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Int. J. Mol. Sci., Volume 11, Issue 12 (December 2010), Pages 4782-5347

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Open AccessArticle Anti-Photoaging Effects of Soy Isoflavone Extract (Aglycone and Acetylglucoside Form) from Soybean Cake
Int. J. Mol. Sci. 2010, 11(12), 4782-4795; doi:10.3390/ijms11124782
Received: 22 October 2010 / Revised: 16 November 2010 / Accepted: 17 November 2010 / Published: 24 November 2010
Cited by 18 | PDF Full-text (318 KB) | HTML Full-text | XML Full-text
Abstract
Soy isoflavones, found in soybean and soybean products, have been reported to possess many physiological activities such as antioxidant activity, inhibition of cancer cell proliferation, reduction of cardiovascular risk, prevention of osteoporosis and alleviation of postmenopausal syndrome. In our previous study, soy isoflavone
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Soy isoflavones, found in soybean and soybean products, have been reported to possess many physiological activities such as antioxidant activity, inhibition of cancer cell proliferation, reduction of cardiovascular risk, prevention of osteoporosis and alleviation of postmenopausal syndrome. In our previous study, soy isoflavone extract ISO-1 (containing 12 soy isoflavones) from soybean cake was demonstrated to prevent skin damage caused by UVB exposure. In this study, soy isoflavone extract from soybean cake was further purified and evaluated for the protective effects on UVB-induced damage. The results revealed that Fraction 3, which contains the aglycone group (daidzein, genistein and glycitein) and acetylglucoside group (acetyldaidzin, acetylgenistin and acetylglycitin) of soy isoflavones, could inhibit UVB-induced death of human keratinocytes and reduce the level of desquamation, transepidermal water loss (TEWL), erythema and epidermal thickness in mouse skin. Furthermore, topical application of Fraction 3 increased the activity of catalase and suppressed cyclooxygenase-2 (COX-2) and proliferating cell nuclear antigen (PCNA) expression in mice exposed to UVB. In addition, in comparison with ISO-1 and genistein, the Fraction 3 possessed much greater protective effects on both UVB-induced oxidative stress and keratinocyte death than other fractions. Therefore, the soy isoflavone extract Fraction 3 from soybean cake is a desirable anti-photoaging agent for skin care. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The lin-4 Gene Controls Fat Accumulation and Longevity in Caenorhabditis elegans
Int. J. Mol. Sci. 2010, 11(12), 4814-4825; doi:10.3390/ijms11124814
Received: 10 October 2010 / Revised: 5 November 2010 / Accepted: 18 November 2010 / Published: 25 November 2010
Cited by 9 | PDF Full-text (537 KB) | HTML Full-text | XML Full-text
Abstract
Previous studies have determined that lin-4, which was the first miRNA to be discovered, controls the timing of cell fate determination and life span in Caenorhabditis elegans. However, the mechanism of lin-4 involvement in these processes remains poorly understood. Fat storage
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Previous studies have determined that lin-4, which was the first miRNA to be discovered, controls the timing of cell fate determination and life span in Caenorhabditis elegans. However, the mechanism of lin-4 involvement in these processes remains poorly understood. Fat storage is an essential aspect of the life cycle of organisms, and the function of lin-4 in fat accumulation is not clear. In this study, we showed that the fat content is reduced remarkably in C. elegans lin-4 mutants. Quantitative RT-PCR analysis revealed a considerable decrease in the levels of SBP-1 and OGA-1 mRNA in lin-4 mutants. We also showed that lin-4 mutants have a significantly shorter life span than wild-type worms. DCF assay experiments showed that the reactive oxygen species (ROS) levels increased and mitochondrial DNA (mtDNA) copy number decreased in loss-of-function lin-4 mutants. These mutants also showed attenuation of locomotion. Taken together, our findings suggest that lin-4 may play an important role in regulating fat accumulation and locomotion and that lin-4 may control the life span of C. elegans by mediating ROS production. Full article
Open AccessArticle An Adsorptive Transfer Technique Coupled with Brdicka Reaction to Reveal the Importance of Metallothionein in Chemotherapy with Platinum Based Cytostatics
Int. J. Mol. Sci. 2010, 11(12), 4826-4842; doi:10.3390/ijms11124826
Received: 11 October 2010 / Revised: 10 November 2010 / Accepted: 24 November 2010 / Published: 26 November 2010
Cited by 17 | PDF Full-text (619 KB) | HTML Full-text | XML Full-text
Abstract
The drugs based on platinum metals represent one of the oldest, but also one of the most effective groups of chemotherapeutic agents. Thanks to many clinical studies it is known that resistance of tumor cells to drugs is a frequent cause of chemotherapy
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The drugs based on platinum metals represent one of the oldest, but also one of the most effective groups of chemotherapeutic agents. Thanks to many clinical studies it is known that resistance of tumor cells to drugs is a frequent cause of chemotherapy failure. With regard to platinum based drugs, multidrug resistance can also be connected with increased expression of low-molecular weight protein metallothionein (MT). This study aimed at investigating the interactions of MT with cisplatin or carboplatin, using the adsorptive transfer technique coupled with differential pulse voltammetry Brdicka reaction (AdTS DPV Brdicka reaction), and a comparison of in vitro results with results obtained in vivo. The results obtained from the in vitro study show a strong affinity between platinum based drugs and MT. Further, we analyzed extracts of neuroblastoma cell lines treated with cisplatin or carboplatin. It is clear that neuroblastoma UKF-NB-4 cisplatin-resistant and cisplatin-sensitive cell lines unlikely respond to the presence of the platinum-based cytostatics cisplatin and carboplatin. Finally, we determined the level of MT in samples from rabbits treated with carboplatin and patients with retinoblastoma treated with the same drug. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle 3,4-Methylenedioxymethamphetamine Alters Left Ventricular Function and Activates Nuclear Factor-Kappa B (NF-kB) in a Time and Dose Dependent Manner
Int. J. Mol. Sci. 2010, 11(12), 4843-4863; doi:10.3390/ijms11124743
Received: 13 October 2010 / Revised: 4 November 2010 / Accepted: 8 November 2010 / Published: 26 November 2010
Cited by 3 | PDF Full-text (336 KB) | HTML Full-text | XML Full-text
Abstract
3,4-Methylenedioxymethamphetamine (MDMA) is an illicit psychoactive drug with cardiovascular effects that have not been fully described. In the current study, we observed the effects of acute MDMA on rabbit left ventricular function. We also observed the effects of MDMA on nuclear factor-kappa B
[...] Read more.
3,4-Methylenedioxymethamphetamine (MDMA) is an illicit psychoactive drug with cardiovascular effects that have not been fully described. In the current study, we observed the effects of acute MDMA on rabbit left ventricular function. We also observed the effects of MDMA on nuclear factor-kappa B (NF-kB) activity in cultured rat ventricular myocytes (H9c2). In the rabbit, MDMA (2 mg/kg) alone caused a significant increase in heart rate and a significant decrease in the duration of the cardiac cycle. Inhibition of nitric oxide synthase (NOS) by pretreatment with L-NAME (10 mg/kg) alone caused significant dysfunction in heart rate, systolic pressure, diastolic pressure, duration of relaxation, duration of cardiac cycle, and mean left ventricular pressure. Pretreatment with L-NAME followed by treatment with MDMA caused significant dysfunction in additional parameters that were not abnormal upon exposure to either compound in isolation: duration of contraction, inotropy, and pulse pressure. Exposure to 1.0 mM MDMA for 6 h or 2.0 mM MDMA for 12 h caused increased nuclear localization of NF-kB in cultured H9c2 cells. The current results suggest that MDMA is acutely detrimental to heart function and that an intact cardiovascular NOS system is important to help mitigate early sequelae in some functional parameters. The delayed timing of NF-kB activation suggests that this factor may be relevant to MDMA induced cardiomyopathy of later onset. Full article
(This article belongs to the Special Issue Advances in Molecular Toxicology)
Open AccessArticle Screening and Initial Binding Assessment of Fumonisin B1 Aptamers
Int. J. Mol. Sci. 2010, 11(12), 4864-4881; doi:10.3390/ijms11124864
Received: 1 November 2010 / Revised: 18 November 2010 / Accepted: 18 November 2010 / Published: 26 November 2010
Cited by 55 | PDF Full-text (416 KB) | HTML Full-text | XML Full-text
Abstract
Fumonisins are mycotoxins produced by Fusarium verticillioides and F. proliferatum, fungi that are ubiquitous in corn (maize). Insect damage and some other environmental conditions result in the accumulation of fumonisins in corn-based products worldwide. Current methods of fumonisin detection rely on the
[...] Read more.
