bluuebunny/crossref_metadata_2025 huggingface dataset:
Different states of synaptotagmin regulate evoked versus spontaneous release
Authors: Bai Hua , Xue Renhao , Bao Huan , Zhang Leili , Yethiraj Arun , Cui Qiang , Chapman Edwin R.
Published: March 2016

The tandem C2-domains of synaptotagmin 1 (syt) function as Ca2+-binding modules that trigger exocytosis; in the absence of Ca2+, syt inhibits spontaneous release. Here, we used proline linkers to constrain and alter the relative orientation of these C2-domains. Short poly-proline helices have a period of three, so large changes in the relative disposition of the C2-domains result from changing the length of the poly-proline linker by a single residue. The length of the linker was varied one residue at a time, revealing a periodicity of three for the ability of the linker mutants to interact with anionic phospholipids and drive evoked synaptic transmission; syt efficiently drove exocytosis when its tandem C2-domains pointed in the same direction. Analysis of spontaneous release revealed a reciprocal relationship between the activation and clamping activities of the linker mutants. Hence, different structural states of syt underlie the control of distinct forms of synaptic transmission.
MicroRNA-378 limits activation of hepatic stellate cells and liver fibrosis by suppressing Gli3 expression
Authors: Hyun Jeongeun , Wang Sihyung , Kim Jieun , Rao Kummara Madhusudana , Park Soo Yong , Chung Ildoo , Ha Chang-Sik , Kim Sang-Woo , Yun Yang H. , Jung Youngmi
Published: March 2016

Hedgehog (Hh) signalling regulates hepatic fibrogenesis. MicroRNAs (miRNAs) mediate various cellular processes; however, their role in liver fibrosis is unclear. Here we investigate regulation of miRNAs in chronically damaged fibrotic liver. MiRNA profiling shows that expression of miR-378 family members (miR-378a-3p, miR-378b and miR-378d) declines in carbon tetrachloride (CCl4)-treated compared with corn-oil-treated mice. Overexpression of miR-378a-3p, directly targeting Gli3 in activated hepatic stellate cells (HSCs), reduces expression of Gli3 and profibrotic genes but induces gfap, the inactivation marker of HSCs, in CCl4-treated liver. Smo blocks transcriptional expression of miR-378a-3p by activating the p65 subunit of nuclear factor-κB (NF-κB). The hepatic level of miR-378a-3p is inversely correlated with the expression of Gli3 in tumour and non-tumour tissues in human hepatocellular carcinoma. Our results demonstrate that miR-378a-3p suppresses activation of HSCs by targeting Gli3 and its expression is regulated by Smo-dependent NF-κB signalling, suggesting miR-378a-3p has therapeutic potential for liver fibrosis.
Discovery of abnormal lithium-storage sites in molybdenum dioxide electrodes
Authors: Shon Jeong Kuk , Lee Hyo Sug , Park Gwi Ok , Yoon Jeongbae , Park Eunjun , Park Gyeong Su , Kong Soo Sung , Jin Mingshi , Choi Jae-Man , Chang Hyuk , Doo Seokgwang , Kim Ji Man , Yoon Won-Sub , Pak Chanho , Kim Hansu , Stucky Galen D.
Published: March 2016

Developing electrode materials with high-energy densities is important for the development of lithium-ion batteries. Here, we demonstrate a mesoporous molybdenum dioxide material with abnormal lithium-storage sites, which exhibits a discharge capacity of 1,814 mAh g−1 for the first cycle, more than twice its theoretical value, and maintains its initial capacity after 50 cycles. Contrary to previous reports, we find that a mechanism for the high and reversible lithium-storage capacity of the mesoporous molybdenum dioxide electrode is not based on a conversion reaction. Insight into the electrochemical results, obtained by in situ X-ray absorption, scanning transmission electron microscopy analysis combined with electron energy loss spectroscopy and computational modelling indicates that the nanoscale pore engineering of this transition metal oxide enables an unexpected electrochemical mass storage reaction mechanism, and may provide a strategy for the design of cation storage materials for battery systems.
Cyanobacterial symbionts diverged in the late Cretaceous towards lineage-specific nitrogen fixation factories in single-celled phytoplankton
Authors: Cornejo-Castillo Francisco M. , Cabello Ana M. , Salazar Guillem , Sánchez-Baracaldo Patricia , Lima-Mendez Gipsi , Hingamp Pascal , Alberti Adriana , Sunagawa Shinichi , Bork Peer , de Vargas Colomban , Raes Jeroen , Bowler Chris , Wincker Patrick , Zehr Jonathan P. , Gasol Josep M. , Massana Ramon , Acinas Silvia G.
Published: March 2016

The unicellular cyanobacterium UCYN-A, one of the major contributors to nitrogen fixation in the open ocean, lives in symbiosis with single-celled phytoplankton. UCYN-A includes several closely related lineages whose partner fidelity, genome-wide expression and time of evolutionary divergence remain to be resolved. Here we detect and distinguish UCYN-A1 and UCYN-A2 lineages in symbiosis with two distinct prymnesiophyte partners in the South Atlantic Ocean. Both symbiotic systems are lineage specific and differ in the number of UCYN-A cells involved. Our analyses infer a streamlined genome expression towards nitrogen fixation in both UCYN-A lineages. Comparative genomics reveal a strong purifying selection in UCYN-A1 and UCYN-A2 with a diversification process ∼91 Myr ago, in the late Cretaceous, after the low-nutrient regime period occurred during the Jurassic. These findings suggest that UCYN-A diversified in a co-evolutionary process, wherein their prymnesiophyte partners acted as a barrier driving an allopatric speciation of extant UCYN-A lineages.
Direct evidence of two interatomic relaxation mechanisms in argon dimers ionized by electron impact
Authors: Ren Xueguang , Jabbour Al Maalouf Elias , Dorn Alexander , Denifl Stephan
Published: March 2016

