bluuebunny/crossref_metadata_2025_split huggingface dataset:
Improving replicability in single-cell RNA-Seq cell type discovery with Dune
Authors: de Bézieux Hector Roux , Street Kelly , Fischer Stephan , Van den Berge Koen , Chance Rebecca , Risso Davide , Gillis Jesse , Ngai John , Purdom Elizabeth , Dudoit Sandrine 
Published: March 2020

AbstractSingle-cell transcriptome sequencing (scRNA-Seq) has allowed many new types of investigations at unprecedented and unique levels of resolution. Among the primary goals of scRNA-Seq is the classification of cells into potentially novel cell types. Many approaches build on the existing clustering literature to develop tools specific to single-cell applications. However, almost all of these methods rely on heuristics or user-supplied parameters to control the number of clusters identified. This affects both the resolution of the clusters within the original dataset as well as their replicability across datasets. While many recommendations exist to select these tuning parameters, most of them are quite ad hoc. In general, there is little assurance that any given set of parameters will represent an optimal choice in the ever-present trade-off between cluster resolution and replicability. For instance, it may be the case that another set of parameters will result in more clusters that are also more replicable, or in fewer clusters that are also less replicable.Here, we propose a new method calledDunefor optimizing the trade-off between the resolution of the clusters and their replicability across datasets. Our method takes as input a set of clustering results on a single dataset, derived from any set of clustering algorithms and associated tuning parameters, and iteratively merges clusters within partitions in order to maximize their concordance between partitions. As demonstrated on a variety of scRNA-Seq datasets from different platforms,Duneoutperforms existing techniques, that rely on hierarchical merging for reducing the number of clusters, in terms of replicability of the resultant merged clusters. It provides an objective approach for identifying replicable consensus clusters most likely to represent common biological features across multiple datasets.
Two new genetically modified mouse alleles labeling distinct phases of retinal ganglion cell development by fluorescent proteins
Authors: Ge Yichen , Wu Fuguo , Cheng Mobin , Mu Xiuqian 
Published: March 2020

AbstractDuring development, retinal progenitor cells (RPCs) take on different trajectories for distinct cell fates. Previous studies have identified key regulators involved in two key steps of retinal ganglion cell (RGC) genesis; Atoh7 functions in a subpopulation of RPCs to render them competent for the RGC fate, whereas Pou4f2 and Isl1 function to specify the RGC fate and promote RGC differentiation. Extensive research has been performed on the roles of these transcription factors in RGC development, but properties of these two phases they represent and the cellular context in which these two factors function have not been thoroughly investigated, largely due to the cellular heterogeneity of developing retina. In this paper, we describe two novel knock-in mouse alleles,Atoh7zsGreenCreERT2andPou4f2FlagtdTomato, which enabled us to label retinal cells in the two phases of RGC development by fluorescent proteins. In addition, theAtoh7zsGreenCreERT2allele also allowed for indirect labeling of RGCs and other cell types upon tamoxifen induction in a dose-dependent manner. Further, these alleles could be used to purify retinal cells of these different phases by fluorescence assisted cell sorting (FACS). Thus, these two alleles can serve as very useful tools for studying the molecular and genetic mechanisms underlying RGC formation.
Hippo signaling promotes Ets21c-dependent apical cell extrusion in theDrosophilawing disc
Authors: Ai Xianlong , Wang Dan , Zhang Junzheng , Shen Jie 
Published: March 2020

ABSTRACTCell extrusion is a crucial regulator of epithelial tissue development and homeostasis. Epithelial cells undergoing apoptosis, bearing pathological mutations, and possessing developmental defects are actively extruded toward elimination. However, the molecular mechanisms ofDrosophilaepithelial cell extrusion are not fully understood. Here, we report that activation of the conserved Hippo (Hpo) signaling pathway induces both apical and basal cell extrusion in theDrosophilawing disc epithelia. We show that canonical Yorki targets Diap1, and that dMyc and Cyclin E are not required for either apical or basal cell extrusion induced by activation of this pathway. Another target gene,bantam, is only involved in basal cell extrusion, suggesting novel Hpo-regulated apical cell extrusion mechanisms. Using RNA-Seq analysis, we found that JNK signaling is activated in the extruding cells. We provide genetic evidence that JNK signaling activation is both sufficient and necessary for Hpo-regulated cell extrusion. Furthermore, we demonstrate that the ETS-domain transcription factor Ets21c, an ortholog of proto-oncogenesFLI1andERG, acts downstream of JNK signaling to mediate apical cell extrusion. Our findings reveal a novel molecular link between Hpo signaling and cell extrusion.SUMMARY STATEMENTActivation of Hippo signaling induces cell extrusion in theDrosophilawing epithelia, in whichbantammediates basal cell extrusion and Ets21c mediates apical cell extrusion.
Vitamin D regulation of a SOD1-to-SOD2 antioxidative switch to prevent osteosarcoma transformation
Authors: Lisse Thomas S. 
Published: March 2020

