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Int. J. Mol. Sci., Volume 13, Issue 4 (April 2012), Pages 4003-5289

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Editorial

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Open AccessEditorial International Journal of Molecular Science Best Paper Award 2012
Int. J. Mol. Sci. 2012, 13(4), 4795-4796; doi:10.3390/ijms13044795
Received: 9 April 2012 / Revised: 10 April 2012 / Accepted: 12 April 2012 / Published: 13 April 2012
Cited by 4 | PDF Full-text (127 KB) | HTML Full-text | XML Full-text
Abstract International Journal of Molecular Science is instituting an annual award to recognize the outstanding papers in the area of chemistry, molecular physics and molecular biology published in the International Journal of Molecular Science. [...] Full article
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Research

Jump to: Editorial, Review, Other

Open AccessArticle Folate Intake and Methylenetetrahydrofolate Reductase Gene Polymorphisms as Predictive and Prognostic Biomarkers for Ovarian Cancer Risk
Int. J. Mol. Sci. 2012, 13(4), 4009-4020; doi:10.3390/ijms13044009
Received: 16 February 2012 / Revised: 12 March 2012 / Accepted: 15 March 2012 / Published: 23 March 2012
Cited by 12 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
Folic acid and methylenetetrahydrofolate reductase (MTHFR) may affect the development of human cancer. However, few studies have evaluated folate intake and MTHFR in susceptibility to and prognosis of patients with ovarian cancer. We conducted a prospective case-control study in 215 ovarian cancer [...] Read more.
Folic acid and methylenetetrahydrofolate reductase (MTHFR) may affect the development of human cancer. However, few studies have evaluated folate intake and MTHFR in susceptibility to and prognosis of patients with ovarian cancer. We conducted a prospective case-control study in 215 ovarian cancer patients and 218 controls (all Chinese) between Jan. 2004 and Jan. 2007. MTHFR C677T genotyping was done by PCR-RFLP. All patients were followed up until Dec. 2010. We found a 2.43-fold increased risk of ovarian cancer among MTHFR 677TT carriers, and a decreased risk of ovarian cancer in individuals with high folate intake (OR = 0.54, 95% CI = 0.32–0.94). Cox regression survival analysis showed that among the ovarian cancer patients, those carrying the 677TT genotype had a higher risk of death (HR = 2.17, 95% CI = 1.20–4.79), while high folate intake was associated with a lower risk of death (HR = 0.43, 95% CI = 0.33–0.88). Moreover, MTHFR 677CC carriers with higher folate intake showed a lower risk of death from ovarian cancer (HR = 0.32, 95% CI = 0.27–0.82). In summary, high folate intake may lessen susceptibility and improve the prognosis of ovarian cancer patients, while the MTHFR 677TT genotype appears to increase ovarian cancer risk and worsen its prognosis in a Chinese population. Full article
Open AccessArticle Isolation and Purification of a Novel Deca-Antifungal Peptide from Potato (Solanum tuberosum L. cv. Jopung) Against Candida albicans
Int. J. Mol. Sci. 2012, 13(4), 4021-4032; doi:10.3390/ijms13044021
Received: 25 February 2012 / Revised: 14 March 2012 / Accepted: 19 March 2012 / Published: 23 March 2012
Cited by 3 | PDF Full-text (829 KB) | HTML Full-text | XML Full-text
Abstract
In a previous study, an antifungal protein, AFP-J, was purified from tubers of the potato (Solanum tuberosum cv. L Jopung) and by gel filtration and HPLC. In this study, the functional peptide was characterized by partial acid digestion using HCl and [...] Read more.
In a previous study, an antifungal protein, AFP-J, was purified from tubers of the potato (Solanum tuberosum cv. L Jopung) and by gel filtration and HPLC. In this study, the functional peptide was characterized by partial acid digestion using HCl and HPLC. We obtained three peaks from the AFP-J, the first and third peaks were not active in the tested fungal strain. However, the second peak, which was named Potide-J, was active (MIC; 6.25 μg/mL) against Candida albicans. The amino acid sequences were analyzed by automated Edman degradation, and the amino acid sequence of Potide-J was determined to be Ala-Val-Cys-Glu-Asn-Asp-Leu-Asn-Cys-Cys. Mass spectrometry showed that its molecular mass was 1083.1 Da. Finally, we confirmed that a disulfide bond was present between Cys3 and Cys9 or Cys10. Using this structure, Potide-J was synthesized via solid-phase methods. In these experiments, only the linear sequence was shown to display strong activity against Candida albicans. These results suggest that Potide-J may be an excellent candidate compound for the development of commercially applicable antibiotic agents. Full article
Open AccessArticle Classification of HCV NS5B Polymerase Inhibitors Using Support Vector Machine
Int. J. Mol. Sci. 2012, 13(4), 4033-4047; doi:10.3390/ijms13044033
Received: 25 November 2011 / Revised: 3 February 2012 / Accepted: 19 March 2012 / Published: 27 March 2012
Cited by 13 | PDF Full-text (256 KB) | HTML Full-text | XML Full-text
Abstract
Using a support vector machine (SVM), three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV) NS5B polymerase NNIs (non-nucleoside analogue inhibitors) fitting into the [...] Read more.
Using a support vector machine (SVM), three classification models were built to predict whether a compound is an active or weakly active inhibitor based on a dataset of 386 hepatitis C virus (HCV) NS5B polymerase NNIs (non-nucleoside analogue inhibitors) fitting into the pocket of the NNI III binding site. For each molecule, global descriptors, 2D and 3D property autocorrelation descriptors were calculated from the program ADRIANA.Code. Three models were developed with the combination of different types of descriptors. Model 2 based on 16 global and 2D autocorrelation descriptors gave the highest prediction accuracy of 88.24% and MCC (Matthews correlation coefficient) of 0.789 on test set. Model 1 based on 13 global descriptors showed the highest prediction accuracy of 86.25% and MCC of 0.732 on external test set (including 80 compounds). Some molecular properties such as molecular shape descriptors (InertiaZ, InertiaX and Span), number of rotatable bonds (NRotBond), water solubility (LogS), and hydrogen bonding related descriptors performed important roles in the interactions between the ligand and NS5B polymerase. Full article
Open AccessArticle Possible Time-Dependent Effect of Ions and Hydrophilic Surfaces on the Electrical Conductivity of Aqueous Solutions
Int. J. Mol. Sci. 2012, 13(4), 4048-4068; doi:10.3390/ijms13044048
Received: 21 January 2012 / Revised: 28 February 2012 / Accepted: 13 March 2012 / Published: 27 March 2012
Cited by 7 | PDF Full-text (541 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The purpose of this work was to determine the influence of mechanical and electrical treatment on the electrical conductivity of aqueous solutions. Solutions were treated mechanically by iteration of two steps: 1:100 dilution and vigorous shaking. These two processes were repeated until [...] Read more.
The purpose of this work was to determine the influence of mechanical and electrical treatment on the electrical conductivity of aqueous solutions. Solutions were treated mechanically by iteration of two steps: 1:100 dilution and vigorous shaking. These two processes were repeated until extremely dilute solutions were obtained. For electrical treatment the solutions were exposed to strong electrical impulses. Effects of mechanical (as well as electrical) treatment could not be demonstrated using electrical conductivity measurements. However, significantly higher conductivity than those of the freshly prepared chemically analogous solutions was found in all aged solutions except for those samples stored frozen. The results surprisingly resemble a previously observed weak gel-like behavior in water stored in closed flasks. We suggest that ions and contact with hydrophilic glass surfaces could be the determinative conditions for the occurrence of this phenomenon. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Elaeis oleifera Genomic-SSR Markers: Exploitation in Oil Palm Germplasm Diversity and Cross-Amplification in Arecaceae
Int. J. Mol. Sci. 2012, 13(4), 4069-4088; doi:10.3390/ijms13044069
Received: 23 December 2011 / Revised: 8 March 2012 / Accepted: 8 March 2012 / Published: 28 March 2012
Cited by 8 | PDF Full-text (486 KB) | HTML Full-text | XML Full-text
Abstract
Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences [...] Read more.
Species-specific simple sequence repeat (SSR) markers are favored for genetic studies and marker-assisted selection (MAS) breeding for oil palm genetic improvement. This report characterizes 20 SSR markers from an Elaeis oleifera genomic library (gSSR). Characterization of the repeat type in 2000 sequences revealed a high percentage of di-nucleotides (63.6%), followed by tri-nucleotides (24.2%). Primer pairs were successfully designed for 394 of the E. oleifera gSSRs. Subsequent analysis showed the ability of the 20 selected E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The average Polymorphism Information Content (PIC) value for the SSRs was 0.402, with the tri-repeats showing the highest average PIC (0.626). Low values of observed heterozygosity (Ho) (0.164) and highly positive fixation indices (Fis) in the E. oleifera germplasm collection, compared to the E. guineensis, indicated an excess of homozygosity in E. oleifera. The transferability of the markers to closely related palms, Elaeis guineensis, Cocos nucifera and ornamental palms is also reported. Sequencing the amplicons of three selected E. oleifera gSSRs across both species and palm taxa revealed variations in the repeat-units. The study showed the potential of E. oleifera gSSR markers to reveal genetic diversity in the genus Elaeis. The markers are also a valuable genetic resource for studying E. oleifera and other genus in the Arecaceae family. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Response Surface Methodology to Optimize Enzymatic Preparation of Deapio-Platycodin D and Platycodin D from Radix Platycodi
Int. J. Mol. Sci. 2012, 13(4), 4089-4100; doi:10.3390/ijms13044089
Received: 3 February 2012 / Revised: 8 March 2012 / Accepted: 19 March 2012 / Published: 28 March 2012
Cited by 4 | PDF Full-text (554 KB) | HTML Full-text | XML Full-text
Abstract
In the present work, we reported the enzymatic preparation of deapio-platycodin D (dPD) and platycodin D (PD) optimized by response surface methodology (RSM) from Radix Platycodi. During investigation of the hydrolysis of crude platycosides by various glycoside hydrolases, snailase showed a strong [...] Read more.
In the present work, we reported the enzymatic preparation of deapio-platycodin D (dPD) and platycodin D (PD) optimized by response surface methodology (RSM) from Radix Platycodi. During investigation of the hydrolysis of crude platycosides by various glycoside hydrolases, snailase showed a strong ability to transform deapio-platycoside E (dPE) and platycoside E (PE) into dPD and PD with 100% conversion. RSM was used to optimize the effects of the reaction temperature (35–45 °C), enzyme load (5–20%), and reaction time (4–24 h) on the conversion process. Validation of the RSM model was verified by the good agreement between the experimental and the predicted values of dPD and PD conversion yield. The optimum preparation conditions were as follows: temperature, 43 °C; enzyme load, 15%; reaction time, 22 h. The biotransformation pathways were dPE→dPD3→dPD and PE→PD3→PD, respectively. The determined method may be highly applicable for the enzymatic preparation of dPD and PD for medicinal purposes and also for commercial use. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Subminimal Inhibitory Concentrations of the Disinfectant Benzalkonium Chloride Select for a Tolerant Subpopulation of Escherichia coli with Inheritable Characteristics
Int. J. Mol. Sci. 2012, 13(4), 4101-4123; doi:10.3390/ijms13044101
Received: 1 December 2011 / Revised: 20 January 2012 / Accepted: 19 March 2012 / Published: 28 March 2012
Cited by 6 | PDF Full-text (586 KB) | HTML Full-text | XML Full-text
Abstract
Exposure of Escherichia coli to a subminimal inhibitory concentration (25% below MIC) of benzalkonium chloride (BC), an antimicrobial membrane-active agent commonly used in medical and food-processing environments, resulted in cell death and changes in cell morphology (filamentation). A small subpopulation (1–5% of [...] Read more.
Exposure of Escherichia coli to a subminimal inhibitory concentration (25% below MIC) of benzalkonium chloride (BC), an antimicrobial membrane-active agent commonly used in medical and food-processing environments, resulted in cell death and changes in cell morphology (filamentation). A small subpopulation (1–5% of the initial population) survived and regained similar morphology and growth rate as non-exposed cells. This subpopulation maintained tolerance to BC after serial transfers in medium without BC. To withstand BC during regrowth the cells up regulated a drug efflux associated gene (the acrB gene, member of the AcrAB-TolC efflux system) and changed expression of outer membrane porin genes (ompFW) and several genes involved in protecting the cell from the osmotic- and oxidative stress. Cells pre-exposed to osmotic- and oxidative stress (sodium chloride, salicylic acid and methyl viologen) showed higher tolerance to BC. A control and two selected isolates showing increased BC-tolerance after regrowth in BC was genome sequenced. No common point mutations were found in the BC- isolates but one point mutation in gene rpsA (Ribosomal protein S1) was observed in one of the isolates. The observed tolerance can therefore not solely be explained by the observed point mutation. The results indicate that there are several different mechanisms responsible for the regrowth of a tolerant subpopulation in BC, both BC-specific and general stress responses, and that sub-MIC of BC may select for phenotypic variants in a sensitive E. coli culture. Full article
Open AccessArticle Antimicrobial, Antiproliferative and Proapoptotic Activities of Extract, Fractions and Isolated Compounds from the Stem of Erythroxylum caatingae Plowman
Int. J. Mol. Sci. 2012, 13(4), 4124-4140; doi:10.3390/ijms13044124
Received: 5 January 2012 / Revised: 11 February 2012 / Accepted: 19 March 2012 / Published: 29 March 2012
Cited by 3 | PDF Full-text (335 KB) | HTML Full-text | XML Full-text
Abstract
In the study, we have examined the antitumor and antimicrobial activities of the methanol extract, the fractions, a fraction of total alkaloids and two alkaloids isolated from the stem of Erythroxylum caatingae Plowman. All test fractions, except the hexane fractions, showed antimicrobial [...] Read more.
In the study, we have examined the antitumor and antimicrobial activities of the methanol extract, the fractions, a fraction of total alkaloids and two alkaloids isolated from the stem of Erythroxylum caatingae Plowman. All test fractions, except the hexane fractions, showed antimicrobial activity on gram-positive bacteria and fungi. The acetate: methanol (95:5), acetate, chloroform and hexane fractions show the highest cytotoxicity activity against the NCI-H292, HEp-2 and K562 cell lines using MTT. The absence of hemolysis in the erythrocytes of mice was observed in these fractions and 6β-Benzoyloxy-3α-(3,4,5-trimethoxybenzoyloxy) tropane (catuabine B). Staining with Annexin V-FITC and JC-1 was used to verify the mechanism of action of the compounds of E. caatingae that showed cytotoxicity less than 30 μg/mL in leukemic cells. After 48 h of incubation, we observed that the acetate: methanol (95:5), acetate, and chloroform fractions, as well as the catuabine B, increased in the number of cells in early apoptosis, from 53.0 to 74.8%. An analysis of the potential of the mitochondrial membrane by incorporation of JC-1 showed that most cells during incubation of the acetate: methanol (95:5) and acetate fractions (63.85 and 59.2%) were stained, suggesting the involvement of an intrinsic pathway of apoptosis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Comparison of Ultrasonic and CO2 Laser Pretreatment Methods on Enzyme Digestibility of Corn Stover
Int. J. Mol. Sci. 2012, 13(4), 4141-4152; doi:10.3390/ijms13044141
Received: 8 February 2012 / Revised: 12 March 2012 / Accepted: 22 March 2012 / Published: 29 March 2012
Cited by 5 | PDF Full-text (491 KB) | HTML Full-text | XML Full-text
Abstract
To decrease the cost of bioethanol production, biomass recalcitrance needs to be overcome so that the conversion of biomass to bioethanol becomes more efficient. CO2 laser irradiation can disrupt the lignocellulosic physical structure and reduce the average size of fiber. Analyses [...] Read more.
To decrease the cost of bioethanol production, biomass recalcitrance needs to be overcome so that the conversion of biomass to bioethanol becomes more efficient. CO2 laser irradiation can disrupt the lignocellulosic physical structure and reduce the average size of fiber. Analyses with Fourier transform infrared spectroscopy, specific surface area, and the microstructure of corn stover were used to elucidate the enhancement mechanism of the pretreatment process by CO2 laser irradiation. The present work demonstrated that the CO2 laser had potential to enhance the bioconversion efficiency of lignocellulosic waste to renewable bioethanol. The saccharification rate of the CO2 laser pretreatment was significantly higher than ultrasonic pretreatment, and reached 27.75% which was 1.34-fold of that of ultrasonic pretreatment. The results showed the impact of CO2 laser pretreatment on corn stover to be more effective than ultrasonic pretreatment. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Labeling of Anti-MUC-1 Binding Single Chain Fv Fragments to Surface Modified Upconversion Nanoparticles for an Initial in Vivo Molecular Imaging Proof of Principle Approach
Int. J. Mol. Sci. 2012, 13(4), 4153-4167; doi:10.3390/ijms13044153
Received: 22 February 2012 / Revised: 7 March 2012 / Accepted: 19 March 2012 / Published: 29 March 2012
Cited by 4 | PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
In vivo optical Imaging is an inexpensive and highly sensitive modality to investigate and follow up diseases like breast cancer. However, fluorescence labels and specific tracers are still works in progress to bring this promising modality into the clinical day-to-day use. In [...] Read more.