In weakly bound systems like liquids and clusters electronically excited states can relax in inter-particle reactions via the interplay of electronic and nuclear dynamics. Here we report on the identification of two prominent examples, interatomic Coulombic decay (ICD) and radiative charge transfer (RCT), which are induced in argon dimers by electron collisions. After initial ionization of one dimer constituent ICD and RCT lead to the ionization of its neighbour either by energy transfer to or by electron transfer from the neighbour, respectively. By full quintuple-coincidence measurements, we unambiguously identify ICD and RCT, and trace the relaxation dynamics as function of the collisional excited state energies. Such interatomic processes multiply the number of electrons and shift their energies down to the critical 1–10 eV range, which can efficiently cause chemical degradation of biomolecules. Therefore, the observed relaxation channels might contribute to cause efficient radiation damage in biological systems.
Subharmonic instability of a self-organized granular jet
Authors: Kollmer J. E. , Pöschel T.
Published: March 2016

Downhill flows of granular matter colliding in the lowest point of a valley, may induce a self-organized jet. By means of a quasi two-dimensional experiment where fine grained sand flows in a vertically sinusoidally agitated cylinder, we show that the emergent jet, that is, a sheet of ejecta, does not follow the frequency of agitation but reveals subharmonic response. The order of the subharmonics is a complex function of the parameters of driving.
Functional Connectome before and following Temporal Lobectomy in Mesial Temporal Lobe Epilepsy
Authors: Liao Wei , Ji Gong-Jun , Xu Qiang , Wei Wei , Wang Jue , Wang Zhengge , Yang Fang , Sun Kangjian , Jiao Qing , Richardson Mark P. , Zang Yu-Feng , Zhang Zhiqiang , Lu Guangming
Published: March 2016

As mesial temporal lobe epilepsy (mTLE) has been recognized as a network disorder, a longitudinal connectome investigation may shed new light on the understanding of the underlying pathophysiology related to distinct surgical outcomes. Resting-state functional MRI data was acquired from mTLE patients before (n = 37) and after (n = 24) anterior temporal lobectomy. According to surgical outcome, patients were classified as seizure-free (SF, n = 14) or non-seizure-free (NSF, n = 10). First, we found higher network resilience to targeted attack on topologically central nodes in the SF group compared to the NSF group, preoperatively. Next, a two-way mixed analysis of variance with between-subject factor ‘outcome’ (SF vs. NSF) and within-subject factor ‘treatment’ (pre-operation vs. post-operation) revealed divergent dynamic reorganization in nodal topological characteristics between groups, in the temporoparietal junction and its connection with the ventral prefrontal cortex. We also correlated the network damage score (caused by surgical resection) with postsurgical brain function and found that the damage score negatively correlated with postoperative global and local parallel information processing. Taken together, dynamic connectomic architecture provides vital information for selecting surgical candidates and for understanding brain recovery mechanisms following epilepsy surgery.
Proteasome activators, PA28γ and PA200, play indispensable roles in male fertility
Authors: Huang Lin , Haratake Kousuke , Miyahara Hatsumi , Chiba Tomoki
Published: March 2016

Protein degradation mediated by the proteasome is important for the protein homeostasis. Various proteasome activators, such as PA28 and PA200, regulate the proteasome function. Here we show double knockout (dKO) mice of Psme3 and Psme4 (genes for PA28γ and PA200), but not each single knockout mice, are completely infertile in male. The dKO sperms exhibited remarkable defects in motility, although most of them showed normal appearance in morphology. The proteasome activity of the mutant sperms decreased notably, and the sperms were strongly positive with ubiquitin staining. Quantitative analyses of proteins expressed in dKO sperms revealed up-regulation of several proteins involved in oxidative stress response. Furthermore, increased 8-OHdG staining was observed in dKO sperms head, suggesting defective response to oxidative damage. This report verified PA28γ and PA200 play indispensable roles in male fertility, and provides a novel insight into the role of proteasome activators in antioxidant response.
Effect of light and nutrient availability on the release of dissolved organic carbon (DOC) by Caribbean turf algae
Authors: Mueller Benjamin , den Haan Joost , Visser Petra M. , Vermeij Mark J. A. , van Duyl Fleur C.
Published: March 2016

Turf algae increasingly dominate benthic communities on coral reefs. Given their abundance and high dissolved organic carbon (DOC) release rates, turf algae are considered important contributors to the DOC pool on modern reefs. The release of photosynthetically fixed carbon as DOC generally, but not always, increases with increased light availability. Nutrient availability was proposed as an additional factor to explain these conflicting observations. To address this proposed but untested hypothesis, we documented the interactive contributions of light and nutrient availability on the release of DOC by turf algae. DOC release rates and oxygen production were quantified in incubation experiments at two light levels (full and reduced light) and two nutrient treatments (natural seawater and enriched seawater). In natural seawater, DOC release at full light was four times higher than at reduced light. When nutrients were added, DOC release rates at both light levels were similar to the natural seawater treatment at full light. Our results therefore show that low light in combination with low nutrient availability reduces the release of DOC by turf algae and that light and nutrient availability interactively determine DOC release rates by this important component of Caribbean reef communities.
Mitochondrial redox and pH signaling occurs in axonal and synaptic organelle clusters
Authors: Breckwoldt Michael O. , Armoundas Antonis A. , Aon Miguel A. , Bendszus Martin , O’Rourke Brian , Schwarzländer Markus , Dick Tobias P. , Kurz Felix T.
Published: March 2016

