bluuebunny/crossref_metadata_2025_split huggingface dataset:
PI-Plat: A high-resolution image-based 3D reconstruction method to estimate growth dynamics of rice inflorescence traits
Authors: Sandhu Jaspreet , Zhu Feiyu , Paul Puneet , Gao Tian , Dhatt Balpreet K. , Ge Yufeng , Staswick Paul , Yu Hongfeng , Walia Harkamal 
Published: December 2019

AbstractBackgroundRecent advances in image-based plant phenotyping have improved our capability to study vegetative stage growth dynamics. However, more complex agronomic traits such as inflorescence architecture (IA), which predominantly contributes to grain crop yield are more challenging to quantify and hence are relatively less explored. Previous efforts to estimate inflorescence-related traits using image-based phenotyping have been limited to destructive end-point measurements. Development of non-destructive inflorescence phenotyping platforms could accelerate the discovery of the phenotypic variation with respect to inflorescence dynamics and mapping of the underlying genes regulating critical yield components.ResultsThe major objective of this study is to evaluate post-fertilization development and growth dynamics of inflorescence at high spatial and temporal resolution in rice. For this, we developed the Panicle Imaging Platform (PI-Plat) to comprehend multi-dimensional features of IA in a non-destructive manner. We used 11 rice genotypes to capture multi-view images of primary panicle on weekly basis after the fertilization. These images were used to reconstruct a 3D point cloud of the panicle, which enabled us to extract digital traits such as voxel count and color intensity. We found that the voxel count of developing panicles is positively correlated with seed number and weight at maturity. The voxel count from developing panicles projected overall volumes that increased during the grain filling phase, wherein quantification of color intensity estimated the rate of panicle maturation. Our 3D based phenotyping solution showed superior performance compared to conventional 2D based approaches.ConclusionsFor harnessing the potential of the existing genetic resources, we need a comprehensive understanding of the genotype-to-phenotype relationship. Relatively low-cost sequencing platforms have facilitated high-throughput genotyping, while phenotyping, especially for complex traits, has posed major challenges for crop improvement. PI-Plat offers a low cost and high-resolution platform to phenotype inflorescence-related traits using 3D reconstruction-based approach. Further, the non-destructive nature of the platform facilitates analyses of the same panicle at multiple developmental time points, which can be utilized to explore the genetic variation for dynamic inflorescence traits in cereals.
Reprogrammed Pteropus Bat Stem Cells Present Distinct Immune Signature and are Highly Permissive for Henipaviruses
Authors: Aurine Noémie , Baquerre Camille , Gaudino Maria , Jean Christian , Dumont Claire , Rival-Gervier Sylvie , Kress Clémence , Horvat Branka , Pain Bertrand 
Published: December 2019

AbstractBats are unique among mammals due to the ability of powered flight and exceptional longevity. They are also asymptomatic hosts for numerous viruses, including recently emerged zoonotic Henipaviruses Nipah and Hendra, which are highly pathogenic for humans and other mammals. Better understanding of how bats control viral infection requires development of relevant permissive cellular experimental models. By applying a somatic reprogramming protocol to Pteropus bat primary cells, using a novel combination of ESRRB, CDX2, and c-MYC transcription factors, we generated bat reprogrammed cells exhibiting stem cell-like characteristics and a neural stem cell-like molecular signature. These cells present a unique interferon-stimulated transcriptomic signature and both produce and respond to interferon type-I, highlighting differences between stem cells from bats and other mammals. In contrast to primary bat cells, these reprogrammed cells are highly susceptible to infection by Henipavirus, thereby enabling isolation of new bat viruses, study of virus-bat interactions, and better understanding of bat biology.Summary sentenceSomatic reprogramming provides new bat stem cells with unique immune properties and original viral permissivness
Adenita: Interactive 3D modeling and visualization of DNA Nanostructures
Authors: de Llano Elisa , Miao Haichao , Ahmadi Yasaman , Wilson Amanda J. , Beeby Morgan , Viola Ivan , Barisic Ivan 
Published: December 2019

