bluuebunny/crossref_metadata_2025_split huggingface dataset:
RNA surveillance via nonsense-mediated mRNA decay is crucial for longevity in daf-2/insulin/IGF-1 mutant C. elegans
Authors: Son Heehwa G. , Seo Mihwa , Ham Seokjin , Hwang Wooseon , Lee Dongyeop , An Seon Woo A. , Artan Murat , Seo Keunhee , Kaletsky Rachel , Arey Rachel N. , Ryu Youngjae , Ha Chang Man , Kim Yoon Ki , Murphy Coleen T. , Roh Tae-Young , Nam Hong Gil , Lee Seung-Jae V. 
Published: March 2017

AbstractLong-lived organisms often feature more stringent protein and DNA quality control. However, whether RNA quality control mechanisms, such as nonsense-mediated mRNA decay (NMD), which degrades both abnormal as well as some normal transcripts, have a role in organismal aging remains unexplored. Here we show that NMD mediates longevity in C. elegans strains with mutations in daf-2/insulin/insulin-like growth factor 1 receptor. We find that daf-2 mutants display enhanced NMD activity and reduced levels of potentially aberrant transcripts. NMD components, including smg-2/UPF1, are required to achieve the longevity of several long-lived mutants, including daf-2 mutant worms. NMD in the nervous system of the animals is particularly important for RNA quality control to promote longevity. Furthermore, we find that downregulation of yars-2/tyrosyl-tRNA synthetase, an NMD target transcript, by daf-2 mutations contributes to longevity. We propose that NMD-mediated RNA surveillance is a crucial quality control process that contributes to longevity conferred by daf-2 mutations.
Specific expression of heme oxygenase-1 by myeloid cells modulates renal ischemia-reperfusion injury
Authors: Rossi Maxime , Thierry Antoine , Delbauve Sandrine , Preyat Nicolas , Soares Miguel P. , Roumeguère Thierry , Leo Oberdan , Flamand Véronique , Le Moine Alain , Hougardy Jean-Michel 
Published: March 2017

AbstractRenal ischemia-reperfusion injury (IRI) is a major risk factor for delayed graft function in renal transplantation. Compelling evidence exists that the stress-responsive enzyme, heme oxygenase-1 (HO-1) mediates protection against IRI. However, the role of myeloid HO-1 during IRI remains poorly characterized. Mice with myeloid-restricted deletion of HO-1 (HO-1M-KO), littermate (LT), and wild-type (WT) mice were subjected to renal IRI or sham procedures and sacrificed after 24 hours or 7 days. In comparison to LT, HO-1M-KO exhibited significant renal histological damage, pro-inflammatory responses and oxidative stress 24 hours after reperfusion. HO-1M-KO mice also displayed impaired tubular repair and increased renal fibrosis 7 days after IRI. In WT mice, HO-1 induction with hemin specifically upregulated HO-1 within the CD11b+ F4/80lo subset of the renal myeloid cells. Prior administration of hemin to renal IRI was associated with significant increase of the renal HO-1+ CD11b+ F4/80lo myeloid cells in comparison to control mice. In contrast, this hemin-mediated protection was abolished in HO-1M-KO mice. In conclusion, myeloid HO-1 appears as a critical protective pathway against renal IRI and could be an interesting therapeutic target in renal transplantation.
Length-dependent gene misexpression is associated with Alzheimer’s disease progression
Authors: Barbash Shahar , Sakmar Thomas P. 
Published: March 2017

AbstractRecent reports show transcription preference for long genes in neuronal tissues compared with non-neuronal tissues, and a gene-length dependent change in expression in the neurodevelopmental disease Rett syndrome (RTT). Whether the gene-length dependent changes in expression seen in RTT might also be seen in neurodegenerative diseases is not yet known. However, a reasonable hypothesis is that similar effects might be seen in neurodegenerative diseases as well as in RTT since a common general feature of both illnesses involves progressive dysfunction of synapses. Here, we demonstrate a clear length-dependent gene misexpression in the most prevalent neurodegenerative disease, Alzheimer’s disease. We show that the effect is associated with disease progression and can be attributed specifically to neurons. In particular, we observed gene length-dependent down regulation on the level of the whole tissue and gene length-dependent up regulation on the level of single cells. Our analysis shows that a gene-length effect on expression can be found in degenerative neurological illnesses, such as Alzheimer’s disease. Additional investigation to elucidate the precise mechanism underlying gene-length dependent changes in expression is warranted.
Considerable knock-on displacement of metal atoms under a low energy electron beam
Authors: Gu Hengfei , Li Geping , Liu Chengze , Yuan Fusen , Han Fuzhou , Zhang Lifeng , Wu Songquan 
Published: March 2017

