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Int. J. Mol. Sci., Volume 12, Issue 8 (August 2011), Pages 4758-5460

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Open AccessArticle Anti-Fatigue Properties of Tartary Buckwheat Extracts in Mice
Int. J. Mol. Sci. 2011, 12(8), 4770-4780; doi:10.3390/ijms12084770
Received: 7 June 2011 / Revised: 15 July 2011 / Accepted: 19 July 2011 / Published: 25 July 2011
Cited by 25 | PDF Full-text (181 KB) | HTML Full-text | XML Full-text
Abstract
Anti-fatigue properties of tartary buckwheat extracts (TBE) was investigated in male Kunming mice. The animals were divided into four groups. The first group, designated as the control group (control), was administered with distilled water by gavage every day for 28 days. The [...] Read more.
Anti-fatigue properties of tartary buckwheat extracts (TBE) was investigated in male Kunming mice. The animals were divided into four groups. The first group, designated as the control group (control), was administered with distilled water by gavage every day for 28 days. The other three groups, designated as TBE treatment groups, were administered with TBE of 60, 120 and 240 mg/kg body weight, respectively, by gavage every day for 28 days. Exhaustive swimming time, blood lactic acid (BLA), blood urea nitrogen (BUN), tissue glycogen, glutathione peroxidase (GPx) and superoxide dismutase (SOD) of mice after swimming were determined. The results showed that tartary buckwheat extracts had anti-fatigue properties, which extended the exhaustive swimming time of mice, effectively inhibiting the increase of BLA, decreasing the level of BUN, increasing the tissue glycogen content and the activities of SOD and GPx of mice. However, further study is needed to elucidate the exact mechanism of the effect of TBE on fatigue. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Molecular Recognition Effects in Atomistic Models of Imprinted Polymers
Int. J. Mol. Sci. 2011, 12(8), 4781-4804; doi:10.3390/ijms12084781
Received: 10 June 2011 / Revised: 8 July 2011 / Accepted: 25 July 2011 / Published: 28 July 2011
Cited by 12 | PDF Full-text (709 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine [...] Read more.
In this article we present a model for molecularly imprinted polymers, which considers both complexation processes in the pre-polymerization mixture and adsorption in the imprinted structures within a single consistent framework. As a case study we investigate MAA/EGDMA polymers imprinted with pyrazine and pyrimidine. A polymer imprinted with pyrazine shows substantial selectivity towards pyrazine over pyrimidine, thus exhibiting molecular recognition, whereas the pyrimidine imprinted structure shows no preferential adsorption of the template. Binding sites responsible for the molecular recognition of pyrazine involve one MAA molecule and one EGDMA molecule, forming associations with the two functional groups of the pyrazine molecule. Presence of these specific sites in the pyrazine imprinted system and lack of the analogous sites in the pyrimidine imprinted system is directly linked to the complexation processes in the pre-polymerization solution. These processes are quite different for pyrazine and pyrimidine as a result of both enthalpic and entropic effects. Full article
(This article belongs to the Special Issue Molecular Imprinting Science and Technology)
Open AccessArticle Solvolyses of Benzoyl Chlorides in Weakly Nucleophilic Media
Int. J. Mol. Sci. 2011, 12(8), 4805-4818; doi:10.3390/ijms12084805
Received: 6 July 2011 / Revised: 22 July 2011 / Accepted: 18 July 2011 / Published: 28 July 2011
Cited by 9 | PDF Full-text (398 KB) | HTML Full-text | XML Full-text
Abstract
Rate constants and activations parameters are reported for solvolyses of p-Z-substituted benzoyl chlorides (1, Z = OMe, Me, H, and Cl) in 97% w/w hexafluoroisopropanol-water (97H). Additional kinetic data are reported for solvolyses in acetic and formic acids. Plots [...] Read more.
Rate constants and activations parameters are reported for solvolyses of p-Z-substituted benzoyl chlorides (1, Z = OMe, Me, H, and Cl) in 97% w/w hexafluoroisopropanol-water (97H). Additional kinetic data are reported for solvolyses in acetic and formic acids. Plots of log k vs. σp in 97H are consistent with previous research showing that a cationic reaction channel is dominant, even for solvolyses of 1, Z = NO2. A benzoyl cation intermediate was trapped by Friedel-Crafts reaction with 1,3,5-trimethoxybenzene in hexafluoroisopropanol. The results are explained by an SN2-SN1 spectrum of mechanisms with variations in nucleophilic solvent assistance. Ab initio calculations of heterolytic bond dissociation energies of various chloro- and fluoro-substituted and other benzoyl chlorides are correlated with log k for solvolyses. Full article
(This article belongs to the Special Issue Correlation Analysis Applied to Solvolysis Reactions)
Open AccessArticle Evaluation of in Vitro and in Vivo Depigmenting Activity of Raspberry Ketone from Rheum officinale
Int. J. Mol. Sci. 2011, 12(8), 4819-4835; doi:10.3390/ijms12084819
Received: 22 June 2011 / Accepted: 21 July 2011 / Published: 28 July 2011
Cited by 16 | PDF Full-text (1099 KB) | HTML Full-text | XML Full-text
Abstract
Melanogenesis inhibition by raspberry ketone (RK) from Rheum officinale was investigated both in vitro in cultivated murine B16 melanoma cells and in vivo in zebrafish and mice. In B16 cells, RK inhibited melanogenesis through a post-transcriptional regulation of tyrosinase gene expression, which [...] Read more.
Melanogenesis inhibition by raspberry ketone (RK) from Rheum officinale was investigated both in vitro in cultivated murine B16 melanoma cells and in vivo in zebrafish and mice. In B16 cells, RK inhibited melanogenesis through a post-transcriptional regulation of tyrosinase gene expression, which resulted in down regulation of both cellular tyrosinase activity and the amount of tyrosinase protein, while the level of tyrosinase mRNA transcription was not affected. In zebrafish, RK also inhibited melanogenesis by reduction of tyrosinase activity. In mice, application of a 0.2% or 2% gel preparation of RK applied to mouse skin significantly increased the degree of skin whitening within one week of treatment. In contrast to the widely used flavoring properties of RK in perfumery and cosmetics, the skin-whitening potency of RK has been demonstrated in the present study. Based on our findings reported here, RK would appear to have high potential for use in the cosmetics industry. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Genetic Characterization of Five Hatchery Populations of the Pacific Abalone (Haliotis discus hannai) Using Microsatellite Markers
Int. J. Mol. Sci. 2011, 12(8), 4836-4849; doi:10.3390/ijms12084836
Received: 22 April 2011 / Revised: 5 July 2011 / Accepted: 19 July 2011 / Published: 29 July 2011
Cited by 8 | PDF Full-text (293 KB) | HTML Full-text | XML Full-text
Abstract
The Pacific abalone, Haliotis discus hannai, is a popular food in Eastern Asia. Aquacultural production of this species has increased because of recent resource declines, the growing consumption, and ongoing government-operated stock release programs. Therefore, the genetic characterization of hatchery populations is necessary to maintain the genetic diversity of this species and to develop more effective aquaculture practices. We analyzed the genetic structures of five cultured populations in Korea using six microsatellite markers. The number of alleles per locus ranged from 15 to 64, with an average of 23.5. The mean observed and expected heterozygosities were 0.797 and 0.904, respectively. The inbreeding coefficient FIS ranged from 0.054 to 0.184 (mean FIS = 0.121 ± 0.056). The genetic differentiation across all populations was low but significant (overall FST = 0.009, P < 0.01). Pairwise multilocus FST tests, estimates of genetic distance, and phylogenetic and principal component analyses did not show a consistent relationship between geographic and genetic distances. These results could reflect extensive aquaculture, the exchange of breeds and eggs between hatcheries and/or genetic drift due to intensive breeding practices. Thus, for optimal resource management, the genetic variation of hatchery stocks should be monitored and inbreeding controlled within the abalone stocks that are being released every year. This genetic information will be useful for the management of both H. discus hannai fisheries and the aquaculture industry. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessArticle Intermediates in the Protein Folding Process: A Computational Model
Int. J. Mol. Sci. 2011, 12(8), 4850-4860; doi:10.3390/ijms11084850
Received: 7 April 2011 / Revised: 7 June 2011 / Accepted: 25 July 2011 / Published: 29 July 2011
Cited by 5 | PDF Full-text (648 KB) | HTML Full-text | XML Full-text
Abstract
The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as [...] Read more.
The paper presents a model for simulating the protein folding process in silico. The two-step model (which consists of the early stage—ES and the late stage—LS) is verified using two proteins, one of which is treated (according to experimental observations) as the early stage and the second as an example of the LS step. The early stage is based solely on backbone structural preferences, while the LS model takes into account the water environment, treated as an external hydrophobic force field and represented by a 3D Gauss function. The characteristics of 1ZTR (the ES intermediate, as compared with 1ENH, which is the LS intermediate) confirm the link between the gradual disappearance of ES characteristics in LS structural forms and the simultaneous emergence of LS properties in the 1ENH protein. Positive verification of ES and LS characteristics in these two proteins (1ZTR and 1ENH respectively) suggest potential applicability of the presented model to in silico protein folding simulations. Full article
(This article belongs to the Special Issue Protein Folding 2011)
Open AccessArticle Silibinin Causes Apoptosis and Cell Cycle Arrest in Some Human Pancreatic Cancer Cells
Int. J. Mol. Sci. 2011, 12(8), 4861-4871; doi:10.3390/ijms12084861
Received: 24 May 2011 / Revised: 5 July 2011 / Accepted: 20 July 2011 / Published: 2 August 2011
Cited by 7 | PDF Full-text (796 KB) | HTML Full-text | XML Full-text
Abstract
Silibinin, an effective anti-cancer and chemopreventive agent in various epithelial cancer models, has been reported to inhibit cancer cell growth through mitogenic signaling pathways. However, whether it can inhibit human pancreatic carcinoma growth and what are the underlying mechanisms is still not [...] Read more.
