bluuebunny/crossref_metadata_2025 huggingface dataset:
The RNA binding protein HuR determines the differential translation of autism-associated FoxP subfamily members in the developing neocortex
Authors: Popovitchenko T. , Thompson K. , Viljetic B. , Jiao X. , Kontonyiannis D. L. , Kiledjian M. , Hart R. P. , Rasin M. R.
Published: July 2016

Forkhead-box domain (Fox) containing family members are known to play a role in neocorticogenesis and have also been associated with disorders on the autism spectrum. Here we show that a single RNA-binding protein, Hu antigen R (HuR), dictates translation specificity of bound mRNAs and is sufficient to define distinct Foxp-characterized subpopulations of neocortical projection neurons. Furthermore, distinct phosphorylation states of HuR differentially regulate translation of Foxp mRNAs in vitro. This demonstrates the importance of RNA binding proteins within the framework of the developing brain and further confirms the role of mRNA translation in autism pathogenesis.
TRPC6 channel activation promotes neonatal glomerular mesangial cell apoptosis via calcineurin/NFAT and FasL/Fas signaling pathways
Authors: Soni Hitesh , Adebiyi Adebowale
Published: July 2016

Glomerular mesangial cell (GMC) proliferation and death are involved in the pathogenesis of glomerular disorders. The mechanisms that control GMC survival are poorly understood, but may include signal transduction pathways that are modulated by changes in intracellular Ca2+([Ca2+]i) concentration. In this study, we investigated whether activation of the canonical transient receptor potential (TRPC) 6 channels and successive [Ca2+]ielevation alter neonatal GMC survival. Hyperforin (HF)-induced TRPC6 channel activation increased [Ca2+]iconcentration, inhibited proliferation and triggered apoptotic cell death in primary neonatal pig GMCs. HF-induced neonatal GMC apoptosis was not associated with oxidative stress. However, HF-induced TRPC6 channel activation stimulated nuclear translocation of the nuclear factor of activated T-cells, cytoplasmic 1 (NFATc1). HF also increased cell death surface receptor Fas ligand (FasL) level and caspase-8 activity in the cells; effects mitigated by [Ca2+]ichelator BAPTA, calcineurin/NFAT inhibitor VIVIT and TRPC6 channel knockdown. Accordingly, HF-induced neonatal GMC apoptosis was attenuated by BAPTA, VIVIT, Fas blocking antibody and a caspase-3/7 inhibitor. These findings suggest that TRPC6 channel-dependent [Ca2+]ielevation and the ensuing induction of the calcineurin/NFAT, FasL/Fas and caspase signaling cascades promote neonatal pig GMC apoptosis.
Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification
Authors: Moudjou Mohammed , Chapuis Jérôme , Mekrouti Mériem , Reine Fabienne , Herzog Laetitia , Sibille Pierre , Laude Hubert , Vilette Didier , Andréoletti Olivier , Rezaei Human , Dron Michel , Béringue Vincent
Published: July 2016

Prions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrPC glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrPC species of interest as substrate. Applying the technique to PrPC glycosylation mutants expressing cells revealed that neither PrPC nor PrPSc glycoform stoichiometry was instrumental to PrPSc formation and strainness perpetuation. Our study supports the view that strain properties, including PrPSc glycotype are enciphered within PrPSc structural backbone, not in the attached glycans.
The effects of cytosine methylation on general transcription factors
Authors: Jin Jianshi , Lian Tengfei , Gu Chan , Yu Kai , Gao Yi Qin , Su Xiao-Dong
Published: July 2016

DNA methylation on CpG sites is the most common epigenetic modification. Recently, methylation in a non-CpG context was found to occur widely on genomic DNA. Moreover, methylation of non-CpG sites is a highly controlled process and its level may vary during cellular development. To study non-CpG methylation effects on DNA/protein interactions, we have chosen three human transcription factors (TFs): glucocorticoid receptor (GR), brain and muscle ARNT-like 1 (BMAL1) - circadian locomotor output cycles kaput (CLOCK) and estrogen receptor (ER) with methylated or unmethylated DNA binding sequences, using single-molecule and isothermal titration calorimetry assays. The results demonstrated that these TFs interact with methylated DNA with different effects compared with their cognate DNA sequences. The effects of non-CpG methylation on transcriptional regulation were validated by cell-based luciferase assay at protein level. The mechanisms of non-CpG methylation influencing DNA-protein interactions were investigated by crystallographic analyses and molecular dynamics simulation. With BisChIP-seq assays in HEK-293T cells, we found that GR can recognize highly methylated sites within chromatin in cells. Therefore, we conclude that non-CpG methylation of DNA can provide a mechanism for regulating gene expression through directly affecting the binding of TFs.
The transcriptomes of novel marmoset monkey embryonic stem cell lines reflect distinct genomic features
Authors: Debowski Katharina , Drummer Charis , Lentes Jana , Cors Maren , Dressel Ralf , Lingner Thomas , Salinas-Riester Gabriela , Fuchs Sigrid , Sasaki Erika , Behr Rüdiger
Published: July 2016

