bluuebunny/crossref_metadata_2025 huggingface dataset:
Life is hard: countering definitional pessimism concerning the definition of life
Authors: Smith Kelly C.
Published: September 2016

Cleland and Chyba published a classic piece in 2002 that began a movement I calldefinitional pessimism,where it is argued that there is no point in attempting anything like a general definition of life. This paper offers a critical response to the pessimist position in general and the influential arguments offered by Cleland and her collaborators in particular. One such argument is that all definitions of life fall short of an ideal in which necessary and sufficient conditions produce unambiguous categorizations that dispose of all counterexamples. But this concept of definition is controversial within philosophy; a fact that greatly diminishes the force of the admonition that biologists should conform to such an ideal. Moreover, biology may well be fundamentally different from logic and the physical sciences from which this ideal is drawn, to the point where definitional conformitymisrepresentsbiological reality. Another idea often pushed is that the prospects for definitional success concerning life are on a par with medieval alchemy's attempts to define matter – that is, doomed to fail for lack of a unifying scientific theory. But this comparison to alchemy is both historically inaccurate and unfair. Planetary science before the discovery of the first exoplanets offers a much better analogy, with much more optimistic conclusions. The pessimists also make much of the desirability of using microbes as models for any universal concept of life, from which they conclude that certain types of ‘Darwinian’ evolutionary definitions are inadequate. But this argument posits an unrealistic ideal, as no account of life can both be universal and do justice to the sorts of precise causal mechanisms microbes exemplify. The character of biology and the demand for universality in definitions of life thus probably accords better with functional rather than structural categories. The bottom line is that there is simply no viablealternative,either pragmatically or theoretically, to the pursuit of definitions. If nothing else, the empirical data the pessimists demand will be a very long time coming and scientists will of necessity continue to employ definitions of life in the interim. Chastising them for this will only drive their ideas underground where they can escape critical analysis, making the problems caused by problematic conceptions of life worse.
European Communities – Definitive Anti-Dumping Measures on Certain Iron or Steel Fasteners from China – Recourse to Article 21.5 of the DSU by China (EC–Fasteners (China) (Article 21.5–China), DS397)
Authors: Carlson Geoffrey
Published: September 2016

This compliance proceeding under Article 21.5 of the Dispute Settlement Understanding (DSU) concerned measures taken by the European Union to implement the recommendations and rulings of the Dispute Settlement Body (DSB) in EC–Fasteners (China). In EC–Fasteners (China), the DSB found, inter alia, that a European Communities measure imposing definitive antidumping duties on imports of certain iron or steel fasteners from China was inconsistent with certain aspects of the Anti-Dumping Agreement (ADA). The European Union's measures taken to comply with the recommendations and rulings of the DSB consisted, inter alia, of an anti-dumping review investigation regarding fasteners from China (the Review Investigation) conducted by the Commission of the European Union (the Commission). The conduct of the Commission in the Review Investigation was the focus of this compliance proceeding.
Climate Change May Reduce Future Corn Supply
Authors: Stanley Sarah
Published: September 2016

A suite of simulations run with a spectrum of starting conditions shows that climate change will reduce corn crop yield, although the degree of reductions varies widely.
Crystal nuclei templated nanostructured membranes prepared by solvent crystallization and polymer migration
Authors: Wang Bo , Ji Jing , Li Kang
Published: September 2016

Currently, production of porous polymeric membranes for filtration is predominated by the phase-separation process. However, this method has reached its technological limit, and there have been no significant breakthrough over the last decade. Here we show, using polyvinylidene fluoride as a sample polymer, a new concept of membrane manufacturing by combining oriented green solvent crystallization and polymer migration is able to obtain high performance membranes with pure water permeation flux substantially higher than those with similar pore size prepared by conventional phase-separation processes. The new manufacturing procedure is governed by fewer operating parameters and is, thus, easier to control with reproducible results. Apart from the high water permeation flux, the prepared membranes also show excellent stable flux after fouling and superior mechanical properties of high pressure load and better abrasion resistance. These findings demonstrate the promise of a new concept for green manufacturing nanostructured polymeric membranes with high performances.
Local microRNA delivery targets Palladin and prevents metastatic breast cancer
Authors: Gilam Avital , Conde João , Weissglas-Volkov Daphna , Oliva Nuria , Friedman Eitan , Artzi Natalie , Shomron Noam
Published: September 2016

Metastasis is the primary cause for mortality in breast cancer. MicroRNAs, gene expression master regulators, constitute an attractive candidate to control metastasis. Here we show that breast cancer metastasis can be prevented by miR-96 or miR-182 treatment, and decipher the mechanism of action. We found that miR-96/miR-182 downregulate Palladin protein levels, thereby reducing breast cancer cell migration and invasion. A common SNP, rs1071738, at the miR-96/miR-182-binding site within the Palladin 3′-UTR abolishes miRNA:mRNA binding, thus diminishing Palladin regulation by these miRNAs. Regulation is successfully restored by applying complimentary miRNAs. A hydrogel-embedded, gold-nanoparticle-based delivery vehicle provides efficient local, selective, and sustained release of miR-96/miR-182, markedly suppressing metastasis in a breast cancer mouse model. Combined delivery of the miRNAs with a chemotherapy drug, cisplatin, enables significant primary tumour shrinkage and metastasis prevention. Our data corroborate the role of miRNAs in metastasis, and suggest miR-96/miR-182 delivery as a potential anti-metastatic drug.
Genome-directed analysis of prophage excision, host defence systems, and central fermentative metabolism in Clostridium pasteurianum
Authors: Pyne Michael E. , Liu Xuejia , Moo-Young Murray , Chung Duane A. , Chou C. Perry
Published: September 2016

