bluuebunny/crossref_metadata_2025_split huggingface dataset:
Coenzyme Engineering of a Hyperthermophilic 6-Phosphogluconate Dehydrogenase from NADP+ to NAD+ with Its Application to Biobatteries
Authors: Chen Hui , Zhu Zhiguang , Huang Rui , Zhang Yi-Heng Percival 
Published: November 2016

AbstractEngineering the coenzyme specificity of redox enzymes plays an important role in metabolic engineering, synthetic biology, and biocatalysis, but it has rarely been applied to bioelectrochemistry. Here we develop a rational design strategy to change the coenzyme specificity of 6-phosphogluconate dehydrogenase (6PGDH) from a hyperthermophilic bacterium Thermotoga maritima from its natural coenzyme NADP+ to NAD+. Through amino acid-sequence alignment of NADP+- and NAD+-preferred 6PGDH enzymes and computer-aided substrate-coenzyme docking, the key amino acid residues responsible for binding the phosphate group of NADP+ were identified. Four mutants were obtained via site-directed mutagenesis. The best mutant N32E/R33I/T34I exhibited a ~6.4 × 104-fold reversal of the coenzyme selectivity from NADP+ to NAD+. The maximum power density and current density of the biobattery catalyzed by the mutant were 0.135 mW cm−2 and 0.255 mA cm−2, ~25% higher than those obtained from the wide-type 6PGDH-based biobattery at the room temperature. By using this 6PGDH mutant, the optimal temperature of running the biobattery was as high as 65 °C, leading to a high power density of 1.75 mW cm−2. This study demonstrates coenzyme engineering of a hyperthermophilic 6PGDH and its application to high-temperature biobatteries.
Metal-coupled folding as the driving force for the extreme stability of Rad50 zinc hook dimer assembly
Authors: Kochańczyk Tomasz , Nowakowski Michał , Wojewska Dominika , Kocyła Anna , Ejchart Andrzej , Koźmiński Wiktor , Krężel Artur 
Published: November 2016

AbstractThe binding of metal ions at the interface of protein complexes presents a unique and poorly understood mechanism of molecular assembly. A remarkable example is the Rad50 zinc hook domain, which is highly conserved and facilitates the Zn2+-mediated homodimerization of Rad50 proteins. Here, we present a detailed analysis of the structural and thermodynamic effects governing the formation and stability (logK12 = 20.74) of this evolutionarily conserved protein assembly. We have dissected the determinants of the stability contributed by the small β-hairpin of the domain surrounding the zinc binding motif and the coiled-coiled regions using peptides of various lengths from 4 to 45 amino acid residues, alanine substitutions and peptide bond-to-ester perturbations. In the studied series of peptides, an >650 000-fold increase of the formation constant of the dimeric complex arises from favorable enthalpy because of the increased acidity of the cysteine thiols in metal-free form and the structural properties of the dimer. The dependence of the enthalpy on the domain fragment length is partially compensated by the entropic penalty of domain folding, indicating enthalpy-entropy compensation. This study facilitates understanding of the metal-mediated protein-protein interactions in which the metal ion is critical for the tight association of protein subunits.
Host-ant specificity of endangered large blue butterflies (Phengaris spp., Lepidoptera: Lycaenidae) in Japan
Authors: Ueda Shouhei , Komatsu Takashi , Itino Takao , Arai Ryusuke , Sakamoto Hironori 
Published: November 2016

AbstractLarge blue butterflies, Phengaris (Maculinea), are an important focus of endangered-species conservation in Eurasia. Later-instar Phengaris caterpillars live in Myrmica ant nests and exploit the ant colony’s resources, and they are specialized to specific host-ant species. For example, local extinction of P. arion in the U. K. is thought to have been due to the replacement of its host-ant species with a less-suitable congener, as a result of changes in habitat. In Japan, Myrmica kotokui hosts P. teleius and P. arionides caterpillars. We recently showed, however, that the morphological species M. kotokui actually comprises four genetic clades. Therefore, to determine to which group of ants the hosts of these two Japanese Phengaris species belong, we used mitochondrial COI-barcoding of M. kotokui specimens from colonies in the habitats of P. teleius and P. arionides to identify the ant clade actually parasitized by the caterpillars of each species. We found that these two butterfly species parasitize different ant clades within M. kotokui.
Bioluminescence as an ecological factor during high Arctic polar night
Authors: Cronin Heather A. , Cohen Jonathan H. , Berge Jørgen , Johnsen Geir , Moline Mark A. 
Published: November 2016

