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Int. J. Mol. Sci., Volume 13, Issue 3 (March 2012), Pages 2535-4002

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Open AccessArticle Comparison of Culture and Molecular Identification of Bacteria in Chronic Wounds
Int. J. Mol. Sci. 2012, 13(3), 2535-2550; doi:10.3390/ijms13032535
Received: 1 November 2011 / Revised: 30 January 2012 / Accepted: 13 February 2012 / Published: 23 February 2012
Cited by 32 | PDF Full-text (137 KB) | HTML Full-text | XML Full-text
Abstract
Clinical diagnostics of chronic polymicrobial infections, such as those found in chronic wounds, represent a diagnostic challenge for both culture and molecular methods. In the current retrospective study, the results of aerobic bacterial cultures and culture-free bacterial identification using DNA analyses were [...] Read more.
Clinical diagnostics of chronic polymicrobial infections, such as those found in chronic wounds, represent a diagnostic challenge for both culture and molecular methods. In the current retrospective study, the results of aerobic bacterial cultures and culture-free bacterial identification using DNA analyses were compared. A total of 168 chronic wounds were studied. The majority of bacteria identified with culture testing were also identified with molecular testing, but the majority of bacteria identified with the molecular testing were not identified with culture testing. Seventeen (17) different bacterial taxa were identified with culture, and 338 different bacterial taxa were identified with molecular testing. This study demonstrates the increased sensitivity that molecular microbial identification can have over culture methodologies, and previous studies suggest that molecular bacterial identification can improve the clinical outcomes of patients with chronic wounds. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Primary Study for the Therapeutic Dose and Time Window of Picroside II in Treating Cerebral Ischemic Injury in Rats
Int. J. Mol. Sci. 2012, 13(3), 2551-2562; doi:10.3390/ijms13032551
Received: 30 December 2011 / Revised: 15 February 2012 / Accepted: 16 February 2012 / Published: 23 February 2012
Cited by 9 | PDF Full-text (141 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to explore the optimal therapeutic dose and time window of picroside II for treating cerebral ischemic injury in rats according to the orthogonal test. The middle cerebral artery occlusion (MCAO) models were established by intraluminally inserting [...] Read more.
The aim of this study was to explore the optimal therapeutic dose and time window of picroside II for treating cerebral ischemic injury in rats according to the orthogonal test. The middle cerebral artery occlusion (MCAO) models were established by intraluminally inserting a thread into middle cerebral artery (MCA) from left external carotid artery (ECA). The successful rat models were randomly divided into 16 groups according to the orthogonal layout of [L16(45)] and treated by injecting picroside II intraperitoneally with different doses at various times. The neurological behavioral function was evaluated by Bederson’s test and the cerebral infarction volume was measured by tetrazolium chloride (TTC) staining. The expressions of neuron specific enolase (NSE) and neuroglial mark-protein S-100 were determined by immunohistochemisty assay. The results indicated that the optimal compositions of the therapeutic dose and time window of picroside II in treating cerebral ischemic injury were ischemia 1.5 h with 20 mg/kg body weight according to Bederson’s test, 1.0 h with 20 mg/kg body weight according to cerebral infarction volume, 1.5 h with 20 mg/kg body weight according to the expressions of NSE and S-100 respectively. Based on the principle of the minimization of medication dose and maximization of therapeutic time window, the optimal composition of the therapeutic dose and time window of picroside II in treating cerebral ischemic injury should be achieved by injecting picroside II intraperitoneally with 20 mg/kg body weight at ischemia 1.5 h. Full article
Open AccessArticle Isolation and Identification of Cellulolytic Bacteria from the Gut of Holotrichia parallela Larvae (Coleoptera: Scarabaeidae)
Int. J. Mol. Sci. 2012, 13(3), 2563-2577; doi:10.3390/ijms13032563
Received: 31 January 2012 / Revised: 17 February 2012 / Accepted: 20 February 2012 / Published: 23 February 2012
Cited by 34 | PDF Full-text (733 KB) | HTML Full-text | XML Full-text
Abstract
In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial isolates were assigned to 21 genotypes by amplified ribosomal DNA restriction analysis (ARDRA). A partial 16S rDNA sequence analysis [...] Read more.
In this study, 207 strains of aerobic and facultatively anaerobic cellulolytic bacteria were isolated from the gut of Holotrichia parallela larvae. These bacterial isolates were assigned to 21 genotypes by amplified ribosomal DNA restriction analysis (ARDRA). A partial 16S rDNA sequence analysis and standard biochemical and physiological tests were used for the assignment of the 21 representative isolates. Our results show that the cellulolytic bacterial community is dominated by the Proteobacteria (70.05%), followed by the Actinobacteria (24.15%), the Firmicutes (4.35%), and the Bacteroidetes (1.45%). At the genus level, Gram-negative bacteria including Pseudomonas, Ochrobactrum, Rhizobium, Cellulosimicrobium, and Microbacterium were the predominant groups, but members of Bacillus, Dyadobacter, Siphonobacter, Paracoccus, Kaistia, Devosia, Labrys, Ensifer, Variovorax, Shinella, Citrobacter, and Stenotrophomonas were also found. Furthermore, our results suggest that a significant amount of bacterial diversity exists among the cellulolytic bacteria, and that Siphonobacter aquaeclarae, Cellulosimicrobium funkei, Paracoccus sulfuroxidans, Ochrobactrum cytisi, Ochrobactrum haematophilum, Kaistia adipata, Devosia riboflavina, Labrys neptuniae, Ensifer adhaerens, Shinella zoogloeoides, Citrobacter freundii, and Pseudomonas nitroreducens are reported to be cellulolytic for the first time in this study. Our results indicate that the scarab gut is an attractive source for the study of novel cellulolytic microorganisms and enzymes useful for cellulose degradation. Full article
Open AccessArticle Inhibitory Action of Antidepressants on Mouse Betaine/GABA Transporter (BGT1) Heterologously Expressed in Cell Cultures
Int. J. Mol. Sci. 2012, 13(3), 2578-2589; doi:10.3390/ijms13032578
Received: 29 December 2011 / Revised: 28 January 2012 / Accepted: 17 February 2012 / Published: 24 February 2012
Cited by 4 | PDF Full-text (462 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Betaine/γ-aminobutyric acid (GABA) transporter (BGT1, SLC6A12) is a member of the Na+- and Cl-dependent neurotransmitter transporter gene family with a homology to the GABA transporters (GATs), GAT1 (SLC6A1), GAT2 (SLC6A13) and GAT3 (SLC6A11) (HUGO nomenclature). Since antidepressants have [...] Read more.
Betaine/γ-aminobutyric acid (GABA) transporter (BGT1, SLC6A12) is a member of the Na+- and Cl-dependent neurotransmitter transporter gene family with a homology to the GABA transporters (GATs), GAT1 (SLC6A1), GAT2 (SLC6A13) and GAT3 (SLC6A11) (HUGO nomenclature). Since antidepressants have been reported to inhibit GABA uptake, we examined those effects on mouse BGT1 (mBGT1) in comparison with other mouse GAT (mGAT) subtypes in the heterologously expressed cell cultures. All antidepressants tested here inhibited the [3H]GABA uptake through mBGT1 and mGATs in a rank order of potency with mBGT1 > mGAT1-3. Kinetic analyses for maprotilline, mianserine and trimipramine revealed that they inhibited mBGT1 and mGAT1 noncompetitively, except that mianserine competitively inhibited mBGT1. These results provided a clue to investigate the structure-function relationship of mBGT1 using antidepressants as a tool, leading to the identification of potential candidates for selective and specific inhibitors of mBGT1. Full article
Open AccessArticle Highly Regio- and Stereoselective Diels-Alder Cycloadditions via Two-Step and Multicomponent Reactions Promoted by Infrared Irradiation under Solvent-Free Conditions
Int. J. Mol. Sci. 2012, 13(3), 2590-2617; doi:10.3390/ijms13032590
Received: 15 December 2011 / Revised: 29 January 2012 / Accepted: 13 February 2012 / Published: 24 February 2012
Cited by 11 | PDF Full-text (461 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Infrared irradiation promoted the Diels-Alder cycloadditions of exo-2-oxazolidinone dienes 13 with the Knoevenagel adducts 46, as dienophiles, leading to the synthesis of new 3,5-diphenyltetrahydrobenzo[d]oxazol-2-one derivatives (7, 9, 11 and 13 [...] Read more.
Infrared irradiation promoted the Diels-Alder cycloadditions of exo-2-oxazolidinone dienes 13 with the Knoevenagel adducts 46, as dienophiles, leading to the synthesis of new 3,5-diphenyltetrahydrobenzo[d]oxazol-2-one derivatives (7, 9, 11 and 1317), under solvent-free conditions. These cycloadditions were performed with good regio- and stereoselectivity, favoring the para-endo cycloadducts. We also evaluated the one-pot three-component reaction of active methylene compounds 20, benzaldehydes 21 and exo-2-oxazolidinone diene 2 under the same reaction conditions. A cascade Knoevenagel condensation/Diels-Alder cycloaddition reaction was observed, resulting in the final adducts 1316 in similar yields. These procedures are environmentally benign, because no solvent and no catalyst were employed in these processes. The regioselectivity of these reactions was rationalized by Frontier Molecular Orbital (FMO) calculations. Full article
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Open AccessArticle Phage Display Approaches for the Isolation of Monoclonal Antibodies Against Dengue Virus Envelope Domain III from Human and Mouse Derived Libraries
Int. J. Mol. Sci. 2012, 13(3), 2618-2635; doi:10.3390/ijms13032618
Received: 29 January 2012 / Revised: 14 February 2012 / Accepted: 20 February 2012 / Published: 27 February 2012
Cited by 6 | PDF Full-text (629 KB) | HTML Full-text | XML Full-text
Abstract
Domain III of the dengue virus envelope protein (EDIII, aa295-395) has an immunoglobulin fold and is the proposed receptor-binding domain of the virus. Previous studies have shown that monoclonal antibodies against EDIII can be neutralizing and have therapeutic potential. Here, cloned Fab-phage [...] Read more.
Domain III of the dengue virus envelope protein (EDIII, aa295-395) has an immunoglobulin fold and is the proposed receptor-binding domain of the virus. Previous studies have shown that monoclonal antibodies against EDIII can be neutralizing and have therapeutic potential. Here, cloned Fab-phage libraries of human and mouse origin were screened for DENV specific antibodies. Firstly, bacterially expressed EDIII or whole virus particles were used as bait in biopanning against a large naïve human Fab-phage library ( > 10 billion independent clones). Multiple panning strategies were employed, and in excess of 1000 clones were screened, but all of the antibodies identified bound the envelope in regions outside EDIII suggesting EDIII antibodies are virtually absent from the naïve human repertoire. Next, a chimeric Fab-phage library was constructed from a panel of EDIII specific mouse hybridomas by pooling the VH and VL chain sequences from the hybridomas and cloning these into the pComb3X phagemid vector with human CH and CL encoding sequences. Biopanning against EDIII identified a unique antibody (C9) that cross-reacts with EDIII from DENV1-3 and, in the IgG format, binds and neutralizes DENV2 in cell-based assays. Sequence analysis and saturation mutagenesis of complementary determining regions (CDR) in the C9 light chain suggest an antigen recognition model in which the LCDR3 is a key determinant of EDIII specificity, while modifications in LCDR1 and LCDR2 affect DENV serotype cross-reactivity. Overall, this study supports the current prevailing opinion that neutralizing anti-EDIII monoclonal antibodies can be readily generated in murine systems, but in humans the anti-DENV immune response is directed away from domain III. Full article
(This article belongs to the Special Issue Phage Display)
Open AccessArticle Increased Activity of Cell Surface Peptidases in HeLa Cells Undergoing UV-Induced Apoptosis Is Not Mediated by Caspase 3
Int. J. Mol. Sci. 2012, 13(3), 2650-2675; doi:10.3390/ijms13032650
Received: 6 December 2011 / Revised: 14 February 2012 / Accepted: 22 February 2012 / Published: 28 February 2012
PDF Full-text (892 KB) | HTML Full-text | XML Full-text
Abstract
We have previously shown that in HeLa cells treated with a variety of agents there is an increase in cell surface peptidase (CSP) activity in those cells undergoing apoptosis. The increase in CSP activity observed in UVB-irradiated cells undergoing apoptosis was unaffected [...] Read more.
We have previously shown that in HeLa cells treated with a variety of agents there is an increase in cell surface peptidase (CSP) activity in those cells undergoing apoptosis. The increase in CSP activity observed in UVB-irradiated cells undergoing apoptosis was unaffected when the cultures were treated with the aminopeptidase inhibitor bestatin, and matrix metalloprotease inhibitor BB3103, but greatly enhanced when treated with the caspase 3 inhibitor-DEVD, and reduced in the presence of the poly(ADP-ribose) polymerase (PARP) inhibitor-3-aminobenzamide (3AB). Neither 3AB nor DEVD had an effect on the gross morphology of the apoptotic cells observed under electron microscopy, nor did they have an effect on phosphatidylserine eversion on the cell membrane, or that of PARP cleavage. All the agents except for DEVD had no effect on the level of caspase 3 activity in the cells. The results suggest that other caspases may cleave PARP in these cells. Both 3AB and DEVD treatment reduced the level of actin cleavage seen in the apoptotic cells. The increase in CSP activity observed in cells undergoing UVB-induced apoptosis appears to involve PARP but not caspase 3. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Sequence Analysis and Potentials of the Native RbcS Promoter in the Development of an Alternative Eukaryotic Expression System Using Green Microalga Ankistrodesmus convolutus
Int. J. Mol. Sci. 2012, 13(3), 2676-2691; doi:10.3390/ijms13032676
Received: 23 December 2011 / Revised: 2 February 2012 / Accepted: 5 February 2011 / Published: 28 February 2012
Cited by 5 | PDF Full-text (509 KB) | HTML Full-text | XML Full-text
Abstract
The availability of highly active homologous promoters is critical in the development of a transformation system and improvement of the transformation efficiency. To facilitate transformation of green microalga Ankistrodesmus convolutus which is considered as a potential candidate for many biotechnological applications, a [...] Read more.
The availability of highly active homologous promoters is critical in the development of a transformation system and improvement of the transformation efficiency. To facilitate transformation of green microalga Ankistrodesmus convolutus which is considered as a potential candidate for many biotechnological applications, a highly-expressed native promoter sequence of ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit (AcRbcS) has been used to drive the expression of β-glucuronidase (gusA) gene in this microalga. Besides the determination of the transcription start site by 5¢-RACE, sequence analysis revealed that AcRbcS promoter contained consensus TATA-box and several putative cis-acting elements, including some representative light-regulatory elements (e.g., G-box, Sp1 motif and SORLIP2), which confer light responsiveness in plants, and several potential conserved motifs (e.g., CAGAC-motif, YCCYTGG-motifs and CACCACA-motif), which may be involved in light responsiveness of RbcS gene in green microalgae. Using AcRbcS promoter::gusA translational fusion, it was demonstrated that this promoter could function as a light-regulated promoter in transgenic A. convolutus, which suggested that the isolated AcRbcS promoter was a full and active promoter sequence that contained all cis-elements required for developmental and light-mediated control of gene expression, and this promoter can be used to drive the expression of heterologous genes in A. convolutus. This achievement therefore advances the development of A. convolutus as an alternative expression system for the production of recombinant proteins. This is the first report on development of gene manipulation system for unicellular green alga A. convolutus. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Flavonoid Biosynthesis Genes Putatively Identified in the Aromatic Plant Polygonum minus via Expressed Sequences Tag (EST) Analysis
Int. J. Mol. Sci. 2012, 13(3), 2692-2706; doi:10.3390/ijms13032692
Received: 11 January 2012 / Revised: 31 January 2012 / Accepted: 2 February 2012 / Published: 28 February 2012
Cited by 10 | PDF Full-text (270 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic [...] Read more.
P. minus is an aromatic plant, the leaf of which is widely used as a food additive and in the perfume industry. The leaf also accumulates secondary metabolites that act as active ingredients such as flavonoid. Due to limited genomic and transcriptomic data, the biosynthetic pathway of flavonoids is currently unclear. Identification of candidate genes involved in the flavonoid biosynthetic pathway will significantly contribute to understanding the biosynthesis of active compounds. We have constructed a standard cDNA library from P. minus leaves, and two normalized full-length enriched cDNA libraries were constructed from stem and root organs in order to create a gene resource for the biosynthesis of secondary metabolites, especially flavonoid biosynthesis. Thus, large‑scale sequencing of P. minus cDNA libraries identified 4196 expressed sequences tags (ESTs) which were deposited in dbEST in the National Center of Biotechnology Information (NCBI). From the three constructed cDNA libraries, 11 ESTs encoding seven genes were mapped to the flavonoid biosynthetic pathway. Finally, three flavonoid biosynthetic pathway-related ESTs chalcone synthase, CHS (JG745304), flavonol synthase, FLS (JG705819) and leucoanthocyanidin dioxygenase, LDOX (JG745247) were selected for further examination by quantitative RT-PCR (qRT-PCR) in different P. minus organs. Expression was detected in leaf, stem and root. Gene expression studies have been initiated in order to better understand the underlying physiological processes. Full article
Open AccessArticle Major Phenolic Compounds, Antioxidant Capacity and Antidiabetic Potential of Rice Bean (Vigna umbellata L.) in China
Int. J. Mol. Sci. 2012, 13(3), 2707-2716; doi:10.3390/ijms13032707
Received: 1 November 2011 / Revised: 1 February 2012 / Accepted: 14 February 2012 / Published: 29 February 2012
Cited by 16 | PDF Full-text (224 KB) | HTML Full-text | XML Full-text
Abstract
Interest in edible beans as nutraceuticals is increasing. In the present study, the individual phenolic acids, the total phenolic content (TPC), the total flavonoid content (TFC), and the antioxidant and antidiabetic potential of 13 varieties of rice beans from China were investigated. [...] Read more.
