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Find video protocols related to scientific articles indexed in Pubmed.
Metallosphaera tengchongensis sp. nov., a novel species of acidothermophilic archaeon isolated from a hot spring.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 11-19-2014
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Two novel acidothermophilic archaea, strain Ric-A(T) and Ric-F, were isolated from the muddy water samples of a sulfuric hot spring located at Tengchong County, Yunnan Province, China. They were aerobic and facultatively chemolithoautotrophic. Both strains could oxidize S(0) and K2S4O6 for autotrophic growth, and also could use organic materials for heterotrophic growth. Growth was observed at 55-75 °C and pH 1.5-6.5. The strains could oxidize metal sulfide ores, showing their potential in bioleaching. The DNA G+C content of Ric-A(T) and Ric-F were 41.8 and 41.6 mol%, respectively. Analysis of 16S rRNA gene sequences showed that the two strains share 99.8% sequence similarity to each other, but < 97% to the other known species of the genus Metallosphaera. DNA-DNA hybridization indicated that the isolates were different strains of a novel species of the genus Metallosphaera. Strains Ric-A(T) and Ric-F also shared a number of physiological and biochemical characteristics that distinguished them from the recognized species of the genus Metallosphaera. On the basis of phenotypic, chemotaxonomic and phylogenetic comparisons with their relatives, it was concluded that the strains Ric-A(T) and Ric-F represent a novel species of the genus Metallosphaera, for which the name Metallosphaera tengchongensis is proposed. The type strain is Ric-A(T) (=NBRC109472(T)=CGMCC1.12287(T)).
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High-power operation of silica-based Raman fiber amplifier at 2147 nm.
Opt Express
PUBLISHED: 11-18-2014
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We demonstrated a 2147 nm silica-based Raman fiber amplifier with output power of 14.3 W directly pumped with a 1963 nm CW thulium-doped all-fiber MOPA. The 1963 nm thulium-doped all-fiber MOPA is seeded with a 2147 nm thulium-doped all-fiber laser at the same time. The Raman Stokes power shift from 1963 nm to 2147 nm is accomplished in a piece of 50 m silica-based highly nonlinear fiber (HNLF). The conversion efficiency was 38.5% from 1963 nm to 2147 nm in the HNLF. The output power achieved was only currently limited by available 1963 nm input power and the architecture has significant scaling potential. To the best of our knowledge, this is the highest power operation of a Raman fiber amplifier at >2 µm wavelength region.
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[Production of mature red blood cell by using peripheral blood mononuclear cells].
Zhongguo Shi Yan Xue Ye Xue Za Zhi
PUBLISHED: 10-24-2014
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Most protocols for in vitro producing red blood cells (RBC) use the CD34(+) cells or embryonic stem cells from cord blood, bone marrow or peripheral blood as the start materials. This study was purposed to produce the mature RBC in vitro by using peripheral blood mononuclear cells as start material. The peripheral blood mononuclear cells (PBMNC) were isolated from buffy coat after blood leukapheresis, the mature red blood cells (RBC) were prepared by a 4-step culture protocol. The results showed that after culture by inducing with the different sets of cytokines and supporting by mouse MS-5 cell line, the expansion of PBMNC reached about 1000 folds at the end of the culture. About 90% of cultured RBC were enucleated mature cells which had the comparable morphological characteristics with normal RBC. Colony-forming assays showed that this culture system could stimulate the proliferation of progenitors in PBMNC and differentiate into erythroid cells. The structure and function analysis indicated that the mean cell volume of in vitro cultured RBC was 118 ± 4 fl, which was slight larger than that of normal RBC (80-100 fl); the mean cell hemoglobin was 36 ± 1.2 pg, which was slight higher than that of normal RBC (27-31 pg); the maximal deformation index was 0.46, which approachs level of normal RBC; the glucose-6-phosphate dehydrogenase and pyrurvate kinase levels was consistant with young RBC. It is concluded that PBMNC are feasble, convenient and low-cost source for producing cultured RBC and this culture system is suitable to generate the RBC from PBMNC.
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Automated analysis of angle closure from anterior chamber angle images.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 10-23-2014
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Purpose:To evaluate a novel software capable of automatically grading angle closure on EyeCamTM (Clarity Medical Systems, Pleasanton, CA) angle images in comparison to manual grading of images, with gonioscopy as the reference standard. Methods:In this hospital-based, prospective study, subjects underwent gonioscopy by a single observer, and EyeCam imaging by a different operator. The anterior chamber angle in a quadrant was classified as closed if the posterior trabecular meshwork could not be seen. An eye was classified as having angle closure if there were 2 or more quadrants of closure. Automated grading of the angle images was performed using customized software. Agreement between the methods was ascertained by kappa statistic and comparison of area under receiver operating characteristic curves (AUC). Results:One hundred and forty subjects (140 eyes) were included, the majority of whom were Chinese (102/140, 72.9%) and females (72/140, 51.5%). Angle closure was detected in 61 eyes (43.6%) with gonioscopy in comparison to 59 eyes (42.1%, p=0.73) using manual grading and 67 eyes (47.9%, p=0.24) with automated grading of EyeCam images. The agreement for angle closure diagnosis between gonioscopy and both manual (k=0.88; 95% Confidence Interval (CI), 0.81-0.96) and automated grading of EyeCam images was good (k=0.74; 95% CI, 0.63-0.85). The AUC for detecting eyes with gonioscopic angle closure was comparable for manual and automated grading (AUC 0.974 vs 0.954, p = 0.31) of EyeCam image. Conclusions:Customized software for automated grading of EyeCam angle images was found to have good agreement with gonioscopy. Human observation of the EyeCam images may still be needed to avoid gross misclassification, especially in eyes with extensive angle closure.
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Optic cup segmentation for glaucoma detection using low-rank superpixel representation.
Med Image Comput Comput Assist Interv
PUBLISHED: 10-22-2014
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We present an unsupervised approach to segment optic cups in fundus images for glaucoma detection without using any additional training images. Our approach follows the superpixel framework and domain prior recently proposed in, where the superpixel classification task is formulated as a low-rank representation (LRR) problem with an efficient closed-form solution. Moreover, we also develop an adaptive strategy for automatically choosing the only parameter in LRR and obtaining the final result for each image. Evaluated on the popular ORIGA dataset, the results show that our approach achieves better performance compared with existing techniques.
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Speckle reduction in optical coherence tomography by image registration and matrix completion.
Med Image Comput Comput Assist Interv
PUBLISHED: 10-22-2014
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Speckle noise is problematic in optical coherence tomography (OCT). With the fast scan rate, swept source OCT scans the same position in the retina for multiple times rapidly and computes an average image from the multiple scans for speckle reduction. However, the eye movement poses some challenges. In this paper, we propose a new method for speckle reduction from multiply-scanned OCT slices. The proposed method applies a preliminary speckle reduction on the OCT slices and then registers them using a global alignment followed by a local alignment based on fast iterative diamond search. After that, low rank matrix completion using bilateral random projection is utilized to iteratively estimate the noise and recover the underlying clean image. Experimental results show that the proposed method achieves average contrast to noise ratio 15.65, better than 13.78 by the baseline method used currently in swept source OCT devices. The technology can be embedded into current OCT machines to enhance the image quality for subsequent analysis.
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High power mid-infrared supercontinuum generation in a single-mode ZBLAN fiber with up to 21.8 W average output power.
Opt Express
PUBLISHED: 10-17-2014
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We report high power mid-infrared (mid-IR) supercontinuum (SC) generation in a single-mode ZBLAN (ZrF4-BaF2-LaF3-AlF3-NaF) fiber with up to 21.8 W average output power from 1.9 to beyond 3.8 ?m pumped by amplified picosecond pulses from a single-mode thulium-doped fiber (TDF) master oscillator power amplifier (MOPA). The optical-optical conversion efficiency from the 793 nm pump laser of the last stage thulium-doped fiber amplifier (TDFA) to mid-IR SC output is 17%. It is, to the best of our knowledge, the highest average power mid-IR SC generation from a ZBLAN fiber to date.
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MethBank: a database integrating next-generation sequencing single-base-resolution DNA methylation programming data.
Nucleic Acids Res.
PUBLISHED: 10-09-2014
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DNA methylation plays crucial roles during embryonic development. Here we present MethBank (http://dnamethylome.org), a DNA methylome programming database that integrates the genome-wide single-base nucleotide methylomes of gametes and early embryos in different model organisms. Unlike extant relevant databases, MethBank incorporates the whole-genome single-base-resolution methylomes of gametes and early embryos at multiple different developmental stages in zebrafish and mouse. MethBank allows users to retrieve methylation levels, differentially methylated regions, CpG islands, gene expression profiles and genetic polymorphisms for a specific gene or genomic region. Moreover, it offers a methylome browser that is capable of visualizing high-resolution DNA methylation profiles as well as other related data in an interactive manner and thus is of great helpfulness for users to investigate methylation patterns and changes of gametes and early embryos at different developmental stages. Ongoing efforts are focused on incorporation of methylomes and related data from other organisms. Together, MethBank features integration and visualization of high-resolution DNA methylation data as well as other related data, enabling identification of potential DNA methylation signatures in different developmental stages and accordingly providing an important resource for the epigenetic and developmental studies.