Fumonisins are mycotoxins produced by Fusarium verticillioides and F. proliferatum, fungi that are ubiquitous in corn (maize). Insect damage and some other environmental conditions result in the accumulation of fumonisins in corn-based products worldwide. Current methods of fumonisin detection rely on the use of immunoaffinity columns and high-performance liquid chromatography (HPLC). The use of aptamers offers a good alternative to the use of antibodies in fumonisin cleanup and detection due to lower costs and improved stability. Aptamers are single-stranded oligonucleotides that are selected using Systematic Evolution of Ligands by EXponential enrichment (SELEX) for their ability to bind to targets with high affinity and specificity. Sequences obtained after 18 rounds of SELEX were screened for their ability to bind to fumonisin B1. Six unique sequences were obtained, each showing improved binding to fumonisin B1 compared to controls. Sequence FB1 39 binds to fumonisin with a dissociation constant of 100 ± 30 nM and shows potential for use in fumonisin biosensors and solid phase extraction columns. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessArticle In Situ and in Vivo Study of Nasal Absorption of Paeonol in Rats
Int. J. Mol. Sci. 2010, 11(12), 4882-4890; doi:10.3390/ijms11124882
Received: 12 October 2010 / Revised: 10 November 2010 / Accepted: 10 November 2010 / Published: 26 November 2010
Cited by 10 | PDF Full-text (196 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this work was to study the in situ and in vivo nasal absorption of paeonol. A novel single pass in situ nasal perfusion technique was applied to examine the rate and extent of nasal absorption of paeonol by rats. Various
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The objective of this work was to study the in situ and in vivo nasal absorption of paeonol. A novel single pass in situ nasal perfusion technique was applied to examine the rate and extent of nasal absorption of paeonol by rats. Various experimental conditions, such as perfusion rate, pH, osmotic pressure and drug concentration, were investigated. The in situ experiments showed that the nasal absorption of paeonol was not dependent on drug concentration, and fitted a first order process. The absorption rate constant, Ka, increased with an increase in perfusion speed. Paeonol was better absorbed in acidic solutions than in neutral or alkaline solutions. The value of Ka was higher in a hypertonic environment than under isotonic or hypotonic conditions. In vivo studies of paeonol absorption were carried out in rats and the pharmacokinetics parameters of intranasal (i.n.) and intragastric (i.g.) administration were compared with intravenous (i.v.) administration. The bioavailabilities of paeonol were 52.37% and 15.81% for i.n. and i.g, respectively, while Tmax values were 3.05 ± 1.46 min and 6.30 ± 0.70 min. MRT (Mean Residence Time) were 23.19 ± 6.46 min, 41.49 ± 2.96 min and 23.09 ± 5.88 min for i.n., i.g. and i.v. methods, respectively. The results demonstrate that paeonol could be absorbed promptly and thoroughly by i.n. administration in rats. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Knockdown of Snail Sensitizes Pancreatic Cancer Cells to Chemotherapeutic Agents and Irradiation
Int. J. Mol. Sci. 2010, 11(12), 4891-4904; doi:10.3390/ijms11124891
Received: 22 October 2010 / Revised: 7 November 2010 / Accepted: 12 November 2010 / Published: 26 November 2010
Cited by 9 | PDF Full-text (734 KB) | HTML Full-text | XML Full-text
Abstract
The prognosis of patients with pancreatic cancer remains poor; only patients with small tumors and complete resection have a chance of a complete cure. Pancreatic cancer responds poorly to conventional therapies, including chemotherapy and irradiation. Snail is a transcription factor that has been
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The prognosis of patients with pancreatic cancer remains poor; only patients with small tumors and complete resection have a chance of a complete cure. Pancreatic cancer responds poorly to conventional therapies, including chemotherapy and irradiation. Snail is a transcription factor that has been associated with anti-apoptotic and chemoresistant properties in pancreatic cancer cells. In this study, we investigated whether knockdown of Snail suppresses growth of and/or sensitizes pancreatic cancer cells to chemotherapeutic agents and irradiation through induction of apoptosis. An adeno-associated virus vector was used to deliver Snail siRNA and knockdown Snail expression in untreated pancreatic cancer cells and in pancreatic cancer cells treated with chemotherapeutic agents or γ-irradiation. Our data indicate that our adeno-associated virus vector can efficiently deliver Snail siRNA into PANC-1 cells both in vitro and in vivo, resulting in the knockdown of Snail expression at the mRNA and protein levels. We further show that knockdown of Snail expression results in potent growth suppression of pancreatic cancer cells and suppresses xenograft tumor growth in vivo through induction of apoptosis. Finally, knockdown of Snail expression significantly sensitizes pancreatic cancer cells to chemotherapeutic agents and γ-irradiation through induction of apoptosis. In conclusion, our findings indicate that Snail is an important modulator of therapeutic responses of pancreatic cancer cells and is potentially useful as a sensitizer in pancreatic cancer therapy. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Proteomic Profiles of Mesenchymal Stem Cells Induced by a Liver Differentiation Protocol
Int. J. Mol. Sci. 2010, 11(12), 4905-4915; doi:10.3390/ijms11124905
Received: 11 October 2010 / Revised: 31 October 2010 / Accepted: 11 November 2010 / Published: 30 November 2010
Cited by 5 | PDF Full-text (652 KB) | HTML Full-text | XML Full-text
Abstract
The replacement of disease hepatocytes and the stimulation of endogenous or exogenous regeneration by human mesenchymal stem cells (MSCs) are promising candidates for liver-directed cell therapy. In this study, we isolated MSCs from adult bone marrow by plastic adhesion and induced differentiation with
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The replacement of disease hepatocytes and the stimulation of endogenous or exogenous regeneration by human mesenchymal stem cells (MSCs) are promising candidates for liver-directed cell therapy. In this study, we isolated MSCs from adult bone marrow by plastic adhesion and induced differentiation with a liver differentiation protocol. Western blot analyses were used to assess the expression of liver-specific markers. Next, MSC-specific proteins were analyzed with two-dimensional (2D) gel electrophoresis and peptide mass fingerprinting matrix-assisted laser desorption/ionization (MALDI)-time of flight (TOF)-mass spectrometry (MS). To confirm the results from the proteomic study, semi-quantitative reverse transcription-polymerase chain reaction (RT-PCR) analyses were performed. We demonstrated that MSCs treated with the liver differentiation protocol expressed significantly more albumin, CK19 and CK20, than did undifferentiated cells. In addition the results of proteomic study demonstrated increases expression of FEM1B, PSMC2 and disulfide-isomerase A3 in MSCs treated with the liver differentiation protocol. These results from proteomic profiling will not only provide insight into the global responses of MSCs to hepatocyte differentiation, but will also lead to in-depth studies on the mechanisms of proteomic changes in MSCs. Full article
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Open AccessArticle Compound K, a Metabolite of Ginseng Saponin, Induces Mitochondria-Dependent and Caspase-Dependent Apoptosis via the Generation of Reactive Oxygen Species in Human Colon Cancer Cells
Int. J. Mol. Sci. 2010, 11(12), 4916-4931; doi:10.3390/ijms11124916
Received: 30 October 2010 / Revised: 19 November 2010 / Accepted: 19 November 2010 / Published: 1 December 2010
Cited by 21 | PDF Full-text (400 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this study was to elucidate the cytotoxic mechanism of Compound K, with respect to the involvement of reactive oxygen species (ROS) and the mitochondrial involved apoptosis, in HT-29 human colon cancer cells. Compound K exhibited a concentration of 50% growth
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The objective of this study was to elucidate the cytotoxic mechanism of Compound K, with respect to the involvement of reactive oxygen species (ROS) and the mitochondrial involved apoptosis, in HT-29 human colon cancer cells. Compound K exhibited a concentration of 50% growth inhibition (IC50) at 20 μg/mL and cytotoxicity in a time dependent manner. Compound K produced intracellular ROS in a time dependent fashion; however, N-acetylcysteine (NAC) pretreatment resulted in the inhibition of this effect and the recovery of cell viability. Compound K induced a mitochondria-dependent apoptotic pathway via the modulation of Bax and Bcl-2 expressions, resulting in the disruption of the mitochondrial membrane potential (Δψm). Loss of the Δψm was followed by cytochrome c release from the mitochondria, resulting in the activation of caspase-9, -3, and concomitant poly ADP-ribosyl polymerase (PARP) cleavage, which are the indicators of caspase-dependent apoptosis. The apoptotic effect of Compound K, exerted via the activation of c-Jun NH2-terminal kinase (JNK) and p38 mitogen-activated protein kinase (MAPK), was abrogated by specific MAPK inhibitors. This study demonstrated that Compound K-mediated generation of ROS led to apoptosis through the modulation of a mitochondria-dependent apoptotic pathway and MAPK pathway. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Computer-Based De Novo Designs of Tripeptides as Novel Neuraminidase Inhibitors
Int. J. Mol. Sci. 2010, 11(12), 4932-4951; doi:10.3390/ijms11124932
Received: 20 October 2010 / Revised: 12 November 2010 / Accepted: 18 November 2010 / Published: 1 December 2010
Cited by 9 | PDF Full-text (966 KB) | HTML Full-text | XML Full-text
Abstract
The latest influenza A (H1N1) pandemic attracted worldwide attention and called for the urgent development of novel antiviral drugs. Here, seven tripeptides are designed and explored as neuraminidase (NA) inhibitors on the structural basis of known inhibitors. Their interactions with NA are studied
[...] Read more.
