bluuebunny/crossref_metadata_2025_split huggingface dataset:
The sheep brain: an interesting translational model for functional MRI studies?
Authors: Just Nathalie , Adriaensen Hans , Chevillard Pierre-Marie , Batailler Martine , Dubois Jean-Philippe , Migaud Martine 
Published: September 2020

AbstractBiomedical investigations in clinically relevant animal models is of crucial interest for faster and appropriate transfer to human. The ovine model has already demonstrated its potential compared to rodents and non-human primates (NHP) in various studies: sheep possess a gyrencephalic brain, captivity is not an issue and can undergo magnetic resonance imaging (MRI) in routine clinical scanners (1.5T, 3T) under identical conditions using similar techniques to humans. To date, the effects of anesthesia have been poorly explored and only few functional MRI (fMRI) studies were conducted in sheep. Here, Blood Oxygen Level dependent fMRI and perfusion MRI were conducted in lambs and adult ewes at 3 T. Robust but weak BOLD responses to visual stimulation were found in the lateral geniculate nucleus (LGN) up to 3% isoflurane anaesthesia. BOLD responses were weaker in adult sheep than in lambs while relative cerebral blood volumes (rCBV) and relative cerebral blood flows (rCBF) were significantly higher in lambs than in adult sheep for both gray and white matter in accordance with previous findings in the human. Assessment of functional responses in healthy individuals under adequate physiological conditions is essential for robust translational studies.
Cellular aging in vitro recapitulates multi-tissue epigenetic aging in vivo
Authors: Minteer Christopher , Morselli Marco , Meer Margarita , Cao Jian , Higgins-Chen Albert , Lang Sabine , Pellegrini Matteo , Yan Qin , Levine Morgan 
Published: September 2020

ii.AbstractAging is known to elicit dramatic changes to DNA methylation (DNAm), although the causes and consequences of such alterations are not clear and require further exploration. Our ability to experimentally uncover mechanisms of epigenetic aging will be greatly enhanced by our ability to study and manipulate these changes usingin vitromodels. However, it remains unclear whether the changes elicited by cells in culture can serve as a model of what is observed in aging tissuesin vivo. To test this, we serially passaged mouse embryonic fibroblasts (MEFs) and assessed changes in DNAm at each time-point via RRBS. By developing a measure that tracked cellular agingin vitro, we tested whether it tracked physiological aging in various mouse tissues and whether anti-aging interventions modulate this measure. Our measure, termed DNAmCULTURE, was shown to strongly increase with age when examined in multiple tissues (liver, lung, kidney, blood, and adipose). As a control, we confirmed that the measure was not a marker of cellular senescence, suggesting that it reflects a distinct yet progressive cellular aging phenomena that can be inducedin vitro. Furthermore, we demonstrated slower epigenetic aging in animals undergoing caloric restriction and a resetting of our measure in lung and kidney fibroblasts when re-programmed to iPSCs. Enrichment and clustering analysis implicated SUZ12, EED and Polycomb group (PcG) factors as potentially important chromatin regulators in translational culture aging phenotypes. Overall, this study supports the concept that physiologically relevant aging changes can be inducedin vitroand moving forward, used to uncover mechanistic insights into epigenetic aging.
Leveraging complex interactions between signaling pathways involved in liver development to robustly improve the maturity and yield of pluripotent stem cell-derived hepatocytes
Authors: Raggi Claudia , M’Callum Marie-Agnès , Pham Quang Toan , Gaub Perrine , Selleri Silvia , Baratang Nissan , Mangahas Chenicka Lyn , Cagnone Gaël , Reversade Bruno , Joyal Jean-Sébastien , Paganelli Massimiliano 
Published: September 2020

SUMMARYPluripotent stem cell (PSC)-derived hepatocyte-like cells (HLC) have shown great potential as an alternative to primary human hepatocytes (PHH) forin vitromodeling. Several differentiation protocols have been described to direct PSC towards the hepatic fate, although the resulting HLC have shown more a fetal than adult phenotype. Here, by leveraging recent knowledge of the signaling pathways involved in liver development, we describe a robust, scalable protocol that allows to consistently generate high-quality HLC from both ESC and iPSC. Such HLC are comparable to adult PHH in terms of key mature liver functions and proved suitable to assess drug hepatotoxicity, as a proof of concept of their potential as a physiologically representative alternative forin vitromodeling.
SUMOylation- and GAR1-dependent regulation of dyskerin nuclear and subnuclear localization
Authors: MacNeil D.E. , Lambert-Lanteigne P. , Qin J. , McManus F. , Bonneil E. , Thibault P. , Autexier C. 
Published: September 2020