Interest in edible beans as nutraceuticals is increasing. In the present study, the individual phenolic acids, the total phenolic content (TPC), the total flavonoid content (TFC), and the antioxidant and antidiabetic potential of 13 varieties of rice beans from China were investigated. Eight phenolic compounds (catechin, epicatechin, p-coumaric acid, ferulic acid, vitexin, isovitexin, sinapic acid, quercetin) were analyzed on an ultra-performance liquid chromatography (UPLC) mass spectrometry (MS) system. The rice bean varieties had significant differences in total phenolic compounds (ranging from 123.09 ± 10.35 to 843.75 ± 30.15 μg/g), in TPC (ranging from 3.27 ± 0.04 to 6.43 ± 0.25 mg gallic acid equivalents (GAE)/g), in TFC (ranging from 55.95 ± 11.16 to 320.39 ± 31.77 mg catechin (CE)/g), in antioxidant activity (ranging from 39.87 ± 1.37 to 46.40 ± 2.18 μM·TE/g), in α-glucosidase inhibition activity (ranging from 44.32 ± 2.12 to 68.71 ± 2.19) and in advanced glycation end products formation inhibition activity (ranging from 34.11 ± 0.59 to 75.75 ± 0.33). This study is the first report on phytochemistry and biological activities in rice beans. Full article
(This article belongs to the Special Issue Advances in Nutraceutical Research)
Open AccessArticle Molecular Mechanisms of (R,R)ZX-5 on NO Synthesis and Its Anti-Angiogenic Effect
Int. J. Mol. Sci. 2012, 13(3), 2717-2726; doi:10.3390/ijms13032717
Received: 24 November 2011 / Revised: 4 February 2012 / Accepted: 14 February 2012 / Published: 29 February 2012
Cited by 2 | PDF Full-text (508 KB) | HTML Full-text | XML Full-text
Abstract
(R,R)ZX-5 is a NO regulatory compound, which could significantly increase choroidal blood flow in New Zealand rabbit. The aim of this paper is to investigate the molecular mechanism of (R,R)ZX-5 promoting NO production. Besides [...] Read more.
(R,R)ZX-5 is a NO regulatory compound, which could significantly increase choroidal blood flow in New Zealand rabbit. The aim of this paper is to investigate the molecular mechanism of (R,R)ZX-5 promoting NO production. Besides this, we also investigated the antiangiogenic activity of (R,R)ZX-5. Analysis of Western blot showed that (R,R)ZX-5 up-regulated the expression of Akt, p-Akt (Thr473), eNOS and p-eNOS (Ser1177), down-regulated the expression of Cyclin D1 in human retinal endothelial cells and escalated the intracellular free Ca2+ concentration. Additionally, (R,R)ZX-5 inhibited the growth of blood vessels in the chick chorioallantoic membrane model. It is concluded that (R,R)ZX-5 promotes choroidal blood flow through PI3K/Akt-eNOS and Akt-Ca2+-eNOS pathways. Additionally, (R,R)ZX-5 can inhibit angiogenesis. Full article
Open AccessArticle Synthesis and Characterization of Privileged Monodentate Phosphoramidite Ligands and Chiral Brønsted Acids Derived from D-Mannitol
Int. J. Mol. Sci. 2012, 13(3), 2727-2743; doi:10.3390/ijms13032727
Received: 28 December 2011 / Revised: 6 February 2012 / Accepted: 20 February 2012 / Published: 29 February 2012
Cited by 4 | PDF Full-text (943 KB) | HTML Full-text | XML Full-text
Abstract
The synthesis of several novel chiral phosphoramidite ligands (L1L8) with C2 symmetric, pseudo C2 symmetric secondary amines and chiral Brønsted acids 1a,b has been achieved. These chiral auxiliaries were obtained from commercially available d-mannitol, and secondary [...] Read more.
The synthesis of several novel chiral phosphoramidite ligands (L1L8) with C2 symmetric, pseudo C2 symmetric secondary amines and chiral Brønsted acids 1a,b has been achieved. These chiral auxiliaries were obtained from commercially available d-mannitol, and secondary amines in moderate to excellent yields. Excellent diastereoselectivites of ten chiral auxiliaries were obtained. The chiral phosphoramidite ligands and chiral Brønsted acids were fully characterized by spectroscopic methods. Full article
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Open AccessArticle Genome-Wide Analysis of a TaLEA-Introduced Transgenic Populus simonii × Populus nigra Dwarf Mutant
Int. J. Mol. Sci. 2012, 13(3), 2744-2762; doi:10.3390/ijms13032744
Received: 10 October 2011 / Revised: 9 November 2011 / Accepted: 3 February 2012 / Published: 1 March 2012
Cited by 4 | PDF Full-text (773 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A dwarf mutant (dwf1) was obtained among 15 transgenic lines, when TaLEA (Tamarix androssowii late embryogenesis abundant gene) was introduced into Populus simonii × Populus nigra by Agrobacterium tumefaciens-mediated transformation. Under the same growth conditions, dwf1 height was [...] Read more.
A dwarf mutant (dwf1) was obtained among 15 transgenic lines, when TaLEA (Tamarix androssowii late embryogenesis abundant gene) was introduced into Populus simonii × Populus nigra by Agrobacterium tumefaciens-mediated transformation. Under the same growth conditions, dwf1 height was significantly reduced compared with the wild type and the other transgenic lines. Because only one transgenic line (dwf1) displayed the dwarf phenotype, we considered that T-DNA insertion sites may play a role in the mutant formation. The mechanisms underlying this effect were investigated using TAIL-PCR (thermal asymmetric interlaced PCR) and microarrays methods. According to the TAIL-PCR results, two flanking sequences located on chromosome IV and VIII respectively, were cloned. The results indicated the integration of two independent T-DNA copies. We searched for the potential genes near to the T-DNA insertions. The nearest gene was a putative poplar AP2 transcription factor (GI: 224073210). Expression analysis showed that AP2 was up-regulated in dwf1 compared with the wild type and the other transgenic lines. According to the microarrays results, a total of 537 genes involved in hydrolase, kinase and transcription factor activities, as well as protein and nucleotide binding, showed significant alterations in gene expression. These genes were expressed in more than 60 metabolic pathways, including starch, sucrose, galactose and glycerolipid metabolism and phenylpropanoids and flavonoid biosyntheses. Our transcriptome and T-DNA insertion sites analyses might provide some useful insights into the dwarf mutant formation. Full article
Open AccessArticle Isolation and Characterization of Polymorphic Microsatellite Loci from Metapenaeopsis barbata Using PCR-Based Isolation of Microsatellite Arrays (PIMA)
Int. J. Mol. Sci. 2012, 13(3), 2763-2768; doi:10.3390/ijms13032763
Received: 19 January 2012 / Revised: 19 February 2012 / Accepted: 21 February 2012 / Published: 1 March 2012
Cited by 4 | PDF Full-text (89 KB) | HTML Full-text | XML Full-text
Abstract
The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of [...] Read more.
The red-spot prawn, Metapenaeopsis barbata, is a commercially important, widely distributed demersal species in the Indo-West Pacific Ocean. Overfishing has made its populations decline in the past decade. To study conservation genetics, eight polymorphic microsatellite loci were isolated. Genetic characteristics of the SSR (simple sequence repeat) fingerprints were estimated in 61 individuals from adjacent seas of Taiwan and China. The number of alleles, ranging from 2 to 4, as well as observed and expected heterozygosities in populations, ranging from 0.048 to 0.538, and 0.048 and 0.654, respectively, were detected. No deviation from Hardy–Weinberg expectations was detected at either locus. No significant linkage disequilibrium was detected in locus pairs. The polymorphic microsatellite loci will be useful for investigations of the genetic variation, population structure, and conservation genetics of this species. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle All-Trans Retinoic Acid Treatment Is Associated with Prohibitin Expression in Renal Interstitial Fibrosis Rats
Int. J. Mol. Sci. 2012, 13(3), 2769-2782; doi:10.3390/ijms13032769
Received: 9 January 2012 / Revised: 23 February 2012 / Accepted: 23 February 2012 / Published: 1 March 2012
Cited by 22 | PDF Full-text (956 KB) | HTML Full-text | XML Full-text | Correction | Supplementary Files
Abstract
This study was performed to investigate the association of prohibitin with renal interstitial fibrosis (RIF) lesion and to explore the association of all-trans retinoic acid (ATRA) treatment with prohibitin expression in RIF rats. Rats were divided into three groups: the sham operation [...] Read more.
This study was performed to investigate the association of prohibitin with renal interstitial fibrosis (RIF) lesion and to explore the association of all-trans retinoic acid (ATRA) treatment with prohibitin expression in RIF rats. Rats were divided into three groups: the sham operation group (SHO), the model group subjected to unilateral ureteral obstruction (UUO), and the model group treated with ATRA (GA). Renal tissues were collected at 14 and 28 days after surgery, and the relevant indicators were detected. In comparison with the SHO group, the RIF index in the UUO group was markedly elevated (p < 0.01), and the RIF index in the GA group was alleviated compared with that in the UUO group (p < 0.01). Compared with the SHO group, the expression of prohibitin (protein or mRNA) in the UUO group was significantly reduced (each p < 0.01). Prohibitin expression in the GA group was markedly increased when compared with that in the UUO (p < 0.01). The expression of TGF-β1 (protein and mRNA), protein expressions of Col-IV, fibronectin, α-SMA and cleaved Caspase-3, ROS generation and cell apoptosis index in the UUO group were markedly higher than those in the SHO group (all p < 0.01), and their expressions in the GA group were markedly down-regulated compared to those in the UUO group (all p < 0.01, respectively). The protein expression of prohibitin was negatively correlated with the RIF index, protein expression of TGF-β1, Col-IV, fibronectin, α-SMA or cleaved Caspase-3, ROS generation and the cell apoptosis index (each p < 0.01). In conclusion, lower expression of prohibitin is associated with the RIF, and ATRA treatment is associated with increased prohibitin, which can prevent the progression of RIF. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Sequence Variants and Haplotype Analysis of Cat ERBB2 Gene: A Survey on Spontaneous Cat Mammary Neoplastic and Non-Neoplastic Lesions
Int. J. Mol. Sci. 2012, 13(3), 2783-2800; doi:10.3390/ijms13032783
Received: 12 December 2011 / Revised: 29 January 2012 / Accepted: 24 February 2012 / Published: 2 March 2012
Cited by 4 | PDF Full-text (472 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The human ERBB2 proto-oncogene is widely considered a key gene involved in human breast cancer onset and progression. Among spontaneous tumors, mammary tumors are the most frequent cause of cancer death in cats and second most frequent in humans. In fact, naturally [...] Read more.
The human ERBB2 proto-oncogene is widely considered a key gene involved in human breast cancer onset and progression. Among spontaneous tumors, mammary tumors are the most frequent cause of cancer death in cats and second most frequent in humans. In fact, naturally occurring tumors in domestic animals, more particularly cat mammary tumors, have been proposed as a good model for human breast cancer, but critical genetic and molecular information is still scarce. The aims of this study include the analysis of the cat ERBB2 gene partial sequences (between exon 17 and 20) in order to characterize a normal and a mammary lesion heterogeneous populations. Cat genomic DNA was extracted from normal frozen samples (n = 16) and from frozen and formalin-fixed paraffin-embedded mammary lesion samples (n = 41). We amplified and sequenced two cat ERBB2 DNA fragments comprising exons 17 to 20. It was possible to identify five sequence variants and six haplotypes in the total population. Two sequence variants and two haplotypes show to be specific for cat mammary tumor samples. Bioinformatics analysis predicts that four of the sequence variants can produce alternative transcripts or activate cryptic splicing sites. Also, a possible association was identified between clinicopathological traits and the variant haplotypes. As far as we know, this is the first attempt to examine ERBB2 genetic variations in cat mammary genome and its possible association with the onset and progression of cat mammary tumors. The demonstration of a possible association between primary tumor size (one of the two most important prognostic factors) and the number of masses with the cat ERBB2 variant haplotypes reveal the importance of the analysis of this gene in veterinary medicine. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle An Electrochemical Method to Detect Gamma Glutamyl Transpeptidase
Int. J. Mol. Sci. 2012, 13(3), 2801-2809; doi:10.3390/ijms13032801
Received: 31 December 2011 / Revised: 3 February 2012 / Accepted: 27 February 2012 / Published: 2 March 2012
Cited by 3 | PDF Full-text (221 KB) | HTML Full-text | XML Full-text
Abstract
Gamma glutamyl transpeptidase (GGT) is a transferase, which is of great importance in sustaining intracellular cysteine and glutathione levels. The abnormal expression of GGT is significantly associated with features of many metabolic syndromes (e.g., hepatocellular carcinoma). Therefore, it is essential to develop [...] Read more.
Gamma glutamyl transpeptidase (GGT) is a transferase, which is of great importance in sustaining intracellular cysteine and glutathione levels. The abnormal expression of GGT is significantly associated with features of many metabolic syndromes (e.g., hepatocellular carcinoma). Therefore, it is essential to develop methods to detect GGT so as to monitor the physiological or pathological phenomena related to this species. In this work, by making use of a complex formed by Cu2+ and glutathione, which may exhibit excellent voltammetric response, we have proposed a novel potential electrochemical method for the detection of the enzyme. Results show that in the presence of GGT, the formation of Cu2+-glutathione complex on a working electrode will be disrupted, resulting in greatly depressed electrochemical signals. The primary method exhibits some advantages, such as it being fast, cost-efficient, and conveniently operated. It also has the potential to be further developed as an effective method in the quantitative detection of GGT in real samples. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Variation in Stability of Endogenous Reference Genes in Fallopian Tubes and Endometrium from Healthy and Ectopic Pregnant Women
Int. J. Mol. Sci. 2012, 13(3), 2810-2826; doi:10.3390/ijms13032810
Received: 5 January 2012 / Revised: 10 February 2012 / Accepted: 27 February 2012 / Published: 2 March 2012
Cited by 7 | PDF Full-text (574 KB) | HTML Full-text | XML Full-text
Abstract
RT-qPCR is commonly employed in gene expression studies in ectopic pregnancy. Most use RN18S1, β-actin or GAPDH as internal controls without validation of their suitability as reference genes. A systematic study of the suitability of endogenous reference genes for gene expression studies [...] Read more.
RT-qPCR is commonly employed in gene expression studies in ectopic pregnancy. Most use RN18S1, β-actin or GAPDH as internal controls without validation of their suitability as reference genes. A systematic study of the suitability of endogenous reference genes for gene expression studies in ectopic pregnancy is lacking. The aims of this study were therefore to evaluate the stability of 12 reference genes and suggest those that are stable for use as internal control genes in fallopian tubes and endometrium from ectopic pregnancy and healthy non-pregnant controls. Analysis of the results showed that the genes consistently ranked in the top six by geNorm and NormFinder algorithms, were UBC, GAPDH, CYC1 and EIF4A2 (fallopian tubes) and UBC and ATP5B (endometrium). mRNA expression of NAPE-PLD as a test gene of interest varied between the groups depending on which of the 12 reference genes was used as internal controls. This study demonstrates that arbitrary selection of reference genes for normalisation in RT-qPCR studies in ectopic pregnancy without validation, risk producing inaccurate data and should therefore be discouraged. Full article
Open AccessArticle Gamma Radiation Induced Oxidation and Tocopherols Decrease in In-Shell, Peeled and Blanched Peanuts
Int. J. Mol. Sci. 2012, 13(3), 2827-2845; doi:10.3390/ijms13032827
Received: 13 January 2012 / Revised: 20 February 2012 / Accepted: 27 February 2012 / Published: 2 March 2012
Cited by 11 | PDF Full-text (496 KB) | HTML Full-text | XML Full-text
Abstract
In-shell, peeled and blanched peanut samples were characterized in relation to proximate composition and fatty acid profile. No difference was found in relation to its proximate composition. The three major fatty acids were palmitic acid, oleic acid, and linoleic acid. In order [...] Read more.
In-shell, peeled and blanched peanut samples were characterized in relation to proximate composition and fatty acid profile. No difference was found in relation to its proximate composition. The three major fatty acids were palmitic acid, oleic acid, and linoleic acid. In order to investigate irradiation and storage effects, peanut samples were submitted to doses of 0.0, 5.0, 7.5 or 10.0 kGy, stored for six months at room temperature and monitored every three months. Peanuts responded differently to irradiation, particularly with regards to tocopherol contents, primary and secondary oxidation products and oil stability index. Induction periods and tocopherol contents were negatively correlated with irradiation doses and decreased moderately during storage. α-Tocopherol was the most gamma radiation sensitive and peeled samples were the most affected. A positive correlation was found among tocopherol contents and the induction period of the oils extracted from irradiated samples. Gamma radiation and storage time increased oxidation compounds production. If gamma radiation is considered an alternative for industrial scale peanut conservation, in-shell samples are the best feedstock. For the best of our knowledge this is the first article with such results; this way it may be helpful as basis for future studies on gamma radiation of in-shell crops. Full article
Open AccessArticle Astragalin from Cassia alata Induces DNA Adducts in Vitro and Repairable DNA Damage in the Yeast Saccharomyces cerevisiae
Int. J. Mol. Sci. 2012, 13(3), 2846-2862; doi:10.3390/ijms13032846
Received: 17 January 2012 / Revised: 22 February 2012 / Accepted: 22 February 2012 / Published: 5 March 2012
Cited by 3 | PDF Full-text (1407 KB) | HTML Full-text | XML Full-text
Abstract
Reverse phase-solid phase extraction from Cassia alata leaves (CaRP) was used to obtain a refined extract. Higher than wild-type sensitivity to CaRP was exhibited by 16 haploid Saccharomyces cerevisiae mutants with defects in DNA repair and membrane transport. CaRP had a strong [...] Read more.
Reverse phase-solid phase extraction from Cassia alata leaves (CaRP) was used to obtain a refined extract. Higher than wild-type sensitivity to CaRP was exhibited by 16 haploid Saccharomyces cerevisiae mutants with defects in DNA repair and membrane transport. CaRP had a strong DPPH free radical scavenging activity with an IC50 value of 2.27 µg mL−1 and showed no pro-oxidant activity in yeast. CaRP compounds were separated by HPLC and the three major components were shown to bind to DNA in vitro. The major HPLC peak was identified as kampferol-3-O-β-D-glucoside (astragalin), which showed high affinity to DNA as seen by HPLC-UV measurement after using centrifugal ultrafiltration of astragalin-DNA mixtures. Astragalin-DNA interaction was further studied by spectroscopic methods and its interaction with DNA was evaluated using solid-state FTIR. These and computational (in silico) docking studies revealed that astragalin-DNA binding occurs through interaction with G-C base pairs, possibly by intercalation stabilized by H-bond formation. Full article
Open AccessArticle Development and Characterization of 18 Novel EST-SSRs from the Western Flower Thrips, Frankliniella occidentalis (Pergande)
Int. J. Mol. Sci. 2012, 13(3), 2863-2876; doi:10.3390/ijms13032863
Received: 6 December 2011 / Revised: 27 February 2012 / Accepted: 28 February 2012 / Published: 5 March 2012
Cited by 11 | PDF Full-text (377 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The western flower thrips, Frankliniella occidentalis (Pergande), is an invasive species and the most economically important pest within the insect order Thysanoptera. For a better understanding of the genetic makeup and migration patterns of F. occidentalis throughout the world, we characterized 18 novel polymorphic EST-derived microsatellites. The mutational mechanism of these EST-SSRs was also investigated to facilitate the selection of appropriate combinations of markers for population genetic studies. Genetic diversity of these novel markers was assessed in 96 individuals from three populations in China (Harbin, Dali, and Guiyang). The results showed that all these 18 loci were highly polymorphic; the number of alleles ranged from 2 to 15, with an average of 5.50 alleles per locus. The observed (HO) and expected (HE) heterozygosities ranged from 0.072 to 0.707 and 0.089 to 0.851, respectively. Furthermore, only two locus/population combinations (WFT144 in Dali and WFT50 in Guiyang) significantly deviated from Hardy–Weinberg equilibrium (HWE). Pairwise FST analysis showed a low but significant differentiation (0.026 < FST < 0.032) among all three pairwise population comparisons. Sequence analysis of alleles per locus revealed a complex mutational pattern of these EST-SSRs. Thus, these EST-SSRs are useful markers but greater attention should be paid to the mutational characteristics of these microsatellites when they are used in population genetic studies. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle An Oligodeoxynucleotide That Induces Differentiation of Bone Marrow Mesenchymal Stem Cells to Osteoblasts in Vitro and Reduces Alveolar Bone Loss in Rats with Periodontitis
Int. J. Mol. Sci. 2012, 13(3), 2877-2892; doi:10.3390/ijms13032877
Received: 6 February 2012 / Revised: 19 February 2012 / Accepted: 24 February 2012 / Published: 5 March 2012
Cited by 4 | PDF Full-text (1093 KB) | HTML Full-text | XML Full-text
Abstract
To investigate the effect of oligodeoxynucleotides (ODNs) on the differentiation of rat bone marrow mesenchymal stem cells (BMSCs) to osteoblasts, in order to find a candidate ODN with potential for the treatment of periodontitis, a series of ODNs were designed and selected [...] Read more.
