bluuebunny/crossref_metadata_2025_split huggingface dataset:
IL-1β induced HIF-1α inhibits the differentiation of human FOXP3+ T cells
Authors: Feldhoff Lea M. , Rueda Cesar M. , Moreno-Fernandez Maria E. , Sauer Johanna , Jackson Courtney M. , Chougnet Claire A. , Rupp Jan 
Published: March 2017

AbstractDifferentiation of regulatory Treg (Treg) in the periphery is critical to control inflammatory processes. Although polarization of inducible Treg (iTreg) often occurs in an inflammatory environment, the effects exerted by inflammation on human iTreg differentiation have not been extensively studied. We observed that IL-1β significantly reduced the frequency of FOXP3+ T cells under iTreg-polarizing conditions. Mechanistically, we show that IL-1β activated mTORC1 and downstream upregulated hypoxia inducible factor-1 (HIF-1α) expression. Using specific inhibitors, we demonstrated that both steps were critical in the deleterious effect of IL-1β on Treg differentiation. Chemical stabilization of HIF-1α by Dimethyloxalylglycine (DMOG) also significantly impaired iTreg differentiation. Interestingly, while IL-1β-treated cells exhibited only minor changes in metabolism, DMOG treatment decreased iTreg mitochondrial respiration and increased their glycolytic capacity. In conclusion, exposure to inflammatory stimuli profoundly inhibits human Treg differentiation HIF-1α dependent, suggesting that targeting HIF-1α could be a strategy to foster iTreg differentiation in an inflammatory milieu. However, IL-1β deleterious effect does not appear to be completely driven by metabolic changes. These data thus suggest that several mechanisms contribute to the regulation of iTreg differentiation, but the timing and respective requirement for each pathway vary depending on the milieu in which iTreg differentiate.
Mining of efficient microbial UDP-glycosyltransferases by motif evolution cross plant kingdom for application in biosynthesis of salidroside
Authors: Fan Bo , Chen Tianyi , Zhang Sen , Wu Bin , He Bingfang 
Published: March 2017

AbstractThe plant kingdom provides a large resource of natural products and various related enzymes are analyzed. The high catalytic activity and easy genetically modification of microbial enzymes would be beneficial for synthesis of natural products. But the identification of functional genes of target enzymes is time consuming and hampered by many contingencies. The potential to mine microbe-derived glycosyltransferases (GTs) cross the plant kingdom was assessed based on alignment and evolution of the full sequences and key motifs of target enzymes, such as Rhodiola-derived UDP-glycosyltransferase (UGT73B6) using in salidroside synthesis. The GTs from Bacillus licheniformis ZSP01 with high PSPG motif similarity were speculated to catalyze the synthesis of salidroside. The UGTBL1, which had similarity (61.4%) PSPG motif to UGT73B6, displayed efficient activity and similar regioselectivity. Highly efficient glycosylation of tyrosol (1 g/L) was obtained by using engineered E. coli harboring UGTBL1 gene, which generated 1.04 g/L salidroside and 0.99 g/L icariside D2. All glycosides were secreted into the culture medium and beneficial for downstream purification. It was the first report on the genome mining of UGTs from microorganisms cross the plant kingdom. The mining approach may have broader applications in the selection of efficient candidate for making high-value natural products.
Bisphenol S negatively affects the meotic maturation of pig oocytes
Authors: Žalmanová Tereza , Hošková Kristýna , Nevoral Jan , Adámková Kateřina , Kott Tomáš , Šulc Miloslav , Kotíková Zora , Prokešová Šárka , Jílek František , Králíčková Milena , Petr Jaroslav 
Published: March 2017

AbstractBisphenol A (BPA), a chemical component of plastics, is a widely distributed environmental pollutant and contaminant of water, air, and food that negatively impacts human health. Concerns regarding BPA have led to the use of BPA-free alternatives, one of which is bisphenol S (BPS). However, the effects of BPS are not well characterized, and its specific effects on reproduction and fertility remain unknown. It is therefore necessary to evaluate any effects of BPS on mammalian oocytes. The present study is the first to demonstrate the markedly negative effects of BPS on pig oocyte maturation in vitro, even at doses lower than those humans are exposed to in the environment. Our results demonstrate (1) an effect of BPS on the course of the meiotic cell cycle; (2) the failure of tubulin fibre formation, which controls proper chromosome movement; (3) changes in the supply of maternal mRNA; (4) changes in the protein amounts and distribution of oestrogen receptors α and β and of aromatase; and (5) disrupted cumulus cell expansion. Thus, these results confirm that BPS is an example of regrettable substitution because this substance exerts similar or even worse negative effects than those of the material it replaced.
Rising fluoroquinolone resistance in Campylobacter isolated from feedlot cattle in the United States
Authors: Tang Yizhi , Sahin Orhan , Pavlovic Nada , LeJeune Jeff , Carlson James , Wu Zuowei , Dai Lei , Zhang Qijing 
Published: March 2017

