bluuebunny/crossref_metadata_2025 huggingface dataset:
Export of piRNA precursors by EJC triggers assembly of cytoplasmic Yb-body in Drosophila
Authors: Dennis Cynthia , Brasset Emilie , Sarkar Arpita , Vaury Chantal
Published: December 2016

PIWI-interacting RNAs (piRNAs) are effectors of transposable element (TE) silencing in the reproductive apparatus. In Drosophila ovarian somatic cells, piRNAs arise from longer single-stranded RNA precursors that are processed in the cytoplasm presumably within the Yb-bodies. piRNA precursors encoded by the flamenco (flam) piRNA cluster accumulate in a single focus away from their sites of transcription. In this study, we identify the exportin complex containing Nxf1 and Nxt1 as required for flam precursor nuclear export. Together with components of the exon junction complex (EJC), it is necessary for the efficient transfer of flam precursors away from their site of transcription. Indeed, depletion of these components greatly affects flam intra-nuclear transit. Moreover, we show that Yb-body assembly is dependent on the nucleo-cytoplasmic export of flam transcripts. These results suggest that somatic piRNA precursors are thus required for the assembly of the cytoplasmic transposon silencing machinery.
Ecdysteroid-containing food supplements from Cyanotis arachnoidea on the European market: evidence for spinach product counterfeiting
Authors: Hunyadi Attila , Herke Ibolya , Lengyel Katalin , Báthori Mária , Kele Zoltán , Simon András , Tóth Gábor , Szendrei Kálmán
Published: December 2016

Phytoecdysteroids like 20-hydroxyecdysone (“ecdysterone”) can exert a mild, non-hormonal anabolic/adaptogenic activity in mammals, and as such, are frequently used in food supplements. Spinach is well-known for its relatively low ecdysteroid content. Cyanotis arachnoidea, a plant native in China, is among the richest sources of phytoecdysteroids, and extracts of this plant are marketed in tons per year amounts via the internet at highly competitive prices. Here we report the investigation of a series of food supplements produced in Germany and claimed to contain spinach extracts. Twelve ecdysteroids including two new compounds were isolated and utilized as marker compounds. A comparative analysis of the products with Cyanotis and spinach extracts provides evidence that they were manufactured from Cyanotis extracts instead of spinach as stated. Based on the chromatographic fingerprints, 20-hydroxyecdysone 2- and 3-acetate are suggested as diagnostic markers for related quality control. This case appears to represent an unusual type of dietary supplement counterfeiting: undeclared extracts from alternative plants would supposedly ‘guarantee’ product efficacy.
Concordance between somatic copy number loss and down-regulated expression: A pan-cancer study of cancer predisposition genes
Authors: Wei Ran , Zhao Ming , Zheng Chun-Hou , Zhao Min , Xia Junfeng
Published: December 2016

Cancer predisposition genes (CPGs) are a class of cancer genes in which germline variants lead to increased risk of cancer. Research has revealed that copy number variation (CNV) may be linked to cancer susceptibility in CPGs. In this pan-cancer analysis, we explored the relationship between somatic CNV and gene expression changes in CPGs. Based on curated 827 human CPGs from literature, we firstly identified 729 CPGs with precise CNV information from 5067 tumor samples using TCGA CNV data. Among them, 128 CPGs tended to have more frequent copy number losses (CNLs) compared with copy number gains (CNGs). Then by correlating these CNV data with TCGA gene expression data, we obtained 49 CPGs with concordant CNLs and gene down-regulation. Intriguingly, five CPGs showed concordance between CNL and down-regulation in 50 or more tumor samples: MTAP (216 samples), PTEN (143), MCPH1 (86), SMAD4 (63), and MINPP1 (51), which may represent the recurrent driving force for gene expression change during oncogenesis. Moreover, network analysis revealed that these 49 CPGs were tightly connected. In summary, this study provides the first observation of concordance between CNLs and down-regulation of CPGs in pan-cancer, which may help better understand the CPG biology in tumorigenesis and cancer progression.
The minimum area requirements (MAR) for giant panda: an empirical study
Authors: Qing Jing , Yang Zhisong , He Ke , Zhang Zejun , Gu Xiaodong , Yang Xuyu , Zhang Wen , Yang Biao , Qi Dunwu , Dai Qiang
Published: December 2016

Habitat fragmentation can reduce population viability, especially for area-sensitive species. The Minimum Area Requirements (MAR) of a population is the area required for the population’s long-term persistence. In this study, the response of occupancy probability of giant pandas against habitat patch size was studied in five of the six mountain ranges inhabited by giant panda, which cover over 78% of the global distribution of giant panda habitat. The probability of giant panda occurrence was positively associated with habitat patch area, and the observed increase in occupancy probability with patch size was higher than that due to passive sampling alone. These results suggest that the giant panda is an area-sensitive species. The MAR for giant panda was estimated to be 114.7 km2based on analysis of its occupancy probability. Giant panda habitats appear more fragmented in the three southern mountain ranges, while they are large and more continuous in the other two. Establishing corridors among habitat patches can mitigate habitat fragmentation, but expanding habitat patch sizes is necessary in mountain ranges where fragmentation is most intensive.
Real time optical Biopsy: Time-resolved Fluorescence Spectroscopy instrumentation and validation
Authors: Kittle David S. , Vasefi Fartash , Patil Chirag G. , Mamelak Adam , Black Keith L. , Butte Pramod V.
Published: December 2016

