bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic and transcriptional analyses of the carbohydrate-active enzymes and secretomes of phytopathogenic fungi reveal their significant roles during infection and development
Authors: Lyu Xueliang , Shen Cuicui , Fu Yanping , Xie Jiatao , Jiang Daohong , Li Guoqing , Cheng Jiasen 
Published: November 2015

AbstractOur comparative genomic analysis showed that the numbers of plant cell wall (PCW)- and fungal cell wall (FCW)-degradation-associated carbohydrate-active enzymes (CAZymes) in necrotrophic and hemibiotrophic fungi are significantly larger than that in most biotrophic fungi. However, our transcriptional analyses of CAZyme-encoding genes inMelampsora larici-populina,Puccinia graminisandSclerotinia sclerotiorumshowed that many genes encoding PCW- and FCW-degradation-associated CAZymes were significantly up-regulated during the infection of both necrotrophic fungi and biotrophic fungi, indicating an existence of a universal mechanism underlying PCW degradation and FCW reorganization or modification, which are both intimately involved in necrotrophic and biotrophic fungal infection. Furthermore, our results showed that the FCW reorganization or modification was also related to the fungal development. Additionally, our transcriptional analysis of the secretome ofS. sclerotiorumshowed that many secreted protein-encoding genes were dramatically induced during infection. Among them, a small, cysteine-rich protein SsCVNH was experimentally confirmed to be essential for the virulence and sclerotial development, indicating that the small secreted proteins might also play crucial roles as potential effectors in host-non-specific necrotrophic fungi.
Glaucumolides A and B, Biscembranoids with New Structural Type from a Cultured Soft Coral Sarcophyton glaucum
Authors: Huang Chiung-Yao , Sung Ping-Jyun , Uvarani Chokkalingam , Su Jui-Hsin , Lu Mei-Chin , Hwang Tsong-Long , Dai Chang-Feng , Wu Shwu-Li , Sheu Jyh-Horng 
Published: November 2015

AbstractGlaucumolides A (1) and B (2), novel biscembranes composed of an unprecedented α,β-unsaturated ε-lactone, along with the known metabolites ximaolide A (3) and isosarcophytonolide D (4), were isolated from the cultured soft coral Sarcophyton glaucum. The structures of the new metabolites were determined by extensive spectroscopic analyses. Compounds 1 and 2 were shown to exhibit cytotoxicity against a limited panel of cancer cell lines. In anti-inflammation assay, compounds 1 and 2 displayed strong inhibition of superoxide anion generation and elastase release in human neutrophils stimulated by fMLP/CB. Furthermore, both 1 and 2 were shown to significantly inhibit the accumulation of the pro-inflammatory inducible nitric oxide synthase protein and compounds 1−3 were found to effectively reduce the expression of cyclooxygenase-2 protein, in lipopolysaccharide-stimulated RAW264.7 macrophage cells.
Highly sensitive image-derived indices of water-stressed plants using hyperspectral imaging in SWIR and histogram analysis
Authors: Kim David M. , Zhang Hairong , Zhou Haiying , Du Tommy , Wu Qian , Mockler Todd C. , Berezin Mikhail Y. 
Published: November 2015

AbstractThe optical signature of leaves is an important monitoring and predictive parameter for a variety of biotic and abiotic stresses, including drought. Such signatures derived from spectroscopic measurements provide vegetation indices – a quantitative method for assessing plant health. However, the commonly used metrics suffer from low sensitivity. Relatively small changes in water content in moderately stressed plants demand high-contrast imaging to distinguish affected plants. We present a new approach in deriving sensitive indices using hyperspectral imaging in a short-wave infrared range from 800 nm to 1600 nm. Our method, based on high spectral resolution (1.56 nm) instrumentation and image processing algorithms (quantitative histogram analysis), enables us to distinguish a moderate water stress equivalent of 20% relative water content (RWC). The identified image-derived indices 15XX nm/14XX nm (i.e. 1529 nm/1416 nm) were superior to common vegetation indices, such as WBI, MSI and NDWI, with significantly better sensitivity, enabling early diagnostics of plant health.
Compressible and monolithic microporous polymer sponges prepared via one-pot synthesis
Authors: Lim Yoonbin , Cha Min Chul , Chang Ji Young 
Published: November 2015