Redox switches are important mediators in neoplastic, cardiovascular and neurological disorders. We recently identified spontaneous redox signals in neurons at the single mitochondrion level where transients of glutathione oxidation go along with shortening and re-elongation of the organelle. We now have developed advanced image and signal-processing methods to re-assess and extend previously obtained data. Here we analyze redox and pH signals of entire mitochondrial populations. In total, we quantified the effects of 628 redox and pH events in 1797 mitochondria from intercostal axons and neuromuscular synapses using optical sensors (mito-Grx1-roGFP2; mito-SypHer). We show that neuronal mitochondria can undergo multiple redox cycles exhibiting markedly different signal characteristics compared to single redox events. Redox and pH events occur more often in mitochondrial clusters (medium cluster size: 34.1 ± 4.8 μm2). Local clusters possess higher mitochondrial densities than the rest of the axon, suggesting morphological and functional inter-mitochondrial coupling. We find that cluster formation is redox sensitive and can be blocked by the antioxidant MitoQ. In a nerve crush paradigm, mitochondrial clusters form sequentially adjacent to the lesion site and oxidation spreads between mitochondria. Our methodology combines optical bioenergetics and advanced signal processing and allows quantitative assessment of entire mitochondrial populations.
Evolution of photoinduced effects in phase-separated Sm0.5Sr0.5Mn1−yCryO3 thin films
Authors: Chai Xiaojie , Xing Hui , Jin Kexin
Published: March 2016

Systematic study on electrical transport properties has been performed in Sm0.5Sr0.5Mn1−yCryO3 thin films illuminated by the light. An evolution of persistent and transient photoinduced effects induced by the impurity doping and temperature has been observed, which is closely related to the number of ferromagnetic clusters. The maximum persistent photoinduced effect is observed at y = 0.08 and the corresponding value is about 61.7% at the power density of 13.7 mW/mm2. The underlying mechanism can be understood by the coexistence and competition of the multiphases in phase-separated manganites induced by Cr-doping. These results would pave the way for practical applications in innovative photoelectric devices of all-oxides.
Single-cell lineage tracking analysis reveals that an established cell line comprises putative cancer stem cells and their heterogeneous progeny
Authors: Sato Sachiko , Rancourt Ann , Sato Yukiko , Satoh Masahiko S.
Published: March 2016

Mammalian cell culture has been used in many biological studies on the assumption that a cell line comprises putatively homogeneous clonal cells, thereby sharing similar phenotypic features. This fundamental assumption has not yet been fully tested; therefore, we developed a method for the chronological analysis of individual HeLa cells. The analysis was performed by live cell imaging, tracking of every single cell recorded on imaging videos, and determining the fates of individual cells. We found that cell fate varied significantly, indicating that, in contrast to the assumption, the HeLa cell line is composed of highly heterogeneous cells. Furthermore, our results reveal that only a limited number of cells are immortal and renew themselves, giving rise to the remaining cells. These cells have reduced reproductive ability, creating a functionally heterogeneous cell population. Hence, the HeLa cell line is maintained by the limited number of immortal cells, which could be putative cancer stem cells.
Splice form variant and amino acid changes in MDR49 confers DDT resistance in transgenic Drosophila
Authors: Seong Keon Mook , Sun Weilin , Clark John M. , Pittendrigh Barry R.
Published: March 2016

The ATP-binding cassette (ABC) transporters represent a superfamily of proteins that have important physiological roles in both prokaryotes and eukaryotes. In insects, ABC transporters have previously been implicated in insecticide resistance. The 91-R strain of Drosophila melanogaster has been intensely selected with DDT over six decades. A recent selective sweeps analysis of 91-R implicated the potential role of MDR49, an ABC transporter, in DDT resistance, however, to date the details of how MDR49 may play a role in resistance have not been elucidated. In this study, we investigated the impact of structural changes and an alternative splicing event in MDR49 on DDT-resistance in 91-R, as compared to the DDT susceptible strain 91-C. We observed three amino acid differences in MDR49 when 91-R was compared with 91-C, and only one isoform (MDR49B) was implicated in DDT resistance. A transgenic Drosophila strain containing the 91-R-MDR49B isoform had a significantly higher LD50 value as compared to the 91-C-MDR49B isoform at the early time points (6 h to 12 h) during DDT exposure. Our data support the hypothesis that the MDR49B isoform, with three amino acid mutations, plays a role in the early aspects of DDT resistance in 91-R.
Beta-tricalcium phosphate granules improve osteogenesis in vitro and establish innovative osteo-regenerators for bone tissue engineering in vivo
Authors: Gao Peng , Zhang Haoqiang , Liu Yun , Fan Bo , Li Xiaokang , Xiao Xin , Lan Pingheng , Li Minghui , Geng Lei , Liu Dong , Yuan Yulin , Lian Qin , Lu Jianxi , Guo Zheng , Wang Zhen
Published: March 2016

The drawbacks of traditional bone-defect treatments have prompted the exploration of bone tissue engineering. This study aimed to explore suitable β-tricalcium phosphate (β-TCP) granules for bone regeneration and identify an efficient method to establish β-TCP-based osteo-regenerators. β-TCP granules with diameters of 1 mm and 1–2.5 mm were evaluated in vitro. The β-TCP granules with superior osteogenic properties were used to establish in vivo bioreactors, referred to as osteo-regenerators, which were fabricated using two different methods. Improved proliferation of bone mesenchymal stem cells (BMSCs), glucose consumption and ALP activity were observed for 1–2.5 mm β-TCP compared with 1-mm granules (P < 0.05). In addition, BMSCs incubated with 1–2.5 mm β-TCP expressed significantly higher levels of the genes for runt-related transcription factor-2, alkaline phosphatase, osteocalcin, osteopontin, and collagen type-1 and the osteogenesis-related proteins alkaline phosphatase, collagen type-1 and runt-related transcription factor-2 compared with BMSCs incubated with 1 mm β-TCP (P < 0.05). Fluorochrome labelling, micro-computed tomography and histological staining analyses indicated that the osteo-regenerator with two holes perforating the femur promoted significantly greater bone regeneration compared with the osteo-regenerator with a periosteum incision (P < 0.05). This study provides an alternative to biofunctionalized bioreactors that exhibits improved osteogenesis.
Improved dialytic removal of protein-bound uraemic toxins with use of albumin binding competitors: an in vitro human whole blood study
Authors: Tao Xia , Thijssen Stephan , Kotanko Peter , Ho Chih-Hu , Henrie Michael , Stroup Eric , Handelman Garry
Published: March 2016

