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Int. J. Mol. Sci., Volume 13, Issue 7 (July 2012) – 94 articles , Pages 7872-9399

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Open AccessArticle
Secretome Survey of Human Plexiform Neurofibroma Derived Schwann Cells Reveals a Secreted form of the RARRES1 Protein
Int. J. Mol. Sci. 2012, 13(7), 9380-9399; https://doi.org/10.3390/ijms13079380 - 24 Jul 2012
Cited by 8 | Viewed by 4185
Abstract
To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified [...] Read more.
To bring insights into neurofibroma biochemistry, a comprehensive secretome analysis was performed on cultured human primary Schwann cells isolated from surgically resected plexiform neurofibroma and from normal nerve tissue. Using a combination of SDS-PAGE and high precision LC-MS/MS, 907 proteins were confidently identified in the conditioned media of Schwann cell cultures combined. Label free proteome profiling revealed consistent release of high levels of 22 proteins by the four biological replicates of NF1 Schwann cell cultures relative to the two normal Schwann cell cultures. Inversely, 9 proteins displayed decreased levels in the conditioned media of NF1 relative to normal Schwann cells. The proteins with increased levels included proteins involved in cell growth, angiogenesis and complement pathway while proteins with decreased levels included those involved in cell adhesion, plasminogen pathway and extracellular matrix remodeling. Retinoic acid receptor responder protein-1 (RARRES1), previously described as an integral membrane tumor suppressor, was found exclusively secreted by NF1 Schwann cells but not by normal Schwann cells. All-trans retinoic acid modulated secretion of RARRES1 in a dose dependent manner. This study shows altered secretion of key proteins in NF1 derived Schwann cells. The potential implication of these proteins in neurofibroma biology is discussed. Full article
(This article belongs to the Collection Advances in Proteomic Research)
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Open AccessArticle
The Apoptotic Volume Decrease Is an Upstream Event of MAP Kinase Activation during Staurosporine-Induced Apoptosis in HeLa Cells
Int. J. Mol. Sci. 2012, 13(7), 9363-9379; https://doi.org/10.3390/ijms13079363 - 24 Jul 2012
Cited by 20 | Viewed by 4501
Abstract
Persistent cell shrinkage, called apoptotic volume decrease (AVD), is a pivotal event of apoptosis. Activation of the volume-sensitive outwardly rectifying Cl channel (VSOR) is involved in the AVD induction. On the other hand, activation of the MAP kinase (MAPK) cascade is also [...] Read more.
Persistent cell shrinkage, called apoptotic volume decrease (AVD), is a pivotal event of apoptosis. Activation of the volume-sensitive outwardly rectifying Cl channel (VSOR) is involved in the AVD induction. On the other hand, activation of the MAP kinase (MAPK) cascade is also known to play a critical role in apoptosis. In the present study, we investigated the relationship between the AVD induction and the stress-responsive MAPK cascade activation during the apoptosis process induced by staurosporine (STS) in HeLa cells. STS was found to induce AVD within 2–5 min and phosphorylation of c-Jun N-terminal kinase (JNK) and p38 MAPK after over 20–30 min. VSOR blockers suppressed not only STS-induced AVD but also phosphorylation of JNK and p38 as well as activation of caspase-3/7. Moreover, a p38 inhibitor, SB203580, and a JNK inhibitor, SP600125, failed to affect STS-induced AVD, whereas these compounds reduced STS-induced activation of caspase-3/7. Also, treatment with ASK1-specific siRNA suppressed STS-induced caspase-3/7 activation without affecting the AVD induction. Furthermore, sustained osmotic cell shrinkage per se was found to trigger phosphorylation of JNK and p38, caspase activation, and cell death. Thus, it is suggested that activation of p38 and JNK is a downstream event of AVD for the STS-induced apoptosis of HeLa cells. Full article
(This article belongs to the Collection Programmed Cell Death and Apoptosis)
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Open AccessArticle
Molecular Characterization and Comparative Sequence Analysis of Defense-Related Gene, Oryza rufipogon Receptor-Like Protein Kinase 1
Int. J. Mol. Sci. 2012, 13(7), 9343-9362; https://doi.org/10.3390/ijms13079343 - 24 Jul 2012
Cited by 5 | Viewed by 4672
Abstract
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within [...] Read more.
Many of the plant leucine rich repeat receptor-like kinases (LRR-RLKs) have been found to regulate signaling during plant defense processes. In this study, we selected and sequenced an LRR-RLK gene, designated as Oryza rufipogon receptor-like protein kinase 1 (OrufRPK1), located within yield QTL yld1.1 from the wild rice Oryza rufipogon (accession IRGC105491). A 2055 bp coding region and two exons were identified. Southern blotting determined OrufRPK1 to be a single copy gene. Sequence comparison with cultivated rice orthologs (OsI219RPK1, OsI9311RPK1 and OsJNipponRPK1, respectively derived from O. sativa ssp. indica cv. MR219, O. sativa ssp. indica cv. 9311 and O. sativa ssp. japonica cv. Nipponbare) revealed the presence of 12 single nucleotide polymorphisms (SNPs) with five non-synonymous substitutions, and 23 insertion/deletion sites. The biological role of the OrufRPK1 as a defense related LRR-RLK is proposed on the basis of cDNA sequence characterization, domain subfamily classification, structural prediction of extra cellular domains, cluster analysis and comparative gene expression. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Open AccessArticle
A Theoretical Study on Reductive Debromination of Polybrominated Diphenyl Ethers
Int. J. Mol. Sci. 2012, 13(7), 9332-9342; https://doi.org/10.3390/ijms13079332 - 24 Jul 2012
Cited by 25 | Viewed by 3700
Abstract
Recent progress has been made in the reductive debromination of polybrominated diphenyl ethers (PBDEs) by nanoscale zero-valent iron (nZVI). To better understand the mechanism of this reaction, seven selected BDE congeners and their anions were investigated at the density functional theory (DFT) level [...] Read more.
