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Int. J. Mol. Sci., Volume 12, Issue 4 (April 2011), Pages 2088-2768

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Open AccessArticle Antimicrobial, Cytotoxic and Antioxidant Activities and Determination of the Total Tannin Content of Bark Extracts Endopleura uchi
Int. J. Mol. Sci. 2011, 12(4), 2757-2768; https://doi.org/10.3390/ijms12042757
Received: 4 January 2011 / Revised: 8 February 2011 / Accepted: 10 February 2011 / Published: 21 April 2011
Cited by 11 | PDF Full-text (206 KB) | HTML Full-text | XML Full-text
Abstract
Endopleura uchi is a typical Amazonian tree and its bark is popularly employed in the preparation of teas against myomas, arthritis, influenza, diarrhea and cancer. In this study, the antioxidant activity, cytotoxicity and antimicrobial activity of five different extracts of the bark, selected
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Endopleura uchi is a typical Amazonian tree and its bark is popularly employed in the preparation of teas against myomas, arthritis, influenza, diarrhea and cancer. In this study, the antioxidant activity, cytotoxicity and antimicrobial activity of five different extracts of the bark, selected by their total tannin content, were assessed. The potential antioxidant activity of the extracts was determined by 2.2-diphenyl-1-picrylhydrazyl radical scavenging assay and the values found were very similar among the extracts and to the standards antioxidants used in the tests. Cytotoxicity analysis in mammalian cells indicated that all the tested extracts exhibited IC50 values higher than the highest concentration used, showing that they do not present a risk when consumed under these conditions. Extract tested against five bacterial strains and one yeast strain did not show satisfactory growth inhibitory activity, and even the extracts that showed some antimicrobial activity were not effective at any dilution to determine the minimum inhibitory concentration. The results may serve as a reference for subsequent works, since such reference values described in the literature for the bark of E. uchi. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle Antimicrobial Activities of Hexane Extract and Decussatin from Stembark Extract of Ficus congensis
Int. J. Mol. Sci. 2011, 12(4), 2750-2756; https://doi.org/10.3390/ijms12042750
Received: 9 February 2011 / Revised: 28 March 2011 / Accepted: 12 April 2011 / Published: 21 April 2011
Cited by 3 | PDF Full-text (168 KB) | HTML Full-text | XML Full-text
Abstract
Ficus congensis (Moraceae) is used traditionally in the treatment of various diseases including infectious diseases, infertility, and gastrointestinal disorders. Investigation of hexane extract of the stem bark using chromatographic techniques led to isolation of a xanthone, 1-hydroxy-3,7,8-trimethoxyxanthone (Decussatin). The compound was elucidated based
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Ficus congensis (Moraceae) is used traditionally in the treatment of various diseases including infectious diseases, infertility, and gastrointestinal disorders. Investigation of hexane extract of the stem bark using chromatographic techniques led to isolation of a xanthone, 1-hydroxy-3,7,8-trimethoxyxanthone (Decussatin). The compound was elucidated based on spectroscopic methods such as nuclear magnetic resonance (NMR), UV, IR, and mass spectrometry (MS). Decussatin and the hexane extract were screened in vitro for antibacterial and antifungal activities using broth microdilution (MHB) and disc Agar diffusion (DAD) techniques against Escheichia coli, Bacilus substilis, Klebsiela pneumonia, Staphylococcus aureus, Aspergillus fumigatus, Trichophyton mentagrophytes, Trichophyton rubrum and Candida albicans. Hexane extracts showed potent antibacterial activity against E. coli and B. subtilis with minimum inhibitory concentrations (MIC) of 8 mg/mL and 5 mg/mL, respectively, while Decussatin of the highest concentration (8 mg/mL) used in this study showed no appreciable antimicrobial activity. Only hexane extract was active against C. albicans with a MIC of 1 mg/mL. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessReview Database Survey of Anti-Inflammatory Plants in South America: A Review