AbstractBioluminescence commonly influences pelagic trophic interactions at mesopelagic depths. Here we characterize a vertical gradient in structure of a generally low species diversity bioluminescent community at shallower epipelagic depths during the polar night period in a high Arctic fjord with in situ bathyphotometric sampling. Bioluminescence potential of the community increased with depth to a peak at 80 m. Community composition changed over this range, with an ecotone at 20–40 m where a dinoflagellate-dominated community transitioned to dominance by the copepod Metridia longa. Coincident at this depth was bioluminescence exceeding atmospheric light in the ambient pelagic photon budget, which we term the bioluminescence compensation depth. Collectively, we show a winter bioluminescent community in the high Arctic with vertical structure linked to attenuation of atmospheric light, which has the potential to influence pelagic ecology during the light-limited polar night.
The role of Internal Solitary Waves on deep-water sedimentary processes: the case of up-slope migrating sediment waves off the Messina Strait
Authors: Droghei R. , Falcini F. , Casalbore D. , Martorelli E. , Mosetti R. , Sannino G. , Santoleri R. , Chiocci F. L. 
Published: November 2016

AbstractSubaqueous, asymmetric sand waves are typically observed in marine channel/canyon systems, tidal environments, and continental slopes exposed to strong currents, where they are formed by current shear resulting from a dominant unidirectional flow. However, sand-wave fields may be readily observed in marine environments where no such current exists; the physical processes driving their formation are enigmatic or not well understood. We propose that internal solitary waves (ISWs) induced by tides can produce an effective, unidirectional boundary “current” that forms asymmetric sand waves. We test this idea by examining a sand-wave field off the Messina Strait, where we hypothesize that ISWs formed at the interface between intermediate and surface waters are refracted by topography. Hence, we argue that the deflected pattern (i.e., the depth-dependent orientation) of the sand-wave field is due to refraction of such ISWs. Combining field observations and numerical modelling, we show that ISWs can account for three key features: ISWs produce fluid velocities capable of mobilizing bottom sediments; the predicted refraction pattern resulting from the interaction of ISWs with bottom topography matches the observed deflection of the sand waves; and predicted migration rates of sand waves match empirical estimates. This work shows how ISWs may contribute to sculpting the structure of continental margins and it represents a promising link between the geological and oceanographic communities.
Essential Oils and Eugenols Inhibit Biofilm Formation and the Virulence of Escherichia coli O157:H7
Authors: Kim Yong-Guy , Lee Jin-Hyung , Gwon Giyeon , Kim Soon-Il , Park Jae Gyu , Lee Jintae 
Published: November 2016

AbstractEnterohemorrhagic Escherichia coli O157:H7 (EHEC) has caused foodborne outbreaks worldwide and the bacterium forms antimicrobial-tolerant biofilms. We investigated the abilities of various plant essential oils and their components to inhibit biofilm formation by EHEC. Bay, clove, pimento berry oils and their major common constituent eugenol at 0.005% (v/v) were found to markedly inhibit EHEC biofilm formation without affecting planktonic cell growth. In addition, three other eugenol derivatives isoeugenol, 2-methoxy-4-propylphenol, and 4-ethylguaiacol had antibiofilm activity, indicating that the C-1 hydroxyl unit, the C-2 methoxy unit, and C-4 alkyl or alkane chain on the benzene ring of eugenol play important roles in antibiofilm activity. Interestingly, these essential oils and eugenol did not inhibit biofilm formation by three laboratory E. coli K-12 strains that reduced curli fimbriae production. Transcriptional analysis showed that eugenol down-regulated 17 of 28 genes analysed, including curli genes (csgABDFG), type I fimbriae genes (fimCDH) and ler-controlled toxin genes (espD, escJ, escR, and tir), which are required for biofilm formation and the attachment and effacement phenotype. In addition, biocompatible poly(lactic-co-glycolic acid) coatings containing clove oil or eugenol exhibited efficient biofilm inhibition on solid surfaces. In a Caenorhabditis elegans nematode model, clove oil and eugenol attenuated the virulence of EHEC.
Transjugular intrahepatic portosystemic shunt for Budd–Chiari syndrome with diffuse occlusion of hepatic veins
Authors: He Fuliang , Zhao Hongwei , Dai Shan , Wu Yingfeng , Wang Lei , Huang Hongdong , Yue Zhendong , Fan Zhenhua , Dong Xiaoqun , Liu Fuquan 
Published: November 2016

