bluuebunny/crossref_metadata_2025_split huggingface dataset:
Romidepsin targets multiple survival signaling pathways in malignant T cells
Authors: Valdez B C , Brammer J E , Li Y , Murray D , Liu Y , Hosing C , Nieto Y , Champlin R E , Andersson B S 
Published: October 2015

AbstractRomidepsin is a cyclic molecule that inhibits histone deacetylases. It is Food and Drug Administration-approved for treatment of cutaneous and peripheral T-cell lymphoma, but its precise mechanism of action against malignant T cells is unknown. To better understand the biological effects of romidepsin in these cells, we exposed PEER and SUPT1 T-cell lines, and a primary sample from T-cell lymphoma patient (Patient J) to romidepsin. We then examined the consequences in some key oncogenic signaling pathways. Romidepsin displayed IC50 values of 10.8, 7.9 and 7.0 nm in PEER, SUPT1 and Patient J cells, respectively. Strong inhibition of histone deacetylases and demethylases, increased production of reactive oxygen species and decreased mitochondrial membrane potential were observed, which may contribute to the observed DNA-damage response and apoptosis. The stress-activated protein kinase/c-Jun N-terminal kinase signaling pathway and unfolded protein response in the endoplasmic reticulum were activated, whereas the phosphatidylinositol 3-kinase/AKT/mammalian target of rapamycin (PI3K/AKT/mTOR) and β-catenin pro-survival pathways were inhibited. The decreased level of β-catenin correlated with the upregulation of its inhibitor SFRP1 through romidepsin-mediated hypomethylation of its gene promoter. Our results provide new insights into how romidepsin invokes malignant T-cell killing, show evidence of its associated DNA hypomethylating activity and offer a rationale for the development of romidepsin-containing combination therapies.
Ectomycorrhizal fungal spore bank recovery after a severe forest fire: some like it hot
Authors: Glassman Sydney I , Levine Carrie R , DiRocco Angela M , Battles John J , Bruns Thomas D 
Published: October 2015

AbstractAfter severe wildfires, pine recovery depends on ectomycorrhizal (ECM) fungal spores surviving and serving as partners for regenerating forest trees. We took advantage of a large, severe natural forest fire that burned our long-term study plots to test the response of ECM fungi to fire. We sampled the ECM spore bank using pine seedling bioassays and high-throughput sequencing before and after the California Rim Fire. We found that ECM spore bank fungi survived the fire and dominated the colonization of in situ and bioassay seedlings, but there were specific fire adapted fungi such as Rhizopogon olivaceotinctus that increased in abundance after the fire. The frequency of ECM fungal species colonizing pre-fire bioassay seedlings, post-fire bioassay seedlings and in situ seedlings were strongly positively correlated. However, fire reduced the ECM spore bank richness by eliminating some of the rare species, and the density of the spore bank was reduced as evidenced by a larger number of soil samples that yielded uncolonized seedlings. Our results show that although there is a reduction in ECM inoculum, the ECM spore bank community largely remains intact, even after a high-intensity fire. We used advanced techniques for data quality control with Illumina and found consistent results among varying methods. Furthermore, simple greenhouse bioassays can be used to determine which fungi will colonize after fires. Similar to plant seed banks, a specific suite of ruderal, spore bank fungi take advantage of open niche space after fires.
Towards a general diastereoselective route to oxabicyclo[3.2.1]octanes via a gold-catalysed cascade reaction
Authors: Fu Junkai , Gu Yueqing , Yuan Hao , Luo Tuoping , Liu Song , Lan Yu , Gong Jianxian , Yang Zhen 
Published: October 2015

AbstractThe development of an efficient diastereoselective synthesis of the oxabicyclo[3.2.1]octane ring system bearing two oxygenated quaternary chiral centres represents a significant challenge. This motif can be found in a wide range of natural products with significant biological activities. Here we report the synthesis of such kind of scaffold using a cyclohexane-trans-1,4-diol with an alkyne side chain in the presence of Au(I) catalyst. This is a domino process in which two C–H, two C–O and one C–C bond is assembled through a sequence of cyclization/semi-pinacol rearrangements. This strategy has been successfully applied to the asymmetric formal total synthesis of (+)-cortistatins.
Optimized measurements of separations and angles between intra-molecular fluorescent markers
Authors: Mortensen Kim I. , Sung Jongmin , Flyvbjerg Henrik , Spudich James A. 
Published: October 2015