In vivo optical Imaging is an inexpensive and highly sensitive modality to investigate and follow up diseases like breast cancer. However, fluorescence labels and specific tracers are still works in progress to bring this promising modality into the clinical day-to-day use. In this study an anti-MUC-1 binding single-chain antibody fragment was screened, produced and afterwards labeled with newly designed and surface modified NaYF4:Yb,Er upconversion nanoparticles as fluorescence reporter constructs. The MUC-1 binding of the conjugate was examined in vitro and in vivo using modified state-of-the-art small animal Imaging equipment. Binding of the newly generated upconversion nanoparticle based probe to MUC-1 positive cells was clearly shown via laser scanning microscopy and in an initial proof of principal small animal optical imaging approach. Full article
Open AccessArticle The Relationship Between Grain Hardness, Dough Mixing Parameters and Bread-Making Quality in Winter Wheat
Int. J. Mol. Sci. 2012, 13(4), 4186-4201; doi:10.3390/ijms13044186
Received: 12 February 2012 / Revised: 13 March 2012 / Accepted: 20 March 2012 / Published: 30 March 2012
Cited by 7 | PDF Full-text (381 KB) | HTML Full-text | XML Full-text
Abstract
The influence of grain hardness, determined by using molecular markers and physical methods (near-infrared (NIR) technique and particle size index—PSI) on dough characteristics, which in turn were determined with the use of a farinograph and reomixer, as well as bread-making properties were [...] Read more.
The influence of grain hardness, determined by using molecular markers and physical methods (near-infrared (NIR) technique and particle size index—PSI) on dough characteristics, which in turn were determined with the use of a farinograph and reomixer, as well as bread-making properties were studied. The material covered 24 winter wheat genotypes differing in grain hardness. The field experiment was conducted at standard and increased levels of nitrogen fertilization. Results of molecular analyses were in agreement with those obtained by the use of physical methods for soft-grained lines. Some lines classified as hard (by physical methods) appeared to have the wild-type Pina and Pinb alleles, similar to soft lines. Differences in dough and bread-making properties between lines classified as hard and soft on the basis of molecular data appeared to be of less significance than the differences between lines classified as hard and soft on the basis of physical analyses of grain texture. Values of relative grain hardness at the increased nitrogen fertilization level were significantly higher. At both fertilization levels the NIR parameter determining grain hardness was significantly positively correlated with the wet gluten and sedimentation values, with most of the rheological parameters and bread yield. Values of this parameter correlated with quality characteristics in a higher degree than values of particle size index. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Carotenoids, Fatty Acid Composition and Heat Stability of Supercritical Carbon Dioxide-Extracted-Oleoresins
Int. J. Mol. Sci. 2012, 13(4), 4233-4254; doi:10.3390/ijms13044233
Received: 31 January 2012 / Revised: 13 March 2012 / Accepted: 19 March 2012 / Published: 30 March 2012
Cited by 9 | PDF Full-text (998 KB) | HTML Full-text | XML Full-text
Abstract
The risk of chronic diseases has been shown to be inversely related to tomato intake and the lycopene levels in serum and tissue. Cis-isomers represent approximately 50%–80% of serum lycopene, while dietary lycopene maintains the isomeric ratio present in the plant [...] Read more.
The risk of chronic diseases has been shown to be inversely related to tomato intake and the lycopene levels in serum and tissue. Cis-isomers represent approximately 50%–80% of serum lycopene, while dietary lycopene maintains the isomeric ratio present in the plant sources with about 95% of all-trans-lycopene. Supercritical CO2 extraction (S-CO2) has been extensively developed to extract lycopene from tomato and tomato processing wastes, for food or pharmaceutical industries, also by using additional plant sources as co-matrices. We compared two S-CO2-extracted oleoresins (from tomato and tomato/hazelnut matrices), which showed an oil-solid bi-phasic appearance, a higher cis-lycopene content, and enhanced antioxidant ability compared with the traditional solvent extracts. Heat-treating, in the range of 60–100 °C, led to changes in the lycopene isomeric composition and to enhanced antioxidant activity in both types of oleoresins. The greater stability has been related to peculiar lycopene isomer composition and to the lipid environment. The results indicate these oleoresins are a good source of potentially healthful lycopene. Full article
Open AccessArticle Pharmacological Assessment of the Medicinal Potential of Acacia mearnsii De Wild.: Antimicrobial and Toxicity Activities
Int. J. Mol. Sci. 2012, 13(4), 4255-4267; doi:10.3390/ijms13044255
Received: 13 February 2012 / Revised: 12 March 2012 / Accepted: 21 March 2012 / Published: 30 March 2012
Cited by 6 | PDF Full-text (217 KB) | HTML Full-text | XML Full-text
Abstract
Acacia mearnsii De Wild. (Fabaceae) is a medicinal plant used in the treatment of microbial infections in South Africa without scientific validation of its bioactivity and toxicity. The antimicrobial activity of the crude acetone extract was evaluated by both agar diffusion and [...] Read more.
Acacia mearnsii De Wild. (Fabaceae) is a medicinal plant used in the treatment of microbial infections in South Africa without scientific validation of its bioactivity and toxicity. The antimicrobial activity of the crude acetone extract was evaluated by both agar diffusion and macrobroth dilution methods while its cytotoxicity effect was assessed with brine shrimp lethality assay. The study showed that both bacterial and fungal isolates were highly inhibited by the crude extract. The MIC values for the gram-positive bacteria (78.1–312.5) µg/mL, gram-negative bacteria (39.1–625) µg/mL and fungal isolates (625–5000) µg/mL differ significantly. The bacteria were more susceptible than the fungal strains tested. The antibiosis determination showed that the extract was more (75%) bactericidal than bacteriostatic (25%) and more fungicidal (66.67%) than fungistatic (33.33%). The cytotoxic activity of the extract was observed between 31.25 µg/mL and 500 µg/mL and the LC50 value (112.36 µg/mL) indicates that the extract was nontoxic in the brine shrimp lethality assay (LC50 > 100 μg/mL). These results support the use of A. mearnsii in traditional medicine for treatment of microbial infections. The extract exhibiting significant broad spectrum antimicrobial activity and nontoxic effects has potential to yield active antimicrobial compounds. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle CARD15/NOD2, CD14 and Toll-like 4 Receptor Gene Polymorphisms in Saudi Patients with Crohn’s Disease
Int. J. Mol. Sci. 2012, 13(4), 4268-4280; doi:10.3390/ijms13044268
Received: 31 December 2011 / Revised: 19 March 2012 / Accepted: 20 March 2012 / Published: 2 April 2012
Cited by 7 | PDF Full-text (309 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Crohn’s disease (CD) is a multifactorial disease with a genetic component and an observed association with genes related to the innate immune response. Polymorphisms in the CARD15/NOD2 gene, in addition to functional variants of the toll-like receptor-4 (TLR4) and CD14 genes, have [...] Read more.
Crohn’s disease (CD) is a multifactorial disease with a genetic component and an observed association with genes related to the innate immune response. Polymorphisms in the CARD15/NOD2 gene, in addition to functional variants of the toll-like receptor-4 (TLR4) and CD14 genes, have been associated with the development of Crohn’s disease. There is no information about the frequency of these polymorphisms in the Saudi population. We examined the frequency of the three major CARD15/NOD2 risk alleles (Leu1007fsinsC, Arg702Trp, and Gly908Arg) and the TLR4 (Thr399Il) polymorphism as well as a functional polymorphism in the promoter of the CD14–159C/T in 46 Saudi CD patients and 50 matched controls. Genotyping was performed by allele-specific PCR or by restriction fragment length polymorphism (PCR-RFLP) analysis. The mutant genotype frequencies of the Leu1007fsinsC, Arg702Trp and Gly908Arg in the patient group were 6.5, 21.7 and 6.5%, respectively, compared with frequencies of 0, 4 and 2%, respectively, in the control group. There were 15 patients who carried the mutant alleles for all three CARD15/NOD2 variants, Leu1007fsinsC, Arg702Trp and Gly908Arg, while none of the control candidates carried the three alleles. This genetic study provides evidence that the three major CARD15/NOD2 variant alleles and the CD14 −159C/T polymorphism are associated with Crohn’s disease (CD) susceptibility in the Saudi population; however, there is no evidence that the TLR4 (Thr399Il) or CARD15/NOD2 polymorphisms can be considered risk factors for Crohn’s disease. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle Evolution of Microsatellite Loci of Tropical and Temperate Anguilla Eels
Int. J. Mol. Sci. 2012, 13(4), 4281-4294; doi:10.3390/ijms13044281
Received: 19 January 2012 / Revised: 13 March 2012 / Accepted: 15 March 2012 / Published: 2 April 2012
Cited by 3 | PDF Full-text (288 KB) | HTML Full-text | XML Full-text
Abstract
Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: [...] Read more.
Anguilla eels are divided into temperate and tropical eels, based on their major distributions. The present study collected two temperate eels, Anguilla japonica and Anguilla anguilla, and two tropical eels, Anguilla marmorata and Anguilla bicolor pacifica, to examine two questions: do temperate and tropical Anguilla eels have different genetic polymorphic patterns?; and do temperate Anguilla japonica and Anguilla anguilla have a closer relationship to each other than to tropical eels? In total, 274 sequences were cloned and sequenced from six conserved microsatellite loci to examine polymorphic patterns of these four catadromous eels. Different mutational events, including substitutions, and repeat-unit deletions and insertions, appeared in major regions, while different point mutations were observed in flanking regions. The results implied that parallel patterns of microsatellite sequences occurred within both tropical and temperate freshwater eels. Consensus flanking sequences of six homologous loci from each of the four species were constructed. Genetic distances ranged from 0.044 (Anguilla bicolor pacifica vs. Anguilla marmorata) to 0.061 (Anguilla marmorata vs. Anguilla anguilla). The tree topology suggests the hypothesis of Anguilla japonica and Anguilla anguilla being a sister group must be rejected. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Toward the Understanding of the Metabolism of Levodopa I. DFT Investigation of the Equilibrium Geometries, Acid-Base Properties and Levodopa-Water Complexes
Int. J. Mol. Sci. 2012, 13(4), 4321-4339; doi:10.3390/ijms13044321
Received: 9 January 2012 / Revised: 13 March 2012 / Accepted: 26 March 2012 / Published: 2 April 2012
Cited by 3 | PDF Full-text (1980 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Levodopa (LD) is used to increase dopamine level for treating Parkinson’s disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP [...] Read more.
Levodopa (LD) is used to increase dopamine level for treating Parkinson’s disease. The major metabolism of LD to produce dopamine is decarboxylation. In order to understand the metabolism of LD; the electronic structure of levodopa was investigated at the Density Functional DFT/B3LYP level of theory using the 6-311+G** basis set, in the gas phase and in solution. LD is not planar, with the amino acid side chain acting as a free rotator around several single bonds. The potential energy surface is broad and flat. Full geometry optimization enabled locating and identifying the global minimum on this Potential energy surface (PES). All possible protonation/deprotonation forms of LD were examined and analyzed. Protonation/deprotonation is local in nature, i.e., is not transmitted through the molecular framework. The isogyric protonation/deprotonation reactions seem to involve two subsequent steps: First, deprotonation, then rearrangement to form H-bonded structures, which is the origin of the extra stability of the deprotonated forms. Natural bond orbital (NBO) analysis of LD and its deprotonated forms reveals detailed information of bonding characteristics and interactions across the molecular framework. The effect of deprotonation on the donor-acceptor interaction across the molecular framework and within the two subsystems has also been examined. Attempts to mimic the complex formation of LD with water have been performed. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle Synthesis of Zinc Oxide Nanoparticles and Their Effect on the Compressive Strength and Setting Time of Self-Compacted Concrete Paste as Cementitious Composites
Int. J. Mol. Sci. 2012, 13(4), 4340-4350; doi:10.3390/ijms13044340
Received: 30 January 2012 / Revised: 15 March 2012 / Accepted: 23 March 2012 / Published: 5 April 2012
Cited by 4 | PDF Full-text (278 KB) | HTML Full-text | XML Full-text
Abstract
In the present study, the mechanical properties of self-compacting concrete were investigated after the addition of different amounts of ZnO nanoparticles. The zinc oxide nanoparticles, with an average particle size of about 30 nm, were synthesized and their properties studied with the [...] Read more.
In the present study, the mechanical properties of self-compacting concrete were investigated after the addition of different amounts of ZnO nanoparticles. The zinc oxide nanoparticles, with an average particle size of about 30 nm, were synthesized and their properties studied with the help of a scanning electron microscope (SEM) and X-ray diffraction. The prepared nanoparticles were partially added to self-compacting concrete at different concentrations (0.05, 0.1, 0.2, 0.5 and 1.0%), and the mechanical (flexural and split tensile) strength of the specimens measured after 7, 14, 21 and 28 days, respectively. The present results have shown that the ZnO nanoparticles were able to improve the flexural strength of self-compacting concrete. The increased ZnO content of more than 0.2% could increase the flexural strength, and the maximum flexural and split tensile strength was observed after the addition of 0.5% nanoparticles. Finally, ZnO nanoparticles could improve the pore structure of the self-compacted concrete and shift the distributed pores to harmless and less-harmful pores, while increasing mechanical strength. Full article
(This article belongs to the Special Issue Composite Materials in Skeletal Engineering)
Open AccessArticle Ultraviolet C Irradiation Induces Different Expression of Cyclooxygenase 2 in NIH 3T3 Cells and A431 Cells: The Roles of COX-2 Are Different in Various Cell Lines
Int. J. Mol. Sci. 2012, 13(4), 4351-4366; doi:10.3390/ijms13044351
Received: 1 February 2012 / Revised: 5 March 2012 / Accepted: 16 March 2012 / Published: 5 April 2012
Cited by 5 | PDF Full-text (466 KB) | HTML Full-text | XML Full-text
Abstract
Ultraviolet C (UVC) is a DNA damage inducer, and 20 J/m2 of UVC irradiation caused cell growth inhibition and induced cell death after exposure for 24–36 h. The growth of NIH 3T3 cells was significantly suppressed at 24 h after UVC [...] Read more.
Ultraviolet C (UVC) is a DNA damage inducer, and 20 J/m2 of UVC irradiation caused cell growth inhibition and induced cell death after exposure for 24–36 h. The growth of NIH 3T3 cells was significantly suppressed at 24 h after UVC irradiation whereas the proliferation of A431 cells was inhibited until 36 h after UVC irradiation. UVC irradiation increased COX-2 expression and such up-regulation reached a maximum during 3–6 h in NIH 3T3 cells. In contrast, UVC-induced COX-2 reached a maximum after 24–36 h in A431 cells. Measuring prostaglandin E2 (PGE2) level showed a biphasic profile that PGE2 release was rapidly elevated in 1–12 h after UVC irradiation and increased again at 24 h in both cell lines. Treatment with the selective COX-2 inhibitor, SC-791, during maximum expression of COX-2 induction, attenuated the UVC induced-growth inhibition in NIH 3T3 cells. In contrast, SC-791 treatment after UVC irradiation enhanced death of A431 cells. These data showed that the patterns of UVC-induced PGE2 secretion from NIH 3T3 cells and A431 cells were similar despite the differential profile in UVC-induced COX-2 up-regulation. Besides, COX-2 might play different roles in cellular response to UVC irradiation in various cell lines. Full article
(This article belongs to the Special Issue UV-Induced Cell Death)
Open AccessArticle Evaluation of the Adenocarcinoma-Associated Gene AGR2 and the Intestinal Stem Cell Marker LGR5 as Biomarkers in Colorectal Cancer
Int. J. Mol. Sci. 2012, 13(4), 4367-4387; doi:10.3390/ijms13044367
Received: 1 March 2012 / Revised: 20 March 2012 / Accepted: 23 March 2012 / Published: 5 April 2012
Cited by 15 | PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
We aim to estimate the diagnostic performances of anterior gradient homolog-2 (AGR2) and Leucine-rich repeat-containing-G-protein-coupled receptor 5 (LGR5) in peripheral blood (PB) as mRNA biomarkers in colorectal cancer (CRC) and to explore their prognostic significance. Real-time PCR was [...] Read more.
We aim to estimate the diagnostic performances of anterior gradient homolog-2 (AGR2) and Leucine-rich repeat-containing-G-protein-coupled receptor 5 (LGR5) in peripheral blood (PB) as mRNA biomarkers in colorectal cancer (CRC) and to explore their prognostic significance. Real-time PCR was used to analyze AGR2 and LGR5 in 54 stages I-IV CRC patients and 19 controls. Both mRNAs were significantly increased in PB from CRC patients compared to controls. The area under the receiver-operating characteristic curves were 0.722 (p = 0.006), 0.376 (p = 0.123) and 0.767 (p = 0.001) for AGR2, LGR5 and combined AGR2/LGR5, respectively. The AGR2/LGR5 assay resulted in 67.4% sensitivity and 94.7% specificity. AGR2 correlated with pT3–pT4 and high-grade tumors. LGR5 correlated with metastasis, R2 resections and high-grade. The progression-free survival (PFS) of patients with high AGR2 was reduced (p = 0.037; HR, 2.32), also in the stage I-III subgroup (p = 0.046). LGR5 indicated a poor prognosis regarding both PFS (p = 0.007; HR, 1.013) and overall survival (p = 0.045; HR, 1.01). High AGR2/LGR5 was associated with poor PFS (p = 0.014; HR, 2.8) by multivariate analysis. Our findings indicate that the assessment of AGR2 and LGR5 in PB might reflect the presence of circulating tumor cells (CTC) and stem cell like CTC in CRC. Increased AGR2 and LGR5 are associated with poor outcomes. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Fly Ash Porous Material using Geopolymerization Process for High Temperature Exposure
Int. J. Mol. Sci. 2012, 13(4), 4388-4395; doi:10.3390/ijms13044388
Received: 13 January 2012 / Revised: 24 February 2012 / Accepted: 19 March 2012 / Published: 10 April 2012
Cited by 16 | PDF Full-text (341 KB) | HTML Full-text | XML Full-text
Abstract
This paper presents the results of a study on the effect of temperature on geopolymers manufactured using pozzolanic materials (fly ash). In this paper, we report on our investigation of the performance of porous geopolymers made with fly ash after exposure to [...] Read more.
