bluuebunny/crossref_metadata_2025_split huggingface dataset:
Endogenous sulfur dioxide is a novel adipocyte-derived inflammatory inhibitor
Authors: Zhang Heng , Huang Yaqian , Bu Dingfang , Chen Selena , Tang Chaoshu , Wang Guang , Du Junbao , Jin Hongfang 
Published: June 2016

AbstractThe present study was designed to determine whether sulfur dioxide (SO2) could be endogenously produced in adipocyte and served as a novel adipocyte-derived inflammatory inhibitor. SO2 was detected in adipose tissue using high-performance liquid chromatography with fluorescence detection. SO2 synthase aspartate aminotransferase (AAT1 and AAT2) mRNA and protein expressions in adipose tissues were measured. For in vitro study, 3T3-L1 adipocytes were cultured, infected with adenovirus carrying AAT1 gene or lentivirus carrying shRNA to AAT1, and then treated with tumor necrosis factor-α (TNF-α). We found that endogenous SO2/AAT pathway existed in adipose tissues including perivascular, perirenal, epididymal, subcutaneous and brown adipose tissue. AAT1 overexpression significantly increased SO2 production and inhibited TNF-α-induced inflammatory factors, monocyte chemoattractant protein-1 (MCP-1) and interleukin-8 (IL-8) secretion from 3T3-L1 adipocytes. By contrast, AAT1 knockdown decreased SO2 production and exacerbated TNF-α-stimulated MCP-1 and IL-8 secretion. Mechanistically, AAT1 overexpression attenuated TNF-α-induced IκBα phosphorylation and degradation, and nuclear factor-κB (NF-κB) p65 phosphorylation, while AAT1 knockdown aggravated TNF-α-activated NF-κB pathway, which was blocked by SO2. NF-κB inhibitors, PDTC or Bay 11-7082, abolished excessive p65 phosphorylation and adipocyte inflammation induced by AAT1 knockdown. This is the first report to suggest that endogenous SO2 is a novel adipocyte-derived inflammatory inhibitor.
A light-controlled switch after dual targeting of proliferating tumor cells via the membrane receptor EGFR and the nuclear protein Ki-67
Authors: Wang Sijia , Hüttmann Gereon , Scholzen Thomas , Zhang Zhenxi , Vogel Alfred , Hasan Tayyaba , Rahmanzadeh Ramtin 
Published: June 2016

AbstractUsing nanotechnology for optical manipulation of molecular processes in cells with high spatial and temporal precision promises new therapeutic options. Especially tumor therapy may profit as it requires a combination of both selectivity and an effective cell killing mechanism. Here we show a dual targeting approach for selective and efficient light-controlled killing of cells which are positive for epidermal growth factor receptor (EGFR) and Ki-67. Liposomes with the covalently linked EGFR antibody Erbitux enabled selective uptake of FITC-labeled Ki-67 antibody TuBB-9 in EGFR-positive cells pre-loaded with the photoactive dye BPD. After irradiation at 690 nm, BPD disrupted the endosomal membranes and delivered the antibodies to the nucleoli of the cells. The second irradiation at 490 nm activated the FITC-labeled TuBB-9, which caused inactivation of the Ki-67 protein and subsequent cell death via apoptosis. Efficient cell killing was possible at nanomolar concentrations of TuBB-9 due to the effective transport by immune liposomes and the high efficacy of the Ki-67 light-inactivation. Delivery of the liposomal constructs and cell destruction correlated well with the EGFR expression pattern of different cell lines (HeLa, OVCAR-5, MCF-7, and human fibroblasts), demonstrating an excellent selectivity.
Prediction of miRNA-disease associations with a vector space model
Authors: Pasquier Claude , Gardès Julien 
Published: June 2016

AbstractMicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are associated with diseases contributes to a better understanding of pathogenicity mechanisms. MicroRNAs also represent a tremendous opportunity in biotechnology for early diagnosis. To date, several in silico methods have been developed to address the issue of microRNA-disease association prediction. However, these methods have various limitations. In this study, we investigate the hypothesis that information attached to miRNAs and diseases can be revealed by distributional semantics. Our basic approach is to represent distributional information on miRNAs and diseases in a high-dimensional vector space and to define associations between miRNAs and diseases in terms of their vector similarity. Cross validations performed on a dataset of known miRNA-disease associations demonstrate the excellent performance of our method. Moreover, the case study focused on breast cancer confirms the ability of our method to discover new disease-miRNA associations and to identify putative false associations reported in databases.
The hydrogen sulfide metabolite trimethylsulfonium is found in human urine
Authors: Lajin Bassam , Francesconi Kevin A. 
Published: June 2016