Int. J. Mol. Sci. 2011, 12(4), 2692-2749; https://doi.org/10.3390/ijms12042692
Received: 1 April 2011 / Revised: 8 April 2011 / Accepted: 11 April 2011 / Published: 21 April 2011
Cited by 23 | PDF Full-text (832 KB) | HTML Full-text | XML Full-text
Abstract
Inflammation is a complex event linked to tissue damage whether by bacteria, physical trauma, chemical, heat or any other phenomenon. This physiological response is coordinated largely by a variety of chemical mediators that are released from the epithelium, the immunocytes and nerves of
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Inflammation is a complex event linked to tissue damage whether by bacteria, physical trauma, chemical, heat or any other phenomenon. This physiological response is coordinated largely by a variety of chemical mediators that are released from the epithelium, the immunocytes and nerves of the lamina propria. However, if the factor that triggers the inflammation persists, the inflammation can become relentless, leading to an intensification of the lesion. The present work is a literature survey of plant extracts from the South American continent that have been reported to show anti-inflammatory activity. This review refers to 63 bacterial families of which the following stood out: Asteraceae, Fabaceae, Euphorbiaceae, Apocynaceae and Celastraceae, with their countries, parts used, types of extract used, model bioassays, organisms tested and their activity. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle Preparation and Physicochemical Properties of 10-Hydroxycamptothecin (HCPT) Nanoparticles by Supercritical Antisolvent (SAS) Process
Int. J. Mol. Sci. 2011, 12(4), 2678-2691; https://doi.org/10.3390/ijms12042678
Received: 14 March 2011 / Revised: 13 April 2011 / Accepted: 18 April 2011 / Published: 20 April 2011
Cited by 13 | PDF Full-text (759 KB) | HTML Full-text | XML Full-text
Abstract
The goal of the present work was to study the feasibility of 10-hydroxycamptothecin (HCPT) nanoparticle preparation using supercritical antisolvent (SAS) precipitation. The influences of various experimental factors on the mean particle size (MPS) of HCPT nanoparticles were investigated. The optimum micronization conditions are
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The goal of the present work was to study the feasibility of 10-hydroxycamptothecin (HCPT) nanoparticle preparation using supercritical antisolvent (SAS) precipitation. The influences of various experimental factors on the mean particle size (MPS) of HCPT nanoparticles were investigated. The optimum micronization conditions are determined as follows: HCPT solution concentration 0.5 mg/mL, the flow rate ratio of CO2 and HCPT solution 19.55, precipitation temperature 35 °C and precipitation pressure 20 MPa. Under the optimum conditions, HCPT nanoparticles with a MPS of 180 ± 20.3 nm were obtained. Moreover, the HCPT nanoparticles obtained were characterized by Scanning electron microscopy, Dynamic light scattering, Fourier-transform infrared spectroscopy, High performance liquid chromatography-mass spectrometry, X-ray diffraction and Differential scanning calorimetry analyses. The physicochemical characterization results showed that the SAS process had not induced degradation of HCPT. Finally, the dissolution rates of HCPT nanoparticles were investigated and the results proved that there is a significant increase in dissolution rate compared to unprocessed HCPT. Full article
(This article belongs to the Section Materials Science)
Open AccessArticle Genetic Variation in Safflower (Carthamus tinctorious L.) for Seed Quality-Related Traits and Inter-Simple Sequence Repeat (ISSR) Markers
Int. J. Mol. Sci. 2011, 12(4), 2664-2677; https://doi.org/10.3390/ijms12042664
Received: 3 March 2011 / Revised: 6 April 2011 / Accepted: 6 April 2011 / Published: 19 April 2011
Cited by 30 | PDF Full-text (338 KB) | HTML Full-text | XML Full-text
Abstract
Safflower (Carthamus tinctorious L.) is an oilseed crop that is valued as a source of high quality vegetable oil. The genetic diversity of 16 safflower genotypes originated from different geographical regions of Iran and some with exotic origin were evaluated. Eight
