bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatiotemporal dynamics of PIEZO1 localization controls keratinocyte migration during wound healing
Authors: Holt Jesse R. , Zeng Wei-Zheng , Evans Elizabeth L. , Woo Seung-Hyun , Ma Shang , Abuwarda Hamid , Loud Meaghan , Patapoutian Ardem , Pathak Medha M. 
Published: October 2020

AbstractKeratinocytes, the predominant cell type of the epidermis, migrate to reinstate the epithelial barrier during wound healing. Mechanical cues are known to regulate keratinocyte re-epithelization and wound healing however, the underlying molecular transducers and biophysical mechanisms remain elusive. Here, we show through molecular, cellular and organismal studies that the mechanically-activated ion channel PIEZO1 regulates keratinocyte migration and wound healing. Epidermal-specificPiezo1knockout mice exhibited faster wound closure while gain-of-function mice displayed slower wound closure compared to littermate controls. By imaging the spatiotemporal localization dynamics of endogenous PIEZO1 channels we find that channel enrichment in sub-cellular regions induces a localized cellular retraction that slows keratinocyte migration. Our findings suggest a potential pharmacological target for wound treatment. More broadly, we show that nanoscale spatiotemporal dynamics of Piezo1 channels can control tissue-scale events, a finding with implications beyond wound healing to processes as diverse as development, homeostasis, disease and repair.
High-resolution cryo-EM structure of photosystem II: Effects of electron beam damage
Authors: Kato Koji , Miyazaki Naoyuki , Hamaguchi Tasuku , Nakajima Yoshiki , Akita Fusamichi , Yonekura Koji , Shen Jian-Ren 
Published: October 2020

AbstractPhotosystem II (PSII) plays a key role in water-splitting and oxygen evolution. X-ray crystallography has revealed its atomic structure and some intermediate structures. However, these structures are in the crystalline state, and its final state structure has not been solved because of the low efficiencies of the S-state transitions in the crystals. Here we analyzed the structure of PSII in solution at 1.95 Å resolution by single-particle cryo-electron microscopy (cryo-EM). The structure obtained is similar to the crystal structure, but a PsbY subunit was visible in the cryo-EM structure, indicating that it represents its physiological state more closely. Electron beam damage was observed at a high-dose in the regions that were easily affected by redox states, which was reduced by reducing the electron dose. This study will serve as a good indicator for determining damage-free cryo-EM structures of not only PSII but also all biological samples, especially redox-active metalloproteins.
Tasmanian devil facial tumor-derived extracellular vesicles reveal mesenchymal transition markers and adhesion molecules related to metastasis
Authors: Espejo Camila , Wilson Richard , Woods Gregory M. , Willms Eduard , Hill Andrew F. , Lyons A. Bruce 
Published: October 2020

AbstractTasmanian devils are threatened with extinction by Devil Facial Tumor Disease (DFTD), which consists of two genetically independent transmissible cancers (DFT1 and DFT2). Both cancers typically cause death due to metastases. However, the mechanisms underpinning DFTD metastasis are not well understood. The nano-sized, membrane-enclosed extracellular vesicles (EVs) released by cancer cells have been implicated in metastasis, thus EVs may yield insights into DFTD metastasis. Here, we characterized EVs derived from cultured DFT1, DFT2, and devil fibroblast cells. The proteome of EVs was determined using data independent acquisition mass spectrometry and an in-house spectral library of >1,500 proteins. Relative to EVs from fibroblast cells, EVs from both DFT1 and DFT2 cell lines expressed higher levels of proteins associated with cell adhesion and focal adhesion functions. Furthermore, hallmark proteins of epithelial mesenchymal transition, which are associated with increased metastatic features in some cancers, were enriched in DFT2 EVs relative to DFT1 EVs, suggesting differential aggressiveness between the cancers and a target for novel differential diagnosis biomarkers. This first EV-based investigation of DFTD increases our understanding of the cancers’ EVs and their possible involvement in the metastatic process. As EVs are found in body fluids, these results offer potential for non-invasive biomarkers for DFTD.
MiRNA-223 Inhibits MouseGallstone Formation by Targeting Key Transporters in Hepatobiliary Cholesterol Secretion Pathway
Authors: Zhao Feng , Ma Shiyu , Shen Wei , Li Yanghao , Peng Zihe , Cui Xiaolin , Xing Lina , Li Xiang , Liu Gang , Jin Lingling , Ma Tonghui , Shi Lei 
Published: October 2020

