bluuebunny/crossref_metadata_2025_split huggingface dataset:
Essential role for SphK1/S1P signaling to regulate hypoxia-inducible factor 2α expression and activity in cancer
Authors: Bouquerel P , Gstalder C , Müller D , Laurent J , Brizuela L , Sabbadini R A , Malavaud B , Pyronnet S , Martineau Y , Ader I , Cuvillier O 
Published: March 2016

AbstractThe sphingosine kinase-1/sphingosine 1-phosphate (SphK1/S1P) signaling pathway has been reported to modulate the expression of the canonical transcription factor hypoxia-inducible HIF-1α in multiple cell lineages. HIF-2α is also frequently overexpressed in solid tumors but its role has been mostly studied in clear cell renal cell carcinoma (ccRCC), the most common form of kidney cancer, where HIF-2α has been established as a driver of a more aggressive disease. In this study, the role of SphK1/S1P signaling with regard to HIF-2α was investigated in various cancer cell models including ccRCC cells. Under hypoxic conditions or in ccRCC lacking a functional von Hippel-Lindau (VHL) gene and expressing high levels of HIF-2α, SphK1 activity controls HIF-2α expression and transcriptional activity through a phospholipase D (PLD)-driven mechanism. SphK1 silencing promotes a VHL-independent HIF-2α loss of expression and activity and reduces cell proliferation in ccRCC. Importantly, downregulation of SphK1 is associated with impaired Akt and mTOR signaling in ccRCC. Taking advantage of a monoclonal antibody neutralizing extracellular S1P, we show that inhibition of S1P extracellular signaling blocks HIF-2α accumulation in ccRCC cell lines, an effect mimicked when the S1P transporter Spns2 or the S1P receptor 1 (S1P1) is silenced. Here, we report the first evidence that the SphK1/S1P signaling pathway regulates the transcription factor hypoxia-inducible HIF-2α in diverse cancer cell lineages notably ccRCC, where HIF-2α has been established as a driver of a more aggressive disease. These findings demonstrate that SphK1/S1P signaling may act as a canonical regulator of HIF-2α expression in ccRCC, giving support to its inhibition as a therapeutic strategy that could contribute to reduce HIF-2 activity in ccRCC.
Configurational space discretization and free energy calculation in complex molecular systems
Authors: Wang Kai , Long Shiyang , Tian Pu 
Published: March 2016

AbstractWe sought to design a free energy calculation scheme with the hope of saving cost for generating dynamical information that is inherent in trajectories. We demonstrated that snapshots in a converged trajectory set are associated with implicit conformers that have invariant statistical weight distribution (ISWD). Since infinite number of sets of implicit conformers with ISWD may be created through independent converged trajectory sets, we hypothesized that explicit conformers with ISWD may be constructed for complex molecular systems through systematic increase of conformer fineness and tested the hypothesis in lipid molecule palmitoyloleoylphosphatidylcholine (POPC). Furthermore, when explicit conformers with ISWD were utilized as basic states to define conformational entropy, change of which between two given macrostates was found to be equivalent to change of free energy except a mere difference of a negative temperature factor and change of enthalpy essentially cancels corresponding change of average intra-conformer entropy. By implicitly taking advantage of entropy enthalpy compensation and forgoing all dynamical information, constructing explicit conformers with ISWD and counting thermally accessible number of which for interested end macrostates is likely to be an efficient and reliable alternative end point free energy calculation strategy.
Independent control of electrical and heat conduction by nanostructure designing for Si-based thermoelectric materials
Authors: Yamasaka Shuto , Watanabe Kentaro , Sakane Shunya , Takeuchi Shotaro , Sakai Akira , Sawano Kentarou , Nakamura Yoshiaki 
Published: March 2016

AbstractThe high electrical and drastically-low thermal conductivities, a vital goal for high performance thermoelectric (TE) materials, are achieved in Si-based nanoarchitecture composed of Si channel layers and epitaxial Ge nanodots (NDs) with ultrahigh areal density (~1012 cm−2). In this nanoarchitecture, the ultrasmall NDs and Si channel layers play roles of phonon scattering sources and electrical conduction channels, respectively. Electron conductivity in n-type nanoacrhitecture shows high values comparable to those of epitaxial Si films despite the existence of epitaxial NDs. This is because Ge NDs mainly scattered not electrons but phonons selectively, which could be attributed to the small conduction band offset at the epitaxially-grown Si/Ge interface and high transmission probability through stacking faults. These results demonstrate an independent control of thermal and electrical conduction for phonon-glass electron-crystal TE materials by nanostructure designing and the energetic and structural interface control.
A genistein-enriched diet neither improves skeletal muscle oxidative capacity nor prevents the transition towards advanced insulin resistance in ZDF rats
Authors: van Bree Bianca W. J. , Lenaers Ellen , Nabben Miranda , Briedé Jacco J. , Jörgensen Johanna A. , Schaart Gert , Schrauwen Patrick , Hoeks Joris , Hesselink Matthijs K. C. 
Published: March 2016

