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Int. J. Mol. Sci., Volume 13, Issue 12 (December 2012), Pages 15496-17295

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Open AccessArticle Microtubule Formation and Activities of Antioxidative Enzymes in PC12 Cells Exposed to Phosphatidylcholine Hydroperoxides
Int. J. Mol. Sci. 2012, 13(12), 15510-15522; doi:10.3390/ijms131215510
Received: 9 November 2012 / Revised: 19 November 2012 / Accepted: 20 November 2012 / Published: 22 November 2012
Cited by 1 | PDF Full-text (279 KB) | HTML Full-text | XML Full-text
Abstract
Aging increases free radical generation and lipid oxidation and, thereby, mediates neurodegenerative diseases. As the brain is rich in lipids (polyunsaturated fatty acids), the antioxidative system plays an important role in protecting brain tissues from oxidative injury. The changes in microtubule formation and
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Aging increases free radical generation and lipid oxidation and, thereby, mediates neurodegenerative diseases. As the brain is rich in lipids (polyunsaturated fatty acids), the antioxidative system plays an important role in protecting brain tissues from oxidative injury. The changes in microtubule formation and antioxidative enzyme activities have been investigated in rat pheochromocytoma PC12 cells exposed to various concentrations of phosphatidylcholine hydroperoxides (PCOOH). We measured three typical antioxidative enzymes, superoxide dismutase (SOD), glutathione peroxidase (GPx), and catalase (CAT). The microtubule assembly system was dependent on the antioxidative enzyme system in cells exposed to oxidative stress. The activities of the three enzymes increased in a PCOOH exposure-dependent manner. In particular, the changes in the activity as a result of PCOOH exposure were similar in the three antioxidative enzymes. This is the first report indicating the compatibility between the tubulin-microtubule and antioxidative enzyme systems in cells that deteriorate as a result of phospholipid hydroperoxide administration from an exterior source. The descending order of sensitivity of the three enzymes to PCOOH is also discussed. Full article
(This article belongs to the Special Issue Oxidative Stress and Ageing)
Open AccessArticle Ginsenoside Rh2 Induces Human Hepatoma Cell Apoptosisvia Bax/Bak Triggered Cytochrome C Release and Caspase-9/Caspase-8 Activation
Int. J. Mol. Sci. 2012, 13(12), 15523-15535; doi:10.3390/ijms131215523
Received: 4 September 2012 / Revised: 13 November 2012 / Accepted: 15 November 2012 / Published: 22 November 2012
Cited by 17 | PDF Full-text (2013 KB) | HTML Full-text | XML Full-text
Abstract
Ginsenoside Rh2 (G-Rh2) has been shown to induce apoptotic cell death in a variety of cancer cells. However, the details of the signal transduction cascade involved in G-Rh2-induced cell death is unclear. In this manuscript we elucidate the molecular mechanism of G-Rh2-induced apoptosis
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Ginsenoside Rh2 (G-Rh2) has been shown to induce apoptotic cell death in a variety of cancer cells. However, the details of the signal transduction cascade involved in G-Rh2-induced cell death is unclear. In this manuscript we elucidate the molecular mechanism of G-Rh2-induced apoptosis in human hepatoma SK-HEP-1 cells by demonstrating that G-Rh2 causes rapid and dramatic translocation of both Bak and Bax, which subsequently triggers mitochondrial cytochrome c release and consequent caspase activation. Interestingly, siRNA-based gene inactivation of caspase-8 effectively delays caspase-9 activation and apoptosis induced by G-Rh2, indicating that caspase-8 also plays an important role in the G-Rh2-induced apoptosis program. Taken together, our results indicate that G-Rh2 employs a multi pro-apoptotic pathway to execute cancer cell death, suggesting a potential role for G-Rh2 as a powerful chemotherapeutic agent. Full article
(This article belongs to the Special Issue Signalling Molecules and Signal Transduction in Cells)
Open AccessArticle Cancer Cell Response to Anthracyclines Effects: Mysteries of the Hidden Proteins Associated with These Drugs
Int. J. Mol. Sci. 2012, 13(12), 15536-15564; doi:10.3390/ijms131215536
Received: 31 August 2012 / Revised: 26 October 2012 / Accepted: 7 November 2012 / Published: 22 November 2012
Cited by 2 | PDF Full-text (2962 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A comprehensive proteome map of T-lymphoblastic leukemia cells and its alterations after daunorubicin, doxorubicin and mitoxantrone treatments was monitored and evaluated either by paired comparison with relevant untreated control and using multivariate classification of treated and untreated samples. With the main focus on
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A comprehensive proteome map of T-lymphoblastic leukemia cells and its alterations after daunorubicin, doxorubicin and mitoxantrone treatments was monitored and evaluated either by paired comparison with relevant untreated control and using multivariate classification of treated and untreated samples. With the main focus on early time intervals when the influence of apoptosis is minimized, we found significantly different levels of proteins, which corresponded to 1%–2% of the total amount of protein spots detected. According to Gene Ontology classification of biological processes, the highest representation of identified proteins for all three drugs belong to metabolic processes of proteins and nucleic acids and cellular processes, mainly cytoskeleton organisation and ubiquitin-proteasome pathway. Importantly, we observed significant proportion of changes in proteins involved in the generation of precursor metabolites and energy typical for daunorubicin, transport proteins participating in response to doxorubicin and a group of proteins of immune system characterising response to mitoxantrone. Both a paired comparison and the multivariate evaluation of quantitative data revealed daunorubicin as a distinct member of the group of anthracycline/anthracenedione drugs. A combination of identified drug specific protein changes, which may help to explain anti-cancer activity, together with the benefit of blocking activation of adaptive cancer pathways, presents important approaches to improving treatment outcomes in cancer. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle An Inverse Relationship Links Temperature and Substrate Apparent Affinity in the Ion-Coupled Cotransporters rGAT1 and KAAT1
Int. J. Mol. Sci. 2012, 13(12), 15565-15574; doi:10.3390/ijms131215565
Received: 19 October 2012 / Revised: 14 November 2012 / Accepted: 15 November 2012 / Published: 22 November 2012
Cited by 1 | PDF Full-text (607 KB) | HTML Full-text | XML Full-text
Abstract
The effects of temperature on the operation of two ion-coupled cotransporters of the SLC6A family, namely rat GAT1 (SLC6A1) and KAAT1 (SLC6A19) from Manduca sexta, have been studied by electrophysiological means in Xenopus laevis oocytes expressing these proteins. The maximal transport-associated current
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The effects of temperature on the operation of two ion-coupled cotransporters of the SLC6A family, namely rat GAT1 (SLC6A1) and KAAT1 (SLC6A19) from Manduca sexta, have been studied by electrophysiological means in Xenopus laevis oocytes expressing these proteins. The maximal transport-associated current (Imax) and the apparent substrate affinity (K05) were measured. In addition to the expected increase in transport rate (Q10 = 3–6), both transporters showed greater K05 values (i.e., a decrease in apparent affinity) at higher temperatures. The transport efficiency, estimated as Imax/K05, increased at negative potentials in both transporters, but did not show statistically significant differences with temperature. The observation that the apparent substrate affinity is inversely related to the transport rate suggests a kinetic regulation of this parameter. Furthermore, the present results indicate that the affinities estimated at room temperature for mammalian cotransporters may not be simply extrapolated to their physiological operating conditions. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genomic DNA Methylation Changes in NYGGF4-Overexpression 3T3-L1 Adipocytes
Int. J. Mol. Sci. 2012, 13(12), 15575-15587; doi:10.3390/ijms131215575
Received: 19 September 2012 / Revised: 6 November 2012 / Accepted: 16 November 2012 / Published: 22 November 2012
Cited by 1 | PDF Full-text (1358 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
NYGGF4, an obesity-related gene, is proposed to be involved in the development of insulin resistance; however, the underlying molecular mechanisms remain unclear. In the present analysis, NimbleGen tiling arrays were used to determine the patterns of genomic DNA methylation at CpG islands
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NYGGF4, an obesity-related gene, is proposed to be involved in the development of insulin resistance; however, the underlying molecular mechanisms remain unclear. In the present analysis, NimbleGen tiling arrays were used to determine the patterns of genomic DNA methylation at CpG islands and promoters in NYGGF4-overexpression adipocytes. A total of 2352 CpG dinucleotides in 2018 genes and 3490 CpG dinucleotides in 3064 genes were found to be hypermethylated or hypomethylated, respectively, in NYGGF4-overexpression adipocytes. Furthermore, gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes(KEGG) pathway analysis revealed enrichment of biological processes associated with energy metabolism and signal transduction events, including the peroxisome proliferator-activated receptor gamma (PPARγ) signaling pathway, and mitogen-activated protein kinases(MAPK) and Ras homolog gene family, member A (RhoA) signaling. These data demonstrate that differentially methylated genes are significantly overrepresented in NYGGF4-overexpression adipocytes, providing valuable clues for further exploration of the role of NYGGF4 in insulin sensitivity regulation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Fabrication of an Electrically-Resistive, Varistor-Polymer Composite
Int. J. Mol. Sci. 2012, 13(12), 15640-15652; doi:10.3390/ijms131215640
Received: 2 September 2012 / Revised: 5 November 2012 / Accepted: 7 November 2012 / Published: 23 November 2012
Cited by 2 | PDF Full-text (538 KB) | HTML Full-text | XML Full-text
Abstract
This study focuses on the fabrication and electrical characterization of a polymer composite based on nano-sized varistor powder. The polymer composite was fabricated by the melt-blending method. The developed nano-composite was characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), field emission scanning
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This study focuses on the fabrication and electrical characterization of a polymer composite based on nano-sized varistor powder. The polymer composite was fabricated by the melt-blending method. The developed nano-composite was characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), field emission scanning electron microscopy (FeSEM), and energy-dispersive X-ray spectroscopy (EDAX). The XRD pattern revealed the crystallinity of the composite. The XRD study also showed the presence of secondary phases due to the substitution of zinc by other cations, such as bismuth and manganese. The TEM picture of the sample revealed the distribution of the spherical, nano-sized, filler particles throughout the matrix, which were in the 10–50 nm range with an average of approximately 11 nm. The presence of a bismuth-rich phase and a ZnO matrix phase in the ZnO-based varistor powder was confirmed by FeSEM images and EDX spectra. From the current-voltage curves, the non-linear coefficient of the varistor polymer composite with 70 wt% of nano filler was 3.57, and its electrical resistivity after the onset point was 861 KΩ. The non-linear coefficient was 1.11 in the sample with 100 wt% polymer content. Thus, it was concluded that the composites established a better electrical non-linearity at higher filler amounts due to the nano-metric structure and closer particle linkages. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessArticle The Pharmacological NF-κB Inhibitor BAY11-7082 Induces Cell Apoptosis and Inhibits the Migration of Human Uveal Melanoma Cells
Int. J. Mol. Sci. 2012, 13(12), 15653-15667; doi:10.3390/ijms131215653
Received: 24 August 2012 / Revised: 12 November 2012 / Accepted: 19 November 2012 / Published: 23 November 2012
Cited by 8 | PDF Full-text (2571 KB) | HTML Full-text | XML Full-text
Abstract
Uveal melanomas are highly metastatic and have high rate of recurrence due to the lack of effective systemic therapy. The identification of important survival pathways in uveal melanomas provides novel therapeutic targets for effective treatment. In the present study, we found that the
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Uveal melanomas are highly metastatic and have high rate of recurrence due to the lack of effective systemic therapy. The identification of important survival pathways in uveal melanomas provides novel therapeutic targets for effective treatment. In the present study, we found that the NF-κB signaling pathway was constitutively and highly activated in uveal melanoma cells. Treatment with the pharmacological NF-κB specific inhibitor BAY11-7082 markedly decreased the nuclear translocation of NF-κB. In a dose-dependent setting, BAY11-7082 inhibited the proliferation and growth of uveal melanoma cells by inducing apoptosis without effect on cell cycle. The migration capacity of uveal melanoma cells was also significantly suppressed by BAY11-7082 treatment. Mechanistically, BAY11-7082 increased the activity of caspase 3 and reduced the expression of anti-apoptotic protein Bcl-2, but did not influence the expression of pro-apoptotic protein Bax. Furthermore, BAY11-7082 induced uveal melanoma cell apoptosis and inhibited xenograft tumor growth in vivo. Collectively, the present study identified NF-κB as an important survival signal for uveal melanoma cells and suggested that administration of specific NF-κB inhibitor BAY11-7082 could serve as an effective treatment for patients with uveal melanoma. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Discovery of Novel Focal Adhesion Kinase Inhibitors Using a Hybrid Protocol of Virtual Screening Approach Based on Multicomplex-Based Pharmacophore and Molecular Docking
Int. J. Mol. Sci. 2012, 13(12), 15668-15678; doi:10.3390/ijms131215668
Received: 19 October 2012 / Revised: 9 November 2012 / Accepted: 19 November 2012 / Published: 23 November 2012
Cited by 10 | PDF Full-text (735 KB) | HTML Full-text | XML Full-text
Abstract
Focal adhesion kinase (FAK) is a tyrosine kinase that functions as a key orchestrator of signals leading to invasion and metastasis. In the current study, the multicomplex-based pharmacophore (MCBP)-guided method has been suggested to generate a comprehensive pharmacophore of FAK kinase based on
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Focal adhesion kinase (FAK) is a tyrosine kinase that functions as a key orchestrator of signals leading to invasion and metastasis. In the current study, the multicomplex-based pharmacophore (MCBP)-guided method has been suggested to generate a comprehensive pharmacophore of FAK kinase based on seven crystal structures of FAK-inhibitor complexes. In this investigation, a hybrid protocol of virtual screening methods, comprising of pharmacophore model-based virtual screening (PB-VS) and docking-based virtual screening (DB-VS), is used for retrieving new FAK inhibitors from commercially available chemical databases. This hybrid virtual screening approach was then applied to screen several chemical databases, including the Specs (202,408 compounds) database. Thirty-five compounds were selected from the final hits and should be shifted to experimental studies. These results may provide important information for further research of novel FAK inhibitors. Full article
Open AccessArticle Effects of Nickel, Chlorpyrifos and Their Mixture on the Dictyostelium discoideum Proteome
Int. J. Mol. Sci. 2012, 13(12), 15679-15705; doi:10.3390/ijms131215679
Received: 31 October 2012 / Revised: 13 November 2012 / Accepted: 15 November 2012 / Published: 23 November 2012
Cited by 2 | PDF Full-text (1644 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based
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Mixtures of chemicals can have additive, synergistic or antagonistic interactions. We investigated the effects of the exposure to nickel, the organophosphate insecticide chlorpyrifos at effect concentrations (EC) of 25% and 50% and their binary mixture (Ec25 + EC25) on Dictyostelium discoideum amoebae based on lysosomal membrane stability (LMS). We treated D. discoideum with these compounds under controlled laboratory conditions and evaluated the changes in protein levels using a two-dimensional gel electrophoresis (2DE) proteomic approach. Nickel treatment at EC25 induced changes in 14 protein spots, 12 of which were down-regulated. Treatment with nickel at EC50 resulted in changes in 15 spots, 10 of which were down-regulated. Treatment with chlorpyrifos at EC25 induced changes in six spots, all of which were down-regulated; treatment with chlorpyrifos at EC50 induced changes in 13 spots, five of which were down-regulated. The mixture corresponding to EC25 of each compound induced changes in 19 spots, 13 of which were down-regulated. The data together reveal that a different protein expression signature exists for each treatment, and that only a few proteins are modulated in multiple different treatments. For a simple binary mixture, the proteomic response does not allow for the identification of each toxicant. The protein spots that showed significant differences were identified by mass spectrometry, which revealed modulations of proteins involved in metal detoxification, stress adaptation, the oxidative stress response and other cellular processes. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle Structure Prediction, Molecular Dynamics Simulation and Docking Studies of D-Specific Dehalogenase from Rhizobium sp. RC1
Int. J. Mol. Sci. 2012, 13(12), 15724-15754; doi:10.3390/ijms131215724
Received: 18 August 2012 / Revised: 16 October 2012 / Accepted: 7 November 2012 / Published: 26 November 2012
Cited by 6 | PDF Full-text (2126 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), d,l-2,3-dichloropropionate (d,l-2,3-DCP), and 3-chloropropionate
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Currently, there is no three-dimensional structure of D-specific dehalogenase (DehD) in the protein database. We modeled DehD using ab initio technique, performed molecular dynamics (MD) simulation and docking of D-2-chloropropionate (D-2CP), D-2-bromopropionate (D-2BP), monochloroacetate (MCA), monobromoacetate (MBA), 2,2-dichloropropionate (2,2-DCP), d,l-2,3-dichloropropionate (d,l-2,3-DCP), and 3-chloropropionate (3-CP) into the DehD active site. The sequences of DehD and D-2-haloacid dehalogenase (HadD) from Pseudomonas putida AJ1 have 15% sequence similarity. The model had 80% of the amino acid residues in the most favored region when compared to the crystal structure of DehI from Pseudomonas putida PP3. Docking analysis revealed that Arg107, Arg134 and Tyr135 interacted with D-2CP, and Glu20 activated the water molecule for hydrolytic dehalogenation. Single residue substitutions at 25–30 °C showed that polar residues of DehD were stable when substituted with nonpolar residues and showed a decrease in activity within the same temperature range. The molecular dynamics simulation of DehD and its variants showed that in R134A variant, Arg107 interacted with D-2CP, while in Y135A, Gln221 and Arg231 interacted with D-2CP. It is our emphatic belief that the new model will be useful for the rational design of DehDs with enhanced potentials. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Cholesterol-Dependent Energy Transfer between Fluorescent Proteins—Insights into Protein Proximity of APP and BACE1 in Different Membranes in Niemann-Pick Type C Disease Cells
Int. J. Mol. Sci. 2012, 13(12), 15801-15812; doi:10.3390/ijms131215801
Received: 18 October 2012 / Revised: 14 November 2012 / Accepted: 15 November 2012 / Published: 26 November 2012
Cited by 1 | PDF Full-text (560 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Förster resonance energy transfer (FRET) -based techniques have recently been applied to study the interactions between β-site APP-cleaving enzyme-GFP (BACE1-GFP) and amyloid precursor protein-mRFP (APP-mRFP) in U373 glioblastoma cells. In this context, the role of APP-BACE1 proximity in Alzheimer’s disease (AD) pathogenesis has
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Förster resonance energy transfer (FRET) -based techniques have recently been applied to study the interactions between β-site APP-cleaving enzyme-GFP (BACE1-GFP) and amyloid precursor protein-mRFP (APP-mRFP) in U373 glioblastoma cells. In this context, the role of APP-BACE1 proximity in Alzheimer’s disease (AD) pathogenesis has been discussed. FRET was found to depend on intracellular cholesterol levels and associated alterations in membrane stiffness. Here, NPC1 null cells (CHO-NPC1−/−), exhibiting increased cholesterol levels and disturbed cholesterol transport similar to that observed in Niemann-Pick type C disease (NPC), were used to analyze the influence of altered cholesterol levels on APP-BACE1 proximity. Fluorescence lifetime measurements of whole CHO-wild type (WT) and CHO-NPC1−/− cells (EPI-illumination microscopy), as well as their plasma membranes (total internal reflection fluorescence microscopy, TIRFM), were performed. Additionally, generalized polarization (GP) measurements of CHO-WT and CHO-NPC1−/− cells incubated with the fluorescence marker laurdan were performed to determine membrane stiffness of plasma- and intracellular-membranes. CHO-NPC1−/− cells showed higher membrane stiffness at intracellular- but not plasma-membranes, equivalent to cholesterol accumulation in late endosomes/lysosomes. Along with higher membrane stiffness, the FRET efficiency between BACE1-GFP and APP-mRFP was reduced at intracellular membranes, but not within the plasma membrane of CHO-NPC1−/−. Our data show that FRET combined with TIRF is a powerful technique to determine protein proximity and membrane fluidity in cellular models of neurodegenerative diseases. Full article
(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET))
Open AccessArticle Muscodor albus Volatiles Control Toxigenic Fungi under Controlled Atmosphere (CA) Storage Conditions
Int. J. Mol. Sci. 2012, 13(12), 15848-15858; doi:10.3390/ijms131215848
Received: 6 November 2012 / Revised: 15 November 2012 / Accepted: 21 November 2012 / Published: 27 November 2012
Cited by 4 | PDF Full-text (237 KB) | HTML Full-text | XML Full-text
Abstract
Muscodor albus, a biofumigant fungus, has the potential to control post-harvest pathogens in storage. It has been shown to produce over 20 volatile compounds with fungicidal, bactericidal and insecticidal properties. However, M. albus is a warm climate endophyte, and its biofumigant activity
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Muscodor albus, a biofumigant fungus, has the potential to control post-harvest pathogens in storage. It has been shown to produce over 20 volatile compounds with fungicidal, bactericidal and insecticidal properties. However, M. albus is a warm climate endophyte, and its biofumigant activity is significantly inhibited at temperatures below 5 °C. Conidia of seven mycotoxin producing fungi, Aspergillus carbonarius, A. flavus, A. niger, A. ochraceus, Penicillium verrucosum, Fusarium culmorum and F. graminearum, were killed or prevented from germinating by exposure to volatiles from 2 g M. albus-colonized rye grain per L of headspace in sealed glass jars for 24 h at 20 °C. Two major volatiles of M. albus, isobutyric acid (IBA) and 2-methyl-1-butanol (2MB) at 50 µL/L and 100 µL/L, respectively, gave differential control of the seven fungi when applied individually at 20 °C. When the fungi were exposed to both IBA and 2MB together, an average of 94% of the conidia were killed or suppressed. In a factorial experiment with controlled atmosphere storage (CA) at 3 °C and 72 h exposure to four concentrations of IBA and 2MB combinations, 50 µL/L IBA plus 100 µL/L 2MB killed or suppressed germination of the conidia of all seven fungi. Controlled atmosphere had no significant effect on conidial viability or volatile efficacy. Major volatiles of M. albus may have significant potential to control plant pathogens in either ambient air or CA storage at temperatures below 5 °C. However, combinations of volatiles may be required to provide a broader spectrum of control than individual volatiles. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessArticle Microsatellites in the Endangered Species Dyckia distachya (Bromeliaceae) and Cross-Amplification in Other Bromeliads
Int. J. Mol. Sci. 2012, 13(12), 15859-15866; doi:10.3390/ijms131215859
Received: 13 October 2012 / Revised: 13 November 2012 / Accepted: 16 November 2012 / Published: 27 November 2012
Cited by 2 | PDF Full-text (160 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Microsatellite markers were isolated in Dyckia distachya, an endangered bromeliad from southern Brazil, which will be useful to assess the population genetic structure and reproductive success in introduced and natural populations of this species. Twenty microsatellite loci were developed from an enriched
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Microsatellite markers were isolated in Dyckia distachya, an endangered bromeliad from southern Brazil, which will be useful to assess the population genetic structure and reproductive success in introduced and natural populations of this species. Twenty microsatellite loci were developed from an enriched genomic library, and nine of these were amplified. The loci were characterized in 43 individuals from introduced and wild D. distachya populations. All nine loci were polymorphic, with four to ten alleles per locus. In an introduced population the observed and expected heterozygosities ranged from 0.136–0.667 and 0.543–0.877, respectively, while in a wild population it ranged from 0.000 to 0.895 and from 0.050 to 0.811, respectively. The development of these microsatellite markers will contribute to investigations of the reproductive potential and viability of introduced populations of D. distachya as well as the single known wild population. Cross-amplification in other Bromeliaceae species was successful, with high rates in four loci, demonstrating the applicability of these microsatellite markers in other taxa. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Impact of Cyanidin-3-Glucoside on Glycated LDL-Induced NADPH Oxidase Activation, Mitochondrial Dysfunction and Cell Viability in Cultured Vascular Endothelial Cells
Int. J. Mol. Sci. 2012, 13(12), 15867-15880; doi:10.3390/ijms131215867
Received: 14 September 2012 / Revised: 14 November 2012 / Accepted: 19 November 2012 / Published: 27 November 2012
Cited by 9 | PDF Full-text (909 KB) | HTML Full-text | XML Full-text
Abstract
Elevated levels of glycated low density lipoprotein (glyLDL) are frequently detected in diabetic patients. Previous studies demonstrated that glyLDL increased the production of reactive oxygen species (ROS), activated NADPH oxidase (NOX) and suppressed mitochondrial electron transport chain (mETC) enzyme activities in vascular endothelial
[...] Read more.