Recent progress has been made in the reductive debromination of polybrominated diphenyl ethers (PBDEs) by nanoscale zero-valent iron (nZVI). To better understand the mechanism of this reaction, seven selected BDE congeners and their anions were investigated at the density functional theory (DFT) level using four different methods, including B3LYP/6-31G(d), B3LYP/6-31+G(d), B3LYP/6-31G(d,p) and B3LYP/6-311G(d,p). The cleaved C–Br bonds observed in the equilibrium structures of anionic PBDEs were adopted as the probe of the susceptible debromination position of PBDEs in the presence of nZVI, and the proposed major reaction pathways based on our calculations can satisfactorily conform to the reported experimental results. The debromination preference is theoretically evaluated as meta-Br > ortho-Br > para-Br. In addition, both the calculated frontier orbital energies and adiabatic electronic affinities were found to be highly related to their experimental reductive debromination rate constants. The highest linear regression coefficient was observed in the case using the energy of lowest unoccupied molecular orbital as the molecular descriptor obtained from B3LYP/6-31G(d) (R2 = 0.961, n = 7) or B3LYP/6-31G(d,p) (R2 = 0.961, n = 7). The results clearly showed the evidence of an electron transfer mechanism associated with this reductive debromination reaction. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessReview
The Immunomodulatory and Neuroprotective Effects of Mesenchymal Stem Cells (MSCs) in Experimental Autoimmune Encephalomyelitis (EAE): A Model of Multiple Sclerosis (MS)
Int. J. Mol. Sci. 2012, 13(7), 9298-9331; https://doi.org/10.3390/ijms13079298 - 24 Jul 2012
Cited by 58 | Viewed by 5327
Abstract
Mesenchymal stem cells (MSCs) are multipotent cells that differentiate into the mesenchymal lineages of adipocytes, osteocytes and chondrocytes. MSCs can also transdifferentiate and thereby cross lineage barriers, differentiating for example into neurons under certain experimental conditions. MSCs have anti-proliferative, anti-inflammatory and anti-apoptotic effects [...] Read more.
Mesenchymal stem cells (MSCs) are multipotent cells that differentiate into the mesenchymal lineages of adipocytes, osteocytes and chondrocytes. MSCs can also transdifferentiate and thereby cross lineage barriers, differentiating for example into neurons under certain experimental conditions. MSCs have anti-proliferative, anti-inflammatory and anti-apoptotic effects on neurons. Therefore, MSCs were tested in experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), for their effectiveness in modulating the pathogenic process in EAE to develop effective therapies for MS. The data in the literature have shown that MSCs can inhibit the functions of autoreactive T cells in EAE and that this immunomodulation can be neuroprotective. In addition, MSCs can rescue neural cells via a mechanism that is mediated by soluble factors, which provide a suitable environment for neuron regeneration, remyelination and cerebral blood flow improvement. In this review, we discuss the effectiveness of MSCs in modulating the immunopathogenic process and in providing neuroprotection in EAE. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
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Open AccessArticle
Activation of Propane C-H and C-C Bonds by Gas-Phase Pt Atom: A Theoretical Study
Int. J. Mol. Sci. 2012, 13(7), 9278-9297; https://doi.org/10.3390/ijms13079278 - 24 Jul 2012
Cited by 9 | Viewed by 3669
Abstract
The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane. [...] Read more.
The reaction mechanism of the gas-phase Pt atom with C3H8 has been systematically investigated on the singlet and triplet potential energy surfaces at CCSD(T)//BPW91/6-311++G(d, p), Lanl2dz level. Pt atom prefers the attack of primary over secondary C-H bonds in propane. For the Pt + C3H8 reaction, the major and minor reaction channels lead to PtC3H6 + H2 and PtCH2 + C2H6, respectively, whereas the possibility to form products PtC2H4 + CH4 is so small that it can be neglected. The minimal energy reaction pathway for the formation of PtC3H6 + H2, involving one spin inversion, prefers to start at the triplet state and afterward proceed along the singlet state. The optimal C-C bond cleavages are assigned to C-H bond activation as the first step, followed by cleavage of a C-C bond. The C-H insertion intermediates are kinetically favored over the C-C insertion intermediates. From C-C to C-H oxidative insertion, the lowering of activation barrier is mainly caused by the more stabilizing transition state interaction ΔEint, which is the actual interaction energy between the deformed reactants in the transition state. Full article
(This article belongs to the Section Materials Science)
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Open AccessArticle
Correlation among Antioxidant, Antimicrobial, Hemolytic, and Antiproliferative Properties of Leiothrix spiralis Leaves Extract
Int. J. Mol. Sci. 2012, 13(7), 9260-9277; https://doi.org/10.3390/ijms13079260 - 24 Jul 2012
Cited by 29 | Viewed by 3570
Abstract
The biological activities of a plant extract depend on a complex sum of individual properties including the antioxidant activity. Several biological activities protect against the harmful action of reactive oxygen species (ROS), and here we focused our attention on the relationship between the [...] Read more.
The biological activities of a plant extract depend on a complex sum of individual properties including the antioxidant activity. Several biological activities protect against the harmful action of reactive oxygen species (ROS), and here we focused our attention on the relationship between the biological activities tested and the antioxidant properties. In this study, the total flavonoid content as well as the antioxidant, antimicrobial, hemolytic and cytotoxicity activities of the methanolic extract of Leitothrix spiralis leaves were evaluated. The extract showed a total flavonoid content of 19.26% and the chemical characterization by HPLC-PAD confirmed the presence of flavonoids as the major secondary metabolite compounds. Significant antioxidant activity (IC50 = 1.743 µg/mL ± 0.063) was demonstrated and was effective against Gram-negative organisms and all Candida strains tested, and showed an ability to inhibit hyphal formation. Non-hemolytic and antiproliferative activity could be demonstrated. Full article
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Open AccessArticle
Enhancing Oxidative Stability of Sunflower Oil during Convective and Microwave Heating Using Grape Seed Extract
Int. J. Mol. Sci. 2012, 13(7), 9240-9259; https://doi.org/10.3390/ijms13079240 - 24 Jul 2012
Cited by 65 | Viewed by 5473
Abstract
This study was performed to investigate the effectiveness of grape seed extract (GSE) compared to butylated hydroxytoluene (BHT) on retarding lipid oxidation of sunflower oil subjected to convection and microwave heating up to 240 min under simulated frying conditions. The progress of lipid [...] Read more.
