bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebellar dopamine D2 receptors regulate preference for social novelty
Authors: Cutando Laura , Puighermanal Emma , Castell Laia , Tarot Pauline , Belle Morgane , Bertaso Federica , Arango-Lievano Margarita , Ango Fabrice , Rubinstein Marcelo , Chédotal Alain , Mameli Manuel , Valjent Emmanuel 
Published: December 2019

SummaryThe cerebellum, a primary center involved in the control of sensorimotor tasks, also contributes to higher cognitive functions including reward, emotion and social interaction. The regulation of these behaviors has been largely ascribed to the monoaminergic system in limbic regions. However, the contribution of cerebellar dopamine signaling in the modulation of these functions remains largely unknown due to the lack of precise characterization of cerebellar dopaminoceptive neurons. By combining cell type-specific transcriptomic and histological analyses, 3D imaging and electrophysiology we demonstrate that cerebellar dopamine D2 receptors (D2R) in mice are preferentially expressed in Purkinje cells (PCs). While activation of D2R regulate synaptic efficacy onto PCs, their deletion or overexpression in PCs bidirectionally controls preference for social novelty without affecting motor functions. Altogether, these findings demonstrate novel D2R’s roles in PC function and causally link cerebellar D2R levels of expression to social behaviors.
Evolutionary conservation and multilevel post-translational control of S-adenosyl-homocysteine-Hydrolase in land plants
Authors: Alegre Sara , Pascual Jesús , Trotta Andrea , Angeleri Martina , Rahikainen Moona , Brosche Mikael , Moffatt Barbara , Kangasjärvi Saijaliisa 
Published: December 2019

AbstractTrans-methylation reactions are intrinsic to cellular metabolism in all living organisms. In land plants, a range of substrate-specific methyltransferases catalyze the methylation of DNA, RNA, proteins, cell wall components and numerous species-specific metabolites, thereby providing means for growth and acclimation in various terrestrial habitats. Trans-methylation reactions consume vast amounts of S-adenosyl-L-methionine (SAM) as a methyl donor in several cellular compartments. The inhibitory reaction by-product, S-adenosyl-L-homocysteine (SAH), is continuously removed by SAH hydrolase (SAHH) activity, and in doing so essentially maintains trans-methylation reactions in all living cells. Here we report on the evolutionary conservation and multilevel post-translational control of SAHH in land plants. We find that SAHH forms oligomeric protein complexes in phylogenetically divergent land plants, and provide evidence that the predominant enzyme is a tetramer. By analyzing light-stress-induced adjustments occurring on SAHH inArabidopsis thalianaandPhyscomitrella patens, we demonstrate that both angiosperms and bryophytes undergo regulatory adjustments in the levels of protein complex formation and post-translational modification of this metabolically central enzyme. Collectively, these data suggest that plant adaptation to terrestrial environments involved evolution of regulatory mechanisms that adjust the trans-methylation machinery in response to environmental cues.
Study on Spatial-temporal Variation of Atmospheric Pollution in China between 2014 and 2019
Authors: Peng Guo , Batalbievna Umarova Aminat , Yunqi Luan 
Published: December 2019

