bluuebunny/crossref_metadata_2025 huggingface dataset:
The Atlantic salmon genome provides insights into rediploidization
Authors: Lien Sigbjørn , Koop Ben F. , Sandve Simen R. , Miller Jason R. , Kent Matthew P. , Nome Torfinn , Hvidsten Torgeir R. , Leong Jong S. , Minkley David R. , Zimin Aleksey , Grammes Fabian , Grove Harald , Gjuvsland Arne , Walenz Brian , Hermansen Russell A. , von Schalburg Kris , Rondeau Eric B. , Di Genova Alex , Samy Jeevan K. A. , Olav Vik Jon , Vigeland Magnus D. , Caler Lis , Grimholt Unni , Jentoft Sissel , Inge Våge Dag , de Jong Pieter , Moen Thomas , Baranski Matthew , Palti Yniv , Smith Douglas R. , Yorke James A. , Nederbragt Alexander J. , Tooming-Klunderud Ave , Jakobsen Kjetill S. , Jiang Xuanting , Fan Dingding , Hu Yan , Liberles David A. , Vidal Rodrigo , Iturra Patricia , Jones Steven J. M. , Jonassen Inge , Maass Alejandro , Omholt Stig W. , Davidson William S.
Published: April 2016

The whole-genome duplication 80 million years ago of the common ancestor of salmonids (salmonid-specific fourth vertebrate whole-genome duplication, Ss4R) provides unique opportunities to learn about the evolutionary fate of a duplicated vertebrate genome in 70 extant lineages. Here we present a high-quality genome assembly for Atlantic salmon (Salmo salar), and show that large genomic reorganizations, coinciding with bursts of transposon-mediated repeat expansions, were crucial for the post-Ss4R rediploidization process. Comparisons of duplicate gene expression patterns across a wide range of tissues with orthologous genes from a pre-Ss4R outgroup unexpectedly demonstrate far more instances of neofunctionalization than subfunctionalization. Surprisingly, we find that genes that were retained as duplicates after the teleost-specific whole-genome duplication 320 million years ago were not more likely to be retained after the Ss4R, and that the duplicate retention was not influenced to a great extent by the nature of the predicted protein interactions of the gene products. Finally, we demonstrate that the Atlantic salmon assembly can serve as a reference sequence for the study of other salmonids for a range of purposes.
Extortion can outperform generosity in the iterated prisoner’s dilemma
Authors: Wang Zhijian , Zhou Yanran , Lien Jaimie W. , Zheng Jie , Xu Bin
Published: April 2016

Zero-determinant (ZD) strategies, as discovered by Press and Dyson, can enforce a linear relationship between a pair of players’ scores in the iterated prisoner’s dilemma. Particularly, the extortionate ZD strategies can enforce and exploit cooperation, providing a player with a score advantage, and consequently higher scores than those from either mutual cooperation or generous ZD strategies. In laboratory experiments in which human subjects were paired with computer co-players, we demonstrate that both the generous and the extortionate ZD strategies indeed enforce a unilateral control of the reward. When the experimental setting is sufficiently long and the computerized nature of the opponent is known to human subjects, the extortionate strategy outperforms the generous strategy. Human subjects’ cooperation rates when playing against extortionate and generous ZD strategies are similar after learning has occurred. More than half of extortionate strategists finally obtain an average score higher than that from mutual cooperation.
Interlayer coupling through a dimensionality-induced magnetic state
Authors: Gibert M. , Viret M. , Zubko P. , Jaouen N. , Tonnerre J.-M. , Torres-Pardo A. , Catalano S. , Gloter A. , Stéphan O. , Triscone J.-M.
Published: April 2016

Dimensionality is known to play an important role in many compounds for which ultrathin layers can behave very differently from the bulk. This is especially true for the paramagnetic metal LaNiO3, which can become insulating and magnetic when only a few monolayers thick. We show here that an induced antiferromagnetic order can be stabilized in the [111] direction by interfacial coupling to the insulating ferromagnet LaMnO3, and used to generate interlayer magnetic coupling of a nature that depends on the exact number of LaNiO3 monolayers. For 7-monolayer-thick LaNiO3/LaMnO3 superlattices, negative and positive exchange bias, as well as antiferromagnetic interlayer coupling are observed in different temperature windows. All three behaviours are explained based on the emergence of a (¼,¼,¼)-wavevector antiferromagnetic structure in LaNiO3 and the presence of interface asymmetry with LaMnO3. This dimensionality-induced magnetic order can be used to tailor a broad range of magnetic properties in well-designed superlattice-based devices.
Fimbrin phosphorylation by metaphase Cdk1 regulates actin cable dynamics in budding yeast
Authors: Miao Yansong , Han Xuemei , Zheng Liangzhen , Xie Ying , Mu Yuguang , Yates John R. , Drubin David G.
Published: April 2016

Actin cables, composed of actin filament bundles nucleated by formins, mediate intracellular transport for cell polarity establishment and maintenance. We previously observed that metaphase cells preferentially promote actin cable assembly through cyclin-dependent kinase 1 (Cdk1) activity. However, the relevant metaphase Cdk1 targets were not known. Here we show that the highly conserved actin filament crosslinking protein fimbrin is a critical Cdk1 target for actin cable assembly regulation in budding yeast. Fimbrin is specifically phosphorylated on threonine 103 by the metaphase cyclin–Cdk1 complex, in vivo and in vitro. On the basis of conformational simulations, we suggest that this phosphorylation stabilizes fimbrin’s N-terminal domain, and modulates actin filament binding to regulate actin cable assembly and stability in cells. Overall, this work identifies fimbrin as a key target for cell cycle regulation of actin cable assembly in budding yeast, and suggests an underlying mechanism.
Signalling couples hair follicle stem cell quiescence with reduced histone H3 K4/K9/K27me3 for proper tissue homeostasis
Authors: Lee Jayhun , Kang Sangjo , Lilja Karin C. , Colletier Keegan J. , Scheitz Cornelia Johanna Franziska , Zhang Ying V. , Tumbar Tudorita
Published: April 2016

