bluuebunny/crossref_metadata_2025 huggingface dataset:
Strain-transcending immune response generated by chimeras of the malaria vaccine candidate merozoite surface protein 2
Authors: Krishnarjuna Bankala , Andrew Dean , MacRaild Christopher A. , Morales Rodrigo A. V. , Beeson James G. , Anders Robin F. , Richards Jack S. , Norton Raymond S.
Published: February 2016

MSP2 is an intrinsically disordered protein that is abundant on the merozoite surface and essential to the parasite Plasmodium falciparum. Naturally-acquired antibody responses to MSP2 are biased towards dimorphic sequences within the central variable region of MSP2 and have been linked to naturally-acquired protection from malaria. In a phase IIb study, an MSP2-containing vaccine induced an immune response that reduced parasitemias in a strain-specific manner. A subsequent phase I study of a vaccine that contained both dimorphic forms of MSP2 induced antibodies that exhibited functional activity in vitro. We have assessed the contribution of the conserved and variable regions of MSP2 to the generation of a strain-transcending antibody response by generating MSP2 chimeras that included conserved and variable regions of the 3D7 and FC27 alleles. Robust anti-MSP2 antibody responses targeting both conserved and variable regions were generated in mice, although the fine specificity and the balance of responses to these regions differed amongst the constructs tested. We observed significant differences in antibody subclass distribution in the responses to these chimeras. Our results suggest that chimeric MSP2 antigens can elicit a broad immune response suitable for protection against different strains of P. falciparum.
Calcium and Magnesium Ions Are Membrane-Active against Stationary-Phase Staphylococcus aureus with High Specificity
Authors: Xie Yuntao , Yang Lihua
Published: February 2016

Staphylococcus aureus (S. aureus) is notorious for its ability to acquire antibiotic-resistance, and antibiotic-resistant S. aureus has become a wide-spread cause of high mortality rate. Novel antimicrobials capable of eradicating S. aureus cells including antibiotic-resistant ones are thus highly desired. Membrane-active bactericides and species-specific antimicrobials are two promising sources of novel anti-infective agents for fighting against bacterial antibiotic-resistance. We herein show that Ca2+ and Mg2+, two alkaline-earth-metal ions physiologically essential for diverse living organisms, both disrupt model S. aureus membranes and kill stationary-phase S. aureus cells, indicative of membrane-activity. In contrast to S. aureus, Escherichia coli and Bacillus subtilis exhibit unaffected survival after similar treatment with these two cations, indicative of species-specific activity against S. aureus. Moreover, neither Ca2+ nor Mg2+ lyses mouse red blood cells, indicative of hemo-compatibility. This works suggests that Ca2+ and Mg2+ may have implications in targeted eradication of S. aureus pathogen including the antibiotic-resistant ones.
Basic FGF or VEGF gene therapy corrects insufficiency in the intrinsic healing capacity of tendons
Authors: Tang Jin Bo , Wu Ya Fang , Cao Yi , Chen Chuan Hao , Zhou You Lang , Avanessian Bella , Shimada Masaru , Wang Xiao Tian , Liu Paul Y.
Published: February 2016

Tendon injury during limb motion is common. Damaged tendons heal poorly and frequently undergo unpredictable ruptures or impaired motion due to insufficient innate healing capacity. By basic fibroblast growth factor (bFGF) or vascular endothelial growth factor (VEGF) gene therapy via adeno-associated viral type-2 (AAV2) vector to produce supernormal amount of bFGF or VEGF intrinsically in the tendon, we effectively corrected the insufficiency of the tendon healing capacity. This therapeutic approach (1) resulted in substantial amelioration of the low growth factor activity with significant increases in bFGF or VEGF from weeks 4 to 6 in the treated tendons (p < 0.05 or p < 0.01), (2) significantly promoted production of type I collagen and other extracellular molecules (p < 0.01) and accelerated cellular proliferation and (3) significantly increased tendon strength by 68–91% from week 2 after AAV2-bFGF treatment and by 82–210% from week 3 after AAV2-VEGF compared with that of the controls (p < 0.05 or p < 0.01). Moreover, the transgene expression dissipated after healing was complete. These findings show that the gene transfers provide an optimistic solution to the insufficiencies of the intrinsic healing capacity of the tendon and offers an effective therapeutic possibility for patients with tendon disunion.
Scavenger receptor B1, the HDL receptor, is expressed abundantly in liver sinusoidal endothelial cells
Authors: Ganesan Latha P. , Mates Jessica M. , Cheplowitz Alana M. , Avila Christina L. , Zimmerer Jason M. , Yao Zhili , Maiseyeu Andrei , Rajaram Murugesan V. S. , Robinson John M. , Anderson Clark L.
Published: February 2016

Cholesterol from peripheral tissue, carried by HDL, is metabolized in the liver after uptake by the HDL receptor, SR-B1. Hepatocytes have long been considered the only liver cells expressing SR-B1; however, in this study we describe two disparate immunofluorescence (IF) experiments that suggest otherwise. Using high-resolution confocal microscopy employing ultrathin (120 nm) sections of mouse liver, improving z-axis resolution, we identified the liver sinusoidal endothelial cells (LSEC), marked by FcγRIIb, as the cell within the liver expressing abundant SR-B1. In contrast, the hepatocyte, identified with β-catenin, expressed considerably weaker levels, although optical resolution of SR-B1 was inadequate. Thus, we moved to a different IF strategy, first separating dissociated liver cells by gradient centrifugation into two portions, hepatocytes (parenchymal cells) and LSEC (non-parenchymal cells). Characterizing both portions for the cellular expression of SR-B1 by flow cytometry, we found that LSEC expressed considerable amounts of SR-B1 while in hepatocytes SR-B1 expression was barely perceptible. Assessing mRNA of SR-B1 by real time PCR we found messenger expression in LSEC to be about 5 times higher than in hepatocytes.
A Trans-omics Mathematical Analysis Reveals Novel Functions of the Ornithine Metabolic Pathway in Cancer Stem Cells
Authors: Koseki Jun , Matsui Hidetoshi , Konno Masamitsu , Nishida Naohiro , Kawamoto Koichi , Kano Yoshihiro , Mori Masaki , Doki Yuichiro , Ishii Hideshi
Published: February 2016

