bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vesalius: high-resolution in silico anatomization of Spatial Transcriptomic data using Image Analysis
Authors: Martin Patrick C.N. , Kim Hyobin , Lövkvist Cecilia , Hong Byung-Woo , Won Kyoung Jae 
Published: August 2021

AbstractCharacterization of tissue architecture promises to deliver insights into development, cell communication and disease. In silico spatial domain retrieval methods have been developed for spatial transcriptomics (ST) data assuming transcriptional similarity of neighboring barcodes. However, domain retrieval approaches with this assumption cannot work in complex tissues composed of multiple cell types. This task becomes especially challenging in cellular resolution ST methods. We developed Vesalius to decipher tissue anatomy from ST data by applying image processing technology. Vesalius uniquely detected territories composed of multiple cell types and successfully recovered tissue structures in high-resolution ST data including in mouse brain, embryo, liver, and colon. Utilizing this tissue architecture, Vesalius identified tissue morphology specific gene expression and regional specific gene expression changes for astrocytes, interneuron, oligodendrocytes, and entorhinal cells in the mouse brain.
Multiplein vivoroles for the C-terminal domain of the RNA chaperone Hfq
Authors: Kavita Kumari , Zhang Aixia , Tai Chin-Hsien , Majdalani Nadim , Storz Gisela , Gottesman Susan 
Published: August 2021

ABSTRACTHfq, a bacterial RNA chaperone, stabilizes small regulatory RNAs (sRNAs) and facilitates sRNA base-pairing with target mRNAs. Hfq has a conserved N-terminal domain and a poorly conserved disordered C-terminal domain (CTD). In a transcriptome-wide examination of the effects of a chromosomal CTD deletion (Hfq1-65), theEscherichia colimutant was most defective for the accumulation of sRNAs that bind the proximal and distal faces of Hfq (Class II sRNAs), but other sRNAs also were affected. There were only modest effects on the levels of mRNAs, suggesting little disruption of sRNA-dependent regulation. However, cells expressing Hfq lacking the CTD deletion in combination with a weak distal face mutation were defective for the function of the Class II sRNA ChiX and repression ofmutS, both dependent upon distal face RNA binding. Loss of the region between amino acids 66-72 was critical for this defect. The CTD region beyond amino acid 72 was not necessary for distal face-dependent regulation, but was needed for functions associated with the Hfq rim, seen most clearly in combination with a rim mutant. Our results suggest that the C-terminus collaborates in various ways with different binding faces of Hfq, leading to distinct outcomes for individual sRNAs.
Drosophila nicotinic acetylcholine receptor subunits and their native interactions with insecticidal peptide toxins
Authors: Korona Dagmara , Dirnberger Benedict , Giachello Carlo N G , Queiroz Rayner M L , Minde David-Paul , Deery Michael J , Johnson Glynnis , Müller Karin H , Firth Lucy C , Earley Fergus G , Russell Steven , Lilley Kathryn S 
Published: August 2021

AbstractDrosophila nicotinic acetylcholine receptors (nAChRs) are ligand-gated ion channels that represent a target for insecticides. Peptide neurotoxins are known to block nAChRs by binding to their target subunits, however, a better understanding of receptor subunit composition is needed for effective design of insecticides. To facilitate the analysis of nAChRs we used a CRISPR/Cas9 strategy to generate null alleles for all ten nAChR subunit genes in a common genetic background. We studied interactions of nAChR subunits with peptide neurotoxins by larval injections and styrene maleic acid lipid particles (SMALPs) pull-down assays. For the null alleles we determined the effects of α-Bungarotoxin (α-Btx) and ω-Hexatoxin-Hv1a (Hv1a) administration, identifying potential receptor subunits implicated in the binding of these toxins. We employed pull-down assays to confirm α-Btx interactions with the Dα5, Dα6, Dα7 subunits. Finally, we report the localization of fluorescent tagged endogenous Dα6 during nervous system development. Taken together this study elucidates native Drosophila nAChR subunit interactions with insecticidal peptide toxins and provides a resource for the in vivo analysis of insect nAChRs.
A short perinuclear amphipathic α-helix in Apq12 promotes nuclear pore complex biogenesis
Authors: Zhang Wanlu , Khan Azqa , Vitale Jlenia , Neuner Annett , Rink Kerstin , Lüchtenborg Christian , Brügger Britta , Söllner Thomas H. , Schiebel Elmar 
Published: August 2021

