bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autophagy activation, lipotoxicity and lysosomal membrane permeabilization synergize to promote pimozide- and loperamide-induced glioma cell death
Authors: Meyer Nina , Henkel Lisa , Linder Benedikt , Zielke Svenja , Tascher Georg , Trautmann Sandra , Geisslinger Gerd , Münch Christian , Fulda Simone , Tegeder Irmgard , Kögel Donat 
Published: September 2020

AbstractIncreasing evidence suggests that induction of lethal autophagy carries potential significance for the treatment of glioblastoma (GBM). In continuation of previous work, we demonstrate that pimozide and loperamide trigger an ATG5- and ATG7-dependent type of cell death that is significantly inhibited with the cathepsin inhibitors E64D/Pepstatin A and the lipid ROS scavenger α-tocopherol in MZ-54 GBM cells. Global proteomic analysis after treatment with both drugs also revealed an increase of proteins related to lipid and cholesterol metabolic processes. These changes were accompanied by AKT1 (AKT serine/threonine kinase 1) inhibition and a massive accumulation of cholesterol and other lipids in the lysosomal compartment, indicative of impaired lipid transport/degradation. In line with these observations, pimozide and loperamide treatment were associated with a pronounced increase of bioactive sphingolipids including ceramides, glucosylceramides and sphingoid bases measured by targeted lipidomic analysis. Furthermore, pimozide and loperamide inhibited the activity of acid sphingomyelinase (ASM), increased lipid-ROS levels and promoted induction of lysosomal membrane permeabilization (LMP), as well as release of cathepsin B into the cytosol in MZ-54 wt cells. While LMP and cell death were significantly attenuated in ATG5/7 KO cells, both events were enhanced by depletion of the lysophagy receptor VCP (valosin containing protein), supporting a pro-survival function of lysophagy under these conditions. Collectively, our data suggest that pimozide and loperamide-driven autophagy and lipotoxicity synergize to induce LMP and lysosomal cell death. The results also support the notion that simultaneous overactivation of autophagy and induction of LMP represents a promising approach for the treatment of GBM.
Nature-inspired Circular-economy Recycling (NaCRe) for Proteins: Proof of Concept
Authors: Giaveri Simone , Schmitt Adeline Marie , Roset Julià Laura , Scamarcio Vincenzo , Murello Anna , Cheng Shiyu , Menin Laure , Ortiz Daniel , Patiny Luc , Bolisetty Sreenath , Mezzenga Raffaele , Maerkl Sebastian Josef , Stellacci Francesco 
Published: September 2020

AbstractThe billion tons of synthetic polymer-based materials (i.e.plastics) produced every year are one of the greatest challenges that humanity has to face. Nature produces even more natural polymers, yet they are sustainable. For example, proteins are sequence-defined natural polymers, that are constantly recycled when living systems feed. Indeed, digestion is the protein depolymerization into amino acids (i.e.the monomers) followed by their re-assembly into new proteins of arbitrarily different sequence and function. This process breaks a common recycling paradigm where a material is recycled into itself. Organisms feed of random protein mixtures that are ‘recycled’ into new proteins whose identity depends on the cell’s needs at the time of protein synthesis. Currently, advanced materials are increasingly made of proteins, but the abovementioned ideal recyclability of such materials has yet to be recognized and established. In this study mixtures of several (up to >30) peptides and/or proteins were depolymerized into their amino acid constituents, and these amino acids were used to synthesize new fluorescent, and bio-active proteins extra-cellularly by using an amino acid-free cell-free transcription-translation system. Proteins with high relevance in materials engineering (β-lactoglobulin films, used for water filtration, or silk fibroin solutions) were successfully recycled into biotechnologically relevant proteins (green, and red fluorescent proteins, catechol 2,3-dioxygenase). The potential long-term impact of this approach to recycling lies in its compatibility with circular-economy models where raw materials remain in use as long as possible, thus reducing the burden on the planet.
Etv5is not required for Schwann cell development but is required to regulate the Schwann cell response to peripheral nerve injury
Authors: Balakrishnan Anjali , Belfiore Lauren , Vasan Lakshmy , Touahri Yacine , Stykel Morgan , Fleming Taylor , Midha Rajiv , Biernaskie Jeff , Schuurmans Carol 
Published: September 2020

