bluuebunny/crossref_metadata_2025_split huggingface dataset:
FastIntegration: a versatile R package for accessing and integrating large-scale single-cell RNA-seq data
Authors: Li Mengwei , Zhang Xiaomeng , Ang Kok Siong , Chen Jinmiao 
Published: May 2022

AbstractConstructing atlas-scale comprehensive cell maps from publicly available data enables extensive data mining to achieve novel biological insights. Data integration to construct such maps require both harmonized datasets and an atlas-scale capable data integration tool. The first requirement is met by DISCO, a comprehensive repository of harmonized publicly available single cell data with standardized annotation. To meet the second requirement, the tool must have the capacity to integrate hundreds if not thousands of samples within an acceptable time frame. Moreover, it should output batch-corrected gene expression values to facilitate downstream analyses. Here, we present FastIntegration, a package which allows users to access and integrate public data in a convenient way. FastIntegration provides a fast and high-capacity version of Seurat Integration which can integrate more than 4 million cells within 2 days. It outputs batch corrected values for all genes that we can use for downstream analyses. For the first time, we demonstrated that using batch corrected values can improve the performance of downstream analyses. In particular, we found more accurately identified differentially expressed genes for cell types that are not shared between batches. Moreover, we also showed that FastIntegration outperforms existing methods for both homogeneous and heterogeneous data integration. FastIntegration also provides an API for programmatic access to data hosted on DISCO, a single-cell RNA-seq database that contains more than 5200 single-cell datasets. Users can filter for data at the sample level by tissue, disease and platform etc., and at cell level by specifying the expressed and unexpressed genes.
Aberrant regulation of serine metabolism drives extracellular vesicle release and cancer progression
Authors: Yamamoto Tomofumi , Nakayama Jun , Urabe Fumihiko , Ito Kagenori , Nishida-Aoki Nao , Kitagawa Masami , Yokoi Akira , Kuroda Masahiko , Hattori Yutaka , Yamamoto Yusuke , Ochiya Takahiro 
Published: May 2022

AbstractCancer cells secrete extracellular vesicles (EVs) to regulate cells in the tumor microenvironment to benefit their own growth and survive in the patient’s body. Although emerging evidence has demonstrated the molecular mechanisms of EV release, regulating cancer-specific EV secretion remains challenging. In this study, we applied a microRNA library to reveal the universal mechanisms of EV secretion from cancer cells. Here, we identified miR-891b and its direct target gene, phosphoserine aminotransferase 1 (PSAT1), which promotes EV secretion through the serine-ceramide synthesis pathway. Inhibition of PSAT1 affected EV secretion in multiple types of cancer, suggesting that the miR-891b/PSAT1 axis shares a common mechanism of EV secretion from cancer cells. Interestingly, aberrant PSAT1 expression also regulated cancer metastasis via EV secretion. Our data link between the PSAT1-controlled EV secretion mechanism and cancer metastasis and show the potential of this mechanism as a therapeutic target in multiple types of cancer.
Pax6 mutant cerebral organoids partially recapitulate phenotypes of Pax6 mutant mouse strains
Authors: Ferdaos Nurfarhana , Lowell Sally , Mason John O. 
Published: May 2022

AbstractCerebral organoids show great promise as tools to unravel the complex mechanisms by which the mammalian brain develops during embryogenesis. We generated mouse cerebral organoids harbouring constitutive or conditional mutations in Pax6, which encodes a transcription factor with multiple important roles in brain development. By comparing the phenotypes of mutant organoids with the well-described phenotypes of Pax6 mutant mouse embryos, we evaluated the extent to which cerebral organoids reproduce phenotypes previously described in vivo. Organoids lacking Pax6 showed multiple phenotypes associated with its activity in mice, including precocious neural differentiation, altered cell cycle and an increase in abventricular mitoses. Neural progenitors in both Pax6 mutant and wild type control organoids cycled more slowly than their in vivo counterparts, but nonetheless we were able to identify clear changes to cell cycle attributable to the absence of Pax6. Our findings support the value of cerebral organoids as tools to explore mechanisms of brain development, complementing the use of mouse models.
Comparing DNA metabarcoding with morphology in the assessment of macrozoobenthos in Portuguese transitional waters in the scope of the Water Framework Directive monitoring
Authors: Duarte Sofia , Vieira Pedro E. , Leite Barbara R. , Teixeira Marcos A.L. , Neto João M. , Costa Filipe O. 
Published: May 2022