Clostridium pasteurianum is emerging as a prospective host for the production of biofuels and chemicals, and has recently been shown to directly consume electric current. Despite this growing biotechnological appeal, the organism’s genetics and central metabolism remain poorly understood. Here we present a concurrent genome sequence for the C. pasteurianum type strain and provide extensive genomic analysis of the organism’s defence mechanisms and central fermentative metabolism. Next generation genome sequencing produced reads corresponding to spontaneous excision of a novel phage, designated φ6013, which could be induced using mitomycin C and detected using PCR and transmission electron microscopy. Methylome analysis of sequencing reads provided a near-complete glimpse into the organism’s restriction-modification systems. We also unveiled the chief C. pasteurianum Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) locus, which was found to exemplify a Type I-B system. Finally, we show that C. pasteurianum possesses a highly complex fermentative metabolism whereby the metabolic pathways enlisted by the cell is governed by the degree of reductance of the substrate. Four distinct fermentation profiles, ranging from exclusively acidogenic to predominantly alcohologenic, were observed through redox consideration of the substrate. A detailed discussion of the organism’s central metabolism within the context of metabolic engineering is provided.
Assimilation of virtual legs and perception of floor texture by complete paraplegic patients receiving artificial tactile feedback
Authors: Shokur Solaiman , Gallo Simone , Moioli Renan C. , Donati Ana Rita C. , Morya Edgard , Bleuler Hannes , Nicolelis Miguel A.L.
Published: September 2016

Spinal cord injuries disrupt bidirectional communication between the patient’s brain and body. Here, we demonstrate a new approach for reproducing lower limb somatosensory feedback in paraplegics by remapping missing leg/foot tactile sensations onto the skin of patients’ forearms. A portable haptic display was tested in eight patients in a setup where the lower limbs were simulated using immersive virtual reality (VR). For six out of eight patients, the haptic display induced the realistic illusion of walking on three different types of floor surfaces: beach sand, a paved street or grass. Additionally, patients experienced the movements of the virtual legs during the swing phase or the sensation of the foot rolling on the floor while walking. Relying solely on this tactile feedback, patients reported the position of the avatar leg during virtual walking. Crossmodal interference between vision of the virtual legs and tactile feedback revealed that patients assimilated the virtual lower limbs as if they were their own legs. We propose that the addition of tactile feedback to neuroprosthetic devices is essential to restore a full lower limb perceptual experience in spinal cord injury (SCI) patients, and will ultimately, lead to a higher rate of prosthetic acceptance/use and a better level of motor proficiency.
Determination by near infrared microscopy of the nitrogen and carbon content of tomato (Solanum lycopersicum L.) leaf powder
Authors: Lequeue Gauthier , Draye Xavier , Baeten Vincent
Published: September 2016

Near infrared microscopy (NIRM) has been developed as a rapid technique to predict the chemical composition of foods, reduce analytical costs and time and ease sample preparation. In this study, NIRM has been evaluated as an alternative to classical chemical analysis to determine the nitrogen and carbon content of small samples of tomato (Solanum lycopersicum L.) leaf powder. Near infrared spectra were obtained by NIRM for independent leaf samples collected on 216 plants grown under six different levels of nitrogen. From these, 30 calibration and 30 validation samples covering the spectral range of the whole set were selected and their nitrogen and carbon contents were determined by a reference method. The calibration model obtained for nitrogen content proved to be excellent, with a coefficient of determination in calibration (R2c) higher than 0.9 and a ratio of performance to deviation (RPDc) higher than 3. Statistical indicators of prediction using the validation set were also very high (R2p values > 0.90). However, the calibration model obtained for carbon content was much less satisfactory (R2c < 0.50). NIRM appears as a promising and suitable tool for a rapid, non-destructive and reliable determination of nitrogen content of tiny samples of tomato leaf powder.
PAH contamination in Beijing’s topsoil: A unique indicator of the megacity’s evolving energy consumption and overall environmental quality
Authors: Li Jinguo , Zheng Yi , Luo Xiaolin , Lin Zhongrong , Zhang Wei , Wang Xuejun
Published: September 2016

To improve its air quality, Beijing, the capital of China, has implemented high-cost pollution control measures mainly focused on shifting its energy mix. However, the effectiveness of these measures has long been questioned, especially given the recent problem of severe haze. The main study objectives are to achieve independent, although indirect, information on Beijing’s air pollution by measuring the level of polycyclic aromatic hydrocarbon (PAH) contamination in topsoil and to examine how soil contamination reflects energy consumption. Soil sampling data from two years, 2004 and 2013, were used. The key findings are as follows: 1) although the total PAH content in the topsoil did not significantly decrease from 2004 to 2013, the composition changed considerably; 2) as of 2013, vehicle emissions replaced coal combustion as the leading source of soil PAHs, which validates the existing policy measures regarding vehicle purchasing and traffic volume; 3) the regional transport of atmospheric pollutants, as indicated by the contribution of coking sources in 2013, is not negligible; and 4) appropriate policy measures are needed to control the growing practice of burning biomass. Overall, this study demonstrates that the PAH contamination in topsoil represents an informative indicator of Beijing’s energy consumption and overall environmental quality.
Investigation of rare and low-frequency variants using high-throughput sequencing with pooled DNA samples
Authors: Wang Jingwen , Skoog Tiina , Einarsdottir Elisabet , Kaartokallio Tea , Laivuori Hannele , Grauers Anna , Gerdhem Paul , Hytönen Marjo , Lohi Hannes , Kere Juha , Jiao Hong
Published: September 2016

