bluuebunny/crossref_metadata_2025_split huggingface dataset:
Intrinsic and extrinsic factors collaborate to activate pharyngeal satellite cells without muscle injury
Authors: Kim Eunhye , Zhang Yiming , Wu Fang , Allen James , Vest Katherine E. , Choo Hyojung J. 
Published: May 2020

AbstractSatellite cells (SCs), adult muscle stem cells in craniofacial muscles proliferate and differentiate/fuse without injury, unlike quiescent SCs in uninjured limb muscle. However, whether intrinsic or extrinsic factors driving their increased basal activity are largely unknown. We compared SCs from the pharynx, which contains constrictor muscles critical for swallowing, to SCs from limb muscle. Pharyngeal SCs are intrinsically more proliferative and contain higher mitochondrial content relative to limb SCs. Pharyngeal SCs occupy less quiescent microenvironments containing collagen V and pharyngeal muscles provide a distinctive SC niche enriched with neighboring resident macrophages and fibroadipogenic progenitors. Loss of SCs impacts pharyngeal myofiber cross-sectional area and the number of neighboring cells, suggesting that SCs are required to maintain pharyngeal muscle homeostasis and its unique niche. Taken together, this study gives new insights to explain the distinctive SC activity of craniofacial muscles, which may explain their unique susceptibility to various muscular dystrophies.
XMAP215 and γ-tubulin additively promote microtubule nucleation in purified solutions
Authors: King Brianna R. , Moritz Michelle , Kim Haein , Agard David A. , Asbury Charles L. , Davis Trisha N. 
Published: May 2020

AbstractMicrotubule nucleation is spatiotemporally regulated in cells by several molecules, including the template γ-tubulin and the polymerase XMAP215. Recently, XMAP215 and the γ-tubulin ring complex were reported to function synergistically, and this synergy was hypothesized to be due to direct binding between XMAP215 and γ-tubulin. Here, we address this hypothesis by 1) probing domain requirements for XMAP215 to promote microtubule nucleation and 2) testing whether XMAP215 functions synergistically with γ-tubulin in the absence of the other ring complex proteins. We confirm that γ-tubulin and XMAP215 are classically defined nucleators that reduce the nucleation lag seen in bulk tubulin assembly. Then, using deletion constructs, we show that XMAP215’s ability to nucleate microtubules in purified solutions correlates with its ability to elongate existing microtubules and does not depend on the number of TOG domains. Finally, we show that XMAP215 and γ-tubulin promote αβ-tubulin assembly in an additive, not synergistic, manner. Thus, their modes of action during microtubule nucleation are distinct, and the synergy reported between XMAP215 and the γ-tubulin ring complex is not due to γ-tubulin alone.
Characterization of extracellular vesicles produced byAspergillus fumigatusprotoplasts
Authors: Rizzo Juliana , Chaze Thibault , Miranda Kildare , Roberson Robert W. , Gorgette Olivier , Nimrichter Leonardo , Matondo Mariette , Latgé Jean-Paul , Beauvais Anne , Rodrigues Marcio L. 
Published: May 2020

AbstractExtracellular vesicles (EVs) are outer membranous compartments produced by yeast and mycelial forms of several fungal species. One of the difficulties to perceive the role of EVs during the fungal life is the fact that an active secretion of these EVs has not been clearly demonstrated in situ due to the presence of a thick cell wall. One alternative to have a better access to these vesicles is to use protoplasts. This approach has been investigated here withAspergillus fumigatus, one of the most common opportunistic fungal pathogens worldwide. Analysis of regenerating protoplasts by scanning electron microscopy and fluorescence microscopy indicated the occurrence of outer membrane projections in association with surface components and the release of particles with properties resembling those of fungal EVs. EVs in culture supernatants were characterized by transmission electron microscopy and nanoparticle tracking analysis. Proteomic and glycome analysis of EVs revealed the presence of a complex array of enzymes related to lipid / sugar metabolism, pathogenic processes, and cell wall biosynthesis. Our data indicate that i) EV production is a common feature of different morphological stages of this major fungal pathogen, and ii) protoplastic EVs are a promising tool to undertake studies of vesicle functions in fungal cells.IMPORTANCEFungal cells use extracellular vesicles (EVs) to export biologically active molecules to the outer space. Since fungal cells are encaged in a thick cell wall, it is reasonable to expect that this structure might impact the vesicle-mediated molecular export. In this study, we used protoplasts ofAspergillus fumigatus, a major fungal pathogen, as a model to evaluate EV production in the absence of a cell wall. Our results demonstrated that wall-lessA. fumigatusexports plasma membrane-derived EVs containing a complex combination of proteins and glycans. Our study is the first to characterize fungal EVs in the absence of a cell wall. Our results suggest that protoplasts are a promising model for functional studies of fungal vesicles.
Cadherin Clusters Stabilized by a Combination of Specific and Nonspecific Cis-Interactions
Authors: Thompson Connor J. , Su Zhaoqian , Vu Vinh H. , Wu Yinghao , Leckband Deborah E. , Schwartz Daniel K. 
Published: May 2020