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Gryllotalpicola reticulitermitis sp. nov. isolated from a termite gut.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 10-05-2014
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Strain TS-56T was isolated from the gut of a wood-feeding termite, Reticulitermes chinensis Snyder. Phylogenetic analyses based on 16S rRNA gene sequences revealed that the strain belonged to the genus Gryllotalpicola of the family Microbacteriaceae, with sequence similarities ranging from 96.6% to 97.8%. The isolate was Gram-stain- positive, non-motile, light yellow, irregular short rod-shaped (0.4-0.6 ?m in diameter, 0.6-1.0 ?m in length). Growth of strain TS-56T occurred at 20-35? (optimum, 30?), and at pH 4.0-8.0 (optimum, pH 5.0). The peptidoglycan of strain TS-56T contained ornithine, glutamic acid, alanine, homoserine and glycine. The acyl type was acetyl. The most abundant cellular fatty acids of strain TS-56T was cyclohexyl-C17:0 (88.79%). The respiratory menaquinone was MK-11. The polar lipid profile contained disphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl choline, phosphatidyl inositol, and two unknown glycolipids. DNA of the type strain had a G+C content of 67.4 mol%. Based on the phylogenetic properties and phenotypic distinctiveness, strain TS-56T represents a novel species of the genus Gryllotalpicola, for which the name Gryllotalpicola reticulitermitis sp. nov. is proposed. The type strain is TS-56T (=CGMCC 1.10363T =NBRC 109838T).
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A survey on computer aided diagnosis for ocular diseases.
BMC Med Inform Decis Mak
PUBLISHED: 08-31-2014
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Computer Aided Diagnosis (CAD), which can automate the detection process for ocular diseases, has attracted extensive attention from clinicians and researchers alike. It not only alleviates the burden on the clinicians by providing objective opinion with valuable insights, but also offers early detection and easy access for patients.
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Clostridium algifaecis sp. nov., an anaerobic bacterial species from decomposing algal scum.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-28-2014
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Two anaerobic bacterial strains, MB9-7(T) and MB9-9, were isolated from decomposing algal scum and were characterized using a polyphasic approach. Phylogenetic analysis of 16S rRNA gene sequences showed that strains MB9-7(T) and MB9-9 are closely related to each other (99.7?% similarity) and they are also closely related to Clostridium tyrobutyricum (96.5?%). The two strains were Gram-stain positive and rod-shaped. Growth occurred at 20-45 °C, at pH 4.0-8.0 and at NaCl concentrations of up to 2?% (w/v). Acid was produced from glucose, xylose and mannose. Products of fermentation in PYG medium were mainly butyrate, acetate, carbon dioxide and hydrogen. The predominant cellular fatty acids were C14?:?0 and C16?:?0. The cellular polar lipids comprised phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, two glycolipids, one phospholipid, one aminophospholipid and two aminolipids. The DNA G+C contents of strain MB9-7(T) and MB9-9 were 27.9 and 28.7 mol%, respectively. These results support the assignment of the new isolates to the genus Clostridium and also distinguish them from other species of the genus Clostridium. Hence, it is proposed that strains MB9-7(T) and MB9-9 represent a novel species of the genus Clostridium, with the suggested name Clostridium algifaecis sp. nov. The type strain is MB9-7(T) (?=?CGMCC 1.5188(T)?=?DSM 28783(T)).
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Integrated metagenomics and metatranscriptomics analyses of root-associated soil from transgenic switchgrass.
Genome Announc
PUBLISHED: 08-14-2014
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The benefits of using transgenic switchgrass with decreased levels of caffeic acid 3-O-methyltransferase (COMT) as biomass feedstock have been clearly demonstrated. However, its effect on the soil microbial community has not been assessed. Here we report metagenomic and metatranscriptomic analyses of root-associated soil from COMT switchgrass compared with nontransgenic counterparts.
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Thiosulfate transfer mediated by DsrE/TusA homologs from acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina.
J. Biol. Chem.
PUBLISHED: 08-13-2014
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Conserved clusters of genes encoding DsrE and TusA homologs occur in many archaeal and bacterial sulfur oxidizers. TusA has a well documented function as a sulfurtransferase in tRNA modification and molybdenum cofactor biosynthesis in Escherichia coli, and DsrE is an active site subunit of the DsrEFH complex that is essential for sulfur trafficking in the phototrophic sulfur-oxidizing Allochromatium vinosum. In the acidothermophilic sulfur (S(0))- and tetrathionate (S4O6(2-))-oxidizing Metallosphaera cuprina Ar-4, a dsrE3A-dsrE2B-tusA arrangement is situated immediately between genes encoding dihydrolipoamide dehydrogenase and a heterodisulfide reductase-like complex. In this study, the biochemical features and sulfur transferring abilities of the DsrE2B, DsrE3A, and TusA proteins were investigated. DsrE3A and TusA proved to react with tetrathionate but not with NaSH, glutathione persulfide, polysulfide, thiosulfate, or sulfite. The products were identified as protein-Cys-S-thiosulfonates. DsrE3A was also able to cleave the thiosulfate group from TusA-Cys(18)-S-thiosulfonate. DsrE2B did not react with any of the sulfur compounds tested. DsrE3A and TusA interacted physically with each other and formed a heterocomplex. The cysteine residue (Cys(18)) of TusA is crucial for this interaction. The single cysteine mutants DsrE3A-C(93)S and DsrE3A-C(101)S retained the ability to transfer the thiosulfonate group to TusA. TusA-C(18)S neither reacted with tetrathionate nor was it loaded with thiosulfate with DsrE3A-Cys-S-thiosulfonate as the donor. The transfer of thiosulfate, mediated by a DsrE-like protein and TusA, is unprecedented not only in M. cuprina but also in other sulfur-oxidizing prokaryotes. The results of this study provide new knowledge on oxidative microbial sulfur metabolism.
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Profilin-1 suppresses tumorigenicity in pancreatic cancer through regulation of the SIRT3-HIF1? axis.
Mol. Cancer
PUBLISHED: 08-07-2014
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Tumor cells exhibit abnormal actin remodeling profiles, which involve the altered expressions of several important actin-binding proteins. Profilin1 (Pfn1), originally identified as an actin-associated protein, has been linked to several human malignancies. Our recent studies suggested that Pfn1 facilitates apoptosis in pancreatic cancer cells. Here, we investigated the exact role of Profilin1 (Pfn1) in pancreatic adenocarcinoma (PDAC) and the underlying mechanisms.
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Organic reprogrammable circuits based on electrochemically formed diodes.
ACS Appl Mater Interfaces
PUBLISHED: 08-04-2014
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We report a method to construct reprogrammable circuits based on organic electrochemical (EC) p-n junction diodes. The diodes are built up from the combination of the organic conjugated polymer poly[2-methoxy-5-(2-ethylhexyloxy)-1,4-phenylenevinylene] and a polymer electrolyte. The p-n diodes are defined by EC doping performed at 70 °C, and then stabilized at -30 °C. The reversible EC reaction allows for in situ reprogramming of the polarity of the organic p-n junction, thus enabling us to reconfigure diode circuits. By combining diodes of specific polarities dedicated circuits have been created, such as various logic gates, a voltage limiter and an AC/DC converter. Reversing the EC reaction allows in situ reprogramming of the p-n junction polarity, thus enabling reconfiguration of diode circuits, for example, from an AND gate to an OR gate. The reprogrammable circuits are based on p-n diodes defined from only two layers, the electrodes and then the active semiconductor:electrolyte composite material. Such simple device structures are promising for large-area and fully printed reconfigurable circuits manufactured using common printing tools. The structure of the reported p-n diodes mimics the architecture of and is based on identical materials used to construct light-emitting electrochemical cells (LEC). Our findings thus provide a robust signal routing technology that is easily integrated with traditional LECs.
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A single-chain magnet based on {Co(II)?} complexes and azido/picolinate ligands.
Inorg Chem
PUBLISHED: 07-24-2014
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A new homonuclear single-chain magnet self-assembles as a one-dimensional coordination network of defective dicubane {Co(II)4} complexes linked by single Co(II) ions with the assistance of azido and picolinate ligands. Dominating intrachain ferromagnetic interactions, intrinsic Ising-like Co(II) anisotropy, and negligible interchain magnetic interactions lead to a thermally activated relaxation time of the magnetization below 8 K. Two thermally activated regimes above and below 3.5 K are observed with the following energy barriers: ?(?1)/k(B) = 66 K (?0 = 3.7 × 10(-11) s) and ?(?2)/k(B) = 51 K (?0 = 2.3 × 10(-9) s), respectively. The difference between the two energy barriers of the relaxation time, 15 K, agrees well with the experimental energy, ?(?), to create a domain wall along the chain.
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Chemical structures of constituents from the flowers of Osmanthus fragrans var. aurantiacus.
J Nat Med
PUBLISHED: 07-17-2014
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Three new megastigmane glycosides named floraosmanosides I-III and a new ?-decalactone named floraosmanolactone I together with 16 known constituents were isolated from the flowers of Osmanthus fragrans var. aurantiacus cultivated in Guangxi Zhuang Autonomous Region, China. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. Among them, ligustroside and (+)-pinoresinol significantly inhibited nitric oxide production in lipopolysaccharide-activated RAW264.7 macrophages.
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Progesterone protects blood-brain barrier function and improves neurological outcome following traumatic brain injury in rats.
Exp Ther Med
PUBLISHED: 07-11-2014
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Inflammatory responses are associated with blood-brain barrier (BBB) dysfunction and neurological deficits following traumatic brain injury (TBI). The aim of the present study was to investigate the effects of progesterone on the expression of the inflammatory mediators prostaglandin E2 (PGE2), cyclooxygenase-2 (COX-2), nuclear factor ?B (NF-?B) and tumor necrosis factor-? (TNF-?) in the brain, BBB permeability, cerebral edema and neurological outcome, as well as to explore the mechanism of its neuroprotective effect. In this study, male rats were randomly divided into three groups: a sham-operated group (SHAM), a TBI group (TBI) and a progesterone treatment group (TBI-PROG). The TBI model was established using a modified Feeney's weight-dropping method. Brain samples were extracted 24 h following injury. The expression levels of COX-2 and NF-?B were examined using immunohistochemistry, whilst the expression levels of PGE2 and TNF-? were detected by enzyme-linked immunosorbent assay. BBB permeability was analyzed using Evans blue and cerebral edema was determined using the dry-wet method. The neurological outcome was evaluated using the modified neurological severity score test. The results revealed that progesterone treatment significantly reduced post-injury inflammatory response, brain edema and Evans blue dye extravasation, and improved neurological scores compared with those in the TBI group. In conclusion, the inhibition of inflammation may be an important mechanism by which progesterone protects the BBB and improves neurological outcome.