High-throughput sequencing using pooled DNA samples can facilitate genome-wide studies on rare and low-frequency variants in a large population. Some major questions concerning the pooling sequencing strategy are whether rare and low-frequency variants can be detected reliably, and whether estimated minor allele frequencies (MAFs) can represent the actual values obtained from individually genotyped samples. In this study, we evaluated MAF estimates using three variant detection tools with two sets of pooled whole exome sequencing (WES) and one set of pooled whole genome sequencing (WGS) data. Both GATK and Freebayes displayed high sensitivity, specificity and accuracy when detecting rare or low-frequency variants. For the WGS study, 56% of the low-frequency variants in Illumina array have identical MAFs and 26% have one allele difference between sequencing and individual genotyping data. The MAF estimates from WGS correlated well (r = 0.94) with those from Illumina arrays. The MAFs from the pooled WES data also showed high concordance (r = 0.88) with those from the individual genotyping data. In conclusion, the MAFs estimated from pooled DNA sequencing data reflect the MAFs in individually genotyped samples well. The pooling strategy can thus be a rapid and cost-effective approach for the initial screening in large-scale association studies.
Evaluation of Glutathione Peroxidase 4 role in Preeclampsia
Authors: Peng Xinguo , Lin Yan , Li Jinling , Liu Mengchun , Wang Jingli , Li Xueying , Liu Jingjing , Jia Xuewen , Jing Zhongcui , Huang Zuzhou , Chu Kaiqiu , Liu Shiguo
Published: September 2016

Preeclampsia (PE) is a pregnancy-specific syndrome that may be lifethreatening to pregnancies and fetus. Glutathione Peroxidase 4 (GPx4) is a powerful antioxidant enzyme that can provide protection from oxidative stress damage which plays a pivotal role in the pathology of PE. Therefore, this study aims to investigate the association between Gpx4 polymorphisms and the susceptibility to PE in Chinese Han women. TaqMan allelic discrimination real-time PCR was used to perform the genotyping of rs713041 and rs4807542 in 1008 PE patients and 1386 normotensive pregnancies. Obviously statistical difference of genotypic and allelic frequencies were found of rs713041 in GPx4 between PE patients and controls and the C allele has the higher risk for pathogenesis of PE (χ2 = 12.292, P = 0.002 by genotype; χ2 = 11.035, P = 0.001, OR = 1.216, 95% CI 1.084–1.365 by allele). Additionally, when subdividing these samples into CC + CT and TT groups, we found a significant difference between the two groups (χ2 = 11.241, P = 0.001, OR = 1.417, 95% CI 1.155–1.738). Furthermore, the genotype of rs713041 was found to be associated with the mild, severe and early-onset PE. Our results suggest that rs713041 in GPx4 may play a key role in the pathogenesis of PE.
Amino-Fe3O4 Microspheres Directed Synthesis of a Series of Polyaniline Hierarchical Nanostructures with Different Wettability
Authors: Ma Yong , Chen Yanhui , Hou Chunping , Zhang Hao , Qiao Mingtao , Zhang Hepeng , Zhang Qiuyu
Published: September 2016

We demonstrated polyaniline (PANI) dimensional transformation by adding trace amino-Fe3O4 microspheres to aniline polymerization. Different PANI nanostructures (i.e., flowers, tentacles, and nanofibers) could be produced by controlling the nucleation position and number on the surface of Fe3O4 microspheres, where hydrogen bonding were spontaneously formed between amino groups of Fe3O4 microspheres and aniline molecules. By additionally introducing an external magnetic field, PANI towers were obtained. These PANI nanostructures displayed distinctly different surface wettability in the range from hydrophobicity to hydrophilicity, which was ascribed to the synergistic effect of their dimension, hierarchy, and size. Therefore, the dimension and property of PANI nanostructures can be largely rationalized and predicted by adjusting the PANI nucleation and growth. Using PANI as a model system, the strategies presented here provide insight into the general scheme of dimension and structure control for other conducting polymers.
Progressive muscle proteome changes in a clinically relevant pig model of Duchenne muscular dystrophy
Authors: Fröhlich Thomas , Kemter Elisabeth , Flenkenthaler Florian , Klymiuk Nikolai , Otte Kathrin A. , Blutke Andreas , Krause Sabine , Walter Maggie C. , Wanke Rüdiger , Wolf Eckhard , Arnold Georg J.
Published: September 2016

Duchenne muscular dystrophy (DMD) is caused by genetic deficiency of dystrophin and characterized by massive structural and functional changes of skeletal muscle tissue, leading to terminal muscle failure. We recently generated a novel genetically engineered pig model reflecting pathological hallmarks of human DMD better than the widely used mdx mouse. To get insight into the hierarchy of molecular derangements during DMD progression, we performed a proteome analysis of biceps femoris muscle samples from 2-day-old and 3-month-old DMD and wild-type (WT) pigs. The extent of proteome changes in DMD vs. WT muscle increased markedly with age, reflecting progression of the pathological changes. In 3-month-old DMD muscle, proteins related to muscle repair such as vimentin, nestin, desmin and tenascin C were found to be increased, whereas a large number of respiratory chain proteins were decreased in abundance in DMD muscle, indicating serious disturbances in aerobic energy production and a reduction of functional muscle tissue. The combination of proteome data for fiber type specific myosin heavy chain proteins and immunohistochemistry showed preferential degeneration of fast-twitch fiber types in DMD muscle. The stage-specific proteome changes detected in this large animal model of clinically severe muscular dystrophy provide novel molecular readouts for future treatment trials.
Experimental Trapped-ion Quantum Simulation of the Kibble-Zurek dynamics in momentum space
Authors: Cui Jin-Ming , Huang Yun-Feng , Wang Zhao , Cao Dong-Yang , Wang Jian , Lv Wei-Min , Luo Le , del Campo Adolfo , Han Yong-Jian , Li Chuan-Feng , Guo Guang-Can
Published: September 2016

