bluuebunny/crossref_metadata_2025_split huggingface dataset:
1-Methyl-tryptophan attenuates regulatory T cells differentiation due to the inhibition of estrogen-IDO1-MRC2 axis in endometriosis
Authors: Wei Chunyan , Mei Jie , Tang Lingli , Liu Yukai , Li Dajin , Li Mingqing , Zhu Xiaoyong 
Published: December 2016

AbstractFoxp3+ regulatory T (Treg) cells contribute to the local dysfunctional immune environment in endometriosis, an estrogen-dependent gynecological disease, which affects the function of ectopic endometrial tissue clearance by the immune system. The reason for the high percentage of peritoneal Treg in endometriosis patients is unknown. Here, we show that the proportion of peritoneal Treg cells increases as endometriosis progresses. To determine the probable mechanism, we established a naive T cell-macrophage-endometrial stromal cell (ESC) co-culture system to mimic the peritoneal cavity microenvironment. After adding 1-methyl-tryptophan (1-MT), a specific inhibitor of indoleamine 2,3-dioxygenase-1 (IDO1), to the co-culture system, we found that the differentiation of Treg cells, mainly IL-10+ Treg cells, decreased. Therefore, 1-MT-pretreated ESCs-educated Treg cells performed impaired suppressive function. Moreover, estrogen promoted the differentiation of Treg cells by elevating IDO1 expression in the ectopic lesion. Subsequently, we examined mannose receptor C, type 2 (MRC2), which is an up-stream molecule of IL-10, by bioinformatics analysis and real-time PCR validation. MRC2 expression in ectopic ESCs was notably lower than that in normal ESCs, which further negatively regulated the expression of IDO1 and Ki-67 in ESCs. Furthermore, MRC2 is required for Treg differentiation in the ectopic lesion, especially that for CD4high Treg. Therefore, MRC2-silenced ESCs-educated Treg manifested a stronger suppressive function in vitro. Consistently, the percentage of Treg increased when MRC2-shRNA was administered in the peritoneal cavity of endometriosis-disease mice model. Besides, 1-MT improved the condition of endometriosis, in terms of reducing the number and weight of total ectopic lesions in vivo. These results indicate that the estrogen-IDO1-MRC2 axis participates in the differentiation and function of Treg and is involved in the development of endometriosis. Thus, blockage of IDO1 in the ectopic lesion, which does not influence physiological functions of estrogen, may be considered a potential therapy for endometriosis.
Therapeutic advantage of pro-electrophilic drugs to activate the Nrf2/ARE pathway in Alzheimer’s disease models
Authors: Lipton Stuart A , Rezaie Tayebeh , Nutter Anthony , Lopez Kevin M , Parker James , Kosaka Kunio , Satoh Takumi , McKercher Scott R , Masliah Eliezer , Nakanishi Nobuki 
Published: December 2016

AbstractAlzheimer’s disease (AD) is characterized by synaptic and neuronal loss, which occurs at least partially through oxidative stress induced by oligomeric amyloid-β (Aβ)-peptide. Carnosic acid (CA), a chemical found in rosemary and sage, is a pro-electrophilic compound that is converted to its active form by oxidative stress. The active form stimulates the Keap1/Nrf2 transcriptional pathway and thus production of phase 2 antioxidant enzymes. We used both in vitro and in vivo models. For in vitro studies, we evaluated protective effects of CA on primary neurons exposed to oligomeric Aβ. For in vivo studies, we used two transgenic mouse models of AD, human amyloid precursor protein (hAPP)-J20 mice and triple transgenic (3xTg AD) mice. We treated these mice trans-nasally with CA twice weekly for 3 months. Subsequently, we performed neurobehavioral tests and quantitative immunohistochemistry to assess effects on AD-related phenotypes, including learning and memory, and synaptic damage. In vitro, CA reduced dendritic spine loss in rat neurons exposed to oligomeric Aβ. In vivo, CA treatment of hAPP-J20 mice improved learning and memory in the Morris water maze test. Histologically, CA increased dendritic and synaptic markers, and decreased astrogliosis, Aβ plaque number, and phospho-tau staining in the hippocampus. We conclude that CA exhibits therapeutic benefits in rodent AD models and since the FDA has placed CA on the ‘generally regarded as safe’ (GRAS) list, thus obviating the need for safety studies, human clinical trials will be greatly expedited.
Alternative splicing of a cryptic exon embedded in intron 6 of SMN1 and SMN2
Authors: Yoshimoto Satomi , Harahap Nur Imma Fatimah , Hamamura Yuko , Ar Rochmah Mawaddah , Shima Ai , Morisada Naoya , Shinohara Masakazu , Saito Toshio , Saito Kayoko , Lai Poh San , Matsuo Masafumi , Awano Hiroyuki , Morioka Ichiro , Iijima Kazumoto , Nishio Hisahide 
Published: December 2016

