bluuebunny/crossref_metadata_2025_split huggingface dataset:
Causal evidence for a cerebellar role in prefrontal-hippocampal interaction in spatial working memory decision-making
Authors: Liu Yu , McAfee Samuel S. , Van Der Heijden Meike E. , Dhamala Mukesh , Sillitoe Roy V. , Heck Detlef H. 
Published: March 2020

ABSTRACTSpatial working memory (SWM) is a cognitive skill supporting survival-relevant behaviors, such as optimizing foraging behavior by remembering recent routes and visited sites. It is known that SWM decision-making in rodents requires the medial prefrontal cortex (mPFC) and dorsal hippocampus. The decision process in SWM tasks carries a specific electrophysiological signature of a brief, decision-related increase in neuronal communication in the form of an increase in the coherence of neuronal theta oscillations (4-12 Hz) between the mPFC and dorsal hippocampus, a finding we replicated here during spontaneous exploration of a plus maze in freely moving mice. We further evaluated SWM decision-related coherence changes within frequency bands above theta. Decision-related coherence increases occurred in seven frequency bands between 4 and 200 Hz and decision-outcome related differences in coherence modulation occurred within the beta and gamma frequency bands and in higher frequency oscillations up to 130 Hz. With recent evidence that Purkinje cells in the cerebellar lobulus simplex (LS) represent information about the phase and phase differences of gamma oscillations in the mPFC and dorsal hippocampus, we hypothesized that LS might be involved in the modulation of mPFC-hippocampal gamma coherence. We show that optical stimulation of LS significantly impairs SWM performance and decision-related mPFC-dCA1 coherence modulation, providing causal evidence for an involvement of cerebellar LS in SWM decision making at the behavioral and neuronal level. Our findings suggest that the cerebellum might contribute to SWM decision-making by optimizing the decision-related modulation of mPFC-dCA1 coherence.
Niche Partitioning Between Coastal and Offshore Shelf Waters Results in Differential Expression of Alkane and PAH Catabolic Pathways
Authors: Doyle Shawn M. , Lin Genmei , Morales-McDevitt Maya , Wade Terry L. , Quigg Antonietta , Sylvan Jason B. 
Published: March 2020

ABSTRACTMarine oil spills can impact both coastal and offshore marine environments, but little information is available on how the microbial response to oil and dispersants might differ between these biomes. Here we describe the compositional and functional response of microbial communities to different concentrations of oil and chemically dispersed oil in coastal and offshore surface waters from the Texas-Louisiana continental shelf. Using a combination of analytical chemistry, 16S rRNA amplicon, and metatranscriptomic sequencing, we provide a broad, comparative overview of the ecological response of hydrocarbon degrading bacteria and their expression of hydrocarbon degrading genes in marine surface waters over time between two oceanic biomes. We found evidence for the existence of different ecotypes of several commonly described hydrocarbon degrading bacterial taxa which behaved differentially in coastal and offshore shelf waters despite being exposed to similar concentrations of oil, dispersants, and nutrients. This resulted in the differential expression of catabolic pathways for n-alkanes and polycyclic aromatic hydrocarbons (PAH)—the two major categories of compounds found in crude oil—with preferential expression of n-alkane degradation genes in coastal waters while offshore microbial communities trended more towards the expression of PAH degradation genes. This was unexpected as it contrasts with the generally held view that n-alkanes, being more labile, are attacked before the more refractory PAHs. Collectively, our results provide new insights into the existence and potential consequences of niche partitioning of hydrocarbon degrading taxa between neighboring marine environments.IMPORTANCEIn the wake of the Deepwater Horizon oil spill, the taxonomic response of marine microbial communities to oil and dispersants has been extensively studied. However, relatively few studies on the functional response of these microbial communities have been reported, especially in a longitudinal fashion. Moreover, despite the fact that marine oil spills typically impact thousands of square kilometers of both coastal and offshore marine environments, little information is available on how the microbial response to oil and dispersants might differ between these biomes. The results of this study help fill this critical knowledge gap and provide valuable insight into how oil spill response efforts, such as chemically dispersing oil, may have differing effects in neighboring coastal and offshore marine environments.
Enhancer and promoter usage in the normal and failed human heart
Authors: Gacita Anthony M. , Dellefave-Castillo Lisa , Page Patrick G. T. , Barefield David Y. , Waserstrom J. Andrew , Puckelwartz Megan J. , Nobrega Marcelo A. , McNally Elizabeth M 
Published: March 2020