AbstractAntibiotic resistance, particularly to fluoroquinolones and macrolides, in the major foodborne pathogen Campylobacter is considered a serious threat to public health. Although ruminant animals serve as a significant reservoir for Campylobacter, limited information is available on antibiotic-resistant Campylobacter of bovine origin. Here, we analyzed the antimicrobial susceptibilities of 320 C. jejuni and 115 C. coli isolates obtained from feedlot cattle farms in multiple states in the U.S. The results indicate that fluoroquinolone resistance reached to 35.4% in C. jejuni and 74.4% in C. coli, which are significantly higher than those previously reported in the U.S. While all fluoroquinolone resistant (FQR) C. coli isolates examined in this study harbored the single Thr-86-Ile mutation in GyrA, FQRC. jejuni isolates had other mutations in GyrA in addition to the Thr-86-Ile change. Notably, most of the analyzed FQRC. coli isolates had similar PFGE (pulsed field gel electrophoresis) patterns and the same MLST (multilocus sequence typing) sequence type (ST-1068) regardless of their geographic sources and time of isolation, while the analyzed C. jejuni isolates were genetically diverse, suggesting that clonal expansion is involved in dissemination of FQRC. coli but not C. jejuni. These findings reveal the rising prevalence of FQRCampylobacter in the U.S. and provide novel information on the epidemiology of antibiotic-resistant Campylobacter in the ruminant reservoir.
Cyclooxygenase-2 Signalling Pathway in the Cortex is Involved in the Pathophysiological Mechanisms in the Rat Model of Depression
Authors: Chen Qi , Luo Ying , Kuang Shengnan , Yang Yang , Tian Xiaoyan , Ma Jie , Mai Shaoshan , Xue Lai , Yang Junqing 
Published: March 2017

AbstractThis study was designed to investigate the effect of the cortical cyclooxygenase-2 (COX2) pathway on depressive behaviour in rats. Meloxicam, COX2 overexpressed lentivirus and COX2 RNAi lentivirus were administered to Sprague-Dawley rats subjected to chronic unpredictable mild stress (CUMS). Behaviour tests, biochemistry and immunohistochemistry methods, enzyme-linked immunosorbent assays, western blotting and reverse transcription polymerase chain reactions were used to evaluate the changes in rat behaviour and the cortical COX2 pathway. CUMS rats showed depressive–like behaviours. The superoxide dismutase activity and cyclic adenosine monophosphate (cAMP) contents were significantly decreased, the contents of malondialdehyde, prostaglandin E2 (PGE2) and inflammatory cytokines were significantly increased. The expressions of protein kinase A (PKA) and cAMP response element-binding protein (CREB) were decreased, and the levels of brain-derived neurotrophic factor (BDNF) and COX2 were significantly increased. Meloxicam and COX2 RNAi lentivirus significantly alleviated the abnormalities induced by CUMS, while COX2 overexpressed lentivirus aggravated these abnormalities. Our results indicated that the cortical COX2 pathway was activated in CUMS rats. Inhibition of COX2 activity/expression can obviously improve depressive behaviours in CUMS rats. Upregulating COX2 expression can increase the susceptibility of rats to CUMS. An imbalance in the cortical COX2-PGE2-cAMP/PKA-CREB-BDNF signalling pathway participates in the pathogenic mechanism of depression.
Revised domain structure of ulvan lyase and characterization of the first ulvan binding domain
Authors: Melcher Rebecca L. J. , Neumann Marten , Fuenzalida Werner Juan Pablo , Gröhn Franziska , Moerschbacher Bruno M. 
Published: March 2017

