bluuebunny/crossref_metadata_2025_split huggingface dataset:
Degradation of recalcitrant polyurethane and xenobiotic additives by a selected landfill microbial community and its biodegradative potential revealed by proximity ligation-based metagenomic analysis
Authors: Gaytán Itzel , Sánchez-Reyes Ayixon , Burelo Manuel , Vargas-Suárez Martín , Liachko Ivan , Press Maximilian , Sullivan Shawn , Javier Cruz-Gómez M. , Loza-Tavera Herminia 
Published: September 2019

ABSTRACTPolyurethanes (PU) are the sixth more produced plastics with around 19-million tons/year, but since they are not recyclable they are burned or landfilled, generating ecological damage. To elucidate the mechanisms that landfill microbial communities perform to attack recalcitrant PU plastic, we studied the BP8 community selected by its capability to grow in a water PU dispersion (WPUD) that contains a polyether-polyurethane-acrylate (PE-PU-A) copolymer and xenobiotic additives (N-methyl 2-pyrrolidone, isopropanol and glycol ethers), and performed a proximity ligation-based metagenomic analysis for revealing the community structure and potential biodegradative capacity. Additives were consumed early whereas the copolymer was cleaved throughout the 25-days incubation. BP8 metagenomic deconvolution reconstructed five genomes, three of them from novel species. Genes encoding enzymes for additives biodegradation were predicted. The chemical and physical analysis of the biodegradation process, and the identified biodegradation products show that BP8 cleaves esters, aromatic urethanes, C-C and ether groups by hydrolytic and oxidative mechanisms. The metagenomic analysis allowed to predicting comprehensive metabolic pathways and enzymes that explain the observed PU biodegradation. This is the first study revealing the metabolic potential of a landfill microbial community that thrives within a WPUD system and shows potential for bioremediation of polyurethane- and xenobiotic additives-contaminated sites.
The circadian clock gene circuit controls protein and phosphoprotein rhythms inArabidopsis thaliana
Authors: Krahmer Johanna , Hindle Matthew , Perby Laura K , Nielsen Tom H , Halliday Karen J , van Ooijen Gerben , Le Bihan Thierry , Millar Andrew J 
Published: September 2019

Abstract24-hour, circadian rhythms control many eukaryotic mRNA levels, whereas the levels of their more stable proteins are not expected to reflect the RNA rhythms, emphasizing the need to test the circadian regulation of protein abundance and modification. Here we present circadian proteomic and phosphoproteomic time-series fromArabidopsis thalianaplants under constant light conditions, estimating that just 0.4% of quantified proteins but a much larger proportion of quantified phospho-sites were rhythmic. Approximately half of the rhythmic phospho-sites were most phosphorylated at subjective dawn, a pattern we term the ‘phospho-dawn’. Members of the SnRK/CDPK family of protein kinases are candidate regulators. ACCA1-over-expressing line that disables the clock gene circuit lacked most circadian protein phosphorylation. However, the few phospho-sites that fluctuated despiteCCA1-over-expression still tended to peak in abundance close to subjective dawn, suggesting that the canonical clock mechanism is necessary for most but perhaps not all protein phosphorylation rhythms. To test the potential functional relevance of our datasets, we conducted phosphomimetic experiments using the bifunctional enzyme fructose-6-phosphate-2-kinase / phosphatase (F2KP), as an example. The rhythmic phosphorylation of diverse protein targets is controlled by the clock gene circuit, implicating post-translational mechanisms in the transmission of circadian timing information in plants.
A nonhomologous end-joining mutant forNeurospora sitophilaresearch
Authors: Rhoades Nicholas A. , Webber Elise K. , Hammond Thomas M. 
Published: September 2019