ABSTRACTThe failed heart is characterized by re-expression of a fetal gene program, which contributes to adaptation and maladaptation in heart failure. To define genomewide enhancer and promoter use in heart failure, Cap Analysis of Gene Expression (CAGE-seq) was applied to healthy and failed human left ventricles to define short RNAs associated with both promoters and enhancers. Integration of CAGE-seq data with RNA sequencing identified a combined ∼17,000 promoters and ∼1,500 enhancers active in healthy and failed human left ventricles. Comparing promoter usage between healthy and failed hearts highlighted promoter shifts which altered amino-terminal protein sequences. Comparing enhancer usage between healthy and failed hearts revealed a majority of differentially utilized heart failure enhancers were intronic and primarily localized within the first intron, identifying this position as a common feature associated with tissue-specific gene expression changes in the heart. This dataset defines the dynamic genomic regulatory landscape underlying heart failure and serves as an important resource for understanding genetic contributions to cardiac dysfunction.
Same same but different: Cluster architecture variation in five ‘Pinot Noir’ clonal selection lines correlates with differential expression of three transcription factors and further growth related genes
Authors: Richter Robert , Rossmann Susanne , Gabriel Doreen , Töpfer Reinhard , Theres Klaus , Zyprian Eva 
Published: March 2020

AbstractGrapevine (Vitis viniferaL.) is an economically important crop that needs to comply with high quality standards for fruit, juice and wine production. Intense plant protection is required to avoid losses caused by fungal infections. Grapevine cultivars with loose cluster architecture enable to reduce protective chemical treatments due to their enhanced resilience against fungal infections such asBotrytis cinereainduced grey mold. A recent study identified transcription factor geneVvGRF4as determinant of inflorescence structure in exemplary samples of loose and compact quasi-isogenic ‘Pinot Noir’ clones. Here, we extended the analysis to 12 differently clustered ‘Pinot Noir’ clones originating from five different clonal selection programs. Differential gene expression of these clones was studied in three different locations over three seasons in demonstrative vineyards. Two phenotypically contrasting clones were grown at all three locations and served for standardization of downstream analyses. Differential gene expression data were correlated to the phenotypic variation of cluster architecture sub-traits. A consistent differential gene expression ofVvGRF4in relation to loose clusters was verified over the different environments and in the extended set of ‘Pinot Noir’ clones. In addition, 14 more genes with consistent expression differences between loosely and compactly clustered clones independent from season and location were identified. These genes show annotations related to cellular growth, cell wall extension, cell division and auxin metabolism. They include two more transcription factor genes.
A novel framework for modeling the evolution of cross-scale ecological assembly
Authors: Gallinat Amanda S. , Pearse William D. 
Published: March 2020

AbstractCommunity assembly can be driven by species’ responses to environmental gradients, and interactions within (e.g., competition) and across (e.g., herbivory) clades. These ecological dynamics are mediated by species’ traits, which are in turn shaped by past evolution. As such, identifying the drivers of species assembly is made difficult by the differing temporal and spatial scales of ecological and evolutionary dynamics. Two recent advances have emerged to address the cross-scale challenge of modeling species assembly: phylogenetic generalized linear mixed modeling (PGLMM) and earth observation networks (EONs). PGLMM integrates through time by modeling the evolution of trait-based community assembly, while EONs synthesize across space by placing standardized site-level species occurrence data within their regional context. Here we describe a framework for combining these tools to investigate the drivers of species assembly, and so address three outstanding questions: (1) Does evolution adapt or constrain regional-scale environmental responses? (2) Do evolved responses to past competition minimize or enhance present-day competition? (3) Are species’ cross-clade associations evolutionarily constrained? We provide a conceptual overview of how PGLMM and EONs can be synthesized to answer these questions, and provide exemplar Bayesian PGLMM code. Finally, we describe the capacity of these tools to aid in conservation and natural resource management, including predicting future colonization by rare and invasive species, vulnerable mutualisms, and pest and pathogen outbreaks.
Changes in group size during resource shifts reveal drivers of sociality across the tree of life
Authors: Kao Albert B. , Hund Amanda K. , Santos Fernando P. , Young Jean-Gabriel , Bhat Deepak , Garland Joshua , Oomen Rebekah A. , McCreery Helen F. 
Published: March 2020

