International Journal of Molecular Sciences

554 KiB

Open AccessArticle

Genistein Inhibition of Topoisomerase IIα Expression Participated by Sp1 and Sp3 in HeLa Cell

by Najing Zhou, Yunli Yan, Wenling Li, Yanling Wang, Lifen Zheng, Shuo Han, Yongxin Yan and Yunzhi Li

Int. J. Mol. Sci. 2009, 10(7), 3255-3268; https://doi.org/10.3390/ijms10073255 - 22 Jul 2009

Cited by 30 | Viewed by 10455

Abstract

Genistein (4′, 5, 7-trihydroxyisoflavone) is an isoflavone compound obtained from plants that has potential applications in cancer therapy. However, the molecular mechanism of the action of genistein on cancer cell apoptosis is not well known. In this study, we investigated the effect of [...] Read more.

Genistein (4′, 5, 7-trihydroxyisoflavone) is an isoflavone compound obtained from plants that has potential applications in cancer therapy. However, the molecular mechanism of the action of genistein on cancer cell apoptosis is not well known. In this study, we investigated the effect of genistein on topoisomerase II-α (Topo IIα), an important protein involved in the processes of DNA replication and cell proliferation. The results revealed that inhibition of Topo IIα expression through the regulation of Specificity protein 1 and Specificity protein 3 may be one of the reasons for genistein’s induction of HeLa cell apoptosis. Full article

(This article belongs to the Section Biochemistry)

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223 KiB

Open AccessArticle

Prediction of Skin Sensitization with a Particle Swarm Optimized Support Vector Machine

by Hua Yuan, Jianping Huang and Chenzhong Cao

Int. J. Mol. Sci. 2009, 10(7), 3237-3254; https://doi.org/10.3390/ijms10073237 - 17 Jul 2009

Cited by 19 | Viewed by 11122

Abstract

Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT) and murine local lymph [...] Read more.

Skin sensitization is the most commonly reported occupational illness, causing much suffering to a wide range of people. Identification and labeling of environmental allergens is urgently required to protect people from skin sensitization. The guinea pig maximization test (GPMT) and murine local lymph node assay (LLNA) are the two most important in vivo models for identification of skin sensitizers. In order to reduce the number of animal tests, quantitative structure-activity relationships (QSARs) are strongly encouraged in the assessment of skin sensitization of chemicals. This paper has investigated the skin sensitization potential of 162 compounds with LLNA results and 92 compounds with GPMT results using a support vector machine. A particle swarm optimization algorithm was implemented for feature selection from a large number of molecular descriptors calculated by Dragon. For the LLNA data set, the classification accuracies are 95.37% and 88.89% for the training and the test sets, respectively. For the GPMT data set, the classification accuracies are 91.80% and 90.32% for the training and the test sets, respectively. The classification performances were greatly improved compared to those reported in the literature, indicating that the support vector machine optimized by particle swarm in this paper is competent for the identification of skin sensitizers. Full article

(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)

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Open AccessEditorial

Fuels for Thought!

by Clifford Louime

Int. J. Mol. Sci. 2009, 10(7), 3235-3236; https://doi.org/10.3390/ijms10073235 - 15 Jul 2009

Viewed by 7313

Abstract

When it comes to the marketing of the bioenergy brand, one of the catchiest slogans out these days is “25 by ‘25”. Adopted and supported by industries, academia and government agencies alike, this organization simply aims to supply 25 percent of our energy [...] Read more.

When it comes to the marketing of the bioenergy brand, one of the catchiest slogans out these days is “25 by ‘25”. Adopted and supported by industries, academia and government agencies alike, this organization simply aims to supply 25 percent of our energy from renewable resources by the year 2025. By focusing its future efforts on wind, solar and biomass resources, the “25 by 25” initiative is expected to create new jobs, develop novel technologies, help mitigate the effects of global warming and reduce our dependence on fossil fuels. [...] Full article

(This article belongs to the Special Issue Biofuels R&D: Securing the Planet's Future Energy Needs)