This study was performed to investigate the effectiveness of grape seed extract (GSE) compared to butylated hydroxytoluene (BHT) on retarding lipid oxidation of sunflower oil subjected to convection and microwave heating up to 240 min under simulated frying conditions. The progress of lipid oxidation was assessed in terms of peroxide value (PV), p-anisidine value (p-AV), conjugated dienes and trienes (CD, CT), inhibition of oil oxidation (IO) and TOTOX value. In addition, total phenolic content (TP) was evaluated in samples before and after heating in order to assess the changes in these compounds relative to the extent of lipid oxidation. The results of this study highlight that GSE showed a significantly inhibitory effect on lipid oxidation during both treatments, although to a different extent. This ability was dose-dependent; therefore, the extent of lipid oxidation was inversely related to GSE level. Convective heating, respective microwave exposure for 240 min of samples supplemented by GSE to a level of 1000 ppm, resulted in significant decreases of investigated indices relative to the control values as follows: PV (48%; 30%), p-AV (29%; 40%), CD (45%; 30%), CT (41%; 36%), TOTOX (35%; 37%). GSE to a level of 600–800 ppm inhibited the lipid oxidation in a similar manner to BHT. These results suggested that GSE can be used as a potential natural extract for improving oxidative stability of sunflower oil during thermal applications. Full article
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Open AccessArticle
Bacterial Motility Measured by a Miniature Chamber for High-Pressure Microscopy
Int. J. Mol. Sci. 2012, 13(7), 9225-9239; https://doi.org/10.3390/ijms13079225 - 24 Jul 2012
Cited by 17 | Viewed by 3491
Abstract
Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on [...] Read more.
Hydrostatic pressure is one of the physical stimuli that characterize the environment of living matter. Many microorganisms thrive under high pressure and may even physically or geochemically require this extreme environmental condition. In contrast, application of pressure is detrimental to most life on Earth; especially to living organisms under ambient pressure conditions. To study the mechanism of how living things adapt to high-pressure conditions, it is necessary to monitor directly the organism of interest under various pressure conditions. Here, we report a miniature chamber for high-pressure microscopy. The chamber was equipped with a built-in separator, in which water pressure was properly transduced to that of the sample solution. The apparatus developed could apply pressure up to 150 MPa, and enabled us to acquire bright-field and epifluorescence images at various pressures and temperatures. We demonstrated that the application of pressure acted directly and reversibly on the swimming motility of Escherichia coli cells. The present technique should be applicable to a wide range of dynamic biological processes that depend on applied pressures. Full article
(This article belongs to the Special Issue Molecular Machines and Nanomachines)
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Open AccessShort Note
Development of 20 Microsatellite Markers for Solenocera crassicornis and Their Cross-Species Application in Solenocera melantho
Int. J. Mol. Sci. 2012, 13(7), 9218-9224; https://doi.org/10.3390/ijms13079218 - 23 Jul 2012
Cited by 5 | Viewed by 3463
Abstract
Twenty microsatellite markers were isolated and characterized for Solenocera crassicornis from a (GT)13-enriched genomic library. Their polymorphisms were investigated using 44 wild individuals from the South Yellow Sea. Our investigation revealed that all the markers were polymorphic. The number of alleles [...] Read more.
Twenty microsatellite markers were isolated and characterized for Solenocera crassicornis from a (GT)13-enriched genomic library. Their polymorphisms were investigated using 44 wild individuals from the South Yellow Sea. Our investigation revealed that all the markers were polymorphic. The number of alleles per locus varied from 6 to 19 with an average of 12.35. The observed and expected heterozygosities ranged from 0.400 to 0.977 and from 0.609 to 0.940, with averages of 0.788 and 0.859, respectively. Four loci significantly deviated from Hardy-Weinberg equilibrium after Bonferroni’s correction. Cross-species amplification was also conducted in Solenocera melantho collected from the East China Sea. The result showed that 14 loci could be amplified from Solenocera melantho DNAs. These polymorphic markers would be useful for assessment of genetic variation and population structure of S. crassicornis and S. melantho. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
Open AccessArticle
3D Structure Elucidation of Thermostable L2 Lipase from Thermophilic Bacillus sp. L2
Int. J. Mol. Sci. 2012, 13(7), 9207-9217; https://doi.org/10.3390/ijms13079207 - 23 Jul 2012
Cited by 8 | Viewed by 3858
Abstract
The crystallization of proteins makes it possible to determine their structure by X-ray crystallography, and is therefore important for the analysis of protein structure-function relationships. L2 lipase was crystallized by using the J-tube counter diffusion method. A crystallization consisting of 20% PEG 6000, [...] Read more.
The crystallization of proteins makes it possible to determine their structure by X-ray crystallography, and is therefore important for the analysis of protein structure-function relationships. L2 lipase was crystallized by using the J-tube counter diffusion method. A crystallization consisting of 20% PEG 6000, 50 mM MES pH 6.5 and 50 mM NaCl was found to be the best condition to produce crystals with good shape and size (0.5 × 0.1 × 0.2 mm). The protein concentration used for the crystallization was 3 mg/mL. L2 lipase crystal has two crystal forms, Shape 1 and Shape 2. Shape 2 L2 lipase crystal was diffracted at 1.5 Å and the crystal belongs to the orthorhombic space group P212121, with unit-cell parameters a = 72.0, b = 81.8, c = 83.4 Å, α = β = γ = 90°. There is one molecule per asymmetric unit and the solvent content of the crystals is 56.9%, with a Matthew’s coefficient of 2.85 Å Da−1. The 3D structure of L2 lipase revealed topological organization of α/β-hydrolase fold consisting of 11 β-strands and 13 α-helices. Ser-113, His-358 and Asp-317 were assigned as catalytic triad residues. One Ca2+ and one Zn2+ were found in the L2 lipase molecule. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
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Open AccessArticle
Antioxidative Properties of Crude Polysaccharides from Inonotus obliquus
Int. J. Mol. Sci. 2012, 13(7), 9194-9206; https://doi.org/10.3390/ijms13079194 - 23 Jul 2012
Cited by 46 | Viewed by 4537
Abstract
The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1 [...] Read more.