AbstractBiomass waste products from green algae have recently been given new life, as these polysaccharides have potential applications in industry, agriculture, and medicine. One such polysaccharide group called ulvans displays many different, potentially useful properties that arise from their structural versatility. Hence, performing structural analyses on ulvan is crucial for future applications. However, chemical reaction–based analysis methods cannot fully characterize ulvan and tend to alter its structure. Thus, better methods require well-characterized ulvan-degrading enzymes. Therefore, we analysed a previously sequenced ulvan lyase (GenebankTM reference number JN104480) and characterized its domains. We suggest that the enzyme consists of a shorter than previously described catalytic domain, a newly identified substrate binding domain, and a C-terminal type 9 secretion system signal peptide. By separately expressing the two domains in E. coli, we confirmed that the binding domain is ulvan specific, having higher affinity for ulvan than most lectins for their ligands (affinity constant: 105 M−1). To our knowledge, this is the first description of an ulvan-binding domain. Overall, identifying this new binding domain is one step towards engineering ulvan enzymes that can be used to characterize ulvan, e.g. through enzymatic/mass spectrometric fingerprinting analyses, and help unlock its full potential.
MicroRNA expression profiles during cotton (Gossypium hirsutum L) fiber early development
Authors: Wang Min , Sun Runrun , Li Chao , Wang Qinglian , Zhang Baohong 
Published: March 2017

AbstractThe role of microRNAs (miRNAs) during cotton fiber development remains unclear. Here, a total of 54 miRNAs belonging to 39 families were selected to characterize miRNA regulatory mechanism in eight different fiber development stages in upland cotton cv BM-1. Among 54 miRNAs, 18 miRNAs were involved in cotton fiber initiation and eight miRNAs were related to fiber elongation and secondary wall biosynthesis. Additionally, 3,576 protein-coding genes were candidate target genes of these miRNAs, which are potentially involved in cotton fiber development. We also investigated the regulatory network of miRNAs and corresponding targets in fiber initiation and elongation, and secondary wall formation. Our Gene Ontology-based term classification and KEGG-based pathway enrichment analyses showed that the miRNA targets covered 220 biological processes, 67 molecular functions, 45 cellular components, and 10 KEGG pathways. Three of ten KEGG pathways were involved in lignan synthesis, cell elongation, and fatty acid biosynthesis, all of which have important roles in fiber development. Overall, our study shows the potential regulatory roles of miRNAs in cotton fiber development and the importance of miRNAs in regulating different cell types. This is helpful to design miRNA-based biotechnology for improving fiber quality and yield.
Calibration-free assays on standard real-time PCR devices
Authors: Debski Pawel R. , Gewartowski Kamil , Bajer Seweryn , Garstecki Piotr 
Published: March 2017

AbstractQuantitative Polymerase Chain Reaction (qPCR) is one of central techniques in molecular biology and important tool in medical diagnostics. While being a golden standard qPCR techniques depend on reference measurements and are susceptible to large errors caused by even small changes of reaction efficiency or conditions that are typically not marked by decreased precision. Digital PCR (dPCR) technologies should alleviate the need for calibration by providing absolute quantitation using binary (yes/no) signals from partitions provided that the basic assumption of amplification a single target molecule into a positive signal is met. Still, the access to digital techniques is limited because they require new instruments. We show an analog-digital method that can be executed on standard (real-time) qPCR devices. It benefits from real-time readout, providing calibration-free assessment. The method combines advantages of qPCR and dPCR and bypasses their drawbacks. The protocols provide for small simplified partitioning that can be fitted within standard well plate format. We demonstrate that with the use of synergistic assay design standard qPCR devices are capable of absolute quantitation when normal qPCR protocols fail to provide accurate estimates. We list practical recipes how to design assays for required parameters, and how to analyze signals to estimate concentration.
Near-surface Heating of Young Rift Sediment Causes Mass Production and Discharge of Reactive Dissolved Organic Matter
Authors: Lin Yu-Shih , Koch Boris P. , Feseker Tomas , Ziervogel Kai , Goldhammer Tobias , Schmidt Frauke , Witt Matthias , Kellermann Matthias Y. , Zabel Matthias , Teske Andreas , Hinrichs Kai-Uwe 
Published: March 2017

