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Int. J. Mol. Sci., Volume 13, Issue 6 (June 2012), Pages 6534-7871

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Open AccessArticle Influence of “Glow Discharge Plasma” as an External Stimulus on the Self-Assembly, Morphology and Binding Affinity of Gold Nanoparticle-Streptavidin Conjugates
Int. J. Mol. Sci. 2012, 13(6), 6534-6547; doi:10.3390/ijms13066534
Received: 27 March 2012 / Revised: 2 May 2012 / Accepted: 15 May 2012 / Published: 29 May 2012
Cited by 2 | PDF Full-text (681 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we investigate the influence of glow discharge plasma (GDP) on the self-assembly, morphology and binding affinity of streptavidin coated gold nanoparticles (Au-NP-SV) and biotinylated antibody (bAb) adsorbed on a highly oriented pyrolytic graphite (HOPG) substrate. Atomic force microscope (AFM) [...] Read more.
In this study, we investigate the influence of glow discharge plasma (GDP) on the self-assembly, morphology and binding affinity of streptavidin coated gold nanoparticles (Au-NP-SV) and biotinylated antibody (bAb) adsorbed on a highly oriented pyrolytic graphite (HOPG) substrate. Atomic force microscope (AFM) was used to image the pre- and post-GDP treated samples. The analysis of the AFM images showed a considerable change in the aggregation and morphology of Au-NP-conjugates after treatment with GDP. To our knowledge, this is the first report on using GDP to enhance and speed-up the aggregation (sintering) of adsorbed NP biomolecular conjugates. These results show a promising route that could be generalized for other NPs and their conjugates. It can also be considered as an alternative and cheap aggregation method for controlling the binding affinity of biomolecular species on different surfaces with interesting applications. Full article
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Open AccessArticle Apoptosis Signaling Is Altered in CD4+CD25+FoxP3+ T Regulatory Lymphocytes in Pre-Eclampsia
Int. J. Mol. Sci. 2012, 13(6), 6548-6560; doi:10.3390/ijms13066548
Received: 17 April 2012 / Revised: 21 May 2012 / Accepted: 22 May 2012 / Published: 29 May 2012
Cited by 10 | PDF Full-text (288 KB) | HTML Full-text | XML Full-text
Abstract
The aim of our study was to estimate the surface expressions of CD95 (APO-1/Fas) antigen and the intracellular expressions of anti-apoptotic protein Bcl-2 and pro-apoptotic protein Bax in CD4+CD25+FoxP3+ T regulatory lymphocytes (Tregs) as well as the [...] Read more.
The aim of our study was to estimate the surface expressions of CD95 (APO-1/Fas) antigen and the intracellular expressions of anti-apoptotic protein Bcl-2 and pro-apoptotic protein Bax in CD4+CD25+FoxP3+ T regulatory lymphocytes (Tregs) as well as the percentage of CD8+CD28+ T cytotoxic cells in peripheral blood of patients with pre-eclampsia in comparison with healthy pregnant women in the third trimester of physiological pregnancy. Twenty-four women with pre-eclampsia and 20 normal third trimester pregnant women were included in the study. The lymphocytes were isolated from peripheral blood samples and labeled with monoclonal antibodies. The expressions of surface antigens and intracellular proteins were estimated using flow cytometry. The population of CD4+CD25+FoxP3+ Treg cells was significantly lower in peripheral blood of patients with pre-eclampsia when compared to normal third trimester pregnant women. The percentages of CD4+CD25+FoxP3+ Treg cells that express Bcl-2 protein were significantly lower in peripheral blood of patients with pre-eclampsia when compared to healthy pregnant women, whereas the percentages of CD4+CD25+FoxP3+ Treg cells with the expressions of Bax protein did not differ in both groups. Moreover, the mean fluorescence intensity (MFI) of Bcl-2 protein in CD4+CD25+FoxP3+ Treg cells was significantly lower and MFI of Bax protein significantly higher in pre-eclampsia when compared to the control group. The percentage of CD8+CD28+ T cells did not differ in both studied groups but MFI of CD28 antigen on T CD8+ cells was significantly higher in pre-eclampsia when compared to the control group. The obtained results suggest that the deficit of CD4+CD25+FoxP3+ Treg lymphocytes which is observed in pre-eclampsia may be associated with altered apoptosis signaling in Tregs. Full article
(This article belongs to the collection Programmed Cell Death and Apoptosis)
Open AccessArticle Identification of Late Embryogenesis Abundant (LEA) Protein Putative Interactors Using Phage Display
Int. J. Mol. Sci. 2012, 13(6), 6582-6603; doi:10.3390/ijms13066582
Received: 29 February 2012 / Revised: 7 April 2012 / Accepted: 17 May 2012 / Published: 29 May 2012
Cited by 6 | PDF Full-text (1234 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Arabidopsis thaliana seeds without functional SEED MATURATION PROTEIN1 (SMP1), a boiling soluble protein predicted to be of intrinsic disorder, presumed to be a LATE EMBRYOGENESIS ABUNDANT (LEA) family protein based on sequence homology, do not enter secondary dormancy after 3 days at [...] Read more.
Arabidopsis thaliana seeds without functional SEED MATURATION PROTEIN1 (SMP1), a boiling soluble protein predicted to be of intrinsic disorder, presumed to be a LATE EMBRYOGENESIS ABUNDANT (LEA) family protein based on sequence homology, do not enter secondary dormancy after 3 days at 40 °C. We hypothesized that SMP1 may protect a heat labile protein involved in the promotion of secondary dormancy. Recombinant SMP1 and GmPM28, its soybean (Glycine max), LEA4 homologue, protected the labile GLUCOSE-6-PHOSPHATE DEHYROGENASE enzyme from heat stress, as did a known protectant, Bovine Serum Albumin, whether the LEA protein was in solution or attached to the bottom of microtiter plates. Maintenance of a biological function for both recombinant LEA proteins when immobilized encouraged a biopanning approach to screen for potential protein interactors. Phage display with two Arabidopsis seed, T7 phage, cDNA libraries, normalized for transcripts present in the mature, dehydrated, 12-, 24-, or 36-h imbibed seeds, were used in biopans against recombinant SMP1 and GmPM28. Phage titer increased considerably over four rounds of biopanning for both LEA proteins, but not for BSA, at both 25 and at 41 °C, regardless of the library used. The prevalence of multiple, independent clones encoding portions of specific proteins repeatedly retrieved from different libraries, temperatures and baits, provides evidence suggesting these LEA proteins are discriminating which proteins they protect, a novel finding. The identification of putative LEA-interacting proteins provides targets for reverse genetic approaches to further dissect the induction of secondary dormancy in seeds in response to heat stress. Full article
(This article belongs to the Special Issue Phage Display)
Open AccessArticle Effect of Calcium and Potassium on Antioxidant System of Vicia faba L. Under Cadmium Stress
Int. J. Mol. Sci. 2012, 13(6), 6604-6619; doi:10.3390/ijms13066604
Received: 5 April 2012 / Revised: 21 May 2012 / Accepted: 22 May 2012 / Published: 29 May 2012
Cited by 19 | PDF Full-text (269 KB) | HTML Full-text | XML Full-text
Abstract
Cadmium (Cd) in soil poses a major threat to plant growth and productivity. In the present experiment, we studied the effect of calcium (Ca2+) and/or potassium (K+) on the antioxidant system, accumulation of proline (Pro), malondialdehyde (MDA), and [...] Read more.
Cadmium (Cd) in soil poses a major threat to plant growth and productivity. In the present experiment, we studied the effect of calcium (Ca2+) and/or potassium (K+) on the antioxidant system, accumulation of proline (Pro), malondialdehyde (MDA), and content of photosynthetic pigments, cadmium (Cd) and nutrients, i.e., Ca2+ and K+ in leaf of Vicia faba L. (cv. TARA) under Cd stress. Plants grown in the presence of Cd exhibited reduced growth traits [root length (RL) plant−1, shoot length (SL) plant−1, root fresh weight (RFW) plant−1, shoot fresh weight (SFW) plant−1, root dry weight (RDW) plant−1 and shoot dry weight (SDW) plant−1] and concentration of Ca2+, K+, Chlorophyll (Chl) a and Chl b content, except content of MDA, Cd and (Pro). The antioxidant enzymes [peroxidase (POD) and superoxide dismutase (SOD)] slightly increased as compared to control under Cd stress. However, a significant improvement was observed in all growth traits and content of Ca2+, K+, Chl a, Chl b ,Pro and activity of antioxidant enzymes catalase (CAT), POD and SOD in plants subjected to Ca2+ and/or K+. The maximum alleviating effect was recorded in the plants grown in medium containing Ca2+ and K+ together. This study indicates that the application of Ca2+ and/or K+ had a significant and synergistic effect on plant growth. Also, application of Ca2+ and/or K+ was highly effective against the toxicity of Cd by improving activity of antioxidant enzymes and solute that led to the enhanced plant growth of faba bean plants. Full article
(This article belongs to the Special Issue Oxidative Stress and Ageing)
Open AccessArticle Pharmacophore and Molecular Docking Guided 3D-QSAR Study of Bacterial Enoyl-ACP Reductase (FabI) Inhibitors
Int. J. Mol. Sci. 2012, 13(6), 6620-6638; doi:10.3390/ijms13066620
Received: 20 March 2012 / Revised: 7 May 2012 / Accepted: 14 May 2012 / Published: 30 May 2012
Cited by 4 | PDF Full-text (1233 KB) | HTML Full-text | XML Full-text
Abstract
Enoyl acyl carrier protein (ACP) reductase (FabI) is a potential target for the development of antibacterial agents. Three-dimensional quantitative structure-activity relationships (3D-QSAR) for substituted formamides series of FabI inhibitors were investigated using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices [...] Read more.
Enoyl acyl carrier protein (ACP) reductase (FabI) is a potential target for the development of antibacterial agents. Three-dimensional quantitative structure-activity relationships (3D-QSAR) for substituted formamides series of FabI inhibitors were investigated using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) techniques. Pharmacophore and molecular docking methods were used for construction of the molecular alignments. A training set of 36 compounds was performed to create the 3D-QSAR models and their external predictivity was proven using a test set of 11 compounds. Graphical interpretation of the results revealed important structural features of the formamides related to the active site of FabI. The results may be exploited for further optimization of the design of new potent FabI inhibitors. Full article
Open AccessArticle Synthesis and Characterization of Polyethylene Glycol Mediated Silver Nanoparticles by the Green Method
Int. J. Mol. Sci. 2012, 13(6), 6639-6650; doi:10.3390/ijms13066639
Received: 19 March 2012 / Revised: 17 May 2012 / Accepted: 17 May 2012 / Published: 30 May 2012
Cited by 71 | PDF Full-text (580 KB) | HTML Full-text | XML Full-text
Abstract
The roles of green chemistry in nanotechnology and nanoscience fields are very significant in the synthesis of diverse nanomaterials. Herein, we report a green chemistry method for synthesized colloidal silver nanoparticles (Ag NPs) in polymeric media. The colloidal Ag NPs were synthesized [...] Read more.
The roles of green chemistry in nanotechnology and nanoscience fields are very significant in the synthesis of diverse nanomaterials. Herein, we report a green chemistry method for synthesized colloidal silver nanoparticles (Ag NPs) in polymeric media. The colloidal Ag NPs were synthesized in an aqueous solution using silver nitrate, polyethylene glycol (PEG), and β-d-glucose as a silver precursor, stabilizer, and reducing agent, respectively. The properties of synthesized colloidal Ag NPs were studied at different reaction times. The ultraviolet-visible spectra were in excellent agreement with the obtained nanostructure studies performed by transmission electron microscopy (TEM) and their size distributions. The Ag NPs were characterized by utilizing X-ray diffraction (XRD), zeta potential measurements and Fourier transform infrared (FT-IR). The use of green chemistry reagents, such as glucose, provides green and economic features to this work. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Proximate Composition and Antioxidant Potential of Leaves from Three Varieties of Mulberry (Morus sp.): A Comparative Study
Int. J. Mol. Sci. 2012, 13(6), 6651-6664; doi:10.3390/ijms13066651
Received: 16 April 2012 / Revised: 9 May 2012 / Accepted: 14 May 2012 / Published: 30 May 2012
Cited by 27 | PDF Full-text (161 KB) | HTML Full-text | XML Full-text
Abstract
In this study, leaves of three indigenous varieties of Mulberry namely, Morus alba L., Morus nigra L. and Morus rubra L. were investigated for their antioxidant potential and their proximate composition was determined. The yields of 80% methanolic extracts ranged between 8.28–13.89%. [...] Read more.
In this study, leaves of three indigenous varieties of Mulberry namely, Morus alba L., Morus nigra L. and Morus rubra L. were investigated for their antioxidant potential and their proximate composition was determined. The yields of 80% methanolic extracts ranged between 8.28–13.89%. The contents of total phenolics (TPC), total flavonoids (TFC) and ascorbic acid (AA) ranged between 16.21–24.37 mg gallic acid equivalent (GAE)/g, 26.41–31.28 mg rutin equivalent (RE)/g and 0.97–1.49 mg/g, respectively. The antioxidant activity of leaf extracts was evaluated by measuring 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging actity, 2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid (ABTS•+) radical cation scavenging capacity and ferric ion reducing power and values ranged between 1.89–2.12, 6.12–9.89 and 0.56–0.97 mM Trolox equivalent/g of dried leaves, respectively. The investigated features reveal good nutritive and antioxidant attributes of all the varieties with mutually significant differences. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pharmacological Classification and Activity Evaluation of Furan and Thiophene Amide Derivatives Applying Semi-Empirical ab initio Molecular Modeling Methods
Int. J. Mol. Sci. 2012, 13(6), 6665-6678; doi:10.3390/ijms13066665
Received: 23 April 2012 / Revised: 16 May 2012 / Accepted: 21 May 2012 / Published: 30 May 2012
Cited by 8 | PDF Full-text (198 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS) based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC) retention data is proposed. Structural parameters obtained from the [...] Read more.
Pharmacological and physicochemical classification of the furan and thiophene amide derivatives by multiple regression analysis and partial least square (PLS) based on semi-empirical ab initio molecular modeling studies and high-performance liquid chromatography (HPLC) retention data is proposed. Structural parameters obtained from the PCM (Polarizable Continuum Model) method and the literature values of biological activity (antiproliferative for the A431 cells) expressed as LD50 of the examined furan and thiophene derivatives was used to search for relationships. It was tested how variable molecular modeling conditions considered together, with or without HPLC retention data, allow evaluation of the structural recognition of furan and thiophene derivatives with respect to their pharmacological properties. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
Open AccessArticle Perforin Expression by CD4+ Regulatory T Cells Increases at Multiple Sclerosis Relapse: Sex Differences
Int. J. Mol. Sci. 2012, 13(6), 6698-6710; doi:10.3390/ijms13066698
Received: 29 February 2012 / Revised: 10 May 2012 / Accepted: 22 May 2012 / Published: 1 June 2012
Cited by 6 | PDF Full-text (523 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis (MS) represents the leading cause of neurological deficit among young adults, affecting women more frequently than men. In MS, the extent of central nervous system lesions is determined by the net balance between self-reactive and regulatory T-cells at any given [...] Read more.
Multiple sclerosis (MS) represents the leading cause of neurological deficit among young adults, affecting women more frequently than men. In MS, the extent of central nervous system lesions is determined by the net balance between self-reactive and regulatory T-cells at any given time, among other factors, as well as by the effect of inflammatory response. Here, we studied both CD4+ and CD8+ TReg in parallel in blood and CSF during MS relapse. A recruitment of both regulatory CD4+ and CD8+ T cells (TReg) within the cerebrospinal fluid (CSF) takes place during MS relapse. Not previously described, the presence of CD4+ TReg in CSF was higher in women than in men, which could account for the sexual dimorphism in the incidence of MS. A direct correlation between plasma oestradiol (E2) and IL-2 levels was observed, in line with a putative circuit of E2 and perforin expression by CD4+ TReg playing a role in MS. Also, serum IFN-alpha was higher in females, with direct correlation with serum E2 levels. This is the first study to analyze perforin expression by CD4+ TReg in MS, which was greatly enhanced in CSF, what points out a relevant role of this molecule in the suppressive effects of the CD4+ TReg in MS, and contributes to the understanding of MS pathophysiology. Full article
Open AccessArticle Rapid Synthesis and Antiviral Activity of (Quinazolin-4-Ylamino)Methyl-Phosphonates Through Microwave Irradiation
Int. J. Mol. Sci. 2012, 13(6), 6730-6746; doi:10.3390/ijms13066730
Received: 31 March 2012 / Revised: 8 May 2012 / Accepted: 8 May 2012 / Published: 1 June 2012
Cited by 5 | PDF Full-text (352 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
This study describes the simple synthesis of new (quinazolin-4-ylamino) methylphosphonates via microwave irradiation. Substituted-2-aminobenzonitrile reacted with 1,1-dimethoxy-N,N-dimethylmethanamine at a reflux condition to obtain N'-(substituted-2-cyanophenyl)-N,N-dimethylformamidine (1). The subsequent reaction of this intermediate product with [...] Read more.