Elevated levels of glycated low density lipoprotein (glyLDL) are frequently detected in diabetic patients. Previous studies demonstrated that glyLDL increased the production of reactive oxygen species (ROS), activated NADPH oxidase (NOX) and suppressed mitochondrial electron transport chain (mETC) enzyme activities in vascular endothelial cells (EC). The present study examined the effects of cyanidin-3-glucoside (C3G), a type of anthocyanin abundant in dark-skinned berries, on glyLDL-induced ROS production, NOX activation and mETC enzyme activity in porcine aortic EC (PAEC). Co-treatment of C3G prevented glyLDL-induced upregulation of NOX4 and intracellular superoxide production in EC. C3G normalized glyLDL-induced inhibition on the enzyme activities of mETC Complex I and III, as well as the abundances of NADH dehydrogenase 1 in Complex I and cytochrome b in Complex III in EC. Blocking antibody for the receptor of advanced glycation end products (RAGE) prevented glyLDL-induced changes in NOX and mETC enzymes. Combination of C3G and RAGE antibody did not significantly enhance glyLDL-induced inhibition of NOX or mETC enzymes. C3G reduced glyLDL-induced RAGE expression with the presence of RAGE antibody. C3G prevented prolonged incubation with the glyLDL-induced decrease in cell viability and the imbalance between key regulators for cell viability (cleaved caspase 3 and B cell Lyphoma-2) in EC. The findings suggest that RAGE plays an important role in glyLDL-induced oxidative stress in vascular EC. C3G may prevent glyLDL-induced NOX activation, the impairment of mETC enzymes and cell viability in cultured vascular EC. Full article
(This article belongs to the Special Issue Advances in Free Radicals in Biology and Medicine)
Open AccessArticle Modulation of Adipogenic Conditions for Prospective Use of hADSCs in Adipose Tissue Engineering
Int. J. Mol. Sci. 2012, 13(12), 15881-15900; doi:10.3390/ijms131215881
Received: 3 August 2012 / Revised: 15 October 2012 / Accepted: 8 November 2012 / Published: 27 November 2012
Cited by 9 | PDF Full-text (2297 KB) | HTML Full-text | XML Full-text
Abstract
Modern strategies in adipose tissue engineering (ATE) take advantage of the easy harvest, abundance and differentiation potential towards mesenchymal lineages of hADSCs. The controlled conversion of hADSCs to committed adipogenic precursors and further mature adipocytes formation is important for good long-term results in
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Modern strategies in adipose tissue engineering (ATE) take advantage of the easy harvest, abundance and differentiation potential towards mesenchymal lineages of hADSCs. The controlled conversion of hADSCs to committed adipogenic precursors and further mature adipocytes formation is important for good long-term results in soft tissue regeneration. Thus, in this study, we report: (i) the isolation of the processed lipoaspirate (PLA) cells from adipose tissue and sanguine fractions; (ii) the phenotypic characterization of the PLA descendants; (iii) the design of a novel protocol for the modulation of adipogenic conditions in the perspectives of ATE applications. To modulate the differentiation rate through our protocol, we propose to selectively modify the formulation of the adipogenic media in accordance with the evolution of the process. Therefore, we aimed to ensure the long-term proliferation of the precursor cells and to delay the late adipogenic events. The status of differentiation was characterized in terms of intracellular lipid accumulation and reorganization of the cytoskeleton simultaneously with perilipin protein expression. Moreover, we studied the sequential activation of PPARγ2, FAS, aP2 and perilipin genes which influence the kinetics of the adipogenic process. The strategies developed in this work are the prerequisites for prospective 3D regenerative systems. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Spectral Inverse Quantum (Spectral-IQ) Method for Modeling Mesoporous Systems: Application on Silica Films by FTIR
Int. J. Mol. Sci. 2012, 13(12), 15925-15941; doi:10.3390/ijms131215925
Received: 26 September 2012 / Revised: 19 November 2012 / Accepted: 22 November 2012 / Published: 28 November 2012
Cited by 10 | PDF Full-text (560 KB) | HTML Full-text | XML Full-text
Abstract
The present work advances the inverse quantum (IQ) structural criterion for ordering and characterizing the porosity of the mesosystems based on the recently advanced ratio of the particle-to-wave nature of quantum objects within the extended Heisenberg uncertainty relationship through employing the quantum fluctuation,
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The present work advances the inverse quantum (IQ) structural criterion for ordering and characterizing the porosity of the mesosystems based on the recently advanced ratio of the particle-to-wave nature of quantum objects within the extended Heisenberg uncertainty relationship through employing the quantum fluctuation, both for free and observed quantum scattering information, as computed upon spectral identification of the wave-numbers specific to the maximum of absorption intensity record, and to left-, right- and full-width at the half maximum (FWHM) of the concerned bands of a given compound. It furnishes the hierarchy for classifying the mesoporous systems from more particle-related (porous, tight or ionic bindings) to more wave behavior (free or covalent bindings). This so-called spectral inverse quantum (Spectral-IQ) particle-to-wave assignment was illustrated on spectral measurement of FT-IR (bonding) bands’ assignment for samples synthesized within different basic environment and different thermal treatment on mesoporous materials obtained by sol-gel technique with n-dodecyl trimethyl ammonium bromide (DTAB) and cetyltrimethylammonium bromide (CTAB) and of their combination as cosolvents. The results were analyzed in the light of the so-called residual inverse quantum information, accounting for the free binding potency of analyzed samples at drying temperature, and were checked by cross-validation with thermal decomposition techniques by endo-exo thermo correlations at a higher temperature. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
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Open AccessArticle Novel Microsatellite Markers of Meretrix petechialis and Cross-species Amplification in Related Taxa (Bivalvia: Veneroida)
Int. J. Mol. Sci. 2012, 13(12), 15942-15954; doi:10.3390/ijms131215942
Received: 17 September 2012 / Revised: 11 November 2012 / Accepted: 14 November 2012 / Published: 28 November 2012
Cited by 2 | PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
The Asian hard clam, Meretrix petechialis, is an economically important bivalve, but its catch and population sizes are decreasing rapidly, owing to many factors, including large-scale reclamation of its natural habitat on the western coast of the Korean peninsula. Attempts to restore
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The Asian hard clam, Meretrix petechialis, is an economically important bivalve, but its catch and population sizes are decreasing rapidly, owing to many factors, including large-scale reclamation of its natural habitat on the western coast of the Korean peninsula. Attempts to restore the resources and production of this species require genetic structure and diversity information. In this study, we developed 15 microsatellite markers from a partial genomic library enriched in GT repeats. Nine of these markers were polymorphic, with an average allele number of six, and six were monomorphic in 95 tested individuals. No linkage disequilibrium was found between any pair of loci (p > 0.05), and deviations from the Hardy–Weinberg equilibrium (HWE) test showing excess of heterozygotes was observed in only one of nine loci. In addition, no null alleles or genetic differentiation between two tested populations were detected. A cross-species amplification in 12 species of four families resulted in two M. petechialis-specific loci and three possible universal markers. This information will be useful in the future development of high-quality artificial seedlings and sustainable resource management. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Differential Expression Profile of MicroRNAs during Differentiation of Cardiomyocytes Exposed to Polychlorinated Biphenyls
Int. J. Mol. Sci. 2012, 13(12), 15955-15966; doi:10.3390/ijms131215955
Received: 14 September 2012 / Revised: 9 November 2012 / Accepted: 20 November 2012 / Published: 28 November 2012
Cited by 4 | PDF Full-text (784 KB) | HTML Full-text | XML Full-text
Abstract
Exposure to persistent environmental pollutants, such as polychlorinated biphenyls (PCBs), is a risk factor for the development of congenital heart defects. MicroRNAs (miRNAs) have been shown to be involved in cardiac development. The objective of this study was to investigate changes in miRNA
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Exposure to persistent environmental pollutants, such as polychlorinated biphenyls (PCBs), is a risk factor for the development of congenital heart defects. MicroRNAs (miRNAs) have been shown to be involved in cardiac development. The objective of this study was to investigate changes in miRNA expression profiles during the differentiation of cardiomyocytes exposed to PCBs. For that purpose, PCBs (Aroclor 1254) at a concentration of 2.5 μmol/L were added on day 0 of differentiation of P19 mouse embryonal carcinoma cells into cardiac myocytes. The relative expression of miRNA genes was determined by miRNA microarray and real-time reverse transcriptase polymerase chain reaction (real-time RT-PCR) analyses. The microarray results revealed that 45 miRNAs, of which 14 were upregulated and 31 were downregulated, were differentially expressed in P19 cells treated with PCBs compared with control cells. The miRNA expression data was validated with real-time RT-PCR. The expression of certain potential target genes (Wnt1) was found to be reduced in P19 cells treated with PCBs, whereas the expression of other potential predicted target genes (GSK3β) was increased. Our results demonstrate a critical role of miRNAs in mediating the effect of PCBs during the differentiation of P19 cells into cardiac myocytes. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Identification and Characterization of the Actin-Binding Motif of Phostensin
Int. J. Mol. Sci. 2012, 13(12), 15967-15982; doi:10.3390/ijms131215967
Received: 20 September 2012 / Revised: 15 November 2012 / Accepted: 19 November 2012 / Published: 28 November 2012
Cited by 3 | PDF Full-text (3073 KB) | HTML Full-text | XML Full-text
Abstract
Phostensin, a protein phosphatase 1 F-actin cytoskeleton-targeting subunit encoded by KIAA1949, consists of 165 amino acids and caps the pointed ends of actin filaments. Sequence alignment analyses suggest that the C-terminal region of phostensin, spanning residues 129 to 155, contains a
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Phostensin, a protein phosphatase 1 F-actin cytoskeleton-targeting subunit encoded by KIAA1949, consists of 165 amino acids and caps the pointed ends of actin filaments. Sequence alignment analyses suggest that the C-terminal region of phostensin, spanning residues 129 to 155, contains a consensus actin-binding motif. Here, we have verified the existence of an actin-binding motif in the C-terminal domain of phostensin using colocalization, F-actin co-sedimentation and single filament binding assays. Our data indicate that the N-terminal region of phostensin (1–129) cannot bind to actin filaments and cannot retard the pointed end elongation of gelsolin-actin seeds. Furthermore, the C-terminal region of phostensin (125–165) multiply bind to the sides of actin filaments and lacks the ability to block the pointed end elongation, suggesting that the actin-binding motif is located in the C-terminal region of the phostensin. Further analyses indicate that phostensin binding to the pointed end of actin filament requires N-terminal residues 35 to 51. These results suggest that phostensin might fold into a rigid structure, allowing the N-terminus to sterically hinder the binding of C-terminus to the sides of actin filament, thus rendering phostensin binding to the pointed ends of actin filaments. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Computational Molecular Nanoscience Study of the Properties of Copper Complexes for Dye-Sensitized Solar Cells
Int. J. Mol. Sci. 2012, 13(12), 16005-16019; doi:10.3390/ijms131216005
Received: 20 August 2012 / Revised: 9 October 2012 / Accepted: 12 November 2012 / Published: 28 November 2012
Cited by 9 | PDF Full-text (1270 KB) | HTML Full-text | XML Full-text
Abstract
In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in
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In this work, we studied a copper complex-based dye, which is proposed for potential photovoltaic applications and is named Cu (I) biquinoline dye. Results of electron affinities and ionization potentials have been used for the correlation between different levels of calculation used in this study, which are based on The Density Functional Theory (DFT) and time-dependent (TD) DFT. Further, the maximum absorption wavelengths of our theoretical calculations were compared with the experimental data. It was found that the M06/LANL2DZ + DZVP level of calculation provides the best approximation. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Isolation and Characterization of Polymorphic Microsatellite Markers from the Chinese Medicinal Herb Atractylodes macrocephala (Asteraceae)
Int. J. Mol. Sci. 2012, 13(12), 16046-16052; doi:10.3390/ijms131216046
Received: 13 September 2012 / Revised: 16 October 2012 / Accepted: 26 October 2012 / Published: 28 November 2012
Cited by 6 | PDF Full-text (196 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Atractylodes macrocephala Koidz. (Asteraceae) is an economically important Chinese medicinal herb. In this study, 15 polymorphic microsatellite markers were developed from A. macrocephala using the compound microsatellite marker technique. Levels of polymorphism within the 15 markers were assessed using 83 individuals from two
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Atractylodes macrocephala Koidz. (Asteraceae) is an economically important Chinese medicinal herb. In this study, 15 polymorphic microsatellite markers were developed from A. macrocephala using the compound microsatellite marker technique. Levels of polymorphism within the 15 markers were assessed using 83 individuals from two wild and two cultivated populations in China. The number of alleles per locus ranged from 2 to 20, with an average of 9.9 alleles. Observed and expected heterozygosities ranged from 0.083 to 1.000 and from 0.097 to 0.938, respectively. These markers will be valuable for germplasm classification and identification, as well as for assessing the genetic diversity and spatial genetic structure among wild and cultivated populations of A. macrocephala. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle MiR-218 Impairs Tumor Growth and Increases Chemo-Sensitivity to Cisplatin in Cervical Cancer
Int. J. Mol. Sci. 2012, 13(12), 16053-16064; doi:10.3390/ijms131216053
Received: 28 August 2012 / Revised: 15 October 2012 / Accepted: 25 October 2012 / Published: 28 November 2012
Cited by 37 | PDF Full-text (1102 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs are noncoding RNA molecules of 18–25 nucleotides that regulate gene expression at the post-transcriptional levels. Recent data revealed that miR-218 played key roles in tumor metastasis. Here, we described the regulation and function of miR-218 in cervical cancer. Overexpression of miR-218 reduced
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MicroRNAs are noncoding RNA molecules of 18–25 nucleotides that regulate gene expression at the post-transcriptional levels. Recent data revealed that miR-218 played key roles in tumor metastasis. Here, we described the regulation and function of miR-218 in cervical cancer. Overexpression of miR-218 reduced the proliferation of the human cervical cancer cell line HeLa and induced cell apoptosis through the AKT-mTOR signaling pathway. In addition, it forced expression of miR-218 suppressed tumor growth in the orthotopic mouse model of HeLa cells. Furthermore, miR-218 increased chemosensitivity to cisplatin (CDDP) in vitro. Our results indicated that targeting miR-218 may provide a strategy for blocking the development of cervical cancer. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Wheat Drought-Responsive Grain Proteome Analysis by Linear and Nonlinear 2-DE and MALDI-TOF Mass Spectrometry
Int. J. Mol. Sci. 2012, 13(12), 16065-16083; doi:10.3390/ijms131216065
Received: 15 October 2012 / Revised: 13 November 2012 / Accepted: 14 November 2012 / Published: 29 November 2012
Cited by 23 | PDF Full-text (542 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the
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A comparative proteomic analysis of drought-responsive proteins during grain development of two wheat varieties Kauz (strong resistance to drought stress) and Janz (sensitive to drought stress) was performed by using linear and nonlinear 2-DE and MALDI-TOF mass spectrometry technologies. Results revealed that the nonlinear 2-DE had much higher resolution than the linear 2-DE. A total of 153 differentially expressed protein spots were detected by both 2-DE maps, of which 122 protein spots were identified by MALDI-TOF and MALDI-TOF/TOF mass spectrometry. The identified differential proteins were mainly involved in carbohydrate metabolism (26%), detoxification and defense (23%), and storage proteins (17%). Some key proteins demonstrated significantly different expression patterns between the two varieties. In particular, catalase isozyme 1, WD40 repeat protein, LEA and alpha-amylase inhibitors displayed an upregulated expression pattern in Kauz, whereas they were downregulated or unchanged in Janz. Small and large subunit ADP glucose pyrophosphorylase, ascorbate peroxidase and G beta-like protein were all downregulated under drought stress in Janz, but had no expression changes in Kauz. Sucrose synthase and triticin precursor showed an upregulated expression pattern under water deficits in both varieties, but their upregulation levels were much higher in Kauz than in Janz. These differentially expressed proteins could be related to the biochemical pathways for stronger drought resistance of Kauz. Full article
(This article belongs to the Special Issue Abiotic and Biotic Stress Tolerance Mechanisms in Plants)
Open AccessArticle Carbohydrate Stress Affecting Fruitlet Abscission and Expression of Genes Related to Auxin Signal Transduction Pathway in Litchi
Int. J. Mol. Sci. 2012, 13(12), 16084-16103; doi:10.3390/ijms131216084
Received: 18 October 2012 / Revised: 6 November 2012 / Accepted: 16 November 2012 / Published: 29 November 2012
Cited by 14 | PDF Full-text (1157 KB) | HTML Full-text | XML Full-text
Abstract
Auxin, a vital plant hormone, regulates a variety of physiological and developmental processes. It is involved in fruit abscission through transcriptional regulation of many auxin-related genes, including early auxin responsive genes (i.e., auxin/indole-3-acetic acid (AUX/IAA), Gretchen Hagen3 (GH3
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Auxin, a vital plant hormone, regulates a variety of physiological and developmental processes. It is involved in fruit abscission through transcriptional regulation of many auxin-related genes, including early auxin responsive genes (i.e., auxin/indole-3-acetic acid (AUX/IAA), Gretchen Hagen3 (GH3) and small auxin upregulated (SAUR)) and auxin response factors (ARF), which have been well characterized in many plants. In this study, totally five auxin-related genes, including one AUX/IAA (LcAUX/IAA1), one GH3 (LcGH3.1), one SAUR (LcSAUR1) and two ARFs (LcARF1 and LcARF2), were isolated and characterized from litchi fruit. LcAUX/IAA1, LcGH3.1, LcSAUR1, LcARF1 and LcARF2 contain open reading frames (ORFs) encoding polypeptides of 203, 613, 142, 792 and 832 amino acids, respectively, with their corresponding molecular weights of 22.67, 69.20, 11.40, 88.20 and 93.16 kDa. Expression of these genes was investigated under the treatment of girdling plus defoliation which aggravated litchi fruitlet abscission due to the blockage of carbohydrates transport and the reduction of endogenous IAA content. Results showed that transcript levels of LcAUX/IAA1, LcGH3.1 and LcSAUR1 mRNAs were increased after the treatment in abscission zone (AZ) and other tissues, in contrast to the decreasing accumulation of LcARF1 mRNA, suggesting that LcAUX/IAA1, LcSAUR1 and LcARF1 may play more important roles in abscission. Our results provide new insight into the process of fruitlet abscission induced by carbohydrate stress and broaden our understanding of the auxin signal transduction pathway in this process at the molecular level. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of Curcumin on the Proliferation and Mineralization of Human Osteoblast-Like Cells: Implications of Nitric Oxide
Int. J. Mol. Sci. 2012, 13(12), 16104-16118; doi:10.3390/ijms131216104
Received: 17 October 2012 / Revised: 19 November 2012 / Accepted: 20 November 2012 / Published: 29 November 2012
Cited by 6 | PDF Full-text (994 KB) | HTML Full-text | XML Full-text
Abstract
Curcumin (diferuloylmethane) is found in the rhizomes of the turmeric plant (Curcuma longa L.) and has been used for centuries as a dietary spice and as a traditional Indian medicine used to treat different conditions. At the cellular level, curcumin modulates important
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Curcumin (diferuloylmethane) is found in the rhizomes of the turmeric plant (Curcuma longa L.) and has been used for centuries as a dietary spice and as a traditional Indian medicine used to treat different conditions. At the cellular level, curcumin modulates important molecular targets: transcription factors, enzymes, cell cycle proteins, cytokines, receptors and cell surface adhesion molecules. Because many of the curcumin targets mentioned above participate in the regulation of bone remodeling, curcumin may affect the skeletal system. Nitric oxide (NO) is a gaseous molecule generated from L-arginine during the catalization of nitric oxide synthase (NOS), and it plays crucial roles in catalization and in the nervous, cardiovascular and immune systems. Human osteoblasts have been shown to express NOS isoforms, and the exact mechanism(s) by which NO regulates bone formation remain unclear. Curcumin has been widely described to inhibit inducible nitric oxide synthase expression and nitric oxide production, at least in part via direct interference in NF-κB activation. In the present study, after exposure of human osteoblast-like cells (MG-63), we have observed that curcumin abrogated inducible NOS expression and decreased NO levels, inhibiting also cell prolifieration. This effect was prevented by the NO donor sodium nitroprusside. Under osteogenic conditions, curcumin also decreased the level of mineralization. Our results indicate that NO plays a role in the osteoblastic profile of MG-63 cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Differential Regulation of CD4+ T Cell Adhesion to Cerebral Microvascular Endothelium by the β-Chemokines CCL2 and CCL3
Int. J. Mol. Sci. 2012, 13(12), 16119-16140; doi:10.3390/ijms131216119
Received: 5 September 2012 / Revised: 15 November 2012 / Accepted: 26 November 2012 / Published: 30 November 2012
Cited by 5 | PDF Full-text (767 KB) | HTML Full-text | XML Full-text
Abstract
In Multiple sclerosis (MS), circulating lymphocytes cross the blood–brain barrier (BBB) and accumulate at sites of antigenic challenge. This process depends on specific interactions between lymphocytes and cerebral microvascular endothelium that involve endothelial activation by cytokines and the presence of chemokines. Chemokines play
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In Multiple sclerosis (MS), circulating lymphocytes cross the blood–brain barrier (BBB) and accumulate at sites of antigenic challenge. This process depends on specific interactions between lymphocytes and cerebral microvascular endothelium that involve endothelial activation by cytokines and the presence of chemokines. Chemokines play a key role in the orchestration of immune responses, acting both as chemoattractants and activators of leukocyte subsets. In the present study, we investigated the effects of the β-chemokines, CCL2 and CCL3, on the adhesion of CD4+ T cell subsets to human brain microvessel endothelial cells (HBMEC). Chemokines added to the lower compartment of a two-chamber chemotaxis system under confluent resting or cytokine-activated HBMEC, diffused through the culture substrate and bound to the basal surface of HBMEC. The low rate of adhesion of naïve, resting and memory CD4+ T cells to resting HBMEC was significantly upregulated following treatment of HBMEC with TNF-α and IFN-g. Recently activated CD4+ T cells readily adhered to resting monolayers. Concentration gradients of CCL2 upregulated the adhesion of activated CD4+ T cells to cytokine treated but not resting HBMEC. The presence of CCL3 in the lower chamber increased the adhesion of memory T cells to both unstimulated and cytokine-treated HBMEC. These findings emphasize the importance of brain endothelial cell activation and the role of CCL2 and CCL3 in regulating the adhesion of CD4+ T cell subsets to BBB endothelium, thus contributing to the specificity of immune responses in MS. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
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Open AccessArticle Förster Resonance Energy Transfer (FRET) between Heterogeneously Distributed Probes: Application to Lipid Nanodomains and Pores
Int. J. Mol. Sci. 2012, 13(12), 16141-16156; doi:10.3390/ijms131216141
Received: 9 October 2012 / Revised: 14 November 2012 / Accepted: 16 November 2012 / Published: 30 November 2012
PDF Full-text (1097 KB) | HTML Full-text | XML Full-text
Abstract
The formation of membrane heterogeneities, e.g., lipid domains and pores, leads to a redistribution of donor (D) and acceptor (A) molecules according to their affinity to the structures formed and the remaining bilayer. If such changes sufficiently influence the Förster resonance energy transfer
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The formation of membrane heterogeneities, e.g., lipid domains and pores, leads to a redistribution of donor (D) and acceptor (A) molecules according to their affinity to the structures formed and the remaining bilayer. If such changes sufficiently influence the Förster resonance energy transfer (FRET) efficiency, these changes can be further analyzed in terms of nanodomain/pore size. This paper is a continuation of previous work on this theme. In particular, it is demonstrated how FRET experiments should be planned and how data should be analyzed in order to achieve the best possible resolution. The limiting resolution of domains and pores are discussed simultaneously, in order to enable direct comparison. It appears that choice of suitable donor/acceptor pairs is the most crucial step in the design of experiments. For instance, it is recommended to use DA pairs, which exhibit an increased affinity to pores (i.e., partition coefficients KD,A > 10) for the determination of pore sizes with radii comparable to the Förster radius R0. On the other hand, donors and acceptors exhibiting a high affinity to different phases are better suited for the determination of domain sizes. The experimental setup where donors and acceptors are excluded from the domains/pores should be avoided. Full article
(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET))
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Open AccessArticle Modelling Translation Initiation under the Influence of sRNA
Int. J. Mol. Sci. 2012, 13(12), 16223-16240; doi:10.3390/ijms131216223
Received: 21 October 2012 / Revised: 21 November 2012 / Accepted: 27 November 2012 / Published: 30 November 2012
Cited by 2 | PDF Full-text (1828 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bacterial small non-coding RNA (sRNA) plays an important role in post-transcriptional gene regulation. Although the number of annotated sRNA is steadily increasing, their functional characterization is still lagging behind. Various computational strategies for finding sRNA–mRNA interactions, and thus putative sRNA targets, were developed.