This paper presents the results of a study on the effect of temperature on geopolymers manufactured using pozzolanic materials (fly ash). In this paper, we report on our investigation of the performance of porous geopolymers made with fly ash after exposure to temperatures from 600 °C up to 1000 °C. The research methodology consisted of pozzolanic materials (fly ash) synthesized with a mixture of sodium hydroxide and sodium silicate solution as an alkaline activator. Foaming agent solution was added to geopolymer paste. The geopolymer paste samples were cured at 60 °C for one day and the geopolymers samples were sintered from 600 °C to 1000 °C to evaluate strength loss due to thermal damage. We also studied their phase formation and microstructure. The heated geopolymers samples were tested by compressive strength after three days. The results showed that the porous geopolymers exhibited strength increases after temperature exposure. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle High Genetic Diversity and Low Differentiation of Michelia coriacea (Magnoliaceae), a Critically Endangered Endemic in Southeast Yunnan, China
Int. J. Mol. Sci. 2012, 13(4), 4396-4411; doi:10.3390/ijms13044396
Received: 20 January 2012 / Revised: 14 March 2012 / Accepted: 15 March 2012 / Published: 10 April 2012
Cited by 13 | PDF Full-text (344 KB) | HTML Full-text | XML Full-text
Abstract
Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) [...] Read more.
Michelia coriacea, a critically endangered tree, has a restricted and fragmented distribution in Southeast Yunnan Province, China. The genetic diversity, genetic structure and gene flow in the three extant populations of this species were detected by 10 inter-simple sequence repeat (ISSR) markers and 11 simple sequence repeat (SSR) markers. Examination of genetic diversity revealed that the species maintained a relatively high level of genetic diversity at the species level (percentage of polymorphic bands) PPB = 96.36% from ISSRs; PPL (percentage of polymorphic loci) = 95.56% from SSRs, despite several fragmental populations. Low levels of genetic differentiation among the populations of M. coriacea were detected by Nei’s Gst = 0.187 for ISSR and Wright’s Fst = 0.090 for SSR markers, which is further confirmed by Bayesian model-based STRUCTURE and PCoA analysis that could not reveal a clear separation between populations, although YKP was differentiated to other two populations by ISSR markers. Meanwhile, AMOVA analysis also indicated that 22.84% and 13.90% of genetic variation existed among populations for ISSRs and SSRs, respectively. The high level of genetic diversity, low genetic differentiation, and the population, structure imply that the fragmented habitat and the isolated population of M. coriacea may be due to recent over-exploitation. Conservation and management of M. coriacea should concentrate on maintaining the high level of genetic variability through both in and ex-situ conservation actions. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Isolation and Characterization of Twelve Polymorphic Microsatellite Loci for the Cocoa Mirid Bug Sahlbergella Singularis
Int. J. Mol. Sci. 2012, 13(4), 4412-4417; doi:10.3390/ijms13044412
Received: 1 March 2012 / Revised: 23 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Cited by 2 | PDF Full-text (133 KB) | HTML Full-text | XML Full-text
Abstract
Mirids are the primary pests affecting cocoa production in Africa, but no genetic studies have been conducted on these insects. Here we report the isolation and characterization of 12 polymorphic microsatellite loci for Sahlbergella singularis. A microsatellite-enriched genomic DNA library was [...] Read more.
Mirids are the primary pests affecting cocoa production in Africa, but no genetic studies have been conducted on these insects. Here we report the isolation and characterization of 12 polymorphic microsatellite loci for Sahlbergella singularis. A microsatellite-enriched genomic DNA library was developed and screened to identify marker loci. Twelve polymorphic loci were identified by screening 28 individuals collected from one presumed population in cocoa plantations in Southern Cameroon. The number of alleles ranged from 5 to 25, whereas the observed and the expected heterozygosities ranged from 0.179 to 0.786 and from 0.671 to 0.946, respectively. Tests showed significant deviations from HW equilibrium for four loci, but no linkage disequilibrium was detected at any of the loci. No cross-species amplification was observed in two other mirid pests in Africa. Full article
Open AccessArticle Density Functional Theory (DFT) Study of Triphenylamine-Based Dyes for Their Use as Sensitizers in Molecular Photovoltaics
Int. J. Mol. Sci. 2012, 13(4), 4418-4432; doi:10.3390/ijms13044418
Received: 6 February 2012 / Revised: 4 March 2012 / Accepted: 20 March 2012 / Published: 10 April 2012
Cited by 13 | PDF Full-text (606 KB) | HTML Full-text | XML Full-text
Abstract
In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation [...] Read more.
In this work we studied three dyes which are proposed for potential photovoltaic applications and named Dye7, Dye7-2t and Dye7-3t. The Density Functional Theory (DFT) was utilized, using the M05-2X hybrid meta-GGA functional and the 6–31+G(d,p) basis set. This level of calculation was used to find the optimized molecular structure and to predict the main molecular vibrations, the absorption and emission spectra, the molecular orbitals energies, dipole moment, isotropic polarizability and the chemical reactivity parameters that arise from Conceptual DFT. Also, the pKa values were calculated with the semi-empirical PM6 method. Full article
(This article belongs to the Special Issue Advances in Density Functional Theory)
Open AccessArticle Expression of Transient Receptor Potential Vanilloid (TRPV) Channels in Different Passages of Articular Chondrocytes
Int. J. Mol. Sci. 2012, 13(4), 4433-4445; doi:10.3390/ijms13044433
Received: 27 February 2012 / Revised: 12 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Cited by 14 | PDF Full-text (395 KB) | HTML Full-text | XML Full-text
Abstract
Ion channels play important roles in chondrocyte mechanotransduction. The transient receptor potential vanilloid (TRPV) subfamily of ion channels consists of six members. TRPV1-4 are temperature sensitive calcium-permeable, relatively non-selective cation channels whereas TRPV5 and TRPV6 show high selectivity for calcium over other [...] Read more.
Ion channels play important roles in chondrocyte mechanotransduction. The transient receptor potential vanilloid (TRPV) subfamily of ion channels consists of six members. TRPV1-4 are temperature sensitive calcium-permeable, relatively non-selective cation channels whereas TRPV5 and TRPV6 show high selectivity for calcium over other cations. In this study we investigated the effect of time in culture and passage number on the expression of TRPV4, TRPV5 and TRPV6 in articular chondrocytes isolated from equine metacarpophalangeal joints. Polyclonal antibodies raised against TRPV4, TRPV5 and TRPV6 were used to compare the expression of these channels in lysates from first expansion chondrocytes (P0) and cells from passages 1–3 (P1, P2 and P3) by western blotting. TRPV4, TRPV5 and TRPV6 were expressed in all passages examined. Immunohistochemistry and immunofluorescence confirmed the presence of these channels in sections of formalin fixed articular cartilage and monolayer cultures of methanol fixed P2 chondrocytes. TRPV5 and TRPV6 were upregulated with time and passage in culture suggesting that a shift in the phenotype of the cells in monolayer culture alters the expression of these channels. In conclusion, several TRPV channels are likely to be involved in calcium signaling and homeostasis in chondrocytes. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessArticle Genetic Diversity and Differentiation of Dendrocalamus membranaceus (Poaceae: Bambusoideae), a Declining Bamboo Species in Yunnan, China, as Based on Inter-Simple Sequence Repeat (ISSR) Analysis
Int. J. Mol. Sci. 2012, 13(4), 4446-4457; doi:10.3390/ijms13044446
Received: 5 January 2012 / Revised: 22 March 2012 / Accepted: 31 March 2012 / Published: 10 April 2012
Cited by 7 | PDF Full-text (342 KB) | HTML Full-text | XML Full-text
Abstract
Dendrocalamus membranaceus Munro is a woody bamboo with a high economic and ecological value that often occurs as natural stands, such as in the large-scale forested areas of China’s Yunnan Province. Due to its overexploitation, the habitat of D. membranaceus in [...] Read more.
Dendrocalamus membranaceus Munro is a woody bamboo with a high economic and ecological value that often occurs as natural stands, such as in the large-scale forested areas of China’s Yunnan Province. Due to its overexploitation, the habitat of D. membranaceus in Yunnan has been dramatically reduced, and the quality of the stands has declined. As a preliminary analysis in considering the effective protection for these germplasm resources, we assessed the genetic diversity of 12 natural populations in Yunnan, using inter-simple sequence repeat (ISSR) markers. From 10 ISSR primers, we generated 155 bands, of which 153 were polymorphic (98.71%). Compared with other species in the genus, this species demonstrated a greater genetic diversity (S = 0.349) and lower genetic differentiation (GST = 0.252). Our analysis of molecular variance revealed that the genetic differentiation among the populations is significant. A large proportion of the genetic variation (78.95%) resides among the individuals within populations, whereas only 21.05% are found among populations. Mantel tests indicated no significant correlation between genetic and geographic distances among the populations. Given the low sexual reproducibility and characteristics of monocarpic plants, we recommend implementing in situ conservation measures for all of the D. membranaceus populations in Yunnan and collecting sufficient samples for ex situ conservation. Furthermore, the conservation area should be extended to its main natural habitats, the Lancang-Mekong River Valley. Full article
Open AccessArticle Combining Molecular Docking and Molecular Dynamics to Predict the Binding Modes of Flavonoid Derivatives with the Neuraminidase of the 2009 H1N1 Influenza A Virus
Int. J. Mol. Sci. 2012, 13(4), 4496-4507; doi:10.3390/ijms13044496
Received: 9 January 2012 / Revised: 22 March 2012 / Accepted: 29 March 2012 / Published: 10 April 2012
Cited by 8 | PDF Full-text (616 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. [...] Read more.
Control of flavonoid derivatives inhibitors release through the inhibition of neuraminidase has been identified as a potential target for the treatment of H1N1 influenza disease. We have employed molecular dynamics simulation techniques to optimize the 2009 H1N1 influenza neuraminidase X-ray crystal structure. Molecular docking of the compounds revealed the possible binding mode. Our molecular dynamics simulations combined with the solvated interaction energies technique was applied to predict the docking models of the inhibitors in the binding pocket of the H1N1 influenza neuraminidase. In the simulations, the correlation of the predicted and experimental binding free energies of all 20 flavonoid derivatives inhibitors is satisfactory, as indicated by R2 = 0.75. Full article
Open AccessArticle Enhancement of Mechanical and Thermal Properties of Polycaprolactone/Chitosan Blend by Calcium Carbonate Nanoparticles
Int. J. Mol. Sci. 2012, 13(4), 4508-4522; doi:10.3390/ijms13044508
Received: 31 January 2012 / Revised: 24 February 2012 / Accepted: 19 March 2012 / Published: 10 April 2012
Cited by 18 | PDF Full-text (915 KB) | HTML Full-text | XML Full-text
Abstract
This study investigates the effects of calcium carbonate (CaCO3) nanoparticles on the mechanical and thermal properties and surface morphology of polycaprolactone (PCL)/chitosan nanocomposites. The nanocomposites of PCL/chitosan/CaCO3 were prepared using a melt blending technique. Transmission electron microscopy (TEM) results indicate the average [...] Read more.
This study investigates the effects of calcium carbonate (CaCO3) nanoparticles on the mechanical and thermal properties and surface morphology of polycaprolactone (PCL)/chitosan nanocomposites. The nanocomposites of PCL/chitosan/CaCO3 were prepared using a melt blending technique. Transmission electron microscopy (TEM) results indicate the average size of nanoparticles to be approximately 62 nm. Tensile measurement results show an increase in the tensile modulus with CaCO3 nanoparticle loading. Tensile strength and elongation at break show gradual improvement with the addition of up to 1 wt% of nano-sized CaCO3. Decreasing performance of these properties is observed for loading of more than 1 wt% of nano-sized CaCO3. The thermal stability was best enhanced at 1 wt% of CaCO3 nanoparticle loading. The fractured surface morphology of the PCL/chitosan blend becomes more stretched and homogeneous in PCL/chitosan/CaCO3 nanocomposite. TEM micrograph displays good dispersion of CaCO3 at lower nanoparticle loading within the matrix. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Extreme Multiple Reticulate Origins of the Pteris cadieri Complex (Pteridaceae)
Int. J. Mol. Sci. 2012, 13(4), 4523-4544; doi:10.3390/ijms13044523
Received: 3 February 2012 / Revised: 21 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Cited by 13 | PDF Full-text (687 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Pteris cadieri complex displays extensive morphological variation and seems to have originated through hybridization. However, the members of this complex reproduce by apogamy, which usually limits genetic variation. To evaluate the hypotheses of hybrid origins, the pattern of evolution in this [...] Read more.
The Pteris cadieri complex displays extensive morphological variation and seems to have originated through hybridization. However, the members of this complex reproduce by apogamy, which usually limits genetic variation. To evaluate the hypotheses of hybrid origins, the pattern of evolution in this species complex is reconstructed. Multiple methodologies were used. Diploids, triploids, and tetraploids were identified by chromosome counts and flow cytometry. Nuclear DNA markers (cytosolic phosphoglucose isomerase gene, PgiC) were used, together with chloroplast DNA markers (atpB-rbcL spacer and rbcL gene) to infer the biparental and maternal lineages of the Pteris cadieri complex. The three cpDNA haplotype groups and five PgiC alleles found in this study indicate that the evolution of the Pteris cadieri complex has been extremely reticulate. Up to 11 taxa belonging to eight morphs were identified. By comparing genetic variation in the Pteris cadieri in two independent areas, Hainan and Taiwan, we inferred that hybridization has occurred independently in different areas. Furthermore, we found evidence for phenological divergence (evergreen and deciduous) within Taiwan. We propose that the Pteris cadieri complex originated from different genetic lineages through multiple hybridizations in different geographical areas, leading to its present morphological diversity. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Identification of Novel Potential β-N-Acetyl-D-Hexosaminidase Inhibitors by Virtual Screening, Molecular Dynamics Simulation and MM-PBSA Calculations
Int. J. Mol. Sci. 2012, 13(4), 4545-4563; doi:10.3390/ijms13044545
Received: 7 February 2012 / Revised: 13 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Cited by 5 | PDF Full-text (685 KB) | HTML Full-text | XML Full-text
Abstract
Chitinolytic β-N-acetyl-D-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-D-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical [...] Read more.
Chitinolytic β-N-acetyl-D-hexosaminidases, as a class of chitin hydrolysis enzyme in insects, are a potential species-specific target for developing environmentally-friendly pesticides. Until now, pesticides targeting chitinolytic β-N-acetyl-D-hexosaminidase have not been developed. This study demonstrates a combination of different theoretical methods for investigating the key structural features of this enzyme responsible for pesticide inhibition, thus allowing for the discovery of novel small molecule inhibitors. Firstly, based on the currently reported crystal structure of this protein (OfHex1.pdb), we conducted a pre-screening of a drug-like compound database with 8 × 106 compounds by using the expanded pesticide-likeness criteria, followed by docking-based screening, obtaining 5 top-ranked compounds with favorable docking conformation into OfHex1. Secondly, molecular docking and molecular dynamics simulations are performed for the five complexes and demonstrate that one main hydrophobic pocket formed by residues Trp424, Trp448 and Trp524, which is significant for stabilization of the ligand–receptor complex, and key residues Asp477 and Trp490, are respectively responsible for forming hydrogen-bonding and π–π stacking interactions with the ligands. Finally, the molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) analysis indicates that van der Waals interactions are the main driving force for the inhibitor binding that agrees with the fact that the binding pocket of OfHex1 is mainly composed of hydrophobic residues. These results suggest that screening the ZINC database can maximize the identification of potential OfHex1 inhibitors and the computational protocol will be valuable for screening potential inhibitors of the binding mode, which is useful for the future rational design of novel, potent OfHex1-specific pesticides. Full article
Open AccessArticle Effect of Maturity on Phenolics (Phenolic Acids and Flavonoids) Profile of Strawberry Cultivars and Mulberry Species from Pakistan
Int. J. Mol. Sci. 2012, 13(4), 4591-4607; doi:10.3390/ijms13044591
Received: 24 February 2012 / Revised: 17 March 2012 / Accepted: 19 March 2012 / Published: 11 April 2012
Cited by 18 | PDF Full-text (261 KB) | HTML Full-text | XML Full-text
Abstract
In this study, we investigated how the extent of ripeness affects the yield of extract, total phenolics, total flavonoids, individual flavonols and phenolic acids in strawberry and mulberry cultivars from Pakistan. In strawberry, the yield of extract (%), total phenolics (TPC) and [...] Read more.
In this study, we investigated how the extent of ripeness affects the yield of extract, total phenolics, total flavonoids, individual flavonols and phenolic acids in strawberry and mulberry cultivars from Pakistan. In strawberry, the yield of extract (%), total phenolics (TPC) and total flavonoids (TFC) ranged from 8.5–53.3%, 491–1884 mg gallic acid equivalents (GAE)/100 g DW and 83–327 mg catechin equivalents (CE)/100 g DW, respectively. For the different species of mulberry the yield of extract (%), total phenolics and total flavonoids of 6.9–54.0%, 201–2287 mg GAE/100 g DW and 110–1021 mg CE/100 g DW, respectively, varied significantly as fruit maturity progressed. The amounts of individual flavonols and phenolic acid in selected berry fruits were analyzed by RP-HPLC. Among the flavonols, the content of myricetin was found to be high in Morus alba (88 mg/100 g DW), the amount of quercetin as high in Morus laevigata (145 mg/100 g DW) while kaempferol was highest in the Korona strawberry (98 mg/100 g DW) at fully ripened stage. Of the six phenolic acids detected, p-hydroxybenzoic and p-coumaric acid were the major compounds in the strawberry. M. laevigata and M. nigra contained p-coumaric acid and vanillic acid while M. macroura and M. alba contained p-hydroxy-benzoic acid and chlorogenic acid as the major phenolic acids. Overall, a trend to an increase in the percentage of extraction yield, TPC, TFC, flavonols and phenolic acids was observed as maturity progressed from un-ripened to fully-ripened stages. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Characterization of High-Value Bioactives in Some Selected Varieties of Pakistani Rice (Oryza sativa L.)
