bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single-cell resolution unravels spatial alterations in metabolism, transcriptome and epigenome of ageing liver
Authors: Nikopoulou Chrysa , Kleinenkuhnen Niklas , Parekh Swati , Sandoval Tonantzi , Schneider Farina , Giavalisco Patrick , Bozukova Mihaela , Vesting Anna Juliane , Altmüller Janine , Wunderlich Thomas , Kondylis Vangelis , Tresch Achim , Tessarz Peter 
Published: December 2021

ABSTRACTEpigenetic ageing clocks have revealed that tissues within an organism can age with different velocity. However, it has not been explored whether cells of one type experience different ageing trajectories within a tissue depending on their location. Here, we employed lipidomics, spatial transcriptomics and single-cell ATAC-seq in conjunction with available single-cell RNA-seq data to address how cells in the murine liver are affected by age-related changes of the microenvironment. Integration of the datasets revealed zonation-specific and age-related changes in metabolic states, the epigenome and transcriptome. Particularly periportal hepatocytes were characterized by decreased mitochondrial function and strong alterations in the epigenetic landscape, while pericentral hepatocytes – despite accumulation of large lipid droplets – did not show apparent functional differences. In general, chromatin alterations did not correlate well with transcriptional changes, hinting at post-transcriptional processes that shape gene expression during ageing. Together, we provide evidence that changing microenvironments within a tissue exert strong influences on their resident cells that can shape epigenetic, metabolic and phenotypic outputs.
NAD+capping of RNA in Archaea and Mycobacteria
Authors: Ruiz-Larrabeiti Olatz , Benoni Roberto , Zemlianski Viacheslav , Hanišáková Nikola , Schwarz Marek , Brezovská Barbora , Benoni Barbora , Hnilicová Jarmila , Kaberdin Vladimir R. , Cahová Hana , Vítězová Monika , Převorovský Martin , Krásný Libor 
Published: December 2021

ABSTRACTChemical modifications of RNA affect essential properties of transcripts, such as their translation, localization and stability. 5’-end RNA capping with the ubiquitous redox cofactor nicotinamide adenine dinucleotide (NAD+) has been discovered in organisms ranging from bacteria to mammals. However, the hypothesis that NAD+capping might be universal in all domains of life has not been proven yet, as information on this RNA modification is missing for Archaea. Likewise, this RNA modification has not been studied in the clinically importantMycobacteriumgenus. Here, we demonstrate that NAD+capping occurs in the archaeal and mycobacterial model organismsMethanosarcina barkeriandMycobacterium smegmatis.Moreover, we identify the NAD+-capped transcripts inM. smegmatis,showing that this modification is more prevalent in stationary phase, and revealing that mycobacterial NAD+-capped transcripts include non-coding small RNAs, such as Ms1. Furthermore, we show that mycobacterial RNA polymerase incorporates NAD+into RNA, and that the genes of NAD+-capped transcripts are preceded by promoter elements compatible with σA/σFdependent expression. Taken together, our findings demonstrate that NAD+capping exists in the archaeal domain of life, suggesting that it is universal to all living organisms, and define the NAD+-capped RNA landscape in mycobacteria, providing a basis for its future exploration.
Cell polarity determinant Dlg1 facilitates epithelial invagination by promoting tissue-scale mechanical coordination
Authors: Fuentes Melisa A. , He Bing 
Published: December 2021

AbstractEpithelial folding mediated by apical constriction serves as a fundamental mechanism to convert flat epithelial sheets into multilayered structures. It remains elusive whether additional mechanical inputs are required for folding mediated by apical constriction. Using Drosophila mesoderm invagination as a model, we identified an important role for the non-constricting, lateral mesodermal cells adjacent to the constriction domain (“flanking cells”) in facilitating epithelial folding. We found that depletion of the basolateral determinant, Dlg1, disrupts the transition between apical constriction and invagination without affecting the rate of apical constriction. Strikingly, the observed delay in invagination is associated with ineffective apical myosin contractions in the flanking cells that lead to overstretching of their apical domain. The defects in the flanking cells impede ventral-directed movement of the lateral ectoderm, suggesting reduced mechanical coupling between tissues. Specifically disrupting the flanking cells in wildtype embryos by laser ablation or optogenetic depletion of cortical actin is sufficient to delay the apical constriction-to-invagination transition. Our findings indicate that effective mesoderm invagination requires intact flanking cells and suggest a role for tissue-scale mechanical coupling during epithelial folding.
Degradation-driven protein level oscillation in the yeast Saccharomyces cerevisiae
Authors: Mahrou Bahareh , Pirhanov Azady , Alijanvand Moluk Hadi , Cho Yong Ku , Shin Yong-Jun 
Published: December 2021