To investigate the effect of oligodeoxynucleotides (ODNs) on the differentiation of rat bone marrow mesenchymal stem cells (BMSCs) to osteoblasts, in order to find a candidate ODN with potential for the treatment of periodontitis, a series of ODNs were designed and selected to test their effect on the promotion of the differentiation of BMSCs to osteoblasts in vitro and on the repair of periodontal tissue in rats with periodontitis. It was found that MT01, one of the ODNs with the sequences of human mitochondrial DNA, stimulated the proliferation of BMSCs, the differentiation of BMSCs to osteoblasts and mRNA expression of bone-associated factors including Runx2, Osterix, OPG, RANKL and collagen I in vitro. In vivo study showed that MT01 prevented the loss of alveolar bone in the rats with periodontitis and induced the production of proteins of OPG and Osterix in the bone tissue. These results indicated that MT01 could induce differentiation of BMSCs to osteoblasts and inhibit the alveolar bone absorption in rats with periodontitis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Computational Identification and Modeling of Crosstalk between Phosphorylation, O-β-glycosylation and Methylation of FoxO3 and Implications for Cancer Therapeutics
Int. J. Mol. Sci. 2012, 13(3), 2918-2938; doi:10.3390/ijms13032918
Received: 30 January 2012 / Revised: 23 February 2012 / Accepted: 28 February 2012 / Published: 5 March 2012
Cited by 4 | PDF Full-text (701 KB) | HTML Full-text | XML Full-text
Abstract
FoxO3 is a member of the forkhead class of transcription factors and plays a major role in the regulation of diverse cellular processes, including cell cycle arrest, DNA repair, and protection from stress stimuli by detoxification of reactive oxygen species. In addition, [...] Read more.
FoxO3 is a member of the forkhead class of transcription factors and plays a major role in the regulation of diverse cellular processes, including cell cycle arrest, DNA repair, and protection from stress stimuli by detoxification of reactive oxygen species. In addition, FoxO3 is a tumor suppressor and has been considered as a novel target for cancer therapeutics. Phosphorylation of FoxO3 via the AKT, IKK, and ERK pathways leads to deregulation, cytoplasmic retention, degradation of FoxO3 and favors tumor progression. Identification of the amino acid residues that are the target of different posttranslational modifications (PTMs) provides a foundation for understanding the molecular mechanisms of FoxO3 modifications and associated outcomes. In addition to phosphorylation, serine and threonine residues of several proteins are regulated by a unique type of PTM known as O-β-glycosylation, which serves as a functional switch. We sought to investigate the crosstalk of different PTMs on the FoxO3 which leads to the onset/progression of various cancers and that could also potentially be targeted as a therapeutic point of intervention. A computational workflow and set of selection parameters have been defined for the identification of target sites and crosstalk between different PTMs. We identified phosphorylation, O-β-GlcNAc modification, and Yin Yang sites on Ser/Thr residues, and propose a potential novel mechanism of crosstalk between these PTMs. Furthermore, methylation potential of human FoxO3 at arginine and lysine residues and crosstalk between methylation and phosphorylation have also been described. Our findings may facilitate the study of therapeutic strategies targeting posttranslational events. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Optimization of Freeze Drying Conditions for Purified Pectinase from Mango (Mangifera indica cv. Chokanan) Peel
Int. J. Mol. Sci. 2012, 13(3), 2939-2950; doi:10.3390/ijms13032939
Received: 6 January 2012 / Revised: 12 February 2012 / Accepted: 14 February 2012 / Published: 6 March 2012
Cited by 3 | PDF Full-text (198 KB) | HTML Full-text | XML Full-text
Abstract
Response surface methodology (RSM) along with central composite design (CCD) was applied to optimize the freeze drying conditions for purified pectinase from mango (Mangifera indica cv. Chokanan) peel. The effect of pectinase content (−2.66, 62.66 mg/mL), Arabic gum (−1.21, 10.21%, w/v), and maltodextrin (0.73, 7.26%, w/v) as independent variables on activity, yield, and storage stability of freeze-dried enzyme was evaluated. Storage stability of pectinase was investigated after one week at 4 °C and yield percentage of the enzyme after encapsulation was also determined. The independent variables had the most significant (p < 0.05) effect on pectinase activity and yield of the enzyme. It was observed that the interaction effect of Arabic gum and maltodextrin improved the enzymatic properties of freeze-dried pectinase. The optimal conditions for freeze-dried pectinase from mango peel were obtained using 30 mg/mL of pectinase content, 4.5 (%, w/v) of Arabic gum, and 4 (%, w/v) of maltodextrin. Under these conditions, the maximum activity (11.12 U/mL), yield (86.4%) and storage stability (84.2%) of encapsulated pectinase were achieved. Full article
Open AccessArticle Characterization of Novel Di-, Tri-, and Tetranucleotide Microsatellite Primers Suitable for Genotyping Various Plant Pathogenic Fungi with Special Emphasis on Fusaria and Mycospherella graminicola
Int. J. Mol. Sci. 2012, 13(3), 2951-2964; doi:10.3390/ijms13032951
Received: 7 November 2011 / Revised: 9 January 2012 / Accepted: 20 February 2012 / Published: 6 March 2012
Cited by 11 | PDF Full-text (1665 KB) | HTML Full-text | XML Full-text
Abstract
The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence [...] Read more.
The goals of this investigation were to identify and evaluate the use of polymorphic microsatellite marker (PMM) analysis for molecular typing of seventeen plant pathogenic fungi. Primers for di-, tri-, and tetranucleotide loci were designed directly from the recently published genomic sequence of Mycospherlla graminicola and Fusarium graminearum. A total of 20 new microsatellite primers as easy-to-score markers were developed. Microsatellite primer PCR (MP-PCR) yielded highly reproducible and complex genomic fingerprints, with several bands ranging in size from 200 to 3000 bp. Of the 20 primers tested, only (TAGG)4, (TCC)5 and (CA)7T produced a high number of polymorphic bands from either F. graminearum or F. culmorum. (ATG)5 led to successful amplifications in M. graminicola isolates collected from Germany. Percentage of polymorphic bands among Fusarium species ranged from 9 to 100%. Cluster analysis of banding patterns of the isolates corresponded well to the established species delineations based on morphology and other methods of phylogenetic analysis. The current research demonstrates that the newly designed microsatellite primers are reliable, sensitive and technically simple tools for assaying genetic variability in plant pathogenic fungi. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Identification and Characterization of MicroRNAs from Barley (Hordeum vulgare L.) by High-Throughput Sequencing
Int. J. Mol. Sci. 2012, 13(3), 2973-2984; doi:10.3390/ijms13032973
Received: 10 February 2012 / Revised: 29 February 2012 / Accepted: 1 March 2012 / Published: 6 March 2012
Cited by 26 | PDF Full-text (547 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae [...] Read more.
MicroRNAs (miRNAs) are a class of endogenous RNAs that regulates the gene expression involved in various biological and metabolic processes. Barley is one of the most important cereal crops worldwide and is a model organism for genetic and genomic studies in Triticeae species. However, the miRNA research in barley has lagged behind other model species in grass family. To obtain more information of miRNA genes in barley, we sequenced a small RNA library created from a pool of equal amounts of RNA from four different tissues using Solexa sequencing. In addition to 126 conserved miRNAs (58 families), 133 novel miRNAs belonging to 50 families were identified from this sequence data set. The miRNA* sequences of 15 novel miRNAs were also discovered, suggesting the additional evidence for existence of these miRNAs. qRT-PCR was used to examine the expression pattern of six randomly selected miRNAs. Some miRNAs involved in drought and salt stress response were also identified. Furthermore, the potential targets of these putative miRNAs were predicted using the psRNATarget tools. Our results significantly increased the number of novel miRNAs in barley, which should be useful for further investigation into the biological functions and evolution of miRNAs in barley and other species. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle BDMC33, A Curcumin Derivative Suppresses Inflammatory Responses in Macrophage-Like Cellular System: Role of Inhibition in NF-κB and MAPK Signaling Pathways
Int. J. Mol. Sci. 2012, 13(3), 2985-3008; doi:10.3390/ijms13032985
Received: 13 January 2012 / Revised: 22 February 2012 / Accepted: 24 February 2012 / Published: 6 March 2012
Cited by 10 | PDF Full-text (1564 KB) | HTML Full-text | XML Full-text
Abstract
Our preliminary screening has shown that curcumin derivative BDMC33 [2,6-bis(2,5-dimethoxybenzylidene)cyclohexanone] exerted promising nitric oxide inhibitory activity in activated macrophages. However, the molecular basis and mechanism for its pharmacological action is yet to be elucidated. The aim of this study was to investigate [...] Read more.
Our preliminary screening has shown that curcumin derivative BDMC33 [2,6-bis(2,5-dimethoxybenzylidene)cyclohexanone] exerted promising nitric oxide inhibitory activity in activated macrophages. However, the molecular basis and mechanism for its pharmacological action is yet to be elucidated. The aim of this study was to investigate the anti-inflammatory properties of BDMC33 and elucidate its underlying mechanism action in macrophage cells. Our current study demonstrated that BDMC33 inhibits the secretion of major pro-inflammatory mediators in stimulated macrophages, and includes NO, TNF-α and IL-1β through interference in both nuclear factor kappaB (NF-κB) and mitogen activator protein kinase (MAPK) signaling cascade in IFN-γ/LPS-stimulated macrophages. Moreover, BDMC33 also interrupted LPS signaling through inhibiting the surface expression of CD-14 accessory molecules. In addition, the inhibitory action of BDMC33 not only restricted the macrophages cell (RAW264.7), but also inhibited the secretion of NO and TNF-α in IFN-γ/LPS-challenged microglial cells (BV-2). The experimental data suggests the inflammatory action of BDMC33 on activated macrophage-like cellular systems, which could be used as a future therapeutic agent in the management of chronic inflammatory diseases. Full article
(This article belongs to the Special Issue Advances in Molecular Immunology)
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Open AccessArticle Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing
Int. J. Mol. Sci. 2012, 13(3), 3009-3021; doi:10.3390/ijms13033009
Received: 9 February 2012 / Revised: 23 February 2012 / Accepted: 27 February 2012 / Published: 6 March 2012
Cited by 27 | PDF Full-text (202 KB) | HTML Full-text | XML Full-text
Abstract
Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. [...] Read more.
Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2%) sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%), which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Supercritical Fluid Extraction of Bacterial and Archaeal Lipid Biomarkers from Anaerobically Digested Sludge
Int. J. Mol. Sci. 2012, 13(3), 3022-3037; doi:10.3390/ijms13033022
Received: 19 December 2011 / Revised: 23 February 2012 / Accepted: 27 February 2012 / Published: 6 March 2012
Cited by 3 | PDF Full-text (863 KB) | HTML Full-text | XML Full-text
Abstract
Supercritical fluid extraction (SFE) was used in the analysis of bacterial respiratory quinone (RQ), bacterial phospholipid fatty acid (PLFA), and archaeal phospholipid ether lipid (PLEL) from anaerobically digested sludge. Bacterial RQ were determined using ultra performance liquid chromatography (UPLC). Determination of bacterial [...] Read more.
Supercritical fluid extraction (SFE) was used in the analysis of bacterial respiratory quinone (RQ), bacterial phospholipid fatty acid (PLFA), and archaeal phospholipid ether lipid (PLEL) from anaerobically digested sludge. Bacterial RQ were determined using ultra performance liquid chromatography (UPLC). Determination of bacterial PLFA and archaeal PLEL was simultaneously performed using gas chromatography-mass spectrometry (GC-MS). The effects of pressure, temperature, and modifier concentration on the total amounts of RQ, PLFA, and PLEL were investigated by 23 experiments with five settings chosen for each variable. The optimal extraction conditions that were obtained through a multiple-response optimization included a pressure of 23.6 MPa, temperature of 77.6 °C, and 10.6% (v/v) of methanol as the modifier. Thirty nine components of microbial lipid biomarkers were identified in the anaerobically digested sludge. Overall, the SFE method proved to be more effective, rapid, and quantitative for simultaneously extracting bacterial and archaeal lipid biomarkers, compared to conventional organic solvent extraction. This work shows the potential application of SFE as a routine method for the comprehensive analysis of microbial community structures in environmental assessments using the lipid biomarkers profile. Full article
(This article belongs to the Special Issue Supercritical Fluid Extraction)
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Open AccessArticle Gamma Radiation Effects on Peanut Skin Antioxidants
Int. J. Mol. Sci. 2012, 13(3), 3073-3084; doi:10.3390/ijms13033073
Received: 21 December 2011 / Revised: 29 February 2012 / Accepted: 1 March 2012 / Published: 7 March 2012
Cited by 17 | PDF Full-text (160 KB) | HTML Full-text | XML Full-text
Abstract
Peanut skin, which is removed in the peanut blanching process, is rich in bioactive compounds with antioxidant properties. The aims of this study were to measure bioactive compounds in peanut skins and evaluate the effect of gamma radiation on their antioxidant activity. [...] Read more.
Peanut skin, which is removed in the peanut blanching process, is rich in bioactive compounds with antioxidant properties. The aims of this study were to measure bioactive compounds in peanut skins and evaluate the effect of gamma radiation on their antioxidant activity. Peanut skin samples were treated with 0.0, 5.0, 7.5, or 10.0 kGy gamma rays. Total phenolics, condensed tannins, total flavonoids, and antioxidant activity were evaluated. Extracts obtained from the peanut skins were added to refined-bleached-deodorized (RBD) soybean oil. The oxidative stability of the oil samples was determined using the Oil Stability Index method and compared to a control and synthetic antioxidants (100 mg/kg BHT and 200 mg/kg TBHQ). Gamma radiation changed total phenolic content, total condensed tannins, total flavonoid content, and the antioxidant activity. All extracts, gamma irradiated or not, presented increasing induction period (h), measured by the Oil Stability Index method, when compared with the control. Antioxidant activity of the peanut skins was higher than BHT. The present study confirmed that gamma radiation did not affect the peanut skin extracts’ antioxidative properties when added to soybean oil. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Comparative Evolution of S7 Intron 1 and Ribosomal Internal Transcribed Spacer in Coilia nasus (Clupeiformes: Engraulidae)
Int. J. Mol. Sci. 2012, 13(3), 3085-3100; doi:10.3390/ijms13033085
Received: 21 October 2011 / Revised: 17 January 2012 / Accepted: 28 February 2012 / Published: 7 March 2012
Cited by 3 | PDF Full-text (258 KB) | HTML Full-text | XML Full-text
Abstract
Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze [...] Read more.
Coilia nasus is widely distributed in the Yangtze River, the coastal waters of China, Korea and the Ariake Sound of Japan. Several ecotypes exist and this provides a useful model for the study of comparative diversity between molecular markers. Here we analyze and compare the nucleotide sequences between single-copy ribosomal protein S7 gene intron 1 (rpS7) and multiple-copy ribosomal internal transcribed spacer 1 (ITS1) in this species to compare the phylogenetic signal of the two nuclear genes. Nucleotide substitutions among the two gene sequences and partial sequence of mitochondrial cytochrome c oxidase subunit I (COI) gene were also analyzed. A total of 115 clones for rpS7 and 122 clones for ITS1 were obtained from 37 specimens. The nucleotide sequence length is 741 to 743 bp for rpS7 and 334 to 348 bp for ITS1. Intra- and inter-specimen variation in rpS7 results from nucleotide substitution, while such variation in ITS1 is mainly due to different numbers of short base repeats. The content of G + C is lower in rpS7 (43.5%) than in ITS1 (68.2%). Our results indicate that the proportion of the sequence variable sites is higher in rpS7 (61) than in ITS1 (23); the informative parsimony of rpS7 is evidently higher than that of ITS1 (26 vs. 2); the overall ratio between transitions and transversions in ITS1 is slightly lower than in rpS7, but remarkably lower than in COI. These results suggest that rpS7 is more suitable than ITS1 as a marker for genetic divergence of this group. Furthermore, gene flow is observed between the different geographic populations of C. nasus from the phylogeny of this species based on rpS7, showing that rpS7 has more evolutionary characteristics for understanding the processes of genomic evolution at the intraspecific level. Full article
(This article belongs to the Section Molecular Diagnostics)
Open AccessArticle Prediction of Genomic Islands in Three Bacterial Pathogens of Pneumonia
Int. J. Mol. Sci. 2012, 13(3), 3134-3144; doi:10.3390/ijms13033134
Received: 31 January 2012 / Revised: 20 February 2012 / Accepted: 1 March 2012 / Published: 7 March 2012
Cited by 3 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
Pneumonia is one kind of common infectious disease, which is usually caused by bacteria, viruses, or fungi. In this paper, we predicted genomic islands in three bacterial pathogens of pneumonia. They are Chlamydophila pneumoniae, Mycoplasma pneumoniae and Streptococcus pneumoniae, respectively. [...] Read more.