Int. J. Mol. Sci. 2012, 13(4), 4608-4622; doi:10.3390/ijms13044608
Received: 5 January 2012 / Revised: 4 March 2012 / Accepted: 19 March 2012 / Published: 11 April 2012
Cited by 11 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
The present study reports the composition and variation of fatty acids, sterols, tocopherols and γ-oryzanol among selected varieties namely Basmati Super, Basmati 515, Basmati 198, Basmati 385, Basmati 2000, Basmati 370, Basmati Pak, KSK-139, KS-282 and Irri-6 of Pakistani rice (Oryza [...] Read more.
The present study reports the composition and variation of fatty acids, sterols, tocopherols and γ-oryzanol among selected varieties namely Basmati Super, Basmati 515, Basmati 198, Basmati 385, Basmati 2000, Basmati 370, Basmati Pak, KSK-139, KS-282 and Irri-6 of Pakistani rice (Oryza sativa L). Oil content extracted with n-hexane from different varieties of brown rice seed (unpolished rice) ranged from 1.92% to 2.72%. Total fatty acid contents among rice varieties tested varied between 18240 and 25840 mg/kg brown rice seed. The rice tested mainly contained oleic (6841–10952 mg/kg) linoleic (5453–7874 mg/kg) and palmitic acid (3613–5489 mg/kg). The amounts of total phytosterols (GC and GC-MS analysis), with main contribution from β-sitosterol (445–656 mg/kg), campesterol (116–242 mg/kg), ∆5-avenasterol (89–178 mg/kg) and stigmasterol (75–180 mg/kg) were established to be 739.4 to 1330.4 mg/kg rice seed. The content of α-, γ- and δ-tocopherols as analyzed by HPLC varied from 39.0–76.1, 21.6–28.1 and 6.5–16.5 mg/kg rice seed, respectively. The amounts of different γ-oryzanol components (HPLC data), identified as cycloartenyl ferulate, 24-methylene cycloartanyl ferulate, campesteryl ferulate and β-sitosteryl ferulate, were in the range of 65.5–103.6, 140.2–183.1, 29.8–45.5 and 8.6–10.4 mg/kg rice seed, respectively. Overall, the concentration of these bioactives was higher in the Basmati rice cultivars showing their functional food superiority. In conclusion, the tested varieties of Pakistani rice, especially the Basmati cultivars, can provide best ingredients for functional foods. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Optical Properties of Bismuth Tellurite Based Glass
Int. J. Mol. Sci. 2012, 13(4), 4623-4631; doi:10.3390/ijms13044623
Received: 16 February 2012 / Revised: 26 March 2012 / Accepted: 26 March 2012 / Published: 11 April 2012
Cited by 19 | PDF Full-text (293 KB) | HTML Full-text | XML Full-text
Abstract
A series of binary tellurite based glasses (Bi2O3)x (TeO2)100−x was prepared by melt quenching method. The density, molar volume and refractive index increase when bismuth ions Bi3+ increase, this is due to [...] Read more.
A series of binary tellurite based glasses (Bi2O3)x (TeO2)100−x was prepared by melt quenching method. The density, molar volume and refractive index increase when bismuth ions Bi3+ increase, this is due to the increased polarization of the ions Bi3+ and the enhanced formation of non-bridging oxygen (NBO). The Fourier transform infrared spectroscopy (FTIR) results show the bonding of the glass sample and the optical band gap, Eopt decreases while the refractive index increases when the ion Bi3+ content increases. Full article
Open AccessArticle Preparation and Elastic Moduli of Germanate Glass Containing Lead and Bismuth
Int. J. Mol. Sci. 2012, 13(4), 4632-4641; doi:10.3390/ijms13044632
Received: 31 January 2012 / Revised: 5 March 2012 / Accepted: 30 March 2012 / Published: 11 April 2012
Cited by 5 | PDF Full-text (293 KB) | HTML Full-text | XML Full-text
Abstract
This paper reports the rapid melt quenching technique preparation for the new family of bismuth-lead germanate glass (BPG) systems in the form of (GeO2)60–(PbO)40−x–(½Bi2O3)x where x = 0 to 40 [...] Read more.
This paper reports the rapid melt quenching technique preparation for the new family of bismuth-lead germanate glass (BPG) systems in the form of (GeO2)60–(PbO)40−x–(½Bi2O3)x where x = 0 to 40 mol%. Their densities with respect of Bi2O3 concentration were determined using Archimedes’ method with acetone as a floatation medium. The current experimental data are compared with those of bismuth lead borate (B2O3)20–(PbO)80−x–(Bi2O3)x. The elastic properties of BPG were studied using the ultrasonic pulse-echo technique where both longitudinal and transverse sound wave velocities have been measured in each glass samples at a frequency of 15 MHz and at room temperature. Experimental data shows that all the physical parameters of BPG including density and molar volume, both longitudinal and transverse velocities increase linearly with increasing of Bi2O3 content in the germanate glass network. Their elastic moduli such as longitudinal, shear and Young’s also increase linearly with addition of Bi2O3 but the bulk modulus did not. The Poisson’s ratio and fractal dimensionality are also found to vary linearly with the Bi2O3 concentration. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Salivary Proteins Associated with Periodontitis in Patients with Type 2 Diabetes Mellitus
Int. J. Mol. Sci. 2012, 13(4), 4642-4654; doi:10.3390/ijms13044642
Received: 20 January 2012 / Revised: 23 March 2012 / Accepted: 31 March 2012 / Published: 12 April 2012
Cited by 11 | PDF Full-text (229 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this study was to investigate the salivary proteins that are associated with periodontitis in patients with Type 2 diabetes mellitus (T2DM). Volunteers for the study were patients from the Diabetic Unit, University of Malaya Medical Centre, whose periodontal status was determined. The diabetic volunteers were divided into two groups, i.e., patients with periodontitis and those who were periodontally healthy. Saliva samples were collected and treated with 10% TCA/acetone/20 mM DTT to precipitate the proteins, which were then separated using two-dimensional polyacrylamide gel electrophoresis. Gel images were scanned using the GS-800TM Calibrated Densitometer. The protein spots were analyzed and expressed in percentage volumes. The percentage volume of each protein spot was subjected to Mann-Whitney statistical analysis using SPSS software and false discovery rate correction. When the expression of the salivary proteins was compared between the T2DM patients with periodontitis with those who were periodontally healthy, seven proteins, including polymeric immunoglobulin receptor, plastin-2, actin related protein 3, leukocyte elastase inhibitor, carbonic anhydrases 6, immunoglobulin J and interleukin-1 receptor antagonist, were found to be differentially expressed (p < 0.01304). This implies that the proteins may have the potential to be used as biomarkers for the prediction of T2DM patients who may be prone to periodontitis. Full article
Open AccessArticle Injurious Effects of Curcumin on Maturation of Mouse Oocytes, Fertilization and Fetal Development via Apoptosis
Int. J. Mol. Sci. 2012, 13(4), 4655-4672; doi:10.3390/ijms13044655
Received: 30 December 2011 / Revised: 31 March 2012 / Accepted: 9 April 2012 / Published: 12 April 2012
Cited by 5 | PDF Full-text (478 KB) | HTML Full-text | XML Full-text
Abstract
Curcumin, a common dietary pigment and spice, is a hydrophobic polyphenol derived from the rhizome of the herb Curcuma longa. Previously, we reported a cytotoxic effect of curcumin on mouse embryonic stem cells and blastocysts and its association with defects in [...] Read more.
Curcumin, a common dietary pigment and spice, is a hydrophobic polyphenol derived from the rhizome of the herb Curcuma longa. Previously, we reported a cytotoxic effect of curcumin on mouse embryonic stem cells and blastocysts and its association with defects in subsequent development. In the present study, we further investigated the effects of curcumin on oocyte maturation and subsequent pre- and post-implantation development, both in vitro and in vivo. Notably, curcumin induced a significant reduction in the rate of oocyte maturation, fertilization, and in vitro embryonic development. Treatment of oocytes with curcumin during in vitro maturation (IVM) led to increased resorption of postimplantation embryos and decreased fetal weight. Experiments with an in vivo mouse model disclosed that consumption of drinking water containing 40 μM curcumin led to decreased oocyte maturation and in vitro fertilization as well as early embryonic developmental injury. Finally, pretreatment with a caspase-3-specific inhibitor effectively prevented curcumin-triggered injury effects, suggesting that embryo impairment by curcumin occurs mainly via a caspase-dependent apoptotic process. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Comparative Study of Essential Oils Extracted from Algerian Myrtus communis L. Leaves Using Microwaves and Hydrodistillation
Int. J. Mol. Sci. 2012, 13(4), 4673-4695; doi:10.3390/ijms13044673
Received: 23 January 2012 / Revised: 3 March 2012 / Accepted: 16 March 2012 / Published: 12 April 2012
Cited by 20 | PDF Full-text (648 KB) | HTML Full-text | XML Full-text
Abstract
Two different extraction methods were used for a comparative study of Algerian Myrtle leaf essential oils: solvent-free-microwave-extraction (SFME) and conventional hydrodistillation (HD). Essential oils analyzed by GC and GC-MS presented 51 components constituting 97.71 and 97.39% of the total oils, respectively. Solvent-Free-Microwave-Extract [...] Read more.
Two different extraction methods were used for a comparative study of Algerian Myrtle leaf essential oils: solvent-free-microwave-extraction (SFME) and conventional hydrodistillation (HD). Essential oils analyzed by GC and GC-MS presented 51 components constituting 97.71 and 97.39% of the total oils, respectively. Solvent-Free-Microwave-Extract Essential oils SFME-EO were richer in oxygenated compounds. Their major compounds were 1,8-cineole, followed by α-pinene as against α-pinene, followed by 1,8-cineole for HD. Their antimicrobial activity was investigated on 12 microorganisms. The antioxidant activities were studied with the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging method. Generally, both essential oils showed high antimicrobial and weak antioxidant activities. Microstructure analyses were also undertaken on the solid residue of myrtle leaves by Scanning Electronic Microscopy (SEM); it showed that the SFME-cellular structure undergoes significant modifications compared to the conventional HD residual solid. Comparison between hydrodistillation and SFME presented numerous distinctions. Several advantages with SFME were observed: faster kinetics and higher efficiency with similar yields: 0.32% dry basis, in 30 min as against 180 min for HD. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Improved Synthesis of 5-Substituted 1H-Tetrazoles via the [3+2] Cycloaddition of Nitriles and Sodium Azide Catalyzed by Silica Sulfuric Acid
Int. J. Mol. Sci. 2012, 13(4), 4696-4703; doi:10.3390/ijms13044696
Received: 20 February 2012 / Revised: 19 March 2012 / Accepted: 30 March 2012 / Published: 12 April 2012
Cited by 21 | PDF Full-text (141 KB) | HTML Full-text | XML Full-text
Abstract
A silica supported sulfuric acid catalyzed [3+2] cycloaddition of nitriles and sodium azide to form 5-substituted 1H-tetrazoles is described. The protocol can provide a series of 5-substituted 1H-tetrazoles using silica sulfuric acid from nitriles and sodium azide in [...] Read more.
A silica supported sulfuric acid catalyzed [3+2] cycloaddition of nitriles and sodium azide to form 5-substituted 1H-tetrazoles is described. The protocol can provide a series of 5-substituted 1H-tetrazoles using silica sulfuric acid from nitriles and sodium azide in DMF in 72%–95% yield. Full article
(This article belongs to the Section Green Chemistry)
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Open AccessArticle Effect of Calcium Sprays on Mechanical Strength and Cell Wall Fractions of Herbaceous Peony (Paeonia Lactiflora Pall.) Inflorescence Stems
Int. J. Mol. Sci. 2012, 13(4), 4704-4713; doi:10.3390/ijms13044704
Received: 2 March 2012 / Revised: 15 March 2012 / Accepted: 19 March 2012 / Published: 13 April 2012
Cited by 7 | PDF Full-text (171 KB) | HTML Full-text | XML Full-text
Abstract
Calcium is an essential element and imparts significant structural rigidity to the plant cell walls, which provide the main mechanical support to the entire plant. In order to increase the mechanical strength of the inflorescence stems of herbaceous peony, the stems are [...] Read more.
Calcium is an essential element and imparts significant structural rigidity to the plant cell walls, which provide the main mechanical support to the entire plant. In order to increase the mechanical strength of the inflorescence stems of herbaceous peony, the stems are treated with calcium chloride. The results shows that preharvest sprays with 4% (w/v) calcium chloride three times after bud emergence are the best at strengthening “Da Fugui” peonies’ stems. Calcium sprays increased the concentrations of endogenous calcium, total pectin content as well as cell wall fractions in herbaceous peonies stems, and significantly increased the contents of them in the top segment. Correlation analysis showed that the breaking force of the top segment of peonies’ stems was positively correlated with the ratio of water insoluble pectin to water soluble pectin (R = 0.673) as well as lignin contents (R = 0.926) after calcium applications. Full article
Open AccessArticle Frequent Gene Amplification Predicts Poor Prognosis in Gastric Cancer
Int. J. Mol. Sci. 2012, 13(4), 4714-4726; doi:10.3390/ijms13044714
Received: 13 March 2012 / Revised: 26 March 2012 / Accepted: 30 March 2012 / Published: 13 April 2012
Cited by 27 | PDF Full-text (390 KB) | HTML Full-text | XML Full-text
Abstract
Gastric cancer is one of the most common malignancies worldwide. However, genetic alterations leading to this disease are largely unknown. Gene amplification is one of the most frequent genetic alterations, which is believed to play a major role in the development and [...] Read more.
Gastric cancer is one of the most common malignancies worldwide. However, genetic alterations leading to this disease are largely unknown. Gene amplification is one of the most frequent genetic alterations, which is believed to play a major role in the development and progression of gastric cancer. In the present study, we identified three frequently amplified genes from 30 candidate genes using real-time quantitative PCR method, including ERBB4, C-MET and CD44, and further explored their association with clinicopathological characteristics and poor survival in a cohort of gastric cancers. Our data showed amplification of these genes was significantly associated with certain clinicopathological characteristics, particularly tumor differentiation and cancer-related death. More importantly, amplification of these genes was significantly related to worse survival, suggesting that these amplified genes may be significant predictors of poor prognosis and potential therapeutic targets in gastric cancer. Targeting these genes may thus provide new possibilities in the treatment of gastric cancer. Full article
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Open AccessArticle An Efficient Intergeneric Conjugation of DNA from Escherichia coli to Mycelia of the Lincomycin-Producer Streptomyces lincolnensis
Int. J. Mol. Sci. 2012, 13(4), 4797-4806; doi:10.3390/ijms13044797
Received: 24 February 2012 / Revised: 5 April 2012 / Accepted: 6 April 2012 / Published: 16 April 2012
Cited by 8 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
Streptomyces lincolnensis is a producer of lincomycin, which is a lincosamide antibiotic for the treatment of infective diseases caused by Gram-positive bacteria. S. lincolnensis is refractory to introducing plasmid DNA into cells because of resistance of foreign DNAs and poor sporulation. In [...] Read more.
Streptomyces lincolnensis is a producer of lincomycin, which is a lincosamide antibiotic for the treatment of infective diseases caused by Gram-positive bacteria. S. lincolnensis is refractory to introducing plasmid DNA into cells because of resistance of foreign DNAs and poor sporulation. In this study, a simple and efficient method of transferring plasmids into S. lincolnensis through the intergeneric Escherichia coli-mycelia conjugation was established and optimized for the first time. The recipient mycelia of S. lincolnensis were prepared in liquid SM medium containing 10.3% sucrose for three days. The dispersed mycelia were conjugated with competent E. coli donor cells. The exconjugants were regenerated efficiently on solid mannitol soya flour (MS) medium containing 20 mM MgCl2. The average conjugation frequency was observed at 1.1 × 10−4 per input donor cell and validated functionally by transferring two types of vectors containing lincomycin resistance genes lmrA, lmrB and lmrC into S. lincolnensis mycelia. The data of fermentation in shaking flasks showed the lincomycin yield of the exconjugants increased by 52.9% for the multiple copy vector and 38.3% for the integrative one, compared with the parental strain. The efficient and convenient method of intergeneric E. coli-mycelia conjugation in this study provides a promising procedure to introduce plasmid DNA into other refractory streptomycetes. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Synthesis and Antibacterial Activities of 1-Alkyl-3-methacryloyl (Acryloyl) of Benzimidazolone (Thione) Derivatives
Int. J. Mol. Sci. 2012, 13(4), 4819-4830; doi:10.3390/ijms13044819
Received: 7 March 2012 / Revised: 24 March 2012 / Accepted: 6 April 2012 / Published: 16 April 2012
Cited by 3 | PDF Full-text (229 KB) | HTML Full-text | XML Full-text
Abstract
A series of (28) 1-alkyl-3-methacryloyl (acryloyl)-benzimidazolone (thione) deriv-atives were synthesized. The structures of the new derivatives were confirmed by 1H-NMR, 13C-NMR and ESI-MS spectral analysis. The antibacterial activities of these compounds against several strains of bacteria, such as Bacillus cereus [...] Read more.