AbstractSuperoxide, a form of reactive oxygen species (ROS), is catabolized by superoxide dismutase (SOD) and contributes to carcinogenesis via the oxidative damage it inflicts on cells. The aim of this research was to analyze the potential vitamin D-mediated regulation of the antioxidative “SOD1-to-SOD2 switch” within the human MG-63 osteosarcoma model. For this study, real-time PCR analysis was performed using MG-63 cells exposed to metabolically active 1,25(OH)2D3. Frist, a sustained statistically significant >2-fold suppression of proliferating cell nuclear antigen (PCNA) transcripts was observed after 10nM but not at 100nM of 1,25(OH)2D3treatment, suggesting a cytostatic effect. In order to assess regulators of mitochondrial oxidative phosphorylation, gene expression ofCOX2andCOX4l1of the mitochondrial complex IV and antioxidative enzymes (SOD1, SOD2andCatalase(CAT)) were monitored. For COX2 and COX4l1, no changes in gene expression were observed. However, a concomitant decrease in CAT and SOD1 mRNA, and increase in SOD2 mRNA after 24 hours of 10nM 1,25(OH)2D3treatment were observed. A ~8-fold increase in SOD2 mRNA was apparent after 48 hours. The significant increase in SOD2 activity in the presence of vitamin D indicates an antioxidant potential and sensitization of vitamin D during osteosarcoma transformation and mitochondrial detoxification over time.
Chemokine receptor 2-targeted molecular imaging in pulmonary fibrosis
Authors: Brody Steven L. , Gunsten Sean P. , Luehmann Hannah P. , Sultan Debbie H. , Hoelscher Michelle , Heo Gyu Seong , Pan Jiehong , Koenitzer Jeffrey R. , Lee Ethan C. , Huang Tao , Mpoy Cedric , Guo Shuchi , Laforest Richard , Salter Amber , Russell Tonya D. , Shifren Adrian , Combadiere Christophe , Lavine Kory J. , Kreisel Daniel , Humphreys Benjamin D. , Rogers Buck E. , Gierada David S. , Byers Derek E. , Gropler Robert J. , Chen Delphine L. , Atkinson Jeffrey J. , Liu Yongjian 
Published: March 2020

AbstractIdiopathic pulmonary fibrosis (IPF) is a progressive, inflammatory lung disease that is monitored clinically by measures of lung function, without effective molecular markers of disease activity or therapeutic efficacy. Lung immune cells active in the pro-fibrotic process include inflammatory monocyte and interstitial macrophages that express the C-C motif chemokine receptor 2 (CCR2). CCR2+monocyte lung influx is essential for disease phenotypes in models of fibrosis and identified in lungs from subjects with IPF. Here, we show that our peptide-based radiotracer64Cu-DOTA-ECL1i identifies CCR2+inflammatory monocytes and interstitial macrophages in multiple preclinical mouse models of lung fibrosis, using positron emission tomography (PET) imaging. Mice with bleomycin-induced fibrosis treated with blocking antibodies to interleukin-1β, a mediator of fibrosis associated with CCR2+cell inflammation, or with pirfenidone, an approved anti-fibrotic agent, demonstrated decreased CCR2-dependent interstitial macrophage accumulation and reduced64Cu-DOTA-ECL1i PET uptake, compared to controls. Lung tissues from patients with fibrotic lung disease demonstrated abundant CCR2+cells surrounding regions of fibrosis, and an ex vivo tissue-binding assay showed correlation between radiotracer localization and CCR2+cells. In a phase 0/1 clinical study of64Cu-DOTA-ECL1i PET, healthy volunteers showed little lung uptake, while subjects with pulmonary fibrosis exhibited increased uptake, notably in zones of subpleural fibrosis, reflecting the distribution of CCR2+cells in the profibrotic niche. These findings support a pathologic role of inflammatory lung monocytes/macrophages in fibrotic lung disease and the translational use of64Cu-DOTA-ECL1i PET to track CCR2-specific inflammation for image-guided therapy.One Sentence SummaryPET imaging of CCR2+cells in lung fibrosis identifies a therapeutic response in mouse models and displays a perifibrotic signal in subjects with IPF.
Quantitative proteomics links the LRRC59 interactome to mRNA translation on the ER membrane
Authors: Hannigan Molly M. , Hoffman Alyson M. , Thompson J. Will , Zheng Tianli , Nicchitta Christopher V. 
Published: March 2020