The Kibble-Zurek mechanism is the paradigm to account for the nonadiabatic dynamics of a system across a continuous phase transition. Its study in the quantum regime is hindered by the requisite of ground state cooling. We report the experimental quantum simulation of critical dynamics in the transverse-field Ising model by a set of Landau-Zener crossings in pseudo-momentum space, that can be probed with high accuracy using a single trapped ion. We test the Kibble-Zurek mechanism in the quantum regime in the momentum space and find the measured scaling of excitations is in accordance with the theoretical prediction.
Biochemical and structural characterization of the interface mediating interaction between the influenza A virus non-structural protein-1 and a monoclonal antibody
Authors: Wu Jianping , Mok Chee-Keng , Chow Vincent Tak Kwong , Yuan Y. Adam , Tan Yee-Joo
Published: September 2016

We have previously shown that a non-structural protein 1 (NS1)-binding monoclonal antibody, termed as 2H6, can significantly reduce influenza A virus (IAV) replication when expressed intracellularly. In this study, we further showed that 2H6 binds stronger to the NS1 of H5N1 than A/Puerto Rico/8/1934(H1N1) because of an amino acid difference at residue 48. A crystal structure of 2H6 fragment antigen-binding (Fab) has also been solved and docked onto the NS1 structure to reveal the contacts between specific residues at the interface of antibody-antigen complex. In one of the models, the predicted molecular contacts between residues in NS1 and 2H6-Fab correlate well with biochemical results. Taken together, residues N48 and T49 in H5N1 NS1 act cooperatively to maintain a strong interaction with mAb 2H6 by forming hydrogen bonds with residues found in the heavy chain of the antibody. Interestingly, the pandemic H1N1-2009 and the majority of seasonal H3N2 circulating in humans since 1968 has N48 in NS1, suggesting that mAb 2H6 could bind to most of the currently circulating seasonal influenza A virus strains. Consistent with the involvement of residue T49, which is well-conserved, in RNA binding, mAb 2H6 was also found to inhibit the interaction between NS1 and double-stranded RNA.
Controlling Directionality and Dimensionality of Radiation by Perturbing Separable Bound States in the Continuum
Authors: Rivera Nicholas , Hsu Chia Wei , Zhen Bo , Buljan Hrvoje , Joannopoulos John D. , Soljačić Marin
Published: September 2016

A bound state in the continuum (BIC) is an unusual localized state that is embedded in a continuum of extended states. Here, we present the general condition for BICs to arise from wave equation separability. Then we show that by exploiting perturbations of certain symmetry such BICs can be turned into resonances that radiate with a tailorable directionality and dimensionality. Using this general framework, we construct new examples of separable BICs and resonances that can exist in optical potentials for ultracold atoms, photonic systems, and systems described by tight binding. Such resonances with easily reconfigurable radiation allow for applications such as the storage and release of waves at a controllable rate and direction, as well systems that switch between different dimensions of confinement.
Chromatin remodeling during the in vivo glial differentiation in early Drosophila embryos
Authors: Ye Youqiong , Gu Liang , Chen Xiaolong , Shi Jiejun , Zhang Xiaobai , Jiang Cizhong
Published: September 2016

Chromatin remodeling plays a critical role in gene regulation and impacts many biological processes. However, little is known about the relationship between chromatin remodeling dynamics and in vivo cell lineage commitment. Here, we reveal the patterns of histone modification change and nucleosome positioning dynamics and their epigenetic regulatory roles during the in vivo glial differentiation in early Drosophila embryos. The genome-wide average H3K9ac signals in promoter regions are decreased in the glial cells compared to the neural progenitor cells. However, H3K9ac signals are increased in a group of genes that are up-regulated in glial cells and involved in gliogenesis. There occurs extensive nucleosome remodeling including shift, loss, and gain. Nucleosome depletion regions (NDRs) form in both promoters and enhancers. As a result, the associated genes are up-regulated. Intriguingly, NDRs form in two fashions: nucleosome shift and eviction. Moreover, the mode of NDR formation is independent of the original chromatin state of enhancers in the neural progenitor cells.
Discovery and Optimization of N-Substituted 2-(4-pyridinyl)thiazole carboxamides against Tumor Growth through Regulating Angiogenesis Signaling Pathways
Authors: Zhou Wenbo , Tang Wenshu , Sun Zhenliang , Li Yunqi , Dong Yanmin , Pei Haixiang , Peng Yangrui , Wang Jinhua , Shao Ting , Jiang Zhenran , Yi Zhengfang , Chen Yihua
Published: September 2016