Pneumonia is one kind of common infectious disease, which is usually caused by bacteria, viruses, or fungi. In this paper, we predicted genomic islands in three bacterial pathogens of pneumonia. They are Chlamydophila pneumoniae, Mycoplasma pneumoniae and Streptococcus pneumoniae, respectively. For each pathogen, one clinical strain is involved. After implementing the cumulative GC profile combined with h and BCN index, eight genomic islands are found in three pathogens. Among them, six genomic islands are found to have mobility elements, which constitute a kind of conserved character of genomic islands, and this introduces the possibility that they are genuine genomic islands. The present results show that the cumulative GC profile when combined with h and BCN indexes is a good method for predicting genomic islands in bacteria and it has lower false positive rate than the SIGI method. Specially, three genomic islands are found to contain clusters of genes coding for production of virulence factors and this is useful for research into the pathogenicity of these pathogens and helpful for the treatment of diseases caused by them. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Arabidopsis Serine Decarboxylase Mutants Implicate the Roles of Ethanolamine in Plant Growth and Development
Int. J. Mol. Sci. 2012, 13(3), 3176-3188; doi:10.3390/ijms13033176
Received: 1 February 2012 / Revised: 20 February 2012 / Accepted: 1 March 2012 / Published: 7 March 2012
Cited by 10 | PDF Full-text (1216 KB) | HTML Full-text | XML Full-text
Abstract
Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to [...] Read more.
Ethanolamine is important for synthesis of choline, phosphatidylethanolamine (PE) and phosphatidylcholine (PC) in plants. The latter two phospholipids are the major phospholipids in eukaryotic membranes. In plants, ethanolamine is mainly synthesized directly from serine by serine decarboxylase. Serine decarboxylase is unique to plants and was previously shown to have highly specific activity to L-serine. While serine decarboxylase was biochemically characterized, its functions and importance in plants were not biologically elucidated due to the lack of serine decarboxylase mutants. Here we characterized an Arabidopsis mutant defective in serine decarboxylase, named atsdc-1 (Arabidopsis thaliana serine decarboxylase-1). The atsdc-1 mutants showed necrotic lesions in leaves, multiple inflorescences, sterility in flower, and early flowering in short day conditions. These defects were rescued by ethanolamine application to atsdc-1, suggesting the roles of ethanolamine as well as serine decarboxylase in plant development. In addition, molecular analysis of serine decarboxylase suggests that Arabidopsis serine decarboxylase is cytosol-localized and expressed in all tissue. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Modulation Role of Abscisic Acid (ABA) on Growth, Water Relations and Glycinebetaine Metabolism in Two Maize (Zea mays L.) Cultivars under Drought Stress
Int. J. Mol. Sci. 2012, 13(3), 3189-3202; doi:10.3390/ijms13033189
Received: 7 February 2012 / Revised: 25 February 2012 / Accepted: 28 February 2012 / Published: 8 March 2012
Cited by 10 | PDF Full-text (230 KB) | HTML Full-text | XML Full-text
Abstract
The role of plant hormone abscisic acid (ABA) in plants under drought stress (DS) is crucial in modulating physiological responses that eventually lead to adaptation to an unfavorable environment; however, the role of this hormone in modulation of glycinebetaine (GB) metabolism in [...] Read more.
The role of plant hormone abscisic acid (ABA) in plants under drought stress (DS) is crucial in modulating physiological responses that eventually lead to adaptation to an unfavorable environment; however, the role of this hormone in modulation of glycinebetaine (GB) metabolism in maize particularly at the seedling stage is still poorly understood. Some hydroponic experiments were conducted to investigate the modulation role of ABA on plant growth, water relations and GB metabolism in the leaves of two maize cultivars, Zhengdan 958 (ZD958; drought tolerant), and Jundan 20 (JD20; drought sensitive), subjected to integrated root-zone drought stress (IR-DS) simulated by the addition of polyethylene glycol (PEG, 12% w/v, MW 6000). The IR-DS substantially resulted in increased betaine aldehyde dehydrogenase (BADH) activity and choline content which act as the key enzyme and initial substrate, respectively, in GB biosynthesis. Drought stress also induced accumulation of GB, whereas it caused reduction in leaf relative water content (RWC) and dry matter (DM) in both cultivars. The contents of ABA and GB increased in drought-stressed maize seedlings, but ABA accumulated prior to GB accumulation under the drought treatment. These responses were more predominant in ZD958 than those in JD20. Addition of exogenous ABA and fluridone (Flu) (ABA synthesis inhibitor) applied separately increased and decreased BADH activity, respectively. Abscisic acid application enhanced GB accumulation, leaf RWC and shoot DM production in both cultivars. However, of both maize cultivars, the drought sensitive maize cultivar (JD20) performed relatively better than the other maize cultivar ZD958 under both ABA and Flu application in view of all parameters appraised. It is, therefore, concluded that increase in both BADH activity and choline content possibly resulted in enhancement of GB accumulation under DS. The endogenous ABA was probably involved in the regulation of GB metabolism by regulating BADH activity, and resulting in modulation of water relations and plant growth under drought, especially in the drought sensitive maize cultivar JD20. Full article
Open AccessArticle Applications of Circular Dichroism for Structural Analysis of Gelatin and Antimicrobial Peptides
Int. J. Mol. Sci. 2012, 13(3), 3229-3244; doi:10.3390/ijms13033229
Received: 31 January 2012 / Revised: 2 March 2012 / Accepted: 5 March 2012 / Published: 8 March 2012
Cited by 21 | PDF Full-text (1425 KB) | HTML Full-text | XML Full-text
Abstract
Circular dichroism (CD) is a useful technique for monitoring changes in the conformation of antimicrobial peptides or gelatin. In this study, interactions between cationic peptides and gelatin were observed without affecting the triple helical content of the gelatin, which was more strongly [...] Read more.
Circular dichroism (CD) is a useful technique for monitoring changes in the conformation of antimicrobial peptides or gelatin. In this study, interactions between cationic peptides and gelatin were observed without affecting the triple helical content of the gelatin, which was more strongly affected by anionic surfactant. The peptides did not adopt a secondary structure in the presence of aqueous solution or Tween 80, but a peptide secondary structure formed upon the addition of sodium dodecyl sulfate (SDS). The peptides bound to the phosphate group of lipopolysaccharide (LPS) and displayed an alpha-helical conformation while (KW)4 adopted a folded conformation. Further, the peptides did not specifically interact with the fungal cell wall components of mannan or laminarin. Tryptophan blue shift assay indicated that these peptides interacted with SDS, LPS, and gelatin but not with Tween 80, mannan, or laminarin. The peptides also displayed antibacterial activity against P. aeruginosa without cytotoxicity against HaCaT cells at MIC, except for HPA3NT3-analog peptide. In this study, we used a CD spectroscopic method to demonstrate the feasibility of peptide characterization in numerous environments. The CD method can thus be used as a screening method of gelatin-peptide interactions for use in wound healing applications. Full article
Open AccessArticle Use of the MLPA Assay in the Molecular Diagnosis of Gene Copy Number Alterations in Human Genetic Diseases
Int. J. Mol. Sci. 2012, 13(3), 3245-3276; doi:10.3390/ijms13033245
Received: 30 December 2011 / Revised: 28 February 2012 / Accepted: 29 February 2012 / Published: 8 March 2012
Cited by 35 | PDF Full-text (295 KB) | HTML Full-text | XML Full-text
Abstract
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is [...] Read more.
Multiplex Ligation-dependent Probe Amplification (MLPA) assay is a recently developed technique able to evidence variations in the copy number of several human genes. Due to this ability, MLPA can be used in the molecular diagnosis of several genetic diseases whose pathogenesis is related to the presence of deletions or duplications of specific genes. Moreover, MLPA assay can also be used in the molecular diagnosis of genetic diseases characterized by the presence of abnormal DNA methylation. Due to the large number of genes that can be analyzed by a single technique, MLPA assay represents the gold standard for molecular analysis of all pathologies derived from the presence of gene copy number variation. In this review, the main applications of the MLPA technique for the molecular diagnosis of human diseases are described. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle A Combined DNA-Affinic Molecule and N-Mustard Alkylating Agent Has an Anti-Cancer Effect and Induces Autophagy in Oral Cancer Cells
Int. J. Mol. Sci. 2012, 13(3), 3277-3290; doi:10.3390/ijms13033277
Received: 2 November 2011 / Revised: 7 January 2012 / Accepted: 21 February 2012 / Published: 9 March 2012
Cited by 3 | PDF Full-text (1183 KB) | HTML Full-text | XML Full-text
Abstract
Although surgery or the combination of chemotherapy and radiation are reported to improve the quality of life and reduce symptoms in patients with oral cancer, the prognosis of oral cancer remains generally poor. DNA alkylating agents, such as N-mustard, play an important [...] Read more.
Although surgery or the combination of chemotherapy and radiation are reported to improve the quality of life and reduce symptoms in patients with oral cancer, the prognosis of oral cancer remains generally poor. DNA alkylating agents, such as N-mustard, play an important role in cancer drug development. BO-1051 is a new 9-anilinoacridine N-mustard-derivative anti-cancer drug that can effectively target a variety of cancer cell lines and inhibit tumorigenesis in vivo. However, the underlying mechanism of BO-1051-mediated tumor suppression remains undetermined. In the present study, BO-1051 suppressed cell viability with a low IC50 in oral cancer cells, but not in normal gingival fibroblasts. Cell cycle analysis revealed that the tumor suppression by BO-1051 was accompanied by cell cycle arrest and downregulation of stemness genes. The enhanced conversion of LC3-I to LC3-II and the formation of acidic vesicular organelles indicated that BO-1501 induced autophagy. The expression of checkpoint kinases was upregulated as demonstrated with Western blot analysis, showing that BO-1051 could induce DNA damage and participate in DNA repair mechanisms. Furthermore, BO-1051 treatment alone exhibited a moderate tumor suppressive effect against xenograft tumor growth in immunocompromised mice. Importantly, the combination of BO-1051 and radiation led to a potent inhibition on xenograft tumorigenesis. Collectively, our findings demonstrated that BO-1051 exhibited a cytotoxic effect via cell cycle arrest and the induction of autophagy. Thus, the combination of BO-1051 and radiotherapy may be a feasible therapeutic strategy against oral cancer in the future. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle The Hypoglycemic Effect of the Kelp on Diabetes Mellitus Model Induced by Alloxan in Rats
Int. J. Mol. Sci. 2012, 13(3), 3354-3365; doi:10.3390/ijms13033354
Received: 25 November 2011 / Revised: 3 February 2012 / Accepted: 8 February 2012 / Published: 12 March 2012
Cited by 4 | PDF Full-text (326 KB) | HTML Full-text | XML Full-text
Abstract
Hypoglycemic effects and the use of kelp in diabetes mellitus (DM) model rats induced by alloxan were investigated. Sixty healthy male rats were used to establish DM models by injecting alloxan intraperitoneally. Kelp powder was added to the general forage for the rats. The levels of fasting blood glucose (FBG) were determined by an automatic blood glucose device. Electrochemiluminescence immunoassay was applied to determine the serum levels of insulin. The serum levels of malondialdehyde (MDA) were measured by thiobarbituric acid assay and nitric oxide (NO) by nitrate reductase assay. The activities of superoxide dismutase (SOD) were determined by xanthinoxidase assay and glutathione peroxidase (GSH-Px) by chemical colorimetry. The shape and structure of islet cells were observed with Hematine-Eosin staining, and the expression of superoxide dismutase (SOD) and inducible nitric oxide synthase (iNOS) in islet cells were detected by immunohistochemical assay. The results showed that the serum levels of insulin after treatment with kelp powder increased significantly compared to those in the DM-model group, while the FBG in the medium-high dose treated groups decreased significantly compared to those in the DM-model group (P < 0.05). The levels of MDA and NO in the kelp powder groups were lower than those in the DM-model group, while the activities of SOD and GSH-Px were higher than those in the DM-model group, of which a significant difference existed between the medium-high dose treated groups and the DM-model group (P < 0.05). The shape and structure of islet cells improved with the up-expressing SOD and down-expressing iNOS in the medium-high dose treated groups compared to those in the DM-model group (P < 0.05). There were no significant differences between the medium and high dose treated groups, all above indexes (P > 0.05). It is suggested that kelp might aid recovery of the the islet cell secreting function and reduce the level of FBG by an antioxidant effect. Full article
Open AccessArticle Preparation and Characterization of New Nano-Composite Scaffolds Loaded With Vascular Stents
Int. J. Mol. Sci. 2012, 13(3), 3366-3381; doi:10.3390/ijms13033366
Received: 1 December 2011 / Revised: 4 January 2012 / Accepted: 20 February 2012 / Published: 12 March 2012
Cited by 8 | PDF Full-text (630 KB) | HTML Full-text | XML Full-text
Abstract
In this study, vascular stents were fabricated from poly (lactide-ε-caprolactone)/collagen/nano-hydroxyapatite (PLCL/Col/nHA) by electrospinning, and the surface morphology and breaking strength were observed or measured through scanning electron microscopy and tensile tests. The anti-clotting properties of stents were evaluated for anticoagulation surfaces modified [...] Read more.
In this study, vascular stents were fabricated from poly (lactide-ε-caprolactone)/collagen/nano-hydroxyapatite (PLCL/Col/nHA) by electrospinning, and the surface morphology and breaking strength were observed or measured through scanning electron microscopy and tensile tests. The anti-clotting properties of stents were evaluated for anticoagulation surfaces modified by the electrostatic layer-by-layer self-assembly technique. In addition, nano-composite scaffolds of poly (lactic-co-glycolic acid)/polycapr-olactone/nano-hydroxyapatite (PLGA/PCL/nHA) loaded with the vascular stents were prepared by thermoforming-particle leaching and their basic performance and osteogenesis were tested in vitro and in vivo. The results show that the PLCL/Col/nHA stents and PLGA/PCL/nHA nano-composite scaffolds had good surface structures, mechanical properties, biocompatibility and could guide bone regeneration. These may provide a new way to build vascularized-tissue engineered bone to repair large bone defects in bone tissue engineering. Full article
(This article belongs to the Special Issue Composite Materials in Skeletal Engineering)
Open AccessArticle Chemical Composition and Antimicrobial Activity of the Essential Oil of Kumquat (Fortunella crassifolia Swingle) Peel
Int. J. Mol. Sci. 2012, 13(3), 3382-3393; doi:10.3390/ijms13033382
Received: 11 January 2012 / Revised: 24 February 2012 / Accepted: 24 February 2012 / Published: 12 March 2012
Cited by 12 | PDF Full-text (301 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to determine the main constituents of the essential oil isolated from Fortunella crassifolia Swingle peel by hydro-distillation, and to test the efficacy of the essential oil on antimicrobial activity. Twenty-five components, representing 92.36% of the total [...] Read more.
The aim of this study was to determine the main constituents of the essential oil isolated from Fortunella crassifolia Swingle peel by hydro-distillation, and to test the efficacy of the essential oil on antimicrobial activity. Twenty-five components, representing 92.36% of the total oil, were identified by GC-MS analysis. The essential oil showed potent antimicrobial activity against both Gram-negative (E. coli and S. typhimurium) and Gram-positive (S. aureus, B. cereus, B. subtilis, L. bulgaricus, and B. laterosporus) bacteria, together with a remarkable antifungal activity against C. albicans. In a food model of beef extract, the essential oil was observed to possess an effective capacity to control the total counts of viable bacteria. Furthermore, the essential oil showed strongly detrimental effects on the growth and morphological structure of the tested bacteria. It was suggested that the essential oil from Fortunella crassifolia Swingle peel might be used as a natural food preservative against bacteria or fungus in the food industry. Full article
Open AccessArticle Dietary Pseudopurpurin Effects on Bone Mineral Density and Bone Geometry Architecture in Rats
Int. J. Mol. Sci. 2012, 13(3), 3431-3443; doi:10.3390/ijms13033431
Received: 19 January 2012 / Revised: 1 March 2012 / Accepted: 2 March 2012 / Published: 13 March 2012
Cited by 1 | PDF Full-text (483 KB) | HTML Full-text | XML Full-text
Abstract
The objective of our study was to evaluate whether feeding pseudopurpurin affects bone mineral density and bone geometry architecture in rats. Pseudopurpurin was extracted, analyzed and purified using an HLPC-ESI-MS. Rats were given 0% and 0.5% pseudopurpurin powder in their diet. Femurs [...] Read more.
The objective of our study was to evaluate whether feeding pseudopurpurin affects bone mineral density and bone geometry architecture in rats. Pseudopurpurin was extracted, analyzed and purified using an HLPC-ESI-MS. Rats were given 0% and 0.5% pseudopurpurin powder in their diet. Femurs of rats were examined at 0.5, 1 and 2 months after pseudopurpurin feeding. Compared with rats in the group 0%, the bone mineral density, and the calcium, magnesium, zinc and manganese concentrations in the rats femur in the group 0.5% increased significantly at 1 month and 2 months after pseudopurpurin feeding. Analytical results of micro-computed tomography showed that the group 0.5% displayed an increase in the trabecular volume fraction, trabecular thickness and trabecular number of the distal femur at 1 and 2 months after pseudopurpurin feeding, and the mean thickness, inner perimeter, outer perimeter, and area of the femur diaphysis were significantly increased at 2 months after pseudopurpurin feeding compared with the group 0%. In parallel, the trabecular separation and structure model index of the distal femur were decreased, compared with the group 0% at 1 and 2 months after pseudopurpurin feeding. In the 0.5% and 0% groups, there was no damage to kidney and liver by histopathology analysis. The long-term feeding of pseudopurpurin is safe for rats. The feeding of 0.5% pseudopurpurin which has specific chemical affinities for calcium for bone improvement and level of bone mineral density, enhances the geometry architecture compared with the 0% group. Full article
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Open AccessArticle Extracts of Phenolic Compounds from Seeds of Three Wild Grapevines—Comparison of Their Antioxidant Activities and the Content of Phenolic Compounds
Int. J. Mol. Sci. 2012, 13(3), 3444-3457; doi:10.3390/ijms13033444
Received: 8 December 2011 / Revised: 29 February 2012 / Accepted: 1 March 2012 / Published: 13 March 2012
Cited by 13 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
Phenolic compounds were extracted from three wild grapevine species: Vitis californica, V. riparia and V. amurensis seeds using 80% methanol or 80% acetone. The total content of phenolic compounds was determined utilizing the Folin-Ciocalteu’s phenol reagent while the content of tannins [...] Read more.