A series of (28) 1-alkyl-3-methacryloyl (acryloyl)-benzimidazolone (thione) deriv-atives were synthesized. The structures of the new derivatives were confirmed by 1H-NMR, 13C-NMR and ESI-MS spectral analysis. The antibacterial activities of these compounds against several strains of bacteria, such as Bacillus cereus, Bacillus subtilis, Escherichia coli, Staphylococcus aureus and Pseudomonas aeruginosa, were evaluated by methods of paper disc-diffusion and broth mciro-dilution. Methacryloyl derivatives displayed higher antibacterial activities against tested bacterial strains than those of acryloyl derivatives in in vitro tests. A structure-activity relationship (SAR) study revealed that the presences of the methacryloyl moieties is essential to the antibacterial activities of the compounds. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Curcumin Enhances Cytotoxic Effects of Bortezomib in Human Multiple Myeloma H929 Cells: Potential Roles of NF-κB/JNK
Int. J. Mol. Sci. 2012, 13(4), 4831-4838; doi:10.3390/ijms13044831
Received: 9 March 2012 / Revised: 31 March 2012 / Accepted: 11 April 2012 / Published: 16 April 2012
Cited by 7 | PDF Full-text (419 KB) | HTML Full-text | XML Full-text
Abstract
Combined curcumin and PS-341 treatment has been reported to enhance cytotoxicity and minimize adverse effects through ERK and p38MAPK mechanisms in human multiple myeloma cells. However, whether JNK plays similar role in this process remains unclear. In the present study, we found [...] Read more.
Combined curcumin and PS-341 treatment has been reported to enhance cytotoxicity and minimize adverse effects through ERK and p38MAPK mechanisms in human multiple myeloma cells. However, whether JNK plays similar role in this process remains unclear. In the present study, we found combined treatment altered NF-κB p65 expressions and distributions in multiple myeloma H929 cells. Western blot analysis showed combined treatment inactivated NF-κB while activated JNK signaling. Pre-treatment with JNK inhibitor SP600125 could attenuate NF-κB inactivation and restored H929 cells’ survival. These results suggested that curcumin might enhance the cytotoxicity of PS-341 by interacting with NF-κB, at least in part, through JNK mechanism. Full article
Open AccessArticle Quercetin and Epigallocatechin Gallate Induce in Vitro a Dose-Dependent Stiffening and Hyperpolarizing Effect on the Cell Membrane of Human Mononuclear Blood Cells
Int. J. Mol. Sci. 2012, 13(4), 4839-4859; doi:10.3390/ijms13044839
Received: 6 February 2012 / Revised: 26 March 2012 / Accepted: 6 April 2012 / Published: 17 April 2012
Cited by 8 | PDF Full-text (291 KB) | HTML Full-text | XML Full-text
Abstract
The bioactivity of polyphenols is closely linked to their ability to interact with biological membranes. The study evaluates the in vitro effect of quercetin and epigallocatechin on the membrane anisotropy and transmembrane potential of peripheral blood mononuclear cells (PBMCs) isolated from 26 [...] Read more.
The bioactivity of polyphenols is closely linked to their ability to interact with biological membranes. The study evaluates the in vitro effect of quercetin and epigallocatechin on the membrane anisotropy and transmembrane potential of peripheral blood mononuclear cells (PBMCs) isolated from 26 type 2 diabetes mellitus patients compared to 25 age matched controls. The in vitro assays were analyzed in correlation with the biochemical and inflammatory profile of the subjects and with insulin resistance parameters (HOMA-IR, plasma resistin) as well. For type 2 diabetes patients, the increase of HOMA-IR and resistin concentration was associated with a significant decrease of the PBMCs membrane anisotropy. The two tested polyphenols induced a dose-dependent hyperpolarizing effect and stiffening of the cell membranes for all tested subjects. Physiological levels of quercetin and epigallocatechin gallate had the tendency to normalize the PBMCs membrane anisotropy of the cells isolated from diabetes patients, bringing it to the level of cells isolated from normoglycemic ones. Epigallocatechin gallate induced higher effects compared to quercetin on the membranes isolated from subjects with higher cardiovascular risk. The decrease of membrane fluidity and the hyperpolarizing effect could explain the cardiovascular protective action of the tested compounds. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Preparation, Characterization and Thermal Degradation of Polyimide (4-APS/BTDA)/SiO2 Composite Films
Int. J. Mol. Sci. 2012, 13(4), 4860-4872; doi:10.3390/ijms13044860
Received: 29 December 2011 / Revised: 27 March 2012 / Accepted: 28 March 2012 / Published: 17 April 2012
Cited by 9 | PDF Full-text (741 KB) | HTML Full-text | XML Full-text
Abstract
Polyimide/SiO2 composite films were prepared from tetraethoxysilane (TEOS) and poly(amic acid) (PAA) based on aromatic diamine (4-aminophenyl sulfone) (4-APS) and aromatic dianhydride (3,3,4,4-benzophenonetetracarboxylic dianhydride) (BTDA) via a sol-gel process in N-methyl-2-pyrrolidinone (NMP). The prepared polyimide/SiO2 composite films were characterized [...] Read more.
Polyimide/SiO2 composite films were prepared from tetraethoxysilane (TEOS) and poly(amic acid) (PAA) based on aromatic diamine (4-aminophenyl sulfone) (4-APS) and aromatic dianhydride (3,3,4,4-benzophenonetetracarboxylic dianhydride) (BTDA) via a sol-gel process in N-methyl-2-pyrrolidinone (NMP). The prepared polyimide/SiO2 composite films were characterized using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), scanning electron microscope (SEM) and thermogravimetric analysis (TGA). The FTIR results confirmed the synthesis of polyimide (4-APS/BTDA) and the formation of SiO2 particles in the polyimide matrix. Meanwhile, the SEM images showed that the SiO2 particles were well dispersed in the polyimide matrix. Thermal stability and kinetic parameters of the degradation processes for the prepared polyimide/SiO2 composite films were investigated using TGA in N2 atmosphere. The activation energy of the solid-state process was calculated using Flynn–Wall–Ozawa’s method without the knowledge of the reaction mechanism. The results indicated that thermal stability and the values of the calculated activation energies increased with the increase of the TEOS loading and the activation energy also varied with the percentage of weight loss for all compositions. Full article
Open AccessArticle Study of Drug Metabolism by Xanthine Oxidase
Int. J. Mol. Sci. 2012, 13(4), 4873-4879; doi:10.3390/ijms13044873
Received: 13 January 2012 / Revised: 31 March 2012 / Accepted: 16 April 2012 / Published: 18 April 2012
Cited by 2 | PDF Full-text (380 KB) | HTML Full-text | XML Full-text
Abstract
In this work, we report the studies of drug metabolism by xanthine oxidase (XOD) with electrochemical techniques. Firstly, a pair of stable, well-defined and quasi-reversible oxidation/reduction peaks is obtained with the formal potential at −413.1 mV (vs. SCE) after embedding XOD [...] Read more.
In this work, we report the studies of drug metabolism by xanthine oxidase (XOD) with electrochemical techniques. Firstly, a pair of stable, well-defined and quasi-reversible oxidation/reduction peaks is obtained with the formal potential at −413.1 mV (vs. SCE) after embedding XOD in salmon sperm DNA membrane on the surface of pyrolytic graphite electrode. Then, a new steady peak can be observed at −730 mV (vs. SCE) upon the addition of 6-mercaptopurine (6-MP) to the electrochemical system, indicating the metabolism of 6-MP by XOD. Furthermore, the chronoamperometric response shows that the current of the catalytic peak located at −730 mV increases with addition of 6-MP in a concentration-dependent manner, and the increase of the chronoamperometric current can be inhibited by an XOD inhibitor, quercetin. Therefore, our results prove that XOD/DNA modified electrode can be efficiently used to study the metabolism of 6-MP, which may provide a convenient approach for in vitro studies on enzyme-catalyzed drug metabolism. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Study on the Immunomodulation Effect of Isodon japonicus Extract via Splenocyte Function and NK Anti-Tumor Activity
Int. J. Mol. Sci. 2012, 13(4), 4880-4888; doi:10.3390/ijms13044880
Received: 4 January 2012 / Revised: 6 March 2012 / Accepted: 5 April 2012 / Published: 18 April 2012
Cited by 4 | PDF Full-text (281 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Here we investigated the potential immune-enhancing activity of Isodon japonicus on murine splenocyte and natural-killer (NK) cells in vitro. The ethanol extract of I. japonicus significantly enhanced the proliferation of splenocyte and induced the significant enhancement of NK cells’ activity [...] Read more.
Here we investigated the potential immune-enhancing activity of Isodon japonicus on murine splenocyte and natural-killer (NK) cells in vitro. The ethanol extract of I. japonicus significantly enhanced the proliferation of splenocyte and induced the significant enhancement of NK cells’ activity against tumor cells (YAC-1). In addition, I. japonicus increased the production of interferon (IFN)-γ and tumor necrosis factor (TNF)-α, suggesting that the increase in NK cell cytotoxicity could be due to the enhancement of the NK cell production of both cytokines. Taken together, I. japonicus extract inhibited the growth of human leukemia cells (K562) by 74%. Our observation indicated that the anti-tumor effects of I. japonicus may be attributed to its ability to serve as a stimulant of NK anti-tumor activity. In addition, our results support the development of functional food studies on I. japonicus. Full article
Open AccessArticle Development of Eighteen Microsatellite Markers in Anemone amurensis (Ranunculaceae) and Cross-Amplification in Congeneric Species
Int. J. Mol. Sci. 2012, 13(4), 4889-4895; doi:10.3390/ijms13044889
Received: 10 February 2012 / Revised: 11 April 2012 / Accepted: 11 April 2012 / Published: 18 April 2012
PDF Full-text (152 KB) | HTML Full-text | XML Full-text
Abstract
Polyploidy plays an important role in the evolution of plant genomes. To enable the investigation of the polyploidy events within the genus Anemone, we developed eighteen microsatellite markers from the hexaploid species A. amurensis (Ranunculaceae), and tested their transferability in five [...] Read more.
Polyploidy plays an important role in the evolution of plant genomes. To enable the investigation of the polyploidy events within the genus Anemone, we developed eighteen microsatellite markers from the hexaploid species A. amurensis (Ranunculaceae), and tested their transferability in five closely related species. The number of total alleles (NA) for each resulting locus varied from one to eight. The polymorphism information content (PIC) and Nei’s genetic diversity (NGD) for these microsatellites ranged from 0.00 to 0.71 and 0.00 to 0.91, respectively. For each population, the NA was one to seven, and the values of PIC and NGD varied from 0.00 to 0.84 and 0.00 to 0.95, respectively. In addition, most of these microsatellites can be amplified successfully in the congeneric species. These microsatellite primers provide us an opportunity to study the polyploid evolution in the genus Anemone. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Risk-Association of CYP11A1 Polymorphisms and Breast Cancer Among Han Chinese Women in Southern China
Int. J. Mol. Sci. 2012, 13(4), 4896-4905; doi:10.3390/ijms13044896
Received: 13 January 2012 / Revised: 20 March 2012 / Accepted: 26 March 2012 / Published: 18 April 2012
Cited by 5 | PDF Full-text (183 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Exposure to endogenous sex hormones has been reported as a risk factor for breast cancer. The CYP11A1 gene encodes the key enzyme that catalyzes the initial and rate-limiting step in steroid hormone synthesis. In this study, the associations between single nucleotide polymorphisms [...] Read more.
Exposure to endogenous sex hormones has been reported as a risk factor for breast cancer. The CYP11A1 gene encodes the key enzyme that catalyzes the initial and rate-limiting step in steroid hormone synthesis. In this study, the associations between single nucleotide polymorphisms (SNPs) in CYP11A1 and breast cancer susceptibility were examined. Six SNPs in CYP11A1 were genotyped using the MassARRAY IPLEX platform in 530 breast cancer patients and 546 healthy controls. Association analyses based on a χ2 test and binary logistic regression were performed to determine the odds ratio (OR) and 95% confidence interval (95% CI) for each SNP. Two loci (rs2959008 and rs2279357) showed evidence of associations with breast cancer risk. The variant genotype C/T-C/C of rs2959008 was significantly associated with a decreased risk (age-adjusted OR, 0.75; 95% CI, 0.58–0.96; P = 0.023) compared with the wild-type TT. However, the homozygous TT variant of rs2279357 exhibited increased susceptibility to breast cancer (age-adjusted OR, 1.44; 95% CI, 1.05–1.98; P = 0.022). The locus rs2959003 also showed an appreciable effect, but no associations were observed for three other SNPs. Our results suggest that polymorphisms of CYP11A1 are related to breast cancer susceptibility in Han Chinese women of South China. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Novel Drug Delivery System Based on Docetaxel-Loaded Nanocapsules as a Therapeutic Strategy Against Breast Cancer Cells
Int. J. Mol. Sci. 2012, 13(4), 4906-4919; doi:10.3390/ijms13044906
Received: 8 February 2012 / Revised: 7 March 2012 / Accepted: 6 April 2012 / Published: 19 April 2012
Cited by 12 | PDF Full-text (466 KB) | HTML Full-text | XML Full-text
Abstract
In the field of cancer therapy, lipid nanocapsules based on a core-shell structure are promising vehicles for the delivery of hydrophobic drugs such as docetaxel. The main aim of this work was to evaluate whether docetaxel-loaded lipid nanocapsules improved the anti-tumor effect [...] Read more.
In the field of cancer therapy, lipid nanocapsules based on a core-shell structure are promising vehicles for the delivery of hydrophobic drugs such as docetaxel. The main aim of this work was to evaluate whether docetaxel-loaded lipid nanocapsules improved the anti-tumor effect of free docetaxel in breast cancer cells. Three docetaxel-loaded lipid nanocapsules were synthesized by solvent displacement method. Cytotoxic assays were evaluated in breast carcinoma (MCF-7) cells treated by the sulforhodamine B colorimetric method. Cell cycle was studied by flow cytometry and Annexin V-FITC, and apoptosis was evaluated by using propidium iodide assays. The anti-proliferative effect of docetaxel appeared much earlier when the drug was encapsulated in lipid nanoparticles than when it was free. Docetaxel-loaded lipid nanocapsules significantly enhanced the decrease in IC50 rate, and the treated cells evidenced apoptosis and a premature progression of the cell cycle from G(1) to G(2)-M phase. The chemotherapeutic effect of free docetaxel on breast cancer cells is improved by its encapsulation in lipid nanocapsules. This approach has the potential to overcome some major limitations of conventional chemotherapy and may be a promising strategy for future applications in breast cancer therapy. Full article
(This article belongs to the Special Issue Nanotoxicology)
Open AccessArticle Structural and Functional Characterization of Two Alternative Splicing Variants of Mouse Endothelial Cell-Specific Chemotaxis Regulator (ECSCR)
Int. J. Mol. Sci. 2012, 13(4), 4920-4936; doi:10.3390/ijms13044920
Received: 8 February 2012 / Revised: 19 March 2012 / Accepted: 20 March 2012 / Published: 19 April 2012
Cited by 4 | PDF Full-text (760 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Endothelial cells (ECs) that line the lumen of blood vessels are important players in blood vessel formation, and EC migration is a key component of the angiogenic process. Thus, identification of genes that are specifically or preferentially expressed in vascular ECs and [...] Read more.
Endothelial cells (ECs) that line the lumen of blood vessels are important players in blood vessel formation, and EC migration is a key component of the angiogenic process. Thus, identification of genes that are specifically or preferentially expressed in vascular ECs and in-depth understanding of their biological functions may lead to discovery of new therapeutic targets. We have previously reported molecular characterization of human endothelial cell-specific molecule 2 (ECSM2)/endothelial cell-specific chemotaxis regulator (ECSCR). In the present study, we cloned two mouse full-length cDNAs by RT-PCR, which encode two putative ECSCR isoform precursors with considerable homology to the human ECSCR. Nucleotide sequence and exon-intron junction analyses suggested that they are alternative splicing variants (ECSCR isoform-1 and -2), differing from each other in the first and second exons. Quantitative RT-PCR results revealed that isoform-2 is the predominant form, which was most abundant in heart, lung, and muscles, and moderately abundant in uterus and testis. In contrast, the expression of isoform-1 seemed to be more enriched in testis. To further explore their potential cellular functions, we expressed GFP- and FLAG-tagged ECSCR isoforms, respectively, in an ECSCR deficient cell line (HEK293). Interestingly, the actual sizes of either ECSCR-GFP or -FLAG fusion proteins detected by immunoblotting are much larger than their predicted sizes, suggesting that both isoforms are glycoproteins. Fluorescence microscopy revealed that both ECSCR isoforms are localized at the cell surface, which is consistent with the structural prediction. Finally, we performed cell migration assays using mouse endothelial MS1 cells overexpressing GFP alone, isoform-1-GFP, and isoform-2-GFP, respectively. Our results showed that both isoforms significantly inhibited vascular epidermal growth factor (VEGF)-induced cell migration. Taken together, we have provided several lines of experimental evidence that two mouse ECSCR splicing variants/isoform precursors exist. They are differentially expressed in a variety of tissue types and likely involved in modulation of vascular EC migration. We have also defined the gene structure of mouse ECSCR using bioinformatics tools, which provides new information towards a better understanding of alternative splicing of ECSCR. Full article
(This article belongs to the Special Issue Hypothetical Proteins)
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Open AccessArticle Generation and Characterization of a Novel Recombinant Antibody Against 15-Ketocholestane Isolated by Phage-Display
Int. J. Mol. Sci. 2012, 13(4), 4937-4948; doi:10.3390/ijms13044937
Received: 1 March 2012 / Revised: 27 March 2012 / Accepted: 11 April 2012 / Published: 19 April 2012
Cited by 3 | PDF Full-text (261 KB) | HTML Full-text | XML Full-text
Abstract
The employment of monoclonal antibodies (Mabs) to identify disease-associated biomarkers in clinical samples represents the underlying principle for many diagnostic tests. To date, these have been principally developed for protein targets with few reported applications for lipids due to their hydrophobicity and [...] Read more.
