bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterization of a Citrus R2R3-MYB Transcription Factor that Regulates the Flavonol and Hydroxycinnamic Acid Biosynthesis
Authors: Liu Chaoyang , Long Jianmei , Zhu Kaijie , Liu Linlin , Yang Wei , Zhang Hongyan , Li Li , Xu Qiang , Deng Xiuxin 
Published: May 2016

AbstractFlavonols and hydroxycinnamic acids are important phenylpropanoid metabolites in plants. In this study, we isolated and characterized a citrus R2R3-MYB transcription factor CsMYBF1, encoding a protein belonging to the flavonol-specific MYB subgroup. Ectopic expression of CsMYBF1 in tomato led to an up-regulation of a series of genes involved in primary metabolism and the phenylpropanoid pathway, and induced a strong accumulation of hydroxycinnamic acid compounds but not the flavonols. The RNAi suppression of CsMYBF1 in citrus callus caused a down-regulation of many phenylpropanoid pathway genes and reduced the contents of hydroxycinnamic acids and flavonols. Transactivation assays indicated that CsMYBF1 activated several promoters of phenylpropanoid pathway genes in tomato and citrus. Interestingly, CsMYBF1 could activate the CHS gene promoter in citrus, but not in tomato. Further examinations revealed that the MYBPLANT cis-elements were essential for CsMYBF1 in activating phenylpropanoid pathway genes. In summary, our data indicated that CsMYBF1 possessed the function in controlling the flavonol and hydroxycinnamic acid biosynthesis, and the regulatory differences in the target metabolite accumulation between two species may be due to the differential activation of CHS promoters by CsMYBF1. Therefore, CsMYBF1 constitutes an important gene source for the engineering of specific phenylpropanoid components.
Cinema audiences reproducibly vary the chemical composition of air during films, by broadcasting scene specific emissions on breath
Authors: Williams Jonathan , Stönner Christof , Wicker Jörg , Krauter Nicolas , Derstroff Bettina , Bourtsoukidis Efstratios , Klüpfel Thomas , Kramer Stefan 
Published: May 2016

AbstractHuman beings continuously emit chemicals into the air by breath and through the skin. In order to determine whether these emissions vary predictably in response to audiovisual stimuli, we have continuously monitored carbon dioxide and over one hundred volatile organic compounds in a cinema. It was found that many airborne chemicals in cinema air varied distinctively and reproducibly with time for a particular film, even in different screenings to different audiences. Application of scene labels and advanced data mining methods revealed that specific film events, namely “suspense” or “comedy” caused audiences to change their emission of specific chemicals. These event-type synchronous, broadcasted human chemosignals open the possibility for objective and non-invasive assessment of a human group response to stimuli by continuous measurement of chemicals in air. Such methods can be applied to research fields such as psychology and biology and be valuable to industries such as film making and advertising.
Recurrent hormone-binding domain truncated ESR1 amplifications in primary endometrial cancers suggest their implication in hormone independent growth
Authors: Holst Frederik , Hoivik Erling A. , Gibson William J. , Taylor-Weiner Amaro , Schumacher Steven E. , Asmann Yan W. , Grossmann Patrick , Trovik Jone , Necela Brian M. , Thompson E. Aubrey , Meyerson Matthew , Beroukhim Rameen , Salvesen Helga B. , Cherniack Andrew D. 
Published: May 2016

AbstractThe estrogen receptor alpha (ERα) is highly expressed in both endometrial and breast cancers, and represents the most prevalent therapeutic target in breast cancer. However, anti-estrogen therapy has not been shown to be effective in endometrial cancer. Recently it has been shown that hormone-binding domain alterations of ERα in breast cancer contribute to acquired resistance to anti-estrogen therapy. In analyses of genomic data from The Cancer Genome Atlas (TCGA), we observe that endometrial carcinomas manifest recurrent ESR1 gene amplifications that truncate the hormone-binding domain encoding region of ESR1 and are associated with reduced mRNA expression of exons encoding the hormone-binding domain. These findings support a role for hormone-binding alterations of ERα in primary endometrial cancer, with potentially important therapeutic implications.
Treponema pallidum Lipoprotein TP0435 Expressed in Borrelia burgdorferi Produces Multiple Surface/Periplasmic Isoforms and mediates Adherence
Authors: Chan Kamfai , Nasereddin Thayer , Alter Laura , Centurion-Lara Arturo , Giacani Lorenzo , Parveen Nikhat 
Published: May 2016