AbstractWe demonstrate a combined experimental and computational approach for the quantitative characterization of lateral interactions between membrane-associated proteins. In particular, weak, lateral (cis) interactions between E-cadherin extracellular domains tethered to supported lipid bilayers, were studied using a combination of dynamic single-molecule Förster Resonance Energy Transfer (FRET) and kinetic Monte Carlo (kMC) simulations. Cadherins are intercellular adhesion proteins that assemble into clusters at cell-cell contacts through cis- and trans- (adhesive) interactions. A detailed and quantitative understanding of cis-clustering has been hindered by a lack of experimental approaches capable of detecting and quantifying lateral interactions between proteins on membranes. Here single-molecule intermolecular FRET measurements of wild-type E-cadherin and cis-interaction mutants combined with simulations demonstrate that both nonspecific and specific cis-interactions contribute to lateral clustering on lipid bilayers. Moreover, the intermolecular binding and dissociation rate constants are quantitatively and independently determined, demonstrating an approach that is generalizable for other interacting proteins.
Compromised nuclear envelope integrity drives tumor cell invasion
Authors: Nader Guilherme P.F. , Agüera-Gonzalez Sonia , Routet Fiona , Gratia Matthieu , Maurin Mathieu , Cancila Valeria , Cadart Clotilde , Gentili Matteo , Yamada Ayako , Lodillinsky Catalina , Lagoutte Emilie , Villard Catherine , Viovy Jean-Louis , Tripodo Claudio , Scita Giorgio , Manel Nicolas , Chavrier Philippe , Piel Matthieu 
Published: May 2020

AbstractWhile mutations leading to a fragile envelope of the cell nucleus are well known to cause diseases such as muscular dystrophies or accelerated aging, the pathophysiological consequences of the recently discovered mechanically induced nuclear envelope ruptures in cells harboring no mutation are less known. Here we show that repeated loss of nuclear envelope integrity in nuclei experiencing mechanical constraints promotes senescence in nontransformed cells, and induces an invasive phenotype including increased collagen degradation in human breast cancer cells, bothin vitroand in a mouse xenograft model of breast cancer progression. We show that these phenotypic changes are due to the presence of chronic DNA damage and activation of the ATM kinase. In addition, we found that depletion of the cytoplasmic exonuclease TREX1 is sufficient to abolish the DNA damage in mechanically challenged nuclei and to suppress the phenotypes associated with the loss of nuclear envelope integrity. Our results also show that TREX1-dependent DNA damage induced by physical confinement of tumor cells inside the mammary duct drives the progression ofin situbreast carcinoma to the invasive stage. We propose that DNA damage in mechanically challenged nuclei could affect the pathophysiology of crowded tissues by modulating proliferation and extracellular matrix degradation of normal and transformed cells.
Improvements on marker-free images alignment for electron tomography
Authors: Sorzano C.O.S. , de Isidro-Gómez F. , Fernández-Giménez E. , Herreros D. , Marco S. , Carazo J.M. , Messaoudi C. 
Published: May 2020

AbstractElectron tomography is a technique to obtain three-dimensional structural information of samples. However, the technique is limited by shifts occurring during acquisition that need to be corrected before the reconstruction process. In 2009, we proposed an approach for post-acquisition alignment of tilt series images. This approach was marker-free, based on patch tracking and integrated in free software. Here, we present improvements to the method to make it more reliable, stable and accurate. In addition, we modified the image formation model underlying the alignment procedure to include different deformations occurring during acquisition. We propose a new way to correct these computed deformations to obtain reconstructions with reduced artifacts. The new approach has demonstrated to improve the quality of the final 3D reconstruction, giving access to better defined structures for different transmission electron tomography methods: resin embedded STEM-tomography and cryo-TEM tomography. The method is freely available in TomoJ software.
Use of the Polo-like kinase 4 (PLK4) inhibitor centrinone to investigate intracellular signaling networks using SILAC-based phosphoproteomics
Authors: Byrne Dominic P , Clarke Christopher J , Brownridge Philip J , Kalyuzhnyy Anton , Perkins Simon , Campbell Amy , Mason David , Jones Andrew R , Eyers Patrick A , Eyers Claire E 
Published: May 2020