The Time-resolved fluorescence spectroscopy (TR-FS) has the potential to differentiate tumor and normal tissue in real time during surgical excision. In this manuscript, we describe the design of a novel TR-FS device, along with preliminary data on detection accuracy for fluorophores in a mixture. The instrument is capable of near real-time fluorescence lifetime acquisition in multiple spectral bands and analysis. It is also able to recover fluorescence lifetime with sub-20ps accuracy as validated with individual organic fluorescence dyes and dye mixtures yielding lifetime values for standard fluorescence dyes that closely match with published data. We also show that TR-FS is able to quantify the relative concentration of fluorescence dyes in a mixture by the unmixing of lifetime decays. We show that the TR-FS prototype is able to identify in near-real time the concentrations of dyes in a complex mixture based on previously trained data. As a result, we demonstrate that in complex mixtures of fluorophores, the relative concentration information is encoded in the fluorescence lifetime across multiple spectral bands. We show for the first time the temporal and spectral measurements of a mixture of fluorochromes and the ability to differentiate relative concentrations of each fluorochrome mixture in real time.
Internal luminescence efficiencies in InGaP/GaAs/Ge triple-junction solar cells evaluated from photoluminescence through optical coupling between subcells
Authors: Tex David M. , Imaizumi Mitsuru , Akiyama Hidefumi , Kanemitsu Yoshihiko
Published: December 2016

In-situ characterization is one of the most powerful techniques to improve material quality and device performance. Especially in view of highly efficient tandem solar cells this is an important issue for improving the cost-performance ratio. Optical techniques are suitable characterization methods, since they are non-destructing and contactless. In this work, we measured the power dependence of photoluminescence (PL) from the InGaP and GaAs subcells of an industry-standard triple-junction solar cell. High luminescence yields enhance the luminescence coupling, which was directly verified by time-resolved PL measurements. We present a new method to determine the internal luminescence efficiencies of InGaP and GaAs subcells with the aid of luminescence coupling. High luminescence efficiencies of 90% for GaAs and more than 20% for InGaP were found, which suggest that the material quality of the grown GaAs layer is excellent while the intrinsic luminescence limit of InGaP is still not reached even for high excitation conditions. The PL method is useful for probing the intrinsic material properties of the subcells in flat band condition, without influence of transport. Since no calibration of absolute PL is required, a fast screening of the material quality is possible, which should be extremely helpful for the solar cell industry.
Methionine sulfoxides in serum proteins as potential clinical biomarkers of oxidative stress
Authors: Suzuki Satoko , Kodera Yoshio , Saito Tatsuya , Fujimoto Kazumi , Momozono Akari , Hayashi Akinori , Kamata Yuji , Shichiri Masayoshi
Published: December 2016

Oxidative stress contributes to the pathophysiology of a variety of diseases, and circulating biomarkers of its severity remains a topic of great interest for researchers. Our peptidomic strategy enables accurate and reproducible analysis of circulating proteins/peptides with or without post-translational modifications. Conventional wisdom holds that hydrophobic methionines exposed to an aqueous environment or experimental handling procedures are vulnerable to oxidation. However, we show that the mass spectra intensity ratio of oxidized to non-oxidized methionine residues in serum tryptic proteins can be accurately quantified using a single drop of human serum and give stable and reproducible results. Our data demonstrate that two methionine residues in serum albumin (Met-111 and Met-147) are highly oxidized to methionine sulfoxide in patients with diabetes and renal failure and in healthy smokers versus non-smoker controls. This label-free mass spectrometry approach to quantify redox changes in methionine residues should facilitate the identification of additional circulating biomarkers suitable for predicting the development or progression of human diseases.
Antimicrobial growth promoters modulate host responses in mice with a defined intestinal microbiota
Authors: Brown Kirsty , Zaytsoff Sarah J. M. , Uwiera Richard R. E. , Inglis G. Douglas
Published: December 2016

Antibiotics can promote growth in livestock (antimicrobial growth promoters, AGPs), however lack of knowledge regarding mechanisms has hampered the development of effective non-antibiotic alternatives. Antibiotics affect eukaryotic cells at therapeutic concentrations, yet effects of AGPs on host physiology are relatively understudied, partially due to the complexity of host-microorganism interactions within the gastrointestinal tract. To determine the direct effects of AGPs on the host, we generated Altered Schaedler Flora (ASF) mice, and administered chlortetracycline (CTC) and tylosin phosphate (TYL) in feed. Mice were challenged with Citrobacter rodentium to determine how AGPs alter host responses to physiological stress. Although CTC and TYL had inconsistent effects on the ASF taxa, AGPs protected mice from weight loss following C. rodentium inoculation. Mice treated with either CTC or TYL had lower expression of βd1 and Il17a in the intestine and had a robust induction of Il17a and Il10. Furthermore, AGP administration resulted in a lower hepatic expression of acute phase proteins (Saa1, Hp, and Cp) in liver tissue, and ameliorated C. rodentium-induced reductions in the expression of genes involved in lipogenesis (Hmgcl and Fabp1). Collectively, this indicates that AGPs directly affect host physiology, and highlights important considerations in the development of non-antibiotic alternatives.
Probing the role of cation-π interaction in the thermotolerance and catalytic performance of endo-polygalacturonases
Authors: Tu Tao , Li Yeqing , Su Xiaoyun , Meng Kun , Ma Rui , Wang Yuan , Yao Bin , Lin Zhemin , Luo Huiying
Published: December 2016