AbstractWe demonstrate a novel, yet simple tool for the study of structure and function of biomolecules by extending two-colour co-localization microscopy to fluorescent molecules with fixed orientations and in intra-molecular proximity. From each colour-separated microscope image in a time-lapse movie and using only simple means, we simultaneously determine both the relative (x,y)-separation of the fluorophores and their individual orientations in space with accuracy and precision. The positions and orientations of two domains of the same molecule are thus time-resolved. Using short double-stranded DNA molecules internally labelled with two fixed fluorophores, we demonstrate the accuracy and precision of our method using the known structure of double-stranded DNA as a benchmark, resolve 10-base-pair differences in fluorophore separations, and determine the unique 3D orientation of each DNA molecule, thereby establishing short, double-labelled DNA molecules as probes of 3D orientation of anything to which one can attach them firmly.
Histone methyltransferase SETDB1 regulates liver cancer cell growth through methylation of p53
Authors: Fei Qi , Shang Ke , Zhang Jianhua , Chuai Shannon , Kong Desheng , Zhou Tianlun , Fu Shijun , Liang Ying , Li Chong , Chen Zhi , Zhao Yuan , Yu Zhengtian , Huang Zheng , Hu Min , Ying Haiyan , Chen Zhui , Zhang Yun , Xing Feng , Zhu Jidong , Xu Haiyan , Zhao Kehao , Lu Chris , Atadja Peter , Xiao Zhi-Xiong , Li En , Shou Jianyong 
Published: October 2015

AbstractSETDB1 is a histone H3K9 methyltransferase that has a critical role in early development. It is located within a melanoma susceptibility locus and facilitates melanoma formation. However, the mechanism by which SETDB1 regulates tumorigenesis remains unknown. Here we report the molecular interplay between SETDB1 and the well-known hotspot gain-of-function (GOF) TP53 R249S mutation. We show that in hepatocellular carcinoma (HCC) SETDB1 is overexpressed with moderate copy number gain, and GOF TP53 mutations including R249S associate with this overexpression. Inactivation of SETDB1 in HCC cell lines bearing the R249S mutation suppresses cell growth. The TP53 mutation status renders cancer cells dependent on SETDB1. Moreover, SETDB1 forms a complex with p53 and catalyses p53K370 di-methylation. SETDB1 attenuation reduces the p53K370me2 level, which subsequently leads to increased recognition and degradation of p53 by MDM2. Together, we provide both genetic and biochemical evidence for a mechanism by which SETDB1 regulates cancer cell growth via methylation of p53.
Water Status Related Root-to-Shoot Communication Regulates the Chilling Tolerance of Shoot in Cucumber (Cucumis sativus L.) Plants
Authors: Zhang Zi-Shan , Liu Mei-Jun , Gao Hui-Yuan , Jin Li-Qiao , Li Yu-Ting , Li Qing-Ming , Ai Xi-Zhen 
Published: October 2015

AbstractAlthough root-to-shoot communication has been intensively investigated in plants under drought, few studies have examined root-to-shoot communication under chilling. Here we explored whether root-to-shoot communication contributes to the chilling-light tolerance of cucumber shoots and clarified the key signal involves in this communication. After leaf discs chilling-light treatment, the photoinhibitions of Photosystem I (PSI) and Photosystem II (PSII) were similar in leaf discs of two cucumber varieties (JY-3 and JC-4). When the whole plants, including roots, were chilled under light, the photosynthetic performances in JC-4 leaves decreased more seriously than that in JY-3 leaves. However, when the water status of leaves was maintained by warming roots or floating the attached leaves on water, the PSII activity and amount of PSI in the leaves of the two varieties were similar after chilling-light treatment. In addition, the differences of PSII activities and amount of PSI between the two varieties under whole plant chilling-light treatment were independent of ABA pretreatment. Above results indicate that (1) the better water status in leaves under chilling contributes to the higher chilling tolerance of JY-3; (2) the water status, rather than an ABA signal, dominates root-to-shoot communication under chilling and the chilling tolerance of cucumber shoot.
Are fish fed with cyanobacteria safe, nutritious and delicious? A laboratory study
Authors: Liang Hualei , Zhou Wenshan , Zhang Yulei , Qiao Qin , Zhang Xuezhen 
Published: October 2015