AbstractCompressible and monolithic microporous polymers (MPs) are reported. MPs were prepared as monoliths via a Sonogashira–Hagihara coupling reaction of 1,3,5-triethynylbenzene (TEB) with the bis(bromothiophene) monomer (PBT-Br). The polymers were reversibly compressible and were easily cut into any form using a knife. Microscopy studies on the MPs revealed that the polymers had tubular microstructures, resembling those often found in marine sponges. Under compression, elastic buckling of the tube bundles was observed using an optical microscope. MP-0.8, which was synthesized using a 0.8:1 molar ratio of PBT-Br to TEB, showed microporosity with a BET surface area as high as 463 m2g–1. The polymer was very hydrophobic, with a water contact angle of 145° and absorbed 7–17 times its own weight of organic liquids. The absorbates were released by simple compression, allowing recyclable use of the polymer. MPs are potential precursors of structured carbon materials; for example, a partially graphitic material was obtained by pyrolysis of MP-0.8, which showed a similar tubular structure to that of MP-0.8.
Designing overall stoichiometric conversions and intervening metabolic reactions
Authors: Chowdhury Anupam , Maranas Costas D. 
Published: November 2015

AbstractExisting computational tools for de novo metabolic pathway assembly, either based on mixed integer linear programming techniques or graph-search applications, generally only find linear pathways connecting the source to the target metabolite. The overall stoichiometry of conversion along with alternate co-reactant (or co-product) combinations is not part of the pathway design. Therefore, global carbon and energy efficiency is in essence fixed with no opportunities to identify more efficient routes for recycling carbon flux closer to the thermodynamic limit. Here, we introduce a two-stage computational procedure that both identifies the optimum overall stoichiometry (i.e., optStoic) and selects for (non-)native reactions (i.e., minRxn/minFlux) that maximize carbon, energy or price efficiency while satisfying thermodynamic feasibility requirements. Implementation for recent pathway design studies identified non-intuitive designs with improved efficiencies. Specifically, multiple alternatives for non-oxidative glycolysis are generated and non-intuitive ways of co-utilizing carbon dioxide with methanol are revealed for the production of C2+ metabolites with higher carbon efficiency.
Extraordinary high ductility/strength of the interface designed bulk W-ZrC alloy plate at relatively low temperature
Authors: Xie Z. M. , Liu R. , Miao S. , Yang X. D. , Zhang T. , Wang X. P. , Fang Q. F. , Liu C. S. , Luo G. N. , Lian Y. Y. , Liu X. 
Published: November 2015

AbstractThe refractory tungsten alloys with high ductility/strength/plasticity are highly desirable for a wide range of critical applications. Here we report an interface design strategy that achieves 8.5 mm thick W-0.5 wt. %ZrC alloy plates with a flexural strength of 2.5 GPa and a strain of 3% at room temperature (RT) and ductile-to-brittle transition temperature of about 100 °C. The tensile strength is about 991 MPa at RT and 582 MPa at 500 °C, as well as total elongation is about 1.1% at RT and as large as 41% at 500 °C, respectively. In addition, the W-ZrC alloy plate can sustain 3.3 MJ/m2 thermal load without any cracks. This processing route offers the special coherent interfaces of grain/phase boundaries (GB/PBs) and the diminishing O impurity at GBs, which significantly strengthens GB/PBs and thereby enhances the ductility/strength/plasticity of W alloy. The design thought can be used in the future to prepare new alloys with higher ductility/strength.
IFNL3 mRNA structure is remodeled by a functional non-coding polymorphism associated with hepatitis C virus clearance
Authors: Lu Yi-Fan , Mauger David M. , Goldstein David B. , Urban Thomas J. , Weeks Kevin M. , Bradrick Shelton S. 
Published: November 2015

