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

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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; https://doi.org/10.3390/ijms11125339 - 22 Dec 2010
Cited by 2 | Viewed by 5966
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 [...] Read more.
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)
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; https://doi.org/10.3390/ijms11125323 - 22 Dec 2010
Cited by 37 | Viewed by 6102
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, [...] Read more.
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)
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; https://doi.org/10.3390/ijms11125310 - 21 Dec 2010
Cited by 26 | Viewed by 5017
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 [...] Read more.
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)
Open AccessReview
Intrinsically Disordered Proteins in a Physics-Based World
Int. J. Mol. Sci. 2010, 11(12), 5292-5309; https://doi.org/10.3390/ijms11125292 - 21 Dec 2010
Cited by 33 | Viewed by 6369
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 [...] Read more.
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 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; https://doi.org/10.3390/ijms11125273 - 21 Dec 2010
Cited by 25 | Viewed by 5156
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 [...] Read more.
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
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; https://doi.org/10.3390/ijms11125256 - 20 Dec 2010
Cited by 51 | Viewed by 6494
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 [...] Read more.
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 Materials Science)
Open AccessArticle
Fe-Chlorophyllin Promotes the Growth of Wheat Roots Associated with Nitric Oxide Generation
Int. J. Mol. Sci. 2010, 11(12), 5246-5255; https://doi.org/10.3390/ijms11125246 - 17 Dec 2010
Cited by 4 | Viewed by 5017
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 [...] Read more.
: 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)
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; https://doi.org/10.3390/ijms11125234 - 17 Dec 2010
Cited by 16 | Viewed by 6173
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. [...] Read more.
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)
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; https://doi.org/10.3390/ijms1112521 - 17 Dec 2010
Cited by 36 | Viewed by 5625
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 [...] Read more.
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 AccessArticle
Anti-Tumor Activity of a Novel Protein Obtained from Tartary Buckwheat
Int. J. Mol. Sci. 2010, 11(12), 5201-5211; https://doi.org/10.3390/ijms11125201 - 17 Dec 2010
Cited by 36 | Viewed by 4786
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 [...] Read more.
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)
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Open AccessReview
Liquid-Liquid Phase Transition and Glass Transition in a Monoatomic Model System
Int. J. Mol. Sci. 2010, 11(12), 5184-5200; https://doi.org/10.3390/ijms11125184 - 16 Dec 2010
Cited by 9 | Viewed by 6646
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 [...] Read more.
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
Protein Microarrays and Biomarkers of Infectious Disease
Int. J. Mol. Sci. 2010, 11(12), 5165-5183; https://doi.org/10.3390/ijms11125165 - 16 Dec 2010
Cited by 22 | Viewed by 5534
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
Applications of Chitin and Its Derivatives in Biological Medicine
Int. J. Mol. Sci. 2010, 11(12), 5152-5164; https://doi.org/10.3390/ijms11125152 - 15 Dec 2010
Cited by 143 | Viewed by 9064
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 Materials Science)
Open AccessArticle
Constitutive Expression of Thermobifida fusca Thermostable Acetylxylan Esterase Gene in Pichia pastoris
Int. J. Mol. Sci. 2010, 11(12), 5143-5151; https://doi.org/10.3390/ijms11125143 - 15 Dec 2010
Cited by 10 | Viewed by 6495
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 [...] Read more.
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 P. pastoris transformant are similar to those of the AXE from an E. coli transformant. Full article
(This article belongs to the Section Biochemistry)
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; https://doi.org/10.3390/ijms11125129 - 13 Dec 2010
Cited by 1 | Viewed by 4870
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 [...] Read more.
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
Clinicopathological Significance of Loss of ARID1A Immunoreactivity in Ovarian Clear Cell Carcinoma
Int. J. Mol. Sci. 2010, 11(12), 5120-5128; https://doi.org/10.3390/ijms11125120 - 13 Dec 2010
Cited by 68 | Viewed by 5952
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 [...] Read more.
