bluuebunny/crossref_metadata_2025_split huggingface dataset:
NOTCH inhibition promotes myoblast fusion by releasing HEYL repression onTMEM8Cregulatory regions in foetal skeletal muscles
Authors: Esteves de Lima Joana , Blavet Cédrine , Bonnin Marie-Ange , Hirsinger Estelle , Havis Emmanuelle , Duprez Delphine 
Published: January 2020

AbstractDifferentiation and fusion are two intricate processes involved in skeletal muscle development. The close association of differentiation and fusion makes it difficult to address the process of fusion independently of differentiation. Using the fusion markermyomaker, namedTMEM8Cin chicken, we found that bothTMEM8Ctranscripts and the differentiated and fusion-competent MYOG+ cells are preferentially regionalized in the central regions of limb foetal muscles in chicken embryos. Because the NOTCH signalling pathway is a potent inhibitor of muscle differentiation during developmental myogenesis, NOTCH function in myoblast fusion was not addressed so far. We analysed the consequences of NOTCH inhibition for myoblast fusion andTMEM8Cexpression during foetal myogenesis using in vitro and in vivo chicken systems. NOTCH inhibition following chicken embryo immobilisation or in myoblast cultures increasedTMEM8Cexpression and myoblast fusion. Moreover, we showed that NOTCH inhibition induced the un-binding of the HEYL transcriptional repressor from theTMEM8Cregulatory regions in limb muscles and myoblast cultures. These results identify a molecular mechanism underlying the fusion-promoting effect of NOTCH-inhibition during foetal myogenesis.
Full-length LINE-1s with functional ORFs are favoured by host-level selection in human genomes
Authors: zu Dohna Heinrich , Zhou Bo , Zhu Xiaowei , Urban Alexander E. 
Published: January 2020

AbstractThe effects of transposable elements, such as LINE-1, on host fitness are still poorly understood. Our analysis of the site frequency spectrum of LINE-1s and SNPs within LINE1s in human genomes shows that selection coefficients are higher for full-length than for fragment LINE-1s and on full-length LINE-1s, SNPs are significantly depleted on ORFs and non-synonymous sites within ORFs. These results suggest that host-level selection maintains transposition competent LINE-1s.
Single-cell mapping reveals new markers and functions of lymphatic endothelial cells in lymph nodes
Authors: Fujimoto Noriki , He Yuliang , D’Addio Marco , Tacconi Carlotta , Detmar Michael , Dieterich Lothar C. 
Published: January 2020

ABSTRACTLymph nodes (LNs) are highly organized secondary lymphoid organs that mediate adaptive immune responses to antigens delivered via afferent lymphatic vessels. Lymphatic endothelial cells (LECs) line intranodal lymphatic sinuses and organize lymph and antigen distribution. LECs also directly regulate T cells, mediating peripheral tolerance to self-antigens, and play a major role in many diseases including cancer metastasis. However, little is known about the phenotypic and functional heterogeneity of LN LECs. Using single-cell RNA sequencing, we comprehensively defined the transcriptome of LECs in murine skin-draining LNs, and identified new markers and functions of distinct LEC subpopulations. We found that LECs residing in the subcapsular sinus have an unanticipated function in scavenging of modified LDL and also identified a specific cortical LEC subtype implicated in rapid lymphocyte egress from LNs. Our data provide new insights into the diversity of LECs in murine lymph nodes and a rich resource for future studies into the regulation of immune responses by lymph node LECs.
ECSIT prevents Alzheimer’s disease pathology by regulating neuronal mitochondrial ROS and mitophagy
Authors: Lepelley Alice , Vaughn Lauren S. , Staniszewski Agnieszka , Zhang Hong , Du Fang , Koppensteiner Peter , Tomljanovic Zeljko , Carneiro Flávia R.G. , Teich Andrew F. , Ninan Ipe , Yan Shirley ShiDu , Postler Thomas S. , Hayden Matthew S. , Arancio Ottavio , Ghosh Sankar 
Published: January 2020