Mechanisms of plasticity to acquire different cell fates are critical for adult stem cell (SC) potential, yet are poorly understood. Reduced global histone methylation is an epigenetic state known to mediate plasticity in cultured embryonic SCs and T-cell progenitors. Here we find histone H3 K4/K9/K27me3 levels actively reduced in adult mouse skin and hair follicle stem cells (HFSCs) during G0 quiescence. The level of marks over specific gene promoters did not correlate to mRNA level changes in quiescent HFSCs. Skin hypomethylation during quiescence was necessary for subsequent progression of hair homeostasis (cycle). Inhibiting BMP signal, a known HFSC anti-proliferative factor, elevated HFSC methylation in vivo during quiescence prior to proliferation onset. Furthermore, removal of proliferation factors and addition of BMP4 reduced histone methylases and increased demethylases mRNAs in cultured skin epithelial cells. We conclude that signalling couples hair follicle stem cell quiescence with reduced H3 K4/K9/K27me3 levels for proper tissue homeostasis.
A mutation in the atrial-specific myosin light chain gene (MYL4) causes familial atrial fibrillation
Authors: Orr Nathan , Arnaout Rima , Gula Lorne J. , Spears Danna A. , Leong-Sit Peter , Li Qiuju , Tarhuni Wadea , Reischauer Sven , Chauhan Vijay S. , Borkovich Matthew , Uppal Shaheen , Adler Arnon , Coughlin Shaun R. , Stainier Didier Y. R. , Gollob Michael H.
Published: April 2016

Atrial fibrillation (AF), the most common arrhythmia, is a growing epidemic with substantial morbidity and economic burden. Mechanisms underlying vulnerability to AF remain poorly understood, which contributes to the current lack of highly effective therapies. Recognizing mechanistic subtypes of AF may guide an individualized approach to patient management. Here, we describe a family with a previously unreported syndrome characterized by early-onset AF (age <35 years), conduction disease and signs of a primary atrial myopathy. Phenotypic penetrance was complete in all mutation carriers, although complete disease expressivity appears to be age-dependent. We show that this syndrome is caused by a novel, heterozygous p.Glu11Lys mutation in the atrial-specific myosin light chain gene MYL4. In zebrafish, mutant MYL4 leads to disruption of sarcomeric structure, atrial enlargement and electrical abnormalities associated with human AF. These findings describe the cause of a rare subtype of AF due to a primary, atrial-specific sarcomeric defect.
FNDC4 acts as an anti-inflammatory factor on macrophages and improves colitis in mice
Authors: Bosma Madeleen , Gerling Marco , Pasto Jenny , Georgiadi Anastasia , Graham Evan , Shilkova Olga , Iwata Yasunori , Almer Sven , Söderman Jan , Toftgård Rune , Wermeling Fredrik , Boström Elisabeth Almer , Boström Pontus Almer
Published: April 2016

FNDC4 is a secreted factor sharing high homology with the exercise-associated myokine irisin (FNDC5). Here we report that Fndc4 is robustly upregulated in several mouse models of inflammation as well as in human inflammatory conditions. Specifically, FNDC4 levels are increased locally at inflamed sites of the intestine of inflammatory bowel disease patients. Interestingly, administration of recombinant FNDC4 in the mouse model of induced colitis markedly reduces disease severity compared with mice injected with a control protein. Conversely, mice lacking Fndc4 develop more severe colitis. Analysis of binding of FNDC4 to different immune cell types reveals strong and specific binding to macrophages and monocytes. FNDC4 treatment of bone marrow-derived macrophages in vitro results in reduced phagocytosis, increased cell survival and reduced proinflammatory chemokine expression. Hence, treatment with FNDC4 results in a state of dampened macrophage activity, while enhancing their survival. Thus, we have characterized FNDC4 as a factor with direct therapeutic potential in inflammatory bowel disease and possibly other inflammatory diseases.
Ablating the aryl hydrocarbon receptor (AhR) in CD11c+ cells perturbs intestinal epithelium development and intestinal immunity
Authors: Chng Song Hui , Kundu Parag , Dominguez-Brauer Carmen , Teo Wei Ling , Kawajiri Kaname , Fujii-Kuriyama Yoshiaki , Mak Tak Wah , Pettersson Sven
Published: April 2016

Diet and microbiome derived indole derivatives are known to activate the ligand induced transcription factor, the Aryl hydrocarbon Receptor (AhR). While the current understanding of AhR biology has confirmed its role in mucosal lymphocytes, its function in intestinal antigen presenting cells (APCs) is poorly understood. Here, we report that Cre-mediated deletion of AhR in CD11c-expressing cells in C57/BL6 mice is associated with altered intestinal epithelial morphogenesis in vivo. Moreover, when co-cultured with AhR-deficient DCs ex vivo, intestinal organoids showed reduced SRY (sex determining region Y)-box 9 and increased Mucin 2 expression, which correlates with reduced Paneth cells and increased goblet cell differentiation, similar to the data obtained in vivo. Further, characterization of intestinal APC subsets, devoid of AhR, revealed an expression pattern associated with aberrant intrinsic Wnt pathway regulation. At a functional level, the loss of AhR in APCs resulted in a dysfunctional epithelial barrier, associated with a more aggressive chemically induced colitis compared to wild type animals. Our results are consistent with a model whereby the AhR signalling pathway may participate in the regulation of innate immunity through intestinal epithelium development and mucosal immunity.
ExtraPEG: A Polyethylene Glycol-Based Method for Enrichment of Extracellular Vesicles
Authors: Rider Mark A. , Hurwitz Stephanie N. , Meckes David G.
Published: April 2016