AbstractUnder electron beam irradiation, knock-on atomic displacement is commonly thought to occur only when the incident electron energy is above the incident-energy threshold of the material in question. However, we report that when exposed to intense electrons at room temperature at a low incident energy of 30 keV, which is far below the theoretically predicted incident-energy threshold of zirconium, Zircaloy-4 (Zr-1.50Sn-0.25Fe-0.15Cr (wt.%)) surfaces can undergo considerable displacement damage. We demonstrate that electron beam irradiation of the bulk Zircaloy-4 surface resulted in a striking radiation effect that nanoscale precipitates within the surface layer gradually emerged and became clearly visible with increasing the irradiation time. Our transmission electron microscope (TEM) observations further reveal that electron beam irradiation of the thin-film Zircaly-4 surface caused the sputtering of surface α-Zr atoms, the nanoscale atomic restructuring in the α-Zr matrix, and the amorphization of precipitates. These results are the first direct evidences suggesting that displacement of metal atoms can be induced by a low incident electron energy below threshold. The presented way to irradiate may be extended to other materials aiming at producing appealing properties for applications in fields of nanotechnology, surface technology, and others.
Inhibition of the mechano-enzymatic amyloidogenesis of transthyretin: role of ligand affinity, binding cooperativity and occupancy of the inner channel
Authors: Verona Guglielmo , Mangione P. Patrizia , Raimondi Sara , Giorgetti Sofia , Faravelli Giulia , Porcari Riccardo , Corazza Alessandra , Gillmore Julian D. , Hawkins Philip N. , Pepys Mark B. , Taylor Graham W. , Bellotti Vittorio 
Published: March 2017

AbstractDissociation of the native transthyretin (TTR) tetramer is widely accepted as the critical step in TTR amyloid fibrillogenesis. It is modelled by exposure of the protein to non-physiological low pH in vitro and is inhibited by small molecule compounds, such as the drug tafamidis. We have recently identified a new mechano-enzymatic pathway of TTR fibrillogenesis in vitro, catalysed by selective proteolytic cleavage, which produces a high yield of genuine amyloid fibrils. This pathway is efficiently inhibited only by ligands that occupy both binding sites in TTR. Tolcapone, which is bound with similar high affinity in both TTR binding sites without the usual negative cooperativity, is therefore of interest. Here we show that TTR fibrillogenesis by the mechano-enzymatic pathway is indeed more potently inhibited by tolcapone than by tafamidis but neither, even in large molar excess, completely prevents amyloid fibril formation. In contrast, mds84, the prototype of our previously reported bivalent ligand TTR ‘superstabiliser’ family, is notably more potent than the monovalent ligands and we show here that this apparently reflects the critical additional interactions of its linker within the TTR central channel. Our findings have major implications for therapeutic approaches in TTR amyloidosis.
Variation-preserving normalization unveils blind spots in gene expression profiling
Authors: Roca Carlos P. , Gomes Susana I. L. , Amorim Mónica J. B. , Scott-Fordsmand Janeck J. 
Published: March 2017

AbstractRNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
Building a 5-HT3A Receptor Expression Map in the Mouse Brain
Authors: Koyama Yoshihisa , Kondo Makoto , Shimada Shoichi 
Published: March 2017

AbstractOf the many serotonin receptors, the type 3 receptors (5-HT3R) are the only ionotropic ones, playing a key role in fast synaptic transmission and cognitive and emotional brain function through controlled neuronal excitation. To better understand the various functions of 5-HT3Rs, it is very important to know their expression pattern in the central nervous system (CNS). To date, many distributional studies have shown localized 5-HT3R expression in the brain and spinal cord. However, an accurate pattern of 5-HT3R expression in the CNS remains to be elucidated. To investigate the distribution of 5-HT3R in the mouse brain in detail, we performed immunofluorescent staining using 5-HT3AR-GFP transgenic mice. We found strong 5-HT3AR expression in the olfactory bulb, cerebral cortex, hippocampus, and amygdala; and partial expression in the pons, medulla, and spinal cord. Meanwhile, the thalamus, hypothalamus, and midbrain exhibited a few 5-HT3AR-expressing cells, and no expression was detected in the cerebellum. Further, double-immunostaining using neural markers confirmed that 5-HT3AR is expressed in GABAergic interneurons containing somatostatin or calretinin. In the present study, we built a 5-HT3AR expression map in the mouse brain. Our findings make significant contributions in elucidating the novel functions of 5-HT3R in the CNS.
The Final (Oral Ebola) Vaccine Trial on Captive Chimpanzees?
Authors: Walsh Peter D. , Kurup Drishya , Hasselschwert Dana L. , Wirblich Christoph , Goetzmann Jason E. , Schnell Matthias J. 
Published: March 2017