AbstractThe ability of Treponema pallidum, the syphilis spirochete to colonize various tissues requires the presence of surface-exposed adhesins that have been difficult to identify due to the inability to culture and genetically manipulate T. pallidum. Using a Borrelia burgdorferi-based heterologous system and gain-in-function approach, we show for the first time that a highly immunogenic lipoprotein TP0435 can be differentially processed into multiple isoforms with one variant stochastically displayed on the spirochete surface. TP0435 was previously believed to be exclusively located in T. pallidum periplasm. Furthermore, non-adherent B. burgdorferi strain expressing TP0435 acquires the ability to bind to a variety of host cells including placental cells and exhibits slow opsonophagocytosis in vitro similar to poor ex vivo phagocytosis of T. pallidum by host macrophages reported previously. This phenomenon of production of both surface and periplasmic immunogenic lipoprotein isoforms has possible implications in immune evasion of the obligate pathogen T. pallidum during infection.
Aberrant expression of the S1P regulating enzymes, SPHK1 and SGPL1, contributes to a migratory phenotype in OSCC mediated through S1PR2
Authors: Patmanathan Sathya Narayanan , Johnson Steven P. , Lai Sook Ling , Panja Bernam Suthashini , Lopes Victor , Wei Wenbin , Ibrahim Maha Hafez , Torta Federico , Narayanaswamy Pradeep , Wenk Markus R. , Herr Deron R. , Murray Paul G. , Yap Lee Fah , Paterson Ian C. 
Published: May 2016

AbstractOral squamous cell carcinoma (OSCC) is a lethal disease with a 5-year mortality rate of around 50%. Molecular targeted therapies are not in routine use and novel therapeutic targets are required. Our previous microarray data indicated sphingosine 1-phosphate (S1P) metabolism and signalling was deregulated in OSCC. In this study, we have investigated the contribution of S1P signalling to the pathogenesis of OSCC. We show that the expression of the two major enzymes that regulate S1P levels were altered in OSCC: SPHK1 was significantly upregulated in OSCC tissues compared to normal oral mucosa and low levels of SGPL1 mRNA correlated with a worse overall survival. Inin vitrostudies, S1P enhanced the migration/invasion of OSCC cells and attenuated cisplatin-induced death. We also demonstrate that S1P receptor expression is deregulated in primary OSCCs and that S1PR2 is over-expressed in a subset of tumours, which in part mediates S1P-induced migration of OSCC cells. Lastly, we demonstrate that FTY720 induced significantly more apoptosis in OSCC cells compared to non-malignant cells and that FTY720 acted synergistically with cisplatin to induce cell death. Taken together, our data show that S1P signalling promotes tumour aggressiveness in OSCC and identify S1P signalling as a potential therapeutic target.
Genetic Relationship between Schizophrenia and Nicotine Dependence
Authors: Chen Jingchun , Bacanu Silviu-Alin , Yu Hui , Zhao Zhongming , Jia Peilin , Kendler Kenneth S. , Kranzler Henry R. , Gelernter Joel , Farrer Lindsay , Minica Camelia , Pool Rene , Milaneschi Yuri , Boomsma Dorret I. , Penninx Brenda W. J. H. , Tyndale Rachel F. , Ware Jennifer J. , Vink Jacqueline M. , Kaprio Jaakko , Munafò Marcus , Chen Xiangning ,   Cotinine meta-analysis group, Ware Jennifer J. , Chen Xiangning , Vink Jacqueline M. , Loukola Anu , Minica Camelia , Pool Rene , Milaneschi Yuri , Mangino Massimo , Menni Cristina , Chen Jingchun , Peterson Roseann , Auro Kirsi , Lyytikäinen Leo-Pekka , Wedenoja Juho , Stiby Alex I. , Hemani Gibran , Willemsen Gonneke , Hottenga Jouke Jan , Korhonen Tellervo , Heliövaara Markku , Perola Markus , Rose Richard , Paternoster Lavinia , Timpson Nic , Wassenaar Catherine A. , Zhu Andy Z. X. , Smith George Davey , Raitakari Olli , Lehtimäki Terho , Kähönen Mika , Koskinen Seppo , Spector Timothy , Penninx Brenda W. J. H. , Salomaa Veikko , Boomsma Dorret I. , Tyndale Rachel F. , Kaprio Jaakko , Munafò Marcus ,   FTND meta-analysis group, Ware Jennifer J. , Chen Xiangning , Vink Jacqueline M. , Loukola Anu , Minica Camelia , Chen Jingchun , Peterson Roseann , Timpson Nic , Taylor Michelle , Boomsma Dorret I. , Kaprio Jaakko , Munafò Marcus , Maes Hermine , Riley Brien , Kendler Kenneth S. , Gelernter Joel , Sherva Richard , Farrer Lindsay , Kranzler Henry R. , Maher Brion , Vanyukov Michael 
Published: May 2016

