bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of thrombospondin-4 on pro-inflammatory phenotype differentiation and apoptosis in macrophages
Authors: Rahman Mohammed Tanjimur , Muppala Santoshi , Wu Jiahui , Krukovets Irene , Solovjev Dmitry , Verbovetskiy Dmitriy , Obiako Chioma , Plow Edward F. , Stenina-Adognravi Olga 
Published: January 2020

AbstractThrombospondin-4 (TSP-4) attracted renewed attention recently as a result of assignment of new functions to this matricellular protein in cardiovascular, muscular, and nervous systems. We have previously reported that TSP-4 promotes local vascular inflammation in a mouse atherosclerosis model. A common variant of TSP-4, P387-TSP-4, was associated with increased cardiovascular disease risk in human population studies. In a mouse atherosclerosis model, TSP-4 had profound effect on accumulation of macrophages in lesions, which prompted us to examine its effects on macrophages in more detail. We examined the effects of A387-TSP-4 and P387-TSP-4 on mouse macrophages in cell culture and in vivo in the model of LPS-induced peritonitis. In tissues and in cell culture, TSP-4 expression was associated with inflammation: TSP-4 expression was upregulated in peritoneal tissues in LPS-induced peritonitis, and pro-inflammatory signals, INFγ, GM-CSF, and LPS, induced TSP-4 expression in macrophages in vivo and in cell culture. Deficiency in TSP-4 in macrophages from Thbs4−/− mice reduced the expression of pro-inflammatory macrophage markers, suggesting that TSP-4 facilitates macrophage differentiation into a pro-inflammatory phenotype. Expression of TSP-4, especially more active P387-TSP-4, was associated with higher cellular apoptosis. Cultured macrophages displayed increased adhesion to TSP-4 and reduced migration in presence of TSP-4, and these responses were further increased with P387 variant. We concluded that TSP-4 expression in macrophages increases their accumulation in tissues during the acute inflammatory process and supports macrophage differentiation into a pro-inflammatory phenotype. In a model of acute inflammation, TSP-4 supports pro-inflammatory macrophage apoptosis, a response that is closely related to their pro-inflammatory activity and release of pro-inflammatory signals. P387-TSP-4 was found to be the more active form of TSP-4 in all examined functions.
Down-regulation of long non-coding RNA HOTAIR promotes angiogenesis via regulating miR-126/SCEL pathways in burn wound healing
Authors: Jiang Bimei , Tang Yuting , Wang Hao , Chen Cheng , Yu Wenchang , Sun Hui , Duan Mengting , Lin Xiaofang , Liang Pengfei 
Published: January 2020

AbstractmiR-126, an endothelial-specific microRNA, is associated to vascular integrity and angiogenesis. It is well established that angiogenesis plays a critical role in burn wound healing. However, there was a lack of understanding of the mechanism by which miR-126 regulates angiogenesis during burn wound healing. HOX transcript antisense intergenic RNA (HOTAIR) is a well-characterized long non-coding RNA (lncRNA) involved in cell proliferation, apoptosis, migration, and invasion of cancer cells. Sciellin (SCEL), a precursor to the cornified envelope of human keratinocytes, has been shown to inhibit migration and invasion capabilities of colorectal cancer cells. In this study, a cohort of 20 burn wound tissues and paired adjacent normal tissues were collected. LncRNA and messenger RNA expression profiles were screened by microarray analysis in five pairs of samples with mostly increased miR-126 levels. miR-126 was highly expressed in burn wound tissues and human umbilical vein endothelial cells (HUVECs) exposed to heat stress, whereas HOTAIR and SCEL were down-regulated after thermal injury. Bioinformatic analysis, dual luciferase reporter assay, and quantitative real-time PCR were conducted to validate that HOTAIR and SCEL competitively bind to miR-126 to function as the competitive endogenous RNA. miR-126 promoted endothelial cell proliferation, migration, and angiogenesis, but suppressed apoptosis, while HOTAIR and SCEL exerted opposite effects in HUVECs. The biological functions were determined by MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) assay, Annexin-V-FITC/PI (propidium iodide/fluorescein isothiocyanate) staining, transwell migration, and tube formation assays. Collectively, our study revealed that HOTAIR/miR-126/SCEL axis contributes to burn wound healing through mediating angiogenesis.
Intravenous immunoglobulin mediates anti-inflammatory effects in peripheral blood mononuclear cells by inducing autophagy
Authors: Das Mrinmoy , Karnam Anupama , Stephen-Victor Emmanuel , Gilardin Laurent , Bhatt Bharat , Kumar Sharma Varun , Rambabu Naresh , Patil Veerupaxagouda , Lecerf Maxime , Käsermann Fabian , Bruneval Patrick , Narayanaswamy Balaji Kithiganahalli , Benveniste Olivier , Kaveri Srini V. , Bayry Jagadeesh 
Published: January 2020