The mushroom Inonotus obliquus has been widely used as a folk medicine in Russia, Poland and most of the Baltic countries. In this study, water-soluble and alkali-soluble crude polysaccharides (IOW and IOA) were isolated from I. obliquus, and the carbohydrate-rich fractions IOW-1 and IOA-1 were obtained respectively after deproteination and depigmentation. Their contents, such as neutral carbohydrate, uronic acid and protein, were measured. Their antioxidant properties against chemicals-induced reactive species (ROS) including 1,1'-Diphenyl-2-picrylhydrazyl (DPPH) radical, hydroxyl radical and superoxide anion radical, as well as their protective effects on H2O2-induced PC12 cell death were investigated. Results showed that I. obliquus polysaccharides can scavenge all ROS tested above in a dose-dependent manner. IOA and its product IOA-1 could rescue PC12 cell viability from 38.6% to 79.8% and 83.0% at a concentration of 20µg/mL. Similarly, IOW and its product IOW-1 at the same dose, can also increase cell viability to 84.9% and 88.6% respectively. The antioxidative activities of water-soluble and alkali-soluble polysaccharide constituents from I. obliquus might contribute to diverse medicinal and nutritional values of this mushroom. Full article
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Open AccessArticle
Effect of β,β-Dimethylacrylshikonin on Inhibition of Human Colorectal Cancer Cell Growth in Vitro and in Vivo
Int. J. Mol. Sci. 2012, 13(7), 9184-9193; https://doi.org/10.3390/ijms13079184 - 23 Jul 2012
Cited by 12 | Viewed by 3323
Abstract
In traditional Chinese medicine, shikonin and its derivatives, has been used in East Asia for several years for the prevention and treatment of several diseases, including cancer. We previously identified that β,β-dimethylacrylshikonin (DA) could inhibit hepatocellular carcinoma growth. In the present study, we [...] Read more.
In traditional Chinese medicine, shikonin and its derivatives, has been used in East Asia for several years for the prevention and treatment of several diseases, including cancer. We previously identified that β,β-dimethylacrylshikonin (DA) could inhibit hepatocellular carcinoma growth. In the present study, we investigated the inhibitory effects of DA on human colorectal cancer (CRC) cell line HCT-116 in vitro and in vivo. A viability assay showed that DA could inhibit tumor cell growth in a time- and dose-dependent manner. Flow cytometry showed that DA blocks the cell cycle at G0/G1 phase. Western blotting results demonstrated that the induction of apoptosis by DA correlated with the induction of pro-apoptotic proteins Bax, and Bid, and a decrease in the expression of anti-apoptotic proteins Bcl-2 and Bcl-xl. Furthermore, treatment of HCT-116 bearing nude mice with DA significantly retarded the growth of xenografts. Consistent with the results in vitro, the DA-mediated suppression of HCT-116 xenografts correlated with Bax and Bcl-2. Taken together, these results suggest that DA could be a novel and promising approach to the treatment of CRC. Full article
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Open AccessArticle
Reduction–Oxidation Photocycle Dynamics of Flavins in Starch Films
Int. J. Mol. Sci. 2012, 13(7), 9157-9183; https://doi.org/10.3390/ijms13079157 - 23 Jul 2012
Cited by 8 | Viewed by 4037
Abstract
The blue-light photo-reduction (conversion of oxidized flavin quinone via flavin semiquinone to fully reduced flavin hydroquinone) and dark re-oxidation of the flavins riboflavin and lumiflavin in starch (α-amylose) films was studied by absorption and luminescence spectroscopy. Blue-light photo-excitation caused an absorption, fluorescence, and [...] Read more.
The blue-light photo-reduction (conversion of oxidized flavin quinone via flavin semiquinone to fully reduced flavin hydroquinone) and dark re-oxidation of the flavins riboflavin and lumiflavin in starch (α-amylose) films was studied by absorption and luminescence spectroscopy. Blue-light photo-excitation caused an absorption, fluorescence, and phosphorescence decrease which recovered in the dark. The photo-reduction dark-oxidation cycle could be repeated. The efficiency of photo-reduction decreased with exposed excitation energy, and the speed of re-oxidation in the dark slowed down with time after excitation. The absorption did not fully recover. The fluorescence efficiency after a long time of storage in the dark increased beyond the initial flavin quinone fluorescence efficiency. Flavin photo-excitation is thought to cause starch-flavin restructuring (static fluorescence quenching center formation), enabling enhanced photo-induced starch to flavin electron transfer with subsequent flavin reduction and starch oxidation. In the dark, after light switch-off, thermal reversion of flavin reduction and starch oxidation occurred. Full article
(This article belongs to the Special Issue Flavins)
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Open AccessArticle
TRAIL and Paclitaxel Synergize to Kill U87 Cells and U87-Derived Stem-Like Cells in Vitro
Int. J. Mol. Sci. 2012, 13(7), 9142-9156; https://doi.org/10.3390/ijms13079142 - 20 Jul 2012
Cited by 23 | Viewed by 4478
Abstract
U87-derived stem-like cells (U87-SLCs) were cultured using serum-free stem cell media and identified by both biological behaviors and markers. Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and paclitaxel (PX), in combination or alone, was used to treat U87-MG human glioma cells (U87 cells) [...] Read more.
U87-derived stem-like cells (U87-SLCs) were cultured using serum-free stem cell media and identified by both biological behaviors and markers. Tumor necrosis factor (TNF)-related apoptosis-inducing ligand (TRAIL) and paclitaxel (PX), in combination or alone, was used to treat U87-MG human glioma cells (U87 cells) or U87-SLCs. The results showed that TRAIL/PX cannot only synergistically inhibit U87 cells but also U87-SLCs. We observed a significantly higher apoptotic rate in U87 cells simultaneously treated with TRAIL/PX for 24 h compared to cells treated with either drug alone. Furthermore, there was a remarkably higher apoptosis rate in U87-SLCs induced by the TRAIL/PX combination compared with either drug alone. Unlike the simultaneous treatment in U87 cells, U87-SLCs were pretreated for 24 h with 1 μmol/L of PX followed by 1000 ng/mL of TRAIL. Protein assays revealed that TRAIL/PX synergy was related to DR4, cleaved caspase-8 and cleaved caspase-3 upregulation, whereas the mitochondrial pathway was not involved in TRAIL-induced apoptosis. The present study indicates that PX can sensitize U87 cells and U87-SLCs to TRAIL treatment through an extrinsic pathway of cell apoptosis. The combined treatment of TRAIL and PX may be a promising glioma chemotherapy because of its successful inhibition of U87-SLCs, which are hypothesized to influence chemotherapeutic outcomes of gliomas. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Pharmacokinetics and Tissue Distribution Study of Praeruptorin D from Radix Peucedani in Rats by High-Performance Liquid Chromatography (HPLC)
Int. J. Mol. Sci. 2012, 13(7), 9129-9141; https://doi.org/10.3390/ijms13079129 - 20 Jul 2012
Cited by 11 | Viewed by 3412
Abstract
Praeruptorin D (PD), a major pyranocoumarin isolated from Radix Peucedani, exhibited antitumor and anti-inflammatory activities. The aim of this study was to investigate the pharmacokinetics and tissue distribution of PD in rats following intravenous (i.v.) administration. The levels of PD in plasma and [...] Read more.