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Bacterial chemotaxis on SlipChip.
Lab Chip
PUBLISHED: 06-27-2014
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This paper describes a simple and reusable microfluidic SlipChip device for studying bacterial chemotaxis based on free interface diffusion. The device consists of two glass plates with reconfigurable microwells and ducts, which can set up 20 parallel chemotaxis units as duplicates. In each unit, three nanoliter microwells and connecting ducts were assembled for pipette loading of a chemoeffector solution, bacterial suspension, and 1X PBS buffer solution. By a simple slipping operation, three microwells were disconnected from other units and interconnected by the ducts, which allowed the formation of diffusion concentration gradients of the chemoeffector for inducing cell migration from the cell microwell towards the other two microwells. The migration of cells in the microwells was monitored and accurately counted to evaluate chemotaxis. Moreover, the migrated cells were easily collected by pipetting for further studies after a slip step to reconnect the chemoeffector microwells. The performance of the device was characterized by comparing chemotaxis of two Escherichia coli species, using aspartic acid as the attractant and nitrate sulfate as the repellent. It also enables the separation of bacterial species from a mixture, based on the difference of chemotactic abilities, and collection of the cells with strong chemotactic phenomena for further studies off the chip.
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The Readout of Base-Pair Information in Adenine-Thymine ?-D-Arabinonucleosides.
Chemistry
PUBLISHED: 06-17-2014
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Structurally modified nucleosides are central players in the field of nucleic acid chemistry. Adenine-thymine (AT) pyrimido[4,5-d]pyrimidine furanosyl and pyranosyl arabinonucleosides have been synthesized for the first time. Single-crystal X-ray diffraction analysis reveals novel base pairs that, in synergy with the sugar residues, direct the emergence of distinct networks containing channels and cavities. The microscopic noncovalent connections can be translated into macroscopic levels in which robust organogels are formed by the furanoside but not the pyranoside. The influences of the sugars are also displayed by the different shaped superstructures of the free nucleosides in solution. The readout of the information in the base moiety is therefore tailored by the sugar configuration, and the interplays exert subtle effects on the structures, from solid to gel and to the solution state. The potential for forming these appealing base pairs and higher structures enables these intriguing nucleosides to serve as unique building blocks in various areas or to construct innovative nucleic acid structures.
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210 W single-frequency, single-polarization, thulium-doped all-fiber MOPA.
Opt Express
PUBLISHED: 06-13-2014
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A high-power single-frequency, single-polarization, thulium-doped all-fiber master-oscillator power-amplifier (MOPA) is demonstrated by using all-polarization-maintaining (all-PM) thulium-doped fiber and all-PM-fiber components. The MOPA yielded 210 W of single-frequency, linear-polarized laser output at central wavelength of 2000.9 nm with a polarization extinction ratio (PER) of >17 dB. No indication of stimulated Brillouin scattering (SBS) could be observed at the highest output power level, and the output power was only currently limited by available pump power. To the best of our knowledge, this is the first demonstration of average output power exceeding 200 W from a single-frequency, single-polarization, thulium-doped all-fiber laser at 2 µm wavelength region.
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[Comparative study on da Vince robotic and laparoscopic radical gastrectomy for gastric cancer].
Zhonghua Wei Chang Wai Ke Za Zhi
PUBLISHED: 05-27-2014
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To compare the short-term clinical outcomes of laparoscopic and da Vince robotic radical gastrectomy for gastric cancer and evaluate the safety and efficacy of robotic system.
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Why did the FDA approve efavirenz 800 mg when co-administered with rifampin?
Int J Clin Pharmacol Ther
PUBLISHED: 05-20-2014
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Literature reports regarding the efficacy of efavirenz (EFV) 600 mg with rifampin (RIF) are not consistent. Evaluation of a drug-drug interaction (DDI) study and supportive semi-mechanistic population pharmacokinetic (PK) analyses were undertaken to help delineate this issue.
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Benzoate metabolism intermediate benzoyl coenzyme A affects gentisate pathway regulation in Comamonas testosteroni.
Appl. Environ. Microbiol.
PUBLISHED: 04-25-2014
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A previous study showed that benzoate was catabolized via a coenzyme A (CoA)-dependent epoxide pathway in Azoarcus evansii (R. Niemetz, U. Altenschmidt, S. Brucker, and G. Fuchs, Eur. J. Biochem. 227:161-168, 1995), but gentisate 1,2-dioxygenase was induced. Similarly, we found that the Comamonas testosteroni strain CNB-1 degraded benzoate via a CoA-dependent epoxide pathway and that gentisate 1,2-dioxygenase (GenA) was also induced when benzoate or 3-hydroxybenzoate served as a carbon source for growth. Genes encoding the CoA-dependent epoxide (box genes) and gentisate (gen genes) pathways were identified. Genetic disruption revealed that the gen genes were not involved in benzoate and 3-hydroxybenzoate degradation. Hence, we investigated gen gene regulation in the CNB-1 strain. The PgenA promoter, a MarR-type regulator (GenR), and the GenR binding site were identified. We found that GenR took gentisate, 3-hydroxybenzoate, and benzoyl-CoA as effectors and that binding of GenR to its target DNA sequence was prohibited when these effectors were present. In vivo studies showed that the CNB-1 mutant that lost benzoyl-CoA synthesis was not able to activate PgenA promoter, while transcription of genA was upregulated in another CNB-1 mutant that lost the ability to degrade benzoyl-CoA. The finding that benzoyl-CoA (a metabolic intermediate of benzoate degradation) and 3-hydroxybenzoate function as GenR effectors explains why GenA was induced when CNB-1 grew on benzoate or 3-hydroxybenzoate. Regulation of gentisate pathways by MarR-, LysR-, and IclR-type regulators in diverse bacterial groups is discussed in detail.
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Reduction of Na/K-ATPase affects cardiac remodeling and increases c-kit cell abundance in partial nephrectomized mice.
Am. J. Physiol. Heart Circ. Physiol.
PUBLISHED: 04-18-2014
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The current study examined the role of Na/K-ATPase ?1-subunit in animals subjected to 5/6th partial nephrectomy (PNx) using Na/K-ATPase ?1-heterozygous (?1(+/-)) mice and their wild-type (WT) littermates. After PNx, both WT and ?1(+/-) animals displayed diastolic dimension increases, increased blood pressure, and increased cardiac hypertrophy. However, in the ?1(+/-) animals we detected significant increases in cardiac cell death in PNx animals. Given that reduction of ?1 elicited increased cardiac cell death with PNx, while at the same time these animals developed cardiac hypertrophy, an examination of cardiac cell number, and proliferative capabilities of those cells was carried out. Cardiac tissues were probed for the progenitor cell marker c-kit and the proliferation marker ki-67. The results revealed that ?1(+/-) mice had significantly higher numbers of c-kit-positive and ki-67-positive cells, especially in the PNx group. We also found that ?1(+/-) mice express higher levels of stem cell factor, a c-kit ligand, in their heart tissue and had higher circulating levels of stem cell factor than WT animals. In addition, PNx induced significant enlargement of cardiac myocytes in WT mice but has much less effect in ?1(+/-) mice. However, the total cell number determined by nuclear counting is higher in ?1(+/-) mice with PNx compared with WT mice. We conclude that PNx induces hypertrophic growth and high blood pressure regardless of Na/K-ATPase content change. However, total cardiac cell number as well as c-kit-positive cell number is increased in ?1(+/-) mice with PNx.
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KNDC1 knockdown protects human umbilical vein endothelial cells from senescence.
Mol Med Rep
PUBLISHED: 04-07-2014
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KNDC1 (kinase noncatalytic C-lobe domain containing 1), a brain-specific Ras guanine nucleotide exchange factor, controls the negative regulation of neuronal dendrite growth. However, the effect of KNDC1 on cellular senescence remains to be elucidated. The present study investigated the impact of KNDC1 knockdown on human endothelial cell senescence and the mechanisms underlying this effect. Human umbilical vein endothelial cells (HUVECs) cultured in vitro were used as a model of biological aging. Senescence?associated ?-galactosidase staining was used to detect cellular senescence and flow cytometry was employed to determine cell cycle progression. Quantitative polymerase chain reaction (qPCR) and western blot analysis were utilized to investigate mRNA transcription and protein expression. In the HUVECs, a senescence-like phenotypes developed with increasing passage number in vitro, which were associated with a progressive increase in the transcription and expression of KNDC1. KNDC1 knockdown promoted cell proliferation and partially reversed cellular senescence and cell cycle arrest in the G0/G1 phase in aging HUVECs. Investigations into the mechanism underlying this effect demonstrated that KNDC1 knockdown promoted HUVEC proliferation via the extracellular signal-regulated kinase signaling pathway and delayed HUVEC senescence by inhibiting the p53-p21-p16 transduction cascade. In addition, the promotion of the capillary tube network formation and the increased expression of endothelial nitric oxide synthase revealed that the activity and function of endothelial cells were enhanced. In conclusion, KNDC1 knockdown delayed endothelial cell senescence and promoted HUVEC activity and function. These results demonstrated that KNDC1 may be a novel therapeutic target for the development of agents to extend human life.
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Anti-EGFR MoAb treatment in colorectal cancer: limitations, controversies, and contradictories.
