bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rapid peat accumulation favours the occurrence of both fen and bog microbial communities within a Mediterranean, free-floating peat island
Authors: Concheri Giuseppe , Stevanato Piergiorgio , Zaccone Claudio , Shotyk William , D’Orazio Valeria , Miano Teodoro , Piffanelli Pietro , Rizzi Valeria , Ferrandi Chiara , Squartini Andrea 
Published: August 2017

AbstractThe unique environment of a 4m-thick, free-floating peat island within the Posta Fibreno lake (Central Italy) was analyzed using DNA-based techniques to assess bacterial and fungal community members identity and abundance. Two depths were sampled at 41 and 279 cm from the surface, the former corresponding to an emerged portion of Sphagnum residues accumulated less than 30 yrs ago, and the latter mainly consisting of silty peat belonging to the deeply submerged part of the island, dating back to 1520–1660 AD. The corresponding communities were very diverse, each of them dominated by a different member of the Delta-proteobacteria class for prokaryotes. Among Eukaryotes, Ascomycota prevailed in the shallow layer while Basidiomycota were abundant in the deep sample. The identity of taxa partitioning between acidic surface layer and neutral core is very reminiscent of the differences reported between bogs and fens respectively, supporting the view of Posta Fibreno as a relic transitional floating mire. Moreover, some microbial taxa show an unusual concurrent species convergence between this sub-Mediterranean site and far Nordic or circumpolar environments. This study represents the first report describing the biotic assemblages of such a peculiar environment, and provides some insights into the possible mechanisms of its evolution.
Functional validation of GPIHBP1 and identification of a functional mutation in GPIHBP1 for milk fat traits in dairy cattle
Authors: Yang Jie , Liu Xuan , Wang Dan , Ning Chao , Wang Haifei , Zhang Qin , Jiang Li 
Published: August 2017

AbstractIn a previous genome-wide association study (GWAS) on milk production traits in a Chinese Holstein population, we revealed that GPIHBP1 is a novel promising candidate gene for milk fat content traits. In this study, we performed over-expression and RNAi experiments on GPIHBP1 in bovine primary mammary epithelial cells. The results showed that the expression of several important milk fat-related genes (LPL, CD36, VLDLR, ACACA and FASN) increased or decreased when the expression of GPIHBP1 was up- or down-regulated. To identify the potential functional SNP involved, we explored the genetic variants of GPIHBP1 and found that a G/A mutation (chr14:2553998) in the promoter region of GPIHBP1 significantly reduced promoter activity and had an effect on transcription factor binding sites. This finding was consistent with the lower expression of GPIHBP1 observed in the mammary gland tissue of cows harboring the homozygous AA mutation compared with wild-type homozygous GG or heterozygous AG. Furthermore, association analysis showed that cows with the AA genotype outperformed those with the GG and AG genotypes in terms of the milk fat percentage. Our study demonstrates that GPIHBP1 could be a strong candidate gene for milk fat content traits and, in particular, the G to A mutation at chr14:2553998 within GPIHBP1 could be a functional mutation related to its effects.
A portable microfluidic platform for rapid molecular diagnostic testing of patients with myeloproliferative neoplasms
Authors: Wang Hua , zhang Xinju , Xu Xiao , Zhang Qunfeng , Wang Hengliang , Li Dong , Kang Zhihua , Wu Zhiyuan , Tang Yigui , An Zhenhua , Guan Ming 
Published: August 2017

AbstractThe ability to simultaneously detect JAK2 V617F and MPL W515K/L mutations would substantially improve the early diagnosis of myeloproliferative neoplasms (MPNs) and decrease the risk of arterial thrombosis. The goal of this study is to achieve a point of care testing platform for simultaneous analysis of major genetic alterations in MPN. Here, we report a microfluidic platform including a glass capillary containing polypropylene matrix that extracts genomic DNA from a drop of whole blood, a microchip for simultaneous multi-gene mutation screening, and a handheld battery-powered heating device. The µmLchip system was successfully used for point-of-care identification of the JAK2 V617F and MPL W515K/L mutations. The µmLchip assays were then validated by mutation analysis with samples from 100 MPN patients who had previously been analyzed via unlabeled probe melting curve analysis or real-time PCR. The results from the µmLchip were in perfect agreement with those from the other methods, except for one discrepant result that was negative in the unlabeled probe melting curve analysis but positive in the µmLchip. After T-A cloning, sequences of cloned PCR products revealed JAK2 V617F mutation in the sample. The portable microfluidic platform may be very attractive in developing point-of-care diagnostics for MPL W515K/L and JAK2 V617F mutations.
Medial prefrontal cortical thinning mediates shifts in other-regarding preferences during adolescence
Authors: Sul Sunhae , Güroğlu Berna , Crone Eveline A. , Chang Luke J. 
Published: August 2017