AbstractBoth survival of motor neuron (SMN) genes are associated with spinal muscular atrophy; mutations in SMN1 cause the disease, and SMN2 modulates its severity. It is established that different alternative splicing of exon 7 occurs for SMN1 and SMN2, and a cryptic exon was recently found in intron 6 of both genes. Here, we characterize this cryptic exon and clarify its alternative splicing pattern in control and spinal muscular atrophy cells.
Nitrous oxide as a function of oxygen and archaeal gene abundance in the North Pacific
Authors: Trimmer Mark , Chronopoulou Panagiota-Myrsini , Maanoja Susanna T. , Upstill-Goddard Robert C. , Kitidis Vassilis , Purdy Kevin J. 
Published: December 2016

AbstractOceanic oxygen minimum zones are strong sources of the potent greenhouse gas N2O but its microbial source is unclear. We characterized an exponential response in N2O production to decreasing oxygen between 1 and 30 μmol O2 l−1 within and below the oxycline using 15NO2−, a relationship that held along a 550 km offshore transect in the North Pacific. Differences in the overall magnitude of N2O production were accounted for by archaeal functional gene abundance. A one-dimensional (1D) model, parameterized with our experimentally derived exponential terms, accurately reproduces N2O profiles in the top 350 m of water column and, together with a strong 45N2O signature indicated neither canonical nor nitrifier–denitrification production while statistical modelling supported production by archaea, possibly via hybrid N2O formation. Further, with just archaeal N2O production, we could balance high-resolution estimates of sea-to-air N2O exchange. Hence, a significant source of N2O, previously described as leakage from bacterial ammonium oxidation, is better described by low-oxygen archaeal production at the oxygen minimum zone’s margins.
LncBRM initiates YAP1 signalling activation to drive self-renewal of liver cancer stem cells
Authors: Zhu Pingping , Wang Yanying , Wu Jiayi , Huang Guanling , Liu Benyu , Ye Buqing , Du Ying , Gao Guangxia , Tian Yong , He Lei , Fan Zusen 
Published: December 2016

AbstractLiver cancer stem cells (CSCs) may contribute to the high rate of recurrence and heterogeneity of hepatocellular carcinoma (HCC). However, the biology of hepatic CSCs remains largely undefined. Through analysis of transcriptome microarray data, we identify a long noncoding RNA (lncRNA) called lncBRM, which is highly expressed in liver CSCs and HCC tumours. LncBRM is required for the self-renewal maintenance of liver CSCs and tumour initiation. In liver CSCs, lncBRM associates with BRM to initiate the BRG1/BRM switch and the BRG1-embedded BAF complex triggers activation of YAP1 signalling. Moreover, expression levels of lncBRM together with YAP1 signalling targets are positively correlated with tumour severity of HCC patients. Therefore, lncBRM and YAP1 signalling may serve as biomarkers for diagnosis and potential drug targets for HCC.
Chirped pulse amplification in an extreme-ultraviolet free-electron laser
Authors: Gauthier David , Allaria Enrico , Coreno Marcello , Cudin Ivan , Dacasa Hugo , Danailov Miltcho Boyanov , Demidovich Alexander , Di Mitri Simone , Diviacco Bruno , Ferrari Eugenio , Finetti Paola , Frassetto Fabio , Garzella David , Künzel Swen , Leroux Vincent , Mahieu Benoît , Mahne Nicola , Meyer Michael , Mazza Tommaso , Miotti Paolo , Penco Giuseppe , Raimondi Lorenzo , Ribič Primož Rebernik , Richter Robert , Roussel Eléonore , Schulz Sebastian , Sturari Luca , Svetina Cristian , Trovò Mauro , Walker Paul Andreas , Zangrando Marco , Callegari Carlo , Fajardo Marta , Poletto Luca , Zeitoun Philippe , Giannessi Luca , De Ninno Giovanni 
Published: December 2016

