bluuebunny/crossref_metadata_2025 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

Differentiation 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

The 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

Bisphenol 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

Antibiotic 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

This 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

Biomass 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

The 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

Quantitative 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

Ocean 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

This 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.
Correction: Corrigendum: Universal stress protein Rv2624c alters abundance of arginine and enhances intracellular survival by ATP binding in mycobacteria
Authors: Jia Qiong , Hu Xinling , Shi Dawei , Zhang Yan , Sun Meihao , Wang Jianwei , Mi Kaixia , Zhu Guofeng
Published: March 2017

Scientific Reports 6: Article number: 35462; published online: 20 October 2016; updated: 22 March 2017. This Article contains errors in Figure 5B where the CFU values for T0 and T1 are incorrect. The correct Figure 5B appears below as Figure 1.
Correction: Corrigendum: Development and Characterization of Lecithin-based Self-assembling Mixed Polymeric Micellar (saMPMs) Drug Delivery Systems for Curcumin
Authors: Chen Ling-Chun , Chen Yin-Chen , Su Chia-Yu , Wong Wan-Ping , Sheu Ming-Thau , Ho Hsiu-O
Published: March 2017

Scientific Reports 6: Article number: 37122; published online: 16 November 2016; updated: 22 March 2017. The authors neglected to cite a previous study related to the giving of a single oral dose of 410 mg micellar curcumin to women and men. This additional reference is listed below as reference 1, and should appear in the text as below.
Continuously Varying Critical Exponents Beyond Weak Universality
Authors: Khan N. , Sarkar P. , Midya A. , Mandal P. , Mohanty P. K.
Published: March 2017

Renormalization 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

The 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

We 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

Multiplex 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

We 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.
In Situ Characterization of the Initial Effect of Water on Molecular Interactions at the Interface of Organic/Inorganic Hybrid Systems
Authors: Pletincx Sven , Trotochaud Lena , Fockaert Laura-Lynn , Mol Johannes M. C. , Head Ashley R. , Karslıoğlu Osman , Bluhm Hendrik , Terryn Herman , Hauffman Tom
Published: March 2017

Probing initial interactions at the interface of hybrid systems under humid conditions has the potential to reveal the local chemical environment at solid/solid interfaces under real-world, technologically relevant conditions. Here, we show that ambient pressure X-ray photoelectron spectroscopy (APXPS) with a conventional X-ray source can be used to study the effects of water exposure on the interaction of a nanometer-thin polyacrylic acid (PAA) layer with a native aluminum oxide surface. The formation of a carboxylate ionic bond at the interface is characterized both with APXPS and in situ attenuated total reflectance Fourier transform infrared spectroscopy in the Kretschmann geometry (ATR-FTIR Kretschmann). When water is dosed in the APXPS chamber up to 5 Torr (~28% relative humidity), an increase in the amount of ionic bonds at the interface is observed. To confirm our APXPS interpretation, complementary ATR-FTIR Kretschmann experiments on a similar model system, which is exposed to an aqueous electrolyte, are conducted. These spectra demonstrate that water leads to an increased wet adhesion through increased ionic bond formation.
Sequential displacement of Type VI Secretion System effector genes leads to evolution of diverse immunity gene arrays in Vibrio cholerae
Authors: Kirchberger Paul C. , Unterweger Daniel , Provenzano Daniele , Pukatzki Stefan , Boucher Yan
Published: March 2017

Type VI secretion systems (T6SS) enable bacteria to engage neighboring cells in contact-dependent competition. In Vibrio cholerae, three chromosomal clusters each encode a pair of effector and immunity genes downstream of those encoding the T6SS structural machinery for effector delivery. Different combinations of effector-immunity proteins lead to competition between strains of V. cholerae, which are thought to be protected only from the toxicity of their own effectors. Screening of all publically available V. cholerae genomes showed that numerous strains possess long arrays of orphan immunity genes encoded in the 3′ region of their T6SS clusters. Phylogenetic analysis reveals that these genes are highly similar to those found in the effector-immunity pairs of other strains, indicating acquisition by horizontal gene transfer. Extensive genomic comparisons also suggest that successive addition of effector-immunity gene pairs replaces ancestral effectors, yet retains the cognate immunity genes. The retention of old immunity genes perhaps provides protection against nearby kin bacteria in which the old effector was not replaced. This mechanism, combined with frequent homologous recombination, is likely responsible for the high diversity of T6SS effector-immunity gene profiles observed for V. cholerae and closely related species.
The influence of environmental factors on communities of arbuscular mycorrhizal fungi associated with Chenopodium ambrosioides revealed by MiSeq sequencing investigation
Authors: Xu Xihui , Chen Chen , Zhang Zhou , Sun Zehua , Chen Yahua , Jiang Jiandong , Shen Zhenguo
Published: March 2017

