bluuebunny/crossref_metadata_2025_split huggingface dataset:
mTOR-RhoA signalling impairments in direct striatal projection neurons induce altered behaviours and striatal physiology in mice
Authors: Rial Daniel , Puighermanal Emma , Valjent Emmanuel , Schiffmann Serge , de Kerchove d’Exaerde Alban 
Published: December 2019

AbstractAs an integrator of molecular pathways, mTOR has been associated with diseases including neurodevelopmental, psychiatric and neurodegenerative disorders as autism, schizophrenia, and Huntington’s disease. An important brain area involved in all these diseases is the striatum. However, the mechanisms behind how mTOR is involved in striatal physiology and its relative role in distinct neuronal populations in these striatal-related diseases still remain to be clarified.Taking advantage of the D1-mTOR KO mice (males), we combined behavioural, biochemical, electrophysiological and morphological analysis aiming to untangle the role of mTOR in direct pathway striatal projection neurons (dMSNs) and how this would impact on striatal physiology.Our results indicate deep behavioural changes in absence of mTOR in dMSNs such as decreased spontaneous locomotion, impaired social interaction and repetitive behaviour. These were accompanied by a Kv1.1-induced increase in the fast phase of afterhyperpolarization and decreased distal spines density that were mechanistically independent of protein synthesis but dependent of RhoA activity.These results identify mTOR RhoA signaling as an important regulator of striatal functions through an intricate mechanism involving RhoA and culminating in Kv1.1 overfunction, which could be targeted to treat striatal-related mTORopathies.
Identification of Genomic Insertion and Flanking Sequences of the Transgenic Drought-tolerant Maize Line “SbSNAC1-382” using the Single Molecular Real-Time (SMRT) Sequencing Method
Authors: Zeng Tingru , Zhang Dengfeng , Li Yongxiang , Li Chunhui , Liu Xuyang , Shi Yunsu , Song Yanchun , Li Yu , Wang Tianyu 
Published: December 2019

AbstractSafety assessment of genetically modified (GM) crops is crucial in the phase of product development before the GM crops are put on the market. Characteristics of flanking sequences of exogenous insertion sequences are essential for the safety assessment and marking of transgenic crops. In this study, we used the methods of genome walking and whole genome sequencing (WGS) to identify the flanking sequence characteristics of aSbSNAC1transgenic drought-tolerant maize line “SbSNAC1-382”, but both of the methods failed. Then, we constructed a genomic fosmid library of the transgenic maize line, which contained 4.18×105clones with an average insertion fragment of 35 kb, covering 5.85 times of the maize genome. Subsequently, three positive clones were screened by pairs of specific primers and one of the three positive clones was sequenced by using the Single Molecule Real-Time (SMRT) sequencing technology. More than 1.95 Gb sequence data (∼105× coverage) for the sequenced clone was generated. The junction reads mapped to the boundaries of T-DNA and the flanking sequences in the transgenic line were identified by comparing all sequencing reads with the maize reference genome and the sequence of transgenic vector. Furthermore, the putative insertion loci and flanking sequences were confirmed by PCR amplification and Sanger sequencing. The results indicated that two copies of the exogenous T-DNA fragments were inserted in the same genomic site. And the exogenous T-DNA fragments were integrated at the position of Chromosome 5: 177155650 to 177155696 in the transgenic line 382. Herein, we have demonstrated the successful application of the SMRT technology for the characterization of genomic insertion and flanking sequences.
Quantifying colour difference in animals with variable patterning
Authors: Dračková Tereza , Smolinský Radovan , Hiadlovská Zuzana , Dolinay Matej , Martínková Natália 
Published: December 2019

AbstractColour pattern influences behaviour and modifies survival of organisms through perception of light reflectance. Spectrophotometric methods used to study colour navigate between precision and accuracy of reflectance across wavelengths, while photographic methods are generally used to assess the complexity of colour patterns. Here, we compare how colours characterised using point measurements (simulating spectrophotometry) on the skin of a sand lizard (Lacerta agilis) differ from colours estimated by clustering pixels in a photograph of the lizard’s body. We found that point measurements adequately represented the dominant colour of the lizard; however, where colour patterning influenced measurement geometry, image analysis outper-formed point measurement as regards stability between technical replicates on the same animal. The greater colour variation established from point measurements increased further under controlled laboratory illumination. Both methods revealed lateral colour asymmetry in sand lizards. We conclude that studies assessing the impact of colour on animal ecology and behaviour should utilise hyperspectral imaging, followed by image analysis that encompasses the whole colour pattern.
Differential propagation of ripples along the proximo-distal and septo-temporal axes of dorsal CA1 of rats
Authors: Kumar Mekhala , Deshmukh Sachin S. 
Published: December 2019