AbstractIt is well known that most schizophrenia patients smoke cigarettes. There are different hypotheses postulating the underlying mechanisms of this comorbidity. We used summary statistics from large meta-analyses of plasma cotinine concentration (COT), Fagerström test for nicotine dependence (FTND) and schizophrenia to examine the genetic relationship between these traits. We found that schizophrenia risk scores calculated at P-value thresholds of 5 × 10−3and larger predicted FTND and cigarettes smoked per day (CPD), suggesting that genes most significantly associated with schizophrenia were not associated with FTND/CPD, consistent with the self-medication hypothesis. The COT risk scores predicted schizophrenia diagnosis at P-values of 5 × 10−3and smaller, implying that genes most significantly associated with COT were associated with schizophrenia. These results implicated that schizophrenia and FTND/CPD/COT shared some genetic liability. Based on this shared liability, we identified multiple long non-coding RNAs and RNA binding protein genes (DA376252, BX089737, LOC101927273, LINC01029, LOC101928622, HY157071, DA902558,RBFOX1andTINCR), protein modification genes (MANBA,UBE2D3, andRANGAP1) and energy production genes (XYLB,MTRF1andENOX1) that were associated with both conditions. Further analyses revealed that these shared genes were enriched in calcium signaling, long-term potentiation and neuroactive ligand-receptor interaction pathways that played a critical role in cognitive functions and neuronal plasticity.
Solid-state supercapacitors with rationally designed heterogeneous electrodes fabricated by large area spray processing for wearable energy storage applications
Authors: Huang Chun , Zhang Jin , Young Neil P. , Snaith Henry J. , Grant Patrick S. 
Published: May 2016

AbstractSupercapacitors are in demand for short-term electrical charge and discharge applications. Unlike conventional supercapacitors, solid-state versions have no liquid electrolyte and do not require robust, rigid packaging for containment. Consequently they can be thinner, lighter and more flexible. However, solid-state supercapacitors suffer from lower power density and where new materials have been developed to improve performance, there remains a gap between promising laboratory results that usually require nano-structured materials and fine-scale processing approaches and current manufacturing technology that operates at large scale. We demonstrate a new, scalable capability to produce discrete, multi-layered electrodes with a different material and/or morphology in each layer and where each layer plays a different, critical role in enhancing the dynamics of charge/discharge. This layered structure allows efficient utilisation of each material and enables conservative use of hard-to-obtain materials. The layered electrode shows amongst the highest combinations of energy and power densities for solid-state supercapacitors. Our functional design and spray manufacturing approach to heterogeneous electrodes provide a new way forward for improved energy storage devices.
Development of a loop-mediated isothermal amplification method for the rapid diagnosis of Ascochyta rabiei L. in chickpeas
Authors: Chen Xiaolu , Ma Lijuan , Qiang Song , Ma Deying 
Published: May 2016

AbstractAscochyta blight (AB) is a devastating fungal disease of chickpeas that has spread to nearly all of the chickpea cultivating regions of the world. The rapid diagnosis of Ascochyta rabiei L. (A. rabiei), the pathogen that causes AB, plays an important role in A. rabiei epidemic tracking and AB management. In this study, a group of loop-mediated isothermal amplification (LAMP) primers was designed to detect A. rabiei in chickpea plants and seeds via a LAMP method and a conventional PCR method based on an internal transcribed spacer (ITS) sequence analysis of A. rabiei. Compared with the conventional PCR method, the LAMP method not only exhibited greater sensitivity and specificity in the detection of A. rabiei but also used simpler equipment and required less operational time. The minimum detectable concentration of the A. rabiei genomic DNA solution with the LAMP method was 6.01 × 10−6 ng/μl, which was 100 times lower than that of the conventional PCR method with the same outer primers. The greatest advantage of the LAMP method is that results can be observed via the visualization of color changes in SYBR Green I dye with the naked eye and it does not require expensive instruments, also with less time consumption.
Dissecting the expression relationships between RNA-binding proteins and their cognate targets in eukaryotic post-transcriptional regulatory networks
Authors: Nishtala Sneha , Neelamraju Yaseswini , Janga Sarath Chandra 
Published: May 2016