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
Astaxanthin Improves Stem Cell Potency via an Increase in the Proliferation of Neural Progenitor Cells
Int. J. Mol. Sci. 2010, 11(12), 5109-5119; https://doi.org/10.3390/ijms11125109 - 09 Dec 2010
Cited by 11 | Viewed by 5444
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 [...] Read more.
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)
Open AccessArticle
Rhamnolipid Biosurfactants as New Players in Animal and Plant Defense against Microbes
Int. J. Mol. Sci. 2010, 11(12), 5095-5108; https://doi.org/10.3390/ijms11125095 - 09 Dec 2010
Cited by 76 | Viewed by 5927
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 [...] Read more.
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 AccessReview
Colorimetric Immunoassay for Detection of Tumor Markers
Int. J. Mol. Sci. 2010, 11(12), 5077-5094; https://doi.org/10.3390/ijms11125077 - 07 Dec 2010
Cited by 28 | Viewed by 7158
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 [...] Read more.
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 AccessArticle
Exploring Kinetics of Phenol Biodegradation by Cupriavidus taiwanesis 187
Int. J. Mol. Sci. 2010, 11(12), 5065-5076; https://doi.org/10.3390/ijms11125065 - 07 Dec 2010
Cited by 7 | Viewed by 6423
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 [...] Read more.
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 Materials Science)
Open AccessTechnical Note
A Simple and Rapid Method for DNA Isolation from Xylophagous Insects
Int. J. Mol. Sci. 2010, 11(12), 5056-5064; https://doi.org/10.3390/ijms11125056 - 07 Dec 2010
Cited by 12 | Viewed by 4895
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 [...] Read more.
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)
Open AccessReview
Matrix-Assisted Laser Desorption/Ionization Imaging Mass Spectrometry
Int. J. Mol. Sci. 2010, 11(12), 5040-5055; https://doi.org/10.3390/ijms11125040 - 07 Dec 2010
Cited by 41 | Viewed by 6635
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, [...] Read more.
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 AccessArticle
Poly[(3-hexylthiophene)-block-(3-semifluoroalkylthiophene)] for Polymer Solar Cells
Int. J. Mol. Sci. 2010, 11(12), 5027-5039; https://doi.org/10.3390/ijms11125027 - 06 Dec 2010
Cited by 11 | Viewed by 5904
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
Binding Ligand Prediction for Proteins Using Partial Matching of Local Surface Patches
Int. J. Mol. Sci. 2010, 11(12), 5009-5026; https://doi.org/10.3390/ijms11125009 - 06 Dec 2010
Cited by 25 | Viewed by 5702
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
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; https://doi.org/10.3390/ijms11124991 - 03 Dec 2010
Cited by 40 | Viewed by 5804
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
Profile and Functional Properties of Seed Proteins from Six Pea (Pisum sativum) Genotypes
Int. J. Mol. Sci. 2010, 11(12), 4973-4990; https://doi.org/10.3390/ijms11124973 - 03 Dec 2010
Cited by 73 | Viewed by 5218
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 [...] Read more.
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)
Open AccessArticle
Optimization of Bacterial Plasmid Transformation Using Nanomaterials Based on the Yoshida Effect
Int. J. Mol. Sci. 2010, 11(12), 4962-4972; https://doi.org/10.3390/ijms11124962 - 03 Dec 2010
Cited by 15 | Viewed by 6622
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 [...] Read more.
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)
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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; https://doi.org/10.3390/ijms11124952 - 02 Dec 2010
Cited by 6 | Viewed by 4900
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 [...] Read more.
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
Computer-Based De Novo Designs of Tripeptides as Novel Neuraminidase Inhibitors
Int. J. Mol. Sci. 2010, 11(12), 4932-4951; https://doi.org/10.3390/ijms11124932 - 01 Dec 2010
Cited by 11 | Viewed by 5324
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
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; https://doi.org/10.3390/ijms11124916 - 01 Dec 2010
Cited by 35 | Viewed by 7356
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 [...] Read more.
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)
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