Embryonic stem cells (ESCs) are useful for the study of embryonic development. However, since research on naturally conceived human embryos is limited, non-human primate (NHP) embryos and NHP ESCs represent an excellent alternative to the corresponding human entities. Though, ESC lines derived from naturally conceived NHP embryos are still very rare. Here, we report the generation and characterization of four novel ESC lines derived from natural preimplantation embryos of the common marmoset monkey (Callithrix jacchus). For the first time we document derivation of NHP ESCs derived from morula stages. We show that quantitative chromosome-wise transcriptome analyses precisely reflect trisomies present in both morula-derived ESC lines. We also demonstrate that the female ESC lines exhibit different states of X-inactivation which is impressively reflected by the abundance of the lncRNA X inactive-specific transcript (XIST). The novel marmoset ESC lines will promote basic primate embryo and ESC studies as well as preclinical testing of ESC-based regenerative approaches in NHP.
The presence of bacteria within tissue provides insights into the pathogenesis of oral lichen planus
Authors: Choi Yun Sik , Kim Yunji , Yoon Hye-Jung , Baek Keum Jin , Alam Jehan , Park Hee Kyung , Choi Youngnim
Published: July 2016

Oral lichen planus (OLP) is a chronic T cell-mediated mucocutaneous disease of unknown etiopathogenesis. Although various antigens have been considered, what actually triggers the inflammatory response of T cells is unknown. In the present study, we propose that intracellular bacteria present within tissues trigger T cell infiltration and provide target antigens. Sections of OLP (n = 36) and normal (n = 10) oral mucosal tissues were subjected to in situ hybridization using a universal probe targeting the bacterial 16S rRNA gene and immunohistochemistry with anti-CD3, anti-CD4, anti-CD8, and anti-macrophage-specific antibodies. Bacteria were abundant throughout the epithelium and the lamina propria of OLP tissues, which exhibited positive correlations with the levels of infiltrated CD3+, CD4+, and CD8+ cells. Furthermore, bacteria were detected within the infiltrated T cells. Pyrosequencing analysis of the mucosal microbiota from OLP patients (n = 13) and control subjects (n = 11) revealed a decrease in Streptococcus and increases in gingivitis/periodontitis-associated bacteria in OLP lesions. Using the selected bacterial species, we demonstrated that certain oral bacteria damage the epithelial physical barrier, are internalized into epithelial cells or T cells, and induce production of T cell chemokines CXCL10 and CCL5. Our findings provide insights into the pathogenesis of OLP.
Amyloid precursor protein expression and processing are differentially regulated during cortical neuron differentiation
Authors: Bergström Petra , Agholme Lotta , Nazir Faisal Hayat , Satir Tugce Munise , Toombs Jamie , Wellington Henrietta , Strandberg Joakim , Bontell Thomas Olsson , Kvartsberg Hlin , Holmström Maria , Boreström Cecilia , Simonsson Stina , Kunath Tilo , Lindahl Anders , Blennow Kaj , Hanse Eric , Portelius Erik , Wray Selina , Zetterberg Henrik
Published: July 2016

Amyloid precursor protein (APP) and its cleavage product amyloid β (Aβ) have been thoroughly studied in Alzheimer’s disease. However, APP also appears to be important for neuronal development. Differentiation of induced pluripotent stem cells (iPSCs) towards cortical neurons enables in vitro mechanistic studies on human neuronal development. Here, we investigated expression and proteolytic processing of APP during differentiation of human iPSCs towards cortical neurons over a 100-day period. APP expression remained stable during neuronal differentiation, whereas APP processing changed. α-Cleaved soluble APP (sAPPα) was secreted early during differentiation, from neuronal progenitors, while β-cleaved soluble APP (sAPPβ) was first secreted after deep-layer neurons had formed. Short Aβ peptides, including Aβ1-15/16, peaked during the progenitor stage, while processing shifted towards longer peptides, such as Aβ1-40/42, when post-mitotic neurons appeared. This indicates that APP processing is regulated throughout differentiation of cortical neurons and that amyloidogenic APP processing, as reflected by Aβ1-40/42, is associated with mature neuronal phenotypes.
Local coexistence of VO2 phases revealed by deep data analysis
Authors: Strelcov Evgheni , Ievlev Anton , Belianinov Alex , Tselev Alexander , Kolmakov Andrei , Kalinin Sergei V.
Published: July 2016

We report a synergistic approach of micro-Raman spectroscopic mapping and deep data analysis to study the distribution of crystallographic phases and ferroelastic domains in a defected Al-doped VO2 microcrystal. Bayesian linear unmixing revealed an uneven distribution of the T phase, which is stabilized by the surface defects and uneven local doping that went undetectable by other classical analysis techniques such as PCA and SIMPLISMA. This work demonstrates the impact of information recovery via statistical analysis and full mapping in spectroscopic studies of vanadium dioxide systems, which is commonly substituted by averaging or single point-probing approaches, both of which suffer from information misinterpretation due to low resolving power.
The adipokine lipocalin-2 in the context of the osteoarthritic osteochondral junction
Authors: Villalvilla Amanda , García-Martín Adela , Largo Raquel , Gualillo Oreste , Herrero-Beaumont Gabriel , Gómez Rodolfo
Published: July 2016