This study describes the simple synthesis of new (quinazolin-4-ylamino) methylphosphonates via microwave irradiation. Substituted-2-aminobenzonitrile reacted with 1,1-dimethoxy-N,N-dimethylmethanamine at a reflux condition to obtain N'-(substituted-2-cyanophenyl)-N,N-dimethylformamidine (1). The subsequent reaction of this intermediate product with α-aminophosphonate (2) in a solution containing glacial acetic acid in 2-propanol through microwave irradiation resulted in the formation of (quinazolin-4-ylamino)methyl-phosphonate derivatives 3a to 3x, which were unequivocally characterized by the spectral data and elemental analysis. The influence of the reaction conditions on the yield of 3a was investigated to optimize the synthetic conditions. The relative optimal conditions for the synthesis of 3a include a 1:1 molar ratio of N’-(2-cyanophenyl)-N,N-dimethylformamidine to diethyl amino(phenyl)methylphosphonate and a 4:1 volume ratio of isopropanol to HOAc in the solvent mixture, at a reaction temperature of 150 °C, with a microwave power of 100 W and a corresponding pressure of 150 psi for 20 min in the microwave synthesizer. The yield of 3a was approximately 79%, whereas those of 3b to 3x were approximately 77% to 86%. Some of the synthesized compounds displayed weak to good anti-Tobacco mosaic virus (TMV) activity. Full article
Open AccessArticle Opuntia humifusa Supplementation Increased Bone Density by Regulating Parathyroid Hormone and Osteocalcin in Male Growing Rats
Int. J. Mol. Sci. 2012, 13(6), 6747-6756; doi:10.3390/ijms13066747
Received: 2 May 2012 / Revised: 24 May 2012 / Accepted: 28 May 2012 / Published: 4 June 2012
Cited by 4 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
We investigated the effect of Opuntia humifusa (O. humifusa) supplementation on bone density and related hormone secretion in growing male rats. Sixteen six-week-old male Sprague-Dawley rats were randomly divided into two groups; control diet group (CG, n = 8), and [...] Read more.
We investigated the effect of Opuntia humifusa (O. humifusa) supplementation on bone density and related hormone secretion in growing male rats. Sixteen six-week-old male Sprague-Dawley rats were randomly divided into two groups; control diet group (CG, n = 8), and experimental diet group (EG, n = 8). The rats in the CG were given a control diet and those in the EG were given 5% O. humifusa added to the control diet for eight weeks. The serum OC level of the EG was significantly higher than that of the CG, and the serum parathyroid hormone (PTH) level of EG was significantly lower than that of the CG. In addition, the femoral and tibial BMD of the EG were significantly higher values than those of the CG, and the tibial BMC of the EG was significantly higher than that of the CG. These results suggest that O. humifusa supplementation has a positive effect on bone density by suppressing PTH and increasing the OC level in growing male rats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of 3β-Acethyl Tormentic Acid (3ATA) on ABCC Proteins Activity
Int. J. Mol. Sci. 2012, 13(6), 6757-6771; doi:10.3390/ijms13066757
Received: 12 March 2012 / Revised: 16 May 2012 / Accepted: 25 May 2012 / Published: 4 June 2012
Cited by 4 | PDF Full-text (359 KB) | HTML Full-text | XML Full-text
Abstract
Multidrug resistance (MDR) is considered the main cause of cancer chemotherapy failure and patient relapse. The active drug efflux mediated by transporter proteins of the ABC (ATP-binding cassette) family is the most investigated mechanism leading to MDR. With the aim of inhibiting [...] Read more.
Multidrug resistance (MDR) is considered the main cause of cancer chemotherapy failure and patient relapse. The active drug efflux mediated by transporter proteins of the ABC (ATP-binding cassette) family is the most investigated mechanism leading to MDR. With the aim of inhibiting this transport and circumventing MDR, a great amount of work has been dedicated to identifying pharmacological inhibitors of specific ABC transporters. We recently showed that 3β-acetyl tormentic acid (3ATA) had no effect on P-gp/ABCB1 activity. Herein, we show that 3ATA strongly inhibited the activity of MRP1/ABCC1. In the B16/F10 and Ma104 cell lines, this effect was either 20X higher or similar to that observed with MK571, respectively. Nevertheless, the low inhibitory effect of 3ATA on A549, a cell line that expresses MRP1-5, suggests that it may not inhibit other MRPs. The use of cells transfected with ABCC2, ABCC3 or ABCC4 showed that 3ATA was also able to modulate these transporters, though with an inhibition ratio lower than that observed for MRP1/ABCC1. These data point to 3ATA as a new ABCC inhibitor and call attention to its potential use as a tool to investigate the function of MRP/ABCC proteins or as a co-adjuvant in the treatment of MDR tumors. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessArticle Ontogenic Expression Pattern and Genetic Polymorphisms of the Fatty Acid Transport Protein 4 (FATP4) Gene in Chinese Chicken Populations
Int. J. Mol. Sci. 2012, 13(6), 6820-6835; doi:10.3390/ijms13066820
Received: 28 February 2012 / Revised: 23 May 2012 / Accepted: 29 May 2012 / Published: 5 June 2012
Cited by 1 | PDF Full-text (192 KB) | HTML Full-text | XML Full-text
Abstract
In the current research, the polymorphism of FATP4 gene was analyzed in Erlang Mountainous chickens. A total of nine genetic variants were identified by FATP4 gene sequencing analysis across the chicken samples. Significant associations (p < 0.05) were observed for two SNPs (g.5608778C>T and g.5608814G>A in exon 6) with certain carcass traits (such as live weight, carcass weight, eviscerated weight) in S01 and S05 populations, respectively. Meanwhile, in S05 population, haplotype 3 (T-G) and haplotype 2 (C-A) were associated with higher and lower partial carcass traits such as live weight, carcass weight, eviscerated weight and semi-eviscerated weight, respectively. Moreover, we investigated the expression profile of this gene during ontogenesis in Mountainous black-boned chicken. Quantitative real-time PCR analysis showed that FATP4 mRNA had the highest expression level in small intestine tissue over all other tissues examined. The FATP4 mRNA levels presented remarkable developmental changes with age in the various tissues. These results suggested that the FATP4 gene might play an important role in controlling chicken carcass traits. Full article
Open AccessArticle Polymorphism in Self-Assembled Structures of 9-Anthracene Carboxylic Acid on Ag(111)
Int. J. Mol. Sci. 2012, 13(6), 6836-6848; doi:10.3390/ijms13066836
Received: 2 May 2012 / Revised: 23 May 2012 / Accepted: 29 May 2012 / Published: 5 June 2012
Cited by 1 | PDF Full-text (563 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Surface self-assembly process of 9-anthracene carboxylic acid (AnCA) on Ag(111) was investigated using STM. Depending on the molecular surface density, four spontaneously formed and one annealed AnCA ordered phases were observed, namely a straight belt phase, a zigzag double-belt phase, two simpler [...] Read more.
Surface self-assembly process of 9-anthracene carboxylic acid (AnCA) on Ag(111) was investigated using STM. Depending on the molecular surface density, four spontaneously formed and one annealed AnCA ordered phases were observed, namely a straight belt phase, a zigzag double-belt phase, two simpler dimer phases, and a kagome phase. The two high-density belt phases possess large unit cells on the scale length of 10 nm, which are seldom observed in molecular self-assembled structures. This structural diversity stems from a complicated competition of different interactions of AnCA molecules on metal surface, including intermolecular and molecular-substrate interactions, as well as the steric demand from high molecular surface density. Full article
(This article belongs to the Special Issue Self-Assembled Soft Matter Nanostructures at Interfaces)
Open AccessArticle Role of Helicity on the Anticancer Mechanism of Action of Cationic-Helical Peptides
Int. J. Mol. Sci. 2012, 13(6), 6849-6862; doi:10.3390/ijms13066849
Received: 20 April 2012 / Revised: 19 May 2012 / Accepted: 22 May 2012 / Published: 5 June 2012
Cited by 14 | PDF Full-text (385 KB) | HTML Full-text | XML Full-text
Abstract
In the present study, the 26-residue amphipathic α-helical peptide A12L/A20L (Ac-KWKSFLKTFKSLKKTVLHTLLKAISS-amide) with strong anticancer activity and specificity was used as the framework to study the effects of helicity of α-helical anticancer peptides on biological activities. Helicity was systematically modulated by introducing D-amino [...] Read more.
In the present study, the 26-residue amphipathic α-helical peptide A12L/A20L (Ac-KWKSFLKTFKSLKKTVLHTLLKAISS-amide) with strong anticancer activity and specificity was used as the framework to study the effects of helicity of α-helical anticancer peptides on biological activities. Helicity was systematically modulated by introducing D-amino acids to replace the original L-amino acids on the non-polar face or the polar face of the helix. Peptide helicity was measured by circular dichroism spectroscopy and was demonstrated to correlate with peptide hydrophobicity and the number of D-amino acid substitutions. Biological studies showed that strong hemolytic activity of peptides generally correlated with high hydrophobicity and helicity. Lower helicity caused the decrease of anti-HeLa activity of peptides. By introducing D-amino acids to replace the original L-amino acids on the non-polar face or the polar face of the helix, we improved the therapeutic index of A12L/A20L against HeLa cells by 9-fold and 22-fold, respectively. These results show that the helicity of anticancer peptides plays a crucial role for biological activities. This specific rational approach of peptide design could be a powerful method to improve the specificity of anticancer peptides as promising therapeutics in clinical practices. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Determination of Aniline and Its Derivatives in Environmental Water by Capillary Electrophoresis with On-Line Concentration
Int. J. Mol. Sci. 2012, 13(6), 6863-6872; doi:10.3390/ijms13066863
Received: 26 March 2012 / Revised: 27 April 2012 / Accepted: 17 May 2012 / Published: 5 June 2012
Cited by 7 | PDF Full-text (316 KB) | HTML Full-text | XML Full-text
Abstract
This paper describes a simple, sensitive and environmentally benign method for the direct determination of aniline and its derivatives in environmental water samples by capillary zone electrophoresis (CZE) with field-enhanced sample injection. The parameters that influenced the enhancement and separation efficiencies were [...] Read more.
This paper describes a simple, sensitive and environmentally benign method for the direct determination of aniline and its derivatives in environmental water samples by capillary zone electrophoresis (CZE) with field-enhanced sample injection. The parameters that influenced the enhancement and separation efficiencies were investigated. Surprisingly, under the optimized conditions, two linear ranges for the calibration plot, 1–50 ng/mL and 50–1000 ng/mL (R > 0.998), were obtained. The detection limit was in the range of 0.29–0.43 ng/mL. To eliminate the effect of the real sample matrix on the stacking efficiency, the standard addition method was applied to the analysis of water samples from local rivers. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle By-Passing Large Screening Experiments Using Sequencing as a Tool to Identify scFv Fragments Targeting Atherosclerotic Lesions in a Novel In Vivo Phage Display Selection
Int. J. Mol. Sci. 2012, 13(6), 6902-6923; doi:10.3390/ijms13066902
Received: 27 March 2012 / Revised: 11 May 2012 / Accepted: 22 May 2012 / Published: 7 June 2012
Cited by 2 | PDF Full-text (1095 KB) | HTML Full-text | XML Full-text
Abstract
Atherosclerosis is a chronic, progressive inflammatory disease that may develop into vulnerable lesions leading to thrombosis. To interrogate the molecular components involved in this process, single-chain variable fragments (scFvs) from a semi-synthetic human antibody library were selected on the lesions induced in [...] Read more.
Atherosclerosis is a chronic, progressive inflammatory disease that may develop into vulnerable lesions leading to thrombosis. To interrogate the molecular components involved in this process, single-chain variable fragments (scFvs) from a semi-synthetic human antibody library were selected on the lesions induced in a rabbit model of atherosclerosis after two rounds of in vivo phage display. Homing Phage-scFvs were isolated from (1) the injured endothelium, (2) the underlying lesional tissue and (3) the cells within the intima. Clones selected on the basis of their redundancy or the presence of key amino acids, as determined by comparing the distribution between the native and the selected libraries, were produced in soluble form, and seven scFvs were shown to specifically target the endothelial cell surface and inflamed intima-related regions of rabbit tissue sections by immunohistology approaches. The staining patterns differed depending on the scFv compartment of origin. This study demonstrates that large-scale scFv binding assays can be replaced by a sequence-based selection of best clones, paving the way for easier use of antibody libraries in in vivo biopanning experiments. Future investigations will be aimed at characterizing the scFv/target couples by mass spectrometry to set the stage for more accurate diagnostic of atherosclerosis and development of therapeutic strategies. Full article
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Open AccessArticle Development of Classification Models for Identifying “True” P-glycoprotein (P-gp) Inhibitors Through Inhibition, ATPase Activation and Monolayer Efflux Assays
Int. J. Mol. Sci. 2012, 13(6), 6924-6943; doi:10.3390/ijms13066924
Received: 22 March 2012 / Revised: 21 May 2012 / Accepted: 31 May 2012 / Published: 7 June 2012
Cited by 6 | PDF Full-text (148 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
P-glycoprotein (P-gp) is an efflux pump involved in the protection of tissues of several organs by influencing xenobiotic disposition. P-gp plays a key role in multidrug resistance and in the progression of many neurodegenerative diseases. The development of new and more effective [...] Read more.
P-glycoprotein (P-gp) is an efflux pump involved in the protection of tissues of several organs by influencing xenobiotic disposition. P-gp plays a key role in multidrug resistance and in the progression of many neurodegenerative diseases. The development of new and more effective therapeutics targeting P-gp thus represents an intriguing challenge in drug discovery. P-gp inhibition may be considered as a valid approach to improve drug bioavailability as well as to overcome drug resistance to many kinds of tumours characterized by the over-expression of this protein. This study aims to develop classification models from a unique dataset of 59 compounds for which there were homogeneous experimental data on P-gp inhibition, ATPase activation and monolayer efflux. For each experiment, the dataset was split into a training and a test set comprising 39 and 20 molecules, respectively. Rational splitting was accomplished using a sphere-exclusion type algorithm. After a two-step (internal/external) validation, the best-performing classification models were used in a consensus predicting task for the identification of compounds named as “true” P-gp inhibitors, i.e., molecules able to inhibit P-gp without being effluxed by P-gp itself and simultaneously unable to activate the ATPase function. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Reference Gene Selection in the Desert Plant Eremosparton songoricum
Int. J. Mol. Sci. 2012, 13(6), 6944-6963; doi:10.3390/ijms13066944
Received: 17 February 2012 / Revised: 3 May 2012 / Accepted: 30 May 2012 / Published: 7 June 2012
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Abstract
Eremosparton songoricum (Litv.) Vass. (E. songoricum) is a rare and extremely drought-tolerant desert plant that holds promise as a model organism for the identification of genes associated with water deficit stress. Here, we cloned and evaluated the expression of eight [...] Read more.
Eremosparton songoricum (Litv.) Vass. (E. songoricum) is a rare and extremely drought-tolerant desert plant that holds promise as a model organism for the identification of genes associated with water deficit stress. Here, we cloned and evaluated the expression of eight candidate reference genes using quantitative real-time reverse transcriptase polymerase chain reactions. The expression of these candidate reference genes was analyzed in a diverse set of 20 samples including various E. songoricum plant tissues exposed to multiple environmental stresses. GeNorm analysis indicated that expression stability varied between the reference genes in the different experimental conditions, but the two most stable reference genes were sufficient for normalization in most conditions. EsEF and Esα-TUB were sufficient for various stress conditions, EsEF and EsACT were suitable for samples of differing germination stages, and EsGAPDHand EsUBQ were most stable across multiple adult tissue samples. The Es18S gene was unsuitable as a reference gene in our analysis. In addition, the expression level of the drought-stress related transcription factor EsDREB2 verified the utility of E. songoricum reference genes and indicated that no single gene was adequate for normalization on its own. This is the first systematic report on the selection of reference genes in E. songoricum, and these data will facilitate future work on gene expression in this species. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A Novel Chemometric Method for the Prediction of Human Oral Bioavailability
Int. J. Mol. Sci. 2012, 13(6), 6964-6982; doi:10.3390/ijms13066964
Received: 15 May 2012 / Revised: 29 May 2012 / Accepted: 29 May 2012 / Published: 7 June 2012
Cited by 39 | PDF Full-text (1040 KB) | HTML Full-text | XML Full-text
Abstract
Orally administered drugs must overcome several barriers before reaching their target site. Such barriers depend largely upon specific membrane transport systems and intracellular drug-metabolizing enzymes. For the first time, the P-glycoprotein (P-gp) and cytochrome P450s, the main line of defense by limiting [...] Read more.
Orally administered drugs must overcome several barriers before reaching their target site. Such barriers depend largely upon specific membrane transport systems and intracellular drug-metabolizing enzymes. For the first time, the P-glycoprotein (P-gp) and cytochrome P450s, the main line of defense by limiting the oral bioavailability (OB) of drugs, were brought into construction of QSAR modeling for human OB based on 805 structurally diverse drug and drug-like molecules. The linear (multiple linear regression: MLR, and partial least squares regression: PLS) and nonlinear (support-vector machine regression: SVR) methods are used to construct the models with their predictivity verified with five-fold cross-validation and independent external tests. The performance of SVR is slightly better than that of MLR and PLS, as indicated by its determination coefficient (R2) of 0.80 and standard error of estimate (SEE) of 0.31 for test sets. For the MLR and PLS, they are relatively weak, showing prediction abilities of 0.60 and 0.64 for the training set with SEE of 0.40 and 0.31, respectively. Our study indicates that the MLR, PLS and SVR-based in silico models have good potential in facilitating the prediction of oral bioavailability and can be applied in future drug design. Full article
Open AccessArticle O6-Methylguanine-Methyltransferase (MGMT) Promoter Methylation Status in Glioma Stem-Like Cells is Correlated to Temozolomide Sensitivity Under Differentiation-Promoting Conditions
Int. J. Mol. Sci. 2012, 13(6), 6983-6994; doi:10.3390/ijms13066983
Received: 7 April 2012 / Revised: 25 May 2012 / Accepted: 1 June 2012 / Published: 7 June 2012
Cited by 15 | PDF Full-text (191 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Glioblastoma (GBM) is the most malignant type of primary brain tumor with a very poor prognosis. The actual standard protocol of treatment for GBM patients consists of radiotherapy and concomitant temozolomide (TMZ). However, the therapeutic efficacy of this treatment is limited due [...] Read more.