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Bacterial small non-coding RNA (sRNA) plays an important role in post-transcriptional gene regulation. Although the number of annotated sRNA is steadily increasing, their functional characterization is still lagging behind. Various computational strategies for finding sRNA–mRNA interactions, and thus putative sRNA targets, were developed. Most of them suffer from a high false positive rate. Here, we present a qualitative model to simulate the effect of an sRNA on the translation initiation of a potential target. Information about the ribosome–mRNA interaction, sRNA–mRNA interaction and expression information from deep sequencing experiments is integrated to calculate the change in translation initiation complex formation, as a proxy for translational activity. This model can be used to post-evaluate predicted targets, hence condensing the list of potential targets. We show that our translation initiation model, under the influence of an sRNA, can successfully simulate thirteen out of fifteen tested sRNA–mRNA interactions in a qualitative manner. To show the gain in specificity, we applied our method to a target search for the Escherichia coli sRNA RyhB. Compared with simple target prediction without post-evaluation, we reduce the number of targets to less than one fourth potential targets, considerably reducing the burden of experimental validation. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessArticle Alterations in Glutathione Redox Metabolism, Oxidative Stress, and Mitochondrial Function in the Left Ventricle of Elderly Zucker Diabetic Fatty Rat Heart
Int. J. Mol. Sci. 2012, 13(12), 16241-16254; doi:10.3390/ijms131216241
Received: 20 September 2012 / Revised: 31 October 2012 / Accepted: 19 November 2012 / Published: 30 November 2012
Cited by 9 | PDF Full-text (1339 KB) | HTML Full-text | XML Full-text
Abstract
The Zucker diabetic fatty (ZDF) rat is a genetic model in which the homozygous (FA/FA) male animals develop obesity and type 2 diabetes. Morbidity and mortality from cardiovascular complications, due to increased oxidative stress and inflammatory signals, are the hallmarks of type 2
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The Zucker diabetic fatty (ZDF) rat is a genetic model in which the homozygous (FA/FA) male animals develop obesity and type 2 diabetes. Morbidity and mortality from cardiovascular complications, due to increased oxidative stress and inflammatory signals, are the hallmarks of type 2 diabetes. The precise molecular mechanism of contractile dysfunction and disease progression remains to be clarified. Therefore, we have investigated molecular and metabolic targets in male ZDF (30–34 weeks old) rat heart compared to age matched Zucker lean (ZL) controls. Hyperglycemia was confirmed by a 4-fold elevation in non-fasting blood glucose (478.43 ± 29.22 mg/dL in ZDF vs. 108.22 ± 2.52 mg/dL in ZL rats). An increase in reactive oxygen species production, lipid peroxidation and oxidative protein carbonylation was observed in ZDF rats. A significant increase in CYP4502E1 activity accompanied by increased protein expression was also observed in diabetic rat heart. Increased expression of other oxidative stress marker proteins, HO-1 and iNOS was also observed. GSH concentration and activities of GSH-dependent enzymes, glutathione S-transferase and GSH reductase, were, however, significantly increased in ZDF heart tissue suggesting a compensatory defense mechanism. The activities of mitochondrial respiratory enzymes, Complex I and Complex IV were significantly reduced in the heart ventricle of ZDF rats in comparison to ZL rats. Western blot analysis has also suggested a decreased expression of IκB-α and phosphorylated-JNK in diabetic heart tissue. Our results have suggested that mitochondrial dysfunction and increased oxidative stress in ZDF rats might be associated, at least in part, with altered NF-κB/JNK dependent redox cell signaling. These results might have implications in the elucidation of the mechanism of disease progression and designing strategies for diabetes prevention. Full article
(This article belongs to the Special Issue Oxidative Stress and Ageing)
Open AccessCommunication Isolation and Characterization of Saponin-Producing Fungal Endophytes from Aralia elata in Northeast China
Int. J. Mol. Sci. 2012, 13(12), 16255-16266; doi:10.3390/ijms131216255
Received: 9 October 2012 / Revised: 2 November 2012 / Accepted: 5 November 2012 / Published: 30 November 2012
Cited by 4 | PDF Full-text (242 KB) | HTML Full-text | XML Full-text
Abstract
The purpose of this study was to investigate the diversity of endophytic fungi of Aralia elata distributed in Northeast China as well as their capacity to produce saponins. Ninety-six strains of endophytic fungi were isolated, and polymerase chain reaction (PCR) and sequencing were
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The purpose of this study was to investigate the diversity of endophytic fungi of Aralia elata distributed in Northeast China as well as their capacity to produce saponins. Ninety-six strains of endophytic fungi were isolated, and polymerase chain reaction (PCR) and sequencing were employed to identify the isolates. The saponin concentrations of the culture filtrates of representative strains were measured. The agar diffusion method was used to test antimicrobial activity, while high-performance liquid chromatography (HPLC) was employed to identify the saponins produced by representative strains. Alternaria, Botryosphaeria, Camarosporium, Cryptosporiopsis, Diaporthe, Dictyochaeta, Penicillium, Fusarium, Nectria, Peniophora, Schizophyllum, Cladosporium and Trichoderma species were isolated in this study. Overall, 25% of the isolates belonged to Diaporthe (Diaporthe eres), and 12.5% belonged to Alternaria. The highest concentration of saponins was produced by G22 (2.049 mg/mL). According to the results of the phylogenetic analysis, G22 belonged to the genus Penicillium. The culture filtrate of G22 exhibited antibacterial activity against Staphylococcus aureus, and ginsenosides Re and Rb2 were detected in G22 culture filtrates by HPLC. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Lysophosphatidylcholine Acyltransferase 3 Is the Key Enzyme for Incorporating Arachidonic Acid into Glycerophospholipids during Adipocyte Differentiation
Int. J. Mol. Sci. 2012, 13(12), 16267-16280; doi:10.3390/ijms131216267
Received: 5 November 2012 / Revised: 26 November 2012 / Accepted: 28 November 2012 / Published: 3 December 2012
Cited by 8 | PDF Full-text (494 KB) | HTML Full-text | XML Full-text
Abstract
Cellular membranes contain glycerophospholipids, which have important structural and functional roles in cells. Glycerophospholipids are first formed in the de novo pathway (Kennedy pathway) and are matured in the remodeling pathway (Lands’ cycle). Recently, lysophospholipid acyltransferases functioning in Lands’ cycle were identified and
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Cellular membranes contain glycerophospholipids, which have important structural and functional roles in cells. Glycerophospholipids are first formed in the de novo pathway (Kennedy pathway) and are matured in the remodeling pathway (Lands’ cycle). Recently, lysophospholipid acyltransferases functioning in Lands’ cycle were identified and characterized. Several enzymes involved in glycerophospholipid biosynthesis have been reported to have important roles in adipocytes. However, the role of Lands’ cycle in adipogenesis has not yet been reported. Using C3H10T1/2, a cell line capable of differentiating to adipocyte-like cells in vitro, changes of lysophospholipid acyltransferase activities were investigated. Lysophosphatidylcholine acyltransferase (LPCAT), lysophosphatidylethanolamine acyltransferase (LPEAT) and lysophosphatidylserine acyltransferase (LPSAT) activities were enhanced, especially with 18:2-CoA and 20:4-CoA as donors. Correspondingly, mRNA expression of LPCAT3, which possesses LPCAT, LPEAT and LPSAT activities with high specificity for 18:2- and 20:4-CoA, was upregulated during adipogenesis. Analysis of acyl-chain compositions of phosphatidylcholine (PC), phosphatidylethanolamine (PE) and phosphatidylserine (PS) showed a change in their profiles between preadipocytes and adipocytes, including an increase in the percentage of arachidonic acid-containing phospholipids. These changes are consistent with the activities of LPCAT3. Therefore, it is possible that enhanced phospholipid remodeling by LPCAT3 may be associated with adipocyte differentiation. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences 2012)
Open AccessArticle Activation Energy of Aggregation-Disaggregation Self-Oscillation of Polymer Chain
Int. J. Mol. Sci. 2012, 13(12), 16281-16290; doi:10.3390/ijms131216281
Received: 8 November 2012 / Revised: 25 November 2012 / Accepted: 30 November 2012 / Published: 3 December 2012
Cited by 10 | PDF Full-text (362 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we investigated the activation energies of the aggregation–disaggregation self-oscillation induced by the Belousov-Zhabotinsky (BZ) reaction by utilizing the nonthermoresponsive polymer chain in a wide temperature range. This is because the conventional type self-oscillating polymer chain, with thermoresponsive poly(Nisopropylacrylamide) (poly(NIPAAm) main-chain
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In this paper, we investigated the activation energies of the aggregation–disaggregation self-oscillation induced by the Belousov-Zhabotinsky (BZ) reaction by utilizing the nonthermoresponsive polymer chain in a wide temperature range. This is because the conventional type self-oscillating polymer chain, with thermoresponsive poly(Nisopropylacrylamide) (poly(NIPAAm) main-chain covalently bonded to the ruthenium catalyst (Ru(bpy)3) of the BZ reaction, cannot evaluate the activation energy over the lower critical solution temperature (LCST). The nonthermoresponsive self-oscillating polymer chain is composed of a poly-vinylpyrrolidone (PVP) main-chain with the ruthenium catalyst (Ru(bpy)3). As a result, we clarified that the activation energy of the aggregation–disaggregation self-oscillation of the polymer chain is hardly affected by the concentrations of the BZ substrates. In addition, the activation energy of the nonthermoresponsive self-oscillating polymer chain was found to be almost the same value as normal BZ reaction, i.e., not including the self-oscillating polymer system with Ru moiety. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle In Vitro Antifungal Activity of Burkholderia gladioli pv. agaricicola against Some Phytopathogenic Fungi
Int. J. Mol. Sci. 2012, 13(12), 16291-16302; doi:10.3390/ijms131216291
Received: 13 November 2012 / Revised: 27 November 2012 / Accepted: 29 November 2012 / Published: 3 December 2012
Cited by 11 | PDF Full-text (366 KB) | HTML Full-text | XML Full-text
Abstract
The trend to search novel microbial natural biocides has recently been increasing in order to avoid the environmental pollution from use of synthetic pesticides. Among these novel natural biocides are the bioactive secondary metabolites of Burkholderia gladioli pv. agaricicola (Bga). The
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The trend to search novel microbial natural biocides has recently been increasing in order to avoid the environmental pollution from use of synthetic pesticides. Among these novel natural biocides are the bioactive secondary metabolites of Burkholderia gladioli pv. agaricicola (Bga). The aim of this study is to determine antifungal activity of Bga strains against some phytopathogenic fungi. The fungicidal tests were carried out using cultures and cell-free culture filtrates against Botrytis cinerea, Aspergillus flavus, Aspergillus niger, Penicillium digitatum, Penicillium expansum, Sclerotinia sclerotiorum and Phytophthora cactorum. Results demonstrated that all tested strains exert antifungal activity against all studied fungi by producing diffusible metabolites which are correlated with their ability to produce extracellular hydrolytic enzymes. All strains significantly reduced the growth of studied fungi and the bacterial cells were more bioactive than bacterial filtrates. All tested Bulkholderia strains produced volatile organic compounds (VOCs), which inhibited the fungal growth and reduced the growth rate of Fusarium oxysporum and Rhizoctonia solani. GC/MS analysis of VOCs emitted by strain Bga 11096 indicated the presence of a compound that was identified as 1-methyl-4-(1-methylethenyl)-cyclohexene, a liquid hydrocarbon classified as cyclic terpene. This compound could be responsible for the antifungal activity, which is also in agreement with the work of other authors. Full article
(This article belongs to the Special Issue Green Biocides)
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Open AccessArticle Sensing and Responding to UV-A in Cyanobacteria
Int. J. Mol. Sci. 2012, 13(12), 16303-16332; doi:10.3390/ijms131216303
Received: 1 November 2012 / Revised: 27 November 2012 / Accepted: 27 November 2012 / Published: 3 December 2012
Cited by 9 | PDF Full-text (527 KB) | HTML Full-text | XML Full-text
Abstract
Ultraviolet (UV) radiation can cause stresses or act as a photoregulatory signal depending on its wavelengths and fluence rates. Although the most harmful effects of UV on living cells are generally attributed to UV-B radiation, UV-A radiation can also affect many aspects of
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Ultraviolet (UV) radiation can cause stresses or act as a photoregulatory signal depending on its wavelengths and fluence rates. Although the most harmful effects of UV on living cells are generally attributed to UV-B radiation, UV-A radiation can also affect many aspects of cellular processes. In cyanobacteria, most studies have concentrated on the damaging effect of UV and defense mechanisms to withstand UV stress. However, little is known about the activation mechanism of signaling components or their pathways which are implicated in the process following UV irradiation. Motile cyanobacteria use a very precise negative phototaxis signaling system to move away from high levels of solar radiation, which is an effective escape mechanism to avoid the detrimental effects of UV radiation. Recently, two different UV-A-induced signaling systems for regulating cyanobacterial phototaxis were characterized at the photophysiological and molecular levels. Here, we review the current understanding of the UV-A mediated signaling pathways in the context of the UV-A perception mechanism, early signaling components, and negative phototactic responses. In addition, increasing evidences supporting a role of pterins in response to UV radiation are discussed. We outline the effect of UV-induced cell damage, associated signaling molecules, and programmed cell death under UV-mediated oxidative stress. Full article
(This article belongs to the Special Issue UV-Induced Cell Death 2012)
Open AccessArticle Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey
Int. J. Mol. Sci. 2012, 13(12), 16333-16345; doi:10.3390/ijms131216333
Received: 26 September 2012 / Revised: 14 November 2012 / Accepted: 21 November 2012 / Published: 3 December 2012
Cited by 6 | PDF Full-text (196 KB) | HTML Full-text | XML Full-text
Abstract
Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated
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Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats) motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%); the second most abundant were the tri-nucleotide repeats (42,657, 30.11%). Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32%) of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR). To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82%) produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2–14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Photodegradable Polyesters for Triggered Release
Int. J. Mol. Sci. 2012, 13(12), 16387-16399; doi:10.3390/ijms131216387
Received: 28 September 2012 / Revised: 14 November 2012 / Accepted: 16 November 2012 / Published: 3 December 2012
Cited by 5 | PDF Full-text (929 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Photodegradable polyesters were synthesized with a photolabile monomer 2-nitrophenylethylene glycol and dioyl chlorides with different lengths. These polymers can be assembled to form polymeric particles with encapsulation of target substances. Light activation can degrade these particles and release payloads in both aqueous solutions
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Photodegradable polyesters were synthesized with a photolabile monomer 2-nitrophenylethylene glycol and dioyl chlorides with different lengths. These polymers can be assembled to form polymeric particles with encapsulation of target substances. Light activation can degrade these particles and release payloads in both aqueous solutions and RAW 264.7 cells. Full article
(This article belongs to the Special Issue Bioactive Nanoparticles 2012)
Open AccessArticle Characterization of in Vitro Modified Human Very Low-Density Lipoprotein Particles and Phospholipids by Capillary Electrophoresis
Int. J. Mol. Sci. 2012, 13(12), 16400-16417; doi:10.3390/ijms131216400
Received: 26 October 2012 / Revised: 24 November 2012 / Accepted: 28 November 2012 / Published: 3 December 2012
Cited by 2 | PDF Full-text (949 KB) | HTML Full-text | XML Full-text
Abstract
A simple capillary zone electrophoresis (CZE) method was used to characterize human very low-density lipoprotein (VLDL) particles for four healthy donors. One major peak was observed for native, in vitro oxidized and glycated VLDL particles. The effective mobilities and peak areas of the
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A simple capillary zone electrophoresis (CZE) method was used to characterize human very low-density lipoprotein (VLDL) particles for four healthy donors. One major peak was observed for native, in vitro oxidized and glycated VLDL particles. The effective mobilities and peak areas of the capillary electrophoresis (CE) profiles showed good reproducibility and precision. The mobility of the oxidized VLDL peak was higher than that of the native VLDL. The mobility of the glycated VLDL peak was similar to that of the native VLDL. Phospholipids isolated from VLDL particles were analyzed by our recently developed micellar electrokinetic chromatography (MEKC) with a high-salt stacking method. At absorbance 200 nm, the native VLDL phospholipids showed a major peak and a minor peak for each donor. For oxidized VLDL phospholipids, the area of the major peak reduced for three donors, possibly due to phospholipid decomposition. For glycated VLDL phospholipids, the peak mobilities were more positive than native VLDL phospholipids for two donors, possibly due to phospholipid-linked advanced glycation end products (AGEs). Very interestingly, at absorbance 234 nm, the major peak of oxidized VLDL phospholipids was resolved as two peaks for each donor, possibly due to conjugated dienes formed upon oxidation. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences 2012)
Open AccessArticle Temporal and Spatial Regulation of Ezrin-Radixin-Moesin-Binding Phosphoprotein-50-kDa (EBP50) during Embryo Implantation in Mouse Uterus
Int. J. Mol. Sci. 2012, 13(12), 16418-16429; doi:10.3390/ijms131216418
Received: 17 October 2012 / Revised: 15 November 2012 / Accepted: 20 November 2012 / Published: 3 December 2012
Cited by 2 | PDF Full-text (833 KB) | HTML Full-text | XML Full-text
Abstract
Embryo implantation is a crucial process for successful pregnancy. To date, the mechanism of embryo implantation remains unclear. Ezrin-radixin-moesin-binding protein-50-kDa (EBP50) is a scaffold protein, which has been shown to play an important role in cancer development. Embryo implantation and cancer follow a
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Embryo implantation is a crucial process for successful pregnancy. To date, the mechanism of embryo implantation remains unclear. Ezrin-radixin-moesin-binding protein-50-kDa (EBP50) is a scaffold protein, which has been shown to play an important role in cancer development. Embryo implantation and cancer follow a similar progression. Thus, in this article, we utilized immunohistochemical staining and western blot analyses to examine the spatiotemporal expression and regulation of EBP50 both in the mouse uterus during embryo implantation as well as in other related models. We found that EBP50 was detected in epithelial cells in all of the groups used in our study. During the peri-implantation period, EBP50 mainly localized in apical membranes. At the implantation site (IS) on day 5 (D5) of pregnancy, EBP50 was mainly expressed in the nuclei of stroma cells, whereas from day 6 to day 8 (D6–D8) of pregnancy, the expression of EBP50 was noted in the cytoplasm of decidual cells. The expression of EBP50 was not significantly different in the pseudopregnant uterus and decreased in the uteri subjected to activation of delayed implantation. Artificial decidualization also decreased EBP50 expression. Thus, the expression levels and location were affected by active blastocysts and decidualization during the window of implantation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Secondary Metabolites from the Roots of Beilschmiedia tsangii and Their Anti-Inflammatory Activities
Int. J. Mol. Sci. 2012, 13(12), 16430-16443; doi:10.3390/ijms131216430
Received: 24 September 2012 / Revised: 19 November 2012 / Accepted: 21 November 2012 / Published: 3 December 2012
Cited by 6 | PDF Full-text (284 KB) | HTML Full-text | XML Full-text
Abstract
Four new endiandric acid analogues, tsangibeilin C (1), tsangibeilin D (2), tricyclotsangibeilin (3) and endiandric acid M (4), one new lignan, beilschminol B (5) and two new sesquiterpenes, (+)-5-hydroxybarbatenal (6) and
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Four new endiandric acid analogues, tsangibeilin C (1), tsangibeilin D (2), tricyclotsangibeilin (3) and endiandric acid M (4), one new lignan, beilschminol B (5) and two new sesquiterpenes, (+)-5-hydroxybarbatenal (6) and (4R,5R)-4,5-dihydroxycaryophyll-8(13)-ene (7), together with four known compounds (811), were isolated from the roots of Beilschmiedia tsangii (Lauraceae). The structures of 17 were determined by spectroscopic techniques. Among the isolates, endiandric acid M (4) exhibited moderate iNOS inhibitory activity, with an IC50 value of 31.70 µM. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A Comparative Analysis of the Photo-Protective Effects of Soy Isoflavones in Their Aglycone and Glucoside Forms
Int. J. Mol. Sci. 2012, 13(12), 16444-16456; doi:10.3390/ijms131216444
Received: 19 September 2012 / Revised: 24 November 2012 / Accepted: 29 November 2012 / Published: 4 December 2012
Cited by 9 | PDF Full-text (1035 KB) | HTML Full-text | XML Full-text
Abstract
Isoflavones exist in nature predominantly as glucosides such as daidzin or genistin and are rarely found in their corresponding aglycone forms daidzein and genistein. The metabolism and absorption of isoflavones ingested with food is well documented, but little is known about their use
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Isoflavones exist in nature predominantly as glucosides such as daidzin or genistin and are rarely found in their corresponding aglycone forms daidzein and genistein. The metabolism and absorption of isoflavones ingested with food is well documented, but little is known about their use as topical photo-protective agents. The aim of this study was to investigate in a comparative analysis the photo-protective effects of isoflavones in both their aglycone and glucoside forms. In human skin fibroblasts irradiated with 60 mJ/cm2 ultraviolet B (UVB), we measured the expression levels of COX-2 and Gadd45, which are involved in inflammation and DNA repair, respectively. We also determined the cellular response to UVB-induced DNA damage using the comet assay. Our findings suggest that both the isoflavone glucosides at a specific concentration and combination with an aglycone mixture exerted an anti-inflammatory and photo-protective effect that prevented 41% and 71% of UVB-induced DNA damage, respectively. The advantages of using either isoflavone glucosides or an aglycone mixture in applications in the field of dermatology will depend on their properties and their different potential uses. Full article
(This article belongs to the Special Issue UV-Induced Cell Death 2012)
Open AccessArticle Molecular Diversity Assessment Using Sequence Related Amplified Polymorphism (SRAP) Markers in Vicia faba L.