Obesity and osteoarthritis (OA) form a vicious circle in which obesity contributes to cartilage destruction in OA, and OA-associated sedentary behaviour promotes weight gain. Lipocalin-2 (LCN2), a novel adipokine with catabolic activities in OA joints, contributes to the obesity and OA pathologies and is associated with other OA risk factors. LCN2 is highly induced in osteoblasts in the absence of mechanical loading, but its role in osteoblast metabolism is unclear. Therefore, because osteochondral junctions play a major role in OA development, we investigated the expression and role of LCN2 in osteoblasts and chondrocytes in the OA osteochondral junction environment. Our results showed that LCN2 expression in human osteoblasts and chondrocytes decreased throughout osteoblast differentiation and was induced by catabolic and inflammatory factors; however, TGF-β1 and IGF-1 reversed this induction. LCN2 reduced osteoblast viability in the presence of iron and enhanced the activity of MMP-9 released by osteoblasts. Moreover, pre-stimulated human osteoblasts induced LCN2 expression in human chondrocytes, but the inverse was not observed. Thus, LCN2 is an important catabolic adipokine in osteoblast and chondrocyte metabolism that is regulated by differentiation, inflammation and catabolic and anabolic stimuli, and LCN2 expression in chondrocytes is regulated in a paracrine manner after osteoblast stimulation.
An investigation of the antibacterial ability and cytotoxicity of a novel cu-bearing 317L stainless steel
Authors: Sun Da , Xu Dake , Yang Chunguang , Shahzad M. Babar , Sun Ziqing , Xia Jin , Zhao Jinlong , Gu Tingyue , Yang Ke , Wang Guixue
Published: July 2016

In order to solve the challenging problem of microbial infections caused by microorganisms on medical implants, it is imperative to develop novel antimicrobial biomaterials. This work demonstrated that 317L-Cu stainless steel (SS), created by adding copper through a solution and aging heat treatment process, exhibited good antibacterial properties against staphylococcus aureus, achieving 2 log reduction of planktonic cells after 5 days of incubation. In this study, the antibacterial test was performed using the plate count method, the fluorescence cell staining method and the quantitative polymerase chain reaction (qPCR) method. It is well known that a high concentration of copper ion can lead to cytotoxicity. This work explored the cytotoxicity of 317L-Cu SS through real-time cell analysis (RTCA). Experimental results demonstrated that the 317L-Cu SS possessed a satisfactory antibacterial ability against S. aureus, and the antibacterial rate based on the reduction of sessile cell count reached 98.3% after 24-hour treatment. The bacterial adhesion and the biofilm thickness were considerably reduced by the 317L-Cu SS. The results of RTCA suggested that 317L-Cu SS did not introduce cytotoxicity to mouse cells, indicating its suitability as a medical implant material.
Evolution equation for quantum coherence
Authors: Hu Ming-Liang , Fan Heng
Published: July 2016

The estimation of the decoherence process of an open quantum system is of both theoretical significance and experimental appealing. Practically, the decoherence can be easily estimated if the coherence evolution satisfies some simple relations. We introduce a framework for studying evolution equation of coherence. Based on this framework, we prove a simple factorization relation (FR) for the l1 norm of coherence and identified the sets of quantum channels for which this FR holds. By using this FR, we further determine condition on the transformation matrix of the quantum channel which can support permanently freezing of the l1 norm of coherence. We finally reveal the universality of this FR by showing that it holds for many other related coherence and quantum correlation measures.
Effect of the environment on the secondary metabolic profile of Tithonia diversifolia: a model for environmental metabolomics of plants
Authors: Sampaio Bruno Leite , Edrada-Ebel RuAngelie , Da Costa Fernando Batista
Published: July 2016

Tithonia diversifolia is an invasive weed commonly found in tropical ecosystems. In this work, we investigate the influence of different abiotic environmental factors on the plant’s metabolite profile by multivariate statistical analyses of spectral data deduced by UHPLC-DAD-ESI-HRMS and NMR methods. Different plant part samples of T. diversifolia which included leaves, stems, roots and inflorescences were collected from two Brazilian states throughout a 24-month period, along with the corresponding monthly environmental data. A metabolomic approach employing concatenated LC-MS and NMR data was utilised for the first time to study the relationships between environment and plant metabolism. A seasonal pattern was observed for the occurrence of metabolites that included sugars, sesquiterpenes lactones and phenolics in the leaf and stem parts, which can be correlated to the amount of rainfall and changes in temperature. The distribution of the metabolites in the inflorescence and root parts were mainly affected by variation of some soil nutrients such as Ca, Mg, P, K and Cu. We highlight the environment-metabolism relationship for T. diversifolia and the combined analytical approach to obtain reliable data that contributed to a holistic understanding of the influence of abiotic environmental factors on the production of metabolites in various plant parts.
Static and Dynamical Properties of heavy actinide Monopnictides of Lutetium
Authors: Mir Showkat H. , Jha Prakash C. , Islam M. S. , Banerjee Amitava , Luo Wei , Dabhi Shweta D. , Jha Prafulla K. , Ahuja R.
Published: July 2016

In this work, density functional theory within the framework of generalized gradient approximation has been used to investigate the structural, elastic, mechanical, and phonon properties of lutetium monopnictides in rock-salt crystal structure. The spin orbit coupling and Hubbard-U corrections are included to correctly predict the essential properties of these compounds. The elastic constants, Young’s modulus E, Poisson’s ratio v, shear modulus G, anisotropy factor A and Pugh’s ratio are computed. We found that all lutetium monopnictides are anisotropic and show brittle character. From the wave velocities along [100], [110] and [111] directions, melting temperature of lutetium monopnictides are predicted. Dynamical stability of these monopnictides has been studied by density functional perturbation theory.
Inferring phylogeny and speciation of Gymnosporangium species and their coevolution with host plants
Authors: Zhao Peng , Liu Fang , Li Ying-Ming , Cai Lei
Published: July 2016