Arbuscular mycorrhizal fungi (AMF) affect multiple ecosystem functions and processes, the assemblages of which vary across ecosystems. However, the influences of environmental factors on AMF communities which may shape these communities are still largely unknown. In this study, AMF communities from roots and rhizosphere soils ofChenopodium ambrosioidesin different natural soils were investigated. The root habitat showed significantly smaller numbers of OTUs and lower community richness compared to the rhizosphere soil habitat. Most OTUs in the root habitat were shared by the soil habitat from the same sampling site, indicating that rhizosphere soils represent a pool of AMF species, a fraction of which is recruited by plants. Most of the AMF in root habitats were Glomeraceae, suggesting recruitment preferences of AMF by plants. The relative contributions of environmental factors to explain variations in AMF community composition and phylogenetic structure were assessed. The results revealed soil properties predominantly explained the variation, followed by geographic and climate parameters which explained a small fraction independently, while the host plant showed few explanations. Overall, our results indicated that soil and root habitats as well as soil characters, especially pH, nitrogen and micronutrients (Zn and Cu) affected AMF communities significantly.
Genetic and functional diversity of ubiquitous DNA viruses in selected Chinese agricultural soils
Authors: Han Li-Li , Yu Dan-Ting , Zhang Li-Mei , Shen Ju-Pei , He Ji-Zheng
Published: March 2017

Viral community structures in complex agricultural soils are largely unknown. Electron microscopy and viromic analyses were conducted on six typical Chinese agricultural soil samples. Tailed bacteriophages, spherical and filamentous viral particles were identified by the morphological analysis. Based on the metagenomic analysis, single-stranded DNA viruses represented the largest viral component in most of the soil habitats, while the double-stranded DNA viruses belonging to the Caudovirales order were predominanted in Jiangxi-maize soils. The majority of functional genes belonged to the subsystem “phages, prophages, transposable elements, and plasmids”. Non-metric multidimensional analysis of viral community showed that the environment medium type was the most important driving factor for the viral community structure. For the major viral groups detected in all samples (Microviridae and Caudovirales), the two groups gathered viruses from different sites and similar genetic composition, indicating that viral diversity was high on a local point but relatively limited on a global scale. This is a novel report of viral diversity in Chinese agricultural soils, and the abundance, taxonomic, and functional diversity of viruses that were observed in different types of soils will aid future soil virome studies and enhance our understanding of the ecological functions of soil viruses.
Thin-film metallic glass: an effective diffusion barrier for Se-doped AgSbTe2 thermoelectric modules
Authors: Yu Chia-Chi , Wu Hsin-jay , Deng Ping-Yuan , Agne Matthias T. , Snyder G. Jeffrey , Chu Jinn P.
Published: March 2017