The latest influenza A (H1N1) pandemic attracted worldwide attention and called for the urgent development of novel antiviral drugs. Here, seven tripeptides are designed and explored as neuraminidase (NA) inhibitors on the structural basis of known inhibitors. Their interactions with NA are studied and compared with each other, using flexible docking and molecular dynamics simulations. The various composed tripeptides have respective binding specificities and their interaction energies with NA decrease in the order of FRI > FRV > FRT > FHV > FRS > FRG > YRV (letters corresponding to amino acid code). The Arg and Phe portions of the tripeptides play important roles during the binding process: Arg has strong electrostatic interactions with the key residues Asp151, Glu119, Glu227 and Glu277, whereas Phe fits well in the hydrophobic cave within the NA active site. Owing to the introduction of hydrophobic property, the interaction energies of FRV and FRI are larger; in particular, FRI demonstrates the best binding quality and shows potential as a lead compound. In addition, the influence of the chemical states of the terminal amino acids are clarified: it is revealed that the charged states of the N-terminus (NH3+) and C-terminus (COO) are crucial for the tripeptide inhibitory activities and longer peptides may not be appropriate. In addition, the medium inhibiting activity by acetylation of the N-terminus indicates the possible chemical modifications of FRI. Experimental efforts are expected in order to actualize the tripeptides as potent NA inhibitors in the near future. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Optimization of Enzymatic Production of Oligopeptides from Apricot Almonds Meal with Neutrase and N120P
Int. J. Mol. Sci. 2010, 11(12), 4952-4961; doi:10.3390/ijms11124952
Received: 9 October 2010 / Revised: 28 October 2010 / Accepted: 10 November 2010 / Published: 2 December 2010
Cited by 3 | PDF Full-text (1368 KB) | HTML Full-text | XML Full-text
Abstract
Neutrase 0.8L and N120P proteases were used for oligopeptide production from apricot almonds meal, and response surface design was carried out to optimize the effect of hydrolysis conditions on hydrolysis degree (DH) and oligopeptide yield rate. Four independent variables were used to optimize
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Neutrase 0.8L and N120P proteases were used for oligopeptide production from apricot almonds meal, and response surface design was carried out to optimize the effect of hydrolysis conditions on hydrolysis degree (DH) and oligopeptide yield rate. Four independent variables were used to optimize the hydrolysis process: hydrolysis temperature (X1), enzyme-to substrate ratio (E/S) (X2), substrate concentration (X3) and reaction time (X4). Statistical analysis indicated that the four variables, quadratic terms of X1, X3, and X4, and the interaction terms with X1 had a significant (p Full article
Open AccessArticle Optimization of Bacterial Plasmid Transformation Using Nanomaterials Based on the Yoshida Effect
Int. J. Mol. Sci. 2010, 11(12), 4962-4972; doi:10.3390/ijms11124962
Received: 21 October 2010 / Revised: 15 November 2010 / Accepted: 1 December 2010 / Published: 3 December 2010
Cited by 8 | PDF Full-text (240 KB) | HTML Full-text | XML Full-text
Abstract
With the help of sepiolite, a unique method for transforming DNA into bacteria, based on the Yoshida effect, has been developed recently. However, we confronted many problems when this newest method was tried. Only a few transformants could be obtained even when 100
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With the help of sepiolite, a unique method for transforming DNA into bacteria, based on the Yoshida effect, has been developed recently. However, we confronted many problems when this newest method was tried. Only a few transformants could be obtained even when 100 ng of plasmid pET15b was used, and a successful result seemed difficult to repeat. To address this problem, we optimized the operating method and could achieve about 15,000 transformants using the same amount of plasmid, which could match the efficiency gained using the calcium chloride transformation method. Meanwhile, the results could also be reproduced well. In the same way, carbon nanotubes were used to attain more than 15,000 transformants in the same situation. Therefore, the transformation method could be extended to other nanomaterials. Meanwhile, compared with the mechanism previously reported, we verified quite a different principle for the mechanism responsible for such a transformation. In sum, this unique transformation can be developed to become the third widely-used transformation method in laboratories in addition to the chemical method and electroporation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Profile and Functional Properties of Seed Proteins from Six Pea (Pisum sativum) Genotypes
Int. J. Mol. Sci. 2010, 11(12), 4973-4990; doi:10.3390/ijms11124973
Received: 5 October 2010 / Revised: 21 October 2010 / Accepted: 16 November 2010 / Published: 3 December 2010
Cited by 27 | PDF Full-text (442 KB) | HTML Full-text | XML Full-text
Abstract
Extractability, extractable protein compositions, technological-functional properties of pea (Pisum sativum) proteins from six genotypes grown in Serbia were investigated. Also, the relationship between these characteristics was presented. Investigated genotypes showed significant differences in storage protein content, composition and extractability. The ratio
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Extractability, extractable protein compositions, technological-functional properties of pea (Pisum sativum) proteins from six genotypes grown in Serbia were investigated. Also, the relationship between these characteristics was presented. Investigated genotypes showed significant differences in storage protein content, composition and extractability. The ratio of vicilin:legumin concentrations, as well as the ratio of vicilin + convicilin: Legumin concentrations were positively correlated with extractability. Our data suggest that the higher level of vicilin and/or a lower level of legumin have a positive influence on protein extractability. The emulsion activity index (EAI) was strongly and positively correlated with the solubility, while no significant correlation was found between emulsion stability (ESI) and solubility, nor between foaming properties and solubility. No association was evident between ESI and EAI. A moderate positive correlation between emulsion stability and foam capacity was observed. Proteins from the investigated genotypes expressed significantly different emulsifying properties and foam capacity at different pH values, whereas low foam stability was detected. It appears that genotype has considerable influence on content, composition and technological-functional properties of pea bean proteins. This fact can be very useful for food scientists in efforts to improve the quality of peas and pea protein products. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Computational Prediction of O-linked Glycosylation Sites that Preferentially Map on Intrinsically Disordered Regions of Extracellular Proteins
Int. J. Mol. Sci. 2010, 11(12), 4991-5008; doi:10.3390/ijms11124991
Received: 28 October 2010 / Revised: 17 November 2010 / Accepted: 30 November 2010 / Published: 3 December 2010
Cited by 24 | PDF Full-text (458 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along
[...] Read more.