AbstractGenerating robust, predictable perturbations in cellular protein levels will advance our understanding of protein function and enable the control of physiological outcomes in biotechnology applications. Timed periodic changes in protein levels play a critical role in the cell division cycle, cellular stress response, and development. Here we report the generation of robust protein level oscillations by controlling the protein degradation rate in the yeast Saccharomyces cerevisiae. Using a photo-sensitive degron and red fluorescent proteins as reporters, we show that under constitutive transcriptional induction, repeated triangular protein level oscillations as fast as 5-10 minute-scale can be generated by modulating the protein degradation rate. Consistent with oscillations generated though transcriptional control, we observed a continuous decrease in the magnitude of oscillations as the input modulation frequency increased, indicating low-pass filtering of input perturbation. By using two red fluorescent proteins with distinct maturation times, we show that the oscillations in protein level is largely unaffected by delays originating from functional protein formation. Our study demonstrates the potential for repeated control of protein levels by controlling the protein degradation rate without altering the transcription rate.
Revisiting the Role of Notch in Nephron Segmentation: Notch is Required for Proximal, Not Distal Fate Selection During Mouse and Human Nephrogenesis
Authors: Duvall Kathryn , Bice Lauren , Perl Alison J. , Shakked Naomi Pode , Chaturvedi Praneet , Kopan Raphael 
Published: December 2021

AbstractNotch signaling promotes maturation of nephron epithelia, but its proposed contribution to nephron segmentation into proximal and distal domains has been called into doubt. We leveraged single cell and bulk RNA-seq, quantitative immunofluorescent lineage/fate tracing, and genetically modified human iPSC to revisit this question in developing mouse kidneys and human kidney organoids. We confirmed that Notch signaling is needed for maturation of all nephron lineages, and thus mature lineage markers fail to detect a fate bias. By contrast, early markers identified a distal fate bias in cells lacking Notch2, and a concomitant increase in early proximal and podocyte fates in cells expressing hyperactive Notch1 was observed. Orthogonal support for a conserved role for Notch signaling in the distal/proximal axis segmentation is provided by the ability of Nicastrin-deficient hiPSCs-derived organoids to differentiate into TFA2B+ distal tubule and CDH1 connecting segment progenitors, but not into HNF4A+ or LTL+ proximal progenitors.SummaryNotch signaling acts in nephron segmentation to select early proximal, but not distal tubule fate downstream of a global role promoting epithelial growth and maturation in mouse and human.
Physiochemically distinct SU-8 surfaces tailor Xylella fastidiosa cell-surface holdfast and colonization
Authors: Anbumani Silambarasan , da Silva Aldeliane M. , Alaferdov Andrei , Puydinger dos Santos Marcos V. , Carvalho Isis G. B. , de Souza e Silva Mariana , Moshkalev Stanislav , Carvalho Hernandes F. , de Souza Alessandra A. , Cotta Monica A. 
Published: December 2021

AbstractSU-8 polymer is an excellent platform for diverse applications due to its high aspect ratio of micro/nanostructures fabrication and exceptional optical, chemical, and biocompatible properties. Although SU-8 has been often investigated for a variety of biological applications, how its surface properties influence both the interaction of bacterial cells with the substrate and its colonization is poorly understood. In this work, we tailor SU-8 nanoscale surface properties to investigate single cell motility, adhesion and successive colonization of a phytopathogenic bacteria, Xylella fastidiosa. Different surface properties of SU-8 thin films have been prepared using photolithography processing and oxygen plasma treatment. We found a significant difference in bacterial cell behavior and subsequent colonization on SU-8 as surface property changes. A larger density of carboxyl groups in hydrophilic plasma-treated SU-8 surfaces promotes faster cell motility in the earlier stage of the growth. The hydrophobic nature of pristine SU-8 surfaces has no trackable bacterial motility with 5 to 10 times more single cells adhered to surface than its plasma-treated counterpart. In fact, plasma-treated SU-8 samples suppressed bacterial adhesion, with surfaces showing less than 5% coverage. These results not only showcase that SU-8 surface properties can impact the bacterial behavior in a spatiotemporal manner, but also provide insights on the prominent ability of pathogens to evolve and adapt to different surface properties.
The intrarenal renin-angiotensin system in hypertension: Insights from mathematical modelling
Authors: Smith Delaney , Layton Anita 
Published: December 2021