AbstractThe functional connectivity of the hippocampus with its primary cortical input, the entorhinal cortex, is organized topographically. In area CA1 of the hippocampus, this leads to different functional gradients along the proximo-distal and septo-temporal axes of spatial/sensory responsivity and spatial resolution respectively. CA1 ripples, a network phenomenon, allows us to test whether the hippocampal neural network shows corresponding gradients in functional connectivity along the two axes. We studied the occurrence and propagation of ripples across the entire proximo-distal axis along with a comparable spatial range of the septo-temporal axis of dorsal CA1. We observed that ripples could occur at any location, but their probability of co-occurrence and amplitude decreased with increasing distance from the reference tetrode. This reduction was greater along the proximo-distal axis than the septo-temporal axis. Furthermore, we found that ripples propagate primarily along the proximo-distal axis. Thus, over a spatial scale of ~1.5 mm, the network is anisotropic along the two axes, complementing the topographically organized cortico-hippocampal connections.
The fecal microbiota of piglets is influenced by the farming environment and is associated with piglet robustness at weaning
Authors: Luise Diana , Le Sciellour Mathilde , Buchet Arnaud , Resmond Rémi , Clement Charlène , Rossignol Marie-Noelle , Jardet Deborah , Zemb Olivier , Belloc Catherine , Merlot Elodie 
Published: December 2019

AbstractThis study describes the response of piglet microbiota to weaning in various environments, and investigates whether microbiota composition is associated with the robustness of piglets. Faecal samples and growth data were collected just before and 7 days after weaning in 288 piglets from 16 commercial farms characterised by their pathogenic status and antimicrobial use. The effect of weaning on the most abundant microbial families of faecal microbiota was roughly the same in all farms and in agreement with previous findings. Four enterotypes, ubiquitous in all farms, were identified, for which the most discriminating genera werePrevotella,Faecalibacterium,Roseburia, andLachnospira.They corresponded to a gradual maturational shift from pre to post-weaning microbiota. Besides antimicrobial use, the pathogenic status of the farm had a major influence on the post-weaning microbial evolution of apparently healthy piglets. Regarding individual characteristics, piglets whose growth was less perturbed by weaning had moreBacteroidetes(P < 0.01) and lessProteobacteria (P < 0.001).In response to weaning, they showed a greater increase inPrevotella(P < 0.01),Coprococcus(P< 0.01) andLachnospira(P < 0.05) than piglets that grew more slowly. Thus, the microbiota of robust piglets shares common characteristics regardless the living environment of animals.
Mathematical model for force and energy of virion-cell interactions during full engulfment in HIV: Impact of virion maturation and host cell morphology
Authors: Kruse Elizabeth , Abdalrahman Tamer , Selhorst Philippe , Franz Thomas 
Published: December 2019

AbstractViral endocytosis involves elastic cell deformation, driven by chemical adhesion energy, and depends on physical interactions between virion and cell membrane. These interactions are not easy to quantify experimentally. Hence, this study aimed to develop a mathematical model of the interactions of HIV particles with host cells and explore the effects of mechanical and morphological parameters during full virion engulfment. The invagination force and engulfment energy were described as viscoelastic and linear-elastic functions of radius and elastic modulus of virion and cell, ligand-receptor energy density and engulfment depth. The influence of changes in the virion-cell contact geometry representing different immune cells and ultrastructural membrane features and the decrease in virion radius and shedding of gp120 proteins during maturation on invagination force and engulfment energy was investigated. A low invagination force and high ligand-receptor energy are associated with high virion entry ability. The required invagination force was the same for immune cells of different sizes but lower for a local convex geometry of the cell membrane at the virion length scale. This suggests that localized membrane features of immune cells play a role in viral entry ability. The available engulfment energy decreased during virion maturation, indicating the involvement of additional biological or biochemical changes in viral entry. The developed mathematical model offers potential for the mechanobiological assessment of the invagination of enveloped viruses towards improving the prevention and treatment of viral infections.
The hematopoietic landscape at single-cell resolution reveals unexpected stem cell features in naked mole-rats
Authors: Emmrich Stephan , Mariotti Marco , Takasugi Masaki , Straight Maggie E. , Trapp Alexandre , Gladyshev Vadim N. , Seluanov Andrei , Gorbunova Vera 
Published: December 2019