Silibinin, an effective anti-cancer and chemopreventive agent in various epithelial cancer models, has been reported to inhibit cancer cell growth through mitogenic signaling pathways. However, whether it can inhibit human pancreatic carcinoma growth and what are the underlying mechanisms is still not well elucidated. Here, we evaluated the inhibitory proliferation effects of Silibinin in pancreatic carcinoma growth and examined whether Silibinin modulates cell cycle and apoptosis. Our results indicate that Silibinin effectively inhibited the pancreatic carcinoma AsPC-1, BxPC-3 and Panc-1 cells’ proliferation and caused apoptosis. Silibinin induced a decrease in S phase and cell cycle arrest in G1 phase in AsPC-1 cells, but had no obvious changes in BxPC-3 and Panc-1 cell cycle. Furthermore, these results suggest that Silibinin might be a candidate chemopreventive agent for pancreatic carcinoma therapy. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Green Synthesis and Characterization of Silver/Chitosan/Polyethylene Glycol Nanocomposites without any Reducing Agent
Int. J. Mol. Sci. 2011, 12(8), 4872-4884; doi:10.3390/ijms12084872
Received: 24 June 2011 / Revised: 18 July 2011 / Accepted: 19 July 2011 / Published: 2 August 2011
Cited by 45 | PDF Full-text (1240 KB) | HTML Full-text | XML Full-text
Abstract
This paper presents the green synthesis of silver nanoparticles (Ag NPs) in aqueous medium. This method was performed by reducing AgNO3 in different stirring times of reaction at a moderate temperature using green agents, chitosan (Cts) and polyethylene glycol (PEG). In [...] Read more.
This paper presents the green synthesis of silver nanoparticles (Ag NPs) in aqueous medium. This method was performed by reducing AgNO3 in different stirring times of reaction at a moderate temperature using green agents, chitosan (Cts) and polyethylene glycol (PEG). In this work, silver nitrate (AgNO3) was used as the silver precursor while Cts and PEG were used as the solid support and polymeric stabilizer. The properties of Ag/Cts/PEG nanocomposites (NCs) were studied under different stirring times of reaction. The developed Ag/Cts/PEG NCs were then characterized by the ultraviolet-visible (UV-Vis) spectroscopy, X-ray diffraction (XRD), transmission electron microscopy (TEM), scanning electron microscopy (SEM) and Fourier transform infrared (FTIR) spectroscopy. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessCommunication The Chemical Composition and Nitrogen Distribution of Chinese Yak (Maiwa) Milk
Int. J. Mol. Sci. 2011, 12(8), 4885-4895; doi:10.3390/ijms12084885
Received: 10 June 2011 / Revised: 13 July 2011 / Accepted: 22 July 2011 / Published: 2 August 2011
Cited by 17 | PDF Full-text (170 KB) | HTML Full-text | XML Full-text
Abstract
The paper surveyed the chemical composition and nitrogen distribution of Maiwa yak milk, and compared the results with reference composition of cow milk. Compared to cow milk, yak milk was richer in protein (especially whey protein), essential amino acids, fat, lactose and minerals (except phosphorus). The contents of some nutrients (total protein, lactose, essential amino acids and casein) were higher in the warm season than in the cold season. Higher ratios of total essential amino acids/total amino acids (TEAA/TAA) and total essential amino acids/total non essential amino acids (TEAA/TNEAA) were found in the yak milk from the warm season. However its annual average ratio of EAA/TAA and that of EAA/NEAA were similar to those of cow milk. Yak milk was rich in calcium and iron (p < 0.05), and thus may serve as a nutritional ingredient with a potential application in industrial processing. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle In Vitro and in Vivo Antioxidant Properties of the Plant-Based Supplement Greens+
Int. J. Mol. Sci. 2011, 12(8), 4896-4908; doi:10.3390/ijms12084896
Received: 17 June 2011 / Revised: 20 July 2011 / Accepted: 21 July 2011 / Published: 3 August 2011
Cited by 7 | PDF Full-text (269 KB) | HTML Full-text | XML Full-text
Abstract
Dietary antioxidants play an important role against oxidation, an underlying mechanism in the incidence of chronic diseases. Greens+ is a commercially available preparation containing a variety of plant-derived ingredients. The aim of the current study was to evaluate the antioxidant potential of the methanolic extract of greens+ powder using in vitro and in vivo techniques. In vitro studies were conducted using a liposome model system to simulate biological cell membranes. Total antioxidant potential and polyphenol content of the herbal preparation was measured. For in vivo analysis, 10 healthy human subjects consumed either three or six teaspoons of greens+ per day for four weeks. Blood samples were analyzed at baseline and at the conclusion of the treatment period for total antioxidant capacity, polyphenol content, protein, lipid and LDL oxidation, and the level of glutathione peroxidase. Results showed that greens+ supplementation was well tolerated and increased serum antioxidant potential at higher levels of intake in a dose-dependent manner. HPLC analysis showed the presence of quercetin, apigenin, kaempferol and luteolin in the supplement. Plasma analysis indicated the presence of kaempferol only. A statistically significant (p < 0.05) reduction in protein and lipid oxidation was observed. Based on its antioxidant properties, the results suggest that greens+ might play a role in reducing the risk of chronic diseases involving a burden of oxidative damage. Full article
(This article belongs to the Special Issue Advances in Nutraceutical Research)
Open AccessArticle Experimental and Theoretical Electron Paramagnetic Resonance (EPR) Study on the Temperature-Dependent Structural Changes of Methylsulfanylmethane
Int. J. Mol. Sci. 2011, 12(8), 4909-4922; doi:10.3390/ijms12084909
Received: 8 June 2011 / Revised: 18 July 2011 / Accepted: 20 July 2011 / Published: 3 August 2011
Cited by 1 | PDF Full-text (623 KB) | HTML Full-text | XML Full-text
Abstract
Methylsulfonylmethane (or dimethyl sulfone), a naturally produced and vitally important organosulfur compound in living organisms, was irradiated with gamma rays, and the produced radicals were investigated using electron paramagnetic resonance spectroscopy at different temperatures. The structure and behavior of the radical changed [...] Read more.
Methylsulfonylmethane (or dimethyl sulfone), a naturally produced and vitally important organosulfur compound in living organisms, was irradiated with gamma rays, and the produced radicals were investigated using electron paramagnetic resonance spectroscopy at different temperatures. The structure and behavior of the radical changed when the temperatures varied. The hyperfine splitting of the CH3 group was small, and the 33S splitting was relatively high between 80 and −50 °C. When the temperature was between −50 and −160 °C, the 33S splitting became small and the CH3 splitting was higher. However, the group kept rotating; therefore, only the isotropic splitting values were measured, and the g-values were anisotropic. When the temperature decreased below −180 °C, the CH3 group stopped rotating, and the hydrogen splitting values became nonequivalent due to an inhomogeneous electron distribution. The observed structures can be explained by referring to both the experimental and theoretically calculated values reported. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle The Langmuir-Blodgett Technique as a Tool for Homeotropic Alignment of Fluorinated Liquid Crystals Mixed with Arachidic Acid
Int. J. Mol. Sci. 2011, 12(8), 4923-4945; doi:10.3390/ijms12084923
Received: 25 May 2011 / Revised: 2 July 2011 / Accepted: 26 July 2011 / Published: 3 August 2011
Cited by 7 | PDF Full-text (2150 KB) | HTML Full-text | XML Full-text
Abstract
Some fluoro-substituted liquid crystals mixed with arachidic acid in monolayers formed at air-liquid (Langmuir films) and air-solid substrate (Langmuir-Blodgett films) interfaces were investigated. Molecular organization in Langmuir films was determined on the basis of the analysis of the shape of the surface [...] Read more.
Some fluoro-substituted liquid crystals mixed with arachidic acid in monolayers formed at air-liquid (Langmuir films) and air-solid substrate (Langmuir-Blodgett films) interfaces were investigated. Molecular organization in Langmuir films was determined on the basis of the analysis of the shape of the surface pressure-mean molecular area isotherm and observations made by means of a Brewster angle microscope. It was found that in the compression process the liquid crystal molecules are pushed out towards the top of the first monolayer being in direct contact with the subphase. Langmuir films were transferred onto the quartz substrates at various surface pressures and mono- and multilayered Langmuir-Blodgett films were obtained. The films were characterized using electronic absorption measurements. The conditions for obtaining the homeotropic orientation of the liquid crystal molecules were determined. Full article
(This article belongs to the Special Issue Liquid Crystals 2011)
Open AccessArticle A New Benzofuran Glucoside from Ficus Tikoua Bur
Int. J. Mol. Sci. 2011, 12(8), 4946-4952; doi:10.3390/ijms12084946
Received: 11 July 2011 / Revised: 22 July 2011 / Accepted: 26 July 2011 / Published: 3 August 2011
Cited by 3 | PDF Full-text (298 KB) | HTML Full-text | XML Full-text
Abstract
From the water-soluble portion of the methanol extract of stems of Ficus tikoua Bur., a new benzofuran glucoside, named 6-carboxyethyl-5-hydroxybenzofuran 5-O-β-D-glucopyranoside (1), together with one known benzofuran glucoside (2) were isolated. Their structures were [...] Read more.