AbstractBackgroudMiRNA-223 has previously been reported to play an essential role in hepatic cholesterol homeostasis by suppressing cholesterol synthesis, attenuating cholesterol uptake by hepatocyte from and promoting cholesterol efflux into the blood. However, its role in regulation of biliary cholesterol secretion and gallstone formation remains unknown.MethodsMice with conventional knockout (KO), hepatocyte-specific knockout (ΔHepa) / knockdown (KD) or gain expression of miRNA-223 were included in the study and were subjected to lithogenic diet (LD) for various weeks. The gallbladders were harvested and subjected to cholesterol crystal imaging and gallstone mass measurement. Liver tissues were collected for western blotting, RT-qPCR, and immunohistochemistry staining. Levels of cholesterol, bile salt, phospholipids, and triglyceride were determined in serum, liver tissues, and bile by enzyme color reactive assays. 3’ UTR reporter gene assays were used to verify the direct target genes for miRNA-223.ResultsLD-induced gallstone formation was remarkably accelerated in miRNA-223 KO, ΔHepa, and KD mice with concurrent enhancement in total cholesterol levels in liver tissue and bile. Key biliary cholesterol transporters ABCG5 and ABCG8 were identified as direct targets of miRNA-223. Reversely, AAV-mediated hepatocyte-specific miRNA-223 overexpression prevented gallstone progression with reduced targets protein expression.ConclusionThe present study demonstrates a novel role of miRNA-223 in the regulation of hepatic bile cholesterol secretion pathway and gallstone formation by targeting ABCG5 and ABCG8 expression. Therefore, elevating miRNA-223 would be a potentially novel approach to overcome the sternness of cholesterol gallstone disease.Graphical Abstract
Evolution of structural dynamics in bilobed proteins
Authors: Gouridis Giorgos , Muthahari Yusran A. , de Boer Marijn , Tassis Konstantinos , Tsirigotaki Alexandra , Zijlstra Niels , Eleftheriadis Nikolaos , Xu Ruixue , Zacharias Martin , Griffith Douglas A. , Sugijo Yovin , Dömling Alexander , Karamanou Spiridoula , Economou Anastasios , Cordes Thorben 
Published: October 2020

AbstractNovel biophysical tools allow the structural dynamics of proteins, and the regulation of such dynamics by binding partners, to be explored in unprecedented detail. Although this has provided critical insights into protein function, the means by which structural dynamics direct protein evolution remains poorly understood. Here, we investigated how proteins with a bilobed structure, composed of two related domains from the type-II periplasmic binding protein domain family, have undergone divergent evolution leading to modification of their structural dynamics and function. We performed a structural analysis of ~600 bilobed proteins with a common primordial structural core, which we complemented with biophysical studies to explore the structural dynamics of selected examples by single-molecule Förster resonance energy transfer and Hydrogen-Deuterium exchange mass spectrometry. We show that evolutionary modifications of the structural core, largely at its termini, enables distinct structural dynamics, allowing the diversification of these proteins into transcription factors, enzymes, and extra-cytoplasmic transport-related proteins. Structural embellishments of the core created new interdomain interactions that stabilized structural states, reshaping the active site geometry, and ultimately, altered substrate specificity. Our findings reveal an as yet unrecognized mechanism for the emergence of functional promiscuity during long periods of protein evolution and are applicable to a large number of domain architectures.
Phylogenetic placement of short reads without sequence alignment
Authors: Blanke Matthias , Morgenstern Burkhard 
Published: October 2020

AbstractPhylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them need a multiple alignment of the reference sequences as input. Most of them also need alignments of the query sequences to the multiple alignment of the reference sequences. A major field of application of phylogenetic placement is taxonomic read assignment in metagenomics.Herein, we proposeApp-SpaM, an efficient alignment-free algorithm for phylogenetic placement of short sequencing reads on a tree of a set of reference genomes.App-SpaMis based on theFiltered Spaced Word Matchesapproach that we previously developed. Unlike other methods, our approach neither requires a multiple alignment of the reference genomes, nor alignments of the queries to the reference sequences. Moreover,App-SpaMworks not only on assembled reference genomes, but can also take reference taxa as input for which only unassembled read sequences are available.The quality of the results achieved withApp-SpaMis comparable to the best available approaches to phylogenetic placement. However, sinceApp-SpaMis not based on sequence alignment, it is between one and two orders of magnitude faster than those existing methods.
DNA methylation-based sex classifier to predict sex and identify sex chromosome aneuploidy
Authors: Wang Yucheng , Hannon Eilis , Grant Olivia A , Gorrie-Stone Tyler J , Kumari Meena , Mill Jonathan , Zhai Xiaojun , McDonald-Maier Klaus D , Schalkwyk Leonard C 
Published: October 2020

AbstractSex is an important covariate of epigenome-wide association studies due to its strong influence on DNA methylation patterns across numerous genomic positions. Nevertheless, many samples on the Gene Expression Omnibus (GEO) frequently lack a sex annotation or are incorrectly labelled. Considering the influence that sex imposes on DNA methylation patterns, it is necessary to ensure that methods for filtering poor samples and checking of sex assignment are accurate and widely applicable. In this paper, we presented a novel method to predict sex using only DNA methylation density signals, which can be readily applied to almost all DNA methylation datasets of different formats (raw IDATs or text files with only density signals) uploaded to GEO. We identified 4345 significantly (p< 0.01) sex-associated CpG sites present on both 450K and EPIC arrays, and constructed a sex classifier based on the two first components of PCAs from the two sex chromosomes. The proposed method is constructed using whole blood samples and exhibits good performance across a wide range of tissues. We further demonstrated that our method can be used to identify samples with sex chromosome aneuploidy, this function is validated by five Turner syndrome cases and one Klinefelter syndrome case. The proposed method has been integrated into thewateRmelonBioconductor package.
The microbiota plays a critical role in the reactivity of lung immune components to innate ligands
Authors: Marquant Quentin , Laubreton Daphné , Drajac Carole , Mathieu Elliot , Bouguyon Edwige , Noordine Marie-Louise , Remot Aude , Riffault Sabine , Thomas Muriel , Descamps Delphyne 
Published: October 2020

AbstractThe microbiota contributes to shaping efficient and safe immune defenses in the gut. However, little is known about the role of the microbiota in the education of pulmonary innate immune responses. Here, we tested whether the endogenous microbiota can modulate reactivity of pulmonary tissue to pathogen stimuli by comparing the response of specific pathogen-free (SPF) and germ-free (GF) mice. Using SPF and GF mice intranasally exposed to lipopolysaccharide (LPS), a component of Gram-negative bacteria, we observed earlier and greater inflammation in the pulmonary compartment of GF mice than that of SPF mice. Toll-like receptor 4 (TLR4) was more abundantly expressed in the lungs of GF mice than those of SPF mice at steady state, which could predispose the innate immunity of GF mice to strongly react to environmental stimuli. Lung explants were stimulated with different TLR agonists or infected with the human airways pathogen, respiratory syncytial virus (RSV), resulting in greater inflammation under almost all conditions for the GF explants. Finally, alveolar macrophages (AM) from GF mice presented a higher innate immune response upon RSV infection than those of SPF mice. Overall, these data suggest that the presence of microbiota in SPF mice induced a process of innate immune tolerance in the lungs by a mechanism which remains to be elucidated. Our study represents a step forward to establishing the link between the microbiota and the immune reactivity of the lungs.Plain Language summaryMicrobiota represents an important partner of immunologic system at the interface between immune cells and epithelium. It is well known, notably in the gut, that the microbiota contributes in shaping efficient and safe defenses. However, little is known about the role of the microbiota in the education of pulmonary innate immune responses. In this study, we postulate that endogenous microbiota could dampen an excessive reactivity of pulmonary tissue to external stimuli. Thus, we sought to study the innate immune reaction switched on by viral or bacterial ligands in respiratory tract cells coming from mice with or without microbiota (germ-free condition, GF). Altogether, our results show a higher inflammatory reaction in GF condition. This study represents a step forward to better establish the link between the microbiota and the reactivity of the lung tissue. Not only these data demonstrate that the microbiota educates the pulmonary innate immune system, but also contributes the emerging concept of using respiratory commensal bacteria as potential next-generation probiotics to prevent susceptibility to respiratory diseases.
Near-cognate initiation generates FMRpolyG from CGG repeats in Fragile X associated Tremor Ataxia Syndrome
Authors: Zhang Yuan , Glineburg M. Rebecca , Basrur Venkatesha , Conlon Kevin , Hall Deborah A. , Todd Peter K. 
Published: October 2020