Phenolic compounds were extracted from three wild grapevine species: Vitis californica, V. riparia and V. amurensis seeds using 80% methanol or 80% acetone. The total content of phenolic compounds was determined utilizing the Folin-Ciocalteu’s phenol reagent while the content of tannins was assayed with the vanillin and BSA precipitation methods. Additionally, the DPPH free radical scavenging activity and the reduction power of the extracts were measured. The RP-HPLC method was applied to identify the phenolic compounds in the extracts, such as phenolic acids and catechins. The seeds contained large amounts of tannins, catechins and gallic acid and observable quantities of p-coumaric acid. The total content of phenolic compounds and tannins was similar in the extracts from V. californica and V. riparia seeds. However, the total content of total phenolic compounds and tannins in the extracts from V. californica and V. riperia seeds were about two-fold higher than that in the extracts from V. amurensis seeds. Extracts from seeds of the American species (V. californica and V. riparia) contained similarly high concentrations of tannins, whereas extracts from seeds of V. amurensis had approximately half that amount of these compounds. The content of catechin and epicatechin was similar in all extracts. The highest DPPH anti-radical scavenging activity was observed in the acetonic and methanolic extracts of V. californica and V. riparia seeds—while the acetonic extract from the V. californica seeds was the strongest reducing agent. Full article
(This article belongs to the Special Issue Antioxidants)
Open AccessArticle Homologous NF-YC2 Subunit from Arabidopsis and Tobacco Is Activated by Photooxidative Stress and Induces Flowering
Int. J. Mol. Sci. 2012, 13(3), 3458-3477; doi:10.3390/ijms13033458
Received: 30 January 2012 / Revised: 29 February 2012 / Accepted: 1 March 2012 / Published: 13 March 2012
Cited by 22 | PDF Full-text (643 KB) | HTML Full-text | XML Full-text
Abstract
The transcription factor NF-Y consists of the three subunits A, B and C, which are encoded in Arabidopsis in large gene families. The multiplicity of the genes implies that NF-Y may act in diverse combinations of each subunit for the transcriptional control. [...] Read more.
The transcription factor NF-Y consists of the three subunits A, B and C, which are encoded in Arabidopsis in large gene families. The multiplicity of the genes implies that NF-Y may act in diverse combinations of each subunit for the transcriptional control. We aimed to assign a function in stress response and plant development to NF-YC subunits by analyzing the expression of NF-Y genes and exploitation of nf-y mutants. Among the subunit family, NF-YC2 showed the strongest inducibility towards oxidative stress, e.g. photodynamic, light, oxidative, heat and drought stress. A tobacco NF-YC homologous gene was found to be inducible by photooxidative stress generated by an accumulation of the tetrapyrrole metabolite, coproporphyrin. Despite the stress induction, an Arabidopsis nf-yc2 mutant and NF-YC2 overexpressors did not show phenotypical differences compared to wild-type seedlings in response to photooxidative stress. This can be explained by the compensatory potential of other members of the NF-YC family. However, NF-YC2 overexpression leads to an early flowering phenotype that is correlated with increased FLOWERING LOCUS T-transcript levels. It is proposed that NF-YC2 functions in floral induction and is a candidate gene among the NF-Y family for the transcriptional activation upon oxidative stress. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Open AccessArticle Expression Analysis of an R3-Type MYB Transcription Factor CPC-LIKE MYB4 (TRICHOMELESS2) and CPL4-Related Transcripts in Arabidopsis
Int. J. Mol. Sci. 2012, 13(3), 3478-3491; doi:10.3390/ijms13033478
Received: 14 February 2012 / Revised: 5 March 2012 / Accepted: 5 March 2012 / Published: 13 March 2012
Cited by 16 | PDF Full-text (570 KB) | HTML Full-text | XML Full-text
Abstract
The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 [...] Read more.
The CAPRICE (CPC)-like MYB gene family encodes R3-type MYB transcription factors in Arabidopsis. There are six additional CPC-like MYB sequences in the Arabidopsis genome, including TRYPTICHON (TRY), ENHANCER OF TRY AND CPC1 and 2 (ETC1 and ETC2), ENHANCER OF TRY AND CPC3/CPC-LIKE MYB3 (ETC3/CPL3), and TRICHOMELESS1 and 2 (TCL1 and TCL2). We independently identified CPC-LIKE MYB4 (CPL4), which was found to be identical to TCL2. RT-PCR analysis showed that CPL4 is strongly expressed in shoots, including true leaves, but not in roots. Promoter-GUS analyses indicated that CPL4 is specifically expressed in leaf blades. Although CPC expression was repressed in 35S::ETC1, 35S::ETC2 and 35S::CPL3 backgrounds, CPL4 expression was not affected by ETC1, ETC2 or CPL3 over-expression. Notably, several chimeric transcripts may result from inter-genic alternative splicing of CPL4 and ETC2, two tandemly repeated genes on chromosome II. At least two chimeric transcripts named CPL4-α and CPL4-β are expected to encode complete CPC-like MYB proteins. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Phenolic Contents and Compositions in Skins of Red Wine Grape Cultivars among Various Genetic Backgrounds and Originations
Int. J. Mol. Sci. 2012, 13(3), 3492-3510; doi:10.3390/ijms13033492
Received: 9 January 2012 / Revised: 8 February 2012 / Accepted: 14 February 2012 / Published: 14 March 2012
Cited by 28 | PDF Full-text (425 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In order to analyze and compare the phenolic characteristics of red wine grapes with diverse genetic backgrounds, skin phenolics among 21 different cultivars belonging to Vitis vinifera L., East Asian and North American Vitis species and hybrids, as well as 2 varieties [...] Read more.
In order to analyze and compare the phenolic characteristics of red wine grapes with diverse genetic backgrounds, skin phenolics among 21 different cultivars belonging to Vitis vinifera L., East Asian and North American Vitis species and hybrids, as well as 2 varieties of muscadine grapes were estimated by HPLC-MS/MS. There were 45 anthocyanins, 28 flavonols, 8 flavan-3-ols, 9 cinnamic acids, 5 benzoic acids, 5 ellagic acids and 2 stilbenes detected in all the samples. Total contents of each phenolic type varied significantly among the different grape cultivars investigated. There was also a large variability in the phenolic compositions of different grape groups. The differences in anthocyanin composition were obvious between V. vinifera and non-V. vinifera grapes and also between the grapes originating from Eurasia and North America. Quercetin-3-glucuronide and quercetin-3-glucoside were marker flavonol compounds for Euvitis grape skins. Flavan-3-ol monomers were dominant in the skins of muscadine and non-V. amurensis East Asian grapes, whereas polymers were more common in V. vinifera and North American grapes. The muscadine grapes were very rich in flavonols, flavan-3-ols and ellagic acids. Via principal component analysis, these grape cultivars were clustered into three groups according to their characteristic phenolic content and composition. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A High Molar Extinction Coefficient Bisterpyridyl Homoleptic Ru(II) Complex with trans-2-Methyl-2-butenoic Acid Functionality: Potential Dye for Dye-Sensitized Solar Cells
Int. J. Mol. Sci. 2012, 13(3), 3511-3526; doi:10.3390/ijms13033511
Received: 16 January 2012 / Revised: 25 February 2012 / Accepted: 6 March 2012 / Published: 14 March 2012
Cited by 7 | PDF Full-text (594 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In our continued efforts in the synthesis of ruthenium(II) polypyridine complexes as potential dyes for use in varied applications, such as the dye-sensitized solar cells (DSSCs), this work particularly describes the synthesis, absorption spectrum, redox behavior and luminescence properties of a new [...] Read more.
In our continued efforts in the synthesis of ruthenium(II) polypyridine complexes as potential dyes for use in varied applications, such as the dye-sensitized solar cells (DSSCs), this work particularly describes the synthesis, absorption spectrum, redox behavior and luminescence properties of a new homoleptic ruthenium(II) complex bearing a simple trans-2-methyl-2-butenoic acid functionality as the anchoring ligand on terpyridine moiety. The functionalized terpyridine ligand: 4’-(trans-2-methyl-2-butenoic acid)-terpyridyl (L1) was synthesized by aryl bromide substitution on terpyridine in a basic reaction condition under palladium carbide catalysis. In particular, the photophysical and redox properties of the complex formulated as: bis-4’-(trans-2-methyl-2-butenoic acid)-terpyridyl ruthenium(II) bis-hexafluorophosphate [Ru(L1)2(PF6)2] are significantly better compared to those of [Ru(tpy)2]2+ and compare well with those of the best emitters of Ru(II) polypyridine family containing tridentate ligands. Reasons for the improved photophysical and redox properties of the complex may be attributed partly to the presence of a substituted α,β-unsaturated carboxylic acid moiety leading to increase in the length of π-conjugation bond thereby enhancing the MLCT-MC (Metal-to-ligand-charge transfer-metal centred) energy gap, and to the reduced difference between the minima of the excited and ground states potential energy surfaces. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle A Comparative Study on the Expression, Purification and Functional Characterization of Human Adiponectin in Pichia pastoris and Escherichia coli
Int. J. Mol. Sci. 2012, 13(3), 3549-3562; doi:10.3390/ijms13033549
Received: 4 January 2012 / Revised: 28 February 2012 / Accepted: 6 March 2012 / Published: 15 March 2012
Cited by 8 | PDF Full-text (429 KB) | HTML Full-text | XML Full-text
Abstract
Adiponectin is one of the most bioactive substances secreted by adipose tissue and is involved in the protection against metabolic syndrome, artherosclerosis and type II diabetes. Research into the use of adiponectin as a promising drug for metabolic syndromes requires production of [...] Read more.
Adiponectin is one of the most bioactive substances secreted by adipose tissue and is involved in the protection against metabolic syndrome, artherosclerosis and type II diabetes. Research into the use of adiponectin as a promising drug for metabolic syndromes requires production of this hormone in high quantities considering its molecular isoforms. The objective of this study is to produce recombinant human adiponectin by Pichia pastoris (P-ADP) as a cheap and convenient eukaryotic expression system for potential application in pharmaceutical therapy. For comparison, adiponectin was also expressed using the Escherichia coli (E-ADP) expression system. Adiponectin was constructed by overlap-extension PCR, and cloned in standard cloning vector and hosts. Recombinant expression vectors were cloned in the P. pastoris and E. coli host strains, respectively. SDS-PAGE and western blotting were used to detect and analyse expressed recombinant protein in both systems. Adiponectin was purified by affinity chromatography and quantified using the Bradford Assay. The results of this study indicated that P-ADP quantity (0.111 mg/mL) was higher than that of E-ADP (0.04 mg/mL) and both were produced in soluble form. However, P-ADP was able to form high molecular weights of adiponectin molecules, whilst E-ADP was not able to form isoforms higher than trimer. In addition, P-ADP was more active in lowering blood glucose compared with E-ADP. The two types of proteins were equally efficient and significantly decreased blood triglyceride and increased high density lipoprotein. We conclude that P. pastoris is able to produce high quantity of bioactive adiponectin for potential use in treatment of metabolic syndromes. Full article
Open AccessArticle Autophagy in Premature Senescent Cells Is Activated via AMPK Pathway
Int. J. Mol. Sci. 2012, 13(3), 3563-3582; doi:10.3390/ijms13033563
Received: 7 February 2012 / Revised: 23 February 2012 / Accepted: 6 March 2012 / Published: 16 March 2012
Cited by 14 | PDF Full-text (777 KB) | HTML Full-text | XML Full-text
Abstract
Autophagy is a highly regulated intracellular process involved in the turnover of most cellular constituents and in the maintenance of cellular homeostasis. In this study, we show that the activity of autophagy increases in H2O2 or RasV12-induced senescent fibroblasts. [...] Read more.
Autophagy is a highly regulated intracellular process involved in the turnover of most cellular constituents and in the maintenance of cellular homeostasis. In this study, we show that the activity of autophagy increases in H2O2 or RasV12-induced senescent fibroblasts. Inhibiting autophagy promotes cell apoptosis in senescent cells, suggesting that autophagy activation plays a cytoprotective role. Furthermore, our data indicate that the increase of autophagy in senescent cells is linked to the activation of transcription factor FoxO3A, which blocks ATP generation by transcriptionally up-regulating the expression of PDK4, an inhibitor of pyruvate dehydrogenase complex, thus leading to AMPK activation and mTOR inhibition. These findings suggest a novel mechanism by which FoxO3A factors can activate autophagy via metabolic alteration. Full article
Open AccessArticle Pharmacokinetic Comparison of Ferulic Acid in Normal and Blood Deficiency Rats after Oral Administration of Angelica sinensis, Ligusticum chuanxiong and Their Combination
Int. J. Mol. Sci. 2012, 13(3), 3583-3597; doi:10.3390/ijms13033583
Received: 19 October 2011 / Revised: 28 February 2012 / Accepted: 2 March 2012 / Published: 16 March 2012
Cited by 28 | PDF Full-text (252 KB) | HTML Full-text | XML Full-text
Abstract
Radix Angelica Sinensis (RAS) and Rhizome Ligusticum (RLC) combination is a popular herb pair commonly used in clinics for treatment of blood deficiency syndrome in China. The aim of this study is to compare the pharmacokinetic properties of ferulic acid (FA), a main bioactive constituent in both RAS and RLC, between normal and blood deficiency syndrome animals, and to investigate the influence of compatibility of RAS and RLC on the pharmacokinetic of FA. The blood deficiency rats were induced by injecting 2% Acetyl phenylhydrazine (APH) on the first day, every other day, to a total of five times, at the dosage of 100, 50, 50, 30, 30 mg/kg body mass, respectively. Quantification of FA in rat plasma was achieved by using a simple and rapid HPLC method. Plasma samples were collected at different time points to construct pharmacokinetic profiles by plotting drug concentration versus time, and estimate pharmacokinetic parameters. Between normal and blood deficiency model groups, both AUC(0–t) and Cmax of FA in blood deficiency rats after RAS-RLC extract administration increased significantly (P < 0.05), while clearance (CL) decreased significantly. Among three blood deficiency model groups, t1/2α, Vd, AUC(0–t) and AUC(0–∞) all increased significantly in the RAS-RLC extract group compared with the RAS group. The results indicated that FA was absorbed better and eliminated slower in blood deficiency rats; RLC could significantly prolong the half-life of distribution, increase the volume of distribution and the absorption amount of FA of RAS in blood deficiency rats, which may be due to the synergic action when RAS and RLC were used together to treat blood deficiency syndrome. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Improvement of Carbon Tetrachloride-Induced Acute Hepatic Failure by Transplantation of Induced Pluripotent Stem Cells without Reprogramming Factor c-Myc
Int. J. Mol. Sci. 2012, 13(3), 3598-3617; doi:10.3390/ijms13033598
Received: 16 January 2012 / Revised: 13 February 2012 / Accepted: 28 February 2012 / Published: 16 March 2012
Cited by 5 | PDF Full-text (920 KB) | HTML Full-text | XML Full-text
Abstract
The only curative treatment for hepatic failure is liver transplantation. Unfortunately, this treatment has several major limitations, as for example donor organ shortage. A previous report demonstrated that transplantation of induced pluripotent stem cells without reprogramming factor c-Myc (3-genes iPSCs) attenuates thioacetamide-induced [...] Read more.
The only curative treatment for hepatic failure is liver transplantation. Unfortunately, this treatment has several major limitations, as for example donor organ shortage. A previous report demonstrated that transplantation of induced pluripotent stem cells without reprogramming factor c-Myc (3-genes iPSCs) attenuates thioacetamide-induced hepatic failure with minimal incidence of tumorigenicity. In this study, we investigated whether 3-genes iPSC transplantation is capable of rescuing carbon tetrachloride (CCl4)-induced fulminant hepatic failure and hepatic encephalopathy in mice. Firstly, we demonstrated that 3-genes iPSCs possess the capacity to differentiate into hepatocyte-like cells (iPSC-Heps) that exhibit biological functions and express various hepatic specific markers. 3-genes iPSCs also exhibited several antioxidant enzymes that prevented CCl4-induced reactive oxygen species production and cell death. Intraperitoneal transplantation of either 3-genes iPSCs or 3-genes iPSC-Heps significantly reduced hepatic necrotic areas, improved hepatic functions, and survival rate in CCl4-treated mice. CCl4-induced hepatic encephalopathy was also improved by 3-genes iPSC transplantation. Hoechst staining confirmed the successful engraftment of both 3-genes iPSCs and 3-genes iPSC-Heps, indicating the homing properties of these cells. The most pronounced hepatoprotective effect of iPSCs appeared to originate from the highest antioxidant activity of 3-gene iPSCs among all transplanted cells. In summary, our findings demonstrated that 3-genes iPSCs serve as an available cell source for the treatment of an experimental model of acute liver diseases. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Optimization of Serine Protease Purification from Mango (Mangifera indica cv. Chokanan) Peel in Polyethylene Glycol/Dextran Aqueous Two Phase System
Int. J. Mol. Sci. 2012, 13(3), 3636-3649; doi:10.3390/ijms13033636
Received: 5 December 2011 / Revised: 29 February 2012 / Accepted: 5 March 2012 / Published: 19 March 2012
Cited by 7 | PDF Full-text (377 KB) | HTML Full-text | XML Full-text
Abstract
Mango peel is a good source of protease but remains an industrial waste. This study focuses on the optimization of polyethylene glycol (PEG)/dextran-based aqueous two-phase system (ATPS) to purify serine protease from mango peel. The activity of serine protease in different phase [...] Read more.
Mango peel is a good source of protease but remains an industrial waste. This study focuses on the optimization of polyethylene glycol (PEG)/dextran-based aqueous two-phase system (ATPS) to purify serine protease from mango peel. The activity of serine protease in different phase systems was studied and then the possible relationship between the purification variables, namely polyethylene glycol molecular weight (PEG, 4000–12,000 g·mol−1), tie line length (−3.42–35.27%), NaCl (−2.5–11.5%) and pH (4.5–10.5) on the enzymatic properties of purified enzyme was investigated. The most significant effect of PEG was on the efficiency of serine protease purification. Also, there was a significant increase in the partition coefficient with the addition of 4.5% of NaCl to the system. This could be due to the high hydrophobicity of serine protease compared to protein contaminates. The optimum conditions to achieve high partition coefficient (84.2) purification factor (14.37) and yield (97.3%) of serine protease were obtained in the presence of 8000 g·mol−1 of PEG, 17.2% of tie line length and 4.5% of NaCl at pH 7.5. The enzymatic properties of purified serine protease using PEG/dextran ATPS showed that the enzyme could be purified at a high purification factor and yield with easy scale-up and fast processing. Full article
Open AccessArticle Prediction of Bioluminescent Proteins Using Auto Covariance Transformation of Evolutional Profiles
Int. J. Mol. Sci. 2012, 13(3), 3650-3660; doi:10.3390/ijms13033650
Received: 10 January 2012 / Revised: 21 February 2012 / Accepted: 5 March 2012 / Published: 19 March 2012
Cited by 7 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Bioluminescent proteins are important for various cellular processes, such as gene expression analysis, drug discovery, bioluminescent imaging, toxicity determination, and DNA sequencing studies. Hence, the correct identification of bioluminescent proteins is of great importance both for helping genome annotation and providing a [...] Read more.