Glioblastoma (GBM) is the most malignant type of primary brain tumor with a very poor prognosis. The actual standard protocol of treatment for GBM patients consists of radiotherapy and concomitant temozolomide (TMZ). However, the therapeutic efficacy of this treatment is limited due to tumor recurrence and TMZ resistance. Recently isolated, glioma stem-like cells (GSCs) are thought to represent the population of tumorigenic cells responsible for GBM resistance and recurrence following surgery and chemotherapy. In addition, MGMT (O6-methylguanine-methyltransferase) methylation is considered as one of the principal mechanisms contributing to TMZ sensitivity of GBM. In this study we have isolated GSCs from 10 adult GBM patients and investigated the relationship between MGMT methylation status and Temozolomide (TMZ) sensitivity of these lines grown either in stem-like or differentiation promoting conditions. Sensitivity to TMZ was significantly associated with MGMT methylation status in cells committed to differentiation but not in stem-like cells. In addition, patients harboring highly methylated MGMT promoters had a longer overall survival. These results reveal the importance of the differentiation process when considering the predictive value of MGMT status in GSCs for clinical response to TMZ. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
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Open AccessArticle Toward the Prediction of FBPase Inhibitory Activity Using Chemoinformatic Methods
Int. J. Mol. Sci. 2012, 13(6), 7015-7037; doi:10.3390/ijms13067015
Received: 23 April 2012 / Revised: 18 May 2012 / Accepted: 31 May 2012 / Published: 7 June 2012
PDF Full-text (592 KB) | HTML Full-text | XML Full-text
Abstract
Currently, Chemoinformatic methods are used to perform the prediction for FBPase inhibitory activity. A genetic algorithm-random forest coupled method (GA-RF) was proposed to predict fructose 1,6-bisphosphatase (FBPase) inhibitors to treat type 2 diabetes mellitus using the Mold2 molecular descriptors. A data [...] Read more.
Currently, Chemoinformatic methods are used to perform the prediction for FBPase inhibitory activity. A genetic algorithm-random forest coupled method (GA-RF) was proposed to predict fructose 1,6-bisphosphatase (FBPase) inhibitors to treat type 2 diabetes mellitus using the Mold2 molecular descriptors. A data set of 126 oxazole and thiazole analogs was used to derive the GA-RF model, yielding the significant non-cross-validated correlation coefficient r2ncv and cross-validated r2cv values of 0.96 and 0.67 for the training set, respectively. The statistically significant model was validated by a test set of 64 compounds, producing the prediction correlation coefficient r2pred of 0.90. More importantly, the building GA-RF model also passed through various criteria suggested by Tropsha and Roy with r2o and r2m values of 0.90 and 0.83, respectively. In order to compare with the GA-RF model, a pure RF model developed based on the full descriptors was performed as well for the same data set. The resulting GA-RF model with significantly internal and external prediction capacities is beneficial to the prediction of potential oxazole and thiazole series of FBPase inhibitors prior to chemical synthesis in drug discovery programs. Full article
Open AccessArticle Generation of a Highly Reactive Chicken-Derived Single-Chain Variable Fragment against Fusarium verticillioides by Phage Display
Int. J. Mol. Sci. 2012, 13(6), 7038-7056; doi:10.3390/ijms13067038
Received: 13 March 2012 / Revised: 14 May 2012 / Accepted: 25 May 2012 / Published: 7 June 2012
Cited by 6 | PDF Full-text (529 KB) | HTML Full-text | XML Full-text
Abstract
Fusarium verticillioides is the primary causal agent of Fusarium ear and kernel rot in maize, producing fumonisin mycotoxins that are toxic to humans and domestic animals. Rapid detection and monitoring of fumonisin-producing fungi are pivotally important for the prevention of mycotoxins from [...] Read more.
Fusarium verticillioides is the primary causal agent of Fusarium ear and kernel rot in maize, producing fumonisin mycotoxins that are toxic to humans and domestic animals. Rapid detection and monitoring of fumonisin-producing fungi are pivotally important for the prevention of mycotoxins from entering into food/feed products. Chicken-derived single-chain variable fragments (scFvs) against cell wall-bound proteins from F. verticillioides were isolated from an immunocompetent phage display library. Comparative phage enzyme-linked immunosorbant assays (ELISAs) and sequencing analyses identified four different scFv antibodies with high sensitivity. Soluble antibody ELISAs identified two highly sensitive scFv antibodies, FvCA3 and FvCA4, with the latter being slightly more sensitive. Three-dimensional modeling revealed that the FvCA4 may hold a better overall structure with CDRH3, CDRL1 and CDRL3 centered in the core region of antibody surface compared with that of other scFvs. Immunofluorescence labeling revealed that the binding of FvCA4 antibody was localized to the cell walls of conidiospores and hyphae of F. verticillioides, confirming the specificity of this antibody for a surface target. This scFv antibody was able to detect the fungal mycelium as low as 10−2 μg/mL and contaminating mycelium at a quantity of 10−2 mg/g maize. This is the first report that scFv antibodies derived from phage display have a wide application for rapid and accurate detection and monitoring of fumonisin-producing pathogens in agricultural samples. Full article
(This article belongs to the Special Issue Phage Display)
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Open AccessArticle A Computational Study on Thiourea Analogs as Potent MK-2 Inhibitors
Int. J. Mol. Sci. 2012, 13(6), 7057-7079; doi:10.3390/ijms13067057
Received: 23 April 2012 / Revised: 25 May 2012 / Accepted: 28 May 2012 / Published: 8 June 2012
Cited by 3 | PDF Full-text (1362 KB) | HTML Full-text | XML Full-text
Abstract
Mitogen-activated protein kinase-activated protein kinase 2 (MK-2) has been identified as a drug target for the treatment of inflammatory diseases. Currently, a series of thiourea analogs as potent MK-2 inhibitors were studied using comprehensive computational methods by 3D-QSAR, molecular docking and molecular [...] Read more.
Mitogen-activated protein kinase-activated protein kinase 2 (MK-2) has been identified as a drug target for the treatment of inflammatory diseases. Currently, a series of thiourea analogs as potent MK-2 inhibitors were studied using comprehensive computational methods by 3D-QSAR, molecular docking and molecular dynamics simulations for a further improvement in activities. The optimal 3D models exhibit high statistical significance of the results, especially for the CoMFA results with r2ncv, q2 values of 0.974, 0.536 for the internal validation, and r2pred, r2m values of 0.910, 0.723 for the external validation and Roy’s index, respectively. In addition, more rigorous validation criteria suggested by Tropsha were also employed to check the built models. Graphic representation of the results, as contoured 3D coefficient plots, also provides a clue to the reasonable modification of molecules: (i) The substituent with a bulky size and electron-rich group at the C5 position of the pyrazine ring is required to enhance the potency; (ii) The H-bond acceptor group in the C3 position of the pyrazine ring is likely to be helpful to increase MK-2 inhibition; (iii) The small and electropositive substituent as a hydrogen bond donor of the C2 position in the oxazolone ring is favored; In addition, several important amino acid residues were also identified as playing an important role in MK-2 inhibition. The agreement between 3D-QSAR, molecular docking and molecular dynamics simulations also proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential MK-2 inhibitors. Full article
Open AccessArticle Genome-Wide DNA Methylation Changes between the Superficial and Deep Backfat Tissues of the Pig
Int. J. Mol. Sci. 2012, 13(6), 7098-7108; doi:10.3390/ijms13067098
Received: 3 May 2012 / Revised: 24 May 2012 / Accepted: 5 June 2012 / Published: 8 June 2012
Cited by 8 | PDF Full-text (324 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different [...] Read more.
Adipose tissue is not only a storage organ involved in fuel metabolism, but also an endocrine organ involved in the regulation of insulin sensitivity, thermogenesis, immunity, and inflammation. There are anatomical, cellular, molecular and physiological differences among adipose tissues deposited in different body sites. However, current understanding of the intrinsic differences between the sub-compartments of the subcutaneous adipose tissue remains rudimentary. Here, we analyzed the genome-wide DNA methylation differences between the porcine superficial and deep backfat tissues using methylated DNA immunoprecipitation combined with high-throughput sequencing. We show that the genes with differentially methylated regions in their promoter are mainly involved in the processes of “lipid metabolism” and “regulation of immune-related cytokines”. Compared with the deep backfat tissue, the promoters of genes related to the ‘positive regulation of cytokine production’ were significantly hypermethylated in the superficial backfat tissue, which reflects the intrinsic functional and metabolic differences between the sub-compartments of the subcutaneous adipose tissue. This study provides epigenetic evidence for functionally relevant methylation differences between different layers of porcine backfat tissues. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessCommunication Target Molecular Simulations of RecA Family Protein Filaments
Int. J. Mol. Sci. 2012, 13(6), 7138-7148; doi:10.3390/ijms13067138
Received: 11 April 2012 / Revised: 10 May 2012 / Accepted: 29 May 2012 / Published: 11 June 2012
Cited by 1 | PDF Full-text (1081 KB) | HTML Full-text | XML Full-text
Abstract
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed [...] Read more.
Modeling of the RadA family mechanism is crucial to understanding the DNA SOS repair process. In a 2007 report, the archaeal RadA proteins function as rotary motors (linker region: I71-K88) such as shown in Figure 1. Molecular simulations approaches help to shed further light onto this phenomenon. We find 11 rotary residues (R72, T75-K81, M84, V86 and K87) and five zero rotary residues (I71, K74, E82, R83 and K88) in the simulations. Inclusion of our simulations may help to understand the RadA family mechanism. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
Open AccessArticle Antioxidant Activities of Extract and Fractions from Receptaculum Nelumbinis and Related Flavonol Glycosides
Int. J. Mol. Sci. 2012, 13(6), 7163-7173; doi:10.3390/ijms13067163
Received: 9 May 2012 / Revised: 29 May 2012 / Accepted: 5 June 2012 / Published: 11 June 2012
Cited by 10 | PDF Full-text (201 KB) | HTML Full-text | XML Full-text
Abstract
The antioxidant activities of ethanolic crude extract (ECE) and its four different solvent sub-fractions (namely, petroleum ether fraction (PEF), ethyl acetate fraction (EAF), n-butanol fraction (BF) and the aqueous fraction (AF) from the receptacles of Nelumbo nucifera Gaertn. (Receptaculum Nelumbinis) were [...] Read more.
The antioxidant activities of ethanolic crude extract (ECE) and its four different solvent sub-fractions (namely, petroleum ether fraction (PEF), ethyl acetate fraction (EAF), n-butanol fraction (BF) and the aqueous fraction (AF) from the receptacles of Nelumbo nucifera Gaertn. (Receptaculum Nelumbinis) were investigated using two in vitro antioxidant assays. BF showed the highest total phenolic content (607.6 mg/g gallic acid equivalents), total flavonoid content (862.7 mg/g rutin equivalents) and total proanthocyanidin content (331.0 mg/g catechin equivalents), accompanied with the highest antioxidant activity compared to other fractions through 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis-(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) radical scavenging assays. Five flavonol glycosides, namely hyperoside (1), isoquercitrin (2), quercetin-3-O-β-D-glucuronide (3), isorhamnetin-3-O-β-D-galactoside (4) and syringetin-3-O-β-D-glucoside (5) were isolated from the Receptaculum Nelumbinis. Compounds 25 were isolated for the first time from the Receptaculum Nelumbinis. The five isolated flavone glycosides, particularly compounds 13, demonstrated significant DPPH and ABTS radical scavenging activity, with IC50 values of 8.9 ± 0.2, 5.2 ± 0.2, 7.5 ± 0.1 for DPPH and 114.2 ± 1.7, 112.8 ± 0.8, 172.5 ± 0.7 µg/mL for ABTS, respectively. These results suggest that Receptaculum Nelumbinis has strong antioxidant potential and may be potentially used as a safe and inexpensive bioactive source of natural antioxidants. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pu-erh Tea Reduces Nitric Oxide Levels in Rats by Inhibiting Inducible Nitric Oxide Synthase Expression through Toll-Like Receptor 4
Int. J. Mol. Sci. 2012, 13(6), 7174-7185; doi:10.3390/ijms13067174
Received: 7 May 2012 / Revised: 28 May 2012 / Accepted: 28 May 2012 / Published: 11 June 2012
Cited by 3 | PDF Full-text (217 KB) | HTML Full-text | XML Full-text
Abstract
Pu-erh tea undergoes a unique fermentation process and contains theabrownins, polysaccharides and caffeine; although it is unclear about which component is associated with the down regulation of nitric oxide levels or how this process is mediated. To address this question we examined [...] Read more.
Pu-erh tea undergoes a unique fermentation process and contains theabrownins, polysaccharides and caffeine; although it is unclear about which component is associated with the down regulation of nitric oxide levels or how this process is mediated. To address this question we examined the effects of pu-erh tea on nitric oxide synthase (NOS) genes. Cohorts of rats were separately given four-week treatments of water as control, pu-erh tea, or the tea components: theabrownins, caffeine or polysaccharides. Five experimental groups were injected with lipopolysaccharides (LPS) to induce nitric oxide (NO) production, while the corresponding five control groups were injected with saline as a negative control. The serum and liver NO concentrations were examined and the NOS expression of both mRNA and protein was measured in liver. The results showed that the rats which were fed pu-erh tea or polysaccharides had lower levels of NO which corresponded with the down-regulation of inducible nitric oxide synthase (iNOS) expression. We further demonstrate that this effect is mediated through reduction of Toll-like receptor 4 (TLR4) signaling. Thus we find that the polysaccharide components in pu-erh tea reduce NO levels in an animal model by inhibiting the iNOS expression via signaling through TLR4. Full article
Open AccessArticle Fly Ash-based Geopolymer Lightweight Concrete Using Foaming Agent
Int. J. Mol. Sci. 2012, 13(6), 7186-7198; doi:10.3390/ijms13067186
Received: 7 April 2012 / Revised: 21 May 2012 / Accepted: 31 May 2012 / Published: 12 June 2012
Cited by 15 | PDF Full-text (1090 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we report the results of our investigation on the possibility of producing foam concrete by using a geopolymer system. Class C fly ash was mixed with an alkaline activator solution (a mixture of sodium silicate and NaOH), and foam [...] Read more.
In this paper, we report the results of our investigation on the possibility of producing foam concrete by using a geopolymer system. Class C fly ash was mixed with an alkaline activator solution (a mixture of sodium silicate and NaOH), and foam was added to the geopolymeric mixture to produce lightweight concrete. The NaOH solution was prepared by dilute NaOH pellets with distilled water. The reactives were mixed to produce a homogeneous mixture, which was placed into a 50 mm mold and cured at two different curing temperatures (60 °C and room temperature), for 24 hours. After the curing process, the strengths of the samples were tested on days 1, 7, and 28. The water absorption, porosity, chemical composition, microstructure, XRD and FTIR analyses were studied. The results showed that the sample which was cured at 60 °C (LW2) produced the maximum compressive strength for all tests, (11.03 MPa, 17.59 MPa, and 18.19 MPa) for days 1, 7, and 28, respectively. Also, the water absorption and porosity of LW2 were reduced by 6.78% and 1.22% after 28 days, respectively. The SEM showed that the LW2 sample had a denser matrix than LW1. This was because LW2 was heat cured, which caused the geopolymerization rate to increase, producing a denser matrix. However for LW1, microcracks were present on the surface, which reduced the compressive strength and increased water absorption and porosity. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Rapid Development of Microsatellite Markers with 454 Pyrosequencing in a Vulnerable Fish, the Mottled Skate, Raja pulchra
Int. J. Mol. Sci. 2012, 13(6), 7199-7211; doi:10.3390/ijms13067199
Received: 7 May 2012 / Revised: 5 June 2012 / Accepted: 6 June 2012 / Published: 12 June 2012
Cited by 15 | PDF Full-text (202 KB) | HTML Full-text | XML Full-text
Abstract
The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers [...] Read more.
The mottled skate, Raja pulchra, is an economically valuable fish. However, due to a severe population decline, it is listed as a vulnerable species by the International Union for Conservation of Nature. To analyze its genetic structure and diversity, microsatellite markers were developed using 454 pyrosequencing. A total of 17,033 reads containing dinucleotide microsatellite repeat units (mean, 487 base pairs) were identified from 453,549 reads. Among 32 loci containing more than nine repeat units, 20 primer sets (62%) produced strong PCR products, of which 14 were polymorphic. In an analysis of 60 individuals from two R. pulchra populations, the number of alleles per locus ranged from 1–10, and the mean allelic richness was 4.7. 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 two of the 28 single-loci after sequential Bonferroni’s correction. Using 11 primer sets, cross-species amplification was demonstrated in nine related species from four families within two classes. Among the 11 loci amplified from three other Rajidae family species; three loci were polymorphic. A monomorphic locus was amplified in all three Rajidae family species and the Dasyatidae family. Two Rajidae polymorphic loci amplified monomorphic target DNAs in four species belonging to the Carcharhiniformes class, and another was polymorphic in two Carcharhiniformes species. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Nec-1 Enhances Shikonin-Induced Apoptosis in Leukemia Cells by Inhibition of RIP-1 and ERK1/2
Int. J. Mol. Sci. 2012, 13(6), 7212-7225; doi:10.3390/ijms13067212
Received: 31 March 2012 / Revised: 23 April 2012 / Accepted: 7 June 2012 / Published: 12 June 2012
Cited by 18 | PDF Full-text (460 KB) | HTML Full-text | XML Full-text
Abstract
Necrostatin-1 (Nec-1) inhibits necroptosis by allosterically inhibiting the kinase activity of receptor-interacting protein 1 (RIP1), which plays a critical role in necroptosis. RIP1 is a crucial adaptor kinase involved in the activation of NF-κB, production of reactive oxygen species (ROS) and the [...] Read more.