The thermal stability of joints in thermoelectric (TE) modules, which are degraded during interdiffusion between the TE material and the contacting metal, needs to be addressed in order to utilize TE technology for competitive, sustainable energy applications. Herein, we deposit a 200 nm-thick Zr-based thin-film metallic glass (TFMG), which acts as an effective diffusion barrier layer with low electrical contact resistivity, on a high-zT Se-doped AgSbTe2 substrate. The reaction couples structured with TFMG/TE are annealed at 673 K for 8–360 hours and analyzed by electron microscopy. No observable IMCs (intermetallic compounds) are formed at the TFMG/TE interface, suggesting the effective inhibition of atomic diffusion that may be attributed to the grain-boundary-free structure of TFMG. The minor amount of Se acts as a tracer species, and a homogeneous Se-rich region is found nearing the TFMG/TE interface, which guarantees satisfactory bonding at the joint. The diffusion of Se, which has the smallest atomic volume of all the elements from the TE substrate, is found to follow Fick’s second law. The calculated diffusivity (D) of Se in TFMG falls in the range of D~10−20–10−23(m2/s), which is 106~107 and 1012~1013 times smaller than those of Ni [10−14–10−17(m2/s)] and Cu [10−8–10−11(m2/s)] in Bi2Te3, respectively.
Quasispecies of Hepatitis C Virus Participate in Cell-Specific Infectivity
Authors: Fukuhara Takasuke , Yamamoto Satomi , Ono Chikako , Nakamura Shota , Motooka Daisuke , Mori Hiroyuki , Kurihara Takeshi , Sato Asuka , Tamura Tomokazu , Motomura Takashi , Okamoto Toru , Imamura Michio , Ikegami Toru , Yoshizumi Tomoharu , Soejima Yuji , Maehara Yoshihiko , Chayama Kazuaki , Matsuura Yoshiharu
Published: March 2017

It is well documented that a variety of viral quasispecies are found in the patients with chronic infection of hepatitis C virus (HCV). However, the significance of quasispecies in the specific infectivity to individual cell types remains unknown. In the present study, we analyzed the role of quasispecies of the genotype 2a clone, JFH1 (HCVcc), in specific infectivity to the hepatic cell lines, Huh7.5.1 and Hep3B. HCV RNA was electroporated into Huh7.5.1 cells and Hep3B/miR-122 cells expressing miR-122 at a high level. Then, we adapted the viruses to Huh7 and Hep3B/miR-122 cells by serial passages and termed the resulting viruses HCVcc/Huh7 and HCVcc/Hep3B, respectively. Interestingly, a higher viral load was obtained in the homologous combination of HCVcc/Huh7 in Huh7.5.1 cells or HCVcc/Hep3B in Hep3B/miR-122 cells compared with the heterologous combination. By using a reverse genetics system and deep sequence analysis, we identified several adaptive mutations involved in the high affinity for each cell line, suggesting that quasispecies of HCV participate in cell-specific infectivity.
PPARβ/δ, a Novel Regulator for Vascular Smooth Muscle Cells Phenotypic Modulation and Vascular Remodeling after Subarachnoid Hemorrhage in Rats
Authors: Zhang Hongrong , Jiang Li , Guo Zongduo , Zhong Jianjun , Wu Jingchuan , He Junchi , Liu Han , He Zhaohui , Wu Haitao , Cheng Chongjie , Sun Xiaochuan
Published: March 2017

Cerebral vascular smooth muscle cell (VSMC) phenotypic switch is involved in the pathophysiology of vascular injury after aneurysmal subarachnoid hemorrhage (aSAH), whereas the molecular mechanism underlying it remains largely speculative. Peroxisome proliferator-activated receptor β/δ (PPARβ/δ) has been implicated to modulate the vascular cells proliferation and vascular homeostasis. In the present study, we investigated the potential role of PPARβ/δ in VSMC phenotypic switch following SAH. Activation of PPARβ/δ by GW0742 and adenoviruses PPARβ/δ (Ad-PPARβ/δ) significantly inhibited hemoglobin-induced VSMC phenotypic switch. However, the effects of PPARβ/δ on VSMC phenotypic switch were partly obstacled in the presence of LY294002, a potent inhibitor of Phosphatidyl-Inositol-3 Kinase-AKT (PI3K/AKT). Furthermore, following study demonstrated that PPARβ/δ-induced PI3K/AKT activation can also contribute to Serum Response Factor (SRF) nucleus localization and Myocardin expression, which was highly associated with VSMC phenotypic switch. Finally, we found that Ad-PPARβ/δ positively modulated vascular remodeling in SAH rats, i.e. the diameter of basilar artery and the thickness of vessel wall. In addition, overexpression of PPARβ/δ by adenoviruses significantly improved neurological outcome. Taken together, this study identified PPARβ/δ as a useful regulator for VSMC phenotypic switch and vascular remodeling following SAH, providing novel insights into the therapeutic strategies of delayed cerebral ischemia.
Microscale coiling in bis-imidazolium supramolecular hydrogel fibres induced by the release of a cationic serine protease inhibitor
Authors: Limón David , Jiménez-Newman Claire , Calpena Ana C. , González-Campo Arántzazu , Amabilino David B. , Pérez-García Lluïsa
Published: March 2017

