bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epigenetic activation during T helper 17 cell differentiation is mediated by Tripartite motif containing 28
Authors: Jiang Yu , Liu Ying , Lu Huiping , Sun Shao-Cong , Jin Wei , Wang Xiaohu , Dong Chen 
Published: April 2018

AbstractEpigenetic regulation is important for T-cell fate decision. Although STAT3 is known to initiate Th17 differentiation program, the downstream mechanism is unclear. Here we show that Tripartite motif containing 28 (Trim28) expression in Th17 cells is required for Th17-mediated cytokine production and experimental autoimmune diseases. Genome-wide occupancy analysis reveals that TRIM28-bound regions overlap with almost all Th17-specific super-enhancers (SE), and that those SEs are impaired by the deficiency of STAT3 or TRIM28, but not of RORγt. Importantly, IL-6-STAT3 signaling facilitates TRIM28 binding to theIl17-Il17flocus, and this process is required for epigenetic activation and high-order chromosomal interaction. TRIM28 also forms a complex with STAT3 and RORγt, and promotes the recruitment of RORγt to its target cytokine genes. Our study thus suggests TRIM28 to be important for the epigenetic activation during Th17 cell differentiation, and prompts the potential use of epigenetic interventions for Th17-related autoimmune diseases.
Fossil black smoker yields oxygen isotopic composition of Neoproterozoic seawater
Authors: Hodel F. , Macouin M. , Trindade R. I. F. , Triantafyllou A. , Ganne J. , Chavagnac V. , Berger J. , Rospabé M. , Destrigneville C. , Carlut J. , Ennih N. , Agrinier P. 
Published: April 2018

AbstractThe evolution of the seawater oxygen isotopic composition (δ18O) through geological time remains controversial. Yet, the past δ18Oseawater is key to assess past seawater temperatures, providing insights into past climate change and life evolution. Here we provide a new and unprecedentedly precise δ18O value of −1.33 ± 0.98‰ for the Neoproterozoic bottom seawater supporting a constant oxygen isotope composition through time. We demonstrate that the Aït Ahmane ultramafic unit of the ca. 760 Ma Bou Azzer ophiolite (Morocco) host a fossil black smoker-type hydrothermal system. In this system we analyzed an untapped archive for the ocean oxygen isotopic composition consisting in pure magnetite veins directly precipitated from a Neoproterozoic seawater-derived fluid. Our results suggest that, while δ18Oseawater and submarine hydrothermal processes were likely similar to present day, Neoproterozoic oceans were 15–30 °C warmer on the eve of the Sturtian glaciation and the major life diversification that followed.
Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria
Authors: Dulin David , Bauer David L. V. , Malinen Anssi M. , Bakermans Jacob J. W. , Kaller Martin , Morichaud Zakia , Petushkov Ivan , Depken Martin , Brodolin Konstantin , Kulbachinskiy Andrey , Kapanidis Achillefs N. 
Published: April 2018

AbstractTranscription in bacteria is controlled by multiple molecular mechanisms that precisely regulate gene expression. It has been recently shown that initial RNA synthesis by the bacterial RNA polymerase (RNAP) is interrupted by pauses; however, the pausing determinants and the relationship of pausing with productive and abortive RNA synthesis remain poorly understood. Using single-molecule FRET and biochemical analysis, here we show that the pause encountered by RNAP after the synthesis of a 6-nt RNA (ITC6) renders the promoter escape strongly dependent on the NTP concentration. Mechanistically, the paused ITC6 acts as a checkpoint that directs RNAP to one of three competing pathways: productive transcription, abortive RNA release, or a new unscrunching/scrunching pathway. The cyclic unscrunching/scrunching of the promoter generates a long-lived, RNA-bound paused state; the abortive RNA release and DNA unscrunching are thus not as tightly linked as previously thought. Finally, our new model couples the pausing with the abortive and productive outcomes of initial transcription.
HOXA9 inhibits HIF-1α-mediated glycolysis through interacting with CRIP2 to repress cutaneous squamous cell carcinoma development
Authors: Zhou Liang , Wang Yinghui , Zhou Meijuan , Zhang Ying , Wang Pengfei , Li Xiaoxing , Yang Jing , Wang Hongmei , Ding Zhenhua 
Published: April 2018