SummaryThe integral membrane protein Apq12 is an important nuclear envelope (NE)/ER modulator that cooperates with the nuclear pore complex (NPC) biogenesis factors Brl1 and Brr6. How Apq12 executes these functions is unknown. Here we identified a short amphipathic α-helix (AαH) in Apq12 that links the two transmembrane domains in the perinuclear space and has liposome-binding properties. Cells expressing an APQ12 (apq12-ah) version in which AαH is disrupted show NPC biogenesis and NE integrity defects, without impacting upon Apq12-ah topology or NE/ER localization. Overexpression of APQ12 but not apq12-ah triggers striking over-proliferation of the outer nuclear membrane (ONM)/ER and promotes accumulation of phosphatidic acid (PA) at the NE. Apq12 and Apq12-ah both associate with NPC biogenesis intermediates and removal of AαH increases both Brl1 levels and the interaction between Brl1 and Brr6. We conclude that the short amphipathic α-helix of Apq12 regulates the function of Brl1 and Brr6 and promotes PA accumulation at the NE during NPC biogenesis.
The Zip4 protein directly couples meiotic crossover formation to synaptonemal complex assembly
Authors: Pyatnitskaya Alexandra , Andreani Jessica , Guérois Raphaël , De Muyt Arnaud , Borde Valérie 
Published: August 2021

SummaryMeiotic recombination is triggered by programmed double-strand breaks (DSBs), a subset of these being repaired as crossovers, promoted by eight evolutionarily conserved proteins, named ZMM. Crossover formation is functionally linked to synaptonemal complex (SC) assembly between homologous chromosomes, but the underlying mechanism is unknown. Here we show that Ecm11, a SC central element protein, localizes on both DSB sites and sites that attach chromatin loops to the chromosome axis, which are the starting points of SC formation, in a way that strictly requires the ZMM protein Zip4. Furthermore, Zip4 directly interacts with Ecm11 and point mutants that specifically abolish this interaction lose Ecm11 binding to chromosomes and exhibit defective SC assembly. This can be partially rescued by artificially tethering interaction-defective Ecm11 to Zip4. Mechanistically, this direct connection ensuring SC assembly from CO sites could be a way for the meiotic cell to shut down further DSB formation once enough recombination sites have been selected for crossovers, thereby preventing excess crossovers. Finally, the mammalian ortholog of Zip4, TEX11, also interacts with the SC central element TEX12, suggesting a general mechanism.
Secreted SARS-CoV-2 ORF8 modulates the cytokine expression profile of human macrophages
Authors: Kriplani Nisha , Clohisey Sara , Fonseca Sonia , Fletcher Sarah , Lee Hui-Min , Ashworth Jordan , Kurian Dominic , Lycett Samantha J. , Tait-Burkard Christine , Kenneth Baillie J. , Woolhouse Mark E. J. , Carding Simon R. , Stewart James P. , Digard Paul 
Published: August 2021

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still adapting to its new human host. Attention has focussed on the viral spike protein, but substantial variation has been seen in the ORF8 gene. Here, we show that SARS-CoV-2 ORF8 protein undergoes signal peptide-mediated processing through the endoplasmic reticulum and is secreted as a glycosylated, disulphide-linked dimer. The secreted protein from the prototype SARS-CoV-2 virus had no major effect on viability of a variety of cell types, or on IFN or NF-κB signalling. However, it modulated cytokine expression from primary CSF1-derived human macrophages, most notably by decreasing IL-6 and IL-8 secretion. Furthermore, a sequence polymorphism L84S that appeared early in the pandemic associated with the Clade S lineage of virus, showed a markedly different effect, of increasing IL-6 production. We conclude that ORF8 sequence polymorphisms can potentially affect SARS-CoV-2 virulence and should therefore be monitored in sequencing-based surveillance.
A cooperative network at the nuclear envelope counteracts LINC-mediated forces during oogenesis in C. elegans
Authors: Liu Chenshu , Lung Zoe , Wang John S. , Wu Fan , Dernburg Abby F. 
Published: August 2021