AbstractAutophagy plays an important role in the regulation of autoimmune and autoinflammatory responses of the immune cells. Defective autophagy process is associated with various autoimmune and inflammatory diseases. Moreover, in many of these diseases, the therapeutic use of normal immunoglobulin G or intravenous immunoglobulin (IVIG), a pooled normal IgG preparation, is well documented. Therefore, we explored if IVIG immunotherapy exerts therapeutic benefits via induction of autophagy in the immune cells. Here we show that IVIG induces autophagy in peripheral blood mononuclear cells (PBMCs). Further dissection of this process revealed that IVIG-induced autophagy is restricted to inflammatory cells like monocytes, dendritic cells, and M1 macrophages but not in cells associated with Th2 immune response like M2 macrophages. IVIG induces autophagy by activating AMP-dependent protein kinase, beclin-1, class III phosphoinositide 3-kinase and p38 mitogen-activated protein kinase and by inhibiting mammalian target of rapamycin. Mechanistically, IVIG-induced autophagy is F(ab′)2-dependent but sialylation independent, and requires endocytosis of IgG by innate cells. Inhibition of autophagy compromised the ability of IVIG to suppress the inflammatory cytokines in innate immune cells. Moreover, IVIG therapy in inflammatory myopathies such as dermatomyositis, antisynthetase syndrome and immune-mediated necrotizing myopathy induced autophagy in PBMCs and reduced inflammatory cytokines in the circulation, thus validating the translational importance of these results. Our data provide insight on how circulating normal immunoglobulins maintain immune homeostasis and explain in part the mechanism by which IVIG therapy benefits patients with autoimmune and inflammatory diseases.
Peptidoglycan reshaping by a noncanonical peptidase for helical cell shape in Campylobacter jejuni
Authors: Min Kyungjin , An Doo Ri , Yoon Hye-Jin , Rana Neha , Park Ji Su , Kim Jinshil , Lee Mijoon , Hesek Dusan , Ryu Sangryeol , Kim B. Moon , Mobashery Shahriar , Suh Se Won , Lee Hyung Ho 
Published: January 2020

AbstractAssembly of the peptidoglycan is crucial in maintaining viability of bacteria and in defining bacterial cell shapes, both of which are important for existence in the ecological niche that the organism occupies. Here, eight crystal structures for a member of the cell-shape-determining class of Campylobacter jejuni, the peptidoglycan peptidase 3 (Pgp3), are reported. Characterization of the turnover chemistry of Pgp3 reveals cell wall d,d-endopeptidase and d,d-carboxypeptidase activities. Catalysis is accompanied by large conformational changes upon peptidoglycan binding, whereby a loop regulates access to the active site. Furthermore, prior hydrolysis of the crosslinked peptide stem from the saccharide backbone of the peptidoglycan on one side is a pre-requisite for its recognition and turnover by Pgp3. These analyses reveal the noncanonical nature of the transformations at the core of the events that define the morphological shape for C. jejuni as an intestinal pathogen.
The Medical Genome Reference Bank contains whole genome and phenotype data of 2570 healthy elderly
Authors: Pinese Mark , Lacaze Paul , Rath Emma M. , Stone Andrew , Brion Marie-Jo , Ameur Adam , Nagpal Sini , Puttick Clare , Husson Shane , Degrave Dmitry , Cristina Tina Navin , Kahl Vivian F. S. , Statham Aaron L. , Woods Robyn L. , McNeil John J. , Riaz Moeen , Barr Margo , Nelson Mark R. , Reid Christopher M. , Murray Anne M. , Shah Raj C. , Wolfe Rory , Atkins Joshua R. , Fitzsimmons Chantel , Cairns Heath M. , Green Melissa J. , Carr Vaughan J. , Cowley Mark J. , Pickett Hilda A. , James Paul A. , Powell Joseph E. , Kaplan Warren , Gibson Greg , Gyllensten Ulf , Cairns Murray J. , McNamara Martin , Dinger Marcel E. , Thomas David M. 
Published: January 2020