AbstractProtein synthesis on the endoplasmic reticulum (ER) requires the dynamic coordination of resident membrane proteins and cytoplasmic translation factors. While ER membrane proteins functioning in ribosome association, mRNA anchoring, and protein translocation, have been identified, little is known regarding the higher order organization of ER-localized translation. Here we utilized proximity proteomics to identify neighboring protein networks for the ribosome interactors SEC61β, RPN1, SEC62, and LRRC59. Whereas the SEC61β and RPN1 BioID reporters revealed translocon-associated networks, the SEC62 and LRRC59 reporters identified divergent interactome networks of previously unexplored functions. Notably, the SEC62 interactome is enriched in redox-linked proteins and ER luminal chaperones, whereas the LRRC59 interactome is enriched in SRP pathway components, translation factors, and ER-localized RNA-binding proteins. Analysis of the LRRC59 interactome by native immunoprecipitation identified similar protein and functional enrichments. Combined, these data reveal a functional domain organization for the ER and suggest a key role for LRRC59 in the organization of mRNA translation on the ER.SummaryHannigan et al. characterize the protein interactomes of four ER ribosome-binding proteins, providing evidence that ER-bound ribosomes reside in distinct molecular environments. Their data link SEC62 to ER redox regulation and chaperone trafficking, and suggest a role for LRRC59 in SRP-coupled protein synthesis.
ZFP423 regulates early patterning and multiciliogenesis in the hindbrain choroid plexus
Authors: Casoni Filippo , Croci Laura , Vincenti Francesca , Podini Paola , Massimino Luca , Cremona Ottavio , Consalez G. Giacomo 
Published: March 2020

ABSTRACTThe choroid plexus (ChP) is a secretory tissue that produces cerebrospinal fluid (CSF) and secretes it into the ventricular system. CSF flows from the lateral to the third ventricle, and then to the fourth ventricle through the cerebral aqueduct. Recent studies have uncovered new, active roles for this structure in the regulation of neural stem cell maintenance and differentiation into neurons.Zfp423,encoding a Kruppel-type zinc finger transcription factor essential for cerebellar development and mutated in rare cases of cerebellar vermis hypoplasia / Joubert syndrome and other ciliopathies, is expressed in the hindbrain roof plate (RP), from which the IV ventricle ChP arises, and in mesenchymal cells giving rise to the stroma and leptomeninges.Zfp423mutants display a marked reduction of the hindbrain ChP (hChP), which fails to express key markers of its secretory function and genes implicated in its development and maintenance (Lmx1a, Otx2). The mutant hChP displays a complete lack of multiciliated ependymal cells. A transcriptome analysis conducted at the earliest stages of hChP development and subsequent validations demonstrate that the mutant hChp displays a strong deregulation of pathways involved in early hindbrain patterning and multiciliated cell fate specification. Our results proposeZfp423as a master gene and one of the earliest known determinants of hChP development.
Strong evolutionary convergence of receptor-binding protein spike between COVID-19 and SARS-related coronaviruses
Authors: Wu Yonghua 
Published: March 2020