AbstractWe present Adenita, a novel software tool for the design of DNA nanostructures in a user-friendly integrated environment for molecular modeling. Adenita is capable of handling large DNA origami structures, re-use them as building blocks of new designs and provide on demand feedback, thus overcoming effectively some of the limitations of existing tools. Additionally, it integrates all major established approaches to DNA nanostructure design (DNA origami, wireframe nanostructures and DNA tiles) and allows to combine them. We show-case Adenita by re-using a large nanorod designed with Cadnano [1] to create a new nanostructure through user interactions that employ different editors to modify the original nanorod.
Elucidating the competition between heterotrophic denitrification and DNRA using the resource-ratio theory
Authors: Jia Mingsheng , Winkler Mari K.H. , Volcke Eveline I.P. 
Published: December 2019

AbstractDenitrification and dissimilatory nitrate reduction to ammonium (DNRA) are two microbial processes competing for nitrate and organic carbon (COD). Their competition has great implications for nitrogen loss, conservation, and greenhouse gas emissions. Nevertheless, a comprehensive and mechanistic understanding of the governing factors for this competition is still lacking. We applied the resource-ratio theory and verified it with competition experiments of denitrification and DNRA reported in the literature. Based on this theory, we revealed how COD/N ratio, influent resource concentrations, dilution rate, and stoichiometric and kinetic parameters individually and collectively define the boundaries for different competition outcomes in continuous cultures. The influent COD/N ratio alone did not drive competition outcome as the boundary COD/N ratio for different competition outcomes changed significantly with influent resource concentrations. The stoichiometry of the two processes was determinative for the boundaries, whereas the affinity for the resources (Ks), maximum specific growth rate (μmax) of the two species and the dilution rate had significant impacts as well but mainly at low influent resource concentrations (e.g., <100 μM nitrate). The proposed approach allows for a more comprehensive understanding of the parameters controlling microbial selection and explains apparently conflicting experimental results. The results from this model also provide testable hypotheses and tools for understanding and managing the fate of nitrate in ecosystems and for other species that compete for two resources.
Intercontinental genomic parallelism in multiple adaptive radiations
Authors: Magalhaes Isabel S. , Whiting James R. , D’Agostino Daniele , Hohenlohe Paul A. , Mahmud Muayad , Bell Michael A. , Skúlason Skúli , MacColl Andrew D.C. 
Published: December 2019

AbstractParallelism, the evolution of similar traits in populations diversifying in similar conditions, provides good evidence of adaptation by natural selection. Many studies of parallelism have focused on comparisons of strongly different ecotypes or sharply contrasting environments, defineda priori, which could upwardly bias the apparent prevalence of parallelism. Here, we estimated genomic parallelism associated with individual components of environmental and phenotypic variation at an intercontinental scale across four adaptive radiations of the three-spined stickleback (Gasterosteus aculeatus), by associating genome-wide allele frequencies with continuous distributions of environmental and phenotypic variation. We found that genomic parallelism was well predicted by parallelism of phenotype-environment associations, suggesting that a quantitative characterization of phenotypes and environments can provide a good prediction of expected genomic parallelism. Further, we examined the explanatory power of genetic, phenotypic, and environmental similarity in predicting parallelism. We found that parallelism tended to be greater for geographically proximate, genetically similar radiations, highlighting the significant contingency of standing variation in the early stages of adaptive radiations, before new mutations accumulate. However, we also demonstrate that distance within multivariate environmental space predicts parallelism, after correction for genetic distance. This study thus demonstrates the relative influences of environment, phenotype and genetic contingency on repeatable signatures of adaptation in the genome.
Changing environments reveal innovative genetic variation in children’s cortisol responses
Authors: Raffington Laurel , Malanchini Margherita , Grotzinger Andrew D. , Madole James W. , Engelhardt Laura E. , Sabhlok Aditi , Youn Cherry , Patterson Megan W. , Harden K. Paige , Tucker-Drob Elliot M. 
Published: December 2019