AbstractChirped pulse amplification in optical lasers is a revolutionary technique, which allows the generation of extremely powerful femtosecond pulses in the infrared and visible spectral ranges. Such pulses are nowadays an indispensable tool for a myriad of applications, both in fundamental and applied research. In recent years, a strong need emerged for light sources producing ultra-short and intense laser-like X-ray pulses, to be used for experiments in a variety of disciplines, ranging from physics and chemistry to biology and material sciences. This demand was satisfied by the advent of short-wavelength free-electron lasers. However, for any given free-electron laser setup, a limit presently exists in the generation of ultra-short pulses carrying substantial energy. Here we present the experimental implementation of chirped pulse amplification on a seeded free-electron laser in the extreme-ultraviolet, paving the way to the generation of fully coherent sub-femtosecond gigawatt pulses in the water window (2.3–4.4 nm).
In silico Mapping of Protein Unfolding Mutations for Inherited Disease
Authors: McCafferty Caitlyn L. , Sergeev Yuri V. 
Published: December 2016

AbstractThe effect of disease-causing missense mutations on protein folding is difficult to evaluate. To understand this relationship, we developed the unfolding mutation screen (UMS) for in silico evaluation of the severity of genetic perturbations at the atomic level of protein structure. The program takes into account the protein-unfolding curve and generates propensities using calculated free energy changes for every possible missense mutation at once. These results are presented in a series of unfolding heat maps and a colored protein 3D structure to show the residues critical to the protein folding and are available for quick reference. UMS was tested with 16 crystal structures to evaluate the unfolding for 1391 mutations from the ProTherm database. Our results showed that the computational accuracy of the unfolding calculations was similar to the accuracy of previously published free energy changes but provided a better scale. Our residue identity control helps to improve protein homology models. The unfolding predictions for proteins involved in age-related macular degeneration, retinitis pigmentosa, and Leber’s congenital amaurosis matched well with data from previous studies. These results suggest that UMS could be a useful tool in the analysis of genotype-to-phenotype associations and next-generation sequencing data for inherited diseases.
A previously unreported impact of a PLA2G7 gene polymorphism on the plasma levels of lipoprotein-associated phospholipase A2 activity and mass
Authors: Qi Yue , Zhao Dong , Jia Zhangrong , Wang Wei , Wang Miao , Sun Jiayi , Liu Jun , Li Yan , Xie Wuxiang , Liu Jing 
Published: December 2016

AbstractLipoprotein-associated phospholipase A2 (Lp-PLA2) levels are associated with the development of atherosclerosis. We aimed to assess the genetic determinants of Lp-PLA2 activity and mass by genotyping multiple polymorphisms in PLA2G7, the gene encoding Lp-PLA2, among 1258 participants from the Chinese Multi-provincial Cohort Study-Beijing Project. The Sequenom MassARRAY system, Taqman assay and direct sequencing were adopted. For the first time, the rs13218408 polymorphism was found to be significantly associated with reduced Lp-PLA2 levels. We also confirmed the significant association of previously validated polymorphisms (rs1421378, rs1805018, rs16874954 and rs2216465), even after adjusting for traditional cardiovascular risk factors and for Bonferroni correction. Percentages of variance attributable to rs13218408 were 7.2% for activity and 13.3% for mass, and were secondary to those of rs16874954 (8.1% for activity and 16.9% for mass). A significant joint effect of rs13218408 and rs16874954 was observed on Lp-PLA2 activity (P = 0.058) and mass (P = 0.003), with their minor alleles together linking to the largest reduction in Lp-PLA2 levels (37.8% reduction in activity and 41.6% reduction in mass). Taken together, our findings show a significant association of a PLA2G7 polymorphism with Lp-PLA2 levels, which was previously unreported in any population. The functionality of this genetic variation deserves further investigations.
Protein-peptide molecular docking with large-scale conformational changes: the p53-MDM2 interaction
Authors: Ciemny Maciej Pawel , Debinski Aleksander , Paczkowska Marta , Kolinski Andrzej , Kurcinski Mateusz , Kmiecik Sebastian 
Published: December 2016

AbstractProtein-peptide interactions are often associated with large-scale conformational changes that are difficult to study either by classical molecular modeling or by experiment. Recently, we have developed the CABS-dock method for flexible protein-peptide docking that enables large-scale rearrangements of the protein chain. In this study, we use CABS-dock to investigate the binding of the p53-MDM2 complex, an element of the cell cycle regulation system crucial for anti-cancer drug design. Experimental data suggest that p53-MDM2 binding is affected by significant rearrangements of a lid region - the N-terminal highly flexible MDM2 fragment; however, the details are not clear. The large size of the highly flexible MDM2 fragments makes p53-MDM2 intractable for exhaustive binding dynamics studies using atomistic models. We performed extensive dynamics simulations using the CABS-dock method, including large-scale structural rearrangements of MDM2 flexible regions. Without a priori knowledge of the p53 peptide structure or its binding site, we obtained near-native models of the p53-MDM2 complex. The simulation results match well the experimental data and provide new insights into the possible role of the lid fragment in p53 binding. The presented case study demonstrates that CABS-dock methodology opens up new opportunities for protein-peptide docking with large-scale changes of the protein receptor structure.
Cellular reactions to long-term volatile organic compound (VOC) exposures
Authors: Gostner Johanna M. , Zeisler Johannes , Alam Mohammad Tauqeer , Gruber Peter , Fuchs Dietmar , Becker Kathrin , Neubert Kerstin , Kleinhappl Markus , Martini Stefan , Überall Florian 
Published: December 2016