AbstractAdolescence is a time of significant cortical changes in the ‘social brain’, a set of brain regions involved in sophisticated social inference. However, there is limited evidence linking the structural changes in social brain to development of social behavior. The present study investigated how cortical development of the social brain relates to other-regarding behavior, in the context of fairness concerns. Participants aged between 9 to 23 years old responded to multiple rounds of ultimatum game proposals. The degree to which each participant considers fairness of intention (i.e., intention-based reciprocity) vs. outcome (i.e., egalitarianism) was quantified using economic utility models. We observed a gradual shift in other-regarding preferences from simple rule-based egalitarianism to complex intention-based reciprocity from early childhood to young adulthood. The preference shift was associated with cortical thinning of the dorsomedial prefrontal cortex and posterior temporal cortex. Meta-analytic reverse-inference analysis showed that these regions were involved in social inference. Importantly, the other-regarding preference shift was statistically mediated by cortical thinning in the dorsomedial prefrontal cortex. Together these findings suggest that development of the ability to perform sophisticated other-regarding social inference is associated with the structural changes of specific social brain regions in late adolescence.
Administration of mesenchymal stromal cells before renal ischemia/reperfusion attenuates kidney injury and may modulate renal lipid metabolism in rats
Authors: Erpicum Pauline , Rowart Pascal , Poma Laurence , Krzesinski Jean-Marie , Detry Olivier , Jouret François 
Published: August 2017

AbstractMesenchymal stromal cells (MSC) have been demonstrated to attenuate renal ischemia/reperfusion (I/R) damage in rodent models. The mechanisms of such nephro-protection remain largely unknown. Furthermore, the optimal timing of MSC administration has been poorly investigated. Here, we compare the impact of MSC injection 7 days before (MSCD − 7) versus 1 day after (MSCD + 1) renal I/R in rats. Control groups received equivalent volumes of saline at similar time-points (SD − 7 and SD + 1). Right nephrectomy was performed, and left renal ischemia lasted 45 min. After 48-hour reperfusion, we observed significantly improved renal function parameters, reduced apoptotic index and neutrophil/macrophage infiltration in kidney parenchyma, and lower expression of tubular damage markers and pro-inflammatory cytokines in MSCD − 7 in comparison to MSCD + 1 and saline control groups. Next, comparative high-throughput RNA sequencing of MSCD − 7 vs. SD − 7 non-ischemic right kidneys highlighted significant down-regulation of fatty acid biosynthesis and up-regulation of PPAR-α pathway. Such a preferential regulation towards lipid catabolism was associated with decreased levels of lipid peroxidation products, i.e. malondialdehyde and 4-hydroxy-2-nonenal, in MSCD − 7 versus SD − 7 ischemic kidneys. Our findings suggest that MSC pretreatment may exert protective effects against renal I/R by modulating lipid metabolism in rats.
Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data
Authors: Ferrero Giulio , Miano Valentina , Beccuti Marco , Balbo Gianfranco , De Bortoli Michele , Cordero Francesca 
Published: August 2017

AbstractIn the study of genomic regulation, strategies to integrate the data produced by Next Generation Sequencing (NGS)-based technologies in a meaningful ensemble are eagerly awaited and must continuously evolve. Here, we describe an integrative strategy for the analysis of data generated by chromatin immunoprecipitation followed by NGS which combines algorithms for data overlap, normalization and epigenetic state analysis. The performance of our strategy is illustrated by presenting the analysis of data relative to the transcriptional regulator Estrogen Receptor alpha (ERα) in MCF-7 breast cancer cells and of Glucocorticoid Receptor (GR) in A549 lung cancer cells. We went through the definition of reference cistromes for different experimental contexts, the integration of data relative to co-regulators and the overlay of chromatin states as defined by epigenetic marks in MCF-7 cells. With our strategy, we identified novel features of estrogen-independent ERα activity, including FoxM1 interaction, eRNAs transcription and a peculiar ontology of connected genes.
Effects of environmental enrichment upon ethanol-induced conditioned place preference and pre-frontal BDNF levels in adolescent and adult mice
Authors: Pautassi Ricardo Marcos , Suárez Andrea B. , Hoffmann Lucas Barbosa , Rueda André Veloso , Rae Mariana , Marianno Priscila , Camarini Rosana 
Published: August 2017