Gymnosporangium species (Pucciniaceae, Pucciniales) cause serious diseases and significant economic losses to apple cultivars. Most of the reported species are heteroecious and complete their life cycles on two different plant hosts belonging to two unrelated genera, i.e. Juniperus and Malus. However, the phylogenetic relationships among Gymnosporangium species and the evolutionary history of Gymnosporangium on its aecial and telial hosts were still undetermined. In this study, we recognized species based on rDNA sequence data by using coalescent method of generalized mixed Yule-coalescent (GMYC) and Poisson Tree Processes (PTP) models. The evolutionary relationships of Gymnosporangium species and their hosts were investigated by comparing the cophylogenetic analyses of Gymnosporangium species with Malus species and Juniperus species, respectively. The concordant results of GMYC and PTP analyses recognized 14 species including 12 known species and two undescribed species. In addition, host alternations of 10 Gymnosporangium species were uncovered by linking the derived sequences between their aecial and telial stages. This study revealed the evolutionary process of Gymnosporangium species and clarified that the aecial hosts played more important roles than telial hosts in the speciation of Gymnosporangium species. Host switch, losses, duplication and failure to divergence all contributed to the speciation of Gymnosporangium species.
Phenol-soluble modulin α4 mediates Staphylococcus aureus-associated vascular leakage by stimulating heparin-binding protein release from neutrophils
Authors: li Lin , Pian Yaya , Chen Shaolong , Hao Huaijie , Zheng Yuling , Zhu Li , Xu Bin , Liu Keke , Li Min , Jiang Hua , Jiang Yongqiang
Published: July 2016

Vascular leakage frequently occurs in patients with severe Staphylococcus aureus infection. However, the mechanism underlying S. aureus infection-induced vascular leakage remains unclear. Here, we identified the S. aureus virulence factor phenol-soluble modulin (PSM)α4 from the culture supernatant of strain USA300 as a stimulator of heparin-binding protein (HBP) release from polymorphonuclear neutrophils (PMNs) and demonstrated that PSMα4-induced HBP release from PMNs leads to vascular leakage. PSMα4 appeared less cytolytic than PSMα1–3 and was insensitive to lipoproteins; it significantly increased myeloperoxidase and elastase release from PMNs and cell surface CD63 expression in PMNs. PSMα4-induced HBP release required formyl peptide receptor 2 (FPR2) and phosphoinositide 3-kinase (PI3K) and depended on Ca2+ influx and cytoskeleton rearrangement. Thus, PSMα4 may stimulate HBP release by activating FPR2 and PI3K to initiate PMN degranulation. PSMα4-induced HBP release from PMNs increased endothelial cell monolayer permeability in vitro and induced vascular leakage in mice. This novel function of PSMα4 may contribute to the pathogenesis of S. aureus and may be a potential therapeutic target.
The relationship between sex change and reproductive success in a protandric marine gastropod
Authors: Brante Antonio , Quiñones Adriana , Silva Francisco
Published: July 2016

Protandric species switch sex during their lifetime. According to theory, the time (body size) at which sex change occurs is determined by the reproductive success of individuals affected by social interactions as well as by post-copulatory factors. Experimental evidence is biased to few social systems making the exploration of general patterns difficult. We used the protandric marine gastropod Crepidula coquimbensis that partakes in intrabrood sibling cannibalism to test the following hypotheses: 1. Male-male competition for access to females and sibling cannibalism determine male reproductive success; 2. Males with greater access to females and with higher reproductive success will have reduced growth rates and will delay sex change. Artificial aggregations with different social structures were constructed and male reproductive success was estimated by paternity analysis. The results supported our expectations showing that male competitive ability for access to the female, time spent by males in the copulatory position and sibling cannibalism affect reproductive success and influence time to sex change, with less successful males hastening sex change. Also, males that spent more time in the copulatory position had reduced growth rates. Comparing these results with those reported for other sequential hermaphrodites provides evidence supporting general patterns of sex change in nature.
Limits of Peripheral Blood Mononuclear Cells for Gene Expression-Based Biomarkers in Juvenile Idiopathic Arthritis
Authors: Wong Laiping , Jiang Kaiyu , Chen Yanmin , Hennon Teresa , Holmes Lucy , Wallace Carol A. , Jarvis James N.
Published: July 2016

Juvenile Idiopathic Arthritis (JIA) is one of the most common chronic disease conditions affecting children in the USA. As with many rheumatic diseases, there is growing interest in using genomic technologies to develop biomarkers for either diagnosis or to guide treatment (“personalized medicine”). Here, we explore the use of gene expression patterns in peripheral blood mononuclear cells (PBMC) as a first step approach to developing such biomarkers. Although PBMC carry many theoretical advantages for translational research, we have found that sample heterogeneity makes RNASeq on PBMC unsuitable as a first-step method for screening biomarker candidates in JIA. RNASeq studies of homogeneous cell populations are more likely to be useful and informative.
Green tea catechins are potent anti-oxidants that ameliorate sodium iodate-induced retinal degeneration in rats
Authors: Yang Yaping , Qin Yong Jie , Yip Yolanda W. Y. , Chan Kwok Ping , Chu Kai On , Chu Wai Kit , Ng Tsz Kin , Pang Chi Pui , Chan Sun On
Published: July 2016