AbstractThe renin-angiotensin system (RAS) plays a pivotal role in the maintenance of volume homeostasis and blood pressure. In addition to the well-studied systemic RAS, local RAS have been documented in various tissues, including the kidney. Given the role of the intrarenal RAS in the pathogenesis of hypertension, a role established via various pharmacologic and genetic studies, substantial efforts have been made to unravel the processes that govern intrarenal RAS activity. In particular, several mechanisms have been proposed to explain the rise in intrarenal angiotensin II (Ang II) that accompanies Ang II infusion, including increased angiotensin type 1 receptor (AT1R)-mediated uptake of Ang II and enhanced intrarenal Ang II production. However, experimentally isolating their contribution to the intrarenal accumulation of Ang II in Ang II–induced hypertension is challenging, given that they are fundamentally connected. Computational modelling is advantageous because the feedback underlying each mechanism can removed and the effect on intrarenal Ang II can be studied. In this work, the mechanisms governing the intrarenal accumulation of Ang II during Ang II infusion experiments are delineated and the role of the intrarenal RAS in Ang II-induced hypertension is studied. To accomplish this, a compartmental ODE model of the systemic and intrarenal RAS is developed and Ang II infusion experiments are simulated. Simulations indicate that AT1Rmediated uptake of Ang II is the primary mechanism by which Ang II accumulates in the kidney during Ang II infusion. Enhanced local Ang II production is unnecessary. The results demonstrate the role of the intrarenal RAS in the pathogenesis of Ang II-induced hypertension and consequently, clinical hypertension associated with an overactive RAS.
Retinoic acid signaling mediates peripheral cone photoreceptor survival in a mouse model of retina degeneration
Authors: Amamoto Ryoji , Wallick Grace K. , Cepko Constance L. 
Published: December 2021

ABSTRACTRetinitis Pigmentosa (RP) is a wide array of progressive, debilitating visual disorders caused by mutations in a diverse set of genes. In both human patients and mouse models of RP, rod photoreceptor dysfunction leads to loss of night vision, and is followed by secondary cone photoreceptor dysfunction and degeneration, leading to loss of daylight color vision. A strategy to prevent secondary cone death could provide a generalized RP therapy to preserve daylight color vision regardless of the underlying mutation. In mouse models of RP, cones in the far peripheral retina survive long-term, despite complete rod loss. The mechanism for such peripheral cone survival had not been explored. Here, we found that active retinoic acid (RA) signaling in peripheral Muller glia is both sufficient and necessary for the extended cone survival. RA depletion by conditional knockout of RA synthesis enzymes, or overexpression of an RA degradation enzyme, abrogated peripheral cone survival. Conversely, constitutive activation of RA signaling in the central retina promoted long-term cone survival. These results indicate that RA signaling mediates the prolonged peripheral cone survival in the rd1 mouse model of retinal degeneration, and provide a basis for a generic strategy for cone survival in the many diseases that lead to loss of cone-mediated vision.
Development and Characterization of Recombinant Vesicular Stomatitis Virus (rVSV)-based Bivalent Vaccine Against COVID-19 Delta Variant and Influenza Virus
Authors: Ao Zhujun , Jing Ouyang Maggie , Olukitibi Titus Abiola , Warner Bryce , Vendramelli Robert , Truong Thang , Zhang Manli , Kung Sam , Fowke Keith R , Kobasa Darwyn , Yao Xiaojian 
Published: December 2021