AbstractGenistein, a natural food compound mainly present in soybeans, is considered a potent antioxidant and to improve glucose homeostasis. However, its mechanism of action remains poorly understood. Here, we analyzed whether genistein could antagonize the progression of the hyperinsulinemic normoglycemic state (pre-diabetes) toward full-blown T2DM in Zucker Diabetic Fatty (ZDF) rats by decreasing mitochondrial oxidative stress and improving skeletal muscle oxidative capacity. Rats were assigned to three groups: (1) lean control (CNTL), (2) fa/fa CNTL and (3) fa/fa genistein (GEN). GEN animals were subjected to a 0.02% (w/w) genistein-enriched diet for 8 weeks, whereas CNTL rats received a standard diet. We show that genistein did not affect the overall response to a glucose challenge in ZDF rats. In fact, genistein may exacerbate glucose intolerance as fasting glucose levels were significantly higher in fa/fa GEN (17.6 ± 0.7 mM) compared with fa/fa CNTL animals (14.9 ± 1.4 mM). Oxidative stress, established by electron spin resonance (ESR) spectroscopy, carbonylated protein content and UCP3 levels, remained unchanged upon dietary genistein supplementation. Furthermore, respirometry measurements revealed no effects of genistein on mitochondrial function. In conclusion, dietary genistein supplementation did not improve glucose homeostasis, alleviate oxidative stress, or augment skeletal muscle metabolism in ZDF rats.
Regulation of cell polarity determinants by the Retinoblastoma tumor suppressor protein
Authors: Payankaulam Sandhya , Yeung Kelvin , McNeill Helen , Henry R. William , Arnosti David N. 
Published: March 2016

AbstractIn addition to their canonical roles in the cell cycle, RB family proteins regulate numerous developmental pathways, although the mechanisms remain obscure. We found that Drosophila Rbf1 associates with genes encoding components of the highly conserved apical–basal and planar cell polarity pathways, suggesting a possible regulatory role. Here, we show that depletion of Rbf1 in Drosophila tissues is indeed associated with polarity defects in the wing and eye. Key polarity genes aPKC, par6, vang, pk and fmi are upregulated and an aPKC mutation suppresses the Rbf1-induced phenotypes. RB control of cell polarity may be an evolutionarily conserved function, with important implications in cancer metastasis.
hTERT promotes cell adhesion and migration independent of telomerase activity
Authors: Liu Haiying , Liu Qianqian , Ge Yuanlong , Zhao Qi , Zheng Xiaohui , Zhao Yong 
Published: March 2016

AbstracthTERT, a catalytic component of human telomerase, is undetectable in normal somatic cells but up-regulated in cancer and stem cells where telomere length is maintained by telomerase. Accumulated evidence indicates that hTERT may have noncanonical functions beyond telomerase by regulating the expression of particular genes. However, comprehensive identification of the genes regulated by hTERT is unavailable. In this report, we expressed WT hTERT and hTERTmut which displays dysfunctional catalytic activity, in human U2OS cancer cells and VA-13 immortalized fibroblast cells, both of which lack endogenous hTERT and hTR expression. Changes in gene expression induced by hTERT and hTERT-mut expression were determined by genome-wide RNA-seq and verified by qPCR. Our results showed that hTERT affects different genes in two cell lines, implying that the regulation of gene expression by hTERT is indirect and cell type dependent. Moreover, functional analysis identifies cell adhesion-related genes that have been changed by hTERT in both cell lines. Adhesion experiments revealed that hTERT expression significantly increases cell adhesion. Monolayer wound healing and transwell assays demonstrated increased cell migration upon hTERT expression. These results provide new evidence to support a noncanonical function for hTERT in promoting tumorigenesis.
Efficient and simple generation of multiple unmarked gene deletions in Mycobacterium smegmatis
Authors: Mao Xu-Jian , Yan Mei-Yi , Zhu Hui , Guo Xiao-Peng , Sun Yi-Cheng 
Published: March 2016

