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Int. J. Mol. Sci., Volume 12, Issue 12 (December 2011) , Pages 8316-9604

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Open AccessArticle
Synthesis and Insecticidal Activities of New Ester-Derivatives of Celangulin-V
Int. J. Mol. Sci. 2011, 12(12), 9596-9604; https://doi.org/10.3390/ijms12129596
Received: 17 August 2011 / Revised: 28 October 2011 / Accepted: 15 December 2011 / Published: 20 December 2011
Cited by 10 | Viewed by 2559 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
In order to develop new biorational pesticides, ten new 6-substituted ester derivatives of Celangulin-V were designed and synthesized. The structures of the new derivatives were confirmed by IR, 1H-NMR, 13C-NMR and ESI-MS spectral analysis. Insecticidal activities of these compounds were tested [...] Read more.
In order to develop new biorational pesticides, ten new 6-substituted ester derivatives of Celangulin-V were designed and synthesized. The structures of the new derivatives were confirmed by IR, 1H-NMR, 13C-NMR and ESI-MS spectral analysis. Insecticidal activities of these compounds were tested against the third-instar larvae of Mythimna separata. Two derivatives (1.1, 1.2) showed higher insecticidal activities than Celangulin-V, with mortality of 75.0% and 83.3%, respectively. While four compounds (1.3, 1.4, 1.7, 1.8) denoted lower insecticidal activities, the others (1.5, 1.6, 1.9, 1.10) revealed no activities at a concentration of 10 mg.mL−1. The results suggest that C-6 substitutions of Celangulin-V are very important in determining the insecticidal activities of its ester-derivatives. That the acetyl (1.1) and propionyl (1.2) derivatives possessed much higher insecticidal activities than Celangulin-V itself supported the view that Celangulin-V has the potential to be a lead structure of semi-synthetic green insecticides. Full article
(This article belongs to the Section Green Chemistry)
Open AccessReview
Advances in Carcinogenic Metal Toxicity and Potential Molecular Markers
Int. J. Mol. Sci. 2011, 12(12), 9576-9595; https://doi.org/10.3390/ijms12129576
Received: 13 September 2011 / Revised: 28 October 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 81 | Viewed by 4083 | PDF Full-text (236 KB) | HTML Full-text | XML Full-text
Abstract
Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in [...] Read more.
Metal compounds such as arsenic, cadmium, chromium, cobalt, lead, mercury, and nickel are classified as carcinogens affecting human health through occupational and environmental exposure. However, the underlying mechanisms involved in tumor formation are not well clarified. Interference of metal homeostasis may result in oxidative stress which represents an imbalance between production of free radicals and the system’s ability to readily detoxify reactive intermediates. This event consequently causes DNA damage, lipid peroxidation, protein modification, and possibly symptomatic effects for various diseases including cancer. This review discusses predominant modes of action and numerous molecular markers. Attention is paid to metal-induced generation of free radicals, the phenomenon of oxidative stress, damage to DNA, lipid, and proteins, responsive signal transduction pathways with major roles in cell growth and development, and roles of antioxidant enzymatic and DNA repair systems. Interaction of non-enzymatic antioxidants (carotenoids, flavonoids, glutathione, selenium, vitamin C, vitamin E, and others) with cellular oxidative stress markers (catalase, glutathione peroxidase, and superoxide dismutase) as well as certain regulatory factors, including AP-1, NF-κB, Ref-1, and p53 is also reviewed. Dysregulation of protective pathways, including cellular antioxidant network against free radicals as well as DNA repair deficiency is related to oncogenic stimulation. These observations provide evidence that emerging oxidative stress-responsive regulatory factors and DNA repair proteins are putative predictive factors for tumor initiation and progression. Full article
(This article belongs to the Special Issue Biomarkers 2011)
Open AccessTechnical Note
Development and Characterization of 20 Microsatellite Markers for Chinese Black Sleeper, Bostrychus sinensis
Int. J. Mol. Sci. 2011, 12(12), 9570-9575; https://doi.org/10.3390/ijms12129570
Received: 12 October 2011 / Revised: 30 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 6 | Viewed by 2723 | PDF Full-text (131 KB) | HTML Full-text | XML Full-text
Abstract
Twenty microsatellite markers were isolated and characterized from the Chinese black sleeper, Bostrychus sinensis. Loci were screened in 30 individuals from Taiwan. For each locus, the number of alleles varied from 4 to 22 with mean expected and observed heterozygosity of 0.79 [...] Read more.
Twenty microsatellite markers were isolated and characterized from the Chinese black sleeper, Bostrychus sinensis. Loci were screened in 30 individuals from Taiwan. For each locus, the number of alleles varied from 4 to 22 with mean expected and observed heterozygosity of 0.79 and 0.66, respectively. One locus significantly deviated from Hardy-Weinberg equilibrium after Bonferroni correction and no significant linkage disequilibrium was detected. This set of microsatellites will provide a suitable tool for population genetic studies of Chinese black sleeper. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Introducing Catastrophe-QSAR. Application on Modeling Molecular Mechanisms of Pyridinone Derivative-Type HIV Non-Nucleoside Reverse Transcriptase Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 9533-9569; https://doi.org/10.3390/ijms12129533
Received: 27 October 2011 / Revised: 28 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 11 | Viewed by 4150 | PDF Full-text (602 KB) | HTML Full-text | XML Full-text
Abstract
The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the [...] Read more.
The classical method of quantitative structure-activity relationships (QSAR) is enriched using non-linear models, as Thom’s polynomials allow either uni- or bi-variate structural parameters. In this context, catastrophe QSAR algorithms are applied to the anti-HIV-1 activity of pyridinone derivatives. This requires calculation of the so-called relative statistical power and of its minimum principle in various QSAR models. A new index, known as a statistical relative power, is constructed as an Euclidian measure for the combined ratio of the Pearson correlation to algebraic correlation, with normalized t-Student and the Fisher tests. First and second order inter-model paths are considered for mono-variate catastrophes, whereas for bi-variate catastrophes the direct minimum path is provided, allowing the QSAR models to be tested for predictive purposes. At this stage, the max-to-min hierarchies of the tested models allow the interaction mechanism to be identified using structural parameter succession and the typical catastrophes involved. Minimized differences between these catastrophe models in the common structurally influential domains that span both the trial and tested compounds identify the “optimal molecular structural domains” and the molecules with the best output with respect to the modeled activity, which in this case is human immunodeficiency virus type 1 HIV-1 inhibition. The best molecules are characterized by hydrophobic interactions with the HIV-1 p66 subunit protein, and they concur with those identified in other 3D-QSAR analyses. Moreover, the importance of aromatic ring stacking interactions for increasing the binding affinity of the inhibitor-reverse transcriptase ligand-substrate complex is highlighted. Full article
(This article belongs to the Special Issue Advances in Molecular Electronic Structure Calculations)
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Open AccessReview
Volatile Compounds in Honey: A Review on Their Involvement in Aroma, Botanical Origin Determination and Potential Biomedical Activities
Int. J. Mol. Sci. 2011, 12(12), 9514-9532; https://doi.org/10.3390/ijms12129514
Received: 2 November 2011 / Revised: 29 November 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 68 | Viewed by 5149 | PDF Full-text (154 KB) | HTML Full-text | XML Full-text
Abstract
Volatile organic compounds (VOCs) in honey are obtained from diverse biosynthetic pathways and extracted by using various methods associated with varying degrees of selectivity and effectiveness. These compounds are grouped into chemical categories such as aldehyde, ketone, acid, alcohol, hydrocarbon, norisoprenoids, terpenes and [...] Read more.