Bioinformatics and computational modelling are expected to offer innovative approaches in human medical science. In the present study, we performed computational analyses and made predictions using transcriptome and metabolome datasets obtained from fluorescence-based visualisations of chemotherapy-resistant cancer stem cells (CSCs) in the human oesophagus. This approach revealed an uncharacterized role for the ornithine metabolic pathway in the survival of chemotherapy-resistant CSCs. The present study fastens this rationale for further characterisation that may lead to the discovery of innovative drugs against robust CSCs.
Histological and transcriptome analyses of testes from Duroc and Meishan boars
Authors: Ding Haisheng , Luo Yan , Liu Min , Huang Jingshu , Xu Dequan
Published: February 2016

Meishan boars are known for their early sexual maturity. However, they exhibit a significantly smaller testicular size and a reduced proportion of Sertoli cells and daily sperm production compared with Duroc boars. The testes of Duroc and Meishan boars at 20, 75 and 270 days of age were used for histological and transcriptome analyses. Haematoxylin-eosin staining was conducted to observe histological structure of the testes in Duroc and Meishan boars at different ages. Although spermatogenesis occurred prior to 75 days in Meishan boars, the number of spermatogonia and Sertoli cells in Meishan boars were less than in Duroc boars at adulthood. The diameters of the seminiferous tubules of the testes differed significantly during the initiation of development of the seminiferous tubules between the two breeds. We obtained differentially expressed functional genes and analysed seven pathways involved in male sexual maturity and spermatogenesis using RNA-seq. We also detected four main alternative splicing events and many single nucleotide polymorphisms from testes. Eight functionally important genes were validated by qPCR and Neurotrophin 3 was subjected to quantification and cellular localization analysis. Our study provides the first transcriptome evidence for the differences in sexual function development between Meishan and Duroc boars.
Intrinsic and membrane-facilitated α-synuclein oligomerization revealed by label-free detection through solid-state nanopores
Authors: Hu Rui , Diao Jiajie , Li Ji , Tang Zhipeng , Li Xiaoqing , Leitz Jeremy , Long Jiangang , Liu Jiankang , Yu Dapeng , Zhao Qing
Published: February 2016

α-Synuclein (α-Syn) is an abundant cytosolic protein involved in the release of neurotransmitters in presynaptic terminal and its aberrant aggregation is found to be associated with Parkinson’s disease. Recent study suggests that the oligomers formed at the initial oligomerization stage may be the root cause of cytotoxicity. While characterizing this stage is challenging due to the inherent difficulties in studying heterogeneous and transient systems by conventional biochemical technology. Here we use solid-state nanopores to study the time-dependent kinetics of α-Syn oligomerization through a label-free and single molecule approach. A tween 20 coating method is developed to inhibit non-specific adsorption between α-Syn and nanopore surface to ensure successful and continuous detection of α-Syn translocation. We identify four types of oligomers formed in oligomerization stage and find an underlying consumption mechanism that the formation of large oligomers consumes small oligomers. Furthermore, the effect of lipid membrane on oligomerization of α-Syn is also investigated and the results show that 1,2-dioleoyl-sn-glycero-3-[phospho-L-serine] (DOPS) small unilamellar vesicles (SUVs) dramatically enhances the aggregation rate of α-Syn while do not alter the aggregation pathway.
A novel solid state photocatalyst for living radical polymerization under UV irradiation
Authors: Fu Qiang , McKenzie Thomas G. , Ren Jing M. , Tan Shereen , Nam Eunhyung , Qiao Greg G.
Published: February 2016

This study presents the development of a novel solid state photocatalyst for the photoinduced controlled radical polymerization of methacrylates under mild UV irradiation (λmax ≈ 365 nm) in the absence of conventional photoinitiators, metal-catalysts or dye sensitizers. The photocatalyst design was based on our previous finding that organic amines can act in a synergistic photochemical reaction with thiocarbonylthio compounds to afford well controlled polymethacrylates under UV irradiation. Therefore, in the current contribution an amine-rich polymer was covalently grafted onto a solid substrate, thus creating a heterogeneous catalyst that would allow for facile removal, recovery and recyclability when employed for such photopolymerization reactions. Importantly, the polymethacrylates synthesized using the solid state photocatalyst (ssPC) show similarly excellent chemical and structural integrity as those catalysed by free amines. Moreover, the ssPC could be readily recovered and re-used, with multiple cycles of polymerization showing minimal effect on the integrity of the catalyst. Finally, the ssPC was employed in various photo-“click” reactions, permitting high yielding conjugations under photochemical control.
Activity Variation of Phanerochaete chrysosporium under Nanosilver Exposure by Controlling of Different Sulfide Sources
Authors: Guo Zhi , Chen Guiqiu , Liu Lingzhi , Zeng Guangming , Huang Zhenzhen , Chen Anwei , Hu Liang
Published: February 2016