AbstractCOVID-19 and influenza are both highly contagious respiratory diseases with a wide range of severe symptoms and cause great disease burdens globally. It has become very urgent and important to develop a bivalent vaccine that is able to target these two infectious diseases simultaneously. In this study, we generated three attenuated replicating recombinant VSV (rVSV) vaccine candidates. These rVSV-based vaccines co-express SARS-CoV-2 Delta variant spike protein (SP) or the receptor binding domain (RBD) and four copies of the highly conserved M2 ectodomain (M2e) of influenza A fused with the Ebola glycoprotein DC-targeting/activation domain. Animal studies have shown that immunization with these bivalent rVSV vaccines induced efficient but variable levels of humoral and cell-mediated immune responses against both SARS-CoV-2 and influenza M2e protein. Significantly, our vaccine candidates induced production of high levels of neutralizing antibodies that protected cells against SARS-CoV-2 Delta and other SP-pseudovirus infections in culture. Furthermore, vaccination with the bivalent VSV vaccine via either intramuscular or intranasal route efficiently protected mice from the lethal challenge of H1N1 and H3N2 influenza viruses and significantly reduced viral load in the lungs. These studies provide convincing evidence for the high efficacy of this bivalent vaccine to prevent influenza replication and initiate robust immune responses against SARS-CoV-2 Delta variants. Further investigation of its efficacy to protect against SARS-CoV-2 Delta variants will provide substantial evidence for new avenues to control two contagious respiratory infections, COVID-19 and influenza.
SARS-CoV-2 Spike protein activates TMEM16F-mediated platelet pro-coagulant activity
Authors: Cappelletto Ambra , Allan Harriet E. , Crescente Marilena , Schneider Edoardo , Bussani Rossana , Ali Hashim , Secco Ilaria , Vodret Simone , Simeone Roberto , Mascaretti Luca , Zacchigna Serena , Warner Timothy D. , Giacca Mauro 
Published: December 2021

ABSTRACTBackgroundThrombosis of the lung micro-vasculature is a characteristic of COVID-19 disease, which is observed in large excess compared to other forms of acute respiratory distress syndrome and thus suggests a trigger for thrombosis endogenous to the lung. Our recent work has shown that the SARS-CoV-2 Spike protein activates the cellular TMEM16F chloride channel and scramblase. Through a screening on >3,000 FDA/EMA approved drugs, we identified Niclosamide and Clofazimine as the most effective molecules at inhibiting this activity. As TMEM16F plays an important role in the stimulation of the pro-coagulant activity of platelets, and considering that platelet abnormalities are common in COVID-19 patients, we investigated whether Spike directly affects platelet activation and pro-thrombotic function and tested the effect of Niclosamide and Clofazimine on these processes.MethodsWe produced SARS-CoV-2 Spike or VSV-G protein-pseudotyped virions, or generated cells expressing Spike on their plasma membrane, and tested their effects on platelet adhesion (fluorescence), aggregation (absorbance), exposure of phosphatidylserine (flow cytometry for annexin V binding), calcium flux (flow cytometry for fluo-4 AM), and clot formation and retraction. These experiments were also conducted in the presence of the TMEM16F activity inhibitors Niclosamide and Clofazimine.ResultsHere we show that exposure to SARS-CoV-2 Spike promotes platelet activation, adhesion and spreading, both when present on the envelope of virions or upon expression on the plasma membrane of cells. Spike was effective both as a sole agonist or by enhancing the effect of known platelet activators, such as collagen and collagen-related peptide. In particular, Spike exerted a noticeable effect on the procoagulant phenotype of platelets, by enhancing calcium flux, phosphatidylserine externalisation, and thrombin generation. Eventually, this resulted in a striking increase in thrombin-induced clot formation and retraction. Both Niclosamide and Clofazimine almost abolished this Spike-induced pro-coagulant response.ConclusionsTogether, these findings provide a pathogenic mechanism to explain thrombosis associated to COVID-19 lung disease, by which Spike present in SARS-CoV-2 virions or exposed on the surface of infected cells, leads to local platelet stimulation and subsequent activation of the coagulation cascade. As platelet TMEM16F is central in this process, these findings reinforce the rationale of repurposing drugs targeting this protein, such as Niclosamide, for COVID-19 therapy.
Qualifying a human Liver-Chip for predictive toxicology: Performance assessment and economic implications
Authors: Ewart Lorna , Apostolou Athanasia , Briggs Skyler A. , Carman Christopher V. , Chaff Jake T. , Heng Anthony R. , Jadalannagari Sushma , Janardhanan Jeshina , Jang Kyung-Jin , Joshipura Sannidhi R. , Kadam Mahika M. , Kanellias Marianne , Kujala Ville J. , Kulkarni Gauri , Le Christopher Y. , Lucchesi Carolina , Manatakis Dimitris V. , Maniar Kairav K. , Quinn Meaghan E. , Ravan Joseph S. , Rizos Ann Catherine , Sauld John F.K. , Sliz Josiah D. , Tien-Street William , Trinidad Dennis Ramos , Velez James , Wendell Max , Irrechukwu Onyi , Mahalingaiah Prathap Kumar , Ingber Donald E. , Scannell Jack W. , Levner Daniel 
Published: December 2021