Cancer Chemother. Pharmacol.
PUBLISHED: 04-01-2014
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Anti-epidermal growth-factor receptor (EGFR) monoclonal antibody (MoAb) treatment for chemotherapy refractory or metastatic colorectal cancer has obtained great achievement. However, not every colorectal patient responds to such molecular-targeted agent well. Biomarkers associated with anti-EGFR resistance are not limited to KRAS mutation up to now. It was recently reported that cross-talking molecular effectors interacted with EGFR-related pathway were also negative predictor for anti-EGFR treatment. However, the limited data, controversial results, and contradictories between in vitro and clinical studies restrict the clinical application of these new biomarkers. Although the current theory of tumor microenvironment supported the application of multi-target treatment, the results from the clinical studies were less than expected. Moreover, WHO or RECIST guideline for response assessment in anti-EGFR MoAb treatment was also queried by recent AIO KRK-0306 trial. This review focuses on these controversies, contradictories, and limitations, in order to uncover the unmet needs in current status of anti-EGFR MoAb treatment in colorectal cancer.
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Programming and inheritance of parental DNA methylomes in mammals.
Cell
PUBLISHED: 03-26-2014
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The reprogramming of parental methylomes is essential for embryonic development. In mammals, paternal 5-methylcytosines (5mCs) have been proposed to be actively converted to oxidized bases. These paternal oxidized bases and maternal 5mCs are believed to be passively diluted by cell divisions. By generating single-base resolution, allele-specific DNA methylomes from mouse gametes, early embryos, and primordial germ cell (PGC), as well as single-base-resolution maps of oxidized cytosine bases for early embryos, we report the existence of 5hmC and 5fC in both maternal and paternal genomes and find that 5mC or its oxidized derivatives, at the majority of demethylated CpGs, are converted to unmodified cytosines independent of passive dilution from gametes to four-cell embryos. Therefore, we conclude that paternal methylome and at least a significant proportion of maternal methylome go through active demethylation during embryonic development. Additionally, all the known imprinting control regions (ICRs) were classified into germ-line or somatic ICRs.
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Effects of Na/K-ATPase and its ligands on bone marrow stromal cell differentiation.
Stem Cell Res
PUBLISHED: 03-21-2014
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Endogenous ligands of Na/K-ATPase have been demonstrated to increase in kidney dysfunction and heart failure. It is also reported that Na/K-ATPase signaling function effects stem cell differentiation. This study evaluated whether Na/K-ATPase activation through its ligands and associated signaling functions affect bone marrow stromal cells (BMSCs, also known as bone marrow-derived mesenchymal stem cells) differentiation capacity. BMSCs were isolated from male Sprague-Dawley rats and cultured in minimal essential medium alpha (MEM-?) supplemented with 15% Fetal Bovine serum (FBS). The results showed that marinobufagenin (MBG), a specific Na/K-ATPase ligand, potentiated rosiglitazone-induced adipogenesis in these BMSCs. Meanwhile, it attenuated BMSC osteogenesis. Mechanistically, MBG increased CCAAT/enhancer binding protein alpha (C/EBP?) protein expression through activation of an extracellular regulated kinase (ERK) signaling pathway, which leads to enhanced rosiglitazone-induced adipogenesis. Inhibition of ERK activation by U0126 blocks the effect of MBG on C/EBP? expression and on rosiglitazone-induced adipogenesis. Reciprocally, MBG reduced runt-related transcription factor 2 (RunX2) expression, which resulted in the inhibition of osteogenesis induced by ?-glycerophosphate/ascorbic acid. MBG also potentiated rosiglitazone-induced adipogenesis in 3T3-L1 cells and in mouse BMSCs. These results suggest that Na/K-ATPase and its signaling functions are involved in the regulation of BMSCs differentiation.
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Resolution of carbon metabolism and sulfur-oxidation pathways of Metallosphaera cuprina Ar-4 via comparative proteomics.
J Proteomics
PUBLISHED: 03-16-2014
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Metallosphaera cuprina is able to grow either heterotrophically on organics or autotrophically on CO2 with reduced sulfur compounds as electron donor. These traits endowed the species desirable for application in biomining. In order to obtain a global overview of physiological adaptations on the proteome level, proteomes of cytoplasmic and membrane fractions from cells grown autotrophically on CO2 plus sulfur or heterotrophically on yeast extract were compared. 169 proteins were found to change their abundance depending on growth condition. The proteins with increased abundance under autotrophic growth displayed candidate enzymes/proteins of M. cuprina for fixing CO2 through the previously identified 3-hydroxypropionate/4-hydroxybutyrate cycle and for oxidizing elemental sulfur as energy source. The main enzymes/proteins involved in semi- and non-phosphorylating Entner-Doudoroff (ED) pathway and TCA cycle were less abundant under autotrophic growth. Also some transporter proteins and proteins of amino acid metabolism changed their abundances, suggesting pivotal roles for growth under the respective conditions.
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Metabolic flux responses to genetic modification for shikimic acid production by Bacillus subtilis strains.
Microb. Cell Fact.
PUBLISHED: 02-21-2014
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Shikimic acid (SA) is a key chiral starting molecule for the synthesis of the neuramidase inhibitor GS4104 against viral influenza. Microbial production of SA has been extensively investigated in Escherichia coli, and to a less extent in Bacillus subtilis. However, metabolic flux of the high SA-producing strains has not been explored. In this study, we constructed with genetic manipulation and further determined metabolic flux with 13C-labeling test of high SA-producing B. subtilis strains.
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SPOP promotes tumorigenesis by acting as a key regulatory hub in kidney cancer.
Cancer Cell
PUBLISHED: 02-14-2014
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Hypoxic stress and hypoxia-inducible factors (HIFs) play important roles in a wide range of tumors. We demonstrate that SPOP, which encodes an E3 ubiquitin ligase component, is a direct transcriptional target of HIFs in clear cell renal cell carcinoma (ccRCC). Furthermore, hypoxia results in cytoplasmic accumulation of SPOP, which is sufficient to induce tumorigenesis. This tumorigenic activity occurs through the ubiquitination and degradation of multiple regulators of cellular proliferation and apoptosis, including the tumor suppressor PTEN, ERK phosphatases, the proapoptotic molecule Daxx, and the Hedgehog pathway transcription factor Gli2. Knockdown of SPOP specifically kills ccRCC cells, indicating that it may be a promising therapeutic target. Collectively, our results indicate that SPOP serves as a regulatory hub to promote ccRCC tumorigenesis.
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LSD1 sustains pancreatic cancer growth via maintaining HIF1?-dependent glycolytic process.
Cancer Lett.
PUBLISHED: 02-12-2014
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The histone demethylase LSD1 (lysine specific demethylase 1) plays an important role in the epigenetic regulation of gene transcription. Our study investigated the role of LSD1 in pancreatic cancer and demonstrated that LSD1 was significantly up-regulated in pancreatic cancer patient tissue samples, and elevated LSD1 protein levels positively correlated with overall survival of pancreatic cancer patients. Using in vitro and in vivo models, we demonstrated that knock-down of LSD1 repressed proliferation and tumorigenicity of pancreatic cancer cells. Mechanistically, our study demonstrated that LSD1 synergized with HIF1? (hypoxia inducible factor-1?) in maintaining glycolytic process, which fueled pancreatic cancer uncontrolled proliferation.
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PKA turnover by the REG?-proteasome modulates FoxO1 cellular activity and VEGF-induced angiogenesis.
J. Mol. Cell. Cardiol.
PUBLISHED: 02-04-2014
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The REG?-proteasome serves as a short-cut for the destruction of certain intact mammalian proteins in the absence of ubiquitin- and ATP. The biological roles of the proteasome activator REG? are not completely understood. Here we demonstrate that REG? controls degradation of protein kinase A catalytic subunit-? (PKAca) both in primary human umbilical vein endothelial cells (HUVECs) and mouse embryonic fibroblast cells (MEFs). Accumulation of PKAca in REG?-deficient HUVECs or MEFs results in phosphorylation and nuclear exclusion of the transcription factor FoxO1, indicating that REG? is involved in preserving FoxO1 transcriptional activity. Consequently, VEGF-induced expression of the FoxO1 responsive genes, VCAM-1 and E-Selectin, was tightly controlled by REG? in a PKA dependent manner. Functionally, REG? is crucial for the migration of HUVECs. REG?(-/-) mice display compromised VEGF-instigated neovascularization in cornea and aortic ring models. Implanted matrigel plugs containing VEGF in REG?(-/-) mice induced fewer capillaries than in REG?(+/+) littermates. Taken together, our study identifies REG? as a novel angiogenic factor that plays an important role in VEGF-induced expression of VCAM-1 and E-Selectin by antagonizing PKA signaling. Identification of the REG?-PKA-FoxO1 pathway in endothelial cells (ECs) provides another potential target for therapeutic intervention in vascular diseases.
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Construction and application of an expression vector from the new plasmid pLAtc1 of Acidithiobacillus caldus.
Appl. Microbiol. Biotechnol.