Initially thought to be a means for cells to eliminate waste, secreted extracellular vesicles, known as exosomes, are now understood to mediate numerous healthy and pathological processes. Though abundant in biological fluids, purifying exosomes has been challenging because their biophysical properties overlap with other secreted cell products. Easy-to-use commercial kits for harvesting exosomes are now widely used, but the relative low-purity and high-cost of the preparations restricts their utility. Here we describe a method for purifying exosomes and other extracellular vesicles by adapting methods for isolating viruses using polyethylene glycol. This technique, called ExtraPEG, enriches exosomes from large volumes of media rapidly and inexpensively using low-speed centrifugation, followed by a single small-volume ultracentrifugation purification step. Total protein and RNA harvested from vesicles is sufficient in quantity and quality for proteomics and sequencing analyses, demonstrating the utility of this method for biomarker discovery and diagnostics. Additionally, confocal microscopy studies suggest that the biological activity of vesicles is not impaired. The ExtraPEG method can be easily adapted to enrich for different vesicle populations, or as an efficient precursor to subsequent purification techniques, providing a means to harvest exosomes from many different biological fluids and for a wide variety of purposes.
Quercetin, a Natural Flavonoid Interacts with DNA, Arrests Cell Cycle and Causes Tumor Regression by Activating Mitochondrial Pathway of Apoptosis
Authors: Srivastava Shikha , Somasagara Ranganatha R. , Hegde Mahesh , Nishana Mayilaadumveettil , Tadi Satish Kumar , Srivastava Mrinal , Choudhary Bibha , Raghavan Sathees C.
Published: April 2016

Naturally occurring compounds are considered as attractive candidates for cancer treatment and prevention. Quercetin and ellagic acid are naturally occurring flavonoids abundantly seen in several fruits and vegetables. In the present study, we evaluate and compare antitumor efficacies of quercetin and ellagic acid in animal models and cancer cell lines in a comprehensive manner. We found that quercetin induced cytotoxicity in leukemic cells in a dose-dependent manner, while ellagic acid showed only limited toxicity. Besides leukemic cells, quercetin also induced cytotoxicity in breast cancer cells, however, its effect on normal cells was limited or none. Further, quercetin caused S phase arrest during cell cycle progression in tested cancer cells. Quercetin induced tumor regression in mice at a concentration 3-fold lower than ellagic acid. Importantly, administration of quercetin lead to ~5 fold increase in the life span in tumor bearing mice compared to that of untreated controls. Further, we found that quercetin interacts with DNA directly and could be one of the mechanisms for inducing apoptosis in both, cancer cell lines and tumor tissues by activating the intrinsic pathway. Thus, our data suggests that quercetin can be further explored for its potential to be used in cancer therapeutics and combination therapy.
Single Cell Transfection through Precise Microinjection with Quantitatively Controlled Injection Volumes
Authors: Chow Yu Ting , Chen Shuxun , Wang Ran , Liu Chichi , Kong Chi-wing , Li Ronald A. , Cheng Shuk Han , Sun Dong
Published: April 2016

Cell transfection is a technique wherein foreign genetic molecules are delivered into cells. To elucidate distinct responses during cell genetic modification, methods to achieve transfection at the single-cell level are of great value. Herein, we developed an automated micropipette-based quantitative microinjection technology that can deliver precise amounts of materials into cells. The developed microinjection system achieved precise single-cell microinjection by pre-patterning cells in an array and controlling the amount of substance delivered based on injection pressure and time. The precision of the proposed injection technique was examined by comparing the fluorescence intensities of fluorescent dye droplets with a standard concentration and water droplets with a known injection amount of the dye in oil. Injection of synthetic modified mRNA (modRNA) encoding green fluorescence proteins or a cocktail of plasmids encoding green and red fluorescence proteins into human foreskin fibroblast cells demonstrated that the resulting green fluorescence intensity or green/red fluorescence intensity ratio were well correlated with the amount of genetic material injected into the cells. Single-cell transfection via the developed microinjection technique will be of particular use in cases where cell transfection is challenging and genetically modified of selected cells are desired.
Accurate binning of metagenomic contigs via automated clustering sequences using information of genomic signatures and marker genes
Authors: Lin Hsin-Hung , Liao Yu-Chieh
Published: April 2016

Metagenomics, the application of shotgun sequencing, facilitates the reconstruction of the genomes of individual species from natural environments. A major challenge in the genome recovery domain is to agglomerate or ‘bin’ sequences assembled from metagenomic reads into individual groups. Metagenomic binning without consideration of reference sequences enables the comprehensive discovery of new microbial organisms and aids in the microbial genome reconstruction process. Here we present MyCC, an automated binning tool that combines genomic signatures, marker genes and optional contig coverages within one or multiple samples, in order to visualize the metagenomes and to identify the reconstructed genomic fragments. We demonstrate the superior performance of MyCC compared to other binning tools including CONCOCT, GroopM, MaxBin and MetaBAT on both synthetic and real human gut communities with a small sample size (one to 11 samples), as well as on a large metagenome dataset (over 250 samples). Moreover, we demonstrate the visualization of metagenomes in MyCC to aid in the reconstruction of genomes from distinct bins. MyCC is freely available at http://sourceforge.net/projects/sb2nhri/files/MyCC/.
Universal quantum gates for photon-atom hybrid systems assisted by bad cavities
Authors: Wang Guan-Yu , Liu Qian , Wei Hai-Rui , Li Tao , Ai Qing , Deng Fu-Guo
Published: April 2016