Bioluminescent proteins are important for various cellular processes, such as gene expression analysis, drug discovery, bioluminescent imaging, toxicity determination, and DNA sequencing studies. Hence, the correct identification of bioluminescent proteins is of great importance both for helping genome annotation and providing a supplementary role to experimental research to obtain insight into bioluminescent proteins’ functions. However, few computational methods are available for identifying bioluminescent proteins. Therefore, in this paper we develop a new method to predict bioluminescent proteins using a model based on position specific scoring matrix and auto covariance. Tested by 10-fold cross-validation and independent test, the accuracy of the proposed model reaches 85.17% for the training dataset and 90.71% for the testing dataset respectively. These results indicate that our predictor is a useful tool to predict bioluminescent proteins. This is the first study in which evolutionary information and local sequence environment information have been successfully integrated for predicting bioluminescent proteins. A web server (BLPre) that implements the proposed predictor is freely available. Full article
Open AccessArticle Synthesis and Antimicrobial Studies of Some Novel Bis-[1,3,4]thiadiazole and Bis-thiazole Pendant to Thieno[2,3-b]thiophene Moiety
Int. J. Mol. Sci. 2012, 13(3), 3661-3670; doi:10.3390/ijms13033661
Received: 16 January 2012 / Revised: 7 March 2012 / Accepted: 13 March 2012 / Published: 19 March 2012
Cited by 13 | PDF Full-text (244 KB) | HTML Full-text | XML Full-text
Abstract
The synthetic utility of 3,3’-(3,4-dimethylthieno[2,3-b]thiophene-2,5-diyl)bis (3-oxopropanenitrile) (1) in the synthesis of some novel bis-[1,3,4-thiadiazole] 6a–g and bis-thiazole 10 and 13 derivatives with thieno[2,3-b]thiophene moiety is reported. Antimicrobial evaluation of some selected examples from the synthesized products was carried out and [...] Read more.
The synthetic utility of 3,3’-(3,4-dimethylthieno[2,3-b]thiophene-2,5-diyl)bis (3-oxopropanenitrile) (1) in the synthesis of some novel bis-[1,3,4-thiadiazole] 6a–g and bis-thiazole 10 and 13 derivatives with thieno[2,3-b]thiophene moiety is reported. Antimicrobial evaluation of some selected examples from the synthesized products was carried out and showed promising results. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Synthesis and Biological Activities of a 3'-Azido Analogue of Doxorubicin Against Drug-Resistant Cancer Cells
Int. J. Mol. Sci. 2012, 13(3), 3671-3684; doi:10.3390/ijms13033671
Received: 13 February 2012 / Revised: 7 March 2012 / Accepted: 13 March 2012 / Published: 19 March 2012
Cited by 3 | PDF Full-text (467 KB) | HTML Full-text | XML Full-text
Abstract
Doxorubicin (DOX), an anthracycline antibiotic, is one of the most active anticancer chemotherapeutic agents. The clinical use of DOX, however, is limited by the dose-dependant P-glycoprotein (P-gp)-mediated resistance. Herein, a 3′-azido analogue of DOX (ADOX) was prepared from daunorubicin (DNR). ADOX exhibited [...] Read more.
Doxorubicin (DOX), an anthracycline antibiotic, is one of the most active anticancer chemotherapeutic agents. The clinical use of DOX, however, is limited by the dose-dependant P-glycoprotein (P-gp)-mediated resistance. Herein, a 3′-azido analogue of DOX (ADOX) was prepared from daunorubicin (DNR). ADOX exhibited potent antitumor activities in drug-sensitive (MCF-7 and K562) and drug-resistant cell lines (MCF-7/DNR, K562/DOX), respectively. The drug resistance index (DRI) values of ADOX were much lower than that of DOX. The cytotoxicity experiments of ADOX or DOX against K562/DOX, with or without P-gp inhibitor, indicated that ADOX circumvents resistance by abolishing the P-gp recognition. This conclusion was further supported by drug influx/efflux flow cytometry experiments, as well as by molecular docking of ADOX to P-gp. In vivo animal tests, ADOX exhibited higher activity and less toxicity than DOX. The current data warranted ADOX for additional pre-clinical evaluations for new drug development. Full article
Open AccessArticle Cellulose Biosynthesis Inhibitors: Comparative Effect on Bean Cell Cultures
Int. J. Mol. Sci. 2012, 13(3), 3685-3702; doi:10.3390/ijms13033685
Received: 1 December 2011 / Revised: 5 January 2012 / Accepted: 8 March 2012 / Published: 20 March 2012
Cited by 6 | PDF Full-text (396 KB) | HTML Full-text | XML Full-text
Abstract
The variety of bioassays developed to evaluate different inhibition responses for cellulose biosynthesis inhibitors makes it difficult to compare the results obtained. This work aims (i) to test a single inhibitory assay for comparing active concentrations of a set of putative cellulose [...] Read more.
The variety of bioassays developed to evaluate different inhibition responses for cellulose biosynthesis inhibitors makes it difficult to compare the results obtained. This work aims (i) to test a single inhibitory assay for comparing active concentrations of a set of putative cellulose biosynthesis inhibitors and (ii) to characterize their effect on cell wall polysaccharides biosynthesis following a short-term exposure. For the first aim, dose-response curves for inhibition of dry-weight increase following a 30 days exposure of bean callus-cultured cells to these inhibitors were obtained. The compound concentration capable of inhibiting dry weight increase by 50% compared to control (I50) ranged from subnanomolar (CGA 325′615) to nanomolar (AE F150944, flupoxam, triazofenamide and oxaziclomefone) and micromolar (dichlobenil, quinclorac and compound 1) concentrations. In order to gain a better understanding of the effect of the putative inhibitors on cell wall polysaccharides biosynthesis, the [14C]glucose incorporation into cell wall fractions was determined after a 20 h exposure of cell suspensions to each inhibitor at their I50 value. All the inhibitors tested decreased glucose incorporation into cellulose with the exception of quinclorac, which increased it. In some herbicide treatments, reduction in the incorporation into cellulose was accompanied by an increase in the incorporation into other fractions. In order to appreciate the effect of the inhibitors on cell wall partitioning, a cluster and Principal Component Analysis (PCA) based on the relative contribution of [14C]glucose incorporation into the different cell wall fractions were performed, and three groups of compounds were identified. The first group included quinclorac, which increased glucose incorporation into cellulose; the second group consisted of compound 1, CGA 325′615, oxaziclomefone and AE F150944, which decreased the relative glucose incorporation into cellulose but increased it into tightly-bound cellulose fractions; and the third group, comprising flupoxam, triazofenamide and dichlobenil, decreased the relative glucose incorporation into cellulose and increased it into a pectin rich fraction. Full article
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Open AccessArticle Effect of Polyethylene Glycol Modification of TiO2 Nanoparticles on Cytotoxicity and Gene Expressions in Human Cell Lines
Int. J. Mol. Sci. 2012, 13(3), 3703-3717; doi:10.3390/ijms13033703
Received: 27 December 2011 / Revised: 13 March 2012 / Accepted: 14 March 2012 / Published: 21 March 2012
Cited by 26 | PDF Full-text (280 KB) | HTML Full-text | XML Full-text
Abstract
Nanoparticles (NPs) are tiny materials used in a wide range of industrial and medical applications. Titanium dioxide (TiO2) is a type of nanoparticle that is widely used in paints, pigments, and cosmetics; however, little is known about the impact of [...] Read more.
Nanoparticles (NPs) are tiny materials used in a wide range of industrial and medical applications. Titanium dioxide (TiO2) is a type of nanoparticle that is widely used in paints, pigments, and cosmetics; however, little is known about the impact of TiO2 on human health and the environment. Therefore, considerable research has focused on characterizing the potential toxicity of nanoparticles such as TiO2 and on understanding the mechanism of TiO2 NP-induced nanotoxicity through the evaluation of biomarkers. Uncoated TiO2 NPs tend to aggregate in aqueous media, and these aggregates decrease cell viability and induce expression of stress-related genes, such as those encoding interleukin-6 (IL-6) and heat shock protein 70B’ (HSP70B’), indicating that TiO2 NPs induce inflammatory and heat shock responses. In order to reduce their toxicity, we conjugated TiO2 NPs with polyethylene glycol (PEG) to eliminate aggregation. Our findings indicate that modifying TiO2 NPs with PEG reduces their cytotoxicity and reduces the induction of stress-related genes. Our results also suggest that TiO2 NP-induced effects on cytotoxicity and gene expression vary depending upon the cell type and surface modification. Full article
(This article belongs to the Special Issue Nanotoxicology)
Open AccessArticle Photosensized Controlling Benzyl Methacrylate-Based Matrix Enhanced Eu3+ Narrow-Band Emission for Fluorescence Applications
Int. J. Mol. Sci. 2012, 13(3), 3718-3737; doi:10.3390/ijms13033718
Received: 3 February 2012 / Revised: 14 March 2012 / Accepted: 15 March 2012 / Published: 21 March 2012
Cited by 2 | PDF Full-text (677 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
This study synthesized a europium (Eu3+) complex Eu(DBM)3Cl-MIP (DBM = dibenzoyl methane; Cl-MIP = 2-(2-chlorophenyl)-1-methyl-1H-imidazo[4,5-f][1,10]phenanthroline) dispersed in a benzyl methacrylate (BMA) monomer and treated with ultraviolet (UV) light for polymerization. Spectral results showed that the europium [...] Read more.
This study synthesized a europium (Eu3+) complex Eu(DBM)3Cl-MIP (DBM = dibenzoyl methane; Cl-MIP = 2-(2-chlorophenyl)-1-methyl-1H-imidazo[4,5-f][1,10]phenanthroline) dispersed in a benzyl methacrylate (BMA) monomer and treated with ultraviolet (UV) light for polymerization. Spectral results showed that the europium complex containing an antenna, Cl-MIP, which had higher triplet energy into the Eu3+ energy level, was an energetically enhanced europium emission. Typical stacking behaviors of π–π interactions between the ligands and the Eu3+-ion were analyzed using single crystal X-ray diffraction. Regarding the luminescence performance of this europium composite, the ligand/defect emission was suppressed by dispersion in a poly-BMA (PBMA) matrix. The underlying mechanism of the effective enhancement of the pure Eu3+ emission was attributed to the combined effects of structural modifications, defect emissions, and carrier charge transfer. Fluorescence spectra were compared to the composite of optimized Eu3+ emission where they were subsequently chelated to four metal ions via carboxylate groups on the BMA unit. The optical enhanced europium composite clearly demonstrated highly efficient optical responses and is, therefore a promising application as an optical detection material. Full article
(This article belongs to the Special Issue Correlation Analysis Applied to Solvolysis Reactions)
Open AccessArticle Antihyperglycemic and Antioxidative Effects of Hydroxyethyl Methylcellulose (HEMC) and Hydroxypropyl Methylcellulose (HPMC) in Mice Fed with a High Fat Diet
Int. J. Mol. Sci. 2012, 13(3), 3738-3750; doi:10.3390/ijms13033738
Received: 2 November 2011 / Revised: 2 March 2012 / Accepted: 16 March 2012 / Published: 21 March 2012
Cited by 4 | PDF Full-text (260 KB) | HTML Full-text | XML Full-text
Abstract
The effect of dietary feeding of hydroxyethyl methylcellulose (HEMC) and hydroxypropyl methylcellulose (HPMC) on the glucose metabolism and antioxidative status in mice under high fat diet conditions was investigated. The mice were randomly divided and given experimental diets for six weeks: normal [...] Read more.
The effect of dietary feeding of hydroxyethyl methylcellulose (HEMC) and hydroxypropyl methylcellulose (HPMC) on the glucose metabolism and antioxidative status in mice under high fat diet conditions was investigated. The mice were randomly divided and given experimental diets for six weeks: normal control (NC group), high fat (HF group), and high fat supplemented with either HEMC (HF+HEMC group) or HPMC (HF+HPMC group). At the end of the experimental period, the HF group exhibited markedly higher blood glucose and insulin levels as well as a higher erythrocyte lipid peroxidation rate relative to the control group. However, diet supplementation of HEMC and HPMC was found to counteract the high fat-induced hyperglycemia and oxidative stress via regulation of antioxidant and hepatic glucose-regulating enzyme activities. These findings illustrate that HEMC and HPMC were similarly effective in improving the glucose metabolism and antioxidant defense system in high fat-fed mice and they may be beneficial as functional biomaterials in the development of therapeutic agents against high fat diet-induced hyperglycemia and oxidative stress. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Expression Analysis of Four Peroxiredoxin Genes from Tamarix hispida in Response to Different Abiotic Stresses and Exogenous Abscisic Acid (ABA)
Int. J. Mol. Sci. 2012, 13(3), 3751-3764; doi:10.3390/ijms13033751
Received: 3 February 2012 / Revised: 3 March 2012 / Accepted: 6 March 2012 / Published: 21 March 2012
Cited by 5 | PDF Full-text (308 KB) | HTML Full-text | XML Full-text
Abstract
Peroxiredoxins (Prxs) are a recently discovered family of antioxidant enzymes that catalyze the reduction of peroxides and alkyl peroxides. In this study, four Prx genes (named as ThPrxII, ThPrxIIE, ThPrxIIF, and Th2CysPrx) were cloned from Tamarix hispida. [...] Read more.
Peroxiredoxins (Prxs) are a recently discovered family of antioxidant enzymes that catalyze the reduction of peroxides and alkyl peroxides. In this study, four Prx genes (named as ThPrxII, ThPrxIIE, ThPrxIIF, and Th2CysPrx) were cloned from Tamarix hispida. Their expression profiles in response to stimulus of NaCl, NaHCO3, PEG, CdCl2 and abscisic acid (ABA) in roots, stems and leaves of T. hispida were investigated using real-time RT-PCR. The results showed that the four ThPrxs were all expressed in roots, stems and leaves. Furthermore, the transcript levels of ThPrxIIE and ThPrxII were the lowest and the highest, respectively, in all tissue types. All the ThPrx genes were induced by both NaCl and NaHCO3 and reached their highest expression levels at the onset of stress in roots. Under PEG and CdCl2 stress, the expression patterns of these ThPrxs showed temporal and spatial specificity. The expressions of the ThPrxs were all differentially regulated by ABA, indicating that they are all involved in the ABA signaling pathway. These findings reveal a complex regulation of Prxs that is dependent on the type of Prx, tissue, and the signaling molecule. The divergence of the stress-dependent transcriptional regulation of the ThPrx gene family in T. hispida may provide an essential basis for the elucidation of Prx function in future work. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessCommunication Production of Protocatechuic Acid in Bacillus Thuringiensis ATCC33679
Int. J. Mol. Sci. 2012, 13(3), 3765-3772; doi:10.3390/ijms13033765
Received: 29 January 2012 / Revised: 16 March 2012 / Accepted: 19 March 2012 / Published: 21 March 2012
Cited by 4 | PDF Full-text (167 KB) | HTML Full-text | XML Full-text
Abstract
Protocatechuic acid, or 3,4-dihydroxybenzoic acid, is produced by both soil and marine bacteria in the free form and as the iron binding component of the siderophore petrobactin. The soil bacterium, Bacillus thuringiensis kurstaki ATCC 33679, contains the asb operon, but does not [...] Read more.
Protocatechuic acid, or 3,4-dihydroxybenzoic acid, is produced by both soil and marine bacteria in the free form and as the iron binding component of the siderophore petrobactin. The soil bacterium, Bacillus thuringiensis kurstaki ATCC 33679, contains the asb operon, but does not produce petrobactin. Iron restriction resulted in diminished B. thuringiensis kurstaki ATCC 33679 growth and the production of catechol(s). The gene product responsible for protocatechuic acid (asbF) and its receptor (fatB) were expressed during stationary phase growth. Gene expression varied with growth temperature, with optimum levels occurring well below the Bacillus anthracis virulence temperature of 37 °C. Regulation of protocatechuic acid suggests a possible role for this compound during soil growth cycles. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Increasing the X-ray Diffraction Power of Protein Crystals by Dehydration: The Case of Bovine Serum Albumin and a Survey of Literature Data
Int. J. Mol. Sci. 2012, 13(3), 3782-3800; doi:10.3390/ijms13033782
Received: 9 February 2012 / Revised: 7 March 2012 / Accepted: 8 March 2012 / Published: 21 March 2012
Cited by 26 | PDF Full-text (390 KB) | HTML Full-text | XML Full-text
Abstract
Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum [...] Read more.
Serum albumin is one of the most widely studied proteins. It is the most abundant protein in plasma with a typical concentration of 5 g/100 mL and the principal transporter of fatty acids in plasma. While the crystal structures of human serum albumin (HSA) free and in complex with fatty acids, hemin, and local anesthetics have been characterized, no crystallographic models are available on bovine serum albumin (BSA), presumably because of the poor diffraction power of existing hexagonal BSA crystals. Here, the crystallization and diffraction data of a new BSA crystal form, obtained by the hanging drop method using MPEG 5K as precipitating agent, are presented. The crystals belong to space group C2, with unit-cell parameters a = 216.45 Å, b = 44.72 Å, c = 140.18 Å, β = 114.5°. Dehydration was found to increase the diffraction limit of BSA crystals from ~8 Å to 3.2 Å, probably by improving the packing of protein molecules in the crystal lattice. These results, together with a survey of more than 60 successful cases of protein crystal dehydration, confirm that it can be a useful procedure to be used in initial screening as a method of improving the diffraction limits of existing crystals. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effect of Osmolytes on Protein Fibrillation
Int. J. Mol. Sci. 2012, 13(3), 3801-3819; doi:10.3390/ijms13033801
Received: 9 February 2012 / Revised: 10 March 2012 / Accepted: 13 March 2012 / Published: 21 March 2012
Cited by 16 | PDF Full-text (413 KB) | HTML Full-text | XML Full-text
Abstract
Osmolytes are small molecules that are exploited by cells as a protective system against stress conditions. They favour compact protein states which makes them stabilize globular proteins in vitro and promote folding. Conversely, this preference for compact states promotes aggregation of unstructured [...] Read more.