Volatile organic compounds (VOCs) in honey are obtained from diverse biosynthetic pathways and extracted by using various methods associated with varying degrees of selectivity and effectiveness. These compounds are grouped into chemical categories such as aldehyde, ketone, acid, alcohol, hydrocarbon, norisoprenoids, terpenes and benzene compounds and their derivatives, furan and pyran derivatives. They represent a fingerprint of a specific honey and therefore could be used to differentiate between monofloral honeys from different floral sources, thus providing valuable information concerning the honey’s botanical and geographical origin. However, only plant derived compounds and their metabolites (terpenes, norisoprenoids and benzene compounds and their derivatives) must be employed to discriminate among floral origins of honey. Notwithstanding, many authors have reported different floral markers for honey of the same floral origin, consequently sensory analysis, in conjunction with analysis of VOCs could help to clear this ambiguity. Furthermore, VOCs influence honey’s aroma described as sweet, citrus, floral, almond, rancid, etc. Clearly, the contribution of a volatile compound to honey aroma is determined by its odor activity value. Elucidation of the aroma compounds along with floral origins of a particular honey can help to standardize its quality and avoid fraudulent labeling of the product. Although only present in low concentrations, VOCS could contribute to biomedical activities of honey, especially the antioxidant effect due to their natural radical scavenging potential. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Q Fever Endocarditis in Romania: The First Cases Confirmed by Direct Sequencing
Int. J. Mol. Sci. 2011, 12(12), 9504-9513; https://doi.org/10.3390/ijms12129504
Received: 18 November 2011 / Revised: 9 December 2011 / Accepted: 12 December 2011 / Published: 20 December 2011
Cited by 2 | Viewed by 3429 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Infective endocarditis (IE) is a serious, life-threatening disease with highly variable clinical signs, making its diagnostic a real challenge. A diagnosis is readily made if blood cultures are positive, but in 2.5 to 31% of all infective endocarditis cases, routine blood cultures are [...] Read more.
Infective endocarditis (IE) is a serious, life-threatening disease with highly variable clinical signs, making its diagnostic a real challenge. A diagnosis is readily made if blood cultures are positive, but in 2.5 to 31% of all infective endocarditis cases, routine blood cultures are negative. In such situations, alternative diagnostic approaches are necessary. Coxiella burnetii and Bartonella spp. are the etiological agents of blood culture-negative endocarditis (BCNE) most frequently identified by serology. The purpose of this study is to investigate the usefulness of molecular assays, as complementary methods to the conventional serologic methods for the rapid confirmatory diagnostic of Q fever endocarditis in patients with BCNE. Currently, detection of C. burnetii by culture or an antiphase I IgG antibody titers >800 represents a major Duke criterion for defining IE, while a titers of >800 for IgG antibodies to either B. henselae or B. quintana is used for the diagnosis of endocarditis due to Bartonella spp. We used indirect immunofluorescence assays for the detection of IgG titers for C. burnetii, B. henselae and B. quintana in 57 serum samples from patients with clinical suspicion of IE. Thirty three samples originated from BCNE patients, whereas 24 were tested before obtaining the blood cultures results, which finally were positive. The results of serologic testing showed that nine out of 33 BCNE cases exhibited antiphase I C. burnetii IgG antibody titer >800, whereas none has IgG for B. henselae or B. quintana. Subsequently, we used nested-PCR assay for the amplification of C. burnetii DNA in the nine positive serum samples, and we obtained positive PCR results for all analyzed cases. Afterwards we used the DNA sequencing of amplicons for the repetitive element associated to htpAB gene to confirm the results of nested-PCR. The results of sequencing allowed us to confirm that C. burnetii is the causative microorganism responsible for BCNE. In conclusion, the nested PCR amplification followed by direct sequencing is a reliable and accurate method when applied to serum samples, and it may be used as an additional test to the serological methods for the confirmatory diagnosis of BCNE cases determined by C. burnetii. Full article
(This article belongs to the Section Molecular Pathology, Diagnostics, and Therapeutics)
Open AccessArticle
Modeling Natural Anti-Inflammatory Compounds by Molecular Topology
Int. J. Mol. Sci. 2011, 12(12), 9481-9503; https://doi.org/10.3390/ijms12129481
Received: 8 November 2011 / Revised: 8 December 2011 / Accepted: 9 December 2011 / Published: 20 December 2011
Cited by 21 | Viewed by 3734 | PDF Full-text (269 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into [...] Read more.
One of the main pharmacological problems today in the treatment of chronic inflammation diseases consists of the fact that anti-inflammatory drugs usually exhibit side effects. The natural products offer a great hope in the identification of bioactive lead compounds and their development into drugs for treating inflammatory diseases. Computer-aided drug design has proved to be a very useful tool for discovering new drugs and, specifically, Molecular Topology has become a good technique for such a goal. A topological-mathematical model, obtained by linear discriminant analysis, has been developed for the search of new anti-inflammatory natural compounds. An external validation obtained with the remaining compounds (those not used in building up the model), has been carried out. Finally, a virtual screening on natural products was performed and 74 compounds showed actual anti-inflammatory activity. From them, 54 had been previously described as anti-inflammatory in the literature. This can be seen as a plus in the model validation and as a reinforcement of the role of Molecular Topology as an efficient tool for the discovery of new anti-inflammatory natural compounds. Full article
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Open AccessArticle
Molecular Diagnosis of 5α-Reductase Type II Deficiency in Brazilian Siblings with 46,XY Disorder of Sex Development
Int. J. Mol. Sci. 2011, 12(12), 9471-9480; https://doi.org/10.3390/ijms12129471
Received: 2 September 2011 / Revised: 28 November 2011 / Accepted: 13 December 2011 / Published: 19 December 2011
Cited by 1 | Viewed by 3274 | PDF Full-text (1297 KB) | HTML Full-text | XML Full-text
Abstract
The steroid 5α-reductase type II enzyme catalyzes the conversion of testosterone (T) to dihydrotestosterone (DHT), and its deficiency leads to undervirilization in 46,XY individuals, due to an impairment of this conversion in genital tissues. Molecular analysis in the steroid 5α-reductase type II gene [...] Read more.