Green tea extracts exhibit anti-oxidative and anti-inflammatory actions in different disease conditions. We hypothesized that green tea extract and its catechin constituents ameliorate sodium iodate-induced retinal degeneration in rats by counteracting oxidative stress. In this study, adult Sprague-Dawley rats were intravenously injected with a single dose of sodium iodate. Green tea extract (GTE; Theaphenon-E) or combinations of its catechin constituents, including (−)-epigallocatechin gallate (EGCG), were administered intra-gastrically before injection. Live imaging analysis using confocal scanning laser ophthalmoscopy and spectral-domain optical coherence tomography showed a progressive increase of degenerating profile across the retinal surface and decrease in thickness of outer nuclear layer (ONL) at Day-14 of post-injection. These lesions were significantly ameliorated by Theaphenon-E and catechin combinations with EGCG. Catechins with exclusion of EGCG did not show obvious protective effect. Histological analyses confirmed that Theaphenon-E and catechins containing EGCG protect the retina by reducing ONL disruption. Retinal protective effects were associated with reduced expression of superoxide dismutase, glutathione peroxidase and caspase-3 and suppression of 8-iso-Prostaglandin F2α generation in the retina. In summary, GTE and its catechin constituents are potent anti-oxidants that offer neuroprotection to the outer retinal degeneration after sodium iodate insult, among which EGCG is the most active constituent.
Investigation of absorptance and emissivity of thermal control coatings on Mg–Li alloys and OES analysis during PEO process
Authors: Yao Zhongping , Xia Qixing , Ju Pengfei , Wang Jiankang , Su Peibo , Li Dongqi , Jiang Zhaohua
Published: July 2016

Thermal control ceramic coatings on Mg–Li alloys have been successfully prepared in silicate electrolyte system by plasma electrolytic oxidation (PEO) method. The PEO coatings are mainly composed of crystallized Mg2SiO4 and MgO, which have typical porous structure with some bulges on the surface; OES analysis shows that the plasma temperature, which is influenced by the technique parameters, determines the formation of the coatings with different crystalline phases and morphologies, combined with “quick cooling effect” by the electrolyte; and the electron concentration is constant, which is related to the electric spark breakdown, determined by the nature of the coating and the interface of coating/electrolyte. Technique parameters influence the coating thickness, roughness and surface morphology, but do not change the coating composition in the specific PEO regime, and therefore the absorptance (αS) and emissivity (ε) of the coatings can be adjusted by the technique parameters through changing thickness and roughness in a certain degree. The coating prepared at 10 A/dm2, 50 Hz, 30 min and 14 g/L Na2SiO3 has the minimum value of αS (0.35) and the maximum value of ε (0.82), with the balance temperature of 320 K.
Ocular biometric parameters among 3-year-old Chinese children: testability, distribution and association with anthropometric parameters
Authors: Huang Dan , Chen Xuejuan , Gong Qi , Yuan Chaoqun , Ding Hui , Bai Jing , Zhu Hui , Fu Zhujun , Yu Rongbin , Liu Hu
Published: July 2016

This survey was conducted to determine the testability, distribution and associations of ocular biometric parameters in Chinese preschool children. Ocular biometric examinations, including the axial length (AL) and corneal radius of curvature (CR), were conducted on 1,688 3-year-old subjects by using an IOLMaster in August 2015. Anthropometric parameters, including height and weight, were measured according to a standardized protocol and body mass index (BMI) was calculated. The testability was 93.7% for the AL and 78.6% for the CR overall and both measures improved with age. Girls performed slightly better in AL measurements (P = 0.08) and the difference in CR was statistically significant (P < 0.05). The AL distribution was normal in girls (P = 0.12), whereas it was not in boys (P < 0.05). For CR1, all subgroups presented normal distributions (P = 0.16 for boys;P = 0.20 for girls), but the distribution varied when the subgroups were combined (P < 0.05). CR2 presented a normal distribution (P = 0.11), whereas the AL/CR ratio was abnormal (P < 0.001). Boys exhibited a significantly longer AL, a greater CR and a greater AL/CR ratio than girls (allP < 0.001).
Hydrogenation of 2-methyl-3-butyn-2-ol over a Pd/ZnO catalyst: kinetic model and selectivity study
Authors: Vernuccio S. , Goy R. , Rudolf von Rohr Ph. , Medlock J. , Bonrath W.
Published: July 2016

The three-phase hydrogenation of 2-methyl-3-butyn-2-ol has been studied over a Pd/ZnO catalyst. A mathematical model has been proposed to predict the behavior of the system in the typical operating ranges if industrial reactors.
Continuous Flow Synthesis of Dimethylalkynylaluminum Reagents
Authors: Piccardi Riccardo , Coffinet Anais , Benedetti Erica , Turcaud Serge , Micouin Laurent
Published: July 2016

A new process for the synthesis of dimethylalkynylaluminum reagents under flow conditions is described. It involves a base-catalyzed alumination of terminal alkynes using a resin-supported organocatalyst. Final organometallic species are obtained in solution, and can further react with various aldehydes or nitrones.
Palladium-Catalyzed C(sp3)–C(sp2) Cross-Couplings of O-(α-Bromoacyl) Cyanohydrins with Boronic Acids: An Entry to Enantio­enriched N-Acylated β-Amino Alcohols
Authors: Hertzberg Robin , Dinér Peter , Moberg Christina
Published: July 2016

