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Find video protocols related to scientific articles indexed in Pubmed.
Transplantation with allograft for rupture of the flexor hallucis longus tendon with subsequent longitudinal tear of the flexor digitorum longus tendon at the master knot of Henry a case report.
J Am Podiatr Med Assoc
PUBLISHED: 10-03-2014
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A rare case of closed complete rupture of the flexor hallucis longus tendon with subsequent longitudinal tear of the flexor digitorum longus tendon is reported in a marathon runner. This is also a first case report of flexor hallucis longus transplant with cadaveric posterior tibial tendon allograft. Two minimal incisions distal and proximal to the malleolus allowed for tunneling with urethral dilators to open the tendon sheath for transplantation, avoiding the need for a large incision. Postoperatively, the patient regained active flexion at the interphalangeal joint of the left hallux. Four months after surgery, full range of motion was observed and dynamometric exam revealed 68% of the strength of the contralateral side. The patient was able to resume competitive running after the surgery and performed well in her age bracket.
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Alignathon: a competitive assessment of whole-genome alignment methods.
Genome Res.
PUBLISHED: 10-01-2014
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Multiple sequence alignments (MSAs) are a prerequisite for a wide variety of evolutionary analyses. Published assessments and benchmark data sets for protein and, to a lesser extent, global nucleotide MSAs are available, but less effort has been made to establish benchmarks in the more general problem of whole-genome alignment (WGA). Using the same model as the successful Assemblathon competitions, we organized a competitive evaluation in which teams submitted their alignments and then assessments were performed collectively after all the submissions were received. Three data sets were used: Two were simulated and based on primate and mammalian phylogenies, and one was comprised of 20 real fly genomes. In total, 35 submissions were assessed, submitted by 10 teams using 12 different alignment pipelines. We found agreement between independent simulation-based and statistical assessments, indicating that there are substantial accuracy differences between contemporary alignment tools. We saw considerable differences in the alignment quality of differently annotated regions and found that few tools aligned the duplications analyzed. We found that many tools worked well at shorter evolutionary distances, but fewer performed competitively at longer distances. We provide all data sets, submissions, and assessment programs for further study and provide, as a resource for future benchmarking, a convenient repository of code and data for reproducing the simulation assessments.
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Stacking patterns of thieno[3,2-b]thiophenes functionalized by sequential palladium-catalyzed Suzuki and Heck cross-coupling reactions.
Acta Crystallogr C Struct Chem
PUBLISHED: 08-27-2014
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The crystal structures of three 5-alkenyl-2-arylthieno[3,2-b]thiophenes, namely 3,6-dibromo-5-(4-tert-butylstyryl)-2-(naphthalen-1-yl)thieno[3,2-b]thiophene, C(28)H(22)Br(2)S(2), (I), 3,6-dibromo-5-(4-methylstyryl)-2-(naphthalen-1-yl)thieno[3,2-b]thiophene, C(25)H(16)Br(2)S(2), (II), and 3,6-dibromo-2-(4-tert-butylphenyl)-5-(4-methylstyryl)thieno[3,2-b]thiophene, C(25)H(22)Br(2)S(2), (III), have been determined in order to evaluate the geometry of the molecules. The ?-conjugated system containing the thieno[3,2-b]thiophene skeleton, the ethylene bridge and the phenyl rings is almost planar. The aromatic ring directly attached to the thieno[3,2-b]thiophene moiety is not coplanar with the thieno[3,2-b]thiophene moiety itself due to steric hindrance of the bromo substituent. The crystal packings are characterized by ?-? stacking [only for (II)] and C-Br...? interactions. The long axes of the molecules in (I) are oriented in two directions; for the two other structures the long axis is oriented in one direction only.
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Comparative assembly hubs: Web-accessible browsers for comparative genomics.
Bioinformatics
PUBLISHED: 08-18-2014
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Researchers now have access to large volumes of genome sequences for comparative analysis, some generated by the plethora of public sequencing projects and, increasingly, from individual efforts. It is not possible, or necessarily desirable, that the public genome browsers attempt to curate all these data. Instead, a wealth of powerful tools is emerging to empower users to create their own visualizations and browsers.
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An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons.
Nature
PUBLISHED: 08-07-2014
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Throughout evolution primate genomes have been modified by waves of retrotransposon insertions. For each wave, the host eventually finds a way to repress retrotransposon transcription and prevent further insertions. In mouse embryonic stem cells, transcriptional silencing of retrotransposons requires KAP1 (also known as TRIM28) and its repressive complex, which can be recruited to target sites by KRAB zinc-finger (KZNF) proteins such as murine-specific ZFP809 which binds to integrated murine leukaemia virus DNA elements and recruits KAP1 to repress them. KZNF genes are one of the fastest growing gene families in primates and this expansion is hypothesized to enable primates to respond to newly emerged retrotransposons. However, the identity of KZNF genes battling retrotransposons currently active in the human genome, such as SINE-VNTR-Alu (SVA) and long interspersed nuclear element 1 (L1), is unknown. Here we show that two primate-specific KZNF genes rapidly evolved to repress these two distinct retrotransposon families shortly after they began to spread in our ancestral genome. ZNF91 underwent a series of structural changes 8-12 million years ago that enabled it to repress SVA elements. ZNF93 evolved earlier to repress the primate L1 lineage until ?12.5 million years ago when the L1PA3-subfamily of retrotransposons escaped ZNF93's restriction through the removal of the ZNF93-binding site. Our data support a model where KZNF gene expansion limits the activity of newly emerged retrotransposon classes, and this is followed by mutations in these retrotransposons to evade repression, a cycle of events that could explain the rapid expansion of lineage-specific KZNF genes.
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Crystal structure of chlorido-(piperidine-?N)(quinoline-2-carboxyl-ato-?(2) N,O)platinum(II).
Acta Crystallogr Sect E Struct Rep Online
PUBLISHED: 06-23-2014
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The title compound, [Pt(C10H6NO2)Cl(C5H11N)], crystallizes with one mol-ecule in the asymmetric unit. The Pt(II) cation has a slightly distorted square-planar coordination environment defined by a chloride anion, the quinoline N atom and a carboxyl-ate O atom of the bidentate quinaldate ligand and a piperidine N atom. An intra-molecular C-H?Cl hydrogen bond occurs. In the crystal, mol-ecules are stacked into columns along the c axis by the formation of N-H?Cl and C-H?O hydrogen bonds.
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Realism, criterion validity, and training capability of simulated diagnostic cerebral angiography.
Stud Health Technol Inform
PUBLISHED: 04-16-2014
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Computer-based simulation is increasingly used in medical education for training, assessment, credentialing, and practice. Compared to medical specialties such as anesthesiology and general surgery, the adoption of simulation for neurointerventional training has been slow. This may be due to the limited number of neurointerventional simulators available and the lack of research assessing their validity and training capability. The objective of this study was to assess the realism, validity, and training capability of computer-based simulation for diagnostic cerebral angiography using a commercially available simulator called the ANGIO Mentor Express.
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Cembranoid diterpenes from the soft coral Lobophytum crassum and their anti-inflammatory activities.
Chem. Pharm. Bull.
PUBLISHED: 02-05-2014
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Nine cembranoid diterpenes 1-9, including four new compounds, crassumols D-G (1-4), were isolated from the methanol extract of the Vietnamese soft coral Lobophytum crassum. Spectroscopic methods were used to elucidate the structures of these compounds. Compound 5 exhibited a potent inhibitory effect on tumor necrosis factor-alpha (TNF?)-induced nuclear factor-kappa B (NF-?B) transcriptional activation in HepG2 cells and significantly inhibited the mRNA expression of cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) in a dose-dependent manner.
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Peroxisome proliferator-activated receptor transactivational effects in HepG2 cells of cembranoids from the soft coral Lobophytum crassum Von Marenzeller.
Arch. Pharm. Res.
PUBLISHED: 01-28-2014
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Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors that regulate the expression of multiple genes involved in metabolic, anti-inflammatory, and developmental processes. This study evaluated the PPARs transactivational effects of thirteen cembranoid diterpenoids 1-13 from the soft coral Lobophytum crassum, using PPAR-responsive elements-luciferase reporter and GAL4-PPAR chimera assays. All isolated compounds activated the transcription of PPARs in a dose-dependent manner, with EC50 values ranging from 2.07 ± 1.73 to 130.20 ± 1.85 ?M. Moreover, compounds 6-9 affected the transactivation of all three PPAR types, PPAR?, ?, ?(?), in a dose-dependent manner, with EC50 values in a ranging from 11.92 ± 1.23 to 122.50 ± 2.12 ?M. These results provide a scientific rationale for further studies on the soft coral L. crassum and its diterpenoid constituents to develop medicinal products against inflammatory and metabolic diseases.