PUBLISHED: 01-21-2014
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In this study, a recently sequenced 9.8-kb plasmid, pLAtc1, from Acidithiobacillus caldus strain SM-1 was characterized and developed into an expression vector. The pLAtc1 backbone carried an oriV, three rep genes, five mob genes, a Nic site, and an addiction system. Multilocus sequence analysis indicated that pLAtc1 was phylogenetically more related to the IncQ-like broad host range plasmids than to other IncQ plasmids. pLAtc1 was able to replicate and reside in Gram-negative Escherichia coli, Comamonas testosteroni, but not in Gram-positive Corynebacterium glutamicum. pLAtc1 was mobilized via conjugation into E. coli BL21 and A. caldus SM-1 from E. coli S17-1. Quantitative PCR revealed seven and four copies of plasmid in A. caldus and E. coli cells, respectively. The expression vector pLAtcE was constructed from pLAtc1 by introducing a regulatable promoter (P tetH ), a transcriptional terminator, a multiple cloning site, a kanamycin resistance gene, and a streptomycin resistance gene. The functionality of pLAtcE was demonstrated by expressing a gene encoding enhanced green fluorescence protein in E. coli and in A. caldus. pLAtcE was used to express ?-ketoglutarate dehydrogenase (sucAB) and succinate dehydrogenase (sdhA) genes in A. caldus. The newly engineered strain that harbored sucAB and sdhA on a plasmid pLAtcE-sucA-sucB-sdhA grew better than the parent strain SM-1/pLAtcE in tetrathionate and glucose-supplemented medium and produced more acidity and resulted in a more oxidative environment. This study created a useful molecular tool for genetic manipulation of the thermoacidophilic and autotrophic A. caldus.
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Histone deacetylase 4 selectively contributes to podocyte injury in diabetic nephropathy.
Kidney Int.
PUBLISHED: 01-18-2014
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Studies have highlighted the importance of histone deacetylase (HDAC)-mediated epigenetic processes in the development of diabetic complications. Inhibitors of HDAC are a novel class of therapeutic agents in diabetic nephropathy, but currently available inhibitors are mostly nonselective inhibit multiple HDACs, and different HDACs serve very distinct functions. Therefore, it is essential to determine the role of individual HDACs in diabetic nephropathy and develop HDAC inhibitors with improved specificity. First, we identified the expression patterns of HDACs and found that, among zinc-dependent HDACs, HDAC2/4/5 were upregulated in the kidney from streptozotocin-induced diabetic rats, diabetic db/db mice, and in kidney biopsies from diabetic patients. Podocytes treated with high glucose, advanced glycation end products, or transforming growth factor-? (common detrimental factors in diabetic nephropathy) selectively increased HDAC4 expression. The role of HDAC4 was evaluated by in vivo gene silencing by intrarenal lentiviral gene delivery and found to reduce renal injury in diabetic rats. Podocyte injury was associated with suppressing autophagy and exacerbating inflammation by HDAC4-STAT1 signaling in vitro. Thus, HDAC4 contributes to podocyte injury and is one of critical components of a signal transduction pathway that links renal injury to autophagy in diabetic nephropathy.
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Hemifacial spasm and trigeminal neuralgia in Chiari's I malformation with hydrocephalus: case report and literature review.
Clin Neurol Neurosurg
PUBLISHED: 01-07-2014
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Chiari's I malformation with hydrocephalus is commonly seen in clinical experience. Trigeminal neuralgia (TN) and hemifacial spasm (HFS) are most commonly related to vascular compression of the root entry/enter zone (REZ). Until now, TN and HFS associated with hydrocephalus caused by Chiari's malformation have not been reported. The patient was a 24-year old male with left HFS and ipsilateral TN. Arnold-Chiari's I malformation with hydrocephalus and platybasia were found in magnetic resonance imaging (MRI) of brain. We underwent a programmable ventriculoperitoneal shunt with complete resolution of all symptoms. This is the first report of one case only presenting as coexistent ipsilateral TN and HFS secondary to Chiari's I malformation with hydrocephalus.
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Genetic characterization of 4-cresol catabolism in Corynebacterium glutamicum.
J. Biotechnol.
PUBLISHED: 01-06-2014
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Corynebacterium glutamicum uses 4-cresol as sole carbon source for growth. Protocatechuate 3,4-dioxygenase activity had been detected when C. glutamicum was grown with 4-cresol. In this work, we found that 4-cresol was catabolized via 4-hydroxybenzoate and protocatechuate as intermediate metabolites, and a genetic cluster called cre (designated for 4-cresol, creABCDEFGHIR, tagged as ncgl0521-ncgl0531 in NCBI) was identified. The cre gene cluster comprises of 11 genes, and six of them were experimentally confirmed to be involving in 4-cresol catabolism. The genes creD, creE, and creJ were involved in oxidation of 4-cresol into 4-hydroxybenzyl alcohol. The creD encoded a protein showing Mg(2+)-dependent phosphohydrolase activity. The genes creE, creF, creJ encoded a putative P450 system. The creG encoded a NAD(+)-dependent dehydrogenase and catalyzed 4-hydroxybenzyl alcohol to 4-hydroxybenzaldehyde. Two other genes creH and creI were involved in conversion of 4-hydroxybenzyl alcohol to 4-hydroxybenzoate, but their catalytic function is still unknown. Similar genetic clusters with high DNA sequence identity were identified in Arthrobacter and additional Corynebacterium species, suggesting that this genetic organization for 4-cresol catabolism might be more widely distributed in Gram-positive bacteria.
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Evolutionary and functional novelty of pancreatic ribonuclease: a study of Musteloidea (order Carnivora).
Sci Rep
PUBLISHED: 01-02-2014
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Pancreatic ribonuclease (RNASE1) is a digestive enzyme that has been one of the key models in studies of evolutionary innovation and functional diversification. It has been believed that the RNASE1 gene duplications are correlated with the plant-feeding adaptation of foregut-fermenting herbivores. Here, we characterized RNASE1 genes from Caniformia, which has a simple digestive system and lacks microbial digestion typical of herbivores, in an unprecedented scope based on both gene sequence and tissue expression analyses. Remarkably, the results yielded new hypotheses regarding the evolution and the function of Caniformia RNASE1 genes. Four independent gene duplication events in the families of superfamily Musteloidea, including Procyonidae, Ailuridae, Mephitidae and Mustelidae, were recovered, rejecting previous Mustelidae-specific duplication hypothesis, but supporting Musteloidea duplication hypothesis. Moreover, our analyses revealed pronounced differences among the RNASE1 gene copies regarding their selection pressures, pI values and tissue expression patterns, suggesting the differences in their physiological functions. Notably, the expression analyses detected the transcription of a RNASE1 pseudogene in several tissues, raising the possibility that pseudogenes are also a potential source during the RNase functional diversification. In sum, the present work demonstrated a far more complex and intriguing evolutionary pattern and functional diversity of mammalian ribonuclease than previously thought.
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TRB3 is involved in free fatty acid-induced INS-1-derived cell apoptosis via the protein kinase C ? pathway.
PLoS ONE
PUBLISHED: 01-01-2014
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Chronic exposure to free fatty acids (FFAs) may induce ? cell apoptosis in type 2 diabetes. However, the precise mechanism by which FFAs trigger ? cell apoptosis is still unclear. Tribbles homolog 3 (TRB3) is a pseudokinase inhibiting Akt, a key mediator of insulin signaling, and contributes to insulin resistance in insulin target tissues. This paper outlined the role of TRB3 in FFAs-induced INS-1 ? cell apoptosis. TRB3 was promptly induced in INS-1 cells after stimulation by FFAs, and this was accompanied by enhanced INS-1 cell apoptosis. The overexpression of TRB3 led to exacerbated apoptosis triggered by FFAs in INS-1-derived cell line and the subrenal capsular transplantation animal model. In contrast, cell apoptosis induced by FFAs was attenuated when TRB3 was knocked down. Moreover, we observed that activation and nuclear accumulation of protein kinase C (PKC) ? was enhanced by upregulation of TRB3. Preventing PKC? nuclear translocation and PKC? selective antagonist both significantly lessened the pro-apoptotic effect. These findings suggest that TRB3 was involved in lipoapoptosis of INS-1 ? cell, and thus could be an attractive pharmacological target in the prevention and treatment of T2DM.
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NrdH-redoxin enhances resistance to multiple oxidative stresses by acting as a peroxidase cofactor in Corynebacterium glutamicum.
Appl. Environ. Microbiol.
PUBLISHED: 12-27-2013
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NrdH-redoxins are small protein disulfide oxidoreductases behaving like thioredoxins but sharing a high amino acid sequence similarity to glutaredoxins. Although NrdH-redoxins are supposed to be another candidate in the antioxidant system, their physiological roles in oxidative stress remain unclear. In this study, we confirmed that the Corynebacterium glutamicum NrdH-redoxin catalytically reduces the disulfides in the class Ib RNR, insulin and DTNB, by exclusively receiving electrons from thioredoxin reductase. Overexpression of NrdH increased the resistance of C. glutamicum to multiple oxidative stresses by reducing ROS accumulation. Accordingly, elevated expression of the nrdH gene was observed when the C. glutamicum wild type strain was exposed to oxidative stress conditions. It was discovered that the NrdH-mediated resistance to oxidative stresses was largely dependent on the presence of the thiol peroxidase Prx, as the increased resistance to oxidative stresses mediated by overexpression of NrdH was largely abrogated in the prx mutant. Furthermore, we showed that NrdH facilitated the hydroperoxides reduction activity of Prx by directly targeting and serving as its electron donor. Thus, we present evidence that the NrdH redoxin can protect against the damaging effects of ROS induced by various exogenous oxidative stresses by acting as a peroxidase cofactor.
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High average power picosecond pulse and supercontinuum generation from a thulium-doped, all-fiber amplifier.
Opt Lett
PUBLISHED: 12-11-2013
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We demonstrate a high-power, picosecond, thulium-doped, all-fiber master oscillator power amplifier with average power of 120.4 W. The compact fiber oscillator is carefully designed with high repetition rate for the purpose of overcoming the detrimental effects of fiber nonlinearity in the later fiber amplifiers. The pulse duration of 16 ps at 333.75 MHz repetition rate results in a peak power of 22.5 kW in the final fiber power amplifier. To the best of our knowledge, this is the first demonstration of average power exceeding 100 W from an ultrashort pulse laser at 2 ?m wavelength. On the other hand, by decreasing the fiber oscillator repetition rate and pulse duration for enhancing the fiber nonlinearity effects, we also demonstrate a high-power supercontinuum source with average power of 36 W from 1.95 ?m to beyond 2.4 ?m in the final fiber power amplifier.