Praeruptorin D (PD), a major pyranocoumarin isolated from Radix Peucedani, exhibited antitumor and anti-inflammatory activities. The aim of this study was to investigate the pharmacokinetics and tissue distribution of PD in rats following intravenous (i.v.) administration. The levels of PD in plasma and tissues were measured by a simple and sensitive reversed-phase high-performance liquid chromatography (HPLC) method. The biosamples were treated by liquid-liquid extraction (LLE) with methyl tert-butyl ether (MTBE) and osthole was used as the internal standard (IS). The chromatographic separation was accomplished on a reversed-phase C18 column using methanol-water (75:25, v/v) as mobile phase at a flow rate of 0.8 mL/min and ultraviolet detection wave length was set at 323 nm. The results demonstrate that this method has excellent specificity, linearity, precision, accuracy and recovery. The pharmacokinetic study found that PD fitted well into a two-compartment model with a fast distribution phase and a relative slow elimination phase. Tissue distribution showed that the highest concentration was observed in the lung, followed by heart, liver and kidney. Furthermore, PD can also be detected in the brain, which indicated that PD could cross the blood-brain barrier after i.v. administration. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
HR4 Gene Is Induced in the Arabidopsis-Trichoderma atroviride Beneficial Interaction
Int. J. Mol. Sci. 2012, 13(7), 9110-9128; https://doi.org/10.3390/ijms13079110 - 20 Jul 2012
Cited by 11 | Viewed by 5301
Abstract
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins [...] Read more.
Plants are constantly exposed to microbes, for this reason they have evolved sophisticated strategies to perceive and identify biotic interactions. Thus, plants have large collections of so-called resistance (R) proteins that recognize specific microbe factors as signals of invasion. One of these proteins is codified by the Arabidopsis thaliana HR4 gene in the Col-0 ecotype that is homologous to RPW8 genes present in the Ms-0 ecotype. In this study, we investigated the expression patterns of the HR4 gene in Arabidopsis seedlings interacting with the beneficial fungus Trichoderma atroviride. We observed the induction of the HR4 gene mainly at 96 hpi when the fungus interaction was established. Furthermore, we found that the HR4 gene was differentially regulated in interactions with the beneficial bacterium Pseudomonas fluorescens and the pathogenic bacterium P. syringae. When hormone treatments were applied to A. thaliana (Col-0), each hormone treatment induced changes in HR4 gene expression. On the other hand, the expression of the RPW8.1 and RPW8.2 genes of Arabidopsis ecotype Ms-0 in interaction with T. atroviride was assessed. Interestingly, these genes are interaction-responsive; in particular, the RPW8.1 gene shows a very high level of expression in the later stages of interaction. These results indicate that HR4 and RPW8 genes could play a role in the establishment of Arabidopsis interactions with beneficial microbes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Open AccessArticle
Curcumin Inhibits Glutamate Release from Rat Prefrontal Nerve Endings by Affecting Vesicle Mobilization
Int. J. Mol. Sci. 2012, 13(7), 9097-9109; https://doi.org/10.3390/ijms13079097 - 20 Jul 2012
Cited by 14 | Viewed by 3640
Abstract
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting [...] Read more.
Curcumin, one of the major constituents of Curcuma longa, has been shown to inhibit depolarization-evoked glutamate release from rat prefrontocortical nerve terminals by reducing voltage-dependent Ca2+ entry. This study showed that curcumin inhibited ionomycin-induced glutamate release and KCl-evoked FM1-43 release, suggesting that some steps after Ca2+ entry are regulated by curcumin. Furthermore, disrupting the cytoskeleton organization using cytochalasin D abolished the inhibitory action of curcumin on ionomycin-induced glutamate release. Mitogen-activated protein kinase kinase (MEK) inhibition also prevented the inhibitory effect of curcumin on ionomycin-induced glutamate release. Western blot analyses showed that curcumin decreased the ionomycin-induced phosphorylation of extracellular signal-regulated kinase 1 and 2 (ERK1/2) and synaptic vesicle-associated protein synapsin I, the main presynaptic target of ERK. These results show that curcumin-mediated inhibition of glutamate release involves modulating downstream events by controlling synaptic vesicle recruitment and exocytosis, possibly through a decrease of MAPK/ERK activation and synapsin I phosphorylation, thereby decreasing synaptic vesicle availability for exocytosis. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming 2012)
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Open AccessArticle
The Structure Lacuna
Int. J. Mol. Sci. 2012, 13(7), 9081-9096; https://doi.org/10.3390/ijms13079081 - 20 Jul 2012
Cited by 2 | Viewed by 3554
Abstract
Molecular symmetry is intimately connected with the classical concept ofthree-dimensional molecular structure. In a non-classical theory of wave-like interactionin four-dimensional space-time, both of these concepts and traditional quantum mechanicslose their operational meaning, unless suitably modified. A required reformulation shouldemphasize the importance of four-dimensional [...] Read more.
Molecular symmetry is intimately connected with the classical concept ofthree-dimensional molecular structure. In a non-classical theory of wave-like interactionin four-dimensional space-time, both of these concepts and traditional quantum mechanicslose their operational meaning, unless suitably modified. A required reformulation shouldemphasize the importance of four-dimensional effects like spin and the symmetry effects ofspace-time curvature that could lead to a fundamentally different understanding of molecularsymmetry and structure in terms of elementary number theory. Isolated single moleculeshave no characteristic shape and macro-biomolecules only develop robust three-dimensionalstructure in hydrophobic response to aqueous cellular media. Full article
(This article belongs to the Special Issue Molecular Symmetry)
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Decidual Macrophages Are Significantly Increased in Spontaneous Miscarriages and Over-Express FasL: A Potential Role for Macrophages in Trophoblast Apoptosis
Int. J. Mol. Sci. 2012, 13(7), 9069-9080; https://doi.org/10.3390/ijms13079069 - 20 Jul 2012
Cited by 42 | Viewed by 4430
Abstract
Decidual macrophages (DM) are the second most abundant population in the fetal-maternal interface. Their role has been so far identified as being local immuno-modulators favoring the maternal tolerance to the fetus. Herein we investigated tissue samples from 11 cases of spontaneous miscarriages and [...] Read more.