ABSTRACTSchwann cells are the principal glial cells of the peripheral nervous system, and their development into myelinating glia is critically dependent on MEK/ERK signaling. Ets-domain transcription factors (Etv1, Etv4, Etv5) are common downstream effectors of MEK/ERK signalling, but so far, onlyEtv1has been ascribed a role in Schwann cell development, and only in non-myelinating cells. Here, we examined the role ofEtv5, which is expressed in Schwann cell precursors, including neural crest cells and satellite glia, in Schwann cell lineage development. We analysedEtv5tm1Kmmmutants (designatedEtv5−/−) at embryonic days (E) 12.5, E15.5 and E18.5, focusing on dorsal root ganglia. At these embryonic stages, satellite glia (glutamine synthetase) and Schwann cell markers, including transcriptional regulators (Sox10, Sox9, Tfap2a, Pou3f1) and non-transcription factors (Ngfr, BFABP, GFAP), were expressed in the DRG of wild-type andEtv5−/−embryos. Furthermore, by E18.5, quantification of Sox10+Schwann cells and NeuN+neurons revealed that these cells were present in normal numbers in theEtv5−/−dorsal root ganglia. We next performed peripheral nerve injuries at postnatal day 21, revealing thatEtv5−/−mice had an enhanced injury response, generating more Sox10+Schwann cells compared to wild-type animals at five days post-injury. Thus, whileEtv5is not required for Schwann cell development, possibly due to genetic redundancy withEtv1and/orEtv4, Etv5is an essential negative regulator of the peripheral nerve injury repair response.SIGNIFICANCE STATEMENTOur study sought to determine whether the ets domain transcription factor,Etv5, plays a role in regulating Schwann cell development and nerve repair. By using an embryonically and postnatally viable hypomorphicEtv5mutant allele, we demonstrated thatEtv5is not required for the development of Schwann cells or other neural crest derivatives in the dorsal root ganglia, including satellite glia and neurons. Surprisingly, loss ofEtv5had a direct impact on the Schwann cell repair response post-injury, resulting in more Schwann cells populating the distal injured nerve site compared to wild-type animals. Thus, this work describes for the first time a role forEtv5in regulating the Schwann cell repair response after peripheral nerve injury.
Extraintestinal pathogenic Escherichia coli (ExPEC) are associated with prolonged carriage of extended-spectrum β-lactamase-producing E. coli acquired during travel
Authors: van der Putten Boas C.L. , van Hattem Jarne M. , Penders John ,   COMBAT Consortium, Mende Daniel R. , Schultsz Constance 
Published: September 2020

AbstractObjectivesExtended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) are frequently acquired during international travel, contributing to the global spread of antimicrobial resistance. Human-adapted ESBL-Ec are predicted to exhibit increased intestinal carriage duration, resulting in a higher likelihood of onward human-to-human transmission. Yet, bacterial determinants of increased carriage duration are unknown. Previous studies analysed small traveler cohorts, with short follow-up times, or did not employ high-resolution molecular typing, and were thus unable to identify bacterial traits associated with long-term carriage.MethodsIn a prospective cohort study of 2001 international travelers, we analysed 160 faecal ESBL-Ec isolates from all 38 travelers who acquired ESBL-Ec during travel and subsequently carried ESBL-Ec for at least 12 months after return, by whole-genome sequencing. For 17 travelers, we confirmed the persistence of ESBL-Ec strains through single nucleotide variant typing. To identify determinants of increased carriage duration, we compared the 17 long-term carriers (≥12 months carriage) with 33 age-, sex- and destination-matched short-term carriers (<1 month carriage). Long-read sequencing was employed to investigate ESBL plasmid persistence.ResultsWe show that in healthy travelers with very low antibiotic usage, extraintestinal pathogenic lineages of E. coli (ExPEC) are significantly more likely to persist than other E. coli lineages. The long-term carriage of E. coli from ExPEC lineages is mainly driven by sequence type 131 and phylogroup D E. coli.ConclusionsAlthough ExPEC frequently cause extra-intestinal infections such as bloodstream infections, our results imply that ExPEC are also efficient intestinal colonizers, which potentially contributes to their onward transmission.
The effects of luminal and trans-endothelial fluid flows on the extravasation and tissue invasion of tumor cells in a 3Din vitromicrovascular platform
Authors: Hajal Cynthia , Ibrahim Lina , Serrano Jean Carlos , Offeddu Giovanni S. , Kamm Roger D. 
Published: September 2020