AbstractResearch on mycobacterial genetics relies heavily on techniques for directed gene mutation, but genetic studies are often hampered by the difficulty of generating gene deletions in mycobacteria. We developed an efficient and improved deletion system, described here in detail, which can be used to construct multiple unmarked recombinants in mycobacteria. We tested this system by using it to sequentially delete four pairs of toxin-antitoxin genes in Mycobacterium smegmatis.
Shape perception enhances perceived contrast: evidence for excitatory predictive feedback?
Authors: Han Biao , VanRullen Rufin 
Published: March 2016

AbstractPredictive coding theory suggests that predictable responses are “explained away” (i.e., reduced) by feedback. Experimental evidence for feedback inhibition, however, is inconsistent: most neuroimaging studies show reduced activity by predictive feedback, while neurophysiology indicates that most inter-areal cortical feedback is excitatory and targets excitatory neurons. In this study, we asked subjects to judge the luminance of two gray disks containing stimulus outlines: one enabling predictive feedback (a 3D-shape) and one impeding it (random-lines). These outlines were comparable to those used in past neuroimaging studies. All 14 subjects consistently perceived the disk with a 3D-shape stimulus brighter; thus, predictive feedback enhanced perceived contrast. Since early visual cortex activity at the population level has been shown to have a monotonic relationship with subjective contrast perception, we speculate that the perceived contrast enhancement could reflect an increase in neuronal activity. In other words, predictive feedback may have had an excitatory influence on neuronal responses. Control experiments ruled out attention bias, local feature differences and response bias as alternate explanations.
Atomic visualization of a flipped-back conformation of bisected glycans bound to specific lectins
Authors: Nagae Masamichi , Kanagawa Mayumi , Morita-Matsumoto Kana , Hanashima Shinya , Kizuka Yasuhiko , Taniguchi Naoyuki , Yamaguchi Yoshiki 
Published: March 2016

AbstractGlycans normally exist as a dynamic equilibrium of several conformations. A fundamental question concerns how such molecules bind lectins despite disadvantageous entropic loss upon binding. Bisected glycan, a glycan possessing bisecting N-acetylglucosamine (GlcNAc), is potentially a good model for investigating conformational dynamics and glycan-lectin interactions, owing to the unique ability of this sugar residue to alter conformer populations and thus modulate the biological activities. Here we analyzed bisected glycan in complex with two unrelated lectins, Calsepa and PHA-E. The crystal structures of the two complexes show a conspicuous flipped back glycan structure (designated ‘back-fold’ conformation) and solution NMR analysis also provides evidence of ‘back-fold’ glycan structure. Indeed, statistical conformational analysis of available bisected and non-bisected glycan structures suggests that bisecting GlcNAc restricts the conformations of branched structures. Restriction of glycan flexibility by certain sugar residues may be more common than previously thought and impinges on the mechanism of glycoform-dependent biological functions.
Quantum probability assignment limited by relativistic causality
Authors: Han Yeong Deok , Choi Taeseung 
Published: March 2016

AbstractQuantum theory has nonlocal correlations, which bothered Einstein, but found to satisfy relativistic causality. Correlation for a shared quantum state manifests itself, in the standard quantum framework, by joint probability distributions that can be obtained by applying state reduction and probability assignment that is called Born rule. Quantum correlations, which show nonlocality when the shared state has an entanglement, can be changed if we apply different probability assignment rule. As a result, the amount of nonlocality in quantum correlation will be changed. The issue is whether the change of the rule of quantum probability assignment breaks relativistic causality. We have shown that Born rule on quantum measurement is derived by requiring relativistic causality condition. This shows how the relativistic causality limits the upper bound of quantum nonlocality through quantum probability assignment.
Terahertz Artificial Dielectric Lens
Authors: Mendis Rajind , Nagai Masaya , Wang Yiqiu , Karl Nicholas , Mittleman Daniel M. 
Published: March 2016