Inhibition of angiogenesis is considered as one of the desirable pathways for the treatment of tumor growth and metastasis. Herein we demonstrated that a series of pyridinyl-thiazolyl carboxamide derivatives were designed, synthesized and examined against angiogenesis through a colony formation and migration assays of human umbilical vein endothelial cells (HUVECs) in vitro. A structure-activity relationship (SAR) study was carried out and optimization toward this series of compounds resulted in the discovery of N-(3-methoxyphenyl)-4-methyl-2-(2-propyl-4-pyridinyl)thiazole-5-carboxamide (3k). The results indicated that compound 3k showed similar or better effects compared to Vandetanib in suppressing HUVECs colony formation and migration as well as VEGF-induced angiogenesis in the aortic ring spreading model and chick embryo chorioallantoic membrane (CAM) model. More importantly, compound 3k also strongly blocked tumor growth with the dosage of 30 mg/kg/day, and subsequent mechanism exploration suggested that this series of compounds took effect mainly through angiogenesis signaling pathways. Together, these results suggested compound 3k may serve as a lead for a novel class of angiogenesis inhibitors for cancer treatments.
A Novel Assay for Screening Inhibitors Targeting HIV Integrase LEDGF/p75 Interaction Based on Ni2+ Coated Magnetic Agarose Beads
Authors: Dawei Zhang , Hongqiu He , Mengmeng Liu , Zhixia Meng , Shunxing Guo
Published: September 2016

HIV-1 integrase (IN) plays an essential role in viral replication and thus serves as an important target for chemotherapeutic intervention against HIV-1 infection. However, the current three clinical IN inhibitors, raltegravir, elvitegravir and dolutegravir share the same inhibitory mechanism, resulting in a common clinical resistance profile which have emerged in infected patients receiving treatment. Therefore, it is important to develop small molecule inhibitors that impair IN function with distinct mechanisms of action. In this work, a magnetic-beads based biochemical assay targeting the protein-protein interaction (PPI) between HIV IN and the cellular cofactor LEDGF/p75 was developed for identification of HIV-1 IN inhibitors. Furthermore, a library containing 1000 US. Food and Drug Administration (FDA)-approved drugs currently used for human medication was screened to identify inhibitors targeting the PPI. The assay was proved to be quite robust and with the novel assay we successfully identified dexlansoprazole (IC50 of 4.8 μM), a FDA-approved proton pump inhibitor, as a potential inhibitor for the PPI between IN and LEDGF/p75, which bound to the LEDGF/p75 partner with a kinetic dissociation (Kd) constant of 330 nM ± 2.6 nM.
Quantitative and combinatory determination of in situ phosphorylation of tau and its FTDP-17 mutants
Authors: Kimura Taeko , Hosokawa Tomohisa , Taoka Masato , Tsutsumi Koji , Ando Kanae , Ishiguro Koichi , Hosokawa Masato , Hasegawa Masato , Hisanaga Shin-ichi
Published: September 2016

Tau is hyperphosphorylated in the brains of patients with tauopathies, such as Alzheimer’s disease and frontotemporal dementia and parkinsonism linked to chromosome 17 (FTDP-17). However, neither the mechanism of hyperphosphorylation nor its contribution to pathogenesis is known. We applied Phos-tag SDS-PAGE, a phosphoaffinity electrophoresis, to the analysis of tau phosphorylation in vitro by Cdk5, in cultured cells and in mouse brain. Here, we found that Cdk5-p25 phosphorylated tau in vitro at Ser404, Ser235, Thr205 and Ser202 in this order. In contrast in cultured cells, Ser404 was preferentially phosphorylated by Cdk5-p35, whereas Thr205 was not phosphorylated. Ser202 and Ser235 were phosphorylated by endogenous kinases. Tau exhibited ~12 phosphorylation isotypes in COS-7 cells with different combinations of phosphorylation at Thr181, Ser202, Thr231, Ser235 and Ser404. These phosphorylation sites were similar to tau phosphorylated in mouse brains. FTDP-17 tau with a mutation in the C-terminal region had different banding patterns, indicating a different phosphorylation pattern. In particular, it was clear that the R406W mutation causes loss of Ser404 phosphorylation. These results demonstrate the usefulness of the Phos-tag technique in the quantitative analysis of site-specific in vivo phosphorylation of tau and provide detailed information on in situ combinatory phosphorylation of tau.
iRSpot-DACC: a computational predictor for recombination hot/cold spots identification based on dinucleotide-based auto-cross covariance
Authors: Liu Bingquan , Liu Yumeng , Jin Xiaopeng , Wang Xiaolong , Liu Bin
Published: September 2016

Meiotic recombination presents an uneven distribution across the genome. Genomic regions that exhibit at relatively high frequencies of recombination are called hotspots, whereas those with relatively low frequencies of recombination are called coldspots. Therefore, hotspots and coldspots would provide useful information for the study of the mechanism of recombination. In this study, we proposed a computational predictor called iRSpot-DACC to predict hot/cold spots across the yeast genome. It combined Support Vector Machines (SVMs) and a feature called dinucleotide-based auto-cross covariance (DACC), which is able to incorporate the global sequence-order information and fifteen local DNA properties into the predictor. Combined with Principal Component Analysis (PCA), its performance was further improved. Experimental results on a benchmark dataset showed that iRSpot-DACC can achieve an accuracy of 82.7%, outperforming some highly related methods.
Lack of adrenomedullin in mouse endothelial cells results in defective angiogenesis, enhanced vascular permeability, less metastasis, and more brain damage
Authors: Ochoa-Callejero Laura , Pozo-Rodrigálvarez Andrea , Martínez-Murillo Ricardo , Martínez Alfredo
Published: September 2016