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Stable passively Q-switched and gain-switched Yb-doped all-fiber laser based on a dual-cavity with fiber Bragg gratings.
Opt Express
PUBLISHED: 11-13-2013
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We demonstrate a stable passively Q-switched and gain-switched Yb-doped all-fiber laser cladding-pumped by a continuous fiber-coupled 976 nm laser diode. By use of an all-fiber dual-cavity, the efficient elements of the laser mainly include the fiber Bragg gratings and rare-earth doped fiber, allowing the oscillator to be integrated in a compact size with reliable and stable output. In this scheme, an efficient laser output with 45 ns pulse width, 62 ?J pulse energy, and 1.4 kW peak power operating at 1081 nm was obtained. To the best of our knowledge, this is the minimum pulse width in this similar kind of all-fiber configuration at present. Sequential nanosecond pulses were obtained at the repetition rate of several to tens of kHz with the variation of the diode pumping power. Effects of laser parameters such as pump power, cavity length, external-cavity wavelength, and FBG reflectivity on laser performance were also presented and discussed.
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Violapyrones A-G, ?-Pyrone Derivatives from Streptomyces violascens Isolated from Hylobates hoolock Feces.
J. Nat. Prod.
PUBLISHED: 11-01-2013
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Seven new 3,4,6-trisubstituted ?-pyrone derivatives, violapyrones A-G (1-7), were isolated from Streptomyces violascens obtained from Hylobates hoolock feces. Their structures were elucidated on the basis of detailed spectroscopic analysis. The antimicrobial activities of 1-7 were evaluated against Gram-positive and Gram-negative bacteria and against fungi. Compounds 1-3 showed moderate antibacterial activities against Bacillus subtilis and Staphylococcus aureus with MIC values of 4-32 ?g/mL.
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[Transcription activator-like effectors(TALEs)based genome engineering].
Zool. Res.
PUBLISHED: 10-12-2013
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Systematic reverse-engineering of functional genome architecture requires precise modifications of gene sequences and transcription levels. The development and application of transcription activator-like effectors(TALEs) has created a wealth of genome engineering possibilities. TALEs are a class of naturally occurring DNA-binding proteins found in the plant pathogen Xanthomonas species. The DNA-binding domain of each TALE typically consists of tandem 34-amino acid repeat modules rearranged according to a simple cipher to target new DNA sequences. Customized TALEs can be used for a wide variety of genome engineering applications, including transcriptional modulation and genome editing. Such "genome engineering" has now been established in human cells and a number of model organisms, thus opening the door to better understanding gene function in model organisms, improving traits in crop plants and treating human genetic disorders.
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Involvement of Reactive Oxygen Species in a Feed-forward Mechanism of Na/K-ATPase-mediated Signaling Transduction.
J. Biol. Chem.
PUBLISHED: 10-11-2013
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Cardiotonic steroids (such as ouabain) signaling through Na/K-ATPase regulate sodium reabsorption in the renal proximal tubule. We report here that reactive oxygen species are required to initiate ouabain-stimulated Na/K-ATPase·c-Src signaling. Pretreatment with the antioxidant N-acetyl-l-cysteine prevented ouabain-stimulated Na/K-ATPase·c-Src signaling, protein carbonylation, redistribution of Na/K-ATPase and sodium/proton exchanger isoform 3, and inhibition of active transepithelial (22)Na(+) transport. Disruption of the Na/K-ATPase·c-Src signaling complex attenuated ouabain-stimulated protein carbonylation. Ouabain-stimulated protein carbonylation is reversed after removal of ouabain, and this reversibility is largely independent of de novo protein synthesis and degradation by either the lysosome or the proteasome pathways. Furthermore, ouabain stimulated direct carbonylation of two amino acid residues in the actuator domain of the Na/K-ATPase ?1 subunit. Taken together, the data indicate that carbonylation modification of the Na/K-ATPase ?1 subunit is involved in a feed-forward mechanism of regulation of ouabain-mediated renal proximal tubule Na/K-ATPase signal transduction and subsequent sodium transport.
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Automated anterior chamber angle localization and glaucoma type classification in OCT images.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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To identify glaucoma type with OCT (optical coherence tomography) images, we present an image processing and machine learning based framework to localize and classify anterior chamber angle (ACA) accurately and efficiently. In digital OCT photographs, our method automatically localizes the ACA region, which is the primary structural image cue for clinically identifying glaucoma type. Next, visual features are extracted from this region to classify the angle as open angle (OA) or angle-closure (AC). This proposed method has three major contributions that differ from existing methods. First, the ACA localization from OCT images is fully automated and efficient for different ACA configurations. Second, it can directly classify ACA as OA/AC based on only visual features, which is different from previous work for ACA measurement that relies on clinical features. Third, it demonstrates that higher dimensional visual features outperform low dimensional clinical features in terms of angle closure classification accuracy. From tests on a clinical dataset comprising of 2048 images, the proposed method only requires 0.26s per image. The framework achieves a 0.921 ± 0.036 AUC (area under curve) value and 84.0% ± 5.7% balanced accuracy at a 85% specificity, which outperforms existing methods based on clinical features.
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Integrating research, clinical practice and translation: The singapore experience.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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We introduce the experiences of the Singapore ocular imaging team, iMED, in integrating image processing and computer-aided diagnosis research with clinical practice and knowledge, towards the development of ocular image processing technologies for clinical usage with potential impact. In this paper, we outline key areas of research with their corresponding image modalities, as well as providing a systematic introduction of the datasets used for validation.
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Self-assessment for optic disc segmentation.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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Optic disc segmentation from retinal fundus image is a fundamental but important step in many applications such as automated glaucoma diagnosis. Very often, one method might work well on many images but fail on some other images and it is difficult to have a single method or model to cover all scenarios. Therefore, it is important to combine results from several methods to minimize the risk of failure. For this purpose, this paper computes confidence scores for three methods and combine their results for an optimal one. The experimental results show that the combined result from three methods is better than the results by any individual method. It reduces the mean overlapping error by 7.4% relatively compared with best individual method. Simultaneously, the number of failed cases with large overlapping errors is also greatly reduced. This is important to enhance the clinical deployment of the automated disc segmentation.
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Synchronous simulation for deformation of liver and gallbladder with stretch and compression compensation.
Conf Proc IEEE Eng Med Biol Soc
PUBLISHED: 10-11-2013
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One challenge in surgical simulation is to design stable deformable models to simulate the dynamics of organs synchronously. In this paper, we develop a novel mass-spring model on the tetrahedral meshes for soft organs such as the liver and gallbladder, which can stably deform with large time steps. We model the contact forces between the organs as a kind of forces generated by the tensions of repulsive springs connecting in between the organs. The simulation system couples a pair of constraints on the length of springs with an implicit integration method. Based on the novel constraints, our simulator can efficiently preserve the volumes and geometric properties of the liver and gallbladder during the simulation. The numerical examples demonstrate that the proposed simulation system can provide realistic and stable deformable results.
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Comamonas testosteroni uses a chemoreceptor for tricarboxylic acid cycle intermediates to trigger chemotactic responses towards aromatic compounds.
Mol. Microbiol.
PUBLISHED: 09-11-2013
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Bacterial chemotaxis towards aromatic compounds has been frequently observed; however, knowledge of how bacteria sense aromatic compounds is limited. Comamonas testosteroni?CNB-1 is able to grow on a range of aromatic compounds. This study investigated the chemotactic responses of CNB-1 to 10 aromatic compounds. We constructed a chemoreceptor-free, non-chemotactic mutant, CNB-1?20, by disruption of all 19 putative methyl-accepting chemotaxis proteins (MCPs) and the atypical chemoreceptor in strain CNB-1. Individual complementation revealed that a putative MCP (tagged MCP2201) was involved in triggering chemotaxis towards all 10 aromatic compounds. The recombinant sensory domain of MCP2201 did not bind to 3- or 4-hydroxybenzoate, protocatechuate, catechol, benzoate, vanillate and gentisate, but bound oxaloacetate, citrate, cis-aconitate, isocitrate, ?-ketoglutarate, succinate, fumarate and malate. The mutant CNB-1?pmdF that lost the ability to metabolize 4-hydroxybenzoate and protocatechuate also lost its chemotactic response to these compounds, suggesting that taxis towards aromatic compounds is metabolism-dependent. Based on the ligand profile, we proposed that MCP2201 triggers taxis towards aromatic compounds by sensing TCA cycle intermediates. Our hypothesis was further supported by the finding that introduction of the previously characterized pseudomonad chemoreceptor (McpS) for TCA cycle intermediates into CNB-1?20 likewise triggered chemotaxis towards aromatic compounds.
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Passive Immunization Against Marinobufagenin Attenuates Renal Fibrosis and Improves Renal Function in Experimental Renal Disease.
Am. J. Hypertens.
PUBLISHED: 09-06-2013
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We have shown that the cardiotonic steroid marinobufagenin (MBG) is elevated in clinical and experimental renal disease, and significantly contributes to the development of experimental uremic cardiomyopathy induced by removal of five-sixths of the kidney (5/6 nephrectomy; PNx) in the rat. We have demonstrated that both active and passive immunization against MBG with an anti-MBG monoclonal antibody (mAb 3E9) significantly attenuated cardiac fibrosis following PNx. In the present study we sought to determine whether the use of mAb 3E9 could improve renal function following PNx.
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Robotic learning of motion using demonstrations and statistical models for surgical simulation.