O-glycosylation of mammalian proteins is one of the important posttranslational modifications. We applied a support vector machine (SVM) to predict whether Ser or Thr is glycosylated, in order to elucidate the O-glycosylation mechanism. O-glycosylated sites were often found clustered along the sequence, whereas other sites were located sporadically. Therefore, we developed two types of SVMs for predicting clustered and isolated sites separately. We found that the amino acid composition was effective for predicting the clustered type, whereas the site-specific algorithm was effective for the isolated type. The highest prediction accuracy for the clustered type was 74%, while that for the isolated type was 79%. The existence frequency of amino acids around the O-glycosylation sites was different in the two types: namely, Pro, Val and Ala had high existence probabilities at each specific position relative to a glycosylation site, especially for the isolated type. Independent component analyses for the amino acid sequences around O-glycosylation sites showed the position-specific existences of the identified amino acids as independent components. The O-glycosylation sites were preferentially located within intrinsically disordered regions of extracellular proteins: particularly, more than 90% of the clustered O-GalNAc glycosylation sites were observed in intrinsically disordered regions. This feature could be the key for understanding the non-conservation property of O-glycosylation, and its role in functional diversity and structural stability. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessArticle Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches
Int. J. Mol. Sci. 2010, 11(12), 5009-5026; doi:10.3390/ijms11125009
Received: 2 November 2010 / Revised: 2 December 2010 / Accepted: 3 December 2010 / Published: 6 December 2010
Cited by 20 | PDF Full-text (779 KB) | HTML Full-text | XML Full-text
Abstract
Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding
[...] Read more.
Functional elucidation of uncharacterized protein structures is an important task in bioinformatics. We report our new approach for structure-based function prediction which captures local surface features of ligand binding pockets. Function of proteins, specifically, binding ligands of proteins, can be predicted by finding similar local surface regions of known proteins. To enable partial comparison of binding sites in proteins, a weighted bipartite matching algorithm is used to match pairs of surface patches. The surface patches are encoded with the 3D Zernike descriptors. Unlike the existing methods which compare global characteristics of the protein fold or the global pocket shape, the local surface patch method can find functional similarity between non-homologous proteins and binding pockets for flexible ligand molecules. The proposed method improves prediction results over global pocket shape-based method which was previously developed by our group. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
Open AccessArticle Poly[(3-hexylthiophene)-block-(3-semifluoroalkylthiophene)] for Polymer Solar Cells
Int. J. Mol. Sci. 2010, 11(12), 5027-5039; doi:10.3390/ijms11125027
Received: 13 September 2010 / Revised: 22 November 2010 / Accepted: 2 December 2010 / Published: 6 December 2010
Cited by 10 | PDF Full-text (406 KB) | HTML Full-text | XML Full-text
Abstract
We report the synthesis of poly[(3-hexylthiophene)-block-(3-(4,4,5,5,6,6,7,7,7-nonafluoroheptyl)thiophene)], P(3HT-b-3SFT), carried out by the Grignard Metathesis Method (GRIM). The copolymers composition was determined by 1H and 19F NMR spectroscopies, and gel permeation chromatography (GPC). The thin films of P(3HT‑b
[...] Read more.
We report the synthesis of poly[(3-hexylthiophene)-block-(3-(4,4,5,5,6,6,7,7,7-nonafluoroheptyl)thiophene)], P(3HT-b-3SFT), carried out by the Grignard Metathesis Method (GRIM). The copolymers composition was determined by 1H and 19F NMR spectroscopies, and gel permeation chromatography (GPC). The thin films of P(3HT‑b‑3SFT) were investigated by ultraviolet-visible absorption spectroscopy and atomic force microscopy (AFM). We also fabricated bulk-hetero junction (BHJ) solar cells based on blends of P(3HT-b-3SFT) and [6,6]-phenyl-C61-butyric acid methyl ester (PCBM). Although the composition ratio of P3SFT in P(3HT-b-3SFT) was low, the influence of P3SFT on the morphology and properties of solar cells was significant. The annealing process for the BHJ solar cells induced the formation of large domains and led to poor solar cell performance. The BHJ solar cells, based on PCBM and P(3HT-b-3SFT), prepared by the non-annealing process, had a maximum power conversion efficiency of 0.84% under 100 mW/cm2 (AM 1.5 solar illumination) in air. Full article
(This article belongs to the Special Issue Solar Cells)
Open AccessArticle Exploring Kinetics of Phenol Biodegradation by Cupriavidus taiwanesis 187
Int. J. Mol. Sci. 2010, 11(12), 5065-5076; doi:10.3390/ijms11125065
Received: 18 November 2010 / Revised: 30 November 2010 / Accepted: 3 December 2010 / Published: 7 December 2010
PDF Full-text (250 KB) | HTML Full-text | XML Full-text
Abstract
Phenol biodegradation in batch systems using Cupriavidus taiwanesis 187 has been experimentally studied. To determine the various parameters of a kinetic model, combinations of rearranged equations have been evaluated using inverse polynomial techniques for parameter estimation. The correlations between lag phase and phase
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Phenol biodegradation in batch systems using Cupriavidus taiwanesis 187 has been experimentally studied. To determine the various parameters of a kinetic model, combinations of rearranged equations have been evaluated using inverse polynomial techniques for parameter estimation. The correlations between lag phase and phase concentration suggest that considering phenol inhibition in kinetic analysis is helpful for characterizing phenol degradation. This study proposes a novel method to determine multiplicity of steady states in continuous stirred tank reactors (CSTRs) in order to identify the most appropriate kinetics to characterize the dynamics of phenol biodegradation. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Rhamnolipid Biosurfactants as New Players in Animal and Plant Defense against Microbes
Int. J. Mol. Sci. 2010, 11(12), 5095-5108; doi:10.3390/ijms11125095
Received: 1 November 2010 / Revised: 15 November 2010 / Accepted: 1 December 2010 / Published: 9 December 2010
Cited by 42 | PDF Full-text (211 KB) | HTML Full-text | XML Full-text
Abstract
Rhamnolipids are known as very efficient biosurfactant molecules. They are used in a wide range of industrial applications including food, cosmetics, pharmaceutical formulations and bioremediation of pollutants. The present review provides an overview of the effect of rhamnolipids in animal and plant defense
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Rhamnolipids are known as very efficient biosurfactant molecules. They are used in a wide range of industrial applications including food, cosmetics, pharmaceutical formulations and bioremediation of pollutants. The present review provides an overview of the effect of rhamnolipids in animal and plant defense responses. We describe the current knowledge on the stimulation of plant and animal immunity by these molecules, as well as on their direct antimicrobial properties. Given their ecological acceptance owing to their low toxicity and biodegradability, rhamnolipids have the potential to be useful molecules in medicine and to be part of alternative strategies in order to reduce or replace pesticides in agriculture. Full article
(This article belongs to the Special Issue Biosurfactants)
Open AccessArticle Astaxanthin Improves Stem Cell Potency via an Increase in the Proliferation of Neural Progenitor Cells
Int. J. Mol. Sci. 2010, 11(12), 5109-5119; doi:10.3390/ijms11125109
Received: 20 October 2010 / Revised: 15 November 2010 / Accepted: 7 December 2010 / Published: 9 December 2010
Cited by 4 | PDF Full-text (404 KB) | HTML Full-text | XML Full-text
Abstract
The present study was designed to investigate the question of whether or not astaxanthin improves stem cell potency via an increase in proliferation of neural progenitor cells (NPCs). Treatment with astaxanthin significantly increased proliferation and colony formation of NPCs. For identification of possible