AbstractDespite the growing use and potential of DNA metabarcoding to improve and expedite macrozoobenthos monitoring, its employment in Water Framework Directive (WFD) monitoring of transitional ecosystems still remains largely unexplored and pending proof-of-concept studies. In the current study, we addressed this research gap by building upon the biomonitoring network program of the Portuguese Environmental Agency (APA) to benchmark metabarcoding against the morphology-based approach for characterizing macrozoobenthic communities. We assessed the ecological condition of 20 sites from four major transitional ecosystems in the west coast of Portugal, namely Minho, Lima, Vouga and Mondego estuaries. A total of 154 marine invertebrate species were detected with both methodologies, distributed by 11 phyla. In the majority of the sites, metabarcoding returned a higher number of species and phyla than the morphology-based approach (up to 2.5 times higher). In parallel, the proportion of species detected concurrently by both methods was low (35 species, 23%). The use of a multi-locus strategy increased recovered diversity through metabarcoding, since 37 species were detected exclusively with COI and 46 with 18S. For about 61% of the species recovered through morphology, metabarcoding failed detection, among which 20% was due to the lack of reference sequences in genetic databases. For the remaining, we did not find any plausible reason for only 10%, which could be due either to inefficient DNA extraction or PCR failure. Although morphological and metabarcoding-derived biotic indices did not match completely, similar responses to the environmental gradient were obtained in morphology and metabarcoding based-datasets. We anticipate that metabarcoding can increase the throughput and quality of the assessments, allowing faster assessments with greater spatial-temporal density and robust identifications of all specimens in a sample including larval stages, juveniles, and cryptic lineages, as well as smaller taxonomic groups that cannot be identified to species level using the traditional approach.
Genome sequence assembly evaluation using long-range sequencing data
Authors: Guan Dengfeng , McCarthy Shane A. , Wood Jonathan M. D. , Sims Ying , Chow William , Ning Zemin , Howe Kerstin , Wang Guohua , Wang Yadong , Durbin Richard 
Published: May 2022

AbstractGenome sequences are computationally assembled from millions of much shorter sequencing reads. Although this process can be impressively accurate with long reads, it is still subject to a variety of types of errors, including large structural misassembly errors in addition to localised base pair substitutions. Recent advances in long single molecule sequencing in combination with other long-range technologies such as synthetic long read clouds and Hi-C have dramatically increased the contiguity of assembly. This makes it all the more important to be able to validate the structural integrity of the chromosomal scale assemblies now being generated. Here we describe a novel assembly evaluation tool, Asset, which evaluates the consistency of a proposed genome assembly with multiple primary long-range data sets, identifying both supported regions and putative structural misassemblies. We present tests on three de novo assemblies from a human, a goat and a fish species, demonstrating that Asset can identify structural misassemblies accurately by combining regionally supported evidence from long read and other raw sequencing data. Not only can Asset be used to assess overall assembly confidence, and discover specific problematic regions for downstream genome curation, a process that leads to improvement in genome quality, but it can also provide feedback to automated assembly pipelines.
The N-terminal domain of MX1 proteins is essential for their antiviral activity against different families of RNA viruses
Authors: McKellar Joe , Arnaud-Arnould Mary , Chaloin Laurent , Tauziet Marine , Arpin-André Charlotte , Pourcelot Oriane , Blaise Mickael , Moncorgé Olivier , Goujon Caroline 
Published: May 2022