AbstractAltered mitochondrial fitness is a potential triggering factor in Alzheimer’s disease (AD). Mitochondrial quality control pathways are dysfunctional and mitochondrially-derived reactive oxygen species (mROS) levels are increased in AD patient brains. However, the pathways responsible for dysregulated mROS accumulation have remained relatively unclear. In this study, we demonstrate that levels of ECSIT, a mitochondrial oxidative phosphorylation (OxPhos) complex I (CI)-associated protein, are reduced in AD-affected brains. Neuronal ECSIT downregulation increased mROS generation and impaired mitophagy of defective mitochondria. Consequently, decreasing neuronal ECSIT caused AD-like changes, including memory loss and neuropathology. In contrast, augmented neuronal expression of ECSIT protected against the development of an AD-like phenotype. Decreased levels of ECSIT in AD patient brains therefore likely contribute to oxidative stress, neuroinflammation and AD pathogenesis.
Defective Function of α-Ketoglutarate Dehydrogenase Exacerbates Mitochondrial ATP Deficits during Complex I Deficiency
Authors: Piroli Gerardo G. , Manuel Allison M. , McCain Richard S. , Smith Holland H. , Ozohanics Oliver , Mellid Sara , Cotham William E. , Walla Michael D. , Cascón Alberto , Ambrus Attila , Frizzell Norma 
Published: January 2020

AbstractTheNDUFS4knockout (KO) mouse phenotype resembles the human Complex I deficiency Leigh Syndrome. The irreversible succination of protein thiols by fumarate is increased in select regions of theNDUFS4KO brain affected by neurodegeneration, suggesting a mechanistic role in neurodegenerative decline. We report that dihydrolipoyllysine-residue succinyltransferase (DLST), a component of the α-ketoglutarate dehydrogenase complex (KGDHC) of the tricarboxylic acid (TCA) cycle, is succinated in theNDUFS4KO brain. Succination of DLST reduced KGDHC activity in the brainstem (BS) and olfactory bulb (OB) of KO mice. The defective production of KGDHC derived succinyl-CoA resulted in decreased mitochondrial substrate level phosphorylation (SLP), further aggravating the OXPHOS ATP deficit. Protein succinylation, an acylation modification that requires succinyl-CoA, was reduced in the KO mice. Modeling succination of a cysteine in the spatial vicinity of the DLST active site or introduction of succinomimetic mutations recapitulates these metabolic deficits. Our data demonstrate that the biochemical deficit extends beyond impaired Complex I assembly and OXPHOS deficiency, functionally impairing select components of the TCA cycle to drive metabolic perturbations in affected neurons.
Altered polarization of PAR-2 signaling during airway epithelial remodeling
Authors: Carey Ryan M. , Freund Jenna R. , Hariri Benjamin M. , Adappa Nithin D. , Palmer James N. , Lee Robert J. 
Published: January 2020

ABSTRACTBackgroundProtease-activated receptor 2 (PAR-2) is activated by proteases involved in allergy and triggers airway epithelial secretion and inflammation. PAR-2 is normally expressed basolaterally in differentiated nasal ciliated cells.ObjectiveWe tested if epithelial remodeling during diseases characterized by loss of cilia and squamous metaplasia may alter PAR-2 polarization.MethodsEndogenous PAR-2 responses were measured by live cell calcium and cilia imaging, measurement of fluid secretion, and quantification of cytokines. We utilized airway squamous cell lines, primary differentiated air-liquid interface cultures, and tissue explants. Cells were exposed to disease-related modifiers that alter epithelial morphology, including IL-13, cigarette smoke condensate, and retinoic acid deficiency. We used concentrations and exposure times that altered epithelial morphology without causing breakdown of the epithelial barrier, likely reflecting early disease states.ResultsPAR-2 signaling in airway squamous cells activated calcium and inflammatory responses. Squamous cells cultured at air liquid interface (ALI) responded to PAR-2 agonists applied both apically and basolaterally. Primary well-differentiated nasal epithelial ALI cultures responded only to basolateral PAR-2 stimulation. Primary cultures exposed to IL-13, cigarette smoke condensate, or reduced retinoic acid responded to both apical and basolateral PAR-2 stimulation. Nasal polyp tissue, but not control middle turbinate, exhibited apical calcium responses to PAR-2 stimulation. However, isolated ciliated cells from both polyp and turbinate maintained basolateral PAR-2 polarization.ConclusionsSquamous metaplasia and/or loss of cilia enhances apical PAR-2 responses. Altered PAR-2 polarization in dedifferentiated or remodeled epithelia may contribute to increased sensitivity to inhaled protease allergens in inflammatory airway diseases.
DNA Features Viewer, a sequence annotations formatting and plotting library for Python
Authors: Zulkower Valentin , Rosser Susan 
Published: January 2020

AbstractMotivationWhile the Python programming language counts many Bioinformatics and Computational Biology libraries, none offers customizable sequence annotations visualizations with layout optimization.ResultsDNA Features Viewer is a sequence annotations plotting library which optimizes plot readability while letting users tailor other visual aspects (colors, labels, highlights, etc.) to their particular use case.AvailabilityOpen-source code and documentation are available on Github under the MIT licence (https://github.com/Edinburgh-Genome-Foundry/DnaFeaturesViewer).Contactvalentin.zulkower@ed.ac.ukSupplementary informationattached.
Cell segmentation using deep learning: comparing label and label-free approaches using hyper-labeled image stacks
Authors: Cameron William D. , Bennett Alex M. , Bui Cindy V. , Chang Huntley H. , Rocheleau Jonathan V. 
Published: January 2020