287 KiB

Open AccessArticle

The Evaluation of the Possibilities of Using PLGA Co-Polymer and Its Composites with Carbon Fibers or Hydroxyapatite in the Bone Tissue Regeneration Process – in Vitro and in Vivo Examinations

by Magdalena Cieślik, Anna Mertas, Anna Morawska-Chochół, Daniel Sabat, Rajmund Orlicki, Aleksander Owczarek, Wojciech Król and Tadeusz Cieślik

Int. J. Mol. Sci. 2009, 10(7), 3224-3234; https://doi.org/10.3390/ijms10073224 - 15 Jul 2009

Cited by 28 | Viewed by 12068

Abstract

Synthetic polymers belonging to the aliphatic polyester group have become highly promising biomaterials for reconstructive medicine. The purpose of the present work is a biological evaluation of lactide-glycolide co-polymer (PLGA) and its composites with carbon fibers (PLGA+CF) or hydroxyapatite (PLGA+HA). The cytotoxicity of [...] Read more.

Synthetic polymers belonging to the aliphatic polyester group have become highly promising biomaterials for reconstructive medicine. The purpose of the present work is a biological evaluation of lactide-glycolide co-polymer (PLGA) and its composites with carbon fibers (PLGA+CF) or hydroxyapatite (PLGA+HA). The cytotoxicity of the evaluated materials towards hFOB 1.19 human osteoblast-like cells was assessed. Moreover, during the one-year contact of the assessed materials with living osseous tissue, the progress of bone formation was analyzed and the accompanying process of the materials’ degradation was evaluated. The materials under evaluation proved to be biocompatible. Full article

(This article belongs to the Special Issue Biocompatibility of Materials)

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Open AccessArticle

Biofouling Growth in Cold Estuarine Waters and Evaluation of Some Chitosan and Copper Anti-Fouling Paints

by Émilien Pelletier, Claudie Bonnet and Karine Lemarchand

Int. J. Mol. Sci. 2009, 10(7), 3209-3223; https://doi.org/10.3390/ijms10073209 - 14 Jul 2009

Cited by 38 | Viewed by 15527

Abstract

Ecological concerns about antifouling paints containing non-green tin and copper compounds have highlighted the need for environmentally friendly alternatives. We report here a field test conducted in estuarine waters over two months designed to evaluate the efficiency of a number of active natural [...] Read more.

Ecological concerns about antifouling paints containing non-green tin and copper compounds have highlighted the need for environmentally friendly alternatives. We report here a field test conducted in estuarine waters over two months designed to evaluate the efficiency of a number of active natural and man-made chemical ingredients added into a silicon-polyurethane marine paint. Early steps of biofouling in cold seawater of the St. Lawrence Estuary (Canada) were observed. Analyses, including dry biomass, flow cytometry and spectrofluorimetry, demonstrated a short-term antibacterial action of chitosan-based paints although no significant anti-algal action was observed. Cuprous oxide paints were efficient against bacteria and algae invasion in the first two weeks, especially those with added organic biocides such as isothiazolone and copper pyrithione. However, the overall dry biomass and chlorophyll a content were similar for all chitosan- and copper-based paints after 63 days. Microscopic observations revealed variation in the highly diverse benthic diatom population including species Navicula, Melosira, Cocconeis, Nitshzcia, Fragilaria and Amphora. Results suggest no real long-term efficiency for tested antifouling paints and highlight a particular need for green antifouling ingredients that are active under northern estuarine conditions. Full article

(This article belongs to the Section Green Chemistry)

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Open AccessArticle

Receptor-Mediated Vascular Smooth Muscle Migration Induced by LPA Involves p38 Mitogen-Activated Protein Kinase Pathway Activation

by Zhi-Bin Zhou, Jian-Ping Niu and Zhi-Jun Zhang

Int. J. Mol. Sci. 2009, 10(7), 3194-3208; https://doi.org/10.3390/ijms10073194 - 13 Jul 2009

Cited by 15 | Viewed by 11012 | Correction

Abstract

Lysophosphatidic acid (LPA), a naturally occurring glycerophospholipid, can evoke various biological responses, including cell migration, proliferation and survival, via activation of G protein-coupled receptors (GPCRs). However, the role of LPA receptors and details of LPA signaling in migration are largely unexplored. In this [...] Read more.