Osmolytes are small molecules that are exploited by cells as a protective system against stress conditions. They favour compact protein states which makes them stabilize globular proteins in vitro and promote folding. Conversely, this preference for compact states promotes aggregation of unstructured proteins. Here we combine a brief review of the effect of osmolytes on protein fibrillation with a report of the effect of osmolytes on the unstructured peptide hormone glucagon. Our results show that osmolytes either accelerate the fibrillation kinetics or leave them unaffected, with the exception of the osmolyte taurine. Furthermore, the osmolytes that affected the shape of the fibrillation time profile led to fibrils with different structure as revealed by CD. The structural changes induced by Pro, Ser and choline-O-sulfate could be due to specific osmolytes binding to the peptides, stabilizing an otherwise labile fibrillation intermediate. Full article
(This article belongs to the Special Issue Protein Aggregation)
Open AccessArticle Antinociceptive and Anti-Inflammatory Effects of Ethanol Extract from Vernonia polyanthes Leaves in Rodents
Int. J. Mol. Sci. 2012, 13(3), 3887-3899; doi:10.3390/ijms13033887
Received: 26 December 2011 / Revised: 2 March 2012 / Accepted: 19 March 2012 / Published: 22 March 2012
Cited by 7 | PDF Full-text (219 KB) | HTML Full-text | XML Full-text
Abstract
The ethanol extract from Vernonia polyanthes leaves (EEVP) was investigated for antinociceptive and anti-inflammatory effects at the doses (p.o.) of 100, 200 and 400 mg/kg in animal models. The extract reduced the number of abdominal contortions by 16.75% and 31.44% at a [...] Read more.
The ethanol extract from Vernonia polyanthes leaves (EEVP) was investigated for antinociceptive and anti-inflammatory effects at the doses (p.o.) of 100, 200 and 400 mg/kg in animal models. The extract reduced the number of abdominal contortions by 16.75% and 31.44% at a dose of 200 and 400 mg/kg, respectively. The results obtained showed that EEVP exerted a significant antinociceptive effect in the two phases of formalin. The EEVP increased the reaction time on a hot plate at the doses of 100, 200 and 400 mg/kg after 90 min of treatment. The paw edema was reduced by EEVP at the doses of 100, 200 and 400 mg/kg after 4 h of application of carrageenan. Doses of 200 and 400 mg/kg, administered 4 h before the carrageenan injection, significantly reduced the exudate volume (29.25 and 45.74%, respectively) and leukocyte migration (18.19 and 27.95%, respectively). These results suggest that V. polyanthes can be an active source of substances with antinociceptive and anti-inflammatory activities. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genetic Diversity of the Endemic and Medicinally Important Plant Rheum officinale as Revealed by Inter-Simpe Sequence Repeat (ISSR) Markers
Int. J. Mol. Sci. 2012, 13(3), 3900-3915; doi:10.3390/ijms13033900
Received: 3 February 2012 / Revised: 8 March 2012 / Accepted: 13 March 2012 / Published: 22 March 2012
Cited by 19 | PDF Full-text (385 KB) | HTML Full-text | XML Full-text
Abstract
Rheum officinale Baill., an important but endangered medicinal herb, is endemic to China. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 12 populations of R. officinale. Thirteen selected primers yielded 189 bright and discernible [...] Read more.
Rheum officinale Baill., an important but endangered medicinal herb, is endemic to China. Inter-simple sequence repeat (ISSR) markers were employed to investigate the genetic diversity and differentiation of 12 populations of R. officinale. Thirteen selected primers yielded 189 bright and discernible bands, with an average of 14.54 per primer. The genetic diversity was low at the population level, but pretty high at the species level (H = 0.1008, I = 0.1505, PPB = 28.95% vs. H = 0.3341, I = 0.5000, PPB = 95.24%, respectively) by POPGENE analysis. Analysis of molecular variance (AMOVA) showed that the genetic variation was found mainly among populations (74.38%), in line with the limited gene flow (Nm = 0.2766) among populations. Mantel test revealed a significant correlation between genetic and geographic distances (r = 0.5381, P = 0.002), indicating the role of geographic isolation in shaping the present population genetic structure. Both Bayesian analysis and UPGMA cluster analysis demonstrated the similar results. Our results imply that the conservation efforts should aim to preserve all the extant populations of this endangered species, and cultivation is proposed in this study. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Enhancement of Biocontrol Efficacy of Pichia carribbica to Postharvest Diseases of Strawberries by Addition of Trehalose to the Growth Medium
Int. J. Mol. Sci. 2012, 13(3), 3916-3932; doi:10.3390/ijms13033916
Received: 13 February 2012 / Revised: 2 March 2012 / Accepted: 19 March 2012 / Published: 22 March 2012
Cited by 7 | PDF Full-text (357 KB) | HTML Full-text | XML Full-text
Abstract
The effects of trehalose on the antagonistic activity of Pichia caribbica against Rhizopus decay and gray mold decay of strawberries and the possible mechanisms involved were investigated. The proteomic analysis and comparison of P. carribbica in response to trehalose was analyzed based [...] Read more.
The effects of trehalose on the antagonistic activity of Pichia caribbica against Rhizopus decay and gray mold decay of strawberries and the possible mechanisms involved were investigated. The proteomic analysis and comparison of P. carribbica in response to trehalose was analyzed based on two-dimensional gel electrophoresis. The antagonistic activity of P. carribbica harvested from the culture media of NYDB amended with trehalose at 0.5% was improved greatly compared with that without trehalose. The PPO (Polyphenoloxidase) and POD (Peroxidase) activity of strawberries treated with P. carribbica cultured in the NYDB media amended with trehalose at 0.5% was higher than that of the strawberries treated with P. carribbica harvested from NYDB. The β-1, 3-glucanase activity of strawberries treated with P. carribbica cultured in the NYDB media amended with trehalose at 0.5% was also higher than that of the strawberries treated with P. carribbica harvested from NYDB and the control. Several differentially expressed proteins of P. carribbica in response to trehalose were identified in the cellular proteome, most of them were related to basic metabolism. Full article
Open AccessArticle A Single-Chamber Microbial Fuel Cell without an Air Cathode
Int. J. Mol. Sci. 2012, 13(3), 3933-3948; doi:10.3390/ijms13033933
Received: 23 November 2011 / Revised: 19 January 2012 / Accepted: 14 March 2012 / Published: 22 March 2012
Cited by 5 | PDF Full-text (679 KB) | HTML Full-text | XML Full-text
Abstract
Microbial fuel cells (MFCs) represent a novel technology for wastewater treatment with electricity production. Electricity generation with simultaneous nitrate reduction in a single-chamber MFC without air cathode was studied, using glucose (1 mM) as the carbon source and nitrate (1 mM) as [...] Read more.
Microbial fuel cells (MFCs) represent a novel technology for wastewater treatment with electricity production. Electricity generation with simultaneous nitrate reduction in a single-chamber MFC without air cathode was studied, using glucose (1 mM) as the carbon source and nitrate (1 mM) as the final electron acceptor employed by Bacillus subtilis under anaerobic conditions. Increasing current as a function of decreased nitrate concentration and an increase in biomass were observed with a maximum current of 0.4 mA obtained at an external resistance (Rext) of 1 KΩ without a platinum catalyst of air cathode. A decreased current with complete nitrate reduction, with further recovery of the current immediately after nitrate addition, indicated the dependence of B. subtilis on nitrate as an electron acceptor to efficiently produce electricity. A power density of 0.0019 mW/cm2 was achieved at an Rext of 220 Ω. Cyclic voltammograms (CV) showed direct electron transfer with the involvement of mediators in the MFC. The low coulombic efficiency (CE) of 11% was mainly attributed to glucose fermentation. These results demonstrated that electricity generation is possible from wastewater containing nitrate, and this represents an alternative technology for the cost-effective and environmentally benign treatment of wastewater. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Cooperative Modulation of Mineral Growth by Prismatic-Associated Asprich Sequences and Mg(II)
Int. J. Mol. Sci. 2012, 13(3), 3949-3958; doi:10.3390/ijms13033949
Received: 14 February 2012 / Revised: 3 March 2012 / Accepted: 19 March 2012 / Published: 22 March 2012
Cited by 5 | PDF Full-text (658 KB) | HTML Full-text | XML Full-text
Abstract
Cooperative effects of magnesium ions and acidic polypeptides originating from a family of proteins known as Asprich (mollusk Atrina rigida) were studied. In our previous studies, these two acidic polypeptides were found to be effective in controlling the morphology of the [...] Read more.
Cooperative effects of magnesium ions and acidic polypeptides originating from a family of proteins known as Asprich (mollusk Atrina rigida) were studied. In our previous studies, these two acidic polypeptides were found to be effective in controlling the morphology of the calcium carbonate mineral, the main inorganic constituent of prismatic layer of the mollusk shell. Since these Asprich sequences are believed to contain a putative magnesium binding domain, the morphology-controlling effects were further investigated with the addition of magnesium ions. The mineral morphology was dramatically changed by the combined influence of each polypeptides and the magnesium ions, substantiating the recognized importance of magnesium in the formation of calcium carbonate-based biominerals. Full article
(This article belongs to the Special Issue Composite Materials in Skeletal Engineering)
Open AccessArticle Therapeutic Effect of Arsenicum album on Leukocytes
Int. J. Mol. Sci. 2012, 13(3), 3979-3987; doi:10.3390/ijms13033979
Received: 14 February 2012 / Revised: 21 February 2012 / Accepted: 15 March 2012 / Published: 22 March 2012
Cited by 4 | PDF Full-text (460 KB) | HTML Full-text | XML Full-text
Abstract
The therapeutic effects of homoeopathic Arsenicum album potencies were investigated in-vitro, using a continuous cell line (MT4), pre-intoxicated with arsenic trioxide (As2O3), and then treated with succussed and unsuccussed homoeopathic potencies, 6CH, 30CH and 200CH. This study [...] Read more.
The therapeutic effects of homoeopathic Arsenicum album potencies were investigated in-vitro, using a continuous cell line (MT4), pre-intoxicated with arsenic trioxide (As2O3), and then treated with succussed and unsuccussed homoeopathic potencies, 6CH, 30CH and 200CH. This study aimed to verify the homoeopathic law of similars and to determine whether potencies diluted beyond Avogadro’s constant had physiological effects on cells; whether various potencies would cause different effects as suggested by the concept of hormesis; whether succussed and unsuccussed homoeopathic potencies had different effects on the cells; and to establish whether a biotechnological method could be used to evaluate the above. As2O3 was used to pre-intoxicate and the MTT assay was used to measure the percentage cytotoxicity and half maximal inhibitory concentration (IC50) of the cells. The homoeopathic potencies of Arsenicum album (6CH, 30CH and 200CH) were prepared by either succussing or allowing to diffuse for 30 s. After pre-intoxication of the MT4 cells with the IC50 As2O3 and treatment with succussed and unsuccussed Arsenicum album (6CH-200CH), the cell viability increased with increasing potency from 81% to 194% (over 72 h). The treatments and the times of exposure were found to be statistically significant determinants of cell viability, whereas succussion did not cause any significant variation in the results. The study provided evidence that a biotechnological method (namely cell viability) may be used to scientifically evaluate the physiological effects of homoeopathic potencies on human cells; it confirmed that the homoeopathic potencies did have therapeutic effects; and that succussion was not required in the potentization method in order to produce a curative remedy. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Dihydrolipoic Acid Induces Cytotoxicity in Mouse Blastocysts through Apoptosis Processes
Int. J. Mol. Sci. 2012, 13(3), 3988-4002; doi:10.3390/ijms13033988
Received: 20 February 2012 / Revised: 15 March 2012 / Accepted: 16 March 2012 / Published: 22 March 2012
Cited by 1 | PDF Full-text (374 KB) | HTML Full-text | XML Full-text
Abstract
α-Lipoic acid (LA) is a thiol with antioxidant properties that protects against oxidative stress-induced apoptosis. LA is absorbed from the diet, taken up by cells and tissues, and subsequently reduced to dihydrolipoic acid (DHLA). In view of the recent application of DHLA [...] Read more.
α-Lipoic acid (LA) is a thiol with antioxidant properties that protects against oxidative stress-induced apoptosis. LA is absorbed from the diet, taken up by cells and tissues, and subsequently reduced to dihydrolipoic acid (DHLA). In view of the recent application of DHLA as a hydrophilic nanomaterial preparation, determination of its biosafety profile is essential. In the current study, we examined the cytotoxic effects of DHLA on mouse embryos at the blastocyst stage, subsequent embryonic attachment and outgrowth in vitro, in vivo implantation by embryo transfer, and early embryonic development in an animal model. Blastocysts treated with 50 μM DHLA exhibited significantly increased apoptosis and a corresponding decrease in total cell number. Notably, the implantation success rates of blastocysts pretreated with DHLA were lower than that of their control counterparts. Moreover, in vitro treatment with 50 μM DHLA was associated with increased resorption of post-implantation embryos and decreased fetal weight. Data obtained using an in vivo mouse model further disclosed that consumption of drinking water containing 100 μM DHLA led to decreased early embryo development, specifically, inhibition of development to the blastocyst stage. However, it appears that concentrations of DHLA lower than 50 μM do not exert a hazardous effect on embryonic development. Our results collectively indicate that in vitro and in vivo exposure to concentrations of DHLA higher than 50 μM DHLA induces apoptosis and retards early pre- and post-implantation development, and support the potential of DHLA to induce embryonic cytotoxicity. Full article
(This article belongs to the Section Molecular Toxicology)

Review

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Open AccessReview Role of SDF1/CXCR4 Interaction in Experimental Hemiplegic Models with Neural Cell Transplantation
Int. J. Mol. Sci. 2012, 13(3), 2636-2649; doi:10.3390/ijms13032636
Received: 1 December 2011 / Revised: 8 February 2012 / Accepted: 14 February 2012 / Published: 28 February 2012
Cited by 5 | PDF Full-text (914 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Much attention has been focused on neural cell transplantation because of its promising clinical applications. We have reported that embryonic stem (ES) cell derived neural stem/progenitor cell transplantation significantly improved motor functions in a hemiplegic mouse model. It is important to understand [...] Read more.
Much attention has been focused on neural cell transplantation because of its promising clinical applications. We have reported that embryonic stem (ES) cell derived neural stem/progenitor cell transplantation significantly improved motor functions in a hemiplegic mouse model. It is important to understand the molecular mechanisms governing neural regeneration of the damaged motor cortex after the transplantation. Recent investigations disclosed that chemokines participated in the regulation of migration and maturation of neural cell grafts. In this review, we summarize the involvement of inflammatory chemokines including stromal cell derived factor 1 (SDF1) in neural regeneration after ES cell derived neural stem/progenitor cell transplantation in mouse stroke models. Full article
Open AccessReview Pro-Inflammatory S100A8 and S100A9 Proteins: Self-Assembly into Multifunctional Native and Amyloid Complexes
Int. J. Mol. Sci. 2012, 13(3), 2893-2917; doi:10.3390/ijms13032893
Received: 9 January 2012 / Revised: 21 February 2012 / Accepted: 22 February 2012 / Published: 5 March 2012
Cited by 35 | PDF Full-text (704 KB) | HTML Full-text | XML Full-text
Abstract
S100A8 and S100A9 are EF-hand Ca2+ binding proteins belonging to the S100 family. They are abundant in cytosol of phagocytes and play critical roles in numerous cellular processes such as motility and danger signaling by interacting and modulating the activity of [...] Read more.
S100A8 and S100A9 are EF-hand Ca2+ binding proteins belonging to the S100 family. They are abundant in cytosol of phagocytes and play critical roles in numerous cellular processes such as motility and danger signaling by interacting and modulating the activity of target proteins. S100A8 and S100A9 expression levels increased in many types of cancer, neurodegenerative disorders, inflammatory and autoimmune diseases and they are implicated in the numerous disease pathologies. The Ca2+ and Zn2+-binding properties of S100A8/A9 have a pivotal influence on their conformation and oligomerization state, including self-assembly into homo- and heterodimers, tetramers and larger oligomers. Here we review how the unique chemical and conformational properties of individual proteins and their structural plasticity at the quaternary level account for S100A8/A9 functional diversity. Additional functional diversification occurs via non-covalent assembly into oligomeric and fibrillar amyloid complexes discovered in the aging prostate and reproduced in vitro. This process is also regulated by Ca2+and Zn2+-binding and effectively competes with the formation of the native complexes. High intrinsic amyloid-forming capacity of S100A8/A9 proteins may lead to their amyloid depositions in numerous ailments characterized by their elevated expression patterns and have additional pathological significance requiring further thorough investigation. Full article
(This article belongs to the Special Issue Protein Aggregation)
Open AccessReview Unraveling the Early Events of Amyloid-β Protein (Aβ) Aggregation: Techniques for the Determination of Aβ Aggregate Size
Int. J. Mol. Sci. 2012, 13(3), 3038-3072; doi:10.3390/ijms13033038
Received: 20 December 2011 / Revised: 9 February 2012 / Accepted: 23 February 2012 / Published: 7 March 2012
Cited by 30 | PDF Full-text (1511 KB) | HTML Full-text | XML Full-text
Abstract
The aggregation of proteins into insoluble amyloid fibrils coincides with the onset of numerous diseases. An array of techniques is available to study the different stages of the amyloid aggregation process. Recently, emphasis has been placed upon the analysis of oligomeric amyloid [...] Read more.
The aggregation of proteins into insoluble amyloid fibrils coincides with the onset of numerous diseases. An array of techniques is available to study the different stages of the amyloid aggregation process. Recently, emphasis has been placed upon the analysis of oligomeric amyloid species, which have been hypothesized to play a key role in disease progression. This paper reviews techniques utilized to study aggregation of the amyloid-β protein (Aβ) associated with Alzheimer’s disease. In particular, the review focuses on techniques that provide information about the size or quantity of oligomeric Aβ species formed during the early stages of aggregation, including native-PAGE, SDS-PAGE, Western blotting, capillary electrophoresis, mass spectrometry, fluorescence correlation spectroscopy, light scattering, size exclusion chromatography, centrifugation, enzyme-linked immunosorbent assay, and dot blotting. Full article
(This article belongs to the Special Issue Protein Aggregation)
Open AccessReview Development of On-Line High Performance Liquid Chromatography (HPLC)-Biochemical Detection Methods as Tools in the Identification of Bioactives
Int. J. Mol. Sci. 2012, 13(3), 3101-3133; doi:10.3390/ijms13033101
Received: 7 December 2011 / Revised: 8 February 2012 / Accepted: 1 March 2012 / Published: 7 March 2012
Cited by 11 | PDF Full-text (460 KB) | HTML Full-text | XML Full-text
Abstract
Biochemical detection (BCD) methods are commonly used to screen plant extracts for specific biological activities in batch assays. Traditionally, bioactives in the most active extracts were identified through time-consuming bio-assay guided fractionation until single active compounds could be isolated. Not only are [...] Read more.