Int J Comput Assist Radiol Surg
PUBLISHED: 08-21-2013
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   In robotic-assisted surgical training, the expertise of surgeons in maneuvering surgical instruments may be utilized to provide the motion trajectories for teaching. However, the motion primitives for trajectory planning are not known until the motion trajectory is generalized. We hypothesize that a generic model that encodes surgical skills using demonstrations and statistical models can be used by the surgical training robot to determine the motion primitive base on the motion trajectory.
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Double-gate light-emitting electrochemical transistor: confining the organic p-n junction.
J. Am. Chem. Soc.
PUBLISHED: 08-12-2013
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In conventional light-emitting electrochemical cells (LECs), an off-centered p-n junction is one of the major drawbacks, as it leads to exciton quenching at one of the charge-injecting electrodes and results in performance instability. To combat this problem, we have developed a new device configuration, the double-gate light-emitting electrochemical transistor (DG-LECT), in which the location of the light-emitting p-n junction can be precisely defined via the position of the two gate terminals. Based on a planar LEC structure, two gate electrodes made from an electrochemically active conducting polymer are employed to predefine the p- and n-doped area of the light-emitting polymer. Thus, a p-n junction is formed in between the p-doped and n-doped regions. We demonstrate a homogeneous and centered p-n junction as well as other predefined junction patterns in these DG-LECT devices. Additionally, we report an electrical model that explains the operation of the DG-LECTs. The DG-LECT device provides a new tool to study the fundamental physics of LECs, as it dissects the key working process of LEC into decoupled p-doping, n-doping, and electroluminescence.
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Structural Optimization of Berberine as a Synergist to Restore Antifungal Activity of Fluconazole against Drug-Resistant Candida albicans.
ChemMedChem
PUBLISHED: 08-09-2013
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We have conducted systematic structural modification, deconstruction, and reconstruction of the berberine core with the aim of lowering its cytotoxicity, investigating its pharmacophore, and ultimately, seeking novel synergistic agents to restore the effectiveness of fluconazole against fluconazole-resistant Candida albicans. A structure-activity relationship study of 95 analogues led us to identify the novel scaffold of N-(2-(benzo[d][1,3]dioxol-5-yl)ethyl)-2-(substituted phenyl)acetamides 7?a-l, which exhibited remarkable levels of in vitro synergistic antifungal activity. Compound 7?d (N-(2-(benzo[d][1,3]dioxol-5-yl)ethyl)-2-(2-fluorophenyl)acetamide) significantly decreased the MIC80 values of fluconazole from 128.0??g?mL(-1) to 0.5??g?mL(-1) against fluconazole-resistant C.?albicans and exhibited much lower levels of cytotoxicity than berberine toward human umbilical vein endothelial cells.
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Insulin-like growth factor-1 induces lymphangiogenesis and facilitates lymphatic metastasis in colorectal cancer.
World J. Gastroenterol.
PUBLISHED: 07-24-2013
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To investigate the expression of insulin-like growth factor-1 (IGF-1)/insulin-like growth factor-1 receptor (IGF-1R) in colorectal cancer (CRC) tissues and to analyze their correlation with lymphangiogenesis and lymphatic metastasis.
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[Feasibility and efficiency of embolization of spinal dural arteriovenous fistula].
Zhonghua Wai Ke Za Zhi
PUBLISHED: 07-18-2013
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To evaluate the feasibility and efficiency of embolization of spinal dural arteriovenous fistula (SDAVF).
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Rung-defected ladder of azido-bridged Cu(II) chains linked by [Cu(picolinate)2] units.
Dalton Trans
PUBLISHED: 07-09-2013
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A novel two-dimensional (2D) azido-based Cu(II) network, [Cu11(pic)6(N3)16] (1), was prepared using picolinic acid (Hpic) as coligand. Interestingly, 1 is composed of symmetric double azido EO-bridged [Cu(N3)2]n chains linked by [Cu(pic)2] units making a regular ladder with a missing rung. These rung-defected ladders are assembled in a layered structure by long azido-Cu(II) contacts between neighboring [Cu(N3)2]n chains. The magnetic properties of 1 are dominated by significantly strong antiferromagnetic coupling (J/kB = -15.4(2) K) between Cu(II) spins through the double EO azido-bridges along the [Cu(N3)2]n chains.
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NOX2 deficiency ameliorates cerebral injury through reduction of complexin II-mediated glutamate excitotoxicity in experimental stroke.
Free Radic. Biol. Med.
PUBLISHED: 06-29-2013
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Although NADPH oxidase (NOX)-mediated oxidative stress is considered one of the major mechanisms triggering the pathogenic actions of ischemic stroke and very recent studies have indicated that NADPH oxidase is a major source of reactive oxygen species (ROS) production controlling glutamate release, how neuronal NADPH oxidase activation is coupled to glutamate release is not well understood. Therefore, in this study, we used an in vivo transient middle cerebral artery occlusion model and in vitro primary cell cultures to test whether complexins, the regulators of soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes necessary for vesicle fusion, are associated with NOX2-derived ROS and contribute to glutamate-mediated excitotoxicity in ischemic stroke. In this study, we first identified the upregulation of complexin II in the ischemic brain and evaluated its potential role in ischemic stroke showing that gene silencing of complexin II ameliorated cerebral injury as evidenced by reduced infarction volume, neurological deficit, and neuron necrosis accompanied by decreased glutamate levels, consistent with the results from NOX2(-/-) mice with ischemic stroke. We further demonstrated that complexin II expression was mediated by NOX2 in primary cultured neurons subjected to oxygen-glucose deprivation (OGD) and contributed to OGD-induced glutamate release and neuron necrosis via SNARE signaling. Taken together, these findings for the first time provide evidence that complexin II is a central target molecule that links NADPH oxidase-derived ROS to glutamate-mediated neuronal excitotoxicity in ischemic stroke.
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Rhein lysinate decreases the generation of ?-amyloid in the brain tissues of Alzheimers disease model mice by inhibiting inflammatory response and oxidative stress.
J Asian Nat Prod Res
PUBLISHED: 06-18-2013
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The protective effect of rhein lysinate (RHL) on Alzheimers disease (AD) was explored in senescence-accelerated mouse prone-8 (SAMP8) mice. SAMP8 mice without treatment were used as the AD-positive control, and senescence-accelerated-resistant mice were used as the AD-negative control. In this study, 4-month-old male SAMP8 mice were orally administered 25 and 50 mg/kg RHL in drinking water for 6 months. The results of brain tissue enzyme-linked immunosorbent assay (ELISA), immunohistochemistry, and Western blot were demonstrated that compared with SAMP8 group, ?-amyloid1-40 and ?-amyloid1-42 were reduced; the levels of tumor necrosis factor-? and interleukin 6 of brain tissues were also significantly decreased; however, the level of sirtuin 1 (SIRT1) was increased in the RHL-treated group. Compared with SAMP8 group, the ROS levels and malondialdehyde levels were decreased; however, superoxide dismutase and glutathione peroxidase levels were increased in the brain tissues of SAMP8 25 and 50 mg/kg RHL-treated groups. In conclusion, the reduction of A? induced by RHL was related to the increase of SIRT1 and the inhibition of the inflammatory response and oxidative stress in SAMP8 mice. It might be a promising biological therapeutic drug for AD.
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Creation and validation of a widely applicable multiple gene transfer vector system for stable transformation in plant.
Plant Mol. Biol.
PUBLISHED: 06-16-2013
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Multiple gene transfer (MGT) technology has become a powerful tool for basic and applied plant biology research in recent years. Despite some notable successes in obtaining plant lines harbouring multiple transgenes, these methods are still generally unwieldy and costly. We report here a straightforward and cost effective strategy, utilizing commonly available restriction enzymes for the transfer of multiple genes into plants, hence greatly widening the accessibility of MGT. This methodology exploits the specific nested arrangement of a pair of isocaudomer restriction enzymes (for example XbaI-AvrII-XbaI) so that through the alternate use of these two enzymes in a reiterative fashion multiple genes/constructs (up to five in this study) could be stacked together with ease. In a proof-of-concept experiment, we constructed a plant transformation vector containing three reporter gene expression cassettes flanked by two matrix attachment region sequences. The expression of all three genes was confirmed in transgenic Arabidopsis thaliana. The usefulness of this technology was further validated by the construction of a plant transformation vector containing five transgenes for the production of eicosapentaenoic acid (EPA, C20??,?,¹¹,¹?,¹?), a polyunsaturated essential fatty acid found in fish oils that is beneficial for health. In addition, we constructed four more vectors, incorporating one seed specific and three promoters conferring constitutive expression. These expression cassettes are flanked by a different isocaudomer pair (AvrII-SpeI-AvrII) and four other unique restriction sites, allowing the exchange of promoters and terminators of choice.
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A modified method for reducing renal injury in zoledronic Acid treatment of hypercalcemia and adverse skeletal events.
Indian J Palliat Care
PUBLISHED: 06-15-2013
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In this paper, we have reported a previously undescribed risk factor of deterioration of renal function in zoledronic acid treatment of skeletal metastasis - high serum calcium level. Based on this consideration, a modified method of treatment of hypercalcemia (HCM) with zoledronic acid is suggested in this paper.