Due to the particular activation and inhibition behavior of silver nanoparticles (AgNPs) on microbes at various concentrations, it’s crucial to exploit the special concentration effect in environment. Here, we studied the viability variation of Phanerochaete chrysosporium (P. chrysosporium) under exposure to citrate-coated AgNPs (Citrate-AgNPs) in the presence of different sulfide sources (an inorganic sulfide, NaHS and an organic sulfide, thioacetamide (TAA)). The results indicated that both NaHS and TAA can promote activation of P. chrysosporium by Citrate-AgNPs at a higher concentration, which was initial at toxic level. Treatment with various concentrations of Citrate-AgNPs (0–9 mg/L) demonstrated a maximum activation concentration (MAC) at 3 mg/L. With the increase in sulfide concentration, MAC transferred to higher concentration significantly, indicating the obvious “toxicity to activation” transformation at a higher concentration. Ag+ testing exhibited that variations in sulfide-induced Ag+ concentration (3−7 μg/L Ag+) accounted for the “toxicity to activation” transformation. In addition, the similar results were observed on antibacterial application using Escherichia coli as the model species. Based on the research results, the application of this transformation in improving antibacterial activity was proposed. Therefore, the antibacterial activity of AgNPs can be controlled, even at concentration, via adjusting for the sulfide concentration.
Persistence in eye movement during visual search
Authors: Amor Tatiana A. , Reis Saulo D. S. , Campos Daniel , Herrmann Hans J. , Andrade José S.
Published: February 2016

As any cognitive task, visual search involves a number of underlying processes that cannot be directly observed and measured. In this way, the movement of the eyes certainly represents the most explicit and closest connection we can get to the inner mechanisms governing this cognitive activity. Here we show that the process of eye movement during visual search, consisting of sequences of fixations intercalated by saccades, exhibits distinctive persistent behaviors. Initially, by focusing on saccadic directions and intersaccadic angles, we disclose that the probability distributions of these measures show a clear preference of participants towards a reading-like mechanism (geometrical persistence), whose features and potential advantages for searching/foraging are discussed. We then perform a Multifractal Detrended Fluctuation Analysis (MF-DFA) over the time series of jump magnitudes in the eye trajectory and find that it exhibits a typical multifractal behavior arising from the sequential combination of saccades and fixations. By inspecting the time series composed of only fixational movements, our results reveal instead a monofractal behavior with a Hurst exponent "Equation missing", which indicates the presence of long-range power-law positive correlations (statistical persistence). We expect that our methodological approach can be adopted as a way to understand persistence and strategy-planning during visual search.
Simultaneous resonant x-ray diffraction measurement of polarization inversion and lattice strain in polycrystalline ferroelectrics
Authors: Gorfman S. , Simons H. , Iamsasri T. , Prasertpalichat S. , Cann D. P. , Choe H. , Pietsch U. , Watier Y. , Jones J. L.
Published: February 2016

Structure-property relationships in ferroelectrics extend over several length scales from the individual unit cell to the macroscopic device, and with dynamics spanning a broad temporal domain. Characterizing the multi-scale structural origin of electric field-induced polarization reversal and strain in ferroelectrics is an ongoing challenge that so far has obscured its fundamental behaviour. By utilizing small intensity differences between Friedel pairs due to resonant scattering, we demonstrate a time-resolved X-ray diffraction technique for directly and simultaneously measuring both lattice strain and, for the first time, polarization reversal during in-situ electrical perturbation. This technique is demonstrated for BaTiO3-BiZn0.5Ti0.5O3 (BT-BZT) polycrystalline ferroelectrics, a prototypical lead-free piezoelectric with an ambiguous switching mechanism. This combines the benefits of spectroscopic and diffraction-based measurements into a single and robust technique with time resolution down to the ns scale, opening a new door to in-situ structure-property characterization that probes the full extent of the ferroelectric behaviour.
ITF2357 transactivates Id3 and regulate TGFβ/BMP7 signaling pathways to attenuate corneal fibrosis
Authors: Lim Rayne R. , Tan Alison , Liu Yu-Chi , Barathi Veluchamy A. , Mohan Rajiv R. , Mehta Jodhbir S. , Chaurasia Shyam S.
Published: February 2016

Corneal fibrosis is often seen in patients with ocular trauma and infection that compromises corneal transparency resulting in vision loss. Treatment strategies including NSAIDs, steroids, MMC and corneal transplants have shown tremendous success but with several side effects and cellular toxicity. Histone deacetylase inhibitors (HDACi) have been shown to inhibit corneal fibrosis via TGFβ signaling pathway. In this study, we investigated safety, efficacy and mechanism of action of a HDACi, ITF2357 in TGFβ-stimulatedin vitroprimary human cornea stromal fibroblasts (pHCSFs) andin vivoin a photorefractive keratectomy-treated rabbit model of corneal fibrosis. We found thatin vivoITF2357 decreased collagen I, collagen IV, fibronectin, integrin αVβ3 expression with a reduction in corneal haze. In addition, ITF2357 reduced myofibroblast formation, suppressed phosphorylation of Smad proteins in TGFβ pathway and inhibited key responsive protein, P4HA1 involved in pro-collagen synthesis. Treatment of pHCSFs with ITF2357 activated BMP7 levels and expressed all the members of inhibitor of differentiation proteins (Id1-Id4), however, it failed to rescue TGFβ-driven transdifferentiation of fibroblasts to myofibroblasts in the presence of siRNA specific to Id3. We conclude that ITF2357 is a potential anti-fibrotic drug that exerts its action via activation of Id3, a downstream target of TGFβ/BMP7 signaling pathways.
Moral judgment modulates neural responses to the perception of other’s pain: an ERP study
Authors: Cui Fang , Ma Ning , Luo Yue-jia
Published: February 2016