Int. J. Mol. Sci. 2012, 13(12), 16457-16471; doi:10.3390/ijms131216457
Received: 2 October 2012 / Revised: 9 November 2012 / Accepted: 12 November 2012 / Published: 4 December 2012
Cited by 20 | PDF Full-text (243 KB) | HTML Full-text | XML Full-text
Abstract
Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with
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Sequence-related amplified polymorphism (SRAP) markers were used to assess the genetic diversity and relationship among 58 faba bean (Vicia faba L.) genotypes. Fourteen SRAP primer combinations amplified a total of 1036 differently sized well-resolved peaks (fragments), of which all were polymorphic with a 0.96 PIC value and discriminated all of the 58 faba bean genotypes. An average pairwise similarity of 21% was revealed among the genotypes ranging from 2% to 65%. At a similarity of 28%, UPGMA clustered the genotypes into three main groups comprising 78% of the genotypes. The local landraces and most of the Egyptian genotypes in addition to the Sudan genotypes were grouped in the first main cluster. The advanced breeding lines were scattered in the second and third main clusters with breeding lines from the ICARDA and genotypes introduced from Egypt. At a similarity of 47%, all the genotypes formed separated clusters with the exceptions of Hassawi 1 and Hassawi 2. Group analysis of the genotypes according to their geographic origin and type showed that the landraces were grouped according to their origin, while others were grouped according to their seed type. To our knowledge, this is the first application of SRAP markers for the assessment of genetic diversity in faba bean. Such information will be useful to determine optimal breeding strategies to allow continued progress in faba bean breeding. Full article
(This article belongs to the Special Issue Molecular Cut and Paste)
Open AccessArticle 1-Benzyl-2-Phenylbenzimidazole (BPB), a Benzimidazole Derivative, Induces Cell Apoptosis in Human Chondrosarcoma through Intrinsic and Extrinsic Pathways
Int. J. Mol. Sci. 2012, 13(12), 16472-16488; doi:10.3390/ijms131216472
Received: 22 October 2012 / Revised: 23 November 2012 / Accepted: 27 November 2012 / Published: 4 December 2012
Cited by 8 | PDF Full-text (802 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we investigated the anticancer effects of a new benzimidazole derivative, 1-benzyl-2-phenyl -benzimidazole (BPB), in human chondrosarcoma cells. BPB-mediated apoptosis was assessed by the MTT assay and flow cytometry analysis. The in vivo efficacy was examined in a JJ012 xenograft model.
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In this study, we investigated the anticancer effects of a new benzimidazole derivative, 1-benzyl-2-phenyl -benzimidazole (BPB), in human chondrosarcoma cells. BPB-mediated apoptosis was assessed by the MTT assay and flow cytometry analysis. The in vivo efficacy was examined in a JJ012 xenograft model. Here we found that BPB induced apoptosis in human chondrosarcoma cell lines (JJ012 and SW1353) but not in primary chondrocytes. BPB induced upregulation of Bax, Bad and Bak, downregulation of Bcl-2, Bid and Bcl-XL and dysfunction of mitochondria in chondrosarcoma. In addition, BPB also promoted cytosolic releases AIF and Endo G. Furthermore, it triggered extrinsic death receptor-dependent pathway, which was characterized by activating Fas, FADD and caspase-8. Most importantly, animal studies revealed a dramatic 40% reduction in tumor volume after 21 days of treatment. Thus, BPB may be a novel anticancer agent for the treatment of chondrosarcoma. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle An Institutional Retrospective Analysis of 93 Patients with Brain Metastases from Breast Cancer: Treatment Outcomes, Diagnosis-Specific Prognostic Factors
Int. J. Mol. Sci. 2012, 13(12), 16489-16499; doi:10.3390/ijms131216489
Received: 1 November 2012 / Revised: 29 November 2012 / Accepted: 3 December 2012 / Published: 5 December 2012
Cited by 8 | PDF Full-text (184 KB) | HTML Full-text | XML Full-text
Abstract
To evaluate the prognostic factors and indexes of a series of 93 patients with breast cancer and brain metastases (BM) in a single institution. Treatment outcomes were evaluated according to the major prognostic indexes (RPA, BSBM, GPA scores) and breast cancer subtypes. Independent
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To evaluate the prognostic factors and indexes of a series of 93 patients with breast cancer and brain metastases (BM) in a single institution. Treatment outcomes were evaluated according to the major prognostic indexes (RPA, BSBM, GPA scores) and breast cancer subtypes. Independent prognostic factors for overall survival (OS) were identified. The median OS values according to GPA 0–1, 1.5–2, 2.5–3 and 3.5–4, were 4.5, 9.5, 14.2 and 19.1 months, respectively (p < 0.0001) and according to genetic subtypes, they were 5, 14.2, 16.5 and 17.1 months for basal-like, luminal A and B and HER, respectively (p = 0.04). Using multivariate analysis, we established a new grading system using the six factors that were identified as indicators of longer survival: age under 60 (p = 0.001), high KPS (p = 0.007), primary tumor control (p = 0.05), low number of extracranial metastases and BM (p = 0.01 and 0.0002, respectively) and triple negative subtype (p = 0.002). Three groups with significantly different median survival times were identified: 4.1, 9.5 and 26.3 months, respectively (p < 0.0001). Our new grading system shows that prognostic indexes could be improved by using more levels of classification and confirms the strength of biological prognostic factors. Full article
(This article belongs to the Special Issue Brain Metastasis)
Open AccessArticle Identification of Candidate Polymorphisms on Stress Oxidative and DNA Damage Repair Genes Related with Clinical Outcome in Breast Cancer Patients
Int. J. Mol. Sci. 2012, 13(12), 16500-16513; doi:10.3390/ijms131216500
Received: 10 October 2012 / Revised: 23 November 2012 / Accepted: 27 November 2012 / Published: 5 December 2012
Cited by 1 | PDF Full-text (507 KB) | HTML Full-text | XML Full-text
Abstract
Diverse polymorphisms have been associated with the predisposition to develop cancer. On fewer occasions, they have been related to the evolution of the disease and to different responses to treatment. Previous studies of our group have associated polymorphisms on genes related to oxidative
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Diverse polymorphisms have been associated with the predisposition to develop cancer. On fewer occasions, they have been related to the evolution of the disease and to different responses to treatment. Previous studies of our group have associated polymorphisms on genes related to oxidative stress (rs3736729 on GCLC and rs207454 on XDH) and DNA damage repair (rs1052133 on OGG1) with a predisposition to develop breast cancer. In the present work, we have evaluated the hypothesis that these polymorphisms also play a role in a patient’s survival. A population-based cohort study of 470 women diagnosed with primary breast cancer and a median follow up of 52.44 months was conducted to examine the disease-free and overall survival in rs3736729, rs207454 and rs1052133 genetic variants. Adjusted Cox regression analysis was used to that end. The Kaplan-Meier analysis shows that rs3736729 on GCLC presents a significant association with disease-free survival and overall survival. The polymorphisms rs1052133 on OGG1 and rs207454 on XDH show a trend of association with overall survival. The analysis based on hormonal receptor status revealed a stronger association. The CC genotype on rs207454 (XDH) was significantly associated with lower time of disease free survival (p = 0.024) in progesterone receptor negative (PGR−) patients and rs3736729 (GCLC) was significantly associated with disease free survival (p = 0.001) and overall survival (p = 0.012) in the subgroup of estrogen receptor negative (ER−) patients. This work suggests that unfavorable genetic variants in the rs207454 (XDH) and rs3736729 (GCLC) polymorphisms may act as predictors of the outcome in negative progesterone receptor and negative estrogen receptor breast cancer patients, respectively. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessArticle Phenolics and Antioxidant Activity of Mulberry Leaves Depend on Cultivar and Harvest Month in Southern China
Int. J. Mol. Sci. 2012, 13(12), 16544-16553; doi:10.3390/ijms131216544
Received: 12 October 2012 / Revised: 15 November 2012 / Accepted: 23 November 2012 / Published: 5 December 2012
Cited by 16 | PDF Full-text (345 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
To elucidate the effects of cultivar and harvest month on the phenolic content and antioxidant activity of mulberry leaves, four major phenolics, including chlorogenic acid (ChA), benzoic acid (BeA), rutin (Rut) and astragalin (Ast), were quantified using an HPLC-UV method. Leaves from six
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To elucidate the effects of cultivar and harvest month on the phenolic content and antioxidant activity of mulberry leaves, four major phenolics, including chlorogenic acid (ChA), benzoic acid (BeA), rutin (Rut) and astragalin (Ast), were quantified using an HPLC-UV method. Leaves from six mulberry cultivars, collected from April to October, were analyzed. The antioxidant activity of mulberry leaves was assessed by ferric reducing antioxidant power (FRAP), hydroxyl radical scavenging activity (HSA) and superoxide radical scavenging activity (SSA) assays. The results showed that the total values of the four phenolic compounds ranged from 2.3 dry weight (DW) to 4.2 mg/g DW, with ChA being the major compound. The mean total phenol (TP) content of the six cultivars ranged from 30.4 equivalents (GAE) mg/g DW to 44.7 GAE mg/g DW. Mulberry leaves harvested in May had the highest TP content. Moreover, the antioxidant activities of mulberry leaves harvested from April to October differed noticeably. In general, Kq 10 and May were considered to be a better cultivar and harvest month concerning phenolic content and antioxidant activity, respectively. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Chemical Composition and Biological Activities of the Essential Oils from Three Melaleuca Species Grown in Tunisia
Int. J. Mol. Sci. 2012, 13(12), 16580-16591; doi:10.3390/ijms131216580
Received: 25 September 2012 / Revised: 25 October 2012 / Accepted: 29 November 2012 / Published: 5 December 2012
Cited by 5 | PDF Full-text (191 KB) | HTML Full-text | XML Full-text
Abstract
The chemical composition of the essential oils of Melaleuca armillaris Sm., Melaleuca styphelioides Sm. and Melaleuca acuminata F. Muell., collected in Tunisia, was studied by means of GC and GC-MS analysis. In all, 46 compounds were identified, 38 for M. armillaris, 20
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The chemical composition of the essential oils of Melaleuca armillaris Sm., Melaleuca styphelioides Sm. and Melaleuca acuminata F. Muell., collected in Tunisia, was studied by means of GC and GC-MS analysis. In all, 46 compounds were identified, 38 for M. armillaris, 20 for M. acuminata and eight for M. styphelioides, respectively. The presence of a sesquiterpenic fraction (52.2%) characterized the oil from M. armillaris; M. sthypheliodes oil was rich in methyl eugenol, a phenolic compound (91.1%), while M. acuminata oil is mainly constituted by oxygenated monoterpenoids (95.6%). The essential oils were evaluated for their in vitro potentially phytotoxic activity against germination and initial radicle growth of Raphanus sativus L., Lepidium sativum L., Sinapis arvensis L., Triticum durum L. and Phalaris canariensis L. seeds. The radicle elongation of five seeds was inhibited at the highest doses tested, while germination of all seeds was not affected. Moreover, the essential oils showed low antimicrobial activity against eight selected microorganisms. Full article
Open AccessArticle Modulation of MDR1 and MRP3 Gene Expression in Lung Cancer Cells after Paclitaxel and Carboplatin Exposure
Int. J. Mol. Sci. 2012, 13(12), 16624-16635; doi:10.3390/ijms131216624
Received: 28 September 2012 / Revised: 20 November 2012 / Accepted: 26 November 2012 / Published: 5 December 2012
Cited by 5 | PDF Full-text (458 KB) | HTML Full-text | XML Full-text
Abstract
Carboplatin-paclitaxel is a reference regimen in the treatment of locally advanced or disseminated non-small cell lung cancer (NSCLC). This paper discusses the multidrug resistance developed with this drug combination, which is one of the major obstacles to successful treatment. In order to understand
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Carboplatin-paclitaxel is a reference regimen in the treatment of locally advanced or disseminated non-small cell lung cancer (NSCLC). This paper discusses the multidrug resistance developed with this drug combination, which is one of the major obstacles to successful treatment. In order to understand and overcome the drug resistance pattern of NSCLC after carboplatin plus paclitaxel exposure, levels of mRNA expression of multidrug resistance 1 (MDR1) and multidrug resistance-associated protein 3 (MRP3) were investigated in primary NSCLC cell lines (A-549 and A-427) and a metastasis-derived NSCLC cell line (NODO). Our results showed that exposure of the three NSCLC lines to plasma concentrations of paclitaxel (5 μM) produced an increase in MDR1 expression, while MRP3 showed no alteration in expression. By contrast, the same cells exposed to carboplatin plasma concentrations (30 μM) showed overexpression of MRP3. In these cells, MDR1 showed no expression changes. Interestingly, the combination of both paclitaxel and carboplatin caused increased expression of the MDR1 drug resistance gene rather than the individual treatments. These results suggest that carboplatin and paclitaxel may induce drug resistance mediated by MDR1 and MRP3, which may be enhanced by the simultaneous use of both drugs. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle XRCC3 Gene Polymorphism Is Associated with Survival in Japanese Lung Cancer Patients
Int. J. Mol. Sci. 2012, 13(12), 16658-16667; doi:10.3390/ijms131216658
Received: 28 September 2012 / Revised: 7 November 2012 / Accepted: 28 November 2012 / Published: 5 December 2012
Cited by 9 | PDF Full-text (247 KB) | HTML Full-text | XML Full-text
Abstract
We focused on OGG1 Ser326Cys, MUTYH Gln324His, APEX1 Asp148Glu, XRCC1 Arg399Gln, and XRCC3 Thr241Met and examined the relationship between the different genotypes and survival of Japanese lung cancer patients. A total of 99 Japanese lung cancer patients were recruited into our study. Clinical
[...] Read more.
We focused on OGG1 Ser326Cys, MUTYH Gln324His, APEX1 Asp148Glu, XRCC1 Arg399Gln, and XRCC3 Thr241Met and examined the relationship between the different genotypes and survival of Japanese lung cancer patients. A total of 99 Japanese lung cancer patients were recruited into our study. Clinical data were collected, and genotypes of the target genes were identified by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP). Survival analysis to verify the impact of these gene polymorphisms on the clinical outcome of lung cancer showed that lung squamous cell carcinoma patients with the Thr/Met genotype at XRCC3 had a significantly shorter survival time than those with the Thr/Thr genotype (13 months versus 48 months; log-rank test, p < 0.0001). Cox regression analysis showed that the carriers of XRCC3 genotypes were at a significantly higher risk [adjusted hazard ratio (HR) = 9.35, 95% confidence interval (CI) = 2.52–34.68, p = 0.001; adjusted HR = 9.05, 95% CI = 1.89–44.39, p = 0.006]. Our results suggest that XRCC3 Thr241Met may act as a favorable prognostic indicator for lung squamous cell carcinoma patients. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle UVA Irradiation of Dysplastic Keratinocytes: Oxidative Damage versus Antioxidant Defense
Int. J. Mol. Sci. 2012, 13(12), 16718-16736; doi:10.3390/ijms131216718
Received: 5 September 2012 / Revised: 13 November 2012 / Accepted: 29 November 2012 / Published: 6 December 2012
Cited by 2 | PDF Full-text (1050 KB) | HTML Full-text | XML Full-text
Abstract
UVA affects epidermal cell physiology in a complex manner, but the harmful effects have been studied mainly in terms of DNA damage, mutagenesis and carcinogenesis. We investigated UVA effects on membrane integrity and antioxidant defense of dysplastic keratinocytes after one and two hours
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UVA affects epidermal cell physiology in a complex manner, but the harmful effects have been studied mainly in terms of DNA damage, mutagenesis and carcinogenesis. We investigated UVA effects on membrane integrity and antioxidant defense of dysplastic keratinocytes after one and two hours of irradiation, both immediately after exposure, and 24 h post-irradiation. To determine the UVA oxidative stress on cell membrane, lipid peroxidation was correlated with changes in fatty acid levels. Membrane permeability and integrity were assessed by propidium iodide staining and lactate dehydrogenase release. The effects on keratinocyte antioxidant protection were investigated in terms of catalase activity and expression. Lipid peroxidation increased in an exposure time-dependent manner. UVA exposure decreased the level of polyunsaturated fatty acids, which gradually returned to its initial value. Lactate dehydrogenase release showed a dramatic loss in membrane integrity after 2 h minimum of exposure. The cell ability to restore membrane permeability was noted at 24 h post-irradiation (for one hour exposure). Catalase activity decreased in an exposure time-dependent manner. UVA-irradiated dysplastic keratinocytes developed mechanisms leading to cell protection and survival, following a non-lethal exposure. The surviving cells gained an increased resistance to apoptosis, suggesting that their pre-malignant status harbors an abnormal ability to control their fate. Full article
(This article belongs to the Special Issue UV-Induced Cell Death 2012)
Open AccessArticle Inhibitor of Apoptosis Protein-Like Protein-2 as a Novel Serological Biomarker for Breast Cancer
Int. J. Mol. Sci. 2012, 13(12), 16737-16750; doi:10.3390/ijms131216737
Received: 28 September 2012 / Revised: 22 November 2012 / Accepted: 30 November 2012 / Published: 7 December 2012
Cited by 7 | PDF Full-text (510 KB) | HTML Full-text | XML Full-text
Abstract
Inhibitor of apoptosis protein-like protein-2 (ILP-2) has only been detected in the testis and in lymphoblastoid cells. Although previous studies have not reported the presence of ILP-2 in breast cancer tissues, this study indicates the presence of ILP-2 in breast cancer serum samples.
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Inhibitor of apoptosis protein-like protein-2 (ILP-2) has only been detected in the testis and in lymphoblastoid cells. Although previous studies have not reported the presence of ILP-2 in breast cancer tissues, this study indicates the presence of ILP-2 in breast cancer serum samples. To validate whether ILP-2 is a novel serological biomarker for breast cancer, we conducted two-dimensional gel electrophoresis (2DE) and matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis on 400 breast cancer serum samples and 40 non-cancer serum samples (i.e., healthy controls). We then performed a Western blot analysis of 10 breast cancer serum samples and 10 non-cancer serum samples. Finally, we analyzed 35 serum samples from healthy controls or subjects with breast cancer, other types of cancer, galactophore hyperplasia or breast cancer post-surgery by using 2DE and enzyme-linked immunosorbent assay. Our results indicate that ILP-2 is a novel breast cancer biomarker in the peripheral blood. Full article
(This article belongs to the Special Issue Advances in Cancer Diagnosis)
Open AccessArticle Isolation and Characterization of Eleven Polymorphic Microsatellite Loci for the Valuable Medicinal Plant Dendrobium huoshanense and Cross-Species Amplification
Int. J. Mol. Sci. 2012, 13(12), 16779-16784; doi:10.3390/ijms131216779
Received: 12 September 2012 / Revised: 14 November 2012 / Accepted: 29 November 2012 / Published: 7 December 2012
Cited by 7 | PDF Full-text (182 KB) | HTML Full-text | XML Full-text
Abstract
Dendrobium huoshanense (Orchidaceae) is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM) endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify
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Dendrobium huoshanense (Orchidaceae) is a perennial herb and a widely used medicinal plant in Traditional Chinese medicine (TCM) endemic to Huoshan County town in Anhui province in Southeast China. A microsatellite-enriched genomic DNA library of D. huoshanense was developed and screened to identify marker loci. Eleven polymorphic loci were isolated and analyzed by screening 25 individuals collected from a natural population. The number of alleles per locus ranged from 2 to 5. The observed and expected heterozygosities ranged from 0.227 to 0.818 and from 0.317 to 0.757, respectively. Two loci showed significant deviations from Hardy-Weinberg equilibrium and four of the pairwise comparisons of loci revealed linkage disequilibrium (p < 0.05). These microsatellite loci were cross-amplified for five congeneric species and seven loci can be amplified in all species. These simple sequence repeats (SSR) markers are useful in genetic studies of D. huoshanense and other related species and in conservation decision-making. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Antiviral Activity of Baicalein and Quercetin against the Japanese Encephalitis Virus
Int. J. Mol. Sci. 2012, 13(12), 16785-16795; doi:10.3390/ijms131216785
Received: 28 September 2012 / Revised: 7 November 2012 / Accepted: 8 November 2012 / Published: 7 December 2012
Cited by 24 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
Japanese encephalitis (JE), a mosquito-borne viral disease, is endemic to the entire east and southeast Asia, and some other parts of the world. Currently, there is no effective therapeutic available for JE; therefore, finding the effective antiviral agent against JEV replication is crucial.