Adrenomedullin (AM) is a vasodilating peptide involved in the regulation of circulatory homeostasis and in the pathophysiology of certain cardiovascular diseases. AM plays critical roles in blood vessels, including regulation of vascular stability and permeability. To elucidate the autocrine/paracrine function of AM in endothelial cells (EC) in vivo, a conditional knockout of AM in EC (AMEC-KO) was used. The amount of vascularization of the matrigel implants was lower in AMEC-KO mice indicating a defective angiogenesis. Moreover, ablation of AM in EC revealed increased vascular permeability in comparison with wild type (WT) littermates. In addition, AMEC-KO lungs exhibited significantly less tumor growth than littermate WT mice using a syngeneic model of metastasis. Furthermore, following middle cerebral artery permanent occlusion, there was a significant infarct size decrease in animals lacking endothelial AM when compared to their WT counterparts. AM is an important regulator of EC function, angiogenesis, tumorigenesis, and brain response to ischemia. Studies of AM should bring novel approaches to the treatment of vascular diseases.
SCOP/PHLPP1β in the basolateral amygdala regulates circadian expression of mouse anxiety-like behavior
Authors: Nakano Jun J. , Shimizu Kimiko , Shimba Shigeki , Fukada Yoshitaka
Published: September 2016

While disruption of the circadian clock triggers a spectrum of affective abnormalities, how the clock regulates mammalian emotionality remains unclear. Here, we characterized the time-of-day-dependent regulation of mouse anxiety-like behaviors. We show that anxiety-like behaviors are expressed in a circadian manner in mice and demonstrate that the clock machineries in the dorsal telencephalon (dTel) are required for the time-of-day-dependent regulation of anxiety-like behaviors. We identify suprachiasmatic nucleus circadian oscillatory protein (SCOP/PHLPP1β) as an essential intracellular signaling molecule mediating this temporal regulation downstream of the clock. Using viral-mediated, basolateral amygdala (BLA)-specific knockout of Scop, we demonstrate that deletion of SCOP in the BLA exerts anxiolytic effects on the elevated plus maze at early subjective night, thereby blunting the circadian variation in the anxiety-like behavior. We conclude that the circadian expression of SCOP in the BLA plays a key role in generating circadian rhythmicity in the anxiety-like behavior. Our results demonstrate SCOP as a regulator of anxiety-like behaviors and reveal its key roles in the anxiogenic functions of the BLA.
TSPO ligands stimulate ZnPPIX transport and ROS accumulation leading to the inhibition of P. falciparum growth in human blood
Authors: Marginedas-Freixa I. , Hattab C. , Bouyer G. , Halle F. , Chene A. , Lefevre S. D. , Cambot M. , Cueff A. , Schmitt M. , Gamain B. , Lacapere J. J. , Egee S. , Bihel F. , Le Van Kim C. , Ostuni M. A.
Published: September 2016

After invading red blood cells (RBCs), Plasmodium falciparum (Pf) can export its own proteins to the host membrane and activate endogenous channels that are present in the membrane of RBCs. This transport pathway involves the Voltage Dependent Anion Channel (VDAC). Moreover, ligands of the VDAC partner TranSlocator PrOtein (TSPO) were demonstrated to inhibit the growth of the parasite. We studied the expression of TSPO and VDAC isoforms in late erythroid precursors, examined the presence of these proteins in membranes of non-infected and infected human RBCs, and evaluated the efficiency of TSPO ligands in inhibiting plasmodium growth, transporting the haem analogue Zn-protoporphyrin-IX (ZnPPIX) and enhancing the accumulation of reactive oxygen species (ROS). TSPO and VDAC isoforms are differentially expressed on erythroid cells in late differentiation states. TSPO2 and VDAC are present in the membranes of mature RBCs in a unique protein complex that changes the affinity of TSPO ligands after Pf infection. TSPO ligands dose-dependently inhibited parasite growth, and this inhibition was correlated to ZnPPIX uptake and ROS accumulation in the infected RBCs. Our results demonstrate that TSPO ligands can induce Pf death by increasing the uptake of porphyrins through a TSPO2–VDAC complex, which leads to an accumulation of ROS.
Automatic Bayesian single molecule identification for localization microscopy
Authors: Tang Yunqing , Hendriks Johnny , Gensch Thomas , Dai Luru , Li Junbai
Published: September 2016

Single molecule localization microscopy (SMLM) is on its way to become a mainstream imaging technique in the life sciences. However, analysis of SMLM data is biased by user provided subjective parameters required by the analysis software. To remove this human bias we introduce here the Auto-Bayes method that executes the analysis of SMLM data automatically. We demonstrate the success of the method using the photoelectron count of an emitter as selection characteristic. Moreover, the principle can be used for any characteristic that is bimodally distributed with respect to false and true emitters. The method also allows generation of an emitter reliability map for estimating quality of SMLM-based structures. The potential of the Auto-Bayes method is shown by the fact that our first basic implementation was able to outperform all software packages that were compared in the ISBI online challenge in 2015, with respect to molecule detection (Jaccard index).
Olive and grape seed extract prevents post-traumatic osteoarthritis damages and exhibits in vitro anti IL-1β activities before and after oral consumption
Authors: Mével Elsa , Merceron Christophe , Vinatier Claire , Krisa Stéphanie , Richard Tristan , Masson Martial , Lesoeur Julie , Hivernaud Vincent , Gauthier Olivier , Abadie Jérôme , Nourissat Geoffroy , Houard Xavier , Wittrant Yohann , Urban Nelly , Beck Laurent , Guicheux Jérôme
Published: September 2016