AbstractGenetic associations with biopsychosocial phenotypes are often interpreted as evidence that the genome codes for fixed end-states. Instead, a given genotype might regulate a dynamic range of phenotypes in response to environmental change. We collected hair cortisol (n = 1,104), salivary cortisol in reaction to an in-laboratory stressor (n = 537), and diurnal salivary cortisol (n = 488) from twins aged 8-15 years in the Texas Twin Project. Baseline genetic variation in both salivary and hair cortisol was not simply magnified after stressor exposure or after waking. Rather, novel genetic influences on cortisol arose over time. Thus, environmental change can reveal genetic variation that would not otherwise be observed in static cortisol levels. These findings are in line with the notion that the genome regulates individuals’ reactions to the environment that differ across environments.
Kidney Function and Blood Pressure: A Bi-directional Mendelian Randomisation Study
Authors: Yu Zhi , Coresh Josef , Qi Guanghao , Grams Morgan , Boerwinkle Eric , Snieder Harold , Teumer Alexander , Pattaro Cristian , Köttgen Anna , Chatterjee Nilanjan , Tin Adrienne 
Published: December 2019

AbstractObjectiveTo evaluate the bi-directional causal relation between kidney function and blood pressure.DesignMendelian randomisation study.SettingWe performed two-sample Mendelian randomisation analyses. Genetic instruments of kidney function traits were selected from summary statistics of genome-wide association studies (GWAS) of glomerular filtration rate estimated from serum creatinine (eGFRcr) and blood urea nitrogen (BUN) and were required to be associated with both eGFRcr and BUN to ensure that the instruments were more likely to represent the underlying kidney function. Genetic instruments of blood pressure were selected from summary statistics of GWAS of systolic and diastolic blood pressure. We investigated Mendelian randomisation hypothesis using several alternative approaches, including methods that are most robust to the presence of horizontal pleiotropy.ParticipantsThe summary statistics of eGFRcr included 567,460 participants from 54 cohorts, and the summary statistics of BUN included 243,031 participants from 48 cohorts from the Chronic Kidney Disease Genetics (CKDGen) Consortium. The summary statistics of systolic and diastolic blood pressure included 757,601 participants from the UK Biobank and 78 cohorts from the International Consortium for Blood Pressure (ICBP).ResultsSignificant evidence supported the causal effects of higher kidney function on lower blood pressure with multiple methods. Based on the mode-based Mendelian randomisation analysis approach, known for its robustness to the presence of pleiotropic effect, the effect estimate for 1 SD higher in eGFRcr was −0.17 SD unit (95 % CI: −0.09 to −0.24) in systolic blood pressure (SBP) and −0.15 SD unit (95% CI: −0.07 to −0.22) in diastolic blood pressure (DBP). In contrast, the causal effects of blood pressure on kidney function were not statistically significant.ConclusionsMendelian randomisation analyses support causal effects of higher kidney function on lower blood pressure. These results suggest preventing kidney function decline can reduce the public health burden of hypertension.
Global analysis of adenylate-forming enzymes reveals β-lactone biosynthesis pathway in pathogenicNocardia
Authors: Robinson Serina L. , Terlouw Barbara R. , Smith Megan D. , Pidot Sacha J. , Stinear Tim P. , Medema Marnix H. , Wackett Lawrence P. 
Published: December 2019

ABSTRACTEnzymes that cleave ATP to activate carboxylic acids play essential roles in primary and secondary metabolism in all domains of life. Class I adenylate-forming enzymes share a conserved structural fold but act on a wide range of substrates to catalyze reactions involved in bioluminescence, nonribosomal peptide biosynthesis, fatty acid activation, and β-lactone formation. Despite their metabolic importance, the substrates and catalytic functions of the vast majority of adenylate-forming enzymes are unknown without tools available to accurately predict them. Given the crucial roles of adenylate-forming enzymes in biosynthesis, this also severely limits our ability to predict natural product structures from biosynthetic gene clusters. Here we used machine learning to predict adenylate-forming enzyme function and substrate specificity from protein sequence. We built a web-based predictive tool and used it to comprehensively map the biochemical diversity of adenylate-forming enzymes across >50,000 candidate biosynthetic gene clusters in bacterial, fungal, and plant genomes. Ancestral enzyme reconstruction and sequence similarity networking revealed a ‘hub’ topology suggesting radial divergence of the adenylate-forming superfamily from a core enzyme scaffold most related to contemporary aryl-CoA ligases. Our classifier also predicted β-lactone synthetases in novel biosynthetic gene clusters conserved across >90 different strains ofNocardia. To test our computational predictions, we purified a candidate β-lactone synthetase fromNocardia brasiliensisand reconstituted the biosynthetic pathwayin vitroto link the gene cluster to the β-lactone natural product, nocardiolactone. We anticipate our machine learning approach will aid in functional classification of enzymes and advance natural product discovery.
Top predator introduction changes the effects of spatial isolation on freshwater community structure
Authors: Pelinson Rodolfo Mei , Leibold Mathew A. , Schiesari Luis 
Published: December 2019