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The present study was designed to investigate the question of whether or not astaxanthin improves stem cell potency via an increase in proliferation of neural progenitor cells (NPCs). Treatment with astaxanthin significantly increased proliferation and colony formation of NPCs. For identification of possible activated signaling molecules involved in active cell proliferation occurring after astaxanthin treatment, total protein levels of several proliferation-related proteins, and expression levels of proliferation-related transcription factors, were assessed in NPCs. In Western blot analysis, astaxanthin induced significant activation of phosphatidylinositol 3-kinase (PI3K) and its downstream mediators in a time‑dependent manner. Results of RT-PCR analysis showed upregulation of proliferation‑related transcription factors and stemness genes. To estimate the relevance of PI3K and mitogen-activated protein, or extracellular signal-regulated kinase kinase (MEK) signaling pathways in cell growth of astaxanthin‑treated NPCs, inhibition assays were performed with LY294002, a specific inhibitor of PI3K, and PD98059, a specific inhibitor of MEK, respectively. These results clearly showed that astaxanthin induces proliferation of NPCs via activation of the PI3K and MEK signaling pathways and improves stem cell potency via stemness acting signals. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Clinicopathological Significance of Loss of ARID1A Immunoreactivity in Ovarian Clear Cell Carcinoma
Int. J. Mol. Sci. 2010, 11(12), 5120-5128; doi:10.3390/ijms11125120
Received: 1 December 2010 / Revised: 8 December 2010 / Accepted: 8 December 2010 / Published: 13 December 2010
Cited by 54 | PDF Full-text (237 KB) | HTML Full-text | XML Full-text
Abstract
Recent genome-wide analysis has demonstrated that somatic mutations in ARID1A (BAF250) are the most common molecular genetic changes in ovarian clear cell carcinoma (OCCC). ARID1A mutations, which occur in approximately half of OCCC cases, lead to deletion of the encoded protein
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Recent genome-wide analysis has demonstrated that somatic mutations in ARID1A (BAF250) are the most common molecular genetic changes in ovarian clear cell carcinoma (OCCC). ARID1A mutations, which occur in approximately half of OCCC cases, lead to deletion of the encoded protein and inactivation of the putative tumor suppressor. In this study, we determined the significance of loss of ARID1A immunoreactivity with respect to several clinicopathological features in a total of 149 OCCCs. First, we demonstrated that ARID1A immunohistochemistry showed concordance with the mutational status in 91% of cases with 100% sensitivity and 66% specificity. Specifically, among 12 OCCC cases for which ARIDA mutational status was known, ARIDIA immunoreactivity was undetectable in all 9 cases harboring ARID1A mutations and was undetectable in one of 3 cases with wild-type ARID1A. With respect to the entire cohort, ARID1A immunoreactivity was undetectable in 88 (59%) of 149 OCCCs. There was no significant difference between ARID1A negative and positive cases in terms of histopathologic features, age, clinical stage, or overall survival. In conclusion, this study provides further evidence that mutations in ARID1A resulted in loss of ARID1A protein expression in OCCC, although no significant differences between ARID1A positive and negative cases were observed with respect to any clinicopathological features examined. Full article
(This article belongs to the Special Issue Cancer Molecules in Ovarian Cancer)
Open AccessArticle Molecular Interactions and Protein-Induced DNA Hairpin in the Transcriptional Control of Bacteriophage Ø29 DNA
Int. J. Mol. Sci. 2010, 11(12), 5129-5142; doi:10.3390/ijms11125129
Received: 8 October 2010 / Revised: 22 November 2010 / Accepted: 7 December 2010 / Published: 13 December 2010
PDF Full-text (507 KB) | HTML Full-text | XML Full-text
Abstract
Studies on the regulation of phage Ø29 gene expression revealed a new mechanism to accomplish simultaneous activation and repression of transcription leading to orderly gene expression. Two phage-encoded early proteins, p4 and p6, bind synergistically to DNA, modifying the topology of the sequences
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Studies on the regulation of phage Ø29 gene expression revealed a new mechanism to accomplish simultaneous activation and repression of transcription leading to orderly gene expression. Two phage-encoded early proteins, p4 and p6, bind synergistically to DNA, modifying the topology of the sequences encompassing early promoters A2c and A2b and late promoter A3 in a hairpin that allows the switch from early to late transcription. Protein p6 is a nucleoid-like protein that binds DNA in a non-sequence specific manner. Protein p4 is a sequence-specific DNA binding protein with multifaceted sequence-readout properties. The protein recognizes the chemical signature of only one DNA base on the inverted repeat of its target sequence through a direct-readout mechanism. In addition, p4 specific binding depends on the recognition of three A-tracts by indirect-readout mechanisms. The biological importance of those three A-tracts resides in their individual properties rather than in the global curvature that they may induce. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessArticle Constitutive Expression of Thermobifida fusca Thermostable Acetylxylan Esterase Gene in Pichia pastoris
Int. J. Mol. Sci. 2010, 11(12), 5143-5151; doi:10.3390/ijms11125143
Received: 17 November 2010 / Revised: 1 December 2010 / Accepted: 9 December 2010 / Published: 15 December 2010
Cited by 6 | PDF Full-text (112 KB) | HTML Full-text | XML Full-text
Abstract
A gene encoding the thermostable acetylxylan esterase (AXE) in Thermobifida fusca NTU22 was amplified by PCR, sequenced and cloned into the Pichia pastoris X-33 host strain using the vector pGAPZαA, allowing constitutive expression and secretion of the protein. Recombinant expression resulted in high
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A gene encoding the thermostable acetylxylan esterase (AXE) in Thermobifida fusca NTU22 was amplified by PCR, sequenced and cloned into the Pichia pastoris X-33 host strain using the vector pGAPZαA, allowing constitutive expression and secretion of the protein. Recombinant expression resulted in high levels of extracellular AXE production, as high as 526 U/mL in the Hinton flask culture broth. The purified enzyme showed a single band at about 28 kDa by SDS-polyacrylamide gel electrophoresis after being treated with endo-β-N-acetylglycosaminidase H; this agrees with the predicted size based on the nucleotide sequence. About 70% of the original activity remained after heat treatment at 60 °C for three hours. The optimal pH and temperature of the purified enzyme were 8.0 and 60 °C, respectively. The properties of the purified AXE from the Ppastoris transformant are similar to those of the AXE from an E. coli transformant. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Anti-Tumor Activity of a Novel Protein Obtained from Tartary Buckwheat
Int. J. Mol. Sci. 2010, 11(12), 5201-5211; doi:10.3390/ijms11125201
Received: 12 November 2010 / Revised: 18 November 2010 / Accepted: 14 December 2010 / Published: 17 December 2010
Cited by 23 | PDF Full-text (311 KB) | HTML Full-text | XML Full-text
Abstract
TBWSP31 is a novel antitumor protein that was isolated from tartary buckwheat water-soluble extracts. The objective of this paper was to investigate the anti-proliferative effects of TBWSP31 on breast cancer Bcap37cells and to explore its possible mechanism. After treatment of Bcap37 cells with
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TBWSP31 is a novel antitumor protein that was isolated from tartary buckwheat water-soluble extracts. The objective of this paper was to investigate the anti-proliferative effects of TBWSP31 on breast cancer Bcap37cells and to explore its possible mechanism. After treatment of Bcap37 cells with TBWSP31, typical apoptotic morphological changes were observed by inverted microscopy and scanning electron microscopy (SEM), such as detachment from the culture plate, change to a round shape, cell shrinkage, the absence of obvious microvilli, plasma membrane blebbing, and formation of apoptotic bodies. Cell-cycle analysis revealed that treatment with TBWSP31 resulted in a G0/G1 arrest and prevented the cells from growing from G0/G1 phase to S phase, which was most prominent at 48 h. The expression of bcl-2 and Fas were detected quantitatively by FCM, which showed that TBWSP31 induced-apoptosis may be involved with the participation of Fas and bcl-2. These results suggest that TBWSP31 is a potential antitumor compound and that apoptosis induced by TBWSP31 is a key antitumor mechanism. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Differential Expression of Copper-Zinc Superoxide Dismutase Gene of Polygonum sibiricum Leaves, Stems and Underground Stems, Subjected to High-Salt Stress
Int. J. Mol. Sci. 2010, 11(12), 5234-5245; doi:10.3390/ijms11125234
Received: 30 September 2010 / Revised: 20 November 2010 / Accepted: 29 November 2010 / Published: 17 December 2010
Cited by 13 | PDF Full-text (388 KB) | HTML Full-text | XML Full-text
Abstract
In aerobic organisms, protection against oxidative damage involves the combined action of highly specialized antioxidant enzymes, such as copper-zinc superoxide dismutase. In this work, a cDNA clone which encodes a copper-zinc superoxide dismutase gene, named PS-CuZnSOD, has been identified from P.