Suzuki-type cross-coupling of enantiomerically enriched O-(α-bromoacyl) cyanohydrins with aromatic boronic acids substituted with electron-withdrawing or electron-donating groups gave the expected coupling products in high yields without racemization. These substrates exhibit higher reactivities than analogous substrates lacking the nitrile function, probably as a result of π-coordination of the nitrile to palladium. Reduction of the nitrile group of the products, with accompanying intramolecular acyl transfer, provides access to biologically interesting N-acylated β-amino alcohols.
Cascade of parametric resonances in coupled Josephson junctions
Authors: Shukrinov Yu. M. , Azemtsa-Donfack H. , Rahmonov I. R. , Botha A. E.
Published: July 2016

We found that the coupled system of Josephson junctions under external electromagnetic radiation demonstrates a cascade of parametric instabilities. These instabilities appear along the IV characteristics within bias current intervals corresponding to Shapiro step subharmonics and lead to charging in the superconducting layers. The amplitudes of the charge oscillations increase with increasing external radiation power. We demonstrate the existence of longitudinal plasma waves at the corresponding bias current values. An essential advantage of the parametric instabilities in the case of subharmonics is the lower amplitude of radiation that is needed for the creation of the longitudinal plasma wave. This fact gives a unique possibility to create and control longitudinal plasma waves in layered superconductors. We propose a novel experiment for studying parametric instabilities and the charging of superconducting layers based on the simultaneous variation of the bias current and radiation amplitude.
Raman scattering in multiferroic SmFe3(BO3)4
Authors: Peschanskii A. V. , Fomin V. I. , Gudim I. A.
Published: July 2016

Raman spectrum of single-crystal SmFe3(BO3)4 was studied in the frequency range from 3 to 1500 cm−1 at temperatures 10–300 K. All the A1 and E phonon modes predicted by the group theory for a given symmetry of the crystal were observed. The magnitudes of splitting between the LO and TO components of polar E phonons were determined. It was found that under the transition to a magnetically ordered phase, the behavior of the intensity of the line corresponding to the A1 vibrational mode is anomalous. It was shown that at low temperatures the spectrum of two-magnon excitations has a complex shape and is observed with both nondiagonal and diagonal components of the scattering tensor. This complex shape reflects the features in the density of states of the magnetic branches. An estimate of the magnon energy Em at the Brillouin zone boundary gave ∼47 cm−1. The structure of the ground multiplet 6H5/2 of a Sm+3 ion in paramagnetic and antiferromagnetic states as well as the effect of the magnetic phase transition on it were studied. Electron-phonon interaction for the electronic excitation at 225 cm−1 was revealed.
Torque magnetometry of perpendicular anisotropy exchange-spring heterostructures
Authors: Vallobra P. , Hauet T. , Montaigne F. , Shipton E. G. , Fullerton E. E. , Mangin S.
Published: July 2016

The field-induced magnetic configurations in a [Co/Pd]15 /TbFeCo exchange-spring system with perpendicular magnetic anisotropy are studied using torque magnetometry. The experimental results are compared to a 1D micromagnetic simulation. The good agreement between experiments and simulations allows us to deduce the evolution of the in-depth magnetic configuration as a function of the applied field orientation and amplitude. The chirality transition of the interfacial domain wall developing in the structure can also be determined with this technique.
Quasi-static magnetic properties and high-frequency energy losses in CoFe2O4 nanoparticles
Authors: Tykhonenko-Polishchuk Yu. O. , Kulyk N. N. , Yelenich O. V. , Bečyte V. , Mažeika K. , Kalita V. M. , Belous A. G. , Tovstolytkin A. I.
Published: July 2016

Two series of nanosized cobalt spinel ferrites CoFe2O4 are synthesized from metal salts using high-energy ball milling with the addition of NaCl as a growth agent (series CFO-NaCl), and without (CFO Series). The particle properties are characterized using atomic force microscopy, as well as magnetic and calorimetric measurements. It is shown that the average sizes of the nanoparticles were ∼5.6 and ∼10.3 nm for CFO and CFO-NaCl series, respectively. We performed magnetostatic measurements and determined the parameters that are required to analyze the magnetic state and remagnetization processes of the nanoparticles. It is shown that the blocking temperature is ≈160 K for CFO samples and ≈300 K for the CFO-NaCl series. It was concluded that at 293 K the CFO series particles exhibit a superparamagnetic state, whereas the CFO-NaCl series are in the blocked state. The specific loss power that is scattered by the synthesized nanoparticle ensembles placed in an alternating magnetic field, is measured experimentally and theoretically assessed. The nature of the processes that determine the thermal characteristics of the nanoparticles is analyzed.
Unintentional indium incorporation into barriers of InGaN/GaN multiple quantum wells studied by photoreflectance and photoluminescence excitation spectroscopy
Authors: Freytag Stefan , Feneberg Martin , Berger Christoph , Bläsing Jürgen , Dadgar Armin , Callsen Gordon , Nippert Felix , Hoffmann Axel , Bokov Pavel Yu. , Goldhahn Rüdiger
Published: July 2016

InxGa1–xN/GaN single and multi quantum well (MQW) structures with x ≈ 0.13 were investigated optically by photoreflectance, photoluminescence excitation spectroscopy, and luminescence. Clear evidence of unintentional indium incorporation into the nominal GaN barrier layers is found. The unintentional In content is found to be around 3%. Inhomogeneous distribution of In atoms occurs within the distinct quantum well (QW) layers, which is commonly described as statistical alloy fluctuation and leads to the characteristic S-shape temperature shift of emission energy. Furthermore, differences in emission energy between the first and the other QWs of a MQW stack are found experimentally. This effect is discussed with the help of model calculations and is assigned to differences in the confining potential due to unwanted indium incorporation for the upper QWs.
Coupled thermomechanical behavior of graphene using the spring-based finite element approach
Authors: Georgantzinos S. K. , Giannopoulos G. I. , Anifantis N. K.
Published: July 2016