Polyphenols exert a large range of beneficial effects in the prevention of age-related diseases. We sought to determine whether an extract of olive and grape seed standardized according to hydroxytyrosol (HT) and procyanidins (PCy) content, exerts preventive anti-osteoathritic effects. To this aim, we evaluated whether the HT/PCy mix could (i) have in vitro anti-inflammatory and chondroprotective actions, (ii) exert anti-osteoarthritis effects in two post-traumatic animal models and (iii) retain its bioactivity after oral administration. Anti-inflammatory and chondroprotective actions of HT/PCy were tested on primary cultured rabbit chondrocytes stimulated by interleukin-1 beta (IL-1β). The results showed that HT/PCy exerts anti-inflammatory and chondroprotective actions in vitro. The preventive effect of HT/PCy association was assessed in two animal models of post-traumatic OA in mice and rabbits. Diet supplementation with HT/PCy significantly decreased the severity of post-traumatic osteoarthritis in two complementary mice and rabbit models. The bioavailability and bioactivity was evaluated following gavage with HT/PCy in rabbits. Regular metabolites from HT/PCy extract were found in sera from rabbits following oral intake. Finally, sera from rabbits force-fed with HT/PCy conserved anti-IL-1β effect, suggesting the bioactivity of this extract. To conclude, HT/PCy extract may be of clinical significance for the preventive treatment of osteoarthritis.
Highly efficient removal of lead and cadmium during wastewater irrigation using a polyethylenimine-grafted gelatin sponge
Authors: Li Bingbing , Zhou Feng , Huang Kai , Wang Yipei , Mei Surong , Zhou Yikai , Jing Tao
Published: September 2016

Wastewater irrigation is a very important resource for heavy metal pollution in soil and then accumulation in vegetable crops. In this study, a polyethylenimine (PEI)-grafted gelatin sponge was prepared to effectively adsorb heavy metals during wastewater irrigation. Based on the strong water adsorption ability, wastewater remained in the PEI-grafted gelatin sponge for a sufficient time for the heavy metals to interact with the sorbents. The binding capacities of Pb(II) ions and Cd(II) ions on the PEI-grafted gelatin sponge were 66 mg g−1 and 65 mg g−1, which were much more than those on the gelatin sponge (9.75 mg g−1 and 9.35 mg g−1). Subsequently, the PEI-grafted gelatin sponge was spread on the surface of soil planted with garlic and then sprayed with synthetic wastewater. The concentrations of cadmium and lead in the garlic leaves were 1.59 mg kg−1 and 5.69 mg kg−1, respectively, which were much lower than those (15.78 mg kg−1 and 27.98 mg kg−1) without the gelatin sponge and the removal efficiencies were 89.9% and 79.7%. The PEI-grafting gelatin sponge could effectively remove heavy metals during wastewater irrigation, which improved the soil environment and reduced human exposure to heavy metals.
The N-terminal domain plays a crucial role in the structure of a full-length human mitochondrial Lon protease
Authors: Kereïche Sami , Kováčik Lubomír , Bednár Jan , Pevala Vladimír , Kunová Nina , Ondrovičová Gabriela , Bauer Jacob , Ambro Ľuboš , Bellová Jana , Kutejová Eva , Raška Ivan
Published: September 2016

Lon is an essential, multitasking AAA+protease regulating many cellular processes in species across all kingdoms of life. Altered expression levels of the human mitochondrial Lon protease (hLon) are linked to serious diseases including myopathies, paraplegia, and cancer. Here, we present the first 3D structure of full-lengthhLon using cryo-electron microscopy.hLon has a unique three-dimensional structure, in which the proteolytic and ATP-binding domains (AP-domain) form a hexameric chamber, while the N-terminal domain is arranged as a trimer of dimers. These two domains are linked by a narrow trimeric channel composed likely of coiled-coil helices. In the presence of AMP-PNP, the AP-domain has a closed-ring conformation and its N-terminal entry gate appears closed, but in ADP binding, it switches to a lock-washer conformation and its N-terminal gate opens, which is accompanied by a rearrangement of the N-terminal domain. We have also found that both the enzymatic activities and the 3D structure of ahLon mutant lacking the first 156 amino acids are severely disturbed, showing thathLon’s N-terminal domains are crucial for the overall structure of thehLon, maintaining a conformation allowing its proper functioning.
Full-length model of the human galectin-4 and insights into dynamics of inter-domain communication
Authors: Rustiguel Joane K. , Soares Ricardo O. S. , Meisburger Steve P. , Davis Katherine M. , Malzbender Kristina L. , Ando Nozomi , Dias-Baruffi Marcelo , Nonato Maria Cristina
Published: September 2016

Galectins are proteins involved in diverse cellular contexts due to their capacity to decipher and respond to the information encoded by β-galactoside sugars. In particular, human galectin-4, normally expressed in the healthy gastrointestinal tract, displays differential expression in cancerous tissues and is considered a potential drug target for liver and lung cancer. Galectin-4 is a tandem-repeat galectin characterized by two carbohydrate recognition domains connected by a linker-peptide. Despite their relevance to cell function and pathogenesis, structural characterization of full-length tandem-repeat galectins has remained elusive. Here, we investigate galectin-4 using X-ray crystallography, small- and wide-angle X-ray scattering, molecular modelling, molecular dynamics simulations and differential scanning fluorimetry assays and describe for the first time a structural model for human galectin-4. Our results provide insight into the structural role of the linker-peptide and shed light on the dynamic characteristics of the mechanism of carbohydrate recognition among tandem-repeat galectins.
In Situ Anabolic Activity of Periodontal Pathogens Porphyromonas gingivalis and Filifactor alocis in Chronic Periodontitis
Authors: Spooner Ralee , Weigel Kris M. , Harrison Peter L. , Lee KyuLim , Cangelosi Gerard A. , Yilmaz Özlem
Published: September 2016