ABSTRACTFrom biofilms to whale pods, organisms have repeatedly converged on sociality as a strategy to improve individual fitness. Yet, it remains challenging to identify the most important drivers—and by extension, the evolutionary mechanisms—of sociality for particular species. Here, we present a conceptual framework, literature review, and model demonstrating that the direction and magnitude of the response of group size to sudden resource shifts provides a strong indication of the underlying drivers of sociality. We catalog six functionally distinct mechanisms related to the acquisition of resources, and we model these mechanisms’ effects on the survival of individuals foraging in groups. We find that whether, and to what degree, optimal group size increases, decreases, or remains constant when resource abundance declines depends strongly on the dominant mechanism. Existing empirical data support our model predictions, and we demonstrate how our framework can be used to predict the dominant social benefit for particular species. Together, our framework and results show that a single easily measurable characteristic, namely, group size under different resource abundances, can illuminate the potential drivers of sociality across the tree of life.
Diffusion property and functional connectivity of superior longitudinal fasciculus underpin human metacognition
Authors: Zheng Yunxuan , Wang Danni , Ye Qun , Zou Futing , Li Yao , Kwok Sze Chai 
Published: March 2020

AbstractMetacognition as the capacity of monitoring one’s own cognition operates across domains. Here, we addressed whether metacognition in different cognitive domains rely on common or distinct neural substrates with combined diffusion tensor imaging (DTI) and functional magnetic resonance imaging (fMRI) techniques. After acquiring DTI and resting-state fMRI data, we asked participants to perform a temporal-order memory task and a perceptual discrimination task, followed by trial-specific confidence judgments. DTI analysis revealed that the structural integrity (indexed by fractional anisotropy) in the anterior portion of right superior longitudinal fasciculus (SLF) was associated with both perceptual and mnemonic metacognitive abilities. Using perturbed mnemonic metacognitive scores produced by inhibiting the precuneus using TMS, the mnemonic metacognition scores did not correlate with individuals’ SLF structural integrity anymore, revealing the relevance of this tract in memory metacognition. In order to further verify the involvement of several cortical regions connected by SLF, we took the TMS-targeted precuneus region as a seed in a functional connectivity analysis and found the functional connectivity between precuneus and two SLF-connected regions (inferior parietal cortex and precentral gyrus) differentially mediated mnemonic but not perceptual metacognition performance. These results illustrate the importance of SLF and a putative white-matter grey-matter circuitry that supports human metacognition.
Gene expression profiling of Tea (Camellia sinensisL.) in response to biotic stress using microarrays
Authors: Ashokraj S. , Raj E. Edwin , Chandrashekara K.N. , Govindaraj R. , Blessia T. Femlin , Radhakrishnan B. 
Published: March 2020

ABSTRACTThe blister blight (BB) and grey blight (GB) diseases are the major biotic stresses, which affecting the plant health, yield and quality of tea. The study aims to understand the gene response of tea plants against destructing foliar diseases in terms of differential gene expression and their pathways through microarray analysis aid by MapMan®software. The results of expression profile analysis showed that 235 in BB and 258 for GB genes were differentially expressed (at P<0.05) which involving in gene regulatory function as biotic stress response. Similarly, 76 and 86 differentially expressed genes involving in cellular response during BB and GB diseases, respectively. However, 28 in BB and 9 in GB differentially expressed (P<0.01) genes were putatively involved in biotic stress response. The study also identified differentially expressed 75 transcription factors (TFs) belongs to 23 TFs superfamily act as either transcriptional activators or repressors. The study helps to understand the differential gene expression pattern and its cellular, molecular and biological mechanisms of tea plants of two different diseases based on microarray analysis. Further studies using biotechnological tools on the stress-responsive genes in the germplasm may enable us for development of disease resistance.
Development of non-destructive methods to estimate functional traits and field evaluation in tea plantations using a smartphone
Authors: Raj Esack Edwin , Kumar Rajagobal Raj , Shanmugam Ashokraj , Radhakrishnan Balakrishnan 
Published: March 2020