Protein-bound uraemic toxins (PBUTs) cause various deleterious effects in end-stage kidney disease patients, because their removal by conventional haemodialysis (HD) is severely limited by their low free fraction in plasma. Here we provide an experimental validation of the concept that the HD dialytic removal of PBUTs can be significantly increased by extracorporeal infusion of PBUT binding competitors. The binding properties of indoxyl sulfate (IS), indole-3-acetic acid (IAA) and hippuric acid (HIPA) and their binding competitors, ibuprofen (IBU), furosemide (FUR) and tryptophan (TRP) were studied in uraemic plasma. The effect of binding competitor infusion on fractional removal of PBUT was then quantified in an ex vivo single-pass HD model using uraemic human whole blood. The infusion of a combination of IBU and FUR increased the fractional removal of IS from 6.4 ± 0.1 to 18.3 ± 0.4%. IAA removal rose from 16.8 ± 0.3 to 34.5 ± 0.7%. TRP infusion increased the removal of IS and IAA to 10.5 ± 0.1% and 27.1 ± 0.3%, respectively. Moderate effects were observed on HIPA removal. Pre-dialyzer infusion of PBUT binding competitors into the blood stream can increase the HD removal of PBUTs. This approach can potentially be applied in current HD settings.
PSCA rs2294008 polymorphism contributes to the decreased risk for cervical cancer in a Chinese population
Authors: Wang Shizhi , Wu Shenshen , Zhu Haixia , Ding Bo , Cai Yunlang , Ni Jing , Wu Qiang , Meng Qingtao , Zhang Xin , Zhang Chengcheng , Li Xiaobo , Wang Meilin , Chen Rui , Jin Hua , Zhang Zhengdong
Published: March 2016

Recently, three genome-wide association studies have identified the PSCA (prostate stem cell antigen) rs2294008 polymorphism (C > T) associated with susceptibility to gastric cancer, bladder cancer, and duodenal ulcers, highlighting its critical role in disease pathogenesis. Given PSCA is reported to be overexpressed in cervical cancer and the rs2294008 can influence PSCA transcription, we aimed to determine the role of rs2294008 in susceptibility to cervical cancer. The genotyping was performed in the 1126 cases and 1237 controls. Our results showed the rs2294008 TT genotype significantly associated with a reduced risk of cervical cancer (adjusted OR = 0.55, 95% CI = 0.38–0.79; recessive model). Stratified analyses revealed that the association was restricted to the subgroups of age > 49 years, parity ≤ 1, abortion and early-stage cervical cancer. Immunohistochemistry assay showed the individuals carrying the TT genotype having lower PSCA expression than those with CC/CT genotypes. In summary, the PSCA rs2294008 polymorphism may serve as a biomarker of cervical cancer, particularly of early-stage cervical cancer.
UniBic: Sequential row-based biclustering algorithm for analysis of gene expression data
Authors: Wang Zhenjia , Li Guojun , Robinson Robert W. , Huang Xiuzhen
Published: March 2016

Biclustering algorithms, which aim to provide an effective and efficient way to analyze gene expression data by finding a group of genes with trend-preserving expression patterns under certain conditions, have been widely developed since Morgan et al. pioneered a work about partitioning a data matrix into submatrices with approximately constant values. However, the identification of general trend-preserving biclusters which are the most meaningful substructures hidden in gene expression data remains a highly challenging problem. We found an elementary method by which biologically meaningful trend-preserving biclusters can be readily identified from noisy and complex large data. The basic idea is to apply the longest common subsequence (LCS) framework to selected pairs of rows in an index matrix derived from an input data matrix to locate a seed for each bicluster to be identified. We tested it on synthetic and real datasets and compared its performance with currently competitive biclustering tools. We found that the new algorithm, named UniBic, outperformed all previous biclustering algorithms in terms of commonly used evaluation scenarios except for BicSPAM on narrow biclusters. The latter was somewhat better at finding narrow biclusters, the task for which it was specifically designed.
Solitonic dynamics and excitations of the nonlinear Schrödinger equation with third-order dispersion in non-Hermitian PT-symmetric potentials
Authors: Chen Yong , Yan Zhenya
Published: March 2016

Solitons are of the important significant in many fields of nonlinear science such as nonlinear optics, Bose-Einstein condensates, plamas physics, biology, fluid mechanics and etc. The stable solitons have been captured not only theoretically and experimentally in both linear and nonlinear Schrödinger (NLS) equations in the presence of non-Hermitian potentials since the concept of the parity-time "Equation missing"-symmetry was introduced in 1998. In this paper, we present novel bright solitons of the NLS equation with third-order dispersion in some complex "Equation missing"-symmetric potentials (e.g., physically relevant "Equation missing"-symmetric Scarff-II-like and harmonic-Gaussian potentials). We find stable nonlinear modes even if the respective linear "Equation missing"-symmetric phases are broken. Moreover, we also use the adiabatic changes of the control parameters to excite the initial modes related to exact solitons to reach stable nonlinear modes. The elastic interactions of two solitons are exhibited in the third-order NLS equation with "Equation missing"-symmetric potentials. Our results predict the dynamical phenomena of soliton equations in the presence of third-order dispersion and "Equation missing"-symmetric potentials arising in nonlinear fiber optics and other physically relevant fields.
Precipitation shapes communities of arbuscular mycorrhizal fungi in Tibetan alpine steppe
Authors: Zhang Jing , Wang Fang , Che Rongxiao , Wang Ping , Liu Hanke , Ji Baoming , Cui Xiaoyong
Published: March 2016