Understanding the dynamics of the key pectinase, polygalacturonase, and improving its thermotolerance and catalytic efficiency are of importance for the cost-competitive bioconversion of pectic materials. By combining structure analysis and molecular dynamics (MD) simulations, eight mutagenesis sites having the potential to form cation-π interactions were identified in the widely used fungal endo-polygalacturonase PG63. In comparison to the wild-type, three single mutants H58Y, T71Y and T304Y showed improved thermostability (the apparentTms increased by 0.6−3.9 °C) and catalytic efficiency (by up to 32-fold). Chromatogram analysis of the hydrolysis products indicated that a larger amount of shorter sugars were released from the polygalacturonic acid by these three mutants than by the wild-type. MD analysis of the enzyme-substrate complexes illustrated that the mutants with introduced cation-π interaction have modified conformations of catalytic crevice, which provide an enviable environment for the catalytic process. Moreover, the lower plasticity of T3 loop 2 at the edge of the subsite tunnel appears to recruit the reducing ends of oligogalacturonide into the active site tunnel and initiates new hydrolysis reactions. This study demonstrates the importance of cation-π interaction in protein conformation and provides a realistic strategy to enhance the thermotolerance and catalytic performance of endo-polygalacturonases.
Magnetic separation of general solid particles realised by a permanent magnet
Authors: Hisayoshi K. , Uyeda C. , Terada K.
Published: December 2016

Most existing solids are categorised as diamagnetic or weak paramagnetic materials. The possibility of magnetic motion has not been intensively considered for these materials. Here, we demonstrate for the first time that ensembles of heterogeneous particles (diamagnetic bismuth, diamond and graphite particles, as well as two paramagnetic olivines) can be dynamically separated into five fractions by the low field produced by neodymium (NdFeB) magnets during short-duration microgravity (μg). This result is in contrast to the generally accepted notion that ordinary solid materials are magnetically inert. The materials of the separated particles are identified by their magnetic susceptibility (χ), which is determined from the translating velocity. The potential of this approach as an analytical technique is comparable to that of chromatography separation because the extraction of new solid phases from a heterogeneous grain ensemble will lead to important discoveries about inorganic materials. The method is applicable for the separation of the precious samples such as lunar soils and/or the Hayabusa particles recovered from the asteroids, because even micron-order grains can be thoroughly separated without sample-loss.
RNA sequencing of chorionic villi from recurrent pregnancy loss patients reveals impaired function of basic nuclear and cellular machinery
Authors: Sõber Siim , Rull Kristiina , Reiman Mario , Ilisson Piret , Mattila Pirkko , Laan Maris
Published: December 2016

Recurrent pregnancy loss (RPL) concerns ~3% of couples aiming at childbirth. In the current study, transcriptomes and miRNomes of 1st trimester placental chorionic villi were analysed for 2 RPL cases (≥6 miscarriages) and normal, but electively terminated pregnancies (ETP; n = 8). Sequencing was performed on Illumina HiSeq 2000 platform. Differential expression analyses detected 51 (27%) transcripts with increased and 138 (73%) with decreased expression in RPL compared to ETP (DESeq: FDR P < 0.1 and DESeq2: <0.05). RPL samples had substantially decreased transcript levels of histones, regulatory RNAs and genes involved in telomere, spliceosome, ribosomal, mitochondrial and intra-cellular signalling functions. Downregulated expression of HIST1H1B and HIST1H4A (Wilcoxon test, fc≤0.372, P≤9.37 × 10−4) was validated in an extended sample by quantitative PCR (RPL, n = 14; ETP, n = 24). Several upregulated genes are linked to placental function and pregnancy complications: ATF4, C3, PHLDA2, GPX4, ICAM1, SLC16A2. Analysis of the miRNA-Seq dataset identified no large disturbances in RPL samples. Notably, nearly 2/3 of differentially expressed genes have binding sites for E2F transcription factors, coordinating mammalian endocycle and placental development. For a conceptus destined to miscarriage, the E2F TF-family represents a potential key coordinator in reprogramming the placental genome towards gradually stopping the maintenance of basic nuclear and cellular functions.
Genetic diversity and population structure in Bactrocera correcta (Diptera: Tephritidae) inferred from mtDNA cox1 and microsatellite markers
Authors: Qin Yu-Jia , Buahom Nopparat , Krosch Matthew N. , Du Yu , Wu Yi , Malacrida Anna R. , Deng Yu-Liang , Liu Jia-Qi , Jiang Xiao-Long , Li Zhi-Hong
Published: December 2016

Bactrocera correcta is one of the most destructive pests of horticultural crops in tropical and subtropical regions. Despite the economic risk, the population genetics of this pest have remained relatively unexplored. This study explores population genetic structure and contemporary gene flow in B. correcta in Chinese Yunnan Province and attempts to place observed patterns within the broader geographical context of the species’ total range. Based on combined data from mtDNA cox1 sequences and 12 microsatellite loci obtained from 793 individuals located in 7 countries, overall genetic structuring was low. The expansion history of this species, including likely human-mediated dispersal, may have played a role in shaping the observed weak structure. The study suggested a close relationship between Yunnan Province and adjacent countries, with evidence for Western and/or Southern Yunnan as the invasive origin of B. correcta within Yunnan Province. The information gleaned from this analysis of gene flow and population structure has broad implications for quarantine, trade and management of this pest, especially in China where it is expanding northward. Future studies should concentrate effort on sampling South Asian populations, which would enable better inferences of the ancestral location of B. correcta and its invasion history into and throughout Asia.
Extraordinary behavioral entrainment following circadian rhythm bifurcation in mice
Authors: Harrison Elizabeth M. , Walbeek Thijs J. , Sun Jonathan , Johnson Jeremy , Poonawala Qays , Gorman Michael R.
Published: December 2016

