bluuebunny/crossref_metadata_2025_split huggingface dataset:
Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification
Authors: Moudjou Mohammed , Chapuis Jérôme , Mekrouti Mériem , Reine Fabienne , Herzog Laetitia , Sibille Pierre , Laude Hubert , Vilette Didier , Andréoletti Olivier , Rezaei Human , Dron Michel , Béringue Vincent 
Published: July 2016

AbstractPrions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrPC glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrPC species of interest as substrate. Applying the technique to PrPC glycosylation mutants expressing cells revealed that neither PrPC nor PrPSc glycoform stoichiometry was instrumental to PrPSc formation and strainness perpetuation. Our study supports the view that strain properties, including PrPSc glycotype are enciphered within PrPSc structural backbone, not in the attached glycans.
The effects of cytosine methylation on general transcription factors
Authors: Jin Jianshi , Lian Tengfei , Gu Chan , Yu Kai , Gao Yi Qin , Su Xiao-Dong 
Published: July 2016

AbstractDNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.
The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Authors: Debowski Katharina , Drummer Charis , Lentes Jana , Cors Maren , Dressel Ralf , Lingner Thomas , Salinas-Riester Gabriela , Fuchs Sigrid , Sasaki Erika , Behr Rüdiger 
Published: July 2016

AbstractEmbryonic stem cells (ESCs) are useful for the study of embryonic development. However, since research on naturally conceived human embryos is limited, non-human primate (NHP) embryos and NHP ESCs represent an excellent alternative to the corresponding human entities. Though, ESC lines derived from naturally conceived NHP embryos are still very rare. Here, we report the generation and characterization of four novel ESC lines derived from natural preimplantation embryos of the common marmoset monkey (Callithrix jacchus). For the first time we document derivation of NHP ESCs derived from morula stages. We show that quantitative chromosome-wise transcriptome analyses precisely reflect trisomies present in both morula-derived ESC lines. We also demonstrate that the female ESC lines exhibit different states of X-inactivation which is impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST). The novel marmoset ESC lines will promote basic primate embryo and ESC studies as well as preclinical testing of ESC-based regenerative approaches in NHP.
The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus
Authors: Choi Yun Sik , Kim Yunji , Yoon Hye-Jung , Baek Keum Jin , Alam Jehan , Park Hee Kyung , Choi Youngnim 
Published: July 2016

AbstractOral lichen planus (OLP) is a chronic T cell-mediated mucocutaneous disease of unknown etiopathogenesis. Although various antigens have been considered, what actually triggers the inflammatory response of T cells is unknown. In the present study, we propose that intracellular bacteria present within tissues trigger T cell infiltration and provide target antigens. Sections of OLP (n = 36) and normal (n = 10) oral mucosal tissues were subjected to in situ hybridization using a universal probe targeting the bacterial 16S rRNA gene and immunohistochemistry with anti-CD3, anti-CD4, anti-CD8, and anti-macrophage-specific antibodies. Bacteria were abundant throughout the epithelium and the lamina propria of OLP tissues, which exhibited positive correlations with the levels of infiltrated CD3+, CD4+, and CD8+ cells. Furthermore, bacteria were detected within the infiltrated T cells. Pyrosequencing analysis of the mucosal microbiota from OLP patients (n = 13) and control subjects (n = 11) revealed a decrease in Streptococcus and increases in gingivitis/periodontitis-associated bacteria in OLP lesions. Using the selected bacterial species, we demonstrated that certain oral bacteria damage the epithelial physical barrier, are internalized into epithelial cells or T cells, and induce production of T cell chemokines CXCL10 and CCL5. Our findings provide insights into the pathogenesis of OLP.
Amyloid precursor protein expression and processing are differentially regulated during cortical neuron differentiation
Authors: Bergström Petra , Agholme Lotta , Nazir Faisal Hayat , Satir Tugce Munise , Toombs Jamie , Wellington Henrietta , Strandberg Joakim , Bontell Thomas Olsson , Kvartsberg Hlin , Holmström Maria , Boreström Cecilia , Simonsson Stina , Kunath Tilo , Lindahl Anders , Blennow Kaj , Hanse Eric , Portelius Erik , Wray Selina , Zetterberg Henrik 
Published: July 2016