AbstractGlycolytic reprogramming is a typical feature of many cancers; however, key regulators of glucose metabolism reengineering are poorly understood, especially in cutaneous squamous cell carcinoma (cSCC). Here, Homeobox A9 (HOXA9), a direct target of onco-miR-365, is identified to be significantly downregulated in cSCC tumors and cell lines. HOXA9 acts as a tumor suppressor and inhibits glycolysis in cSCC in vitro and in vivo by negatively regulating HIF-1α and its downstream glycolytic regulators, HK2, GLUT1 and PDK1. Mechanistic studies show that HOXA9-CRIP2 interaction at glycolytic gene promoters impeds HIF-1α binding, repressing gene expression in trans. Our results reveal a miR-365-HOXA9-HIF-1α regulatory axis that contributes to the enhanced glycolysis in cSCC development and may represent an intervention target for cSCC therapy.
Genome-wide excision repair in Arabidopsis is coupled to transcription and reflects circadian gene expression patterns
Authors: Oztas Onur , Selby Christopher P. , Sancar Aziz , Adebali Ogun 
Published: April 2018

AbstractPlants are exposed to numerous DNA-damaging stresses including the exposure to ultraviolet (UV) component of solar radiation. They employ nucleotide excision repair to remove DNA-bulky adducts and to help eliminate UV-induced DNA lesions, so as to maintain their genome integrity and their fitness. Here, we generated genome-wide single-nucleotide resolution excision repair maps of UV-induced DNA damage in Arabidopsis at different circadian time points. Our data show that the repair of UV lesions for a large fraction of the genome is controlled by the joint actions of the circadian clock and transcription by RNA polymerase II. Our findings reveal very strong repair preference for the transcribed strands of active genes in Arabidopsis, and 10–30% of the transcription-coupled repair is circadian time-dependent. This dynamic range in nucleotide excision repair levels throughout the day enables Arabidopsis to cope with the bulky DNA lesion-inducing environmental factors including UV.
Modular assembly of proteins on nanoparticles
Authors: Ma Wenwei , Saccardo Angela , Roccatano Danilo , Aboagye-Mensah Dorothy , Alkaseem Mohammad , Jewkes Matthew , Di Nezza Francesca , Baron Mark , Soloviev Mikhail , Ferrari Enrico 
Published: April 2018

AbstractGenerally, the high diversity of protein properties necessitates the development of unique nanoparticle bio-conjugation methods, optimized for each different protein. Here we describe a universal bio-conjugation approach which makes use of a new recombinant fusion protein combining two distinct domains. The N-terminal part is Glutathione S-Transferase (GST) from Schistosoma japonicum, for which we identify and characterize the remarkable ability to bind gold nanoparticles (GNPs) by forming gold–sulfur bonds (Au–S). The C-terminal part of this multi-domain construct is the SpyCatcher from Streptococcus pyogenes, which provides the ability to capture recombinant proteins encoding a SpyTag. Here we show that SpyCatcher can be immobilized covalently on GNPs through GST without the loss of its full functionality. We then show that GST-SpyCatcher activated particles are able to covalently bind a SpyTag modified protein by simple mixing, through the spontaneous formation of an unusual isopeptide bond.
A geometric approach to characterize the functional identity of single cells
Authors: Mohammadi Shahin , Ravindra Vikram , Gleich David F. , Grama Ananth 
Published: April 2018

AbstractSingle-cell transcriptomic data has the potential to radically redefine our view of cell-type identity. Cells that were previously believed to be homogeneous are now clearly distinguishable in terms of their expression phenotype. Methods for automatically characterizing the functional identity of cells, and their associated properties, can be used to uncover processes involved in lineage differentiation as well as sub-typing cancer cells. They can also be used to suggest personalized therapies based on molecular signatures associated with pathology. We develop a new method, called ACTION, to infer the functional identity of cells from their transcriptional profile, classify them based on their dominant function, and reconstruct regulatory networks that are responsible for mediating their identity. Using ACTION, we identify novel Melanoma subtypes with differential survival rates and therapeutic responses, for which we provide biomarkers along with their underlying regulatory networks.
Non-invasive detection of human cardiomyocyte death using methylation patterns of circulating DNA
Authors: Zemmour Hai , Planer David , Magenheim Judith , Moss Joshua , Neiman Daniel , Gilon Dan , Korach Amit , Glaser Benjamin , Shemer Ruth , Landesberg Giora , Dor Yuval 
Published: April 2018