AbstractDeep learning provides an opportunity to automatically segment and extract cellular features from high-throughput microscopy images. Many labeling strategies have been developed for this purpose, ranging from the use of fluorescent markers to label-free approaches. However, differences in the channels available to each respective training dataset make it difficult to directly compare the effectiveness of these strategies across studies. Here we explore training models using subimage stacks composed of channels sampled from larger, ‘hyper-labeled’, image stacks. This allows us to directly compare a variety of labeling strategies and training approaches on identical cells. This approach revealed that fluorescence-based strategies generally provide higher segmentation accuracies but were less accurate than label-free models when labeling was inconsistent. The relative strengths of label and label-free techniques could be combined through the use of merging fluorescence channels and out-of-focus brightfield images. Beyond comparing labeling strategies, using subimage stacks for training was also found to provide a method of simulating a wide range of labeling conditions, increasing the ability of the final model to accommodate a greater range of experimental setups.
A role for theMEGF6gene in predisposition to osteoporosis
Authors: Teerlink Craig C. , Jurynec Michael J , Hernandez Rolando , Stevens Jeff , Hughes Dana C. , Brunker Cherie P. , Rowe Kerry , Grunwald David J. , Facelli Julio C. , Cannon-Albright Lisa A. 
Published: January 2020

ABSTRACTOsteoporosis is a common skeletal disorder characterized by deterioration of bone tissue in later life. The set of genetic factors contributing to osteoporosis is not completely specified. High-risk osteoporosis pedigrees were analyzed to identify genes that may confer susceptibility to disease. Candidate predisposition variants were identified initially by whole exome sequencing of affected-relative-pairs, approximately cousins, from ten pedigrees. Variants were filtered on the basis of population frequency, concordance between pairs of cousins, affecting a gene associated with osteoporosis, and likelihood to have functionally damaging, pathogenic consequences. Subsequently variants were tested for segregation in 68 additional relatives of the index carriers. A rare variant inMEGF6(rs755467862) showed strong evidence of segregation with the disease phenotype. Predicted protein folding indicated the variant (Cys200Tyr) may disrupt structure of an EGF-like calcium-binding domain of MEGF6. Functional analyses demonstrated that complete loss of the paralogous genesmegf6aandmegf6bin zebrafish resulted in significant delay of cartilage and bone formation. Segregation analyses, in-silico protein structure modeling, and functional assays support a role forMEGF6in predisposition to osteoporosis.
Mutation of the Galectin-3 Glycan Binding Domain (Lgals3-R200S) Enhances Cortical Bone Expansion in Male and Trabecular Bone Mass in Female Mice
Authors: Maupin Kevin A. , Dick Daniel , Vivarium VARI , Core Transgenics , Williams Bart O. 
Published: January 2020

AbstractThe study of galectin-3 is complicated by its ability to function both intracellularly and extracellularly. While the mechanism of galectin-3 secretion is unclear, studies have shown that the mutation of a highly conserved arginine to a serine in human galectin-3 (LGALS3-R186S) blocks glycan binding and secretion. To gain insight into the roles of extracellular and intracellular functions of galectin-3, we generated mice with the equivalent mutation (Lgals3-R200S) using CRISPR/Cas9-directed homologous recombination. Consistent with a reduction in galectin-3 secretion, we observed significantly reduced galectin-3 protein levels in the plasma of heterozygous and homozygous mutant mice. We observed a similar increased bone mass phenotype inLgals3-R200S mutant mice at 36 weeks as we previously observed inLgals3-KO mice with slight variation. LikeLgals3-KO mice,Lgals3-R200S females, but not males, had significantly increased trabecular bone mass. However, only maleLgals3-R200S mice showed increased cortical bone expansion, which we had previously observed in both male and femaleLgals3-KO mice and only in female mice using a separateLgals3null allele (Lgals3). These results suggest that the trabecular bone phenotype ofLgals3-KO mice was driven primarily by loss of extracellular galectin-3. However, the cortical bone phenotype ofLgals3-KO mice may have also been influenced by loss of intracellular galectin-3. Future analyses of these mice will aid in identifying the cellular and molecular mechanisms that contribute to theLgals3-deficient bone phenotype as well as aid in distinguishing the extracellular vs. intracellular roles of galectin-3 in various signaling pathways.
Design and demonstration in vitro of a mouse-specific Transcranial Magnetic Stimulation coil
Authors: Khokhar Farah A. , Voss Logan J. , Steyn-Ross D. Alistair , Wilson Marcus T. 
Published: January 2020