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Japanese encephalitis (JE), a mosquito-borne viral disease, is endemic to the entire east and southeast Asia, and some other parts of the world. Currently, there is no effective therapeutic available for JE; therefore, finding the effective antiviral agent against JEV replication is crucial. In the present study, the in vitro antiviral activity of baicalein and quercetin, two purportedly antiviral bioflavonoids, was evaluated against Japanese encephalitis virus (JEV) replication in Vero cells. Anti-JEV activities of these compounds were examined on different stages of JEV replication cycle. The effects of the compounds on virus replication were determined by foci forming unit reduction assay (FFURA) and quantitative RT-PCR. Baicalein showed potent antiviral activity with IC50 = 14.28 µg/mL when it was introduced to the Vero cells after adsorption of JEV. Quercetin exhibited weak anti-JEV effects with IC50 = 212.1 µg/mL when the JEV infected cells were treated with the compound after virus adsorption. However, baicalein exhibited significant effect against JEV adsorption with IC50 = 7.27 µg/mL while quercetin did not show any anti-adsorption activity. Baicalein also exhibited direct extracellular virucidal activity on JEV with IC50 = 3.44 µg/mL. However, results of quantitative RT-PCR experiments confirmed the findings from FFURA. This study demonstrated that baicalein should be considered as an appropriate candidate for further investigations, such as the study of molecular and cellular mechanism(s) of action and in vivo evaluation for the development of an effective antiviral compound against Japanese encephalitis virus. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Actinopyga lecanora Hydrolysates as Natural Antibacterial Agents
Int. J. Mol. Sci. 2012, 13(12), 16796-16811; doi:10.3390/ijms131216796
Received: 25 October 2012 / Accepted: 1 December 2012 / Published: 7 December 2012
Cited by 9 | PDF Full-text (424 KB) | HTML Full-text | XML Full-text
Abstract
Actinopyga lecanora, a type of sea cucumber commonly known as stone fish with relatively high protein content, was explored as raw material for bioactive peptides production. Six proteolytic enzymes, namely alcalase, papain, pepsin, trypsin, bromelain and flavourzyme were used to hydrolyze A.
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Actinopyga lecanora, a type of sea cucumber commonly known as stone fish with relatively high protein content, was explored as raw material for bioactive peptides production. Six proteolytic enzymes, namely alcalase, papain, pepsin, trypsin, bromelain and flavourzyme were used to hydrolyze A. lecanora at different times and their respective degrees of hydrolysis (DH) were calculated. Subsequently, antibacterial activity of the A. lecanora hydrolysates, against some common pathogenic Gram positive bacteria (Bacillus subtilis and Staphylococcus aureus) and Gram negative bacteria (Escherichia coli, Pseudomonas aeruginosa, and Pseudomonas sp.) were evaluated. Papain hydrolysis showed the highest DH value (89.44%), followed by alcalase hydrolysis (83.35%). Bromelain hydrolysate after one and seven hours of hydrolysis exhibited the highest antibacterial activities against Pseudomonas sp., P. aeruginosa and E. coli at 51.85%, 30.07% and 30.45%, respectively compared to the other hydrolysates. Protein hydrolysate generated by papain after 8 h hydrolysis showed maximum antibacterial activity against S. aureus at 20.19%. The potent hydrolysates were further fractionated using RP-HPLC and antibacterial activity of the collected fractions from each hydrolysate were evaluated, wherein among them only three fractions from the bromelain hydrolysates exhibited inhibitory activities against Pseudomonas sp., P. aeruginosa and E. coli at 24%, 25.5% and 27.1%, respectively and one fraction of papain hydrolysate showed antibacterial activity of 33.1% against S. aureus. The evaluation of the relationship between DH and antibacterial activities of papain and bromelain hydrolysates revealed a meaningful correlation of four and six order functions. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Phase Transformations of α-Alumina Made from Waste Aluminum via a Precipitation Technique
Int. J. Mol. Sci. 2012, 13(12), 16812-16821; doi:10.3390/ijms131216812
Received: 27 August 2012 / Revised: 23 November 2012 / Accepted: 30 November 2012 / Published: 7 December 2012
Cited by 11 | PDF Full-text (227 KB) | HTML Full-text | XML Full-text
Abstract
We report on a recycling project in which α-Al2O3 was produced from aluminum cans because no such work has been reported in literature. Heated aluminum cans were mixed with 8.0 M of H2SO4 solution to form an
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We report on a recycling project in which α-Al2O3 was produced from aluminum cans because no such work has been reported in literature. Heated aluminum cans were mixed with 8.0 M of H2SO4 solution to form an Al2(SO4)3 solution. The Al2(SO4)3 salt was contained in a white semi-liquid solution with excess H2SO4; some unreacted aluminum pieces were also present. The solution was filtered and mixed with ethanol in a ratio of 2:3, to form a white solid of Al2(SO4)3·18H2O. The Al2(SO4)3·18H2O was calcined in an electrical furnace for 3 h at temperatures of 400–1400 °C. The heating and cooling rates were 10 °C /min. XRD was used to investigate the phase changes at different temperatures and XRF was used to determine the elemental composition in the alumina produced. A series of different alumina compositions, made by repeated dehydration and desulfonation of the Al2(SO4)3·18H2O, is reported. All transitional alumina phases produced at low temperatures were converted to α-Al2O3 at high temperatures. The X-ray diffraction results indicated that the α-Al2O3 phase was realized when the calcination temperature was at 1200 °C or higher. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Turn-On Fluorescent Chemosensor for Hg2+ Based on Multivalent Rhodamine Ligands
Int. J. Mol. Sci. 2012, 13(12), 16822-16832; doi:10.3390/ijms131216822
Received: 22 November 2012 / Accepted: 4 December 2012 / Published: 7 December 2012
Cited by 6 | PDF Full-text (1357 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rhodamine-based fluorescent chemosensors 1 and 2 exhibit selective fluorescence enhancement to Fe3+ and Hg2+ over other metal ions at 580 nm in CH3CN/H2O (3/1, v/v) solution. Bis(rhodamine) chemosensor 1, under optimized conditions (CH
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Rhodamine-based fluorescent chemosensors 1 and 2 exhibit selective fluorescence enhancement to Fe3+ and Hg2+ over other metal ions at 580 nm in CH3CN/H2O (3/1, v/v) solution. Bis(rhodamine) chemosensor 1, under optimized conditions (CH3CN/HEPES buffer (0.02 M, pH = 7.0) (95/5, v/v)), shows a high selectivity and sensitivity to Hg2+, with a linear working range of 0–50 μM, a wide pH span of 4–10, and a detection limit of 0.4 μM Hg2+. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle Changes in Molecular Characteristics of Cereal Carbohydrates after Processing and Digestion
Int. J. Mol. Sci. 2012, 13(12), 16833-16852; doi:10.3390/ijms131216833
Received: 11 October 2012 / Revised: 30 November 2012 / Accepted: 4 December 2012 / Published: 10 December 2012
Cited by 11 | PDF Full-text (616 KB) | HTML Full-text | XML Full-text
Abstract
Different extraction, purification and digestion methods were used to investigate the molecular properties of carbohydrates in arabinoxylan and β-glucan concentrates, dietary fiber (DF) rich breads and ileum content of bread fed pigs. The breads studied were: a low DF wheat bread (WF), whole
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Different extraction, purification and digestion methods were used to investigate the molecular properties of carbohydrates in arabinoxylan and β-glucan concentrates, dietary fiber (DF) rich breads and ileum content of bread fed pigs. The breads studied were: a low DF wheat bread (WF), whole meal rye bread (GR), rye bread with kernels (RK), wheat bread supplemented with wheat arabinoxylan concentrate (AX) and wheat bread supplemented with oat β-glucan concentrate (BG). The weight average molecular weight (Mw) of extractable carbohydrates in β-glucan concentrate decreased eight-fold after inclusion in the BG bread when exposed to in vitro digestion, while the Mw of purified extractable carbohydrates in AX bread was reduced two-fold, and remained almost unaffected until reaching the terminal ileum of pigs. Similarly, the Mw of purified extractable carbohydrates in GR and RK bread was not significantly changed in the ileum. The AX bread resulted in the highest concentration of dissolved arabinoxylan in the ileum among all the breads that caused a substantial increased in ileal AX viscosity. Nevertheless, for none of the breads, the Mw of extractable carbohydrates was related neither to the bread extract nor ileal viscosity. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Bacterial Over-Expression and Purification of the 3'phosphoadenosine 5'phosphosulfate (PAPS) Reductase Domain of Human FAD Synthase: Functional Characterization and Homology Modeling
Int. J. Mol. Sci. 2012, 13(12), 16880-16898; doi:10.3390/ijms131216880
Received: 10 October 2012 / Revised: 14 November 2012 / Accepted: 20 November 2012 / Published: 11 December 2012
Cited by 5 | PDF Full-text (1119 KB) | HTML Full-text | XML Full-text
Abstract
FAD synthase (FADS, EC 2.7.7.2) is a key enzyme in the metabolic pathway that converts riboflavin into the redox cofactor, FAD. Human FADS is organized in two domains: -the 3'phosphoadenosine 5'phosphosulfate (PAPS) reductase domain, similar to yeast Fad1p, at the C-terminus, and
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FAD synthase (FADS, EC 2.7.7.2) is a key enzyme in the metabolic pathway that converts riboflavin into the redox cofactor, FAD. Human FADS is organized in two domains: -the 3'phosphoadenosine 5'phosphosulfate (PAPS) reductase domain, similar to yeast Fad1p, at the C-terminus, and -the resembling molybdopterin-binding domain at the N-terminus. To understand whether the PAPS reductase domain of hFADS is sufficient to catalyze FAD synthesis, per se, and to investigate the role of the molybdopterin-binding domain, a soluble “truncated” form of hFADS lacking the N-terminal domain (Δ1-328-hFADS) has been over-produced and purified to homogeneity as a recombinant His-tagged protein. The recombinant Δ1-328-hFADS binds one mole of FAD product very tightly as the wild-type enzyme. Under turnover conditions, it catalyzes FAD assembly from ATP and FMN and, at a much lower rate, FAD pyrophosphorolytic hydrolysis. The Δ1-328-hFADS enzyme shows a slight, but not significant, change of Km values (0.24 and 6.23 µM for FMN and ATP, respectively) and of kcat (4.2 × 10−2 s−1) compared to wild-type protein in the forward direction. These results demonstrate that the molybdopterin-binding domain is not strictly required for catalysis. Its regulatory role is discussed in light of changes in divalent cations sensitivity of the Δ1-328-hFADS versus wild-type protein. Full article
(This article belongs to the Special Issue Flavins)
Open AccessArticle Electrochemical Characterization of Escherichia coli Adaptive Response Protein AidB
Int. J. Mol. Sci. 2012, 13(12), 16899-16915; doi:10.3390/ijms131216899
Received: 7 October 2012 / Revised: 26 November 2012 / Accepted: 3 December 2012 / Published: 11 December 2012
PDF Full-text (653 KB) | HTML Full-text | XML Full-text
Abstract
When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB) in repairing DNA lesions has been well characterized, while the function of
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When exposed to known DNA-damaging alkylating agents, Escherichia coli cells increase production of four DNA repair enzymes: Ada, AlkA, AlkB, and AidB. The role of three enzymes (Ada, AlkA, and AlkB) in repairing DNA lesions has been well characterized, while the function of AidB is poorly understood. AidB has a distinct cofactor that is potentially related to the elusive role of AidB in adaptive response: a redox active flavin adenine dinucleotide (FAD). In this study, we report the thermodynamic redox properties of the AidB flavin for the first time, both for free protein and in the presence of potential substrates. We find that the midpoint reduction potential of the AidB flavin is within a biologically relevant window for redox chemistry at −181 mV, that AidB significantly stabilizes the flavin semiquinone, and that small molecule binding perturbs the observed reduction potential. Our electrochemical results combined with structural analysis allow for fresh comparisons between AidB and the homologous acyl-coenzyme A dehydrogenase (ACAD) family of enzymes. AidB exhibits several discrepancies from ACADs that suggest a novel catalytic mechanism distinct from that of the ACAD family enzymes. Full article
(This article belongs to the Special Issue Flavins)
Open AccessArticle Evaporation Rate of Water as a Function of a Magnetic Field and Field Gradient
Int. J. Mol. Sci. 2012, 13(12), 16916-16928; doi:10.3390/ijms131216916
Received: 3 October 2012 / Revised: 9 November 2012 / Accepted: 3 December 2012 / Published: 11 December 2012
Cited by 9 | PDF Full-text (1018 KB) | HTML Full-text | XML Full-text
Abstract
The effect of magnetic fields on water is still a highly controversial topic despite the vast amount of research devoted to this topic in past decades. Enhanced water evaporation in a magnetic field, however, is less disputed. The underlying mechanism for this phenomenon
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The effect of magnetic fields on water is still a highly controversial topic despite the vast amount of research devoted to this topic in past decades. Enhanced water evaporation in a magnetic field, however, is less disputed. The underlying mechanism for this phenomenon has been investigated in previous studies. In this paper, we present an investigation of the evaporation of water in a large gradient magnetic field. The evaporation of pure water at simulated gravity positions (0 gravity level (ab. g), 1 g, 1.56 g and 1.96 g) in a superconducting magnet was compared with that in the absence of the magnetic field. The results showed that the evaporation of water was indeed faster in the magnetic field than in the absence of the magnetic field. Furthermore, the amount of water evaporation differed depending on the position of the sample within the magnetic field. In particular, the evaporation at 0 g was clearly faster than that at other positions. The results are discussed from the point of view of the evaporation surface area of the water/air interface and the convection induced by the magnetization force due to the difference in the magnetic susceptibility of water vapor and the surrounding air. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Oxidative Stress Mediated-Alterations of the MicroRNA Expression Profile in Mouse Hippocampal Neurons
Int. J. Mol. Sci. 2012, 13(12), 16945-16960; doi:10.3390/ijms131216945
Received: 1 November 2012 / Revised: 21 November 2012 / Accepted: 29 November 2012 / Published: 11 December 2012
Cited by 24 | PDF Full-text (1148 KB) | HTML Full-text | XML Full-text
Abstract
Oxidative stress plays a critical role in the etiology and pathogenesis of neurodegenerative disorders, and the molecular mechanisms that control the neuron response to ROS have been extensively studied. However, the oxidative stress-effect on miRNA expression in hippocampal neurons has not been investigated,
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Oxidative stress plays a critical role in the etiology and pathogenesis of neurodegenerative disorders, and the molecular mechanisms that control the neuron response to ROS have been extensively studied. However, the oxidative stress-effect on miRNA expression in hippocampal neurons has not been investigated, and little is known on the effect of ROS-modulated miRNAs on cell function. In this study, H2O2 was used to stimulate the mouse primary hippocampal neurons to develop an oxidative stress cell model. The alterations of miRNAs expression were detected by microarray analysis and five miRNAs were validated by real-time RT-PCR. The bioinformatic analysis of deregulated miRNAs was performed to determine their potential roles in the pathogenesis of neurological disorders. We found that H2O2 mediated a total of 101 deregulated miRNAs, which mainly took part in the regulation of the MAPK pathway. Among them, miR-135b and miR-708 were up-regulated significantly and their targets were predicted to be involved in DNA recombination, protein ubiquitination, protein autophosphorylation and development of neurons. These results demonstrated that oxidative stress alters the miRNA expression profile of hippocampal neurons, and the deregulated miRNAs might play a potential role in the pathogenesis of neurodegenerative diseases, such as Alzheimer’s disease (AD). Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of Sesamin on Streptozotocin (STZ)-Induced NIT-1 Pancreatic β-Cell Damage
Int. J. Mol. Sci. 2012, 13(12), 16961-16970; doi:10.3390/ijms131216961
Received: 14 November 2012 / Revised: 4 December 2012 / Accepted: 5 December 2012 / Published: 11 December 2012
Cited by 6 | PDF Full-text (748 KB) | HTML Full-text | XML Full-text
Abstract
The protective effect of sesamin (SES) from sesame meal on NIT-1 pancreatic β-cells damaged by streptozotocin (STZ) in vitro was investigated. The cell viability, insulin secretion, the activity of superoxide dismutase(SOD), glutathione peroxidase (GSHpx) and the content of reduced glutathione (GSH) increased significantly
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The protective effect of sesamin (SES) from sesame meal on NIT-1 pancreatic β-cells damaged by streptozotocin (STZ) in vitro was investigated. The cell viability, insulin secretion, the activity of superoxide dismutase(SOD), glutathione peroxidase (GSHpx) and the content of reduced glutathione (GSH) increased significantly when incubated with SES (400, 200 µg mL−1). The content of malondialdehyde (MDA), nitric oxide (NO) production, and the activity of NO synthase (NOS), inducible NOS (iNOS), decreased significantly when incubated with SES. The destructive changes of NIT-1 cells were ameliorated when treated with SES under microscopic observation. These data suggested that SES had obvious protective effect on NIT-1 pancreatic β-cells damaged by STZ, which might be related to its effects of decreasing levels of β-cell-destroying factors such as oxidative stress and NO synthesis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Increased Insulin Sensitivity and Distorted Mitochondrial Adaptations during Muscle Unloading
Int. J. Mol. Sci. 2012, 13(12), 16971-16985; doi:10.3390/ijms131216971
Received: 23 September 2012 / Revised: 27 November 2012 / Accepted: 29 November 2012 / Published: 11 December 2012
Cited by 4 | PDF Full-text (382 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
We aimed to further investigate mitochondrial adaptations to muscle disuse and the consequent metabolic disorders. Male rats were submitted to hindlimb unloading (HU) for three weeks. Interestingly, HU increased insulin sensitivity index (ISI) and decreased blood level of triglyceride and insulin. In skeletal
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We aimed to further investigate mitochondrial adaptations to muscle disuse and the consequent metabolic disorders. Male rats were submitted to hindlimb unloading (HU) for three weeks. Interestingly, HU increased insulin sensitivity index (ISI) and decreased blood level of triglyceride and insulin. In skeletal muscle, HU decreased expression of pyruvate dehydrogenase kinase 4 (PDK4) and its protein level in mitochondria. HU decreased mtDNA content and mitochondrial biogenesis biomarkers. Dynamin-related protein (Drp1) in mitochondria and Mfn2 mRNA level were decreased significantly by HU. Our findings provide more extensive insight into mitochondrial adaptations to muscle disuse, involving the shift of fuel utilization towards glucose, the decreased mitochondrial biogenesis and the distorted mitochondrial dynamics. Full article
(This article belongs to the Special Issue Advances in Free Radicals in Biology and Medicine)
Open AccessArticle Effects of Schizonepetin on Activity and mRNA Expression of Cytochrome P450 Enzymes in Rats
Int. J. Mol. Sci. 2012, 13(12), 17006-17018; doi:10.3390/ijms131217006
Received: 20 August 2012 / Revised: 16 November 2012 / Accepted: 3 December 2012 / Published: 12 December 2012
Cited by 6 | PDF Full-text (262 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to find out whether Schizonepetin influences the pharmacokinetics of the main substrates drugs of CYP1A2, CYP3A1/2, CYP2E1, CYP2C19 and CYP2D6 in rats; the influence on the levels of CYP mRNA was also studied. Phenacetin, dapsone, chlorzoxazone, omeprazole
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The aim of this study was to find out whether Schizonepetin influences the pharmacokinetics of the main substrates drugs of CYP1A2, CYP3A1/2, CYP2E1, CYP2C19 and CYP2D6 in rats; the influence on the levels of CYP mRNA was also studied. Phenacetin, dapsone, chlorzoxazone, omeprazole and metoprolol were selected as probe substrates for CYP1A2, CYP3A1/2, CYP2E1, CYP2C19 and CYP2D6 respectively. HPLC methods were employed for the determination of these substrates in plasma and the pharmacokinetic parameters were calculated. Real-time RT-PCR was used to determine the effects of Schizonepetin on the mRNA expression of CYP3A1, CYP1A2 and CYP2E1 in the rat liver. After the rats were orally administrated with Schizonepetin once a day for seven consecutive days, there were significant differences in plasma concentration of phenacetin, dapsone, chlorzoxazone and metoprolol, but not omeprazole, as compared with pre-administration. In addition, Schizonepetin induced the expression of CYP3A1, CYP1A and CYP2E1 at dosages of 24 and 48 mg/kg. Our results indicated that Schizonepetin had significant induction effects on CYP3A1/2 and inhibition effects on CYP1A2, CYP2E1 or CYP2D6 as oriented from the pharmacokinetic profiles of the substrates. Moreover, in the mRNA expression levels, Schizonepetin could induce the mRNA expression of CYP3A1, CYP1A and CYP2E1. In conclusion, co-administration of some CYP substrates with Schizonepetin may lead to an undesirable herb-drug interaction. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Anti-Legionella dumoffii Activity of Galleria mellonella Defensin and Apolipophorin III
Int. J. Mol. Sci. 2012, 13(12), 17048-17064; doi:10.3390/ijms131217048
Received: 24 September 2012 / Revised: 21 November 2012 / Accepted: 5 December 2012 / Published: 12 December 2012
Cited by 18 | PDF Full-text (2024 KB) | HTML Full-text | XML Full-text
Abstract
The gram-negative bacterium Legionella dumoffii is, beside Legionella pneumophila, an etiological agent of Legionnaires’ disease, an atypical form of pneumonia. The aim of this study was to determine the antimicrobial activity of Galleria mellonella defense polypeptides against L. dumoffii. The extract
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The gram-negative bacterium Legionella dumoffii is, beside Legionella pneumophila, an etiological agent of Legionnaires’ disease, an atypical form of pneumonia. The aim of this study was to determine the antimicrobial activity of Galleria mellonella defense polypeptides against L. dumoffii. The extract of immune hemolymph, containing a mixture of defense peptides and proteins, exhibited a dose-dependent bactericidal effect on L. dumoffii. The bacterium appeared sensitive to a main component of the hemolymph extract, apolipophorin III, as well as to a defense peptide, Galleria defensin, used at the concentrations 0.4 mg/mL and 40 μg/mL, respectively. L. dumoffii cells cultured in the presence of choline were more susceptible to both defense factors analyzed. A transmission electron microscopy study of bacterial cells demonstrated that Galleria defensin and apolipophorin III induced irreversible cell wall damage and strong intracellular alterations, i.e., increased vacuolization, cytoplasm condensation and the appearance of electron-white spaces in electron micrographs. Our findings suggest that insects, such as G. mellonella, with their great diversity of antimicrobial factors, can serve as a rich source of compounds for the testing of Legionella susceptibility to defense-related peptides and proteins. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences 2012)
Open AccessArticle Plant Regeneration and Somatic Embryogenesis from Immature Embryos Derived through Interspecific Hybridization among Different Carica Species
Int. J. Mol. Sci. 2012, 13(12), 17065-17076; doi:10.3390/ijms131217065
Received: 5 September 2012 / Revised: 15 November 2012 / Accepted: 4 December 2012 / Published: 12 December 2012
Cited by 2 | PDF Full-text (1625 KB) | HTML Full-text | XML Full-text
Abstract
Plant regeneration and somatic embryogenesis through interspecific hybridization among different Carica species were studied for the development of a papaya ringspot virus-resistant variety. The maximum fruit sets were recorded from the cross of the native variety C. papaya cv. Shahi with the wild