From the water-soluble portion of the methanol extract of stems of Ficus tikoua Bur., a new benzofuran glucoside, named 6-carboxyethyl-5-hydroxybenzofuran 5-O-β-D-glucopyranoside (1), together with one known benzofuran glucoside (2) were isolated. Their structures were elucidated by 1D and 2D (1H-1H COSY, HMQC, and HMBC) NMR spectroscopy and HRMS techniques. The antioxidant activities of the isolated compounds were assayed based on the scavenging activities of DPPH free radical. Compounds 1 and 2 exhibited moderate antioxidant activities, and the IC50 values were 242.8 μg·mL1 and 324.9 μg·mL−1, respectively. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Low Expression of TBX4 Predicts Poor Prognosis in Patients with Stage II Pancreatic Ductal Adenocarcinoma
Int. J. Mol. Sci. 2011, 12(8), 4953-4963; doi:10.3390/ijms12084953
Received: 28 June 2011 / Revised: 21 July 2011 / Accepted: 27 July 2011 / Published: 3 August 2011
Cited by 4 | PDF Full-text (462 KB) | HTML Full-text | XML Full-text
Abstract
This study was designed to investigate the expression of the T-box transcription factor 4 (TBX4), a tumor biomarker that was previously identified by proteomics, in pancreatic ductal adenocarcinoma (PDAC) and evaluate its clinical utility as a potential prognostic biomarkers for PDAC. The [...] Read more.
This study was designed to investigate the expression of the T-box transcription factor 4 (TBX4), a tumor biomarker that was previously identified by proteomics, in pancreatic ductal adenocarcinoma (PDAC) and evaluate its clinical utility as a potential prognostic biomarkers for PDAC. The expression of TBX4 was detected in 77 stage II PDAC tumors by immunohistochemistry, and the results were analyzed with regard to clinicopathological characteristics and overall survival. Moreover, Tbx4 promoter methylation status in primary PDAC tumors and normal adjacent pancreas tissues was measured by bisulfite sequencing. Among 77 stage II PDAC tumors, 48 cases (62.3%) expressed TBX4 at a high level. No significant correlation between TBX4 expression and other clinicopathological parameters, except tumor grade and liver metastasis recurrence, was found. The survival of patients with TBX4-high expression was significantly longer than those with TBX4-low expression (P = 0.010). In multivariate analysis, low TBX4 expression was an independent prognostic factor for overall survival in patients with stage II PDAC. TBX4 promoter methylation status was frequently observed in both PDAC and normal adjacent pancreas. We conclude that a low level of TBX4 expression suggests a worse prognosis for patients with stage II PDAC. Down-regulation of the TBX4 gene in pancreas is less likely to be regulated by DNA methylation. Full article
(This article belongs to the Special Issue Biomarkers 2011)
Open AccessArticle Interaction of Human Serum Album and C60 Aggregates in Solution
Int. J. Mol. Sci. 2011, 12(8), 4964-4974; doi:10.3390/ijms12084964
Received: 30 March 2011 / Revised: 12 July 2011 / Accepted: 27 July 2011 / Published: 4 August 2011
Cited by 16 | PDF Full-text (533 KB) | HTML Full-text | XML Full-text
Abstract
An important property of C60 in aquatic ecotoxicology is that it can form stable aggregates with nanoscale dimensions, namely nC60. Aggregation allows fullerenes to remain suspended for a long time, and the reactivity of individual C60 is substantially [...] Read more.
An important property of C60 in aquatic ecotoxicology is that it can form stable aggregates with nanoscale dimensions, namely nC60. Aggregation allows fullerenes to remain suspended for a long time, and the reactivity of individual C60 is substantially altered in this aggregate form. Herein, we investigated the interaction of nC60 and human serum album (HSA) using the methods of fluorescence, fluorescence dynamics, circular dichroism (CD), and site marker competitive experiments. We proposed a binding model consistent with the available experimental results for the interactions of nC60 with HSA. During the interaction process, the structure and conformation of HSA were affected, leading to functional changes of drug binding sites of HSA. Full article
(This article belongs to the Special Issue Bioactive Nanoparticles (special issue))
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Open AccessArticle Transient Co-Expression of Post-Transcriptional Gene Silencing Suppressors for Increased in Planta Expression of a Recombinant Anthrax Receptor Fusion Protein
Int. J. Mol. Sci. 2011, 12(8), 4975-4990; doi:10.3390/ijms12084975
Received: 1 April 2011 / Revised: 18 June 2011 / Accepted: 20 July 2011 / Published: 5 August 2011
Cited by 10 | PDF Full-text (572 KB) | HTML Full-text | XML Full-text
Abstract
Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that [...] Read more.
Potential epidemics of infectious diseases and the constant threat of bioterrorism demand rapid, scalable, and cost-efficient manufacturing of therapeutic proteins. Molecular farming of tobacco plants provides an alternative for the recombinant production of therapeutics. We have developed a transient production platform that uses Agrobacterium infiltration of Nicotiana benthamiana plants to express a novel anthrax receptor decoy protein (immunoadhesin), CMG2-Fc. This chimeric fusion protein, designed to protect against the deadly anthrax toxins, is composed of the von Willebrand factor A (VWA) domain of human capillary morphogenesis 2 (CMG2), an effective anthrax toxin receptor, and the Fc region of human immunoglobulin G (IgG). We evaluated, in N. benthamiana intact plants and detached leaves, the expression of CMG2-Fc under the control of the constitutive CaMV 35S promoter, and the co-expression of CMG2-Fc with nine different viral suppressors of post-transcriptional gene silencing (PTGS): p1, p10, p19, p21, p24, p25, p38, 2b, and HCPro. Overall, transient CMG2-Fc expression was higher on intact plants than detached leaves. Maximum expression was observed with p1 co-expression at 3.5 days post-infiltration (DPI), with a level of 0.56 g CMG2-Fc per kg of leaf fresh weight and 1.5% of the total soluble protein, a ten-fold increase in expression when compared to absence of suppression. Co-expression with the p25 PTGS suppressor also significantly increased the CMG2-Fc expression level after just 3.5 DPI. Full article
(This article belongs to the Special Issue Plant-Derived Pharmaceuticals by Molecular Farming)
Open AccessArticle Resveratrol Protects against 2-Bromopropane-Induced Apoptosis and Disruption of Embryonic Development in Blastocysts
Int. J. Mol. Sci. 2011, 12(8), 4991-5010; doi:10.3390/ijms12084991
Received: 27 May 2011 / Revised: 18 July 2011 / Accepted: 28 July 2011 / Published: 5 August 2011
Cited by 2 | PDF Full-text (1434 KB) | HTML Full-text | XML Full-text
Abstract
2-Bromopropane (2-BP) is used as an alternative to ozone-depleting cleaning solvents. Previously, we reported that 2-BP has cytotoxic effects on mouse blastocysts and is associated with defects in subsequent development. In the present work, we show that 2-BP induces apoptosis in the [...] Read more.
2-Bromopropane (2-BP) is used as an alternative to ozone-depleting cleaning solvents. Previously, we reported that 2-BP has cytotoxic effects on mouse blastocysts and is associated with defects in subsequent development. In the present work, we show that 2-BP induces apoptosis in the inner cell mass of mouse blastocysts, and inhibits cell proliferation. Both effects are suppressed by resveratrol, a grape-derived phytoalexin with known antioxidant and anti-inflammatory properties. 2-BP-treated blastocysts displayed lower levels of implantation (compared to controls) when plated on culture dishes in vitro, and a reduced ability to proceed to later stages of embryonic development. Pretreatment with resveratrol prevented 2-BP-induced disruption of embryonic development, both in vitro and in vivo. Further investigation of these processes revealed that 2-BP directly promotes ROS generation, loss of mitochondrial membrane potential (MMP), and activation of caspase-3, whereas resveratrol effectively blocks 2-BP-induced ROS production and the accompanying apoptotic biochemical changes. Our results collectively imply that 2-BP triggers the mitochondrion-dependent apoptotic pathway via ROS generation, and the antioxidant activity of resveratrol prevents 2-BP-induced toxicity. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Investigation of the Structure Requirement for 5-HT6 Binding Affinity of Arylsulfonyl Derivatives: A Computational Study
Int. J. Mol. Sci. 2011, 12(8), 5011-5030; doi:10.3390/ijms12085011
Received: 8 July 2011 / Revised: 19 July 2011 / Accepted: 29 July 2011 / Published: 8 August 2011
Cited by 7 | PDF Full-text (1791 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
5-HT6 receptor has been implicated in a series of diseases including anxiety, depression, schizophrenia and cognitive dysfunctions. 5-HT6 ligands have been reported to play a significant role in the treatment for central nervous system (CNS) diseases. Presently, a large series [...] Read more.