Morality and empathy are both crucial in building human society. Yet the relationship between them has been merely explored. The present study revealed how the morality influenced empathy for pain by comparing the ERPs elicited by pictures showing the targets’ in pain primed by different moral information about the targets. We found that when the target was a moral one or a neutral one, the painful pictures elicited significantly larger amplitude in N2 than the non-painful pictures, but when the target was an immoral one, the difference between the amplitudes of N2 component elicited by painful and non-painful pictures became insignificant. We proposed that this effect was induced by the decreased affective arousal when observing an immoral person in pain. The reduced neural response towards the immoral one’s pain can keep us alert when we face the potentially dangerous people thereby increasing our chance of survival. SLORTEA results showed the source of this difference in N2 localized in the ventral medial prefrontal cortex (vmPFC) and the rostral anterior cingulate cortex (rACC) areas.
Progranulin suppresses titanium particle induced inflammatory osteolysis by targeting TNFα signaling
Authors: Zhao Yun-peng , Wei Jian-lu , Tian Qing-yun , Liu Alexander Tianxing , Yi Young-Su , Einhorn Thomas A. , Liu Chuan-ju
Published: February 2016

Aseptic loosening is a major complication of prosthetic joint surgery, characterized by chronic inflammation, pain and osteolysis surrounding the bone-implant interface. Progranulin (PGRN) is known to have anti-inflammatory action by binding to Tumor Necrosis Factor (TNF) receptors and antagonizing TNFα. Here we report that titanium particles significantly induced PGRN expression in RAW264.7 cells and also in a mouse air-pouch model of inflammation. PGRN-deficiency enhanced, whereas administration of recombinant PGRN effectively inhibited, titanium particle-induced inflammation in an air pouch model. In addition, PGRN also significantly inhibited titanium particle-induced osteoclastogenesis and calvarial osteolysis in vitro, ex vivo and in vivo. Mechanistic studies demonstrated that the inhibition of PGRN on titanium particle induced-inflammation is primarily via neutralizing the titanium particle-activated TNFα/NF-κB signaling pathway and this is evidenced by the suppression of particle-induced IκB phosphorylation, NF-κB p65 nuclear translocation and activity of the NF-κB-specific reporter gene. Collectively, these findings not only demonstrate that PGRN plays an important role in inhibiting titanium particle-induced inflammation, but also provide a potential therapeutic agent for the prevention of wear debris-induced inflammation and osteolysis.
Effects of three permeases on arginine utilization in Saccharomyces cerevisiae
Authors: Zhang Peng , Du Guocheng , Zou Huijun , Chen Jian , Xie Guangfa , Shi Zhongping , Zhou Jingwen
Published: February 2016

Arginine plays an important role in cellular function and metabolism. Arginine uptake mainly occurs through three amino acid permeases, Alp1p, Gap1p and Can1p, which act as both transporters and receptors for amino acid utilization. In this study, seven mutants were constructed with different combinations of permease deficiencies that inhibit arginine utilization. Their effects on arginine metabolism were measured. The three amino acid permeases were also individually overexpressed in wild-type (WT), Δalp1Δgap1Δcan1 and Δnpr1 strains. The growth and arginine utilization of Δcan1, Δgap1Δcan1 and Δalp1Δgap1Δcan1 mutants were suppressed in YNB medium when arginine was the sole nitrogen source. Meanwhile, overexpression of Alp1p and Can1p enhanced growth and arginine utilization in WT, Δalp1Δgap1Δcan1 and Δnpr1. Besides, overexpression of Can1p caused a 26.7% increase in OD600 and 29.3% increase in arginine utilization compared to that of Alp1p in Δalp1Δgap1Δcan1. Transcription analysis showed that the effects of three amino acid permeases on the arginine utilization and the regulation of related genes, were tightly related to their individual characteristics. However, their overall effects were different for different combinations of mutants. The results presented here suggest some possible synergistic effects of different amino acid permeases on regulation of amino acid utilization and metabolism.
Multifunctional flexible free-standing titanate nanobelt membranes as efficient sorbents for the removal of radioactive 90Sr2+ and 137Cs+ ions and oils
Authors: Wen Tao , Zhao Zhiwei , Shen Congcong , Li Jiaxing , Tan Xiaoli , Zeb Akif , Wang Xiangke , Xu An-Wu
Published: February 2016

For the increasing attention focused on saving endangered environments, there is a growing need for developing membrane materials able to perform complex functions such as removing radioactive pollutants and oil spills from water. A major challenge is the scalable fabrication of membranes with good mechanical and thermal stability, superior resistance to radiation, and excellent recyclability. In this study, we constructed a multifunctional flexible free-standing sodium titanate nanobelt (Na-TNB) membrane that was assembled as advanced radiation-tainted water treatment and oil uptake. We compared the adsorption behavior of 137Cs+ and 90Sr2+ on Na-TNB membranes under various environmental conditions. The maximum adsorption coefficient value (Kd) for Sr2+ reaches 107 mL g−1. The structural collapse of the exchange materials were confirmed by XRD, FTIR and XPS spectroscopy as well as Raman analysis. The adsorption mechanism of Na-TNB membrane is clarified by forming a stable solid with the radioactive cations permanently trapped inside. Besides, the engineered multilayer membrane is exceptionally capable in selectively and rapidly adsorbing oils up to 23 times the adsorbent weight when coated with a thin layer of hydrophobic molecules. This multifunctional membrane has exceptional potential as a suitable material for next generation water treatment and separation technologies.
Highly bendable bilayer-type photo-actuators comprising of reduced graphene oxide dispersed in hydrogels
Authors: Kim Dowan , Lee Heon Sang , Yoon Jinhwan
Published: February 2016