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Plant regeneration and somatic embryogenesis through interspecific hybridization among different Carica species were studied for the development of a papaya ringspot virus-resistant variety. The maximum fruit sets were recorded from the cross of the native variety C. papaya cv. Shahi with the wild species C. cauliflora. The highest hybrid embryos were recorded at 90 days after pollination and the embryos were aborted at 150 days after pollination. The immature hybrid embryos were used for plant regeneration and somatic embryogenesis. The 90-day-old hybrid embryos from the cross of C. papaya cv. Shahi × C. cauliflora showed the highest percentage of germination, as well as plant regeneration on growth regulators free culture medium after 7 days pre-incubation on half-strength MS medium supplemented with 0.2 mg/L BAP, 0.5 mg/L NAA and 60 g/L sucrose. The 90-day-old hybrid embryos from the cross of C. papaya cv. Shahi × C. cauliflora produced maximum callus, as well as somatic embryos when cultured on half-strength MS medium containing 5 mg/L 2,4-D, 100 mg/L glutamine, 100 mg/L casein hydrolysate and 60 g/L sucrose. The somatic embryos were transferred into half-strength MS medium containing 0.5 mg/L BAP and 0.2 mg/L NAA and 60 g/L sucrose for maturation. The highest number of regenerated plants per hybrid embryo (10.33) was recorded from the cross of C. papaya cv. Shahi × C. cauliflora. Isoenzyme and dendrogram cluster analysis using UPGMA of the regenerated F1 plantlets confirmed the presence of the hybrid plantlets. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle High Density Lipoprotein Protects Mesenchymal Stem Cells from Oxidative Stress-Induced Apoptosis via Activation of the PI3K/Akt Pathway and Suppression of Reactive Oxygen Species
Int. J. Mol. Sci. 2012, 13(12), 17104-17120; doi:10.3390/ijms131217104
Received: 26 September 2012 / Revised: 11 November 2012 / Accepted: 4 December 2012 / Published: 13 December 2012
Cited by 30 | PDF Full-text (1917 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The therapeutic effect of transplantation of mesenchymal stem cells (MSCs) in myocardial infarction (MI) appears to be limited by poor cell viability in the injured tissue, which is a consequence of oxidative stress and pro-apoptotic factors. High density lipoprotein (HDL) reverses cholesterol transport
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The therapeutic effect of transplantation of mesenchymal stem cells (MSCs) in myocardial infarction (MI) appears to be limited by poor cell viability in the injured tissue, which is a consequence of oxidative stress and pro-apoptotic factors. High density lipoprotein (HDL) reverses cholesterol transport and has anti-oxidative and anti-apoptotic properties. We, therefore, investigated whether HDL could protect MSCs from oxidative stress-induced apoptosis. MSCs derived from the bone marrow of rats were pre-incubated with or without HDL, and then were exposed to hydrogen peroxide (H2O2) in vitro, or were transplanted into experimentally infarcted hearts of rats in vivo. Pre-incubation of MSCs with HDL increased cell viability, reduced apoptotic indices and resulted in parallel decreases in reactive oxygen species (ROS) in comparison with control MSCs. Each of the beneficial effects of HDL on MSCs was attenuated by inhibiting the PI3K/Akt pathway. Preconditioning with HDL resulted in higher MSC survival rates, improved cardiac remodeling and better myocardial function than in the MSC control group. Collectively, these results suggest that HDL may protect against H2O2-induced apoptosis in MSCs through activation of a PI3K/Akt pathway, and by suppressing the production of ROS. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Aptamer-Based Molecular Recognition of Lysergamine, Metergoline and Small Ergot Alkaloids
Int. J. Mol. Sci. 2012, 13(12), 17138-17159; doi:10.3390/ijms131217138
Received: 18 September 2012 / Revised: 26 November 2012 / Accepted: 5 December 2012 / Published: 14 December 2012
Cited by 10 | PDF Full-text (1122 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to
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Ergot alkaloids are mycotoxins produced by fungi of the genus Claviceps, which infect cereal crops and grasses. The uptake of ergot alkaloid contaminated cereal products can be lethal to humans and animals. For food safety assessment, analytical techniques are currently used to determine the presence of ergot alkaloids in food and feed samples. However, the number of samples which can be analyzed is limited, due to the cost of the equipment and the need for skilled personnel. In order to compensate for the lack of rapid tests for the detection of ergot alkaloids, the aim of this study was to develop a specific recognition element for ergot alkaloids, which could be further applied to produce a colorimetric reaction in the presence of these toxins. As recognition elements, single-stranded DNA ligands were selected by using an iterative selection procedure named SELEX, i.e., Systematic Evolution of Ligands by EXponential enrichment. After several selection cycles, the resulting aptamers were cloned and sequenced. A surface plasmon resonance analysis enabled determination of the dissociation constants of the complexes of aptamers and lysergamine. Dissociation constants in the nanomolar range were obtained with three selected aptamers. One of the selected aptamers, having a dissociation constant of 44 nM, was linked to gold nanoparticles and it was possible to produce a colorimetric reaction in the presence of lysergamine. This system could also be applied to small ergot alkaloids in an ergot contaminated flour sample. Full article
(This article belongs to the Section Molecular Recognition)
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Open AccessArticle Virtual Screening of Specific Insulin-Like Growth Factor 1 Receptor (IGF1R) Inhibitors from the National Cancer Institute (NCI) Molecular Database
Int. J. Mol. Sci. 2012, 13(12), 17185-17209; doi:10.3390/ijms131217185
Received: 10 October 2012 / Revised: 21 November 2012 / Accepted: 11 December 2012 / Published: 14 December 2012
PDF Full-text (675 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Insulin-like growth factor 1 receptor (IGF1R) is an attractive drug target for cancer therapy and research on IGF1R inhibitors has had success in clinical trials. A particular challenge in the development of specific IGF1R inhibitors is interference from insulin receptor (IR), which has
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Insulin-like growth factor 1 receptor (IGF1R) is an attractive drug target for cancer therapy and research on IGF1R inhibitors has had success in clinical trials. A particular challenge in the development of specific IGF1R inhibitors is interference from insulin receptor (IR), which has a nearly identical sequence. A few potent inhibitors that are selective for IGF1R have been discovered experimentally with the aid of computational methods. However, studies on the rapid identification of IGF1R-selective inhibitors using virtual screening and confidence-level inspections of ligands that show different interactions with IGF1R and IR in docking analysis are rare. In this study, we established virtual screening and binding-mode prediction workflows based on benchmark results of IGF1R and several kinase receptors with IGF1R-like structures. We used comprehensive analysis of the known complexes of IGF1R and IR with their binding ligands to screen specific IGF1R inhibitors. Using these workflows, 17 of 139,735 compounds in the NCI (National Cancer Institute) database were identified as potential specific inhibitors of IGF1R. Calculations of the potential of mean force (PMF) with GROMACS were further conducted for three of the identified compounds to assess their binding affinity differences towards IGF1R and IR. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Analysis of the Endoplasmic Reticulum Subproteome in the Livers of Type 2 Diabetic Mice
Int. J. Mol. Sci. 2012, 13(12), 17230-17243; doi:10.3390/ijms131217230
Received: 27 September 2012 / Revised: 30 November 2012 / Accepted: 12 December 2012 / Published: 17 December 2012
Cited by 4 | PDF Full-text (794 KB) | HTML Full-text | XML Full-text
Abstract
Type 2 diabetes is a chronic metabolic disease that results from insulin resistance in the liver, muscle, and adipose tissue and relative insulin deficiency. The endoplasmic reticulum (ER) plays a crucial role in the regulation of the cellular response to insulin. Recently, ER
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Type 2 diabetes is a chronic metabolic disease that results from insulin resistance in the liver, muscle, and adipose tissue and relative insulin deficiency. The endoplasmic reticulum (ER) plays a crucial role in the regulation of the cellular response to insulin. Recently, ER stress has been known to reduce the insulin sensitivity of the liver and lead to type 2 diabetes. However, detailed mechanisms of ER stress response that leads to type 2 diabetes remains unknown. To obtain a global view of ER function in type 2 diabetic liver and identify proteins that may be responsible for hepatic ER stress and insulin resistance, we performed proteomics analysis of mouse liver ER using nano UPLC-MSE. A total of 1584 proteins were identified in control C57 and type 2 diabetic db/db mice livers. Comparison of the rER and sER proteomes from normal mice showed that proteins involved in protein synthesis and metabolic process were enriched in the rER, while those associated with transport and cellular homeostasis were localized to the sER. In addition, proteins involved in protein folding and ER stress were found only in the rER. In the livers of db/db mice, however, the functions of the rER and sER were severely disrupted, including the capacity to resolve ER stress. These results provide new insight into the research on hepatic insulin resistance and type 2 diabetes and are suggestive of the potential use of the differentially expressed hepatic ER proteins as biomarkers for hepatic insulin resistance and type 2 diabetes. Full article
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Open AccessArticle Optimization of Synthesis, Characterization and Cytotoxic Activity of Seleno-Capparis spionosa L. Polysaccharide
Int. J. Mol. Sci. 2012, 13(12), 17275-17289; doi:10.3390/ijms131217275
Received: 21 August 2012 / Revised: 17 November 2012 / Accepted: 4 December 2012 / Published: 17 December 2012
Cited by 4 | PDF Full-text (1245 KB) | HTML Full-text | XML Full-text
Abstract
In this study, an experiment was designed to optimize the synthesis of seleno-Capparis spionosa L. polysaccharide (Se-CSPS) by response surface methodology. Three independent variables (reaction time, reaction temperature and ratio of Na2SeO3 to CSPS) were tested. Furthermore, the thermal
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In this study, an experiment was designed to optimize the synthesis of seleno-Capparis spionosa L. polysaccharide (Se-CSPS) by response surface methodology. Three independent variables (reaction time, reaction temperature and ratio of Na2SeO3 to CSPS) were tested. Furthermore, the thermal stability, particle size, shape and cytotoxic activity of Se-CSPS in vitro were investigated. The optimum reaction conditions were obtained shown as follows: reaction time 7.5 h, reaction temperature 71 °C, and ratio of Na2SeO3 to CSPS 0.9 g/g. Under these conditions, the Se content in Se-CSPS reached 5.547 mg/g, which was close to the predicted value (5.518 mg/g) by the model. The thermal stability, particle size and shape of Se-CSPS were significantly different from those of CSPS. Additionally, a MTT assay indicated that the Se-CSPS could inhibit the proliferation of human gastric cancer SGC-7901 cells in a dose-dependent manner. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessReview Identification of kakusei, a Nuclear Non-Coding RNA, as an Immediate Early Gene from the Honeybee, and Its Application for Neuroethological Study
Int. J. Mol. Sci. 2012, 13(12), 15496-15509; doi:10.3390/ijms131215496
Received: 29 October 2012 / Revised: 16 November 2012 / Accepted: 19 November 2012 / Published: 22 November 2012
Cited by 7 | PDF Full-text (4197 KB) | HTML Full-text | XML Full-text
Abstract
The honeybee is a social insect that exhibits various social behaviors. To elucidate the neural basis of honeybee behavior, we detected neural activity in freely-moving honeybee workers using an immediate early gene (IEG) that is expressed in a neural activity-dependent manner. In European
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The honeybee is a social insect that exhibits various social behaviors. To elucidate the neural basis of honeybee behavior, we detected neural activity in freely-moving honeybee workers using an immediate early gene (IEG) that is expressed in a neural activity-dependent manner. In European honeybees (Apis mellifera), we identified a novel nuclear non-coding RNA, termed kakusei, as the first insect IEG, and revealed the neural activity pattern in foragers. In addition, we isolated a homologue of kakusei, termed Acks, from the Japanese honeybee (Apis cerana), and detected active neurons in workers fighting with the giant hornet. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessReview Elevated Levels of Lewis Y and Integrin α5β1 Correlate with Chemotherapeutic Drug Resistance in Epithelial Ovarian Carcinoma
Int. J. Mol. Sci. 2012, 13(12), 15588-15600; doi:10.3390/ijms131215588
Received: 22 October 2012 / Revised: 9 November 2012 / Accepted: 12 November 2012 / Published: 23 November 2012
Cited by 8 | PDF Full-text (645 KB) | HTML Full-text | XML Full-text
Abstract
Objective: To measure Lewis y and integrin α5β1 expression in epithelial ovarian carcinoma and to correlate the levels of these molecules with ovarian carcinoma chemotherapy and prognosis. Methods: The study population included 34 ovarian carcinoma patients with chemotherapeutic drug-resistance, six
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Objective: To measure Lewis y and integrin α5β1 expression in epithelial ovarian carcinoma and to correlate the levels of these molecules with ovarian carcinoma chemotherapy and prognosis. Methods: The study population included 34 ovarian carcinoma patients with chemotherapeutic drug-resistance, six partially drug-sensitive cases, and 52 drug-sensitive cases (92 total). Immunochemistry was used to determine expression of Lewis y antigen and integrin α5β1 in ovarian carcinoma tissues, and correlation of these molecules with chemotherapy resistance was further investigated, Multi-factor logistic regression analysis was applied to investigate: age, surgical stage, grade, subtype of patient cases, metastasis of lymph nodes, residual tumor size, expression levels of Lewis y antigen and integrin α5β1 correlation with ovarian carcinoma chemotherapy resistance. Results: The expression rates of Lewis y antigen and integrins α5 and β1 were significantly greater in the drug-resistant group (91.17%, 85.29%, 88.24%) than the partially sensitive (50.00%, 33.33%, 50.00%) or sensitive groups (61.54%, 57.69%, 55.77%). Binary logistic regression analysis revealed that surgical stage, residual tumor size, and expression of integrin α5 and Lewis y in ovarian carcinoma tissues were independent risk factors for chemotherapeutic drug resistance. Conclusions: Overexpression of Lewis y and integrin α5 are strong risk factors for chemotherapeutic drug resistance in ovarian carcinoma patients. Full article
Open AccessReview Form Follows Function: Structural and Catalytic Variation in the Class A Flavoprotein Monooxygenases
Int. J. Mol. Sci. 2012, 13(12), 15601-15639; doi:10.3390/ijms131215601
Received: 21 September 2012 / Revised: 8 November 2012 / Accepted: 9 November 2012 / Published: 23 November 2012
Cited by 9 | PDF Full-text (2595 KB) | HTML Full-text | XML Full-text
Abstract
Flavoprotein monooxygenases (FPMOs) exhibit an array of mechanistic solutions to a common chemical objective; the monooxygenation of a target substrate. Each FPMO efficiently couples reduction of a flavin cofactor by NAD(P)H to oxygenation of the target substrate via a (hydro)peroxyflavin intermediate. This purpose
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Flavoprotein monooxygenases (FPMOs) exhibit an array of mechanistic solutions to a common chemical objective; the monooxygenation of a target substrate. Each FPMO efficiently couples reduction of a flavin cofactor by NAD(P)H to oxygenation of the target substrate via a (hydro)peroxyflavin intermediate. This purpose of this review is to describe in detail the Class A flavoprotein hydroxylases (FPMO) in the context of the other FPMO classes (B–F). Both one and two component FPMOs are found in nature. Two-component enzymes require, in addition to the monooxygenase, the involvement of a reductase that first catalyzes the reduction of the flavin by NAD(P)H. The Class A and B FPMOs are single-component and manage to orchestrate the same net reaction within a single peptide. The Class A enzymes have, by some considerable margin, the most complete research record. These enzymes use choreographed movements of the flavin ring that facilitate access of the organic substrates to the active site, provide a means for interaction of NADPH with the flavin, offer a mechanism to sequester the dioxygen reduction chemistry from solvent and a means to release the product. The majority of the discrete catalytic events of the catalytic cycle can be observed directly in exquisite detail using spectrophotometric kinetic methods and many of the key mechanistic conclusions are further supported by structural data. This review attempts to compile each of the key observations made for both paradigm and newly discovered examples of Class A FPMOs into a complete catalytic description of one enzymatic turnover. Full article
(This article belongs to the Special Issue Flavins)
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Open AccessReview Heat Shock Protein 90 in Plants: Molecular Mechanisms and Roles in Stress Responses
Int. J. Mol. Sci. 2012, 13(12), 15706-15723; doi:10.3390/ijms131215706
Received: 28 September 2012 / Revised: 29 October 2012 / Accepted: 29 October 2012 / Published: 23 November 2012
Cited by 16 | PDF Full-text (238 KB) | HTML Full-text | XML Full-text
Abstract
The heat shock protein 90 (Hsp90) family mediates stress signal transduction, and plays important roles in the control of normal growth of human cells and in promoting development of tumor cells. Hsp90s have become a currently important subject in cellular immunity, signal transduction,
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The heat shock protein 90 (Hsp90) family mediates stress signal transduction, and plays important roles in the control of normal growth of human cells and in promoting development of tumor cells. Hsp90s have become a currently important subject in cellular immunity, signal transduction, and anti-cancer research. Studies on the physiological functions of Hsp90s began much later in plants than in animals and fungi. Significant progress has been made in understanding complex mechanisms of HSP90s in plants, including ATPase-coupled conformational changes and interactions with cochaperone proteins. A wide range of signaling proteins interact with HSP90s. Recent studies revealed that plant Hsp90s are important in plant development, environmental stress response, and disease and pest resistance. In this study, the plant HSP90 family was classified into three clusters on the basis of phylogenetic relationships, gene structure, and biological functions. We discuss the molecular functions of Hsp90s, and systematically review recent progress of Hsp90 research in plants. Full article
Open AccessReview RORα, a Potential Tumor Suppressor and Therapeutic Target of Breast Cancer
Int. J. Mol. Sci. 2012, 13(12), 15755-15766; doi:10.3390/ijms131215755
Received: 12 October 2012 / Revised: 17 November 2012 / Accepted: 19 November 2012 / Published: 26 November 2012
Cited by 9 | PDF Full-text (269 KB) | HTML Full-text | XML Full-text
Abstract
The function of the nuclear receptor (NR) in breast cancer progression has been investigated for decades. The majority of the nuclear receptors have well characterized natural ligands, but a few of them are orphan receptors for which no ligand has been identified. RORα,
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The function of the nuclear receptor (NR) in breast cancer progression has been investigated for decades. The majority of the nuclear receptors have well characterized natural ligands, but a few of them are orphan receptors for which no ligand has been identified. RORα, one member of the retinoid orphan nuclear receptor (ROR) subfamily of orphan receptors, regulates various cellular and pathological activities. RORα is commonly down-regulated and/or hypoactivated in breast cancer compared to normal mammary tissue. Expression of RORα suppresses malignant phenotypes in breast cancer cells, in vitro and in vivo. Activity of RORα can be categorized into the canonical and non-canonical nuclear receptor pathways, which in turn regulate various breast cancer cellular function, including cell proliferation, apoptosis and invasion. This information suggests that RORα is a potent tumor suppressor and a potential therapeutic target for breast cancer. Full article
(This article belongs to the Special Issue Signalling Molecules and Signal Transduction in Cells)
Open AccessReview The Role of Sox Genes in Lung Morphogenesis and Cancer
Int. J. Mol. Sci. 2012, 13(12), 15767-15783; doi:10.3390/ijms131215767
Received: 25 September 2012 / Revised: 26 October 2012 / Accepted: 14 November 2012 / Published: 26 November 2012
Cited by 11 | PDF Full-text (442 KB) | HTML Full-text | XML Full-text
Abstract
The human lung consists of multiple cell types derived from early embryonic compartments. The morphogenesis of the lung, as well as the injury repair of the adult lung, is tightly controlled by a network of signaling pathways with key transcriptional factors. Lung cancer
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The human lung consists of multiple cell types derived from early embryonic compartments. The morphogenesis of the lung, as well as the injury repair of the adult lung, is tightly controlled by a network of signaling pathways with key transcriptional factors. Lung cancer is the third most cancer-related death in the world, which may be developed due to the failure of regulating the signaling pathways. Sox (sex-determining region Y (Sry) box-containing) family transcriptional factors have emerged as potent modulators in embryonic development, stem cells maintenance, tissue homeostasis, and cancerogenesis in multiple processes. Recent studies demonstrated that the members of the Sox gene family played important roles in the development and maintenance of lung and development of lung cancer. In this context, we summarize our current understanding of the role of Sox family transcriptional factors in the morphogenesis of lung, their oncogenic potential in lung cancer, and their potential impact in the diagnosis, prognosis, and targeted therapy of lung cancer. Full article
(This article belongs to the Special Issue Advances in Cancer Diagnosis)
Open AccessReview Brain Metastases from Colorectal Cancer: Microenvironment and Molecular Mechanisms
Int. J. Mol. Sci. 2012, 13(12), 15784-15800; doi:10.3390/ijms131215784
Received: 8 October 2012 / Revised: 5 November 2012 / Accepted: 12 November 2012 / Published: 26 November 2012
Cited by 5 | PDF Full-text (189 KB) | HTML Full-text | XML Full-text
Abstract
Colorectal cancer is one of the most common digestive tract malignancies in the world. Owing to the newer and more effective systemic therapies, the life of colorectal cancer patients can be remarkably prolonged, and the incidence of brain metastases is increasing. However, little
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Colorectal cancer is one of the most common digestive tract malignancies in the world. Owing to the newer and more effective systemic therapies, the life of colorectal cancer patients can be remarkably prolonged, and the incidence of brain metastases is increasing. However, little is known about the underlying mechanisms of brain metastasis from colorectal cancer. Here we review the tumor microenvironment and metastasis associated molecules in brain metastases from colorectal cancer. A further understanding of these mechanisms will help us to propose better strategies for colorectal cancer patients with brain metastasis and improve their life quality. Full article
(This article belongs to the Special Issue Brain Metastasis)
Open AccessReview DNA Damage and Repair in Epithelium after Allogeneic Hematopoietic Stem Cell Transplantation
Int. J. Mol. Sci. 2012, 13(12), 15813-15825; doi:10.3390/ijms131215813
Received: 19 October 2012 / Revised: 18 November 2012 / Accepted: 19 November 2012 / Published: 27 November 2012
Cited by 2 | PDF Full-text (1247 KB) | HTML Full-text | XML Full-text
Abstract
Allogeneic hematopoietic stem cell transplantation (allo-HSCT) in humans, following hematoablative treatment, results in biological chimeras. In this case, the transplanted hematopoietic, immune cells and their derivatives can be considered the donor genotype, while the other tissues are the recipient genotype. The first sequel,
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Allogeneic hematopoietic stem cell transplantation (allo-HSCT) in humans, following hematoablative treatment, results in biological chimeras. In this case, the transplanted hematopoietic, immune cells and their derivatives can be considered the donor genotype, while the other tissues are the recipient genotype. The first sequel, which has been recognized in the development of chimerical organisms after allo-HSCT, is the graft versus host (GvH) reaction, in which the new developed immune cells from the graft recognize the host’s epithelial cells as foreign and mount an inflammatory response to kill them. There is now accumulating evidence that this chronic inflammatory tissue stress may contribute to clinical consequences in the transplant recipient. It has been recently reported that host epithelial tissue acquire genomic alterations and display a mutator phenotype that may be linked to the occurrence of a GvH reaction. The current review discusses existing data on this recently discovered phenomenon and focuses on the possible pathogenesis, clinical significance and therapeutic implications. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview MicroRNAs in Metal Stress: Specific Roles or Secondary Responses?