5-HT6 receptor has been implicated in a series of diseases including anxiety, depression, schizophrenia and cognitive dysfunctions. 5-HT6 ligands have been reported to play a significant role in the treatment for central nervous system (CNS) diseases. Presently, a large series of 223 5-HT6 ligands were studied using a combinational method by 3D-QSAR, molecular docking and molecular dynamics calculations for further improvement of potency. The optimal 3D models exhibit satisfying statistical results with r2ncv, q2 values of 0.85 and 0.50 for CoMFA, 0.81 and 0.53 for CoMSIA, respectively. Their predictive powers were validated by external test set, showing r2pred of 0.71 and 0.76. The contour maps also provide a visual representation of contributions of steric, electrostatic, hydrophobic and hydrogen bond fields as well as the prospective binding models. In addition, the agreement between 3D-QSAR, molecular docking and molecular dynamics simulation proves the rationality of the developed models. These results, we hope, may be helpful in designing novel and potential 5-HT6 ligands. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Comparative Clinical Study of Bactigras and Telfa AMD for Skin Graft Donor-Site Dressing
Int. J. Mol. Sci. 2011, 12(8), 5031-5038; doi:10.3390/ijms12085031
Received: 24 April 2011 / Revised: 22 July 2011 / Accepted: 1 August 2011 / Published: 8 August 2011
Cited by 6 | PDF Full-text (258 KB) | HTML Full-text | XML Full-text
Abstract
The Bactigras® paraffin tulle coated with chlorhexidine is normally used for the treatment of donor-site wounds in burn patients who received split-thickness skin grafts in several centers. It has some disadvantages, such as adhesion to wound surfaces and pain from the irritation caused by this dressing. The Telfa AMD®, a non-adherent wound dressing which consists of absorbent cotton fibers impregnated with polyhexamethylene biguanide enclosed in a sleeve of thermoplastic polymers, is a new option for donor-site wound care which causes less adherence to the wound. The purpose of this study was to compare clinical efficacy of these two dressings for the management of donor-site wounds. Thirty-two patients who received split-thickness skin grafts by donor site harvesting from the thigh were enrolled in this study and randomized into two groups receiving either the Bactigras® or the Telfa AMD® wound treatment. Re-epithelialization, pain, infection and cost-effectiveness analyses were compared between both groups. The results showed that there was no significant difference in age, area of donor sites or length of hospital stays between the groups (p > 0.05). However, the day of re-epithelialization (≥90%) was significantly shorter in patients treated with the Telfa AMD® compared to the Bactigras® group (14.00 ± 3.05 vs. 9.25 ± 1.88 days for Bactigras® and Telfa AMD® groups, respectively, p < 0.001). The average pain score was also significantly lower in the Telfa AMD® group (1.57 ± 0.55 vs. 4.70 ± 1.16, p < 0.001). There was no difference in the cost of treatment between the groups (4.64 ± 1.97 vs. 5.72 ± 2.54 USD, p = 0.19). This study indicated that the Telfa AMD® was an effective dressing for the treatment of donor-site wounds. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Potential Antibacterial Activity of Carvacrol-Loaded Poly(DL-lactide-co-glycolide) (PLGA) Nanoparticles against Microbial Biofilm
Int. J. Mol. Sci. 2011, 12(8), 5039-5051; doi:10.3390/ijms12085039
Received: 30 May 2011 / Revised: 25 July 2011 / Accepted: 26 July 2011 / Published: 8 August 2011
Cited by 37 | PDF Full-text (319 KB) | HTML Full-text | XML Full-text
Abstract
The ability to form biofilms contributes significantly to the pathogenesis of many microbial infections, including a variety of ocular diseases often associated with the biofilm formation on foreign materials. Carvacrol (Car.) is an important component of essential oils and recently has attracted [...] Read more.
The ability to form biofilms contributes significantly to the pathogenesis of many microbial infections, including a variety of ocular diseases often associated with the biofilm formation on foreign materials. Carvacrol (Car.) is an important component of essential oils and recently has attracted much attention pursuant to its ability to promote microbial biofilm disruption. In the present study Car. has been encapsulated in poly(DL-lactide-co-glycolide (PLGA) nanocapsules in order to obtain a suitable drug delivery system that could represent a starting point for developing new therapeutic strategies against biofilm-associated infections, such as improving the drug effect by associating an antimicrobial agent with a biofilm viscoelasticity modifier. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle A Pilot Study of the Association of Tumor Necrosis Factor Alpha Polymorphisms with Psoriatic Arthritis in the Romanian Population
Int. J. Mol. Sci. 2011, 12(8), 5052-5059; doi:10.3390/ijms12085052
Received: 6 April 2011 / Revised: 12 July 2011 / Accepted: 1 August 2011 / Published: 8 August 2011
Cited by 4 | PDF Full-text (158 KB) | HTML Full-text | XML Full-text
Abstract
Tumor necrosis factor alpha (TNF-alpha) is an important pro-inflammatory cytokine implicated in the pathogenesis of psoriatic arthritis. We have performed a case-control association study of three TNF-alpha gene polymorphisms in a group of Romanian psoriatic arthritis patients versus ethnically matched controls. A [...] Read more.
Tumor necrosis factor alpha (TNF-alpha) is an important pro-inflammatory cytokine implicated in the pathogenesis of psoriatic arthritis. We have performed a case-control association study of three TNF-alpha gene polymorphisms in a group of Romanian psoriatic arthritis patients versus ethnically matched controls. A second group of patients with undifferentiated spondyloarthritis was used in order to look for similarities in the genetic background of the two rheumatic disorders. The −857C/T polymorphism was associated with susceptibility to psoriatic arthritis in our population at the individual level (p = 0.03, OR 1.65, 95% CI 1.05–2.57) and in combined haplotypes with the −238G/A and −308G/A SNPs. Regarding the investigated polymorphisms and derived haplotypes, no potential association was found with the susceptibility to undifferentiated spondyloarthritis in Romanian patients. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effect of Cistanches Herba Aqueous Extract on Bone Loss in Ovariectomized Rat
Int. J. Mol. Sci. 2011, 12(8), 5060-5069; doi:10.3390/ijms12085060
Received: 14 June 2011 / Revised: 21 July 2011 / Accepted: 4 August 2011 / Published: 8 August 2011
Cited by 8 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
To assess the ability of traditional Chinese medicine Cistanches Herba extract (CHE) to prevent bone loss in the ovariectomized (OVX) rat, Cistanches Herba extract (CHE) was administered intragastrically to the rats. Female rats were anesthetized with pentobarbital sodium (40 mg kg−1 [...] Read more.
To assess the ability of traditional Chinese medicine Cistanches Herba extract (CHE) to prevent bone loss in the ovariectomized (OVX) rat, Cistanches Herba extract (CHE) was administered intragastrically to the rats. Female rats were anesthetized with pentobarbital sodium (40 mg kg−1, i.p.), and their ovaries were removed bilaterally. The rats in the sham-operated group were anesthetized, laparotomized, and sutured without removing their ovaries. After 1 week of recovery from surgery, the OVX rats were randomly divided into three groups and orally treated with H2O (OVX group) or CHE (100 or 200 mg kg−1 daily) for 3 months. The sham-operated group (n = 8) was orally treated with H2O. After 3 months, the total body bone mineral density (BMD), bone mineral content (BMC), Bone biomechanical index, blood mineral levels and blood antioxidant enzymes activities were examined in sham-operated, ovariectomized and Cistanches Herba extract treated rats. Results showed that Cistanches Herba extract treatment significantly dose-dependently enhanced bone mineral density (BMD), bone mineral content (BMC), maximum load, displacement at maximum load, stress at maximum load, load at auto break, displacement at auto break, and stress at auto break, and blood antioxidant enzymes activities, decreased blood Ca, Zn and Cu levels compared to the OVX group. This experiment demonstrates that the administration of Cistanches Herba extract to ovariectomized rats reverses bone loss and prevents osteoporosis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Combined 3D-QSAR and Docking Modelling Study on Indolocarbazole Series Compounds as Tie-2 Inhibitors
Int. J. Mol. Sci. 2011, 12(8), 5080-5097; doi:10.3390/ijms12085080
Received: 24 May 2011 / Revised: 1 August 2011 / Accepted: 2 August 2011 / Published: 10 August 2011
Cited by 4 | PDF Full-text (851 KB) | HTML Full-text | XML Full-text
Abstract
Tie-2, a kind of endothelial cell tyrosine kinase receptor, is required for embryonic blood vessel development and tumor angiogenesis. Several compounds that showed potent activity toward this attractive anticancer drug target in the assay have been reported. In order to investigate the [...] Read more.
Tie-2, a kind of endothelial cell tyrosine kinase receptor, is required for embryonic blood vessel development and tumor angiogenesis. Several compounds that showed potent activity toward this attractive anticancer drug target in the assay have been reported. In order to investigate the structure-activity correlation of indolocarbazole series compounds and modify them to improve their selectivity and activity, 3D-QSAR models were built using CoMFA and CoMSIA methods and molecular docking was used to check the results. Based on the common sketch align, two good QSAR models with high predictabilities (CoMFA model: q2 = 0.823, r2 = 0.979; CoMSIA model: q2 = 0.804, r2 = 0.967) were obtained and the contour maps obtained from both models were applied to identify the influence on the biological activity. Molecular docking was then used to confirm the results. Combined with the molecular docking results, the detail binding mode between the ligands and Tie-2 was elucidated, which enabled us to interpret the structure-activity relationship. These satisfactory results not only offered help to comprehend the action mechanism of indolocarbazole series compounds, but also provide new information for the design of new potent inhibitors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle Alert-QSAR. Implications for Electrophilic Theory of Chemical Carcinogenesis
Int. J. Mol. Sci. 2011, 12(8), 5098-5134; doi:10.3390/ijms12085098
Received: 1 June 2011 / Revised: 30 June 2011 / Accepted: 3 August 2011 / Published: 11 August 2011
Cited by 21 | PDF Full-text (490 KB) | HTML Full-text | XML Full-text
Abstract
Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations ASA of electrophilic molecular structures with observed carcinogenic potencies in rats [...] Read more.
Given the modeling and predictive abilities of quantitative structure activity relationships (QSARs) for genotoxic carcinogens or mutagens that directly affect DNA, the present research investigates structural alert (SA) intermediate-predicted correlations ASA of electrophilic molecular structures with observed carcinogenic potencies in rats (observed activity, A = Log[1/TD50], i.e., ASA=f(X1SA,X2SA,...)). The present method includes calculation of the recently developed residual correlation of the structural alert models, i.e., ARASA=f(A-ASA,X1SA,X2SA,...) . We propose a specific electrophilic ligand-receptor mechanism that combines electronegativity with chemical hardness-associated frontier principles, equality of ligand-reagent electronegativities and ligand maximum chemical hardness for highly diverse toxic molecules against specific receptors in rats. The observed carcinogenic activity is influenced by the induced SA-mutagenic intermediate effect, alongside Hansch indices such as hydrophobicity (LogP), polarizability (POL) and total energy (Etot), which account for molecular membrane diffusion, ionic deformation, and stericity, respectively. A possible QSAR mechanistic interpretation of mutagenicity as the first step in genotoxic carcinogenesis development is discussed using the structural alert chemoinformation and in full accordance with the Organization for Economic Co-operation and Development QSAR guidance principles. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
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Open AccessArticle Self-Assembly of Protein Monolayers Engineered for Improved Monoclonal Immunoglobulin G Binding
Int. J. Mol. Sci. 2011, 12(8), 5157-5167; doi:10.3390/ijms12085157
Received: 4 July 2011 / Revised: 4 July 2011 / Accepted: 10 August 2011 / Published: 15 August 2011
Cited by 2 | PDF Full-text (467 KB) | HTML Full-text | XML Full-text
Abstract
Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs [...] Read more.