SUMMARYNaked mole-rats are the longest-lived rodents endowed with resistance to cancer and age-related diseases, yet their stem cell characteristics remain enigmatic. We profiled the naked mole-rat hematopoietic system down to single-cell resolution, and identified several unique features likely contributing to longevity. In adult naked mole-rats red blood cells are formed in spleen and marrow, a neotenic feature beneficial for hypoxic environments and to prevent anemia. Platelet numbers are lower compared to short-lived mice, which may preclude age-related platelet increase and thrombosis. T cells mature in thymus and lymph nodes, providing a supply of T cells after age-related thymus involution. The pool of quiescent stem cells is higher than in mice, and HSCs overexpress an oxidative phosphorylation signature, revealing a new paradigm of stem cell metabolism to benefit longevity and oppose oncogenesis. Our work provides a platform to study immunology and stem cell biology in an animal model of healthy aging.HIGHLIGHTSFlow cytometry labelling panel to purify viable naked mole-rat HSPCsThe spleen as the major site of erythropoiesis in the naked mole-ratNaked mole-rats show extrathymic T-cell development under homeostatic conditionsNaked mole-rat hematopoietic stem cells (HSCs) have high OXPHOS activity
Multi-parametric quantitative spinal cord MRI with unified signal readout and image denoising
Authors: Grussu Francesco , Battiston Marco , Veraart Jelle , Schneider Torben , Cohen-Adad Julien , Shepherd Timothy M. , Alexander Daniel C. , Novikov Dmitry S. , Fieremans Els , Wheeler-Kingshott Claudia A. M. Gandini 
Published: December 2019

AbstractMulti-parametric quantitative MRI (qMRI) of the spinal cord is a promising non-invasive tool to probe early microstructural damage in neurological disorders. It is usually performed by combining acquisitions with multiple signal readouts, which exhibit different thermal noise levels, geometrical distortions and susceptibility to physiological noise. This ultimately hinders joint multi-contrast modelling and makes the geometric correspondence of parametric maps challenging. We propose an approach to overcome these limitations, by implementing state-of-the-art microstructural MRI of the spinal cord with a unified signal readout. We base our acquisition on single-shot echo planar imaging with reduced field-of-view, and obtain data from two different vendors (vendor 1: Philips Achieva; vendor 2: Siemens Prisma). Importantly, the unified acquisition allows us to compare signal and noise across contrasts, thus enabling overall quality enhancement via Marchenko-Pastur (MP) Principal Component Analysis (PCA) denoising. MP-PCA is a recent method relying on redundant acquisitions, i.e. such that the number of measurements is much larger than the number of informative principal components. Here we used in vivo and synthetic data to test whether a unified readout enables more efficient denoising of less redundant acquisitions, since these can be denoised jointly with more redundant ones. We demonstrate that a unified readout provides robust multi-parametric maps, including diffusion and kurtosis tensors from diffusion MRI, myelin metrics from two-pool magnetisation transfer, and T1 and T2 from relaxometry. Moreover, we show that MP-PCA improves the quality of our multi-contrast acquisitions, since it reduces the coefficient of variation (i.e. variability) by up to 15% for mean kurtosis, 8% for bound pool fraction (BPF, myelin-sensitive), and 13% for T1, while enabling more efficient denoising of modalities limited in redundancy (e.g. relaxometry). In conclusion, multi-parametric spinal cord qMRI with unified readout is feasible and provides robust microstructural metrics with matched resolution and distortions, whose quality benefits from MP-PCA denoising, a useful pre-processing tool for spinal cord MRI.
Golgi anti-apoptotic proteins are evolutionarily conserved ion channels that regulate cell death in plants
Authors: Sierla Maija , Prole David L. , Saraiva Nuno , Carrara Guia , Dinischiotu Natalia , Vaattovaara Aleksia , Wrzaczek Michael , Taylor Colin W. , Smith Geoffrey L. , Feys Bart 
Published: December 2019