We present two deterministic schemes for constructing a CNOT gate and a Toffoli gate on photon-atom and photon-atom-atom hybrid quantum systems assisted by bad cavities, respectively. They are achieved by cavity-assisted photon scattering and work in the intermediate coupling region with bad cavities, which relaxes the difficulty of their implementation in experiment. Also, bad cavities are feasible for fast quantum operations and reading out information. Compared with previous works, our schemes do not need any auxiliary qubits and measurements. Moreover, the schematic setups for these gates are simple, especially that for our Toffoli gate as only a quarter wave packet is used to interact the photon with each of the atoms every time. These atom-cavity systems can be used as the quantum nodes in long-distance quantum communication as their relatively long coherence time is suitable for multi-time operations between the photon and the system. Our calculations show that the average fidelities and efficiencies of our two universal hybrid quantum gates are high with current experimental technology.
Adsorbing/dissolving Lyoprotectant Matrix Technology for Non-cryogenic Storage of Archival Human Sera
Authors: Solivio Morwena J. , Less Rebekah , Rynes Mathew L. , Kramer Marcus , Aksan Alptekin
Published: April 2016

Despite abundant research conducted on cancer biomarker discovery and validation, to date, less than two-dozen biomarkers have been approved by the FDA for clinical use. One main reason is attributed to inadvertent use of low quality biospecimens in biomarker research. Most proteinaceous biomarkers are extremely susceptible to pre-analytical factors such as collection, processing and storage. For example, cryogenic storage imposes very harsh chemical, physical and mechanical stresses on biospecimens, significantly compromising sample quality. In this communication, we report the development of an electrospun lyoprotectant matrix and isothermal vitrification methodology for non-cryogenic stabilization and storage of liquid biospecimens. The lyoprotectant matrix was mainly composed of trehalose and dextran (and various low concentration excipients targeting different mechanisms of damage) and it was engineered to minimize heterogeneity during vitrification. The technology was validated using five biomarkers; LDH, CRP, PSA, MMP-7 and C3a. Complete recovery of LDH, CRP and PSA levels was achieved post-rehydration while more than 90% recovery was accomplished for MMP-7 and C3a, showing promise for isothermal vitrification as a safe, efficient and low-cost alternative to cryogenic storage.
An Integrative Platform for Three-dimensional Quantitative Analysis of Spatially Heterogeneous Metastasis Landscapes
Authors: Guldner Ian H. , Yang Lin , Cowdrick Kyle R. , Wang Qingfei , Alvarez Barrios Wendy V. , Zellmer Victoria R. , Zhang Yizhe , Host Misha , Liu Fang , Chen Danny Z. , Zhang Siyuan
Published: April 2016

Metastatic microenvironments are spatially and compositionally heterogeneous. This seemingly stochastic heterogeneity provides researchers great challenges in elucidating factors that determine metastatic outgrowth. Herein, we develop and implement an integrative platform that will enable researchers to obtain novel insights from intricate metastatic landscapes. Our two-segment platform begins with whole tissue clearing, staining and imaging to globally delineate metastatic landscape heterogeneity with spatial and molecular resolution. The second segment of our platform applies our custom-developed SMART 3D (Spatial filtering-based background removal and Multi-chAnnel forest classifiers-based 3D ReconsTruction), a multi-faceted image analysis pipeline, permitting quantitative interrogation of functional implications of heterogeneous metastatic landscape constituents, from subcellular features to multicellular structures, within our large three-dimensional (3D) image datasets. Coupling whole tissue imaging of brain metastasis animal models with SMART 3D, we demonstrate the capability of our integrative pipeline to reveal and quantify volumetric and spatial aspects of brain metastasis landscapes, including diverse tumor morphology, heterogeneous proliferative indices, metastasis-associated astrogliosis and vasculature spatial distribution. Collectively, our study demonstrates the utility of our novel integrative platform to reveal and quantify the global spatial and volumetric characteristics of the 3D metastatic landscape with unparalleled accuracy, opening new opportunities for unbiased investigation of novel biological phenomena in situ.
Systematic characterization of seminal plasma piRNAs as molecular biomarkers for male infertility
Authors: Hong Yeting , Wang Cheng , Fu Zheng , Liang Hongwei , Zhang Suyang , Lu Meiling , Sun Wu , Ye Chao , Zhang Chen-Yu , Zen Ke , Shi Liang , Zhang Chunni , Chen Xi
Published: April 2016

Although piwi-interacting RNAs (piRNAs) play pivotal roles in spermatogenesis, little is known about piRNAs in the seminal plasma of infertile males. In this study, we systematically investigated the profiles of seminal plasma piRNAs in infertile males to identify piRNAs that are altered during infertility and evaluate their diagnostic value. Seminal plasma samples were obtained from 211 infertile patients (asthenozoospermia and azoospermia) and 91 fertile controls. High-throughput sequencing technology was employed to screen piRNA profiles in seminal plasma samples pooled from healthy controls and infertile patients. The results identified 61 markedly altered piRNAs in infertile patient groups compared with control group. Next, a quantitative RT-PCR assay was conducted in the training and validation sets to measure and confirm the concentrations of altered piRNAs. The results identified a panel of 5 piRNAs that were significantly decreased in seminal plasma of infertile patients compared with healthy controls. ROC curve analysis and risk score analysis revealed that the diagnostic potential of these 5 piRNAs to distinguish asthenozoospermic and azoospermic individuals from healthy controls was high. In summary, this study identifies a panel of piRNAs that can accurately distinguish fertile from infertile males. This finding may provide pathophysiological clues about the development of infertility.
C/EBPβ-Thr217 Phosphorylation Stimulates Macrophage Inflammasome Activation and Liver Injury
Authors: Buck Martina , Solis-Herruzo Jose , Chojkier Mario
Published: April 2016