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Safflower (Carthamus tinctorious L.) is an oilseed crop that is valued as a source of high quality vegetable oil. The genetic diversity of 16 safflower genotypes originated from different geographical regions of Iran and some with exotic origin were evaluated. Eight different seed quality-related traits including fatty acid composition of seed oil (stearic acid, palmitic acid, oleic acid and linoleic acid), the contents of, oil, protein, fiber and ash in its seeds, as well as 20 inter-simple sequence repeat (ISSR) polymorphic primers were used in this study. Analysis of variance showed significant variation in genotypes for the seed quality-related traits. Based on ISSR markers, a total of 204 bands were amplified and 149 bands (about 70%) of these were polymorphic. Cluster analysis based on either biochemical or molecular markers classified the genotypes into four groups, showing some similarities between molecular and biochemical markers for evaluated genotypes. A logical similarity between the genotype clusters based on molecular data with their geographical origins was observed. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle In Vivo Anti-Tumor Activity of Polypeptide HM-3 Modified by Different Polyethylene Glycols (PEG)
Int. J. Mol. Sci. 2011, 12(4), 2650-2663; https://doi.org/10.3390/ijms12042650
Received: 12 February 2011 / Revised: 8 March 2011 / Accepted: 1 April 2011 / Published: 19 April 2011
Cited by 13 | PDF Full-text (346 KB) | HTML Full-text | XML Full-text
Abstract
HM-3, designed by our laboratory, is a polypeptide composed of 18 amino acids. Pharmacodynamic studies in vivo and in vitro indicated that HM-3 could inhibit endothelial cell migration and angiogenesis, thereby inhibiting tumor growth. However, the half-life of HM-3 is short. In this
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HM-3, designed by our laboratory, is a polypeptide composed of 18 amino acids. Pharmacodynamic studies in vivo and in vitro indicated that HM-3 could inhibit endothelial cell migration and angiogenesis, thereby inhibiting tumor growth. However, the half-life of HM-3 is short. In this study, we modified HM-3 with different polyethylene glycols (PEG) in order to reduce the plasma clearance rate, extend the half-life in the body, maintain a high concentration of HM-3 in the blood and increase the therapeutic efficiency. HM-3 was modified with four different types of PEG with different molecular weights (ALD-mPEG5k, ALD-mPEG10k, SC-mPEG10k and SC-mPEG20k), resulting in four modified products (ALD-mPEG5k-HM-3, ALD-mPEG10k-HM-3, SC-mPEG10k-HM-3 and SC-mPEG20k-HM-3, respectively). Anti-tumor activity of these four modified HM-3 was determined in BALB/c mice with Taxol as a positive control and normal saline as a negative control. Tumor weight inhibition rates of mice treated with Taxol, HM-3, ALD-mPEG5k-HM-3, ALD-mPEG10k-HM-3, SC-mPEG10k-HM-3 and SC-mPEG20k-HM-3 were 44.50%, 43.92%, 37.95%, 31.64%, 20.27% and 50.23%, respectively. Tumor inhibition rates in the Taxol, HM-3 and SC-mPEG20k-HM-3 groups were significantly higher than that in the negative control group. The efficiency of tumor inhibition in the SC-mPEG20k-HM-3 group (drug treatment frequency: once per two days) was better than that in the HM-3 group (drug treatment frequency: twice per day). In addition, tumor inhibition rate in the SC-mPEG20k-HM-3 group was higher than that in the taxol group. We conclude that SC-mPEG20k-HM-3 had a low plasma clearance rate and long half-life, resulting in high anti-tumor therapeutic efficacy in vivo. Therefore, SC-mPEG20k-HM-3 could be potentially developed as new anti-tumor drugs. Full article
(This article belongs to the Special Issue Conjugated Polymers)
Open AccessArticle Infrared Assisted Production of 3,4-Dihydro-2(1H)-pyridones in Solvent-Free Conditions
Int. J. Mol. Sci. 2011, 12(4), 2641-2649; https://doi.org/10.3390/ijms12042641
Received: 10 February 2011 / Revised: 14 March 2011 / Accepted: 30 March 2011 / Published: 18 April 2011
Cited by 17 | PDF Full-text (170 KB) | HTML Full-text | XML Full-text
Abstract
A green approach for the synthesis of a set of ten 4-aryl substituted-5-alcoxy carbonyl-6-methyl-3,4-dihydro-2(1H)-pyridones using Meldrum’s acid has been devised, the absence of solvent and the activation with infrared irradiation in addition to a multicomponent protocol are the main reaction conditions.