ABSTRACTOogenesis involves meiosis and oocyte maturation. Both processes rely on mechanical forces (Lee et al., 2015; Nagamatsu et al., 2019; Rog and Dernburg, 2015; Sato et al., 2009; Tsatskis et al., 2020; Wynne et al., 2012), which can be transduced from the cytoskeleton to the nuclear envelope (NE) through linker of nucleoskeleton and cytoskeleton (LINC) complexes (Burke, 2018; Chang et al., 2015; Fan et al., 2020; Link et al., 2014). Gametes must protect their genomes from damage in this mechanically stressful environment. In C. elegans, oocyte nuclei lacking the single lamin protein LMN-1 are vulnerable to nuclear collapse. Here we deploy the auxin-inducible degradation system to investigate the balance of forces that drive this collapse and protect oocyte nuclei. We find that nuclear collapse is not a consequence of apoptosis. It is promoted by dynein and a LINC complex comprised of SUN-1 and ZYG-12, which assumes polarized distribution at the NE in response to dynein-mediated forces. We also show that the lamin meshwork works in parallel with other inner nuclear membrane (INM) proteins to counteract mechanical stress at the NE during oogenesis. We speculate that a similar network may protect oocyte integrity during the long arrest period in mammals.
Comparative Analysis and Rational Design of dCas9-VP64 Variants for CRISPR Activation
Authors: Omachi Kohei , Miner Jeffrey H. 
Published: August 2021

ABSTRACTCRISPR/Cas9-mediated transcriptional activation (CRISPRa) is a powerful tool for investigating complex biological phenomena. Although CRISPRa approaches based on VP64 have been widely studied in both cultured cells and in animal models and exhibit great versatility for various cell types and developmental stages in vivo, different dCas9-VP64 versions have not been rigorously compared. Here, we compared different dCas9-VP64 constructs in identical contexts, including the cell lines used and the transfection conditions, for their ability to activate endogenous and exogenous genes. Moreover, we investigated the optimal approach for VP64 addition to VP64- and p300-based constructs. We found that MS2-MCP-scaffolded VP64 enhanced dCas9-VP64 and dCas9-p300 activity better than did direct VP64 fusion to the N-terminus of dCas9. dCas9-VP64+MCP-VP64 and dCas9-p300+MCP-VP64 were superior to VP64-dCas9-VP64 for all target genes tested. Furthermore, multiplexing gRNA expression with dCas9-VP64+MCP-VP64 or dCas9-p300+MCP-VP64 significantly enhanced endogenous gene activation to a level comparable to CRISPRa-SAM with a single gRNA. Our findings demonstrate improvement of the dCas9-VP64 CRISPRa system and contribute to development of a versatile, efficient CRISPRa platform.
Laboratory analysis of glucose, fructose, and sucrose contents in Japanese common beverages for the exact assessment of beverage-derived sugar intake
Authors: Ando Yoshitaka , Ohta Yoshiji , Munetsuna Eiji , Yamada Hiroya , Nouchi Yuki , Kageyama Itsuki , Mizuno Genki , Yamazaki Mirai , Fujii Ryosuke , Ishikawa Hiroaki , Suzuki Koji , Ohashi Koji 
Published: August 2021

AbstractBackgroundThe adverse health effects of sugar-sweetened beverage consumption have been studied worldwide. There are several reports on actual sugar contents in sugar-sweetened beverages. However, there is no recent report on actual sugar contents in Japanese sugar-sweetened beverages. Therefore, we attempted to analyze glucose, fructose, and sucrose contents in Japanese common beverages.MethodsGlucose, fructose, and sucrose contents in 49 beverages including 8 energy drinks, 11 sodas, 4 fruit juices, 7 probiotic drinks, 4 sports drinks, 5 coffee drinks, 6 green tea drinks, and 4 tea drinks were determined using the enzymatic methods.ResultsTow zero calorie drinks, 2 sugarless coffee drinks, and 6 green tea drinks contained no sugar. Three coffee drinks contained only sucrose. The orders of median glucose, fructose, and sucrose contents in categorized beverages containing sugars were as follows: for glucose, fruit juice > energy drink ≥ soda >> probiotic drink > black tea drink > sports drink; for fructose, probiotic drink ≥ energy drink > fruit juice > soda >> sports drink > black tea drink; and for sucrose, black tea drink > energy drink ≥ probiotic drink > fruit juice > soda > coffee drink >> sports drink. The rate of total fructose content in total sugar content in 38 sugar-containing beverages was approximately 40-60%. The total sugar content analyzed was not always equivalent to carbohydrate content indicated on the nutrition label.ConclusionsThese results indicate that actual sugar content in Japanese common beverages is necessary for the exact assessment of beverage-derived sugar intake.
Antimicrobial interactions between the phytoextracts of Callistemon citrinus and Eriobotrya japonica against Streptococcus mutans
Authors: Kavuo J. S , Namboko Jerald Kutosi , Bukusuba Samuel , Onen Healy 
Published: August 2021