To avoid the problem of reduced graphene oxide (rGO) restacking in aqueous solution, the preparation of light-responsive poly(N-isopropylacrylamide) incorporating rGO (PNIPAm/rGO) was achieved by the chemical reduction of GO dispersed in the hydrogel matrix. Due to the enhanced photothermal efficiency of the rGO, the prepared PNIPAm/rGO underwent large volume reductions in response to irradiation by visible light of modest intensity. With respect to potential applications, bilayer-type photo-actuators comprising a PNIPAm/rGO active layer and poly(acrylamide) passive layer were fabricated; these achieved a full bending motion upon visible-light exposure. Adjusting the swelling ratio of each layer in the initial state yielded bidirectional photo-actuators that showed the active motion of turning inside out. Furthermore, we demonstrated that the fabricated actuation system would exhibit controlled bending motion in response to solar radiation.
Protective efficacy of the chimeric Staphylococcus aureus vaccine candidate IC in sepsis and pneumonia models
Authors: Yang Liuyang , Cai Changzhi , Feng Qiang , Shi Yun , Zuo Qianfei , Yang Huijie , Jing Haiming , Wei Chao , Zhuang Yuan , Zou Quanming , Zeng Hao
Published: February 2016

Staphylococcus aureus causes serious sepsis and necrotic pneumonia worldwide. Due to the spread of multidrug-resistant strains, developing an effective vaccine is the most promising method for combating S. aureus infection. In this study, based on the immune-dominant areas of the iron surface determinant B (IsdB) and clumping factor A (ClfA), we designed the novel chimeric vaccine IsdB151-277ClfA33-213 (IC). IC formulated with the AlPO4 adjuvant induced higher protection in an S. aureus sepsis model compared with the single components alone and showed broad immune protection against several clinical S. aureus isolates. Immunisation with IC induced strong antibody responses. The protective effect of antibodies was demonstrated through the opsonophagocytic assay (OPA) and passive immunisation experiment. Moreover, this new chimeric vaccine induced Th1/Th17-skewed cellular immune responses based on cytokine profiles and CD4+ T cell stimulation tests. Neutralisation of IL-17A alone (but not IFN-γ) resulted in a significant decrease in vaccine immune protection. Finally, we found that IC showed protective efficacy in a pneumonia model. Taken together, these data provide evidence that IC is a potentially promising vaccine candidate for combating S. aureus sepsis and pneumonia.
Evolution of short inverted repeat in cupressophytes, transfer of accD to nucleus in Sciadopitys verticillata and phylogenetic position of Sciadopityaceae
Authors: Li Jia , Gao Lei , Chen Shanshan , Tao Ke , Su Yingjuan , Wang Ting
Published: February 2016

Sciadopitys verticillata is an evergreen conifer and an economically valuable tree used in construction, which is the only member of the family Sciadopityaceae. Acquisition of the S. verticillata chloroplast (cp) genome will be useful for understanding the evolutionary mechanism of conifers and phylogenetic relationships among gymnosperm. In this study, we have first reported the complete chloroplast genome of S. verticillata. The total genome is 138,284 bp in length, consisting of 118 unique genes. The S. verticillata cp genome has lost one copy of the canonical inverted repeats and shown distinctive genomic structure comparing with other cupressophytes. Fifty-three simple sequence repeat loci and 18 forward tandem repeats were identified in the S. verticillata cp genome. According to the rearrangement of cupressophyte cp genome, we proposed one mechanism for the formation of inverted repeat: tandem repeat occured first, then rearrangement divided the tandem repeat into inverted repeats located at different regions. Phylogenetic estimates inferred from 59-gene sequences and cpDNA organizations have both shown that S. verticillata was sister to the clade consisting of Cupressaceae, Taxaceae and Cephalotaxaceae. Moreover, accD gene was found to be lost in the S. verticillata cp genome and a nucleus copy was identified from two transcriptome data.
Femtosecond laser for cavity preparation in enamel and dentin: ablation efficiency related factors
Authors: Chen H. , Li H. , Sun YC. , Wang Y. , Lü PJ.
Published: February 2016

To study the effects of laser fluence (laser energy density), scanning line spacing and ablation depth on the efficiency of a femtosecond laser for three-dimensional ablation of enamel and dentin. A diode-pumped, thin-disk femtosecond laser (wavelength 1025 nm, pulse width 400 fs) was used for the ablation of enamel and dentin. The laser spot was guided in a series of overlapping parallel lines on enamel and dentin surfaces to form a three-dimensional cavity. The depth and volume of the ablated cavity was then measured under a 3D measurement microscope to determine the ablation efficiency. Different values of fluence, scanning line spacing and ablation depth were used to assess the effects of each variable on ablation efficiency. Ablation efficiencies for enamel and dentin were maximized at different laser fluences and number of scanning lines and decreased with increases in laser fluence or with increases in scanning line spacing beyond spot diameter or with increases in ablation depth. Laser fluence, scanning line spacing and ablation depth all significantly affected femtosecond laser ablation efficiency. Use of a reasonable control for each of these parameters will improve future clinical application.
Broadband perfect light trapping in the thinnest monolayer graphene-MoS2 photovoltaic cell: the new application of spectrum-splitting structure
Authors: Wu Yun-Ben , Yang Wen , Wang Tong-Biao , Deng Xin-Hua , Liu Jiang-Tao
Published: February 2016