AbstractAmyloid precursor protein (APP) and its cleavage product amyloid β (Aβ) have been thoroughly studied in Alzheimer’s disease. However, APP also appears to be important for neuronal development. Differentiation of induced pluripotent stem cells (iPSCs) towards cortical neurons enables in vitro mechanistic studies on human neuronal development. Here, we investigated expression and proteolytic processing of APP during differentiation of human iPSCs towards cortical neurons over a 100-day period. APP expression remained stable during neuronal differentiation, whereas APP processing changed. α-Cleaved soluble APP (sAPPα) was secreted early during differentiation, from neuronal progenitors, while β-cleaved soluble APP (sAPPβ) was first secreted after deep-layer neurons had formed. Short Aβ peptides, including Aβ1-15/16, peaked during the progenitor stage, while processing shifted towards longer peptides, such as Aβ1-40/42, when post-mitotic neurons appeared. This indicates that APP processing is regulated throughout differentiation of cortical neurons and that amyloidogenic APP processing, as reflected by Aβ1-40/42, is associated with mature neuronal phenotypes.
Local coexistence of VO2 phases revealed by deep data analysis
Authors: Strelcov Evgheni , Ievlev Anton , Belianinov Alex , Tselev Alexander , Kolmakov Andrei , Kalinin Sergei V. 
Published: July 2016

AbstractWe report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffer from information misinterpretation due to low resolving power.
The adipokine lipocalin-2 in the context of the osteoarthritic osteochondral junction
Authors: Villalvilla Amanda , García-Martín Adela , Largo Raquel , Gualillo Oreste , Herrero-Beaumont Gabriel , Gómez Rodolfo 
Published: July 2016

AbstractObesity and osteoarthritis (OA) form a vicious circle in which obesity contributes to cartilage destruction in OA, and OA-associated sedentary behaviour promotes weight gain. Lipocalin-2 (LCN2), a novel adipokine with catabolic activities in OA joints, contributes to the obesity and OA pathologies and is associated with other OA risk factors. LCN2 is highly induced in osteoblasts in the absence of mechanical loading, but its role in osteoblast metabolism is unclear. Therefore, because osteochondral junctions play a major role in OA development, we investigated the expression and role of LCN2 in osteoblasts and chondrocytes in the OA osteochondral junction environment. Our results showed that LCN2 expression in human osteoblasts and chondrocytes decreased throughout osteoblast differentiation and was induced by catabolic and inflammatory factors; however, TGF-β1 and IGF-1 reversed this induction. LCN2 reduced osteoblast viability in the presence of iron and enhanced the activity of MMP-9 released by osteoblasts. Moreover, pre-stimulated human osteoblasts induced LCN2 expression in human chondrocytes, but the inverse was not observed. Thus, LCN2 is an important catabolic adipokine in osteoblast and chondrocyte metabolism that is regulated by differentiation, inflammation and catabolic and anabolic stimuli, and LCN2 expression in chondrocytes is regulated in a paracrine manner after osteoblast stimulation.
An investigation of the antibacterial ability and cytotoxicity of a novel cu-bearing 317L stainless steel
Authors: Sun Da , Xu Dake , Yang Chunguang , Shahzad M. Babar , Sun Ziqing , Xia Jin , Zhao Jinlong , Gu Tingyue , Yang Ke , Wang Guixue 
Published: July 2016

AbstractIn order to solve the challenging problem of microbial infections caused by microorganisms on medical implants, it is imperative to develop novel antimicrobial biomaterials. This work demonstrated that 317L-Cu stainless steel (SS), created by adding copper through a solution and aging heat treatment process, exhibited good antibacterial properties against staphylococcus aureus, achieving 2 log reduction of planktonic cells after 5 days of incubation. In this study, the antibacterial test was performed using the plate count method, the fluorescence cell staining method and the quantitative polymerase chain reaction (qPCR) method. It is well known that a high concentration of copper ion can lead to cytotoxicity. This work explored the cytotoxicity of 317L-Cu SS through real-time cell analysis (RTCA). Experimental results demonstrated that the 317L-Cu SS possessed a satisfactory antibacterial ability against S. aureus, and the antibacterial rate based on the reduction of sessile cell count reached 98.3% after 24-hour treatment. The bacterial adhesion and the biofilm thickness were considerably reduced by the 317L-Cu SS. The results of RTCA suggested that 317L-Cu SS did not introduce cytotoxicity to mouse cells, indicating its suitability as a medical implant material.
Evolution equation for quantum coherence
Authors: Hu Ming-Liang , Fan Heng 
Published: July 2016