AbstractHydrogen sulfide is the third and most recently discovered gaseous signaling molecule following nitric oxide and carbon monoxide, playing important roles both in normal physiological conditions and disease progression. The trimethylsulfonium ion (TMS) can result from successive methylation reactions of hydrogen sulfide. No report exists so far about the presence or quantities of TMS in human urine. We developed a method for determining TMS in urine using liquid chromatography-electrospray ionization-triple quadrupole mass spectrometry (LC-ESI-QQQ) and applied the method to establish the urinary levels of TMS in a group of human volunteers. The measured urinary levels of TMS were in the nanomolar range, which is commensurate with the steady-state tissue concentrations of hydrogen sulfide previously reported in the literature. The developed method can be used in future studies for the quantification of urinary TMS as a potential biomarker for hydrogen sulfide body pools.
The Wheat GT Factor TaGT2L1D Negatively Regulates Drought Tolerance and Plant Development
Authors: Zheng Xin , Liu Haipei , Ji Hongtao , Wang Youning , Dong Baodi , Qiao Yunzhou , Liu Mengyu , Li Xia 
Published: June 2016

AbstractGT factors are trihelix transcription factors that specifically regulate plant development and stress responses. Recently, several GT factors have been characterized in different plant species; however, little is known about the role of GT factors in wheat. Here, we show that TaGT2L1A, TaGT2L1B, and TaGT2L1D are highly homologous in hexaploid wheat, and are localized to wheat chromosomes 2A, 2B, and 2D, respectively. These TaGT2L1 genes encode proteins containing two SANT domains and one central helix. All three homologs were ubiquitously expressed during wheat development and were responsive to osmotic stress. Functional analyses demonstrated that TaGT2L1D acts as a transcriptional repressor; it was able to suppress the expression of AtSDD1 in Arabidopsis by binding directly to the GT3 box in its promoter that negatively regulates drought tolerance. TaGT2L1D overexpression markedly increased the number of stomata and reduced drought tolerance in gtl1-3 plants. Notably, ectopic expression of TaGT2L1D also affected floral organ development and overall plant growth. These results demonstrate that TaGT2L1 is an ortholog of AtGTL1, and that it plays an evolutionarily conserved role in drought resistance by fine tuning stomatal density in wheat. Our data also highlight the role of TaGT2L1 in plant growth and development.
Differences in DNA Repair Capacity, Cell Death and Transcriptional Response after Irradiation between a Radiosensitive and a Radioresistant Cell Line
Authors: Borràs-Fresneda Mireia , Barquinero Joan-Francesc , Gomolka Maria , Hornhardt Sabine , Rössler Ute , Armengol Gemma , Barrios Leonardo 
Published: June 2016

AbstractNormal tissue toxicity after radiotherapy shows variability between patients, indicating inter-individual differences in radiosensitivity. Genetic variation probably contributes to these differences. The aim of the present study was to determine if two cell lines, one radiosensitive (RS) and another radioresistant (RR), showed differences in DNA repair capacity, cell viability, cell cycle progression and, in turn, if this response could be characterised by a differential gene expression profile at different post-irradiation times. After irradiation, the RS cell line showed a slower rate of γ-H2AX foci disappearance, a higher frequency of incomplete chromosomal aberrations, a reduced cell viability and a longer disturbance of the cell cycle when compared to the RR cell line. Moreover, a greater and prolonged transcriptional response after irradiation was induced in the RS cell line. Functional analysis showed that 24 h after irradiation genes involved in “DNA damage response”, “direct p53 effectors” and apoptosis were still differentially up-regulated in the RS cell line but not in the RR cell line. The two cell lines showed different response to IR and can be distinguished with cell-based assays and differential gene expression analysis. The results emphasise the importance to identify biomarkers of radiosensitivity for tailoring individualized radiotherapy protocols.
Seven wood-inhabiting new species of the genus Trichoderma (Fungi, Ascomycota) in Viride clade
Authors: Qin Wen-Tao , Zhuang Wen-Ying 
Published: June 2016