AbstractDetection of cardiomyocyte death is crucial for the diagnosis and treatment of heart disease. Here we use comparative methylome analysis to identify genomic loci that are unmethylated specifically in cardiomyocytes, and develop these as biomarkers to quantify cardiomyocyte DNA in circulating cell-free DNA (cfDNA) derived from dying cells. Plasma of healthy individuals contains essentially no cardiomyocyte cfDNA, consistent with minimal cardiac turnover. Patients with acute ST-elevation myocardial infarction show a robust cardiac cfDNA signal that correlates with levels of troponin and creatine phosphokinase (CPK), including the expected elevation-decay dynamics following coronary angioplasty. Patients with sepsis have high cardiac cfDNA concentrations that strongly predict mortality, suggesting a major role of cardiomyocyte death in mortality from sepsis. A cfDNA biomarker for cardiomyocyte death may find utility in diagnosis and monitoring of cardiac pathologies and in the study of normal human cardiac physiology and development.
Variation in Wolbachia effects on Aedes mosquitoes as a determinant of invasiveness and vectorial capacity
Authors: King Jessica G. , Souto-Maior Caetano , Sartori Larissa M. , Maciel-de-Freitas Rafael , Gomes M. Gabriela M. 
Published: April 2018

AbstractWolbachia has been introduced into Aedes aegypti mosquitoes to control the spread of arboviruses, such as dengue, chikungunya and Zika. Studies showed that certain Wolbachia strains (such as wMel) reduce replication of dengue viruses in the laboratory, prompting the release of mosquitoes carrying the bacterium into the field, where vectorial capacity can be realistically assessed in relation to native non-carriers. Here we apply a new analysis to two published datasets, and show that wMel increases the mean and the variance in Ae. aegypti susceptibility to dengue infection when introgressed into Brazil and Vietnam genetic backgrounds. In the absence of other processes, higher mean susceptibility should lead to enhanced viral transmission. The increase in variance, however, widens the basis for selection imposed by unexplored natural forces, retaining the potential for reducing transmission overall.
Variable density dependence and the restructuring of coral-reef fisheries across 25 years of exploitation
Authors: Houk Peter , Cuetos-Bueno Javier , Tibbatts Brent , Gutierrez Jay 
Published: April 2018

AbstractVariable density dependence within multispecies fisheries results in species restructuring as exploitation intensifies that is poorly understood. We examined unique species-based records across 25 years of exploitation to evaluate patterns, consequences, and predictions of species replacements within three coral-reef fisheries. Body-size was an expected determinant of species replacements, as larger fishes were consistently replaced by smaller, faster-growing counterparts. However, many species with similar sizes and growth rates responded differently. Naso unicornis, a primary component of coral-reef fisheries across the Pacific, was one of the most resilient species to exploitation despite having a similar maximum size and growth as many large parrotfishes that slowly disappeared from landings. Assessments conducted for all primary target species revealed clear distinctions in compensatory responses: 31% had diminishing size structures, 18% had diminishing proportional contribution, but only 5% showed both. Standard approaches to fisheries management assume constant rates of size-and-age restructuring and rely upon metrics such as fishing-versus-natural mortality. Instead, a deeper appreciation for varying recruitment rates may help to (re)define fisheries management units and reduce complexity in multispecies fisheries. We last consider our results alongside traditional knowledge and management in the Pacific that clearly appreciated species responses, but have been lost over the years.
Identification of Morus notabilis MADS-box genes and elucidation of the roles of MnMADS33 during endodormancy
Authors: Luo Yiwei , Li Hongshun , Xiang Zhonghuai , He Ningjia 
Published: April 2018

AbstractThe MADS-box genes encode transcriptional regulators with various functions especially during floral development. A total of 54 putative Morus notabilis MADS-box genes (MnMADSs) were identified and phylogenetically classified as either type I (17 genes) or type II (37 genes). The detected genes included three FLOWERING LOCUS C-like (MnFLC-like) genes, MnMADS33, MnMADS50, and MnMADS7. MnFLC-like proteins could directly or indirectly repress promoter activity of the mulberry FLOWERING LOCUS T-like (MnFT) gene. Transgenic Arabidopsis thaliana overexpressing MnFLC-like genes exhibited delayed flowering and down-regulated expression of FT and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS1 (SOC1). The gene expression analyses in floral bud indicated that MnMADS33 expression increased, while MnFT expression decreased during the induction of dormancy in response to cold conditions. Dormancy release resulted in the down-regulation of MnMADS33 expression and the up-regulation of MnFT expression. Furthermore, abscisic acid promoted the transcription of MnMADS33 and MnFT, although the expression level of MnFT gradually decreased. These results are consistent with the hypothesis that MnMADS33 negatively regulated the expression of MnFT to repress dormancy release and flowering in mulberry. This study may be relevant for future investigations regarding the effects of MnMADS genes on mulberry flowering development.
A Highly Efficient Adsorbent Cu-Perusian Blue@Nanodiamond for Cesium in Diluted Artificial Seawater and Soil-Treated Wastewater
Authors: Matsumoto Kazuko , Yamato Hideyuki , Kakimoto Seishiro , Yamashita Takeshi , Wada Ryutaro , Tanaka Yoshiaki , Akita Masakazu , Fujimura Tadamasa 
Published: April 2018