AbstractEnvironmental enrichment (EE) provides a non-pharmacological tool to alter drug-induced reward, yet its effects on ethanol-induced reward remain controversial. We analyzed adolescent vs. adult (mice) differences in the influence of EE on ethanol-induced conditioned place preference (CPP). The effects of these treatments on brain-derived neurotrophic factor (BDNF) levels in the prefrontal cortex were examined in a separate group of animals. Ethanol-induced CPP was found in adults, and it was similar in EE and in animals reared under standard housing conditions (SC). Adolescents kept under EE, but not those in SC, exhibited CPP. Among SC, but not among EE, adolescents, BDNF levels were significantly lower in those treated with ethanol than in those given vehicle. These results indicate that, compared to adults, adolescent exhibited reduced sensitivity to ethanol’s rewarding effects, yet the youth but not the adults exhibited sensitivity to the promoting effect of EE upon CPP by ethanol. Ethanol significantly reduced BDNF levels in adolescents reared under standard housing conditions, but not in adult mice nor in adolescents given EE housing conditions. The present results add to the plethora of adolescent-specific responses to ethanol or to environmental stimuli that may put the youth at risk for escalation of ethanol intake.
Human cytomegalovirus escapes immune recognition by NK cells through the downregulation of B7-H6 by the viral genes US18 and US20
Authors: Charpak-Amikam Yoav , Kubsch Tobias , Seidel Einat , Oiknine-Djian Esther , Cavaletto Noemi , Yamin Rachel , Schmiedel Dominik , Wolf Dana , Gribaudo Giorgio , Messerle Martin , Cicin-Sain Luka , Mandelboim Ofer 
Published: August 2017

AbstractHuman cytomegalovirus (HCMV) is a major human pathogen, causing serious diseases in immunocompromised populations and congenially infected neonates. One of the main immune cells acting against the virus are Natural Killer (NK) cells. Killing by NK cells is mediated by a small family of activating receptors such as NKp30 that interact with the cellular ligand B7-H6. The outcome of B7-H6-NKp30 interaction was, so far, mainly studied with regard to NK recognition and killing of tumors. Here, we demonstrated that the expression of B7-H6 is upregulated following HCMV infection and that HCMV uses two of its genes: US18 and US20, to interfere with B7-H6 surface expression, in a mechanism involving endosomal degradation, in order to evade NK cell recognition.
Shared peptide binding of HLA Class I and II alleles associate with cutaneous nevirapine hypersensitivity and identify novel risk alleles
Authors: Pavlos Rebecca , McKinnon Elizabeth J. , Ostrov David A. , Peters Bjoern , Buus Soren , Koelle David , Chopra Abha , Schutte Ryan , Rive Craig , Redwood Alec , Restrepo Susana , Bracey Austin , Kaever Thomas , Myers Paisley , Speers Ellen , Malaker Stacy A. , Shabanowitz Jeffrey , Jing Yuan , Gaudieri Silvana , Hunt Donald F. , Carrington Mary , Haas David W. , Mallal Simon , Phillips Elizabeth J. 
Published: August 2017

AbstractGenes of the human leukocyte antigen (HLA) system encode cell-surface proteins involved in regulation of immune responses, and the way drugs interact with the HLA peptide binding groove is important in the immunopathogenesis of T-cell mediated drug hypersensitivity syndromes. Nevirapine (NVP), is an HIV-1 antiretroviral with treatment-limiting hypersensitivity reactions (HSRs) associated with multiple class I and II HLA alleles. Here we utilize a novel analytical approach to explore these multi-allelic associations by systematically examining HLA molecules for similarities in peptide binding specificities and binding pocket structure. We demonstrate that primary predisposition to cutaneous NVP HSR, seen across ancestral groups, can be attributed to a cluster of HLA-C alleles sharing a common binding groove F pocket withHLA-C*04:01. An independent association with a group of class II alleles which share the HLA-DRB1-P4 pocket is also observed. In contrast, NVP HSR protection is afforded by a cluster of HLA-B alleles defined by a characteristic peptide binding groove B pocket. The results suggest drug-specific interactions within the antigen binding cleft can be shared across HLA molecules with similar binding pockets. We thereby provide an explanation for multiple HLA associations with cutaneous NVP HSR and advance insight into its pathogenic mechanisms.
Use of Biocompatible Sorafenib-gold Nanoconjugates for Reversal of Drug Resistance in Human Hepatoblatoma Cells
Authors: Vishwakarma Sandeep Kumar , Sharmila Priyanka , Bardia Avinash , Chandrakala Lakkireddy , Raju N. , Sravani G. , Sastry B. V. S. , Habeeb Md Aejaz , Khan Aleem Ahmed , Dhayal Marshal 
Published: August 2017