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Green-to-red photoconvertible Dronpa mutant for multimodal super-resolution fluorescence microscopy.
ACS Nano
PUBLISHED: 01-21-2014
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Advanced imaging techniques crucially depend on the labels used. In this work, we present the structure-guided design of a fluorescent protein that displays both reversibly photochromic and green-to-red photoconversion behavior. We first designed ffDronpa, a mutant of the photochromic fluorescent protein Dronpa that matures up to three times faster while retaining its interesting photochromic features. Using a combined evolutionary and structure-driven rational design strategy, we developed a green-to-red photoconvertible ffDronpa mutant, called pcDronpa, and explored different optimization strategies that resulted in its improved version, pcDronpa2. This fluorescent probe combines a high brightness with low photobleaching and photoblinking. We herein show that, despite its tetrameric nature, pcDronpa2 allows for multimodal subdiffraction imaging by sequentially imaging a given sample using both super-resolution fluctuation imaging and localization microscopy.
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Hydrogen-bonded chains in three cis-dichloridoplatinum(II) complexes bearing piperidine and amine ligands.
Acta Crystallogr C Struct Chem
PUBLISHED: 01-06-2014
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The crystal structures of cis-dichlorido(ethylamine-?N)(piperidine-?N)platinum(II), [PtCl2(C2H7N)(C5H11N)], (I), cis-dichlorido(3-methoxyaniline-?N)(piperidine-?N)platinum(II), [PtCl2(C5H11N)(C7H9NO)], (II), and cis-dichlorido(piperidine-?N)(quinoline-?N)platinum(II), [PtCl2(C5H11N)(C9H7N)], (III), have been determined at 100?K in order to verify the influence of the nonpiperidine ligand on the geometry and crystal packing. The crystal packing is characterized by N-H...Cl hydrogen bonding, resulting in the formation of chains of molecules connected in a head-to-tail fashion. Hydrogen-bonding interactions play a major role in the packing of (I), where the chains further aggregate into planes, but less so in the case of (II) and (III), where ?-? stacking interactions are of greater importance.
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Addition of valproic acid to CHO cell fed-batch cultures improves monoclonal antibody titers.
Mol. Biotechnol.
PUBLISHED: 01-02-2014
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Improving the productivity of a biopharmaceutical Chinese hamster ovary (CHO) fed-batch cell culture can enable cost savings and more efficient manufacturing capacity utilization. One method for increasing CHO cell productivity is the addition of histone deacetylase (HDAC) inhibitors to the cell culture process. In this study, we examined the effect of valproic acid (VPA, 2-propylpentanoic acid), a branched-chain carboxylic acid HDAC inhibitor, on the productivity of three of our CHO cell lines that stably express monoclonal antibodies. Fed-batch shake flask VPA titrations on the three different CHO cell lines yielded cell line-specific results. Cell line A responded highly positively, cell line B responded mildly positively, and cell line C did not respond. We then performed factorial experiments to identify the optimal VPA concentration and day of addition for cell line A. After identifying the optimal conditions for cell line A, we performed verification experiments in fed-batch bioreactors for cell lines A and B. These experiments confirmed that a high dose of VPA late in the culture can increase harvest titer >20 % without greatly changing antibody aggregation, charge heterogeneity, and N-linked glycosylation profiles. Our results suggest that VPA is an attractive and viable small molecule enhancer of protein production for biopharmaceutical CHO cell culture processes.
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Track data hubs enable visualization of user-defined genome-wide annotations on the UCSC Genome Browser.
Bioinformatics
PUBLISHED: 11-13-2013
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Track data hubs provide an efficient mechanism for visualizing remotely hosted Internet-accessible collections of genome annotations. Hub datasets can be organized, configured and fully integrated into the University of California Santa Cruz (UCSC) Genome Browser and accessed through the familiar browser interface. For the first time, individuals can use the complete browser feature set to view custom datasets without the overhead of setting up and maintaining a mirror.Availability and implementation: Source code for the BigWig, BigBed and Genome Browser software is freely available for non-commercial use at http://hgdownload.cse.ucsc.edu/admin/jksrc.zip, implemented in C and supported on Linux. Binaries for the BigWig and BigBed creation and parsing utilities may be downloaded at http://hgdownload.cse.ucsc.edu/admin/exe/. Binary Alignment/Map (BAM) and Variant Call Format (VCF)/tabix utilities are available from http://samtools.sourceforge.net/ and http://vcftools.sourceforge.net/. The UCSC Genome Browser is publicly accessible at http://genome.ucsc.edu.
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Identification of KvLQT1 K+ channels as new regulators of non-small cell lung cancer cell proliferation and migration.
Int. J. Oncol.
PUBLISHED: 10-24-2013
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K+ channels, which are overexpressed in several cancers, have been identified as regulators of cell proliferation and migration, key processes in cancer development/propagation. Their role in lung cancer has not been studied extensively; but we showed previously that KvLQT1 channels are involved in cell migration, proliferation and repair of normal lung epithelial cells. We now investigated the role of these channels in lung cancer cell lines and their expression levels in human lung adenocarcinoma (AD) tissues. First, we observed that the wound-healing rates of A549 lung adenocarcinoma cell monolayers were reduced by clofilium and chromanol or after silencing with KvLQT1-specific siRNA. Dose-dependent decrease of A549 cell growth and cell accumulation in G0/G1 phase were seen after KvLQT1 inhibition. Clofilium also affected 2D and 3D migration of A549 cells. Similarly, H460 cell growth, migration and wound healing were diminished by this drug. Because K+ channel overexpression has been encountered in some cancers, we assessed KvLQT1 expression levels in tumor tissues from patients with lung AD. KvLQT1 protein expression in tumor samples was increased by 1.5- to 7-fold, compared to paired non-neoplastic tissues, in 17 of 26 patients. In summary, our data reveal that KvLQT1 channel blockade efficiently reduces A549 and H460 cell proliferation and migration. Moreover, KvLQT1 overexpression in AD samples suggests that it could be a potential therapeutic target in lung cancer.
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New anti-inflammatory cembranoid diterpenoids from the Vietnamese soft coral Lobophytum crassum.
Bioorg. Med. Chem. Lett.
PUBLISHED: 10-13-2013
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Four new cembranoid diterpenes lobocrasols A-D (1-4), were isolated from the methanol extract of the soft coral Lobophytum crassum. Their structures were elucidated by spectroscopic analysis and by comparison of the spectroscopic data with those of similar compounds previously reported in literature. The anti-inflammatory effects of isolated compounds were evaluated using NF-?B luciferase and reverse transcription polymerase chain reaction (RT-PCR). Compounds 1 and 2 significantly inhibited TNF?-induced NF-?B transcriptional activity in HepG2 cells in a dose-dependent manner, with IC50 values of 6.30±0.42 and 6.63±0.11?M, respectively. Furthermore, the transcriptional inhibition of these compounds was confirmed by a decrease in cyclooxygenase-2 (COX-2) and inducible nitric oxide synthase (iNOS) gene expression levels in HepG2 cells.
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Submicrometer 3D structures fabrication enabled by one-photon absorption direct laser writing.
Opt Express
PUBLISHED: 10-10-2013
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We demonstrate a new 3D fabrication method to achieve the same results as those obtained by the two-photon excitation technique, by using a simple one-photon elaboration method in a very low absorption regime. Desirable 2D and 3D submicrometric structures, such as spiral, chiral, and woodpile architectures, with feature size as small as 190 nm have been fabricated, by using just a few milliwatts of a continuous-wave laser at 532 nm and a commercial SU8 photoresist. Different aspects of the direct laser writing based on ultralow one-photon absorption (LOPA) technique are investigated and compared with the TPA technique, showing several advantages, such as simplicity and low cost.
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Visuospatial anatomy comprehension: The role of spatial visualization ability and problem-solving strategies.
Anat Sci Educ
PUBLISHED: 04-03-2013
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The present study explored the problem-solving strategies of high- and low-spatial visualization ability learners on a novel spatial anatomy task to determine whether differences in strategies contribute to differences in task performance. The results of this study provide further insights into the processing commonalities and differences among learners beyond the classification of spatial visualization ability alone, and help elucidate what, if anything, high- and low-spatial visualization ability learners do differently while solving spatial anatomy task problems. Forty-two students completed a standardized measure of spatial visualization ability, a novel spatial anatomy task, and a questionnaire involving personal self-analysis of the processes and strategies used while performing the spatial anatomy task. Strategy reports revealed that there were different ways students approached answering the spatial anatomy task problems. However, chi-square test analyses established that differences in problem-solving strategies did not contribute to differences in task performance. Therefore, underlying spatial visualization ability is the main source of variation in spatial anatomy task performance, irrespective of strategy. In addition to scoring higher and spending less time on the anatomy task, participants with high spatial visualization ability were also more accurate when solving the task problems. Anat Sci Educ. © 2013 American Association of Anatomists.