The light absorption of a monolayer graphene-molybdenum disulfide photovoltaic (GM-PV) cell in a wedge-shaped microcavity with a spectrum-splitting structure is investigated theoretically. The GM-PV cell, which is three times thinner than the traditional photovoltaic cell, exhibits up to 98% light absorptance in a wide wavelength range. This rate exceeds the fundamental limit of nanophotonic light trapping in solar cells. The effects of defect layer thickness, GM-PV cell position in the microcavity, incident angle, and lens aberration on the light absorptance of the GM-PV cell are explored. Despite these effects, the GM-PV cell can still achieve at least 90% light absorptance with the current technology. Our proposal provides different methods to design light-trapping structures and apply spectrum-splitting systems.
Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry
Authors: Zhang Wenyang , Yuan Zhiwei , Huang Lulu , Kang Jie , Jiang Ruowei , Zhong Hongying
Published: February 2016

Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.
Integration of lipidomics and transcriptomics unravels aberrant lipid metabolism and defines cholesteryl oleate as potential biomarker of prostate cancer
Authors: Li Jia , Ren Shancheng , Piao Hai-long , Wang Fubo , Yin Peiyuan , Xu Chuanliang , Lu Xin , Ye Guozhu , Shao Yaping , Yan Min , Zhao Xinjie , Sun Yinghao , Xu Guowang
Published: February 2016

In-depth delineation of lipid metabolism in prostate cancer (PCa) is significant to open new insights into prostate tumorigenesis and progression, and provide potential biomarkers with greater accuracy for improved diagnosis. Here, we performed lipidomics and transcriptomics in paired prostate cancer tumor (PCT) and adjacent nontumor (ANT) tissues, followed by external validation of biomarker candidates. We identified major dysregulated pathways involving lipogenesis, lipid uptake and phospholipids remodeling, correlated with widespread lipid accumulation and lipid compositional reprogramming in PCa. Specifically, cholesteryl esters (CEs) were most prominently accumulated in PCa, and significantly associated with cancer progression and metastasis. We showed that overexpressed scavenger receptor class B type I (SR-BI) may contribute to CEs accumulation. In discovery set, CEs robustly differentiated PCa from nontumor (area under curve (AUC) of receiver operating characteristics (ROC), 0.90–0.94). In validation set, CEs potently distinguished PCa and non-malignance (AUC, 0.84–0.91), and discriminated PCa and benign prostatic hyperplasia (BPH) (AUC, 0.90–0.96), superior to serum prostate-specific antigen (PSA) (AUC = 0.83). Cholesteryl oleate showed highest AUCs in distinguishing PCa from non-malignance or BPH (AUC = 0.91 and 0.96). Collectively, our results unravel the major lipid metabolic aberrations in PCa and imply the potential role of CEs, particularly, cholesteryl oleate, as molecular biomarker for PCa detection.
Illuminating necrosis: From mechanistic exploration to preclinical application using fluorescence molecular imaging with indocyanine green
Authors: Fang Cheng , Wang Kun , Zeng Chaoting , Chi Chongwei , Shang Wenting , Ye Jinzuo , Mao Yamin , Fan Yingfang , Yang Jian , Xiang Nan , Zeng Ning , Zhu Wen , Fang Chihua , Tian Jie
Published: February 2016

Tissue necrosis commonly accompanies the development of a wide range of serious diseases. Therefore, highly sensitive detection and precise boundary delineation of necrotic tissue via effective imaging techniques are crucial for clinical treatments; however, no imaging modalities have achieved satisfactory results to date. Although fluorescence molecular imaging (FMI) shows potential in this regard, no effective necrosis-avid fluorescent probe has been developed for clinical applications. Here, we demonstrate that indocyanine green (ICG) can achieve high avidity of necrotic tissue owing to its interaction with lipoprotein (LP) and phospholipids. The mechanism was explored at the cellular and molecular levels through a series of in vitro studies. Detection of necrotic tissue and real-time image-guided surgery were successfully achieved in different organs of different animal models with the help of FMI using in house-designed imaging devices. The results indicated that necrotic tissue with a 0.6 mm diameter could be effectively detected with precise boundary definition. We believe that the new discovery and the associated imaging techniques will improve personalized and precise surgery in the near future.
Satellite gravity gradient grids for geophysics
Authors: Bouman Johannes , Ebbing Jörg , Fuchs Martin , Sebera Josef , Lieb Verena , Szwillus Wolfgang , Haagmans Roger , Novak Pavel
Published: February 2016

The Gravity field and steady-state Ocean Circulation Explorer (GOCE) satellite aimed at determining the Earth’s mean gravity field. GOCE delivered gravity gradients containing directional information, which are complicated to use because of their error characteristics and because they are given in a rotating instrument frame indirectly related to the Earth. We compute gravity gradients in grids at 225 km and 255 km altitude above the reference ellipsoid corresponding to the GOCE nominal and lower orbit phases respectively and find that the grids may contain additional high-frequency content compared with GOCE-based global models. We discuss the gradient sensitivity for crustal depth slices using a 3D lithospheric model of the North-East Atlantic region, which shows that the depth sensitivity differs from gradient to gradient. In addition, the relative signal power for the individual gradient component changes comparing the 225 km and 255 km grids, implying that using all components at different heights reduces parameter uncertainties in geophysical modelling. Furthermore, since gravity gradients contain complementary information to gravity, we foresee the use of the grids in a wide range of applications from lithospheric modelling to studies on dynamic topography and glacial isostatic adjustment, to bedrock geometry determination under ice sheets.
An integrated platform for large-scale data collection and precise perturbation of live Drosophila embryos
Authors: Levario Thomas J. , Zhao Charles , Rouse Tel , Shvartsman Stanislav Y. , Lu Hang
Published: February 2016