AbstractThe study in this paper reveals that the atmospheric contaminants in mainland China is of concentricity in spatial distribution, persistence in temporal distribution and correlation between different parameters. This spatial-temporal variation law plays an important role in improving and addressing the problem with atmospheric environment of given cities and regions by employing focused and pointed measures. In this paper, seven kinds of atmospheric pollution parameters including PM2.5, PM10, AQI, CO, NO2, O3 and SO2 in 370 Chinese cities from 2014 to 2019 are analyzed based on their hourly mass concentration. The spatial-temporal variations of each parameter in each separated year are obtained by using interpolation calculation towards the annual atmospheric pollution parameters. The results show that higher mass concentration (including the highest mass concentration) of PM2.5, AQI, PM10, CO, NO2, SO2 mainly concentrated in Beijing-Tianjin-Hebei region in the northeast of mainland China and its neighboring regions and Xinjiang region in the northwest of mainland China. The spatial variation of PM2.5, AQI, PM10, CO, NO2, SO2 experienced similar trend. Higher mass concentration (including the highest mass concentration) of O3 mainly concentrated in Qinghai and Inner Mongolia in the central north of mainland China and Shandong on the right side of Beijing-Tianjin-Hebei region. The spatial variation of O3 experienced different trend from that of other parameters. PM2.5, AQI, PM10 indicated increase and decrease, followed by increase and decrease again with time, which was a S-shaped change. Almost the same temporal variation happened to PM2.5, AQI, PM10 and to CO, NO2, SO2, which was opposite to O3. The analysis from the perspective of the annual highest mass concentration of PM2.5, AQI, PM10, NO2 and O3 indicates the atmospheric environment of mainland China had not been authentically improved by 2019. The analysis from the perspective of the annual highest mass concentration of CO and SO2 indicates the atmospheric environment of mainland China had been authentically improved by 2019. What should we do immediately is to strengthen environmental governance and address the source of contamination in Beijing-Tianjin-Hebei region in the northeast of China, Xinjiang region in the northwest of China, Qinghai and Inner Mongolia regions in the central north of China.
Endosperm and seed transcriptomes reveal possible roles for small RNA pathways in wild tomato hybrid seed failure
Authors: Florez-Rueda Ana Marcela , Fiscalini Flurin , Roth Morgane , Grossniklaus Ueli , Städler Thomas 
Published: December 2019

AbstractCrosses between the wild tomato speciesSolanum peruvianumandS. chilenseresult in hybrid seed failure (HSF), characterized by endosperm misdevelopment and embryo arrest. We previously showed that genomic imprinting, the parent-of-origin–dependent expression of alleles, is perturbed in hybrid endosperm, with many of the normally paternally expressed genes losing their imprinted status. Here, we report transcriptome-based analyses of gene and small RNA expression levels. We identified 2,295 genes and 468 small RNAs (sRNAs) as differentially expressed (DE) when comparing reciprocal hybrid seed to seeds and endosperms from the two within-species crosses. Our analyses uncovered a pattern of overdominance in endosperm gene expression in both cross directions, in marked contrast to the patterns of sRNA expression in whole seeds. Intriguingly, patterns of increased gene expression resembled the previously reported increased maternal expression proportions in hybrid endosperms. We identified physical clusters of sRNAs; DE sRNAs exhibited reduced levels of expression in hybrid seeds from both cross directions. Moreover, sRNAs mapped to genes coding for key proteins involved in epigenetic regulation of gene expression, suggesting a regulatory feedback mechanism. We describe examples of genes that are targets of sRNA-mediated gene silencing; in these cases, reduced sRNA expression was concomitant with increased gene expression in hybrid seeds. Our analyses also show thatS. peruvianumdominance impacts gene and sRNA expression in hybrid seeds. Overall, our study indicates roles for sRNA-mediated epigenetic regulation in HSF between closely related wild tomato species.
metabolisHMM: Phylogenomic analysis for exploration of microbial phylogenies and metabolic pathways
Authors: McDaniel E.A. , Anantharaman K. , McMahon K.D. 
Published: December 2019

AbstractSummaryAdvances in high-throughput sequencing technologies and bioinformatic pipelines have exponentially increased the amount of data that can be obtained from uncultivated microbial lineages inhabiting diverse ecosystems. Various annotation tools and databases currently exist for predicting the functional potential of sequenced genomes or microbial communities based upon sequence identity. However, intuitive, reproducible, and user-friendly tools for further exploring and visualizing functional guilds of microbial community metagenomic sequencing datasets remains lacking. Here, we present metabolisHMM, a series of workflows for visualizing the distribution of curated and user-provided Hidden Markov Models (HMMs) to understand metabolic characteristics and evolutionary histories of microbial lineages. metabolisHMM performs functional annotations with a set of curated or user-defined HMMs to 1) construct ribosomal protein and single marker gene phylogenies, 2) summarize the presence/absence of metabolic pathway markers, and 3) create heatmap visualizations of presence/absence summaries.Availability and ImplementationmetabolisHMM is freely available on Github athttps://github.com/elizabethmcd/metabolisHMMand on PyPi athttps://pypi.org/project/metabolisHMM/under the GNU General Public License v3.0.
Optimisation of a Novel Bio-Substrate as a Treatment for Atrophic Age-Related Macular Degeneration
Authors: McCormick Rachel , Pearce Ian , Kaye Stephen , Haneef Atikah 
Published: December 2019