AbstractOcean margin sediments have been considered as important sources of dissolved organic carbon (DOC) to the deep ocean, yet the contribution from advective settings has just started to be acknowledged. Here we present evidence showing that near-surface heating of sediment in the Guaymas Basin, a young extensional depression, causes mass production and discharge of reactive dissolved organic matter (DOM). In the sediment heated up to ~100 °C, we found unexpectedly low DOC concentrations in the pore waters, reflecting the combined effect of thermal desorption and advective fluid flow. Heating experiments suggested DOC production to be a rapid, abiotic process with the DOC concentration increasing exponentially with temperature. The high proportions of total hydrolyzable amino acids and presence of chemical species affiliated with activated hydrocarbons, carbohydrates and peptides indicate high reactivity of the DOM. Model simulation suggests that at the local scale, near-surface heating of sediment creates short and massive DOC discharge events that elevate the bottom-water DOC concentration. Because of the heterogeneous distribution of high heat flow areas, the expulsion of reactive DOM is spotty at any given time. We conclude that hydrothermal heating of young rift sediments alter deep-ocean budgets of bioavailable DOM, creating organic-rich habitats for benthic life.
Comparison of multivariate analysis methods for extracting the paraffin component from the paraffin-embedded cancer tissue spectra for Raman imaging
Authors: Meksiarun Phiranuphon , Ishigaki Mika , Huck-Pezzei Verena A.C. , Huck Christian W. , Wongravee Kanet , Sato Hidetoshi , Ozaki Yukihiro 
Published: March 2017

AbstractThis study aimed to extract the paraffin component from paraffin-embedded oral cancer tissue spectra using three multivariate analysis (MVA) methods; Independent Component Analysis (ICA), Partial Least Squares (PLS) and Independent Component - Partial Least Square (IC-PLS). The estimated paraffin components were used for removing the contribution of paraffin from the tissue spectra. These three methods were compared in terms of the efficiency of paraffin removal and the ability to retain the tissue information. It was found that ICA, PLS and IC-PLS could remove the paraffin component from the spectra at almost the same level while Principal Component Analysis (PCA) was incapable. In terms of retaining cancer tissue spectral integrity, effects of PLS and IC-PLS on the non-paraffin region were significantly less than that of ICA where cancer tissue spectral areas were deteriorated. The paraffin-removed spectra were used for constructing Raman images of oral cancer tissue and compared with Hematoxylin and Eosin (H&E) stained tissues for verification. This study has demonstrated the capability of Raman spectroscopy together with multivariate analysis methods as a diagnostic tool for the paraffin-embedded tissue section.
Continuously Varying Critical Exponents Beyond Weak Universality
Authors: Khan N. , Sarkar P. , Midya A. , Mandal P. , Mohanty P. K. 
Published: March 2017

AbstractRenormalization group theory does not restrict the form of continuous variation of critical exponents which occurs in presence of a marginal operator. However, the continuous variation of critical exponents, observed in different contexts, usually follows a weak universality scenario where some of the exponents (e.g., β, γ, ν) vary keeping others (e.g., δ, η) fixed. Here we report ferromagnetic phase transition in (Sm1−yNdy)0.52Sr0.48MnO3 (0.5 ≤ y ≤ 1) single crystals where all three exponents β, γ, δ vary with Nd concentration y. Such a variation clearly violates both universality and weak universality hypothesis. We propose a new scaling theory that explains the present experimental results, reduces to the weak universality as a special case, and provides a generic route leading to continuous variation of critical exponents and multi-criticality.
Global identification and analysis of isozyme-specific possible substrates crosslinked by transglutaminases using substrate peptides in mouse liver fibrosis
Authors: Tatsukawa Hideki , Tani Yuji , Otsu Risa , Nakagawa Haruka , Hitomi Kiyotaka 
Published: March 2017

AbstractThe transglutaminase (TG) family comprises eight isozymes that form the isopeptide bonds between glutamine and lysine residues and contribute to the fibrotic diseases via crosslinking-mediated stabilization of ECM and the activation of TGF-β in several tissues. However, despite a growing body of evidence implicating TG2 as a key enzyme in fibrosis, the causative role of TG2 and the involvement of the other isozymes have not yet been fully elucidated. Therefore, here we clarified the distributions of TG isozymes and their in situ activities and identified the isozyme-specific possible substrates for both TG1 and TG2 using their substrate peptides in mouse fibrotic liver. We found that TG1 activity was markedly enhanced intracellularly over a widespread area, whereas TG2 activity increased in the extracellular space. In total, 43 and 42 possible substrates were identified for TG1 and TG2, respectively, as involved in chromatin organization and cellular component morphogenesis. These included keratin 18, a biomarker for hepatic injury, which was accumulated in the fibrotic liver and showed the partly similar distribution with TG1 activity. These findings suggest that TG1 activity may be involved in the functional modification of intracellular proteins, whereas TG2 activity contributes to the stabilization of extracellular proteins during liver fibrosis.
Impact of temperature on mortality in Hubei, China: a multi-county time series analysis
Authors: Zhang Yunquan , Yu Chuanhua , Bao Junzhe , Li Xudong 
Published: March 2017