The mammalian circadian timing system uses light to synchronize endogenously generated rhythms with the environmental day. Entrainment to schedules that deviate significantly from 24 h (T24) has been viewed as unlikely because the circadian pacemaker appears capable only of small, incremental responses to brief light exposures. Challenging this view, we demonstrate that simple manipulations of light alone induce extreme plasticity in the circadian system of mice. Firstly, exposure to dim nocturnal illumination (<0.1 lux), rather than completely dark nights, permits expression of an altered circadian waveform wherein mice in light/dark/light/dark (LDLD) cycles “bifurcate” their rhythms into two rest and activity intervals per 24 h. Secondly, this bifurcated state enables mice to adopt stable activity rhythms under 15 or 30 h days (LDLD T15/T30), well beyond conventional limits of entrainment. Continuation of dim light is unnecessary for T15/30 behavioral entrainment following bifurcation. Finally, neither dim light alone nor a shortened night is sufficient for the extraordinary entrainment observed under bifurcation. Thus, we demonstrate in a non-pharmacological, non-genetic manipulation that the circadian system is far more flexible than previously thought. These findings challenge the current conception of entrainment and its underlying principles, and reveal new potential targets for circadian interventions.
Involvement of P2X7 receptor in neuronal degeneration triggered by traumatic injury
Authors: Nadal-Nicolás Francisco M. , Galindo-Romero Caridad , Valiente-Soriano Francisco J. , Barberà-Cremades María , deTorre-Minguela Carlos , Salinas-Navarro Manuel , Pelegrín Pablo , Agudo-Barriuso Marta
Published: December 2016

Axonal injury is a common feature of central nervous system insults that culminates with the death of the affected neurons, and an irreversible loss of function. Inflammation is an important component of the neurodegenerative process, where the microglia plays an important role by releasing proinflammatory factors as well as clearing the death neurons by phagocytosis. Here we have identified the purinergic signaling through the P2X7 receptor as an important component for the neuronal death in a model of optic nerve axotomy. We have found that in P2X7 receptor deficient mice there is a delayed loss of retinal ganglion cells and a decrease of phagocytic microglia at early times points after axotomy. In contralateral to the axotomy retinas, P2X7 receptor controlled the numbers of phagocytic microglia, suggesting that extracellular ATP could act as a danger signal activating the P2X7 receptor in mediating the loss of neurons in contralateral retinas. Finally, we show that intravitreal administration of the selective P2X7 receptor antagonist A438079 also delays axotomy-induced retinal ganglion cell death in retinas from wild type mice. Thus, our work demonstrates that P2X7 receptor signaling is involved in neuronal cell death after axonal injury, being P2X7 receptor antagonism a potential therapeutic strategy.
Universalities of thermodynamic signatures in topological phases
Authors: Kempkes S. N. , Quelle A. , Smith C. Morais
Published: December 2016

Topological insulators (superconductors) are materials that host symmetry-protected metallic edge states in an insulating (superconducting) bulk. Although they are well understood, a thermodynamic description of these materials remained elusive, firstly because the edges yield a non-extensive contribution to the thermodynamic potential, and secondly because topological field theories involve non-local order parameters, and cannot be captured by the Ginzburg-Landau formalism. Recently, this challenge has been overcome: by using Hill thermodynamics to describe the Bernevig-Hughes-Zhang model in two dimensions, it was shown that at the topological phase transition the thermodynamic potential does not scale extensively due to boundary effects. Here, we extend this approach to different topological models in various dimensions (the Kitaev chain and Su-Schrieffer-Heeger model in one dimension, the Kane-Mele model in two dimensions and the Bernevig-Hughes-Zhang model in three dimensions) at zero temperature. Surprisingly, all models exhibit the same universal behavior in the order of the topological-phase transition, depending on the dimension. Moreover, we derive the topological phase diagram at finite temperature using this thermodynamic description, and show that it displays a good agreement with the one calculated from the Uhlmann phase. Our work reveals unexpected universalities and opens the path to a thermodynamic description of systems with a non-local order parameter.
Broadband photodetector based on carbon nanotube thin film/single layer graphene Schottky junction
Authors: Zhang Teng-Fei , Li Zhi-Peng , Wang Jiu-Zhen , Kong Wei-Yu , Wu Guo-An , Zheng Yu-Zhen , Zhao Yuan-Wei , Yao En-Xu , Zhuang Nai-Xi , Luo Lin-Bao
Published: December 2016

In this study, we present a broadband nano-photodetector based on single-layer graphene (SLG)-carbon nanotube thin film (CNTF) Schottky junction. It was found that the as-fabricated device exhibited obvious sensitivity to a wide range of illumination, with peak sensitivity at 600 and 920 nm. In addition, the SLG-CNTF device had a fast response speed (τr = 68 μs, τf = 78 μs) and good reproducibility in a wide range of switching frequencies (50–5400 Hz). The on-off ratio, responsivity, and detectivity of the device were estimated to be 1 × 102, 209 mAW−1 and 4.87 × 1010 cm Hz1/2 W−1, respectively. What is more, other device parameters including linear performance θ and linear dynamic range (LDR) were calculated to be 0.99 and 58.8 dB, respectively, which were relatively better than other carbon nanotube based devices. The totality of the above study signifies that the present SLG-CNTF Schottky junction broadband nano-photodetector may have promising application in future nano-optoelectronic devices and systems.
Channel morphology effect on water transport through graphene bilayers
Authors: Liu Bo , Wu Renbing , Law Adrian Wing-Keung , Feng Xi-Qiao , Bai Lichun , Zhou Kun
Published: December 2016