AbstractAtrophic age-related macular degeneration (AMD) is the most common form of AMD accounting for 90% of patients. During atrophic AMD the waste/exchange pathway between the blood supply (choroid) and the retinal pigment epithelium (RPE) is compromised. This results in atrophy and death of the RPE cells and subsequently the photoreceptors leading to central blindness. Although the mechanisms behind AMD are unknown, the growth of fatty deposits known as drusen, have been shown to play a role in the disease. There is currently no treatment or cure for atrophic AMD. Much research focuses on developing a synthetic substrate in order to transplant healthy cells to the native Bruch’s membrane (BM), however, the diseased native BM and related structures still leave the potential for transplanted cells to succumb to disease. In this work we electrospun poly(ethylene terephthalate) (PET) to fabricate a nanofibrous cytocompatible synthetic BM. The apical surface of the membrane was cultured with ARPE-19 cells and the basal surface was decorated with poly(lactic acid-co-glycolic acid) (PLGA) or poly(glycolic acid) (PGA) degradable nanoparticles by electrospraying. The membrane exhibited hydrophilicity, high tensile strength and structurally resembled the native BM. ARPE-19 cells were able to form a monolayer on the surface of the membrane and no cell invasion into the membrane was seen. The presence of both PLGA and PGA nanoparticles increased ARPE-19 cell metabolism but had no effect on cell viability. There was a decrease in pH of ARPE-19 cell culture media 7 days following culturing with the PLGA nanoparticles but this change was eliminated by 2 weeks; PGA nanoparticles had no effect on cell culture media pH. The fluorescent dye FITC was encapsulated into nanoparticles and showed sustained release from PLGA nanoparticles for two weeks and PGA nanoparticles for 1 day. Future work will focus on encapsulating biologically active moieties to target drusen. This would allow this novel bioactive substrate to be a potential treatment for atrophic AMD that would function two-fold: deliver the required monolayer of healthy RPE cells to the macula on a synthetic BM and remove diseased structures within the retina, restoring the waste/exchange pathway and preventing vision loss.
The open bar is closed: restructuration of a native parasitoid community following successful control of an invasive pest
Authors: Muru David , Borowiec Nicolas , Thaon Marcel , Ris Nicolas , Viciriuc Madalina I. , Warot Sylvie , Vercken Elodie 
Published: December 2019

AbstractThe rise of the Asian chestnut gall waspDryocosmus kuriphilusin France has benefited the native community of parasitoids originally associated with oak gall wasps by becoming an additional trophic subsidy and therefore perturbing population dynamics of local parasitoids. However, the successful biological control of this pest has then led to significant decreases in its population densities. Here we investigate how the invasion of the Asian chestnut gall waspDryocosmus kuriphilusin France and its subsequent control by the exotic parasitoidTorymus sinensishas impacted the local community of native parasitoids.We explored 5 years of native community dynamics within 26 locations during the rise and fall of the invasive pest. In an attempt to understand how mechanisms such as local extinction or competition come into play, we analyzed how the patterns of co-occurrence between the different native parasitoid species changed through time.Our results demonstrate that native parasitoid communities experienced increased competition as theD. kuriphiluslevels of infestation decreased. During the last year of the survey, two alternative patterns were observed depending on the sampled location: either native parasitoid communities were represented by an extremely limited number of species occurring at low densities, in some cases no native parasitoid species at all, or they were dominated by one main parasitoid:Mesopolobus sericeus. These two patterns seemed to correlate with the habitat type,M. sericeusbeing more abundant in semi-natural habitats compared to agricultural lands, the former known to be natural reservoirs for native parasitoids. These results highlight how the “boom-and-bust” dynamics of an invasive pest followed by successful biological control can deeply alter the structure of native communities of natural enemies.This article has been peer-reviewed and recommended byPeer Community in Zoologyhttps://doi.org/10.24072/pci.zool.100004
A single-cell survey ofDrosophilablood
Authors: Tattikota Sudhir Gopal , Hu Yanhui , Liu Yifang , Cho Bumsik , Barrera Victor , Steinbaugh Michael , Yoon Sang-Ho , Comjean Aram , Li Fangge , Dervis Franz , Hung Ruei-Jiun , Nam Jin-Wu , Sui Shannan Ho , Shim Jiwon , Perrimon Norbert 
Published: December 2019