AbstractMyxovirus resistance protein 1 (MX1) and MX2, are homologous, dynamin-like large GTPases, induced upon interferon (IFN) exposure. Human MX1 (HsMX1) is known to inhibit many viruses, including influenza A virus (IAV), by likely acting at various steps of their life cycles. Despite decades of studies, the mechanism(s) of action with which MX1 proteins manage to inhibit target viruses is not fully understood. MX1 proteins are mechano-enzymes and share a similar organization to dynamin, with an amino-terminal GTPase domain and a carboxy-terminal stalk domain, connected by a Bundle Signalling Element (BSE). These three elements are known to be essential for antiviral activity. HsMX1 has two unstructured regions, the L4 loop, also essential for antiviral activity, and a short amino (N)-terminal region, which greatly varies between MX1 proteins of different species. The role of this N-terminal domain in antiviral activity is not known. Herein, using mutagenesis, imaging and biochemical approaches, we demonstrate that the N-terminal domain of HsMX1 is essential for antiviral activity against IAV and Vesicular Stomatitis Virus (VSV), and for the ability to aggregate Orthobunyavirus nucleoproteins. Furthermore, we pinpoint a highly conserved leucine within this region, which is absolutely crucial for human, mouse and bat MX1 protein antiviral activity. Importantly, mutation of this leucine does not compromise GTPase activity or oligomerization capabilities, but does modify MX1 protein subcellular localisation. The discovery of this essential and highly conserved residue defines this region as key and may reveal insights as to the mechanism of action of MX1 proteins.
Macrophages inhibit Coxiella burnetii by the ACOD1-itaconate pathway for containment of Q fever
Authors: Kohl Lisa , Alam Siddique Md. Nur A , Bodendorfer Barbara , Berger Raffaela , Preikschat Annica , Daniel Christoph , Ölke Martha , Mauermeir Michael , Yang Kai-Ting , Hayek Inaya , Szperlinski Manuela , Schulze-Luehrmann Jan , Schleicher Ulrike , Bozec Aline , Krönke Gerhard , Murray Peter J. , Wirtz Stefan , Yamamoto Masahiro , Schatz Valentin , Jantsch Jonathan , Oefner Peter , Degrandi Daniel , Pfeffer Klaus , Rauber Simon , Bogdan Christian , Dettmer Katja , Lührmann Anja , Lang Roland 
Published: May 2022

AbstractInfection with the intracellular bacterium Coxiella (C.) burnetii can cause chronic Q fever with severe complications and limited treatment options. Here, we identify the enzyme cis- aconitate decarboxylase 1 (ACOD1 or IRG1) and its product itaconate as protective host immune pathway in Q fever. Infection of mice with C. burnetii induced expression of several anti-microbial candidate genes, including Acod1. In macrophages, Acod1 was essential for restricting C. burnetii replication, while other antimicrobial pathways were dispensable. Intratracheal or intraperitoneal infection of Acod1-/- mice caused increased C. burnetii burden, significant weight loss and stronger inflammatory gene expression. Exogenously added itaconate restored pathogen control in Acod1-/- mouse macrophages and blocked replication in human macrophages. In axenic cultures, itaconate directly inhibited growth of C. burnetii. Finally, treatment of infected Acod1-/-mice with itaconate efficiently reduced the tissue pathogen load. Thus, ACOD1-derived itaconate is a key factor in the macrophage-mediated defense against C. burnetii and may be exploited for novel therapeutic approaches in chronic Q fever.
Selectively expressed RNA molecules: a new dimension in functionalized cell targeting
Authors: Hoffmann Marco , Schüle Sylvie , Hoffmann Christina , Rastfeld Frederik , Gerlach Sven , Hersch N. , Walter Helene L. , Wiedermann Dirk , Fink Gereon R. , Merkel Rudolf , Bohlen Heribert , Rueger Maria A. , Hoffmann Bernd 
Published: May 2022

AbstractExact targeting of specific mammalian cell types or diseased cells is one of the most urgently needed prerequisites for a new generation of potent pharmaceuticals. Different approaches have been pursued, failing mainly due to a lack of specific surface markers in most cases. Developing a completely novel RNA-based methodology, we can now ensure exact cell targeting and simultaneously combine this with selective expression of effector proteins, thereby functionalization of the target cell for therapy, diagnostics or cell steering. The specific combination of the molecular properties of antisense technology and mRNA therapy with functional RNA secondary structures allowed us to develop selectively expressed RNA molecules for medical applications. These so-called seRNAs remain inactive in non-target cells and are only activated by partial degradation to induce translation in preselected cell types of interest. Cell type specificity and type of functionalization are easily adaptable based on a simple modular system. In proof of concept in vitro and in vivo studies we used seRNAs as a highly selective platform technology for powerful glioblastoma cancer cell targeting and significantly reduce brain tumors of mice without detectable side effects with just a single treatment within days. Our data open up new potential avenues for the efficient treatment of various cancers and other human diseases.
Molecular Mechanisms of Steric Pressure Generation and Membrane Remodeling by Intrinsically Disordered Proteins
Authors: Houser Justin R. , Cho Hyun Woo , Hayden Carl C. , Yang Noel X. , Wang Liping , Lafer Eileen M. , Thirumalai D. , Stachowiak Jeanne C. 
Published: May 2022