Amplification of liver injury is mediated by macrophages but the signaling by which the macrophage inflammasome enhances liver injury is not completely understood. The CCAAT/Enhancer Binding Protein-β (C/EBPβ) is a critical signaling molecule for macrophages because expression of a dominant inhibitor of C/EBPβ DNA-binding sites or a targeted deletion of C/EBPβ results in impaired macrophage differentiation. We reported that expression of the phosphorylation-mutant C/EBPβ-Glu217, which mimics phosphorylated C/EBPβ-Thr217, was sufficient to confer macrophage survival to Anthrax lethal toxin. Here, using primary hepatocytes, primary liver macrophages, dominant positive and negative transgenic mice of the C/EBPβ-Thr217 phosphoacceptor, macrophage ablation and an inhibitory peptide of C/EBPβ-Thr217 phosphorylation, we determined that this phosphorylation is essential for the activation of the inflammasome in liver macrophages and for the hepatocyte apoptosis induced by hepatotoxins that results in liver injury. Similar findings were observed in the livers of patients with acute injury induced by Toxic Oil Syndrome.
Molar concentration from sequential 2-D water-window X-ray ptychography and X-ray fluorescence in hydrated cells
Authors: Jones M. W. M. , Elgass K. D. , Junker M. D. , de Jonge M. D. , van Riessen G. A.
Published: April 2016

Recent developments in biological X-ray microscopy have allowed structural information and elemental distribution to be simultaneously obtained by combining X-ray ptychography and X-ray fluorescence microscopy. Experimentally, these methods can be performed simultaneously; however, the optimal conditions for each measurement may not be compatible. Here, we combine two distinct measurements of ultrastructure and elemental distribution, with each measurement performed under optimised conditions. By combining optimised ptychography and fluorescence information we are able to determine molar concentrations from two-dimensional images, allowing an investigation into the interactions between the environment sensing filopodia in fibroblasts and extracellular calcium. Furthermore, the biological ptychography results we present illustrate a point of maturity where the technique can be applied to solve significant problems in structural biology.
Theory of Thomson scattering in inhomogeneous media
Authors: Kozlowski P. M. , Crowley B. J. B. , Gericke D. O. , Regan S. P. , Gregori G.
Published: April 2016

Thomson scattering of laser light is one of the most fundamental diagnostics of plasma density, temperature and magnetic fields. It relies on the assumption that the properties in the probed volume are homogeneous and constant during the probing time. On the other hand, laboratory plasmas are seldom uniform and homogeneous on the temporal and spatial dimensions over which data is collected. This is particularly true for laser-produced high-energy-density matter, which often exhibits steep gradients in temperature, density and pressure, on a scale determined by the laser focus. Here, we discuss the modification of the cross section for Thomson scattering in fully-ionized media exhibiting steep spatial inhomogeneities and/or fast temporal fluctuations. We show that the predicted Thomson scattering spectra are greatly altered compared to the uniform case, and may lead to violations of detailed balance. Therefore, careful interpretation of the spectra is necessary for spatially or temporally inhomogeneous systems.
Nox Complex signal and MAPK cascade pathway are cross-linked and essential for pathogenicity and conidiation of mycoparasite Coniothyrium minitans
Authors: Wei Wei , Zhu Wenjun , Cheng Jiasen , Xie Jiatao , Jiang Daohong , Li Guoqing , Chen Weidong , Fu Yanping
Published: April 2016

The NADPH oxidase complex of a sclerotial mycoparasite Coniothyrium minitans, an important biocontrol agent against crop diseases caused by Sclerotinia sclerotiorum, was identified and its functions involved in conidiation and mycoparasitism were studied. Gene knock-out and complementary experiments indicated that CmNox1, but not CmNox2, is necessary for conidiation and parasitism, and its expression could be significantly induced by its host fungus. CmNox1 is regulated by CmRac1-CmNoxR and interacts with CmSlt2, a homolog of Saccharomyces cerevisiae Slt2 encoding cell wall integrity-related MAP kinase. In ΔCmNox1, CmSlt2-GFP fusion protein lost the ability to localize to the cell nucleus accurately. The defect of conidiation in ΔCmRac1 could be partially restored by over-expressing CmSlt2, indicating that CmSlt2 was a downstream regulatory factor of CmNox1 and was involved in conidiation and parasitism. The expressions of mycoparasitism-related genes CmPks1, Cmg1 and CH1 were suppressed in the knock-out mutants of the genes in CmNox1-CmSlt2 signal pathway when cultivated either on PDA. Therefore, our study infers that CmRac1-CmNoxR regulates CmNox1-CmSlt2 pathway in regulating conidiation and pathogenicity of C. minitans.
Matrine displayed antiviral activity in porcine alveolar macrophages co-infected by porcine reproductive and respiratory syndrome virus and porcine circovirus type 2
Authors: Sun Na , Sun Panpan , Lv Haipeng , Sun Yaogui , Guo Jianhua , Wang Zhirui , Luo Tiantian , Wang Shaoyu , Li Hongquan
Published: April 2016

The co-infection of porcine reproductive respiratory syndrome virus (PRRSV) and porcine circovirus type 2 (PCV2) is quite common in clinical settings and no effective treatment to the co-infection is available. In this study, we established the porcine alveolar macrophages (PAM) cells model co-infected with PRRSV/PCV2 with modification in vitro, and investigated the antiviral activity of Matrine on this cell model and further evaluated the effect of Matrine on virus-induced TLR3,4/NF-κB/TNF-α pathway. The results demonstrated PAM cells inoculated with PRRSV followed by PCV2 2 h later enhanced PRRSV and PCV2 replications. Matrine treatment suppressed both PRRSV and PCV2 infection at 12 h post infection. Furthermore, PRRSV/PCV2 co- infection induced IκBα degradation and phosphorylation as well as the translocation of NF-κB from the cytoplasm to the nucleus indicating that PRRSV/PCV2 co-infection induced NF-κB activation. Matrine treatment significantly down-regulated the expression of TLR3, TLR4 and TNF-α although it, to some extent, suppressed p-IκBα expression, suggesting that TLR3,4/NF-κB/TNF-α pathway play an important role of Matrine in combating PRRSV/PCV2 co-infection. It is concluded that Matrine possesses activity against PRRSV/PCV2 co-infection in vitro and suppression of the TLR3,4/NF-κB/TNF-α pathway as an important underlying molecular mechanism. These findings warrant Matrine to be further explored for its antiviral activity in clinical settings.
Genipin cross-linked decellularized tracheal tubular matrix for tracheal tissue engineering applications
Authors: Sun Fei , Jiang Yuan , Xu Yanfei , Shi Hongcan , Zhang Siquan , Liu Xingchen , Pan Shu , Ye Gang , Zhang Weidong , Zhang Fangbiao , Zhong Chonghao
Published: April 2016