Porphyromonas gingivalis and Filifactor alocis are fastidious anaerobic bacteria strongly associated with chronic forms of periodontitis. Our understanding of the growth activities of these microorganisms in situ is very limited. Previous studies have shown that copy numbers of ribosomal-RNA precursor (pre-rRNA) of specific pathogen species relative to genomic-DNA (gDNA) of the same species (P:G ratios) are greater in actively growing bacterial cells than in resting cells. The method, so-called steady-state pre-rRNA-analysis, represents a novel culture-independent approach to study bacteria. This study employed this technique to examine the in situ growth activities of oral bacteria in periodontitis before and after non-surgical periodontal therapy. Sub-gingival paper-point samples were taken at initial and re-evaluation appointments. Pre-rRNA and gDNA levels of P. gingivalis and F. alocis were quantified and compared using reverse-transcriptase qPCR. The results indicate significantly reduced growth activity of P. gingivalis, but not F. alocis, after therapy. The P:G ratios of P. gingivalis and F. alocis were compared and a low-strength, but statistically significant inter-species correlation was detected. Our study demonstrates that steady-state pre-rRNA-analysis can be a valuable culture-independent approach to studying opportunistic bacteria in periodontitis.
Size-Exclusion Chromatography-based isolation minimally alters Extracellular Vesicles’ characteristics compared to precipitating agents
Authors: Gámez-Valero Ana , Monguió-Tortajada Marta , Carreras-Planella Laura , Franquesa Marcel·la , Beyer Katrin , Borràs Francesc E.
Published: September 2016

Extracellular vesicles (EVs) have become an attractive field among the scientific community. Yet, a major challenge is to define a consensus method for EVs isolation. Ultracentrifugation has been the most widely used methodology but rapid methods, including Size Exclusion Chromatography (SEC) and/or precipitating agents such as Polyethylene glycol (PEG) or PRotein Organic Solvent PRecipitation (PROSPR) have emerged. To evaluate the impact of these different methods on the resulting EV preparations, plasma EVs were isolated using SEC, PEG and PROSPR and their total protein content, NTA and Cryo-electron microscopy profiles and EV-markers were compared. Also, their effect on recipient cells was tested. Low protein content and Cryo-EM analysis showed that SEC removed most of the overabundant soluble plasma proteins, which were not removed using PEG and partially by PROSPR. Moreover, only SEC allowed the detection of the EV-markers CD9, CD63 and CD81, LGALS3BP and CD5L, suggesting a putative interference of the precipitating agents in the structure/composition of the EVs. Furthermore, PEG and PROSPR-based EV isolation resulted in reduced cell viability in vitro. These results stress that appropriate EV-isolation method should be considered depending on the forthcoming application of the purified EVs.
Thermal stress depletes energy reserves in Drosophila
Authors: Klepsatel Peter , Gáliková Martina , Xu Yanjun , Kühnlein Ronald P.
Published: September 2016

Understanding how environmental temperature affects metabolic and physiological functions is of crucial importance to assess the impacts of climate change on organisms. Here, we used different laboratory strains and a wild-caught population of the fruit flyDrosophila melanogasterto examine the effect of temperature on the body energy reserves of an ectothermic organism. We found that permanent ambient temperature elevation or transient thermal stress causes significant depletion of body fat stores. Surprisingly, transient thermal stress induces a lasting “memory effect” on body fat storage, which also reduces survivorship of the flies upon food deprivation later after stress exposure. Functional analyses revealed that an intact heat-shock response is essential to protect flies from temperature-dependent body fat decline. Moreover, we found that the temperature-dependent body fat reduction is caused at least in part by apoptosis of fat body cells, which might irreversibly compromise the fat storage capacity of the flies. Altogether, our results provide evidence that thermal stress has a significant negative impact on organismal energy reserves, which in turn might affect individual fitness.
RETRACTED ARTICLE: Silencing of Histone Deacetylase 9 Expression in Podocytes Attenuates Kidney Injury in Diabetic Nephropathy
Authors: Liu Feng , Zong Ming , Wen Xiaofei , Li Xuezhu , Wang Jun , Wang Yi , Jiang Wei , Li Xiaojun , Guo Zhongliang , Qi Hualin
Published: September 2016

Podocyte dysfunction is important in the onset and development of diabetic nephropathy (DN). Histone deacetylases (HDACs) have been recently proved to play critical roles in the pathogenesis of DN. As one subtype of the class IIa HDACs, HDAC9 is capable to repress/de-repress their target genes in tumor, inflammation, atherosclerosis and metabolic diseases. In the present study, we investigate whether HDAC9 is involved in the pathophysiologic process of DN, especially the podocyte injury. Firstly, we explored the expression patterns and localization of HDAC9 and found that HDAC9 expression was significantly up-regulated in high glucose (HG)-treated mouse podocytes, as well as kidney tissues from diabetic db/db mice and patients with DN. Secondly, knockdown of HDAC9 in mouse podocytes significantly suppressed HG-induced reactive oxygen species (ROS) generation, cell apoptosis and inflammation through JAK2/STAT3 pathway and reduced the podocytes injury by decreasing the expression levels of Nephrin and Podocin. Moreover, in diabetic db/db mice, silencing of HDAC9 attenuated the glomerulosclerosis, inflammatory cytokine release, podocyte apoptosis and renal injury. Collectively, these data indicate that HDAC9 may be involved in the process of DN, especially podocyte injury. Our study suggest that inhibition of HDAC9 may have a therapeutic potential in DN treatment.