ABSTRACTPolo-like kinase 4 (PLK4) is the master regulator of centriole duplication in metazoan organisms. Catalytic activity and protein turnover of PLK4 are tightly coupled in human cells, since changes in PLK4 concentration and catalysis have profound effects on centriole duplication and supernumerary centrosomes, which are associated with aneuploidy and cancer. Recently, PLK4 has been targeted with a variety of small molecule kinase inhibitors exemplified by centrinone, which rapidly induces inhibitory effects on PLK4 and leads to on-target centrosome depletion. Despite this, relatively few PLK4 substrates have been identified unequivocally in human cells, and PLK4 signaling outside centriolar networks remains poorly characterised. We report an unbiased mass spectrometry (MS)-based quantitative analysis of cellular protein phosphorylation in stable PLK4-expressing U2OS human cells exposed to centrinone. PLK4 phosphorylation was itself sensitive to brief exposure to the compound, resulting in PLK4 stabilization. Analysing asynchronous cell populations, we report hundreds of centrinone-regulated cellular phosphoproteins, including centrosomal and cell cycle proteins and a variety of likely ‘non-canonical’ substrates. Surprisingly, sequence interrogation of ~300 significantly down-regulated phosphoproteins reveals an extensive network of centrinone-sensitive [Ser/Thr]Pro phosphorylation sequence motifs, which based on our analysis might be either direct or indirect targets of PLK4. In addition, we confirm that NMYC and PTPN12 are PLK4 substrates, bothin vitroand in human cells. Our findings suggest that PLK4 catalytic output directly controls the phosphorylation of a diverse set of cellular proteins, including Pro-directed targets that are likely to be important in PLK4-mediated cell signaling.
Defective Trafficking of Annexins to the Site of Injury in ANO5-Knockout Muscle Fibers
Authors: Foltz Steven J. , Cui YuanYuan , Choo Hyojung J. , Hartzell H. Criss 
Published: May 2020

AbstractMutations inANO5(TMEM16E) cause limb-girdle muscular dystrophy R12 (limb-girdle muscular dystrophy type 2L). Recent evidence implicates defective plasma membrane repair as a likely mechanism for the disorder. Here, we probe the ANO5-dependency of the membrane repair pathway using a laser wounding assay inAno5knockout mouse muscle fibers. Wounded myofibers fromAno5knockout mice exhibit delayed membrane resealing relative to wild type fibers as revealed by an increased uptake of the membrane-impermeant FM1-43 dye and a prolonged elevation of intracellular Ca2+. The trafficking of several annexin proteins, which together form a cap at the site of injury, is altered inAno5knockout fibers. Annexin A2 accumulates at the wound to nearly twice the level observed in WT fibers, while annexin A6 accumulation is substantially inhibited in the absence of ANO5. Furthermore, trafficking of annexins A1 and A5 to the cap is decreased in theAno5knockout. These changes are correlated with an alteration in the fine structure of the annexin repair cap and the shedding of annexin-positive extracellular vesicles. Our results suggest that the meticulous coordination of the annexin repair machinery required to effectively reseal wounded sarcolemma is disrupted inAno5knockout mice. ANO5 is a putative phospholipid scramblase, responsible for exposure of intracellular phospholipids to the extracellular leaflet of the plasma membrane. However, because the membrane repair defect is rescued by overexpression of wild type ANO5 or a scramblase-defective mutant, we suggest that ANO5-mediated phospholipid scrambling is not essential for membrane repair.Significance StatementMutations inANO5/TMEM16Ecause myopathies of variable severity, with some patients losing ambulation entirely. Unfortunately, relatively little is known about the function of ANO5 at the protein level, but it has been suggested that ANO5 plays a role in the repair of injured muscle plasma membranes. Here, we investigate the mechanism of ANO5-mediated repair and find that annexin proteins, which in normal muscle form a cap to seal wounds, traffic abnormally to the cap when ANO5 is not expressed. Muscle fibers lacking ANO5 reseal more slowly and thus are exposed to prolonged intracellular calcium elevation that can damage the fibers. Our findings contribute to the growing literature implicating failed repair as a probable pathogenic mechanism in patients withANO5mutations.
Intravital imaging reveals cell cycle-dependent satellite cell migration during muscle regeneration
Authors: Konagaya Yumi , Takakura Kanako , Sogabe Maina , Bisaria Anjali , Liu Chad , Meyer Tobias , Sehara-Fujisawa Atsuko , Matsuda Michiyuki , Terai Kenta 
Published: May 2020