Decellularization techniques have been widely used as an alternative strategy for organ reconstruction. This study investigated the mechanical, pro-angiogenic and in vivo biocompatibility properties of decellularized airway matrices cross-linked with genipin. New Zealand rabbit tracheae were decellularized and cross-linked with genipin, a naturally derived agent. The results demonstrated that, a significant (p < 0.05) increase in the secant modulus was computed for the cross-linked tracheae, compared to the decellularized samples. Angiogenic assays demonstrated that decellularized tracheal scaffolds and cross-linked tracheae treated with 1% genipin induce strong in vivo angiogenic responses (CAM analysis). Seven, 15 and 30 days after implantation, decreased (p < 0.01) inflammatory reactions were observed in the xenograft models for the genipin cross-linked tracheae matrices compared with control tracheae and no increase in the IgM or IgG content was observed in rats. In conclusion, treatment with genipin improves the mechanical properties of decellularized airway matrices without altering the pro-angiogenic properties or eliciting an in vivo inflammatory response.
Functional traits help to explain half-century long shifts in pollinator distributions
Authors: Aguirre-Gutiérrez Jesús , Kissling W. Daniel , Carvalheiro Luísa G. , WallisDeVries Michiel F. , Franzén Markus , Biesmeijer Jacobus C.
Published: April 2016

Changes in climate and land use can have important impacts on biodiversity. Species respond to such environmental modifications by adapting to new conditions or by shifting their geographic distributions towards more suitable areas. The latter might be constrained by species’ functional traits that influence their ability to move, reproduce or establish. Here, we show that functional traits related to dispersal, reproduction, habitat use and diet have influenced how three pollinator groups (bees, butterflies and hoverflies) responded to changes in climate and land-use in the Netherlands since 1950. Across the three pollinator groups, we found pronounced areal range expansions (>53%) and modelled range shifts towards the north (all taxa: 17–22 km), west (bees: 14 km) and east (butterflies: 11 km). The importance of specific functional traits for explaining distributional changes varied among pollinator groups. Larval diet preferences (i.e. carnivorous vs. herbivorous/detritivorous and nitrogen values of host plants, respectively) were important for hoverflies and butterflies, adult body size for hoverflies and flight period length for all groups. Moreover, interactions among multiple traits were important to explain species’ geographic range shifts, suggesting that taxon-specific multi-trait analyses are needed to predict how global change will affect biodiversity and ecosystem services.
Facile fabrication of properties-controllable graphene sheet
Authors: Choi Jin Sik , Choi Hongkyw , Kim Ki-Chul , Jeong Hu Young , Yu Young-Jun , Kim Jin Tae , Kim Jin-Soo , Shin Jin-Wook , Cho Hyunsu , Choi Choon-Gi
Published: April 2016

Graphene has been received a considerable amount of attention as a transparent conducting electrode (TCE) which may be able to replace indium tin oxide (ITO) to overcome the significant weakness of the poor flexibility of ITO. Given that graphene is the thinnest 2-dimensional (2D) material known, it shows extremely high flexibility, and its lateral periodic honeycomb structure of sp2-bonded carbon atoms enables ~2.3% of incident light absorption per layer. However, there is a trade-off between the electrical resistance and the optical transmittance, and the fixed absorption rate in graphene limits is use when fabricating devices. Therefore, a more efficient method which continuously controls the optical and electrical properties of graphene is needed. Here, we introduce a method which controls the optical transmittance and the electrical resistance of graphene through various thicknesses of the top Cu layers with a Cu/Ni metal catalyst structure used to fabricate a planar mesh pattern of single and multi-layer graphene. We exhibit a continuous transmittance change from 85% (MLG) to 97.6% (SLG) at an incident light wavelength of 550 nm on graphene samples simultaneously grown in a CVD quartz tube. We also investigate the relationships between the sheet resistances.
Simultaneous Determination of Size and Quantification of Gold Nanoparticles by Direct Coupling Thin layer Chromatography with Catalyzed Luminol Chemiluminescence
Authors: Yan Neng , Zhu Zhenli , He Dong , Jin Lanlan , Zheng Hongtao , Hu Shenghong
Published: April 2016