AbstractDisruption of the nonhomologous end-joining (NHEJ) pathway has been shown to increase the efficiency of transgene integration into targeted genomic locations ofNeurospora crassaand other fungi. Here, we report that a similar phenomenon occurs in a second Neurospora species:N. sitophila. Specifically, we show that deletion ofN. sitophila mus-51increases the efficiency of targeted-transgene integration, presumably by disrupting NHEJ. Researchers interested in obtaining theN. sitophila mus-51Δstrains described in this study can obtain them from the Fungal Genetics Stock Center (FGSC).
A missing link in mutualistic networks: symbiotic fungi in plant-animal interactions
Authors: Chaverri Priscila , Chaverri Gloriana 
Published: September 2019

AbstractWe explored the hypothesis of an indirect mutualistic relationship (i.e., when the association between two species is modified by a third one) within a plant-animal seed dispersal network. Bats are important long-distance dispersers of many tropical plants, yet, by consuming fruits they may disperse not only the plant’s seeds, but also the endosymbiotic fungi within those fruits. We characterized fungal communities in fruits ofFicus colubrinaeand in feces ofEctophylla albato determine if passage through the digestive tract of the bats affected the total mycobiome. Results show a significant reduction, after passage through the gut, of fungi known to be plant pathogenic, while abundance of species known to have beneficial properties significantly increased. These findings suggest that the role of frugivores in plant-animal mutualistic networks may extend beyond seed dispersal: they also promote the dispersal of potentially beneficial microbial symbionts while hindering those that can cause plant disease.
Evolution of generalists by phenotypic plasticity
Authors: Fraebel David T. , Gowda Karna , Mani Madhav , Kuehn Seppe 
Published: September 2019

AbstractAdapting organisms face a tension between specializing their phenotypes for certain ecological tasks or developing generalist strategies which permit persistence in multiple environmental conditions. Understanding when and how generalists or specialists evolve is therefore an important question in evolutionary dynamics. Here we study the evolution of bacterial range expansions by selectingEscherichia colifor faster migration through porous media containing one of four different sugars supporting growth and chemotaxis. We find that selection in any one sugar drives the evolution of faster migration in all sugars relative to the ancestral strain. Measurements of growth and motility of all evolved lineages in all nutrient conditions reveal that the ubiquitous evolution of fast migration arises via phenotypic plasticity. Phenotypic plasticity permits evolved strains to exploit distinct phenotypic strategies to achieve fast migration in each environment irrespective of the environment in which they were evolved. Our work suggests that plasticity plays an important role in the evolution of generalist phenotypes.
Collective behaviour is not robust to disturbance, yet parent and offspring colonies resemble each other in social spiders
Authors: Fisher David N. , Lichtenstein James L.L. , Costa-Pereira Raul , Yeager Justin , Pruitt Jonathan N. 
Published: September 2019

AbstractGroups of animals possess phenotypes such as collective behaviour, which may determine the fitness of group members. However, the stability and robustness to perturbations of collective phenotypes in natural conditions is not established. Furthermore, whether group phenotypes are transmitted from parent to offspring groups is required for understanding how selection on group phenotypes contributes to evolution, but parent-offspring resemblance at the group level is rarely estimated. We evaluated robustness to perturbation and parent-offspring resemblance of collective foraging aggressiveness in colonies of the social spiderAnelosimus eximius. Among-colony differences in foraging aggressiveness were consistent over time but changed if the colony was perturbed through the removal of individuals, or via their removal and subsequent return. Offspring and parent colony behaviour were correlated, but only once the offspring colony had settled after being translocated. The parent-offspring resemblance was not driven by a shared elevation but could be due to other environmental factors. Laboratory collective behaviour was not correlated with behaviour in the field. Colony aggression seems sensitive to initial conditions and easily perturbed between behavioural states. Despite this sensitivity, offspring colonies have collective behaviour that resembles that of their parent colony, provided they are given enough time to settle into the environment.
A dual function of the IDA peptide in regulating cell separation and modulating plant immunity at the molecular level
Authors: Lalun Vilde Olsson , Breiden Maike , Galindo-Trigo Sergio , Smakowska-Luzan Elwira , Simon Rüdiger , Butenko Melinka A. 
Published: September 2019