AbstractThe present study identifies the potential of highly biocompatible SF-GNP nano-conjugate to enhance the chemotherapeutic response to combat drug resistance in cancer cells. We developed a stable colloidal suspension of sorafenib-gold nanoconjugate (SF-GNP) of <10 nm size in aqueous medium for reverting the cancer drug resistance in SF-resistant HepG2 cells in a 3D ex-vivo model system. In-vivo biocompatibility assay of SF-GNPs showed absence of systemic toxicological effects including hematological, biochemical and histological parameters. More importantly, the histopathological analysis of vital organs such as liver, brain, lung, kidney and heart showed very least or no sign of inflammation, cell infiltration, necrosis, tissue disorganization or fibrotic reactions after intra-peritoneal administration of SF-GNP nanoconjugates in animals. However, SF-GNP nanoconjugates significantly reduced (>80%) the percentage cell survival and the size and number of SF resistant solid tumor colonies of HepG2 cells in 3D model system. The exposure of SF-GNP nanoconjugate to SF resistant HepG2 cell colonies also provided evidence for anti-proliferative effect and reversal of drug resistance by elucidating the molecular regulatory mechanisms of extracellular matrix factor (CD147), tumor growth factor (TGF-β), hepatoma upregulated protein (hURP) and drug transporter (ABCG-2).
A single-molecule assessment of the protective effect of DMSO against DNA double-strand breaks induced by photo-and γ-ray-irradiation, and freezing
Authors: Noda Masami , Ma Yue , Yoshikawa Yuko , Imanaka Tadayuki , Mori Toshiaki , Furuta Masakazu , Tsuruyama Tatsuaki , Yoshikawa Kenichi 
Published: August 2017

AbstractDimethyl sulfoxide (DMSO) is widely used as a cryoprotectant for organs, tissues, and cell suspension in storage. In addition, DMSO is known to be a useful free radical scavenger and a radio-protectant. To date, many in vitro assays using cultured cells have been performed for analysing the protective effect of DMSO against genomic DNA damage; however, currently it has been rather difficult to detect DNA double strand breaks (DSBs) in a quantitative manner. In the present study, we aimed to observe the extent of DNA damage by use of single molecular observation with a fluorescence microscope to evaluate DSBs induced by photo- and γ-ray-irradiation, or freeze/thawing in variable concentrations of DMSO. As a result, we found that 2% DMSO conferred the maximum protective effect against all of the injury sources tested, and these effects were maintained at higher concentrations. Further, DMSO showed a significantly higher protective effect against freezing-induced damage than against photo- and γ-ray-irradiation-induced damage. Our study provides significant data for the optimization of DNA cryopreservation with DMSO, as well as for the usage of DNA as the protective agent against the injuries caused by active oxygen and radiations.
Fusion protein analysis reveals the precise regulation between Hsp70 and Hsp100 during protein disaggregation
Authors: Hayashi Sayaka , Nakazaki Yosuke , Kagii Kei , Imamura Hiromi , Watanabe Yo-hei 
Published: August 2017

AbstractClpB, a bacterial Hsp100, is a ring-shaped AAA+ chaperone that can reactivate aggregated proteins in cooperation with DnaK, a bacterial Hsp70, and its co-factors. ClpB subunits comprise two AAA+ modules with an interstitial rod-shaped M-domain. The M-domain regulates ClpB ATPase activity and interacts directly with the DnaK nucleotide-binding domain (NBD). Here, to clarify how these functions contribute to the disaggregation process, we constructed ClpB, DnaK, and aggregated YFP fusion proteins in various combinations. Notably, i) DnaK activates ClpB only when the DnaK substrate-binding domain (SBD) is in the closed conformation, affording high DnaK-peptide affinity; ii) although NBD alone can activate ClpB, SBD is required for disaggregation; and iii) tethering aggregated proteins to the activated ClpB obviates SBD requirements. These results indicate that DnaK activates ClpB only when the SBD tightly holds aggregated proteins adjacent to ClpB for effective disaggregation.
A Preliminary Investigation of the Association of Sleep With Inflammation and Oxidative Stress Biomarkers and Functional Outcomes After Stroke Rehabilitation
Authors: Yeh Ting-ting , Hsieh Yu-wei , Wu Ching-yi , Wang Jong-shyan , Lin Keh-chung , Chen Chia-ling 
Published: August 2017