The increasing use of metal-based nanoparticle products has raised concerns in particular for the aquatic environment and thus the quantification of such nanomaterials released from products should be determined to assess their environmental risks. In this study, a simple, rapid and sensitive method for the determination of size and mass concentration of gold nanoparticles (AuNPs) in aqueous suspension was established by direct coupling of thin layer chromatography (TLC) with catalyzed luminol-H2O2 chemiluminescence (CL) detection. For this purpose, a moving stage was constructed to scan the chemiluminescence signal from TLC separated AuNPs. The proposed TLC-CL method allows the quantification of differently sized AuNPs (13 nm, 41 nm and 100 nm) contained in a mixture. Various experimental parameters affecting the characterization of AuNPs, such as the concentration of H2O2, the concentration and pH of the luminol solution, and the size of the spectrometer aperture were investigated. Under optimal conditions, the detection limits for AuNP size fractions of 13 nm, 41 nm and 100 nm were 38.4 μg L−1, 35.9 μg L−1 and 39.6 μg L−1, with repeatabilities (RSD, n = 7) of 7.3%, 6.9% and 8.1% respectively for 10 mg L−1 samples. The proposed method was successfully applied to the characterization of AuNP size and concentration in aqueous test samples.
The combination of three molecular markers can be a valuable predictive tool for the prognosis of hepatocellular carcinoma patients
Authors: Chen Sheng-Sen , Yu Kang-Kang , Ling Qing-Xia , Huang Chong , Li Ning , Zheng Jian-Ming , Bao Su-Xia , Cheng Qi , Zhu Meng-Qi , Chen Ming-Quan
Published: April 2016

Based on molecular profiling, several prognostic markers for HCC are also used in clinic, but only a few genes have been identified as useful. We collected 72 post-operative liver cancer tissue samples. Genes expression were tested by RT-PCR. Multilayer perceptron and discriminant analysis were built and their ability to predict the prognosis of HCC patients were tested. Receiver operating characteristic (ROC) analysis was performed and multivariate analysis with Cox’s Proportional Hazard Model was used for confirming the markers’predictive efficiency for HCC patients’survival. A simple risk scoring system devised for further predicting the prognosis of liver tumor patients. Multilayer perceptron and discriminant analysis showed a very strong predictive value in evaluating liver cancer patients’prognosis. Cox multivariate regression analysis demonstrated that DUOX1, GLS2, FBP1 and age were independent risk factors for the prognosis of HCC patients after surgery. Finally, the risk scoring system revealed that patients whose total score >1 and >3 are more likely to relapse and die than patients whose total score ≤1 and ≤3. The three genes model proposed proved to be highly predictive of the HCC patients’ prognosis. Implementation of risk scoring system in clinical practice can help in evaluating survival of HCC patients after operation.
Cage-bell Pt-Pd nanostructures with enhanced catalytic properties and superior methanol tolerance for oxygen reduction reaction
Authors: Chen Dong , Ye Feng , Liu Hui , Yang Jun
Published: April 2016

Precisely tailoring the structure and fully making use of the components of nanoparticles are effective to enhance their catalytic performance for a given reaction. We herein demonstrate the design of cage-bell structured Pt-Pd nanoparticles, where a Pd shell is deliberately selected to enhance the catalytic property and methanol tolerance of Pt for oxygen reduction reaction. This strategy starts with the synthesis of core-shell Pt@Ag nanoparticles, followed by galvanic replacement reaction between the Ag shell and Pd2+ ions to form core-shell-shell Pt@Ag@Ag-Pd nanoparticles with a Pt core and double shells composed of Ag at inner and alloy Ag-Pd at outer, respectively. Then, the core-shell-shell templates are agitated with saturated NaCl solution to eliminate the Ag component from the double shells, leading to the formation of bimetallic Pt-Pd nanoparticles with a cage-bell structure, defined as a movable Pt core enclosed by a porous Pd shell, which show enhanced catalytic activity for oxygen reduction compared with that of the Pt seeds due to the additional catalysis from Pd shell. In addition, owing to the different diffusion behavior of methanol and oxygen molecules in the porous Pd shell, the Pt-Pd cage-bell nanostructures also exhibit superior methanol tolerant property in catalyzing the oxygen reduction.
A new strategy to prepare giant vesicles from surface active ionic liquids (SAILs): a study of protein dynamics in a crowded environment using a fluorescence correlation spectroscopic technique
Authors: Banerjee Chiranjib , Roy Arpita , Kundu Niloy , Banik Debasis , Sarkar Nilmoni
Published: April 2016

A simple procedure for the preparation of giant vesicles using surface active ionic liquids (SAILs) has been provided in this paper.
Synthesis and evaluation of the sensitivity and vibrational lifetimes of thiocyanate and selenocyanate infrared reporters
Authors: Levin Daniel E. , Schmitz Andrew J. , Hines Shawn M. , Hines Kevin J. , Tucker Matthew J. , Brewer Scott H. , Fenlon Edward E.
Published: April 2016

Infrared spectroscopy demonstrates that thiocyanate and selenocyanate groups are sensitive reporters with vibrational lifetimes in the 100–300 ps range.
N-Heterocyclic carbene-catalyzed desymmetrization of functionalized 1,4-dienes via Stetter Reaction
Authors: Lin Qiqiao , Li Yuanzhen , Das Deb Kumar , Zhang Guoxiang , Zhao Zhifei , Yang Shuang , Fang Xinqiang
Published: April 2016

The asymmetric desymmetrization of 1,4-dienesviachiral N-heterocyclic carbene catalyzed Stetter-type umpolung reaction was demonstrated.
Fluorescent supracolloidal polymer chains with quantum dots
Authors: Chae Seungyong , Lee Sanghwa , Kim Kyungtae , Jang Suk Woo , Sohn Byeong-Hyeok
Published: April 2016

We demonstrate the fabrication of fluorescent supracolloidal chains functionalized with quantum dots, which were polymerized from patched micelles of diblock copolymers by adjusting the polarity of the solvent. Supracolloidal random and block chains with green- and red-emitting quantum dots were also synthesized.
A switchable dual organocatalytic system and the enantioselective total synthesis of the quadrane sesquiterpene suberosanone
Authors: Ren Yajun , Presset Marc , Godemert Jeremy , Vanthuyne Nicolas , Naubron Jean-Valère , Giorgi Michel , Rodriguez Jean , Coquerel Yoann
Published: April 2016