AbstractWe examined the impact of extreme temperatures on mortality in 12 counties across Hubei Province, central China, during 2009–2012. Quasi-Poisson generalized linear regression combined with distributed lag non-linear model was first applied to estimate county-specific relationship between temperature and mortality. A multivariable meta-analysis was then used to pool the estimates of county-specific mortality effects of extreme cold temperature (1st percentile) and hot temperature (99th percentile). An inverse J-shaped relationship was observed between temperature and mortality at the provincial level. Heat effect occurred immediately and persisted for 2–3 days, whereas cold effect was 1–2 days delayed and much longer lasting. Higher mortality risks were observed among females, the elderly aged over 75 years, persons dying outside the hospital and those with high education attainment, especially for cold effects. Our data revealed some slight differences in heat- and cold- related mortality effects on urban and rural residents. These findings may have important implications for developing locally-based preventive and intervention strategies to reduce temperature-related mortality, especially for those susceptible subpopulations. Also, urbanization should be considered as a potential influence factor when evaluating temperature-mortality association in future researches.
Evaluation of Different Oligonucleotide Base Substitutions at CpG Binding sites in Multiplex Bisulfite-PCR sequencing
Authors: Lu Jennifer , Ru Kelin , Candiloro Ida , Dobrovic Alexander , Korbie Darren , Trau Matt 
Published: March 2017

AbstractMultiplex bisulfite-PCR sequencing is a convenient and scalable method for the quantitative determination of the methylation state of target DNA regions. A challenge of this application is the presence of CpGs in the same region where primers are being placed. A common solution to the presence of CpGs within a primer-binding region is to substitute a base degeneracy at the cytosine position. However, the efficacy of different substitutions and the extent to which bias towards methylated or unmethylated templates may occur has never been evaluated in bisulfite multiplex sequencing applications. In response, we examined the performance of four different primer substitutions at the cytosine position of CpG’s contained within the PCR primers. In this study, deoxyinosine-, 5-nitroindole-, mixed-base primers and primers with an abasic site were evaluated across a series of methylated controls. Primers that contained mixed- or deoxyinosine- base modifications performed most robustly. Mixed-base primers were further selected to determine the conditions that induce bias towards methylated templates. This identified an optimized set of conditions where the methylated state of bisulfite DNA templates can be accurately assessed using mixed-base primers, and expands the scope of bisulfite resequencing assays when working with challenging templates.
Biomimetic surface structuring using cylindrical vector femtosecond laser beams
Authors: Skoulas Evangelos , Manousaki Alexandra , Fotakis Costas , Stratakis Emmanuel 
Published: March 2017

AbstractWe report on a new, single-step and scalable method to fabricate highly ordered, multi-directional and complex surface structures that mimic the unique morphological features of certain species found in nature. Biomimetic surface structuring was realized by exploiting the unique and versatile angular profile and the electric field symmetry of cylindrical vector (CV) femtosecond (fs) laser beams. It is shown that, highly controllable, periodic structures exhibiting sizes at nano-, micro- and dual- micro/nano scales can be directly written on Ni upon line and large area scanning with radial and azimuthal polarization beams. Depending on the irradiation conditions, new complex multi-directional nanostructures, inspired by the Shark’s skin morphology, as well as superhydrophobic dual-scale structures mimicking the Lotus’ leaf water repellent properties can be attained. It is concluded that the versatility and features variations of structures formed is by far superior to those obtained via laser processing with linearly polarized beams. More important, by exploiting the capabilities offered by fs CV fields, the present technique can be further extended to fabricate even more complex and unconventional structures. We believe that our approach provides a new concept in laser materials processing, which can be further exploited for expanding the breadth and novelty of applications.