Understanding the fundamental principles governing embryogenesis is a key goal of developmental biology. Direct observation of embryogenesis via in vivo live imaging is vital to understanding embryogenesis; yet, tedious sample preparation makes it difficult to acquire large-scale imaging data that is often required to overcome experimental and biological noises for quantitative studies. Furthermore, it is often difficult and sometimes impossible, to incorporate environmental perturbation for understanding developmental responses to external stimuli. To address this issue, we have developed a method for high-throughput imaging of live embryos, delivering precise environmental perturbations and unbiased data extraction. This platform includes an optimized microfluidic device specifically for live embryos and also for precise perturbations in the microenvironment of the developing embryos. In addition, we developed software for simple, yet accurate, automated segmentation of fluorescent images and automated data extraction. Using a quantitative assessment we find that embryos develop normally within the microfluidic device. Finally, we show an application of the high-throughput assay for monitoring developmental responses to external stimuli: anoxia-induced developmental arrest in Drosophila embryos. With slight modifications, the method developed in this work can be applied to many other models of development and other stimulus-response behaviors during development.
Real-time kinetics of electrogenic Na+ transport by rhodopsin from the marine flavobacterium Dokdonia sp. PRO95
Authors: Bogachev Alexander V. , Bertsova Yulia V. , Verkhovskaya Marina L. , Mamedov Mahir D. , Skulachev Vladimir P.
Published: February 2016

Discovery of the light-driven sodium-motive pump Na+-rhodopsin (NaR) has initiated studies of the molecular mechanism of this novel membrane-linked energy transducer. In this paper, we investigated the photocycle of NaR from the marine flavobacterium Dokdonia sp. PRO95 and identified electrogenic and Na+-dependent steps of this cycle. We found that the NaR photocycle is composed of at least four steps: NaR519 + hv → K585 → (L450↔M495) → O585 → NaR519. The third step is the only step that depends on the Na+ concentration inside right-side-out NaR-containing proteoliposomes, indicating that this step is coupled with Na+ binding to NaR. For steps 2, 3, and 4, the values of the rate constants are 4×104 s–1, 4.7 × 103 M–1 s–1, and 150 s–1, respectively. These steps contributed 15, 15, and 70% of the total membrane electric potential (Δψ ~ 200 mV) generated by a single turnover of NaR incorporated into liposomes and attached to phospholipid-impregnated collodion film. On the basis of these observations, a mechanism of light-driven Na+ pumping by NaR is suggested.
Temporal retinal transcriptome and systems biology analysis identifies key pathways and hub genes in Staphylococcus aureus endophthalmitis
Authors: Rajamani Deepa , Singh Pawan Kumar , Rottmann Bruce G. , Singh Natasha , Bhasin Manoj K. , Kumar Ashok
Published: February 2016

Bacterial endophthalmitis remains a devastating inflammatory condition associated with permanent vision loss. Hence, assessing the host response in this disease may provide new targets for intervention. Using a mouse model ofStaphylococcus aureus(SA) endophthalmitis and performing retinal transcriptome analysis, we discovered progressive changes in the expression of 1,234 genes. Gene ontology (GO) and pathway analyses revealed the major pathways impacted in endophthalmitis includes: metabolism, inflammatory/immune, antimicrobial, cell trafficking, and lipid biosynthesis. Among the immune/inflammation pathways, JAK/Stat and IL-17A signaling were the most significantly affected. Interactive network-based analyses identified 13 focus hub genes (IL-6, IL-1β, CXCL2, STAT3, NUPR1, Jun, CSF1, CYR61, CEBPB, IGF-1, EGFR1, SPP1, and TGM2) within these important pathways. The expression of hub genes confirmed by qRT-PCR, ELISA (IL-6, IL-1β, and CXCL2), and Western blot or immunostaining (CEBP, STAT3, NUPR1, and IGF1) showed strong correlation with transcriptome data. Since TLR2 plays an important role in SA endophthalmitis, counter regulation analysis of TLR2 ligand pretreated retina or the use of retinas from TLR2 knockout mice showed the down-regulation of inflammatory regulatory genes. Collectively, our study provides, for the first time, a comprehensive analysis of the transcriptomic response and identifies key pathways regulating retinal innate responses in staphylococcal endophthalmitis.
Comparison of chemometric approaches for near-infrared spectroscopic data
Authors: Yang Liming , Sun Qun
Published: February 2016

Near-infrared (NIR) spectroscopy technology has demonstrated great potential in the analysis of complex samples owing to its simplicity, rapidity and being nondestructive.
Non enzymatic colorimetric detection of glucose using cyanophenyl boronic acid included β-cyclodextrin stabilized gold nanoparticles
Authors: Nair Priya A. , Sreenivasan K.
Published: February 2016

Gold nanoparticles generated and stabilized by a β-cyclodextrin–cyano phenyl boronic acid complex enable the colorimetric detection of glucose.
Expeditious quantitative analysis of λ-cyhalothrin depending on fluorescence quenching of fluorescent surface molecularly imprinted sensors
Authors: Gao Lin , Han Wenjuan , Yan Yongsheng , Li Xiuying , Li Chunxiang , Hu Bo
Published: February 2016