AbstractRNA-binding proteins (RBPs) are pivotal in orchestrating several steps in the metabolism of RNA in eukaryotes thereby controlling an extensive network of RBP-RNA interactions. Here, we employed CLIP (cross-linking immunoprecipitation)-seq datasets for 60 human RBPs and RIP-ChIP (RNP immunoprecipitation-microarray) data for 69 yeast RBPs to construct a network of genome-wide RBP- target RNA interactions for each RBP. We show in humans that majority (~78%) of the RBPs are strongly associated with their target transcripts at transcript level while ~95% of the studied RBPs were also found to be strongly associated with expression levels of target transcripts when protein expression levels of RBPs were employed. At transcript level, RBP - RNA interaction data for the yeast genome, exhibited a strong association for 63% of the RBPs, confirming the association to be conserved across large phylogenetic distances. Analysis to uncover the features contributing to these associations revealed the number of target transcripts and length of the selected protein-coding transcript of an RBP at the transcript level while intensity of the CLIP signal, number of RNA-Binding domains, location of the binding site on the transcript, to be significant at the protein level. Our analysis will contribute to improved modelling and prediction of post-transcriptional networks.
Taste substance binding elicits conformational change of taste receptor T1r heterodimer extracellular domains
Authors: Nango Eriko , Akiyama Shuji , Maki-Yonekura Saori , Ashikawa Yuji , Kusakabe Yuko , Krayukhina Elena , Maruno Takahiro , Uchiyama Susumu , Nuemket Nipawan , Yonekura Koji , Shimizu Madoka , Atsumi Nanako , Yasui Norihisa , Hikima Takaaki , Yamamoto Masaki , Kobayashi Yuji , Yamashita Atsuko 
Published: May 2016

AbstractSweet and umami tastes are perceived by T1r taste receptors in oral cavity. T1rs are class C G-protein coupled receptors (GPCRs), and the extracellular ligand binding domains (LBDs) of T1r1/T1r3 and T1r2/T1r3 heterodimers are responsible for binding of chemical substances eliciting umami or sweet taste. However, molecular analyses of T1r have been hampered due to the difficulties in recombinant expression and protein purification, and thus little is known about mechanisms for taste perception. Here we show the first molecular view of reception of a taste substance by a taste receptor, where the binding of the taste substance elicits a different conformational state of T1r2/T1r3 LBD heterodimer. Electron microscopy has showed a characteristic dimeric structure. Förster resonance energy transfer and X-ray solution scattering have revealed the transition of the dimerization manner of the ligand binding domains, from a widely spread to compactly organized state upon taste substance binding, which may correspond to distinct receptor functional states.
Heat-Treatment-Induced Switching of Magnetic States in the Doped Polar Semiconductor Ge1−xMnxTe
Authors: Kriener M. , Nakajima T. , Kaneko Y. , Kikkawa A. , Yu X. Z. , Endo N. , Kato K. , Takata M. , Arima T. , Tokura Y. , Taguchi Y. 
Published: May 2016

AbstractCross-control of a material property - manipulation of a physical quantity (e.g., magnetisation) by a nonconjugate field (e.g., electrical field) – is a challenge in fundamental science and also important for technological device applications. It has been demonstrated that magnetic properties can be controlled by electrical and optical stimuli in various magnets. Here we find that heat-treatment allows the control over two competing magnetic phases in the Mn-doped polar semiconductor GeTe. The onset temperatures Tc of ferromagnetism vary at low Mn concentrations by a factor of five to six with a maximum Tc ≈ 180 K, depending on the selected phase. Analyses in terms of synchrotron x-ray diffraction and energy dispersive x-ray spectroscopy indicate a possible segregation of the Mn ions, which is responsible for the high-Tc phase. More importantly, we demonstrate that the two states can be switched back and forth repeatedly from either phase by changing the heat-treatment of a sample, thereby confirming magnetic phase-change-memory functionality.
Redox potential driven aeration during very-high-gravity ethanol fermentation by using flocculating yeast
Authors: Liu Chen-Guang , Hao Xue-Mi , Lin Yen-Han , Bai Feng-Wu 
Published: May 2016