SummaryDyskerin, a telomerase-associated protein and H/ACA ribonucleoprotein complex component plays an essential role in human telomerase assembly and activity. The nuclear and subnuclear compartmentalization of dyskerin and the H/ACA complex is an important though incompletely understood aspect of H/ACA ribonucleoprotein function. The posttranslational modification, SUMOylation, targets a wide variety of proteins, including numerous RNA-binding proteins, and most identified targets reported to date localize to the nucleus. Four SUMOylation sites were previously identified in the C-terminal Nuclear/Nucleolar Localization Signal (N/NoLS) of dyskerin, each located within one of two lysine-rich clusters. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS and both lysine-rich clusters represents an under-SUMOylated variant of dyskerin compared to wildtype dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3-fusion construct can drive nuclear accumulation of this variant, and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein involved in rRNA and snRNA biogenesis.
The Combination of Morphology and Surface Chemistry Defines the Biological Identity of Nanocarriers in Human Blood
Authors: Karabin Nicholas B. , Vincent Michael P. , Allen Sean D. , Bobbala Sharan , Frey Molly A. , Yi Sijia , Yang Yufan , Scott Evan A. 
Published: September 2020

AbstractFollowing intravenous administration, an adsorbed corona of blood proteins immediately forms on the surfaces of nanocarriers to confer a distinct biological identity that dictates interactions with the immune system. While the nanocarrier surface chemistry has long been the focus of protein corona formation, the influence of the nanocarrier structure has remained unclear despite well-documented influences on biodistribution, clearance and inflammation. Here, we present design rules for the combined engineering of both nanocarrier structure and surface chemistry derived from a comprehensive proteomic analysis of protein corona formation in human blood. A library of nine soft PEGylated nanocarriers that differ in their combination of morphology (spheres, vesicles, and cylinders) and surface chemistry (methoxy, hydroxyl, and phosphate) were synthesized to represent properties of commonly employed drug delivery vehicles. Using label-free proteomics and high-throughput techniques, we examined the relationship between physicochemical properties and the resulting nanocarrier biological identity, including dynamic changes in protein corona composition, differential immunostimulation and uptake by relevant immune cell populations. In human blood, non-polar spherical micelles developed a similar biological identity to polar vesicles, whereas the identities of polar spheres and cylinders resembled that of non-polar vesicles. The formed protein coronas were compositionally dynamic and morphology-dependent, and these time-dependent fingerprints altered nanocarrier complement activation as well as their uptake by human monocytes, macrophages, and dendritic cells. This comprehensive analysis provides mechanistic insights into rational design choices that impact nanocarrier fate in human blood.One Sentence SummaryWe demonstrate that not only the surface chemistry, but the combined chemical and structural properties of soft drug delivery vehicles impact the composition of blood proteins that adsorb to their surfaces, and these differences specify their interactions with and modulation of human immune cells.
Genome-wide SNP detection in Darjeeling tea: unravelling genetic structure, functional impact and trait associations
Authors: Hazra Anjan , Kumar Rakesh , Sengupta Chandan , Das Sauren 
Published: September 2020

AbstractGenotyping by sequencing and identification of functionally relevant nucleotide variations in crop accessions are the key steps to unravel genetic control of desirable traits. In the scope of present work, elite cultivars of Darjeeling tea were undergone SNP genotyping by double-digest restriction site associated DNA sequencing method. This study reports a set of 54,206 high-quality SNP markers discovered from ∼10.4 GB sequence data, encompassing 15 chromosomes of reference tea genome. Genetic relatedness among the accessions conforms to the analyses of Bayesian clustering, UPGMA, and PCoA methods. High percent of heterozygous loci in the majority of the cultivars reflect their ‘hybrid’ ancestry as reported earlier. Genomic positions of the discovered SNPs and their putative effect on annotated genes designated a thoughtful understanding of their functional aspects in tea system biology. A group of 95 genes was identified to be affected by high impact variants, most of them are involved in signal transduction, biosynthesis of secondary metabolite, transcriptional and translational regulation. Genome-wide association analyses of 21 agronomic and biochemical phenotypes resulted in trait-linked polymorphic loci with strong confidence (p< 0.05 and 0.001). The selection of significant marker-trait associations with the Bonferroni correction threshold retained a set of 57 SNPs distributed across 14 chromosomes to be linked with eight phenotypic traits. High impact and trait-associated nucleotide polymorphisms perceived in this study can be exploited in worldwide germplasm of contrasting origin to depict their heritability and to unlock their potentiality in marker-assisted breeding.
Evolution and regulation of microbial secondary metabolism
Authors: Santamaria Guillem , Liao Chen , Wang Zhe , Rhee Kyu , Pinto Francisco , Yan Jinyuan , Xavier Joao B. 
Published: September 2020