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Comparison of 3D reconstructive technologies used for morphometric research and the translation of knowledge using a decision matrix.
Anat Sci Educ
PUBLISHED: 03-12-2013
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The use of three-dimensional (3D) models for education, pre-operative assessment, presurgical planning, and measurement have become more prevalent. With the increase in prevalence of 3D models there has also been an increase in 3D reconstructive software programs that are used to create these models. These software programs differ in reconstruction concepts, operating system requirements, user features, cost, and no one program has emerged as the standard. The purpose of this study was to conduct a systematic comparison of three widely available 3D reconstructive software programs, Amira(®), OsiriX, and Mimics(®) , with respect to the softwares ability to be used in two broad themes: morphometric research and education to translate morphological knowledge. Cost, system requirements, and inherent features of each program were compared. A novel concept selection tool, a decision matrix, was used to objectify comparisons of usability of the interface, quality of the output, and efficiency of the tools. Findings indicate that Mimics was the best-suited program for construction of 3D anatomical models and morphometric analysis, but for creating a learning tool the results were less clear. OsiriX was very user-friendly; however, it had limited capabilities. Conversely, although Amira had endless potential and could create complex dynamic videos, it had a challenging interface. These results provide a resource for morphometric researchers and educators to assist the selection of appropriate reconstruction programs when starting a new 3D modeling project.
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Improving the second-order nonlinear optical response of fluorescent proteins: the symmetry argument.
J. Am. Chem. Soc.
PUBLISHED: 03-01-2013
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We have successfully designed and expressed a new fluorescent protein with improved second-order nonlinear optical properties. It is the first time that a fluorescent protein has been rationally altered for this particular characteristic. On the basis of the specific noncentrosymmetry requirements for second-order nonlinear optical effects, we had hypothesized that the surprisingly low first hyperpolarizability (?) of the enhanced yellow fluorescent protein (eYFP) could be explained by centrosymmetric stacking of the chromophoric Tyr66 and the neighboring Tyr203 residue. The inversion center was removed by mutating Tyr203 into Phe203, with minor changes in the linear optical properties and even an improved fluorescence quantum yield. Structure determination by X-ray crystallography as well as linear optical characterization corroborate a correct folding and maturation. Measurement of ? by means of hyper-Rayleigh scattering (HRS) as well as their analysis using quantum chemistry calculations validate our hypothesis. This observation can eventually lead to improved red fluorescent proteins for even better performance. On the basis of the specific function (second-harmonic generation), the color of its emission, and in analogy with the "fruit" names, we propose SHardonnay as the name for this Tyr203Phe mutant of eYFP.
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Inhibitory effects of oleanane-type triterpenes and saponins from the stem bark of Kalopanax pictus on LPS-stimulated pro-inflammatory cytokine production in bone marrow-derived dendritic cells.
Arch. Pharm. Res.
PUBLISHED: 02-27-2013
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Kalopanax pictus (Araliaceae) is a deciduous tree distributed in Korea, Japan, and China. The stem bark of K. pictus has been functionally used as a traditional crude drug for the treatment of various inflammatory diseases. In the present study, we describe the inhibitory effects of oleanane-type triterpenes and saponins isolated from the stem bark of K. pictus on production of pro-inflammatory cytokines in LPS-stimulated bone marrow-derived dendritic cells. Of the compounds tested, 16,23,29-trihydroxy-3-oxo-olean-12-en-28-oic acid (1), 4,23,29-trihydroxy-3,4-seco-olean-12-en-3-oate-28-oic acid (2), 3?,6?,23-trihydroxyolean-12-en-28-oic acid 28-O-?-D-glucopyranoside (3), nipponogenin E (6), 3?,6?,23-trihydroxyolean-12-en-28-oic acid (7), and caulophyllogenin (19) significantly inhibited the production of IL-12 p40 and IL-6 with IC50 values ranging from 3.3 to 9.1 ?M. Compounds 2, 3, 7, and 19 significantly suppressed the secretion of TNF-? with IC50 ranging from 8.8 to 20.0 ?M. These data provide scientific support for the use of K. pictus stem bark and its triterpene and saponin components in the inhibition of pro-inflammatory cytokine secretion, including IL-12 p40, IL-6, and TNF-?, and for prevention and treatment of inflammatory diseases.
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Oleanolic triterpene saponins from the roots of Panax bipinnatifidus.
Chem. Pharm. Bull.
PUBLISHED: 11-02-2011
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Ten oleanane-type saponins (1-10), including three new compounds, namely bifinosides A-C (1-3), were isolated from the roots of Panax bipinnatifidus SEEM. Their structures were elucidated on the basis of chemical and spectroscopic methods.
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Discovery of a linear cyclotide from the bracelet subfamily and its disulfide mapping by top-down mass spectrometry.
J. Biol. Chem.
PUBLISHED: 10-06-2011
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Cyclotides are heat-stable macrocyclic peptides from plants that display a wide range of biological activities. They can be divided into two subfamilies: Möbius or bracelet, based on the presence or absence of a cis-proline residue in loop 5, respectively. Currently, over 150 cyclotides have been discovered, but only four linear variants of the Möbius subfamily have been hitherto isolated. In this study, we report the discovery of two novel cyclotides, hedyotide B1 and hedyotide B2, from the aerial parts of Hedyotis biflora. Hedyotide B1 has a cyclic cystine knot structure typical of cyclotides. Interestingly, hedyotide B2 possesses a linear backbone and is the first linear representative of the bracelet subfamily. Disulfide mapping of hedyotide B2 by a top-down MS/MS approach showed that it shares the same knotted disulfide arrangement as conventional cyclotides. Its unfolding pathway also showed that the penetrating disulfide bond Cys III-VI is the most stable disulfide linkage. Cloning of the gene encoding hedyotide B2 revealed a nonsense mutation that introduces a premature stop codon at the conserved Asn residue position, which is essential for an end-to-end backbone ligation. Biophysical characterization showed that hedyotide B2 was more susceptible to exopeptidase degradation as compared with hedyotide B1. Hedyotide B2 was also inactive against all four tested bacterial strains, whereas hedyotide B1 was bactericidal to Escherichia coli and Streptococcus salivarius at low micromolar concentration. Our results provide a deeper understanding of the structures, functions, and biosynthetic processing of cyclotides and uncyclotides in plants.
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Assemblathon 1: a competitive assessment of de novo short read assembly methods.
Genome Res.
PUBLISHED: 09-16-2011
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Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe the Assemblathon 1 competition, which aimed to comprehensively assess the state of the art in de novo assembly methods when applied to current sequencing technologies. In a collaborative effort, teams were asked to assemble a simulated Illumina HiSeq data set of an unknown, simulated diploid genome. A total of 41 assemblies from 17 different groups were received. Novel haplotype aware assessments of coverage, contiguity, structure, base calling, and copy number were made. We establish that within this benchmark: (1) It is possible to assemble the genome to a high level of coverage and accuracy, and that (2) large differences exist between the assemblies, suggesting room for further improvements in current methods. The simulated benchmark, including the correct answer, the assemblies, and the code that was used to evaluate the assemblies is now public and freely available from http://www.assemblathon.org/.
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Regulation of normal and cystic fibrosis airway epithelial repair processes by TNF-? after injury.
Am. J. Physiol. Lung Cell Mol. Physiol.
PUBLISHED: 09-09-2011
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Chronic infection and inflammation have been associated with progressive airway epithelial damage in patients with cystic fibrosis (CF). However, the effect of inflammatory products on the repair capacity of respiratory epithelia is unclear. Our objective was to study the regulation of repair mechanisms by tumor necrosis factor-? (TNF-?), a major component of inflammation in CF, in a model of mechanical wounding, in two bronchial cell lines, non-CF NuLi and CF CuFi. We observed that TNF-? enhanced the NuLi and CuFi repair rates. Chronic exposure (24-48 h) to TNF-? augmented this stimulation as well as the migration rate during repair. The cellular mechanisms involved in this stimulation were then evaluated. First, we discerned that TNF-? induced metalloproteinase-9 release, epidermal growth factor (EGF) shedding, and subsequent EGF receptor transactivation. Second, TNF-?-induced stimulation of the NuLi and CuFi wound-closure rates was prevented by GM6001 (metalloproteinase inhibitor), EGF antibody (to titrate secreted EGF), and EGF receptor tyrosine kinase inhibitors. Furthermore, we recently reported a relationship between the EGF response and K(+) channel function, both controlling bronchial repair. We now show that TNF-? enhances KvLQT1 and K(ATP) currents, while their inhibition abolishes TNF-?-induced repair stimulation. These results indicate that the effect of TNF-? is mediated, at least in part, through EGF receptor transactivation and K(+) channel stimulation. In contrast, cell proliferation during repair was slowed by TNF-?, suggesting that TNF-? could exert contrasting actions on repair mechanisms of CF airway epithelia. Finally, the stimulatory effect of TNF-? on airway wound repair was confirmed on primary airway epithelial cells, from non-CF and CF patients.