AbstractDuring muscle regeneration, extracellular signal-regulated kinase (ERK) promotes both proliferation and migration. However, the relationship between proliferation and migration is poorly understood in this context. To elucidate this complex relationship on a physiological level, we established an intravital imaging system for measuring ERK activity, migration speed, and cell-cycle phases in mouse muscle satellite cells. We found thatin vivo, ERK was maximally activated in satellite cells two days after injury, and this is then followed by increases in cell number and motility. With limited effects of immediate ERK activity on migration, we hypothesized that ERK increases migration speed in the later phase by promoting cell-cycle progression. Our cell-cycle analysis further revealed that in satellite cells, ERK activity is critical for the G1/S transition, and cells migrate more rapidly in the S/G2 phase three days after injury. Finally, migration speed of satellite cells was suppressed after CDK1/2, but not CDK1, inhibitor treatment, demonstrating a critical role of CDK2 in satellite cell migration. Overall, our study demonstrates that in satellite cells, the ERK-CDK2 axis not only promotes the G1/S transition, but also migration speed, which may provide a novel mechanism for efficient muscle regeneration.
Learning What a Good Structural Variant Looks Like
Authors: Chowdhury Murad , Layer Ryan M. 
Published: May 2020

AbstractStructural variations (SVs) are an important class of genetic mutations, yet SV detectors still suffer from high false-positive rates. In many cases, humans can quickly determine whether a putative SV is real by merely looking at a visualization of the SV’s coverage profile. To that end, we developed Samplot-ML, a convolutional neural network (CNN) trained to genotype genomic deletions using Samplot visualizations that incorporate various forms of evidence such as genome coverage, discordant pairs, and split reads. Using Samplot-ML, we were able to reduce false positives by 47% while keeping 97% of true positives on average across several test samples.
NTR 2.0: a rationally-engineered prodrug converting enzyme with substantially enhanced efficacy for targeted cell ablation
Authors: Sharrock Abigail V. , Mulligan Timothy S. , Hall Kelsi R. , Williams Elsie M. , White David T. , Zhang Liyun , Matthews Frazer , Nimmagadda Saumya , Washington Selena , Le Katherine , Meir-Levi Danielle , Cox Olivia L. , Saxena Meera T. , Calof Anne L. , Lopez-Burks Martha E. , Lander Arthur D. , Ding Ding , Ji Hongkai , Ackerley David F. , Mumm Jeff S. 
Published: May 2020

ABSTRACTHeterologously-expressed bacterial nitroreductase (NTR) enzymes sensitize eukaryotic cells to prodrugs such as metronidazole (MTZ), enabling selective cell ablation paradigms that have expanded studies of cell function and regeneration in vertebrate systems. However, first-generation NTRs require confoundingly toxic prodrug treatments (e.g. 10 mM MTZ) and some cell types have proven resistant. We used rational engineering and cross-species screening to develop a NTR variant, NTR 2.0, which exhibits ~100-fold improvement in MTZ-mediated cell-specific ablation efficacy. Toxicity tests in zebrafish showed no deleterious effects of prolonged MTZ treatments of ≤1 mM. NTR 2.0 therefore enables sustained cell loss paradigms and ablation of previously resistant cell types. These properties permit enhanced interrogations of cell function, extended challenges to the regenerative capacities of discrete stem cell niches, and enable modeling of chronic degenerative diseases. Accordingly, we have created a series of bipartite transgenic resources to facilitate dissemination of NTR 2.0 to the research community.
Clustering method for spread pattern analysis of corona-virus (COVID-19) infection in Iran
Authors: Azarafza Mehdi , Azarafza Mohammad , Akgün Haluk 
Published: May 2020

AbstractThe COVID-19 is outbreak from China and infected more than 131,652 people and caused 7,300 deaths in Iran. Unfortunately, the infection numbers and deaths are still increasing rapidly which has put the world on the catastrophic abyss edge. Application of data mining to perform pattern recognition of infection is mainly used for peparing the spread mapping which considred in this work for spatiotemporal distribution assessment and spread pattern analysis of corona-virus (COVID-19) infection in Iran.
High-Throughput Human Primary Cell-Based Airway Model for Evaluating Influenza, Coronavirus, or other Respiratory Virusesin vitro
Authors: Gard A.L. , Maloney R. , Cain B.P. , Miller C.R. , Luu R.J. , Coppeta J.R. , Liu P. , Wang J.P. , Azizgolshani H. , Fezzie R.F. , Balestrini J.L. , Isenberg B.C. , Finberg R.W. , Borenstein J.T. 
Published: May 2020