AbstractWe have designed, fabricated and experimentally characterized a lens for the THz regime based on artificial dielectrics. These are man-made media that mimic properties of naturally occurring dielectric media, or even manifest properties that cannot generally occur in nature. For example, the well-known dielectric property, the refractive index, which usually has a value greater than unity, can have a value less than unity in an artificial dielectric. For our lens, the artificial-dielectric medium is made up of a parallel stack of 100 μm thick metal plates that form an array of parallel-plate waveguides. The convergent lens has a plano-concave geometry, in contrast to conventional dielectric lenses. Our results demonstrate that this lens is capable of focusing a 2 cm diameter beam to a spot size of 4 mm, at the design frequency of 0.17 THz. The results further demonstrate that the overall power transmission of the lens can be better than certain conventional dielectric lenses commonly used in the THz regime. Intriguingly, we also observe that under certain conditions, the lens boundary demarcated by the discontinuous plate edges actually resembles a smooth continuous surface. These results highlight the importance of this artificial-dielectric technology for the development of future THz-wave devices.
Discovery of a Novel Seminal Fluid Microbiome and Influence of Estrogen Receptor Alpha Genetic Status
Authors: Javurek Angela B. , Spollen William G. , Ali Amber M. Mann , Johnson Sarah A. , Lubahn Dennis B. , Bivens Nathan J. , Bromert Karen H. , Ellersieck Mark R. , Givan Scott A. , Rosenfeld Cheryl S. 
Published: March 2016

AbstractBacteria harbored in the male reproductive system may influence reproductive function and health of the male and result in developmental origins of adult health and disease (DOHaD) effects in his offspring. Such effects could be due to the seminal fluid, which is slightly basic and enriched with carbohydrates; thereby, creating an ideal habitat for microbes or a potential seminal fluid microbiome (SFM). Using wild-type (WT) and estrogen receptor-alpha (ESR1) knockout (KO) male mice, we describe a unique SFM whose inhabitants differ from gut microbes. The bacterial composition of the SFM is influenced according to whether mice have functional Esr1 genes. Propionibacterium acnes, causative agent of chronic prostatitis possibly culminating in prostate cancer, is reduced in SFM of ESR1 KO compared to WT mice (P ≤ 0.0007). In certain genetic backgrounds, WT mice show a greater incidence of prostate cancer than ESR1 KO, which may be due to increased abundance of P. acnes. Additionally, select gut microbiome residents in ESR1 KO males, such as Lachnospiraceae and Christensenellaceae, might contribute to previously identified phenotypes, especially obesity, in these mutant mice. Understanding how genetics and environmental factors influence the SFM may provide the next frontier in male reproductive disorders and possibly paternal-based DOHaD diseases.
High-pressure Gas Activation for Amorphous Indium-Gallium-Zinc-Oxide Thin-Film Transistors at 100 °C
Authors: Kim Won-Gi , Tak Young Jun , Du Ahn Byung , Jung Tae Soo , Chung Kwun-Bum , Kim Hyun Jae 
Published: March 2016

AbstractWe investigated the use of high-pressure gases as an activation energy source for amorphous indium-gallium-zinc-oxide (a-IGZO) thin film transistors (TFTs). High-pressure annealing (HPA) in nitrogen (N2) and oxygen (O2) gases was applied to activate a-IGZO TFTs at 100 °C at pressures in the range from 0.5 to 4 MPa. Activation of the a-IGZO TFTs during HPA is attributed to the effect of the high-pressure environment, so that the activation energy is supplied from the kinetic energy of the gas molecules. We reduced the activation temperature from 300 °C to 100 °C via the use of HPA. The electrical characteristics of a-IGZO TFTs annealed in O2 at 2 MPa were superior to those annealed in N2 at 4 MPa, despite the lower pressure. For O2 HPA under 2 MPa at 100 °C, the field effect mobility and the threshold voltage shift under positive bias stress were improved by 9.00 to 10.58 cm2/V.s and 3.89 to 2.64 V, respectively. This is attributed to not only the effects of the pressurizing effect but also the metal-oxide construction effect which assists to facilitate the formation of channel layer and reduces oxygen vacancies, served as electron trap sites.
Decoding regulatory landscape of somatic embryogenesis reveals differential regulatory networks between japonica and indica rice subspecies
Authors: Indoliya Yuvraj , Tiwari Poonam , Chauhan Abhisekh Singh , Goel Ridhi , Shri Manju , Bag Sumit Kumar , Chakrabarty Debasis 
Published: March 2016