SummaryDrosophilablood cells, called hemocytes, are classified into plasmatocytes, crystal cells, and lamellocytes based on the expression of a few marker genes and cell morphologies, which are inadequate to classify the complete hemocyte repertoire. Here, we used single-cell RNA sequencing (scRNA-seq) to map hemocytes across different inflammatory conditions in larvae. We resolved plasmatocytes into different states based on the expression of genes involved in cell cycle, antimicrobial response, and metabolism together with the identification of intermediate states. Further, we discovered rare subsets within crystal cells and lamellocytes that express fibroblast growth factor (FGF) ligandbranchlessand receptorbreathless, respectively. We demonstrate that these FGF components are required for mediating effective immune responses against parasitoid wasp eggs, highlighting a novel role for FGF signaling in inter-hemocyte crosstalk. Our scRNA-seq analysis reveals the diversity of hemocytes and provides a rich resource of gene expression profiles for a systems-level understanding of their functions.HighlightsscRNA-seq ofDrosophilablood recovers plasmatocytes, crystal cells, and lamellocytesscRNA-seq identifies different plasmatocyte states based on the expression of genes involved in cell cycle regulation, antimicrobial response, and metabolismPseudotemporal ordering of single cells identifies crystal cell and lamellocyte intermediate statesscRNA-seq uncovers a novel role for FGF signaling in inter-hemocyte crosstalk
A modified two-color flow cytometry assay to quantify in-vitro reinvasion and determine invasion phenotypes at lowPlasmodium falciparumparasitemia
Authors: Atuh Ngoh Ines , Nota Anong Damian , Cho Fru Jerome , Bojang Fatoumata , Mbye Haddijatou , Amambua-Ngwa Alfred 
Published: December 2019

ABSTRACTTwo-color flow cytometry(2cFCM) is the most accessible method for phenotyping parasite invasion. However, current protocols require samples of field isolates at ∼1% parasitemia for assay set-up, which are becoming more uncommon in low transmission settings. Current protocols, therefore, have to be adapted for low parasitemia if the method must have continued applicability in this era of elimination. Optimizing the protocol requires addressing; interference from young uninfected RBCs background fluorescence and biased phenotypes due to limited labeled RBCs availability and/or parasite density per assay. Here, we used SYBR Green I and CTFR Proliferation fluorescent dyes to set-up invasion assays withPlasmodium falciparum3D7, Dd2 and field isolates cultures (diluted at 0.05% to 2.0% parasitemia) against varying unlabeled to labeled RBC ratios (1:1 to 1:4). We showed that a shorter SYBR Green I staining time of 20 minutes, down from 1hour, minimized background fluorescence from uninfected RBCs (mean= 0.03% events) and allowed 2cFCM to accurately quantify reinvasion for an assay at 0.02% parasitemia. An increase in labeled target RBCs to 1:3 per assays significantly increased heterologous reinvasion (p<0.001). This resulted in a 10% greater invasion inhibition by enzyme treatments (p<0.05). Strain-specific invasion phenotype could be accurately determined for samples with as low as 0.3% parasitemia. Samples above 0.8% parasitemia were less accurate. These findings show that invasion pathway phenotypes can be obtained for field samples with low parasitemia at greater sensitivity and reproducibility by increasing the proportion of labeled RBCs per assay by at least 2-fold what is in current methods.
Human follicular helper T cell promoter connectomes reveal novel genes and regulatory elements at SLE GWAS loci
Authors: Su Chun , Johnson Matthew E. , Torres Annabel , Thomas Rajan M. , Manduchi Elisabetta , Sharma Prabhat , Le Coz Carole , Leonard Michelle E. , Lu Sumei , Hodge Kenyaita M. , Chesi Alessandra , Pippin James , Romberg Neil , Grant Struan F. A. , Wells Andrew D. 
Published: December 2019