AbstractInvestigations of cellular processes initiated by volatile organic compounds (VOCs) are limited when modelling realistic long-term exposure scenarios at low concentrations. Exposure to indoor VOCs is associated with a range of adverse effects, but data on molecular changes at regulatory threshold limits are lacking. Activity analysis of VOC in vitro can be a valuable complement to inhalation toxicological evaluations. We developed an exposure platform that generates a stable VOC atmosphere and allows the exposure of cells for longer periods. Using formaldehyde as a model analyte, air-liquid interface cultured A549 lung epithelial cells were exposed to critical concentrations of 0.1 and 0.5 ppm for 3 days. Owing to the lack of known exposure biomarkers, we applied a genome-wide transcriptional analysis to investigate cellular responses at these sublethal concentrations. We demonstrate a minor overlap of differentially expressed transcripts for both treatment concentrations, which can be further analyzed for their use as exposure biomarkers. Moreover, distinct expression patterns emerge for 0.1 and 0.5 ppm formaldehyde exposure, which is reflected in significant enrichment of distinct biological processes. More specifically, metabolism of specific compound classes, lipid biosynthesis and lung-associated functions are affected by lower exposure levels and processes affecting proliferation and apoptosis dominate the higher exposure levels.
Hallucinations in schizophrenia and Parkinson’s disease: an analysis of sensory modalities involved and the repercussion on patients
Authors: Llorca P. M. , Pereira B. , Jardri R. , Chereau-Boudet I. , Brousse G. , Misdrahi D. , Fénelon G. , Tronche A.-M. , Schwan R. , Lançon C. , Marques A. , Ulla M. , Derost P. , Debilly B. , Durif F. , de Chazeron I. 
Published: December 2016

AbstractHallucinations have been described in various clinical populations, but they are neither disorder nor disease specific. In schizophrenia patients, hallucinations are hallmark symptoms and auditory ones are described as the more frequent. In Parkinson’s disease, the descriptions of hallucination modalities are sparse, but the hallucinations do tend to have less negative consequences. Our study aims to explore the phenomenology of hallucinations in both hallucinating schizophrenia patients and Parkinson’s disease patients using the Psycho-Sensory hAllucinations Scale (PSAS). The main objective is to describe the phenomena of these clinical symptoms in those two specific populations. Each hallucinatory sensory modality significantly differed between Parkinson’s disease and schizophrenia patients. Auditory, olfactory/gustatory and cœnesthetic hallucinations were more frequent in schizophrenia than visual hallucinations. The guardian angel item, usually not explored in schizophrenia, was described by 46% of these patients. The combination of auditory and visual hallucinations was the most frequent for both Parkinson’s disease and schizophrenia. The repercussion index summing characteristics of each hallucination (frequency, duration, negative aspects, conviction, impact, control and sound intensity) was always higher for schizophrenia. A broader view including widespread characteristics and interdisciplinary works must be encouraged to better understand the complexity of the process involved in hallucinations.
Early-onset epileptic encephalopathy caused by a reduced sensitivity of Kv7.2 potassium channels to phosphatidylinositol 4,5-bisphosphate
Authors: Soldovieri Maria Virginia , Ambrosino Paolo , Mosca Ilaria , De Maria Michela , Moretto Edoardo , Miceli Francesco , Alaimo Alessandro , Iraci Nunzio , Manocchio Laura , Medoro Alessandro , Passafaro Maria , Taglialatela Maurizio 
Published: December 2016