The application of few-layered graphene-derived functional thin films for molecular filtration and separation has recently attracted intensive interests. In practice, the morphology of the nanochannel formed by the graphene (GE) layers is not ideally flat and can be affected by various factors. This work investigates the effect of channel morphology on the water transport behaviors through the GE bilayers via molecular dynamics simulations. The simulation results show that the water flow velocity and transport resistance highly depend on the curvature of the graphene layers, particularly when they are curved in non-synergic patterns. To understand the channel morphology effect, the distributions of water density, dipole moment orientation and hydrogen bonds inside the channel are investigated, and the potential energy surface with different distances to the basal GE layer is analyzed. It shows that the channel morphology significantly changes the distribution of the water molecules and their orientation and interaction inside the channel. The energy barrier for water molecules transport through the channel also significantly depends on the channel morphology.
A novel method to visualise and quantify circadian misalignment
Authors: Fischer Dorothee , Vetter Céline , Roenneberg Till
Published: December 2016

The circadian clock governs virtually all processes in the human body, including sleep-wake behaviour. Circadian misalignment describes the off-set between sleep-wake cycles and clock-regulated physiology. This strain is predominantly caused by external (societal) demands including shift work, early school start times and fast travels across time zones. Sleeping at the ‘wrong’ internal time can jeopardise health and safety, and we therefore need a good quantification of this phenomenon. Here, we propose a novel method to quantify the mistiming of sleep-wake rhythms and demonstrate its versatility in day workers and shift workers. Based on a single time series, our Composite Phase Deviation method unveils distinct, subject- and schedule-specific geometries (‘islands and pancakes’) that illustrate how modern work times interfere with sleep. With increasing levels of circadian strain, the resulting shapes change systematically from small, connected forms to large and fragmented patterns. Our method shows good congruence with published measures of circadian misalignment (i.e., Inter-daily Stability and ‘Behavioural Entrainment’), but offers added value as to its requirements, e.g., being computable for sleep logs and questionnaires. Composite Phase Deviations will help to understand the mechanisms that link ‘living against the clock’ with health and disease on an individual basis.
TGF-β regulates phosphorylation and stabilization of Sox9 protein in chondrocytes through p38 and Smad dependent mechanisms
Authors: Coricor George , Serra Rosa
Published: December 2016

Members of the TGF-β superfamily are important regulators of chondrocyte function. Sox9, a key transcriptional regulator of chondrogenesis, is required for TGF-β-mediated regulation of specific cartilage genes. TGF-β can signal through a canonical, Smad-mediated pathway or non-conical pathways, including p38. Here we show that both pathways are activated in chondrocytes after treatment with TGF-β and that TGF-β stabilizes Sox9 protein and increases phosphorylation of Sox9. Mutagenesis of potential serine phosphorylation sites on Sox9 was used to demonstrate that serine 211 is required to maintain normal basal levels of Sox9 as well as mediate increased Sox9 levels in response to TGF-β. The serine 211 site is in a motif that is targeted by p38 kinase. We used siRNA and pharmacological agents to show that p38 and Smad3 independently regulate the phosphorylation and stability of Sox9. Previously, we demonstrated that Papss2 is a downstream transcriptional target of Sox9 and TGF-β. Here we show that p38 is required for TGF-β-mediated regulation of Papss2 mRNA. Together the results suggest a new mechanism for TGF-β-mediated gene regulation in chondrocytes via p38 and phosphorylation and stabilization of Sox9. Understanding how TGF-β regulates Sox9 may lead to identification of therapeutic targets for OA.
Single Molecular Demonstration of Modulating Charge Inversion of DNA
Authors: Wang Yanwei , Wang Ruxia , Cao Bozhi , Guo Zilong , Yang Guangcan
Published: December 2016

Charge inversion of DNA is a counterintuitive phenomenon in which the effective charge of DNA switches its sign from negative to positive in the presence of multivalent counterions. The underlying microscopic mechanism is still controversial whether it is driven by a specific chemical affinity or electrostatic ion correlation. It is well known that DNA shows no charge inversion in normal aqueous solution of trivalent counterions though they can induce the conformational compaction of DNA. However, in the same trivalent counterion condition, we demonstrate for the first time the occurrence of DNA charge inversion by decreasing the dielectric constant of solution to make the electrophoretic mobility of DNA increase from a negative value to a positive value. In contrast, the charge inversion of DNA induced by quadrivalent counterions can be canceled out by increasing the dielectric constant of solution. The physical modulation of DNA effective charge in two ways unambiguously demonstrates that charge inversion of DNA is a predominantly electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. This conclusion is also supported by the measurement of condensing and unraveling forces of DNA condensates by single molecular MT.
Magnetic domains driving a Q-switched laser
Authors: Morimoto Ryohei , Goto Taichi , Pritchard John , Takagi Hiroyuki , Nakamura Yuichi , Lim Pang Boey , Uchida Hironaga , Mina Mani , Taira Takunori , Inoue Mitsuteru
Published: December 2016