AbstractThe abscission of floral organs and emergence of lateral roots in Arabidopsis is regulated by the peptide ligand INFLORESCENCE DEFICIENT IN ABSCISSION (IDA) and the receptor protein kinases HAESA (HAE) and HAESA-LIKE 2 (HSL2). During these cell separation processes, the plant induces defense-associated genes to protect against pathogen invasion. However, the molecular coordination between abscission and immunity has not been thoroughly explored. Here we show that IDA induces a release of cytosolic calcium ions (Ca2+) and apoplastic production of reactive oxygen species, which are signatures of early defense responses. In addition, we find that IDA promotes late defense responses by the transcriptional upregulation of genes known to be involved in immunity. When comparing the IDA induced early immune responses to known immune responses, such as those elicited by flagellin22 treatment, we observe both similarities and differences. We propose a molecular mechanism by which IDA promotes signatures of an immune response in cells destined for separation to guard them from pathogen attack.
Locally acting transcription factors are required for p53-dependent cis-regulatory element activity
Authors: Catizone Allison N. , Uzunbas Gizem Karsli , Celadova Petra , Kuang Sylvia , Bose Daniel , Sammons Morgan A. 
Published: September 2019

AbstractThe master tumor suppressor p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, DNA damage repair, and senescence. Recent studies revealed pervasive binding of p53 to cis-regulatory elements (CRE), which are non-coding segments of DNA that spatially and temporally control transcription through the combinatorial binding of local transcription factors (TFs). Although the role of p53 as a strong trans-activator of gene expression is well known, the co-regulatory factors and local sequences acting at p53-bound CREs are comparatively understudied. We designed and executed a massively parallel reporter assay (MPRA) to investigate the effect of transcription factor binding motifs and local sequence context on p53-bound CRE activity. Our data indicate that p53-bound CREs are both positively and negatively affected by alterations in local sequence context and changes to co-regulatory TF motifs. We identified a SP1/KLF family motif located in an intronic p53 CRE that is required for the endogenous expression of the p53-dependent gene CCNG1. We also identified ATF3 as a factor that co-regulates the expression of the p53-dependent gene GDF15 through binding with p53 in an upstream CRE. Loss of either p53 or ATF3 severely reduces CRE activity and alters endogenous GDF15 mRNA levels in the cell. Our data suggests that p53 has the flexibility to cooperate with a variety of transcription factors in order to regulate CRE activity. By utilizing different sets of co-factors across CREs, we hypothesize that p53 activity is guarded against loss of any one regulatory partner allowing for dynamic and redundant control of p53-mediated transcription.
JAM-A functions as a female microglial tumor suppressor in glioblastoma
Authors: Turaga Soumya M. , Silver Daniel J. , Bayik Defne , Paouri Evi , Peng Sen , Borjini Nozha , Stanko Sarah , Naik Ulhas , Keri Ruth A. , Connor James R. , Barnholtz-Sloan Jill S. , Rubin Joshua B. , Berens Michael , Davalos Dimitrios , Lathia Justin D. 
Published: September 2019

AbstractGlioblastoma (GBM) remains refractory to treatment. In addition to its cellular and molecular heterogeneity, epidemiological studies indicate the presence of additional complexity associated with biological sex. GBM is more prevalent and aggressive in male compared to female patients, suggesting the existence of sex-specific growth, invasion, and therapeutic resistance mechanisms. While sex-specific molecular mechanisms have been reported at a tumor cell-intrinsic level, sex-specific differences in the tumor microenvironment have not been investigated. Using transgenic mouse models, we demonstrate that deficiency of junctional adhesion molecule-A (JAM-A) in female mice enhances microglia activation, GBM cell proliferation, and tumor growth. Mechanistically, JAM-A suppresses anti-inflammatory/pro-tumorigenic gene activation via interferon-activated gene 202b (Ifi202b) and found in inflammatory zone (Fizz1) in female microglia. Our findings suggest that cell adhesion mechanisms function to suppress pathogenic microglial activation in the female tumor microenvironment, which highlights an emerging role for sex differences in the GBM microenvironment and suggests that sex differences extend beyond previously reported tumor cell intrinsic differences.SummaryTuraga et al. demonstrate that female microglia drive a more aggressive glioblastoma phenotype in the context of JAM-A deficiency. These findings highlight a sex-specific role for JAM-A and represent the first evidence of sexual dimorphism in the glioblastoma microenvironment.
Mother knows best: maternal egg-clutch size predicts larval group size in pine sawflies (genusNeodiprion)
Authors: Terbot John W. , Linnen Catherine R. 
Published: September 2019