AbstractThe estimation of the decoherence process of an open quantum system is of both theoretical significance and experimental appealing. Practically, the decoherence can be easily estimated if the coherence evolution satisfies some simple relations. We introduce a framework for studying evolution equation of coherence. Based on this framework, we prove a simple factorization relation (FR) for the l1 norm of coherence and identified the sets of quantum channels for which this FR holds. By using this FR, we further determine condition on the transformation matrix of the quantum channel which can support permanently freezing of the l1 norm of coherence. We finally reveal the universality of this FR by showing that it holds for many other related coherence and quantum correlation measures.
Effect of the environment on the secondary metabolic profile of Tithonia diversifolia: a model for environmental metabolomics of plants
Authors: Sampaio Bruno Leite , Edrada-Ebel RuAngelie , Da Costa Fernando Batista 
Published: July 2016

AbstractTithonia diversifolia is an invasive weed commonly found in tropical ecosystems. In this work, we investigate the influence of different abiotic environmental factors on the plant’s metabolite profile by multivariate statistical analyses of spectral data deduced by UHPLC-DAD-ESI-HRMS and NMR methods. Different plant part samples of T. diversifolia which included leaves, stems, roots and inflorescences were collected from two Brazilian states throughout a 24-month period, along with the corresponding monthly environmental data. A metabolomic approach employing concatenated LC-MS and NMR data was utilised for the first time to study the relationships between environment and plant metabolism. A seasonal pattern was observed for the occurrence of metabolites that included sugars, sesquiterpenes lactones and phenolics in the leaf and stem parts, which can be correlated to the amount of rainfall and changes in temperature. The distribution of the metabolites in the inflorescence and root parts were mainly affected by variation of some soil nutrients such as Ca, Mg, P, K and Cu. We highlight the environment-metabolism relationship for T. diversifolia and the combined analytical approach to obtain reliable data that contributed to a holistic understanding of the influence of abiotic environmental factors on the production of metabolites in various plant parts.
Static and Dynamical Properties of heavy actinide Monopnictides of Lutetium
Authors: Mir Showkat H. , Jha Prakash C. , Islam M. S. , Banerjee Amitava , Luo Wei , Dabhi Shweta D. , Jha Prafulla K. , Ahuja R. 
Published: July 2016

AbstractIn this work, density functional theory within the framework of generalized gradient approximation has been used to investigate the structural, elastic, mechanical, and phonon properties of lutetium monopnictides in rock-salt crystal structure. The spin orbit coupling and Hubbard-U corrections are included to correctly predict the essential properties of these compounds. The elastic constants, Young’s modulus E, Poisson’s ratio v, shear modulus G, anisotropy factor A and Pugh’s ratio are computed. We found that all lutetium monopnictides are anisotropic and show brittle character. From the wave velocities along [100], [110] and [111] directions, melting temperature of lutetium monopnictides are predicted. Dynamical stability of these monopnictides has been studied by density functional perturbation theory.
Inferring phylogeny and speciation of Gymnosporangium species and their coevolution with host plants
Authors: Zhao Peng , Liu Fang , Li Ying-Ming , Cai Lei 
Published: July 2016

AbstractGymnosporangium species (Pucciniaceae, Pucciniales) cause serious diseases and significant economic losses to apple cultivars. Most of the reported species are heteroecious and complete their life cycles on two different plant hosts belonging to two unrelated genera, i.e. Juniperus and Malus. However, the phylogenetic relationships among Gymnosporangium species and the evolutionary history of Gymnosporangium on its aecial and telial hosts were still undetermined. In this study, we recognized species based on rDNA sequence data by using coalescent method of generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP) models. The evolutionary relationships of Gymnosporangium species and their hosts were investigated by comparing the cophylogenetic analyses of Gymnosporangium species with Malus species and Juniperus species, respectively. The concordant results of GMYC and PTP analyses recognized 14 species including 12 known species and two undescribed species. In addition, host alternations of 10 Gymnosporangium species were uncovered by linking the derived sequences between their aecial and telial stages. This study revealed the evolutionary process of Gymnosporangium species and clarified that the aecial hosts played more important roles than telial hosts in the speciation of Gymnosporangium species. Host switch, losses, duplication and failure to divergence all contributed to the speciation of Gymnosporangium species.
Phenol-soluble modulin α4 mediates Staphylococcus aureus-associated vascular leakage by stimulating heparin-binding protein release from neutrophils
Authors: li Lin , Pian Yaya , Chen Shaolong , Hao Huaijie , Zheng Yuling , Zhu Li , Xu Bin , Liu Keke , Li Min , Jiang Hua , Jiang Yongqiang 
Published: July 2016