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Anti-inflammatory triterpenoid saponins from the stem bark of Kalopanax pictus.
J. Nat. Prod.
PUBLISHED: 08-26-2011
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Five new compounds, 16,23,29-trihydroxy-3-oxo-olean-12-en-28-oic acid (1), 4,23,29-trihydroxy-3,4-seco-olean-12-en-3-oate-28-oic acid (2), 3?,6?,23-trihydroxyolean-12-en-28-oic acid 28-O-?-D-glucopyranoside (3), 3-O-[2,3-di-O-acetyl-?-L-arabinopyranosyl]hederagenin 28-O-?-L-rhamnopyranosyl-(1?4)-?-D-glucopyranosyl-(1?6)-?-D-glucopyranoside (4), and 3-O-[3,4-di-O-acetyl-?-L-arabinopyranosyl]hederagenin 28-O-?-L-rhamnopyranosyl-(1?4)-?-D-glucopyranosyl-(1?6)-?-D-glucopyranoside (5), as well as 10 known compounds (6-15), were isolated from the stem bark of Kalopanax pictus. Compounds 1-5 and 7-14 inhibited TNF?-induced NF-?B transcriptional activity in HepG2 cells in a dose-dependent manner, with IC50 values ranging from 0.6 to 16.4 ?M. Furthermore, the transcriptional inhibitory function of these compounds was confirmed on the basis of decreases in COX-2 and iNOS gene expression in HepG2 cells. The structure-activity relationship of the compounds with respect to anti-inflammatory activity is also discussed.
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Embryological methods in ascidians: the Villefranche-sur-Mer protocols.
Methods Mol. Biol.
PUBLISHED: 08-02-2011
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Ascidians (marine invertebrates: urochordates) are thought to be the closest sister groups of vertebrates. They are particularly attractive models because of their non-duplicated genome and the fast and synchronous development of large populations of eggs into simple tadpoles made of about 3,000 cells. As a result of stereotyped asymmetric cleavage patterns all blastomeres become fate restricted between the 16- and 110 cell stage through inheritance of maternal determinants and/or cellular interactions. These advantageous features have allowed advances in our understanding of the nature and role of maternal determinants, inductive interactions, and gene networks that are involved in cell lineage specification and differentiation of embryonic tissues. Ascidians have also contributed to our understanding of fertilization, cell cycle control, self-recognition, metamorphosis, and regeneration. In this chapter we provide basic protocols routinely used at the marine station in Villefranche-sur-Mer using the cosmopolitan species of reference Ciona intestinalis and the European species Phallusia mammillata. These two models present complementary advantages with regard to molecular, functional, and imaging approaches. We describe techniques for basic culture of embryos, micro-injection, in vivo labelling, micro-manipulations, fixation, and immuno-labelling. These methods allow analysis of calcium signals, reorganizations of cytoplasmic and cortical domains, meiotic and mitotic cell cycle and cleavages as well as the roles of specific genes and cellular interactions. Ascidians eggs and embryos are also an ideal material to isolate cortical fragments and to isolate and re-associate individual blastomeres. We detail the experimental manipulations which we have used to understand the structure and role of the egg cortex and of specific blastomeres during development.
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Effect of triterpenes and triterpene saponins from the stem bark of Kalopanax pictus on the transactivational activities of three PPAR subtypes.
Carbohydr. Res.
PUBLISHED: 06-16-2011
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Kalopanax pictus (Araliaceae) is a deciduous tree that grows in East Asian countries. Its stem bark and leaves have been used in traditional medicine to treat rheumatic arthritis, neurotic pain, and diabetes mellitus. A phytochemical study on a methanol extract of the stem bark of K. pictus resulted in the isolation of three new compounds, 6?,16?-dihydroxy-hederagenin 3-O-?-D-glucuronopyranoside (1), 3-O-?-D-glucuronopyranosyl-28-O-?-D-glucopyranosyl-6?,16?-dihydroxy-oleanolic acid (2), and 3-O-?-D-galactopyranosyl(1?3)-?-L-arabinopyranosyl hederagenin 28-O-?-D-glucopyranosyl-(1?6)-?-D-glucopyranosyl ester (3), along with eight known compounds (4-11). Their structures were established on the basis of chemical and spectroscopic methods (IR, 1D and 2D NMR, and HRESITOFMS). Compounds 1-6 and 8-10 upregulated PPARs transcriptional activity in a dose-dependent manner in HepG2 cells, with EC(50) values in the range 0.20-15.5 ?M. Moreover, the specific PPAR transactivational effects of compounds 1-6 and 8-10 on separate PPAR subtypes, PPAR?, -?, and -?(?) were further investigated. Compounds 4, 5, 8, and 10 showed significant PPAR? transactivational activity, with EC(50) values of 7.8, 8.0, 10.3, and 17.3 ?M, respectively. Compounds 2, 4, 6, and 8-10 exhibited PPAR? dose-dependent transactivational activity, with EC(50) values of 14.7, 15.5, 14.8, 10.9, 17.1, and 16.3 ?M, whereas compounds 8 and 10 significantly upregulated PPAR?(?) transcriptional activity, with EC(50) values of 15.7 and 17.7 ?M, respectively.
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Cactus: Algorithms for genome multiple sequence alignment.
Genome Res.
PUBLISHED: 06-10-2011
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Much attention has been given to the problem of creating reliable multiple sequence alignments in a model incorporating substitutions, insertions, and deletions. Far less attention has been paid to the problem of optimizing alignments in the presence of more general rearrangement and copy number variation. Using Cactus graphs, recently introduced for representing sequence alignments, we describe two complementary algorithms for creating genomic alignments. We have implemented these algorithms in the new "Cactus" alignment program. We test Cactus using the Evolver genome evolution simulator, a comprehensive new tool for simulation, and show using these and existing simulations that Cactus significantly outperforms all of its peers. Finally, we make an empirical assessment of Cactuss ability to properly align genes and find interesting cases of intra-gene duplication within the primates.
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An evaluation of the RNase H inhibitory effects of Vietnamese medicinal plant extracts and natural compounds.
Pharm Biol
PUBLISHED: 05-20-2011
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Acquired immune deficiency syndrome (AIDS) is a severe pandemic disease especially prevalent in poor and developing countries. Thus, developing specific, potent antiviral drugs that restrain infection by human immunodeficiency virus type 1 (HIV-1), a major cause of AIDS, remains an urgent priority.
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Discovery and characterization of novel cyclotides originated from chimeric precursors consisting of albumin-1 chain a and cyclotide domains in the Fabaceae family.
J. Biol. Chem.
PUBLISHED: 05-19-2011
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The tropical plant Clitoria ternatea is a member of the Fabaceae family well known for its medicinal values. Heat extraction of C. ternatea revealed that the bioactive fractions contained heat-stable cysteine-rich peptides (CRPs). The CRP family of A1b (Albumin-1 chain b/leginsulins), which is a linear cystine knot CRP, has been shown to present abundantly in the Fabaceae. In contrast, the cyclotide family, which also belongs to the cystine knot CRPs but with a cyclic structure, is commonly found in the Rubiaceae, Violaceae, and Cucurbitaceae families. In this study, we report the discovery of a panel of 15 heat-stable CRPs, of which 12 sequences (cliotide T1-T12) are novel. We show unambiguously that the cliotides are cyclotides and not A1bs, as determined by their sequence homology, disulfide connectivity, and membrane active properties indicated by their antimicrobial activities against Escherichia coli and cytotoxicities to HeLa cells. We also show that cliotides are prevalent in C. ternatea and are found in every plant tissue examined, including flowers, seeds, and nodules. In addition, we demonstrate that their precursors are chimeras, half from cyclotide and the other half from Albumin-1, with the cyclotide domain displacing the A1b domain in the precursor. Their chimeric structures likely originate from either horizontal gene transfer or convergent evolution in plant nuclear genomes, which are exceedingly rare events. Such atypical genetic arrangement also implies a different mechanism of biosynthetic processing of cyclotides in the Fabaceae and provides new understanding of their evolution in plants.