ABSTRACTProgrammed cell death regulates developmental and stress responses in eukaryotes. Golgi anti-apoptotic proteins (GAAPs) are evolutionarily conserved cell death regulators. Human and viral GAAPs inhibit apoptosis and modulate intracellular Ca2+fluxes, and viral GAAPs form cation-selective channels. Although most mammalian cell death regulators are not conserved at the sequence level in plants, the GAAP gene family shows expansion, with five paralogues (AtGAAP1-5) in the Arabidopsis genome. We pursued molecular and physiological characterization of AtGAAPs making use of the advanced knowledge of their human and viral counterparts. Structural modeling of AtGAAPs predicted the presence of a channel-like pore, and electrophysiological recordings from purified AtGAAP3 reconstituted into lipid bilayers confirmed that plant GAAPs can function as ion channels. AtGAAP1 and AtGAAP4 localized exclusively to the Golgi within the plant cell, while AtGAAP2, AtGAAP3 and AtGAAP5 also showed tonoplastic localization. Gene expression analysis revealed differential spatial expression and abundance of transcript forAtGAAPparalogues in Arabidopsis tissues. We demonstrate that AtGAAP1-5 inhibit Bax-induced cell death in yeast. However, overexpression of AtGAAP1 induces cell death inNicotiana benthamianaleaves and lesion mimic phenotype in Arabidopsis. We propose that AtGAAPs function as Golgi-localized ion channels that regulate cell death by affecting ionic homeostasis within the cell.HighlightArabidopsis Golgi anti-apoptotic proteins (GAAPs) share functional conservation with their human and viral counterparts in cell death regulation and ion channel activityAbbreviationsAtGAAP,Arabidopsis thalianaGAAP; BI-1, Bax inhibitor-1; CFP, cyan fluorescent protein; CMLV, camelpox virus; ER, Endoplasmic reticulum; GAAP, Golgi anti-apoptotic protein; GFP, green fluorescent protein; hGAAP, human GAAP; LFG, Lifeguard; LMM, lesion mimic mutant; PCD, programmed cell death; TMBIM, transmembrane Bax inhibitor-1 motif-containing; TMDs, transmembrane domains; vGAAP, viral GAAP; YFP, yellow fluorescent protein
Alignment of time-course single-cell RNA-seq data with CAPITAL
Authors: Sugihara Reiichi , Kato Yuki , Mori Tomoya , Kawahara Yukio 
Published: December 2019

AbstractRecent techniques on single-cell RNA sequencing have boosted transcriptome-wide observation of gene expression dynamics of time-course data at a single-cell scale. Typical examples of such analysis include inference of a pseudotime cell trajectory, and comparison of pseudotime trajectories between different experimental conditions will tell us how feature genes regulate a dynamic cellular process. Existing methods for comparing pseudotime trajectories, however, force users to select trajectories to be compared because they can deal only with simple linear trajectories, leading to the possibility of making a biased interpretation. Here we present CAPITAL, a method for comparing pseudotime trajectories with tree alignment whereby trajectories including branching can be compared without any knowledge of paths to be compared. Computational tests on time-series public data indicate that CAPITAL can align non-linear pseudotime trajectories and reveal gene expression dynamics.
Interplay betweenTERTpromoter mutations and methylation culminates in chromatin accessibility andTERTexpression
Authors: Salgado Catarina , Roelse Celine , Nell Rogier , Gruis Nelleke , van Doorn Remco , van der Velden Pieter 
Published: December 2019