ABSTRACTThroughout the process of metastatic dissemination, tumor cells are continuously subjected to mechanical forces resulting from complex fluid flows due to changes in pressures in their local microenvironments. While these forces have been associated with invasive phenotypes in 3D matrices, their role in key steps of the metastatic cascade, namely extravasation and subsequent interstitial migration, remains poorly understood. In this study, anin vitromodel of the human microvasculature was employed to subject tumor cells to physiological luminal, trans-endothelial, and interstitial flows to evaluate their effects on those key steps of metastasis. Luminal flow promoted the extravasation potential of tumor cells, possibly as a result of their increased intravascular migration speed. Trans-endothelial flow increased the speed with which tumor cells transmigrated across the endothelium as well as their migration speed in the matrix following extravasation. In addition, tumor cells possessed a greater propensity to migrate in close proximity to the endothelium when subjected to physiological flows, which may promote the successful formation of metastatic foci. These results show important roles of fluid flow during extravasation and invasion, which could determine the local metastatic potential of tumor cells.
A joint reaction coordinate for computing the free energy landscape of pore nucleation and pore expansion in lipid membranes
Authors: Hub Jochen S. 
Published: September 2020

AbstractTopological transitions of membranes, such as pore formation or membrane fusion, play key roles in biology, biotechnology, and in medical applications. Calculating the related free energy landscapes has been complicated by the fact that such processes involve a sequence of transitions along highly distinct directions in conformational space, making it difficult to define good reaction coordinates (RCs) for the overall process. In this study, we present a new RC capable of driving both pore nucleation and pore expansion in lipid membranes. The potential of mean force (PMF) along the RC computed with molecular dynamics (MD) simulations provides a comprehensive view on the free-energy landscape of pore formation, including a barrier for pore nucleation, the size, free energy, and metastability of the open pore, and the energetic cost for further pore expansion against the line tension of the pore rim. We illustrate the RC by quantifying the effects (i) of simulation system size and (ii) of the addition of dimethyl sulfoxide (DMSO) on the free energy landscape of pore formation. PMF calculations along the RC provide mechanistic and energetic understanding of pore formation, hence they will be useful to rationalize the effects of membrane-active peptides, electric fields, and membrane composition on transmembrane pores.
lncRNA-RMST functioned as a SOX2 transcription co-regulator to regulate miR-1251 in the progression of Hirschsprung’s disease
Authors: Zhou Lingling , Zhi Zhengke , Chen Pingfa , Wei Zhonghong , Du Chunxia , Wang Binyu , Fang Xiang , Tang Weibing , Li Hongxing 
Published: September 2020

ABSTRACTHirschsprung’s disease (HSCR) is a congenital disorder characterized by the absence of enteric neural crest cells (ENCCs). Non-coding RNAs including long non-coding RNAs (lncRNAs) and microRNAs (miRNAs) have been authenticated as important regulators of biological functions. We conducted a microarray analysis and found lncRNA Rhabdomyosarcoma 2-associated transcript (RMST) was down-regulated in the stenotic segment of HSCR patients. MiR-1251 is transcribed from the intron region of RMST and was also low-expressed. When the expression of RMST or miR-1251 was reduced, the cell proliferation and migration were attenuated. However, RMST didn’t affect the expression of miR-1251 directly found in this study. Through bioinformatic analysis, transcription factor SOX2 was predicted to bind to the promoter region of miR-1251 which was confirmed by CHIP assay. Herein, we demonstrated that RMST exerted as a co-regulator of SOX2 to regulate the expression of miR-1251. Furtherly, AHNAK was proved to be the target gene of miR-1251 in this study. Taken together, we revealed the role of RMST/SOX2/miR-1251/AHNAK pathway in the occurrence of Hirschsprung’s disease and provided a potential therapeutic target for this disease.SUMMARY STATEMENTHirschsprung disease (HSCR) is characterized by a deficit in enteric neurons, however, the underlying mechanism remains unclear. This study revealed the role of lnc-RMST during the occurrence of HSCR.
Evenness-richness scatter plots: a graphical, intuitive approach to alpha diversity analysis
Authors: Gauthier Jeff , Derome Nicolas 
Published: September 2020