AbstractRepeat associated non-AUG (RAN) translation ofFMR15’ UTR CGG repeats produces toxic homo-polymeric proteins that accumulate within ubiquitinated inclusions in Fragile X-associated tremor/ataxia syndrome (FXTAS) patient brains and model systems. The most abundant RAN product, FMRpolyG, initiates predominantly at an ACG codon located just 5’ to the repeat. Methods to accurately measure FMRpolyG in FXTAS patients are lacking. Here we used data dependent acquisition (DDA) and parallel reaction monitoring (PRM) mass spectrometry coupled with stable isotope labeled standard peptides (SIS) to identify potential signature FMRpolyG fragments in patient cells and tissues. Following immunoprecipitation (IP) enrichment, we detected FMRpolyG signature peptides by PRM in transfected cells, FXTAS human samples and patient derived stem cells, but not in controls. Surprisingly, we identified two amino-terminal peptides: one beginning with methionine (Ac-MEAPLPGGVR) initiating at an ACG, and a second beginning with threonine (Ac-TEAPLPGGVR), initiating at a GUG. Abundance of the threonine peptide was enhanced relative to the methionine peptide upon activation of the integrated stress response. In addition, loss of the eIF2 alternative factor, eIF2A, or enhanced expression of initiation factor eIF1, preferentially suppressed GUG initiated FMRpolyG synthesis. These data demonstrate that FMRpolyG is quantifiable in human samples and that RAN translation onFMR1initiates at specific near cognate codons dependent on available initiation factors and cellular environment.
Glycosylphosphatidylinositol-anchoring is required for the proper transport and glycosylation of classical arabinogalactan protein precursor in tobacco BY-2 cells
Authors: Nagasato Daiki , Sugita Yuto , Tsuno Yuhei , Tanaka Rutsuko , Fukuda Maki , Matsuoka Ken 
Published: October 2020

AbstractArabinogalactan proteins (AGPs) are extracellular proteoglycans with many O-linked glycan chains. Precursors to many AGPs contain a C-terminal signal for the addition of a glycosylphosphatidylinositol(GPI)-anchor, but the role of this modification has not been elucidated. NtAGP1, a tobacco precursor to AGP, comprises a signal peptide, an AGP-coding region, and a GPI-anchoring signal, and it is classified as a member of the classical AGP family. Using green fluorescent protein (GFP) and sweet potato sporamin (SPO) as tags and tobacco BY-2 cells as the host, we analysed the transport and modification of NtAGP1. The fusion protein of GFP or SPO and NtAGP1 expressed in BY-2 cells migrated as a large smear on SDS-polyacrylamide gel. A confocal microscopic analysis indicated that the GFP and NtAGP1 fusion protein localized to the plasma membrane (PM) and intracellular structures. Fractionation studies of microsomes indicated that most of the fusion protein of SPO and NtAGP1 (SPO-AGP) localized to the PM. In contrast, the expression of mutants without a GPI-anchoring signal yielded several forms. The largest forms migrating as large smears on the gel were secreted into the culture medium, whereas other forms were recovered in the endomembrane organelles. A comparison of the glycan structures of the microsomal SPO-AGP and the secreted mutant SPO-AGP without a GPI-anchoring signal using antibodies against AGP glycan epitopes indicated that the glycan structures of these proteins differ. These observations indicate that a GPI-anchoring signal is required for both the proper transport and glycosylation of the AGP precursor.
Urbanization as taxidermy: “Man”hattanization of Mannahatta
Authors: Sadri Hossein 
Published: October 2020