A gemini dicationic amphiphile forms gels with a serine protease inhibitor, which could be used in a new approach to the treatment of Rosacea, and the release of the drug causes remarkable gel fibre coiling.
Elemental two-dimensional nanosheets beyond graphene
Authors: Kong Xiangkai , Liu Qiangchun , Zhang Changlin , Peng Zhenmeng , Chen Qianwang
Published: March 2017

The recent progress of elemental two-dimensional nanosheets, beyond graphene, has been summarized with the focus on their preparation and applications.
Al-Based coordination polymer nanotubes: simple preparation, post-modification and application in Fe3+ ions sensing
Authors: Dao Xiaoyao , Ni Yonghong
Published: March 2017

Aluminum-based coordination polymers, MIL-110(Al) nanotubes, were successfully prepared from a mixed solution of methanol and ethanol with the volume ratio of 10 : 10 at room temperature in the absence of any template or surfactant; AlCl3 and sodium 1,3,5-benzenetricarboxylate (Na3BTC) were employed as the initial reactants.
Kinetics of the hydrogen evolution reaction on a highly porous three-dimensional Ni catalyst in the presence of a Mo ion activator in alkaline solution
Authors: Madram Ali Reza , Asadi Samane
Published: March 2017

In situ activated 3D-Ni by Mo ions in alkaline solution studied by various electrochemical methods for the hydrogen evolution reaction (HER).
Structure comparison and optical properties of Na7Mg4.5(P2O7)4: a sodium magnesium phosphate with isolated P2O7units
Authors: Ma Ruru , Yang Yun , Pan Shilie , Sun Yanzhou , Yang Zhihua
Published: March 2017

The crystal structure of Na7Mg4.5(P2O7)4comprises a parallelogram channel composed of corner/edge-sharing isolated [P2O7] dimers and a Na(2)O5polyhedra to form a 3D framework and has an ultraviolet (UV) cut-off edge of about 210 nm.
MoOx–pyridine organic–inorganic hybrid wires as a reusable and highly selective catalyst for the oxidation of alcohols: a comparison study between reaction-controlled phase-transfer catalysis and heterogeneous catalysis
Authors: Malakooti R. , Feghhi A.
Published: March 2017

The different catalytic behaviors of Mo3O10(C5H6N)2·H2O wires (MoOx–pyridine) in the selective oxidation of alcohols by means of molecular oxygen (O2) and hydrogen peroxide (H2O2) as green oxidants were investigated.
The convergent chemical synthesis of histone H3 protein for site-specific acetylation at Lys56 and ubiquitination at Lys122
Authors: Qi Yun-Kun , He Qiao-Qiao , Ai Hua-Song , Guo Jing , Li Jia-Bin
Published: March 2017

The first total chemical synthesis of modified H3 bearing Lys56 acetylation and Lys122 ubiquitination.
Distinct mechanisms for the upconversion of NaYF4:Yb3+,Er3+ nanoparticles revealed by stimulated emission depletion
Authors: Shin Kyujin , Jung Taeyoung , Lee Eunsang , Lee Gibok , Goh Yeongchang , Heo Junseok , Jung Minhyuk , Jo Eun-Jung , Lee Hohjai , Kim Min-Gon , Lee Kang Taek
Published: March 2017

We demonstrated that the visible emission of NaYF4:Yb3+,Er3+ upconversion nanoparticles could be modulated by external emission depletion (ED), the efficiency of which was much higher for the red band than the green.
Blue light effect on retinal pigment epithelial cells by display devices
Authors: Moon Jiyoung , Yun Jieun , Yoon Yeo Dae , Park Sang-Il , Seo Young-Jun , Park Won-Sang , Chu Hye Yong , Park Keun Hong , Lee Myung Yeol , Lee Chang Woo , Oh Soo Jin , Kwak Young-Shin , Jang Young Pyo , Kang Jong Soon
Published: March 2017