AbstractCoronavirus Disease 2019 (COVID-19) and severe acute respiratory syndrome (SARS)-related coronaviruses (e.g., 2019-nCoV and SARS-CoV) are phylogenetically distantly related, but both are capable of infecting human hosts via the same receptor, angiotensin-converting enzyme 2, and cause similar clinical and pathological features, suggesting their phenotypic convergence. Yet, the molecular basis that underlies their phenotypic convergence remains unknown. Here, we used a recently developed molecular phyloecological approach to examine the molecular basis leading to their phenotypic convergence. Our genome-level analyses show that the spike protein, which is responsible for receptor binding, has undergone significant Darwinian selection along the branches related to 2019-nCoV and SARS-CoV. Further examination shows an unusually high proportion of evolutionary convergent amino acid sites in the receptor binding domain (RBD) of the spike protein between COVID-19 and SARS-related CoV clades, leading to the phylogenetic uniting of their RBD protein sequences. In addition to the spike protein, we also find the evolutionary convergence of its partner protein,ORF3a, suggesting their possible co-evolutionary convergence. Our results demonstrate a strong adaptive evolutionary convergence between COVID-19 and SARS-related CoV, possibly facilitating their adaptation to similar or identical receptors. Finally, it should be noted that many observed bat SARS-like CoVs that have an evolutionary convergent RBD sequence with 2019-nCoV and SARS-CoV may be pre-adapted to human host receptor ACE2, and hence would be potential new coronavirus sources to infect humans in the future.
Structural basis underlying strong interactions between ankyrins and spectrins
Authors: Li Jianchao , Chen Keyu , Zhu Ruichi , Zhang Mingjie 
Published: March 2020

AbstractAnkyrins (encoded byANK1/2/3corresponding to Ankyrin-R/B/G or AnkR/B/G), via binding to spectrins, connect plasma membranes with actin cytoskeleton to maintain mechanical strengths and to modulate excitabilities of diverse cells such as neurons, muscle cells, and erythrocytes. Cellular and genetic evidences suggest that each isoform of ankyrins pairs with a specific β-spectrin in discrete subcellular membrane microdomains for distinct functions, though the molecular mechanisms underlying such ankyrin/β-spectrin pairings are unknown. In this study, we discover that a conserved and short extension N-terminal to the ZU5N-ZU5C-UPA tandem (exZZU) is critical for each ankyrin to bind to β-spectrins with high affinities. Structures of AnkB/G exZZU in complex with spectrin repeats13-15 of β2/β4-spectrins solved here reveal that the extension sequence of exZZU forms an additional β-strand contributing to the structural stability and enhanced affinity of each ZU5N/spectrin repeat interaction. The junction site between the extension and ZU5Nis exactly the position of a splicing-mediated miniexon insertion site of AnkB/G. The complex structures further reveal that the UPA domain of exZZU directly participates in spectrin binding. Formation of the exZZU supramodule juxtaposes the ZU5Nand UPA domains for simultaneous interacting with spectrin repeats 14 and 15. However, our biochemical and structural investigations indicate that the direct and strong interactions between ankyrins and β-spectrins do not appear to determine their pairing specificities. Therefore, there likely exists additional mechanism(s) for modulating functional pairings between ankyrins and β-spectrins in cells.
A global barley panel revealing genomic signatures of breeding in modern cultivars
Authors: Hill Camilla Beate , Angessa Tefera Tolera , Zhang Xiao-Qi , Chen Kefei , Zhou Gaofeng , Tan Cong , Wang Penghao , Westcott Sharon , Li Chengdao 
Published: March 2020

AbstractThe future of plant cultivar improvement lies in the evaluation of genetic resources from currently available germplasm. Recent efforts in plant breeding have been aimed at developing new and improved varieties from poorly adapted crops to suit local environments. However, the impact of these breeding efforts is poorly understood. Here, we assess the contributions of both historical and recent breeding efforts to local adaptation and crop improvement in a global barley panel by analysing the distribution of genetic variants with respect to geographic region or historical breeding category. By tracing the impact breeding had on the genetic diversity of barley released in Australia, where the history of barley production is relatively young, we identify 69 candidate regions within 922 genes that were under selection pressure. We also show that modern Australian barley varieties exhibit 12% higher genetic diversity than historical cultivars. Finally, field-trialling and phenotyping for agriculturally relevant traits across a diverse range of Australian environments suggests that genomic regions under strong breeding selection and their candidate genes are closely associated with key agronomic traits. In conclusion, our combined dataset and germplasm collection provide a rich source of genetic diversity that can be applied to understanding and improving environmental adaptation and enhanced yields.Author summaryToday’s gene pool of crop genetic diversity has been shaped during domestication and more recently by breeding. Genetic diversity is vital for crop species to be able to adapt to changing environments. There is concern that recent breeding efforts have eroded the genetic diversity of many domesticated crops including barley. The present study assembled a global panel of barley genotypes with a focus on historical and modern Australian varieties.Genome-wide data was used to detect genes that are thought to have been under selection during crop breeding in Australian barley. The results demonstrate that despite being more extensively bred, modern Australian barley varieties exhibit higher genetic diversity than historical cultivars, countering the common perception that intensive breeding leads to genetic erosion of adaptive diversity in modern cultivars. In addition, some loci (particularly those related to phenology) were subject to selection during the introduction of other barley varieties to Australia – these genes might continue to be important targets in breeding efforts in the face of changing climatic conditions.
Rapid formation of peptide/lipid co-aggregates by the amyloidogenic seminal peptide PAP248-286
Authors: Vane E.W. , He S. , Maibaum L. , Nath A. 
Published: March 2020