BackgroundTranscranial Magnetic Stimulation (TMS) is a technique used to treat different neurological disorders non-invasively. A pulsed current to a coil generates a magnetic field (B-field) which induces an electric field (E-field). Underlying biophysical effects of TMS are unclear. Therefore, animal experiments are needed; however, making small TMS coils suitable for mice is difficult and their field strengths are typically much lower than for human sized coils.Objectives/HypothesisWe aimed to design and demonstrate a mouse-specific coil that can generate high and focused E-field.MethodsWe designed a tapered TMS coil of 50 turns of 0.2 mm diameter copper wire around a 5 mm diameter tapered powdered iron core and discharged a 220 μF capacitor at 50 V through it. We measured B-field with a Hall probe and induced E-field with a wire loop. We measured temperature rise with a thermocouple. We applied 1200 pulses of continuous theta burst stimulation (cTBS) and intermittent theta burst stimulation (iTBS) to mouse brain slices and analysed how spontaneous electrical activity changed.ResultsThe coil gave maximum B-field of 685 mT at the base of the coil and 340 mT at 2 mm below the coil, and maximum E-field 2 mm below the coil of approximately 10 V/m, at 50 V power supply, with a temperature increase of 20 degrees after 1200 pulses of cTBS. We observed no changes in B-field with heating. cTBS reduced frequency of spontaneous population events in mouse brain slices up to 20 minutes after stimulation and iTBS increased frequency up to 20 minutes after stimulation. No frequency changes occurred after 20 minutes. No changes in amplitude of spontaneous events were found.ConclusionThe design generated fields strong enough to modulate brain activity in vitro.
Developmental hourglass and heterochronic shifts in fin and limb development
Authors: Onimaru Koh , Tatsumi Kaori , Tanegashima Chiharu , Kadota Mitsutaka , Nishimura Osamu , Kuraku Shigehiro 
Published: January 2020

AbstractHow genetic changes are linked to morphological novelties and developmental constraints remains elusive. Here we investigate genetic apparatuses that distinguish fish fins from tetrapod limbs by analyzing transcriptomes and open chromatin regions (OCRs). Specifically, we compare mouse forelimb buds with pectoral fin buds of a slowly evolving species, the brown-banded bamboo shark (Chiloscyllium punctatum). A transcriptomic comparison with an accurate orthology map reveals both a mass heterochrony and hourglass-shaped conservation of gene expression between fins and limbs. Furthermore, chromatin-accessibility data indicate that conserved regulatory sequences are most active during mid-stage limb development. During this stage, stage-specific and tissue-specific OCRs are also enriched. Together, early and late stages of fin/limb development are more permissive to mutations, which may have contributed to the major morphological changes during the fin-to-limb evolution. We also hypothesize that the middle stages are constrained by regulatory complexity that results from dynamic and tissue-specific transcriptional controls.
Complement and coagulation cascades are potentially involved in dopaminergic neurodegeneration in α-synuclein-based mouse models of Parkinson’s disease
Authors: Ma Shi-Xun , Kim Donghoon , Xiong Yulan , Kwon Seung-Hwan , Brahmachari Saurav , Kim Sangjune , Kam Tae-In , Nirujogi Raja Sekhar , Kwon Sang Ho , Dawson Valina L. , Dawson Ted M. , Pandey Akhilesh , Na Chan Hyun , Ko Han Seok 
Published: January 2020

AbstractParkinson’s disease (PD) is the second most common neurodegenerative disorder that results in motor dysfunction and eventually, cognitive impairment. α-Synuclein protein has been known to be the most culprit protein, but the underlying pathological mechanism still remains to be elucidated. As an effort to clarify the pathogenesis mechanism by α-synuclein, various PD mouse models with α-synuclein overexpression have been developed. However, the systemic analysis of protein abundance change by the overexpressed α-synuclein in the whole proteome level has been still lacking. To address this issue, we established two sophisticated mouse models of PD by injecting α-synuclein preformed fibrils (PFF) or by inducing overexpression of human A53T α-synuclein to discover overlapping pathways, which could be altered in the two different types of PD mouse model. For more accurate quantification of mouse brain proteome, stable isotope labeling with amino acid in mammal-based quantification was implemented. As a result, we have successfully identified a total of 8,355 proteins from both of the mouse models; ∼6,800 and ∼7,200 proteins from α-synuclein PFF injected mice and human A53T α-synuclein transgenic mice, respectively. From the pathway analysis of the differentially expressed proteins in common, the complement and coagulation cascade pathway were determined as the most enriched ones. This is the first study that highlights the significance of the complement and coagulation pathway in the pathogenesis of PD through proteome analyses with two sophisticated mouse models of PD.
SPARC promotes insulin secretion through down-regulation of RGS4 protein in pancreatic β-cells
Authors: Hu Li , He Fengli , Huang Meifeng , Zhao Qian , Cheng Lamei , Said Neveen , Zhou Zhiguang , Liu Feng , Dai Yan-Shan 
Published: January 2020