AbstractEither acute or sub-acute Budd–Chiari syndrome (BCS) with diffuse occlusion of hepatic veins has a high mortality rate and remains challenging for clinical treatment. We aimed to evaluate the feasibility and safety of transjugular intrahepatic portosystemic shunt (TIPS) as a treatment for BCS with diffuse occlusion of hepatic veins. From January 2007 to December 2010, 100 patients were randomly recruited onto this study and 91 patients were treated with TIPS. 14 patients were defined as acute BCS group and 86 patients as sub-acute group. Patients with acute BCS had a significantly higher rate of jaundice whereas a lower rate of abdominal and chest varices, gastroesophageal variceal bleeding and refractory ascites than sub-acute group (P < 0.001). TIPS was technically successful in all 91 patients (12 in acute group). The portosystemic pressure gradient (PSG) was decreased to normal level, while total bilirubin (TBIL) and liver function were significantly improved. During follow-up period, the mortality rate of 91 patients who underwent TIPS was 6.59% (6/91), whereas 88.89% of 9 patients who didn’t receive TIPS procedure (2 in acute group). Collectively, TIPS is an effective and safe approach in treating BCS with diffuse occlusion of hepatic veins, which should be performed in time.
Transcriptome Analysis of the Signalling Networks in Coronatine-Induced Secondary Laticifer Differentiation from Vascular Cambia in Rubber Trees
Authors: Wu Shaohua , Zhang Shixin , Chao Jinquan , Deng Xiaomin , Chen Yueyi , Shi Minjing , Tian Wei-Min 
Published: November 2016

AbstractThe secondary laticifer in rubber tree (Hevea brasiliensis Muell. Arg.) is a specific tissue within the secondary phloem. This tissue differentiates from the vascular cambia, and its function is natural rubber biosynthesis and storage. Given that jasmonates play a pivotal role in secondary laticifer differentiation, we established an experimental system with jasmonate (JA) mimic coronatine (COR) for studying the secondary laticifer differentiation: in this system, differentiation occurs within five days of the treatment of epicormic shoots with COR. In the present study, the experimental system was used to perform transcriptome sequencing and gene expression analysis. A total of 67,873 unigenes were assembled, and 50,548 unigenes were mapped at least in one public database. Of these being annotated unigenes, 15,780 unigenes were differentially expressed early after COR treatment, and 19,824 unigenes were differentially expressed late after COR treatment. At the early stage, 8,646 unigenes were up-regulated, while 7,134 unigenes were down-regulated. At the late stage, the numbers of up- and down-regulated unigenes were 7,711 and 12,113, respectively. The annotation data and gene expression analysis of the differentially expressed unigenes suggest that JA-mediated signalling, Ca2+ signal transduction and the CLAVATA-MAPK-WOX signalling pathway may be involved in regulating secondary laticifer differentiation in rubber trees.
A short insertion mutation disrupts genesis of miR-16 and causes increased body weight in domesticated chicken
Authors: Jia Xinzheng , Lin Huiran , Nie Qinghua , Zhang Xiquan , Lamont Susan J. 
Published: November 2016

AbstractBody weight is one of the most important quantitative traits with high heritability in chicken. We previously mapped a quantitative trait locus (QTL) for body weight by genome-wide association study (GWAS) in an F2 chicken resource population. To identify the causal mutations linked to this QTL, expression profiles were determined on livers of high-weight and low-weight chicken lines by microarray. Combining the expression pattern with SNP effects by GWAS, miR-16 was identified as the most likely potential candidate with a 3.8-fold decrease in high-weight lines. Re-sequencing revealed that a 54-bp insertion mutation in the upstream region of miR-15a-16 displayed high allele frequencies in high-weight commercial broiler line. This mutation resulted in lower miR-16 expression by introducing three novel splicing sites instead of the missing 5′ terminal splicing of mature miR-16. Elevating miR-16 significantly inhibited DF-1 chicken embryo cell proliferation, consistent with a role in suppression of cellular growth. The 54-bp insertion was significantly associated with increased body weight, bone size and muscle mass. Also, the insertion mutation tended towards fixation in commercial broilers (Fst > 0.4). Our findings revealed a novel causative mutation for body weight regulation that aids our basic understanding of growth regulation in birds.
Manipulation of small particles at solid liquid interface: light driven diffusioosmosis
Authors: Feldmann David , Maduar Salim R. , Santer Mark , Lomadze Nino , Vinogradova Olga I. , Santer Svetlana 
Published: November 2016