Necrostatin-1 (Nec-1) inhibits necroptosis by allosterically inhibiting the kinase activity of receptor-interacting protein 1 (RIP1), which plays a critical role in necroptosis. RIP1 is a crucial adaptor kinase involved in the activation of NF-κB, production of reactive oxygen species (ROS) and the phosphorylation of mitogen activated protein kinases (MAPKs). NF-κB, ROS and MAPKs all play important roles in apoptotic signaling. Nec-1 was regarded as having no effect on apoptosis. Here, we report that Nec-1 increased the rate of nuclear condensation and caspases activation induced by a low concentration of shikonin (SHK) in HL60, K562 and primary leukemia cells. siRNA-mediated knockdown of RIP1 significantly enhanced shikonin-induced apoptosis in K562 and HL60 cells. Shikonin treatment alone could slightly inhibit the phosphorylation of ERK1/2 in leukemia cells, and the inhibitory effect on ERK1/2 was significantly augmented by Nec-1. We also found that Nec-1 could inhibit NF-κB p65 translocation to the nucleus at a later stage of SHK treatment. In conclusion, we found that Nec-1 can promote shikonin-induced apoptosis in leukemia cells. The mechanism by which Nec-1 sensitizes shikonin-induced apoptosis appears to be the inhibition of RIP1 kinase-dependent phosphorylation of ERK1/2. To our knowledge, this is the first study to document Nec-1 sensitizes cancer cells to apoptosis. Full article
Open AccessArticle Biosysthesis of Corn Starch Palmitate by Lipase Novozym 435
Int. J. Mol. Sci. 2012, 13(6), 7226-7236; doi:10.3390/ijms13067226
Received: 23 April 2012 / Revised: 12 May 2012 / Accepted: 23 May 2012 / Published: 12 June 2012
Cited by 14 | PDF Full-text (412 KB) | HTML Full-text | XML Full-text
Abstract
Esterification of starch was carried out to expand the usefulness of starch for a myriad of industrial applications. Lipase B from Candida antarctica, immobilized on macroporous acrylic resin (Novozym 435), was used for starch esterification in two reaction systems: micro-solvent system [...] Read more.
Esterification of starch was carried out to expand the usefulness of starch for a myriad of industrial applications. Lipase B from Candida antarctica, immobilized on macroporous acrylic resin (Novozym 435), was used for starch esterification in two reaction systems: micro-solvent system and solvent-free system. The esterification of corn starch with palmitic acid in the solvent-free system and micro-solvent system gave a degree of substitution (DS) of 1.04 and 0.0072 respectively. Esterification of corn starch with palmitic acid was confirmed by UV spectroscopy and IR spectroscopy. The results of emulsifying property analysis showed that the starch palmitate with higher DS contributes to the higher emulsifying property (67.6%) and emulsion stability (79.6%) than the native starch (5.3% and 3.9%). Modified starch obtained by esterification that possesses emulsifying properties and has long chain fatty acids, like palmitic acid, has been widely used in the food, pharmaceutical and biomedical applications industries. Full article
(This article belongs to the Special Issue Organic Synthesis Using Biocatalyst)
Open AccessArticle Evaluation of the Antioxidant Capacity of Synthesized Coumarins
Int. J. Mol. Sci. 2012, 13(6), 7260-7270; doi:10.3390/ijms13067260
Received: 14 May 2012 / Revised: 25 May 2012 / Accepted: 28 May 2012 / Published: 13 June 2012
Cited by 9 | PDF Full-text (278 KB) | HTML Full-text | XML Full-text
Abstract
Coumarins are secondary metabolites that are widely distributed within the plant kingdom, some of which have been extensively studied for their antioxidant properties. The antioxidant activity of coumarins assayed in the present study was measured by different methods, namely the 1,1-diphenyl-2-picryl-hydrazyl (DPPH [...] Read more.
Coumarins are secondary metabolites that are widely distributed within the plant kingdom, some of which have been extensively studied for their antioxidant properties. The antioxidant activity of coumarins assayed in the present study was measured by different methods, namely the 1,1-diphenyl-2-picryl-hydrazyl (DPPH) method, cyclic voltammetry and the antioxidant capacity against peroxyl radicals (ACAP) method. The 7,8-dihydroxy-4-methylcoumarin (LaSOM 78), 5-carboxy-7,8-dihydroxy-4-methylcoumarin (LaSOM 79), and 6,7-dihydroxycoumarin (Esculetin) compounds proved to be the most active, showing the highest capacity to deplete the DPPH radicals, the highest antioxidant capacity against peroxyl radicals, and the lowest values of potential oxidation. Full article
Open AccessArticle Oral Administration of Apigenin Inhibits Metastasis through AKT/P70S6K1/MMP-9 Pathway in Orthotopic Ovarian Tumor Model
Int. J. Mol. Sci. 2012, 13(6), 7271-7282; doi:10.3390/ijms13067271
Received: 27 April 2012 / Revised: 28 May 2012 / Accepted: 29 May 2012 / Published: 13 June 2012
Cited by 19 | PDF Full-text (872 KB) | HTML Full-text | XML Full-text
Abstract
Apigenin, a flavonoid commonly present in the daily diet, is known for its potential anti-tumor properties. However, the effect of apigenin via oral administration on tumor growth and metastasis remains unknown. In this study we developed an orthotopic ovarian tumor model in [...] Read more.
Apigenin, a flavonoid commonly present in the daily diet, is known for its potential anti-tumor properties. However, the effect of apigenin via oral administration on tumor growth and metastasis remains unknown. In this study we developed an orthotopic ovarian tumor model in nude mice to test the effect of apigenin oral administration, and showed that apigenin inhibited the micrometastasis of cancer cells in the animal tumor model. To understand the mechanism of apigenin in inhibiting metastasis, we found that apigenin greatly inhibited MMP-9 expression and p-AKT and p-p70S6K1 levels in the tumor tissues compared to the control group. We further demonstrated that the downregulation of MMP-9 by apigenin was mediated by the AKT/p70S6K1 pathway. These findings help to address the question with common interests to the public of whether oral uptake of flavonoids is effective in preventing cancer. Our results demonstrate for the first time that oral uptake of apigenin can inhibit tumor metastasis through MMP-9 expression using the orthotopic ovarian tumor model. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Function Prediction and Analysis of Mycobacterium tuberculosis Hypothetical Proteins
Int. J. Mol. Sci. 2012, 13(6), 7283-7302; doi:10.3390/ijms13067283
Received: 2 April 2012 / Revised: 28 May 2012 / Accepted: 7 June 2012 / Published: 13 June 2012
Cited by 19 | PDF Full-text (656 KB) | HTML Full-text | XML Full-text
Abstract
High-throughput biology technologies have yielded complete genome sequences and functional genomics data for several organisms, including crucial microbial pathogens of humans, animals and plants. However, up to 50% of genes within a genome are often labeled “unknown”, “uncharacterized” or “hypothetical”, limiting our [...] Read more.
High-throughput biology technologies have yielded complete genome sequences and functional genomics data for several organisms, including crucial microbial pathogens of humans, animals and plants. However, up to 50% of genes within a genome are often labeled “unknown”, “uncharacterized” or “hypothetical”, limiting our understanding of virulence and pathogenicity of these organisms. Even though biological functions of proteins encoded by these genes are not known, many of them have been predicted to be involved in key processes in these organisms. In particular, for Mycobacterium tuberculosis, some of these “hypothetical” proteins, for example those belonging to the Pro-Glu or Pro-Pro-Glu (PE/PPE) family, have been suspected to play a crucial role in the intracellular lifestyle of this pathogen, and may contribute to its survival in different environments. We have generated a functional interaction network for Mycobacterium tuberculosis proteins and used this to predict functions for many of its hypothetical proteins. Here we performed functional enrichment analysis of these proteins based on their predicted biological functions to identify annotations that are statistically relevant, and analysed and compared network properties of hypothetical proteins to the known proteins. From the statistically significant annotations and network information, we have tried to derive biologically meaningful annotations relatedto infection and disease. This quantitative analysis provides an overview of the functional contributions of Mycobacterium tuberculosis “hypothetical” proteins to many basic cellular functions, including its adaptability in the host system and its ability to evade the host immune response. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Herbicide-Intercalated Zinc Layered Hydroxide Nanohybrid for a Dual-Guest Controlled Release Formulation
Int. J. Mol. Sci. 2012, 13(6), 7328-7342; doi:10.3390/ijms13067328
Received: 11 April 2012 / Revised: 6 June 2012 / Accepted: 7 June 2012 / Published: 13 June 2012
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Abstract
Herbicides, namely 4-(2,4-dichlorophenoxy) butyrate (DPBA) and 2-(3-chlorophenoxy) propionate (CPPA), were intercalated simultaneously into the interlayers of zinc layered hydroxide (ZLH) by direct reaction of zinc oxide with both anions under aqueous environment to form a new nanohybrid containing both herbicides labeled as [...] Read more.
Herbicides, namely 4-(2,4-dichlorophenoxy) butyrate (DPBA) and 2-(3-chlorophenoxy) propionate (CPPA), were intercalated simultaneously into the interlayers of zinc layered hydroxide (ZLH) by direct reaction of zinc oxide with both anions under aqueous environment to form a new nanohybrid containing both herbicides labeled as ZCDX. Successful intercalation of both anions simultaneously into the interlayer gallery space of ZLH was studied by PXRD, with basal spacing of 28.7 Å and supported by FTIR, TGA/DTG and UV-visible studies. Simultaneous release of both CPPA and DPBA anions into the release media was found to be governed by a pseudo second-order equation. The loading and percentage release of the DPBA is higher than the CPPA anion, which indicates that the DPBA anion was preferentially intercalated into and released from the ZLH interlayer galleries. This work shows that layered single metal hydroxide, particularly ZLH, is a suitable host for the controlled release formulation of two herbicides simultaneously. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessArticle Solution NMR Structure of Hypothetical Protein CV_2116 Encoded by a Viral Prophage Element in Chromobacterium violaceum
Int. J. Mol. Sci. 2012, 13(6), 7354-7364; doi:10.3390/ijms13067354
Received: 20 April 2012 / Revised: 25 May 2012 / Accepted: 4 June 2012 / Published: 14 June 2012
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Abstract
CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07) corresponding to a hypothetical protein OR16_04617 [...] Read more.
CV_2116 is a small hypothetical protein of 82 amino acids from the Gram-negative coccobacillus Chromobacterium violaceum. A PSI-BLAST search using the CV_2116 sequence as a query identified only one hit (E = 2e−07) corresponding to a hypothetical protein OR16_04617 from Cupriavidus basilensis OR16, which failed to provide insight into the function of CV_2116. The CV_2116 gene was cloned into the p15TvLic expression plasmid, transformed into E. coli, and 13C- and 15N-labeled NMR samples of CV_2116 were overexpressed in E. coli and purified for structure determination using NMR spectroscopy. The resulting high-quality solution NMR structure of CV_2116 revealed a novel α + β fold containing two anti-parallel β -sheets in the N-terminal two-thirds of the protein and one α-helix in the C-terminal third of the protein. CV_2116 does not belong to any known protein sequence family and a Dali search indicated that no similar structures exist in the protein data bank. Although no function of CV_2116 could be derived from either sequence or structural similarity searches, the neighboring genes of CV_2116 encode various proteins annotated as similar to bacteriophage tail assembly proteins. Interestingly, C. violaceum exhibits an extensive network of bacteriophage tail-like structures that likely result from lateral gene transfer by incorporation of viral DNA into its genome (prophages) due to bacteriophage infection. Indeed, C. violaceum has been shown to contain four prophage elements and CV_2116 resides in the fourth of these elements. Analysis of the putative operon in which CV_2116 resides indicates that CV_2116 might be a component of the bacteriophage tail-like assembly that occurs in C. violaceum. Full article
(This article belongs to the Special Issue Hypothetical Proteins)
Open AccessArticle New Antifungal Pyranoisoflavone from Ficus tikoua Bur.
Int. J. Mol. Sci. 2012, 13(6), 7375-7382; doi:10.3390/ijms13067375
Received: 4 May 2012 / Revised: 5 June 2012 / Accepted: 7 June 2012 / Published: 14 June 2012
Cited by 5 | PDF Full-text (201 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Considering the undesirable attributes of synthetic fungicides and the availability of Ficus species in China, the stem of Ficus tikoua Bur. was investigated. One new antifungal pyranoisoflavone, 5,3',4'-trihydroxy-2",2"-dimethylpyrano (5",6":7,8) isoflavone (1), together with two known isoflavones, wighteone (2) [...] Read more.
Considering the undesirable attributes of synthetic fungicides and the availability of Ficus species in China, the stem of Ficus tikoua Bur. was investigated. One new antifungal pyranoisoflavone, 5,3',4'-trihydroxy-2",2"-dimethylpyrano (5",6":7,8) isoflavone (1), together with two known isoflavones, wighteone (2) and lupiwighteone (3) (with previously reported antifungal activities), were isolated from ethyl acetate extract by bioassay-guided fractionation. Their structures were determined by spectroscopic analysis, such as NMR (1H-1H COSY, HMQC, HMBC and NOESY), IR, UV and HRMS, as well as ESI-MSn analyses. The antifungal activities of 13 against Phytophthora infestans were evaluated by direct spore germination assay, and the IC50 values were 262.442, 198.153 and 90.365 µg·mL−1, respectively. Full article
Open AccessArticle Aroma Volatile Compounds from Two Fresh Pineapple Varieties in China
Int. J. Mol. Sci. 2012, 13(6), 7383-7392; doi:10.3390/ijms13067383
Received: 13 April 2012 / Revised: 13 May 2012 / Accepted: 28 May 2012 / Published: 14 June 2012
Cited by 9 | PDF Full-text (162 KB) | HTML Full-text | XML Full-text
Abstract
Volatile compounds from two pineapples varieties (Tainong No.4 and No.6) were isolated by headspace solid phase microextraction (HS-SPME) and identified and quantified by gas chromatography-mass spectrometry (GC/MS). In the Tainong No. 4 and No. 6 pineapples, a total of 11 and 28 [...] Read more.
Volatile compounds from two pineapples varieties (Tainong No.4 and No.6) were isolated by headspace solid phase microextraction (HS-SPME) and identified and quantified by gas chromatography-mass spectrometry (GC/MS). In the Tainong No. 4 and No. 6 pineapples, a total of 11 and 28 volatile compounds were identified according to their retention time on capillary columns and their mass spectra, and quantified with total concentrations of 1080.44 µg·kg−1 and 380.66 µg·kg−1 in the Tainong No.4 and No. 6 pineapples, respectively. The odor active values (OAVs) of volatile compounds from pineapples were also calculated. According to the OAVs, four compounds were defined as the characteristic aroma compounds for the Tainong No. 4 pineapple, including furaneol, 3-(methylthio)propanoic acid methyl ester, 3-(methylthio)propanoic acid ethyl ester and δ-octalactone. The OAVs of five compounds including ethyl-2-methylbutyrate, methyl-2-methylbutyrate, 3-(methylthio)propanoic acid ethyl ester, ethyl hexanoate and decanal were considered to be the characteristic aroma compounds for the Tainong No. 6 pineapple. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Identification of Intensity Ratio Break Points from Photon Arrival Trajectories in Ratiometric Single Molecule Spectroscopy
Int. J. Mol. Sci. 2012, 13(6), 7445-7465; doi:10.3390/ijms13067445
Received: 19 April 2012 / Revised: 7 June 2012 / Accepted: 12 June 2012 / Published: 18 June 2012
Cited by 2 | PDF Full-text (636 KB) | HTML Full-text | XML Full-text
Abstract
We describe a statistical method to analyze dual-channel photon arrival trajectories from single molecule spectroscopy model-free to identify break points in the intensity ratio. Photons are binned with a short bin size to calculate the logarithm of the intensity ratio for each bin. Stochastic photon counting [...] Read more.
We describe a statistical method to analyze dual-channel photon arrival trajectories from single molecule spectroscopy model-free to identify break points in the intensity ratio. Photons are binned with a short bin size to calculate the logarithm of the intensity ratio for each bin. Stochastic photon counting noise leads to a near-normal distribution of this logarithm and the standard student t-test is used to find statistically significant changes in this quantity. In stochastic simulations we determine the significance threshold for the t-test’s p-value at a given level of confidence.We test the method’s sensitivity and accuracy indicating that the analysis reliably locates break points with significant changes in the intensity ratio with little or no error in realistic trajectories with large numbers of small change points, while still identifying a large fraction of the frequent break points with small intensity changes. Based on these results we present an approach to estimate confidence intervals for the identified break point locations and recommend a bin size to choose for the analysis. The method proves powerful and reliable in the analysis of simulated and actual data of single molecule reorientation in a glassy matrix. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessArticle Vibrational Stark Effect of the Electric-Field Reporter 4-Mercaptobenzonitrile as a Tool for Investigating Electrostatics at Electrode/SAM/Solution Interfaces
Int. J. Mol. Sci. 2012, 13(6), 7466-7482; doi:10.3390/ijms13067466
Received: 9 May 2012 / Revised: 6 June 2012 / Accepted: 11 June 2012 / Published: 18 June 2012
Cited by 11 | PDF Full-text (580 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
4-mercaptobenzonitrile (MBN) in self-assembled monolayers (SAMs) on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE). Using MBN SAMs in [...] Read more.