AbstractMore than 200 recent collections of Trichoderma from China were examined and 16 species belonging to the Viride clade were identified based on integrated studies of phenotypic and molecular data. Among them, seven wood-inhabiting new species, T. albofulvopsis, T. densum, T. laevisporum, T. sinokoningii, T. sparsum, T. sphaerosporum and T. subviride, are found. They form trichoderma- to verticillium-like conidiophores, lageniform to subulate phialides and globose to ellipsoidal conidia, but vary greatly in colony features, growth rates, and sizes of phialides and conidia. To explore their taxonomic positions, the phylogenetic tree including all the known species of the Viride clade is constructed based on sequence analyses of the combined RNA polymerase II subunit b and translation elongation factor 1 alpha exon genes. Our results indicated that the seven new species were well-located in the Koningii, Rogersonii and Neorufum subclades as well as a few independent terminal branches. They are clearly distinguishable from any existing species. Morphological distinctions and sequence divergences between the new species and their close relatives were discussed.
The Role of Trap-assisted Recombination in Luminescent Properties of Organometal Halide CH3NH3PbBr3 Perovskite Films and Quantum Dots
Authors: Zhang Zhen-Yu , Wang Hai-Yu , Zhang Yan-Xia , Hao Ya-Wei , Sun Chun , Zhang Yu , Gao Bing-Rong , Chen Qi-Dai , Sun Hong-Bo 
Published: June 2016

AbstractHybrid metal halide perovskites have been paid enormous attentions in photophysics research, whose excellent performances were attributed to their intriguing charge carriers proprieties. However, it still remains far from satisfaction in the comprehensive understanding of perovskite charge-transport properities, especially about trap-assisted recombination process. In this Letter, through time-resolved transient absorption (TA) and photoluminescence (PL) measurements, we provided a relative comprehensive investigation on the charge carriers recombination dynamics of CH3NH3PbBr3 (MAPbBr3) perovskite films and quantum dots (QDs), especially about trap-assisted recombination. It was found that the integral recombination mode of MAPbBr3 films was highly sensitive to the density distribution of generated charge carriers and trap states. Additional, Trap effects would be gradually weakened with elevated carrier densities. Furthermore, the trap-assisted recombination can be removed from MAPbBr3 QDs through its own surface passivation mechanism and this specialty may render the QDs as a new material in illuminating research. This work provides deeper physical insights into the dynamics processes of MAPbBr3 materials and paves a way toward more light-harvesting applications in future.
Development of a high-affinity peptide that prevents phospholemman (PLM) inhibition of the sodium/calcium exchanger 1 (NCX1)
Authors: Wanichawan Pimthanya , Hodne Kjetil , Hafver Tandekile Lubelwana , Lunde Marianne , Martinsen Marita , Louch William Edward , Sejersted Ole Mathias , Carlson Cathrine Rein 
Published: June 2016

NCX1 (Na+/Ca2+ exchanger 1) is an important regulator of intracellular Ca2+ and a potential therapeutic target for brain ischaemia and for diastolic heart failure with preserved ejection fraction. PLM (phospholemman), a substrate for protein kinases A and C, has been suggested to regulate NCX1 activity. However, although several studies have demonstrated that binding of phosphorylated PLM (pSer68-PLM) leads to NCX1 inhibition, other studies have failed to demonstrate a functional interaction of these proteins. In the present study, we aimed to analyse the biological function of the pSer68-PLM–NCX1 interaction by developing high-affinity blocking peptides. PLM was observed to co-fractionate and co-immunoprecipitate with NCX1 in rat left ventricle, and in co-transfected HEK (human embryonic kidney)-293 cells. For the first time, the NCX1–PLM interaction was also demonstrated in the brain. PLM binding sites on NCX1 were mapped to two regions by peptide array assays, containing the previously reported PASKT and QKHPD motifs. Conversely, the two NCX1 regions bound identical sequences in the cytoplasmic domain of PLM, suggesting that NCX1-PASKT and NCX1-QKHPD might bind to each PLM monomer. Using two-dimensional peptide arrays of the native NCX1 sequence KHPDKEIEQLIELANYQVLS revealed that double substitution of tyrosine for positions 1 and 4 (K1Y and D4Y) enhanced pSer68-PLM binding 8-fold. The optimized peptide blocked binding of NCX1-PASKT and NCX1-QKHPD to PLM and reversed PLM(S68D) inhibition of NCX1 activity (both forward and reverse mode) in HEK-293 cells. Altogether our data indicate that PLM interacts directly with NCX1 and inhibits NCX1 activity when phosphorylated at Ser68.
Involvement of matrix metalloproteinases (MMPs) and inflammasome pathway in molecular mechanisms of fibrosis
Authors: Robert Sacha , Gicquel Thomas , Victoni Tatiana , Valença Samuel , Barreto Emiliano , Bailly-Maître Béatrice , Boichot Elisabeth , Lagente Vincent 
Published: June 2016