AbstractSmartphones are equipped with various types of sensors which make them a promising tool to assist diverse digital farming tasks because of their mobility, cost, accessibility, and computing power allow us to perform real-time practical applications. This paper presents the utilization of various non-destructive methods of nutrient and disease classification techniques using smartphone collected images, processed through various image segmentation algorithms. Bothin vivoandin vitroestimations shows comparable results with both chlorophyll and nitrogen contents of a crop shoot. Moreover, the correlation between SPAD measured values and nitrogen of crop shoot showed a significant linear association (R2=0.7309), revealing the potency ofin vivoobservation for prediction of actual chlorophyll content in tea crop. SPAD values and yield have a strong linear relationship (R2=0.7103), in which SPAD-meter performed better detection at very low values. The study concluded that the proposed techniques could be used for automatic detection as well as classification of foliar diseases and nutrients in tea.
Phosphatidylinositol 3-phosphate and Hsp70 protectPlasmodium falciparumfrom heat-induced cell death
Authors: Lu Kuan-Yi , Pasaje Charisse Flerida A. , Srivastava Tamanna , Loiselle David R. , Niles Jacquin C. , Derbyshire Emily R. 
Published: March 2020

AbstractPhosphatidylinositol 3-phosphate (PI(3)P) levels inPlasmodium falciparumcorrelate with tolerance to cellular stresses caused by artemisinin, a first-line malaria treatment, and environmental factors. However, the functional role of PI(3)P in thePlasmodiumstress response and a possible mechanism of protection were unknown. Here, we used multiple chemical probes including PI3K inhibitors and known antimalarial drugs to examine the importance of PI(3)P under thermal conditions that recapitulate malaria fever. Live cell microscopy using both chemical and genetic reporters revealed that PI(3)P stabilizes the acidic and proteolytic digestive vacuole (DV) under heat stress. We demonstrate that heat-induced DV destabilization in PI(3)P-deficientP. falciparumprecedes cell death and is reversible after withdrawal of the stress condition and the PI3K inhibitor. These phenotypes are not observed with an inactive structural analog of the PI3K inhibitor. A chemoproteomic and biochemical approach identified PfHsp70-1 as a parasite PI(3)P-binding protein. Targeting PfHsp70-1 with a small molecule inhibitor phenocopied PI(3)P-deficient parasites under heat shock. Furthermore, tunable knockdown of PfHsp70-1 showed that PfHsp70-1 downregulation causes DV destabilization and hypersensitizes parasites to heat shock and PI3K inhibitors. Our findings underscore a mechanistic link between PI(3)P and PfHsp70-1, and present a novel PI(3)P function in stabilizing the DV compartment during heat stress.
Testing the pathogenic potential ofCryphonectria parasiticaand related species on three common European Fagaceae
Authors: Dennert Francesca , Rigling Daniel , Meyer Joana B. , Schefer Christopher , Augustiny Eva , Prospero Simone 
Published: March 2020