A 10-mm cavity length magnetooptically Q-switched Nd:GdVO4 laser was demonstrated using a single-crystalline ferrimagnetic rare-earth iron garnet film. To design the Q-switching system, the magnetic, optical, and magnetooptical properties of the garnet film were measured. The diode pumped solid-state laser cavity was constructed using a 190-μm-thick garnet film with 58% transmittance. The garnet film had maze-shaped magnetic domains, and the domain walls disappeared when a field of over 200 Oe was applied. Therefore, the polarization state of the transmitted light was modified by modulating the magnetization, and a Q-switched pulse output with a pulse width of 5 ns and peak power of 255 W was achieved in the 10-mm-long cavity. The physical limitation of the pulse width was discussed with the calculated results.
Caveolin-1 is an aggresome-inducing protein
Authors: Tiwari Ajit , Copeland Courtney A. , Han Bing , Hanson Caroline A. , Raghunathan Krishnan , Kenworthy Anne K.
Published: December 2016

Caveolin-1 (Cav1) drives the formation of flask-shaped membrane invaginations known as caveolae that participate in signaling, clathrin-independent endocytosis and mechanotransduction. Overexpression or mutations of Cav1 can lead to its mistrafficking, including its accumulation in a perinuclear compartment previously identified as the Golgi complex. Here, we show that in the case of overexpressed Cav1-GFP, this perinuclear compartment consists of cytoplasmic inclusion bodies generated in response to the accumulation of aggregates of misfolded proteins, known as aggresomes. Aggresomes containing Cav1-GFP are encased within vimentin cages, form in a microtubule-dependent manner, and are enriched in a number of key regulators of protein turnover, including ubiquitin, VCP/p97 and proteasomes. Interestingly, aggresome induction was cell-type dependent and was observed for many but not all Cav1 constructs tested. Furthermore, endogenous Cav1 accumulated in aggresomes formed in response to proteosomal inhibition. Our finding that Cav1 is both an aggresome-inducing and aggresome-localized protein provides new insights into how cells handle and respond to misfolded Cav1. They also raise the possibility that aggresome formation may contribute to some of reported phenotypes associated with overexpressed and/or mutant forms of Cav1.
Effects of nitrogen and biochar amendment on soil methane concentration profiles and diffusion in a rice-wheat annual rotation system
Authors: Xu Xin , Wu Zhen , Dong Yubing , Zhou Ziqiang , Xiong Zhengqin
Published: December 2016

The CH4 emissions from soil were influenced by the changeable CH4 concentrations and diffusions in soil profiles, but that have been subjected to nitrogen (N) and biochar amendment over seasonal and annual time frames. Accordingly, a two-year field experiment was conducted in southeastern China to determine the amendment effects on CH4 concentrations and diffusive effluxes as measured by a multilevel sampling probe in paddy soil during two cycles of rice-wheat rotations. The results showed that the top 7-cm soil layers were the primary CH4 production sites during the rice-growing seasons. This layer acted as the source of CH4 generation and diffusion, and the deeper soil layers and the wheat season soil acted as the sink. N fertilization significantly increased the CH4 concentration and diffusive effluxes in the top 7-cm layers during the 2013 and 2014 rice seasons. Following biochar amendment, the soil CH4 concentrations significantly decreased during the rice season in 2014, relative to the single N treatment. Moreover, 40 t ha−1 biochar significantly decreased the diffusive effluxes during the rice seasons in both years. Therefore, our results showed that biochar amendment is a good strategy for reducing the soil profile CH4 concentrations and diffusive effluxes induced by N in paddy fields.
Reduced expression of monocyte CD200R is associated with enhanced proinflammatory cytokine production in sarcoidosis
Authors: Fraser Simon D. , Sadofsky Laura R. , Kaye Paul M. , Hart Simon P.
Published: December 2016

In sarcoidosis, the proinflammatory cytokines interferon gamma, tumour necrosis factor and interleukin-6 are released by monocyte-derived macrophages and lymphocytes in the lungs and other affected tissues. Regulatory receptors expressed on monocytes and macrophages act to suppress cytokine production, and reduced expression of regulatory receptors may thus promote tissue inflammation. The aim of this study was to characterise the role of regulatory receptors on blood monocytes in patients with sarcoidosis. Cytokine release in response to stimulation of whole blood was measured in healthy controls and Caucasian non-smoking patients with sarcoidosis who were not taking disease modifying therapy. Expression of the regulatory molecules IL-10R, SIRP-α/β, CD47, CD200R, and CD200L was measured by flow cytometry, and functional activity was assessed using blocking antibodies. Stimulated whole blood and monocytes from patients with sarcoidosis produced more TNF and IL-6 compared with healthy controls. 52.9% of sarcoidosis patients had monocytes characterised by low expression of CD200R, compared with 11.7% of controls (p < 0.0001). Patients with low monocyte CD200R expression produced higher levels of proinflammatory cytokines. In functional studies, blocking the CD200 axis increased production of TNF and IL-6. Reduced expression of CD200R on monocytes may be a mechanism contributing to monocyte and macrophage hyper-activation in sarcoidosis.
First complete mitochondrial genome data from ancient South American camelids - The mystery of the chilihueques from Isla Mocha (Chile)
Authors: Westbury Michael , Prost Stefan , Seelenfreund Andrea , Ramírez José-Miguel , Matisoo-Smith Elizabeth A. , Knapp Michael
Published: December 2016