AbstractVascular leakage frequently occurs in patients with severe Staphylococcus aureus infection. However, the mechanism underlying S. aureus infection-induced vascular leakage remains unclear. Here, we identified the S. aureus virulence factor phenol-soluble modulin (PSM)α4 from the culture supernatant of strain USA300 as a stimulator of heparin-binding protein (HBP) release from polymorphonuclear neutrophils (PMNs) and demonstrated that PSMα4-induced HBP release from PMNs leads to vascular leakage. PSMα4 appeared less cytolytic than PSMα1–3 and was insensitive to lipoproteins; it significantly increased myeloperoxidase and elastase release from PMNs and cell surface CD63 expression in PMNs. PSMα4-induced HBP release required formyl peptide receptor 2 (FPR2) and phosphoinositide 3-kinase (PI3K) and depended on Ca2+ influx and cytoskeleton rearrangement. Thus, PSMα4 may stimulate HBP release by activating FPR2 and PI3K to initiate PMN degranulation. PSMα4-induced HBP release from PMNs increased endothelial cell monolayer permeability in vitro and induced vascular leakage in mice. This novel function of PSMα4 may contribute to the pathogenesis of S. aureus and may be a potential therapeutic target.
The relationship between sex change and reproductive success in a protandric marine gastropod
Authors: Brante Antonio , Quiñones Adriana , Silva Francisco 
Published: July 2016

AbstractProtandric species switch sex during their lifetime. According to theory, the time (body size) at which sex change occurs is determined by the reproductive success of individuals affected by social interactions as well as by post-copulatory factors. Experimental evidence is biased to few social systems making the exploration of general patterns difficult. We used the protandric marine gastropod Crepidula coquimbensis that partakes in intrabrood sibling cannibalism to test the following hypotheses: 1. Male-male competition for access to females and sibling cannibalism determine male reproductive success; 2. Males with greater access to females and with higher reproductive success will have reduced growth rates and will delay sex change. Artificial aggregations with different social structures were constructed and male reproductive success was estimated by paternity analysis. The results supported our expectations showing that male competitive ability for access to the female, time spent by males in the copulatory position and sibling cannibalism affect reproductive success and influence time to sex change, with less successful males hastening sex change. Also, males that spent more time in the copulatory position had reduced growth rates. Comparing these results with those reported for other sequential hermaphrodites provides evidence supporting general patterns of sex change in nature.
Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis
Authors: Wong Laiping , Jiang Kaiyu , Chen Yanmin , Hennon Teresa , Holmes Lucy , Wallace Carol A. , Jarvis James N. 
Published: July 2016

AbstractJuvenile Idiopathic Arthritis (JIA) is one of the most common chronic disease conditions affecting children in the USA. As with many rheumatic diseases, there is growing interest in using genomic technologies to develop biomarkers for either diagnosis or to guide treatment (“personalized medicine”). Here, we explore the use of gene expression patterns in peripheral blood mononuclear cells (PBMC) as a first step approach to developing such biomarkers. Although PBMC carry many theoretical advantages for translational research, we have found that sample heterogeneity makes RNASeq on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA. RNASeq studies of homogeneous cell populations are more likely to be useful and informative.
Green tea catechins are potent anti-oxidants that ameliorate sodium iodate-induced retinal degeneration in rats
Authors: Yang Yaping , Qin Yong Jie , Yip Yolanda W. Y. , Chan Kwok Ping , Chu Kai On , Chu Wai Kit , Ng Tsz Kin , Pang Chi Pui , Chan Sun On 
Published: July 2016

AbstractGreen tea extracts exhibit anti-oxidative and anti-inflammatory actions in different disease conditions. We hypothesized that green tea extract and its catechin constituents ameliorate sodium iodate-induced retinal degeneration in rats by counteracting oxidative stress. In this study, adult Sprague-Dawley rats were intravenously injected with a single dose of sodium iodate. Green tea extract (GTE; Theaphenon-E) or combinations of its catechin constituents, including (−)-epigallocatechin gallate (EGCG), were administered intra-gastrically before injection. Live imaging analysis using confocal scanning laser ophthalmoscopy and spectral-domain optical coherence tomography showed a progressive increase of degenerating profile across the retinal surface and decrease in thickness of outer nuclear layer (ONL) at Day-14 of post-injection. These lesions were significantly ameliorated by Theaphenon-E and catechin combinations with EGCG. Catechins with exclusion of EGCG did not show obvious protective effect. Histological analyses confirmed that Theaphenon-E and catechins containing EGCG protect the retina by reducing ONL disruption. Retinal protective effects were associated with reduced expression of superoxide dismutase, glutathione peroxidase and caspase-3 and suppression of 8-iso-Prostaglandin F2α generation in the retina. In summary, GTE and its catechin constituents are potent anti-oxidants that offer neuroprotection to the outer retinal degeneration after sodium iodate insult, among which EGCG is the most active constituent.