Decidual macrophages (DM) are the second most abundant population in the fetal-maternal interface. Their role has been so far identified as being local immuno-modulators favoring the maternal tolerance to the fetus. Herein we investigated tissue samples from 11 cases of spontaneous miscarriages and from 9 cases of elective terminations of pregnancy. Using immunohistochemistry and dual immunofluorescence we have demonstrated that in spontaneous miscarriages the DM are significantly increased. Additionally, we noted a significant up-regulation of macrophage FasL expression. Our results further support a dual role for DM during pregnancy and miscarriages. We hypothesize that the baseline DM population in normal pregnancy is in line with an M2 phenotype supporting the ongoing gestation. In contrast, during spontaneous miscarriages, the increased FasL-expressing population could be a part of an M1 phenotype participating in Fas/FasL-related apoptosis. Our results highlight a new aspect of macrophage biology in pregnancy physiology and pathophysiology. Further studies with larger samples are needed to verify the current results and evaluate their clinical impact. Full article
(This article belongs to the Collection Programmed Cell Death and Apoptosis)
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Ultrasonic-Assisted Enzymolysis to Improve the Antioxidant Activities of Peanut (Arachin conarachin L.) Antioxidant Hydrolysate
Int. J. Mol. Sci. 2012, 13(7), 9051-9068; https://doi.org/10.3390/ijms13079051 - 20 Jul 2012
Cited by 32 | Viewed by 3914
Abstract
The objective of this work is to provide a theoretical basis for preparing peanut antioxidant hydrolysate in order to improve its antioxidant activities. Therefore, response surface methodology (RSM) based on the Box-Behnken design was used to optimize ultrasonic-assisted enzymolysis for the purpose of [...] Read more.
The objective of this work is to provide a theoretical basis for preparing peanut antioxidant hydrolysate in order to improve its antioxidant activities. Therefore, response surface methodology (RSM) based on the Box-Behnken design was used to optimize ultrasonic-assisted enzymolysis for the purpose of preparing peanut antioxidant hydrolysate. Results indicated that the DPPH free radical scavenging activity of peanut hydrolysate could reach 90.06% under the following optimum conditions: ultrasonic power of 150.0 w, reaction temperature of 62.0 °C, incubation time of 25.0 min, and initial pH value of 8.5. The DPPH free radical scavenging rate of peanut hydrolysate from ultrasonic-assisted enzymolysis improved comparing with that of peanut hydrolysate from protease hydrolysis alone. The peanut antioxidant hydrolysate was found to display eight improved kinds of antioxidant activities. In conclusion, the optimal ultrasonic-assisted enzymolysis technology conditions described in this paper, appear to be beneficial for preparing peanut antioxidant hydrolysate. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Quantitative and Chemical Fingerprint Analysis for the Quality Evaluation of Isatis indigotica based on Ultra-Performance Liquid Chromatography with Photodiode Array Detector Combined with Chemometric Methods
Int. J. Mol. Sci. 2012, 13(7), 9035-9050; https://doi.org/10.3390/ijms13079035 - 20 Jul 2012
Cited by 27 | Viewed by 4373
Abstract
A simple and reliable method of ultra-performance liquid chromatography with photodiode array detector (UPLC-PDA) was developed to control the quality of Radix Isatidis (dried root of Isatis indigotica) for chemical fingerprint analysis and quantitative analysis of eight bioactive constituents, including R, [...] Read more.
A simple and reliable method of ultra-performance liquid chromatography with photodiode array detector (UPLC-PDA) was developed to control the quality of Radix Isatidis (dried root of Isatis indigotica) for chemical fingerprint analysis and quantitative analysis of eight bioactive constituents, including R,S-goitrin, progoitrin, epiprogoitrin, gluconapin, adenosine, uridine, guanosine, and hypoxanthine. In quantitative analysis, the eight components showed good regression (R > 0.9997) within test ranges, and the recovery method ranged from 99.5% to 103.0%. The UPLC fingerprints of the Radix Isatidis samples were compared by performing chemometric procedures, including similarity analysis, hierarchical clustering analysis, and principal component analysis. The chemometric procedures classified Radix Isatidis and its finished products such that all samples could be successfully grouped according to crude herbs, prepared slices, and adulterant Baphicacanthis cusiae Rhizoma et Radix. The combination of quantitative and chromatographic fingerprint analysis can be used for the quality assessment of Radix Isatidis and its finished products. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Hepatoprotective Effects of Berberis vulgaris L. Extract/β Cyclodextrin on Carbon Tetrachloride–Induced Acute Toxicity in Mice
Int. J. Mol. Sci. 2012, 13(7), 9014-9034; https://doi.org/10.3390/ijms13079014 - 19 Jul 2012
Cited by 27 | Viewed by 4288
Abstract
The present study investigated the capacity of formulated Berberis vulgaris extract/β-cyclodextrin to protect liver against CCl4-induced hepatotoxicity in mice. Formulated and non-formulated extracts were given orally (50 mg/kg/day) to mice for 7 days and were then intra-peritoneally injected with 1.0 mL/kg [...] Read more.
The present study investigated the capacity of formulated Berberis vulgaris extract/β-cyclodextrin to protect liver against CCl4-induced hepatotoxicity in mice. Formulated and non-formulated extracts were given orally (50 mg/kg/day) to mice for 7 days and were then intra-peritoneally injected with 1.0 mL/kg CCl4 on the 8th day. After 24 h of CCl4 administration, an increase in the levels of apartate-amino-transferase (AST), alanine-amino-transferase (ALT) and malondialdehyde (MDA) was found and a significant decrease in superoxide-dismutase (SOD), catalase (CAT), glutathione (GSH) and glutathione-peroxidase (GPx) levels could be detected. This was accompanied by extended centrilobular necrosis, steatosis, fibrosis and an altered ultrastructure of hepatocytes. Pre-treatment with formulated or non-formulated extract suppressed the increase in ALT, AST and MDA levels and restored the level of antioxidant enzymes at normal values. Histopathological and electron-microscopic examination showed milder liver damage in both pre-treated groups and the protective effect was more pronounced after the formulated extract was administered. Internucleosomal DNA fragmentation induced by CCl4 was reduced in the group which received non-formulated extract and absent in the group which received formulated extract. Taken together, our results suggest that Berberis vulgaris/β-cyclodextrin treatment prevents hepatic injury induced by CCl4 and can be considered for further nutraceutical studies. Full article
(This article belongs to the Section Biochemistry)
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Homology Modeling and Analysis of Structure Predictions of the Bovine Rhinitis B Virus RNA Dependent RNA Polymerase (RdRp)
Int. J. Mol. Sci. 2012, 13(7), 8998-9013; https://doi.org/10.3390/ijms13078998 - 19 Jul 2012
Cited by 6 | Viewed by 4330
Abstract
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence [...] Read more.