AbstractToxic cyanobacterial blooms, which produce cyclic heptapeptide toxins known as microcystins, are worldwide environmental problems. On the other hand, the cyanobacteria protein (30–50%) has been recommended as substitute protein for aquaculture. The present laboratory study verified the feasibility of cyanobacteria protein substitution and risk assessment. Goldfish were fed diets supplemented lyophilised cyanobacteria powder for 16 weeks with the various doses: 0% (control), 10%, 20%, 30% and 40%. Low doses (10% and 20%) promoted growth whereas high doses (30% and 40%) inhibited growth. In cyanobacteria treated fish, the proximate composition of ash, crude fat content and crude protein content decreased in 16 weeks; the saturated fatty acid (SFA) content significantly increased; the n-3 polyunsaturated fatty acid content, collagen content and muscle pH significantly decreased; cooking loss percents increased significantly. Muscle fiber diameter and myofibril length were negatively correlation. Additionally, flavour compounds (e.g., amino acids, nucleotides, organic acids and carnosine) changed significantly in the treated fish and odour compounds geosmin and 2-methylisoborneol increased significantly. The estimated daily intake (EDI) of microcystins in muscle was close to or exceeded the World Health Organization (WHO) tolerable daily intake (TDI), representing a great health risk. Cyanobacterie is not feasible for protein sources use in aquaculture.
Dynamic manipulation of particles via transformative optofluidic waveguides
Authors: Lee Kang Soo , Lee Kyung Heon , Kim Sang Bok , Ha Byung Hang , Jung Jin Ho , Sung Hyung Jin , Kim Sang Soo 
Published: October 2015

AbstractOptofluidics is one of the most remarkable areas in the field of microfluidic research. Particle manipulation with optofluidic platforms has become central to optical chromatography, biotechnology and μ-total analysis systems. Optical manipulation of particles depends on their sizes and refractive indices (n), which occasionally leads to undesirable separation consequences when their optical mobilities are identical. Here, we demonstrate rapid and dynamic particle manipulation according to n, regardless of size. Integrated liquid-core/solid-cladding (LS) and liquid-core/liquid-cladding (L2) waveguides were fabricated and their characteristics were experimentally and theoretically determined. The high and low n particles showed the opposite behaviors by controlling the contrast of their n values to those of the working fluids. The LS waveguide was found to successfully manipulate particles according to n and the L2 waveguide was found to provide additional system stability and flexibility, compared to the LS system.
Ruthenium nanoparticles confined in SBA-15 as highly efficient catalyst for hydrolytic dehydrogenation of ammonia borane and hydrazine borane
Authors: Yao Qilu , Lu Zhang-Hui , Yang Kangkang , Chen Xiangshu , Zhu Meihua 
Published: October 2015

AbstractUltrafine ruthenium nanoparticles (NPs) within the mesopores of the SBA-15 have been successfully prepared by using a “double solvents” method, in which n-hexane is used as a hydrophobic solvent and RuCl3 aqueous solution is used as a hydrophilic solvent. After the impregnation and reduction processes, the samples were characterized by XRD, TEM, EDX, XPS, N2 adsorption-desorption and ICP techniques. The TEM images show that small sized Ru NPs with an average size of 3.0 ± 0.8 nm are uniformly dispersed in the mesopores of SBA-15. The as-synthesized Ru@SBA-15 nanocomposites (NCs) display exceptional catalytic activity for hydrogen generation by the hydrolysis of ammonia borane (NH3BH3, AB) and hydrazine borane (N2H4BH3, HB) at room temperature with the turnover frequency (TOF) value of 316 and 706 mol H2 (mol Ru min)−1, respectively, relatively high values reported so far for the same reaction. The activation energies (Ea) for the hydrolysis of AB and HB catalyzed by Ru@SBA-15 NCs are measured to be 34.8 ± 2 and 41.3 ± 2 kJ mol−1, respectively. Moreover, Ru@SBA-15 NCs also show satisfied durable stability for the hydrolytic dehydrogenation of AB and HB, respectively.
Chitosan nanoparticles: A positive modulator of innate immune responses in plants
Authors: Chandra Swarnendu , Chakraborty Nilanjan , Dasgupta Adhiraj , Sarkar Joy , Panda Koustubh , Acharya Krishnendu 
Published: October 2015

