bluuebunny/crossref_metadata_2025_split huggingface dataset:
Choosing variant interpretation tools for clinical applications: context matters
Authors: Aguirre Josu , Padilla Natàlia , Özkan Selen , Riera Casandra , Feliubadaló Lidia , de la Cruz Xavier 
Published: February 2022

AbstractOur inability to solve the Variant Interpretation Problem (VIP) has become a bottleneck in the biomedical/clinical application of Next-Generation Sequencing. This situation has favored the development and use of bioinformatics tools for the VIP. However, choosing the optimal tool for our purposes is difficult because of the high variability of clinical contexts across and within countries.Here, we introduce the use of cost models as a new approach to compare pathogenicity predictors that considers clinical context. An interesting feature of this approach, absent in standard performance measures, is that it treats pathogenicity predictors as rejection classifiers. These classifiers, commonly found in machine learning applications to healthcare, reject low-confidence predictions. Finally, to explore whether context has any impact on predictor selection, we have developed a computational procedure that solves the problem of comparing an arbitrary number of tools across all possible clinical scenarios.We illustrate our approach using a set of seventeen pathogenicity predictors for missense variants. Our results show that there is no optimal predictor for all possible clinical scenarios. We also find that considering rejection gives a view of classifiers contrasting with that of standard performance measures. The Python code for comparing pathogenicity predictors across the clinical space using cost models is available to any interested user at:https://github.com/ClinicalTranslationalBioinformatics/clinical_space_partitionSummariesJosu Aguirre earned his doctorate at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).Natàlia Padilla earned is a post-doctoral researcher at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).Selen Özkan is a Ph.D. student at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).Casandra Riera earned her doctorate at the Clinical and Translational Bioinformatics group, at the Vall d’Hebron Institute of Research (VHIR).Lidia Feliubadalo earned her doctorate at the Universitat de Barcelona, presently she is a high-level technician working at the Catalan Institute of Oncology (ICO) in the diagnosis of hereditary cancers.Xavier de la Cruz is ICREA Research Professor at the Vall d’Hebron Institute of Research (VHIR). His research interests revolve around the application of machine learning methods to healthcare problems.
Spatially resolved epigenomic profiling of single cells in complex tissues
Authors: Lu Tian , Ang Cheen Euong , Zhuang Xiaowei 
Published: February 2022

SUMMARYThe recent development of spatial omics methods enables single-cell profiling of the transcriptome and the 3D genome organization in a spatially resolved manner. Expanding the repertoire of spatial omics tools, a spatial epigenomics method will accelerate our understanding of the spatial regulation of cell and tissue functions. Here, we report a method for spatially resolved profiling of epigenomes in single cells using in-situ tagmentation and transcription followed by highly multiplexed imaging. We profiled histone modifications marking active promoters and enhancers, H3K4me3 and H3K27ac, and generated high-resolution spatial atlas of hundreds of active promoters and putative enhancers in embryonic and adult mouse brains. Our results further revealed putative promoter-enhancer pairs and enhancer hubs regulating the expression of developmentally important genes. We envision this approach will be generally applicable to spatial profiling of epigenetic modifications and DNA-binding proteins, advancing our understanding of how gene expression is spatiotemporally regulated by the epigenome.
Nuclear envelope disruption triggers hallmarks of aging in lung alveolar macrophages
Authors: De Silva Nilushi S. , Nader Guilherme P.F. , Nadalin Francesca , de Azevedo Kevin , Couty Mickaël , Bhargava Anvita , Conrad Cécile , Maurin Mathieu , Fouillade Charles , Londono-Vallejo Arturo , Behrendt Rayk , Gallwitz Lisa , Saftig Paul , Fernández Beatriz Herrero , González-Granado José María , van Niel Guillaume , Boissonnas Alexandre , Piel Mathieu , Manel Nicolas 
Published: February 2022