AbstractThetelomerase reverse transcriptase(TERT) gene is responsible for telomere maintenance in germline and stem cells, and is re-expressed in 90% of human cancers. Contrary to common concepts, CpG methylation in theTERTpromoter (TERTp), was correlated withTERTmRNA expression. Furthermore, two hotspot mutations inTERTp, dubbed C228T and C250T, have been revealed to assist binding of transcription factor ETS/TCF and subsequentTERTexpression. This study aimed to elucidate the combined contribution of epigenetic (promoter methylation and higher-order chromatin structure) and genetic (promoter mutations) mechanisms in regulatingTERTgene expression in healthy skin and in melanoma cell lines (n=61). We unexpectedly observed that the methylation ofTERTp was as high in a subset of healthy skin cells, mainly keratinocytes, as in cutaneous melanoma cell lines. In spite of the high promoter methylation fraction in wild-type (WT) samples,TERTmRNA was only expressed in the melanoma cell lines with high methylation or intermediate methylation in combination withTERTmutations.TERTp methylation was positively correlated with chromatin accessibility and expression in 8 melanoma cell lines. Cooperation between epigenetic and genetic mechanisms were best observed in heterozygous mutant cell lines as chromosome accessibility preferentially concerned the mutant allele. Combined, these results suggest a complex model in whichTERTexpression requires either a widely open chromatin state throughout the promoter inTERTp-WT samples due to high methylation or a combination of moderate methylation fraction/chromatin accessibility in the presence of the C228T/C250T mutations.Author summaryPvdV and RvD formulated research goals and aims and supervised the overall progress. Wet-lab experiments, preparation of the manuscript and statistical analysis were performed by CS and CR. CS designed the novel assays. RN was involved in the experimental setup. RvD, NG and PvdV were responsible for funding acquisition. CR, RN, NG, RvD and PvdV critically reviewed the manuscript.
wg-blimp: an end-to-end analysis pipeline for whole genome bisulfite sequencing data
Authors: Wöste Marius , Leitão Elsa , Laurentino Sandra , Horsthemke Bernhard , Rahmann Sven , Schröder Christopher 
Published: December 2019

BackgroundAnalysing whole genome bisulfite sequencing datasets is a data-intensive task that requires comprehensive and reproducible workflows to generate valid results. While many algorithms have been developed for tasks such as alignment, comprehensive end-to-end pipelines are still sparse. Furthermore, previous pipelines lack features or show technical deficiencies, thus impeding analyses.ResultsWe developed wg-blimp (whole genome bisulfite sequencing methylation analysis pipeline) as an end-to-end pipeline to ease whole genome bisulfite sequencing data analysis. It integrates established algorithms for alignment, quality control, methylation calling, detection of differentially methylated regions, and methylome segmentation, requiring only a reference genome and raw sequencing data as input. Comparing wg-blimp to previous end-to-end pipelines reveals similar setups for common sequence processing tasks, but shows differences for post-alignment analyses. We improve on previous pipelines by providing a more comprehensive analysis workflow as well as an interactive user interface. To demonstrate wg-blimp’s ability to produce correct results we used it to call differentially methylated regions for two publicly available datasets. We were able to replicate 112 of 114 previously published regions, and found results to be consistent with previous findings. We further applied wg-blimp to a publicly available sample of embryonic stem cells to showcase methylome segmentation. As expected, unmethylated regions were in close proximity of transcription start sites. Segmentation results were consistent with previous analyses, despite different reference genomes and sequencing techniques.Conclusionswg-blimp provides a comprehensive analysis pipeline for whole genome bisulfite sequencing data as well as a user interface for simplified result inspection. We demonstrated its applicability by analysing multiple publicly available datasets. Thus, wg-blimp is a relevant alternative to previous analysis pipelines and may facilitate future epigenetic research.
On the prediction of DNA-binding preferences of C2H2-ZF domains using structural models: application on human CTCF
Authors: Meseguer Alberto , Årman Filip , Fornes Oriol , Molina Ruben , Bonet Jaume , Fernandez-Fuentes Narcis , Oliva Baldo 
Published: December 2019

ABSTRACTCis2-His2 zinc finger (C2H2-ZF) proteins are the largest family of transcription factors in human and higher metazoans. However, the DNA-binding preferences of many members of this family remain unknown. We have developed a computational method to predict these DNA-binding preferences. We combine information from crystal structures composed by C2H2-ZF domains and from bacterial one-hybrid experiments to compute scores for protein-DNA binding based on statistical potentials. We apply the scores to compute theoretical position weight matrices (PWMs) of proteins with a DNA-binding domain composed by C2H2-ZF domains, with the only requirement of an input structure (experimentally determined or modelled). We have tested the capacity to predict PWMs of zinc finger domains, successfully predicting 3-2 nucleotides of a trinucleotide binding site for about 70% variants of single zinc-finger domains of Zif268. We have also tested the capacity to predict the PWMs of proteins composed by three C2H2-ZF domains, successfully matching between 60% and 90% of the binding-site motif according to the JASPAR database. The tests are used as a proof of the capacity to scan a DNA fragment and find the potential binding sites of transcription-factors formed by C2H2-ZF domains. As an example, we have tested the approach to predict the DNA-binding preferences of the human chromatin binding factor CTCF.