A highly selective and sensitive molecular imprinted polymer sensor suitable for fluorescence detection of cyhalothrin samples has been successfully fabricated via atom transfer radical polymerization.
Reorganization energy and Stokes shift calculations from spectral data as new efficient approaches in distinguishing the end point of micellization/aggregation
Authors: Halder Mintu , Datta Shubhashis , Bolel Priyanka , Mahapatra Niharendu , Panja Sudipta , Vardhan Harsh , Kayal Saurav , Khatua Deb Kumar , Das Ishita
Published: February 2016

Variation of the reorganization energy with surfactant concentrations.
The use of PAMAM dendrimers as a dynamic coating for cyclodextrin mediated enantioseparation of selected basic drugs
Authors: Znaleziona J. , Maier V.
Published: February 2016

A dynamic coating using polyamidoamine (PAMAM) dendrimers was used to change the direction and magnitude of electroosmotic flow.
Development of an analytical method by defining a design space: a case study of saponin determination for Panax notoginseng extracts
Authors: Gong Xingchu , Zhang Ying , Chen Huali , Chen Teng , Pan Jianyang , Wang Xiaoyu , Qu Haibin
Published: February 2016

A reversed-phase HPLC-UV method was developed using a design space approach for the simultaneous determination of five saponins in the extracts of Panax notoginseng, which were notoginsenoside R1, ginsenosides Rg1, Re, Rb1, and Rd.
Raising the (metastable) bar: 100% photo-switching in [Pd(Bu4dien)(η1-N̲O2)]+ approaches ambient temperature
Authors: Hatcher Lauren E.
Published: February 2016

Rapid, fully-reversible photo-switching is observed under near-ambient conditions for the first time in crystals of a novel palladium–nitrite linkage isomer.
Predicting long term cooperativity and specific modulators of receptor interactions in human transferrin from dynamics within a single microstate
Authors: Abdizadeh Haleh , Atilgan Canan
Published: February 2016

PRS identifies regions contacting rapidly evolving residues that mechanically manipulate dissociation from the pathogen in the human transferrin–bacterial receptor complex.
A general and efficient method for the palladium-catalysed conversion of allylic alcohols into their corresponding dienes
Authors: Ostrowski Karoline A. , Vogelsang Dennis , Vorholt Andreas J.
Published: February 2016

A broad range of allylic alcohols underwent palladium-catalysed conversion into their corresponding dienes with water as the sole co-product.
Mononuclear and polynuclear complexes ligated by an iminodiacetic acid derivative: synthesis, structure, solution studies and magnetic properties
Authors: Puentes Roberto , Torres Julia , Kremer Carlos , Cano Joan , Lloret Francesc , Capucci Davide , Bacchi Alessia
Published: February 2016

Two novel families of coordination polymers, [Ln(bzlida)(Hbzlida)]·H2O (Ln = La, Nd) and [Ln2(bzlida)3]·3H2O (Ln = Nd, Sm, Eu, Gd) were prepared by hydrothermal reaction of Ln2O3 with benzyliminodiacetic acid.
High-rate in-plane micro-supercapacitors scribed onto photo paper using in situ femtolaser-reduced graphene oxide/Au nanoparticle microelectrodes
Authors: Li R.-Z. , Peng Rui , Kihm K. D. , Bai S. , Bridges D. , Tumuluri U. , Wu Z. , Zhang T. , Compagnini G. , Feng Z. , Hu A.
Published: February 2016

Direct laser-reduction of graphene oxide (GO), as a lithography-free approach, has been proven effective in manufacturing in-plane micro-supercapacitors (MSCs) with fast ion diffusion.
OH reactivity in urban and suburban regions in Seoul, South Korea – an East Asian megacity in a rapid transition
Authors: Kim Saewung , Sanchez Dianne , Wang Mark , Seco Roger , Jeong Daun , Hughes Stacey , Barletta Barbara , Blake Donald R. , Jung Jinsang , Kim Deugsoo , Lee Gangwoong , Lee Meehye , Ahn Joonyoung , Lee Sang-Deok , Cho Gangnam , Sung Min-Young , Lee Yong-Hwan , Kim Dan Bi , Kim Younha , Woo Jung-Hun , Jo Duseong , Park Rokjin , Park Jeong-Hoo , Hong You-Deog , Hong Ji-Hyung
Published: February 2016

South Korea has recently achieved developed country status with the second largest megacity in the world, the Seoul Metropolitan Area (SMA). This study provides insights into future changes in air quality for rapidly emerging megacities in the East Asian region. We present total OH reactivity observations in the SMA conducted at an urban Seoul site (May–June, 2015) and a suburban forest site (Sep, 2015). The total OH reactivity in an urban site during the daytime was observed at similar levels (∼15 s−1) to those previously reported from other East Asian megacity studies. Trace gas observations indicate that OH reactivity is largely accounted for by NOX (∼50%) followed by volatile organic compounds (VOCs) (∼35%). Isoprene accounts for a substantial fraction of OH reactivity among the comprehensive VOC observational dataset (25–47%). In general, observed total OH reactivity can be accounted for by the observed trace gas dataset. However, observed total OH reactivity in the suburban forest area cannot be largely accounted for (∼70%) by the trace gas measurements. The importance of biogenic VOC (BVOCs) emissions and oxidations used to evaluate the impacts of East Asian megacity outflows for the regional air quality and climate contexts are highlighted in this study.