AbstractCellular membranes, which are densely crowded by proteins, take on an elaborate array of highly curved shapes. Steric pressure generated by protein crowding plays a significant role in shaping membrane surfaces. It is increasingly clear that many proteins involved in membrane remodeling contain substantial regions of intrinsic disorder. These domains have large hydrodynamic radii, suggesting that they may contribute significantly to steric congestion on membrane surfaces. However, it has been unclear to what extent they are capable of generating steric pressure, owing to their conformational flexibility. To address this gap, we use a recently developed sensor based on Förster resonance energy transfer to measure steric pressure generated at membrane surfaces by the intrinsically disordered domain of the endocytic protein, AP180. We find that disordered domains generate substantial steric pressure that arises from both entropic and electrostatic components. Interestingly, this steric pressure is largely invariant with the molecular weight of the disordered domain, provided that coverage of the membrane surface is held constant. Moreover, equivalent levels of steric pressure result in equivalent degrees of membrane remodeling, regardless of protein molecular weight. This result, which is consistent with classical polymer scaling relationships for semi-dilute solutions, helps to explain the molecular and physical origins of steric pressure generation by intrinsically disordered domains. From a physiological perspective, these findings suggest that a broad range of membrane-associated disordered domains are likely to play a significant and previously unknown role in controlling membrane shape.SignificanceWith nearly half their surfaces covered by proteins, biological membranes are highly crowded. Rapid diffusion and collision of membrane-bound proteins generates substantial steric pressure that is capable of shaping membrane surfaces. Many proteins involved in membrane remodeling, are intrinsically disordered. Having large hydrodynamic radii, disordered domains could contribute substantially to membrane crowding. However, it is unclear to what extent they are capable of generating steric pressure, owing to their conformational flexibility. Toward resolving this uncertainty, we have measured steric pressure at membrane surfaces during dynamic membrane remodeling events. Our data indicate that disordered domains generate significant steric pressure through entropic and electrostatic mechanisms, suggesting that they may constitute a critical, yet previously neglected class of membrane remodeling proteins.
SpatialDEG: Identification of differentially expressed genes by leveraging spatial information in spatially resolved transcriptomic studies
Authors: Yang Yi , Lim Jeffrey ChunTatt , Ng Cedric Chuan Young , Lee Jing Yi , Yeong Joe , Sun Lei , Liu Jin 
Published: May 2022

AbstractMotivationSpatially resolved transcriptomics (SRT) technologies have been developed to simultaneously profile gene expression while retaining physical information. To explore differentially expressed genes using SRT in the context of various conditions, statistical methods are needed to perform spatial differential expression analysis.ResultsWe propose that a new probabilistic framework, spatialDEG, can perform differential expression analysis by leveraging spatial information on gene expression with spatial information. SpatialDEG utilizes the average information algorithm and can be scalable to tens of thousands of genes. Comprehensive simulations demonstrated that spatialDEG can identify genes differentially expressed in tissues across different conditions with a controlled type-I error rate. We further applied spatialDEG to analyze datasets for human dorsolateral prefrontal cortex and mouse whole liver.AvailabilityThe R package spatialDEG can be downloaded from https://github.com/Shufeyangyi2015310117/spatialDEG.
Optogenetics and electron tomography for structure-function analysis of cochlear ribbon synapses
Authors: Chakrabarti Rituparna , Jaime Tobon Lina Maria , Slitin Loujin , Redondo-Canales Magdalena , Hoch Gerhard , Slashcheva Marina , Fritsch Elisabeth , Bodensiek Kai , Özçete Özge Demet , Gültas Mehmet , Michanski Susann , Opazo Felipe , Neef Jakob , Pangrsic Tina , Moser Tobias , Wichmann Carolin 
Published: May 2022