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REG? deficiency promotes premature aging via the casein kinase 1 pathway.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 06-13-2013
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Our recent studies suggest a role for the proteasome activator REG (11S regulatory particles, 28-kDa proteasome activator)? in the regulation of tumor protein 53 (p53). However, the molecular details and in vivo biological significance of REG?-p53 interplay remain elusive. Here, we demonstrate that REG?-deficient mice develop premature aging phenotypes that are associated with abnormal accumulation of casein kinase (CK) 1? and p53. Antibody array analysis led us to identify CK1? as a direct target of REG?. Silencing CK1? or inhibition of CK1? activity prevented decay of murine double minute (Mdm)2. Interestingly, a massive increase of p53 in REG?(-/-) tissues is associated with reduced Mdm2 protein levels despite that Mdm2 transcription is enhanced. Allelic p53 haplodeficiency in REG?-deficient mice attenuated premature aging features. Furthermore, introducing exogenous Mdm2 to REG?(-/-) MEFs significantly rescues the phenotype of cellular senescence, thereby establishing a REG?-CK1-Mdm2-p53 regulatory pathway. Given the conflicting evidence regarding the "antiaging" and "proaging" effects of p53, our results indicate a key role for CK1?-Mdm2-p53 regulation in the cellular aging process. These findings reveal a unique model that mimics acquired aging in mammals and indicates that modulating the activity of the REG?-proteasome may be an approach for intervention in aging-associated disorders.
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Medicinal flowers. XXXX . Structures of dihydroisocoumarin glycosides and inhibitory effects on aldose reducatase from the flowers of Hydrangea macrophylla var.thunbergii.
Chem. Pharm. Bull.
PUBLISHED: 06-04-2013
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Six dihydroisocoumarin glycosides, florahydrosides I and II, thunberginol G 8-O-?-d-glucopyranoside, thunberginol C 8-O-?-d-glucopyranoside, 4-hydroxythunberginol G 3-O-?-d-glucopyranoside, and thunberginol D 3-O-?-d-glucopyranoside, have been isolated from the flowers of Hydrangea macrophylla Seringe var. thunbergii Makino (Saxifragaceae) together with 20 known compounds. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. Among the constituents, acylated quinic acid analog, neochlorogenic acid, was shown to substantially inhibit aldose reductase [IC50=5.6?µm]. In addition, the inhibitory effects on aldose reductase of several caffeoylquinic acid analogs were examined for structure-activity relationship study. As the results, 4,5-O-trans-p-dicaffeoyl-d-quinic acid was found to exhibit a potent inhibitory effect [IC50=0.29?µm].
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Differential regulation of the REG?-proteasome pathway by p53/TGF-? signalling and mutant p53 in cancer cells.
Nat Commun
PUBLISHED: 05-31-2013
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Proteasome activity is frequently enhanced in cancer to accelerate metastasis and tumorigenesis. REG?, a proteasome activator known to promote p53/p21/p16 degradation, is often overexpressed in cancer cells. Here we show that p53/TGF-? signalling inhibits the REG?-20S proteasome pathway by repressing REG? expression. Smad3 and p53 interact on the REG? promoter via the p53RE/SBE region. Conversely, mutant p53 binds to the REG? promoter and recruits p300. Importantly, mutant p53 prevents Smad3/N-CoR complex formation on the REG? promoter, which enhances the activity of the REG?-20S proteasome pathway and contributes to mutant p53 gain of function. Depletion of REG? alters the cellular response to p53/TGF-? signalling in drug resistance, proliferation, cell cycle progression and proteasome activity. Moreover, p53 mutations show a positive correlation with REG? expression in cancer samples. These findings suggest that targeting REG?-20S proteasome for cancer therapy may be applicable to human tumours with abnormal p53/Smad protein status. Furthermore, this study demonstrates a link between p53/TGF-? signalling and the REG?-20S proteasome pathway, and provides insight into the REG?/p53 feedback loop.
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Rhein inhibits the expression of vascular cell adhesion molecule 1 in human umbilical vein endothelial cells with or without lipopolysaccharide stimulation.
Am. J. Chin. Med.
PUBLISHED: 05-29-2013
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Reducing the expression of endothelial cell adhesion molecules (ECAMs) is known to decrease inflammation-induced vascular complications. In this study, we explored whether rhein can reduce the inflammation-induced expression of ECAMs in human umbilical vein endothelial cells (HUVECs) with or without lipopolysaccharide (LPS) stimulation. HUVECs were treated with different concentrations of rhein with or without 2.5 ?g/ml LPS stimulation. Cell viability was assayed using the MTT method. Real-time PCR and Western blot analysis were used to measure the transcription and expression levels of ECAMs, including intercellular adhesion molecule-1 (ICAM-1), vascular cell adhesion molecule-1 (VCAM-1), E-SELECTIN and related signaling proteins. The results indicated that rhein (0-20 ?mol/L) and LPS (0-10 ?g/ml) had no effect on the viability of HUVECs. LPS could promote the expression of VCAM-1, ICAM-1 and E-SELECTIN. Rhein appeared to target VCAM-1, ICAM-1 and E-SELECTIN, with the transcription and expression of all three factors being reduced by the rhein treatment (10 and 20 ?mol/L). The transcription and expression of VCAM-1 were also reduced by treatment with rhein (10 and 20 ?mol/L) in the presence of LPS stimulation. In conclusion, rhein treatment reduced the expression of VCAM-1 in HUVECs via a p38-dependent pathway.
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Parapedobacter pyrenivorans sp. nov., isolated from a pyrene-degrading microbial enrichment, and emended description of the genus Parapedobacter.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 05-24-2013
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A novel pyrene-degrading, Gram-negative bacterium, designated strain P-4(T), was isolated from a polycyclic aromatic hydrocarbon-degrading enrichment of polluted soils from a coking chemical plant. Cells of strain P-4(T) were non-motile rods. Strain P-4(T) grew at 15-45 °C (optimum, 37 °C), pH 6.0-10.0 (optimum, pH 8.5) and 0-4?% (w/v) NaCl. Analysis of the 16S rRNA gene sequence showed that strain P-4(T) was related phylogenetically to members of the genus Parapedobacter, with sequence similarity of 93.7-95.1?%. The cellular fatty acids of strain P-4(T) were iso-C15?:?0, summed feature 3 (C16?:?1?7c and/or C16?:?1?6c), iso-C17?:?0 3-OH, summed feature 9 (iso-C17?:?1?9c and/or 10-methyl C16?:?0), anteiso-C15?:?0, iso-C15?:?0 3-OH, C16?:?0, iso-C15?:?1 G, C16?:?0 3-OH and C17?:?0 2-OH. Cells contained menaquinone 7 as the major quinone. The polyamine of strain P-4(T) was homospermidine, and the main polar lipids were phosphatidylethanolamine and a sphingolipid. The G+C content of the DNA was 45.4 mol%. Strain P-4(T) showed a range of phenotypic characteristics that differentiated it from previously recognized Parapedobacter species, particularly its ability to use pyrene as a sole carbon source for growth and its alkaline optimal pH for growth (pH 8.5). On the basis of these results, it is concluded that strain P-4(T) represents a novel species of the genus Parapedobacter, for which the name Parapedobacter pyrenivorans (type strain P-4(T)?=?NBRC 109113(T)?=?CGMCC 1.12195(T)) is proposed. An emended description of the genus Parapedobacter is also provided.
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Paenibacillus taihuensis sp. nov., isolated from an eutrophic lake.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 04-26-2013
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Two Gram-stain-negative, facultatively anaerobic and endospore-forming rod-shaped bacterial strains, THMBG22(T) and R24, were isolated from decomposing algal scum. Phylogenetic analysis of 16S rRNA gene sequences showed that the two strains were closely related to each other (99.7?% similarity) and that they were also closely related to Paenibacillus sacheonensis DSM 23054(T) (97-97.1?%) and Paenibacillus phyllosphaerae DSM 17399(T) (96.1-96.4?%). This affiliation was also supported by rpoB-based phylogenetic analyses. Growth was observed at 20-40 °C (optimum, 30-37 °C) and at pH 5.0-9.0 (optimum, pH 6.0-7.0). The cells contained MK-7 as the sole respiratory quinone and anteiso-C15?:?0 as the major cellular fatty acid. Their cellular polar lipids were composed of phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine and 12 unidentified polar lipids. The diamino acid of their cell-wall peptidoglycan was meso-diaminopimelic acid. The DNA-DNA hybridization value between THMBG22(T) and R24 was 84?%, and DNA-DNA relatedness to the most closely related species with a validly published name (P. sacheonensis) was 35-37?%. These results supported the assignment of the new isolates to the genus Paenibacillus and also distinguished them from the previously described species of the genus Paenibacillus. Hence, it is proposed that strains THMBG22(T) and R24 represent a novel species of the genus Paenibacillus, with the name Paenibacillus taihuensis sp. nov. The type strain is THMBG22(T) (?=?CGMCC 1.10966(T)?=?NBRC 108766(T)).
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Site-specific acetylation of the proteasome activator REG? directs its heptameric structure and functions.
J. Biol. Chem.
PUBLISHED: 04-23-2013
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The proteasome activator REG? has been reported to promote degradation of steroid receptor coactivator-3 and cyclin-dependent kinase inhibitors p21, p16, and p19 in a ubiquitin- and ATP-independent manner. A recent comparative analysis of REG? expression in mouse and human tissues reveals a unique pattern of REG? in specific cell types, suggesting undisclosed functions and biological importance of this molecule. Despite the emerging progress made in REG?-related studies, how REG? function is regulated remains to be explored. In this study, we report for the first time that REG? can be acetylated mostly on its lysine 195 (Lys-195) residue by CREB binding protein (CBP), which can be reversed by sirtuin 1 (SIRT1) in mammalian cells. Site-directed mutagenesis abrogated acetylation at Lys-195 and significantly attenuated the capability of REG? to degrade its target substrates, p21 and hepatitis C virus core protein. Mechanistically, acetylation at Lys-195 is important for the interactions between REG? monomers and ultimately influences REG? heptamerization. Biological analysis of cells containing REG?-WT or REG?-K195R mutant indicates an impact of acetylation on REG?-mediated regulation of cell proliferation and cell cycle progression. These findings reveal a previously unknown mechanism in the regulation of REG? assembly and activity, suggesting a potential venue for the intervention of the ubiquitin-independent REG? proteasome activity.
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