AbstractSPARC-deficient mice have been shown to exhibit impaired glucose tolerance and insulin secretion, but the underlying mechanism remains unknown. Here, we show that SPARC enhanced the promoting effect of Muscarinic receptor agonist oxotremorine-M on insulin secretion in cultured mouse islets. Overexpression of SPARC down-regulated RGS4, a negative regulator of β-cell M3 muscarinic receptors. Conversely, knockdown of SPARC up-regulated RGS4 in Min6 cells. RGS4 was up-regulated in islets fromsparc-/- mice, which correlated with decreased glucose-stimulated insulin secretion (GSIS). Furthermore, inhibition of RGS4 restored GSIS insparc-/- mice, and knockdown of RGS4 partially decreased the promoting effect of SPARC on oxotremorine-M stimulated insulin secretion. Phosphoinositide 3-kinase (PI3K) inhibitor LY-294002 abolished SPARC-induced down-regulation of RGS4. Taken together, our data revealed that SPARC promoted GSIS by inhibiting RGS4 in pancreatic β cells.
Targeting Aryl Hydrocarbon Receptor with small molecule, 1′H-indole-3′-carbonyl-thiazole-4-carboxylic acid methyl ester blocked human glioma cell invasion via MYH9
Authors: Zhao Lijiao , Shu Qiuting , Sun Hui , Ma Yunlong , Kang Dandan , Zhao Yating , Lu Jing , Gong Pei , Yang Fan , Wan Fang 
Published: January 2020

AbstractAryl hydrocarbon receptor (AHR) was a master regulator of anti-tumor cell migration in various cell types. Whether and how AHR regulates glioma cell migration is largely unknown. We found that small molecule 2-(1′H-indole-3′-carbonyl)-thiazole-4-carboxylic acid methyl ester (ITE), an endogenous AHR ligand, can significantly block glioma cell migration and invasionin vitro,ex vivoandin vivo. Knocking down AHR by siRNA abolished ITE’s migration-inhibiting effects. ITE increased the number of filopodia-like protrusion formation, but reduced protrusion attachment to the extracellular matrix, and inhibited the rear retraction of migrating glioma cells. Moreover, both mesenchymal and amoeboid migrating cells were observed in the DMSO control group while none of the cells display amoeboid migration in the ITE treated group. MYH9 was significantly reduced by ITE treatment in human glioma cells. Over-expression of MYH9 abrogated ITE’s migration-inhibiting effects, with the expression level of MYH9 correlated with cell migration ability. Since MYH9 is a component of non-muscle myosin IIA (NMIIA), which is essential for cell migration in 3D confined space, and not a discovered target of AHR, the fact that ITE affects MYH9 via AHR opens a new research and development avenue.
TQM for Greek SMEs: an alternative in facing crisis conditions
Authors: Sainis George , Haritos George , Kriemadis Thanos , Papasolomou Ioanna 
Published: January 2020

PurposeThis study aims to bridge the gap left by earlier studies regarding the issue of whether the International Organization for Standardization (ISO) certification is a stepping stone that ultimately leads to instilling a total quality management (TQM) culture, or whether it is the end-point in their journey toward quality.Design/methodology/approachThe study was primarily quantitative in nature supported from a qualitative survey following the triangulation approach, as the aim was to test a number of hypotheses related to TQM’s role in the operation of Greek ISO certified small and medium-sized enterprises (SMEs). A questionnaire was developed based on the critical success factors that were used in the self-assessment instrument developed by Hunt (1992) and Sashkin (1996) to assess the level of TQM implementation in approximately 400 Greek SMEs.FindingsThe study revealed that Greek ISO certified SMEs, emphasize performance appraisal, invest in quality elements that require minimum usage of their resources and prioritize their ISO certification.Originality/valueTQM is one of the most powerful concepts available to businesses today. However, most of the literature focuses on the practice of TQM within large manufacturing organizations. This paper aims to readdress the situation by outlining a study on TQM in the SME sector in Greece.