The prediction of the thermomechanical behavior of graphene using a new coupled thermomechanical spring-based finite element approach is the aim of this work. Graphene sheets are modeled in nanoscale according to their atomistic structure. Based on molecular theory, the potential energy is defined as a function of temperature, describing the interatomic interactions in different temperature environments. The force field is approached by suitable straight spring finite elements. Springs simulate the interatomic interactions and interconnect nodes located at the atomic positions. Their stiffness matrix is expressed as a function of temperature. By using appropriate boundary conditions, various different graphene configurations are analyzed and their thermo-mechanical response is approached using conventional finite element procedures. A complete parametric study with respect to the geometric characteristics of graphene is performed, and the temperature dependency of the elastic material properties is finally predicted. Comparisons with available published works found in the literature demonstrate the accuracy of the proposed method.
Establishing the temperature dependency of vegetative and reproductive growth processes and their threshold temperatures of vineyard-grown Vitis vinifera cv. Semillon vines across the growing season
Authors: Greer Dennis H. , Weedon Mark M.
Published: July 2016

A hydrocooling system provided canopy temperature control of Vitis vinifera L. cv. Semillon vines at set points of 30, 35 and 40°C. The impacts on vegetative and reproductive growth over the growing season were assessed. Dynamics and rates of leaf expansion, bunch biomass and sugar accumulation were strongly affected by canopy temperatures – being highest at 30°C and lowest at 40°C. Leaf and stem biomass accumulation at 40°C was detrimentally affected but was otherwise little affected by temperature. Leaf expansion was earliest, leaf sizes greatest and rates of expansion all optimal at 30°C and all were strongly temperature dependent. Bunch biomass accumulation was earliest at 35°C but amount of biomass in bunches and rates were both highly temperature dependent and optimal at 30°C. Rates of sugar accumulation and total amounts accumulated at harvest were both highly temperature-dependent processes: fastest and greatest at 30°C. Many of the temperature-dependent processes decreased in rates and amounts linearly between 30 and 40°C. Despite the effects of temperature on bunch and berry growth, there were no treatment effects on the yield per vine. The study confirms that the threshold temperature for most processes was 35°C, where some depreciation in dry matter and sugar accumulation occurred, whereas 40°C was detrimental to all growth processes.
Susceptibility of coral assemblages to successive bleaching events at Moorea, French Polynesia
Authors: Carroll A. G. , Harrison P. L. , Adjeroud M.
Published: July 2016

In 2002, bleaching was reported throughout many Indo-Pacific coral-reef regions, including French Polynesia. Bleaching occurred again in French Polynesia in 2003, providing an opportunity to compare the effects of successive bleaching events on coral susceptibility. During 2002 and 2003, underwater video surveys were completed in stations at four depths (lagoon: 0–2, 2–4m; outer reef slope: 6–8, 12–14m) at two locations on the northern and north-western coast of Moorea (Society Archipelago) to compare the cover of healthy-appearing, the cover of partially bleached and the cover of fully bleached coral. Bleaching patterns were genus specific and differences in susceptibility among major genera were generally consistent between 2002 and 2003, with Acropora showing the greatest susceptibility. Some genera exhibited substantial spatial variability in bleaching susceptibility between years (e.g. Pocillopora, Montipora); however, this variability was significant only for fully bleached and partially bleached Acropora. Multivariate analyses showed that spatial patterns in the proportion of healthy-appearing coral were similar over time within the assemblages, whereas the cover of partially bleached and the cover of fully bleached coral were more variable among depths and locations. This variability has important implications for assessing changes to coral community structure over time and for estimating coral-reef resistance and resilience to future bleaching disturbance.
Influence of selected environmental factors on seed germination and seedling survival of the arid zone invasive species tobacco bush (Nicotiana glauca R. Graham)
Authors: Florentine Singarayer K. , Weller Sandra , Graz Patrick F. , Westbrooke Martin , Florentine Arunthathy , Javaid Mansoor , Fernando Nimesha , Chauhan Bhagirath S. , Dowling Kim
Published: July 2016

Tobacco bush (Nicotiana glauca R. Graham) is an aggressive invading species, which is active after disturbances such as high rainfall events and flooding. Past studies have focussed on population dynamics and allelopathic effects associated with the species, but little is known about its seed ecology. To address this dearth of information, this study aimed to investigate: (i) the effect of various stress factors (temperature, light, osmotic potential, salt stress, heat-shock, a combination of heat-shock and smoke, pH buffer, and burial depth of seed) on seed germination and seedling emergence, and (ii) factors affecting the fate of seedlings. The results show that N. glauca was able to germinate over a broad range of temperatures with highest seed germination occurring at 30/20°C with 12 h of light and 12 h of dark conditions. Seed germination was greatest (89%) when seeds were placed on the soil surface and emergence decreased considerably as planting depth increased from 0.5 to 1.5 cm. Water stress greatly reduced seed germination (58% germination at osmotic potentials below –0.2 MPa) and germination was completely inhibited at water potentials of –0.4 to –0.6 MPa. Although increasing salinity reduced the seed germination of this invasive species, N. glauca seed was able to germinate in both alkaline (81% at pH 10) and acidic (80% at pH 4) conditions. The trial on the effect of seed age and field seed burial on seed germination showed a slight decline in seed germination after 120 days of burial compared with non-buried seeds. Further, the combined effect of heat-shock and smoke effectively inhibited the germination of N. glauca seeds; however, our study shows that seedlings of N. glauca can withstand heat-shock of up to 130°C. Studies such as this will assist in the development of control strategies to prevent the spread of this invasive species into arid landscapes.
Prelude to War: The Russian Siege and Storming of the Fortress of Ganjeh, 1803–4
Authors: Bournoutian George
Published: July 2016