AbstractEvolutionary conflicts are pervasive in nature and have the potential to drive antagonistic coevolution of conflict-related traits. However, when such conflicts are weak or idiosyncratic, phenotypic signatures of coevolutionary arms races may be absent. Here, we ask whether variation in group-living traits among pine-sawfly species in the genusNeodiprionis consistent with a history of parent-offspring conflict. To address this question, we compile data on adult female clutch size, larval aggregation behavior, and larval group size for a monophyletic group of 19 eastern North AmericanNeodiprionspecies from field observations, laboratory assays, and published descriptions. We then evaluate the extent to which each trait exhibits phylogenetic signal and, based on these results, examine correlations between group-size traits both with and without phylogenetic correction. Although female oviposition behavior and larval grouping behavior varies among species and variation in these traits is decoupled from phylogeny, we find no evidence of antagonistic coevolution between these traits. Furthermore, while larvae are physically capable of dispersal, female clutch size is a strong predictor of larval colony size, indicating that larvae do not substantially alter initial group size after hatching. Thus, although theoretical work demonstrates the potential for parent-offspring conflict over group size in animals that lack parental care, our data suggest that this type of conflict is not likely to be a long-term driver of phenotypic evolution.
Deamidation in Moxetumomab Pasudotox Leading to Conformational Change and Immunotoxin Activity Loss
Authors: Lu X. , Lin S. , De Mel N. , Parupudi A. , Pandey M. , Delmar J. , Wang X. , Wang J. 
Published: September 2019

ABSTRACTAsparagine deamidation is a common posttranslational modification in which asparagine is converted to aspartic acid or isoaspartic acid. By introducing a negative charge, deamidation could potentially impact the binding interface and biological activities of protein therapeutics. We identified a deamidation variant in moxetumomab pasudotox, an immunotoxin Fv fusion protein drug derived from a 38-kilodalton (kDa) truncated Pseudomonas exotoxin A (PE38) for the treatment of hairy-cell leukemia. Although the deamidation site, Asn-358, was outside of the binding interface, the modification had a significant impact on the biological activity of moxetumomab pasudotox. Surprisingly, the variant eluted earlier than its unmodified form on anion exchange chromatography, which suggests a higher positive charge. Here we describe the characterization of the deamidation variant with differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry, which revealed that the Asn-358 deamidation caused the conformational changes in the catalytic domain of the PE38 region. These results provide a possible explanation for why the deamidation affected the biological activity of moxetumomab pasudotox and suggest an approach that can be used for process control to ensure product quality and process consistency.Statement of SignificanceAsparagine deamidation can have a potentially significant impact on protein therapeutics. Previous studies have revealed that deamidation at a single site significantly reduces the biological activity of moxetumomab pasudotox, a recombinant anti-CD22 immunotoxin developed for the treatment of B-cell malignancies. Surprisingly, despite the fact that deamidation introduced a negative charge, the deamidated variant eluted earlier than its unmodified form on anion exchange chromatography. In order to understand these observations, we isolated the deamidated variant using an anion exchange column and characterized it by differential scanning calorimetry and hydrogen-deuterium exchange mass spectrometry. The results revealed the conformational change caused by the deamidation, which explains the diminished biological activity of the variant and its early elution time on anion exchange chromatography.
Mental geometry of 3D size and shape perception
Authors: Maruya Akihito , Zaidi Qasim 
Published: September 2019