AbstractSomatic embryogenesis is a unique process in plants and has considerable interest for biotechnological application. Compare to japonica, indica rice has been less responsive to in vitro culture. We used Illumina Hiseq 2000 sequencing platform for comparative transcriptome analysis between two rice subspecies at six different developmental stages combined with a tag-based digital gene expression profiling. Global gene expression among different samples showed greater complexity in japonica rice compared to indica which may be due to polyphyletic origin of two rice subspecies. Expression pattern in initial stage indicate major differences in proembryogenic callus induction phase that may serve as key regulator to observe differences between both subspecies. Our data suggests that phytohormone signaling pathways consist of elaborate networks with frequent crosstalk, thereby allowing plants to regulate somatic embryogenesis pathway. However, this crosstalk varies between the two rice subspecies. Down regulation of positive regulators of meristem development (i.e. KNOX, OsARF5) and up regulation of its counterparts (OsRRs, MYB, GA20ox1/GA3ox2) in japonica may be responsible for its better regeneration and differentiation of somatic embryos. Comprehensive gene expression information in the present experiment may also facilitate to understand the monocot specific meristem regulation for dedifferentiation of somatic cell to embryogenic cells.
Functional characterization of ent-copalyl diphosphate synthase, kaurene synthase and kaurene oxidase in the Salvia miltiorrhiza gibberellin biosynthetic pathway
Authors: Su Ping , Tong Yuru , Cheng Qiqing , Hu Yating , Zhang Meng , Yang Jian , Teng Zhongqiu , Gao Wei , Huang Luqi 
Published: March 2016

AbstractSalvia miltiorrhiza Bunge is highly valued in traditional Chinese medicine for its roots and rhizomes. Its bioactive diterpenoid tanshinones have been reported to have many pharmaceutical activities, including antibacterial, anti-inflammatory and anticancer properties. Previous studies found four different diterpenoid biosynthetic pathways from the universal diterpenoid precursor (E,E,E)-geranylgeranyl diphosphate (GGPP) in S. miltiorrhiza. Here, we describe the functional characterization of ent-copalyl diphosphate synthase (SmCPSent), kaurene synthase (SmKS) and kaurene oxidase (SmKO) in the gibberellin (GA) biosynthetic pathway. SmCPSent catalyzes the cyclization of GGPP to ent-copalyl diphosphate (ent-CPP), which is converted to ent-kaurene by SmKS. Then, SmKO catalyzes the three-step oxidation of ent-kaurene to ent-kaurenoic acid. Our results show that the fused enzyme SmKS-SmCPSent increases ent-kaurene production by several fold compared with separate expression of SmCPSent and SmKS in yeast strains. In this study, we clarify the GA biosynthetic pathway from GGPP to ent-kaurenoic acid and provide a foundation for further characterization of the subsequent enzymes involved in this pathway. These insights may allow for better growth and the improved accumulation of bioactive tanshinones in S. miltiorrhiza through the regulation of the expression of these genes during developmental processes.
RETRACTED ARTICLE: Overexpression of miR-499-5p inhibits non-small cell lung cancer proliferation and metastasis by targeting VAV3
Authors: Li Ming , Zhang Shenjun , Wu Ning , Wu Liang , Wang Changhui , Lin Yinping 
Published: March 2016

AbstractDysregulation of miRNAs is reported to be involved in the invasion and metastasis of lung cancer. Previous studies showed that low serum miR-499 expression was associated with advanced TNM stage and poor prognosis. The present study is carried out to evaluate the biological functions of miR-499-5p in lung cancer. We demonstrated that miR-499-5p was significantly reduced in NSCLC tissues and correlated with poor clinical outcomes. Overexpression of miR-499-5p inhibited cell proliferation and induced apoptosis in vitro and in vivo. Furthermore, miR-499-5p overexpression also inhibited NSCLC metastasis in vitro and in vivo. Using bioinformatics tools, we identified VAV3 as a candidate target of miR-499-5p and demonstrated that restoration of miR-499-5p expression in NSCLC cells downregulated VAV3 expression while inhibition of miR-499-5p upregulated VAV3 expression. Luciferase reporter assays showed that miR-499-5p targeted 3′-UTR of VAV3. Moreover, cancer growth, proliferation and metastasis were decreased and apoptosis was increased after VAV3 blockage induced by miR-499-5p overexpression. We conclude that miR-499-5p functions as a tumor suppressor by targeting VAV3. This finding may provide a therapeutic approach for future treatment of NSCLC.