ABSTRACTSystemic lupus erythematosus (SLE) is a complex inflammatory disease mediated by autoreactive antibodies that damages multiple tissues in children and adults. Genome-wide association studies (GWAS) have statistically implicated hundreds of loci in the susceptibility to human disease, including SLE, but the majority have failed to identify the causal variants or the effector genes. As a physicochemical approach to detecting functional variants and connecting them to target genes, we generated comprehensive, high-resolution maps of SLE variant accessibility and gene connectivity in the context of the three-dimensional chromosomal architecture of human tonsillar follicular helper T cells (TFH), a cell type required for the production of anti-nuclear antibodies characteristic of SLE. These spatial epigenomic maps identified a shortlist of over 400 potentially functional variants across 48 GWAS-implicated SLE loci. Twenty percent of these variants were located in open promoters of highly-expressed TFH genes, while 80% reside in non-promoter genomic regions that are connected in 3D to genes that likewise tend to be highly expressed in TFH. Importantly, we find that 90% of SLE-associated variants exhibit spatial proximity to genes that are not nearby in the 1D sequence of the genome, and over 60% of variants ‘skip’ the nearest gene to physically interact only with the promoters of distant genes. Gene ontology confirmed that genes in spatial proximity to SLE variants reside in highly SLE-relevant networks, including accessible variants that loop 200-1000 kb to interact with the promoters of the canonical TFH genesBCL6andCXCR5. CRISPR-Cas9 genome editing confirmed that these variants reside in novel, distal regulatory elements required for normalBCL6andCXCR5expression by T cells. Furthermore, SLE-associated SNP-promoter interactomes implicated a set of novel genes with no known role in TFH or SLE disease biology, including the homeobox-interacting protein kinase HIPK1 and the Ste kinase homolog MINK1. Targeting these kinases in primary human TFH cells inhibited production of IL-21, a requisite cytokine for production of class-switched antibodies by B cells. This 3D-variant-to-gene mapping approach gives mechanistic insight into the SLE-associated regulatory architecture of the human genome.
PiVR: an affordable and versatile closed-loop platform to study unrestrained sensorimotor behavior
Authors: Tadres David , Louis Matthieu 
Published: December 2019

AbstractTools enabling closed-loop experiments are crucial to delineate causal relationships between the activity of genetically-labeled neurons and specific behaviors. We developed the RaspberryPiVirtualReality system (PiVR) to conduct closed-loop optogenetic stimulation of neural functions in unrestrained animals. PiVR is an experimental platform that operates at high-temporal resolution (>50 Hz) with low latencies (~10 ms), while being affordable (<$500) and easy to build (<6 hours). This tool was designed to be accessible to a wide public, from highschool students to professional researchers studying systems neuroscience. We illustrate the functionality of PiVR by focusing on sensory navigation in response to gradients of chemicals (chemotaxis) and light (phototaxis). We show howDrosophilaflies perform negative chemotaxis by modulating their locomotor speed to avoid locations associated with optogenetically-evoked bitter taste. InDrosophilalarvae, we use innate positive chemotaxis to compare orientation behavior elicited by real- and virtual-odor gradients with static shapes as well as by turbulent virtual-odor plumes. Finally, we examine how positive phototaxis emerges in zebrafish larvae from the modulation of turning maneuvers during the ascent of virtual white-light gradients. Besides its application to study chemotaxis and phototaxis, PiVR is a versatile tool designed to bolster efforts to map and to functionally characterize neural circuits.
High-throughput cryo-EM enabled by user-free preprocessing routines
Authors: Li Yilai , Cash Jennifer N. , Tesmer John. J.G. , Cianfrocco Michael A. 
Published: December 2019

ABSTRACTThe growth of single-particle cryo-EM into a mainstream structural biology tool has allowed for many important biological discoveries. Continued developments in data collection strategies alongside new sample preparation devices heralds a future where users will collect multiple datasets per microscope session. To make cryo-EM data processing more automatic and user-friendly, we have developed an automatic pipeline for cryo-EM data preprocessing and assessment using a combination of deep learning and image analysis tools. We have verified the performance of this pipeline on a number of datasets and extended its scope to include sample screening by the user-free assessment of the qualities of a series of datasets under different conditions. We propose that our workflow provides a decision-free solution for cryo-EM, making data preprocessing more generalized and robust in the high-throughput era as well as more convenient for users from a range of backgrounds.