Bacterial outer membrane proteins, along with a filling lipid molecule can be modified to form stable self-assembled monolayers on gold. The transmembrane domain of Escherichia coli outer membrane protein A has been engineered to create a scaffold protein to which functional motifs can be fused. In earlier work we described the assembly and structure of an antibody-binding array where the Z domain of Staphylococcus aureus protein A was fused to the scaffold protein. Whilst the binding of rabbit polyclonal immunoglobulin G (IgG) to the array is very strong, mouse monoclonal IgG dissociates from the array easily. This is a problem since many immunodiagnostic tests rely upon the use of mouse monoclonal antibodies. Here we describe a strategy to develop an antibody-binding array that will bind mouse monoclonal IgG with lowered dissociation from the array. A novel protein consisting of the scaffold protein fused to two pairs of Z domains separated by a long flexible linker was manufactured. Using surface plasmon resonance the self-assembly of the new protein on gold and the improved binding of mouse monoclonal IgG were demonstrated. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
Open AccessArticle Syntheses and Self-assembling Behaviors of Pentagonal Conjugates of Tryptophane Zipper-Forming Peptide
Int. J. Mol. Sci. 2011, 12(8), 5187-5199; doi:10.3390/ijms12085187
Received: 13 June 2011 / Revised: 30 July 2011 / Accepted: 10 August 2011 / Published: 15 August 2011
Cited by 5 | PDF Full-text (1429 KB) | HTML Full-text | XML Full-text
Abstract
Pentagonal conjugates of tryptophane zipper-forming peptide (CKTWTWTE) with a pentaazacyclopentadecane core (Pentagonal-Gly-Trpzip and Pentagonal-Ala-Trpzip) were synthesized and their self-assembling behaviors were investigated in water. Pentagonal-Gly-Trpzip self-assembled into nanofibers with the width of about 5 nm in neutral water (pH 7) via formation [...] Read more.
Pentagonal conjugates of tryptophane zipper-forming peptide (CKTWTWTE) with a pentaazacyclopentadecane core (Pentagonal-Gly-Trpzip and Pentagonal-Ala-Trpzip) were synthesized and their self-assembling behaviors were investigated in water. Pentagonal-Gly-Trpzip self-assembled into nanofibers with the width of about 5 nm in neutral water (pH 7) via formation of tryptophane zipper, which irreversibly converted to nanoribbons by heating. In contrast, Pentagonal-Ala-Trpzip formed irregular aggregates in water. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
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Open AccessArticle A Comparative Reverse Docking Strategy to Identify Potential Antineoplastic Targets of Tea Functional Components and Binding Mode
Int. J. Mol. Sci. 2011, 12(8), 5200-5212; doi:10.3390/ijms12085200
Received: 6 March 2011 / Revised: 19 July 2011 / Accepted: 22 July 2011 / Published: 15 August 2011
Cited by 14 | PDF Full-text (633 KB) | HTML Full-text | XML Full-text
Abstract
The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. [...] Read more.
The main functional components of green tea, such as epigallocatechin gallate (EGCG), epigallocatechin (EGC), epicatechin gallate (ECG) and epicatechin (EC), are found to have a broad antineoplastic activity. The discovery of their targets plays an important role in revealing the antineoplastic mechanism. Therefore, to identify potential target proteins for tea polyphenols, we have taken a comparative virtual screening approach using two reverse docking systems, one based on Autodock software and the other on Tarfisdock. Two separate in silico workflows were implemented to derive a set of target proteins related to human diseases and ranked by the binding energy score. Several conventional clinically important proteins with anti-tumor effects are screened out from the PDTD protein database as the potential receptors by both procedures. To further analyze the validity of docking results, we study the binding mode of EGCG and the potential target protein Leukotriene A4 hydrolase in detail. We indicate that interactions mediated by electrostatic and hydrogen bond play a key role in ligand binding. EGCG binds to the enzyme with certain orientation and conformation that is suitable for nucleophilic attacks by several electrical residues inside the enzyme’s activity cavity. This study provides useful information for studying the antitumor mechanism of tea’s functional components. The comparative reverse docking strategy presented generates a tractable set of antineoplastic proteins for future experimental validation as drug targets against tumors. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Effects of Nitrogen Fertilization on Synthesis of Primary and Secondary Metabolites in Three Varieties of Kacip Fatimah (Labisia Pumila Blume)
Int. J. Mol. Sci. 2011, 12(8), 5238-5254; doi:10.3390/ijms12085238
Received: 8 July 2011 / Revised: 28 July 2011 / Accepted: 4 August 2011 / Published: 16 August 2011
Cited by 28 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
A split plot 3 by 4 experiment was designed to examine the impact of 15-week variable levels of nitrogen fertilization (0, 90, 180 and 270 kg N/ha) on the characteristics of total flavonoids (TF), total phenolics (TP), total non structurable carbohydrate (TNC), [...] Read more.
A split plot 3 by 4 experiment was designed to examine the impact of 15-week variable levels of nitrogen fertilization (0, 90, 180 and 270 kg N/ha) on the characteristics of total flavonoids (TF), total phenolics (TP), total non structurable carbohydrate (TNC), net assimilation rate, leaf chlorophyll content, carbon to nitrogen ratio (C/N), phenyl alanine lyase activity (PAL) and protein content, and their relationships, in three varieties of Labisia pumila Blume (alata, pumila and lanceolata). The treatment effects were solely contributed by nitrogen application; there was neither varietal nor interaction effect observed. As nitrogen levels increased from 0 to 270 kg N/ha, the production of TNC was found to decrease steadily. Production of TF and TP reached their peaks under 0 followed by 90, 180 and 270 kg N/ha treatment. However, net assimilation rate was enhanced as nitrogen fertilization increased from 0 to 270 kg N/ha. The increase in production of TP and TF under low nitrogen levels (0 and 90 kg N/ha) was found to be correlated with enhanced PAL activity. The enhancement in PAL activity was followed by reduction in production of soluble protein under low nitrogen fertilization indicating more availability of amino acid phenyl alanine (phe) under low nitrogen content that stimulate the production of carbon based secondary metabolites (CBSM). The latter was manifested by high C/N ratio in L. pumila plants. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Sinanodonta woodiana (Mollusca: Bivalvia: Unionidae): Isolation and Characterization of the First Microsatellite Markers
Int. J. Mol. Sci. 2011, 12(8), 5255-5260; doi:10.3390/ijms12085255
Received: 6 July 2011 / Revised: 25 July 2011 / Accepted: 4 August 2011 / Published: 17 August 2011
Cited by 5 | PDF Full-text (140 KB) | HTML Full-text | XML Full-text
Abstract
Sinanodonta woodiana (Lea, 1834) is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to [...] Read more.
Sinanodonta woodiana (Lea, 1834) is a large Unionid species with a real invasion success. It colonized Europe, Central America, the Indonesian Islands and recently North America. The species life cycle involves a larval parasitic stage on freshwater fish species which contributes to the spread of the mussel. In this paper we describe, for the first time, eight polymorphic microsatellite loci for the species Sinanodonta woodiana. The genetic screening of individuals confirmed that all loci were highly polymorphic. The number of alleles per locus ranged from 7 to 14 and the observed heterozygosity ranged from 0.650 to 0.950. These loci should prove useful to study the species population genetics which could help to infer important aspects of the invasion process. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Characterization of Thermophilic Halotolerant Aeribacillus pallidus TD1 from Tao Dam Hot Spring, Thailand
Int. J. Mol. Sci. 2011, 12(8), 5294-5303; doi:10.3390/ijms12085294
Received: 24 June 2011 / Revised: 28 July 2011 / Accepted: 5 August 2011 / Published: 17 August 2011
Cited by 10 | PDF Full-text (589 KB) | HTML Full-text | XML Full-text
Abstract
The bacterial strain TD1 was isolated from Tao Dam hot spring in Thailand. Strain TD1 was Gram positive, rod-shaped, aerobic, motile, and endospore forming. The cell was 2.0–40 mm in length and about 0.4 mm in diameter. The optimum growth occurred at [...] Read more.