AbstractPopulation health research is increasingly focused on the genetic determinants of healthy ageing, but there is no public resource of whole genome sequences and phenotype data from healthy elderly individuals. Here we describe the first release of the Medical Genome Reference Bank (MGRB), comprising whole genome sequence and phenotype of 2570 elderly Australians depleted for cancer, cardiovascular disease, and dementia. We analyse the MGRB for single-nucleotide, indel and structural variation in the nuclear and mitochondrial genomes. MGRB individuals have fewer disease-associated common and rare germline variants, relative to both cancer cases and the gnomAD and UK Biobank cohorts, consistent with risk depletion. Age-related somatic changes are correlated with grip strength in men, suggesting blood-derived whole genomes may also provide a biologic measure of age-related functional deterioration. The MGRB provides a broadly applicable reference cohort for clinical genetics and genomic association studies, and for understanding the genetics of healthy ageing.
A biphasic growth model for cell pole elongation in mycobacteria
Authors: Hannebelle Mélanie T. M. , Ven Joëlle X. Y. , Toniolo Chiara , Eskandarian Haig A. , Vuaridel-Thurre Gaëlle , McKinney John D. , Fantner Georg E. 
Published: January 2020

AbstractMycobacteria grow by inserting new cell wall material in discrete zones at the cell poles. This pattern implies that polar growth zones must be assembled de novo at each division, but the mechanisms that control the initiation of new pole growth are unknown. Here, we combine time-lapse optical and atomic force microscopy to measure single-cell pole growth in mycobacteria with nanometer-scale precision. We show that single-cell growth is biphasic due to a lag phase of variable duration before the new pole transitions from slow to fast growth. This transition and cell division are independent events. The difference between the lag and interdivision times determines the degree of single-cell growth asymmetry, which is high in fast-growing species and low in slow-growing species. We propose a biphasic growth model that is distinct from previous unipolar and bipolar models and resembles “new end take off” (NETO) dynamics of polar growth in fission yeast.
Easy access to medium-sized lactones through metal carbene migratory insertion enabled 1,4-palladium shift
Authors: Yu Yinghua , Chakraborty Pushkin , Song Jinshuai , Zhu Lei , Li Chunsen , Huang Xueliang 
Published: January 2020

AbstractReactions that efficiently construct medium-sized lactones are significant, as they overcome the unfavorable entropic factor and transannular interactions for ring closure, and the lactones produced are common structural motifs recurring in many biologically active compounds. Herein, we describe a valuable strategy for medium-sized lactone synthesis by accomplishing site-selective C–H bond functionalization via a palladium carbene migratory insertion enabled 1,4-palladium shift. The overall process achieves the formal dimerization of two readily available benzaldehyde derivatives, providing value-added products medium-sized lactones. Our method is amenable to late-stage modification of approved drugs and other complex molecules. Mechanistic studies including deuterium-labeling experiments and DFT calculation shed light on the reaction pathways.
Neural dynamics of the attentional blink revealed by encoding orientation selectivity during rapid visual presentation
Authors: Tang Matthew F. , Ford Lucy , Arabzadeh Ehsan , Enns James T. , Visser Troy A. W. , Mattingley Jason B. 
Published: January 2020

AbstractThe human brain is inherently limited in the information it can make consciously accessible. When people monitor a rapid stream of visual items for two targets, they typically fail to see the second target if it occurs within 200–500 ms of the first, a phenomenon called the attentional blink (AB). The neural basis for the AB is poorly understood, partly because conventional neuroimaging techniques cannot resolve visual events displayed close together in time. Here we introduce an approach that characterises the precise effect of the AB on behaviour and neural activity. We employ multivariate encoding analyses to extract feature-selective information carried by randomly-oriented gratings. We show that feature selectivity is enhanced for correctly reported targets and suppressed when the same items are missed, whereas irrelevant distractor items are unaffected. The findings suggest that the AB involves both short- and long-range neural interactions between visual representations competing for access to consciousness.
Synergistic effect of quinary molten salts and ruthenium catalyst for high-power-density lithium-carbon dioxide cell
Authors: Baek Kyungeun , Jeon Woo Cheol , Woo Seongho , Kim Jin Chul , Lee Jun Gyeong , An Kwangjin , Kwak Sang Kyu , Kang Seok Ju 
Published: January 2020