Tibetan Plateau is one of the largest and most unique habitats for organisms including arbuscular mycorrhizal fungi (AMF). However, it remains unclear how AMF communities respond to key environmental changes in this harsh environment. To test if precipitation could be a driving force in shaping AMF community structures at regional scale, we examined AMF communities associated with dominant plant species along a precipitation gradient in Tibetan alpine steppe. Rhizosphere soils were collected from five sites with annual precipitation decreasing from 400 to 50 mm. A total of 31 AMF operational taxonomic units (OTUs) were identified. AMF community composition varied significantly among sites, whereas AMF community composition did not vary among plant species. Path analysis revealed that precipitation directly affected AMF hyphal length density, and indirectly influenced AMF species richness likely through the mediation of plant coverage. Our results suggested that water availability could drive the changes of AMF communities at regional scale. Given the important roles AMF could play in the dynamics of plant communities, exploring the changes of AMF communities along key environmental gradients would help us better predict the ecosystem level responses of the Tibetan vegetation to future climate change.
BRE plays an essential role in preventing replicative and DNA damage-induced premature senescence
Authors: Shi Wenting , Tang Mei Kuen , Yao Yao , Tang Chengcheng , Chui Yiu Loon , Lee Kenneth Ka Ho
Published: March 2016

The BRE gene, alias BRCC45, produces a 44 kDa protein that is normally distributed in both cytoplasm and nucleus. In this study, we used adult fibroblasts isolated from wild-type (WT) and BRE knockout (BRE−/−) mice to investigate the functional role of BRE in DNA repair and cellular senescence. We compared WT with BRE−/− fibroblasts at different cell passages and observed that the mutant fibroblasts entered replicative senescence earlier than the WT fibroblasts. With the use of gamma irradiation to induce DNA damage in fibroblasts, the percentage of SA-β-Gal+ cells was significantly higher in BRE−/− fibroblasts compared with WT cells, suggesting that BRE is also associated with DNA damage-induced premature senescence. We also demonstrated that the gamma irradiation induced γ-H2AX foci, a DNA damage marker, persisted significantly longer in BRE−/− fibroblasts than in WT fibroblasts, confirming that the DNA repair process is impaired in the absence of BRE. In addition, the BRCA1-A complex recruitment and homologous recombination (HR)-dependent DNA repair process upon DNA damage were impaired in BRE−/− fibroblasts. Taken together, our results demonstrate a role for BRE in both replicative senescence and DNA damage-induced premature senescence. This can be attributed to BRE being required for BRCA1-A complex-driven HR DNA repair.
DephosSite: a machine learning approach for discovering phosphotase-specific dephosphorylation sites
Authors: Wang Xiaofeng , Yan Renxiang , Song Jiangning
Published: March 2016

Protein dephosphorylation, which is an inverse process of phosphorylation, plays a crucial role in a myriad of cellular processes, including mitotic cycle, proliferation, differentiation and cell growth. Compared with tyrosine kinase substrate and phosphorylation site prediction, there is a paucity of studies focusing on computational methods of predicting protein tyrosine phosphatase substrates and dephosphorylation sites. In this work, we developed two elegant models for predicting the substrate dephosphorylation sites of three specific phosphatases, namely, PTP1B, SHP-1 and SHP-2. The first predictor is called MGPS-DEPHOS, which is modified from the GPS (Group-based Prediction System) algorithm with an interpretable capability. The second predictor is called CKSAAP-DEPHOS, which is built through the combination of support vector machine (SVM) and the composition of k-spaced amino acid pairs (CKSAAP) encoding scheme. Benchmarking experiments using jackknife cross validation and 30 repeats of 5-fold cross validation tests show that MGPS-DEPHOS and CKSAAP-DEPHOS achieved AUC values of 0.921, 0.914 and 0.912, for predicting dephosphorylation sites of the three phosphatases PTP1B, SHP-1 and SHP-2, respectively. Both methods outperformed the previously developed kNN-DEPHOS algorithm. In addition, a web server implementing our algorithms is publicly available at http://genomics.fzu.edu.cn/dephossite/ for the research community.
Omnidirectional optical attractor in structured gap-surface plasmon waveguide
Authors: Sheng Chong , Liu Hui , Zhu Shining , Genov Dentcho A.
Published: March 2016

An optical attractor based on a simple and easy to fabricate structured metal-dielectric-metal (SMDM) waveguide is proposed. The structured waveguide has a variable thickness in the vicinity of an embedded microsphere and allow for adiabatic nano-focusing of gap-surface plasmon polaritons (GSPPs). We show that the proposed system acts as an omnidirectional absorber across a broad spectral range. The geometrical optics approximation is used to provide a description of the ray trajectories in the system and identify the singularity of the deflection angle at the photon sphere. The analytical theory is validated by full-wave numerical simulations demonstrating adiabatic, deep sub-wavelength focusing of GSPPs and high local field enhancement. The proposed structured waveguide is an ideal candidate for the demonstration of reflection free omnidirectional absorption of GSPP in the optical and infrared frequency ranges.
Two phases of aging separated by the Smurf transition as a public path to death
Authors: Dambroise E. , Monnier L. , Ruisheng L. , Aguilaniu H. , Joly J.-S. , Tricoire H. , Rera M.
Published: March 2016