The steroid 5α-reductase type II enzyme catalyzes the conversion of testosterone (T) to dihydrotestosterone (DHT), and its deficiency leads to undervirilization in 46,XY individuals, due to an impairment of this conversion in genital tissues. Molecular analysis in the steroid 5α-reductase type II gene (SRD5A2) was performed in two 46,XY female siblings. SRD5A2 gene sequencing revealed that the patients were homozygous for p.Gln126Arg missense mutation, which results from the CGA > CAA nucleotide substitution. The molecular result confirmed clinical diagnosis of 46,XY disorder of sex development (DSD) for the older sister and directed the investigation to other family members. Studies on SRD5A2 protein structure showed severe changes at NADPH binding region indicating that structural modeling analysis can be useful to evaluate the deleterious role of a mutation as causing 5α-reductase type II enzyme deficiency. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
Open AccessArticle
Use of Peroxyacetic Acid as Green Chemical on Yield and Sensorial Quality in Watercress (Nasturtium officinale R. Br.) Under Soilless Culture
Int. J. Mol. Sci. 2011, 12(12), 9463-9470; https://doi.org/10.3390/ijms12129463
Received: 26 October 2011 / Revised: 8 December 2011 / Accepted: 12 December 2011 / Published: 19 December 2011
Cited by 4 | Viewed by 3604 | PDF Full-text (103 KB) | HTML Full-text | XML Full-text
Abstract
The goal of this research was to evaluate the effect of different doses of peroxyacetic acid on the productivity of watercress (Nasturtium officinale R. Br.) cultivated hydroponically using a constant nutritive solution. Green chemistry in protected horticulture seeks compatibility with the environment [...] Read more.
The goal of this research was to evaluate the effect of different doses of peroxyacetic acid on the productivity of watercress (Nasturtium officinale R. Br.) cultivated hydroponically using a constant nutritive solution. Green chemistry in protected horticulture seeks compatibility with the environment through the creation of biodegradable byproducts. In hydroponics, appropriate doses of peroxyacetic mixtures deliver these byproducts while also oxygenating the roots. Watercress producers who recirculate the nutritive solution can use these mixtures in order to increase oxygenation in the hydroponic system. The experiment took place between August and December 2009, beginning with the planting of the watercress seeds and concluding with the completion of the sensory panels. A completely random design was used, including three treatments and four repetitions, with applications of 0, 20 and 40 mg L−1 of the peroxyacetic mixture. Measured variables were growth (plant height, leaf length and stem diameter), yield (weight per plant and dry matter) and organoleptic quality (color and sensory panel). The application of 40 mg L−1 of the peroxyacetic mixture had a greater effect on the growth and development of the plants, which reached an average height of 29.3 cm, stem diameter of 3.3 mm and leaf length of 7.6 cm, whereas the control group reached an average height of only 20.2 cm, stem diameter of 1.9 mm and leaf length of 5.7 cm. The application of the peroxyacetic mixtures resulted in an improvement in growth parameters as well as in yield. Individual weights achieved using the 40 mg L−1 dose were 1.3 g plant−1 in the control group and 3.4 g plant−1 in the experimental group (62% yield increase). Sensory analysis revealed no differences in organoleptic quality. Full article
(This article belongs to the Special Issue Advances in Green Chemistry and Sustainable Chemistry 2011)
Open AccessArticle
Dynamic Structure-Based Pharmacophore Model Development: A New and Effective Addition in the Histone Deacetylase 8 (HDAC8) Inhibitor Discovery
Int. J. Mol. Sci. 2011, 12(12), 9440-9462; https://doi.org/10.3390/ijms12129440
Received: 29 August 2011 / Revised: 15 November 2011 / Accepted: 8 December 2011 / Published: 19 December 2011
Cited by 20 | Viewed by 4214 | PDF Full-text (1041 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this [...] Read more.
Histone deacetylase 8 (HDAC8) is an enzyme involved in deacetylating the amino groups of terminal lysine residues, thereby repressing the transcription of various genes including tumor suppressor gene. The over expression of HDAC8 was observed in many cancers and thus inhibition of this enzyme has emerged as an efficient cancer therapeutic strategy. In an effort to facilitate the future discovery of HDAC8 inhibitors, we developed two pharmacophore models containing six and five pharmacophoric features, respectively, using the representative structures from two molecular dynamic (MD) simulations performed in Gromacs 4.0.5 package. Various analyses of trajectories obtained from MD simulations have displayed the changes upon inhibitor binding. Thus utilization of the dynamically-responded protein structures in pharmacophore development has the added advantage of considering the conformational flexibility of protein. The MD trajectories were clustered based on single-linkage method and representative structures were taken to be used in the pharmacophore model development. Active site complimenting structure-based pharmacophore models were developed using Discovery Studio 2.5 program and validated using a dataset of known HDAC8 inhibitors. Virtual screening of chemical database coupled with drug-like filter has identified drug-like hit compounds that match the pharmacophore models. Molecular docking of these hits reduced the false positives and identified two potential compounds to be used in future HDAC8 inhibitor design. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessReview
Genetic and Epigenetic Traits as Biomarkers in Colorectal Cancer
Int. J. Mol. Sci. 2011, 12(12), 9426-9439; https://doi.org/10.3390/ijms12129426
Received: 17 October 2011 / Revised: 28 November 2011 / Accepted: 7 December 2011 / Published: 16 December 2011
Cited by 33 | Viewed by 4019 | PDF Full-text (312 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has, [...] Read more.
Colorectal cancer is a major health burden, and a leading cause of cancer-related deaths in industrialized countries. The steady improvements in surgery and chemotherapy have improved survival, but the ability to identify high- and low-risk patients is still somewhat poor. Molecular biology has, over the years, given insight into basic principles of colorectal cancer initiation and development. These findings include aberrations increasing risk of tumor development, genetic changes associated with the stepwise progression of the disease, and errors predicting response to a specific treatment. Potential biomarkers in colorectal cancer are extensively studied, and how the molecular aberrations relate to clinical features. Yet, little of this knowledge has been possible to transfer into clinical practice. In this review, an overview of colorectal cancer genetics will be given, as well as how aberrations found in this tumor type are proposed as biomarkers for risk prediction, as diagnostic tools, for prognosis or prediction of treatment outcome. Full article
(This article belongs to the Section Biochemistry)
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Open AccessReview
Chiral Vibrational Structures of Proteins at Interfaces Probed by Sum Frequency Generation Spectroscopy
Int. J. Mol. Sci. 2011, 12(12), 9404-9425; https://doi.org/10.3390/ijms12129404
Received: 8 November 2011 / Revised: 13 December 2011 / Accepted: 13 December 2011 / Published: 16 December 2011
Cited by 41 | Viewed by 4701 | PDF Full-text (963 KB) | HTML Full-text | XML Full-text
Abstract
We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. [...] Read more.