Biochemical detection (BCD) methods are commonly used to screen plant extracts for specific biological activities in batch assays. Traditionally, bioactives in the most active extracts were identified through time-consuming bio-assay guided fractionation until single active compounds could be isolated. Not only are isolation procedures often tedious, but they could also lead to artifact formation. On-line coupling of BCD assays to high performance liquid chromatography (HPLC) is gaining ground as a high resolution screening technique to overcome problems associated with pre-isolation by measuring the effects of compounds post-column directly after separation. To date, several on-line HPLC-BCD assays, applied to whole plant extracts and mixtures, have been published. In this review the focus will fall on enzyme-based, receptor-based and antioxidant assays. Full article
(This article belongs to the Special Issue Advances in Nutraceutical Research)
Open AccessReview Glutathione Is a Key Player in Metal-Induced Oxidative Stress Defenses
Int. J. Mol. Sci. 2012, 13(3), 3145-3175; doi:10.3390/ijms13033145
Received: 21 December 2011 / Revised: 10 February 2012 / Accepted: 23 February 2012 / Published: 7 March 2012
Cited by 104 | PDF Full-text (592 KB) | HTML Full-text | XML Full-text
Abstract
Since the industrial revolution, the production, and consequently the emission of metals, has increased exponentially, overwhelming the natural cycles of metals in many ecosystems. Metals display a diverse array of physico-chemical properties such as essential versus non-essential and redox-active versus non-redox-active. In [...] Read more.
Since the industrial revolution, the production, and consequently the emission of metals, has increased exponentially, overwhelming the natural cycles of metals in many ecosystems. Metals display a diverse array of physico-chemical properties such as essential versus non-essential and redox-active versus non-redox-active. In general, all metals can lead to toxicity and oxidative stress when taken up in excessive amounts, imposing a serious threat to the environment and human health. In order to cope with different kinds of metals, plants possess defense strategies in which glutathione (GSH; γ-glu-cys-gly) plays a central role as chelating agent, antioxidant and signaling component. Therefore, this review highlights the role of GSH in: (1) metal homeostasis; (2) antioxidative defense; and (3) signal transduction under metal stress. The diverse functions of GSH originate from the sulfhydryl group in cysteine, enabling GSH to chelate metals and participate in redox cycling. Full article
Figures

Open AccessReview Tannins, Peptic Ulcers and Related Mechanisms
Int. J. Mol. Sci. 2012, 13(3), 3203-3228; doi:10.3390/ijms13033203
Received: 29 January 2012 / Revised: 26 February 2012 / Accepted: 28 February 2012 / Published: 8 March 2012
Cited by 17 | PDF Full-text (255 KB) | HTML Full-text | XML Full-text
Abstract
This review of the current literature aims to study correlations between the chemical structure and gastric anti-ulcer activity of tannins. Tannins are used in medicine primarily because of their astringent properties. These properties are due to the fact that tannins react with [...] Read more.
This review of the current literature aims to study correlations between the chemical structure and gastric anti-ulcer activity of tannins. Tannins are used in medicine primarily because of their astringent properties. These properties are due to the fact that tannins react with the tissue proteins with which they come into contact. In gastric ulcers, this tannin-protein complex layer protects the stomach by promoting greater resistance to chemical and mechanical injury or irritation. Moreover, in several experimental models of gastric ulcer, tannins have been shown to present antioxidant activity, promote tissue repair, exhibit anti Helicobacter pylori effects, and they are involved in gastrointestinal tract anti-inflammatory processes. The presence of tannins explains the anti-ulcer effects of many natural products. Full article
Open AccessReview Valuable Nutrients and Functional Bioactives in Different Parts of Olive (Olea europaea L.)—A Review
Int. J. Mol. Sci. 2012, 13(3), 3291-3340; doi:10.3390/ijms13033291
Received: 21 December 2011 / Revised: 13 February 2012 / Accepted: 16 February 2012 / Published: 12 March 2012
Cited by 55 | PDF Full-text (674 KB) | HTML Full-text | XML Full-text
Abstract
The Olive tree (Olea europaea L.), a native of the Mediterranean basin and parts of Asia, is now widely cultivated in many other parts of the world for production of olive oil and table olives. Olive is a rich source of [...] Read more.
The Olive tree (Olea europaea L.), a native of the Mediterranean basin and parts of Asia, is now widely cultivated in many other parts of the world for production of olive oil and table olives. Olive is a rich source of valuable nutrients and bioactives of medicinal and therapeutic interest. Olive fruit contains appreciable concentration, 1–3% of fresh pulp weight, of hydrophilic (phenolic acids, phenolic alchohols, flavonoids and secoiridoids) and lipophilic (cresols) phenolic compounds that are known to possess multiple biological activities such as antioxidant, anticarcinogenic, antiinflammatory, antimicrobial, antihypertensive, antidyslipidemic, cardiotonic, laxative, and antiplatelet. Other important compounds present in olive fruit are pectin, organic acids, and pigments. Virgin olive oil (VOO), extracted mechanically from the fruit, is also very popular for its nutritive and health-promoting potential, especially against cardiovascular disorders due to the presence of high levels of monounsaturates and other valuable minor components such as phenolics, phytosterols, tocopherols, carotenoids, chlorophyll and squalene. The cultivar, area of production, harvest time, and the processing techniques employed are some of the factors shown to influence the composition of olive fruit and olive oil. This review focuses comprehensively on the nutrients and high-value bioactives profile as well as medicinal and functional aspects of different parts of olives and its byproducts. Various factors affecting the composition of this food commodity of medicinal value are also discussed. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Generating Aptamers by Cell-SELEX for Applications in Molecular Medicine
Int. J. Mol. Sci. 2012, 13(3), 3341-3353; doi:10.3390/ijms13033341
Received: 19 January 2012 / Revised: 1 February 2012 / Accepted: 1 March 2012 / Published: 12 March 2012
Cited by 38 | PDF Full-text (481 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are single-stranded oligonucleotides of DNA or RNA that bind to target molecules with high affinity and specificity. Typically, aptamers are generated by an iterative selection process, called systematic evolution of ligands by exponential enrichment (SELEX). Recent advancements in SELEX technology have [...] Read more.
Aptamers are single-stranded oligonucleotides of DNA or RNA that bind to target molecules with high affinity and specificity. Typically, aptamers are generated by an iterative selection process, called systematic evolution of ligands by exponential enrichment (SELEX). Recent advancements in SELEX technology have extended aptamer selection from comparatively simple mixtures of purified proteins to whole living cells, and now cell-based SELEX (or cell-SELEX) can isolate aptamers that bind to specific target cells. Combined with nanotechnology, microchips, microfluidic devices, RNAi and other advanced technologies, cell-SELEX represents an integrated platform providing ultrasensitive and highly specific tools for clinical medicine. In this review, we describe the recent progress made in the application of cell-SELEX for diagnosis, therapy and biomarker discovery. Full article
Open AccessReview Conformational Changes in DNA upon Ligand Binding Monitored by Circular Dichroism
Int. J. Mol. Sci. 2012, 13(3), 3394-3413; doi:10.3390/ijms13033394
Received: 21 January 2012 / Revised: 22 February 2012 / Accepted: 24 February 2012 / Published: 12 March 2012
Cited by 41 | PDF Full-text (728 KB) | HTML Full-text | XML Full-text
Abstract
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor [...] Read more.
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future. Full article
(This article belongs to the Special Issue Applications of Circular Dichroism)
Open AccessReview Computational Analysis of Axonal Transport: A Novel Assessment of Neurotoxicity, Neuronal Development and Functions
Int. J. Mol. Sci. 2012, 13(3), 3414-3430; doi:10.3390/ijms13033414
Received: 11 January 2012 / Revised: 25 January 2012 / Accepted: 23 February 2012 / Published: 12 March 2012
Cited by 4 | PDF Full-text (328 KB) | HTML Full-text | XML Full-text
Abstract
Axonal transport plays a crucial role in neuronal morphogenesis, survival and function. Despite its importance, however, the molecular mechanisms of axonal transport remain mostly unknown because a simple and quantitative assay system for monitoring this cellular process has been lacking. In order [...] Read more.
Axonal transport plays a crucial role in neuronal morphogenesis, survival and function. Despite its importance, however, the molecular mechanisms of axonal transport remain mostly unknown because a simple and quantitative assay system for monitoring this cellular process has been lacking. In order to better characterize the mechanisms involved in axonal transport, we formulate a novel computer-assisted monitoring system of axonal transport. Potential uses of this system and implications for future studies will be discussed. Full article
Open AccessReview Arsenic and Antimony Transporters in Eukaryotes
Int. J. Mol. Sci. 2012, 13(3), 3527-3548; doi:10.3390/ijms13033527
Received: 10 February 2012 / Revised: 29 February 2012 / Accepted: 7 March 2012 / Published: 15 March 2012
Cited by 21 | PDF Full-text (713 KB) | HTML Full-text | XML Full-text
Abstract
Arsenic and antimony are toxic metalloids, naturally present in the environment and all organisms have developed pathways for their detoxification. The most effective metalloid tolerance systems in eukaryotes include downregulation of metalloid uptake, efflux out of the cell, and complexation with phytochelatin [...] Read more.
Arsenic and antimony are toxic metalloids, naturally present in the environment and all organisms have developed pathways for their detoxification. The most effective metalloid tolerance systems in eukaryotes include downregulation of metalloid uptake, efflux out of the cell, and complexation with phytochelatin or glutathione followed by sequestration into the vacuole. Understanding of arsenic and antimony transport system is of high importance due to the increasing usage of arsenic-based drugs in the treatment of certain types of cancer and diseases caused by protozoan parasites as well as for the development of bio- and phytoremediation strategies for metalloid polluted areas. However, in contrast to prokaryotes, the knowledge about specific transporters of arsenic and antimony and the mechanisms of metalloid transport in eukaryotes has been very limited for a long time. Here, we review the recent advances in understanding of arsenic and antimony transport pathways in eukaryotes, including a dual role of aquaglyceroporins in uptake and efflux of metalloids, elucidation of arsenic transport mechanism by the yeast Acr3 transporter and its role in arsenic hyperaccumulation in ferns, identification of vacuolar transporters of arsenic-phytochelatin complexes in plants and forms of arsenic substrates recognized by mammalian ABC transporters. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessReview The Intriguing Life of Autophagosomes
Int. J. Mol. Sci. 2012, 13(3), 3618-3635; doi:10.3390/ijms13033618
Received: 30 January 2012 / Revised: 2 March 2012 / Accepted: 7 March 2012 / Published: 19 March 2012
Cited by 9 | PDF Full-text (418 KB) | HTML Full-text | XML Full-text
Abstract
Autophagosomes are double-membrane vesicles characteristic of macroautophagy, a degradative pathway for cytoplasmic material and organelles terminating in the lysosomal or vacuole compartment for mammals and yeast, respectively. This highly dynamic, multi-step process requires significant membrane reorganization events at different stages of the [...] Read more.
Autophagosomes are double-membrane vesicles characteristic of macroautophagy, a degradative pathway for cytoplasmic material and organelles terminating in the lysosomal or vacuole compartment for mammals and yeast, respectively. This highly dynamic, multi-step process requires significant membrane reorganization events at different stages of the macroautophagic process. Such events include exchange and flow of lipids and proteins between membranes and vesicles (e.g., during initiation and growth of the phagophore), vesicular positioning and trafficking within the cell (e.g., autophagosome location and movement) and fusion of autophagosomes with the boundary membranes of the degradative compartment. Here, we review current knowledge on the contribution of different organelles to the formation of autophagosomes, their trafficking and fate within the cell. We will consider some of the unresolved questions related to the molecular mechanisms that regulate the “life and death” of the autophagosome. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessReview Recent Advances of Flowering Locus T Gene in Higher Plants
Int. J. Mol. Sci. 2012, 13(3), 3773-3781; doi:10.3390/ijms13033773
Received: 25 January 2012 / Revised: 9 March 2012 / Accepted: 13 March 2012 / Published: 21 March 2012
Cited by 7 | PDF Full-text (106 KB) | HTML Full-text | XML Full-text
Abstract
Flowering Locus T (FT) can promote flowering in the plant photoperiod pathway and also facilitates vernalization flowering pathways and other ways to promote flowering. The expression of products of the FT gene is recognized as important parts of the flowering [...] Read more.
Flowering Locus T (FT) can promote flowering in the plant photoperiod pathway and also facilitates vernalization flowering pathways and other ways to promote flowering. The expression of products of the FT gene is recognized as important parts of the flowering hormone and can induce flowering by long-distance transportation. In the present study, many FT-like genes were isolated, and the transgenic results show that FT gene can promote flowering in plants. This paper reviews the progress of the FT gene and its expression products to provide meaningful information for further studies of the functions of FT genes. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessReview Inroads to Predict in Vivo Toxicology—An Introduction to the eTOX Project
Int. J. Mol. Sci. 2012, 13(3), 3820-3846; doi:10.3390/ijms13033820
Received: 11 October 2011 / Revised: 30 January 2012 / Accepted: 14 March 2012 / Published: 21 March 2012
Cited by 34 | PDF Full-text (1051 KB) | HTML Full-text | XML Full-text
Abstract
There is a widespread awareness that the wealth of preclinical toxicity data that the pharmaceutical industry has generated in recent decades is not exploited as efficiently as it could be. Enhanced data availability for compound comparison (“read-across”), or for data mining to [...] Read more.
There is a widespread awareness that the wealth of preclinical toxicity data that the pharmaceutical industry has generated in recent decades is not exploited as efficiently as it could be. Enhanced data availability for compound comparison (“read-across”), or for data mining to build predictive tools, should lead to a more efficient drug development process and contribute to the reduction of animal use (3Rs principle). In order to achieve these goals, a consortium approach, grouping numbers of relevant partners, is required. The eTOX (“electronic toxicity”) consortium represents such a project and is a public-private partnership within the framework of the European Innovative Medicines Initiative (IMI). The project aims at the development of in silico prediction systems for organ and in vivo toxicity. The backbone of the project will be a database consisting of preclinical toxicity data for drug compounds or candidates extracted from previously unpublished, legacy reports from thirteen European and European operation-based pharmaceutical companies. The database will be enhanced by incorporation of publically available, high quality toxicology data. Seven academic institutes and five small-to-medium size enterprises (SMEs) contribute with their expertise in data gathering, database curation, data mining, chemoinformatics and predictive systems development. The outcome of the project will be a predictive system contributing to early potential hazard identification and risk assessment during the drug development process. The concept and strategy of the eTOX project is described here, together with current achievements and future deliverables. Full article
(This article belongs to the Special Issue Advances in Computational Toxicology)
Open AccessReview Functionalized Nanostructures with Application in Regenerative Medicine
Int. J. Mol. Sci. 2012, 13(3), 3847-3886; doi:10.3390/ijms13033847
Received: 29 January 2012 / Revised: 3 March 2012 / Accepted: 6 March 2012 / Published: 22 March 2012
Cited by 36 | PDF Full-text (721 KB) | HTML Full-text | XML Full-text
Abstract
In the last decade, both regenerative medicine and nanotechnology have been broadly developed leading important advances in biomedical research as well as in clinical practice. The manipulation on the molecular level and the use of several functionalized nanoscaled materials has application in [...] Read more.
In the last decade, both regenerative medicine and nanotechnology have been broadly developed leading important advances in biomedical research as well as in clinical practice. The manipulation on the molecular level and the use of several functionalized nanoscaled materials has application in various fields of regenerative medicine including tissue engineering, cell therapy, diagnosis and drug and gene delivery. The themes covered in this review include nanoparticle systems for tracking transplanted stem cells, self-assembling peptides, nanoparticles for gene delivery into stem cells and biomimetic scaffolds useful for 2D and 3D tissue cell cultures, transplantation and clinical application. Full article
(This article belongs to the Special Issue From Molecules to Nanomaterials)
Open AccessReview Curcumin: Updated Molecular Mechanisms and Intervention Targets in Human Lung Cancer
Int. J. Mol. Sci. 2012, 13(3), 3959-3978; doi:10.3390/ijms13033959
Received: 6 February 2012 / Revised: 5 March 2012 / Accepted: 15 March 2012 / Published: 22 March 2012
Cited by 22 | PDF Full-text (385 KB) | HTML Full-text | XML Full-text
Abstract
Curcumin, a yellow pigment derived from Curcuma longa Linn, has attracted great interest in the research of cancer during the past decades. Extensive studies documented that curcumin attenuates cancer cell proliferation and promotes apoptosis in vivo and in vitro. Curcumin [...] Read more.
Curcumin, a yellow pigment derived from Curcuma longa Linn, has attracted great interest in the research of cancer during the past decades. Extensive studies documented that curcumin attenuates cancer cell proliferation and promotes apoptosis in vivo and in vitro. Curcumin has been demonstrated to interact with multiple molecules and signal pathways, which makes it a potential adjuvant anti-cancer agent to chemotherapy. Previous investigations focus on the mechanisms of action for curcumin, which is shown to manipulate transcription factors and induce apoptosis in various kinds of human cancer. Apart from transcription factors and apoptosis, emerging studies shed light on latent targets of curcumin against epidermal growth factor receptor (EGFR), microRNAs (miRNA), autophagy and cancer stem cell. The present review predominantly discusses significance of EGFR, miRNA, autophagy and cancer stem cell in lung cancer therapy. Curcumin as a natural phytochemicals could communicate with these novel targets and show synergism to chemotherapy. Additionally, curcumin is well tolerated in humans. Therefore, EGFR-, miRNA-, autophagy- and cancer stem cell-based therapy in the presence of curcumin might be promising mechanisms and targets in the therapeutic strategy of lung cancer. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

Other

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Open AccessCommentary Management of Diabetes Mellitus: Could Simultaneous Targeting of Hyperglycemia and Oxidative Stress Be a Better Panacea?
Int. J. Mol. Sci. 2012, 13(3), 2965-2972; doi:10.3390/ijms13032965
Received: 16 November 2011 / Revised: 23 January 2012 / Accepted: 29 January 2012 / Published: 6 March 2012
Cited by 10 | PDF Full-text (96 KB) | HTML Full-text | XML Full-text
Abstract
The primary aim of the current management of diabetes mellitus is to achieve and/or maintain a glycated hemoglobin level of ≤6.5%. However, recent evidence indicates that intensive treatment of hyperglycemia is characterized by increased weight gain, severe hypoglycemia and higher mortality. Besides, [...] Read more.
The primary aim of the current management of diabetes mellitus is to achieve and/or maintain a glycated hemoglobin level of ≤6.5%. However, recent evidence indicates that intensive treatment of hyperglycemia is characterized by increased weight gain, severe hypoglycemia and higher mortality. Besides, evidence suggests that it is difficult to achieve and/or maintain optimal glycemic control in many diabetic patients; and that the benefits of intensively-treated hyperglycemia are restricted to microvascular complications only. In view of these adverse effects and limitations of intensive treatment of hyperglycemia in preventing diabetic complications, which is linked to oxidative stress, this commentary proposes a hypothesis that “simultaneous targeting of hyperglycemia and oxidative stress” could be more effective than “intensive treatment of hyperglycemia” in the management of diabetes mellitus. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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