Even low-intensity blue light emitted by display devices exerts hazardous effects on RPE cells, which might be solved if display devices contain less short wavelength blue light.
Biophysical isolation and identification of circulating tumor cells
Authors: Che James , Yu Victor , Garon Edward B. , Goldman Jonathan W. , Di Carlo Dino
Published: March 2017

The integrated vortex enrichment–deformability cytometry device may enable automated enumeration of circulating tumor cells from blood by mechanophenotyping.
Magnetic fluidized bed for solid phase extraction in microfluidic systems
Authors: Pereiro Iago , Tabnaoui Sanae , Fermigier Marc , du Roure Olivia , Descroix Stéphanie , Viovy Jean-Louis , Malaquin Laurent
Published: March 2017

Fluidization of micromagnetic beads in microfluidics for flow-through bioanalytical operations at low driving pressures, high clogging resistance and favorable binding kinetics.
Domino reaction of cyclic sulfamidate imines with Morita–Baylis–Hillman acetates promoted by DABCO: a metal-free approach to functionalized nicotinic acid derivatives
Authors: Majee Debashis , Biswas Soumen , Mobin Shaikh M. , Samanta Sampak
Published: March 2017

A series of 4,6-diarylnicotinates have been prepared in good to excellent yields via a domino reaction of cyclic sulfamidate imines with MBH acetates in 2-MeTHF promoted by DABCO under an O2 atmosphere.
Thiolysis of NBD-based dyes for colorimetric and fluorescence detection of H2S and biothiols: design and biological applications
Authors: Yi Long , Xi Zhen
Published: March 2017

H2S-specific fluorescent/colorimetric probes based on the thiolysis of NBD dyes are summarized.
Metabolism of 2,3-dihydroxypropane-1-sulfonate by marine bacteria
Authors: Celik Ersin , Maczka Michael , Bergen Nils , Brinkhoff Thorsten , Schulz Stefan , Dickschat Jeroen S.
Published: March 2017

The uptake and conversion of the algal sulfoquinovose catabolite 2,3-dihydroxypropane-1-sulfonate by marine bacteria was studied in isotopic labelling experiments.
A threonine turnstile defines a dynamic amphiphilic binding motif in the AAA ATPase p97 allosteric binding site
Authors: Burnett James C. , Lim Chaemin , Peyser Brian D. , Samankumara Lalith P. , Kovaliov Marina , Colombo Raffaele , Bulfer Stacie L. , LaPorte Matthew G. , Hermone Ann R. , McGrath Connor F. , Arkin Michelle R. , Gussio Rick , Huryn Donna M. , Wipf Peter
Published: March 2017

The turnstile motion of two neighboring threonines accommodates both polar and apolar ligands.
Physico-mechanical properties of plywood bonded with ecological adhesives from Acacia mollissima tannins and lignosulfonates
Authors: Rhazi Naima , Oumam Mina , Sesbou Abdessadek , Hannache Hassan , Charrier-El Bouhtoury Fatima
Published: March 2017

The objective of this research was to develop ecological adhesives for bonding plywood panels using lignosulfonates, a common waste product of the wood pulp industry, and natural tannin extracted from Moroccan bark of Acacia mollissima using different process. Natural tannin and lignin were used in wood adhesives formulation to substitute resins based on phenol and formaldehyde. To achieve this, the lignosulfonates were glyoxalated to enhance their reactivity and the used tannins obtained by three different extraction methods were compared with commercial mimosa tannin. The proportion of Acacia mollissima tannins and lignosulfonates, the pressing time, the pressing temperature, and the pressure used were studied to improve mechanical properties, and bonding quality of plywood panel. The properties of plywood panels produced with these adhesives were tested in accordance with normative tests. Thus, the tensile strength, and the shear strength were measured. The results showed that the performance of the plywood panels made using biobased tannin adhesives was influenced by physical conditions such as pressure, press temperature as well as by chemical conditions, such as the tannin-lignin ratio. It exhibited excellent mechanical properties comparable to commercially available phenol-formaldehyde plywood adhesives. This study showed that biobased adhesives formulations presented good and higher mechanical performance and no formaldehyde emission.
Ultrasound-Accelerated Amide Coupling Reactions Directed toward the Synthesis of 1-Acetyl-3-carboxamide-β-carboline Derivatives of Biological Importance
Authors: Sharma N. , Kumari P. , Sharma P. , Bhagat N. , Bhagat S.
Published: March 2017