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In aerobic organisms, protection against oxidative damage involves the combined action of highly specialized antioxidant enzymes, such as copper-zinc superoxide dismutase. In this work, a cDNA clone which encodes a copper-zinc superoxide dismutase gene, named PS-CuZnSOD, has been identified from P. sibiricum Laxm. by the rapid amplification of cDNA ends method (RACE). Analysis of the nucleotide sequence reveals that the PS-CuZnSOD gene cDNA clone consists of 669 bp, containing 87 bp in the 5' untranslated region; 459 bp in the open reading frame (ORF) encoding 152 amino acids; and 123 bp in 3' untranslated region. The gene accession nucleotide sequence number in GenBank is GQ472846. Sequence analysis indicates that the protein, like most plant superoxide dismutases (SOD), includes two conserved ecCuZnSOD signatures that are from the amino acids 43 to 51, and from the amino acids 137 to 148, and it has a signal peptide extension in the front of the N-terminus (1–16 aa). Expression analysis by real-time quantitative PCR reveals that the PS-CuZnSOD gene is expressed in leaves, stems and underground stems. PS-CuZnSOD gene expression can be induced by 3% NaHCO3. The different mRNA levels’ expression of PS-CuZnSOD show the gene’s different expression modes in leaves, stems and underground stems under the salinity-alkalinity stress. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Fe-Chlorophyllin Promotes the Growth of Wheat Roots Associated with Nitric Oxide Generation
Int. J. Mol. Sci. 2010, 11(12), 5246-5255; doi:10.3390/ijms11125246
Received: 1 November 2010 / Revised: 7 December 2010 / Accepted: 14 December 2010 / Published: 17 December 2010
Cited by 3 | PDF Full-text (499 KB) | HTML Full-text | XML Full-text
Abstract
: Effects of Fe-chlorophyllin on the growth of wheat root were investigated in this study. We found that Fe-chlorophyllin can promote root growth. The production of nitric oxide in wheat root was detected using DAF-2DA fluorescent emission. The intensity of fluorescent in the
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: Effects of Fe-chlorophyllin on the growth of wheat root were investigated in this study. We found that Fe-chlorophyllin can promote root growth. The production of nitric oxide in wheat root was detected using DAF-2DA fluorescent emission. The intensity of fluorescent in the presence of 0.1 mg/L Fe-chlorophyllin was near to that observed with the positive control of sodium nitroprusside (SNP), the nitric oxide donor. IAA oxidase activity decreased with all treatments of Fe-chlorophyllin from 0.01 to 10 mg/L. At the relatively lower Fe-chlorophyllin concentration of 0.1 mg/L, the activity of IAA oxidase displayed a remarkable decrease, being 40.1% lower than the control. Meanwhile, Fe-chlorophyllin treatment could increase the activities of reactive oxygen scavenging enzymes, such as superoxide dismutase (SOD) and peroxidase (POD), as determined using non-denaturing polyacrylamide gel electrophoresis. These results indicate that Fe-chlorophyllin contributes to the growth of wheat root associated with nitric oxide generation. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle In Vitro Response of Retinal Pigment Epithelial Cells Exposed to Chitosan Materials Prepared with Different Cross-Linkers
Int. J. Mol. Sci. 2010, 11(12), 5256-5272; doi:10.3390/ijms11125256
Received: 18 November 2010 / Revised: 13 December 2010 / Accepted: 20 December 2010 / Published: 20 December 2010
Cited by 33 | PDF Full-text (502 KB) | HTML Full-text | XML Full-text
Abstract
The interaction between cells and biopolymers is the evaluation indicator of the biocompatibility of materials. The purpose of this work was to examine the responses of retinal pigment epithelial (RPE) cells to genipin (GP) or glutaraldehyde (GTA) cross-linked chitosan by means of cell
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The interaction between cells and biopolymers is the evaluation indicator of the biocompatibility of materials. The purpose of this work was to examine the responses of retinal pigment epithelial (RPE) cells to genipin (GP) or glutaraldehyde (GTA) cross-linked chitosan by means of cell viability assays, cytokine expression analyses, and apoptosis assays. Evaluations of non-cross-linked chitosan were conducted simultaneously for comparison. Both GP and GTA treated samples with the same extent of cross-linking (around 80%) were prepared by varying cross-linking time. Our results showed that GP cross-linking was carried out by either radical polymerization of the monomers or SN2 nucleophilic substitution reaction involving the replacement of the ester group on the monomer with a secondary amide linkage. On the other hand, GTA could react with free amino groups of chitosan, leading to the formation of either the Schiff bases or the Michael-type adducts with terminal aldehydes. The biocompatibility of non-cross-linked chitosan membranes was demonstrated by the absence of any signs of toxicity or inflammation reaction. The present study showed that the ARPE-19 cells exposed to GTA cross-linked chitosan membranes had significantly higher cytotoxicity, interleukin-6 levels, and number of TUNEL-positive nuclei than did those exposed to GP treated samples. In addition, the materials modified with GTA trigger apoptosis at an early stage and may induce toxicity in the RPE cells later. The findings suggest that while the chitosan molecules bridged by GP are satisfactorily cytocompatible, the counterparts treated by GTA do not seem to be tolerated. In terms of material safety, the GP cross-linked chitosan may be compatible with human RPE cells and may have a potential application as delivery carriers in the treatment of posterior segment diseases. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Screening of Molecular Virulence Markers in Staphylococcus aureus and Pseudomonas aeruginosa Strains Isolated from Clinical Infections
Int. J. Mol. Sci. 2010, 11(12), 5273-5291; doi:10.3390/ijms11125273
Received: 12 November 2010 / Revised: 2 December 2010 / Accepted: 3 December 2010 / Published: 21 December 2010
Cited by 11 | PDF Full-text (538 KB) | HTML Full-text | XML Full-text
Abstract
Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new
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Staphylococcus (S.) aureus and Pseudomonas (Ps.) aeruginosa are two of the most frequently opportunistic pathogens isolated in nosocomial infections, responsible for severe infections in immunocompromised hosts. The frequent emergence of antibiotic-resistant S. aureus and Ps. aeruginosa strains has determined the development of new strategies in order to elucidate the different mechanisms used by these bacteria at different stages of the infectious process, providing the scientists with new procedures for preventing, or at least improving, the control of S. aureus and Ps. aeruginosa infections. The purpose of this study was to characterize the molecular markers of virulence in S. aureus and Ps. aeruginosa strains isolated from different clinical specimens. We used multiplex and uniplex PCR assays to detect the genes encoding different cell-wall associated and extracellular virulence factors, in order to evaluate potential associations between the presence of putative virulence genes and the outcome of infections caused by these bacteria. Our results demonstrate that all the studied S. aureus and Ps. aeruginosa strains synthesize the majority of the investigated virulence determinants, probably responsible for different types of infections. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Chronic Mild Stress Induces Fluoxetine-Reversible Decreases in Hippocampal and Cerebrospinal Fluid Levels of the Neurotrophic Factor S100B and Its Specific Receptor
Int. J. Mol. Sci. 2010, 11(12), 5310-5322; doi:10.3390/ijms11125310
Received: 8 November 2010 / Revised: 3 December 2010 / Accepted: 18 December 2010 / Published: 21 December 2010
Cited by 15 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
Chronic mild stress (CMS) affects the hippocampal structure and function in the rat. S100B, a calcium-binding protein secreted by astrocytes, has been shown to be increased in serum of patients with depression and associated with good therapeutic response and clinical outcome. This work
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Chronic mild stress (CMS) affects the hippocampal structure and function in the rat. S100B, a calcium-binding protein secreted by astrocytes, has been shown to be increased in serum of patients with depression and associated with good therapeutic response and clinical outcome. This work aimed to study the impact of CMS and fluoxetine on depressive-like behaviors in rats, as well as the concomitant expression of the astroglial protein S100B and of its receptor RAGE (receptor for advanced glycation end products) in the hippocampus and Cerebrospinal fluid of the same group of animals. S100B and sRAGE (circulating soluble form of RAGE) were measured in CSF by ELISA, and S100B and RAGE were measured in hippocampal slices by Western blot. Our study has demonstrated that stress and depression decrease S100B and RAGE/SRAGE expression and antidepressant treatment reverses or blocks these effects. This result suggested that S100B/RAGE interactions may be involved in the development and maintenance of depression and may play an important role in the mechanism of antidepressants’ therapeutic action. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Antiproliferative Effects of Cucurbitacin B in Breast Cancer Cells: Down-Regulation of the c-Myc/hTERT/Telomerase Pathway and Obstruction of the Cell Cycle
Int. J. Mol. Sci. 2010, 11(12), 5323-5338; doi:10.3390/ijms11125323