We review the recent development of chiral sum frequency generation (SFG) spectroscopy and its applications to study chiral vibrational structures at interfaces. This review summarizes observations of chiral SFG signals from various molecular systems and describes the molecular origins of chiral SFG response. It focuses on the chiral vibrational structures of proteins and presents the chiral SFG spectra of proteins at interfaces in the C-H stretch, amide I, and N-H stretch regions. In particular, a combination of chiral amide I and N-H stretches of the peptide backbone provides highly characteristic vibrational signatures, unique to various secondary structures, which demonstrate the capacity of chiral SFG spectroscopy to distinguish protein secondary structures at interfaces. On the basis of these recent developments, we further discuss the advantages of chiral SFG spectroscopy and its potential application in various fields of science and technology. We conclude that chiral SFG spectroscopy can be a new approach to probe chiral vibrational structures of protein at interfaces, providing structural and dynamic information to study in situ and in real time protein structures and dynamics at interfaces. Full article
(This article belongs to the Special Issue Applications of Circular Dichroism)
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Open AccessArticle
Identification of (−)(E)-N-[2(S)-Hydroxy-2-(4-hydroxyphenyl) ethyl]ferulamide, a Natural Product Isolated from Croton Pullei: Theoretical and Experimental Analysis
Int. J. Mol. Sci. 2011, 12(12), 9389-9403; https://doi.org/10.3390/ijms12129389
Received: 31 August 2011 / Revised: 23 November 2011 / Accepted: 5 December 2011 / Published: 15 December 2011
Cited by 5 | Viewed by 3335 | PDF Full-text (652 KB) | HTML Full-text | XML Full-text
Abstract
Ferulic acid (FA) and its derivatives (FADs) are known for a variety of biological activities, such as photo-protective agent, antioxidant, antiatherogenic and antiplasmodial activities. During structural definition of a FAD isolated from Croton pullei, the possibility of a heterologous series made this [...] Read more.
Ferulic acid (FA) and its derivatives (FADs) are known for a variety of biological activities, such as photo-protective agent, antioxidant, antiatherogenic and antiplasmodial activities. During structural definition of a FAD isolated from Croton pullei, the possibility of a heterologous series made this definition difficult. In this regard, computational simulations were performed using theoretical calculations at DFT level to predict Infrared (IR) and Nuclear Magnetic Resonance (NMR) data. The IR and NMR 13C and 1H data were compared with the theoretical calculations performed for three structural possibilities of a heterologous series. The theoretical results were compared with the experimental data through linear regression in order to define the most probable structure and showed satisfactory values. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessArticle
Monitoring Insulin Aggregation via Capillary Electrophoresis
Int. J. Mol. Sci. 2011, 12(12), 9369-9388; https://doi.org/10.3390/ijms12129369
Received: 22 October 2011 / Revised: 6 December 2011 / Accepted: 12 December 2011 / Published: 14 December 2011
Cited by 10 | Viewed by 4006 | PDF Full-text (621 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE) [...] Read more.
Early stages of insulin aggregation, which involve the transient formation of oligomeric aggregates, are an important aspect in the progression of Type II diabetes and in the quality control of pharmaceutical insulin production. This study is the first to utilize capillary electrophoresis (CE) with ultraviolet (UV) detection to monitor insulin oligomer formation at pH 8.0 and physiological ionic strength. The lag time to formation of the first detected species in the aggregation process was evaluated by UV-CE and thioflavin T (ThT) binding for salt concentrations from 100 mM to 250 mM. UV-CE had a significantly shorter (5–8 h) lag time than ThT binding (15–19 h). In addition, the lag time to detection of the first aggregated species via UV-CE was unaffected by salt concentration, while a trend toward an increased lag time with increased salt concentration was observed with ThT binding. This result indicates that solution ionic strength impacts early stages of aggregation and β-sheet aggregate formation differently. To observe whether CE may be applied for the analysis of biological samples containing low insulin concentrations, the limit of detection using UV and laser induced fluorescence (LIF) detection modes was determined. The limit of detection using LIF-CE, 48.4 pM, was lower than the physiological insulin concentration, verifying the utility of this technique for monitoring biological samples. LIF-CE was subsequently used to analyze the time course for fluorescein isothiocyanate (FITC)-labeled insulin oligomer formation. This study is the first to report that the FITC label prevented incorporation of insulin into oligomers, cautioning against the use of this fluorescent label as a tag for following early stages of insulin aggregation. Full article
(This article belongs to the Special Issue Protein Aggregation)
Open AccessArticle
QSAR Study and Molecular Design of Open-Chain Enaminones as Anticonvulsant Agents
Int. J. Mol. Sci. 2011, 12(12), 9354-9368; https://doi.org/10.3390/ijms12129354
Received: 15 September 2011 / Revised: 7 November 2011 / Accepted: 24 November 2011 / Published: 14 December 2011
Cited by 43 | Viewed by 3383 | PDF Full-text (262 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches [...] Read more.
Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches are applied with the purpose of comparing the consistency of our results: (a) the search of molecular descriptors via multivariable linear regressions; and (b) the calculation of flexible descriptors with the CORAL (CORrelation And Logic) program. Among the results found, we propose some potent candidate open-chain enaminones having ED50 values lower than 10 mg·kg−1 for corresponding pharmacological studies. These compounds are classified as Class 1 and Class 2 according to the Anticonvulsant Selection Project. Full article
(This article belongs to the Special Issue Atoms in Molecules and in Nanostructures)
Open AccessArticle
The Relationships Between Biological Activities and Structure of Flavan-3-Ols
Int. J. Mol. Sci. 2011, 12(12), 9342-9353; https://doi.org/10.3390/ijms12129342
Received: 27 October 2011 / Revised: 23 November 2011 / Accepted: 5 December 2011 / Published: 13 December 2011
Cited by 30 | Viewed by 3712 | PDF Full-text (405 KB) | HTML Full-text | XML Full-text
Abstract
Flavan-3-ols are involved in multiple metabolic pathways that induce inhibition of cell proliferation. We studied the structure-activity relationship of gallic acid (GA) and four flavan-3-ols: epigallocatechin gallate (EGCG), epigallocatechin (EGC), catechin (C), and epicatechin (EC). We measured the cell viability by the MTT [...] Read more.