Fibrosis is a basic connective tissue lesion defined by the increase in the fibrillar extracellular matrix (ECM) components in tissue or organ. Matrix metalloproteinases (MMPs) are a major group of proteases known to regulate the turn-over of ECM and so they are suggested to be important in tissue remodelling observed during fibrogenic process associated with chronic inflammation. Tissue remodelling is the result of an imbalance in the equilibrium of the normal processes of synthesis and degradation of ECM components markedly controlled by the MMPs/TIMP imbalance. We previously showed an association of the differences in collagen deposition in the lungs of bleomycin-treated mice with a reduced molar pro-MMP-9/TIMP-1 ratio. Using the carbon tetrachloride (CCl4) preclinical model of liver fibrosis in mice, we observed a significant increase in collagen deposition with increased expression and release of tissue inhibitors of metalloproteinase (TIMP)-1 both at 24 h and 3 weeks later. This suggests an early altered regulation of matrix turnover involved in the development of fibrosis. We also demonstrated an activation of NLRP3-inflammasome pathway associated with the IL-1R/MyD88 signalling in the development of experimental fibrosis both in lung and liver. This was also associated with an increased expression of purinergic receptors mainly P2X7. Finally, these observations emphasize those effective therapies for these disorders must be given early in the natural history of the disease, prior to the development of tissue remodelling and fibrosis.
Spatial scale modulates the strength of ecological processes driving disease distributions
Authors: Cohen Jeremy M. , Civitello David J. , Brace Amber J. , Feichtinger Erin M. , Ortega C. Nicole , Richardson Jason C. , Sauer Erin L. , Liu Xuan , Rohr Jason R. 
Published: June 2016

Significance
For four decades, ecologists have hypothesized that biotic interactions predominantly control species’ distributions at local scales, whereas abiotic factors operate more at regional scales. Here, we demonstrate that the drivers of three emerging diseases (amphibian chytridiomycosis, West Nile virus, and Lyme disease) in the United States support the predictions of this fundamental hypothesis. Humans are contributing to biodiversity loss, changes in dispersal patterns, and global climate change at an unprecedented rate. Our results highlight that common single-scale analyses can misestimate the impact that humans are having on biodiversity, disease, and the environment.
Heme dynamics and trafficking factors revealed by genetically encoded fluorescent heme sensors
Authors: Hanna David A. , Harvey Raven M. , Martinez-Guzman Osiris , Yuan Xiaojing , Chandrasekharan Bindu , Raju Gheevarghese , Outten F. Wayne , Hamza Iqbal , Reddi Amit R. 
Published: June 2016

SignificanceAll heme-dependent functions require the mobilization of labile heme (LH), of which there is little understanding of its nature and dynamics. To probe LH pools, we developed genetically encoded fluorescent heme sensors and deployed them in the unicellular eukaryoteSaccharomyces cerevisiae. We find that LH is relatively abundant in the cytosol, but exceedingly low in the mitochondria and nucleus. Further, we find that LH can be mobilized by signaling molecules like nitric oxide. We also find that the glycolytic enzyme glyceraldehyde phosphate dehydrogenase constitutes a major heme buffer and is responsible for regulating the activity of a heme-dependent transcription factor. Altogether, our work will have profound implications for understanding the mechanisms of heme utilization.
Teaching a lay theory before college narrows achievement gaps at scale
Authors: Yeager David S. , Walton Gregory M. , Brady Shannon T. , Akcinar Ezgi N. , Paunesku David , Keane Laura , Kamentz Donald , Ritter Gretchen , Duckworth Angela Lee , Urstein Robert , Gomez Eric M. , Markus Hazel Rose , Cohen Geoffrey L. , Dweck Carol S. 
Published: June 2016