AbstractStreptococcus mutans is a gram-positive bacterium in the oral cavity that is most implicated in the dental caries progression. The condition is very expensive to manage and the most commonly used products such as fluoride tooth pastes and alcohol-based mouth washes are associated with many side effects. The current study therefore focused on providing a scientific evidence to guide the use of a combination of Eriobotrya japonica (EJ) and Callistemon citrinus (CC) as actives in development of an effective and cheaper herbal formulation for management of dental caries. The objective of this study was to determine antimicrobial interactions of Eriobotrya japonica and Callistemon citrinus phytoextracts proportions against Streptococcus mutans bacteria. The leaves of both plants (EJ and CC) were shade-dried and pulverized into a coarse powder which were then cold macerated using ethanol (60 %) for 24 h. Phytochemical screening was conducted for the two dry extracts obtained after fan drying before they were mixed in to five different proportions (1:0, 3:1, 1:1, 1:3 and 0:1). Minimum inhibitory concentrations (MIC) and minimum bactericidal concentration (MBC) assays against Streptococcus mutans were done for all the proportions above with ciprofloxacin and 2.5 % Dimethyl sulfoxide (DMSO) as the positive and negative controls respectively. Antimicrobial interactions between the two extracts were also evaluated using Fractional Inhibitory and Bacterial Concentration Indices (FICI/FBCI). Results showed that EJ and CC had percentage yields of 20.05 % and 15.45 % respectively. All the extracts showed similar phytochemical profiles. They also demonstrated an inhibitory effect on Streptococcus mutans with MIC and MBC values ranging from 521 to 3333 μg/ml and 1042 to 3667 μg/ml respectively. However, CC: EJ (1:0) had the lowest MIC and MBC comparable to that of the standard drug at P <0.05. The FICI/FBCI were between 1.5 and 3.917. Therefore, CC: EJ (1:0) proportion markedly demonstrated better antimicrobial activity against the test organism and there are no beneficial antimicrobial interactions between the two plant extracts to inform their combination as actives for dental caries product formulation.
Evidence for the Presence of Hyphae and Fruiting Body Calcium Oxalate Crystallites in Schizophyllum commune
Authors: Xiao Xiangyue , Huang Tianji , Zhang Jingyi , Su Qiuyi , Tao Lin , Chen Xiaojie , Zhang Yuchen , Jiang Yufan , Ding Yan , Yu Xiaoming , Liu Wei , Ji Hong , Song Chi 
Published: August 2021

AbstractBiomineralization is a phenomenon in which organisms form crystals. Studies have shown that many fungi have the ability to biomineralize, it can exhibit calcium oxalate crystals on their hyphae and fruiting body. Schizophyllum commune is a common saprophytic fungus distributed all over the world, but there is little research on its biomineralization. In this paper, S. commune fruiting body from three different provinces of China were collected, and isolation for hyphal cultured to obtain several samples. Utilizing light microscope, FE-SEM, and EDAX, the existence of crystals on the fruiting body and mycelium of each strain was found, and their morphological characteristics and ion content were analyzed. It was ultimately established that biomineralization occurs on S. commune.
Non-Invasive Confocal Fluorescence Imaging of Mice Beyond 1700 nm Using Superconducting Nanowire Single-Photon Detectors
Authors: Wang Feifei , Ren Fuqiang , Ma Zhuoran , Qu Liangqiong , Gourgues Ronan , Xu Chun , Baghdasaryan Ani , Li Jiachen , Zadeh Iman Esmaeil , Los Johannes WN , Fognini Andreas , Qin-Dregely Jessie , Dai Hongjie 
Published: August 2021