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A green approach for the synthesis of a set of ten 4-aryl substituted-5-alcoxy carbonyl-6-methyl-3,4-dihydro-2(1H)-pyridones using Meldrum’s acid has been devised, the absence of solvent and the activation with infrared irradiation in addition to a multicomponent protocol are the main reaction conditions. The transformations proceeded with moderated yields (50–75%) with a reasonable reaction rate (3 h). It is worth noting that two novel molecules of the new class of the bis-3,4-dihydropyridones were also obtained. In addition, a comparison without the use of infrared irradiation was performed. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessArticle Assessment of Acetylcholinesterase Activity Using Indoxylacetate and Comparison with the Standard Ellman’s Method
Int. J. Mol. Sci. 2011, 12(4), 2631-2640; https://doi.org/10.3390/ijms12042631
Received: 20 February 2011 / Revised: 1 March 2011 / Accepted: 29 March 2011 / Published: 18 April 2011
Cited by 27 | PDF Full-text (218 KB) | HTML Full-text | XML Full-text
Abstract
Assay of acetylcholinesterase (AChE) activity plays an important role in diagnostic, detection of pesticides and nerve agents, in vitro characterization of toxins and drugs including potential treatments for Alzheimer’s disease. These experiments were done in order to determine whether indoxylacetate could be an
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Assay of acetylcholinesterase (AChE) activity plays an important role in diagnostic, detection of pesticides and nerve agents, in vitro characterization of toxins and drugs including potential treatments for Alzheimer’s disease. These experiments were done in order to determine whether indoxylacetate could be an adequate chromogenic reactant for AChE assay evaluation. Moreover, the results were compared to the standard Ellman’s method. We calculated Michaelis constant Km (2.06 × 10−4 mol/L for acetylthiocholine and 3.21 × 10−3 mol/L for indoxylacetate) maximum reaction velocity Vmax (4.97 × 10−7 kat for acetylcholine and 7.71 × 10−8 kat for indoxylacetate) for electric eel AChE. In a second part, inhibition values were plotted for paraoxon, and reactivation efficacy was measured for some standard oxime reactivators: obidoxime, pralidoxime (2-PAM) and HI-6. Though indoxylacetate is split with lower turnover rate, this compound appears as a very attractive reactant since it does not show any chemical reactivity with oxime antidots and thiol used for the Ellman’s method. Thus it can be advantageously used for accurate measurement of AChE activity. Suitability of assay for butyrylcholinesterase activity assessment is also discussed. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle Antioxidant Effects of the Ethanol Extract from Flower of Camellia japonica via Scavenging of Reactive Oxygen Species and Induction of Antioxidant Enzymes
Int. J. Mol. Sci. 2011, 12(4), 2618-2630; https://doi.org/10.3390/ijms12042618
Received: 24 March 2011 / Revised: 11 April 2011 / Accepted: 12 April 2011 / Published: 18 April 2011
Cited by 15 | PDF Full-text (588 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to investigate the antioxidant properties of the ethanol extract of the flower of Camellia japonica (Camellia extract). Camellia extract exhibited 1,1-diphenyl-2-picrylhydrazyl radical and intracellular reactive oxygen species (ROS) scavenging activity in human HaCaT keratinocytes. In addition,
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The aim of this study was to investigate the antioxidant properties of the ethanol extract of the flower of Camellia japonica (Camellia extract). Camellia extract exhibited 1,1-diphenyl-2-picrylhydrazyl radical and intracellular reactive oxygen species (ROS) scavenging activity in human HaCaT keratinocytes. In addition, Camellia extract scavenged superoxide anion generated by xanthine/xanthine oxidase and hydroxyl radical generated by the Fenton reaction (FeSO4 + H2O2) in a cell-free system, which was detected by electron spin resonance spectrometry. Furthermore, Camellia extract increased the protein expressions and activity of cellular antioxidant enzymes, such as superoxide dismutase, catalase and glutathione peroxidase. These results suggest that Camellia extract exhibits antioxidant properties by scavenging ROS and enhancing antioxidant enzymes. Camellia extract contained quercetin, quercetin-3-O-glucoside, quercitrin and kaempferol, which are antioxidant compounds. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle Effect of Temperature on the Physico-Chemical Properties of a Room Temperature Ionic Liquid (1-Methyl-3-pentylimidazolium Hexafluorophosphate) with Polyethylene Glycol Oligomer