AbstractCould new oral vaccine technologies protect endangered wildlife against a rising tide of infectious disease? We used captive chimpanzees to test oral delivery of a rabies virus (RABV) vectored vaccine against Ebola virus (EBOV), a major threat to wild chimpanzees and gorillas. EBOV GP and RABV GP-specific antibody titers increased exponentially during the trial, with rates of increase for six orally vaccinated chimpanzees very similar to four intramuscularly vaccinated controls. Chimpanzee sera also showed robust neutralizing activity against RABV and pseudo-typed EBOV. Vaccination did not induce serious health complications. Blood chemistry, hematologic, and body mass correlates of psychological stress suggested that, although sedation induced acute stress, experimental housing conditions did not induce traumatic levels of chronic stress. Acute behavioral and physiological responses to sedation were strongly correlated with immune responses to vaccination. These results suggest that oral vaccination holds great promise as a tool for the conservation of apes and other endangered tropical wildlife. They also imply that vaccine and drug trials on other captive species need to better account for the effects of stress on immune response.
Immunogenicity is preferentially induced in sparse dendritic cell cultures
Authors: Nasi Aikaterini , Bollampalli Vishnu Priya , Sun Meng , Chen Yang , Amu Sylvie , Nylén Susanne , Eidsmo Liv , Rothfuchs Antonio Gigliotti , Réthi Bence 
Published: March 2017

AbstractWe have previously shown that human monocyte-derived dendritic cells (DCs) acquired different characteristics in dense or sparse cell cultures. Sparsity promoted the development of IL-12 producing migratory DCs, whereas dense cultures increased IL-10 production. Here we analysed whether the density-dependent endogenous breaks could modulate DC-based vaccines. Using murine bone marrow-derived DC models we show that sparse cultures were essential to achieve several key functions required for immunogenic DC vaccines, including mobility to draining lymph nodes, recruitment and massive proliferation of antigen-specific CD4+ T cells, in addition to their TH1 polarization. Transcription analyses confirmed higher commitment in sparse cultures towards T cell activation, whereas DCs obtained from dense cultures up-regulated immunosuppressive pathway components and genes suggesting higher differentiation plasticity towards osteoclasts. Interestingly, we detected a striking up-regulation of fatty acid and cholesterol biosynthesis pathways in sparse cultures, suggesting an important link between DC immunogenicity and lipid homeostasis regulation.
Principal Components Analysis Based Unsupervised Feature Extraction Applied to Gene Expression Analysis of Blood from Dengue Haemorrhagic Fever Patients
Authors: Taguchi Y-h. 
Published: March 2017

AbstractDengue haemorrhagic fever (DHF) sometimes occurs after recovery from the disease caused by Dengue virus (DENV), and is often fatal. However, the mechanism of DHF has not been determined, possibly because no suitable methodologies are available to analyse this disease. Therefore, more innovative methods are required to analyse the gene expression profiles of DENV-infected patients. Principal components analysis (PCA)-based unsupervised feature extraction (FE) was applied to the gene expression profiles of DENV-infected patients, and an integrated analysis of two independent data sets identified 46 genes as critical for DHF progression. PCA using only these 46 genes rendered the two data sets highly consistent. The application of PCA to the 46 genes of an independent third data set successfully predicted the progression of DHF. A fourth in vitro data set confirmed the identification of the 46 genes. These 46 genes included interferon- and heme-biosynthesis-related genes. The former are enriched in binding sites for STAT1, STAT2, and IRF1, which are associated with DHF-promoting antibody-dependent enhancement, whereas the latter are considered to be related to the dysfunction of spliceosomes, which may mediate haemorrhage. These results are outcomes that other type of bioinformatic analysis could hardly achieve.
Widespread platinum anomaly documented at the Younger Dryas onset in North American sedimentary sequences
Authors: Moore Christopher R. , West Allen , LeCompte Malcolm A. , Brooks Mark J. , Daniel I. Randolph , Goodyear Albert C. , Ferguson Terry A. , Ivester Andrew H. , Feathers James K. , Kennett James P. , Tankersley Kenneth B. , Adedeji A. Victor , Bunch Ted E. 
Published: March 2017