AbstractProtein/lipid co-assembly is an understudied phenomenon that is important to the function of antimicrobial peptides as well as the pathological effects of amyloid. Here we study the co-assembly process of PAP248-286, a seminal peptide that displays both amyloid-forming and antimicrobial activity. PAP248-286is a fragment of prostatic acid phosphatase and has been reported to form amyloid fibrils, known as semen-derived enhancer of viral infection (SEVI), that enhance the viral infectivity of HIV. We find that in addition to forming amyloid, PAP248-286much more readily assembles with lipid vesicles into peptide/lipid co-aggregates that resemble amyloid fibrils in some important ways but are a distinct species. The formation of these co-aggregates, which we term “messicles”, is controlled by the peptide:lipid (P:L) ratio and by the lipid composition. The optimal P:L ratio is around 1:10 and at least 70% anionic lipid is required for co-aggregate formation. Once formed, messicles are not disrupted by subsequent changes in P:L ratio. We propose that messicles form through a polyvalent assembly mechanism, where a critical surface density of PAP248-286on liposomes enables peptide-mediated particle bridging into larger species. Even at ~100-fold lower PAP248-286concentrations, messicles form at least 10-fold faster than amyloid fibrils. It is therefore possible that, some or all of the biological activities assigned to SEVI, the amyloid form of PAP248-286, could instead be attributed to a PAP248-286/lipid co-aggregate. More broadly speaking, this work provides a potential framework for the discovery and characterization of peptide/lipid co-aggregates by other amyloid-forming proteins and antimicrobial peptides.Statement of SignificancePAP248-286, a fragment of prostatic acid phosphatase, forms amyloid thought to enhances the infectivity of many viruses, including HIV. This amyloid, termed semen-derived enhancer of viral infection (SEVI), has been assigned responsibility for all of PAP248-286’s biological activities, while the monomer is thought to be inactive. However, SEVI formation is quite slow and requires very high concentrations of PAP248-286. Here, we show that PAP248-286can instead assemble much more rapidly with lipid membranes to form another species, mechanistically and morphologically distinct from both monomer and SEVI amyloid. We have characterized this new species, which could play a role in the biological activities currently ascribed to SEVI. Additionally, our proposed mechanism for peptide/lipid co-assembly could apply to other biologically important systems.
Septin Roles and Mechanisms in Organization of Endothelial Cell Junctions
Authors: Kim Joanna , Cooper John A. 
Published: March 2020

AbstractSeptins play an important role in regulating the barrier function of the endothelial monolayer of the microvasculature. Depletion of septin 2 protein alters the organization of vascular endothelial (VE)-cadherin at cell-cell adherens junctions as well as the dynamics of membrane protrusions at endothelial cell-cell contact sites. Here, we report the discovery that localization of septin 2 at endothelial cell junctions is important for the distribution of a number of other junctional molecules. We also found that treatment of microvascular endothelial cells with the inflammatory mediator TNF-α led to sequestration of septin 2 away from cell junctions and into the cytoplasm, without an effect on the overall level of septin 2 protein. Interestingly, TNF-α treatment of endothelial monolayers produced effects similar to those of depletion of septin 2 on various molecular components of adherens junctions (AJs) and tight junctions (TJs). Immunofluorescence staining revealed disruption of the integrity of AJs and TJs at cell-cell junctions without significant changes in protein expression except for VE-cadherin and nectin-2. To investigate the mechanism of junctional localization of septin 2, we mutated the polybasic motif of septin 2, which is proposed to interact with PIP2in the plasma membrane. Overexpression of PIP2-binding mutant (PIP2BM) septin 2 led to loss of septin 2 from cell junctions with accumulation in the cytoplasm. This redistribution of septin 2 away from the membrane led to effects on cell junction molecules similar to those observed for depletion of septin 2. We conclude that septin localization to the membrane is essential for function and that septins support the localization of multiple cell junction molecules in endothelial cells.