AbstractWith a recent increase in interest in metal-gas batteries, the lithium-carbon dioxide cell has attracted considerable attention because of its extraordinary carbon dioxide-capture ability during the discharge process and its potential application as a power source for Mars exploration. However, owing to the stable lithium carbonate discharge product, the cell enables operation only at low current densities, which significantly limits the application of lithium-carbon dioxide batteries and effective carbon dioxide-capture cells. Here, we investigate a high-performance lithium-carbon dioxide cell using a quinary molten salt electrolyte and ruthenium nanoparticles on the carbon cathode. The nitrate-based molten salt electrolyte allows us to observe the enhanced carbon dioxide-capture rate and the reduced discharge-charge over-potential gap with that of conventional lithium-carbon dioxide cells. Furthermore, owing to the ruthernium catalyst, the cell sustains its performance over more than 300 cycles at a current density of 10.0 A g−1 and exhibits a peak power density of 33.4 mW cm−2.
Transcription reinitiation by recycling RNA polymerase that diffuses on DNA after releasing terminated RNA
Authors: Kang Wooyoung , Ha Kook Sun , Uhm Heesoo , Park Kyuhyong , Lee Ja Yil , Hohng Sungchul , Kang Changwon 
Published: January 2020

AbstractDespite extensive studies on transcription mechanisms, it is unknown how termination complexes are disassembled, especially in what order the essential components dissociate. Our single-molecule fluorescence study unveils that RNA transcript release precedes RNA polymerase (RNAP) dissociation from the DNA template much more often than their concurrent dissociations in intrinsic termination of bacterial transcription. As termination is defined by the release of product RNA from the transcription complex, the subsequent retention of RNAP on DNA constitutes a previously unidentified stage, termed here as recycling. During the recycling stage, post-terminational RNAPs one-dimensionally diffuse on DNA in downward and upward directions, and can initiate transcription again at the original and nearby promoters in the case of retaining a sigma factor. The efficiency of this event, termed here as reinitiation, increases with supplement of a sigma factor. In summary, after releasing RNA product at intrinsic termination, recycling RNAP diffuses on the DNA template for reinitiation most of the time.
Alternative transcription cycle for bacterial RNA polymerase
Authors: Harden Timothy T. , Herlambang Karina S. , Chamberlain Mathew , Lalanne Jean-Benoît , Wells Christopher D. , Li Gene-Wei , Landick Robert , Hochschild Ann , Kondev Jane , Gelles Jeff 
Published: January 2020

AbstractRNA polymerases (RNAPs) transcribe genes through a cycle of recruitment to promoter DNA, initiation, elongation, and termination. After termination, RNAP is thought to initiate the next round of transcription by detaching from DNA and rebinding a new promoter. Here we use single-molecule fluorescence microscopy to observe individual RNAP molecules after transcript release at a terminator. Following termination, RNAP almost always remains bound to DNA and sometimes exhibits one-dimensional sliding over thousands of basepairs. Unexpectedly, the DNA-bound RNAP often restarts transcription, usually in reverse direction, thus producing an antisense transcript. Furthermore, we report evidence of this secondary initiation in live cells, using genome-wide RNA sequencing. These findings reveal an alternative transcription cycle that allows RNAP to reinitiate without dissociating from DNA, which is likely to have important implications for gene regulation.
TGFβ2-induced formation of lipid droplets supports acidosis-driven EMT and the metastatic spreading of cancer cells
Authors: Corbet Cyril , Bastien Estelle , Santiago de Jesus Joao Pedro , Dierge Emeline , Martherus Ruben , Vander Linden Catherine , Doix Bastien , Degavre Charline , Guilbaud Céline , Petit Laurenne , Michiels Carine , Dessy Chantal , Larondelle Yvan , Feron Olivier 
Published: January 2020

AbstractAcidosis, a common characteristic of the tumor microenvironment, is associated with alterations in metabolic preferences of cancer cells and progression of the disease. Here we identify the TGF-β2 isoform at the interface between these observations. We document that acidic pH promotes autocrine TGF-β2 signaling, which in turn favors the formation of lipid droplets (LD) that represent energy stores readily available to support anoikis resistance and cancer cell invasiveness. We find that, in cancer cells of various origins, acidosis-induced TGF-β2 activation promotes both partial epithelial-to-mesenchymal transition (EMT) and fatty acid metabolism, the latter supporting Smad2 acetylation. We show that upon TGF-β2 stimulation, PKC-zeta-mediated translocation of CD36 facilitates the uptake of fatty acids that are either stored as triglycerides in LD through DGAT1 or oxidized to generate ATP to fulfill immediate cellular needs. We also address how, by preventing fatty acid mobilization from LD, distant metastatic spreading may be inhibited.
A common wild rice-derived BOC1 allele reduces callus browning in indica rice transformation
Authors: Zhang Kun , Su Jingjing , Xu Min , Zhou Zhihui , Zhu Xiaoyang , Ma Xin , Hou Jingjing , Tan Lubin , Zhu Zuofeng , Cai Hongwei , Liu Fengxia , Sun Hongying , Gu Ping , Li Chen , Liang Yuntao , Zhao Wensheng , Sun Chuanqing , Fu Yongcai 
Published: January 2020