AbstractShannon’s diversity index is a popular alpha diversity metric because it estimates both richness and evenness in a single equation. However, since its value is dependent of both those parameters, there is theoretically an infinite number of richness / evenness value combinations translating into the same index score. By decoupling both components measured by Shannon’s index, two communities having identical indices can be differentiated by mapping richness and evenness coordinates on a scatter plot. In such graphs, confidence ellipses would allow testing significant differences between groups of samples. Multivariate statistical tests such as PERMANOVA can be performed on distance matrices calculated from richness and evenness coordinates and detect statistically significant differences that would have remained unforeseen otherwise.
Dynamic Mechanochemical feedback between curved membranes and BAR protein self-organization
Authors: Le Roux Anabel-Lise , Tozzi Caterina , Walani Nikhil , Quiroga Xarxa , Zalvidea Dobryna , Trepat Xavier , Staykova Margarita , Arroyo Marino , Roca-Cusachs Pere 
Published: September 2020

AbstractIn many physiological situations, BAR proteins interact with, and reshape, pre-existing curved membranes, contributing to essential cellular processes. However, the non-equilibrium and timedependent process of reshaping, and its dependence on initial membrane shape, remains largely unknown. Here we explain, both experimentally and through modelling, how a BAR protein dynamically interacts with mechanically bent lipid membranes. We capture protein binding to curved membranes, and characterize a variety of dynamical reshaping events depending on membrane shape and protein arrangement. The events can be generally understood by an isotropic-to-nematic phase transition, in which low curvature templates with isotropic protein orientation progress towards highly curved lipid tubes with nematic protein arrangement. Our findings also apply in cells, where mechanical stretch triggers BAR-protein-membrane interactions that enable potential mechanotransduction mechanisms. Our results characterize and broaden the reshaping processes of BAR proteins on mechanically constrained membranes, demonstrating the interplay between membrane mechanical stimuli and BAR protein response.
The Kappa Opioid Receptor is required for some intermittent alcohol drinking induced changes in stress and threat responding in male C57BL/6J mice
Authors: Hwa Lara S. , Bowling Morgan , Calloway Rachel , Kash Thomas L. 
Published: September 2020

AbstractThe dynorphin/kappa opioid receptor (KOR) system in the brain regulates both stressful experiences and negative, aversive states during withdrawal from drugs of abuse. We explored the role of this system during acute withdrawal from long-term alcohol drinking. Male C57BL/6J mice were subjected to repeated forced swim tests, home cage exposure to a predator odor, and a visual threat after intermittent access to alcohol or water. Systemic injection of KOR antagonist norBNI reversed alcohol-related differences in immobility time during the second swim test and reduced burying behavior in response to predator odor, but did not affect behavioral response to visual threat.HighlightsIntermittent alcohol drinking changed stress reactions in mice.KOR antagonist norBNI altered some, but not all, stress responses in alcohol drinkers
Across kingdom biased CYP-mediated metabolism via small-molecule ligands docking on P450 oxidoreductase
Authors: Jensen Simon Bo , Thodberg Sara , Parween Shaheena , Moses Matias E. , Hansen Cecilie C. , Thomsen Johannes , Sletfjerding Magnus B. , Knudsen Camilla , Giudice Rita Del , Lund Philip M. , Castaño Patricia R. , Bustamante Yanet G. , Jørgensen Flemming S. , Pandey Amit V. , Laursen Tomas , Møller Birger Lindberg , Hatzakis Nikos S. 
Published: September 2020

AbstractMetabolic control is mediated by the dynamic assemblies and function of multiple redox enzymes. A key element in these assemblies, the P450 oxidoreductase (POR), donates electrons and selectively activates numerous (>50 in humans and >300 in plants) cytochromes P450 (CYPs) controlling metabolism of drugs, steroids and xenobiotics in humans and natural product biosynthesis in plants. The mechanisms underlying POR-mediated CYP metabolism remain poorly understood and to date no ligand binding has been described to regulate the specificity of POR. Here, using a combination of computational modeling and functional assays, we identified ligands that dock on POR and bias its specificity towards CYP redox partners. Single molecule FRET studies revealed ligand docking to alter POR conformational sampling, which resulted in biased activation of metabolic cascades in whole cell assays. We propose the model ofbiased metabolism, a mechanism akin to biased signaling of GPCRs, where ligand docking on POR stabilizes different conformational states that are linked to distinct metabolic outcomes. Biased metabolism may allow designing pathway-specific therapeutics or personalized food suppressing undesired, disease related, metabolic pathways.
Can quantifying morphology and TMEM119 expression distinguish between microglia and infiltrating macrophages after ischemic stroke and reperfusion in male and female mice?
Authors: Young Kimberly F. , Gardner Rebeca , Sariana Victoria , Whitman Susan A. , Bartlett Mitchell J. , Falk Torsten , Morrison Helena W. 
Published: September 2020