Int. J. Mol. Sci. 2012, 13(12), 15826-15847; doi:10.3390/ijms131215826
Received: 1 November 2012 / Revised: 20 November 2012 / Accepted: 21 November 2012 / Published: 27 November 2012
Cited by 34 | PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
In plants, microRNAs (miRNAs) control various biological processes by negatively regulating the expression of complementary target genes, either (1) post-transcriptionally by cleavage or translational inhibition of target mRNA, or (2) transcriptionally by methylation of target DNA. Besides their role in developmental processes, miRNAs
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In plants, microRNAs (miRNAs) control various biological processes by negatively regulating the expression of complementary target genes, either (1) post-transcriptionally by cleavage or translational inhibition of target mRNA, or (2) transcriptionally by methylation of target DNA. Besides their role in developmental processes, miRNAs are main players in stress responses, including metal stress responses. Exposure of plants to excess metal concentrations disturbs the cellular redox balance and enhances ROS accumulation, eventually leading to oxidative damage or signaling. Plants modify their gene expression by the activity of miRNAs in response to metal toxicity to regulate (1) complexation of excess metals, (2) defense against oxidative stress and (3) signal transduction for controlling various biological responses. This review focuses on the biogenesis, working mechanisms and functioning of miRNAs in plants. In a final part, our current knowledge on the regulatory roles of miRNAs in plant metal stress responses is highlighted, and whether stress-regulated miRNAs have specific roles or are secondary consequences is discussed. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessReview Optimization of the Bacterial Cytochrome P450 BM3 System for the Production of Human Drug Metabolites
Int. J. Mol. Sci. 2012, 13(12), 15901-15924; doi:10.3390/ijms131215901
Received: 27 September 2012 / Revised: 1 November 2012 / Accepted: 13 November 2012 / Published: 28 November 2012
Cited by 23 | PDF Full-text (461 KB) | HTML Full-text | XML Full-text
Abstract
Drug metabolism in human liver is a process involving many different enzymes. Among them, a number of cytochromes P450 isoforms catalyze the oxidation of most of the drugs commercially available. Each P450 isoform acts on more than one drug, and one drug may
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Drug metabolism in human liver is a process involving many different enzymes. Among them, a number of cytochromes P450 isoforms catalyze the oxidation of most of the drugs commercially available. Each P450 isoform acts on more than one drug, and one drug may be oxidized by more than one enzyme. As a result, multiple products may be obtained from the same drug, and as the metabolites can be biologically active and may cause adverse drug reactions (ADRs), the metabolic profile of a new drug has to be known before this can be commercialized. Therefore, the metabolites of a certain drug must be identified, synthesized and tested for toxicity. Their synthesis must be in sufficient quantities to be used for metabolic tests. This review focuses on the progresses done in the field of the optimization of a bacterial self-sufficient and efficient cytochrome P450, P450 BM3 from Bacillus megaterium, used for the production of metabolites of human enzymes. The progress made in the improvement of its catalytic performance towards drugs, the substitution of the costly NADPH cofactor and its immobilization and scale-up of the process for industrial application are reported. Full article
(This article belongs to the Special Issue Enzyme Optimization and Immobilization)
Open AccessReview Asymmetric Dimethyarginine as Marker and Mediator in Ischemic Stroke
Int. J. Mol. Sci. 2012, 13(12), 15983-16004; doi:10.3390/ijms131215983
Received: 28 September 2012 / Revised: 14 November 2012 / Accepted: 21 November 2012 / Published: 28 November 2012
Cited by 25 | PDF Full-text (334 KB) | HTML Full-text | XML Full-text
Abstract
Asymmetric dimethylarginine (ADMA), an endogenous nitric oxide synthase (NOS) inhibitor, is known as mediator of endothelial cell dysfunction and atherosclerosis. Circulating ADMA levels are correlated with cardiovascular risk factors such as hypercholesterolemia,arterial hypertension, diabetes mellitus, hyperhomocysteinemia, age and smoking. Accordingly, clinical studies
[...] Read more.
Asymmetric dimethylarginine (ADMA), an endogenous nitric oxide synthase (NOS) inhibitor, is known as mediator of endothelial cell dysfunction and atherosclerosis. Circulating ADMA levels are correlated with cardiovascular risk factors such as hypercholesterolemia, arterial hypertension, diabetes mellitus, hyperhomocysteinemia, age and smoking. Accordingly, clinical studies found evidence that increased ADMA levels are associated with a higher risk of cerebrovascular events. After the acute event of ischemic stroke, levels of ADMA and its analog symmetric dimethylarginine (SDMA) are elevated through augmentation of protein methylation and oxidative stress. Furthermore, cleavage of ADMA through dimethylarginine dimethylaminohydrolases (DDAHs) is reduced. This increase of dimethylarginines might be predictive for adverse clinical outcome. However, the definite role of ADMA after acute ischemic stroke still needs to be clarified. On the one hand, ADMA might contribute to brain injury by reduction of cerebral blood flow. On the other hand, ADMA might be involved in NOS-induced oxidative stress and excitotoxic neuronal death. In the present review, we highlight the current knowledge from clinical and experimental studies on ADMA and its role for stroke risk and ischemic brain injury in the hyperacute stage after stroke. Finally, further studies are warranted to unravel the relevance of the close association of dimethylarginines with stroke. Full article
(This article belongs to the Special Issue ADMA and Nitrergic System)
Open AccessReview Drug Conjugates Such as Antibody Drug Conjugates (ADCs), Immunotoxins and Immunoliposomes Challenge Daily Clinical Practice
Int. J. Mol. Sci. 2012, 13(12), 16020-16045; doi:10.3390/ijms131216020
Received: 17 September 2012 / Revised: 15 November 2012 / Accepted: 19 November 2012 / Published: 28 November 2012
Cited by 18 | PDF Full-text (273 KB) | HTML Full-text | XML Full-text
Abstract
Drug conjugates have been studied extensively in preclinical in vitro and in vivo models but to date only a few compounds have progressed to the clinical setting. This situation is now changing with the publication of studies demonstrating a significant impact on clinical
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Drug conjugates have been studied extensively in preclinical in vitro and in vivo models but to date only a few compounds have progressed to the clinical setting. This situation is now changing with the publication of studies demonstrating a significant impact on clinical practice and highlighting the potential of this new class of targeted therapies. This review summarizes the pharmacological and molecular background of the main drug conjugation systems, namely antibody drug conjugates (ADCs), immunotoxins and immunoliposomes. All these compounds combine the specific targeting moiety of an antibody or similar construct with the efficacy of a toxic drug. The aim of this strategy is to target tumor cells specifically while sparing normal tissue, thus resulting in high efficacy and low toxicity. Recently, several strategies have been investigated in phase I clinical trials and some have entered phase III clinical development. This review provides a detailed overview of various strategies and critically discusses the most relevant achievements. Examples of the most advanced compounds include T-DM1 and brentuximab vedotin. However, additional promising strategies such as immunotoxins and immunoliposmes are already in clinical development. In summary, targeted drug delivery by drug conjugates is a new emerging class of anti-cancer therapy that may play a major role in the future. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview The Phorbol Ester Fraction from Jatropha curcas Seed Oil: Potential and Limits for Crop Protection against Insect Pests
Int. J. Mol. Sci. 2012, 13(12), 16157-16171; doi:10.3390/ijms131216157
Received: 24 September 2012 / Revised: 23 November 2012 / Accepted: 27 November 2012 / Published: 30 November 2012
Cited by 10 | PDF Full-text (216 KB) | HTML Full-text | XML Full-text
Abstract
The physic nut shrub, Jatropha curcas (Euphorbiaceae), has been considered as a “miracle tree”, particularly as a source of alternate fuel. Various extracts of the plant have been reported to have insecticidal/acaricidal or molluscicidal/anthelminthic activities on vectors of medical or veterinary interest or
[...] Read more.
The physic nut shrub, Jatropha curcas (Euphorbiaceae), has been considered as a “miracle tree”, particularly as a source of alternate fuel. Various extracts of the plant have been reported to have insecticidal/acaricidal or molluscicidal/anthelminthic activities on vectors of medical or veterinary interest or on agricultural or non-agricultural pests. Among those extracts, the phorbol ester fraction from seed oil has been reported as a promising candidate for use as a plant-derived protectant of a variety of crops, from a range of pre-harvest and post-harvest insect pests. However, such extracts have not been widely used, despite the “boom” in the development of the crop in the tropics during recent years, and societal concerns about overuse of systemic chemical pesticides. There are many potential explanations to such a lack of use of Jatropha insecticidal extracts. On the one hand, the application of extracts potentially harmful to human health on stored food grain, might not be relevant. The problem of decomposition of phorbol esters and other compounds toxic to crop pests in the field needing further evaluation before such extracts can be widely used, may also be a partial explanation. High variability of phorbol ester content and hence of insecticidal activity among physic nut cultivars/ecotypes may be another. Phytotoxicity to crops may be further limitation. Apparent obstacles to a wider application of such extracts are the costs and problems involved with registration and legal approval. On the other hand, more studies should be conducted on molluscicidal activity on slugs and land snails which are major pests of crops, particularly in conservation agriculture systems. Further evaluation of toxicity to natural enemies of insect pests and studies on other beneficial insects such as pollinators are also needed. Full article
(This article belongs to the Special Issue Green Biocides)
Open AccessReview Base Excision Repair in Physiology and Pathology of the Central Nervous System
Int. J. Mol. Sci. 2012, 13(12), 16172-16222; doi:10.3390/ijms131216172
Received: 21 September 2012 / Revised: 6 November 2012 / Accepted: 12 November 2012 / Published: 30 November 2012
Cited by 6 | PDF Full-text (742 KB) | HTML Full-text | XML Full-text
Abstract
Relatively low levels of antioxidant enzymes and high oxygen metabolism result in formation of numerous oxidized DNA lesions in the tissues of the central nervous system. Accumulation of damage in the DNA, due to continuous genotoxic stress, has been linked to both aging
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Relatively low levels of antioxidant enzymes and high oxygen metabolism result in formation of numerous oxidized DNA lesions in the tissues of the central nervous system. Accumulation of damage in the DNA, due to continuous genotoxic stress, has been linked to both aging and the development of various neurodegenerative disorders. Different DNA repair pathways have evolved to successfully act on damaged DNA and prevent genomic instability. The predominant and essential DNA repair pathway for the removal of small DNA base lesions is base excision repair (BER). In this review we will discuss the current knowledge on the involvement of BER proteins in the maintenance of genetic stability in different brain regions and how changes in the levels of these proteins contribute to aging and the onset of neurodegenerative disorders. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview Oxidative Stress in Malaria
Int. J. Mol. Sci. 2012, 13(12), 16346-16372; doi:10.3390/ijms131216346
Received: 17 October 2012 / Revised: 8 November 2012 / Accepted: 23 November 2012 / Published: 3 December 2012
Cited by 35 | PDF Full-text (256 KB) | HTML Full-text | XML Full-text
Abstract
Malaria is a significant public health problem in more than 100 countries and causes an estimated 200 million new infections every year. Despite the significant effort to eradicate this dangerous disease, lack of complete knowledge of its physiopathology compromises the success in this
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Malaria is a significant public health problem in more than 100 countries and causes an estimated 200 million new infections every year. Despite the significant effort to eradicate this dangerous disease, lack of complete knowledge of its physiopathology compromises the success in this enterprise. In this paper we review oxidative stress mechanisms involved in the disease and discuss the potential benefits of antioxidant supplementation as an adjuvant antimalarial strategy. Full article
(This article belongs to the Special Issue Advances in Free Radicals in Biology and Medicine)
Open AccessReview Integration of DNA Damage and Repair with Murine Double-Minute 2 (Mdm2) in Tumorigenesis
Int. J. Mol. Sci. 2012, 13(12), 16373-16386; doi:10.3390/ijms131216373
Received: 27 September 2012 / Revised: 27 November 2012 / Accepted: 27 November 2012 / Published: 3 December 2012
Cited by 2 | PDF Full-text (184 KB) | HTML Full-text | XML Full-text
Abstract
The alteration of tumorigenic pathways leading to cancer is a degenerative disease process typically involving inactivation of tumor suppressor proteins and hyperactivation of oncogenes. One such oncogenic protein product is the murine double-minute 2, or Mdm2. While, Mdm2 has been primarily associated as
[...] Read more.
The alteration of tumorigenic pathways leading to cancer is a degenerative disease process typically involving inactivation of tumor suppressor proteins and hyperactivation of oncogenes. One such oncogenic protein product is the murine double-minute 2, or Mdm2. While, Mdm2 has been primarily associated as the negative regulator of the p53 tumor suppressor protein there are many p53-independent roles demonstrated for this oncogene. DNA damage and chemotherapeutic agents are known to activate Mdm2 and DNA repair pathways. There are five primary DNA repair pathways involved in the maintenance of genomic integrity: Nucleotide excision repair (NER), Base excision repair (BER), Mismatch repair (MMR), Non-homologous end joining (NHEJ) and homologous recombination (HR). In this review, we will briefly describe these pathways and also delineate the functional interaction of Mdm2 with multiple DNA repair proteins. We will illustrate the importance of these interactions with Mdm2 and discuss how this is important for tumor progression, cellular proliferation in cancer. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview Biotransformations Utilizing β-Oxidation Cycle Reactions in the Synthesis of Natural Compounds and Medicines
Int. J. Mol. Sci. 2012, 13(12), 16514-16543; doi:10.3390/ijms131216514
Received: 31 August 2012 / Revised: 19 November 2012 / Accepted: 21 November 2012 / Published: 5 December 2012
Cited by 6 | PDF Full-text (3412 KB) | HTML Full-text | XML Full-text
Abstract
β-Oxidation cycle reactions, which are key stages in the metabolism of fatty acids in eucaryotic cells and in processes with a significant role in the degradation of acids used by microbes as a carbon source, have also found application in biotransformations. One of
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β-Oxidation cycle reactions, which are key stages in the metabolism of fatty acids in eucaryotic cells and in processes with a significant role in the degradation of acids used by microbes as a carbon source, have also found application in biotransformations. One of the major advantages of biotransformations based on the β-oxidation cycle is the possibility to transform a substrate in a series of reactions catalyzed by a number of enzymes. It allows the use of sterols as a substrate base in the production of natural steroid compounds and their analogues. This route also leads to biologically active compounds of therapeutic significance. Transformations of natural substrates via β-oxidation are the core part of the synthetic routes of natural flavors used as food additives. Stereoselectivity of the enzymes catalyzing the stages of dehydrogenation and addition of a water molecule to the double bond also finds application in the synthesis of chiral biologically active compounds, including medicines. Recent advances in genetic, metabolic engineering, methods for the enhancement of bioprocess productivity and the selectivity of target reactions are also described. Full article
(This article belongs to the Special Issue Organic Synthesis Using Biocatalyst)
Open AccessReview Epigenetic Deregulation of MicroRNAs in Rhabdomyosarcoma and Neuroblastoma and Translational Perspectives
Int. J. Mol. Sci. 2012, 13(12), 16554-16579; doi:10.3390/ijms131216554
Received: 29 October 2012 / Revised: 21 November 2012 / Accepted: 21 November 2012 / Published: 5 December 2012
Cited by 2 | PDF Full-text (564 KB) | HTML Full-text | XML Full-text
Abstract
Gene expression control mediated by microRNAs and epigenetic remodeling of chromatin are interconnected processes often involved in feedback regulatory loops, which strictly guide proper tissue differentiation during embryonal development. Altered expression of microRNAs is one of the mechanisms leading to pathologic conditions, such
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Gene expression control mediated by microRNAs and epigenetic remodeling of chromatin are interconnected processes often involved in feedback regulatory loops, which strictly guide proper tissue differentiation during embryonal development. Altered expression of microRNAs is one of the mechanisms leading to pathologic conditions, such as cancer. Several lines of evidence pointed to epigenetic alterations as responsible for aberrant microRNA expression in human cancers. Rhabdomyosarcoma and neuroblastoma are pediatric cancers derived from cells presenting features of skeletal muscle and neuronal precursors, respectively, blocked at different stages of differentiation. Consistently, tumor cells express tissue markers of origin but are unable to terminally differentiate. Several microRNAs playing a key role during tissue differentiation are often epigenetically downregulated in rhabdomyosarcoma and neuroblastoma and behave as tumor suppressors when re-expressed. Recently, inhibition of epigenetic modulators in adult tumors has provided encouraging results causing re-expression of anti-tumor master gene pathways. Thus, a similar approach could be used to correct the aberrant epigenetic regulation of microRNAs in rhabdomyosarcoma and neuroblastoma. The present review highlights the current insights on epigenetically deregulated microRNAs in rhabdomyosarcoma and neuroblastoma and their role in tumorigenesis and developmental pathways. The translational clinical implications and challenges regarding modulation of epigenetic chromatin remodeling/microRNAs interconnections are also discussed. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessReview Recent Advances in Nanoparticle-Based Förster Resonance Energy Transfer for Biosensing, Molecular Imaging and Drug Release Profiling
Int. J. Mol. Sci. 2012, 13(12), 16598-16623; doi:10.3390/ijms131216598
Received: 11 October 2012 / Revised: 15 November 2012 / Accepted: 16 November 2012 / Published: 5 December 2012
Cited by 36 | PDF Full-text (1637 KB) | HTML Full-text | XML Full-text
Abstract
Förster resonance energy transfer (FRET) may be regarded as a “smart” technology in the design of fluorescence probes for biological sensing and imaging. Recently, a variety of nanoparticles that include quantum dots, gold nanoparticles, polymer, mesoporous silica nanoparticles and upconversion nanoparticles have been
[...] Read more.
Förster resonance energy transfer (FRET) may be regarded as a “smart” technology in the design of fluorescence probes for biological sensing and imaging. Recently, a variety of nanoparticles that include quantum dots, gold nanoparticles, polymer, mesoporous silica nanoparticles and upconversion nanoparticles have been employed to modulate FRET. Researchers have developed a number of “visible” and “activatable” FRET probes sensitive to specific changes in the biological environment that are especially attractive from the biomedical point of view. This article reviews recent progress in bringing these nanoparticle-modulated energy transfer schemes to fruition for applications in biosensing, molecular imaging and drug delivery. Full article
(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET))
Open AccessReview The Implications of Cancer Stem Cells for Cancer Therapy
Int. J. Mol. Sci. 2012, 13(12), 16636-16657; doi:10.3390/ijms131216636
Received: 11 October 2012 / Revised: 21 November 2012 / Accepted: 27 November 2012 / Published: 5 December 2012
Cited by 19 | PDF Full-text (334 KB) | HTML Full-text | XML Full-text
Abstract
Surgery, radiotherapy and chemotherapy are universally recognized as the most effective anti-cancer therapies. Despite significant advances directed towards elucidating molecular mechanisms and developing clinical trials, cancer still remains a major public health issue. Recent studies have showed that cancer stem cells (CSCs), a
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Surgery, radiotherapy and chemotherapy are universally recognized as the most effective anti-cancer therapies. Despite significant advances directed towards elucidating molecular mechanisms and developing clinical trials, cancer still remains a major public health issue. Recent studies have showed that cancer stem cells (CSCs), a small subpopulation of tumor cells, can generate bulk populations of nontumorigenic cancer cell progeny through the self-renewal and differentiation processes. As CSCs are proposed to persist in tumors as a distinct population and cause relapse and metastasis by giving rise to new tumors, development of CSC-targeted therapeutic strategies holds new hope for improving survival and quality of life in patients with cancer. Therapeutic innovations will emerge from a better understanding of the biology and environment of CSCs, which, however, are largely unexplored. This review summarizes the characteristics, evidences and development of CSCs, as well as implications and challenges for cancer treatment. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Class IIa Bacteriocins: Diversity and New Developments
Int. J. Mol. Sci. 2012, 13(12), 16668-16707; doi:10.3390/ijms131216668
Received: 10 September 2012 / Revised: 10 October 2012 / Accepted: 12 November 2012 / Published: 6 December 2012
Cited by 22 | PDF Full-text (676 KB) | HTML Full-text | XML Full-text
Abstract
Class IIa bacteriocins are heat-stable, unmodified peptides with a conserved amino acids sequence YGNGV on their N-terminal domains, and have received much attention due to their generally recognized as safe (GRAS) status, their high biological activity, and their excellent heat stability. They
[...] Read more.
Class IIa bacteriocins are heat-stable, unmodified peptides with a conserved amino acids sequence YGNGV on their N-terminal domains, and have received much attention due to their generally recognized as safe (GRAS) status, their high biological activity, and their excellent heat stability. They are promising and attractive agents that could function as biopreservatives in the food industry. This review summarizes the new developments in the area of class IIa bacteriocins and aims to provide uptodate information that can be used in designing future research. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Long Non-Coding RNAs and p53 Regulation
Int. J. Mol. Sci. 2012, 13(12), 16708-16717; doi:10.3390/ijms131216708
Received: 5 November 2012 / Revised: 3 December 2012 / Accepted: 3 December 2012 / Published: 6 December 2012
Cited by 10 | PDF Full-text (299 KB) | HTML Full-text | XML Full-text
Abstract
The advent of novel and high-throughput sequencing (next generation) technologies allowed for the sequencing of the genome at an unprecedented depth. The majority of transcribed RNAs have been classified as non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) are emerging as important regulators
[...] Read more.
The advent of novel and high-throughput sequencing (next generation) technologies allowed for the sequencing of the genome at an unprecedented depth. The majority of transcribed RNAs have been classified as non-coding RNAs. Among them, long non-coding RNAs (lncRNAs) are emerging as important regulators in many biological processes. Here, we discuss the role of those lncRNAs which are under the control of p53 or that are able to regulate its activity, due to the central role of p53 pathway in many conditions. We also briefly discussed the emerging need of having novel strategies and computational tools to completely unravel the multifaceted roles of lncRNAs and to pave the way to the development of novel diagnostic and therapeutic applications based on these peculiar molecules. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessReview Flavin-Dependent Enzymes in Cancer Prevention
Int. J. Mol. Sci. 2012, 13(12), 16751-16768; doi:10.3390/ijms131216751
Received: 20 September 2012 / Revised: 26 November 2012 / Accepted: 4 December 2012 / Published: 7 December 2012
Cited by 5 | PDF Full-text (1684 KB) | HTML Full-text | XML Full-text
Abstract
Statistical studies have demonstrated that various agents may reduce the risk of cancer’s development. One of them is activity of flavin-dependent enzymes such as flavin-containing monooxygenase (FMO)GS-OX1, FAD-dependent 5,10-methylenetetrahydrofolate reductase and flavin-dependent monoamine oxidase. In the last decade, many papers concerning
[...] Read more.