Received: 19 November 2010 / Revised: 20 December 2010 / Accepted: 21 December 2010 / Published: 22 December 2010
Cited by 25 | PDF Full-text (648 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Naturally occurring cucurbitacins have been shown to have anticancer, antimicrobial and anti-inflammatory activities. In this study, we determined the effects of cucurbitacin B extracted from the Thai herb Trichosanthes cucumerina L. on telomerase regulation in three human breast cancer cell lines (T47D, SKBR-3,
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Naturally occurring cucurbitacins have been shown to have anticancer, antimicrobial and anti-inflammatory activities. In this study, we determined the effects of cucurbitacin B extracted from the Thai herb Trichosanthes cucumerina L. on telomerase regulation in three human breast cancer cell lines (T47D, SKBR-3, and MCF-7) and a mammary epithelium cell line (HBL-100). Cell viability after treatment with cucurbitacin B, which is an active ingredient of this herb, was assessed. Telomeric Repeat Amplification Protocol (TRAP) assays and RT-PCR (qualitative and realtime) were performed to investigate activity of telomerase as well as expression of human telomerase reverse transcriptase (hTERT) and c-Myc. The c-Myc protein level was also determined in SKBR-3 and HBL-100 cells. Our results show that the cucurbitacin B inhibits growth and telomerase activity in the three breast cancer cell lines and exerts an obvious inhibitory effect in the estrogen receptor (ER)-negative breast cancer SKBR-3 cells. The expression of hTERT and c-Myc were also inhibited by cucurbitacin B, In addition, a clear reduction of c-Myc protein was observed after treatment in SKBR-3 cells even with a concentration of cucurbitacin B that was ten-times lower compared to the concentration used for HBL-100. Our findings imply that cucurbitacin B exerts an anticancer effect by inhibiting telomerase via down regulating both the hTERT and c-Myc expression in breast cancer cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Mouse Plasminogen Has Oxidized Phosphatidylcholine Adducts That Are Not Metabolized by Lipoprotein-Associated Phospholipase A2 under Basal Conditions
Int. J. Mol. Sci. 2010, 11(12), 5339-5347; doi:10.3390/ijms11125339
Received: 12 November 2010 / Revised: 15 December 2010 / Accepted: 17 December 2010 / Published: 22 December 2010
Cited by 1 | PDF Full-text (263 KB) | HTML Full-text | XML Full-text
Abstract
We previously showed that plasminogen (Plg) isolated from the plasma of normal human subjects contains 1–2 moles of oxidized phosphatidylcholine (oxPtdPC) adducts/mole of protein. Moreover, we suggested that these species are generated at the hepatic site and speculated that they may play a
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We previously showed that plasminogen (Plg) isolated from the plasma of normal human subjects contains 1–2 moles of oxidized phosphatidylcholine (oxPtdPC) adducts/mole of protein. Moreover, we suggested that these species are generated at the hepatic site and speculated that they may play a role in the reported cardiovascular pathogenicity of Plg. We aimed to determine whether mouse Plg also harbors linked oxPtdPCs and whether these molecules are metabolized by lipoprotein-associated phospholipase A2/PAF acetylhydrolase (Lp-PLA2/PAF-AH), an enzyme specific for hydrolysis of oxPtdPCs. We determined the total concentration of Plg in plasma samples from control (WT) and Lp-PLA2-deficient (KO) mice, we isolated Plg, and assessed its content of oxPtdPCs by immunoblot analyses. We also evaluated whether human recombinant Lp-PLA2 metabolized Plg-linked oxPtdPCs in vivo and in vitro. WT and KO mice expressed comparable levels (14.4–15.8 mg/dL) of plasma Plg, as determined by ELISA. We observed no differences in the content of oxPtdPC in Plg isolated from the two mouse strains and in parallel no changes in oxPtdPC content in mouse Plg following incubation with pure recombinant Lp-PLA2. Plg from mouse plasma contains oxPtdPC adducts that are not affected by the action of Lp-PLA2, suggesting that linkage to Plg protects oxPtdPCs from metabolism during their transport in the plasma. This modification may have important physio-pathological implications related to the function of Plg, oxPtdPCs, or both. Full article
(This article belongs to the Special Issue Phospholipids: Molecular Sciences)

Review

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Open AccessReview Functional Toxicogenomics: Mechanism-Centered Toxicology
Int. J. Mol. Sci. 2010, 11(12), 4796-4813; doi:10.3390/ijms11124796
Received: 29 September 2010 / Revised: 22 November 2010 / Accepted: 22 November 2010 / Published: 24 November 2010
Cited by 23 | PDF Full-text (147 KB) | HTML Full-text | XML Full-text
Abstract
Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered
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Traditional toxicity testing using animal models is slow, low capacity, expensive and assesses a limited number of endpoints. Such approaches are inadequate to deal with the increasingly large number of compounds found in the environment for which there are no toxicity data. Mechanism-centered high-throughput testing represents an alternative approach to meet this pressing need but is limited by our current understanding of toxicity pathways. Functional toxicogenomics, the global study of the biological function of genes on the modulation of the toxic effect of a compound, can play an important role in identifying the essential cellular components and pathways involved in toxicity response. The combination of the identification of fundamental toxicity pathways and mechanism-centered targeted assays represents an integrated approach to advance molecular toxicology to meet the challenges of toxicity testing in the 21st century. Full article
(This article belongs to the Special Issue Advances in Molecular Toxicology)
Open AccessReview Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry
Int. J. Mol. Sci. 2010, 11(12), 5040-5055; doi:10.3390/ijms11125040
Received: 10 November 2010 / Revised: 25 November 2010 / Accepted: 27 November 2010 / Published: 7 December 2010
Cited by 29 | PDF Full-text (372 KB) | HTML Full-text | XML Full-text
Abstract
Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-mass spectrometric technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation,
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Matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) is a powerful tool that enables the simultaneous detection and identification of biomolecules in analytes. MALDI-imaging mass spectrometry (MALDI-IMS) is a two-dimensional MALDI-mass spectrometric technique used to visualize the spatial distribution of biomolecules without extraction, purification, separation, or labeling of biological samples. MALDI-IMS has revealed the characteristic distribution of several biomolecules, including proteins, peptides, amino acids, lipids, carbohydrates, and nucleotides, in various tissues. The versatility of MALDI-IMS has opened a new frontier in several fields such as medicine, agriculture, biology, pharmacology, and pathology. MALDI-IMS has a great potential for discovery of unknown biomarkers. In this review, we describe the methodology and applications of MALDI-IMS for biological samples. Full article
(This article belongs to the Special Issue Biomarkers)
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Open AccessReview Colorimetric Immunoassay for Detection of Tumor Markers
Int. J. Mol. Sci. 2010, 11(12), 5077-5094; doi:10.3390/ijms11125077
Received: 7 November 2010 / Revised: 24 November 2010 / Accepted: 25 November 2010 / Published: 7 December 2010
Cited by 17 | PDF Full-text (317 KB) | HTML Full-text | XML Full-text
Abstract
Tumor markers are substances, usually proteins, produced by the body in response to cancer growth, or by the cancer tissue itself. They can be detected in blood, urine, or tissue samples, and the discovery and detection of tumor markers may provide earlier diagnosis
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Tumor markers are substances, usually proteins, produced by the body in response to cancer growth, or by the cancer tissue itself. They can be detected in blood, urine, or tissue samples, and the discovery and detection of tumor markers may provide earlier diagnosis of cancer and improved therapeutic intervention. Colorimetric immunoassays for tumor marker detection have attracted considerable attention, due to their simplicity and high efficiency. The traditionally used colorimetric immunoassays for the detection of tumor markers are based on enzyme-linked immunosorbent assays, and the great achievement of nanotechnology has further opened opportunities for the development of such kind of immunoassays. This paper will summarize recent advances in the field of colorimetric immunoassays for detecting tumor markers, which is aimed to provide an overview in this field, as well as experimental guidance for the learner. Full article
(This article belongs to the Special Issue Biomarkers)
Open AccessReview Applications of Chitin and Its Derivatives in Biological Medicine
Int. J. Mol. Sci. 2010, 11(12), 5152-5164; doi:10.3390/ijms11125152
Received: 1 November 2010 / Revised: 2 December 2010 / Accepted: 6 December 2010 / Published: 15 December 2010
Cited by 69 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Chitin and its derivatives—as a potential resource as well as multiple functional substrates—have generated attractive interest in various fields such as biomedical, pharmaceutical, food and environmental industries, since the first isolation of chitin in 1811. Moreover, chitosan and its chitooligosaccharides (COS) are degraded
[...] Read more.