AbstractThe immunomodulatory role of the natural biopolymer, chitosan, has already been demonstrated in plants, whilst its nanoparticles have only been examined for biomedical applications. In our present study, we have investigated the possible ability and mechanism of chitosan nanoparticles (CNP) to induce and augment immune responses in plants. CNP-treatment of leaves produced significant improvement in the plant’s innate immune response through induction of defense enzyme activity, upregulation of defense related genes including that of several antioxidant enzymes as well as elevation of the levels of total phenolics. It is also possible that the extracellular localization of CNP may also play a role in the observed upregulation of defense response in plants. Nitric oxide (NO), an important signaling molecule in plant defense, was also observed to increase following CNP treatment. However, such CNP-mediated immuno-stimulation was significantly mitigated when NO production was inhibited, indicating a possible role of NO in such immune induction. Taken together, our results suggest that CNP may be used as a more effective phytosanitary or disease control agent compared to natural chitosan for sustainable organic cultivation.
Notch Signaling in Inflammation-Induced Preterm Labor
Authors: Jaiswal Mukesh K. , Agrawal Varkha , Pamarthy Sahithi , Katara Gajendra K. , Kulshrestha Arpita , Gilman-Sachs Alice , Beaman Kenneth D. , Hirsch Emmet 
Published: October 2015

AbstractNotch signaling plays an important role in regulation of innate immune responses and trophoblast function during pregnancy. To identify the role of Notch signaling in preterm labor, Notch receptors (Notch1-4), its ligands (DLL (Delta-like protein)-1/3/4), Jagged 1/2) and Notch-induced transcription factor Hes1 were assessed during preterm labor. Preterm labor was initiated on gestation day 14.5 by intrauterine (IU) injection of peptidoglycan (PGN) and polyinosinic:cytidylic acid (poly(I:C). Notch1, Notch2, Notch4, DLL-1 and nuclear localization of Hes1 were significantly elevated in uterus and placenta during PGN+poly(I:C)-induced preterm labor. Ex vivo, Gamma secretase inhibitor (GSI) (inhibitor of Notch receptor processing) significantly diminished the PGN+poly(I:C)-induced secretion of M1- and M2-associated cytokines in decidual macrophages and of proinflammatory cytokines (IFN-γ, TNF-α and IL-6) and chemokines (MIP-1β) in decidual and placental cells. Conversely, angiogenesis factors including Notch ligands Jagged 1/2 and DLL-4 and VEGF were significantly reduced in uterus and placenta during PGN+poly(I:C)-induced preterm labor. In vivo GSI treatment prevents PGN+poly(I:C)-induced preterm delivery by 55.5% and increased the number of live fetuses in-utero significantly compared to respective controls 48 hrs after injections. In summary, Notch signaling is activated during PGN+poly(I:C)-induced preterm labor, resulting in upregulation of pro-inflammatory responses and its inhibition improves in-utero survival of live fetuses.
Development and external validation of a prostate health index-based nomogram for predicting prostate cancer
Authors: Zhu Yao , Han Cheng-Tao , Zhang Gui-Ming , Liu Fang , Ding Qiang , Xu Jian-Feng , Vidal Adriana C. , Freedland Stephen J. , Ng Chi-Fai , Ye Ding-Wei 
Published: October 2015

AbstractTo develop and externally validate a prostate health index (PHI)-based nomogram for predicting the presence of prostate cancer (PCa) at biopsy in Chinese men with prostate-specific antigen 4–10 ng/mL and normal digital rectal examination (DRE). 347 men were recruited from two hospitals between 2012 and 2014 to develop a PHI-based nomogram to predict PCa. To validate these results, we used a separate cohort of 230 men recruited at another center between 2008 and 2013. Receiver operator curves (ROC) were used to assess the ability to predict PCa. A nomogram was derived from the multivariable logistic regression model and its accuracy was assessed by the area under the ROC (AUC). PHI achieved the highest AUC of 0.839 in the development cohort compared to the other predictors (p < 0.001). Including age and prostate volume, a PHI-based nomogram was constructed and rendered an AUC of 0.877 (95% CI 0.813–0.938). The AUC of the nomogram in the validation cohort was 0.786 (95% CI 0.678–0.894). In clinical effectiveness analyses, the PHI-based nomogram reduced unnecessary biopsies from 42.6% to 27% using a 5% threshold risk of PCa to avoid biopsy with no increase in the number of missed cases relative to conventional biopsy decision.
Biophysical optimality of the golden angle in phyllotaxis
Authors: Okabe Takuya 
Published: October 2015