In South American societies, domesticated camelids were of great cultural importance and subject to trade and translocation. South American camelids were even found on remote and hard to reach islands, emphasizing their importance to historic and pre-historic South American populations. Isla Mocha, a volcanic island 35 km offshore of Central-South Chile, is an example of such an island. When Dutch and Spanish explorers reached the island in the early 17th century, they found that domesticated camelids called “chilihueque” played a major role in the island’s society. The origin and taxonomy of these enigmatic camelids is unclear and controversial. This study aims to resolve this controversy through genetic analyses of Isla Mocha camelid remains dating from pre-Columbian to early historic times. A recent archaeological excavation of site P21-3 on Isla Mocha yielded a number of camelid remains. Three complete mitochondrial genomes were successfully recovered and analysed. Phylogenetic analyses suggest that “chilihueque” was a local term for a domesticated guanaco. Results from phylogeographic analyses are consistent with Isla Mocha camelids being sourced from Southern Chilean guanaco populations. Our data highlights the capability of ancient DNA to answer questions about extinct populations which includes species identity, potential translocation events and origins of founding individuals.
Depth resolved lattice-charge coupling in epitaxial BiFeO3 thin film
Authors: Lee Hyeon Jun , Lee Sung Su , Kwak Jeong Hun , Kim Young-Min , Jeong Hu Young , Borisevich Albina Y. , Lee Su Yong , Noh Do Young , Kwon Owoong , Kim Yunseok , Jo Ji Young
Published: December 2016

For epitaxial films, a critical thickness (tc) can create a phenomenological interface between a strained bottom layer and a relaxed top layer. Here, we present an experimental report of how the tc in BiFeO3 thin films acts as a boundary to determine the crystalline phase, ferroelectricity, and piezoelectricity in 60 nm thick BiFeO3/SrRuO3/SrTiO3 substrate. We found larger Fe cation displacement of the relaxed layer than that of strained layer. In the time-resolved X-ray microdiffraction analyses, the piezoelectric response of the BiFeO3 film was resolved into a strained layer with an extremely low piezoelectric coefficient of 2.4 pm/V and a relaxed layer with a piezoelectric coefficient of 32 pm/V. The difference in the Fe displacements between the strained and relaxed layers is in good agreement with the differences in the piezoelectric coefficient due to the electromechanical coupling.
Peptidylarginine deiminase 1-catalyzed histone citrullination is essential for early embryo development
Authors: Zhang Xiaoqian , Liu Xiaoqiu , Zhang Mei , Li Tingting , Muth Aaron , Thompson Paul R. , Coonrod Scott A. , Zhang Xuesen
Published: December 2016

Peptidylarginine deiminase (PADI) enzymes are increasingly being associated with the regulation of chromatin structure and gene activity via histone citrullination. As one of the PADI family members, PADI1 has been mainly reported to be expressed in the epidermis and uterus, where the protein in keratinocytes is thought to promote differentiation by citrullinating filament proteins. However, the roles of PADI1 in preimplantation development have not been addressed. Using a PADI1-specific inhibitor and Padi1-morpholino knockdown, we found that citrullination of histone tails at H4R3 and H3R2/8/17 were markedly reduced in the 2- and 4-cell embryos. Consistent with this observation, early embryo development was also arrested at the 4-cell stage upon depletion of PADI1 or inhibition of PADI1 enzyme activity. Additionally, by employing 5-ethynyl uridine (EU) incorporation analysis, ablation of PADI1 function led to a dramatic decrease in overall transcriptional activity, correlating well with the reduced levels of phosphorylation of RNA Pol II at Ser2 observed at 2- or 4-cell stage of embryos under Padi1 knockdown or inhibiting PADI1. Thus, our data reveal a novel function of PADI1 during early embryo development transitions by catalyzing histone tail citrullination, which facilitates early embryo genome transactivation.
Neurofilaments in blood and CSF for diagnosis and prediction of onset in Creutzfeldt-Jakob disease
Authors: Steinacker Petra , Blennow Kaj , Halbgebauer Steffen , Shi Song , Ruf Viktoria , Oeckl Patrick , Giese Armin , Kuhle Jens , Slivarichova Dana , Zetterberg Henrik , Otto Markus
Published: December 2016

While cerebrospinal fluid (CSF) biomarkers for Creutzfeldt-Jakob disease (CJD) are established and partly included in the diagnostic criteria, no blood biomarkers are available. Here, we assessed the utility of serum neurofilament light chain (NF-L) and tau protein in comparison to CSF markers (NF-L and phosphorylated NF heavy chain (pNF-H), tau, S100B, 14-3-3) and prion conversion assay (real-time quaking induced conversion (RT-QuIC)) for sporadic and genetic CJD. Importantly, a Gerstmann-Sträussler-Scheinker mutation carrier in the asymptomatic phase and at disease onset was included as well. Both NF-L and tau were markedly increased in CJD serum, reaching similar or even better performance as in CSF (sensitivity and specificity for serum NF-L 100% and 85.5%, and for serum tau 84.6% and 96.2%, respectively). Serum S100B showed high sensitivity as well (84.2%), but lower specificity (63%). CSF neurofilaments were increased before symptom onset, while prion seeding assay was negative. Just before a clinical diagnosis could be made, all CSF markers and NF-L in the serum were increased and CSF prion conversion assay was positive. The data suggest that neurofilaments are sensitive and specific blood markers for the diagnosis of genetic and sporadic CJD and might represent promising tools to predict disease onset.
Exosomal microRNA miR-1246 induces cell motility and invasion through the regulation of DENND2D in oral squamous cell carcinoma
Authors: Sakha Sujata , Muramatsu Tomoki , Ueda Koji , Inazawa Johji
Published: December 2016