AbstractMicrobes have disproportionate impacts on the macroscopic world. This is in part due to their ability to grow to large groups and cooperatively secrete massive amounts of secondary metabolites that impact their environment. Yet, the conditions enabling secondary metabolism without compromising primary needs remain unclear. Here we investigated the biosynthesis of rhamnolipids, a secondary metabolite thatPseudomonas aeruginosamakes to decrease the surface tension of surrounding liquid. Using a combination of genomics, metabolomics, transcriptomics, and mathematical modeling we show that biosynthesis of rhamnolipids from glycerol varies inconsistently across the phylogenetic tree; instead, non-producer lineages are also those worse at reducing the oxidative stress of primary glycerol metabolism. The link to oxidative stress explains the inconsistent distribution across theP. aeruginosatree, adding a new layer to the regulation of rhamnolipids—a microbial secondary metabolite important for fitness in natural and clinical settings.SignificanceThe bacteriumPseudomonas aeruginosais a major source of hospital-acquired infections. This pathogen’s knack for virulence relies on its ability to multiply and secrete massive amounts of substances that overwhelm microbial competitors and weaken host defenses. It remains unclear how the bacteria conciliate their need to grow and multiply—a need at the individual-level— with their ability to secrete products—a need of the population. Here we combined genomics, metabolomics and mathematical modeling to study the biosynthesis of rhamnolipids, a surfactant thatP. aeruginosamakes to reduce the surface tension of surrounding liquids. Our study reveals a new link between oxidative stress and rhamnolipid synthesis, which helps explain how this important bacterial product has evolved and how it persists in many lineages of pathogens.
Identification of a novel cobamide remodeling enzyme in the beneficial human gut bacteriumAkkermansia muciniphila
Authors: Mok Kenny C. , Sokolovskaya Olga M. , Nicolas Alexa M. , Hallberg Zachary F. , Deutschbauer Adam , Carlson Hans K. , Taga Michiko E. 
Published: September 2020

AbstractThe beneficial human gut bacteriumAkkermansia muciniphilaprovides metabolites to other members of the gut microbiota by breaking down host mucin, but most of its other metabolic functions have not been investigated.A. muciniphilais known to use cobamides, the vitamin B12family of cofactors with structural diversity in the lower ligand, though the specific cobamides it can use have not been examined. We found that growth ofA. muciniphilastrain MucTwas nearly identical with each of seven cobamides tested, in contrast to nearly all bacteria that have been studied. Unexpectedly, this promiscuity is due to cobamide remodeling – the removal and replacement of the lower ligand – despite the absence of the canonical remodeling enzyme CbiZ inA. muciniphila. We identified a novel enzyme, CbiR, that is capable of initiating the remodeling process by hydrolyzing the phosphoribosyl bond in the nucleotide loop of cobamides. CbiR does not share homology with other cobamide remodeling enzymes or B12-binding domains, and instead is a member of the AP endonuclease 2 enzyme superfamily. We speculate that CbiR enables bacteria to repurpose cobamides they otherwise cannot use in order to grow under a cobamide-requiring condition; this function was confirmed by heterologous expression ofcbiRinE. coli. Homologs of CbiR are found in over 200 microbial taxa across 22 phyla, suggesting that many bacteria may use CbiR to gain access to the diverse cobamides present in their environment.ImportanceCobamides, the vitamin B12family of cobalt-containing cofactors, are required for metabolism in all domains of life, including most bacteria. Cobamides have structural variability in the lower ligand, and selectivity for particular cobamides has been observed in most organisms studied to date. Here, we discover that the beneficial human gut bacteriumAkkermansia muciniphilacan use a diverse range of cobamides due to its ability to change the cobamide structure via “cobamide remodeling”. We identify and characterize the novel enzyme CbiR that is necessary for initiating the cobamide remodeling process. The discovery of this enzyme has implications not only for understanding the ecological role ofA. muciniphilain the gut, but for other bacteria that carry this enzyme as well.
A balance between matrix deformation and the coordination of turning events governs directed neutrophil migration in 3-D matrices
Authors: François Joshua , Kandasamy Adithan , Yeh Yi-Ting , Ayala Cindy , Meili Ruedi , Chien Shu , Lasheras Juan C. , del Álamo Juan C. 
Published: September 2020