AbstractEthanol fermentation requires oxygen to maintain high biomass and cell viability, especially under very-high-gravity (VHG) condition. In this work, fermentation redox potential (ORP) was applied to drive the aeration process at low dissolved oxygen (DO) levels, which is infeasible to be regulated by a DO sensor. The performance and characteristics of flocculating yeast grown under 300 and 260 g glucose/L conditions were subjected to various aeration strategies including: no aeration; controlled aeration at −150, −100 and −50 mV levels; and constant aeration at 0.05 and 0.2 vvm. The results showed that anaerobic fermentation produced the least ethanol and had the highest residual glucose after 72 h of fermentation. Controlled aerations, depending on the real-time oxygen demand, led to higher cell viability than the no-aeration counterpart. Constant aeration triggered a quick biomass formation, and fast glucose utilization. However, over aeration at 0.2 vvm caused a reduction of final ethanol concentration. The controlled aeration driven by ORP under VHG conditions resulted in the best fermentation performance. Moreover, the controlled aeration could enhance yeast flocculating activity, promote an increase of flocs size, and accelerate yeast separation near the end of fermentation.
Fatal influenza A (H5N1) virus Infection in zoo-housed Tigers in Yunnan Province, China
Authors: Hu Tingsong , Zhao Huanyun , Zhang Yan , Zhang Wendong , Kong Qiang , Zhang Zhixiao , Cui Qinghua , Qiu Wei , Deng Bo , Fan Quanshui , Zhang Fuqiang 
Published: May 2016

AbstractFrom 2014 to 2015, three cases of highly pathogenic avian influenza infection occurred in zoo-housed north-east China tigers (Panthera tigris ssp.altaica) and four tigers died of respiratory distress in succession in Yunnan Province, China. We isolated and characterized three highly pathogenic avian influenza A(H5N1) viruses from these tigers. Phylogenetic analysis indicated that A/tiger /Yunnan /tig1404 /2014(H5N1) belongs to the provisional subclade 2.3.4.4e which were novel reassortant influenza A (H5N1) viruses with six internal genes from avian influenza A (H5N2) viruses. The HA gene of the isolated A/tiger /Yunnan /tig1412 /2014(H5N1) virus belongs to the subclade 2.3.2.1b. The isolated A/tiger /Yunnan /tig1508/2015 (H5N1) virus was a novel reassortant influenza A (H5N1) virus with three internal genes (PB2, PB1 and M) from H9N2 virus and belongs to the subclade 2.3.2.1c.
Novel European free-living, non-diazotrophic Bradyrhizobium isolates from contrasting soils that lack nodulation and nitrogen fixation genes – a genome comparison
Authors: Jones Frances Patricia , Clark Ian M. , King Robert , Shaw Liz J. , Woodward Martin J. , Hirsch Penny R. 
Published: May 2016

AbstractThe slow-growing genus Bradyrhizobium is biologically important in soils, with different representatives found to perform a range of biochemical functions including photosynthesis, induction of root nodules and symbiotic nitrogen fixation and denitrification. Consequently, the role of the genus in soil ecology and biogeochemical transformations is of agricultural and environmental significance. Some isolates of Bradyrhizobium have been shown to be non-symbiotic and do not possess the ability to form nodules. Here we present the genome and gene annotations of two such free-living Bradyrhizobium isolates, named G22 and BF49, from soils with differing long-term management regimes (grassland and bare fallow respectively) in addition to carbon metabolism analysis. These Bradyrhizobium isolates are the first to be isolated and sequenced from European soil and are the first free-living Bradyrhizobium isolates, lacking both nodulation and nitrogen fixation genes, to have their genomes sequenced and assembled from cultured samples. The G22 and BF49 genomes are distinctly different with respect to size and number of genes; the grassland isolate also contains a plasmid. There are also a number of functional differences between these isolates and other published genomes, suggesting that this ubiquitous genus is extremely heterogeneous and has roles within the community not including symbiotic nitrogen fixation.
Hot spots of DNA double-strand breaks in human rDNA units are produced in vivo
Authors: Tchurikov Nickolai A. , Yudkin Dmitry V. , Gorbacheva Maria A. , Kulemzina Anastasia I. , Grischenko Irina V. , Fedoseeva Daria M. , Sosin Dmitri V. , Kravatsky Yuri V. , Kretova Olga V. 
Published: May 2016

AbstractEndogenous hot spots of DNA double-strand breaks (DSBs) are tightly linked with transcription patterns and cancer genomics1,2. There are nine hot spots of DSBs located in human rDNA units3–6. Here we describe that the profiles of these hot spots coincide with the profiles of γ-H2AX or H2AX, strongly suggesting a high level of in vivo breakage inside rDNA genes. The data were confirmed by microscopic observation of the largest γ-H2AX foci inside nucleoli in interphase chromosomes. In metaphase chromosomes, we observed that only some portion of rDNA clusters possess γ-H2AX foci and that all γ-H2AX foci co-localize with UBF-1 binding sites, which strongly suggests that only active rDNA units possess the hot spots of DSBs. Both γ-H2AX and UBF-1 are epigenetically inherited and thus indicate the rDNA units that were active in the previous cell cycle. These results have implications for diverse fields, including epigenetics and cancer genomics.