Significance
In the United States, large, persistent gaps exist in the rates at which racial, ethnic, and socioeconomic groups complete postsecondary education, even when groups are equated on prior preparation. We test a method for preventing some of those gaps by providing individuals with a lay theory about the meaning of commonplace difficulties before college matriculation. Across three experiments, lay theory interventions delivered to over 90% of students increased full-time enrollment rates, improved grade point averages, and reduced the overrepresentation of socially disadvantaged students among the bottom 20% of class rank. The interventions helped disadvantaged students become more socially and academically integrated in college. Broader tests can now be conducted to understand in which settings lay theories can help remedy postsecondary inequality at scale.
Hierarchy of prediction errors for auditory events in human temporal and frontal cortex
Authors: Dürschmid Stefan , Edwards Erik , Reichert Christoph , Dewar Callum , Hinrichs Hermann , Heinze Hans-Jochen , Kirsch Heidi E. , Dalal Sarang S. , Deouell Leon Y. , Knight Robert T. 
Published: June 2016

Significance
To survive, organisms must constantly form predictions of the future based on past regularities. When predictions are violated, action may be needed. Different scales of environmental regularity need to encompass both subsecond repetitions and complex structures spanning longer timescales. How different parts of the brain monitor these temporal regularities and produce prediction error signals is unclear. Utilizing subdural electrocorticographic electrodes with an auditory paradigm involving local and global regularities, we show that frontal cortex is sensitive to the big picture, responding with high γ-band activity exclusively to globally unpredictable changes, whereas the temporal cortex equally responds to any change in the immediate history. These results reveal a hierarchy of predictive coding recorded directly from the human brain.
Draft genome of the peanut A-genome progenitor (Arachis duranensis) provides insights into geocarpy, oil biosynthesis, and allergens
Authors: Chen Xiaoping , Li Hongjie , Pandey Manish K. , Yang Qingli , Wang Xiyin , Garg Vanika , Li Haifen , Chi Xiaoyuan , Doddamani Dadakhalandar , Hong Yanbin , Upadhyaya Hari , Guo Hui , Khan Aamir W. , Zhu Fanghe , Zhang Xiaoyan , Pan Lijuan , Pierce Gary J. , Zhou Guiyuan , Krishnamohan Katta A. V. S. , Chen Mingna , Zhong Ni , Agarwal Gaurav , Li Shuanzhu , Chitikineni Annapurna , Zhang Guo-Qiang , Sharma Shivali , Chen Na , Liu Haiyan , Janila Pasupuleti , Li Shaoxiong , Wang Min , Wang Tong , Sun Jie , Li Xingyu , Li Chunyan , Wang Mian , Yu Lina , Wen Shijie , Singh Sube , Yang Zhen , Zhao Jinming , Zhang Chushu , Yu Yue , Bi Jie , Zhang Xiaojun , Liu Zhong-Jian , Paterson Andrew H. , Wang Shuping , Liang Xuanqiang , Varshney Rajeev K. , Yu Shanlin 
Published: June 2016

SignificanceWe present a draft genome of the peanut A-genome progenitor,Arachis duranensis, providing details on total genes present in the genome. Genome analysis suggests that the peanut lineage was affected by at least three polyploidizations since the origin of eudicots. Resequencing of syntheticArachistetraploids reveals extensive gene conversion since their formation by human hands. TheA. duranensisgenome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants. This study also provides millions of structural variations that can be used as genetic markers for the development of improved peanut varieties through genomics-assisted breeding.
Mechanosensory hairs in bumblebees (
Bombus terrestris
) detect weak electric fields
Authors: Sutton Gregory P. , Clarke Dominic , Morley Erica L. , Robert Daniel 
Published: June 2016

Significance
Electroreception in terrestrial animals is poorly understood. In bumblebees, the mechanical response of filiform hairs in the presence of electric fields provides key evidence for electrosensitivity to ecologically relevant electric fields. Mechanosensory hairs in arthropods have been shown to function as fluid flow or sound particle velocity receivers. The present work provides direct evidence for additional, nonexclusive functionality involving electrical Coulomb-force coupling between distant charged objects and mechanosensory hairs. Thus, the sensory mechanism is proposed to rely on electromechanical coupling, whereby many light thin hairs serve the detection of the electrical field surrounding a bumblebee approaching a flower. This finding prompts the possibility that other terrestrial animals use such sensory hairs to detect and respond to electric fields.