Flavan-3-ols are involved in multiple metabolic pathways that induce inhibition of cell proliferation. We studied the structure-activity relationship of gallic acid (GA) and four flavan-3-ols: epigallocatechin gallate (EGCG), epigallocatechin (EGC), catechin (C), and epicatechin (EC). We measured the cell viability by the MTT assay and we determined the concentration of testing compound required to reduce cell viability by 50% (IC50). All tested compounds showed a dose-dependent and time-dependent inhibitory antiproliferative effect on Hs578T cells; IC50 values varying from the 15.81 to 326.8 µM. Intracellular ROS (reactive oxygen species) were quantified using a fluorescent probe 2’,7’-dichlorofluorescin diacetate (DCFH-DA). Only the treatment with 10 µM EGC and EGCG was able to induce a significant decrease of ROS concentration and increased levels of ROS were registered for 100 µM EGCG, EGC and GA. Flavans-3-ols and GA induced apoptosis in a dose- and time-dependent manner, which indicated that the induction of apoptosis mediated their cytotoxic activity at least partially. The galloylated catechins have shown a stronger antiproliferative activity and apoptotic effect than the one produced by non galloylated catechins. The galloylated flavan-3-ols are potential therapeutic agents for patients with triple negative breast cancer via induction of apoptosis. Full article
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Open AccessArticle
Combined Extraction Processes of Lipid from Chlorella vulgaris Microalgae: Microwave Prior to Supercritical Carbon Dioxide Extraction
Int. J. Mol. Sci. 2011, 12(12), 9332-9341; https://doi.org/10.3390/ijms12129332
Received: 1 September 2011 / Revised: 21 October 2011 / Accepted: 2 December 2011 / Published: 13 December 2011
Cited by 52 | Viewed by 3767 | PDF Full-text (1401 KB) | HTML Full-text | XML Full-text
Abstract
Extraction yields and fatty acid profiles from freeze-dried Chlorella vulgaris by microwave pretreatment followed by supercritical carbon dioxide (MW-SCCO2) extraction were compared with those obtained by supercritical carbon dioxide extraction alone (SCCO2). Work performed with pressure range of 20–28 [...] Read more.
Extraction yields and fatty acid profiles from freeze-dried Chlorella vulgaris by microwave pretreatment followed by supercritical carbon dioxide (MW-SCCO2) extraction were compared with those obtained by supercritical carbon dioxide extraction alone (SCCO2). Work performed with pressure range of 20–28 Mpa and temperature interval of 40–70 °C, gave the highest extraction yield (w/w dry weight) at 28 MPa/40 °C. MW-SCCO2 allowed to obtain the highest extraction yield (4.73%) compared to SCCO2 extraction alone (1.81%). Qualitative and quantitative analyses of microalgae oil showed that palmitic, oleic, linoleic and α-linolenic acid were the most abundant identified fatty acids. Oils obtained by MW-SCCO2 extraction had the highest concentrations of fatty acids compared to SCCO2 extraction without pretreatment. Native form, and microwave pretreated and untreated microalgae were observed by scanning electronic microscopy (SEM). SEM micrographs of pretreated microalgae present tearing wall agglomerates. After SCCO2, microwave pretreated microalgae presented several micro cracks; while native form microalgae wall was slightly damaged. Full article
(This article belongs to the Section Green Chemistry)
Open AccessEditorial
Molecular System Bioenergics of the Heart: Experimental Studies of Metabolic Compartmentation and Energy Fluxes versus Computer Modeling
Int. J. Mol. Sci. 2011, 12(12), 9296-9331; https://doi.org/10.3390/ijms12129296
Received: 10 November 2011 / Revised: 30 November 2011 / Accepted: 30 November 2011 / Published: 13 December 2011
Cited by 17 | Viewed by 4300 | PDF Full-text (801 KB) | HTML Full-text | XML Full-text
Abstract
In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We [...] Read more.
In this review we analyze the recent important and remarkable advancements in studies of compartmentation of adenine nucleotides in muscle cells due to their binding to macromolecular complexes and cellular structures, which results in non-equilibrium steady state of the creatine kinase reaction. We discuss the problems of measuring the energy fluxes between different cellular compartments and their simulation by using different computer models. Energy flux determinations by 18O transfer method have shown that in heart about 80% of energy is carried out of mitochondrial intermembrane space into cytoplasm by phosphocreatine fluxes generated by mitochondrial creatine kinase from adenosine triphosphate (ATP), produced by ATP Synthasome. We have applied the mathematical model of compartmentalized energy transfer for analysis of experimental data on the dependence of oxygen consumption rate on heart workload in isolated working heart reported by Williamson et al. The analysis of these data show that even at the maximal workloads and respiration rates, equal to 174 µmol O2 per min per g dry weight, phosphocreatine flux, and not ATP, carries about 80–85% percent of energy needed out of mitochondria into the cytosol. We analyze also the reasons of failures of several computer models published in the literature to correctly describe the experimental data. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics 2011)
Open AccessReview
The Slowly Aggregating Salmon Calcitonin: A Useful Tool for the Study of the Amyloid Oligomers Structure and Activity
Int. J. Mol. Sci. 2011, 12(12), 9277-9295; https://doi.org/10.3390/ijms12129277
Received: 28 October 2011 / Revised: 17 November 2011 / Accepted: 24 November 2011 / Published: 13 December 2011
Cited by 16 | Viewed by 3835 | PDF Full-text (3581 KB) | HTML Full-text | XML Full-text
Abstract
Amyloid proteins of different aminoacidic composition share the tendency to misfold and aggregate in a similar way, following common aggregation steps. The process includes the formation of dimers, trimers, and low molecular weight prefibrillar oligomers, characterized by the typical morphology of globules less [...] Read more.
Amyloid proteins of different aminoacidic composition share the tendency to misfold and aggregate in a similar way, following common aggregation steps. The process includes the formation of dimers, trimers, and low molecular weight prefibrillar oligomers, characterized by the typical morphology of globules less than 10 nm diameter. The globules spontaneously form linear or annular structures and, eventually, mature fibers. The rate of this process depends on characteristics intrinsic to the different proteins and to environmental conditions (i.e., pH, ionic strength, solvent composition, temperature). In the case of neurodegenerative diseases, it is now generally agreed that the pathogenic aggregates are not the mature fibrils, but the intermediate, soluble oligomers. However, the molecular mechanism by which these oligomers trigger neuronal damage is still unclear. Inparticular, it is not clear if there is a peculiar structure at the basis of the neurotoxic effect and how this structure interacts with neurons. This review will focus on the results we obtained using salmon Calcitonin, an amyloid protein characterized by a very slow aggregation rate, which allowed us to closely monitor the aggregation process. We used it as a tool to investigate the characteristics of amyloid oligomers formation and their interactions with neuronal cells. Our results indicate that small globules of about 6 nm could be the responsible for the neurotoxic effects. Moreover, our data suggest that the rich content in lipid rafts of neuronal cell plasma membrane may render neurons particularly vulnerable to the amyloid protein toxic effect. Full article
(This article belongs to the Special Issue Protein Aggregation)
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Open AccessArticle
Inference of Gene Regulation via miRNAs During ES Cell Differentiation Using MiRaGE Method
Int. J. Mol. Sci. 2011, 12(12), 9265-9276; https://doi.org/10.3390/ijms12129265
Received: 24 October 2011 / Revised: 22 November 2011 / Accepted: 29 November 2011 / Published: 12 December 2011
Cited by 7 | Viewed by 5064 | PDF Full-text (321 KB) | HTML Full-text | XML Full-text
Abstract
MicroRNA (miRNA) is a critical regulator of cell growth, differentiation, and development. To identify important miRNAs in a biological process, many bioinformatical tools have been developed. We have developed MiRaGE (MiRNA Ranking by Gene Expression) method to infer the regulation of gene expression [...] Read more.