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Predictors of fatigue severity in early systemic sclerosis: a prospective longitudinal study of the GENISOS cohort.
PLoS ONE
PUBLISHED: 04-13-2011
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Longitudinal studies examining the baseline predictors of fatigue in SSc have not been reported. Our objectives were to examine the course of fatigue severity over time and to identify baseline clinical, demographic, and psychosocial predictors of sequentially obtained fatigue scores in early SSc. We also examined baseline predictors of change in fatigue severity over time.
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Bi-polarized translation of ascidian maternal mRNA determinant pem-1 associated with regulators of the translation machinery on cortical Endoplasmic Reticulum (cER).
Dev. Biol.
PUBLISHED: 04-05-2011
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Polarized cortical mRNA determinants such as maternal macho-1 and pem-1 in ascidians, like budding yeast mating factor ASH1 reside on the cER-mRNA domain a subdomain of cortical Endoplasmic Reticulum(ER) and are translated in its vicinity. Using high resolution imaging and isolated cortical fragments prepared from eggs and embryos we now find that macho-1 and pem-1 RNAs co-localize with phospho-protein regulators of translation initiation (MnK/4EBP/S6K). Translation of cortical pem-1 RNA follows its bi-polarized relocalization. About 10 min after fertilization or artificial activation with a calcium ionophore, PEM1 protein is detected in the vegetal cortex in the vicinity of pem-1 RNA. About 40 min after fertilization-when pem-1 RNA and P-MnK move to the posterior pole-PEM1 protein remains in place forming a network of cortical patches anchored at the level of the zygote plasma membrane before disappearing. Cortical PEM1 protein is detected again at the 4 cell stage in the posterior centrosome attracting body (CAB) region where the cER-mRNA domain harboring pem-1/P-MnK/P-4EBP/P-S6K is concentrated. Bi-polarized PEM1 protein signals are not detected when pem-1 morpholinos are injected into eggs or zygotes or when MnK is inhibited. We propose that localized translation of the pem-1 RNA determinant is triggered by the fertilization/calcium wave and that the process is controlled by phospho-protein regulators of translation initiation co-localized with the RNA determinant on a sub-domain of the cortical Endoplasmic Reticulum.
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Amniotic membrane transplantation for Moorens ulcer.
Clin. Experiment. Ophthalmol.
PUBLISHED: 03-16-2011
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To describe the outcome of surgery using amniotic membrane transplantation for Moorens ulcer.
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A new iridoid and effect on the rat aortic vascular smooth muscle cell proliferation of isolated compounds from Buddleja officinalis.
Bioorg. Med. Chem. Lett.
PUBLISHED: 03-04-2011
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A new iridoid, named methylscutelloside (1) together with 19 known compounds belonging to the iridoids (2-4), monoterpenoids (5), flavonoids (6-8), triterpenoids (9-14), and phenylethanoids (15-20) were isolated from the flowers of Buddleja officinalis. Their chemical structures were elucidated on the basis of physicochemical properties, and by spectroscopic methods including 1D, 2D NMR, and MS. All isolated compounds were tested in vitro for their effects on the proliferation of rat aortic vascular smooth muscle cells (VSMCs). Among them, iridoids were the main active components and showed significant inhibitory effects on PDGF-BB-induced proliferation in rat aortic VSMCs.
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Prevalence of cervical human papillomavirus infection among married women in Hanoi, Vietnam, 2010.
Asia Pac J Public Health
PUBLISHED: 02-28-2011
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Human papillomavirus (HPV) is a necessary cause of cervical cancer. This study examined the prevalence of cervical HPV infection and the distribution of HPV specific types among married women in Hanoi to provide updated data for planning cancer preventive activities. Sample of 750 married women aged 15 to 69 years were interviewed and had gynecological examination. HPV infection status and HPV genotyping tests were done for all participants.
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Cytotoxic and PPARs transcriptional activities of sterols from the Vietnamese soft coral Lobophytum laevigatum.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-26-2011
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A new unusual sterol, named lobophytosterol (1), and five known metabolites (2-6) were isolated from the methanol extract of the soft coral Lobophytum laevigatum. Their chemical structures were elucidated by extensive spectroscopic analysis and comparison with those reported in the literature. The absolute stereochemistry of 1 was determined using a modified Moshers method. Compounds 1-3 showed cytotoxic activity against HCT-116 cells with IC(50) values of 3.2, 6.9 and 18.1 ?M, respectively. Compound 1 additionally displayed cytotoxic effects on A549 and HL-60 cells with IC(50) values of 4.5 and 5.6 ?M, respectively. Treatment of these cells with compound 1 resulted in an induction of apoptosis evident by chromatin condensation in treated cells. Besides, compounds 2, 4, and 6 significantly upregulated PPARs transcriptional activity dose-dependently in Hep-G2 cells. Taken together, these data suggest that compound 1 might inhibit the growth of the cancer cells by the induction of apoptosis, and compounds 2, 4, and 6 might act as specific agonists for PPAR?, PPAR?, and PPAR? and may therefore regulate cellular glucose, lipid, and cholesterol metabolism.
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Cytotoxic and anti-inflammatory cembranoids from the Vietnamese soft coral Lobophytum laevigatum.
Bioorg. Med. Chem.
PUBLISHED: 01-14-2011
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Four new cembranoids, namely laevigatol A-D (1-4), and six known metabolites (5-10), were isolated from the Vietnamese soft coral Lobophytum laevigatum. The structures of these compounds were elucidated by extensive spectroscopic analyses, and the absolute stereochemistry of 1 was determined using the modified Moshers method. Compounds 5, and 7-10 exhibited cytotoxic activity against selected human cancer cell lines. Compounds 1, 2, 8, and 9 showed dose-dependent inhibitory effects on the TNF?-induced NF-?B transcriptional activity in Hep-G2 cells. Moreover, compounds 1, 2, 8, and 9 significantly inhibited the induction of COX-2 and iNOS mRNA dose-dependently, indicating that these compounds attenuated the synthesis of these transcripts at the transcriptional level.
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A head in virtual reality: development of a dynamic head and neck model.
Anat Sci Educ
PUBLISHED: 11-06-2009
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Advances in computer and interface technologies have made it possible to create three-dimensional (3D) computerized models of anatomical structures for visualization, manipulation, and interaction in a virtual 3D environment. In the past few decades, a multitude of digital models have been developed to facilitate complex spatial learning of the human body. However, there is limited empirical evidence to guide the development and integration of effective computer models for teaching and learning. The purpose of this article is to describe the development of a dynamic head and neck model with flexible displays (2D, 3D, and stereoscopic 3D) and interactive control features that can be later used to design and test the efficacy of computer models as a means of improving student learning. The model was created using computer tomography scans of a human cadaver. Anatomical structures captured on the scans were segmented into discreet areas, and then reconstructed in three-dimensions using specialized software. The final model consists of 70 distinct anatomical structures that can be displayed in 2D, 3D, or stereoscopic 3D. In 3D mode, a mouse can be used to actively and continuously interact with the model by manipulating viewer orientation, altering surface transparency, superimposing 2D scans with 3D reconstructions, removing or adding structures sequentially, and customizing animated scenes to show complex anatomical pathways or relationships.
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[K+ channels and lung epithelial physiology].
Med Sci (Paris)
PUBLISHED: 05-05-2009
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Transcripts of more than 30 different K(+) channels have been detected in the respiratory epithelium lining airways and alveoli. These channels belong to the 3 main classes of K(+) channels, i.e. i) voltage-dependent or calcium-activated, 6 transmembrane segments (TM), ii) 2-pores 4-TM and iii) inward-rectified 2-TM channels. The physiological and functional significance of this high molecular diversity of lung epithelial K(+) channels is not well understood. Surprisingly, relatively few studies are focused on K(+) channel function in lung epithelial physiology. Nevertheless, several studies have shown that KvLQT1, KCa and K(ATP) K(+) channels play a crucial role in ion and fluid transport, contributing to the control of airway and alveolar surface liquid composition and volume. K(+) channels are involved in other key functions, such as O(2) sensing or the capacity of the respiratory epithelia to repair after injury. This mini-review aims to discuss potential functions of lung K(+) channels.
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Molecular diversity and function of K+ channels in airway and alveolar epithelial cells.
Am. J. Physiol. Lung Cell Mol. Physiol.