Metastasis is associated with poor prognosis in cancers. Exosomes, which are packed with RNA and proteins and are released in all biological fluids, are emerging as an important mediator of intercellular communication. However, the function of exosomes remains poorly understood in cancer metastasis. Here, we demonstrate that exosomes isolated by size-exclusion chromatography from a highly metastatic human oral cancer cell line, HOC313-LM, induced cell growth through the activation of ERK and AKT as well as promoted cell motility of the poorly metastatic cancer cell line HOC313-P. MicroRNA (miRNA) array analysis identified two oncogenic miRNAs, miR-342–3p and miR-1246, that were highly expressed in exosomes. These miRNAs were transferred to poorly metastatic cells by exosomes, which resulted in increased cell motility and invasive ability. Moreover, miR-1246 increased cell motility by directly targeting DENN/MADD Domain Containing 2D (DENND2D). Taken together, our findings support the metastatic role of exosomes and exosomal miRNAs, which highlights their potential for applications in miRNA-based therapeutics.
All-inorganic large-area low-cost and durable flexible perovskite solar cells using copper foil as a substrate
Authors: Abdollahi Nejand B. , Nazari P. , Gharibzadeh S. , Ahmadi V. , Moshaii A.
Published: December 2016

All-inorganic large-area, low-cost, and durable flexible perovskite solar cells using copper foil as a substrate are introduced.
Synthesis of sialic acid derivatives based on chiral substrate-controlled stereoselective aldol reactions using pyruvic acid oxabicyclo[2.2.2]octyl orthoester
Authors: Norimura Yusuke , Yamamoto Daisuke , Makino Kazuishi
Published: December 2016

The synthesis of sialic acids and their analogs was accomplished based on substrate-controlled asymmetric aldol reactions using pyruvic acid oxabicyclo[2.2.2]octyl orthoester.
Manipulation of cellular orientation and migration by internalized magnetic particles
Authors: Liu Jiaojiao , Tian Xiaodong , Bao Meimei , Li Jingliang , Dou Yujiang , Yuan Bing , Yang Kai , Ma Yuqiang
Published: December 2016

Cellular orientation and migration are mediated by internalized Fe3O4 nanoparticles with an external magnetic field in a particle-concentration dependent manner.
IR-polarizing film containing a new quinoline dye and Fe3O4 nanoparticles: optical and thermophysical investigations
Authors: Shahab Siyamak , Filippovich Liudmila , Borzehandani Mostafa Yousefzadeh , Kumar Rakesh , Lugovsky Anatoliy , Eryomin Alexandr , Mashayekhi Mahsa
Published: December 2016

Monosodium mono(4-(2-(2-(2-chloro-1-(2-(1-(4-sulfonatobutyl)-3,4-dihydroquinolin-2(1H)-ylidene)ethyliden)-1H-inden-3-yl)vinyl)-3,4-dihydroquinolin-1(2H)-yl)butane-1-sulfonate) (M), with a strong maximum absorption at 764 nm was synthesized and modeled using DFT.
Atomic layer deposition of vanadium oxides for thin-film lithium-ion battery applications
Authors: Mattelaer Felix , Geryl Kobe , Rampelberg Geert , Dobbelaere Thomas , Dendooven Jolien , Detavernier Christophe
Published: December 2016

A wide range of vanadium oxides is demostrated as lithium ion cathodes by a combination of ALD and post-ALD anneal, with lithium insertion capacities up to 1380 mAh cm−3.
Effect of interionic interactions on the structure and dynamics of ionic solvation shells in aqueous electrolyte solutions
Authors: Kumar Parveen , Bharadwaj Mridula Dixit , Yashonath S.
Published: December 2016

Molecular dynamics (MD) simulations to explore the structure and dynamics of the ionic solvation shell of alkali ions and halide ions in aqueous solution.
Facile synthesis of hierarchical fern leaf-like Sb and its application as an additive-free anode for fast reversible Na-ion storage
Authors: Liang Liying , Xu Yang , Li Yueliang , Dong Huishuang , Zhou Min , Zhao Huaping , Kaiser Ute , Lei Yong
Published: December 2016

Hierarchical Sb as an additive-free anode was fabricated to show excellent electrochemical performance for both Na-ion half and full cells.
Size changeable nanosystems for precise drug controlled release and efficient overcoming of cancer multidrug resistance
Authors: Fang Xueyang , Jiang Wenting , Huang Yanyu , Yang Fang , Chen Tianfeng
Published: December 2016

Herein we demonstrate the rational design of a size changeable nanosystem for precise drug controlled release and efficient overcoming of cancer multidrug resistance in cancer cells by enhancing the cellular uptake and inhibiting the expression of ABC family proteins.
Highly reliable and highly conductive submicron Cu particle patterns fabricated by low temperature heat-welding and subsequent flash light sinter-reinforcement
Authors: Li Wanli , Zhang Hao , Gao Yue , Jiu Jinting , Li Cai-Fu , Chen Chuantong , Hu Dawei , Goya Yusuke , Wang Yutao , Koga Hirotaka , Nagao Shijo , Suganuma Katsuaki
Published: December 2016

An optimized two-step sintering process is developed to achieve highly reliable submicron Cu particle patterns on low-cost, transparent, and flexible substrates.