The employment of monoclonal antibodies (Mabs) to identify disease-associated biomarkers in clinical samples represents the underlying principle for many diagnostic tests. To date, these have been principally developed for protein targets with few reported applications for lipids due to their hydrophobicity and poor immunogenicity. Oxysterols represent a family of lipids implicated in diverse human diseases where Mab-based detection assays could have a profound effect on their utility as clinical biomarkers. These are usually identified in patients’ samples by mass- spectrometry based approaches. Here, we describe an antibody phage-library based screening methodology for generating a recombinant monoclonal antibody (RAb) targeting the oxysterol-15-ketocholestane (15-KA), a lipid implicated in multiple sclerosis and Autoimmune Encephalomyelitis (EAE). The antibody is highly specific for 15-KA and shows little or no binding activity for other closely related oxysterols. We employ RAb2E9 to address the controversy over whether 15-KA is a true biomarker for MS/EAE and show that 15-KA is undetectable in serum taken from mice with EAE using antibody based detection methodologies; a finding confirmed by mass-spectrometry analysis. This study demonstrates the technical feasibility of using phage display to isolate highly specific antibodies against poorly immunogenic, small molecule lipids. Full article
(This article belongs to the Special Issue Phage Display)
Open AccessArticle Mycoflora and Ochratoxin A Control in Wheat Grain Using Natural Extracts Obtained from Wine Industry By-Products
Int. J. Mol. Sci. 2012, 13(4), 4949-4967; doi:10.3390/ijms13044949
Received: 20 March 2012 / Revised: 9 April 2012 / Accepted: 13 April 2012 / Published: 19 April 2012
Cited by 4 | PDF Full-text (354 KB) | HTML Full-text | XML Full-text
Abstract
The aim of this study was to evaluate the effect of some natural extracts obtained from grape pomace (GPE) and grape seeds (GSE) as compared to a synthetic food, antioxidant-butylated hydroxytoluene (BHT), in order to control fungal population and ochratoxin A (OTA) [...] Read more.
The aim of this study was to evaluate the effect of some natural extracts obtained from grape pomace (GPE) and grape seeds (GSE) as compared to a synthetic food, antioxidant-butylated hydroxytoluene (BHT), in order to control fungal population and ochratoxin A (OTA) production in naturally contaminated wheat. The results showed that the addition of these extracts was efficient with OTA content decreasing. On treatment with these extracts the loss of OTA content after 14 days was in the range 7.8–28.3% relative to the control sample, but increased up to 26.48–37% after 28 days. The highest loss in OTA content was recorded for treatment with GPE at the 500 ppm level. Regarding the fungal development, the obtained results show that the total fungal populations were significantly reduced by using natural extracts. The most efficient extract was GPE. Both BHT and GPE inhibit the growth of Penicillium verrrucosum, for all doses, but less with Aspergillus genera. GPE affects the growth of other types of moulds such as Rhizopus microsporus, Fusarium graminearum, Alternaria infectoria and Cladosporium herbarum. Our data suggested that GPE and GSE are able to provide fungicidal and fungistatic protection and to control the OTA accumulation in wheat, at least in a similar manner to BHT. Full article
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Open AccessArticle 2-Decenoic Acid Ethyl Ester, a Compound That Elicits Neurotrophin-like Intracellular Signals, Facilitating Functional Recovery from Cerebral Infarction in Mice
Int. J. Mol. Sci. 2012, 13(4), 4968-4981; doi:10.3390/ijms13044968
Received: 12 March 2012 / Revised: 6 April 2012 / Accepted: 11 April 2012 / Published: 19 April 2012
Cited by 1 | PDF Full-text (718 KB) | HTML Full-text | XML Full-text
Abstract
In our previous study, we found that trans-2-decenoic acid ethyl ester (DAEE), a derivative of a medium-chain fatty acid, elicits neurotrophin-like signals including the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) in cultured mouse cortical neurons. Here, we examined the [...] Read more.
In our previous study, we found that trans-2-decenoic acid ethyl ester (DAEE), a derivative of a medium-chain fatty acid, elicits neurotrophin-like signals including the activation of extracellular signal-regulated kinases 1 and 2 (ERK1/2) in cultured mouse cortical neurons. Here, we examined the efficacy of intraperitoneal administration of DAEE on the treatment of a mouse model of the cerebral infarction caused by unilateral permanent middle cerebral artery occlusion (PMCAO). DAEE-treatment (100 µg/kg body weight injected at 0.5, 24, 48, 72 h after PMCAO) significantly restored the mice from PMCAO-induced neurological deficits including motor paralysis when evaluated 48, 72, and 96 h after the PMCAO. Furthermore, DAEE facilitated the phosphorylation of ERK1/2 on the infarction side of the brain when analyzed by Western immunoblot analysis, and it enhanced the number of phosphorylated ERK1/2-positive cells in the border areas between the infarction and non-infarction regions of the cerebral cortex, as estimated immunohistochemically. As the infarct volume remained unchanged after DAEE-treatment, it is more likely that DAEE improved the neurological condition through enhanced neuronal functions of the remaining neurons in the damaged areas rather than by maintaining neuronal survival. These results suggest that DAEE has a neuro-protective effect on cerebral infarction. Full article
Open AccessArticle Synthesis, Spectral and Antibacterial Studies of Copper(II) Tetraaza Macrocyclic Complexes
Int. J. Mol. Sci. 2012, 13(4), 4982-4992; doi:10.3390/ijms13044982
Received: 8 March 2012 / Revised: 11 April 2012 / Accepted: 12 April 2012 / Published: 19 April 2012
Cited by 12 | PDF Full-text (221 KB) | HTML Full-text | XML Full-text
Abstract
A novel family of tetraaza macrocyclic Cu(II) complexes [CuLX2] (where L = N4 donor macrocyclic ligands) and (X = Cl, NO3) have been synthesized and characterized by elemental analysis, magnetic moments, IR, EPR, mass, [...] Read more.
A novel family of tetraaza macrocyclic Cu(II) complexes [CuLX2] (where L = N4 donor macrocyclic ligands) and (X = Cl, NO3) have been synthesized and characterized by elemental analysis, magnetic moments, IR, EPR, mass, electronic spectra and thermal studies. The magnetic moments and electronic spectral studies suggest square planar geometry for [Cu(DBACDT)]Cl2 and [Cu(DBACDT)](NO3)2 complexes and distorted octahedral geometry to the rest of the ten complexes. The biological activity of all these complexes against gram-positive and gram-negative bacteria was compared with the activity of existing commercial antibacterial compounds like Linezolid and Cefaclor. Six complexes out of twelve were found to be most potent against both gram-positive as well as gram-negative bacteria due to the presence of thio group in the coordinated ligands. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Effects of Inflorescence Stem Structure and Cell Wall Components on the Mechanical Strength of Inflorescence Stem in Herbaceous Peony
Int. J. Mol. Sci. 2012, 13(4), 4993-5009; doi:10.3390/ijms13044993
Received: 5 March 2012 / Revised: 31 March 2012 / Accepted: 5 April 2012 / Published: 19 April 2012
Cited by 4 | PDF Full-text (4011 KB) | HTML Full-text | XML Full-text
Abstract
Herbaceous peony (Paeonia lactiflora Pall.) is a traditional famous flower, but its poor inflorescence stem quality seriously constrains the development of the cut flower. Mechanical strength is an important characteristic of stems, which not only affects plant lodging, but also plays [...] Read more.
Herbaceous peony (Paeonia lactiflora Pall.) is a traditional famous flower, but its poor inflorescence stem quality seriously constrains the development of the cut flower. Mechanical strength is an important characteristic of stems, which not only affects plant lodging, but also plays an important role in stem bend or break. In this paper, the mechanical strength, morphological indices and microstructure of P. lactiflora development inflorescence stems were measured and observed. The results showed that the mechanical strength of inflorescence stems gradually increased, and that the diameter of inflorescence stem was a direct indicator in estimating mechanical strength. Simultaneously, with the development of inflorescence stem, the number of vascular bundles increased, the vascular bundle was arranged more densely, the sclerenchyma cell wall thickened, and the proportion of vascular bundle and pith also increased. On this basis, cellulose and lignin contents were determined, PlCesA3, PlCesA6 and PlCCoAOMT were isolated and their expression patterns were examined including PlPAL. The results showed that cellulose was not strictly correlated with the mechanical strength of inflorescence stem, and lignin had a significant impact on it. In addition, PlCesA3 and PlCesA6 were not key members in cellulose synthesis of P. lactiflora and their functions were also different, but PlPAL and PlCCoAOMT regulated the lignin synthesis of P. lactiflora. These data indicated that PlPAL and PlCCoAOMT could be applied to improve the mechanical strength of P. lactiflora inflorescence stem in genetic engineering. Full article
Open AccessArticle Aristolactam-Type Alkaloids from Orophea enterocarpa and Their Cytotoxicities
Int. J. Mol. Sci. 2012, 13(4), 5010-5018; doi:10.3390/ijms13045010
Received: 7 March 2012 / Revised: 27 March 2012 / Accepted: 12 April 2012 / Published: 20 April 2012
Cited by 3 | PDF Full-text (752 KB) | HTML Full-text | XML Full-text
Abstract
A new aristolactam, named enterocarpam-III (10-amino-2,3,4,6-tetramethoxy phenanthrene-1-carboxylic acid lactam, 1) together with the known alkaloid stigmalactam (2), were isolated from Orophea enterocarpa. Their structures were elucidated on the basis of interpretation of their spectroscopic data. Compounds 1 and [...] Read more.
A new aristolactam, named enterocarpam-III (10-amino-2,3,4,6-tetramethoxy phenanthrene-1-carboxylic acid lactam, 1) together with the known alkaloid stigmalactam (2), were isolated from Orophea enterocarpa. Their structures were elucidated on the basis of interpretation of their spectroscopic data. Compounds 1 and 2 exhibited significant cytotoxicities against human colon adenocarcinoma (HCT15) cell line with IC50 values of 1.68 and 1.32 μM, respectively. Full article
Open AccessArticle Na+, K+-ATPase Subunit Composition in a Human Chondrocyte Cell Line; Evidence for the Presence of α1, α3, β1, β2 and β3 Isoforms
Int. J. Mol. Sci. 2012, 13(4), 5019-5034; doi:10.3390/ijms13045019
Received: 7 March 2012 / Revised: 6 April 2012 / Accepted: 12 April 2012 / Published: 20 April 2012
Cited by 2 | PDF Full-text (1217 KB) | HTML Full-text | XML Full-text
Abstract
Membrane transport systems participate in fundamental activities such as cell cycle control, proliferation, survival, volume regulation, pH maintenance and regulation of extracellular matrix synthesis. Multiple isoforms of Na+, K+-ATPase are expressed in primary chondrocytes. Some of these isoforms [...] Read more.
Membrane transport systems participate in fundamental activities such as cell cycle control, proliferation, survival, volume regulation, pH maintenance and regulation of extracellular matrix synthesis. Multiple isoforms of Na+, K+-ATPase are expressed in primary chondrocytes. Some of these isoforms have previously been reported to be expressed exclusively in electrically excitable cells (i.e., cardiomyocytes and neurons). Studying the distribution of Na+, K+-ATPase isoforms in chondrocytes makes it possible to document the diversity of isozyme pairing and to clarify issues concerning Na+, K+-ATPase isoform abundance and the physiological relevance of their expression. In this study, we investigated the expression of Na+, K+-ATPase in a human chondrocyte cell line (C-20/A4) using a combination of immunological and biochemical techniques. A panel of well-characterized antibodies revealed abundant expression of the α1, β1 and β2 isoforms. Western blot analysis of plasma membranes confirmed the above findings. Na+, K+-ATPase consists of multiple isozyme variants that endow chondrocytes with additional homeostatic control capabilities. In terms of Na+, K+-ATPase expression, the C-20/A4 cell line is phenotypically similar to primary and in situ chondrocytes. However, unlike freshly isolated chondrocytes, C-20/A4 cells are an easily accessible and convenient in vitro model for the study of Na+, K+-ATPase expression and regulation in chondrocytes. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessArticle A Novel and Expedient Approach to New Thiazoles, Thiazolo[3,2-a]pyridines, Dihydrothiophenes, and Hydrazones Incorporating Thieno[2,3-b]thiophene Moiety
Int. J. Mol. Sci. 2012, 13(4), 5035-5047; doi:10.3390/ijms13045035
Received: 1 March 2012 / Revised: 31 March 2012 / Accepted: 12 April 2012 / Published: 23 April 2012
Cited by 6 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
This paper reports details about the synthesis of a series of novel functionalized symmetrical bis-heterocyclic compounds containing a thieno[2,3-b]thiophene motif. Bis-thiazole derivatives 2, 3a-c and thiazolo[3,2-a]pyridine derivatives 4a-c are achieved. The hitherto unknown dihydrothiophene derivatives 6a-d via [...] Read more.
This paper reports details about the synthesis of a series of novel functionalized symmetrical bis-heterocyclic compounds containing a thieno[2,3-b]thiophene motif. Bis-thiazole derivatives 2, 3a-c and thiazolo[3,2-a]pyridine derivatives 4a-c are achieved. The hitherto unknown dihydrothiophene derivatives 6a-d via bis-pyridimium salt 5 are obtained. Additionally, the novel hydrazonothieno[2,3-b]thiophene derivatives 10a-c are obtained via bis-tosylacetylthieno[2,3-b]thiophene derivative 9. All compounds are characterized by 1H-, 13C-NMR, GCMS, IR, and UV-vis spectrometry. These compounds represent a new class of sulfur and nitrogen containing heterocycles that should also be of interest as new materials. Full article
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Open AccessArticle Nonselective Blocking of the Sympathetic Nervous System Decreases Detrusor Overactivity in Spontaneously Hypertensive Rats
Int. J. Mol. Sci. 2012, 13(4), 5048-5059; doi:10.3390/ijms13045048
Received: 5 March 2012 / Revised: 20 April 2012 / Accepted: 20 April 2012 / Published: 23 April 2012
Cited by 2 | PDF Full-text (223 KB) | HTML Full-text | XML Full-text
Abstract
The involuntary dual control systems of the autonomic nervous system (ANS) in the bladder of awake spontaneously hypertensive rats (SHRs) were investigated through simultaneous registrations of intravesical and intraabdominal pressures to observe detrusor overactivity (DO) objectively as a core symptom of an overactive bladder. SHRs (n = 6) showed the features of overactive bladder syndrome during urodynamic study, especially DO during the filling phase. After injection of the nonselective sympathetic blocking agent labetalol, DO disappeared in 3 of 6 SHRs (50%). DO frequency decreased from 0.98 ± 0.22 min−1 to 0.28 ± 0.19 min−1 (p < 0.01), and DO pressure decreased from 3.82 ± 0.57 cm H2O to 1.90 ± 0.86 cm H2O (p < 0.05). This suggests that the DO originating from the overactive parasympathetic nervous system is attenuated by the nonselective blocking of the sympathetic nervous system. The detailed mechanism behind this result is still not known, but parasympathetic overactivity seems to require overactive sympathetic nervous system activity in a kind of balance between these two systems. These findings are consistent with recent clinical findings suggesting that patients with idiopathic overactive bladder may have ANS dysfunction, particularly a sympathetic dysfunction. The search for newer and better drugs than the current anticholinergic drugs as the mainstay for overactive bladder will be fueled by our research on these sympathetic mechanisms. Further studies of this principle are required. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Preparation and Characterization of Micronized Artemisinin via a Rapid Expansion of Supercritical Solutions (RESS) Method
Int. J. Mol. Sci. 2012, 13(4), 5060-5073; doi:10.3390/ijms13045060
Received: 12 March 2012 / Revised: 4 April 2012 / Accepted: 11 April 2012 / Published: 23 April 2012
Cited by 4 | PDF Full-text (731 KB) | HTML Full-text | XML Full-text
Abstract
The particle sizes of pharmaceutical substances are important for their bioavailability. Bioavailability can be improved by reducing the particle size of the drug. In this study, artemisinin was micronized by the rapid expansion of supercritical solutions (RESS). The particle size of the [...] Read more.