SummaryAging is characterized by gradual immune dysfunction and increased risk for many diseases, including respiratory infections. Genomic instability is thought to play a central role in the aging process but the mechanisms that damage nuclear DNA in aging are insufficiently defined. Cells that migrate or reside within confined environments experience forces applied to their nucleus, leading to transient nuclear envelope (NE) ruptures. NE ruptures are associated with DNA damage, and Lamin A/C is required to limit these events. Here, we show that Lamin A/C protects lung alveolar macrophages from NE rupture and hallmarks of aging. Lamin A/C ablation in immune cells results in a selective depletion of lung alveolar macrophages (AM) and a heightened susceptibility to influenza infection. Lamin A/C-deficient AM that persist display constitutive nuclear envelope rupture marks, DNA damage and p53-dependent senescence. In wild-type mice, we found that AM migrate within constricted spaces in vivo, at heights that induce NE rupture and DNA damage. AM from aged wild-type mice and from Lamin A/C-deficient mice share an upregulated lysosomal signature with CD63 expression, and we find that CD63 is required to clear damaged DNA in macrophages. We propose that induction of genomic instability by NE disruption represents a mechanism of aging in alveolar macrophages.
Comparison of fitness effects in the earthworm Eisenia fetida after exposure to single or multiple anthropogenic pollutants
Authors: Holzinger Anja , Mair Magdalena M. , Lücker Darleen , Seidenath Dimitri , Opel Thorsten , Langhof Nico , Otti Oliver , Feldhaar Heike 
Published: February 2022

AbstractTerrestrial ecosystems are exposed to many anthropogenic pollutants. Non-target effects of pesticides and fertilizers have put agricultural intensification in the focus as a driver for biodiversity loss. However, other pollutants, such as heavy metals, particulate matter, or microplastic also enter the environment, e.g. via traffic and industrial activities in urban areas. As soil acts as a potential sink for such pollutants, soil invertebrates like earthworms may be particularly affected by them. Under natural conditions soil invertebrates will likely be confronted with combinations of pollutants simultaneously, which may result in stronger negative effects if pollutants act synergistically.Within this work we study how multiple pollutants affect the soil-dwelling, substrate feeding earthworm Eisenia fetida. We compared the effects of the single stressors, polystyrene microplastic fragments, polystyrene fibers, brake dust and soot, with the combined effect of these pollutants when applied as a mixture. Endpoints measured were survival, growth, reproductive fitness, and changes in three oxidative stress markers. We found that among single pollutant treatments, brake dust imposed the strongest negative effects on earthworms in all measured endpoints including increased mortality rates. Sub-lethal effects were found for all pollutants. Exposing earthworms to all four pollutants simultaneously led to effects on mortality and oxidative stress markers that were smaller than expected by the respective null models. These antagonistic effects are likely a result of the adsorption of toxic substances found in brake dust to the other pollutants. With this study we show that effects of combinations of pollutants cannot necessarily be predicted from their individual effects and that combined effects will likely depend on identity and concentration of the pollutants.
Dependence of diffusion in Escherichia coli cytoplasm on protein size, environmental conditions and cell growth
Authors: Bellotto N. , Agudo-Canalejo J. , Colin R. , Golestanian R. , Malengo G. , Sourjik V. 
Published: February 2022

AbstractInside prokaryotic cells, passive translational diffusion typically limits the rates with which cytoplasmic proteins can reach their locations. Diffusion is thus fundamental to most cellular processes, but the understanding of protein mobility in the highly crowded and non-homogeneous environment of a bacterial cell is still limited. Here we investigated the mobility of a large set of proteins in the cytoplasm of Escherichia coli, by employing fluorescence correlation spectroscopy (FCS) combined with simulations and theoretical modeling. We conclude that cytoplasmic protein mobility could be well described by Brownian diffusion in the confined geometry of the bacterial cell and at the high viscosity imposed by macromolecular crowding. We observed similar size dependence of protein diffusion for the majority of tested proteins, whether native or foreign to E. coli, and, for the faster-diffusing proteins, it is well consistent with the Stokes-Einstein relation once taking into account the specific dumbbell shape of protein fusions. Pronounced subdiffusion and hindered mobility are only observed for proteins with extensive interactions within the cytoplasm. Finally, while protein diffusion becomes markedly faster in actively growing cells, at high temperature, or upon treatment with rifampicin, and slower at high osmolarity, all of these perturbations affect proteins of different sizes in the same proportions, which could thus be described as changes of a well-defined cytoplasmic viscosity.
Molecular characteristics and laminar distribution of prefrontal neurons projecting to the mesolimbic system
Authors: Babiczky Ákos , Mátyás Ferenc 
Published: February 2022