AbstractPolymorphisms near the interferon lambda 3 (IFNL3) gene strongly predict clearance of hepatitis C virus (HCV) infection. We analyzed a variant (rs4803217 G/T) located within the IFNL3 mRNA 3′ untranslated region (UTR); the G allele (protective allele) is associated with elevated therapeutic HCV clearance. We show that the IFNL3 3′ UTR represses mRNA translation and the rs4803217 allele modulates the extent of translational regulation. We analyzed the structures of IFNL3 variant mRNAs at nucleotide resolution by SHAPE-MaP. The rs4803217 G allele mRNA forms well-defined 3′ UTR structure while the T allele mRNA is more dynamic. The observed differences between alleles are among the largest possible RNA structural alterations that can be induced by a single nucleotide change and transform the UTR from a single well-defined conformation to one with multiple dynamic interconverting structures. These data illustrate that non-coding genetic variants can have significant functional effects by impacting RNA structure.
Light-matter decoupling and A2 term detection in superconducting circuits
Authors: García-Ripoll J. J. , Peropadre B. , De Liberato S. 
Published: November 2015

AbstractThe spontaneous and stimulated emission of a superconducting qubit in the presence of propagating microwaves originates from an effective light-matter interaction that, similarly to the case of the atomic case, can contain a diamagnetic term proportional to the square vector potential A2. In the present work we prove that an increase in the strength of the diamagnetic term leads to an effective decoupling of the qubit from the electromagnetic field and that this effect is observable at any range of qubit-photon coupling. To measure this effect we propose to use a transmon suspended over a transmission line, where the relative strength of the A2 term is controlled by the qubit-line separation. We show that the spontaneous emission rate of the suspended transmon onto the line can, at short distances, increase with such a separation, instead of decreasing.
Comparative genomics and experimental evolution of Escherichia coli BL21(DE3) strains reveal the landscape of toxicity escape from membrane protein overproduction
Authors: Kwon Soon-Kyeong , Kim Seong Keun , Lee Dae-Hee , Kim Jihyun F. 
Published: November 2015

AbstractAchieving sufficient yields of proteins in their functional form represents the first bottleneck in contemporary bioscience and biotechnology. To accomplish successful overexpression of membrane proteins in a workhorse organism such as E. coli, defined and rational optimization strategies based on an understanding of the genetic background of the toxicity-escape mechanism are desirable. To this end, we sequenced the genomes of E. coli C41(DE3) and its derivative C43(DE3), which were developed for membrane protein production. Comparative analysis of their genomes with those of their ancestral strain E. coli BL21(DE3) revealed various genetic changes in both strains. A series of E. coli variants that are able to tolerate transformation with or overexpression of membrane proteins were generated by in vitro evolution. Targeted sequencing of the evolved strains revealed the mutational hotspots among the acquired genetic changes. By these combinatorial approaches, we found non-synonymous changes in the lac repressor gene of the lac operon as well as nucleotide substitutions in the lacUV5 promoter of the DE3 region, by which the toxic effect to the host caused by overexpression of membrane proteins could be relieved. A mutation in lacI was demonstrated to be crucial for conferring tolerance to membrane protein overexpression.
Modifying the thermal conductivity of small molecule organic semiconductor thin films with metal nanoparticles
Authors: Wang Xinyu , Parrish Kevin D. , Malen Jonathan A. , Chan Paddy K. L. 
Published: November 2015

AbstractThermal properties of organic semiconductors play a significant role in the performance and lifetime of organic electronic devices, especially for scaled-up large area applications. Here we employ silver nanoparticles (Ag NPs) to modify the thermal conductivity of the small molecule organic semiconductor, dinaphtho[2,3-b:2’,3’-f]thieno[3,2-b]thiophene (DNTT). The differential 3-ω method was used to measure the thermal conductivity of Ag-DNTT hybrid thin films. We find that the thermal conductivity of pure DNTT thin films do not vary with the deposition temperature over a range spanning 24 °C to 80 °C. The thermal conductivity of the Ag-DNTT hybrid thin film initially decreases and then increases when the Ag volume fraction increases from 0% to 32%. By applying the effective medium approximation to fit the experimental results of thermal conductivity, the extracted thermal boundary resistance of the Ag-DNTT interface is 1.14 ± 0.98 × 10−7 m2-K/W. Finite element simulations of thermal conductivity for realistic film morphologies show good agreement with experimental results and effective medium approximations.
Abnormalities in synaptic dynamics during development in a mouse model of spinocerebellar ataxia type 1
Authors: Hatanaka Yusuke , Watase Kei , Wada Keiji , Nagai Yoshitaka 
Published: November 2015