The particle sizes of pharmaceutical substances are important for their bioavailability. Bioavailability can be improved by reducing the particle size of the drug. In this study, artemisinin was micronized by the rapid expansion of supercritical solutions (RESS). The particle size of the unprocessed white needle-like artemisinin particles was 30 to 1200 µm. The optimum micronization conditions are determined as follows: extraction temperature of 62 °C, extraction pressure of 25 MPa, precipitation temperature 45 °C and nozzle diameter of 1000 μm. Under the optimum conditions, micronized artemisinin with a (mean particle size) MPS of 550 nm is obtained. By analysis of variance (ANOVA), extraction temperature and pressure have significant effects on the MPS of the micronized artemisinin. The particle size of micronized artemisinin decreased with increasing extraction temperature and pressure. Moreover, the SEM, LC-MS, FTIR, DSC and XRD allowed the comparison between the crystalline initial state and the micronization particles obtained after the RESS process. The results showed that RESS process has not induced degradation of artemisinin and that processed artemisinin particles have lower crystallinity and melting point. The bulk density of artemisinin was determined before and after RESS process and the obtained results showed that it passes from an initial density of 0.554 to 0.128 g·cm−3 after the processing. The decrease in bulk density of the micronized powder can increase the liquidity of drug particles when they are applied for medicinal preparations. These results suggest micronized powder of artemisinin can be of great potential in drug delivery systems. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Rhinacanthus nasutus Extracts Prevent Glutamate and Amyloid-β Neurotoxicity in HT-22 Mouse Hippocampal Cells: Possible Active Compounds Include Lupeol, Stigmasterol and β-Sitosterol
Int. J. Mol. Sci. 2012, 13(4), 5074-5097; doi:10.3390/ijms13045074
Received: 20 January 2012 / Revised: 17 March 2012 / Accepted: 20 March 2012 / Published: 23 April 2012
Cited by 17 | PDF Full-text (1732 KB) | HTML Full-text | XML Full-text
Abstract
The Herb Rhinacanthus nasutus (L.) Kurz, which is native to Thailand and Southeast Asia, has become known for its antioxidant properties. Neuronal loss in a number of diseases including Alzheimer’s disease is thought to result, in part, from oxidative stress. Glutamate causes [...] Read more.
The Herb Rhinacanthus nasutus (L.) Kurz, which is native to Thailand and Southeast Asia, has become known for its antioxidant properties. Neuronal loss in a number of diseases including Alzheimer’s disease is thought to result, in part, from oxidative stress. Glutamate causes cell death in the mouse hippocampal cell line, HT-22, by unbalancing redox homeostasis, brought about by a reduction in glutathione levels, and amyloid-β has been shown to induce reactive oxygen species (ROS) production. Here in, we show that ethanol extracts of R. nasutus leaf and root are capable of dose dependently attenuating the neuron cell death caused by both glutamate and amyloid-β treatment. We used free radical scavenging assays to measure the extracts antioxidant activities and as well as quantifying phenolic, flavonoid and sterol content. Molecules found in R. nasutus, lupeol, stigmasterol and β-sitosterol are protective against glutamate toxicity. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Establishment of a Primary Culture System of Proximal Tubule Segments Using Specific Markers from Normal Mouse Kidneys
Int. J. Mol. Sci. 2012, 13(4), 5098-5111; doi:10.3390/ijms13045098
Received: 21 March 2012 / Revised: 5 April 2012 / Accepted: 18 April 2012 / Published: 23 April 2012
Cited by 11 | PDF Full-text (404 KB) | HTML Full-text | XML Full-text
Abstract
The proximal tubule contains the highest expression of angiotensinogen mRNA and protein within the kidney and plays a vital role in the renal renin-angiotensin system. To study the regulation of angiotensinogen expression in the kidney in more detail, the proximal tubule needs [...] Read more.
The proximal tubule contains the highest expression of angiotensinogen mRNA and protein within the kidney and plays a vital role in the renal renin-angiotensin system. To study the regulation of angiotensinogen expression in the kidney in more detail, the proximal tubule needs to be accurately isolated from the rest of the nephron and separated into its three segments. The purpose of this study was to design a novel protocol using specific markers for the separation of proximal tubule cells into the three proximal tubule segments and to determine angiotensinogen expression in each segment. Kidneys were removed from C57BL/6J mice. The proximal tubules were aspirated from region of a Percoll gradient solution of the appropriate density. The proximal tubule was then separated into its three segments using segment-specific membrane proteins, after which each segment was characterized by a different specific marker (sodium-glucose transporter 2 for Segment 1; carbonic anhydrase IV for Segment 2; ecto-adenosine triphosphatase for Segment 3). The isolation of proximal tubules into three segments was successful, and angiotensinogen mRNA in Segment 2 and 3 and angiotensinogen protein in all three segments were confirmed. This protocol will be helpful for future studies of the detailed mechanisms of the intrarenal renin-angiotensin system. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genome-Wide Identification and in Silico Analysis of Poplar Peptide Deformylases
Int. J. Mol. Sci. 2012, 13(4), 5112-5124; doi:10.3390/ijms13045112
Received: 17 January 2012 / Revised: 12 April 2012 / Accepted: 18 April 2012 / Published: 23 April 2012
Cited by 3 | PDF Full-text (858 KB) | HTML Full-text | XML Full-text
Abstract
Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs [...] Read more.
Peptide deformylases (PDF) behave as monomeric metal cation hydrolases for the removal of the N-formyl group (Fo). This is an essential step in the N-terminal Met excision (NME) that occurs in these proteins from eukaryotic mitochondria or chloroplasts. Although PDFs have been identified and their structure and function have been characterized in several herbaceous species, it remains as yet unexplored in poplar. Here, we report on the first identification of two genes (PtrPDF1A and PtrPDF1B) respectively encoding two putative PDF polypeptides in Populus trichocarpa by genome-wide investigation. One of them (XP_002300047.1) encoded by PtrPDF1B (XM_002300011.1) was truncated, and then revised into a complete sequence based on its ESTs support with high confidence. We document that the two PDF1s of Populus are evolutionarily divergent, likely as a result of independent duplicated events. Furthermore, in silico simulations demonstrated that PtrPDF1A and PtrPDF1B should act as similar PDF catalytic activities to their corresponding PDF orthologs in Arabidopsis. This result would be value of for further assessment of their biological activities in poplar, and further experiments are now required to confirm them. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A DNA Network as an Information Processing System
Int. J. Mol. Sci. 2012, 13(4), 5125-5137; doi:10.3390/ijms13045125
Received: 29 February 2012 / Revised: 31 March 2012 / Accepted: 17 April 2012 / Published: 23 April 2012
Cited by 6 | PDF Full-text (691 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic [...] Read more.
Biomolecular systems that can process information are sought for computational applications, because of their potential for parallelism and miniaturization and because their biocompatibility also makes them suitable for future biomedical applications. DNA has been used to design machines, motors, finite automata, logic gates, reaction networks and logic programs, amongst many other structures and dynamic behaviours. Here we design and program a synthetic DNA network to implement computational paradigms abstracted from cellular regulatory networks. These show information processing properties that are desirable in artificial, engineered molecular systems, including robustness of the output in relation to different sources of variation. We show the results of numerical simulations of the dynamic behaviour of the network and preliminary experimental analysis of its main components. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessArticle Identification of Important Chemical Features of 11β-Hydroxysteroid Dehydrogenase Type1 Inhibitors: Application of Ligand Based Virtual Screening and Density Functional Theory
Int. J. Mol. Sci. 2012, 13(4), 5138-5162; doi:10.3390/ijms13045138
Received: 30 January 2012 / Revised: 19 March 2012 / Accepted: 5 April 2012 / Published: 23 April 2012
Cited by 9 | PDF Full-text (929 KB) | HTML Full-text | XML Full-text
Abstract
11ß-Hydroxysteroid dehydrogenase type1 (11ßHSD1) regulates the conversion from inactive cortisone to active cortisol. Increased cortisol results in diabetes, hence quelling the activity of 11ßHSD1 has been thought of as an effective approach for the treatment of diabetes. Quantitative hypotheses were developed and [...] Read more.
11ß-Hydroxysteroid dehydrogenase type1 (11ßHSD1) regulates the conversion from inactive cortisone to active cortisol. Increased cortisol results in diabetes, hence quelling the activity of 11ßHSD1 has been thought of as an effective approach for the treatment of diabetes. Quantitative hypotheses were developed and validated to identify the critical chemical features with reliable geometric constraints that contribute to the inhibition of 11ßHSD1 function. The best hypothesis, Hypo1, which contains one-HBA; one-Hy-Ali, and two-RA features, was validated using Fischer’s randomization method, a test and a decoy set. The well validated, Hypo1, was used as 3D query to perform a virtual screening of three different chemical databases. Compounds selected by Hypo1 in the virtual screening were filtered by applying Lipinski’s rule of five, ADMET, and molecular docking. Finally, five hit compounds were selected as virtual novel hit molecules for 11ßHSD1 based on their electronic properties calculated by Density functional theory. Full article
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Open AccessArticle Application of Ionic Liquids in the Microwave-Assisted Extraction of Proanthocyanidins from Larix gmelini Bark
Int. J. Mol. Sci. 2012, 13(4), 5163-5178; doi:10.3390/ijms13045163
Received: 5 March 2012 / Revised: 23 March 2012 / Accepted: 20 April 2012 / Published: 24 April 2012
Cited by 21 | PDF Full-text (673 KB) | HTML Full-text | XML Full-text
Abstract
Ionic liquid based, microwave-assisted extraction (ILMAE) was successfully applied to the extraction of proanthocyanidins from Larix gmelini bark. In this work, in order to evaluate the performance of ionic liquids in the microwave-assisted extraction process, a series of 1-alkyl-3-methylimidazolium ionic liquids with [...] Read more.
Ionic liquid based, microwave-assisted extraction (ILMAE) was successfully applied to the extraction of proanthocyanidins from Larix gmelini bark. In this work, in order to evaluate the performance of ionic liquids in the microwave-assisted extraction process, a series of 1-alkyl-3-methylimidazolium ionic liquids with different cations and anions were evaluated for extraction yield, and 1-butyl-3-methylimidazolium bromide was selected as the optimal solvent. In addition, the ILMAE procedure for the proanthocyanidins was optimized and compared with other conventional extraction techniques. Under the optimized conditions, satisfactory extraction yield of the proanthocyanidins was obtained. Relative to other methods, the proposed approach provided higher extraction yield and lower energy consumption. The Larix gmelini bark samples before and after extraction were analyzed by Thermal gravimetric analysis, Fourier-transform infrared spectroscopy and characterized by scanning electron microscopy. The results showed that the ILMAE method is a simple and efficient technique for sample preparation. Full article
(This article belongs to the Section Green Chemistry)
Open AccessArticle Poisson Parameters of Antimicrobial Activity: A Quantitative Structure-Activity Approach
Int. J. Mol. Sci. 2012, 13(4), 5207-5229; doi:10.3390/ijms13045207
Received: 22 March 2012 / Revised: 17 April 2012 / Accepted: 19 April 2012 / Published: 24 April 2012
Cited by 2 | PDF Full-text (519 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
A contingency of observed antimicrobial activities measured for several compounds vs. a series of bacteria was analyzed. A factor analysis revealed the existence of a certain probability distribution function of the antimicrobial activity. A quantitative structure-activity relationship analysis for the overall [...] Read more.
A contingency of observed antimicrobial activities measured for several compounds vs. a series of bacteria was analyzed. A factor analysis revealed the existence of a certain probability distribution function of the antimicrobial activity. A quantitative structure-activity relationship analysis for the overall antimicrobial ability was conducted using the population statistics associated with identified probability distribution function. The antimicrobial activity proved to follow the Poisson distribution if just one factor varies (such as chemical compound or bacteria). The Poisson parameter estimating antimicrobial effect, giving both mean and variance of the antimicrobial activity, was used to develop structure-activity models describing the effect of compounds on bacteria and fungi species. Two approaches were employed to obtain the models, and for every approach, a model was selected, further investigated and found to be statistically significant. The best predictive model for antimicrobial effect on bacteria and fungi species was identified using graphical representation of observed vs. calculated values as well as several predictive power parameters. Full article
(This article belongs to the Special Issue Advances in Biomolecular Simulation)
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Open AccessArticle Enhanced Production of a Novel Cyclic Hexapeptide Antibiotic (NW-G01) by Streptomyces alboflavus 313 Using Response Surface Methodology
Int. J. Mol. Sci. 2012, 13(4), 5230-5241; doi:10.3390/ijms13045230
Received: 6 January 2012 / Revised: 16 April 2012 / Accepted: 17 April 2012 / Published: 24 April 2012
Cited by 10 | PDF Full-text (417 KB) | HTML Full-text | XML Full-text
Abstract
NW-G01, produced by Streptomyces alboflavus 313, is a novel cyclic hexapeptide antibiotic with many potential applications, including antimicrobial activity and antitumor agents. This study developed a system for optimizing medium components in order to enhance NW-G01 production. In this study, Plackett-Burman design [...] Read more.
NW-G01, produced by Streptomyces alboflavus 313, is a novel cyclic hexapeptide antibiotic with many potential applications, including antimicrobial activity and antitumor agents. This study developed a system for optimizing medium components in order to enhance NW-G01 production. In this study, Plackett-Burman design (PBD) was used to find the key ingredients of medium components, and then response surface methodology (RSM) was implemented to determine their optimal concentrations. The results of PBD revealed that the crucial ingredients related to the production of NW-G01 were (NH4)2SO4, peptone and CaCO3. A prediction model has been built in the experiments of central composite design and response surface methodology, and its validation has been further verified. The optimal medium composition was determined (g/L): corn starch 15, glucose 15, peptone 3.80, (NH4)2SO4 0.06, NaCl 1.5, CaCO3 1.30, MgSO4·7H2O 0.015, K2HPO4·3H2O 0.015, MnCl2·4H2O 0.015, FeSO4·7H2O 0.015, and ZnSO4·7H2O 0.015. Compared with NW-G01 production (5.707 mg/L) in non-optimized fermentation medium, the production of NW-G01 (15.564 mg/L) in optimized fermentation medium had a 2.73-fold increase. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Sol-Gel-Derived Hydroxyapatite-Carbon Nanotube/Titania Coatings on Titanium Substrates
Int. J. Mol. Sci. 2012, 13(4), 5242-5253; doi:10.3390/ijms13045242
Received: 29 February 2012 / Revised: 9 March 2012 / Accepted: 18 April 2012 / Published: 24 April 2012
Cited by 12 | PDF Full-text (638 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, hydroxyapatite-carbon nanotube/titania (HA-CNT/TiO2) double layer coatings were successfully developed on titanium (Ti) substrates intended for biomedical applications. A TiO2 coating was firstly developed by anodization to improve bonding between HA and Ti, and then the layer [...] Read more.
In this paper, hydroxyapatite-carbon nanotube/titania (HA-CNT/TiO2) double layer coatings were successfully developed on titanium (Ti) substrates intended for biomedical applications. A TiO2 coating was firstly developed by anodization to improve bonding between HA and Ti, and then the layer of HA and CNTs was coated on the surface by the sol-gel process to improve the biocompatibility and mechanical properties of Ti. The surfaces of double layer coatings were uniform and crack-free with a thickness of about 7 μm. The bonding strength of the HA-CNT/TiO2 coating was higher than that of the pure HA and HA-CNT coatings. Additionally, in vitro cell experiments showed that CNTs promoted the adhesion of preosteoblasts on the HA-CNT/TiO2 double layer coatings. These unique surfaces combined with the osteoconductive properties of HA exhibited the excellent mechanical properties of CNTs. Therefore, the developed HA-CNT/TiO2 coatings on Ti substrates might be a promising material for bone replacement. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Synthesis Mechanism of Low-Voltage Praseodymium Oxide Doped Zinc Oxide Varistor Ceramics Prepared Through Modified Citrate Gel Coating
Int. J. Mol. Sci. 2012, 13(4), 5278-5289; doi:10.3390/ijms13045278
Received: 20 February 2012 / Revised: 31 March 2012 / Accepted: 12 April 2012 / Published: 24 April 2012
Cited by 4 | PDF Full-text (1058 KB) | HTML Full-text | XML Full-text
Abstract
High demands on low-voltage electronics have increased the need for zinc oxide (ZnO) varistors with fast response, highly non-linear current-voltage characteristics and energy absorption capabilities at low breakdown voltage. However, trade-off between breakdown voltage and grain size poses a critical bottle-neck in [...] Read more.
High demands on low-voltage electronics have increased the need for zinc oxide (ZnO) varistors with fast response, highly non-linear current-voltage characteristics and energy absorption capabilities at low breakdown voltage. However, trade-off between breakdown voltage and grain size poses a critical bottle-neck in the production of low-voltage varistors. The present study highlights the synthesis mechanism for obtaining praseodymium oxide (Pr6O11) based ZnO varistor ceramics having breakdown voltages of 2.8 to 13.3 V/mm through employment of direct modified citrate gel coating technique. Precursor powder and its ceramics were examined by means of TG/DTG, FTIR, XRD and FESEM analyses. The electrical properties as a function of Pr6O11 addition were analyzed on the basis of I-V characteristic measurement. The breakdown voltage could be adjusted from 0.01 to 0.06 V per grain boundary by controlling the amount of Pr6O11 from 0.2 to 0.8 mol%, without alteration of the grain size. The non-linearity coefficient, α, varied from 3.0 to 3.5 and the barrier height ranged from 0.56 to 0.64 eV. Breakdown voltage and α lowering with increasing Pr6O11 content were associated to reduction in the barrier height caused by variation in O vacancies at grain boundary. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)

Review

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Open AccessReview Congenital Diarrheal Disorders: An Updated Diagnostic Approach
Int. J. Mol. Sci. 2012, 13(4), 4168-4185; doi:10.3390/ijms13044168
Received: 18 February 2012 / Revised: 2 March 2012 / Accepted: 19 March 2012 / Published: 29 March 2012
Cited by 17 | PDF Full-text (319 KB) | HTML Full-text | XML Full-text
Abstract
Congenital diarrheal disorders (CDDs) are a group of inherited enteropathies with a typical onset early in the life. Infants with these disorders have frequently chronic diarrhea of sufficient severity to require parenteral nutrition. For most CDDs the disease-gene is known and molecular [...] Read more.