AbstractKv7.2 and Kv7.3 subunits underlie the M-current, a neuronal K+ current characterized by an absolute functional requirement for phosphatidylinositol 4,5-bisphosphate (PIP2). Kv7.2 gene mutations cause early-onset neonatal seizures with heterogeneous clinical outcomes, ranging from self-limiting benign familial neonatal seizures to severe early-onset epileptic encephalopathy (Kv7.2-EE). In this study, the biochemical and functional consequences prompted by a recurrent variant (R325G) found independently in four individuals with severe forms of neonatal-onset EE have been investigated. Upon heterologous expression, homomeric Kv7.2 R325G channels were non-functional, despite biotin-capture in Western blots revealed normal plasma membrane subunit expression. Mutant subunits exerted dominant-negative effects when incorporated into heteromeric channels with Kv7.2 and/or Kv7.3 subunits. Increasing cellular PIP2 levels by co-expression of type 1γ PI(4)P5-kinase (PIP5K) partially recovered homomeric Kv7.2 R325G channel function. Currents carried by heteromeric channels incorporating Kv7.2 R325G subunits were more readily inhibited than wild-type channels upon activation of a voltage-sensitive phosphatase (VSP), and recovered more slowly upon VSP switch-off. These results reveal for the first time that a mutation-induced decrease in current sensitivity to PIP2 is the primary molecular defect responsible for Kv7.2-EE in individuals carrying the R325G variant, further expanding the range of pathogenetic mechanisms exploitable for personalized treatment of Kv7.2-related epilepsies.
Serbian Language version of the Modified Checklist for Autism in Toddlers, Revised, with Follow-Up: Cross-Cultural Adaptation and Assessment of Reliability
Authors: Carakovac Mia , Jovanovic Jelena , Kalanj Marko , Rudic Nenad , Aleksic–Hil Olivera , Aleksic Branko , Villalobos Itzel Bustos , Kasuya Hideki , Ozaki Norio , Lecic–Tosevski Dusica , Pejovic–Milovancevic Milica 
Published: December 2016

AbstractEarly detection of Autism Spectrum Disorder (ASD) has proven to be of high significance, however there is a limited availability of ASD screening tools in Serbian language. In this study we aim to translate, assess reliability and, in part, test the applicability of Modified Checklist for Autism in Toddlers, Revised, with Follow-Up (M-CHAT R/F) in Serbian Healthcare environment. We screened 128 children in three primary healthcare centres and 20 children in a tertiary psychiatric center, using M-CHAT R/F translated into Serbian language, between December 2014 and October 2015. At the end of the screening process 80% of participants in the risk group screened positive for ASD, while in the control group 4 (3.1%) participants screened positive, with a mean total scores of 8.25 and 0.66 respectively. The Cronbach’s α coefficient was 0.91 and Guttman’s λ6 was 0.93. Test – retest reliability was deemed as acceptable, and no significant correlation was found between M-CHAT-R/F scores and Epworth Sleepiness Scale for children scores. The Serbian version of the M-CHAT-R/F has shown satisfactory reliability. We can therefore assert that it is a reliable tool for identifying ASD and it can be used in clinical practice to improve early detection, assessment and treatment.
Defining an olfactory receptor function in airway smooth muscle cells
Authors: Aisenberg William H. , Huang Jessie , Zhu Wanqu , Rajkumar Premraj , Cruz Randy , Santhanam Lakshmi , Natarajan Niranjana , Yong Hwan Mee , De Santiago Breann , Oh Jung Jin , Yoon A-Rum , Panettieri Reynold A. , Homann Oliver , Sullivan John K. , Liggett Stephen B. , Pluznick Jennifer L. , An Steven S. 
Published: December 2016

AbstractPathways that control, or can be exploited to alter, the increase in airway smooth muscle (ASM) mass and cellular remodeling that occur in asthma are not well defined. Here we report the expression of odorant receptors (ORs) belonging to the superfamily of G-protein coupled receptors (GPCRs), as well as the canonical olfaction machinery (Golf and AC3) in the smooth muscle of human bronchi. In primary cultures of isolated human ASM, we identified mRNA expression for multiple ORs. Strikingly, OR51E2 was the most highly enriched OR transcript mapped to the human olfactome in lung-resident cells. In a heterologous expression system, OR51E2 trafficked readily to the cell surface and showed ligand selectivity and sensitivity to the short chain fatty acids (SCFAs) acetate and propionate. These endogenous metabolic byproducts of the gut microbiota slowed the rate of cytoskeletal remodeling, as well as the proliferation of human ASM cells. These cellular responses in vitro were found in ASM from non-asthmatics and asthmatics, and were absent in OR51E2-deleted primary human ASM. These results demonstrate a novel chemo-mechanical signaling network in the ASM and serve as a proof-of-concept that a specific receptor of the gut-lung axis can be targeted to treat airflow obstruction in asthma.