AbstractHuman organ-on-a-chip (Organ-Chip) technology has the potential to disrupt preclinical drug discovery and improve success in drug development pipelines as it can recapitulate organ-level pathophysiology and clinical responses. The Innovation and Quality (IQ) consortium formed by multiple pharmaceutical and biotechnology companies to confront this challenge has published guidelines that define criteria for qualifying preclinical models, however, systematic and quantitative evaluation of the predictive value of Organ-Chips has not yet been reported. Here, 870 Liver-Chips were analyzed to determine their ability to predict drug-induced liver injury (DILI) caused by small molecules identified as benchmarks by the IQ consortium. The Liver-Chip met the qualification guidelines across a blinded set of 27 known hepatotoxic and non-toxic drugs with a sensitivity of 87% and a specificity of 100%. A computational economic value analysis suggests that with this performance the Liver-Chip could generate $3 billion annually for the pharmaceutical industry due to increased R&D productivity.
Using Deep Clustering to Improve fMRI Dynamic Functional Connectivity Analysis
Authors: Spencer Arthur P C , Goodfellow Marc 
Published: December 2021

AbstractDynamic functional connectivity (dFC) analysis of resting-state fMRI data is commonly performed by calculating sliding-window correlations (SWC), followed by k-means clustering in order to assign each window to a given state. Studies using synthetic data have shown that k-means performance is highly dependent on sliding window parameters and signal-to-noise ratio. Additionally, sources of heterogeneity between subjects may affect the accuracy of group-level clustering, thus affecting measurements of dFC state temporal properties such as dwell time and fractional occupancy. This may result in spurious conclusions regarding differences between groups (e.g. when comparing a clinical population to healthy controls). Therefore, is it important to quantify the ability of k-means to estimate dFC state temporal properties when applied to cohorts of multiple subjects, and to explore ways in which clustering performance can be maximised.Here, we explore the use of dimensionality reduction methods prior to clustering in order to map high-dimensional data to a lower dimensional space, providing salient features to the subsequent clustering step. We assess the use of deep autoencoders for feature selection prior to applying k-means clustering to the encoded data. We compare this deep clustering method to feature selection using principle component analysis (PCA), uniform manifold approximation and projection (UMAP), as well as applying k-means to the original feature space using either L1 or L2 distance. We provide extensive quantitative evaluation of clustering performance using synthetic datasets, representing data from multiple heterogeneous subjects. In synthetic data we find that deep clustering gives the best performance, while other approaches are often insufficient to capture temporal properties of dFC states. We then demonstrate the application of each method to real-world data from human subjects and show that the choice of feature selection method has a significant effect on group-level measurements of state temporal properties. We therefore advocate for the use of deep clustering as a precursor to clustering in dFC.
Mice identify subgoal locations through an action-driven mapping process
Authors: Shamash Philip , Branco Tiago 
Published: December 2021

AbstractMammals instinctively explore and form mental maps of their spatial environments. Models of cognitive mapping in neuroscience mostly depict map-learning as a process of random or biased diffusion. In practice, however, animals explore spaces using structured, purposeful, sensory-guided actions. Here we test the hypothesis that executing specific exploratory actions is a key strategy for building a cognitive map. Previous work has shown that in arenas with obstacles and a shelter, mice spontaneously learn efficient multi-step escape routes by memorizing allocentric subgoal locations. We thus used threat-evoked escape to probe the relationship between ethological exploratory behavior and allocentric spatial memory. Using closed-loop neural manipulations to interrupt running movements during exploration, we found that blocking runs targeting an obstacle edge abolished subgoal learning. In contrast, blocking other movements while sparing edge-directed runs had no effect on memorizing subgoals. Finally, spatial analyses suggest that the decision to use a subgoal during escape takes into account the mouse’s starting position relative to the layout of the environment. We conclude that mice use an action-driven learning process to identify subgoals and that these subgoals are then integrated into a map-based planning process. We suggest a conceptual framework for spatial learning that is compatible with the successor representation from reinforcement learning and sensorimotor enactivism from cognitive science.