Several biologically important 1-acetyl-3-carboxamide-β-carboline derivatives were rapidly synthesized by ultrasound-promoted amide coupling of 1-acetyl-9H-pyrido[3,4-b]indole-3-carboxylic acid with substituted aromatic amines. The major advantages of the proposed method are that use of ultrasound irradiations afforded the desired products in a drastically reduced reaction time and in excellent yields compared with conventional stirring.
Cervical Vestibular-Evoked Myogenic Potentials in Sedated Toddlers
Authors: Ibraheem Ola , Hassaan Mohammad
Published: March 2017

Introduction Cervical vestibular-evoked myogenic potentials (cVEMPs) are difficult to test in toddlers who cannot follow instructions or stay calm.

Objective Due to the growing need for vestibular testing in very young children as a part of a delayed walking assessment battery, this study aimed to provide a solution to this problem by recording the cVEMPs in toddlers during sedation.

Method The cVEMPs measures were assessed in 30 toddlers aged 12 to 36 months with normal motor milestones. They were sedated with chloral hydrate. Then, the head was retracted ∼ 30° backward with a pillow under the shoulders, and turned 45° contralateral to the side of stimulation to put the sternocleidomastoid (SCM) muscle in a state of tension.

Results The P13 and N23 waves of the cVEMPs were recordable in all sedated toddlers. The cVEMPs measures resulted in the following: P13 latency of 17.5 ± 1.41 milliseconds, N23 latency of 25.58 ± 2.02 milliseconds, and peak-to-peak amplitude of 15.39 ± 3.45 µV. One-sample t-test revealed statistically significant longer latencies and smaller amplitude of the toddlers' cVEMPs relative to the normative data for adults.

Conclusions The difficulty of cVEMPs testing in toddlers can be overcome by sedating them and attaining a position that contracts the SCM muscle. However, the toddlers' recordings revealed delayed latencies and smaller amplitudes than those of adults.
Charge transfer excitations from particle-particle random phase approximation—Opportunities and challenges arising from two-electron deficient systems
Authors: Yang Yang , Dominguez Adriel , Zhang Du , Lutsker Vitalij , Niehaus Thomas A. , Frauenheim Thomas , Yang Weitao
Published: March 2017

The particle-particle random phase approximation (pp-RPA) is a promising method for studying charge transfer (CT) excitations. Through a detailed analysis on two-electron deficient systems, we show that the pp-RPA is always able to recover the long-distance asymptotic −1/R trend for CT excitations as a result of the concerted effect between orbital energies and the pp-RPA kernel. We also provide quantitative results for systems with relatively short donor-acceptor distances. With conventional hybrid or range-separated functionals, the pp-RPA performs much better than time-dependent density functional theory (TDDFT), although it still gives underestimated results which are not as good as TDDFT with system-dependent tuned functionals. For pp-RPA, there remain three great challenges in dealing with CT excitations. First, the delocalized frontier orbitals in strongly correlated systems often lead to difficulty with self-consistent field convergence as well as an incorrect picture with about half an electron transferred. Second, the commonly used density functionals often underestimate the energy gap between the highest occupied molecular orbital and the lowest unoccupied molecular orbital (LUMO) for the two-electron deficient species, resulting in systems with delocalized orbitals. Third, the performance of pp-RPA greatly depends on the energy difference between the LUMO and a higher virtual orbital. However, the meaning of the orbital energies for higher virtual orbitals is still not clear. We also discuss the performance of an approximate pp-RPA scheme that uses density functional tight binding (pp-DFTB) as reference and demonstrate that the aforementioned challenges can be overcome by adopting suitable range-separated hybrid functionals. The pp-RPA and pp-DFTB are thus promising general approaches for describing charge transfer excitations.