AbstractPrefrontal cortical influence over the mesolimbic system – including the nucleus accumbens (NAc) and the ventral tegmental area (VTA) - is implicated in various cognitive processes and behavioral malfunctions. The functional versatility of this system could be explained by an underlying anatomical complexity; however, the detailed characterization of the medial prefrontal cortical (mPFC) innervation of the NAc and VTA is still lacking. Therefore, combining classical retrograde and conditional viral tracing techniques with multiple fluorescent immunohistochemistry, we sought to deliver a precise, cell- and layer-specific anatomical description of the cortico-mesolimbic pathways. We demonstrated that NAc- (mPFCNAc) and VTA-projecting mPFC (mPFCVTA) populations show different laminar distribution (layers 2/3-5a and 5b-6, respectively) and express different molecular markers. Specifically, calbindin and Ntsr1 are specific to mPFCNAc neurons, while mPFCVTA neurons express high levels of Ctip2 and FoxP2, indicating that these populations are mostly separated at the cellular level. We directly tested this with double retrograde tracing and Canine adenovirus type 2-mediated viral labelling and found that there is indeed minimal overlap between the two populations. Furthermore, whole-brain analysis revealed that the projection patter of these populations is also different throughout the brain. Taken together, we demonstrated that the NAc and the VTA are innervated by two, mostly non-overlapping mPFC populations with different laminar distribution and molecular profile. These results can contribute to the advancement in our understanding of mesocorticolimbic functions and its disorders in future studies.
Noninvasive sampling for comparisons of wildlife microbiomes may be more reliable than sampling trapped animals
Authors: Turjeman Sondra , Pekarsky Sasha , Corl Ammon , Kamath Pauline L. , Getz Wayne M. , Bowie Rauri C. K. , Markin Yuri , Nathan Ran 
Published: February 2022

AbstractIn ecological and conservation studies, responsible researchers strive to obtain rich data while minimizing disturbance to wildlife and ecosystems. We assessed if samples collected noninvasively can be used for microbiome research, comparing microbiota of noninvasively collected fecal samples to those collected from trapped common cranes at the same sites over the same periods. We found significant differences in microbial composition (alpha and beta diversity), which were not accounted for by noninvasive samples’ exposure to soil contaminants, as manually assessed by comparing differentially abundant taxa. They could result from trapped birds’ exposure to sedatives. We conclude that if all samples are collected in the same manner, comparative analyses are valid, and noninvasive sampling may better represent host microbiota because there are no trapping effects. Experiments with fresh and delayed sample collection can elucidate effects of environmental exposures on microbiota. Further, stressing or sedation may unravel how trapping affects wildlife microbiota.
PKD-1 Signaling Is Required for the Maintenance of CSCs with Epithelial-mesenchymal Plasticity in Pancreatic Neuroendocrine Tumors
Authors: Guo Yichen , Jiang Yinan , Rose J. Bart , Jaskula-Sztul Renata , Hjelmeland Anita B. , Chen Herbert , Ren Bin 
Published: February 2022

AbstractPancreatic neuroendocrine tumors (pNETs) are extremely heterogeneous and highly vascularized neoplasms that arise from endocrine cells in the pancreas. pNETs harbor a subpopulation of stem cell-like cancer cells (cancer stem cells/CSCs), which contribute to intratumoral heterogeneity and promote tumor maintenance and recurrence. In this study we demonstrated that CSCs in human pNETs co-expressed PKD-1 and CD44. We further identified PKD-1 signaling as a critical pathway in the regulation of CSC maintenance in pNET cells. PKD-1 signaling regulated the expression of a CSC-related gene signature and promoted CSC self-renewal. Intriguingly, pharmacological or genetic disruption of PKD-1 signaling in human pNET cells impaired lysophosphatidic acid-induced expression of genes associated with epithelial to mesenchymal transition (EMT), specifically E-cadherin and vimentin. This study indicates that PKD-1 signaling is essential for the maintenance of a subpopulation of CSCs in pNETs at an intermediate state along the epithelial–mesenchymal spectrum, thereby leading to a CSC phenotype with plasticity and partial EMT. Inhibiting the PKD-1 pathway may facilitate the elimination of CSC subpopulations to curb pNET progression, therapeutic resistance and metastasis. Given that the signaling networks associated with CSC maintenance and EMT are complex and extend across multiple levels of gene regulation, this study provides insight into signaling regulation of partial EMT in determining CSC fate and aids in developing potential therapeutic strategies that target different subsets of CSCs in a variety of cancers.
DeepMinimizer: A Differentiable Framework for Optimizing Sequence-Specific Minimizer Schemes
Authors: Hoang Minh , Zheng Hongyu , Kingsford Carl 
Published: February 2022