Aging’s most obvious characteristic is the time dependent increase of an individual’s probability to die. This lifelong process is accompanied by a large number of molecular and physiological changes. Although numerous genes involved in aging have been identified in the past decades its leading factors have yet to be determined. To identify the very processes driving aging we have developed in the past years an assay to identify physiologically old individuals in a synchronized population of Drosophila melanogaster. Those individuals show an age-dependent increase of intestinal permeability followed by a high risk of death. Here we show that this physiological marker of aging is conserved in 3 invertebrate species Drosophila mojavensis, Drosophila virilis, Caenorhabditis elegans as well as in 1 vertebrate species Danio rerio. Our findings suggest that intestinal barrier dysfunction may be an important event in the aging process conserved across a broad range of species, thus raising the possibility that it may also be the case in Homo sapiens.
NR2A contributes to genesis and propagation of cortical spreading depression in rats
Authors: Bu Fan , Du Ruoxing , Li Yi , Quinn John P , Wang Minyan
Published: March 2016

Cortical spreading depression (CSD) is a transient propagating excitation of synaptic activity followed by depression, which is implicated in migraine. Increasing evidence points to an essential role of NR2A-containing NMDA receptors in CSD propagation in vitro; however, whether these receptors mediate CSD genesis in vivo requires clarification and the role of NR2A on CSD propagation is still under debate. Using in vivo CSD in rats with electrophysiology and in vitro CSD in chick retina with intrinsic optical imaging, we addressed the role of NR2A in CSD. We demonstrated that NVP-AAM077, a potent antagonist for NR2A-containing receptors, perfused through microdialysis probes, markedly reduced cortex susceptibility to CSD, but also reduced magnitude of CSD genesis in rats. Additionally, NVP-AAM077 at 0.3 nmol perfused into the contralateral ventricle, considerably suppressed the magnitude of CSD propagation wave and propagation rate in rats. This reduction in CSD propagation was also observed with TCN-201, a negative allosteric modulator selective for NR2A, at 3 μM, in the chick retina. Our data provides strong evidence that NR2A subunit contributes to CSD genesis and propagation, suggesting drugs selectively antagonizing NR2A-containing receptors might constitute a highly specific strategy treating CSD associated migraine with a likely better safety profile.
Functional magnetic resonance imaging in awake transgenic fragile X rats: evidence of dysregulation in reward processing in the mesolimbic/habenular neural circuit
Authors: Kenkel W M , Yee J R , Moore K , Madularu D , Kulkarni P , Gamber K , Nedelman M , Ferris C F
Published: March 2016

Anxiety and social deficits, often involving communication impairment, are fundamental clinical features of fragile X syndrome. There is growing evidence that dysregulation in reward processing is a contributing factor to the social deficits observed in many psychiatric disorders. Hence, we hypothesized that transgenic fragile X mental retardation 1 gene (fmr1) KO (FX) rats would display alterations in reward processing. To this end, awake control and FX rats were imaged for changes in blood oxygen level dependent (BOLD) signal intensity in response to the odor of almond, a stimulus to elicit the innate reward response. Subjects were ‘odor naive’ to this evolutionarily conserved stimulus. The resulting changes in brain activity were registered to a three-dimensional segmented, annotated rat atlas delineating 171 brain regions. Both wild-type (WT) and FX rats showed robust brain activation to a rewarding almond odor, though FX rats showed an altered temporal pattern and tended to have a higher number of voxels with negative BOLD signal change from baseline. This pattern of greater negative BOLD was especially apparent in the Papez circuit, critical to emotional processing and the mesolimbic/habenular reward circuit. WT rats showed greater positive BOLD response in the supramammillary area, whereas FX rats showed greater positive BOLD response in the dorsal lateral striatum, and greater negative BOLD response in the retrosplenial cortices, the core of the accumbens and the lateral preoptic area. When tested in a freely behaving odor-investigation paradigm, FX rats failed to show the preference for almond odor which typifies WT rats. However, FX rats showed investigation profiles similar to WT when presented with social odors. These data speak to an altered processing of this highly salient novel odor in the FX phenotype and lend further support to the notion that altered reward systems in the brain may contribute to fragile X syndrome symptomology.
Isotope-labelling derivatisation: a broadly applicable approach to quantitation of algal toxins by isotope dilution LC-MS/MS
Authors: Beach Daniel G. , Hollingdale Christie , Quilliam Michael A.
Published: March 2016

Derivatisation with a labelled reagent allows for isotope dilution calibration of algal toxins for which no labelled standard is available.
Effects of Pt dispersion on electronic and oxide ionic conductivity in Pr1.90Ni0.71Cu0.24Ga0.05O4
Authors: Ishihara T. , Hyodo J. , Schraknepper H. , Tominaga K. , Ida S.
Published: March 2016

Pt dispersion in Pr2NiO4 based oxides formed compressed strain and electrical conductivity decreases, however, the oxide ion conductivity increases by the compressed strain due to the decreased hole and the increased interstitial oxygen concentration.
Phase evolution in sonochemically synthesized Fe3+ doped BaTiO3 nanocrystallites: structural, magnetic and ferroelectric characterisation
Authors: Dutta Dimple P. , Roy Mainak , Maiti Nandita , Tyagi Avesh K.
Published: March 2016

Sonochemically synthesized Fe3+ doped BaTiO3 nanostructures exhibiting phase transition and room temperature ferromagnetic and ferroelectric behaviour.
Layer-by-layer assembly of versatile nanoarchitectures with diverse dimensionality: a new perspective for rational construction of multilayer assemblies
Authors: Xiao Fang-Xing , Pagliaro Mario , Xu Yi-Jun , Liu Bin
Published: March 2016

Layer-by-layer (LbL) assembly of versatile nanoarchitectures with diverse dimensionality was systematically elucidated and future perspectives and challenges were discussed.
Catalytic conversion of cellulose to C2–C3glycols by dual association of a homogeneous metallic salt and a perovskite-supported platinum catalyst
Authors: Girard E. , Delcroix D. , Cabiac A.
Published: March 2016

Dual combinations of homogeneous metallic salts and heterogeneous platinum catalysts were explored for the conversion of cellulose to C2–C3glycols.
Large and porous carbon sheets derived from water hyacinth for high-performance supercapacitors
Authors: Wu Kai , Gao Biao , Su Jianjun , Peng Xiang , Zhang Xuming , Fu Jijiang , Peng Shunjin , Chu Paul K.
Published: March 2016