AbstractThe importance of local selective pressures on community structure is predicted to increase with spatial isolation when species favored by local conditions also have higher dispersal rates. In freshwater habitats, the introduction of predatory fish can produce trophic cascades because fish tend to prey upon intermediate predatory taxa, such as predatory insects, which indirectly benefits herbivores and detritivores. Similarly, spatial isolation is known to limit predatory insect's colonization rates more strongly than of herbivores and detritivores, thus generating similar effects. Here we tested the hypothesis that the effect of introduced predatory fish on macroinvertebrate community structure increases across a gradient of spatial isolation by conducting a field experiment where artificial ponds with and without fish (the Redbreast Tilapia) were constructed at three different distances from a source wetland. Overall results show that fish do reduce the abundance of predatory insects but have no effect on the abundance of herbivores and detritivores. Spatial isolation, however, does strengthen the trophic cascade caused by dispersal limitation of predatory insects, but only in the absence of fish. More importantly, macroinvertebrate communities with and without fish tend to diverge more strongly at higher spatial isolation, however, this pattern was not due to an increase in the magnitude of the effect of fish, as initially hypothesized, but to a change in the effect of isolation in the presence of fish. We argue that as spatial isolation increases, suitable prey, such as predatory insects become scarce and fish increases predation pressure upon herbivores and detritivores, dampening the positive effect of spatial isolation on them. Our results highlight the importance of considering interspecific variation in dispersal and multiple trophic levels to better understand the processes generating metacommunity structures.
Integration of absolute multi-omics reveals translational and metabolic interplay in mixed-kingdom microbiomes
Authors: Delogu F. , Kunath B.J. , Arntzen M.Ø. , Hvidsten T.R. , Pope P.B. 
Published: December 2019

AbstractMicrobiology is founded on well-known model organisms. For example, the majority of our fundamental knowledge regarding the quantitative levels of DNA, RNA, and protein backdates to keystone pure culture-based studies. Nowadays, meta-omic approaches allow us to directly access the molecules that constitute microbes and microbial communities, however due to a lack of absolute measurements, many original culture-derived “microbiology statutes” have not been updated or adapted to more complex microbiome settings. Within a cellulose-degrading and methanogenic consortium, we temporally measured genome-centric absolute RNA and protein levels per gene, and obtained a protein-to-RNA ratio of 102-104 for bacterial populations, whereas Archaeal RNA/protein dynamics (103-105: Methanothermobacter thermoautotrophicus) were more comparable to Eukaryotic representatives humans and yeast. The linearity between transcriptome and proteome had a population-specific change over time, highlighting a minimal subset of four functional carriers (cellulose degrader, fermenter, syntrophic acetate-oxidizer and methanogen) that coordinated their respective metabolisms, cumulating in the overarching community phenotype of converting polysaccharides to methane. Our findings show that upgrading multi-omic toolkits with traditional absolute measurements unlocks the scaling of core biological questions to dynamic and complex microbiomes, creating a deeper insight into inter-organismal relationships that drive the greater community function.
Skap2 Regulates Atherosclerosis through Macrophage Polarization and Efferocytosis
Authors: Hyatt Danielle , Schroeder Allison E. , Bhatnagar Ashita , Golan David E. , Swanson Kenneth D. , Alenghat Francis J. 
Published: December 2019