AbstractMinimizers are k-mer sampling schemes designed to generate sketches for large sequences that preserve sufficiently long matches between sequences. Despite their widespread application, learning an effective minimizer scheme with optimal sketch size is still an open question. Most work in this direction focuses on designing schemes that work well on expectation over random sequences, which have limited applicability to many practical tools. On the other hand, several methods have been proposed to construct minimizer schemes for a specific target sequence. These methods, however, require greedy approximations to solve an intractable discrete optimization problem on the permutation space of k-mer orderings. To address this challenge, we propose: (a) a reformulation of the combinatorial solution space using a deep neural network re-parameterization; and (b) a fully differentiable approximation of the discrete objective. We demonstrate that our framework, DeepMinimizer, discovers minimizer schemes that significantly outperform state-of-the-art constructions on genomic sequences.
Modulation of sleep by trafficking of lipids through the Drosophila blood brain barrier
Authors: Artiushin Gregory , Li Fu , Sehgal Amita 
Published: February 2022

AbstractEndocytosis through Drosophila glia is a significant determinant of sleep amount and occurs preferentially during sleep in glia of the blood brain barrier (BBB). To identify metabolites whose trafficking is mediated by sleep-dependent endocytosis, we conducted metabolomic analysis of flies that have increased sleep due to a block in glial endocytosis. We report that acylcarnitines, molecules that conjugate with long chain fatty acids to promote their transport, accumulate in heads of these animals. In parallel, to identify transporters and receptors whose loss contributes to the sleep phenotype caused by blocked endocytosis, we screened genes enriched in barrier glia for effects on sleep. We find that knockdown of lipid transporters LRP1&2 as well as carnitine transporters ORCT1&2 increases sleep. In support of the idea that the block in endocytosis affects trafficking through specific transporters, knockdown of LRP or ORCT transporters also increases acylcarnitines in heads. We propose that lipid species, such as acylcarnitines, are trafficked through the BBB via sleep-dependent endocytosis, and their accumulation in the brain increases the need for sleep.
Regulatory mechanisms of the dynein-2 motility by post-translational modification revealed by MD simulation
Authors: Kubo Shintaroh , Bui Khanh Huy 
Published: February 2022

AbstractIntraflagellar transport for ciliary assembly and maintenance is driven by dynein and kinesins specific for the cilia. It has been shown that anterograde and retrograde transports run on different regions of the doublet microtubule, i.e., separate train tracks. However, little is known about the regulatory mechanism of this selective process. Since the doublet microtubule is known to display specific post-translational modifications of tubulins, i.e. “tubulin code”, for molecular motor regulations, we investigated the motility of ciliary specific dynein-2 under different post-translational modification by coarse-grained molecular dynamics. Our setup allows us to simulate the stochastic stepping behaviors of dynein-2 on un-modified, detyrosinated, poly-glutamylated and poly-glycylated microtubules in silico. Our study revealed that poly-glutamylation can play an inhibitory effect on dynein-2 motility. Our result indicates that poly-glutamylation of the B-tubule of the doublet microtubule can be used as an efficient means to target retrograde intraflagellar transport onto the A-tubule.
Eurasian Stone-curlews Burhinus oedicnemus breeding in Italy show a remarkable inter and intra-population variability of migratory behaviour
Authors: Falchi Valentina , Barbon Andrea , Catoni Carlo , Cerritelli Giulia , Cutroneo Alice , Dell’omo Giacomo , Dragonetti Marco , Giovacchini Pietro , Meschini Angelo , Panzarin Lucio , Picciau Angela , Giunchi Dimitri 
Published: February 2022