The bacterial strain TD1 was isolated from Tao Dam hot spring in Thailand. Strain TD1 was Gram positive, rod-shaped, aerobic, motile, and endospore forming. The cell was 2.0–40 mm in length and about 0.4 mm in diameter. The optimum growth occurred at 55–60 °C and at pH 7–8. Strain TD1 was able to grow on medium containing up to 10% NaCl. The DNA G+C content was 38.9 mol%. The cellular fatty acid content was mainly C16:0, which comprised 25.04% of the total amount of cellular fatty acid. 16S rDNA showed 99% identity to Aeribacillus pallidus DSM 3670T. Bayesian tree analysis strongly supported the idea that strain TD1 is affiliated with genus Aeribacillus, as Aeribacillus pallidus strain TD1. Although the 16S rDNA of A. pallidus strain TD1 is similar to that of A. pallidus DSM 3670T, some physiological properties and the cellular fatty acid profiles differ significantly. A. pallidus strain TD1 can produce extracellular pectate lyase, which has not been reported elsewhere for other bacterial strains in the genus Aeribacillus. A. pallidus strain TD1 may be a good candidate as a pectate lyase producer, which may have useful industrial applications. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Microwave-Assisted Extraction of Oleanolic Acid and Ursolic Acid from Ligustrum lucidum Ait
Int. J. Mol. Sci. 2011, 12(8), 5319-5329; doi:10.3390/ijms12085319
Received: 7 July 2011 / Revised: 9 August 2011 / Accepted: 12 August 2011 / Published: 18 August 2011
Cited by 22 | PDF Full-text (221 KB) | HTML Full-text | XML Full-text
Abstract
Oleanolic acid and ursolic acid are the main active components in fruit of Ligustrum lucidum Ait, and possess anticancer, antimutagenic, anti-inflammatory, antioxidative and antiprotozoal activities. In this study, microwave-assisted extraction of oleanolic acid and ursolic acid from Ligustrum lucidum was investigated with HPLC-photodiode array detection. Effects of several experimental parameters, such as type and concentration of extraction solvent, ratio of liquid to material, microwave power, extraction temperature and microwave time, on the extraction efficiencies of oleanolic acid and ursolic acid from Ligustrum lucidum were evaluated. The influence of experimental parameters on the extraction efficiency of ursolic acid was more significant than that of oleanolic acid (p < 0.05). The optimal extraction conditions were 80% ethanol aqueous solution, the ratio of material to liquid was 1:15, and extraction for 30 min at 70 °C under microwave irradiation of 500 W. Under optimal conditions, the yields of oleanolic acid and ursolic acid were 4.4 ± 0.20 mg/g and 5.8 ± 0.15 mg/g, respectively. The results obtained are helpful for the full utilization of Ligustrum lucidum, which also indicated that microwave-assisted extraction is a very useful method for extraction of oleanolic acid and ursolic acid from plant materials. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Effect of Filler Size and Temperature on Packing Stress and Viscosity of Resin-composites
Int. J. Mol. Sci. 2011, 12(8), 5330-5338; doi:10.3390/ijms12085330
Received: 28 June 2011 / Revised: 12 July 2011 / Accepted: 12 August 2011 / Published: 18 August 2011
Cited by 2 | PDF Full-text (743 KB) | HTML Full-text | XML Full-text
Abstract
The objective of this study was to investigate the effect of filler size on the packing stress and viscosity of uncured resin-composite at 23 °C and 37 °C. A precision instrument used was designed upon the penetrometer principle. Eight resin-composite materials were tested. Packing-stress ranged from 2.60 to 0.43 MPa and viscosity ranged from 2.88 to 0.02 MPa.s at 23 °C. Values for both properties were reduced significantly at 37 °C. Statistical analysis, by ANOVA and post hoc methods, were carried out to check any significant differences between materials tested (P < 0.05). Conclusions: Filler size and distribution will affect the viscosity and packing of resin-composites during cavity placement. Full article
(This article belongs to the Special Issue Dental Materials)
Open AccessCommunication Spin Transition Sensors Based on β-Amino-Acid 1,2,4-Triazole Derivative
Int. J. Mol. Sci. 2011, 12(8), 5339-5351; doi:10.3390/ijms12085339
Received: 11 July 2011 / Revised: 11 August 2011 / Accepted: 12 August 2011 / Published: 18 August 2011
Cited by 15 | PDF Full-text (850 KB) | HTML Full-text | XML Full-text
Abstract
A β-aminoacid ester was successfully derivatized to yield to 4H-1,2-4-triazol-4-yl-propionate (βAlatrz) which served as a neutral bidentate ligand in the 1D coordination polymer [Fe(βAlatrz)3](CF3SO3)2·0.5H2O (1· [...] Read more.
A β-aminoacid ester was successfully derivatized to yield to 4H-1,2-4-triazol-4-yl-propionate (βAlatrz) which served as a neutral bidentate ligand in the 1D coordination polymer [Fe(βAlatrz)3](CF3SO3)2·0.5H2O (1·0.5H2O). The temperature dependence of the high-spin molar fraction derived from 57Fe Mossbauer spectroscopy recorded on cooling below room temperature reveals an exceptionally abrupt single step transition between high-spin and low-spin states with a hysteresis loop of width 4 K (Tc = 232 K and Tc = 228 K) in agreement with magnetic susceptibility measurements. The material presents striking reversible thermochromism from white, at room temperature, to pink on quench cooling to liquid nitrogen, and acts as an alert towards temperature variations. The phase transition is of first order, as determined by differential scanning calorimetry, with transition temperatures matching the ones determined by SQUID and Mössbauer spectroscopy. The freshly prepared sample of 1·0.5H2O, dried in air, was subjected to annealing at 390 K, and the obtained white compound [Fe(βAlatrz)3](CF3SO3)2 (1) was found to exhibit a similar spin transition curve however much temperature was increased by (Tc = 252 K and Tc = 248 K). The removal of lattice water molecules from 1·0.5H2O is not accompanied by a change of the morphology and of the space group, and the chain character is preserved. However, an internal pressure effect stabilizing the low-spin state is evidenced. Full article
(This article belongs to the Special Issue Recent Advances in Molecular Electronics)
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Open AccessArticle The hsp 16 Gene of the Probiotic Lactobacillus acidophilus Is Differently Regulated by Salt, High Temperature and Acidic Stresses, as Revealed by Reverse Transcription Quantitative PCR (qRT-PCR) Analysis
Int. J. Mol. Sci. 2011, 12(8), 5390-5405; doi:10.3390/ijms12085390
Received: 17 June 2011 / Revised: 8 August 2011 / Accepted: 15 August 2011 / Published: 22 August 2011
Cited by 7 | PDF Full-text (1210 KB) | HTML Full-text | XML Full-text
Abstract
Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock [...] Read more.
Small heat shock proteins (sHsps) are ubiquitous conserved chaperone-like proteins involved in cellular proteins protection under stressful conditions. In this study, a reverse transcription quantitative PCR (RT-qPCR) procedure was developed and used to quantify the transcript level of a small heat shock gene (shs) in the probiotic bacterium Lactobacillus acidophilus NCFM, under stress conditions such as heat (45 °C and 53 °C), bile (0.3% w/v), hyperosmosis (1 M and 2.5 M NaCl), and low pH value (pH 4). The shs gene of L. acidophilus NCFM was induced by salt, high temperature and acidic stress, while repression was observed upon bile stress. Analysis of the 5' noncoding region of the hsp16 gene reveals the presence of an inverted repeat (IR) sequence (TTAGCACTC-N9-GAGTGCTAA) homologue to the controlling IR of chaperone expression (CIRCE) elements found in the upstream regulatory region of Gram-positive heat shock operons, suggesting that the hsp16 gene of L. acidophilus might be transcriptionally controlled by HrcA. In addition, the alignment of several small heat shock proteins identified so far in lactic acid bacteria, reveals that the Hsp16 of L. acidophilus exhibits a strong evolutionary relationship with members of the Lactobacillus acidophilus group. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Preparation and Microcosmic Structural Analysis of Recording Coating on Inkjet Printing Media
Int. J. Mol. Sci. 2011, 12(8), 5422-5427; doi:10.3390/ijms12085422
Received: 16 July 2011 / Revised: 5 August 2011 / Accepted: 16 August 2011 / Published: 23 August 2011
PDF Full-text (794 KB) | HTML Full-text | XML Full-text
Abstract
Preparation of recording coating on inkjet printing (RC-IJP) media was proposed. The microstructure and roughness of RC-IJP was analyzed by scanning electron microscopy (SEM) and atomic force microscope (AFM). The surface infiltration process of RC-IJP was studied by a liquid infiltration instrument. [...] Read more.
Preparation of recording coating on inkjet printing (RC-IJP) media was proposed. The microstructure and roughness of RC-IJP was analyzed by scanning electron microscopy (SEM) and atomic force microscope (AFM). The surface infiltration process of RC-IJP was studied by a liquid infiltration instrument. The distribution of C, O and Si composites on recording coating surface is analyzed by energy dispersive spectrum (EDS). The transmission electron microscopy (TEM) analysis showed that the nanoscale silica could be dissolved uniformly in water. Finally, the print color is shown clearly by the preparative recording coating. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessArticle Antioxidant, Antimicrobial and Antiproliferative Activities of Five Lichen Species
Int. J. Mol. Sci. 2011, 12(8), 5428-5448; doi:10.3390/ijms12085428
Received: 23 June 2011 / Revised: 15 August 2011 / Accepted: 19 August 2011 / Published: 23 August 2011
Cited by 46 | PDF Full-text (631 KB) | HTML Full-text | XML Full-text
Abstract
The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of [...] Read more.