AbstractThe strong adhesion of sub-micron sized particles to surfaces is a nuisance, both for removing contaminating colloids from surfaces and for conscious manipulation of particles to create and test novel micro/nano-scale assemblies. The obvious idea of using detergents to ease these processes suffers from a lack of control: the action of any conventional surface-modifying agent is immediate and global. With photosensitive azobenzene containing surfactants we overcome these limitations. Such photo-soaps contain optical switches (azobenzene molecules), which upon illumination with light of appropriate wavelength undergo reversible trans-cis photo-isomerization resulting in a subsequent change of the physico-chemical molecular properties. In this work we show that when a spatial gradient in the composition of trans- and cis- isomers is created near a solid-liquid interface, a substantial hydrodynamic flow can be initiated, the spatial extent of which can be set, e.g., by the shape of a laser spot. We propose the concept of light induced diffusioosmosis driving the flow, which can remove, gather or pattern a particle assembly at a solid-liquid interface. In other words, in addition to providing a soap we implement selectivity: particles are mobilized and moved at the time of illumination, and only across the illuminated area.
Physiological response and sulfur metabolism of the V. dahliae-infected tomato plants in tomato/potato onion companion cropping
Authors: Fu Xuepeng , Li Chunxia , Zhou Xingang , Liu Shouwei , Wu Fengzhi 
Published: November 2016

AbstractCompanion cropping with potato onions (Allium cepa var. agrogatum Don.) can enhance the disease resistance of tomato plants (Solanum lycopersicum) to Verticillium dahliae infection by increasing the expressions of genes related to disease resistance. However, it is not clear how tomato plants physiologically respond to V. dahliae infection and what roles sulfur plays in the disease-resistance. Pot experiments were performed to examine changes in the physiology and sulfur metabolism of tomato roots infected by V. dahliae under the companion cropping (tomato/potato onion). The results showed that the companion cropping increased the content of total phenol, lignin and glutathione and increased the activities of peroxidase, polyphenol oxidase and phenylalanine ammonia lyase in the roots of tomato plants. RNA-seq analysis showed that the expressions of genes involved in sulfur uptake and assimilation, and the formation of sulfur-containing defense compounds (SDCs) were up-regulated in the V. dahlia-infected tomatoes in the companion cropping. In addition, the interactions among tomato, potato onion and V. dahliae induced the expression of the high- affinity sulfate transporter gene in the tomato roots. These results suggest that sulfur may play important roles in tomato disease resistance against V. dahliae.
Ultra-Smooth, Fully Solution-Processed Large-Area Transparent Conducting Electrodes for Organic Devices
Authors: Jin Won-Yong , Ginting Riski Titian , Ko Keum-Jin , Kang Jae-Wook 
Published: November 2016

AbstractA novel approach for the fabrication of ultra-smooth and highly bendable substrates consisting of metal grid-conducting polymers that are fully embedded into transparent substrates (ME-TCEs) was successfully demonstrated. The fully printed ME-TCEs exhibited ultra-smooth surfaces (surface roughness ~1.0 nm), were highly transparent (~90% transmittance at a wavelength of 550 nm), highly conductive (sheet resistance ~4 Ω ◻−1), and relatively stable under ambient air (retaining ~96% initial resistance up to 30 days). The ME-TCE substrates were used to fabricate flexible organic solar cells and organic light-emitting diodes exhibiting devices efficiencies comparable to devices fabricated on ITO/glass substrates. Additionally, the flexibility of the organic devices did not degrade their performance even after being bent to a bending radius of ~1 mm. Our findings suggest that ME-TCEs are a promising alternative to indium tin oxide and show potential for application toward large-area optoelectronic devices via fully printing processes.
Surface-bound bovine serum albumin carrier protein as present in recombinant cytokine preparations amplifies T helper 17 cell polarization
Authors: Dong Lei , Helmke Alexandra , Waisman Ari , Haller Hermann , Pich Andreas , von Vietinghoff Sibylle 
Published: November 2016