AbstractInfluenza and other respiratory viruses represent a significant threat to public health, national security, and the world economy, and can lead to the emergence of global pandemics such as the current COVID-19 crisis. One of the greatest barriers to the development of effective therapeutic agents to treat influenza, coronaviruses, and many other infections of the respiratory tract is the absence of a robust preclinical model. Preclinical studies currently rely on high-throughput, low-fidelityin vitroscreening with cell lines and/or low-throughput animal models that often provide a poor correlation to human clinical responses. Here, we introduce a human primary airway epithelial cell-based model integrated into a high-throughput platform where tissues are cultured at an air-liquid interface (PREDICT96-ALI). We present results on the application of this platform to influenza and coronavirus infections, providing multiple readouts capable of evaluating viral infection kinetics and potentially the efficacy of therapeutic agents in anin vitrosystem. Several strains of influenza A virus are shown to successfully infect the human primary cell-based airway tissue cultured at an air-liquid interface (ALI), and as a proof-of-concept, the effect of the antiviral oseltamivir on one strain of Influenza A is evaluated. Human coronaviruses NL63 (HCoV-NL63) and SARS-CoV-2 enter host cells via ACE2 and utilize the protease TMPRSS2 for protein priming, and we confirm expression of both in our ALI model. We also demonstrate coronavirus infection in this system with HCoV-NL63, observing sufficient viral propagation over 96 hours post-infection to indicate successful infection of the primary cell-based model. This new capability has the potential to address a gap in the rapid assessment of therapeutic efficacy of various small molecules and antiviral agents against influenza and other respiratory viruses including coronaviruses.
TuNR: Orthogonal Control of Mean and Variability of Endogenous Genes in a Human Cell Line
Authors: Bonny Alain R. , Fonseca João Pedro , Park Jesslyn E. , El-Samad Hana 
Published: May 2020

AbstractStochastic fluctuations at the transcriptional level contribute to isogenic cell-to-cell heterogeneity in mammalian cell populations. However, we still have no clear understanding of the repercussions of this heterogeneity, given the lack of tools to independently control mean expression and variability of a gene. Here, we engineered a synthetic circuit to independently modulate mean expression and heterogeneity of transgenes and endogenous human genes. The circuit, a Tunable Noise Rheostat (TuNR), consists of a transcriptional cascade of two inducible transcriptional activators, where the output mean and variance can be modulated by two orthogonal small molecule inputs. In this fashion, different combinations of the inputs can achieve the same mean but with different population variability. With TuNR, we achieve low basal expression, over 1000-fold expression of a transgene product, and up to 7-fold induction of the endogenous geneNGFR. Importantly, for the same mean expression level, we are able to establish varying degrees of heterogeneity in expression within an isogenic population, thereby decoupling gene expression noise from its mean. TuNR is therefore a modular tool that can be used in mammalian cells to enable direct interrogation of the implications of cell-to-cell variability.
Editorial: increasing burden of nonalcoholic fatty liver disease—a call to action
Authors: Chuah Kee‐Huat , Chan Wah‐Kheong 
Published: May 2020

LINKED CONTENTThis article is linked to Estes et al papers. To view these articles, visit https://doi.org/10.1111/apt.15673 and https://doi.org/10.1111/apt.15718.
Letter: how can we reduce mortality in elderly patients with acute severe ulcerative colitis?
Authors: Li Wai Suen Christopher F.D. , Choy Matthew C. , De Cruz Peter 
Published: May 2020

LINKED CONTENTThis article is linked to Dong et al papers. To view these articles, visit https://doi.org/10.1111/apt.15592 and https://doi.org/10.1111/apt.15776.
Editorial: increasing burden of nonalcoholic fatty liver disease—a call to action. Authors' reply
Authors: Estes Chris , Chan Henry L. Y. , Chien Rong N. , Chuang Wan‐Long , Fung James , Goh George Boon‐Bee , Hu Tsung H. , Huang Jee‐Fu , Jang Byoung K. , Jun Dae W. , Kao Jia H. , Lee Jin‐Woo , Lin Han‐Chieh , Razavi‐Shearer Kathryn , Seto Wai‐Kay , Wong Grace L.‐H. , Wong Vincent W.‐S. , Razavi Homie 
Published: May 2020

LINKED CONTENTThis article is linked to Estes et al and Chuah and Chan papers. To view these articles, visit https://doi.org/10.1111/apt.15673 and https://doi.org/10.1111/apt.15700.