ABSTRACTBackgroundIschemic stroke is an acquired brain injury with gender dependent outcomes. A persistent obstacle in understanding the sex-specific neuroinflammatory contributions to ischemic brain injury is distinguishing between resident microglia versus infiltrating macrophages—both phagocytes—and determining cell population specific contributions to injury evolution and recovery processes. Our purpose was to identify microglial and macrophage populations regulated by ischemic stroke using morphology analysis and the presence of microglia transmembrane protein 119 (TMEM119). Second, we examined sex and menopause differences in microglia/macrophage cell populations after an ischemic stroke.MethodsMale and female, premenopausal and postmenopausal, mice underwent either 60-min of middle cerebral artery occlusion and 24-h of reperfusion or sham surgery. The accelerated ovarian failure model was used to model post-menopause. Brain tissue was collected to quantify infarct area and for immunohistochemistry and western blot methods. Ionized calcium-binding adapter molecule, TMEM119, and confocal microscopy were used to analyze microglia morphology and TMEM119 area in ipsilateral brain regions. Western blot was used to quantify protein quantity.ResultsPost-stroke injury is increased in male and female post-menopause mice versus pre-menopause female mice (p<0.05) with differences primarily occurring in caudal sections. After stroke, microglia underwent a region, but not sex group, dependent transformation into less ramified cells (p<0.0001). However, the number of phagocytic microglia were increased in distal ipsilateral regions of postmenopausal mice versus the other sex groups (p<0.05). The number of TMEM119 positive cells was decreased in proximity to the infarct (p<0.0001) but without a sex group effect. Two key findings prevented distinguishing microglia from systemic macrophages. First, morphological data were not congruent with TMEM119 immunofluorescence data. Cells with severely decreased TMEM119 immunofluorescence were ramified, a distinguishing microglia characteristic. Second, whereas TMEM119 immunofluorescence area decreased in proximity to the infarcted area, TMEM119 protein quantity was unchanged in ipsilateral hemisphere regions using western blot methods.ConclusionsOur findings suggest that TMEM119 is not a stable microglia marker in male and female mice in the context of ischemic stroke. Until TMEM119 function in the brain is elucidated, its use to distinguish between cell populations following brain injury with cell infiltration is cautioned.
CHARTS: A web application for characterizing and comparing tumor subpopulations in publicly available single-cell RNA-seq datasets
Authors: Bernstein Matthew N. , Ni Zijian , Collins Michael , Burkard Mark E. , Kendziorski Christina , Stewart Ron 
Published: September 2020

AbstractBackgroundSingle-cell RNA-seq (scRNA-seq) enables the profiling of genome-wide gene expression at the single-cell level and in so doing facilitates insight into and information about cellular heterogeneity within a tissue. Perhaps nowhere is this more important than in cancer, where tumor and tumor microenvironment heterogeneity directly impact development, maintenance, and progression of disease. While publicly available scRNA-seq cancer datasets offer unprecedented opportunity to better understand the mechanisms underlying tumor progression, metastasis, drug resistance, and immune evasion, much of the available information has been underutilized, in part, due to the lack of tools available for aggregating and analysing these data.ResultsWe present CHARacterizing Tumor Subpopulations (CHARTS), a computational pipeline and web application for analyzing, characterizing, and integrating publicly available scRNA-seq cancer datasets. CHARTS enables the exploration of individual gene expression, cell type, malignancy-status, differentially expressed genes, and gene set enrichment results in subpopulations of cells across multiple tumors and datasets.ConclusionCHARTS is an easy to use, comprehensive platform for exploring single-cell subpopulations within tumors across the ever-growing collection of public scRNA-seq cancer datasets. CHARTS is freely available atcharts.morgridge.org.