AbstractPreviously, a large platinum (Pt) anomaly was reported in the Greenland ice sheet at the Younger Dryas boundary (YDB) (12,800 Cal B.P.). In order to evaluate its geographic extent, fire-assay and inductively coupled plasma mass spectrometry (FA and ICP-MS) elemental analyses were performed on 11 widely separated archaeological bulk sedimentary sequences. We document discovery of a distinct Pt anomaly spread widely across North America and dating to the Younger Dryas (YD) onset. The apparent synchroneity of this widespread YDB Pt anomaly is consistent with Greenland Ice Sheet Project 2 (GISP2) data that indicated atmospheric input of platinum-rich dust. We expect the Pt anomaly to serve as a widely-distributed time marker horizon (datum) for identification and correlation of the onset of the YD climatic episode at 12,800 Cal B.P. This Pt datum will facilitate the dating and correlating of archaeological, paleontological, and paleoenvironmental data between sequences, especially those with limited age control.
Simple Risk Score for Prediction of Early Recurrence of Hepatocellular Carcinoma within the Milan Criteria after Orthotopic Liver Transplantation
Authors: Feng Jiliang , Wu Jushan , Zhu Ruidong , Feng Dezhao , Yu Lu , Zhang Yan , Bu Dayu , Li Chenlei , Zhou Yuyan , Si Lianghao , Liu Yuhan , Liang Ziwei , Xu Jianing , Wu Tianjun 
Published: March 2017

AbstractTen to twenty percent of the hepatocellular carcinoma (HCC) patients fulfilling the Milan criteria (MC) recurred within three years after orthotopic liver transplantation (OLT). We therefore utilize a training cohort to develop an improved prognostic model for predicting the recurrence in these patients. By univariate and multivariate analysis, AFP level [cut-off value: 321 ng/mL, area under the curve (AUC) = 0.724, 95% confidence interval (CI) = 0.604–0.843, P < 0.001] and cytokeratin-19 (CK19) and glypican-3 (GPC3) expression pattern from nine putative prognostic factors were entered in risk factor scoring model to conjecture the tumor recurrence. In the training cohort, the AUC value of the model was 0.767 (95% CI = 0.645–0.890, P < 0.001), which was the highest among all the elements. The model’s performance was then assessed using a validation cohort. In the validation cohort, the AUC value of the model was 0.843 (95% CI = 0.720−0.966, P < 0.001) which was higher than any other elements. The results indicated that model had high performance with good discrimination ability and significantly improved the predictive capacity for the recurrence of HCC patients within MC after OLT.
Suppression of autophagy by mycophenolic acid contributes to inhibition of HCV replication in human hepatoma cells
Authors: Fang Shoucai , Su Jinming , Liang Bingyu , Li Xu , Li Yu , Jiang Junjun , Huang Jiegang , Zhou Bo , Ning Chuanyi , Li Jieliang , Ho Wenzhe , Li Yiping , Chen Hui , Liang Hao , Ye Li 
Published: March 2017

AbstractPrevious studies have shown that mycophenolic acid (MPA) has an anti-HCV activity. However, the mechanism of MPA-mediated inhibition of HCV replication remains to be determined. This study investigated whether MPA has an effect on autophagy, a cellular machinery required for HCV replication, thereby, inhibits HCV replication in Huh7 cells. MPA treatment of Huh7 cells could suppress autophagy, evidenced by decreased LC3B-II level and conversion of LC3B-I to LC3B-II, decreased autophagosome formation, and increased p62 level compared to MPA-untreated cells. Tunicamycin treatment or HCV infection could induce cellular autophagy, however, MPA also exhibited its inhibitory effect on tunicamycin- or HCV infection-induced autophagy. The expression of three autophagy-related genes, Atg3, Atg5, and Atg7 were identified to be inhibited by MPA treatment. Over-expression of these genes could partly recover HCV replication inhibited by MPA; however, silencing their expression by siRNAs could enhance the inhibitory effect of MPA on HCV. Collectively, these results reveal that suppression of autophagy by MPA plays a role in its anti-HCV activity. Down-regulating the expression of three autophagy-related genes by MPA involves in its antiviral mechanism.
The effect of cold priming on the fitness of Arabidopsis thaliana accessions under natural and controlled conditions
Authors: Cvetkovic Jelena , Müller Klaus , Baier Margarete 
Published: March 2017