AbstractThree-dimensional (3-D) neutrophil migration is essential for immune surveillance and inflammatory responses. During 3-D migration, especially through extravascular spaces, neutrophils rely on frontal protrusions and rear contractions to squeeze and maneuver through extracellular matrices containing narrow pores. However, the role of matrix density and the cells’ ability to probe and remodel matrix pores during 3-D chemotaxis are far from being understood. We investigated these processes by tracking the trajectories of over 20,000 neutrophils in a 3-D migration device containing collagen matrices of varying concentrations and analyzing the shape of these trajectories at multiple scales. Additionally, we quantified the transient 3-D matrix deformations caused by the migrating cells. The mean pore size of our reconstituted collagen matrices decreased when the collagen concentration ([col]) was increased. In low-[col] matrices, neutrophils exerted large transient deformations and migrated in relatively straight trajectories. In contrast, they were not able to appreciably deform high- [col] matrices and adapted to this inability by turning more often to circumvent these narrow matrix pores. While this adaptation resulted in slower migration, the cells were able to balance the more frequent turning with the long-range directional bias necessary for chemotaxis. Based on our statistical analysis of cell trajectories, we postulate that neutrophils achieve this balance by using matrix obstacles as pivoting points to steer their motion towards the chemoattractant. Inhibiting myosin-II contractility or Arp2/3-mediated pseudopod protrusions not only compromised the cells’ ability to deform the matrix, but also made them switch to increased turning in more restrictive matrices when compared to untreated control cells. Both myosin-II contractility and Arp2/3-mediated branched polymerization of actin played a role in fast migration, but Arp2/3 was also crucial for neutrophils when coordinating the orientations of successive turns to prevent veering away from the chemotactic path. These results may contribute to an improved understanding of the mechanisms employed by migrating neutrophils in confined 3-D environments, as well as the molecular and environmental regulators for maintaining persistent motion.
Optimization of negative stage bias potential for faster imaging in large-scale electron microscopy
Authors: Lane Ryan , Vos Yoram , Wolters Anouk H. G. , van Kessel Luc , Giepmans Ben N.G. , Hoogenboom Jacob P. 
Published: September 2020

AbstractLarge-scale electron microscopy (EM) allows analysis of both tissues and macromolecules in a semi-automated manner, but acquisition rate forms a bottleneck. We reasoned that a negative bias potential may be used to enhance signal collection, allowing shorter dwell times and thus increasing imaging speed. Negative bias potential has previously been used to tune penetration depth in block-face imaging. However, optimization of negative bias potential for application in thin section imaging will be needed prior to routine use and application in large-scale EM. Here, we present negative bias potential optimized through a combination of simulations and empirical measurements. We find that the use of a negative bias potential generally results in improvement of image quality and signal-to-noise ratio (SNR). The extent of these improvements depends on the presence and strength of a magnetic immersion field. Maintaining other imaging conditions and aiming for the same image quality and SNR, the use of a negative stage bias can allow for a 20-fold decrease in dwell time, thus reducing the time for a week long acquisition to less than 8 hours. We further show that negative bias potential can be applied in an integrated correlative light electron microscopy (CLEM) application, allowing fast acquisition of a high precision overlaid LM-EM dataset. Application of negative stage bias potential will thus help to solve the current bottleneck of image acquisition of large fields of view at high resolution in large-scale microscopy.
Massive expansion of human gut bacteriophage diversity
Authors: Camarillo-Guerrero Luis F. , Almeida Alexandre , Rangel-Pineros Guillermo , Finn Robert D. , Lawley Trevor D. 
Published: September 2020

SUMMARYBacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database (GPD), a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent novel phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalogue of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.
Testing methods of linguistic homeland detection using synthetic data
Authors: Wichmann Søren , Rama Taraka 
Published: September 2020

AbstractTwo families of quantitative methods have been used to infer geographical homelands of language families: Bayesian phylogeography and the ‘diversity method’. Bayesian methods model how populations may have moved using a phylogenetic tree as a backbone, while the diversity method assumes that the geographical area where linguistic diversity is highest likely corresponds to the homeland. No systematic tests of the performances of the different methods in a linguistic context have so far been published. Here we carry out performance testing by simulating language families, including branching structures and word lists, along with speaker populations moving in space. We test six different methods: two versions of BayesTraits; the relaxed random walk model of BEAST 2; our own RevBayes implementations of a fixed rates and a variable rates random walk model; and the diversity method. As a result of the tests we propose a hierarchy of performance of the different methods. Factors such as geographical idiosyncrasies, incomplete sampling, tree imbalance, and small family sizes all have a negative impact on performance, but mostly across the board, the performance hierarchy generally being impervious to such factors.