Int. J. Mol. Sci. 2011, 12(4), 2598-2617; https://doi.org/10.3390/ijms12042598
Received: 30 March 2011 / Revised: 7 April 2011 / Accepted: 7 April 2011 / Published: 18 April 2011
Cited by 24 | PDF Full-text (916 KB) | HTML Full-text | XML Full-text
Abstract
A systematic study of the effect of composition on the thermo-physical properties of the binary mixtures of 1-methyl-3-pentyl imidazolium hexafluorophosphate [MPI][PF6] with poly(ethylene glycol) (PEG) [Mw = 400] is presented. The excess molar volume, refractive index deviation, viscosity deviation, and
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A systematic study of the effect of composition on the thermo-physical properties of the binary mixtures of 1-methyl-3-pentyl imidazolium hexafluorophosphate [MPI][PF6] with poly(ethylene glycol) (PEG) [Mw = 400] is presented. The excess molar volume, refractive index deviation, viscosity deviation, and surface tension deviation values were calculated from these experimental density, ρ, refractive index, n, viscosity, η, and surface tension, γ, over the whole concentration range, respectively. The excess molar volumes are negative and continue to become increasingly negative with increasing temperature; whereas the viscosity and surface tension deviation are negative and become less negative with increasing temperature. The surface thermodynamic functions, such as surface entropy, enthalpy, as well as standard molar entropy, Parachor, and molar enthalpy of vaporization for pure ionic liquid, have been derived from the temperature dependence of the surface tension values. Full article
(This article belongs to the Section Materials Science)
Open AccessReview Droplets Formation and Merging in Two-Phase Flow Microfluidics
Int. J. Mol. Sci. 2011, 12(4), 2572-2597; https://doi.org/10.3390/ijms12042572
Received: 17 February 2011 / Revised: 11 March 2011 / Accepted: 2 April 2011 / Published: 15 April 2011
Cited by 97 | PDF Full-text (839 KB) | HTML Full-text | XML Full-text
Abstract
Two-phase flow microfluidics is emerging as a popular technology for a wide range of applications involving high throughput such as encapsulation, chemical synthesis and biochemical assays. Within this platform, the formation and merging of droplets inside an immiscible carrier fluid are two key
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Two-phase flow microfluidics is emerging as a popular technology for a wide range of applications involving high throughput such as encapsulation, chemical synthesis and biochemical assays. Within this platform, the formation and merging of droplets inside an immiscible carrier fluid are two key procedures: (i) the emulsification step should lead to a very well controlled drop size (distribution); and (ii) the use of droplet as micro-reactors requires a reliable merging. A novel trend within this field is the use of additional active means of control besides the commonly used hydrodynamic manipulation. Electric fields are especially suitable for this, due to quantitative control over the amplitude and time dependence of the signals, and the flexibility in designing micro-electrode geometries. With this, the formation and merging of droplets can be achieved on-demand and with high precision. In this review on two-phase flow microfluidics, particular emphasis is given on these aspects. Also recent innovations in microfabrication technologies used for this purpose will be discussed. Full article
(This article belongs to the Special Issue Microfluidics)
Open AccessArticle Simultaneous Structural Identification of Natural Products in Fractions of Crude Extract of the Rare Endangered Plant Anoectochilus roxburghii Using 1H NMR/RRLC-MS Parallel Dynamic Spectroscopy
Int. J. Mol. Sci. 2011, 12(4), 2556-2571; https://doi.org/10.3390/ijms12042556
Received: 18 March 2011 / Revised: 11 April 2011 / Accepted: 12 April 2011 / Published: 15 April 2011
Cited by 7 | PDF Full-text (631 KB) | HTML Full-text | XML Full-text
Abstract
Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to 1H NMR and rapid resolution liquid chromatography-mass