PUBLISHED: 03-11-2009
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Multiple K(+) channels are expressed in the respiratory epithelium lining airways and alveoli. Of the three main classes [1) voltage-dependent or Ca(2+)-activated, 6-transmembrane domains (TMD), 2) 2-pores 4-TMD, and 3) inward-rectified 2-TMD K(+) channels], almost 40 different transcripts have already been detected in the lung. The physiological and functional significance of this high molecular diversity of lung epithelial K(+) channels is intriguing. As detailed in the present review, K(+) channels are located at both the apical and basolateral membranes in the respiratory epithelium, where they mediate K(+) currents of diverse electrophysiological and regulatory properties. The main recognized function of K(+) channels is to control membrane potential and to maintain the driving force for transepithelial ion and liquid transport. In this manner, KvLQT1, KCa and K(ATP) channels, for example, contribute to the control of airway and alveolar surface liquid composition and volume. Thus, K(+) channel activation has been identified as a potential therapeutic strategy for the resolution of pathologies characterized by ion transport dysfunction. K(+) channels are also involved in other key functions in lung physiology, such as oxygen-sensing, inflammatory responses and respiratory epithelia repair after injury. The purpose of this review is to summarize and discuss what is presently known about the molecular identity of lung K(+) channels with emphasis on their role in lung epithelial physiology.
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[Dispersal of Staphylococcus aureus from nasal carriers].
Ugeskr. Laeg.
PUBLISHED: 02-12-2009
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Staphylococcus aureus (Sa) is an important cause of hospital-acquired infections, and nasal carriage of Sa is common among health care workers. This study was designed to measure the airborne dispersal of Sa and other bacteria from such carriers and to investigate whether the use of cap, gown, gloves, and mask could reduce this dispersal.
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Cytokines correlate with age in healthy volunteers, dialysis patients and kidney-transplant patients.
Cytokine
PUBLISHED: 01-14-2009
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T-cell functions are currently used as biomarkers for the pharmacodynamic monitoring of immunosuppressive drugs or as disease biomarkers of inflammation/sepsis and organ rejection. In order to evaluate co-factors potentially influencing the expression of the immunological biomarkers, we explored T-cell proliferation, T-cell activation (CD25 and CD71 expressions) and intra-lymphocyte cytokine production (interleukin (IL)-2 and tumor necrosis factor (TNF)-alpha) in healthy volunteers, dialysis patients and stable kidney-transplant patients treated with standard immunosuppressive therapy, i.e. tacrolimus, mycophenolic acid with or without steroids. Age was positively correlated with TNF-alpha expression in all three patient populations, and with IL-2 expression in healthy volunteers and kidney-transplant patients. Further age was correlated with inhibition of lymphocyte proliferation in healthy volunteers and with the T-cell activation marker CD25 in kidney-transplant patients. In healthy volunteers lymphocyte proliferation was higher in woman as compared to men. Other biomarkers of T-cell function were independent of the gender. In the kidney-transplant patient group a significantly lower expression of all biomarkers of T-cell functions compared to healthy volunteers and dialysis patients. In dialysis patients we found significant increased IL-2 expression compared to healthy volunteers, while the other T-cell functions were not significantly different. Further time on dialysis had no effect on the level of biomarker expression. In conclusion we found decreased T-cell functions in kidney-transplant patients compared to healthy volunteers and dialysis patients, increased IL-2 expression in dialysis patients compared to healthy volunteers and in all three populations we found a correlation of age and intra-T-lymphocyte TNF-alpha expression.
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Does sleep really influence face recognition memory?
PLoS ONE
PUBLISHED: 01-10-2009
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Mounting evidence implicates sleep in the consolidation of various kinds of memories. We investigated the effect of sleep on memory for face identity, a declarative form of memory that is indispensable for nearly all social interaction. In the acquisition phase, observers viewed faces that they were required to remember over a variable retention period (0-36 hours). In the test phase, observers viewed intermixed old and new faces and judged seeing each before. Participants were classified according to acquisition and test times into seven groups. Memory strength (d) and response bias (c) were evaluated. Substantial time spent awake (12 hours or more) during the retention period impaired face recognition memory evaluated at test, whereas sleep per se during the retention period did little to enhance the memory. Wakefulness during retention also led to a tightening of the decision criterion. Our findings suggest that sleep passively and transiently shelters face recognition memory from waking interference (exposure) but does not actively aid in its long-term consolidation.
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Inhibition of the KCa3.1 channels by AMP-activated protein kinase in human airway epithelial cells.
Am. J. Physiol., Cell Physiol.
PUBLISHED: 01-07-2009
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The vectorial transport of ions and water across epithelial cells depends to a large extent on the coordination of the apical and basolateral ion fluxes with energy supply. In this work we provide the first evidence for a regulation by the 5-AMP-activated protein kinase (AMPK) of the calcium-activated potassium channel KCa3.1 expressed at the basolateral membrane of a large variety of epithelial cells. Inside-out patch-clamp experiments performed on human embryonic kidney (HEK) cells stably transfected with KCa3.1 first revealed a decrease in KCa3.1 activity following the internal addition of AMP at a fixed ATP concentration. This effect was dose dependent with half inhibition at 140 muM AMP in 1 mM ATP. Evidence for an interaction between the COOH-terminal region of KCa3.1 and the gamma1-subunit of AMPK was next obtained by two-hybrid screening and pull-down experiments. Our two-hybrid analysis confirmed in addition that the amino acids extending from Asp(380) to Ala(400) in COOH-terminal were essential for the interaction AMPK-gamma1/KCa3.1. Inside-out experiments on cells coexpressing KCa3.1 with the dominant negative AMPK-gamma1-R299G mutant showed a reduced sensitivity of KCa3.1 to AMP, arguing for a functional link between KCa3.1 and the gamma1-subunit of AMPK. More importantly, coimmunoprecipitation experiments carried out on bronchial epithelial NuLi cells provided direct evidence for the formation of a KCa3.1/AMPK-gamma1 complex at endogenous AMPK and KCa3.1 expression levels. Finally, treating NuLi monolayers with the membrane permeant AMPK activator 5-aminoimidazole-4-carboxamide-1-beta-d-ribofuranoside (AICAR) caused a significant decrease of the KCa3.1-mediated short-circuit currents, an effect reversible by coincubation with the AMPK inhibitor Compound C. These observations argue for a regulation of KCa3.1 by AMPK in a functional epithelium through protein/protein interactions involving the gamma1-subunit of AMPK.
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Inhibition of TNF-?-mediated NF-?B Transcriptional Activity in HepG2 Cells by Dammarane-type Saponins from Panax ginseng Leaves.
J Ginseng Res
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Panax ginseng (PG) is a globally utilized medicinal herb. The medicinal effects of PG are primarily attributable to ginsenosides located in the root and leaf. The leaves of PG are known to be rich in various bioactive ginsenosides, and the therapeutic effects of ginseng extract and ginsenosides have been associated with immunomodulatory and anti-inflammatory activities. We examined the effect of PG leaf extract and the isolated ginsenosides, on nuclear factor (NF)-?B transcriptional activity and target gene expression by applying a luciferase assay and reverse transcription polymerase chain reaction in tumor necrosis factor (TNF)-?-treated hepatocarcinoma HepG2 cells. Air-dried PG leaf extract inhibited TNF-?-induced NF-?B transcription activity and NF-?B-dependent cyclooxygenase (COX)-2 and inducible nitric oxide synthase (iNOS) gene expression more efficiently than the steamed extract. Of the 10 ginsenosides isolated from PG leaves, Rd and Km most significantly inhibited activity in a dose-dependent manner, with IC50 values of 12.05±0.82 and 8.84±0.99 ?M, respectively. Furthermore, the ginsenosides Rd and Km inhibited the TNF-?-induced expression levels of the COX-2 and iNOS gene in HepG2 cells. Air-dried leaf extracts and their chemical components, ginsenoside Rd and Km, are involved in the suppression of TNF-?-induced NF-?B activation and NF-?B-dependent iNOS and COX-2 gene expression. Consequently, air-dried leaf extract from PG, and the purified ginsenosides, have therapeutic potential as anti-inflammatory.
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Plantagiolides I and J, two new withanolide glucosides from Tacca plantaginea with nuclear factor-kappaB inhibitory and peroxisome proliferator-activated receptor transactivational activities.
Chem. Pharm. Bull.