4-mercaptobenzonitrile (MBN) in self-assembled monolayers (SAMs) on Au and Ag electrodes was studied by surface enhanced infrared absorption and Raman spectroscopy, to correlate the nitrile stretching frequency with the local electric field exploiting the vibrational Stark effect (VSE). Using MBN SAMs in different metal/SAM interfaces, we sorted out the main factors controlling the nitrile stretching frequency, which comprise, in addition to external electric fields, the metal-MBN bond, the surface potential, and hydrogen bond interactions. On the basis of the linear relationships between the nitrile stretching and the electrode potential, an electrostatic description of the interfacial potential distribution is presented that allows for determining the electric field strengths on the SAM surface, as well as the effective potential of zero-charge of the SAM-coated metal. Comparing this latter quantity with calculated values derived from literature data, we note a very good agreement for Au/MBN but distinct deviations for Ag/MBN which may reflect either the approximations and simplifications of the model or the uncertainty in reported structural parameters for Ag/MBN. The present electrostatic model consistently explains the electric field strengths for MBN SAMs on Ag and Au as well as for thiophenol and mercaptohexanoic acid SAMs with MBN incorporated as a VSE reporter. Full article
(This article belongs to the Special Issue Self-Assembled Soft Matter Nanostructures at Interfaces)
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Open AccessArticle Optimization of Glutamine Peptide Production from Soybean Meal and Analysis of Molecular Weight Distribution of Hydrolysates
Int. J. Mol. Sci. 2012, 13(6), 7483-7495; doi:10.3390/ijms13067483
Received: 5 May 2012 / Revised: 5 June 2012 / Accepted: 8 June 2012 / Published: 18 June 2012
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Abstract
The process parameters of enzymatic hydrolysis and molecular weight distribution of glutamine (Gln) peptides from soybean meal were investigated. The Protamex® hydrolysis pH of 6.10, temperature of 56.78 °C, enzyme to substrate ratio (E/S) of 1.90 and hydrolysis time of 10.72 h were found to be the optimal conditions by response surface methodology (RSM) for a maximal degree of hydrolysis (DH) value of 16.63% and Gln peptides content at 5.95 mmol/L. The soybean meal was hydrolyzed by a combination of Protamex® and trypsinase so that DH and Gln peptides would reach 22.02% and 6.05 mmol/mL, respectively. The results of size exclusion chromatography indicated that the relative proportion of the molecular weight < 1000 Da fraction increased with DH values from 6.76%, 11.13%, 17.89% to 22.02%, most notably the 132–500 Da fractions of hydrolysates were 42.14%, 46.57%, 58.44% and 69.65%. High DH values did not lead to high Gln peptides content of the hydrolysate but to the low molecular weight Gln peptides. Full article
(This article belongs to the Special Issue Enzyme Optimization and Immobilization)
Open AccessArticle Simulated Gastrointestinal pH Condition Improves Antioxidant Properties of Wheat and Rice Flours
Int. J. Mol. Sci. 2012, 13(6), 7496-7507; doi:10.3390/ijms13067496
Received: 16 April 2012 / Revised: 31 May 2012 / Accepted: 1 June 2012 / Published: 18 June 2012
Cited by 6 | PDF Full-text (271 KB) | HTML Full-text | XML Full-text
Abstract
The present study was conducted to evaluate the antioxidant properties of wheat and rice flours under simulated gastrointestinal pH condition. After subjecting the wheat and rice flour slurries to simulated gastrointestinal pH condition, both slurries were centrifuged to obtain the crude phenolic extracts for further analyses. Extraction yield, total contents of phenolic and flavonoids were determined as such (untreated) and under simulated gastrointestinal pH condition (treated). 1,1-diphenyl-2-picrylhydrazyl radical (DPPH) scavenging activity, 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) radical cation (ABTS•+) scavenging activity, ferric reducing antioxidant power (FRAP), beta-carotene bleaching (BCB) and iron chelating activity assays were employed for the determination of antioxidant activity of the tested samples. In almost all of the assays performed, significant improvements in antioxidant properties (p < 0.05) were observed in both flours after treatment, suggesting that wheat and rice flours contain considerably heavy amounts of bound phenolics, and that their antioxidant properties might be improved under gastrointestinal digestive conditions. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effect of Toll-Like Receptor 4 on Macrophage Cytokines During Endotoxin Induced Uveitis
Int. J. Mol. Sci. 2012, 13(6), 7508-7520; doi:10.3390/ijms13067508
Received: 23 April 2012 / Revised: 4 June 2012 / Accepted: 13 June 2012 / Published: 18 June 2012
Cited by 8 | PDF Full-text (1107 KB) | HTML Full-text | XML Full-text
Abstract
Toll-like receptor 4 (TLR4) signal activation of macrophages can lead to endotoxin-induced uveitis (EIU). Previously, our research group has demonstrated a higher expression of TLR4 in vivo during EIU than normal. In this study, we analyzed levels of peritoneal macrophage cytokines from [...] Read more.
Toll-like receptor 4 (TLR4) signal activation of macrophages can lead to endotoxin-induced uveitis (EIU). Previously, our research group has demonstrated a higher expression of TLR4 in vivo during EIU than normal. In this study, we analyzed levels of peritoneal macrophage cytokines from C3H/HeN mice with LPS stimulation in vitro to elucidate the effect of TLR4 on cytokines during EIU. Full article
Open AccessArticle Mechanism of Cellular Oxidation Stress Induced by Asymmetric Dimethylarginine
Int. J. Mol. Sci. 2012, 13(6), 7521-7531; doi:10.3390/ijms13067521
Received: 2 May 2012 / Revised: 7 June 2012 / Accepted: 13 June 2012 / Published: 18 June 2012
Cited by 11 | PDF Full-text (256 KB) | HTML Full-text | XML Full-text
Abstract
The mechanism by which asymmetric dimethylarginine (ADMA) induces vascular oxidative stress is not well understood. In this study, we utilized human umbilical vein endothelial cells (HUVEC) to examine the roles of ADMA cellular transport and the uncoupling of endothelial nitric oxide synthase [...] Read more.
The mechanism by which asymmetric dimethylarginine (ADMA) induces vascular oxidative stress is not well understood. In this study, we utilized human umbilical vein endothelial cells (HUVEC) to examine the roles of ADMA cellular transport and the uncoupling of endothelial nitric oxide synthase (eNOS) in contributing to this phenomenon. Dihydroethidium (DHE) fluorescence was used as an index of oxidative stress. Whole cells and their isolated membrane fractions exhibited measureable increased DHE fluorescence at ADMA concentrations greater than 10 µM. ADMA-induced DHE fluorescence was inhibited by co-incubation with L-lysine, tetrahydrobiopterin (BH4), or L-nitroarginine methyl ester (L-NAME). Oxidative stress induced in these cells by angiotensin II (Ang II) were unaffected by the same concentrations of L-lysine, L-NAME and BH4. ADMA-induced reduction in cellular nitrite or nitrite/nitrate production was reversed in the presence of increasing concentrations of BH4. These results suggest that ADMA-induced DHE fluorescence involves the participation of both the cationic transport system in the cellular membrane and eNOS instead of the Ang II-NADPH oxidase pathway. Full article
(This article belongs to the Special Issue ADMA and Nitrergic System)
Open AccessArticle Prediction of a New Ligand-Binding Site for Type 2 Motif based on the Crystal Structure of ALG-2 by Dry and Wet Approaches
Int. J. Mol. Sci. 2012, 13(6), 7532-7549; doi:10.3390/ijms13067532
Received: 5 April 2012 / Revised: 6 June 2012 / Accepted: 13 June 2012 / Published: 18 June 2012
Cited by 3 | PDF Full-text (938 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
ALG-2 is a penta-EF-hand Ca2+-binding protein and interacts with a variety of intracellular proteins. Two types of ALG-2-binding motifs have been determined: type 1, PXYPXnYP (X, variable; n = 4), in ALIX and PLSCR3; [...] Read more.
ALG-2 is a penta-EF-hand Ca2+-binding protein and interacts with a variety of intracellular proteins. Two types of ALG-2-binding motifs have been determined: type 1, PXYPXnYP (X, variable; n = 4), in ALIX and PLSCR3; type 2, PXPGF, in Sec31A and PLSCR3. The previously solved X-ray crystal structure of the complex between ALG-2 and an ALIX peptide containing type 1 motif showed that the peptide binds to Pocket 1 and Pocket 2. Co-crystallization of ALG-2 and type 2 motif-containing peptides has not been successful. To gain insights into the molecular basis of type 2 motif recognition, we searched for a new hydrophobic cavity by computational algorithms using MetaPocket 2.0 based on 3D structures of ALG-2. The predicted hydrophobic pocket designated Pocket 3 fits with N-acetyl-ProAlaProGlyPhe-amide, a virtual penta-peptide derived from one of the two types of ALG-2-binding sites in PLSCR3 (type 2 motif), using the molecular docking software AutoDock Vina. We investigated effects of amino acid substitutions of the predicted binding sites on binding abilities by pulldown assays using glutathione-S-transferase -fused ALG-2 of wild-type and mutant proteins and lysates of cells expressing green fluorescent protein -fused PLSCR3 of wild-type and mutants. Substitution of either L52 with Ala or F148 with Ser of ALG-2 caused loss of binding abilities to PLSCR3 lacking type 1 motif but retained those to PLSCR3 lacking type 2 motif, strongly supporting the hypothesis that Pocket 3 is the binding site for type 2 motif. Full article
(This article belongs to the Section Molecular Recognition)
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Open AccessArticle Effect of ZnO on the Physical Properties and Optical Band Gap of Soda Lime Silicate Glass
Int. J. Mol. Sci. 2012, 13(6), 7550-7558; doi:10.3390/ijms13067550
Received: 18 April 2012 / Revised: 18 May 2012 / Accepted: 22 May 2012 / Published: 18 June 2012
Cited by 13 | PDF Full-text (230 KB) | HTML Full-text | XML Full-text
Abstract
This manuscript reports on the physical properties and optical band gap of five samples of soda lime silicate (SLS) glass combined with zinc oxide (ZnO) that were prepared by a melting and quenching process. To understand the role of ZnO in this [...] Read more.
This manuscript reports on the physical properties and optical band gap of five samples of soda lime silicate (SLS) glass combined with zinc oxide (ZnO) that were prepared by a melting and quenching process. To understand the role of ZnO in this glass structure, the density, molar volume and optical band gaps were investigated. The density and absorption spectra in the Ultra-Violet-Visible (UV-Visible) region were recorded at room temperature. The results show that the densities of the glass samples increased as the ZnO weight percentage increased. The molar volume of the glasses shows the same trend as the density: the molar volume increased as the ZnO content increased. The optical band gaps were calculated from the absorption edge, and it was found that the optical band gap decreased from 3.20 to 2.32 eV as the ZnO concentration increased. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle DNA Polymorphisms of the Lipoprotein Lipase Gene and Their Association with Coronary Artery Disease in the Saudi Population
Int. J. Mol. Sci. 2012, 13(6), 7559-7574; doi:10.3390/ijms13067559
Received: 20 March 2012 / Revised: 30 May 2012 / Accepted: 8 June 2012 / Published: 18 June 2012
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Abstract
Coronary heart disease (CHD) is a major health problem and a major cause of death in most countries. Evidence has been presented that gene polymorphisms (HindIII, PvuII and Ser447Ter) of lipoprotein lipase (LPL) are risk factors of coronary artery disease (CAD). Aim: Our objective of the present investigation was to determine whether 3 LPL polymorphisms (LPL-HindIII, LPL-PvuII and LPL-Ser447Ter) can be considered as independent risk factors for CAD in the Saudi population. Methods: We recruited 120 CAD subjects, confirmed angiographically with identical ethnic backgrounds and 65 control subjects. Polymerase chain reaction-restriction fragment length polymorphisms (RFLP) technique was used to detect the polymorphisms of the LPL gene. Results and conclusion: For the HindIII genotype, within the CAD group, the frequencies of the H+H+ were found in 50.8%, whereas 44.2% carried the HH+ genotype, and 5% carried the HH genotype. Within the control group, the H+H+ genotype was found in 44.6%, whereas 35.4% carried the HH+ genotype, 20% carried the HHgenotype. The odds ratio (OR) of HindIII genotype H+H+ vs. HH genotype at 95% Confidence Interval (CI) were 4.6 (1.57–13.2) and p < 0.005, hence showing no significant association with CAD. For the PvuII genotype, within the CAD group the frequencies of the P+P+ found in 41.7% whereas 43.3.2% carried the PP+ genotype, and 15% carried the PP genotype. Within the control group the P+P+ was found in 38.5%, 43.0% carried the PP+ genotype, and 18.5% carried the PP genotype. The OR of PvuII genotype P+P+ vs. PP genotypes (95% CI) is 1.33 and p = 0.52; hence, it was also insignificant to show association with the disease. For the Ser447Ter genotype, within the CAD group, the frequencies of the C/C found in 83.3%, whereas 16.7% carried the C/G genotype. Within the control group, the C/C was found in 87.7% and 12.3% carried the C/G genotype. We did not get any GG genotypes in control as well as patients for this gene. It can be concluded that C allele of gene masks the presence of G allele in the Saudi population. The OR of CG + GG vs. CC (95% CI) is 1.43 from 0.59 to 3.44 which is insignificant. Hence this gene also has no significant association with CAD in the Saudi population. Full article
Open AccessArticle Carrier Injection and Transport in Blue Phosphorescent Organic Light-Emitting Device with Oxadiazole Host
Int. J. Mol. Sci. 2012, 13(6), 7575-7585; doi:10.3390/ijms13067575
Received: 27 March 2012 / Revised: 25 May 2012 / Accepted: 13 June 2012 / Published: 19 June 2012
Cited by 19 | PDF Full-text (203 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, we investigate the carrier injection and transport characteristics in iridium(III)bis[4,6-(di-fluorophenyl)-pyridinato-N,C2']picolinate (FIrpic) doped phosphorescent organic light-emitting devices (OLEDs) with oxadiazole (OXD) as the bipolar host material of the emitting layer (EML). When doping Firpic inside the OXD, the driving voltage [...] Read more.
In this paper, we investigate the carrier injection and transport characteristics in iridium(III)bis[4,6-(di-fluorophenyl)-pyridinato-N,C2']picolinate (FIrpic) doped phosphorescent organic light-emitting devices (OLEDs) with oxadiazole (OXD) as the bipolar host material of the emitting layer (EML). When doping Firpic inside the OXD, the driving voltage of OLEDs greatly decreases because FIrpic dopants facilitate electron injection and electron transport from the electron-transporting layer (ETL) into the EML. With increasing dopant concentration, the recombination zone shifts toward the anode side, analyzed with electroluminescence (EL) spectra. Besides, EL redshifts were also observed with increasing driving voltage, which means the electron mobility is more sensitive to the electric field than the hole mobility. To further investigate carrier injection and transport characteristics, FIrpic was intentionally undoped at different positions inside the EML. When FIrpic was undoped close to the ETL, driving voltage increased significantly which proves the dopant-assisted-electron-injection characteristic in this OLED. When the undoped layer is near the electron blocking layer, the driving voltage is only slightly increased, but the current efficiency is greatly reduced because the main recombination zone was undoped. However, non-negligible FIrpic emission is still observed which means the recombination zone penetrates inside the EML due to certain hole-transporting characteristics of the OXD. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Isolation and Characterization of Simple Sequence Repeats (SSR) Markers from the Moss Genus Orthotrichum Using a Small Throughput Pyrosequencing Machine
Int. J. Mol. Sci. 2012, 13(6), 7586-7593; doi:10.3390/ijms13067586
Received: 10 May 2012 / Revised: 12 June 2012 / Accepted: 13 June 2012 / Published: 19 June 2012
Cited by 5 | PDF Full-text (138 KB) | HTML Full-text | XML Full-text
Abstract
Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment) genomic library and small-scale 454 pyrosequencing, we determined [...] Read more.
Here, we report the results of next-generation sequencing on the GS Junior system to identify a large number of microsatellites from the epiphytic moss Orthotrichum speciosum. Using a combination of a total (non-enrichment) genomic library and small-scale 454 pyrosequencing, we determined 5382 contigs whose length ranged from 103 to 5445 bp. In this dataset we identified 92 SSR (simple sequence repeats) motifs in 89 contigs. Forty-six of these had flanking regions suitable for primer design. We tested PCR amplification, reproducibility, and the level of polymorphism of 46 primer pairs for Orthotrichum speciosum using 40 individuals from two populations. As a result, the designed primers revealed 35 polymorphic loci with more than two alleles detected. This method is cost- and time-effective in comparison with traditional approaches involving cloning and sequencing. Full article
Open AccessArticle Density Functional Theory (DFT) Study of Edaravone Derivatives as Antioxidants
Int. J. Mol. Sci. 2012, 13(6), 7594-7606; doi:10.3390/ijms13067594
Received: 18 May 2012 / Revised: 9 June 2012 / Accepted: 11 June 2012 / Published: 20 June 2012
Cited by 8 | PDF Full-text (531 KB) | HTML Full-text | XML Full-text
Abstract
Quantum chemical calculations at the B3LYP/6–31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E), ionization potential (IP), bond dissociation energy (BDE), and stabilization energies [...] Read more.