Chitin and its derivatives—as a potential resource as well as multiple functional substrates—have generated attractive interest in various fields such as biomedical, pharmaceutical, food and environmental industries, since the first isolation of chitin in 1811. Moreover, chitosan and its chitooligosaccharides (COS) are degraded products of chitin through enzymatic and acidic hydrolysis processes; and COS, in particular, is well suited for potential biological application, due to the biocompatibility and nontoxic nature of chitosan. In this review, we investigate the current bioactivities of chitin derivatives, which are all correlated with their biomedical properties. Several new and cutting edge insights here may provide a molecular basis for the mechanism of chitin, and hence may aid its use for medical and pharmaceutical applications. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessReview Protein Microarrays and Biomarkers of Infectious Disease
Int. J. Mol. Sci. 2010, 11(12), 5165-5183; doi:10.3390/ijms11125165
Received: 19 November 2010 / Revised: 11 December 2010 / Accepted: 15 December 2010 / Published: 16 December 2010
Cited by 13 | PDF Full-text (277 KB) | HTML Full-text | XML Full-text
Abstract
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have
[...] Read more.
Protein microarrays are powerful tools that are widely used in systems biology research. For infectious diseases, proteome microarrays assembled from proteins of pathogens will play an increasingly important role in discovery of diagnostic markers, vaccines, and therapeutics. Distinct formats of protein microarrays have been developed for different applications, including abundance-based and function-based methods. Depending on the application, design issues should be considered, such as the need for multiplexing and label or label free detection methods. New developments, challenges, and future demands in infectious disease research will impact the application of protein microarrays for discovery and validation of biomarkers. Full article
(This article belongs to the Special Issue Biomarkers)
Open AccessReview Liquid-Liquid Phase Transition and Glass Transition in a Monoatomic Model System
Int. J. Mol. Sci. 2010, 11(12), 5184-5200; doi:10.3390/ijms11125184
Received: 16 November 2010 / Revised: 13 December 2010 / Accepted: 13 December 2010 / Published: 16 December 2010
Cited by 6 | PDF Full-text (304 KB) | HTML Full-text | XML Full-text
Abstract
We review our recent study on the polyamorphism of the liquid and glass states in a monatomic system, a two-scale spherical-symmetric Jagla model with both attractive and repulsive interactions. This potential with a parametrization for which crystallization can be avoided and both the
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We review our recent study on the polyamorphism of the liquid and glass states in a monatomic system, a two-scale spherical-symmetric Jagla model with both attractive and repulsive interactions. This potential with a parametrization for which crystallization can be avoided and both the glass transition and the liquid-liquid phase transition are clearly separated, displays water-like anomalies as well as polyamorphism in both liquid and glassy states, providing a unique opportunity to study the interplay between the liquid-liquid phase transition and the glass transition. Our study on a simple model may be useful in understanding recent studies of polyamorphism in metallic glasses. Full article
(This article belongs to the Special Issue Amorphous Alloys)
Open AccessReview Deleted in Malignant Brain Tumors-1 Protein (DMBT1): A Pattern Recognition Receptor with Multiple Binding Sites
Int. J. Mol. Sci. 2010, 11(12), 5212-5233; doi:10.3390/ijms1112521
Received: 11 November 2010 / Revised: 9 December 2010 / Accepted: 9 December 2010 / Published: 17 December 2010
Cited by 23 | PDF Full-text (423 KB) | HTML Full-text | XML Full-text
Abstract
Deleted in Malignant Brain Tumors-1 protein (DMBT1), salivary agglutinin (DMBT1SAG), and lung glycoprotein-340 (DMBT1GP340) are three names for glycoproteins encoded by the same DMBT1 gene. All these proteins belong to the scavenger receptor cysteine-rich (SRCR) superfamily of proteins: a
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Deleted in Malignant Brain Tumors-1 protein (DMBT1), salivary agglutinin (DMBT1SAG), and lung glycoprotein-340 (DMBT1GP340) are three names for glycoproteins encoded by the same DMBT1 gene. All these proteins belong to the scavenger receptor cysteine-rich (SRCR) superfamily of proteins: a superfamily of secreted or membrane-bound proteins with SRCR domains that are highly conserved down to sponges, the most ancient metazoa. In addition to SRCR domains, all DMBT1s contain two CUB domains and one zona pellucida domain. The SRCR domains play a role in the function of DMBT1s, which is the binding of a broad range of pathogens including cariogenic streptococci, Helicobacter pylori and HIV. Mucosal defense proteins like IgA, surfactant proteins and lactoferrin also bind to DMBT1s through their SRCR domains. The binding motif on the SRCR domains comprises an 11-mer peptide in which a few amino acids are essential for binding (GRVEVLYRGSW). Adjacent to each individual SRCR domain are glycosylation domains, where the attached carbohydrate chains play a role in the binding of influenza A virus and Helicobacter pylori. The composition of the carbohydrate chains is not only donor specific, but also varies between different organs. These data demonstrate a role for DMBT1s as pattern recognition molecules containing various peptide and carbohydrate binding motifs. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
Open AccessReview Intrinsically Disordered Proteins in a Physics-Based World
Int. J. Mol. Sci. 2010, 11(12), 5292-5309; doi:10.3390/ijms11125292
Received: 19 October 2010 / Revised: 17 December 2010 / Accepted: 17 December 2010 / Published: 21 December 2010
Cited by 24 | PDF Full-text (203 KB) | HTML Full-text | XML Full-text
Abstract
Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play fundamental roles, and are extensively involved in human diseases. For signaling and regulation, IDPs
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Intrinsically disordered proteins (IDPs) are a newly recognized class of functional proteins that rely on a lack of stable structure for function. They are highly prevalent in biology, play fundamental roles, and are extensively involved in human diseases. For signaling and regulation, IDPs often fold into stable structures upon binding to specific targets. The mechanisms of these coupled binding and folding processes are of significant importance because they underlie the organization of regulatory networks that dictate various aspects of cellular decision-making. This review first discusses the challenge in detailed experimental characterization of these heterogeneous and dynamics proteins and the unique and exciting opportunity for physics-based modeling to make crucial contributions, and then summarizes key lessons from recent de novo simulations of the structure and interactions of several regulatory IDPs. Full article
(This article belongs to the Special Issue Advances in Molecular Recognition)
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Open AccessTechnical Note A Simple and Rapid Method for DNA Isolation from Xylophagous Insects
Int. J. Mol. Sci. 2010, 11(12), 5056-5064; doi:10.3390/ijms11125056
Received: 8 October 2010 / Revised: 22 November 2010 / Accepted: 30 November 2010 / Published: 7 December 2010
Cited by 11 | PDF Full-text (320 KB) | HTML Full-text | XML Full-text
Abstract
Published methods to isolate DNA from insects are not always effective in xylophagous insects because they have high concentrations of phenolics and other secondary plant compounds in their digestive tracts. A simple, reliable and labor-effective cetyltrimethylammonium bromide-polyvinylpyrrolidone (CTAB-PVP) method for isolation of high
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Published methods to isolate DNA from insects are not always effective in xylophagous insects because they have high concentrations of phenolics and other secondary plant compounds in their digestive tracts. A simple, reliable and labor-effective cetyltrimethylammonium bromide-polyvinylpyrrolidone (CTAB-PVP) method for isolation of high quality DNA from xylophagous insects is described. This method was successfully applied to PCR and restriction analysis, indicating removal of common inhibitors. DNA isolated by the CTAB-PVP method could be used in most molecular analyses. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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