AbstractInvasions by non-native pathogens represent a major threat to managed and natural ecosystems worldwide. Although necessary for adopting preventive strategies, the identification of invasive species before they are introduced is particularly difficult. Indeed, most pathogenic species that have become established in the last decades were first described only after they became invasive. To prevent further biological invasions, not only the early identification of potential new invasive plant pathogens is crucial, but also the assessment of their potential host range. In this study, we determined the pathogenicity and the saprotrophic ability of threeCryphonectriaspecies towards three potential hosts in the family Fagaceae. For this, seedlings and dormant stems of European chestnut (Castanea sativa), pedunculate oak (Quercus robur) and European beech (Fagus sylvatica) were inoculated with different genotypes ofC. parasitica(Asian species, invasive in Europe),C. naterciae(European species), andC. japonica(Asian species, not present in Europe). Lesion growth was measured and mortality assessed for four months. The highest damage was caused byC. parasiticaon European chestnut, whileC. japonicaandC. naterciaeinduced significantly smaller lesions on this host species. All threeCryphonectriaspecies did not grow saprophytically onF. sylvaticaandQ. robur, but successfully colonized dormant stems ofC. sativa. In the context of biological invasions, our study shows that the AsianC. japonicamost likely represents a much less severe threat thanC. parasiticafor the tested European host species. Nonetheless, the ability ofC. naterciaeandC. japonicato saprotrophically colonize fresh chestnut wood may suggest that they could become established in chestnut forests and eventually infect weakened chestnut trees or other hosts not tested in this study.
Cell-free protein synthesis enables one-pot cascade biotransformation in an aqueous-organic biphasic system
Authors: Liu Wan-Qiu , Wu Changzhu , Jewett Michael C. , Li Jian 
Published: March 2020

AbstractBiocatalytic cascade reactions have become increasingly important and useful for chemical synthesis. However, biocatalysts are often incompatible with organic solvents, which prohibits many cascade reactions involving nonpolar substrates. In this work, we used cell-free protein synthesis (CFPS) to express enzymes in an aqueous-organic biphasic system for the construction of an artificial enzymatic pathway. CFPS-expressed enzymes without purification performed efficiently to convert styrene (below 20 mM) to (S)-1-phenyl-1,2-ethanediol (two steps in one pot) with 100% conversion. In addition, our CFPS system showed great tolerance to different organic solvents and, importantly, the entire biocatalytic system can be consistently scaled up without reduction of the substrate conversion rate. We therefore anticipate that our cell-free approach will make possible cost-effective, high-yielding synthesis of valuable chemicals.
CYCA3;4 Is a Post-Prophase Target of the APC/CCCS52A2E3-Ligase Controlling Formative Cell Divisions in Arabidopsis
Authors: Willems Alex , Heyman Jefri , Eekhout Thomas , Achon Ignacio , Pedroza-Garcia Jose Antonio , Zhu Tingting , Li Lei , Vercauteren Ilse , Van den Daele Hilde , van de Cotte Brigitte , De Smet Ive , De Veylder Lieven 
Published: March 2020

ABSTRACTThe Anaphase Promoting Complex/Cyclosome (APC/C) controls unidirectional progression through the cell cycle by marking key cell cycle proteins for proteasomal turnover. Its activity is temporally regulated by the docking of different activating subunits, known in plants as CDC20 and CCS52. Despite the importance of the APC/C during cell proliferation, the number of identified targets in the plant cell cycle is limited. Here, we used the growth and meristem phenotypes of Arabidopsis CCS52A2-deficient plants in a suppressor mutagenesis screen to identify APC/CCCS52A2substrates or regulators, resulting in the identification of a mutant cyclinCYCA3;4allele. CYCA3;4 deficiency partially rescues the earlyccs52a2-1phenotypes, whereas increased CYCA3;4 levels enhances them. Furthermore, whereas CYCA3;4 proteins are promptly broken down after prophase in wild-type plants, they remain present in later stages of mitosis inccs52a2-1mutant plants, marking them as APC/CCCS52A2substrates. Strikingly,CYCA3;4overexpression results in aberrant root meristem and stomatal divisions, mimicking phenotypes of plants with reduced RBR1 activity. Correspondingly, RBR1 hyperphosphorylation was observed in CYCA3;4-overproducing plants. Our data thus demonstrate that an inability to timely destroy CYCA3;4 attributes to disorganized formative divisions, likely in part caused by the inactivation of RBR1.ONE-SENTENCE SUMMARYTimely post-prophase breakdown of the Arabidopsis cyclin CYCA3;4 by the Anaphase Promoting Complex/Cyclosome is essential for meristem organization and development.