AbstractA new adsorbent Cu-Perussian blue@Nanodiamond (Cu-PB@DND) for Cs+ removal was prepared and characterized with IR, SEM, X-ray diffraction, particle size analysis, and zeta-potential. The adsorbent consists of a core of aggregated detonation nanodiamond (DND) particles with the surface treated with Cu-PB. Cesium adsorption was studied in two modes; a co-precipitation mode and a batch mode. In the co-precipitation mode, DND, CuCl2, and K4[Fe(CN)6] were added sequentially to a Cs+ solution in diluted artificial seawater. In the batch mode, adsorbent Cu-PB@DND was dispersed into a Cs+ solution with stirring. The distribution coefficient (Kd) of the co-precipitation mode was 8.8 × 107 (mL/g) at Cs+ 6.6 ppm in 0.07% seawater. The Kd value of the batch mode was 1.3 × 106 (mL/g). Precipitation of Cs+-incorporated particles was complete, and post filtration was not necessary. Excess copper and iron ions were completely removed and were not detected in the supernatant. The adsorption data for Cu-PB@DND were analyzed by assuming Langmuir isotherm and a good fit was obtained with a maximum adsorption capacity Qmax of 759 mg/g. The co-precipitation method was also applied to soil-treated wastewater.
Novel Indole-fused benzo-oxazepines (IFBOs) inhibit invasion of hepatocellular carcinoma by targeting IL-6 mediated JAK2/STAT3 oncogenic signals
Authors: Singh Ashok K. , Bhadauria Archana S. , Kumar Umesh , Raj Vinit , Rai Amit , Kumar Pranesh , Keshari Amit K. , Kumar Dinesh , Maity Biswanath , Nath Sneha , Prakash Anand , Saha Sudipta 
Published: April 2018

AbstractInspired by the well-documented tumor protecting ability of paullones, recently, we synthesized novel paullone-like scaffolds, indole-fused benzo-oxazepines (IFBOs), and screened them against hepatocellular carcinoma (HCC) specific Hep-G2 cells. Three of the synthesized compounds significantly attenuated the progression of HCCin vitro. By computational studies, we further discovered that IFBOs exhibited a stable binding complex with the IL-6 receptor. In this context, we investigatedin vivostudy using the nitrosodiethyl amine (NDEA)-induced HCC model, which strengthened our previous findings by showing the blockade of the IL-6 mediated JAK2/STAT3 oncogenic signaling pathway. Treatment with IFBOs showed remarkable attenuation of cellular proliferation, as evidenced through a decrease in the number of nodules, restoration of body weight, oxidative stress parameters, liver marker enzymes and histological architecture. Interestingly, using a metabolomic approach we further discovered that IFBOs can restore the perturbed metabolic profile associated with the HCC condition to normalcy. Particularly, the efficacy of compound6afor an anti-HCC response was significantly better than the marketed chemotherapeutic drug, 5-fluorouracil. Altogether, these remarkable findings open up possibilities of developing IFBOs as novel future candidate molecules for plausible alternatives for HCC treatment.
Efficient white phosphorescent organic light-emitting diodes using ultrathin emissive layers (<1 nm)
Authors: Yu Haojian , Dai Xudong , Yao Fangnan , Wei Xiang , Cao Jin , Jhun Chulgyu 
Published: April 2018