AbstractLate-onset neurodegenerative diseases are characterized by neurological symptoms and progressive neuronal death. Accumulating evidence suggests that neuronal dysfunction, rather than neuronal death, causes the symptoms of neurodegenerative diseases. However, the mechanisms underlying the dysfunction that occurs prior to cell death remain unclear. To investigate the synaptic basis of this dysfunction, we employed in vivo two-photon imaging to analyse excitatory postsynaptic dendritic protrusions. We used Sca1154Q/2Q mice, an established knock-in mouse model of the polyglutamine disease spinocerebellar ataxia type 1 (SCA1), which replicates human SCA1 features including ataxia, cognitive impairment and neuronal death. We found that Sca1154Q/2Q mice exhibited greater synaptic instability than controls, without synaptic loss, in the cerebral cortex, where obvious neuronal death is not observed, even before the onset of distinct symptoms. Interestingly, this abnormal synaptic instability was evident in Sca1154Q/2Q mice from the synaptic developmental stage and persisted into adulthood. Expression of synaptic scaffolding proteins was also lower in Sca1154Q/2Q mice than controls before synaptic maturation. As symptoms progressed, synaptic loss became evident. These results indicate that aberrant synaptic instability, accompanied by decreased expression of scaffolding proteins during synaptic development, is a very early pathology that precedes distinct neurological symptoms and neuronal cell death in SCA1.
Compartmentalized microchannel array for high-throughput analysis of single cell polarized growth and dynamics
Authors: Geng Tao , Bredeweg Erin L. , Szymanski Craig J. , Liu Bingwen , Baker Scott E. , Orr Galya , Evans James E. , Kelly Ryan T. 
Published: November 2015

AbstractInterrogating polarized growth is technologically challenging due to extensive cellular branching and uncontrollable environmental conditions in conventional assays. Here we present a robust and high-performance microfluidic system that enables observations of polarized growth with enhanced temporal and spatial control over prolonged periods. The system has built-in tunability and versatility to accommodate a variety of scientific applications requiring precisely controlled environments. Using the model filamentous fungus, Neurospora crassa, our microfluidic system enabled direct visualization and analysis of cellular heterogeneity in a clonal fungal cell population, nuclear distribution and dynamics at the subhyphal level and quantitative dynamics of gene expression with single hyphal compartment resolution in response to carbon source starvation and exchange. Although the microfluidic device is demonstrated on filamentous fungi, the technology is immediately extensible to a wide array of other biosystems that exhibit similar polarized cell growth, with applications ranging from bioenergy production to human health.
CD44 deficiency inhibits unloading-induced cortical bone loss through downregulation of osteoclast activity
Authors: Li Yuheng , Zhong Guohui , Sun Weijia , Zhao Chengyang , Zhang Pengfei , Song Jinping , Zhao Dingsheng , Jin Xiaoyan , Li Qi , Ling Shukuan , Li Yingxian 
Published: November 2015

AbstractThe CD44 is cellular surface adhesion molecule that is involved in physiological processes such as hematopoiesis, lymphocyte homing and limb development. It plays an important role in a variety of cellular functions including adhesion, migration, invasion and survival. In bone tissue, CD44 is widely expressed in osteoblasts, osteoclasts and osteocytes. However, the mechanisms underlying its role in bone metabolism remain unclear. We found that CD44 expression was upregulated during osteoclastogenesis. CD44 deficiency in vitro significantly inhibited osteoclast activity and function by regulating the NF-κB/NFATc1-mediated pathway. In vivo, CD44 mRNA levels were significantly upregulated in osteoclasts isolated from the hindlimb of tail-suspended mice. CD44 deficiency can reduce osteoclast activity and counteract cortical bone loss in the hindlimb of unloaded mice. These results suggest that therapeutic inhibition of CD44 may protect from unloading induced bone loss by inhibiting osteoclast activity.
No effect on pharmacokinetics of tamoxifen and 4-hydroxytamoxifen by multiple doses of red clover capsule in rats
Authors: Raju Kanumuri Siva Rama , Taneja Isha , Valicherla Guru Raghavendra , Challagundla Murali Krishna , Rashid Mamunur , Syed Anees Ahmed , Gayen Jiaur Rahman , Singh Sheelendra Pratap , Wahajuddin Muhammad 
Published: November 2015