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A novel withanolide glucoside, plantagiolide I (1), a new withanolide glucoside, plantagiolide J (2), and six known compounds (3-8) were isolated from the whole plant of Tacca plantaginea. Their structures were determined by spectroscopic and chemical methods. Compound 3 significantly inhibited tumor necrosis factor alpha (TNF?)-induced nuclear factor-kappaB (NF-?B) transcriptional activity in HepG2 cells in a dose-dependent manner, with IC(50) values of 9.0?µM. Compounds 1-8 enhanced the transcriptional activity of peroxisome proliferator-activated receptors (PPARs) in a dose-dependent manner, with EC(50) values ranging from 1.6 to 49.7?µM. In addition, the transactivational effects of compounds 1-8 on three individual PPAR subtypes, including PPAR?, ?(?), and ? were evaluated. Compounds 1-8 significantly activated the transcriptional activity of PPAR?(?), with EC(50) values in a ranging from 4.1 to 29.6?µM. These results provide scientific support for the use of T. plantaginea and its components for the prevention and treatment of inflammatory and metabolic diseases.
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Improving protein coreference resolution by simple semantic classification.
BMC Bioinformatics
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Current research has shown that major difficulties in event extraction for the biomedical domain are traceable to coreference. Therefore, coreference resolution is believed to be useful for improving event extraction. To address coreference resolution in molecular biology literature, the Protein Coreference (COREF) task was arranged in the BioNLP Shared Task (BioNLP-ST, hereafter) 2011, as a supporting task. However, the shared task results indicated that transferring coreference resolution methods developed for other domains to the biological domain was not a straight-forward task, due to the domain differences in the coreference phenomena.
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Structural basis for the influence of a single mutation K145N on the oligomerization and photoswitching rate of Dronpa.
Acta Crystallogr. D Biol. Crystallogr.
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The crystal structure of the on-state of PDM1-4, a single-mutation variant of the photochromic fluorescent protein Dronpa, is reported at 1.95 Å resolution. PDM1-4 is a Dronpa variant that possesses a slower off-switching rate than Dronpa and thus can effectively increase the image resolution in subdiffraction optical microscopy, although the precise molecular basis for this change has not been elucidated. This work shows that the Lys145Asn mutation in PDM1-4 stabilizes the interface available for dimerization, facilitating oligomerization of the protein. No significant changes were observed in the chromophore environment of PDM1-4 compared with Dronpa, and the ensemble absorption and emission properties of PDM1-4 were highly similar to those of Dronpa. It is proposed that the slower off-switching rate in PDM1-4 is caused by a decrease in the potential flexibility of certain ?-strands caused by oligomerization along the AC interface.
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Tyrosinase Inhibitors from the Wood of Artocarpus heterophyllus.
J. Nat. Prod.
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From the methanolic-soluble extract of the wood of Artocarpus heterophyllus, four new flavones, artocarmins A-D (1-4), and three new chalcones, artocarmitins A-C (5-7), have been isolated together with 13 known compounds. Their structures were determined on the basis of the spectroscopic data. Compounds 1-4, 6, 7, 9-16, and 20 displayed significant tyrosinase inhibitory activity. The most active compound, morachalcone A (12) (IC50, 0.013 ?M), was 3000 times more active as a tyrosinase inhibitor than a positive control, kojic acid (IC50, 44.6 ?M).
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Anti-Inflammatory and PPAR transactivational properties of flavonoids from the roots of Sophora flavescens.
Phytother Res
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Anti-inflammatory and peroxisome proliferator-activated receptors (PPARs) transactivational effects of nine compounds (1?-?9) from the roots of Sophora flavescens were evaluated using NF-?B-luciferase, reverse transcriptase polymerase chain reaction, peroxisome proliferator response element (PPRE)-luciferase, and GAL-4-PPAR chimera assays. Compounds 4 and 8 significantly inhibited TNF?-induced NF-?B transcriptional activity in HepG2 cells in a dose-dependent manner, with IC?? values of 4.0 and 4.4??M, respectively. Furthermore, the transcriptional inhibitory function of these compounds was confirmed by a decrease in cyclooxgenase 2 and inducible nitric oxide synthase gene expression levels in HepG2 cells. Compounds 1, 3, 5, 6, 8, and 9 significantly activated the transcription of PPARs in a dose-dependent manner, with EC?? values ranging from 1.1 to 13.0??M. Compounds 1, 3, 5, 6, 8, and 9 exhibited dose-dependent PPAR? transactivational activity, with EC?? values in a range of 0.9?-?16.0??M. Compounds 1, 3, 8, and 9 also significantly upregulated PPAR? activity in a dose-dependent manner, with EC?? values of 10.5, 6.6, 15.7, and 1.6??M, whereas compounds 1, 8, and 9 demonstrated transactivational PPAR?(?) effects with EC?? values of 11.4, 10.3, and 1.5??M, respectively. These results provide a scientific rationale for the use of the roots of S. flavescens and warrant further studies to develop new agents for the prevention and treatment of inflammatory and metabolic diseases.
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Diarylheptanoid glycosides from Tacca plantaginea and their effects on NF-?B activation and PPAR transcriptional activity.
Bioorg. Med. Chem. Lett.
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In the screening search for NF-?B inhibitory and PPAR transactivational agents from medicinal plants, a methanol extract of the whole plant of Tacca plantaginea and its aqueous fraction showed the significant activities. Bioassay-guided fractionation combined with repeated chromatographic separation of the aqueous fraction of the methanol extract of T. plantaginea resulted in the isolation of two new diarylheptanoid glycosides, plantagineosides A (1) and B (2), an unusual new cyclic diarylheptanoid glycoside, plantagineoside C (3), and three known compounds (4-6). Their structures were determined by extensive spectroscopic and chemical methods. Compounds 3-6 significantly inhibited TNF?-induced NF-?B transcriptional activity in HepG2 cells in a dose-dependent manner, with IC(50) values ranging from 0.9 to 9.4 ?M. Compounds 1-6 significantly activated the transcriptional activity of PPARs in a dose-dependent manner, with EC(50) values ranging from 0.30 to 10.4 ?M. In addition, the transactivational effects of compounds 1-6 were evaluated on three individual PPAR subtypes, including PPAR?, ?, and ?(?). Compounds 1-6 significantly enhanced the transcriptional activity of PPAR?(?), with EC(50) values in a range of 11.0-30.1 ?M. These data provide the rationale for using T. plantaginea and its components for the prevention and treatment of inflammatory and metabolic diseases.
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Computed tomography (CT) bone segmentation of an ancient Egyptian mummy: a comparison of automated and semiautomated threshold and dual-energy techniques.
J Comput Assist Tomogr
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Dual-energy computed tomography (CT) enables 3-dimensional,noninvasive, and nondestructive imaging with material separation. Dual-energy CT is generally used to segment hydrated tissues within the clinical context. We apply dual-energy CT to an ancient Egyptian mummy and present several techniques designed to separate bone from desiccated tissue and resin. Automated and semiautomated dual-energy CT techniques are compared to manual segmentation and thresholding-based techniques. Semiautomated techniques enable substantial reductions in operator time compared to manual segmentation.
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Tyrosine phosphorylation of DEP-1/CD148 as a mechanism controlling Src kinase activation, endothelial cell permeability, invasion, and capillary formation.
Blood
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DEP-1/CD148 is a receptor-like protein tyrosine phosphatase with antiproliferative and tumor-suppressive functions. Interestingly, it also positively regulates Src family kinases in hematopoietic and endothelial cells, where we showed it promotes VE-cadherin-associated Src activation and endothelial cell survival upon VEGF stimulation. However, the molecular mechanism involved and its biologic functions in endothelial cells remain ill-defined. We demonstrate here that DEP-1 is phosphorylated in a Src- and Fyn-dependent manner on Y1311 and Y1320, which bind the Src SH2 domain. This allows DEP-1-catalyzed dephosphorylation of Src inhibitory Y529 and favors the VEGF-induced phosphorylation of Src substrates VE-cadherin and Cortactin. Accordingly, RNA interference (RNAi)-mediated knockdown of DEP-1 or expression of DEP-1 Y1311F/Y1320F impairs Src-dependent biologic responses mediated by VEGF including permeability, invasion, and branching capillary formation. In addition, our work further reveals that above a threshold expression level, DEP-1 can also dephosphorylate Src Y418 and attenuate downstream signaling and biologic responses, consistent with the quiescent behavior of confluent endothelial cells that express the highest levels of endogenous DEP-1. Collectively, our findings identify the VEGF-dependent phosphorylation of DEP-1 as a novel mechanism controlling Src activation, and show this is essential for the proper regulation of permeability and the promotion of the angiogenic response.
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The Genia Event and Protein Coreference tasks of the BioNLP Shared Task 2011.
BMC Bioinformatics
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The Genia task, when it was introduced in 2009, was the first community-wide effort to address a fine-grained, structural information extraction from biomedical literature. Arranged for the second time as one of the main tasks of BioNLP Shared Task 2011, it aimed to measure the progress of the community since 2009, and to evaluate generalization of the technology to full text papers. The Protein Coreference task was arranged as one of the supporting tasks, motivated from one of the lessons of the 2009 task that the abundance of coreference structures in natural language text hinders further improvement with the Genia task.