Quantum chemical calculations at the B3LYP/6–31G* level of theory were employed for the structure-activity relationship and prediction of the antioxidant activity of edaravone and structurally related derivatives using energy (E), ionization potential (IP), bond dissociation energy (BDE), and stabilization energies (∆Eiso). Spin density calculations were also performed for the proposed antioxidant activity mechanism. The electron abstraction is related to electron-donating groups (EDG) at position 3, decreasing the IP when compared to substitution at position 4. The hydrogen abstraction is related to electron-withdrawing groups (EDG) at position 4, decreasing the BDECH when compared to other substitutions, resulting in a better antioxidant activity. The unpaired electron formed by the hydrogen abstraction from the C–H group of the pyrazole ring is localized at 2, 4, and 6 positions. The highest scavenging activity prediction is related to the lowest contribution at the carbon atom. The likely mechanism is related to hydrogen transfer. It was found that antioxidant activity depends on the presence of EDG at the C2 and C4 positions and there is a correlation between IP and BDE. Our results identified three different classes of new derivatives more potent than edaravone. Full article
(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)
Open AccessCommunication Ultrasound-Assisted Extraction of Syringin from the Bark of Ilex rotunda Thumb Using Response Surface Methodology
Int. J. Mol. Sci. 2012, 13(6), 7607-7616; doi:10.3390/ijms13067607
Received: 28 April 2012 / Revised: 12 May 2012 / Accepted: 15 May 2012 / Published: 20 June 2012
Cited by 9 | PDF Full-text (690 KB) | HTML Full-text | XML Full-text
Abstract
In this work, a rapid extraction method based on ultrasound-assisted extraction (UAE) of syringin from the bark of Ilex rotunda Thumb using response surface methodology (RSM) is described. The syringin was analyzed and quantified by high performance liquid chromatography coupled with UV [...] Read more.
In this work, a rapid extraction method based on ultrasound-assisted extraction (UAE) of syringin from the bark of Ilex rotunda Thumb using response surface methodology (RSM) is described. The syringin was analyzed and quantified by high performance liquid chromatography coupled with UV detection (HPLC-UV). The extraction solvent, extraction temperature and extraction time, the three main factors for UAE, were optimized with Box-Behnken design (BBD) to obtain the highest extraction efficiency. The optimal conditions were the use of a sonication frequency of 40 kHz, 65% methanol as the solvent, an extraction time of 30 min and an extraction temperature of 40 °C. Using these optimal conditions, the experimental values agreed closely with the predicted values. The analysis of variance (ANOVA) indicated a high goodness of model fit and the success of the RSM method for optimizing syringin extraction from the bark of I. rotunda. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Biodegradation Study of Microcrystalline Chitosan and Microcrystalline Chitosan/β-TCP Complex Composites
Int. J. Mol. Sci. 2012, 13(6), 7617-7628; doi:10.3390/ijms13067617
Received: 18 April 2012 / Revised: 25 May 2012 / Accepted: 30 May 2012 / Published: 21 June 2012
Cited by 2 | PDF Full-text (478 KB) | HTML Full-text | XML Full-text
Abstract
Bone repair or regeneration is a common and complicated clinical problem in orthopedic surgery. The importance of natural polymers, such as microcrystalline chitosan, and minerals such as HAp and β-TCP, has grown significantly over the last two decades due to their renewable [...] Read more.
Bone repair or regeneration is a common and complicated clinical problem in orthopedic surgery. The importance of natural polymers, such as microcrystalline chitosan, and minerals such as HAp and β-TCP, has grown significantly over the last two decades due to their renewable and biodegradable source, increasing the knowledge and functionality of composites in technological and biomedical applications. This study compares the biodegradation process, bioactivity, structure, morphology, and mechanical properties of microcrystalline chitosan and microcrystalline chitosan/β-TCP complex; the latter according to the new method of preparation. The complex showed a homogeneous network structure with regular pores, good bioactivity, even after 60 days of conducting the hydrolytic and enzymatic degradation process, showing a bacteriostatic and bactericidal activity. The complex indicates that it could be used successfully as a base for implants and scaffolds production in orthopedic surgery. Full article
(This article belongs to the Special Issue Composite Materials in Skeletal Engineering)
Open AccessArticle Supercritical Fluid Extraction of Eucalyptus globulus Bark—A Promising Approach for Triterpenoid Production
Int. J. Mol. Sci. 2012, 13(6), 7648-7662; doi:10.3390/ijms13067648
Received: 10 May 2012 / Revised: 30 May 2012 / Accepted: 8 June 2012 / Published: 21 June 2012
Cited by 19 | PDF Full-text (258 KB) | HTML Full-text | XML Full-text
Abstract
Eucalyptus bark contains significant amounts of triterpenoids with demonstrated bioactivity, namely triterpenic acids and their acetyl derivatives (ursolic, betulinic, oleanolic, betulonic, 3-acetylursolic, and 3-acetyloleanolic acids). In this work, the supercritical fluid extraction (SFE) of Eucalyptus globulus deciduous bark was carried out with [...] Read more.
Eucalyptus bark contains significant amounts of triterpenoids with demonstrated bioactivity, namely triterpenic acids and their acetyl derivatives (ursolic, betulinic, oleanolic, betulonic, 3-acetylursolic, and 3-acetyloleanolic acids). In this work, the supercritical fluid extraction (SFE) of Eucalyptus globulus deciduous bark was carried out with pure and modified carbon dioxide to recover this fraction, and the results were compared with those obtained by Soxhlet extraction with dichloromethane. The effects of pressure (100–200 bar), co-solvent (ethanol) content (0, 5 and 8% wt), and multistep operation were studied in order to evaluate the applicability of SFE for their selective and efficient production. The individual extraction curves of the main families of compounds were measured, and the extracts analyzed by GC-MS. Results pointed out the influence of pressure and the important role played by the co-solvent. Ethanol can be used with advantage, since its effect is more important than increasing pressure by several tens of bar. At 160 bar and 40 °C, the introduction of 8% (wt) of ethanol greatly improves the yield of triterpenoids more than threefold. Full article
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Open AccessArticle Expression of Sox2 and Oct4 and Their Clinical Significance in Human Non-Small-Cell Lung Cancer
Int. J. Mol. Sci. 2012, 13(6), 7663-7675; doi:10.3390/ijms13067663
Received: 11 April 2012 / Revised: 15 June 2012 / Accepted: 19 June 2012 / Published: 21 June 2012
Cited by 30 | PDF Full-text (407 KB) | HTML Full-text | XML Full-text
Abstract
Sox2 and Oct4 are transcription factors with the characteristics of regulating self-renewal and differentiation of embryonic stem cell. The aim of this study was to detect the expression of Sox2 and Oct4 and analyze their clinical significance in human non-small-cell lung cancer (NSCLC). Expression of Sox2 and Oct4 were assayed in cancer tissues and their corresponding paracancerous tissues from 44 patients with NSCLC and 21 patients with benign tumors using immunohistochemistry, Western blot, reverse transcription polymerase chain reaction (RT-PCR). The correlation between the expression of Sox2 and Oct4 and tumor type, grade and prognosis and the utility of the two genes in discriminating between benign and malignant tumors were analyzed as well. The results showed that Sox2 and Oct4 positive staining was only seen in the nuclei of cancer cells but not in either the precancerous tissues or benign tumor tissues by immunohistochemistry (p < 0.01). Furthermore, in the lung cancer tissue, the positive rate for Sox2 and Oct4 was 70.5% and 54.5%, respectively. Meanwhile, clinicopathological correlations showed that the Oct4 expression level was significantly associated with poorer differentiation and higher TNM stage of the cancer (p < 0.05). Western blot and RT-PCR analysis showed similar results to immunohistochemistry. Follow-up analysis revealed that expression of Oct4 was significantly associated with poor prognosis of lung cancer. The conclusion is that Sox2 and Oct4 may act as the promising unit markers in directing NSCLC diagnosis and therapy. Also, Oct4 can be regarded as a novel predictor of poor prognosis for NSCLC patients undergoing resection. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Proteomic Analysis of Cerebrospinal Fluid in a Fulminant Case of Multiple Sclerosis
Int. J. Mol. Sci. 2012, 13(6), 7676-7693; doi:10.3390/ijms13067676
Received: 27 March 2012 / Revised: 19 April 2012 / Accepted: 5 June 2012 / Published: 21 June 2012
Cited by 9 | PDF Full-text (970 KB) | HTML Full-text | XML Full-text
Abstract
Multiple Sclerosis (MS) is a chronic disease, but in rare fulminant cases rapid progression may lead to death shortly after diagnosis. Currently there is no diagnostic test to predict disease course. The aim of this study was to identify potential biomarkers/proteins related [...] Read more.
Multiple Sclerosis (MS) is a chronic disease, but in rare fulminant cases rapid progression may lead to death shortly after diagnosis. Currently there is no diagnostic test to predict disease course. The aim of this study was to identify potential biomarkers/proteins related to rapid progression. We present the case history of a 15-year-old male MS patient. Cerebrospinal fluid (CSF) was taken at diagnosis and at the time of rapid progression leading to the patient’s death. Using isobaric tag labeling and nanoflow liquid chromatography in conjunction with matrix assisted laser desorption/ionization time of flight tandem mass spectrometry we quantitatively analyzed the protein content of two CSF samples from the patient with fulminant MS as well as one relapsing-remitting (RR) MS patient and one control headache patient, whose CSF analysis was normal. Seventy-eight proteins were identified and seven proteins were found to be more abundant in both fulminant MS samples but not in the RR MS sample compared to the control. These proteins are involved in the immune response, blood coagulation, cell proliferation and cell adhesion. In conclusion, in this pilot study we were able to show differences in the CSF proteome of a rapidly progressing MS patient compared to a more typical clinical form of MS and a control subject. Full article
Open AccessArticle The Role of PPARα in Metformin-Induced Attenuation of Mitochondrial Dysfunction in Acute Cardiac Ischemia/Reperfusion in Rats
Int. J. Mol. Sci. 2012, 13(6), 7694-7709; doi:10.3390/ijms13067694
Received: 9 May 2012 / Revised: 31 May 2012 / Accepted: 18 June 2012 / Published: 21 June 2012
Cited by 14 | PDF Full-text (428 KB) | HTML Full-text | XML Full-text
Abstract
Metformin, an anti-diabetic drug, exerts cardioprotection against ischemia-reperfusion (IR) through the activation of AMPK. However, the molecular mechanisms underlying these beneficial effects remain elusive. In this study, we examined the role of PPARα in mediating cardioprotective effects of metformin on mitochondria. Hearts of male Sprague-Dawley rats perfused by Langendorff were subjected to IR in the presence or absence of metformin and the PPARα inhibitor, GW6471. IR reduced cardiac function and compromised the structural integrity of cardiac cells evidenced by increased LDH release from the hearts. In addition, IR induced mitochondrial dysfunction as evidenced by reduced respiration and increased mitochondrial permeability transition pore (PTP) opening. However, metformin-treated hearts demonstrated improved post-ischemic recovery of cardiac function and reduced cell death that were associated with increased state 3 respiration at complexes I and II (by 27% and 32%, respectively, both p < 0.05) and decreased PTP opening (by 27%, p < 0.05) compared to untreated hearts. The protective effects of metformin on cardiac function and mitochondria were blocked by GW6471. Thus, our results demonstrate that inhibition of PPARα attenuates the beneficial effects of metformin on mitochondria in acute IR. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effects of Methylmercury Contained in a Diet Mimicking the Wayana Amerindians Contamination through Fish Consumption: Mercury Accumulation, Metallothionein Induction, Gene Expression Variations, and Role of the Chemokine CCL2
Int. J. Mol. Sci. 2012, 13(6), 7710-7738; doi:10.3390/ijms13067710
Received: 1 May 2012 / Revised: 11 June 2012 / Accepted: 14 June 2012 / Published: 21 June 2012
Cited by 5 | PDF Full-text (1667 KB) | HTML Full-text | XML Full-text
Abstract
Methylmercury (MeHg) is a potent neurotoxin, and human beings are mainly exposed to this pollutant through fish consumption. We addressed the question of whether a diet mimicking the fish consumption of Wayanas Amerindians from French Guiana could result in observable adverse effects [...] Read more.
Methylmercury (MeHg) is a potent neurotoxin, and human beings are mainly exposed to this pollutant through fish consumption. We addressed the question of whether a diet mimicking the fish consumption of Wayanas Amerindians from French Guiana could result in observable adverse effects in mice. Wayanas adult men are subjected to a mean mercurial dose of 7 g Hg/week/kg of body weight. We decided to supplement a vegetarian-based mice diet with 0.1% of lyophilized Hoplias aimara fish, which Wayanas are fond of and equivalent to the same dose as that afflicting the Wayanas Amerindians. Total mercury contents were 1.4 ± 0.2 and 5.4 ± 0.5 ng Hg/g of food pellets for the control and aimara diets, respectively. After 14 months of exposure, the body parts and tissues displaying the highest mercury concentration on a dry weight (dw) basis were hair (733 ng/g) and kidney (511 ng/g), followed by the liver (77 ng/g). Surprisingly, despite the fact that MeHg is a neurotoxic compound, the brain accumulated low levels of mercury (35 ng/g in the cortex). The metallothionein (MT) protein concentration only increased in those tissues (kidney, muscles) in which MeHg demethylation had occurred. This can be taken as a molecular sign of divalent mercurial contamination since only Hg2+ has been reported yet to induce MT accumulation in contaminated tissues. The suppression of the synthesis of the chemokine CCL2 in the corresponding knockout (KO) mice resulted in important changes in gene expression patterns in the liver and brain. After three months of exposure to an aimara-containing diet, eight of 10 genes selected (Sdhb, Cytb, Cox1, Sod1, Sod2, Mt2, Mdr1a and Bax) were repressed in wild-type mice liver whereas none presented a differential expression in KO Ccl2/ mice. In the wild-type mice brain, six of 12 genes selected (Cytb, Cox1, Sod1, Sod2, Mdr1a and Bax) presented a stimulated expression, whereas all remained at the basal level of expression in KO Ccl2/ mice. In the liver of aimara-fed mice, histological alterations were observed for an accumulated mercury concentration as low as 32 ng/g, dw, and metal deposits were observed within the cytoplasm of hepatic cells. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessArticle Preparation of Porous Scaffolds from Silk Fibroin Extracted from the Silk Gland of Bombyx mori (B. mori)
Int. J. Mol. Sci. 2012, 13(6), 7762-7775; doi:10.3390/ijms13067762
Received: 25 April 2012 / Revised: 14 June 2012 / Accepted: 15 June 2012 / Published: 21 June 2012
Cited by 9 | PDF Full-text (634 KB) | HTML Full-text | XML Full-text
Abstract
In order to use a simple and ecofriendly method to prepare porous silk scaffolds, aqueous silk fibroin solution (ASF) was extracted from silk gland of 7-day-old fifth instar larvae of Bombyx mori (B. mori). SDS-page analysis indicated that the obtained [...] Read more.
In order to use a simple and ecofriendly method to prepare porous silk scaffolds, aqueous silk fibroin solution (ASF) was extracted from silk gland of 7-day-old fifth instar larvae of Bombyx mori (B. mori). SDS-page analysis indicated that the obtained fibroin had a molecular weight higher than 200 kDa. The fabrication of porous scaffolds from ASF was achieved by using the freeze-drying method. The pore of porous scaffolds is homogenous and tends to become smaller with an increase in the concentration of ASF. Conversely, the porosity is decreased. The porous scaffolds show impressive compressive strength which can be as high as 6.9 ± 0.4 MPa. Furthermore, ASF has high cell adhesion and growth activity. It also exhibits high ALP activity. This implies that porous scaffolds prepared from ASF have biocompatibility. Therefore, the porous scaffolds prepared in this study have potential application in tissue engineering due to the impressive compressive strength and biocompatibility. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Polydatin Attenuates Hypoxic Pulmonary Hypertension and Reverses Remodeling through Protein Kinase C Mechanisms
Int. J. Mol. Sci. 2012, 13(6), 7776-7787; doi:10.3390/ijms13067776
Received: 10 April 2012 / Revised: 11 May 2012 / Accepted: 12 June 2012 / Published: 21 June 2012
Cited by 4 | PDF Full-text (447 KB) | HTML Full-text | XML Full-text
Abstract
Hypoxic pulmonary hypertension is a life-threatening emergency if untreated. Consistent pulmonary hypertension also leads to arteries and ventricular remodeling. The clinical therapeutic strategy for pulmonary hypertension and the corresponding remodeling mainly interacts with NO, angiotensin II (Ang II) and elevated endothelin (ET) [...] Read more.
Hypoxic pulmonary hypertension is a life-threatening emergency if untreated. Consistent pulmonary hypertension also leads to arteries and ventricular remodeling. The clinical therapeutic strategy for pulmonary hypertension and the corresponding remodeling mainly interacts with NO, angiotensin II (Ang II) and elevated endothelin (ET) targets. In the present study, we evaluated the effects of polydatin on hypoxia-induced pulmonary hypertension. It was observed that polydatin attenuated hypoxic pulmonary hypertension, reversed remodeling, and regulated NO, Ang II, ET contents in the serum and lung samples. However, forced activation of PKC signaling by its selective activator thymeleatoxin (THX) could abate the effects of polydatain. These results suggest that polydatin might be a promising candidate for hypoxic pulmonary treatment through interaction with PKC mechanisms. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Plasma Depolymerization of Chitosan in the Presence of Hydrogen Peroxide
Int. J. Mol. Sci. 2012, 13(6), 7788-7797; doi:10.3390/ijms13067788
Received: 23 April 2012 / Revised: 16 June 2012 / Accepted: 18 June 2012 / Published: 21 June 2012
Cited by 5 | PDF Full-text (266 KB) | HTML Full-text | XML Full-text
Abstract
The depolymerization of chitosan by plasma in the presence of hydrogen peroxide (H2O2) was investigated. The efficiency of the depolymerization was demonstrated by means of determination of viscosity-average molecular weight and gel permeation chromatography (GPC). The structure of [...] Read more.