Congenital diarrheal disorders (CDDs) are a group of inherited enteropathies with a typical onset early in the life. Infants with these disorders have frequently chronic diarrhea of sufficient severity to require parenteral nutrition. For most CDDs the disease-gene is known and molecular analysis may contribute to an unequivocal diagnosis. We review CDDs on the basis of the genetic defect, focusing on the significant contribution of molecular analysis in the complex, multistep diagnostic work-up. Full article
Open AccessReview Scientific Evidence and Rationale for the Development of Curcumin and Resveratrol as Nutraceutricals for Joint Health
Int. J. Mol. Sci. 2012, 13(4), 4202-4232; doi:10.3390/ijms13044202
Received: 27 February 2012 / Revised: 12 March 2012 / Accepted: 19 March 2012 / Published: 30 March 2012
Cited by 15 | PDF Full-text (728 KB) | HTML Full-text | XML Full-text
Abstract
Interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α) are key cytokines that drive the production of inflammatory mediators and matrix-degrading enzymes in osteoarthritis (OA). These proinflammatory cytokines bind to their respective cell surface receptors and activate inflammatory signaling pathways culminating with [...] Read more.
Interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α) are key cytokines that drive the production of inflammatory mediators and matrix-degrading enzymes in osteoarthritis (OA). These proinflammatory cytokines bind to their respective cell surface receptors and activate inflammatory signaling pathways culminating with the activation of nuclear factor κB (NF-κB), a transcription factor that can be triggered by a host of stress-related stimuli including, excessive mechanical stress and ECM degradation products. Once activated, NF-κB regulates the expression of many cytokines, chemokines, adhesion molecules, inflammatory mediators, and several matrix-degrading enzymes. Therefore, proinflammatory cytokines, their cell surface receptors, NF-κB and downstream signaling pathways are therapeutic targets in OA. This paper critically reviews the recent literature and outlines the potential prophylactic properties of plant-derived phytochemicals such as curcumin and resveratrol for targeting NF-κB signaling and inflammation in OA to determine whether these phytochemicals can be used as functional foods. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Salivary Defense Proteins: Their Network and Role in Innate and Acquired Oral Immunity
Int. J. Mol. Sci. 2012, 13(4), 4295-4320; doi:10.3390/ijms13044295
Received: 5 March 2012 / Revised: 15 March 2012 / Accepted: 19 March 2012 / Published: 2 April 2012
Cited by 50 | PDF Full-text (242 KB) | HTML Full-text | XML Full-text
Abstract
There are numerous defense proteins present in the saliva. Although some of these molecules are present in rather low concentrations, their effects are additive and/or synergistic, resulting in an efficient molecular defense network of the oral cavity. Moreover, local concentrations of these [...] Read more.
There are numerous defense proteins present in the saliva. Although some of these molecules are present in rather low concentrations, their effects are additive and/or synergistic, resulting in an efficient molecular defense network of the oral cavity. Moreover, local concentrations of these proteins near the mucosal surfaces (mucosal transudate), periodontal sulcus (gingival crevicular fluid) and oral wounds and ulcers (transudate) may be much greater, and in many cases reinforced by immune and/or inflammatory reactions of the oral mucosa. Some defense proteins, like salivary immunoglobulins and salivary chaperokine HSP70/HSPAs (70 kDa heat shock proteins), are involved in both innate and acquired immunity. Cationic peptides and other defense proteins like lysozyme, bactericidal/permeability increasing protein (BPI), BPI-like proteins, PLUNC (palate lung and nasal epithelial clone) proteins, salivary amylase, cystatins, prolin-rich proteins, mucins, peroxidases, statherin and others are primarily responsible for innate immunity. In this paper, this complex system and function of the salivary defense proteins will be reviewed. Full article
Open AccessReview The Ascorbate-glutathione-α-tocopherol Triad in Abiotic Stress Response
Int. J. Mol. Sci. 2012, 13(4), 4458-4483; doi:10.3390/ijms13044458
Received: 25 February 2012 / Revised: 22 March 2012 / Accepted: 26 March 2012 / Published: 10 April 2012
Cited by 42 | PDF Full-text (692 KB) | HTML Full-text | XML Full-text
Abstract
The life of any living organism can be defined as a hurdle due to different kind of stresses. As with all living organisms, plants are exposed to various abiotic stresses, such as drought, salinity, extreme temperatures and chemical toxicity. These primary stresses [...] Read more.
The life of any living organism can be defined as a hurdle due to different kind of stresses. As with all living organisms, plants are exposed to various abiotic stresses, such as drought, salinity, extreme temperatures and chemical toxicity. These primary stresses are often interconnected, and lead to the overproduction of reactive oxygen species (ROS) in plants, which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA, which ultimately results in oxidative stress. Stress-induced ROS accumulation is counteracted by enzymatic antioxidant systems and non-enzymatic low molecular weight metabolites, such as ascorbate, glutathione and α-tocopherol. The above mentioned low molecular weight antioxidants are also capable of chelating metal ions, reducing thus their catalytic activity to form ROS and also scavenge them. Hence, in plant cells, this triad of low molecular weight antioxidants (ascorbate, glutathione and α-tocopherol) form an important part of abiotic stress response. In this work we are presenting a review of abiotic stress responses connected to these antioxidants. Full article
Open AccessReview Biochemistry of Bacterial Multidrug Efflux Pumps
Int. J. Mol. Sci. 2012, 13(4), 4484-4495; doi:10.3390/ijms13044484
Received: 24 February 2012 / Revised: 9 March 2012 / Accepted: 15 March 2012 / Published: 10 April 2012
Cited by 17 | PDF Full-text (213 KB) | HTML Full-text | XML Full-text
Abstract
Bacterial pathogens that are multi-drug resistant compromise the effectiveness of treatment when they are the causative agents of infectious disease. These multi-drug resistance mechanisms allow bacteria to survive in the presence of clinically useful antimicrobial agents, thus reducing the efficacy of chemotherapy [...] Read more.
Bacterial pathogens that are multi-drug resistant compromise the effectiveness of treatment when they are the causative agents of infectious disease. These multi-drug resistance mechanisms allow bacteria to survive in the presence of clinically useful antimicrobial agents, thus reducing the efficacy of chemotherapy towards infectious disease. Importantly, active multi-drug efflux is a major mechanism for bacterial pathogen drug resistance. Therefore, because of their overwhelming presence in bacterial pathogens, these active multi-drug efflux mechanisms remain a major area of intense study, so that ultimately measures may be discovered to inhibit these active multi-drug efflux pumps. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessReview Cell Adhesion and Its Endocytic Regulation in Cell Migration during Neural Development and Cancer Metastasis
Int. J. Mol. Sci. 2012, 13(4), 4564-4590; doi:10.3390/ijms13044564
Received: 7 February 2012 / Revised: 23 March 2012 / Accepted: 26 March 2012 / Published: 11 April 2012
Cited by 32 | PDF Full-text (791 KB) | HTML Full-text | XML Full-text
Abstract
Cell migration is a crucial event for tissue organization during development, and its dysregulation leads to several diseases, including cancer. Cells exhibit various types of migration, such as single mesenchymal or amoeboid migration, collective migration and scaffold cell-dependent migration. The migration properties [...] Read more.
Cell migration is a crucial event for tissue organization during development, and its dysregulation leads to several diseases, including cancer. Cells exhibit various types of migration, such as single mesenchymal or amoeboid migration, collective migration and scaffold cell-dependent migration. The migration properties are partly dictated by cell adhesion and its endocytic regulation. While an epithelial-mesenchymal transition (EMT)-mediated mesenchymal cell migration requires the endocytic recycling of integrin-mediated adhesions after the disruption of cell-cell adhesions, an amoeboid migration is not dependent on any adhesions to extracellular matrix (ECM) or neighboring cells. In contrast, a collective migration is mediated by both cell-cell and cell-ECM adhesions, and a scaffold cell-dependent migration is regulated by the endocytosis and recycling of cell-cell adhesion molecules. Although some invasive carcinoma cells exhibit an EMT-mediated mesenchymal or amoeboid migration, other cancer cells are known to maintain cadherin-based cell-cell adhesions and epithelial morphology during metastasis. On the other hand, a scaffold cell-dependent migration is mainly utilized by migrating neurons in normal developing brains. This review will summarize the structures of cell adhesions, including adherens junctions and focal adhesions, and discuss the regulatory mechanisms for the dynamic behavior of cell adhesions by endocytic pathways in cell migration in physiological and pathological conditions, focusing particularly on neural development and cancer metastasis. Full article
Figures

Open AccessReview Phages and HIV-1: From Display to Interplay
Int. J. Mol. Sci. 2012, 13(4), 4727-4794; doi:10.3390/ijms13044727
Received: 1 March 2012 / Revised: 26 March 2012 / Accepted: 30 March 2012 / Published: 13 April 2012
Cited by 3 | PDF Full-text (848 KB) | HTML Full-text | XML Full-text
Abstract
The complex hide-and-seek game between HIV-1 and the host immune system has impaired the development of an efficient vaccine. In addition, the high variability of the virus impedes the long-term control of viral replication by small antiviral drugs. For more than 20 [...] Read more.
The complex hide-and-seek game between HIV-1 and the host immune system has impaired the development of an efficient vaccine. In addition, the high variability of the virus impedes the long-term control of viral replication by small antiviral drugs. For more than 20 years, phage display technology has been intensively used in the field of HIV-1 to explore the epitope landscape recognized by monoclonal and polyclonal HIV-1-specific antibodies, thereby providing precious data about immunodominant and neutralizing epitopes. In parallel, biopanning experiments with various combinatorial or antibody fragment libraries were conducted on viral targets as well as host receptors to identify HIV-1 inhibitors. Besides these applications, phage display technology has been applied to characterize the enzymatic specificity of the HIV-1 protease. Phage particles also represent valuable alternative carriers displaying various HIV-1 antigens to the immune system and eliciting antiviral responses. This review presents and summarizes the different studies conducted with regard to the nature of phage libraries, target display mode and biopanning procedures. Full article
(This article belongs to the Special Issue Phage Display)
Figures

Open AccessReview Structural Features of Caspase-Activating Complexes
Int. J. Mol. Sci. 2012, 13(4), 4807-4818; doi:10.3390/ijms13044807
Received: 7 March 2012 / Revised: 28 March 2012 / Accepted: 10 April 2012 / Published: 16 April 2012
Cited by 24 | PDF Full-text (406 KB) | HTML Full-text | XML Full-text
Abstract
Apoptosis, also called programmed cell death, is an orderly cellular suicide program that is critical for the development, immune regulation and homeostasis of a multi-cellular organism. Failure to control this process can lead to serious human diseases, including many types of cancer, [...] Read more.
Apoptosis, also called programmed cell death, is an orderly cellular suicide program that is critical for the development, immune regulation and homeostasis of a multi-cellular organism. Failure to control this process can lead to serious human diseases, including many types of cancer, neurodegenerative diseases, and autoimmununity. The process of apoptosis is mediated by the sequential activation of caspases, which are cysteine proteases. Initiator caspases, such as caspase-2, -8, -9, and -10, are activated by formation of caspase-activating complexes, which function as a platform to recruit caspases, providing proximity for self-activation. Well-known initiator caspase-activating complexes include (1) DISC (Death Inducing Signaling Complex), which activates caspases-8 and 10; (2) Apoptosome, which activates caspase-9; and (3) PIDDosome, which activates caspase-2. Because of the fundamental biological importance of capases, many structural and biochemical studies to understand the molecular basis of assembly mechanism of caspase-activating complexes have been performed. In this review, we summarize previous studies that have examined the structural and biochemical features of caspase-activating complexes. By analyzing the structural basis for the assembly mechanism of the caspase-activating complex, we hope to provide a comprehensive understanding of caspase activation by these important oligomeric complexes. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Open AccessReview Filamentous Bacteriophage Fd as an Antigen Delivery System in Vaccination
Int. J. Mol. Sci. 2012, 13(4), 5179-5194; doi:10.3390/ijms13045179
Received: 28 January 2012 / Revised: 29 February 2012 / Accepted: 19 April 2012 / Published: 24 April 2012
Cited by 14 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Peptides displayed on the surface of filamentous bacteriophage fd are able to induce humoral as well as cell-mediated immune responses, which makes phage particles an attractive antigen delivery system to design new vaccines. The immune response induced by phage-displayed peptides can be [...] Read more.
Peptides displayed on the surface of filamentous bacteriophage fd are able to induce humoral as well as cell-mediated immune responses, which makes phage particles an attractive antigen delivery system to design new vaccines. The immune response induced by phage-displayed peptides can be enhanced by targeting phage particles to the professional antigen presenting cells, utilizing a single-chain antibody fragment that binds dendritic cell receptor DEC-205. Here, we review recent advances in the use of filamentous phage fd as a platform for peptide vaccines, with a special focus on the use of phage fd as an antigen delivery platform for peptide vaccines in Alzheimer’s Disease and cancer. Full article
(This article belongs to the Special Issue Phage Display)
Figures

Open AccessReview Localization of Axonal Motor Molecules Machinery in Neurodegenerative Disorders
Int. J. Mol. Sci. 2012, 13(4), 5195-5206; doi:10.3390/ijms13045195
Received: 26 February 2012 / Revised: 2 April 2012 / Accepted: 18 April 2012 / Published: 24 April 2012
Cited by 3 | PDF Full-text (386 KB) | HTML Full-text | XML Full-text
Abstract
Axonal transport and neuronal survival depend critically on active transport and axon integrity both for supplying materials and communication to different domains of the cell body. All these actions are executed through cytoskeleton, transport and regulatory elements that appear to be disrupted [...] Read more.
Axonal transport and neuronal survival depend critically on active transport and axon integrity both for supplying materials and communication to different domains of the cell body. All these actions are executed through cytoskeleton, transport and regulatory elements that appear to be disrupted in neurodegenerative diseases. Motor-driven transport both supplies and clears distal cellular portions with proteins and organelles. This transport is especially relevant in projection and motor neurons, which have long axons to reach the farthest nerve endings. Thus, any disturbance of axonal transport may have severe consequences for neuronal function and survival. A growing body of literature indicates the presence of alterations to the motor molecules machinery, not only in expression levels and phosphorylation, but also in their subcellular distribution within populations of neurons, which are selectively affected in the course of neurodegenerative diseases. The implications of this altered subcellular localization and how this affects axon survival and neuronal death still remain poorly understood, although several hypotheses have been suggested. Furthermore, cytoskeleton and transport element localization can be selectively disrupted in some disorders suggesting that specific loss of the axonal functionality could be a primary hallmark of the disorder. This can lead to axon degeneration and neuronal death either directly, through the functional absence of essential axonal proteins, or indirectly, through failures in communication among different cellular domains. This review compares the localization of cytoskeleton and transport elements in some neurodegenerative disorders to ask what aspects may be essential for axon survival and neuronal death. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Phage Displayed Peptides/Antibodies Recognizing Growth Factors and Their Tyrosine Kinase Receptors as Tools for Anti-Cancer Therapeutics
Int. J. Mol. Sci. 2012, 13(4), 5254-5277; doi:10.3390/ijms13045254
Received: 9 February 2012 / Revised: 9 April 2012 / Accepted: 20 April 2012 / Published: 24 April 2012
Cited by 3 | PDF Full-text (390 KB) | HTML Full-text | XML Full-text
Abstract
The basic idea of displaying peptides on a phage, introduced by George P. Smith in 1985, was greatly developed and improved by McCafferty and colleagues at the MRC Laboratory of Molecular Biology and, later, by Barbas and colleagues at the Scripps Research [...] Read more.
The basic idea of displaying peptides on a phage, introduced by George P. Smith in 1985, was greatly developed and improved by McCafferty and colleagues at the MRC Laboratory of Molecular Biology and, later, by Barbas and colleagues at the Scripps Research Institute. Their approach was dedicated to building a system for the production of antibodies, similar to a naïve B cell repertoire, in order to by-pass the standard hybridoma technology that requires animal immunization. Both groups merged the phage display technology with an antibody library to obtain a huge number of phage variants, each of them carrying a specific antibody ready to bind its target molecule, allowing, later on, rare phage (one in a million) to be isolated by affinity chromatography. Here, we will briefly review the basis of the technology and the therapeutic application of phage-derived bioactive molecules when addressed against key players in tumor development and progression: growth factors and their tyrosine kinase receptors. Full article
(This article belongs to the Special Issue Phage Display)

Other

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Open AccessShort Note Development of 16 Microsatellite Markers for Prince’s Pine, Chimaphila japonica (Pyroleae, Monotropoideae, Ericaceae)
Int. J. Mol. Sci. 2012, 13(4), 4003-4008; doi:10.3390/ijms13044003
Received: 6 February 2012 / Revised: 15 March 2012 / Accepted: 19 March 2012 / Published: 23 March 2012
PDF Full-text (130 KB) | HTML Full-text | XML Full-text
Abstract
The perennial evergreen herb, Chimaphila japonica is found exclusively in East Asian temperate coniferous or sometimes in deciduous forests. By using the Fast Isolation by Amplified Fragment Length Polymorphism (AFLP) of Sequences Containing repeats (FIASCO) protocol, 20 microsatellite primer sets were identified [...] Read more.
The perennial evergreen herb, Chimaphila japonica is found exclusively in East Asian temperate coniferous or sometimes in deciduous forests. By using the Fast Isolation by Amplified Fragment Length Polymorphism (AFLP) of Sequences Containing repeats (FIASCO) protocol, 20 microsatellite primer sets were identified in two wild populations. Of these primers, 16 displayed polymorphisms and 4 were monomorphic. The number of alleles per locus ranged from one to six among populations, values for expected and observed heterozygosities ranged from 0.000 to 0.848 and from 0.000 to 1.000, respectively. The new SSR markers will be useful in obtaining estimates of population-level genetic diversity and in phylogeographic studies of C. japonica. Full article

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