MicroRNA (miRNA) is a critical regulator of cell growth, differentiation, and development. To identify important miRNAs in a biological process, many bioinformatical tools have been developed. We have developed MiRaGE (MiRNA Ranking by Gene Expression) method to infer the regulation of gene expression by miRNAs from changes of gene expression profiles. The method does not require precedent array normalization. We applied the method to elucidate possibly important miRNAs during embryonic stem (ES) cell differentiation to neuronal cells and we infer that certain miRNAs, including miR-200 family, miR-429, miR-302 family, and miR-17-92 cluster members may be important to the maintenance of undifferentiated status in ES cells. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
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Open AccessArticle
3D QSAR Pharmacophore Modeling, in Silico Screening, and Density Functional Theory (DFT) Approaches for Identification of Human Chymase Inhibitors
Int. J. Mol. Sci. 2011, 12(12), 9236-9264; https://doi.org/10.3390/ijms12129236
Received: 24 October 2011 / Revised: 18 November 2011 / Accepted: 23 November 2011 / Published: 12 December 2011
Cited by 43 | Viewed by 4761 | PDF Full-text (861 KB) | HTML Full-text | XML Full-text
Abstract
Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify [...] Read more.
Human chymase is a very important target for the treatment of cardiovascular diseases. Using a series of theoretical methods like pharmacophore modeling, database screening, molecular docking and Density Functional Theory (DFT) calculations, an investigation for identification of novel chymase inhibitors, and to specify the key factors crucial for the binding and interaction between chymase and inhibitors is performed. A highly correlating (r = 0.942) pharmacophore model (Hypo1) with two hydrogen bond acceptors, and three hydrophobic aromatic features is generated. After successfully validating “Hypo1”, it is further applied in database screening. Hit compounds are subjected to various drug-like filtrations and molecular docking studies. Finally, three structurally diverse compounds with high GOLD fitness scores and interactions with key active site amino acids are identified as potent chymase hits. Moreover, DFT study is performed which confirms very clear trends between electronic properties and inhibitory activity (IC50) data thus successfully validating “Hypo1” by DFT method. Therefore, this research exertion can be helpful in the development of new potent hits for chymase. In addition, the combinational use of docking, orbital energies and molecular electrostatic potential analysis is also demonstrated as a good endeavor to gain an insight into the interaction between chymase and inhibitors. Full article
(This article belongs to the Section Biochemistry)
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Open AccessArticle
The Effect of the Acetone Extract of Arctotis arctotoides (Asteraceae) on the Growth and Ultrastructure of Some Opportunistic Fungi Associated with HIV/AIDS
Int. J. Mol. Sci. 2011, 12(12), 9226-9235; https://doi.org/10.3390/ijms12129226
Received: 18 October 2011 / Revised: 23 November 2011 / Accepted: 24 November 2011 / Published: 9 December 2011
Cited by 8 | Viewed by 3097 | PDF Full-text (1256 KB) | HTML Full-text | XML Full-text
Abstract
In this study, the effect of the acetone extract of Arctotis arctotoides (L.f.) O. Hoffm. (Asteraceae) on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM). Remarkable morphological alterations in the fungal [...] Read more.
In this study, the effect of the acetone extract of Arctotis arctotoides (L.f.) O. Hoffm. (Asteraceae) on the growth and ultrastructure of some opportunistic fungi associated with HIV/AIDS was analyzed by means of scanning electron microscope (SEM). Remarkable morphological alterations in the fungal mycelia which were attributed to the loss of cell wall strength ranged from loss of turgidity and uniformity, collapse of entire hyphae to evident destruction of the hyphae. The elements responsible for giving the fungi their characteristic virulence were detected and quantified by energy dispersive X-ray microanalysis techniques. X-ray microanalysis showed the specific spectra of sodium, potassium and sulfur as the principal intersection of the four pathogenic fungi studied. Since these ions have the potential of fostering fungal invasion by altering the permeability of hosts’ membranes, their presence was considered inherent to the pathogenicity of the opportunistic fungi. Hence, these findings indicate the potential of the crude extract of A. arctotoides in preventing fungal invasion and subsequent infection of host’s membranes. Full article
Open AccessReview
Hormonal Influence on Coenzyme Q10 Levels in Blood Plasma
Int. J. Mol. Sci. 2011, 12(12), 9216-9225; https://doi.org/10.3390/ijms12129216
Received: 1 November 2011 / Revised: 19 November 2011 / Accepted: 29 November 2011 / Published: 9 December 2011
Cited by 13 | Viewed by 3393 | PDF Full-text (364 KB) | HTML Full-text | XML Full-text
Abstract
Coenzyme Q10 (CoQ10), also known as ubiquinone for its presence in all body cells, is an essential part of the cell energy-producing system. However, it is also a powerful lipophilic antioxidant protecting lipoproteins and cell membranes. Due to these two [...] Read more.
Coenzyme Q10 (CoQ10), also known as ubiquinone for its presence in all body cells, is an essential part of the cell energy-producing system. However, it is also a powerful lipophilic antioxidant protecting lipoproteins and cell membranes. Due to these two actions, CoQ10 is commonly used in clinical practice in chronic heart failure, male infertility, and neurodegenerative disease. However, it is also taken as an anti-aging substance by healthy people aiming for long-term neuroprotection and by sportsmen to improve endurance. Many hormones are known to be involved in body energy regulation, in terms of production, consumption and dissipation, and their influence on CoQ10 body content or blood values may represent an important pathophysiological mechanism. We summarize the main findings of the literature about the link between hormonal systems and circulating CoQ10 levels. In particular the role of thyroid hormones, directly involved in the regulation of energy homeostasis, is discussed. There is also a link with gonadal and adrenal hormones, partially due to the common biosynthetic pathway with CoQ10, but also to the increased oxidative stress found in hypogonadism and hypoadrenalism. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics 2011)
Open AccessArticle
Differential Motor Neuron Impairment and Axonal Regeneration in Sporadic and Familiar Amyotrophic Lateral Sclerosis with SOD-1 Mutations: Lessons from Neurophysiology
Int. J. Mol. Sci. 2011, 12(12), 9203-9215; https://doi.org/10.3390/ijms12129203
Received: 9 October 2011 / Revised: 11 November 2011 / Accepted: 29 November 2011 / Published: 9 December 2011
Cited by 3 | Viewed by 3854 | PDF Full-text (147 KB) | HTML Full-text | XML Full-text
Abstract
Amyotrophic Lateral Sclerosis (ALS) is a degenerative disorder of the motor system. About 10% of cases are familial and 20% of these families have point mutations in the Cu/Zn superoxide dismutase 1 (SOD-1) gene. SOD-1 catalyses the superoxide radical (O2) [...] Read more.