PurposeThis article unveils the similarities of today's space production systems with taxidermy. Giving examples from the transformation of natural environment during the history of Mannahatta (Manhattan), the article discusses the process of metamorphosis of habitats and ecosystems to anthropocentric artificial objects.Design/methodology/approachReferencing Lefebvre, urbanization is conceptualized as the production of abstract space that ultimately stifles life; by analogy, space taxidermy.FindingsUsing the analogy of taxidermy and abstract space production processes, the article introduces the necessity and the principles of restoring natural habitats.Originality/valueRe-writing the urban and architectural history of Manhattan by focusing on four different scenes from its life-span, the article introduces a novel; a new narrative of the history of the city from the perspective of human-nature relations and the various ways habitats were shaped on this island during history.
The decision usefulness of reported changes in fair values and fair value measurement-related disclosure for debtholders: evidence from Australian real estate industry
Authors: Sangchan Pinprapa , Jiang Haiyan , Bhuiyan Md. Borhan Uddin 
Published: October 2020

PurposeThis paper aims to examine the information content of changes in fair values of investment property reported under international accounting standards (IAS) 40 and International Financial Reporting Standards (IFRS) 13 to debtholders. This study further examines the effect of fair value hierarchy inputs, valuer types and the quality of fair value measurement-related disclosure on the information usefulness of changes in fair value.Design/methodology/approachThis paper performs a panel regression on the cost of debt capital and changes in fair value of investment properties, and fair value measurement features using data covering periods 2007–2015 from Australian real estate companies.FindingsThe findings suggest that changes in fair value of investment property are informative about the real estate firm’s future cash flow to debtholders. Also, the findings show that the use of unobservable inputs in an active market (Level 3 inputs) and Level 2 has no different impacts on the cost of debts. Also, this paper documents that employing the directors solely in valuation may lead to a higher cost of debts. Furthermore, this paper reports that an extensive fair value disclosure appears no additional value in the debt decision.Originality/valueCollectively, the findings indicate that although the use of unobservable inputs is common in the real estate sector, information on the changes of the fair value of investment properties are informative to debtholders. The findings have important implications for accounting standard setters to consider revisiting the IAS 40 and IFRS 13 on whether the independent valuation should be required and whether the extensive disclosure requirement is worthwhile.
Barriers to development of private sector investment in water and sewage industry
Authors: Sarvari Hadi , Chan Daniel W.M. , Banaitiene Nerija , Noor Norhazilan Md , Beer Michael 
Published: October 2020

PurposePrivatization is a complex issue in many developing countries; therefore, it is vital to examine the obstacles that prevent its proper implementation. The goal of this study is to identify and analyze the barriers to private sector investment in the Water and Sewage Industry (WSI) and to suggest effective ways to attract the private investors to this sector.Design/methodology/approachThe obstacles to private sector investment in the WSI were identified by conducting a desktop literature review and interviewing an expert panel, using the fuzzy Delphi technique. The most important barriers were identified and categorized. A structured survey was then developed and distributed to private sector investment experts. The Fuzzy Analytic Hierarchy Process (FAHP) was applied to further examine the responses and to rank the identified barriers.FindingsThe results showed that the greatest barrier to privatization is the weakness of insurance companies in controlling investment risks, and the second greatest barrier is the weakness of the country's capitalist culture. A review of recent success stories revealed that these barriers can be overcome with transparent price policies and increased interaction between the public and private sectors, which motivate private investors to invest in the WSI.Originality/valueThe elicitation of this study can be useful to both private and public sectors for the development of infrastructure projects, particularly for the WSI.