The antioxidative, antimicrobial and antiproliferative potentials of the methanol extracts of the lichen species Parmelia sulcata, Flavoparmelia caperata, Evernia prunastri, Hypogymnia physodes and Cladonia foliacea were evaluated. The total phenolic content of the tested extracts varied from 78.12 to 141.59 mg of gallic acid equivalent (GA)/g of extract and the total flavonoid content from 20.14 to 44.43 mg of rutin equivalent (Ru)/g of extract. The antioxidant capacities of the lichen extracts were determined by 2,2-diphenyl-1-picrylhydrazyl (DPPH) radicals scavenging. Hypogymnia physodes with the highest phenolic content showed the strongest DPPH radical scavenging effect. Further, the antimicrobial potential of the lichen extracts was determined by a microdilution method on 29 microorganisms, including 15 strains of bacteria, 10 species of filamentous fungi and 4 yeast species. A high antimicrobial activity of all the tested extracts was observed with more potent inhibitory effects on the growth of Gram (+) bacteria. The highest antimicrobial activity among lichens was demonstrated by Hypogymnia physodes and Cladonia foliacea. Finally, the antiproliferative activity of the lichen extracts was explored on the colon cancer adenocarcinoma cell line HCT-116 by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide) viability assay and acridine orange/ethidium bromide staining. The methanol extracts of Hypogymnia physodes and Cladonia foliacea showed a better cytotoxic activity than the other extracts. All lichen species showed the ability to induce apoptosis of HCT-116 cells. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Estimation of the Genetic Diversity in Tetraploid Alfalfa Populations Based on RAPD Markers for Breeding Purposes
Int. J. Mol. Sci. 2011, 12(8), 5449-5460; doi:10.3390/ijms12085449
Received: 19 May 2011 / Revised: 25 July 2011 / Accepted: 16 August 2011 / Published: 24 August 2011
Cited by 9 | PDF Full-text (536 KB) | HTML Full-text | XML Full-text
Abstract
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five [...] Read more.
Alfalfa is an autotetraploid, allogamous and heterozygous forage legume, whose varieties are synthetic populations. Due to the complex nature of the species, information about genetic diversity of germplasm used in any alfalfa breeding program is most beneficial. The genetic diversity of five alfalfa varieties, involved in progeny tests at Institute of Field and Vegetable Crops, was characterized based on RAPD markers. A total of 60 primers were screened, out of which 17 were selected for the analysis of genetic diversity. A total of 156 polymorphic bands were generated, with 10.6 bands per primer. Number and percentage of polymorphic loci, effective number of alleles, expected heterozygosity and Shannon’s information index were used to estimate genetic variation. Variety Zuzana had the highest values for all tested parameters, exhibiting the highest level of variation, whereas variety RSI 20 exhibited the lowest. Analysis of molecular variance (AMOVA) showed that 88.39% of the total genetic variation was attributed to intra-varietal variance. The cluster analysis for individual samples and varieties revealed differences in their population structures: variety Zuzana showed a very high level of genetic variation, Banat and Ghareh were divided in subpopulations, while Pecy and RSI 20 were relatively uniform. Ways of exploiting the investigated germplasm in the breeding programs are suggested in this paper, depending on their population structure and diversity. The RAPD analysis shows potential to be applied in analysis of parental populations in semi-hybrid alfalfa breeding program in both, development of new homogenous germplasm, and identification of promising, complementary germplasm. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

Review

Jump to: Research

Open AccessReview Interplay of Dynamic Transcription and Chromatin Remodeling: Lessons from Yeast
Int. J. Mol. Sci. 2011, 12(8), 4758-4769; doi:10.3390/ijms12084758
Received: 1 June 2011 / Revised: 15 July 2011 / Accepted: 20 July 2011 / Published: 25 July 2011
Cited by 2 | PDF Full-text (233 KB) | HTML Full-text | XML Full-text
Abstract
Regulation of transcription involves dynamic rearrangements of chromatin structure. The budding yeast Saccharomyces cerevisiae has a variety of highly conserved factors necessary for these reconstructions. Chromatin remodelers, histone modifiers and histone chaperones directly associate to promoters and open reading frames of exposed [...] Read more.
Regulation of transcription involves dynamic rearrangements of chromatin structure. The budding yeast Saccharomyces cerevisiae has a variety of highly conserved factors necessary for these reconstructions. Chromatin remodelers, histone modifiers and histone chaperones directly associate to promoters and open reading frames of exposed genes and facilitate activation and repression of transcription. We compare two distinct patterns of induced transcription: Sustained transcribed genes switch to an activated state where they remain as long as the induction signal is present. In contrast, single pulsed transcribed genes show a quick and strong induction pulse resulting in high transcript levels followed by adaptation and repression to basal levels. We discuss intensively studied promoters and coding regions from both groups for their co-factor requirements during transcription. Interplay between chromatin restructuring factors and dynamic transcription is highly variable and locus dependent. Full article
(This article belongs to the Special Issue Chromatin Assembly)
Open AccessReview Identification and Role of Regulatory Non-Coding RNAs in Listeria monocytogenes
Int. J. Mol. Sci. 2011, 12(8), 5070-5079; doi:10.3390/ijms12085070
Received: 28 June 2011 / Revised: 15 July 2011 / Accepted: 8 August 2011 / Published: 10 August 2011
Cited by 9 | PDF Full-text (173 KB) | HTML Full-text | XML Full-text
Abstract
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- [...] Read more.
Bacterial regulatory non-coding RNAs control numerous mRNA targets that direct a plethora of biological processes, such as the adaption to environmental changes, growth and virulence. Recently developed high-throughput techniques, such as genomic tiling arrays and RNA-Seq have allowed investigating prokaryotic cis- and trans-acting regulatory RNAs, including sRNAs, asRNAs, untranslated regions (UTR) and riboswitches. As a result, we obtained a more comprehensive view on the complexity and plasticity of the prokaryotic genome biology. Listeria monocytogenes was utilized as a model system for intracellular pathogenic bacteria in several studies, which revealed the presence of about 180 regulatory RNAs in the listerial genome. A regulatory role of non-coding RNAs in survival, virulence and adaptation mechanisms of L. monocytogenes was confirmed in subsequent experiments, thus, providing insight into a multifaceted modulatory function of RNA/mRNA interference. In this review, we discuss the identification of regulatory RNAs by high-throughput techniques and in their functional role in L. monocytogenes. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
Open AccessReview Enhancing Single Molecule Imaging in Optofluidics and Microfluidics
Int. J. Mol. Sci. 2011, 12(8), 5135-5156; doi:10.3390/ijms12085135
Received: 31 March 2011 / Revised: 23 May 2011 / Accepted: 25 July 2011 / Published: 12 August 2011
Cited by 11 | PDF Full-text (781 KB) | HTML Full-text | XML Full-text
Abstract
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the [...] Read more.
Microfluidics and optofluidics have revolutionized high-throughput analysis and chemical synthesis over the past decade. Single molecule imaging has witnessed similar growth, due to its capacity to reveal heterogeneities at high spatial and temporal resolutions. However, both resolution types are dependent on the signal to noise ratio (SNR) of the image. In this paper, we review how the SNR can be enhanced in optofluidics and microfluidics. Starting with optofluidics, we outline integrated photonic structures that increase the signal emitted by single chromophores and minimize the excitation volume. Turning then to microfluidics, we review the compatible functionalization strategies that reduce noise stemming from non-specific interactions and architectures that minimize bleaching and blinking. Full article
(This article belongs to the Special Issue Microfluidics)
Open AccessReview Major Histocompatibility Complex (MHC) Markers in Conservation Biology
Int. J. Mol. Sci. 2011, 12(8), 5168-5186; doi:10.3390/ijms12085168
Received: 11 May 2011 / Revised: 27 June 2011 / Accepted: 5 August 2011 / Published: 15 August 2011
Cited by 22 | PDF Full-text (226 KB) | HTML Full-text | XML Full-text
Abstract
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a [...] Read more.
Human impacts through habitat destruction, introduction of invasive species and climate change are increasing the number of species threatened with extinction. Decreases in population size simultaneously lead to reductions in genetic diversity, ultimately reducing the ability of populations to adapt to a changing environment. In this way, loss of genetic polymorphism is linked with extinction risk. Recent advances in sequencing technologies mean that obtaining measures of genetic diversity at functionally important genes is within reach for conservation programs. A key region of the genome that should be targeted for population genetic studies is the Major Histocompatibility Complex (MHC). MHC genes, found in all jawed vertebrates, are the most polymorphic genes in vertebrate genomes. They play key roles in immune function via immune-recognition and -surveillance and host-parasite interaction. Therefore, measuring levels of polymorphism at these genes can provide indirect measures of the immunological fitness of populations. The MHC has also been linked with mate-choice and pregnancy outcomes and has application for improving mating success in captive breeding programs. The recent discovery that genetic diversity at MHC genes may protect against the spread of contagious cancers provides an added impetus for managing and protecting MHC diversity in wild populations. Here we review the field and focus on the successful applications of MHC-typing for conservation management. We emphasize the importance of using MHC markers when planning and executing wildlife rescue and conservation programs but stress that this should not be done to the detriment of genome-wide diversity. Full article
(This article belongs to the Special Issue Advances in Molecular Ecology)
Open AccessReview Mechanisms of Mycotoxin-Induced Neurotoxicity through Oxidative Stress-Associated Pathways
Int. J. Mol. Sci. 2011, 12(8), 5213-5237; doi:10.3390/ijms12085213
Received: 7 June 2011 / Revised: 21 July 2011 / Accepted: 4 August 2011 / Published: 15 August 2011
Cited by 28 | PDF Full-text (261 KB) | HTML Full-text | XML Full-text
Abstract
Among many mycotoxins, T-2 toxin, macrocyclic trichothecenes, fumonisin B1 (FB1) and ochratochin A (OTA) are known to have the potential to induce neurotoxicity in rodent models. T-2 toxin induces neuronal cell apoptosis in the fetal and adult brain. Macrocyclic [...] Read more.