AbstractCallus browning, a common trait derived from the indica rice cultivar (Oryza sativa L.), is a challenge to transformation regeneration. Here, we report the map-based cloning of BROWNING OF CALLUS1 (BOC1) using a population derived from crossing Teqing, an elite indica subspecies exhibiting callus browning, and Yuanjiang, a common wild rice accession (Oryza rufipogon Griff.) that is less susceptible to callus browning. We show that BOC1 encodes a SIMILAR TO RADICAL-INDUCED CELL DEATH ONE (SRO) protein. Callus browning can be reduced by appropriate upregulation of BOC1, which consequently improves the genetic transformation efficiency. The presence of a Tourist-like miniature inverted-repeat transposable element (Tourist MITE) specific to wild rice in the promoter of BOC1 increases the expression of BOC1 in callus. BOC1 may decrease cell senescence and death caused by oxidative stress. Our study provides a gene target for improving tissue culturability and genetic transformation.
Dissecting transcriptomic signatures of neuronal differentiation and maturation using iPSCs
Authors: Burke Emily E. , Chenoweth Joshua G. , Shin Joo Heon , Collado-Torres Leonardo , Kim Suel-Kee , Micali Nicola , Wang Yanhong , Colantuoni Carlo , Straub Richard E. , Hoeppner Daniel J. , Chen Huei-Ying , Sellers Alana , Shibbani Kamel , Hamersky Gregory R. , Diaz Bustamante Marcelo , Phan BaDoi N. , Ulrich William S. , Valencia Cristian , Jaishankar Amritha , Price Amanda J. , Rajpurohit Anandita , Semick Stephen A. , Bürli Roland W. , Barrow James C. , Hiler Daniel J. , Page Stephanie C. , Martinowich Keri , Hyde Thomas M. , Kleinman Joel E. , Berman Karen F. , Apud Jose A. , Cross Alan J. , Brandon Nicholas J. , Weinberger Daniel R. , Maher Brady J. , McKay Ronald D. G. , Jaffe Andrew E. 
Published: January 2020

AbstractHuman induced pluripotent stem cells (hiPSCs) are a powerful model of neural differentiation and maturation. We present a hiPSC transcriptomics resource on corticogenesis from 5 iPSC donor and 13 subclonal lines across 9 time points over 5 broad conditions: self-renewal, early neuronal differentiation, neural precursor cells (NPCs), assembled rosettes, and differentiated neuronal cells. We identify widespread changes in the expression of both individual features and global patterns of transcription. We next demonstrate that co-culturing human NPCs with rodent astrocytes results in mutually synergistic maturation, and that cell type-specific expression data can be extracted using only sequencing read alignments without cell sorting. We lastly adapt a previously generated RNA deconvolution approach to single-cell expression data to estimate the relative neuronal maturity of iPSC-derived neuronal cultures and human brain tissue. Using many public datasets, we demonstrate neuronal cultures are maturationally heterogeneous but contain subsets of neurons more mature than previously observed.
Controlled release of H2S and NO gases through CO2-stimulated anion exchange
Authors: Ishihara Shinsuke , Iyi Nobuo 
Published: January 2020

AbstractDifficulties related to handling gases are a common bottleneck for applications. Although solid materials that release gas molecules under external stimuli exist, they require an external energy or a device for reliable operation. Herein, we report a CO2 stimulus for controlled release of p.p.m.-level functional gases from solid materials. A CO2-preferential anion-exchange property of layered double hydroxides and redox reactions in gas molecules are combined to release various gases (including H2S and NO) under ambient air from HS− and NO2−-incorporated layered double hydroxides, respectively. The profiles of gas release are mainly governed by the difference of pKa between H2CO3 and resulting acids (formed through protonation of interlayer anions), and are not so susceptible to the variation of relative humidity in air. Moreover, structural modulation of solid materials enables fine control of the gas release profiles. The use of safe, ubiquitous, and nearly constant (~400 p.p.m. in atmosphere) CO2 stimulus offers broad applications for functional gases.