The depolymerization of chitosan by plasma in the presence of hydrogen peroxide (H2O2) was investigated. The efficiency of the depolymerization was demonstrated by means of determination of viscosity-average molecular weight and gel permeation chromatography (GPC). The structure of the depolymerized chitosan was characterized by Fourier-transform infrared spectra (FT-IR), ultraviolet spectra (UV) and X-ray diffraction (XRD). The results showed that chitosan can be effectively degradated by plasma in the presence of H2O2. The chemical structure of the depolymerized chitosan was not obviously modified. The combined plasma/H2O2 method is significantly efficient for scale-up manufacturing of low molecular weight chitosan. Full article
Open AccessArticle Diffusivity Maximum in a Reentrant Nematic Phase
Int. J. Mol. Sci. 2012, 13(6), 7854-7871; doi:10.3390/ijms13067854
Received: 28 April 2012 / Revised: 11 June 2012 / Accepted: 13 June 2012 / Published: 21 June 2012
Cited by 2 | PDF Full-text (734 KB) | HTML Full-text | XML Full-text
Abstract
We report molecular dynamics simulations of confined liquid crystals using the Gay–Berne–Kihara model. Upon isobaric cooling, the standard sequence of isotropic–nematic–smectic A phase transitions is found. Upon further cooling a reentrant nematic phase occurs. We investigate the temperature dependence of the self-diffusion [...] Read more.
We report molecular dynamics simulations of confined liquid crystals using the Gay–Berne–Kihara model. Upon isobaric cooling, the standard sequence of isotropic–nematic–smectic A phase transitions is found. Upon further cooling a reentrant nematic phase occurs. We investigate the temperature dependence of the self-diffusion coefficient of the fluid in the nematic, smectic and reentrant nematic phases. We find a maximum in diffusivity upon isobaric cooling. Diffusion increases dramatically in the reentrant phase due to the high orientational molecular order. As the temperature is lowered, the diffusion coefficient follows an Arrhenius behavior. The activation energy of the reentrant phase is found in reasonable agreement with the reported experimental data. We discuss how repulsive interactions may be the underlying mechanism that could explain the occurrence of reentrant nematic behavior for polar and non-polar molecules. Full article
(This article belongs to the Special Issue Self-Assembled Soft Matter Nanostructures at Interfaces)

Review

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Open AccessReview State of the Art in Silico Tools for the Study of Signaling Pathways in Cancer
Int. J. Mol. Sci. 2012, 13(6), 6561-6581; doi:10.3390/ijms13066561
Received: 27 March 2012 / Revised: 3 May 2012 / Accepted: 10 May 2012 / Published: 29 May 2012
Cited by 3 | PDF Full-text (672 KB) | HTML Full-text | XML Full-text
Abstract
In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical [...] Read more.
In the last several years, researchers have exhibited an intense interest in the evolutionarily conserved signaling pathways that have crucial roles during embryonic development. Interestingly, the malfunctioning of these signaling pathways leads to several human diseases, including cancer. The chemical and biophysical events that occur during cellular signaling, as well as the number of interactions within a signaling pathway, make these systems complex to study. In silico resources are tools used to aid the understanding of cellular signaling pathways. Systems approaches have provided a deeper knowledge of diverse biochemical processes, including individual metabolic pathways, signaling networks and genome-scale metabolic networks. In the future, these tools will be enormously valuable, if they continue to be developed in parallel with growing biological knowledge. In this study, an overview of the bioinformatics resources that are currently available for the analysis of biological networks is provided. Full article
Open AccessReview Intravascular Targets for Molecular Contrast-Enhanced Ultrasound Imaging
Int. J. Mol. Sci. 2012, 13(6), 6679-6697; doi:10.3390/ijms13066679
Received: 19 April 2012 / Revised: 21 May 2012 / Accepted: 22 May 2012 / Published: 1 June 2012
Cited by 16 | PDF Full-text (1754 KB) | HTML Full-text | XML Full-text
Abstract
Molecular targeting of contrast agents for ultrasound imaging is emerging as a new medical imaging modality. It combines advances in ultrasound technology with principles of molecular imaging, thereby allowing non-invasive assessment of biological processes in vivo. Preclinical studies have shown that [...] Read more.
Molecular targeting of contrast agents for ultrasound imaging is emerging as a new medical imaging modality. It combines advances in ultrasound technology with principles of molecular imaging, thereby allowing non-invasive assessment of biological processes in vivo. Preclinical studies have shown that microbubbles, which provide contrast during ultrasound imaging, can be targeted to specific molecular markers. These microbubbles accumulate in tissue with target (over) expression, thereby significantly increasing the ultrasound signal. This concept offers safe and low-cost imaging with high spatial resolution and sensitivity. It is therefore considered to have great potential in cancer imaging, and early-phase clinical trials are ongoing. In this review, we summarize the current literature on targets that have been successfully imaged in preclinical models using molecularly targeted ultrasound contrast agents. Based on preclinical experience, we discuss the potential clinical utility of targeted microbubbles. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
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Open AccessReview 8-Oxoguanine DNA Glycosylases: One Lesion, Three Subfamilies
Int. J. Mol. Sci. 2012, 13(6), 6711-6729; doi:10.3390/ijms13066711
Received: 20 April 2012 / Revised: 14 May 2012 / Accepted: 24 May 2012 / Published: 1 June 2012
Cited by 8 | PDF Full-text (2831 KB) | HTML Full-text | XML Full-text
Abstract
Amongst the four bases that form DNA, guanine is the most susceptible to oxidation, and its oxidation product, 7,8-dihydro-8-oxoguanine (8-oxoG) is the most prevalent base lesion found in DNA. Fortunately, throughout evolution cells have developed repair mechanisms, such as the 8-oxoguanine DNA [...] Read more.
Amongst the four bases that form DNA, guanine is the most susceptible to oxidation, and its oxidation product, 7,8-dihydro-8-oxoguanine (8-oxoG) is the most prevalent base lesion found in DNA. Fortunately, throughout evolution cells have developed repair mechanisms, such as the 8-oxoguanine DNA glycosylases (OGG), which recognize and excise 8-oxoG from DNA thereby preventing the accumulation of deleterious mutations. OGG are divided into three subfamilies, OGG1, OGG2 and AGOG, which are all involved in the base excision repair (BER) pathway. The published structures of OGG1 and AGOG, as well as the recent availability of OGG2 structures in both apo- and liganded forms, provide an excellent opportunity to compare the structural and functional properties of the three OGG subfamilies. Among the observed differences, the three-dimensional fold varies considerably between OGG1 and OGG2 members, as the latter lack the A-domain involved in 8-oxoG binding. In addition, all three OGG subfamilies bind 8-oxoG in a different manner even though the crucial interaction between the enzyme and the protonated N7 of 8-oxoG is conserved. Finally, the three OGG subfamilies differ with respect to DNA binding properties, helix-hairpin-helix motifs, and specificity for the opposite base. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Open AccessReview Mechanistic Insights into Neurotoxicity Induced by Anesthetics in the Developing Brain
Int. J. Mol. Sci. 2012, 13(6), 6772-6799; doi:10.3390/ijms13066772
Received: 28 March 2012 / Revised: 12 May 2012 / Accepted: 25 May 2012 / Published: 4 June 2012
Cited by 9 | PDF Full-text (235 KB) | HTML Full-text | XML Full-text
Abstract
Compelling evidence has shown that exposure to anesthetics used in the clinic can cause neurodegeneration in the mammalian developing brain, but the basis of this is not clear. Neurotoxicity induced by exposure to anesthestics in early life involves neuroapoptosis and impairment of [...] Read more.
Compelling evidence has shown that exposure to anesthetics used in the clinic can cause neurodegeneration in the mammalian developing brain, but the basis of this is not clear. Neurotoxicity induced by exposure to anesthestics in early life involves neuroapoptosis and impairment of neurodevelopmental processes such as neurogenesis, synaptogenesis and immature glial development. These effects may subsequently contribute to behavior abnormalities in later life. In this paper, we reviewed the possible mechanisms of anesthetic-induced neurotoxicity based on new in vitro and in vivo findings. Also, we discussed ways to protect against anesthetic-induced neurotoxicity and their implications for exploring cellular and molecular mechanisms of neuroprotection. These findings help in improving our understanding of developmental neurotoxicology and in avoiding adverse neurological outcomes in anesthesia practice. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessReview Fragment C of Tetanus Toxin: New Insights into Its Neuronal Signaling Pathway
Int. J. Mol. Sci. 2012, 13(6), 6883-6901; doi:10.3390/ijms13066883
Received: 28 March 2012 / Revised: 8 May 2012 / Accepted: 23 May 2012 / Published: 7 June 2012
Cited by 9 | PDF Full-text (4043 KB) | HTML Full-text | XML Full-text
Abstract
When Clostridium tetani was discovered and identified as a Gram-positive anaerobic bacterium of the genus Clostridium, the possibility of turning its toxin into a valuable biological carrier to ameliorate neurodegenerative processes was inconceivable. However, the non-toxic carboxy-terminal fragment of the tetanus [...] Read more.
When Clostridium tetani was discovered and identified as a Gram-positive anaerobic bacterium of the genus Clostridium, the possibility of turning its toxin into a valuable biological carrier to ameliorate neurodegenerative processes was inconceivable. However, the non-toxic carboxy-terminal fragment of the tetanus toxin heavy chain (fragment C) can be retrogradely transported to the central nervous system; therefore, fragment C has been used as a valuable biological carrier of neurotrophic factors to ameliorate neurodegenerative processes. More recently, the neuroprotective properties of fragment C have also been described in vitro and in vivo, involving the activation of Akt kinase and extracellular signal-regulated kinase (ERK) signaling cascades through neurotrophin tyrosine kinase (Trk) receptors. Although the precise mechanism of the molecular internalization of fragment C in neuronal cells remains unknown, fragment C could be internalized and translocated into the neuronal cytosol through a clathrin-mediated pathway dependent on proteins, such as dynamin and AP-2. In this review, the origins, molecular properties and possible signaling pathways of fragment C are reviewed to understand the biochemical characteristics of its intracellular and synaptic transport. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
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Open AccessReview Neuroglobin, a Novel Target for Endogenous Neuroprotection against Stroke and Neurodegenerative Disorders
Int. J. Mol. Sci. 2012, 13(6), 6995-7014; doi:10.3390/ijms13066995
Received: 28 April 2012 / Revised: 25 May 2012 / Accepted: 31 May 2012 / Published: 7 June 2012
Cited by 20 | PDF Full-text (248 KB) | HTML Full-text | XML Full-text
Abstract
Brain neurons and tissues respond to sublethal injury by activating endogenous protective pathways. Recently, following the failure of a large number of clinical trials for protective strategies against stroke that aim to inhibit a specific ischemia response pathway, endogenous neuroprotection has emerged [...] Read more.
Brain neurons and tissues respond to sublethal injury by activating endogenous protective pathways. Recently, following the failure of a large number of clinical trials for protective strategies against stroke that aim to inhibit a specific ischemia response pathway, endogenous neuroprotection has emerged as a more promising and hopeful strategy for development of therapeutics against stroke and neurodegenerative disorders. Neuroglobin (Ngb) is an oxygen-binding globin protein that is highly and specifically expressed in brain neurons. Accumulating evidence have clearly demonstrated that Ngb is an endogenous neuroprotective molecule against hypoxic/ischemic and oxidative stress-related insults in cultured neurons and animals, as well as neurodegenerative disorders such as Alzheimer’s disease, thus any pharmacological strategy that can up-regulate endogenous Ngb expression may lead to novel therapeutics against these brain disorders. In this review, we summarize recent studies about the biological function, regulation of gene expression, and neuroprotective mechanisms of Ngb. Furthermore, strategies for identification of chemical compounds that can up-regulate endogenous Ngb expression for neuroprotection against stroke and neurodegenerative disorders are discussed. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
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Open AccessReview Structural Analysis of Hypothetical Proteins from Helicobacter pylori: An Approach to Estimate Functions of Unknown or Hypothetical Proteins
Int. J. Mol. Sci. 2012, 13(6), 7109-7137; doi:10.3390/ijms13067109
Received: 9 March 2012 / Revised: 29 May 2012 / Accepted: 1 June 2012 / Published: 8 June 2012
Cited by 6 | PDF Full-text (2870 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc [...] Read more.
Helicobacter pylori (H. pylori) have a unique ability to survive in extreme acidic environments and to colonize the gastric mucosa. It can cause diverse gastric diseases such as peptic ulcers, chronic gastritis, mucosa-associated lymphoid tissue (MALT) lymphoma, gastric cancer, etc. Based on genomic research of H. pylori, over 1600 genes have been functionally identified so far. However, H. pylori possess some genes that are uncharacterized since: (i) the gene sequences are quite new; (ii) the function of genes have not been characterized in any other bacterial systems; and (iii) sometimes, the protein that is classified into a known protein based on the sequence homology shows some functional ambiguity, which raises questions about the function of the protein produced in H. pylori. Thus, there are still a lot of genes to be biologically or biochemically characterized to understand the whole picture of gene functions in the bacteria. In this regard, knowledge on the 3D structure of a protein, especially unknown or hypothetical protein, is frequently useful to elucidate the structure-function relationship of the uncharacterized gene product. That is, a structural comparison with known proteins provides valuable information to help predict the cellular functions of hypothetical proteins. Here, we show the 3D structures of some hypothetical proteins determined by NMR spectroscopy and X-ray crystallography as a part of the structural genomics of H. pylori. In addition, we show some successful approaches of elucidating the function of unknown proteins based on their structural information. Full article
(This article belongs to the Special Issue Hypothetical Proteins)
Open AccessReview Structural DNA Nanotechnology: From Design to Applications
Int. J. Mol. Sci. 2012, 13(6), 7149-7162; doi:10.3390/ijms13067149
Received: 2 May 2012 / Revised: 29 May 2012 / Accepted: 4 June 2012 / Published: 11 June 2012
Cited by 23 | PDF Full-text (757 KB) | HTML Full-text | XML Full-text
Abstract
The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct [...] Read more.
The exploitation of DNA for the production of nanoscale architectures presents a young yet paradigm breaking approach, which addresses many of the barriers to the self-assembly of small molecules into highly-ordered nanostructures via construct addressability. There are two major methods to construct DNA nanostructures, and in the current review we will discuss the principles and some examples of applications of both the tile-based and DNA origami methods. The tile-based approach is an older method that provides a good tool to construct small and simple structures, usually with multiply repeated domains. In contrast, the origami method, at this time, would appear to be more appropriate for the construction of bigger, more sophisticated and exactly defined structures. Full article
(This article belongs to the Special Issue Self-Assembled Soft Matter Nanostructures at Interfaces)
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Open AccessReview Plants versus Fungi and Oomycetes: Pathogenesis, Defense and Counter-Defense in the Proteomics Era
Int. J. Mol. Sci. 2012, 13(6), 7237-7259; doi:10.3390/ijms13067237
Received: 3 May 2012 / Revised: 29 May 2012 / Accepted: 30 May 2012 / Published: 13 June 2012
Cited by 5 | PDF Full-text (238 KB) | HTML Full-text | XML Full-text
Abstract
Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as [...] Read more.
Plant-fungi and plant-oomycete interactions have been studied at the proteomic level for many decades. However, it is only in the last few years, with the development of new approaches, combined with bioinformatics data mining tools, gel staining, and analytical instruments, such as 2D-PAGE/nanoflow-LC-MS/MS, that proteomic approaches thrived. They allow screening and analysis, at the sub-cellular level, of peptides and proteins resulting from plants, pathogens, and their interactions. They also highlight post-translational modifications to proteins, e.g., glycosylation, phosphorylation or cleavage. However, many challenges are encountered during in planta studies aimed at stressing details of host defenses and fungal and oomycete pathogenicity determinants during interactions. Dissecting the mechanisms of such host-pathogen systems, including pathogen counter-defenses, will ensure a step ahead towards understanding current outcomes of interactions from a co-evolutionary point of view, and eventually move a step forward in building more durable strategies for management of diseases caused by fungi and oomycetes. Unraveling intricacies of more complex proteomic interactions that involve additional microbes, i.e., PGPRs and symbiotic fungi, which strengthen plant defenses will generate valuable information on how pathosystems actually function in nature, and thereby provide clues to solving disease problems that engender major losses in crops every year. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessReview The Toxicity of Amyloid ß Oligomers
Int. J. Mol. Sci. 2012, 13(6), 7303-7327; doi:10.3390/ijms13067303
Received: 2 May 2012 / Revised: 1 June 2012 / Accepted: 8 June 2012 / Published: 13 June 2012
Cited by 34 | PDF Full-text (1741 KB) | HTML Full-text | XML Full-text
Abstract
Abstract: In this review, we elucidate the mechanisms of Aβ oligomer toxicity which may contribute to Alzheimer’s disease (AD). In particular, we discuss on the interaction of Aβ oligomers with the membrane through the process of adsorption and insertion. Such interaction gives [...] Read more.
Abstract: In this review, we elucidate the mechanisms of Aβ oligomer toxicity which may contribute to Alzheimer’s disease (AD). In particular, we discuss on the interaction of Aβ oligomers with the membrane through the process of adsorption and insertion. Such interaction gives rises to phase transitions in the sub-structures of the Aβ peptide from α-helical to β-sheet structure. By means of a coarse-grained model, we exhibit the tendency of β-sheet structures to aggregate, thus providing further insights to the process of membrane induced aggregation. We show that the aggregated oligomer causes membrane invagination, which is a precursor to the formation of pore structures and ion channels. Other pathological progressions to AD due to Aβ oligomers are also covered, such as their interaction with the membrane receptors, and their direct versus indirect effects on oxidative stress and intraneuronal accumulation. We further illustrate that the molecule curcumin is a potential Aβ toxicity inhibitor as a β-sheet breaker by having a high propensity to interact with certain Aβ residues without binding to them. The comprehensive understanding gained from these current researches on the various toxicity mechanisms show promises in the provision of better therapeutics and treatment strategies in the near future. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Figures

Open AccessReview Role of Microglia in Oxidative Toxicity Associated with Encephalomycarditis Virus Infection in the Central Nervous System
Int. J. Mol. Sci. 2012, 13(6), 7365-7374; doi:10.3390/ijms13067365
Received: 2 May 2012 / Revised: 28 May 2012 / Accepted: 5 June 2012 / Published: 14 June 2012
Cited by 6 | PDF Full-text (172 KB) | HTML Full-text | XML Full-text
Abstract
The single-stranded RNA encephalomyocarditis virus (EMCV) can replicate in the central nervous system (CNS) and lead to prominent brain lesions in the stratum pyramidale hippocampus and the stratum granulosum cerebelli. Activated microglia cells infected by EMCV produce a massive burst of reactive [...] Read more.