AbstractPlant leaves are arranged around a stem axis in a regular pattern characterized by common fractions, a phenomenon known as phyllotaxis or phyllotaxy. As plants grow, these fractions often transition according to simple rules related to Fibonacci sequences. This mathematical regularity originates from leaf primordia at the shoot tip (shoot apical meristem), which successively arise at fixed intervals of a divergence angle, typically the golden angle of 137.5°. Algebraic and numerical interpretations have been proposed to explain the golden angle observed in phyllotaxis. However, it remains unknown whether phyllotaxis has adaptive value, even though two centuries have passed since the phenomenon was discovered. Here, I propose a new adaptive mechanism explaining the presence of the golden angle. This angle is the optimal solution to minimize the energy cost of phyllotaxis transition. This model accounts for not only the high precision of the golden angle but also the occurrences of other angles observed in nature. The model also effectively explains the observed diversity of rational and irrational numbers in phyllotaxis.
Effects of Stretching Speed on Mechanical Rupture of Phospholipid/Cholesterol Bilayers: Molecular Dynamics Simulation
Authors: Shigematsu Taiki , Koshiyama Kenichiro , Wada Shigeo 
Published: October 2015

AbstractRupture of biological cell membrane under mechanical stresses is critical for cell viability. It is triggered by local rearrangements of membrane molecules. We investigated the effects of stretching speed on mechanical rupture of phospholipid/cholesterol bilayers using unsteady molecular dynamics simulations. We focused on pore formation, the trigger of rupture, in a 40 mol% cholesterol-including bilayer. The unsteady stretching was modeled by proportional and temporal scaling of atom positions at stretching speeds from 0.025 to 30 m/s. The effects of the stretching speed on the critical areal strain, where the pore forms, is composed of two regimes. At low speeds (<1.0 m/s), the critical areal strain is insensitive to speed, whereas it significantly increases at higher speeds. Also, the strain is larger than that of a pure bilayer, regardless of the stretching speeds, which qualitatively agrees with available experimental data. Transient recovery of the cholesterol and phospholipid molecular orientations was evident at lower speeds, suggesting the formation of a stretch-induced interdigitated gel-like phase. However, this recovery was not confirmed at higher speeds or for the pure bilayer. The different responses of the molecular orientations may help explain the two regimes for the effect of stretching speed on pore formation.
Density Functional Theory for Steady-State Nonequilibrium Molecular Junctions
Authors: Liu Shuanglong , Nurbawono Argo , Zhang Chun 
Published: October 2015

AbstractWe present a density functional theory (DFT) for steady-state nonequilibrium quantum systems such as molecular junctions under a finite bias. Based on the steady-state nonequilibrium statistics that maps nonequilibrium to an effective equilibrium, we show that ground-state DFT (GS-DFT) is not applicable in this case and two densities, the total electron density and the density of current-carrying electrons, are needed to uniquely determine the properties of the corresponding nonequilibrium system. A self-consistent mean-field approach based on two densities is then derived. The theory is implemented into SIESTA computational package and applied to study nonequilibrium electronic/transport properties of a realistic carbon-nanotube (CNT)/Benzene junction. Results obtained from our steady-state DFT (SS-DFT) are compared with those of conventional GS-DFT based transport calculations. We show that SS-DFT yields energetically more stable nonequilibrium steady state, predicts significantly lower electric current and is able to produce correct electronic structures in local equilibrium under a limiting case.
Revealing crosstalk of plant and fungi in the symbiotic roots of sewage-cleaning Eichhornia crassipes using direct de novo metatranscriptomic analysis
Authors: Luo Bin , Gu Wei , Zhong Jiayong , Wang Ying , Zhang Gong 
Published: October 2015

AbstractCultivation and environmental changes can induce development of novel phenotypes in plants. For example, the root morphology of cultivated purple rootEichhornia crassipesdiffers remarkably from normalEichhornia crassipesand also shows an enhanced ability to absorb heavy metal from groundwater. However, the changes in gene expression associated with these processes are unknown because of the lack of information on its large and unsequenced genome and its complex plant-rhizosphere symbiotic system. To investigate these gene expression changes, we applied a new strategy, directde novometatranscriptome analysis. Using this approach, we assembled the metatranscriptome of the entire rhizosphere and identified species-specific differentially expressed genes (DEGs) via hyper-accurate algorithms, showing a polarized plant/fungus distribution: the plant genes were responsible for morphological changes to the root system, offering a greater volume and surface area that hosts more fungi; while genes associated with heavy metal response in the fungusFusariumwere upregulated more than 3600-fold. These results suggested a distinct and synergistic functional response by the plant and fungal transcriptomes, indicating significant plant/fungal crosstalk during environmental changes. This study demonstrates that the metatranscriptomic approach adopted here offers a cost-efficient strategy to study symbiosis systems without the need fora priorigenomic knowledge.