Large and porous carbon sheets derived from water hyacinths owns high specific surface and desirable microstructures ensuring large specific capacitance, excellent rate capability and superior cyclic stability for high performance supercapacitors.
Effect of hybridization of organoclay with carbon black on the transport, mechanical, and adhesion properties of nanocomposites based on bromobutyl/epoxidized natural rubber blends
Authors: Sankaran Kumar , Manoharan Partheban , Chattopadhyay Santanu , Nair Sujith , Govindan Unnikrishnan , Arayambath Sreejesh , Nando Golok B.
Published: March 2016

The formation of hybrid nanostructures improves the barrier properties significantly by increasing the path of diffusion of the permeant.
Cadmium and lead accumulation and low-molecular-weight organic acids secreted by roots in an intercropping of a cadmium accumulator Sonchus asper L. with Vicia faba L.
Authors: Zhan Fang-dong , Qin Li , Guo Xian-hua , Tan Jian-bo , Liu Ning-ning , Zu Yan-qun , Li Yuan
Published: March 2016

Intercropping reduced the crop Cd contents and enhanced the remediation, which was related to the roots LMWOAs exudation in soils.
Zinc ion-doped carbon dots with strong yellow photoluminescence
Authors: Cheng Jian , Wang Cai-Feng , Zhang Yan , Yang Shengyang , Chen Su
Published: March 2016

Carbon dots doped with zinc ions and displaying strong yellow photoluminescence and a QY of 51.2% were produced, as were various applications of these carbon dots.
Structure elucidation of a complex CO2-based organic framework material by NMR crystallography
Authors: Leclaire Julien , Poisson Guillaume , Ziarelli Fabio , Pepe Gerard , Fotiadu Frédéric , Paruzzo Federico M. , Rossini Aaron J. , Dumez Jean-Nicolas , Elena-Herrmann Bénédicte , Emsley Lyndon
Published: March 2016

A three-dimensional structural model of a complex CO2-based organic framework made from high molecular weight, self-assembled, flexible and multi-functional oligomeric constituents has been determined de novo by solid-state NMR including DNP-enhanced experiments.
Quantitative morphological characterization of bicontinuous Pickering emulsions via interfacial curvatures
Authors: Reeves Matthew , Stratford Kevin , Thijssen Job H. J.
Published: March 2016

Bicontinuous Pickering emulsions (bijels) are a physically interesting class of soft materials with many potential applications including catalysis, microfluidics and tissue engineering.
Microfluidic fabrication of stimuli-responsive microdroplets for acoustic and optical droplet vaporization
Authors: Zhu Zhiqiang , Wu Qiang , Li Guangbin , Han Shuya , Si Ting , Xu Ronald X.
Published: March 2016

We developed a flow-focusing microfluidic assay for fabricating stimuli-responsive microdroplets (SRMs) for imaging and therapeutic applications.
Modeling of phosphorus diffusion in silicon oxide and incorporation in silicon nanocrystals
Authors: Mastromatteo Massimo , De Salvador Davide , Napolitani Enrico , Arduca Elisa , Seguini Gabriele , Frascaroli Jacopo , Perego Michele , Nicotra Giuseppe , Spinella Corrado , Lenardi Cristina , Carnera Alberto
Published: March 2016

A complete description and modelization of P diffusion in SiO2 and P trapping in Si NCs embedded in the SiO2 matrix.
Visible-light-initiated difluoromethylation of arene diazonium tetrafluoroborates
Authors: Wu Ye-bin , Lu Guo-ping , Zhou Bao-jing , Bu Mei-jie , Wan Li , Cai Chun
Published: March 2016

A mild and efficient method for the radical addition of α-aryl-β,β-difluoroenol silyl with arene diazonium tetrafluoroborates at room temperature has been disclosed.
Pd(0)@UiO-68-AP: chelation-directed bifunctional heterogeneous catalyst for stepwise organic transformations
Authors: Li Yan-An , Yang Song , Liu Qi-Kui , Chen Gong-Jun , Ma Jian-Ping , Dong Yu-Bin
Published: March 2016

A bifunctional heterogeneous catalyst Pd(0)@UiO-68-AP based on a chelation-directed post-synthetic approach is reported.
Vertically aligned graphitic carbon nanosheet arrays fabricated from graphene oxides for supercapacitors and Li–O2 batteries
Authors: Zhao Guangyu , Zhang Li , Lv Jixian , Li Changle , Sun Kening
Published: March 2016

Vertically aligned graphitic carbon nanosheet arrays fabricated from graphene oxide by a facile and accessible method.
Transformation of zincblende nanoparticles into wurtzite microrods by a dissolution–regrowth process: an intergrowth homojunction with enhanced photocatalytic activity
Authors: Liu Maochang , Wang Bin , Zheng Yiqun , Xue Fei , Chen Yubin , Guo Liejin
Published: March 2016

A CdS intergrowth homojunction in the form of zincblende nanoparticle-decorated wurtzite microrods was prepared and showed superior activity for solar H2production.
O,S-Heterocyclic stannylenes: synthesis and reactivity
Authors: Karwasara Surendar , Jha Chandan Kumar , Sinhababu Soumen , Nagendran Selvarajan
Published: March 2016

Commercially availableN-oxide (2-mercaptopyridine-N-oxide) is used as a ligand instead of an oxidizing agent to stabilize the compounds of main group elements in low-valent states.
Translating diagnostic assays from the laboratory to the clinic: analytical and clinical metrics for device development and evaluation
Authors: Borysiak Mark D. , Thompson Matthew J. , Posner Jonathan D.
Published: March 2016