AbstractRibbon synapses of cochlear inner hair cells (IHCs) are specialized to indefatigably transmit sound information at high rates. To understand the underlying mechanisms, structure-function analysis of the active zone (AZ) of these synapses is essential. Previous electron microscopy studies of synaptic vesicle (SV) dynamics at the IHC AZ used potassium stimulation, which limited the temporal resolution to minutes. Here, we established optogenetic IHC stimulation followed by quick freezing within milliseconds and electron tomography to study the ultrastructure of functional synapse states with good temporal resolution. We characterized optogenetic IHC stimulation by patch-clamp recordings from IHCs and postsynaptic boutons revealing robust IHC depolarization and transmitter release. Ultrastructurally, the number of docked SVs increased and distances to the presynaptic density decreased upon short (17-25 ms) and long (48-76 ms) light stimulation paradigms. We did not observe enlarged SVs or other morphological correlates of homotypic fusion events. Our results suggest a rapid replenishment of docked SVs at IHC ribbon synapses and argue against synchronized multiquantal release under our experimental conditions.
A neural code for spatiotemporal context
Authors: Schonhaut Daniel R. , Aghajan Zahra M. , Kahana Michael J. , Fried Itzhak 
Published: May 2022

AbstractTime and space are principle organizing dimensions of human experience. Whereas separate lines of study have identified neural correlates of time and space, little is known about how these representations converge during self-guided experience. Here we asked how neurons in the human brain represent time and space concurrently. Subjects fitted with intracranial microelectrodes played a timed navigation game where they alternated between searching for and retrieving objects in a virtual environment. Significant proportions of both time- and place-selective neurons were present during navigation, and distinct time-selective neurons appeared during task-free delays absent movement. We find that temporal and spatial codes are dissociable, with time cells remapping between search and retrieval tasks while place cells maintained stable firing fields. Other neurons tracked the context unique to each task phase, independent of time or space. Together these neuronal classes comprise a biological basis for the cognitive map of spatiotemporal context.
“Human platelet lysate derived extracellular vesicles enhance angiogenesis through miR-126”
Authors: Bordin Antonella , Chirivì Maila , Pagano Francesca , Milan Marika , Iuliano Marco , Scaccia Eleonora , Fortunato Orazio , Mangino Giorgio , Dhori Xhulio , De Marinis Elisabetta , D’Amico Alessandra , Miglietta Selenia , Picchio Vittorio , Rizzi Roberto , Romeo Giovanna , Pulcinelli Fabio , Chimenti Isotta , Frati Giacomo , De Falco Elena 
Published: May 2022

ABSTRACTObjectivesextracellular vesicles (EVs) are key biological mediators of several physiological functions within the cell microenvironment. Platelets are the most abundant source of EVs in the blood. Similarly, platelet lysate (PL), the best platelet derivative and angiogenic performer for regenerative purposes, is enriched of EVs, but their role is still too poorly discovered to be suitably exploited. Here we explored the contribution of the EVs in PL, by investigating the angiogenic features extrapolated from that possessed by PL.Methodswe tested angiogenic ability and molecular cargo in 3D bioprinted models and by RNA sequencing analysis of PL-derived EVs.Resultsa subset of small vesicles is highly represented in PL. The EVs do not retain aggregation ability, preserving a low redox state in HUVEC and increasing the angiogenic tubularly-like structures in 3D endothelial bioprinted constructs. EVs resembled the miRNome profile of PL, mainly enriched of small RNAs and a high amount of miR-126, the most abundant angiogenic miRNA in platelets. The transfer of miR-126 by EVs in HUVEC after the in vitro inhibition of the endogenous form, restored angiogenesis, without involving VEGF as downstream target in this system.ConclusionsPL is a biological source of available EVs with angiogenic effects involving a miRNAs-based cargo. These properties can be exploited for targeted molecular/biological manipulation of PL, by potentially developing a product exclusively manufactured of EVs.