AbstractTamoxifen is used in clinical practice for breast cancer patients and to prevent osteoporosis. Red clover (Trifolium pratense) preparations are consumed worldwide as dietary supplements for relieving postmenopausal symptoms. In the present study we investigated the possible herb-drug interaction between red clover and tamoxifen in rats. 15 days pre-treatment with red clover did not alter the tamoxifen and its active metabolite 4-hydroxytamoxifen pharmacokinetics significantly (p > 0.05). Therefore the therapeutic efficacy of the tamoxifen may not be compromised by the co-administration with red clover. Tamoxifen metabolism is primarily mediated by CYP2D6, CYP3A4 with minor contribution from CYP2C9, CYP2E1 and CYP1A2 isoforms. Although, red clover pre-treatment significantly (p < 0.05) decreased the mRNA expression and activity of CYP3a2, no effect on CYP2d4 and increased expression and activity of CYP2c11 could be the plausible reasons for lack of effect on tamoxifen and its metabolite pharmacokinetics in rats. CYP1a1 and CYP2b2 mRNA expression and activity were also significantly reduced by red clover. To extend the clinical utility of the present study, effect of red clover extract on major CYPs using human liver microsomes and HepG2 cell lines were also determined. Similar finding were observed in the human liver preparations as in rats.
Targeted DNA Sequencing Detects Mutations Related to Susceptibility among Familial Non-medullary Thyroid Cancer
Authors: Yu Yang , Dong Li , Li Dapeng , Chuai Shaokun , Wu Zhigang , Zheng Xiangqian , Cheng Yanan , Han Lei , Yu Jinpu , Gao Ming 
Published: November 2015

AbstractSome studies have demonstrated that familial non-medullary thyroid cancer (FNMTC) has a more aggressive clinical behavior compared to sporadic NMTC (SNMTC). However, FNMTC is difficult to differentiate from SNMTC by the morphology and immunohistochemistry. Although genes responsible for FNMTC were unclear, screening for rare germline mutations on known important tumor suppressor genes might offer more insights on predicting susceptibility to FNMTC. Here, a customized panel was designed to capture all exons of 31 cancer susceptive genes possibly related to FNMTC. Using next-generation sequencing we performed deep sequencing to achieve 500× coverage of the targeted regions. At the end 45 variants were identified in 29 of 47 familial patients and 6 of 16 sporadic patients. Notably, several germline mutations were found matching between paired FNMTC patients from the same family, including APC L292F and A2778S, BRAF D22N, MSH6 G355S and A36V, MSH2 L719F, MEN1 G508D, BRCA1 SS955S, BRCA2 G2508S and a GNAS inframe insertion. We demonstrated a novel approach to help diagnose and elucidate the genetic cause of the FNMTC patients and assess whether their family members are exposed to a higher genetic risk. The findings would also provide insights on monitoring the potential second cancers for thyroid cancer patients.
Adaptation of the autotrophic acetogen Sporomusa ovata to methanol accelerates the conversion of CO2 to organic products
Authors: Tremblay Pier-Luc , Höglund Daniel , Koza Anna , Bonde Ida , Zhang Tian 
Published: November 2015

AbstractAcetogens are efficient microbial catalysts for bioprocesses converting C1 compounds into organic products. Here, an adaptive laboratory evolution approach was implemented to adapt Sporomusa ovata for faster autotrophic metabolism and CO2 conversion to organic chemicals. S. ovata was first adapted to grow quicker autotrophically with methanol, a toxic C1 compound, as the sole substrate. Better growth on different concentrations of methanol and with H2-CO2 indicated the adapted strain had a more efficient autotrophic metabolism and a higher tolerance to solvent. The growth rate on methanol was increased 5-fold. Furthermore, acetate production rate from CO2 with an electrode serving as the electron donor was increased 6.5-fold confirming that the acceleration of the autotrophic metabolism of the adapted strain is independent of the electron donor provided. Whole-genome sequencing, transcriptomic and biochemical studies revealed that the molecular mechanisms responsible for the novel characteristics of the adapted strain were associated with the methanol oxidation pathway and the Wood-Ljungdahl pathway of acetogens along with biosynthetic pathways, cell wall components and protein chaperones. The results demonstrate that an efficient strategy to increase rates of CO2 conversion in bioprocesses like microbial electrosynthesis is to evolve the microbial catalyst by adaptive laboratory evolution to optimize its autotrophic metabolism.