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Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to 1H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in 1H NMR/RRLC–MS PDS spectrum, 1H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. 1H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessArticle An Oligodeoxynucleotide with Promising Modulation Activity for the Proliferation and Activation of Osteoblast
Int. J. Mol. Sci. 2011, 12(4), 2543-2555; https://doi.org/10.3390/ijms12042543
Received: 11 March 2011 / Revised: 6 April 2011 / Accepted: 7 April 2011 / Published: 15 April 2011
Cited by 7 | PDF Full-text (412 KB) | HTML Full-text | XML Full-text
Abstract
The paper explored the regulatory role of oligodeoxynucleotides (ODNs) with specific sequences in the proliferation and activation of osteoblast, using human osteoblast-like cell line MG 63 as the model. Through the administration of ODNs to MG 63 cells at a concentration of 1.0
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The paper explored the regulatory role of oligodeoxynucleotides (ODNs) with specific sequences in the proliferation and activation of osteoblast, using human osteoblast-like cell line MG 63 as the model. Through the administration of ODNs to MG 63 cells at a concentration of 1.0 µg/mL, ODN MT01 with positive effects on proliferation and activation of osteoblast was selected from 11 different ODNs by methyl thiazolyl tetrazolium (MTT) assay and alkaline phosphatase (ALP) activity measurement. To get a deeper insight into the molecular mechanism, effects of ODN MT01 treatment on the expression level of Sp7, runx-2, collagen-I, osteoprotegerin (OPG) and RANK ligand (RANKL) were determined using quantitative real time PCR and Western blotting. Remarkably, the mRNA and protein expression levels of Sp7, runx-2, collagen-I and OPG were improved after ODN MT01 treatment. Meanwhile, the protein expression level of RANKL was dramatically decreased. These results suggested that ODN MT01 had a significant impact in facilitating osteogenic proliferation and activation, and provided a direct evidence for the notion that single strand ODN could regulate the balance of bone formation and resorption, and thus was of great potential in the rebuilding of alveolar bone. Full article
(This article belongs to the Section Biochemistry, Molecular and Cellular Biology)
Open AccessReview Functioning Nanomachines Seen in Real-Time in Living Bacteria Using Single-Molecule and Super-Resolution Fluorescence Imaging
Int. J. Mol. Sci. 2011, 12(4), 2518-2542; https://doi.org/10.3390/ijms12042518
Received: 28 February 2011 / Revised: 7 April 2011 / Accepted: 11 April 2011 / Published: 15 April 2011
Cited by 22 | PDF Full-text (634 KB) | HTML Full-text | XML Full-text
Abstract
Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the
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Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry. Full article
(This article belongs to the Special Issue Molecular Machines and Nanomachines)
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Open AccessArticle Global Transcriptomic Profiling Using Small Volumes of Whole Blood: A Cost-Effective Method for Translational Genomic Biomarker Identification in Small Animals
Int. J. Mol. Sci. 2011, 12(4), 2502-2517; https://doi.org/10.3390/ijms12042502
Received: 2 March 2011 / Revised: 28 March 2011 / Accepted: 1 April 2011 / Published: 13 April 2011
Cited by 6 | PDF Full-text (291 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin
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Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total RNA samples were further processed using the NuGEN Ovation Whole Blood Solution system and cDNA was hybridized to Affymetrix Rat Genome 230 2.0 Arrays. The microarray QC parameters using RNA isolated with the QSI method were within the acceptable range for microarray analysis. The transcriptomic profiles were highly correlated with those using RNA isolated with the PAXgene method and were consistent with expected LPS-induced inflammatory responses. The present study demonstrated that the QSI method coupled with NuGEN Ovation Whole Blood Solution system is cost-effective and particularly suitable for transcriptomic profiling of minimal volumes of whole blood, typical of those obtained with small animal species. Full article
(This article belongs to the Special Issue Toxicogenomics)
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