AbstractThis study examined the association of sleep with inflammation and oxidative stress biomarkers, and with functional outcomes, after stroke rehabilitation. The rehabilitation effects on biomarkers and functional outcomes were also evaluated. Twenty subacute stroke survivors received 4 weeks of upper limb rehabilitation. Baseline inflammatory (i.e., soluble intercellular adhesion molecule-1, sICAM-1) and oxidative stress biomarkers (i.e., glutathione peroxidase, GPx and malondialdehyde, MDA) were assessed, as were sleep outcomes. Positive correlations were observed between baseline level of sICAM-1 and number of awakenings at post-treatment (ρ = 0.51,p < 0.05) as well as between baseline level of MDA and post-performance time of the Wolf Motor Function Test (WMFT-time) (ρ = 0.46,p < 0.05). In addition, MDA levels were significantly decreased, and functional outcomes of the modified Rankin Scale (mRS), functional ability scale of the WMFT, and Stroke Impact Scale (SIS-total, and SIS-physical function) were improved after the rehabilitation. This pilot study emphasizes the relationship among biomarkers, sleep, and functional outcomes after stroke rehabilitation. Oxidative stress markers may be useful predictors of functional outcomes in subacute stroke survivors.
The Role of Rho-GTPases and actin polymerization during Macrophage Tunneling Nanotube Biogenesis
Authors: Hanna Samer J. , McCoy-Simandle Kessler , Miskolci Veronika , Guo Peng , Cammer Michael , Hodgson Louis , Cox Dianne 
Published: August 2017

AbstractMacrophage interactions with other cells, either locally or at distances, are imperative in both normal and pathological conditions. While soluble means of communication can transmit signals between different cells, it does not account for all long distance macrophage interactions. Recently described tunneling nanotubes (TNTs) are membranous channels that connect cells together and allow for transfer of signals, vesicles, and organelles. However, very little is known about the mechanism by which these structures are formed. Here we investigated the signaling pathways involved in TNT formation by macrophages using multiple imaging techniques including super-resolution microscopy (3D-SIM) and live-cell imaging including the use of FRET-based Rho GTPase biosensors. We found that formation of TNTs required the activity and differential localization of Cdc42 and Rac1. The downstream Rho GTPase effectors mediating actin polymerization through Arp2/3 nucleation, Wiskott-Aldrich syndrome protein (WASP) and WASP family verprolin-homologous 2 (WAVE2) proteins are also important, and both pathways act together during TNT biogenesis. Finally, TNT function as measured by transfer of cellular material between cells was reduced following depletion of a single factor demonstrating the importance of these factors in TNTs. Given that the characterization of TNT formation is still unclear in the field; this study provides new insights and would enhance the understanding of TNT formation towards investigating new markers.
Mortierella alpina CS10E4, an oleaginous fungal endophyte of Crocus sativus L. enhances apocarotenoid biosynthesis and stress tolerance in the host plant
Authors: Wani Zahoor Ahmed , Kumar Amit , Sultan Phalisteen , Bindu Kushal , Riyaz-Ul-Hassan Syed , Ashraf Nasheeman 
Published: August 2017

AbstractCrocus sativus is the only plant species which produces apocarotenoids like crocin, picrocrocin and safranal in significant amounts. These compounds impart organoleptic properties to saffron (dried stigmas of Crocus flower) making it world’s costliest spice. Crocus apocarotenoids have tremendous medicinal properties as well. Effect of endophytes on Crocus apocarotenoid production and the molecular mechanism involved has not been reported so far. Here we studied the effect of an oleaginous fungal endophyte, Mortierella alpina CS10E4 on Crocus growth, apocarotenoid metabolism and tolerance to corm rot disease. The results demonstrated that there was a significant improvement in many morphological and physiological traits in endophyte treated Crocus plants including total biomass and size of corms, stigma biomass, number of apical sprouting buds, and number of adventitious roots. The endophyte also shifted metabolic flux towards enhanced production of apocarotenoids by modulating the expression of key pathway genes. Further, M. alpina CS10E4 enhanced tolerance to corm rot disease by releasing arachidonic acid which acts as conserved defense signal and induces jasmonic acid production in endophyte treated Crocus corms. This is first report on effect of a fungal endophyte on Crocus apocarotenoid metabolism and stress tolerance.