AbstractPriming improves an organism's performance upon a future stress. To test whether cold priming supports protection in spring and how it is affected by cold acclimation, we compared seven Arabidopsis accessions with different cold acclimation potentials in the field and in the greenhouse for growth, photosynthetic performance and reproductive fitness in March and May after a 14 day long cold-pretreatment at 4 °C. In the plants transferred to the field in May, the effect of the cold pretreatment on the seed yield correlated with the cold acclimation potential of the accessions. In the March transferred plants, the reproductive fitness was most supported by the cold pretreatment in the accessions with the weakest cold acclimation potential. The fitness effect was linked to long-term effects of the cold pretreatment on photosystem II activity stabilization and leaf blade expansion. The study demonstrated that cold priming stronger impacts on plant fitness than cold acclimation in spring in accessions with intermediate and low cold acclimation potential.
Comparison of human adipose stromal vascular fraction and adipose-derived mesenchymal stem cells for the attenuation of acute renal ischemia/reperfusion injury
Authors: Zhou Liuhua , Song Qun , Shen Jiangwei , Xu Luwei , Xu Zheng , Wu Ran , Ge Yuzheng , Zhu Jiageng , Wu Jianping , Dou Quanliang , Jia Ruipeng 
Published: March 2017

AbstractStem cells therapy has been suggested as a promising option for the treatment of acute kidney injury (AKI). This study was performed to compare the abilities of xenogenic transplantation of human adipose stromal vascular fraction (SVF) and adipose-derived mesenchymal stem cells (AdMSCs) to facilitate the recovery of renal function and structure in a rat model of ischemia/reperfusion (IR) induced AKI. SVF or AdMSCs were transplanted to the injured kidney through intra-parenchymal injection. Significantly improved renal function and reduced tubular injury were observed in SVF and AdMSCs groups. Administration of SVF or AdMSCs contributed to significantly improved cell proliferation and markedly reduced cell apoptosis in parallel with reduced microvascular rarefaction in injured kidney. IR injury resulted in higher levels of inflammatory cytokines, whereas xenogenic transplantation of SVF or AdMSCs reduced but not induced inflammatory cytokines expression. Additionally, in vitro study showed that administration of SVF or AdMSCs could also significantly promote the proliferation and survival of renal tubular epithelial cells underwent hypoxia/reoxygenation injury through secreting various growth factors. However, cell proliferation was significantly promoted in SVF group than in AdMSCs group. In conclusion, our study demonstrated that administration of SVF or AdMSCs was equally effective in attenuating acute renal IR injury.
Acetylation and phosphorylation control both local and global stability of the chloroplast F1 ATP synthase
Authors: Schmidt Carla , Beilsten-Edmands Victoria , Mohammed Shabaz , Robinson Carol V. 
Published: March 2017

AbstractATP synthases (ATPases) are enzymes that produce ATP and control the pH in the cell or cellular compartments. While highly conserved over different species, ATPases are structurally well-characterised but the existence and functional significance of many post-translational modifications (PTMs) is not well understood. We combined a range of mass spectrometric techniques to unravel the location and extent of PTMs in the chloroplast ATP synthase (cATPase) purified from spinach leaves. We identified multiple phosphorylation and acetylation sites and found that both modifications stabilise binding of ε and δ subunits. Comparing cross-linking of naturally modified cATPase with the in vitro deacetylated enzyme revealed a major conformational change in the ε subunit in accord with extended and folded forms of the subunit. Locating modified residues within the catalytic head we found that phosphorylated and acetylated residues are primarily on α/β and β/α interfaces respectively. By aligning along different interfaces the higher abundance acetylated residues are proximal to the regulatory sites while the lower abundance phosphorylation sites are more densely populated at the catalytic sites. We propose that modifications in the catalytic head, together with the conformational change in subunit ε, work in synergy to fine-tune the enzyme during adverse conditions.