This tutorial review focuses on analytical and clinical metrics related to the design and evaluation of lab-on-a-chip diagnostic devices. We aim to provide standardized definitions and practical guidance for researchers working in this area.
Efficient visualization of H2S via a fluorescent probe with three electrophilic centres
Authors: Asthana Sharad Kumar , Kumar Ajit , Neeraj Neeraj , Shweta Shweta , Upadhyay K. K.
Published: March 2016

A meticulous design strategy of incorporating three electrophilic centres in an optical probe (FLA) led to the achievement of high sensitivity and rapid response time (40 s) towards H2S detection.
A surprising switch in absolute configuration of anti-inflammatory macrolactones
Authors: Tauber Johannes , Rohr Markus , Walter Thorsten , Schollmeyer Dieter , Rahn-Hotze Karin , Erkel Gerhard , Opatz Till
Published: March 2016

The absolute configuration of the strongly anti-inflammatory 14-deoxyoxacyclododecindione was determined as (14S,15R) which is opposite to the configuration of the structurally related but less bioactive (S)-curvularin.
Supermolecular assembly of polyoxoanion and metal–organic cationic units towards a model for core–shell nanostructures
Authors: Zhou Yang-Yang , Kong Ya-jie , Jia Qian-Qian , Yao Shuang , Yan Jing-Hui
Published: March 2016

Two novel core–shell-like molecular composites [NiL3]4[HVIV12VV6O42(PO4)] and [NiL2]4[HVIV12VV6O42(PO4)] were designed and synthesized, which exhibited electrocatalytic activity for the reduction of H2O2 and oxidation of NO2−.
Formation of calcium phosphate nanostructures under the influence of self-assembling hybrid elastin-like-statherin recombinamers
Authors: Misbah M. Hamed , Espanol M. , Quintanilla Luis , Ginebra M. P. , Rodríguez-Cabello J. Carlos
Published: March 2016

The self-assembly properties of elastin-like-statherin recombinamers have great influence on calcium phosphate mineralization.
Palladium nanoparticles modified electrospun CoFe2O4 nanotubes with enhanced peroxidase-like activity for colorimetric detection of hydrogen peroxide
Authors: Yang Zezhou , Zhang Zhen , Jiang Yanzhou , Chi Maoqiang , Nie Guangdi , Lu Xiaofeng , Wang Ce
Published: March 2016

Herein, we report a simple procedure to decorate small palladium nanoparticles (Pd NPs) on the surface of CoFe2O4 nanotubes; the decorated nanotubes possess intrinsic peroxidase-like activity for the sensitive detection of H2O2.
Green synthesis of palladium nanoparticles via branched polymers: a bio-based nanocomposite for C–C coupling reactions
Authors: Wu Changyan , Peng Xinwen , Zhong Linxin , Li Xuehui , Sun Runcang
Published: March 2016

Renewable and sustainable CMH was the natural ligand for CMH–Pd(0) nanocomposite which was as an efficient and recyclable catalyst for Heck reaction.
Growth and highly efficient third harmonic generation of ammonium dihydrogen phosphate crystals
Authors: Feng Xi , Zhu Lili , Li Fuquan , Wang Fang , Han Wei , Wang Zhengping , Zhu Qihua , Sun Xun
Published: March 2016

ADP crystals were grown, and their optical properties including third harmonic generation were measured.
Increasing cell viability using Cd-free – InP/ZnS@silica@layered double hydroxide – materials for biological labeling
Authors: Serrano Iván Castelló , Stoica Georgiana , Palomares Emilio
Published: March 2016

In this work we describe the synthesis and characterization of InP/ZnS@silica@LDH nanoparticles and, moreover, their use as biomarkers.
Hierarchical LiNi0.8Co0.15Al0.05O2 plates with exposed {010} active planes as a high performance cathode material for Li-ion batteries
Authors: Wang Zhen , Liu Heng , Wu Jian , Lau Woon-Ming , Mei Jun , Liu Hao , Liu Guobiao
Published: March 2016

Hierarchical LiNi0.8Co0.15Al0.05O2 plates with exposed {010} active planes deliver a discharge capacity of 124 mA h g−1 at 10C.
Tuning the electronic properties in TaNx/Ag nanocomposite thin films
Authors: Gao Haitao , Li Yanhuai , Li Cuilan , Ma Fei , Song Zhongxiao , Xu Kewei
Published: March 2016

The temperature coefficient of resistance (TCR) of TaNx/Ag nanocomposite thin films could be substantially tuned by changing the components, even down to zero.
Reversible coupling of 4-nitroaniline molecules to 4-aminothiophenol functionalized on Ag nanoparticle/graphene oxide nanocomposites through the plasmon assisted chemical reaction
Authors: Tasi Ting-Ti , Lin Tsung-Wu , Shao Li-Dong , Shen Hsin-Hui
Published: March 2016

In this study, we demonstrate the formation of azo compounds on a composite of silver nanoparticles and graphene oxides (Ag@G) through a plasmon-assisted coupling reaction between different amine compounds.
Proton induced aggregation of water soluble isophthalic acid appended arylene diimides: justification with perylene derivative
Authors: Bag Kausik , Sukul Pradip Kumar , Chandra Santra Dines , Roy Arkapal , Malik Sudip
Published: March 2016

We report the self-assembly behaviour of five water soluble arylene diimides based on benzene, naphthalene and perylene moieties, by utilizing the essentiality of two major reversible supramolecular interactions, π-stacking and hydrogen bonding.
Enhanced sensitivity of quartz tuning fork sensors using electrospun polymer wires
Authors: Kim Wuseok , Yun Minhyuk , Lee Seongjae , Jeon Sangmin
Published: March 2016

A PMMA nanowire was prepared by electrospinning and attached to a quartz tuning fork. We investigated the PMMA wire-coated QTF as a humidity sensor and enhanced the sensitivity without affecting the response time by increasing the number of wires.