Bovine Rhinitis B Virus (BRBV) is a picornavirus responsible for mild respiratory infection of cattle. It is probably the least characterized among the aphthoviruses. BRBV is the closest relative known to Foot and Mouth Disease virus (FMDV) with a ~43% identical polyprotein sequence and as much as 67% identical sequence for the RNA dependent RNA polymerase (RdRp), which is also known as 3D polymerase (3Dpol). In the present study we carried out phylogenetic analysis, structure based sequence alignment and prediction of three-dimensional structure of BRBV 3Dpol using a combination of different computational tools. Model structures of BRBV 3Dpol were verified for their stereochemical quality and accuracy. The BRBV 3Dpol structure predicted by SWISS-MODEL exhibited highest scores in terms of stereochemical quality and accuracy, which were in the range of 2Å resolution crystal structures. The active site, nucleic acid binding site and overall structure were observed to be in agreement with the crystal structure of unliganded as well as template/primer (T/P), nucleotide tri-phosphate (NTP) and pyrophosphate (PPi) bound FMDV 3Dpol (PDB, 1U09 and 2E9Z). The closest proximity of BRBV and FMDV 3Dpol as compared to human rhinovirus type 16 (HRV-16) and rabbit hemorrhagic disease virus (RHDV) 3Dpols is also substantiated by phylogeny analysis and root-mean square deviation (RMSD) between C-α traces of the polymerase structures. The absence of positively charged α-helix at C terminal, significant differences in non-covalent interactions especially salt bridges and CH-pi interactions around T/P channel of BRBV 3Dpol compared to FMDV 3Dpol, indicate that despite a very high homology to FMDV 3Dpol, BRBV 3Dpol may adopt a different mechanism for handling its substrates and adapting to physiological requirements. Our findings will be valuable in the design of structure-function interventions and identification of molecular targets for drug design applicable to Aphthovirus RdRps. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Antioxidant Property Enhancement of Sweet Potato Flour under Simulated Gastrointestinal pH
Int. J. Mol. Sci. 2012, 13(7), 8987-8997; https://doi.org/10.3390/ijms13078987 - 19 Jul 2012
Cited by 14 | Viewed by 3493
Abstract
Sweet potato is known to be rich in healthful antioxidants, but the stability of its antioxidant properties under gastrointestinal pH is very much unknown. Hence, this study aimed to evaluate the changes in antioxidant properties (total contents of phenolics and flavonoids as well [...] Read more.
Sweet potato is known to be rich in healthful antioxidants, but the stability of its antioxidant properties under gastrointestinal pH is very much unknown. Hence, this study aimed to evaluate the changes in antioxidant properties (total contents of phenolics and flavonoids as well as antioxidant activity) of sweet potato flour (SPF) under simulated gastrointestinal pH conditions. It was found that the yield of SPF crude phenolic extract increased from 0.29 to 3.22 g/100 g SPF upon subjection to gastrointestinal pH conditions (p < 0.05). Also elevated significantly were the total phenolic content (TPC), total flavonoid content (TFC) and antioxidant activity of SPF (p < 0.05). In summary, the antioxidant properties of SPF were enhanced under gastrointestinal pH conditions, suggesting that SPF might possess a considerable amount of bound phenolic and other antioxidative compounds. The antioxidant properties of SPF are largely influenced by pH and thus might be enhanced during the in vivo digestive process. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Enrichment and Purification of Syringin, Eleutheroside E and Isofraxidin from Acanthopanax senticosus by Macroporous Resin
Int. J. Mol. Sci. 2012, 13(7), 8970-8986; https://doi.org/10.3390/ijms13078970 - 18 Jul 2012
Cited by 14 | Viewed by 3853
Abstract
In order to screen a suitable resin for the preparative simultaneous separation and purification of syringin, eleutheroside E and isofraxidin from Acanthopanax senticosus, the adsorption and desorption properties of 17 widely used commercial macroporous resins were evaluated. According to our results, HPD100C, [...] Read more.
In order to screen a suitable resin for the preparative simultaneous separation and purification of syringin, eleutheroside E and isofraxidin from Acanthopanax senticosus, the adsorption and desorption properties of 17 widely used commercial macroporous resins were evaluated. According to our results, HPD100C, which adsorbs by the molecular tiers model, was the best macroporous resin, offering higher adsorption and desorption capacities and higher adsorption speed for syringin, eleutheroside E and isofraxidin than other resins. Dynamic adsorption and desorption tests were carried out to optimize the process parameters. The optimal conditions were as follows: for adsorption, processing volume: 24 BV, flow rate: 2 BV/h; for desorption, ethanol–water solution: 60:40 (v/v), eluent volume: 4 BV, flow rate: 3 BV/h. Under the above conditions, the contents of syringin, eleutheroside E and isofraxidin increased 174-fold, 20-fold and 5-fold and their recoveries were 80.93%, 93.97% and 93.79%, respectively. Full article
(This article belongs to the Section Materials Science)
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Open AccessArticle
Binding Mode Prediction of Evodiamine within Vanilloid Receptor TRPV1
Int. J. Mol. Sci. 2012, 13(7), 8958-8969; https://doi.org/10.3390/ijms13078958 - 18 Jul 2012
Cited by 15 | Viewed by 3284
Abstract
Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 [...] Read more.