AbstractUnderstanding of T helper 17 lineage (TH17) polarization has been significantly promoted by cell culture experiments that reduce the complexity of the in vivo environment. We here investigated TH17 amplification by coating of cytokine preparations. Cytokine preparations coated to the surface compared to the same amount given in solution significantly enhanced TH17 polarization assessed by flow cytometry and interleukin (IL)-17A, IL-17F and RORγt mRNA expression. T cell proliferation and TH1 polarization were similarly enhanced while TREG polarization was impeded. TH17 amplification was replicated by coating the plate with low amounts of FCS or albumin as used as carrier protein for cytokines (0.5 μl 0.1%). It was unaltered by filtration, protein digestion and arylhydrocarbon receptor blockade, not replicated by LPS and independent of integrin stimulation. TH17 amplification required anti-CD3 stimulation and was T cell intrinsic. Supernatants of CD4+ cells polarized on coated cytokine preparations with carrier albumin conferred amplification to fresh splenocytes. Coating markedly elevated CD4+ IL-22 mRNA expression and IL-22 blockade significantly reduced TH17 amplification. Our data show TH17 amplification by coated albumin in the low amounts present in recombinant cytokine preparations. This unexpected adjuvant like effect underscores the need for controls also for temporal and spatial factors in cell culture.
The role of carbon in structural evolution during single step synthesis of nano tantalum carbide
Authors: Brar Loveleen K. , Singla Gourav , Pandey O. P. 
Published: November 2016

Carbon-coated nano TaC has been synthesized at 800 °C in single step from TaO2. Structural features of synthesized cubic TaC depend on the initial carbon concentration. The reaction analysis depicts the role of Mg in lowering the reaction temperature.
Homocysteine deteriorates intrahepatic derangement and portal-systemic collaterals in cirrhotic rats
Authors: Tung Hung-Chun , Hsu Shao-Jung , Tsai Ming-Hung , Lin Te-Yueh , Hsin I-Fang , Huo Te-Ia , Lee Fa-Yauh , Huang Hui-Chun , Ho Hsin-Ling , Lin Han-Chieh , Lee Shou-Dong 
Published: November 2016

In liver cirrhosis, the altered levels of vasoactive substances, especially endothelin-1 (ET-1) and nitric oxide (NO) lead to elevated intrahepatic resistance, increased portal-systemic collaterals and abnormal intra- and extra-hepatic vascular responsiveness. These derangements aggravate portal hypertension-related complications such as gastro-oesophageal variceal bleeding. Homocysteine, a substance implicated in cardiovascular diseases, has been found with influences on vasoresponsiveness and angiogenesis. However, their relevant effects in liver cirrhosis have not been investigated. In the present study, liver cirrhosis was induced by common bile duct ligation (BDL) in Sprague–Dawley rats. In acute study, the results showed that homocysteine enhanced hepatic vasoconstriction to ET-1 but decreased portal-systemic collateral vasocontractility to arginine vasopressin (AVP). Homocysteine down-regulated hepatic phosphorylated endothelial NO synthase (p-eNOS) and p-Akt protein expressions. Inducible NOS (iNOS) and cyclooxygenase (COX)-2 expressions were up-regulated by homocysteine in splenorenal shunt (SRS), the most prominent intra-abdominal collateral vessel. In chronic study, BDL or thioacetamide (TAA) rats received homocysteine or vehicle for 14 days. The results revealed that homocysteine increased hepatic collagen fibre deposition and fibrotic factors expressions in both BDL- and TAA-induced liver fibrotic rats. Portal-systemic shunting and expressions of mesenteric angiogenetic factors [vascular endothelial growth factor (VEGF), platelet-derived growth factor (PDGF), PDGF receptor β (PDGFRβ) and p-eNOS] were also increased in BDL rats. In conclusion, homocysteine is harmful to vascular derangements and liver fibrosis in cirrhosis.