Lysophosphatidic acid (LPA), a naturally occurring glycerophospholipid, can evoke various biological responses, including cell migration, proliferation and survival, via activation of G protein-coupled receptors (GPCRs). However, the role of LPA receptors and details of LPA signaling in migration are largely unexplored. In this study we detect the expression of LPA1 and LPA3 receptors in rat aortic smooth muscle cells (RASMCs). LPA stimulated RASMCs migration in a dose-dependent manner and induced the phosphorylation of p38 mitogen-activated protein kinase (p38MAPK) and extracellular signal-regulated kinase (ERK). LPA-induced cell migration was significantly inhibited by specific LPA1/LPA3-receptor antagonist Dioctylglycerol pyrophosphate (8:0) (DGPP8.0) at higher concentration. Migration of cells toward LPA was partially, but significantly, reduced in the presence of SB-203580, a p38 MAPK inhibitor, but not PD98059, an ERK inhibitor. In addition, pertussis toxin (PTX), a Gi protein inhibitor, induced an inhibitory effect on p38 MAPK,ERK phosphorylation and RASMCs migration. These data suggest that LPA-induced migration is mediated through the Gi-protein-coupled LPA1 receptor involving activation of a PTX-sensitive Gi / p38MAPK pathway. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

A TD-DFT Study on the Photo-Physicochemical Properties of Chrysophanol from Rheum

by Xue Zhao, Zebao Zheng, Shuai Feng, Zhiqiang Shi and Dezhan Chen

Int. J. Mol. Sci. 2009, 10(7), 3186-3193; https://doi.org/10.3390/ijms10073186 - 13 Jul 2009

Cited by 9 | Viewed by 13792

Abstract

As a naturally occurring anthraquinone pigment, chrysophanol (MHAQ) has attracted considerable attention in recent years owing to its efficient photosensitivity under the solar spectrum. Considering the successful use of time-dependent density functional theory (TD-DFT) in investigating the photo-physicochemical behaviors of dyes and pigments, [...] Read more.

As a naturally occurring anthraquinone pigment, chrysophanol (MHAQ) has attracted considerable attention in recent years owing to its efficient photosensitivity under the solar spectrum. Considering the successful use of time-dependent density functional theory (TD-DFT) in investigating the photo-physicochemical behaviors of dyes and pigments, we performed a study by means of TD-DFT calculations, which provided us with various excited state properties of chrysophanol, including absorption spectrum, lowest triplet excited-state energy, vertical electron affinity and vertical ionization potential. On the basis of the calculated results, the photosensitive mechanisms of chrysophanol were discussed and some deeper insights were gained. First, we indicated that the experimentally observed chrysophanol’s photo-damage to DNA in oxygen-free media is more likely to arise from MHAQ^•+ rather than from T₁ state chrysophanol. Second, we revealed that it is the MHAQ^•−that is responsible for the O₂^•−generation in solvents. Based on the photosensitive activities, chrysophanol may be potentially used as the photodynamic medicine for clinical therapy of the diseases occurring on the shallow surface and vascular capillary diseases. Full article

(This article belongs to the Special Issue Applications of Density Functional Theory)

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Open AccessReview

Post-transcriptional Regulation of Gene Expression in Plants during Abiotic Stress

by Maïna Floris, Hany Mahgoub, Elodie Lanet, Christophe Robaglia and Benoît Menand

Int. J. Mol. Sci. 2009, 10(7), 3168-3185; https://doi.org/10.3390/ijms10073168 - 10 Jul 2009

Cited by 117 | Viewed by 21759

Abstract

Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on [...] Read more.