AbstractIn this paper, efficient phosphorescent white organic light-emitting diodes (WOLEDs) were fabricated based on ultrathin doping-free emissive layers and mixed bipolar interlayers. The energy transfer processes were proved via the research of WOLEDs with different interlayer thicknesses and transient photoluminescence lifetime. WOLEDs with optimized thickness of doping-free emissive layers show maximum current efficiency of 47.8 cd/A and 44.9 cd/A for three-colors and four-colors WOLEDs, respectively. The Commission Internationale de L’Eclairage coordinates shows a very slight variation of ( ± 0.02, ± 0.02) from 5793 cd/m2to 11370 cd/m2for three-colors WOLEDs and from 3038 cd/m2to 13720 cd/m2for four-colors WOLEDs, respectively. The stability of the spectra is attributed to the stable and sequential energy transfer among the various dyes. The color temperature of four-colors WOLEDs can be obtained from 2659 to 6636 by adjusting the thickness of ultrathin emissive layer.
Spatial fishing restrictions benefit demersal stocks in the northeastern Mediterranean Sea
Authors: Dimarchopoulou Donna , Dogrammatzi Aikaterini , Karachle Paraskevi K. , Tsikliras Athanassios C. 
Published: April 2018

AbstractThe multi-level benefits that marine organisms gain when protected from fishing are well acknowledged. Here, we investigated the effects of a 40-year trawling ban on the status of targeted and non-targeted marine species within a major fishing ground in the northeastern Mediterranean Sea (Thermaikos Gulf, Aegean Sea). Biomass and somatic length of fish and invertebrates (six commercial and three non-commercial demersal species) were measured in three areas of varying fishing pressure, depending on the temporal and spatial operational regimes of fishing vessels. The positive effects of fishing restrictions on the studied demersal stocks were clearly revealed, as the commercial fish species exhibited higher biomass in the intermediate and low pressure areas, as well as increasing maximum and mean total length (and other length indicators) with decreasing fishing effort. The mean total length of non-commercial species generally did not differ among areas, except for species caught and discarded at high rates. The present study shows that fishing does alter the population structure and biomass of commercial demersal species, and that fishing restrictions greatly contribute to improving the status of demersal populations within the restricted areas by providing a refuge for large individuals and their important contribution to the gene pool.
Tracing of the fecal microbiota of commercial pigs at five growth stages from birth to shipment
Authors: Han Geon Goo , Lee Jun-Yeong , Jin Gwi-Deuk , Park Jongbin , Choi Yo Han , Kang Sang-Kee , Chae Byung Jo , Kim Eun Bae , Choi Yun-Jaie 
Published: April 2018

AbstractThe intestinal microbiota affect various physiological traits of host animals such as brain development, obesity, age, and the immune system. In the swine industry, understanding the relationship between intestinal microbiota and growth stage is essential because growth stage is directly related to the feeding system of pigs, thus we studied the intestinal microbiota of 32 healthy pigs across five sows at 10, 21, 63, 93, and 147 d of ages. The intestinal microbiota were altered with growth of pigs and were separated into three distinct clusters. The relative abundance of several phyla and genera were significantly different between growth stages. We observed co-occurrence pattern of the intestinal microbiota at each growth stage. In addition, we predicted the functions of the intestinal microbiota and confirmed that several KEGG pathways were significantly different between growth stages. We also explored the relationship between the intestinal microbiota and innate factors such as the maternal effect and gender. When pigs were young, innate factors affected on construction of intestinal microbiota, however this tendency was disappeared with growth. Our findings broaden the understanding of microbial ecology, and the results will be used as a reference for investigating host-microbe interactions in the swine industry.
Electronic and optical responses of quasi-one-dimensional phosphorene nanoribbons to strain and electric field
Authors: Zhang Longlong , Hao Yuying 
Published: April 2018

AbstractElectronic and optical responses of zigzag- and armchair-edge quasi-one-dimensional phosphorene nanoribbons (Q1D-PNRs) to strain and external field are comparatively studied based on the tight-binding calculations. The results show that: (i) Zigzag-edge Q1D-PNR has the metallic ground state; applying global strains can not open the gap at the Fermi level but applying the electric field can achieve it; the direct/indirect character of the field-induced gap is determined by the electron-hole symmetry; an electric-field-enhanced optical absorption of low-energy photons is also predicted. (ii) Armchair-edge Q1D-PNR turns out an insulator with the large direct band gap; the inter-plane strain modulates this gap non monotonically while the in-plane one modulates it monotonically; in addition, the gap responses to electric fields also show strong direction dependence, i. e., increasing the inter-plane electric field will monotonically enlarge the gap but the electric field along the width direction modulates the gap non monotonically with three characteristic response regions.