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Improvement of defective cystic fibrosis airway epithelial wound repair after CFTR rescue.
Eur. Respir. J.
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Airway damage and remodelling are important components of lung pathology progression in cystic fibrosis (CF). Although repair mechanisms are engaged to restore the epithelial integrity, these processes are obviously insufficient to maintain lung function in CF airways. Our aims were therefore to study how the basic cystic fibrosis transmembrane conductance regulator (CFTR) defect could impact epithelial wound healing and to determine if CFTR correction could improve it. Wound-healing experiments, as well as cell migration and proliferation assays, were performed to study the early phases of epithelial repair in human CF and non-CF airway cells. CFTR function was evaluated using CFTR small interferring (si)RNA and inhibitor GlyH101 in non-CF cells, and conversely after CFTR rescue with the CFTR corrector VRT-325 in CF cells. Wound-healing experiments first showed that airway cells from CF patients repaired slower than non-CF cells. CFTR inhibition or silencing in non-CF primary airway cells significantly inhibited wound closure. GlyH101 also decreased cell migration and proliferation. Interestingly, wild-type CFTR transduction in CF airway cell lines or CFTR correction with VRT-325 in CFBE-?F508 and primary CF bronchial monolayers significantly improved wound healing. Altogether our results demonstrated that functional CFTR plays a critical role in wound repair, and CFTR correction may represent a novel strategy to promote the airway repair processes in CF.
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Drimane-type sesquiterpenes with a dioxabicyclooctane skeleton from the fruiting bodies of Nigrofomes melanoporus and their cytotoxicity.
Planta Med.
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Two new drimane-type compounds, nigrofomins A ( 1) and B ( 2), possessing a rare dioxabicyclooctane moiety, were purified from the fruiting bodies of Nigrofomes melanoporus. Their structures were determined using 1D-, 2D-NMR and HR-ESI-MS spectroscopic analyses. In addition, 1 was established by X-ray crystallographic studies. Both nigrofomins A ( 1) and B ( 2) exhibited cytotoxicity on acute T-cell leukemia (Jurkat), human nasopharyngeal carcinoma (NPC-TW01), and lung cancer (NCI-H661) cells with IC (50) values in the range of 99.44-246.32 µM. Furthermore, the effects of 1 and 2 on cell-cycle progression of Jurkat cells displayed a concentration-dependent accumulation in the G (0)/G (1) phase.
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Anti-inflammatory and PPAR transactivational effects of secondary metabolites from the roots of Asarum sieboldii.
Bioorg. Med. Chem. Lett.
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Phytochemical study on the roots of Asarum sieboldii resulted in the isolation of one new compound, (1R,2S,5R,6R)-5-O-methylpluviatilol (1) and 12 known compounds (2-13). Their structures were determined by extensive spectroscopic methods, including 1D and 2D NMR, and MS spectra. The absolute configuration of compound 1 was established using CD spectrum. Compounds 4, 5, and 12/13 significantly inhibited TNF?-induced NF-?B transcriptional activity in HepG2 cells in a dose-dependent manner, with IC(50) values ranging from 6.4 to 9.4 ?M. Furthermore, the transcriptional inhibitory function of these compounds was confirmed based on decreases in COX-2 and iNOS gene expression in HepG2 cells. Compounds 1-3, 6,7, 10, and 11 significantly activated the transcriptional activity of PPARs in a dose-dependent manner, with EC(50) values ranging from 1.7 to 20.9 ?M. Compounds 7, 10, and 11 exhibited significant dose-dependent PPAR? transactivational activity, with EC(50) values of 19.5, 15.7, and 4.0 ?M, respectively. Compounds 1, 6, 7, 10, and 11 activated PPAR? transcriptional activity, with EC(50) values ranging from 3.6 to 22.6 ?M, whereas compounds 10 and 11 significantly increased PPAR?(?) transactivational activity, with EC(50) values of 22.6 and 4.9 ?M, respectively. These results provide a scientific support for the use of the roots of A. sieboldii and warrant further studies to develop new agents for the prevention and treatment of the inflammatory and metabolic diseases.
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Anti-inflammatory and PPAR transactivational effects of components from the stem bark of Ginkgo biloba.
J. Agric. Food Chem.
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Ginkgo biloba, which is considered a "living fossil", has been used for medicinal purposes for thousands of years. Currently, extracts of G. biloba are some of the most widely used herbal products and/or dietary supplements in the world. In this study, three new compounds, (2E,4E,1R,3S,5R,8S)-dihydrophaseic acid 3-O-?-D-glucopyranoside (1), 7,8-dihydro-(R)-7-methoxyconiferyl alcohol (2), and (8S)-3-methoxy-8,4-oxyneolignan-4,9,9-triol 3-O-?-D-glucopyranoside (3), and 13 known compounds (4-16) were isolated from the stem bark of G. biloba. Their structures were determined by extensive spectroscopic methods, including 1D and 2D NMR, MS, and circular dichroism spectra. Four of the compounds (1, 2, 7, and 10) inhibited TNF?-induced NF-?B transcriptional activity significantly in HepG2 cells in a dose-dependent manner, with IC?? values ranging from 6.9 to 9.1 ?M. Furthermore, the transcriptional inhibitory function of these compounds was confirmed based on decreases in COX-2 and iNOS gene expression in HepG2 cells. Compounds 1-5, 7, 9, 10, and 12-14 significantly activated the transcriptional activity of PPARs in a dose-dependent manner, with EC?? values ranging from 0.7 to 12.8 ?M. Compounds 2, 3, and 12 exhibited dose-dependent PPAR? transactivational activity, with EC?? values of 7.0, 3.3, and 10.1 ?M, respectively. Compounds 1-3 activated PPAR? transcriptional activity, with EC?? values of 11.9, 11.0, and 15.3 ?M, whereas compounds 1 and 3 promoted the transactivational activity of PPAR?(?) with EC?? values of 10.7 and 11.2 ?M, respectively. These results provide a scientific support for the use of G. biloba stem bark for the prevention and treatment of inflammatory and metabolic diseases. Moreover, these data provide the rationale for further studies of the potential of G. biloba stem bark in functional foods.
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Inhibition of nuclear transcription factor-?B and activation of peroxisome proliferator-activated receptors in HepG2 cells by cucurbitane-type triterpene glycosides from Momordica charantia.
J Med Food
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Momordica charantia is used to treat various diseases, including inflammatory conditions. Previous reports indicated that the extract of this plant inhibits activation of nuclear transcription factor-?B (NF-?B) but activates peroxisome proliferator-activated receptor (PPAR). Additionally, cucurbitane-type triterpene glycosides are the main bioactive components of the fruit of M. charantia. Therefore, we investigated the anti-inflammatory activity of 17 cucurbitane-type triterpene glycosides (1-17) isolated from this plant. Their inhibition of NF-?B and activation of PPAR activities in HepG2 cells were measured using luciferase reporter and PPAR subtype transactivation assays. Compounds 6 and 8 were found to inhibit NF-?B activation stimulated by tumor necrosis factor-? (TNF?) in a dose-dependent manner. With 50% inhibition concentration (IC(50)) values of 0.4??M, compounds 6 and 8 were more potent inhibitors than the positive control, sulfasalazine (IC(50)=0.9??M). Compounds 4, 6, and 8 also inhibited TNF?-induced expressions of inducible nitric oxide synthase and cyclooxygenase-2 mRNA. However, only compound 13 significantly increased PPAR? transactivation.
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Computer visualizations: factors that influence spatial anatomy comprehension.
Anat Sci Educ
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Computer visualizations are increasingly common in education across a range of subject disciplines, including anatomy. Despite optimism about their educational potential, students sometime have difficulty learning from these visualizations. The purpose of this study was to explore a range of factors that influence spatial anatomy comprehension before and after instruction with different computer visualizations. Three major factors were considered: (1) visualization ability (VZ) of learners, (2) dynamism of the visual display, and (3) interactivity of the system. Participants (N = 60) of differing VZs (high, low) studied a group of anatomical structures in one of three visual conditions (control, static, dynamic) and one of two interactive conditions (interactive, non-interactive). Before and after the study phase, participants comprehension of spatial anatomical information was assessed using a multiple-choice spatial anatomy task (SAT) involving the mental rotation of the anatomical structures, identification of the structures in 2D cross-sections, and localization of planes corresponding to given cross-sections. Results indicate that VZ had a positive influence on SAT performance but instruction with different computer visualizations could modulate the effect of VZ on task performance.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.