Switch it! The combination of aminocatalysis and N-heterocyclic carbene catalysis has been extended to a switchable dual catalytic system.
Gold and diazo reagents: a fruitful tool for developing molecular complexity
Authors: Fructos Manuel R. , Díaz-Requejo M. Mar , Pérez Pedro J.
Published: April 2016

After a decade since its discovery and being yet at its sunrise, the use of gold catalysis for the transfer of carbene groups from diazo compounds is becoming a powerful synthetic tool. The main advances in the area and future directions are provided in thisFeature Article.
Photoenergy storage and power amplification strategy in membrane-less photoelectrochemical biofuel cells
Authors: Yu You , Xu Miao , Dong Shaojun
Published: April 2016

We proposed a novel integrated PBFC by insetting a third electrode with high efficiency energy storage and release between the bioelectrode and the photoelectrode, resulting in a higher power output than that of the original PBFC.
Bis-phosphine allene ligand: coordination chemistry and preliminary applications in catalysis
Authors: Vanitcha Avassaya , Damelincourt Cecilia , Gontard Geoffrey , Vanthuyne Nicolas , Mouriès-Mansuy Virginie , Fensterbank Louis
Published: April 2016

A 1,3-bis-diphenylphosphine allene provided new coordination complexes with palladium, platinum and gold salts. The dinuclear gold(i) complex gave promising results in asymmetric catalysis.
Enantiopure phosphonic acids as chiral inducers: homochiral crystallization of cobalt coordination polymers showing field-induced slow magnetization relaxation
Authors: Feng Jian-Shen , Ren Min , Cai Zhong-Sheng , Fan Kun , Bao Song-Song , Zheng Li-Min
Published: April 2016

Homochiral crystallization of (M)- or (P)-Co(SO4)(1,3-bbix)(H2O)3 (1M or 1P) from an achiral precursor is achieved in the presence of a catalytic amount of (S)- or (R)-3-phenyl-2-((phosphonomethyl)amino) propanoic acid.
Hydrophilic Pt nanoflowers: synthesis, crystallographic analysis and catalytic performance
Authors: Mourdikoudis Stefanos , Altantzis Thomas , Liz-Marzán Luis M. , Bals Sara , Pastoriza-Santos Isabel , Pérez-Juste Jorge
Published: April 2016

A 3D-tomography reconstructed image of a water-soluble Pt nanoflower, synthesized in diethyleneglycol in the presence of PEI.
Use of the PIXEL method to investigate gas adsorption in metal–organic frameworks
Authors: Maloney Andrew G. P. , Wood Peter A. , Parsons Simon
Published: April 2016

The PIXEL method can be applied to MOFs, yielding binding energies and optimised guest locations similar to more costly DFT calculations.
Synthesis of barbituric acid containing nucleotides and their implications for the origin of primitive informational polymers
Authors: Mungi Chaitanya V. , Singh Sachin Kumar , Chugh Jeetender , Rajamani Sudha
Published: April 2016

Nucleotides containing barbituric acid were synthesized and polymerized under prebiotically relevant conditions. This study demonstrates the plausibility of the emergence of primitive informational polymers from ribonucleotides with alternate heterocycles.
Photoactive bile salts with critical micellar concentration in the micromolar range
Authors: Gomez-Mendoza Miguel , Marin M. Luisa , Miranda Miguel A.
Published: April 2016

The aggregation behavior of bile salts is strongly dependent on the number of hydroxyl groups.
Analysis of constant tension-induced rupture of lipid membranes using activation energy
Authors: Karal Mohammad Abu Sayem , Levadnyy Victor , Yamazaki Masahito
Published: April 2016

Experimentally determined activation energy explains the tension dependence of the rate constant of tension-induced rupture of charged and neutral lipid membranes.
Enhanced photoelectrochemical performance of quantum dot-sensitized TiO2 nanotube arrays with Al2O3 overcoating by atomic layer deposition
Authors: Zeng Min , Peng Xiange , Liao Jianjun , Wang Guizhen , Li Yanfang , Li Jianbao , Qin Yong , Wilson Joshua , Song Aimin , Lin Shiwei
Published: April 2016

Conformal Al2O3 overcoating by ALD can drastically enhance the PEC performance of quantum dot-sensitized TiO2 nanotube arrays.
Heads or tails: how do chemically substituted fullerenes melt?
Authors: Armstrong Jeff , Mukhopadhyay Sanghamitra , Bresme Fernando , Fernandez-Alonso Felix
Published: April 2016

The melting of the substituted fullerene PCBM is driven by the tail, not the head.
A complex-polarization-propagator protocol for magneto-chiral axial dichroism and birefringence dispersion
Authors: Cukras Janusz , Kauczor Joanna , Norman Patrick , Rizzo Antonio , Rikken Geert L. J. A. , Coriani Sonia
Published: April 2016

A schematic representation of magneto-chiral effects.
Incorporation of Mn into the vacant T-atom sites of a BEA zeolite as isolated, mononuclear Mn: FTIR, XPS, EPR and DR UV-Vis studies
Authors: Baran R. , Valentin L. , Dzwigaj S.
Published: April 2016

A MnSiBEA zeolite has been prepared via a two-step postsynthesis procedure which consisted, in the first step, of the treatment of a tetraethylammonium BEA zeolite with nitric acid for the formation of vacant T-atom sites and then, in the second step, of the incorporation of Mn ions into the framework, resulting in a SiBEA zeolite, through their reaction with the silanol group of the vacant T-atom sites.
High catalytic activity of mesoporous Co–N/C catalysts for aerobic oxidative synthesis of nitriles
Authors: Shang Sensen , Wang Lianyue , Dai Wen , Chen Bo , Lv Ying , Gao Shuang
Published: April 2016

We report the synthesis and assessment of novel mesoporous cobalt-coordinated nitrogen-doped carbon catalysts (meso-Co–N/C) for highly efficient synthesis of nitriles.