Among many mycotoxins, T-2 toxin, macrocyclic trichothecenes, fumonisin B1 (FB1) and ochratochin A (OTA) are known to have the potential to induce neurotoxicity in rodent models. T-2 toxin induces neuronal cell apoptosis in the fetal and adult brain. Macrocyclic trichothecenes bring about neuronal cell apoptosis and inflammation in the olfactory epithelium and olfactory bulb. FB1 induces neuronal degeneration in the cerebral cortex, concurrent with disruption of de novo ceramide synthesis. OTA causes acute depletion of striatal dopamine and its metabolites, accompanying evidence of neuronal cell apoptosis in the substantia nigra, striatum and hippocampus. This paper reviews the mechanisms of neurotoxicity induced by these mycotoxins especially from the viewpoint of oxidative stress-associated pathways. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessReview FK506-Binding Protein 22 from a Psychrophilic Bacterium, a Cold Shock-Inducible Peptidyl Prolyl Isomerase with the Ability to Assist in Protein Folding
Int. J. Mol. Sci. 2011, 12(8), 5261-5284; doi:10.3390/ijms12085261
Received: 12 May 2011 / Revised: 28 July 2011 / Accepted: 9 August 2011 / Published: 17 August 2011
Cited by 9 | PDF Full-text (834 KB) | HTML Full-text | XML Full-text
Abstract
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization [...] Read more.
Adaptation of microorganisms to low temperatures remains to be fully elucidated. It has been previously reported that peptidyl prolyl cis-trans isomerases (PPIases) are involved in cold adaptation of various microorganisms whether they are hyperthermophiles, mesophiles or phsycrophiles. The rate of cis-trans isomerization at low temperatures is much slower than that at higher temperatures and may cause problems in protein folding. However, the mechanisms by which PPIases are involved in cold adaptation remain unclear. Here we used FK506-binding protein 22, a cold shock protein from the psychrophilic bacterium Shewanella sp. SIB1 (SIB1 FKBP22) as a model protein to decipher the involvement of PPIases in cold adaptation. SIB1 FKBP22 is homodimer that assumes a V-shaped structure based on a tertiary model. Each monomer consists of an N-domain responsible for dimerization and a C-catalytic domain. SIB1 FKBP22 is a typical cold-adapted enzyme as indicated by the increase of catalytic efficiency at low temperatures, the downward shift in optimal temperature of activity and the reduction in the conformational stability. SIB1 FKBP22 is considered as foldase and chaperone based on its ability to catalyze refolding of a cis-proline containing protein and bind to a folding intermediate protein, respectively. The foldase and chaperone activites of SIB1 FKBP22 are thought to be important for cold adaptation of Shewanella sp. SIB1. These activities are also employed by other PPIases for being involved in cold adaptation of various microorganisms. Despite other biological roles of PPIases, we proposed that foldase and chaperone activities of PPIases are the main requirement for overcoming the cold-stress problem in microorganisms due to folding of proteins. Full article
(This article belongs to the Special Issue Protein Folding 2011)
Open AccessReview New Aspects of Mitochondrial Uncoupling Proteins (UCPs) and Their Roles in Tumorigenesis
Int. J. Mol. Sci. 2011, 12(8), 5285-5293; doi:10.3390/ijms12085285
Received: 26 July 2011 / Revised: 9 August 2011 / Accepted: 10 August 2011 / Published: 17 August 2011
Cited by 19 | PDF Full-text (166 KB) | HTML Full-text | XML Full-text
Abstract
Uncoupling proteins (UCPs) belong to a family of mitochondrial carrier proteins that are present in the mitochondrial inner membrane. UCP1 was first identified followed by its two homologs, UCP2 and UCP3. The physiological functions of UCP include lowering mitochondrial membrane potential and [...] Read more.
Uncoupling proteins (UCPs) belong to a family of mitochondrial carrier proteins that are present in the mitochondrial inner membrane. UCP1 was first identified followed by its two homologs, UCP2 and UCP3. The physiological functions of UCP include lowering mitochondrial membrane potential and dissipating metabolic energy as heat. However, UCP can be dysregulated and may contribute to the pathogenesis of metabolic disorders and obesity. Recent studies suggest that UCP also plays a role in neurodegenerative diseases and atherosclerosis. In addition, the widely expressed UCP, UCP2, has been shown to be upregulated in a number of aggressive human cancers. One mechanism of UCP2 upregulation in these cancers is due to oxidative stress, and elevated UCP2 in turn reduces oxidative stress, which provides a growth advantage for these cancers. Nevertheless, new studies suggest UCP2 may interact with oncogenes and tumor suppressor genes, providing a potential new mechanism of how UCP2 contributes to cancer development. In this review, the evidence supporting the role of UCPs in diseases other than diabetes and obesity, the reports on how UCP is regulated in cancer cells, and how UCP may regulate p53 will be discussed. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Reviewing Ligand-Based Rational Drug Design: The Search for an ATP Synthase Inhibitor
Int. J. Mol. Sci. 2011, 12(8), 5304-5318; doi:10.3390/ijms12085304
Received: 23 February 2011 / Revised: 4 August 2011 / Accepted: 11 August 2011 / Published: 17 August 2011
Cited by 7 | PDF Full-text (586 KB) | HTML Full-text | XML Full-text
Abstract
Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design [...] Read more.
Following major advances in the field of medicinal chemistry, novel drugs can now be designed systematically, instead of relying on old trial and error approaches. Current drug design strategies can be classified as being either ligand- or structure-based depending on the design process. In this paper, by describing the search for an ATP synthase inhibitor, we review two frequently used approaches in ligand-based drug design: The pharmacophore model and the quantitative structure-activity relationship (QSAR) method. Moreover, since ATP synthase ligands are potentially useful drugs in cancer therapy, pharmacophore models were constructed to pave the way for novel inhibitor designs. Full article
(This article belongs to the Special Issue A Systematic Development Method for Rational Drug Design)
Open AccessReview Structure and Dynamics of Reentrant Nematics: Any Open Questions after Almost 40 Years?
Int. J. Mol. Sci. 2011, 12(8), 5352-5372; doi:10.3390/ijms12085352
Received: 6 July 2011 / Revised: 9 August 2011 / Accepted: 11 August 2011 / Published: 22 August 2011
Cited by 10 | PDF Full-text (855 KB) | HTML Full-text | XML Full-text
Abstract
Liquid crystals have attracted enormous interest because of the variety of their phases and richness of their application. The interplay of general physical symmetries and specific molecular features generates a myriad of different phenomena. A surprising behavior of liquid crystals is the [...] Read more.
Liquid crystals have attracted enormous interest because of the variety of their phases and richness of their application. The interplay of general physical symmetries and specific molecular features generates a myriad of different phenomena. A surprising behavior of liquid crystals is the reentrancy of phases as temperature, pressure, or concentration are varied. Here, we review the main experimental facts and the different theoretical scenarios that have guided the understanding of bulk reentrant nematics. Recently, some computer simulations of a system confined to nanoscopic scales have found new dynamical features of the reentrant nematic phase. We discuss this prediction in relation with the available experimental evidence on reentrant nematics and with the dynamics of liquids in strongly confined environments. Full article
(This article belongs to the Special Issue Liquid Crystals 2011)
Open AccessReview p66Shc Aging Protein in Control of Fibroblasts Cell Fate
Int. J. Mol. Sci. 2011, 12(8), 5373-5389; doi:10.3390/ijms12085373
Received: 6 July 2011 / Revised: 2 August 2011 / Accepted: 15 August 2011 / Published: 22 August 2011
Cited by 8 | PDF Full-text (586 KB) | HTML Full-text | XML Full-text
Abstract
Reactive oxygen species (ROS) are wieldy accepted as one of the main factors of the aging process. These highly reactive compounds modify nucleic acids, proteins and lipids and affect the functionality of mitochondria in the first case and ultimately of the cell. [...] Read more.
Reactive oxygen species (ROS) are wieldy accepted as one of the main factors of the aging process. These highly reactive compounds modify nucleic acids, proteins and lipids and affect the functionality of mitochondria in the first case and ultimately of the cell. Any agent or genetic modification that affects ROS production and detoxification can be expected to influence longevity. On the other hand, genetic manipulations leading to increased longevity can be expected to involve cellular changes that affect ROS metabolism. The 66-kDa isoform of the growth factor adaptor Shc (p66Shc) has been recognized as a relevant factor to the oxygen radical theory of aging. The most recent data indicate that p66Shc protein regulates life span in mammals and its phosphorylation on serine 36 is important for the initiation of cell death upon oxidative stress. Moreover, there is strong evidence that apart from aging, p66Shc may be implicated in many oxidative stress-associated pathologies, such as diabetes, mitochondrial and neurodegenerative disorders and tumorigenesis. This article summarizes recent knowledge about the role of p66Shc in aging and senescence and how this protein can influence ROS production and detoxification, focusing on studies performed on skin and skin fibroblasts. Full article
(This article belongs to the Special Issue Oxidative Stress and Mitochondria)
Open AccessReview Self-Assembly in the Ferritin Nano-Cage Protein Superfamily
Int. J. Mol. Sci. 2011, 12(8), 5406-5421; doi:10.3390/ijms12085406
Received: 20 July 2011 / Revised: 9 August 2011 / Accepted: 15 August 2011 / Published: 22 August 2011
Cited by 26 | PDF Full-text (801 KB) | HTML Full-text | XML Full-text
Abstract
Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these [...] Read more.
Protein self-assembly, through specific, high affinity, and geometrically constraining protein-protein interactions, can control and lead to complex cellular nano-structures. Establishing an understanding of the underlying principles that govern protein self-assembly is not only essential to appreciate the fundamental biological functions of these structures, but could also provide a basis for their enhancement for nano-material applications. The ferritins are a superfamily of well studied proteins that self-assemble into hollow cage-like structures which are ubiquitously found in both prokaryotes and eukaryotes. Structural studies have revealed that many members of the ferritin family can self-assemble into nano-cages of two types. Maxi-ferritins form hollow spheres with octahedral symmetry composed of twenty-four monomers. Mini-ferritins, on the other hand, are tetrahedrally symmetric, hollow assemblies composed of twelve monomers. This review will focus on the structure of members of the ferritin superfamily, the mechanism of ferritin self-assembly and the structure-function relations of these proteins. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2011)
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