AbstractLight scattering by biological tissues sets a limit to the penetration depth of high-resolution optical microscopy imaging of live mammals in vivo. An effective approach to reduce light scattering and increase imaging depth is by extending the excitation and emission wavelengths to the > 1000 nm second near-infrared (NIR-II), also called the short-wavelength infrared (SWIR) window. Here, we developed biocompatible core-shell lead sulfide/cadmium sulfide (PbS/CdS) quantum dots emitting at ~1880 nm and superconducting nanowire single photon detectors (SNSPD) for single-photon detection up to 2000 nm, enabling one-photon fluorescence imaging window in the 1700-2000 nm (NIR-IIc) range. Confocal fluorescence imaging in NIR-IIc reached an imaging depth of ~ 800 μm through intact mouse head, and enabled non-invasive imaging of inguinal lymph nodes (LNs) without any surgery. In vivo molecular imaging of high endothelial venules (HEVs) with diameter down to ~ 6.6 μm in the lymph nodes was achieved, opening the possibility of non-invasive imaging of immune trafficking in lymph nodes at the single-cell/vessel level longitudinally.
Assembled chromosomes of the blood fluke Schistosoma mansoni provide insight into the evolution of its ZW sex-determination system
Authors: Buddenborg Sarah K , Tracey Alan , Berger Duncan J , Lu Zhigang , Doyle Stephen R , Fu Beiyuan , Yang Fengtang , Reid Adam J , Rodgers Faye H , Rinaldi Gabriel , Sankaranarayanan Geetha , Böhme Ulrike , Holroyd Nancy , Berriman Matthew 
Published: August 2021

ABSTRACTBackgroundSchistosoma mansoni is a flatworm that causes a neglected tropical disease affecting millions worldwide. Most flatworms are hermaphrodites but schistosomes have genotypically determined male (ZZ) and female (ZW) sexes. Sex is essential for pathology and transmission, however, the molecular determinants of sex remain unknown and is limited by poorly resolved sex chromosomes in previous genome assemblies.ResultsWe assembled the 391.4 Mb S. mansoni genome into individual, single-scaffold chromosomes, including Z and W. Manual curation resulted in a vastly improved gene annotation, resolved gene and repeat arrays, trans-splicing, and almost all UTRs. The sex chromosomes each comprise pseudoautosomal regions and single sex-specific regions. The Z-specific region contains 932 genes, but on W all but 29 of these genes have been lost and the presence of five pseudogenes indicates that degeneration of W is ongoing. Synteny analysis reveals an ancient chromosomal fusion corresponding to the oldest part of Z, where only a single gene—encoding the large subunit of pre-mRNA splicing factor U2AF—has retained an intact copy on W. The sex-specific copies of U2AF have divergent N-termini and show sex-biased gene expression.ConclusionOur assembly with fully resolved chromosomes provides evidence of an evolutionary path taken to create the Z and W sex chromosomes of schistosomes. Sex-linked divergence of the single U2AF gene, which has been present in the sex-specific regions longer than any other extant gene with distinct male and female specific copies and expression, may have been a pivotal step in the evolution of gonorchorism and genotypic sex determination of schistosomes.
Artists as cultural intermediaries? Remediating practices of production and consumption
Authors: Hadley Steven 
Published: August 2021

PurposeThe purpose of this paper is to discuss findings from an Arts and Humanities Research Council (AHRC)-funded research project into the heritage culture of British folk tales. The project investigated how such archival source material might be made relevant to contemporary audience via processes of artistic remediation. The research considered artists as “cultural intermediaries”, i.e. as actors occupying the conceptual space between production and consumption in an artistic process.Design/methodology/approachInterview data is drawn from a range of 1‐2‐1 and group interviews with the artists. These interviews took place throughout the duration of the project.FindingsWhen artists are engaged in a process of remediation which has a distinct arts marketing/audience development focus, they begin to intermediate between themselves and the audience/consumer. Artist perceptions of their role as “professionals of qualification” is determined by the subjective disposition required by the market context in operation at the time (in the case of this project, as commissioned artists working to a brief). Artists’ ability (and indeed willingness) to engage in this process is to a great extent proscribed by their “sense-of-self-as-artist” and an engagement with Romantic ideas of artistic autonomy.Originality/valueA consideration of the relationship between cultural intermediation and both cultural policy and arts marketing. The artist-as-intermediary role, undertaking creative processes to mediate how goods are perceived by others, enables value-adding processes to be undertaken at the point of remediation, rather than at the stage of intermediation.