ABSTRACTRationaleAtherosclerosis causes more deaths than any other pathophysiologic process. It has a well-established inflammatory, macrophage-mediated component, but important and potentially protective intracellular macrophage processes in atherosclerosis remain enigmatic. Src Kinase-Associated Phosphoprotein 2 (Skap2) is a macrophage-predominant adaptor protein critical for cytoskeletal reorganization, and thereby, for macrophage migration and chemotaxis. The role of macrophage Skap2 in atherosclerosis is unknown and deserves exploration.ObjectiveTo establish the critical role of Skap2 in macrophage-mediated atherosclerotic plaque homeostasis.ResultsIn human arterial gene expression analysis, Skap2 expression is enriched in macrophage-containing areas of human atheroma, and the transcript level varies with plaque characteristics. We have discovered that deletion of Skap2 accelerates atherosclerosis by threefold in ApoE-/- mice on standard diet. Skap2 expression is switched on only as monocytes differentiate into macrophages, so Skap2-/- monocytes have no defect in infiltrating the atheroma. On the other hand, once they fully differentiate, Skap2-deficient macrophages cannot polarize efficiently into alternatively-activated, regulatory cells, and instead they preferentially polarize toward the classical pro-inflammatory phenotype both ex vivo and within the developing atheroma. This defect extends to polarized effector functions, as ex vivo analysis of macrophage phagocytosis of dying foam cells indicates that Skap2 is required for the regulatory process of efferocytosis.ConclusionsTaken together, our findings support a model in which Skap2 drives a regulatory, efferocytic mode of behavior to quell atherosclerosis.CONDENSED ABSTRACT / SUMMARYSkap2—a macrophage protein found in the human atheroma—is atheroprotective. Skap2-null mice, whose foam cells do not migrate well due to a defect in integrin-induced cytoskeletal rearrangement, have accelerated atherosclerosis. Skap2 is not expressed in monocytes but becomes important once they reach the atheroma and become macrophage foam cells, at which point it drives toward a regulatory, anti-inflammatory polarization state required for efficient efferocytosis of dying foam cells. Thus, Skap2 drives a protective, regulatory mode of behavior, supporting the fact that macrophages are not solely deleterious in atherosclerosis, and further pointing to efferocytosis as a target for therapy.There are no relationships to disclose.
CofActor: A light and redox-gated optogenetic clustering tool to study abnormal cytoskeletal dynamics in stressed cells
Authors: Salem Fatema B. , Prabhu V. V. , Kuyateh Abu-Bakarr , Bunner Wyatt Paul , Murashov Alexander , Szatmari Erzsebet M. , Hughes Robert M. 
Published: December 2019

AbstractThe biochemical hallmarks of neurodegenerative diseases (neural fibrils, clumps, and tangles; heightened reactive oxygen species (ROS); cofilin-actin rods) have presented numerous challenges for development of in vivo diagnostic tools (1–7). Biomarkers such as amyloid beta (Aβ) fibrils and Tau tangles in Alzheimer’s Disease (AD) are only accessible via invasive cerebrospinal fluid assay for peptide mass fingerprinting or post-mortem diagnosis (8–11), while ROS can be fleeting and thus challenging to monitor in vivo (12–15). While remaining a challenge for in vivo detection, the unique protein-protein interactions underlying these disease-specific biomarkers also present rich opportunities for the engineering of in vitro pathology-sensitive biosensors and bioactuators. These tools can be useful for the investigation of critical, early stage events in neurodegenerative diseases in both cellular and animal models (16, 17), while potentially leading to advanced detection reagents with clinical applications. In this report, we describe a light and redox-gated protein switch inspired by the phenomenon of cofilin-actin rod formation, which occurs in stressed neurons in the AD brain and following brain ischemia (18). By coupling the redox-sensitive interaction of cofilin and actin with the light responsive Cry2-CIB blue light switch, we accomplish both light- and ROS-gated control of this interaction. The resulting switch is referred to as the “CofActor” system. Site-directed mutagenesis of both cofilin and actin partners demonstrate which residues are critical for sustaining or abrogating the light and redox gated response. Furthermore, switch response varies depending on whether oxidative stress is generated via glycolytic inhibition or a combination of glycolytic inhibition and azide-induced oxidative stress. Finally, light and redox gated switch function was demonstrated in cultured hippocampal neurons. As a dual input biosensor, CofActor holds promise for the tracking of early stage events in neurodegeneration and the investigation of actin-binding protein interactions under oxidative stress.