Amyotrophic Lateral Sclerosis (ALS) is a degenerative disorder of the motor system. About 10% of cases are familial and 20% of these families have point mutations in the Cu/Zn superoxide dismutase 1 (SOD-1) gene. SOD-1 catalyses the superoxide radical (O2) into hydrogen peroxide and molecular oxygen. The clinical neurophysiology in ALS plays a fundamental role in differential diagnosis between the familial and sporadic forms and in the assessment of its severity and progression. Sixty ALS patients (34 males; 26 females) were enrolled in the study and examined basally (T0) and every 4 months (T1, T2, and T3). Fifteen of these patients are SOD-1 symptomatic mutation carriers (nine males, six females). We used Macro-EMG and Motor Unit Number Estimation (MUNE) in order to evaluate the neuronal loss and the re-innervation process at the onset of disease and during follow-up period. Results and Discussion: SOD-1 mutation carriers have a higher number of motor units at the moment of diagnosis when compared with the sporadic form, despite a more dramatic drop in later stages. Moreover, in familiar SOD-1 ALS there is not a specific time interval in which the axonal regeneration can balance the neuronal damage. Taken together, these results strengthen the idea of a different pathogenetic mechanism at the base of sALS and fALS. Full article
(This article belongs to the Special Issue Studies of Motor Molecules)
Open AccessArticle
Wild and Hatchery Populations of Korean Starry Flounder (Platichthys stellatus) Compared Using Microsatellite DNA Markers
Int. J. Mol. Sci. 2011, 12(12), 9189-9202; https://doi.org/10.3390/ijms12129189
Received: 22 November 2011 / Revised: 2 December 2011 / Accepted: 5 December 2011 / Published: 9 December 2011
Cited by 16 | Viewed by 2904 | PDF Full-text (612 KB) | HTML Full-text | XML Full-text
Abstract
Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool [...] Read more.
Starry flounder (Platichthys stellatus) is an important sport and food fish found around the margins of the North Pacific. Aquaculture production of this species in Korea has increased because of its commercial value. Microsatellite DNA markers are a useful DNA-based tool for monitoring the genetic variation of starry flounder populations. In this study, 12 polymorphic microsatellite DNA markers were identified from a partial genomic starry flounder DNA library enriched in CA repeats, and used to compare allelic variation between wild and hatchery starry flounder populations in Korea. All loci were readily amplified and demonstrated high allelic diversity, with the number of alleles ranging from 6 to 18 in the wild population and from 2 to 12 in the farmed population. A total of 136 alleles were detected at the 12 microsatellite loci in the two populations. The mean observed and expected heterozygosities were 0.62 and 0.68, respectively, in the hatchery samples and 0.67 and 0.75, respectively, in the wild samples. These results indicate lower genetic variability in the hatchery population as compared to the wild population. Significant shifts in allelic frequencies were detected at eight loci, which resulted in a small but significant genetic differences between the wild and hatchery populations (FST = 0.043, P < 0.05). Further studies with additional starry flounder sample collections are needed for comprehensive determinations of the genetic varieties between the wild and hatchery populations. These microsatellite loci may be valuable for future population genetic studies, monitoring the genetic variation for successful aquaculture management and the preservation of aquatic biodiversity. Full article
(This article belongs to the Section Biochemistry)
Open AccessArticle
Dynamics of Protein Phosphatase Gene Expression in Corbicula fluminea Exposed to Microcystin-LR and to Toxic Microcystis aeruginosa Cells
Int. J. Mol. Sci. 2011, 12(12), 9172-9188; https://doi.org/10.3390/ijms12129172
Received: 1 August 2011 / Revised: 21 November 2011 / Accepted: 30 November 2011 / Published: 8 December 2011
Cited by 11 | Viewed by 3559 | PDF Full-text (316 KB) | HTML Full-text | XML Full-text
Abstract
This study investigated the in vivo effects of microcystins on gene expression of several phosphoprotein phosphatases (PPP) in the freshwater clam Corbicula fluminea with two different exposure scenarios. Clams were exposed for 96 h to 5 µg L−1 of dissolved microcystin-LR and [...] Read more.
This study investigated the in vivo effects of microcystins on gene expression of several phosphoprotein phosphatases (PPP) in the freshwater clam Corbicula fluminea with two different exposure scenarios. Clams were exposed for 96 h to 5 µg L−1 of dissolved microcystin-LR and the relative changes of gene expression of three different types of PPP (PPP1, 2 and 4) were analyzed by quantitative real-time PCR. The results showed a significant induction of PPP2 gene expression in the visceral mass. In contrast, the cyanotoxin did not cause any significant changes on PPP1 and PPP4 gene expression. Based on these results, we studied alterations in transcriptional patterns in parallel with enzymatic activity of C. fluminea for PPP2, induced by a Microcystis aeruginosa toxic strain (1 × 105 cells cm−3) during 96 h. The relative changes of gene expression and enzyme activity in visceral mass were analyzed by quantitative real-time PCR and colorimetric assays respectively. The clams exhibited a significant reduction of PPP2 activity with a concomitant enhancement of gene expression. Considering all the results we can conclude that the exposure to an ecologically relevant concentration of pure or intracellular microcystins (-LR) promoted an in vivo effect on PPP2 gene expression in C. fluminea. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessReview
RNA Aptamer Evolution: Two Decades of SELEction
Int. J. Mol. Sci. 2011, 12(12), 9155-9171; https://doi.org/10.3390/ijms12129155
Received: 24 October 2011 / Revised: 24 November 2011 / Accepted: 28 November 2011 / Published: 8 December 2011
Cited by 39 | Viewed by 4470 | PDF Full-text (444 KB) | HTML Full-text | XML Full-text
Abstract
Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First [...] Read more.