The single-stranded RNA encephalomyocarditis virus (EMCV) can replicate in the central nervous system (CNS) and lead to prominent brain lesions in the stratum pyramidale hippocampus and the stratum granulosum cerebelli. Activated microglia cells infected by EMCV produce a massive burst of reactive oxygen species (ROS) via NADPH oxidase 2 (NOX2) activation, leading to neuronal death. Balancing this effect is mechanisms by which ROS are eliminated from the CNS. Cellular prion protein (PrPC) plays an important antioxidant role and contributes to cellular defense against EMCV infection. This review introduces recent knowledge on brain injury induced by EMCV infection via ROS generation as well as the involvement of various mediators and regulators in the pathogenesis. Full article
Open AccessReview Hierarchical Assembly of Multifunctional Oxide-based Composite Nanostructures for Energy and Environmental Applications
Int. J. Mol. Sci. 2012, 13(6), 7393-7423; doi:10.3390/ijms13067393
Received: 23 March 2012 / Revised: 31 May 2012 / Accepted: 1 June 2012 / Published: 15 June 2012
Cited by 19 | PDF Full-text (5772 KB) | HTML Full-text | XML Full-text
Abstract
Composite nanoarchitectures represent a class of nanostructured entities that integrates various dissimilar nanoscale building blocks including nanoparticles, nanowires, and nanofilms toward realizing multifunctional characteristics. A broad array of composite nanoarchitectures can be designed and fabricated, involving generic materials such as metal, ceramics, [...] Read more.
Composite nanoarchitectures represent a class of nanostructured entities that integrates various dissimilar nanoscale building blocks including nanoparticles, nanowires, and nanofilms toward realizing multifunctional characteristics. A broad array of composite nanoarchitectures can be designed and fabricated, involving generic materials such as metal, ceramics, and polymers in nanoscale form. In this review, we will highlight the latest progress on composite nanostructures in our research group, particularly on various metal oxides including binary semiconductors, ABO3-type perovskites, A2BO4 spinels and quaternary dielectric hydroxyl metal oxides (AB(OH)6) with diverse application potential. Through a generic template strategy in conjunction with various synthetic approaches—such as hydrothermal decomposition, colloidal deposition, physical sputtering, thermal decomposition and thermal oxidation, semiconductor oxide alloy nanowires, metal oxide/perovskite (spinel) composite nanowires, stannate based nanocompostes, as well as semiconductor heterojunction—arrays and networks have been self-assembled in large scale and are being developed as promising classes of composite nanoarchitectures, which may open a new array of advanced nanotechnologies in solid state lighting, solar absorption, photocatalysis and battery, auto-emission control, and chemical sensing. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessReview Dietary Supplementations as Neuroprotective Therapies: Focus on NT-020 Diet Benefits in a Rat Model of Stroke
Int. J. Mol. Sci. 2012, 13(6), 7424-7444; doi:10.3390/ijms13067424
Received: 9 March 2012 / Revised: 4 June 2012 / Accepted: 5 June 2012 / Published: 15 June 2012
Cited by 1 | PDF Full-text (433 KB) | HTML Full-text | XML Full-text
Abstract
Stroke remains the number one cause of disability in the adult population. Despite scientific progress in our understanding of stroke pathology, only one treatment (tissue plasminogen activator or tPA) is able to afford benefits but to less than 3% of ischemic stroke [...] Read more.
Stroke remains the number one cause of disability in the adult population. Despite scientific progress in our understanding of stroke pathology, only one treatment (tissue plasminogen activator or tPA) is able to afford benefits but to less than 3% of ischemic stroke patients. The development of experimental dietary supplement therapeutics designed to stimulate endogenous mechanisms that confer neuroprotection is likely to open new avenues for exploring stroke therapies. The present review article evaluates the recent literature supporting the benefits of dietary supplementation for the therapy of ischemic stroke. This article focuses on discussing the medical benefits of NT-020 as an adjunct agent for stroke therapy. Based on our preliminary data, a pre-stroke treatment with dietary supplementation promotes neuroprotection by decreasing inflammation and enhancing neurogenesis. However, we recognize that a pre-stroke treatment holds weak clinical relevance. Thus, the main goal of this article is to provide information about recent data that support the assumption of natural compounds as neuroprotective and to evaluate the therapeutic effects of a dietary supplement called NT-020 as in a stroke model. We focus on a systematic assessment of practical treatment parameters so that NT-020 and other dietary supplementations can be developed as an adjunct agent for the prevention or treatment of chronic diseases. We offer rationale for determining the optimal dosage, therapeutic window, and mechanism of action of NT-020 as a dietary supplement to produce neuroprotection when administered immediately after stroke onset. We highlight our long-standing principle in championing both translational and basic science approaches in an effort to fully reveal the therapeutic potential of NT-020 as dietary supplementation in the treatment of stroke. We envision dietary supplementation as an adjunct therapy for stroke at acute, subacute, and even chronic periods. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessReview WIP Remodeling Actin behind the Scenes: How WIP Reshapes Immune and Other Functions
Int. J. Mol. Sci. 2012, 13(6), 7629-7647; doi:10.3390/ijms13067629
Received: 16 May 2012 / Revised: 7 June 2012 / Accepted: 14 June 2012 / Published: 21 June 2012
Cited by 4 | PDF Full-text (241 KB) | HTML Full-text | XML Full-text
Abstract
Actin polymerization is a fundamental cellular process regulating immune cell functions and the immune response. The Wiskott-Aldrich syndrome protein (WASp) is an actin nucleation promoting factor, which is exclusively expressed in hematopoietic cells, where it plays a key regulatory role in cytoskeletal [...] Read more.
Actin polymerization is a fundamental cellular process regulating immune cell functions and the immune response. The Wiskott-Aldrich syndrome protein (WASp) is an actin nucleation promoting factor, which is exclusively expressed in hematopoietic cells, where it plays a key regulatory role in cytoskeletal dynamics. WASp interacting protein (WIP) was first discovered as the binding partner of WASp, through the use of the yeast two hybrid system. WIP was later identified as a chaperone of WASp, necessary for its stability. Mutations occurring at the WASp homology 1 domain (WH1), which serves as the WIP binding site, were found to cause the Wiskott-Aldrich syndrome (WAS) and X-linked thrombocytopenia (XLT). WAS manifests as an immune deficiency characterized by eczema, thrombocytopenia, recurrent infections, and hematopoietic malignancies, demonstrating the importance of WIP for WASp complex formation and for a proper immune response. WIP deficiency was found to lead to different abnormalities in the activity of various lymphocytes, suggesting differential cell-dependent roles for WIP. Additionally, WIP deficiency causes cellular abnormalities not found in WASp-deficient cells, indicating that WIP fulfills roles beyond stabilizing WASp. Indeed, WIP was shown to interact with various binding partners, including the signaling proteins Nck, CrkL and cortactin. Recent studies have demonstrated that WIP also takes part in non immune cellular processes such as cancer invasion and metastasis, in addition to cell subversion by intracellular pathogens. Understanding of numerous functions of WIP can enhance our current understanding of activation and function of immune and other cell types. Full article
(This article belongs to the Special Issue Advances in Molecular Immunology)
Open AccessReview Clinical Neuroprotective Drugs for Treatment and Prevention of Stroke
Int. J. Mol. Sci. 2012, 13(6), 7739-7761; doi:10.3390/ijms13067739
Received: 15 May 2012 / Revised: 15 June 2012 / Accepted: 19 June 2012 / Published: 21 June 2012
Cited by 3 | PDF Full-text (170 KB) | HTML Full-text | XML Full-text
Abstract
Stroke is an enormous public health problem with an imperative need for more effective therapies. In therapies for ischemic stroke, tissue plasminogen activators, antiplatelet agents and anticoagulants are used mainly for their antithrombotic effects. However, free radical scavengers, minocycline and growth factors [...] Read more.
Stroke is an enormous public health problem with an imperative need for more effective therapies. In therapies for ischemic stroke, tissue plasminogen activators, antiplatelet agents and anticoagulants are used mainly for their antithrombotic effects. However, free radical scavengers, minocycline and growth factors have shown neuroprotective effects in the treatment of stroke, while antihypertensive drugs, lipid-lowering drugs and hypoglycemic drugs have shown beneficial effects for the prevention of stroke. In the present review, we evaluate the treatment and prevention of stroke in light of clinical studies and discuss new anti-stroke effects other than the main effects of drugs, focusing on optimal pharmacotherapy. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessReview Spatial Simulations in Systems Biology: From Molecules to Cells
Int. J. Mol. Sci. 2012, 13(6), 7798-7827; doi:10.3390/ijms13067798
Received: 2 May 2012 / Revised: 8 June 2012 / Accepted: 12 June 2012 / Published: 21 June 2012
Cited by 16 | PDF Full-text (6798 KB) | HTML Full-text | XML Full-text
Abstract
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled [...] Read more.
Cells are highly organized objects containing millions of molecules. Each biomolecule has a specific shape in order to interact with others in the complex machinery. Spatial dynamics emerge in this system on length and time scales which can not yet be modeled with full atomic detail. This review gives an overview of methods which can be used to simulate the complete cell at least with molecular detail, especially Brownian dynamics simulations. Such simulations require correct implementation of the diffusion-controlled reaction scheme occurring on this level. Implementations and applications of spatial simulations are presented, and finally it is discussed how the atomic level can be included for instance in multi-scale simulation methods. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
Open AccessReview Mitogen-Activated Protein (MAP) Kinases in Plant Metal Stress: Regulation and Responses in Comparison to Other Biotic and Abiotic Stresses
Int. J. Mol. Sci. 2012, 13(6), 7828-7853; doi:10.3390/ijms13067828
Received: 31 May 2012 / Revised: 16 June 2012 / Accepted: 18 June 2012 / Published: 21 June 2012
Cited by 32 | PDF Full-text (189 KB) | HTML Full-text | XML Full-text
Abstract
Exposure of plants to toxic concentrations of metals leads to disruption of the cellular redox status followed by an accumulation of reactive oxygen species (ROS). ROS, like hydrogen peroxide, can act as signaling molecules in the cell and induce signaling via mitogen-activated [...] Read more.
Exposure of plants to toxic concentrations of metals leads to disruption of the cellular redox status followed by an accumulation of reactive oxygen species (ROS). ROS, like hydrogen peroxide, can act as signaling molecules in the cell and induce signaling via mitogen-activated protein kinase (MAPK) cascades. MAPK cascades are evolutionary conserved signal transduction modules, able to convert extracellular signals to appropriate cellular responses. In this review, our current understanding about MAPK signaling in plant metal stress is discussed. However, this knowledge is scarce compared to research into the role of MAPK signaling in the case of other abiotic and biotic stresses. ROS production is a common response induced by different stresses and undiscovered analogies may exist with metal stress. Therefore, further attention is given to MAPK signaling in other biotic and abiotic stresses and its interplay with other signaling pathways to create a framework in which the involvement of MAPK signaling in metal stress may be studied. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)

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Open AccessOpinion The Kiss-and-Run Model of Intra-Golgi Transport
Int. J. Mol. Sci. 2012, 13(6), 6800-6819; doi:10.3390/ijms13066800
Received: 9 April 2012 / Revised: 9 May 2012 / Accepted: 22 May 2012 / Published: 5 June 2012
Cited by 10 | PDF Full-text (231 KB) | HTML Full-text | XML Full-text
Abstract
The Golgi apparatus (GA) is the main station along the secretory pathway. Mechanisms of intra-Golgi transport remain unresolved. Three models compete with each other for the right to be defined as the paradigm. The vesicular model cannot explain the following: (1) lipid [...] Read more.
The Golgi apparatus (GA) is the main station along the secretory pathway. Mechanisms of intra-Golgi transport remain unresolved. Three models compete with each other for the right to be defined as the paradigm. The vesicular model cannot explain the following: (1) lipid droplets and aggregates of procollagen that are larger than coatomer I (COPI)-dependent vesicles are transported across the GA; and (2) most anterograde cargoes are depleted in COPI vesicles. The compartment progression/maturation model has the following problems: (1) most Golgi-resident proteins are depleted in COPI vesicles; (2) there are no COPI vesicles for the recycling of the resident proteins in the trans-most-Golgi cisterna; and (3) different proteins have different rates of intra-Golgi transport. The diffusion model based on permanent inter-cisternal connections cannot explain the existence of lipid, ionic and protein gradients across the Golgi stacks. In contrast, the kiss-and-run model has the potential to explain most of the experimental observations. The kiss-and-run model can be symmetric when fusion and then fission occurs in the same place, and asymmetric when fusion takes place in one location, whereas fission takes place in another. The asymmetric kiss-and-run model resembles the carrier maturation mechanism, and it can be used to explain the transport of large cargo aggregates. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessOpinion Inflammation Amplification by Versican: The First Mediator
Int. J. Mol. Sci. 2012, 13(6), 6873-6882; doi:10.3390/ijms13066873
Received: 20 April 2012 / Revised: 3 May 2012 / Accepted: 29 May 2012 / Published: 6 June 2012
Cited by 12 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
The effects of inflammation may not always benefit the individual. Its amplifying nature represents a highly regulated biological program, and the inflammatory microenvironment is its essential component. Growing evidence suggests that the ECM (extracellular matrix) is important for the early steps of [...] Read more.
The effects of inflammation may not always benefit the individual. Its amplifying nature represents a highly regulated biological program, and the inflammatory microenvironment is its essential component. Growing evidence suggests that the ECM (extracellular matrix) is important for the early steps of inflammation. Versican, a ubiquitous component of the ECM, contributes to the formation of the inflammatory response and is highly regulated by cytokines. Certain cytokines exert their initial effects on versican to alter the homeostasis of the inflammatory milieu, and inappropriate production of versican may promote the next inflammatory response. Therefore, versican could be the first step in the amplification of the inflammatory response, and ongoing research of this molecule may help to explain the pathogenesis of inflammation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessShort Note Development of 101 Gene-based Single Nucleotide Polymorphism Markers in Sea Cucumber, Apostichopus japonicus
Int. J. Mol. Sci. 2012, 13(6), 7080-7097; doi:10.3390/ijms13067080
Received: 25 April 2012 / Revised: 25 May 2012 / Accepted: 25 May 2012 / Published: 8 June 2012
Cited by 3 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
Single nucleotide polymorphisms (SNPs) are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM) genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for [...] Read more.
Single nucleotide polymorphisms (SNPs) are currently the marker of choice in a variety of genetic studies. Using the high resolution melting (HRM) genotyping approach, 101 gene-based SNP markers were developed for Apostichopus japonicus, a sea cucumber species with economic significance for the aquaculture industry in East Asian countries. HRM analysis revealed that all the loci showed polymorphisms when evaluated using 40 A. japonicus individuals collected from a natural population. The minor allele frequency ranged from 0.035 to 0.489. The observed and expected heterozygosities ranged from 0.050 to 0.833 and 0.073 to 0.907, respectively. Thirteen loci were found to depart significantly from Hardy–Weinberg equilibrium (HWE) after Bonferroni corrections. Significant linkage disequilibrium (LD) was detected in one pair of markers. These SNP markers are expected to be useful for future quantitative trait loci (QTL) analysis, and to facilitate marker-assisted selection (MAS) in A. japonicus. Full article
Open AccessShort Note Development and Characterization of New Single Nucleotide Polymorphism Markers from Expressed Sequence Tags in Common Carp (Cyprinus carpio)
Int. J. Mol. Sci. 2012, 13(6), 7343-7353; doi:10.3390/ijms13067343
Received: 16 February 2012 / Revised: 17 May 2012 / Accepted: 22 May 2012 / Published: 14 June 2012
Cited by 6 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The common carp (Cyprinus carpio) is an important aquaculture fish worldwide but only limited single nucleotide polymorphism (SNP) markers are characterized from expressed sequence tags (ESTs) in this species. In this study, 1487 putative SNPs were bioinformatically mined from 14,066 [...] Read more.
The common carp (Cyprinus carpio) is an important aquaculture fish worldwide but only limited single nucleotide polymorphism (SNP) markers are characterized from expressed sequence tags (ESTs) in this species. In this study, 1487 putative SNPs were bioinformatically mined from 14,066 online ESTs mainly from the European common carp, with the occurrence rate of about one SNP every 173 bp. One hundred and twenty-one of these SNPs were selected for validation using PCR fragment sequencing, and 48 out of 81 primers could amplify the expected fragments in the Chinese common carp genome. Only 26 (21.5%) putative SNPs were validated, however, 508 new SNPs and 68 indels were identified. The ratios of transitions to transversions were 1.77 for exon SNPs and 1.05 for intron SNPs. All the 23 SNPs selected for population tests were polymorphic, with the observed heterozygosity (Ho) ranging from 0.053 to 0.526 (mean 0.262), polymorphism information content (PIC) from 0.095 to 0.357 (mean 0.246), and 21 SNPs were in Hardy–Weinberg equilibrium. These results suggest that different common carp populations with geographic isolation have significant genetic variation at the SNP level, and these new EST-SNP markers are readily available for genetics and breeding studies in common carp. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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