Accurate assessment of the potential binding mode of drugs is crucial to computer-aided drug design paradigms. It has been reported that evodiamine acts as an agonist of the vanilloid receptor Transient receptor potential vanilloid-1 (TRPV1). However, the precise interaction between evodiamine and TRPV1 was still not fully understood. In this perspective, the homology models of TRPV1 were generated using the crystal structure of the voltage-dependent shaker family K+ channel as a template. We then performed docking and molecular dynamics simulation to gain a better understanding of the probable binding modes of evodiamine within the TRPV1 binding pocket. There are no significant interspecies differences in evodiamine binding in rat, human and rabbit TRPV1 models. Pharmacophore modeling further provided confidence for the validity of the docking studies. This study is the first to shed light on the structural determinants required for the interaction between TRPV1 and evodiamine, and gives new suggestions for the rational design of novel TRPV1 ligands. Full article
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Antioxidant Activity of Brazilian Vegetables and Its Relation with Phenolic Composition
Int. J. Mol. Sci. 2012, 13(7), 8943-8957; https://doi.org/10.3390/ijms13078943 - 18 Jul 2012
Cited by 85 | Viewed by 4913
Abstract
Vegetables are widely consumed in Brazil and exported to several countries. This study was performed to evaluate the phenolic content and antioxidant activity of vegetables commonly consumed in Brazil using five different methods, namely DPPH and ABTS free radical, β-carotene bleaching, reduction of [...] Read more.
Vegetables are widely consumed in Brazil and exported to several countries. This study was performed to evaluate the phenolic content and antioxidant activity of vegetables commonly consumed in Brazil using five different methods, namely DPPH and ABTS free radical, β-carotene bleaching, reduction of Fe3+ (FRAP), oxidative stability in Rancimat, and the chemical composition using gas chromatography-mass spectrometry (GC-MS). The content of phenolic compounds ranged from 1.2 mg GA/g (carrot) to 16.9 mg GA/g (lettuce). Vegetables presenting the highest antioxidant activity were lettuce (77.2 µmol Trolox/g DPPH; 447.1 µmol F2+/g FRAP), turmeric (118.6 µmol Trolox/g ABTS•+; 92.8% β-carotene), watercress and broccoli (protective factor 1.29—Rancimat method). Artichoke, spinach, broccoli, and asparagus also showed considerable antioxidant activity. The most frequent phenolic compounds identified by GC-MS were ferulic, caffeic, p-coumaric, 2-dihydroxybenzoic, 2,5-dihydroxybenzoic acids, and quercetin. We observed antioxidant activity in several vegetables and our results point out their importance in the diet. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
Exome Enrichment and SOLiD Sequencing of Formalin Fixed Paraffin Embedded (FFPE) Prostate Cancer Tissue
Int. J. Mol. Sci. 2012, 13(7), 8933-8942; https://doi.org/10.3390/ijms13078933 - 17 Jul 2012
Cited by 25 | Viewed by 4850
Abstract
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) [...] Read more.
Next generation sequencing (NGS) technologies have revolutionized cancer research allowing the comprehensive study of cancer using high throughput deep sequencing methodologies. These methods detect genomic alterations, nucleotide substitutions, insertions, deletions and copy number alterations. SOLiD (Sequencing by Oligonucleotide Ligation and Detection, Life Technologies) is a promising technology generating billions of 50 bp sequencing reads. This robust technique, successfully applied in gene identification, might be helpful in detecting novel genes associated with cancer initiation and progression using formalin fixed paraffin embedded (FFPE) tissue. This study’s aim was to compare the validity of whole exome sequencing of fresh-frozen vs. FFPE tumor tissue by normalization to normal prostatic FFPE tissue, obtained from the same patient. One primary fresh-frozen sample, corresponding FFPE prostate cancer sample and matched adjacent normal prostatic tissue was subjected to exome sequencing. The sequenced reads were mapped and compared. Our study was the first to show comparable exome sequencing results between FFPE and corresponding fresh-frozen cancer tissues using SOLiD sequencing. A prior study has been conducted comparing the validity of sequencing of FFPE vs. fresh frozen samples using other NGS platforms. Our validation further proves that FFPE material is a reliable source of material for whole exome sequencing. Full article
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Synergistic Interactions of Methanolic Extract of Acacia mearnsii De Wild. with Antibiotics against Bacteria of Clinical Relevance
Int. J. Mol. Sci. 2012, 13(7), 8915-8932; https://doi.org/10.3390/ijms13078915 - 17 Jul 2012
Cited by 42 | Viewed by 4194
Abstract
With the emergence of multidrug-resistant organisms, combining medicinal plants with synthetic or orthodox medicines against resistant bacteria becomes necessary. In this study, interactions between methanolic extract of Acacia mearnsii and eight antibiotics were investigated by agar diffusion and checkerboard assays. The minimum inhibitory [...] Read more.
With the emergence of multidrug-resistant organisms, combining medicinal plants with synthetic or orthodox medicines against resistant bacteria becomes necessary. In this study, interactions between methanolic extract of Acacia mearnsii and eight antibiotics were investigated by agar diffusion and checkerboard assays. The minimum inhibitory concentrations (MICs) of all the antibiotics ranged between 0.020 and 500 µg/mL while that of the crude extract varied between 0.156 and 1.25 mg/mL. The agar diffusion assay showed that extract-kanamycin combination had zones of inhibition ≥20 ± 1.0 mm in all the bacteria tested (100%), followed by extract-chloramphenicol (90%) > extract-ciprofloxacin = extract-tetracycline (70%) > extract-amoxicillin (60%) > extract-nalidixic acid (50%) > extract-erythromycin (40%) > extract-metronidazole (20%). The checkerboard showed synergistic interaction (61.25%), additivity/indifference (23.75%) and antagonistic (15%) effects. The synergistic interaction was most expressed by combining the extract with tetracycline, metronidazole, amoxicillin, ciprofloxacin, chloramphenicol and nalidixic acid against E. coli (ATCC 25922), erythromycin, metronidazole, amoxicillin, chloramphenicol and kanamycin against S. aureus (ATCC 6538), erythromycin, tetracycline, amoxicillin, nalidixic acid and chloramphenicol against B. subtilis KZN, erythromycin, metronidazole and amoxicillin against E. faecalis KZN, erythromycin, tetracycline, nalidixic acid and chloramphenicol against K. pneumoniae (ATCC 10031), erythromycin, tetracycline, metronidazole and chloramphenicol against P. vulgaris (ATCC 6830), erythromycin, tetracycline, amoxicillin and chloramphenicol against S. sonnei (ATCC 29930), metronidazole, amoxicillin and chloramphenicol against E. faecalis (ATCC 29212) and ciprofloxacin and chloramphenicol against Proteus vulgaris KZN. The synergistic interactions indicated that the bactericidal potentials of the antibacterial agents were improved and combining natural products with antibiotic could be potential sources for resistance-modifying agents useful against infectious multi-drug resistant bacteria. Full article
(This article belongs to the Section Biochemistry)
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