Aptamers are small non-coding RNAs capable of recognizing, with high specificity and affinity, a wide variety of molecules in a manner that resembles antibodies. This class of nucleic acids is the resulting product of applying a well-established screening method known as SELEX. First developed in 1990, the SELEX process has become a powerful tool to select structured oligonucleotides for the recognition of targets, starting with small molecules, going through protein complexes until whole cells. SELEX has also evolved along with new technologies positioning itself as an alternative in the design of a new class of therapeutic agents in modern molecular medicine. This review is an historical follow-up of SELEX method over the two decades since its first appearance. Full article
(This article belongs to the Special Issue Non-Coding RNAs)
Open AccessArticle
Effect of Tween Series on Growth and cis-9, trans-11 Conjugated Linoleic Acid Production of Lactobacillus acidophilus F0221 in the Presence of Bile Salts
Int. J. Mol. Sci. 2011, 12(12), 9138-9154; https://doi.org/10.3390/ijms12129138
Received: 20 October 2011 / Revised: 8 November 2011 / Accepted: 16 November 2011 / Published: 8 December 2011
Cited by 16 | Viewed by 3734 | PDF Full-text (197 KB) | HTML Full-text | XML Full-text
Abstract
Cis-9, trans-11 conjugated linoleic acid (c9, t11 CLA) producing bacteria have attracted much attention as novel probiotics which have shown beneficial effects on host health. However, bile salts are able to inhibit bacterial growth and c9, t [...] Read more.
Cis-9, trans-11 conjugated linoleic acid (c9, t11 CLA) producing bacteria have attracted much attention as novel probiotics which have shown beneficial effects on host health. However, bile salts are able to inhibit bacterial growth and c9, t11 CLA production. For recovering growth and c9, t11 CLA production of Lactobacillus acidophilus F0221 in the presence of bile salts, Tween series (Tween 20, Tween 40, Tween 60 and Tween 80) were added in growth culture containing 0.3% oxgall. Results showed that the viable counts were significantly (P < 0.05) recovered to 8.58–8.75 log CFU/mL in the presence of all Tween treatments. However, recovery of c9, t11 CLA production was only demonstrated in the presence of Tween 80 (72.89 μg/mL). Stepwise increasing oxgall in a concentrations range from 0.1% to 0.9% according to human intestinal physiological environments, Tween 80 still showed significant (P < 0.05) recovery ability on growth (8.91–8.04 log CFU/mL) and c9, t11 CLA (69.22–34.27 μg/mL) production. The effect of Tween 80 on growth and production was also investigated in the presence of different types of bile salts (sodium salts of cholic acid (CA), deoxycholic acid (DCA), chendeoxycholic acid (CDCA), glycocholic acid (GCA) and taurocholic acid (TCA)). Results showed that Tween 80 could significantly (P < 0.05) recover c9, t11 CLA production in the presence of all types of bile salts, but the Tween 80 could only significantly (P < 0.05) recover viable counts of the strain in the presence of CA, DCA and CDCA. This recovery ability could be attributed to the protection of leakage of intracellular material. Additionally, although bile salts inhibited growth and c9, t11 CLA production by the growing cell, it promoted the c9, t11 CLA production by the resting cell. Full article
Open AccessArticle
Swelling-Activated Anion Channels Are Essential for Volume Regulation of Mouse Thymocytes
Int. J. Mol. Sci. 2011, 12(12), 9125-9137; https://doi.org/10.3390/ijms12129125
Received: 25 October 2011 / Revised: 10 November 2011 / Accepted: 24 November 2011 / Published: 8 December 2011
Cited by 16 | Viewed by 3290 | PDF Full-text (158 KB) | HTML Full-text | XML Full-text
Abstract
Channel-mediated trans-membrane chloride movement is a key process in the active cell volume regulation under osmotic stress in most cells. However, thymocytes were hypothesized to regulate their volume by activating a coupled K-Cl cotransport mechanism. Under the patch-clamp, we found that osmotic swelling [...] Read more.
Channel-mediated trans-membrane chloride movement is a key process in the active cell volume regulation under osmotic stress in most cells. However, thymocytes were hypothesized to regulate their volume by activating a coupled K-Cl cotransport mechanism. Under the patch-clamp, we found that osmotic swelling activates two types of macroscopic anion conductance with different voltage-dependence and pharmacology. At the single-channel level, we identified two types of events: one corresponded to the maxi-anion channel, and the other one had characteristics of the volume-sensitive outwardly rectifying (VSOR) chloride channel of intermediate conductance. A VSOR inhibitor, phloretin, significantly suppressed both macroscopic VSOR-type conductance and single-channel activity of intermediate amplitude. The maxi-anion channel activity was largely suppressed by Gd3+ ions but not by phloretin. Surprisingly, [(dihydroindenyl)oxy] alkanoic acid (DIOA), a known antagonist of K-Cl cotransporter, was found to significantly suppress the activity of the VSOR-type single-channel events with no effect on the maxi-anion channels at 10 μM. The regulatory volume decrease (RVD) phase of cellular response to hypotonicity was mildly suppressed by Gd3+ ions and was completely abolished by phloretin suggesting a major impact of the VSOR chloride channel and modulatory role of the maxi-anion channel. The inhibitory effect of DIOA was also strong, and, most likely, it occurred via blocking the VSOR Cl channels. Full article
(This article belongs to the Special Issue Membrane Transport)
Open AccessArticle
Loop-Mediated Amplification Accelerated by Stem Primers
Int. J. Mol. Sci. 2011, 12(12), 9108-9124; https://doi.org/10.3390/ijms12129108
Received: 31 August 2011 / Revised: 6 November 2011 / Accepted: 29 November 2011 / Published: 8 December 2011
Cited by 22 | Viewed by 4676 | PDF Full-text (931 KB) | HTML Full-text | XML Full-text
Abstract
Isothermal nucleic acid amplifications (iNAATs) have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP) has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance [...] Read more.
Isothermal nucleic acid amplifications (iNAATs) have become an important alternative to PCR for in vitro molecular diagnostics in all fields. Amongst iNAATs Loop-mediated amplification (LAMP) has gained much attention over the last decade because of the simplicity of hardware requirements. LAMP demonstrates performance equivalent to that of PCR, but its application has been limited by the challenging primer design. The design of six primers in LAMP requires a selection of eight priming sites with significant restrictions imposed on their respective positioning and orientation. In order to relieve primer design constraints we propose an alternative approach which uses Stem primers instead of Loop primers and demonstrate the application of STEM-LAMP in assaying for Clostridium difficile, Listeria monocytogenes and HIV. Stem primers used in LAMP in combination with loop-generating and displacement primers gave significant benefits in speed and sensitivity, similar to those offered by Loop primers, while offering additional options of forward and reverse orientations, multiplexing, use in conjunction with Loop primers or even omission of one or two displacement primers, where necessary. Stem primers represent a valuable alternative to Loop primers and an additional tool for IVD assay development by offering more choices for primer design at the same time increasing assay speed, sensitivity, and reproducibility. Full article
(This article belongs to the Special Issue Advances in Molecular Diagnostics)
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