This essay is the full account, the first in English, of the correspondence between the Russian general, Paul Tsitsianov, and the governor of the khanate of Ganjeh, Javād Khān Qajar. Drawing on contemporary Russian and Iranian records, it includes a daily account of Tsitsianov’s preparation, siege and the storming of the fortress of Ganjeh, which led to the First Russo-Iranian War (1804–13). The essay further includes two special maps—the first is the map of the South Caucasus in 1800 and the route of the invasion; while the second is based on a rare Russian military map that reveals the siege and storming of the fortress.
Comparative assessment of fluorescent proteins for in vivo imaging in an animal model system
Authors: Heppert Jennifer K. , Dickinson Daniel J. , Pani Ariel M. , Higgins Christopher D. , Steward Annette , Ahringer Julie , Kuhn Jeffrey R. , Goldstein Bob
Published: July 2016

Fluorescent protein tags are fundamental tools used to visualize gene products and analyze their dynamics in vivo. Recent advances in genome editing have expedited the precise insertion of fluorescent protein tags into the genomes of diverse organisms. These advances expand the potential of in vivo imaging experiments and facilitate experimentation with new, bright, photostable fluorescent proteins. Most quantitative comparisons of the brightness and photostability of different fluorescent proteins have been made in vitro, removed from biological variables that govern their performance in cells or organisms. To address the gap, we quantitatively assessed fluorescent protein properties in vivo in an animal model system. We generated transgenic Caenorhabditis elegans strains expressing green, yellow, or red fluorescent proteins in embryos and imaged embryos expressing different fluorescent proteins under the same conditions for direct comparison. We found that mNeonGreen was not as bright in vivo as predicted based on in vitro data but is a better tag than GFP for specific kinds of experiments, and we report on optimal red fluorescent proteins. These results identify ideal fluorescent proteins for imaging in vivo in C. elegans embryos and suggest good candidate fluorescent proteins to test in other animal model systems for in vivo imaging experiments.
Improved reconstitution of yeast vacuole fusion with physiological SNARE concentrations reveals an asymmetric Rab(GTP) requirement
Authors: Zick Michael , Wickner William
Published: July 2016

In vitro reconstitution of homotypic yeast vacuole fusion from purified components enables detailed study of membrane fusion mechanisms. Current reconstitutions have yet to faithfully replicate the fusion process in at least three respects: 1) The density of SNARE proteins required for fusion in vitro is substantially higher than on the organelle. 2) Substantial lysis accompanies reconstituted fusion. 3) The Rab GTPase Ypt7 is essential in vivo but often dispensable in vitro. Here we report that changes in fatty acyl chain composition dramatically lower the density of SNAREs that are required for fusion. By providing more physiological lipids with a lower phase transition temperature, we achieved efficient fusion with SNARE concentrations as low as on the native organelle. Although fused proteoliposomes became unstable at elevated SNARE concentrations, releasing their content after fusion had occurred, reconstituted proteoliposomes with substantially reduced SNARE concentrations fused without concomitant lysis. The Rab GTPase Ypt7 is essential on both membranes for proteoliposome fusion to occur at these SNARE concentrations. Strikingly, it was only critical for Ypt7 to be GTP loaded on membranes bearing the R-SNARE Nyv1, whereas the bound nucleotide of Ypt7 was irrelevant on membranes bearing the Q-SNAREs Vam3 and Vti1.
Direct Regulation of Extracellular Chitinase Production by the Transcription Factor LeClp in Lysobacter enzymogenes OH11
Authors: Xu Huiyong , Chen Hongfu , Shen Yuemao , Du Liangcheng , Chou Shan-Ho , Liu Hongxia , Qian Guoliang , Liu Fengquan
Published: July 2016

Lysobacter enzymogenes is a gram-negative bacterial biological control agent that produces abundant extracellular enzymes capable of degrading the cell walls of fungal pathogens. In strain OH11, an isolate from China, the global regulator LeClp controls the production of extracellular chitinase by regulating the transcription of the chitinase-encoding gene chiA. Using a combination of bioinformatic, genetic, and biochemical methods, we show that LeClp regulates chiA transcription by directly binding to the chiA promoter region. Although LeClp appears to be important in this role, it is not the sole regulator of chiA transcription. Furthermore, the sequence analysis of putative LeClp binding sites indicated that the LeClp homolog could be involved in the regulation of extracellular chitinase production in diverse Lysobacter spp. by a mechanism similar to that in L. enzymogenes. Our findings present new insights into the molecular mechanism of LeClp in controlling extracellular chitinase activity, providing a fundamental road to elucidate how LeClp regulates the production of other extracellular lytic enzymes in L. enzymogenes.