AbstractMigratory behaviour in birds shows a remarkable variability at species, population and individual levels. Short-distance migrants, in particular, often adopt a partial migratory strategy and tend to have a rather flexible migration schedule which allows them to respond more effectively to extreme environmental variations, like those due to climate change. Weather seasonality and environmental heterogeneity at regional and local scales have been reported as significant factors in the diversification of migratory behaviour for some species of Mediterranean migrants. Relatively few studies, however, investigated the migration patterns of non-passerine birds migrating within this area. In this study we investigated the migratory strategy of the Eurasian Stone-curlewBurhinus oedicnemususing data collected on 40 individuals tagged with geolocators and GPS-GSM tags, belonging to two continental and two Mediterranean populations of the Italian peninsula. The proportion of migrants was significantly higher in continental populations, but we observed a significant variability also within Mediterranean populations. GPS-tagged migrants traveled less than 1000 km, spending the winter within the Mediterranean basin. Continental Stone-curlews i) departed earlier in spring and later in autumn and ii) covered longer distances than those from Mediterranean areas. The speed of migration did not change between seasons for continental birds, while Mediterranean individuals tended to migrate faster in spring. The likelihood of departure for autumn migration of GPS-tagged birds significantly increased when temperatures were near or below 0 °C suggesting that Stone-curlews tend to delay departure weather conditions worsen abruptly. Thus it can be speculated that the frequency of migratory birds in the considered populations may decrease in the near future due to the effect of global warming in the Mediterranean. This could have a significant effect on the distribution of species throughout the year and should be taken into account when targeting conservation measures.
Deep phenotyping platform for microscopic plant-pathogen interactions
Authors: Lück Stefanie , Douchkov Dimitar 
Published: February 2022

1SummaryThe initial phases of plant-pathogen interactions are critical since they are often decisive for the successful infection. However, these early stages of interaction are typically microscopic, making it challenging to study on a large scale.For this reason, using the powdery mildew fungi of cereals as a model, we have developed an automated microscopy pipeline coupled with deep learning-based image analysis for the high-throughput phenotyping of plant-pathogen interactions.The system can quantify fungal microcolony count and density, the precise area of the secondary hyphae of each colony, and different morphological parameters. Moreover, the high throughput and sensitivity allow quantifying rare microscopic phenotypes in a large sample size. One of these phenotypes is the cryptic infection of non-adapted pathogens, marking the hidden transition stages of pathogen adaptation and breaking the nonhost barrier. Thus, our tool opens the nonhost resistance phenomenon to genetics and genomics studies.We have developed an open-source high-throughput automated microscopy system for phenotyping the initial stages of plant-pathogen interactions, extendable to other microscopic phenotypes and hardware platforms. Furthermore, we have validated the system’s performance in disease resistance screens of genetically diverse barley material and performed Genome-wide associations scans (GWAS), discovering several resistance-associated loci, including conferring nonhost resistance.
Reconstruction of hundreds of reference ancestral genomes across the eukaryotic kingdom
Authors: Muffato Matthieu , Louis Alexandra , Nguyen Nga Thi Thuy , Lucas Joseph , Berthelot Camille , Crollius Hugues Roest 
Published: February 2022

AbstractAncestral sequence reconstruction is a fundamental aspect of molecular evolution studies, and can trace small-scale sequence modifications through the evolution of genomes and species. In contrast, fine-grained reconstructions of ancestral genome organisations are still in their infancy, limiting our ability to draw comprehensive views of genome and karyotype evolution. Here we reconstruct the detailed gene contents and organisations of 624 ancestral vertebrate, plant, fungi, metazoan and protist genomes, 183 of which are near-complete chromosomal reconstructions. Reconstructed ancestral genomes are similar to their descendants in terms of gene content as expected and agree precisely with reference cytogenetic andin silicoreconstructions when available. By comparing successive ancestral genomes along the phylogenetic tree, we estimate the intra- and inter-chromosomal rearrangement history of all major vertebrate clades at high resolution. This freely available resource introduces the possibility to follow evolutionary processes at genomic scales in chronological order, across multiple clades and without relying on a single extant species as reference.