Statistical studies have demonstrated that various agents may reduce the risk of cancer’s development. One of them is activity of flavin-dependent enzymes such as flavin-containing monooxygenase (FMO)GS-OX1, FAD-dependent 5,10-methylenetetrahydrofolate reductase and flavin-dependent monoamine oxidase. In the last decade, many papers concerning their structure, reaction mechanism and role in the cancer prevention were published. In our work, we provide a more in-depth analysis of flavin-dependent enzymes and their contribution to the cancer prevention. We present the actual knowledge about the glucosinolate synthesized by flavin-containing monooxygenase (FMO)GS-OX1 and its role in cancer prevention, discuss the influence of mutations in FAD-dependent 5,10-methylenetetrahydrofolate reductase on the cancer risk, and describe FAD as an important cofactor for the demethylation of histons. We also present our views on the role of riboflavin supplements in the prevention against cancer. Full article
(This article belongs to the Special Issue Flavins)
Open AccessReview The Role of Dicer in DNA Damage Repair
Int. J. Mol. Sci. 2012, 13(12), 16769-16778; doi:10.3390/ijms131216769
Received: 29 September 2012 / Revised: 9 November 2012 / Accepted: 12 November 2012 / Published: 7 December 2012
Cited by 4 | PDF Full-text (166 KB) | HTML Full-text | XML Full-text
Abstract
Dicer is the key component of the RNA interference pathway. Our group and others have reported that knockdown or knockout of Dicer leads to DNA damage in mammalian cells. Two groups recently showed that efficiency of DNA damage repair was greatly reduced in
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Dicer is the key component of the RNA interference pathway. Our group and others have reported that knockdown or knockout of Dicer leads to DNA damage in mammalian cells. Two groups recently showed that efficiency of DNA damage repair was greatly reduced in Dicer-deficient cells and that Dicer-dependent small RNAs (~21 nucleotides) produced from the sequences in the vicinity of DNA double-strand break sites were essential for DNA damage repair. Moreover, accumulating data have suggested that miroRNAs play pivotal roles in DNA damage repair. In this review, we discuss the molecular mechanisms by which loss of Dicer leads to DNA damage, as well as the role of Dicer in tumorigenesis. Full article
Open AccessReview DNA Damage Due to Oxidative Stress in Chronic Obstructive Pulmonary Disease (COPD)
Int. J. Mol. Sci. 2012, 13(12), 16853-16864; doi:10.3390/ijms131216853
Received: 28 September 2012 / Revised: 31 October 2012 / Accepted: 19 November 2012 / Published: 10 December 2012
Cited by 15 | PDF Full-text (177 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
According to the American Thorasic Society (ATS)/European Respiratory Society (ERS) Statement, chronic obstructive pulmonary disease (COPD) is defined as a preventable and treatable disease with a strong genetic component, characterized by airflow limitation that is not fully reversible, but is usually progressive and
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According to the American Thorasic Society (ATS)/European Respiratory Society (ERS) Statement, chronic obstructive pulmonary disease (COPD) is defined as a preventable and treatable disease with a strong genetic component, characterized by airflow limitation that is not fully reversible, but is usually progressive and associated with an enhanced inflammatory response of the lung to noxious particles or gases. The main features of COPD are chronic inflammation of the airways and progressive destruction of lung parenchyma and alveolar structure. The pathogenesis of COPD is complex due to the interactions of several mechanisms, such as inflammation, proteolytic/antiproteolytic imbalance, oxidative stress, DNA damage, apoptosis, enhanced senescence of the structural cells and defective repair processes. This review focuses on the effects of oxidative DNA damage and the consequent immune responses in COPD. In susceptible individuals, cigarette smoke injures the airway epithelium generating the release of endogenous intracellular molecules or danger-associated molecular patterns from stressed or dying cells. These signals are captured by antigen presenting cells and are transferred to the lymphoid tissue, generating an adaptive immune response and enhancing chronic inflammation. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
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Open AccessReview UBE4B: A Promising Regulatory Molecule in Neuronal Death and Survival
Int. J. Mol. Sci. 2012, 13(12), 16865-16879; doi:10.3390/ijms131216865
Received: 7 October 2012 / Revised: 22 November 2012 / Accepted: 27 November 2012 / Published: 10 December 2012
Cited by 1 | PDF Full-text (200 KB) | HTML Full-text | XML Full-text
Abstract
Neuronal survival and death of neurons are considered a fundamental mechanism in the regulation of the nervous system during early development of the system and in adulthood. Defects in this mechanism are highly problematic and are associated with many neurodegenerative diseases. Because neuronal
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Neuronal survival and death of neurons are considered a fundamental mechanism in the regulation of the nervous system during early development of the system and in adulthood. Defects in this mechanism are highly problematic and are associated with many neurodegenerative diseases. Because neuronal programmed death is apoptotic in nature, indicating that apoptosis is a key regulatory process, the p53 family members (p53, p73, p63) act as checkpoints in neurons due to their role in apoptosis. The complexity of this system is due to the existence of different naturally occurring isoforms that have different functions from the wild types (WT), varying from apoptotic to anti-apoptotic effects. In this review, we focus on the role of UBE4B (known as Ube4b or Ufd2a in mouse), an E3/E4 ligase that triggers substrate polyubiquitination, as a master regulatory ligase associated with the p53 family WT proteins and isoforms in regulating neuronal survival. UBE4B is also associated with other pathways independent of the p53 family, such as polyglutamine aggregation and Wallerian degeneration, both of which are critical in neurodegenerative diseases. Many of the hypotheses presented here are gateways to understanding the programmed death/survival of neurons regulated by UBE4B in normal physiology, and a means of introducing potential therapeutic approaches with implications in treating several neurodegenerative diseases. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview DNA Damage and Repair in Atherosclerosis: Current Insights and Future Perspectives
Int. J. Mol. Sci. 2012, 13(12), 16929-16944; doi:10.3390/ijms131216929
Received: 28 September 2012 / Revised: 20 November 2012 / Accepted: 5 December 2012 / Published: 11 December 2012
Cited by 14 | PDF Full-text (440 KB) | HTML Full-text | XML Full-text
Abstract
Atherosclerosis is the leading cause of morbidity and mortality among Western populations. Over the past two decades, considerable evidence has supported a crucial role for DNA damage in the development and progression of atherosclerosis. These findings support the concept that the prolonged exposure
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Atherosclerosis is the leading cause of morbidity and mortality among Western populations. Over the past two decades, considerable evidence has supported a crucial role for DNA damage in the development and progression of atherosclerosis. These findings support the concept that the prolonged exposure to risk factors (e.g., dyslipidemia, smoking and diabetes mellitus) leading to reactive oxygen species are major stimuli for DNA damage within the plaque. Genomic instability at the cellular level can directly affect vascular function, leading to cell cycle arrest, apoptosis and premature vascular senescence. The purpose of this paper is to review current knowledge on the role of DNA damage and DNA repair systems in atherosclerosis, as well as to discuss the cellular response to DNA damage in order to shed light on possible strategies for prevention and treatment. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview Intelligent Design of Nano-Scale Molecular Imaging Agents
Int. J. Mol. Sci. 2012, 13(12), 16986-17005; doi:10.3390/ijms131216986
Received: 21 September 2012 / Accepted: 26 November 2012 / Published: 12 December 2012
Cited by 5 | PDF Full-text (792 KB) | HTML Full-text | XML Full-text
Abstract
Visual representation and quantification of biological processes at the cellular and subcellular levels within living subjects are gaining great interest in life science to address frontier issues in pathology and physiology. As intact living subjects do not emit any optical signature, visual representation
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Visual representation and quantification of biological processes at the cellular and subcellular levels within living subjects are gaining great interest in life science to address frontier issues in pathology and physiology. As intact living subjects do not emit any optical signature, visual representation usually exploits nano-scale imaging agents as the source of image contrast. Many imaging agents have been developed for this purpose, some of which exert nonspecific, passive, and physical interaction with a target. Current research interest in molecular imaging has mainly shifted to fabrication of smartly integrated, specific, and versatile agents that emit fluorescence or luminescence as an optical readout. These agents include luminescent quantum dots (QDs), biofunctional antibodies, and multifunctional nanoparticles. Furthermore, genetically encoded nano-imaging agents embedding fluorescent proteins or luciferases are now gaining popularity. These agents are generated by integrative design of the components, such as luciferase, flexible linker, and receptor to exert a specific on–off switching in the complex context of living subjects. In the present review, we provide an overview of the basic concepts, smart design, and practical contribution of recent nano-scale imaging agents, especially with respect to genetically encoded imaging agents. Full article
(This article belongs to the Special Issue Bioactive Nanoparticles 2012)
Open AccessReview Organic Solar Cells: Understanding the Role of Förster Resonance Energy Transfer
Int. J. Mol. Sci. 2012, 13(12), 17019-17047; doi:10.3390/ijms131217019
Received: 7 October 2012 / Revised: 3 December 2012 / Accepted: 5 December 2012 / Published: 12 December 2012
Cited by 35 | PDF Full-text (1072 KB) | HTML Full-text | XML Full-text
Abstract
Organic solar cells have the potential to become a low-cost sustainable energy source. Understanding the photoconversion mechanism is key to the design of efficient organic solar cells. In this review, we discuss the processes involved in the photo-electron conversion mechanism, which may be
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Organic solar cells have the potential to become a low-cost sustainable energy source. Understanding the photoconversion mechanism is key to the design of efficient organic solar cells. In this review, we discuss the processes involved in the photo-electron conversion mechanism, which may be subdivided into exciton harvesting, exciton transport, exciton dissociation, charge transport and extraction stages. In particular, we focus on the role of energy transfer as described by F¨orster resonance energy transfer (FRET) theory in the photoconversion mechanism. FRET plays a major role in exciton transport, harvesting and dissociation. The spectral absorption range of organic solar cells may be extended using sensitizers that efficiently transfer absorbed energy to the photoactive materials. The limitations of F¨orster theory to accurately calculate energy transfer rates are discussed. Energy transfer is the first step of an efficient two-step exciton dissociation process and may also be used to preferentially transport excitons to the heterointerface, where efficient exciton dissociation may occur. However, FRET also competes with charge transfer at the heterointerface turning it in a potential loss mechanism. An energy cascade comprising both energy transfer and charge transfer may aid in separating charges and is briefly discussed. Considering the extent to which the photo-electron conversion efficiency is governed by energy transfer, optimisation of this process offers the prospect of improved organic photovoltaic performance and thus aids in realising the potential of organic solar cells. Full article
(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET))
Open AccessReview Plant Glandular Trichomes as Targets for Breeding or Engineering of Resistance to Herbivores
Int. J. Mol. Sci. 2012, 13(12), 17077-17103; doi:10.3390/ijms131217077
Received: 6 November 2012 / Revised: 28 November 2012 / Accepted: 5 December 2012 / Published: 12 December 2012
Cited by 41 | PDF Full-text (1172 KB) | HTML Full-text | XML Full-text
Abstract
Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant’s secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products
[...] Read more.
Glandular trichomes are specialized hairs found on the surface of about 30% of all vascular plants and are responsible for a significant portion of a plant’s secondary chemistry. Glandular trichomes are an important source of essential oils, i.e., natural fragrances or products that can be used by the pharmaceutical industry, although many of these substances have evolved to provide the plant with protection against herbivores and pathogens. The storage compartment of glandular trichomes usually is located on the tip of the hair and is part of the glandular cell, or cells, which are metabolically active. Trichomes and their exudates can be harvested relatively easily, and this has permitted a detailed study of their metabolites, as well as the genes and proteins responsible for them. This knowledge now assists classical breeding programs, as well as targeted genetic engineering, aimed to optimize trichome density and physiology to facilitate customization of essential oil production or to tune biocide activity to enhance crop protection. We will provide an overview of the metabolic diversity found within plant glandular trichomes, with the emphasis on those of the Solanaceae, and of the tools available to manipulate their activities for enhancing the plant’s resistance to pests. Full article
(This article belongs to the Special Issue Green Biocides)
Open AccessReview Natural Biomolecules and Protein Aggregation: Emerging Strategies against Amyloidogenesis
Int. J. Mol. Sci. 2012, 13(12), 17121-17137; doi:10.3390/ijms131217121
Received: 29 November 2012 / Revised: 12 December 2012 / Accepted: 12 December 2012 / Published: 14 December 2012
Cited by 15 | PDF Full-text (281 KB) | HTML Full-text | XML Full-text
Abstract
Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way,
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Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way, giving rise to non-native aggregated structures responsible for severe, progressive human diseases that have a serious social impact. Different neurodegenerative disorders, like Huntington’s, Alzheimer’s, and spongiform encephalopathy diseases, have in common the presence of insoluble protein aggregates, generally termed “amyloid,” that share several physicochemical features: a fibrillar morphology, a predominantly beta-sheet secondary structure, birefringence upon staining with the dye Congo red, insolubility in common solvents and detergents, and protease resistance. Conformational constrains, hydrophobic and stacking interactions can play a key role in the fibrillogenesis process and protein–protein and peptide–peptide interactions—resulting in self-assembly phenomena of peptides yielding fibrils—that can be modulated and influenced by natural biomolecules. Small organic molecules, which possess both hydrophilic and hydrophobic moieties able to bind to peptide/protein molecules through hydrogen bonds and hydrophobic and aromatic interactions, are potential candidates against amyloidogenesis. In this review some significant case examples will be critically discussed. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessReview Nitric Oxide in Skeletal Muscle: Role on Mitochondrial Biogenesis and Function
Int. J. Mol. Sci. 2012, 13(12), 17160-17184; doi:10.3390/ijms131217160
Received: 1 November 2012 / Revised: 4 December 2012 / Accepted: 5 December 2012 / Published: 14 December 2012
Cited by 20 | PDF Full-text (782 KB) | HTML Full-text | XML Full-text
Abstract
Nitric oxide (NO) has been implicated in several cellular processes as a signaling molecule and also as a source of reactive nitrogen species (RNS). NO is produced by three isoenzymes called nitric oxide synthases (NOS), all present in skeletal muscle. While neuronal NOS
[...] Read more.
Nitric oxide (NO) has been implicated in several cellular processes as a signaling molecule and also as a source of reactive nitrogen species (RNS). NO is produced by three isoenzymes called nitric oxide synthases (NOS), all present in skeletal muscle. While neuronal NOS (nNOS) and endothelial NOS (eNOS) are isoforms constitutively expressed, inducible NOS (iNOS) is mainly expressed during inflammatory responses. Recent studies have demonstrated that NO is also involved in the mitochondrial biogenesis pathway, having PGC-1α as the main signaling molecule. Increased NO synthesis has been demonstrated in the sarcolemma of skeletal muscle fiber and NO can also reversibly inhibit cytochrome c oxidase (Complex IV of the respiratory chain). Investigation on cultured skeletal myotubes treated with NO donors, NO precursors or NOS inhibitors have also showed a bimodal effect of NO that depends on the concentration used. The present review will discuss the new insights on NO roles on mitochondrial biogenesis and function in skeletal muscle. We will also focus on potential therapeutic strategies based on NO precursors or analogs to treat patients with myopathies and mitochondrial deficiency. Full article
(This article belongs to the Special Issue Advances in Free Radicals in Biology and Medicine)
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Open AccessReview X-Ray Repair Cross Complementing Protein 1 in Base Excision Repair
Int. J. Mol. Sci. 2012, 13(12), 17210-17229; doi:10.3390/ijms131217210
Received: 9 November 2012 / Revised: 6 December 2012 / Accepted: 7 December 2012 / Published: 17 December 2012
Cited by 6 | PDF Full-text (520 KB) | HTML Full-text | XML Full-text
Abstract
X-ray Repair Cross Complementing protein 1 (XRCC1) acts as a scaffolding protein in the converging base excision repair (BER) and single strand break repair (SSBR) pathways. XRCC1 also interacts with itself and rapidly accumulates at sites of DNA damage. XRCC1 can thus mediate
[...] Read more.
X-ray Repair Cross Complementing protein 1 (XRCC1) acts as a scaffolding protein in the converging base excision repair (BER) and single strand break repair (SSBR) pathways. XRCC1 also interacts with itself and rapidly accumulates at sites of DNA damage. XRCC1 can thus mediate the assembly of large multiprotein DNA repair complexes as well as facilitate the recruitment of DNA repair proteins to sites of DNA damage. Moreover, XRCC1 is present in constitutive DNA repair complexes, some of which associate with the replication machinery. Because of the critical role of XRCC1 in DNA repair, its common variants Arg194Trp, Arg280His and Arg399Gln have been extensively studied. However, the prevalence of these variants varies strongly in different populations, and their functional influence on DNA repair and disease remains elusive. Here we present the current knowledge about the role of XRCC1 and its variants in BER and human disease/cancer. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview Prodrugs of Nonsteroidal Anti-Inflammatory Drugs (NSAIDs), More Than Meets the Eye: A Critical Review
Int. J. Mol. Sci. 2012, 13(12), 17244-17274; doi:10.3390/ijms131217244
Received: 13 July 2012 / Revised: 29 November 2012 / Accepted: 10 December 2012 / Published: 17 December 2012
Cited by 23 | PDF Full-text (525 KB) | HTML Full-text | XML Full-text
Abstract
The design and the synthesis of prodrugs for nonsteroidal anti-inflammatory drugs (NSAIDs) have been given much attention by medicinal chemists, especially in the last decade. As a therapeutic group, NSAIDs are among the most widely used prescribed and over the counter (OTC) medications.
[...] Read more.
The design and the synthesis of prodrugs for nonsteroidal anti-inflammatory drugs (NSAIDs) have been given much attention by medicinal chemists, especially in the last decade. As a therapeutic group, NSAIDs are among the most widely used prescribed and over the counter (OTC) medications. The rich literature about potential NSAID prodrugs clearly shows a shift from alkyl, aryalkyl or aryl esters with the sole role of masking the carboxylic acid group, to more elaborate conjugates that contain carefully chosen groups to serve specific purposes, such as enhancement of water solubility and dissolution, nitric oxide release, hydrogen sulfide release, antioxidant activity, anticholinergic and acetylcholinesterase inhibitory (AChEI) activity and site-specific targeting and delivery. This review will focus on NSAID prodrugs that have been designed or were, later, found to possess intrinsic pharmacological activity as an intact chemical entity. Such intrinsic activity might augment the anti-inflammatory activity of the NSAID, reduce its side effects or transform the potential therapeutic use from classical anti-inflammatory action to something else. Reports discussed in this review will be those of NO-NSAIDs, anticholinergic and AChEI-NSAIDs, Phospho-NSAIDs and some miscellaneous agents. In most cases, this review will cover literature dealing with these NSAID prodrugs from the year 2006 and later. Older literature will be used when necessary, e.g., to explain the chemical and biological mechanisms of action. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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Open AccessShort Note Isolation and Characterization of Microsatellite Markers in the Domestic Ferret (Mustela putorius furo)
Int. J. Mol. Sci. 2012, 13(12), 16592-16597; doi:10.3390/ijms131216592
Received: 25 September 2012 / Revised: 22 October 2012 / Accepted: 23 November 2012 / Published: 5 December 2012
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Abstract
The domestic ferret (Mustela putorius furo) is an important model organism for the study of avian influenza and other diseases of humans and animals, as well as a popular pet animal. In order to evaluate genetic diversity and study disease relationships
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The domestic ferret (Mustela putorius furo) is an important model organism for the study of avian influenza and other diseases of humans and animals, as well as a popular pet animal. In order to evaluate genetic diversity and study disease relationships in ferrets, 22 nuclear microsatellite loci (17 dinucleotide and 5 tetranucleotide) were developed from ferret genomic libraries and organized into seven multiplex sets. Polymorphism was preliminarily assessed in one population in Australia and one in the USA, sampled with 25 individuals each. The loci displayed allelic diversity ranging from 1 to 5 alleles, and expected and observed heterozygosities ranging from 0.04 to 0.65 and 0.04 to 0.76, respectively. Additionally, the loci amplified products in 15 samples from the wild ancestor, European polecat (Mustela putorius) and domestic ferret-polecat hybrids. In polecat/hybrid samples, allelic diversity ranged from 3 to 8 alleles, and expected and observed heterozygosities ranged from 0.13 to 0.81 and 0.13 to 0.80 respectively. These markers will be useful for molecular assessments of genetic diversity and applications to evolution, ecology, and health in domestic ferrets and wild polecats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCorrection Zarogouldis, P., et al., Vectors for Inhaled Gene Therapy in Lung Cancer. Application for Nano Oncology and Safety of Bio Nanotechnology. Int. J. Mol. Sci. 2012, 13, 10828-10862
Int. J. Mol. Sci. 2012, 13(12), 17290-17291; doi:10.3390/ijms131217290
Received: 28 October 2012 / Revised: 30 October 2012 / Accepted: 30 October 2012 / Published: 18 December 2012
Cited by 3 | PDF Full-text (129 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The authors wish to add this correction on their paper published in IJMS [1]. The first author’s name is misspelled and the correct name is Paul Zarogoulidis. In addition, the 6th author’s name is incorrect and should be corrected to Wolfgang Hohenforst-Schmidt. These
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The authors wish to add this correction on their paper published in IJMS [1]. The first author’s name is misspelled and the correct name is Paul Zarogoulidis. In addition, the 6th author’s name is incorrect and should be corrected to Wolfgang Hohenforst-Schmidt. These errors have been amended in an amended version of the manuscript, which is available from the International Journal of Molecular Sciences website. The authors and publisher apologize for the inconvenience. [...] Full article
Open AccessCorrection Kasprzak, M.M., et al., Correction: Effect of Enzymatic Treatment of Different Starch Sources on the in Vitro Rate and Extent of Starch Digestion. Int. J. Mol. Sci. 2012, 13, 929-942.
Int. J. Mol. Sci. 2012, 13(12), 17292-17293; doi:10.3390/ijms131217292
Received: 28 November 2012 / Revised: 6 December 2012 / Accepted: 17 December 2012 / Published: 18 December 2012
Cited by 2 | PDF Full-text (123 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract The authors wish to change the description of preparation of samples at Experimental Section on their paper published in IJMS [1]. [...] Full article
Open AccessCorrection Lech, M., et al., Quantitative Expression of C-Type Lectin Receptors in Humans and Mice. Int. J. Mol. Sci. 2012, 13, 10113-10131.
Int. J. Mol. Sci. 2012, 13(12), 17294; doi:10.3390/ijms131217294
Received: 15 October 2012 / Revised: 18 October 2012 / Accepted: 18 October 2012 / Published: 18 December 2012
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Abstract
The authors wish to add this correction on their paper published in IJMS [1]. Galectin-1 was misclassified as a C-type lectin. Galectin-1 belongs to the family of the S-type lectins, i.e., the galectins. These errors have been amended in an amended version
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The authors wish to add this correction on their paper published in IJMS [1]. Galectin-1 was misclassified as a C-type lectin. Galectin-1 belongs to the family of the S-type lectins, i.e., the galectins. These errors have been amended in an amended version of the manuscript, which is available from the International Journal of Molecular Sciences website. The authors and publisher apologize for the inconvenience. [...] Full article
Open AccessCorrection Zhou, T.B., et al., Correction: All-Trans Retinoic Acid Treatment Is Associated with Prohibitin Expression in Renal Interstitial Fibrosis Rats. Int. J. Mol. Sci. 2012, 13, 2769-2782.
Int. J. Mol. Sci. 2012, 13(12), 17295; doi:10.3390/ijms131217295
Received: 24 September 2012 / Revised: 8 October 2012 / Accepted: 24 October 2012 / Published: 18 December 2012
PDF Full-text (107 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The authors wish to change Figure 2 of the paper published in IJMS [1]. The positions of H1 and H2 in the previous article were reversed. These errors have been amended in an amended version of the manuscript, which is available
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The authors wish to change Figure 2 of the paper published in IJMS [1]. The positions of H1 and H2 in the previous article were reversed. These errors have been amended in an amended version of the manuscript, which is available from the International Journal of Molecular Sciences website. The authors and publisher apologize for the inconvenience. [...] Full article

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