationship of OT half-life and OT concentration in maternal circulation identified.OTR Desensitization related to Pitocin infusion time and OT override concentration.Weak correlations for autism development in epidemiological studies explained.Examination called for of medical records of Pitocin use in epidemiological studies.OUTLINE OF PAPERIntroductionDevelopment and application of mathematical model – Sections 1 through 6, notably: Figures 1 through 4Discussion of oxytocin receptor desensitization as it pertains to mathematical model – Sections 7 and 8Influence of mathematical model on interpretation of epidemiological studies – Sections 9 and 10Research considerations – Section 11, notably:Subsection 11.1 – Call for detailed epidemiological analysis of selected medical information indicated by mathematical model Subsection 11.2 – Review of pulsatile Pitocin infusion to mitigate possible offspring autism development indicated by mathematical model
RAxML-NG: A fast, scalable, and user-friendly tool for maximum likelihood phylogenetic inference
Authors: Kozlov Alexey M. , Darriba Diego , Flouri Tomáš , Morel Benoit , Stamatakis Alexandros 
Published: October 2018

AbstractMotivationPhylogenies are important for fundamental biological research, but also have numerous applications in biotechnology, agriculture, and medicine. Finding the optimal tree under the popular maximum like-lihood (ML) criterion is known to be NP-hard. Thus, highly optimized and scalable codes are needed to analyze constantly growing empirical datasets.ResultsWe present RAxML-NG, a from scratch re-implementation of the established greedy tree search algorithm of RAxML/ExaML. RAxML- NG offers improved accuracy, flexibility, speed, scalability, and usability compared to RAxML/ExaML. On taxon-rich datasets, RAxML-NG typically finds higher-scoring trees than IQTree, an increasingly popular recent tool for ML-based phylogenetic inference (although IQ-Tree shows better stability). Finally, RAxML-NG introduces several new features, such as the detection of terraces in tree space and a the recently introduced transfer bootstrap support metric.AvailabilityThe code is available under GNU GPL athttps://github.com/amkozlov/raxml-ng.RAxML-NGweb service (maintained by Vital- IT) is available athttps://raxml-ng.vital-it.ch/.Contactalexey.kozlov@h-its.org
Vigour/tolerance trade-off in cultivated sunflower (Helianthus annuus) response to salinity stress is linked to leaf elemental composition
Authors: Temme Andries A. , Kerr Kelly L. , Donovan Lisa A. 
Published: October 2018

AbstractDeveloping more stress-tolerant crops will require greater knowledge of the physiological basis of stress tolerance. Here we explore how biomass declines in response to salinity relate to leaf traits across twenty genotypes of cultivated sunflower (Helianthus annuus). Plant growth, leaf physiological traits, and leaf elemental composition were assessed after 21 days of salinity treatments (0, 50, 100, 150, or 200 mM NaCl) in a greenhouse study. There was a trade-off in performance such that vigorous genotypes, those with higher biomass at zero mM NaCl, had both a larger absolute decrease and proportional decrease in biomass due to increased salinity. More vigorous genotypes at control were less tolerant to salinity. Contrary to expectation, genotypes with a low increase in leaf Na and decrease in K:Na were not better at maintaining biomass with increasing salinity. Rather, genotypes with a greater reduction in leaf S and K content were better at maintaining biomass at increased salinity. While we found an overall trade-off between sunflower vigour and salt tolerance, some genotypes were more tolerant than expected. Further analysis of the traits and mechanisms underlying this trade-off may allow us to breed these into high vigour genotypes in order to increase their salt tolerance.