AbstractJudging poses, sizes and shapes of objects accurately is necessary for organisms and machines to operate successfully in the world. Retinal images of 3D objects are mapped by the rules of projective geometry, and preserve the invariants of that geometry. Since Plato, it has been debated whether geometry is innate to the human brain, and Poincare and Einstein thought it worth examining whether formal geometry arises from experience with the world. We examine if humans have learned to exploit projective geometry to estimate sizes and shapes of objects in 3D scenes.Numerous studies have examined size invariance as a function of physical distance, which changes scale on the retina, but surprisingly, possible constancy or inconstancy of relative size seems not to have been investigated for object pose, which changes retinal image size differently along different axes. We show systematic underestimation of length for extents pointing towards or away from the observer, both for static objects and dynamically rotating objects. Observers do correct for projected shortening according to the optimal back-transform, obtained by inverting the projection function, but the correction is inadequate by a multiplicative factor. The clue is provided by the greater underestimation for longer objects, and the observation that they appear more slanted towards the observer. Adding a multiplicative factor for perceived slant in the back-transform model provides good fits to the corrections used by observers. We quantify the slant illusion with relative slant measurements, and use a dynamic demonstration to show the power of the slant illusion.In biological and mechanical objects, distortions of shape are manifold, and changes in aspect ratio and relative limb sizes are functionally important. Our model shows that observers try to retain invariance of these aspects of shape to 3D rotation by correcting retinal image distortions due to perspective projection, but the corrections can fall short. We discuss how these results imply that humans have internalized particular aspects of projective geometry through evolution or learning, and how assuming that images are preserving the continuity, collinearity, and convergence invariances of projective geometry, supplements the Generic Viewpoint assumption, and simply explains other illusions, such as Ames’ Chair.
Individual Learning Phenotypes Drive Collective Cognition
Authors: Cook Chelsea N. , Lemanski Natalie J. , Mosqueiro Thiago , Ozturk Cahit , Gadau Jürgen , Pinter-Wollman Noa , Smith Brian H. 
Published: September 2019

AbstractVariation in cognition can influence how individuals respond to and communicate about their environment, which may scale to shape how a collective solves a cognitive task. However, few empirical examples of variation in collective cognition emerges from variation in individual cognition exist. Here, we show that interactions among individuals that differ in the performance of a cognitive task drives collective foraging behavior in honey bee colonies by utilizing a naturally variable and heritable learning behavior called latent inhibition (LI). We artificially selected two distinct phenotypes: high LI bees that are better at ignoring previously unrewarding familiar stimuli, and low LI bees that can learn previously unrewarding and novel stimuli equally well. We then provided colonies composed of these distinct phenotypes with a choice between a familiar feeder or a novel feeder. Colonies of high LI individuals preferred to visit familiar food locations, while low LI colonies visited novel and familiar food locations equally. However, in colonies of mixed learning phenotypes, the low LI bees showed a preference to visiting familiar feeders, which contrasts with their behavior when in a uniform low LI group. We show that the shift in feeder preference of low LI bees is driven by foragers of the high LI phenotype dancing more intensely and attracting more followers. Our results reveal that cognitive abilities of individuals and their interactions drive emergent collective outcomes.Significance StatementVariation in individual cognition affects how animals perceive their environment and which information they share with others. Here we provide empirical evidence that how individual honey bees learn contributes to collective cognition of a colony. By creating colonies of distinct learning phenotypes, we evaluated how bees make foraging choices in the field. Colonies containing individuals that learn to ignore unimportant information preferred familiar food locations, however colonies of individuals that are unable to ignore familiar information visit novel and familiar feeders equally. A 50/50 mix of these phenotypes prefer familiar food locations, because individuals who learn the familiar location recruit nestmates by dancing more intensely. Our results reveal that variation in individual cognition scales non-linearly to shape collective outcomes.