Land plants are anchored in one place for most of their life cycle and therefore must constantly adapt their growth and metabolism to abiotic stresses such as light intensity, temperature and the availability of water and essential minerals. Thus, plants’ subsistence depends on their ability to regulate rapidly gene expression in order to adapt their physiology to their environment. Recent studies indicate that post-transcriptional regulations of gene expression play an important role in how plants respond to abiotic stresses. We will review the different mechanisms of post-transcriptional regulation of nuclear genes expression including messenger RNA (mRNA) processing, stability, localization and protein translation, and discuss their relative importance for plant adaptation to abiotic stress. Full article

(This article belongs to the Special Issue Biotic and Abiotic Stress)

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Open AccessReview

Bax Inhibitor-1, a Conserved Cell Death Suppressor, Is a Key Molecular Switch Downstream from a Variety of Biotic and Abiotic Stress Signals in Plants

by Naohide Watanabe and Eric Lam

Int. J. Mol. Sci. 2009, 10(7), 3149-3167; https://doi.org/10.3390/ijms10073149 - 10 Jul 2009

Cited by 81 | Viewed by 21718

Abstract

In Nature plants are constantly challenged by a variety of environmental stresses that could lead to disruptions in cellular homeostasis. Programmed cell death (PCD) is a fundamental cellular process that is often associated with defense responses to pathogens, during development and in response [...] Read more.

In Nature plants are constantly challenged by a variety of environmental stresses that could lead to disruptions in cellular homeostasis. Programmed cell death (PCD) is a fundamental cellular process that is often associated with defense responses to pathogens, during development and in response to abiotic stresses in fungi, animals and plants. Although there are many characteristics shared between different types of PCD events, it remains unknown whether a common mechanism drives various types of PCD in eukaryotes. One candidate regulator for such a mechanism is Bax Inhibitor-1 (BI-1), an evolutionary conserved, endoplasmic reticulum (ER)-resident protein that represents an ancient cell death regulator that potentially regulates PCD in all eukaryotes. Recent findings strongly suggested that BI-1 plays an important role in the conserved ER stress response pathway to modulate cell death induction in response to multiple types of cell death signals. As ER stress signaling pathways has been suggested to play important roles not only in the control of ER homeostasis but also in other biological processes such as the response to pathogens and abiotic stress in plants, BI-1 might function to control the convergence point that modulates the level of the “pro-survival and pro-death” signals under multiple stress conditions. Full article

(This article belongs to the Special Issue Biotic and Abiotic Stress)

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383 KiB

Open AccessArticle

Density Functional Study of Structures and Electron Affinities of BrO₄F/BrO₄F^-

by Liangfa Gong, Jieming Xiong, Xinmin Wu, Chuansong Qi, Wei Li and Wenli Guo

Int. J. Mol. Sci. 2009, 10(7), 3128-3148; https://doi.org/10.3390/ijms10073128 - 8 Jul 2009

Cited by 1 | Viewed by 25717

Abstract

The structures, electron affinities and bond dissociation energies of BrO₄F/BrO₄F⁻ species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O₂…O₂ complexes possess ³A' electronic state for [...] Read more.

The structures, electron affinities and bond dissociation energies of BrO₄F/BrO₄F⁻ species have been investigated with five density functional theory (DFT) methods with DZP++ basis sets. The planar F-Br…O₂…O₂ complexes possess ³A' electronic state for neutral molecule and ⁴A' state for the corresponding anion. Three types of the neutral-anion energy separations are the adiabatic electron affinity (EA_ad), the vertical electron affinity (EA_vert), and the vertical detachment energy (VDE). The EA_ad value predicted by B3LYP method is 4.52 eV. The bond dissociation energies D_e (BrO₄F → BrO_4-mF + O_m) (m = 1-4) and D_e^- (BrO₄F^-→ BrO_4-mF^- + O_m and BrO₄F^-→ BrO_4-mF + O_m^-) are predicted. The adiabatic electron affinities (EA_ad) were predicted to be 4.52 eV for F-Br…O₂…O₂ (³A'← ⁴A') (B3LYP method). Full article

(This article belongs to the Special Issue Applications of Density Functional Theory)

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375 KiB

Open AccessArticle

Additive SMILES-Based Carcinogenicity Models: Probabilistic Principles in the Search for Robust Predictions

by Andrey A. Toropov, Alla P. Toropova and Emilio Benfenati

Int. J. Mol. Sci. 2009, 10(7), 3106-3127; https://doi.org/10.3390/ijms10073106 - 8 Jul 2009

Cited by 42 | Viewed by 15547

Abstract

Optimal descriptors calculated with the simplified molecular input line entry system (SMILES) have been utilized in modeling of carcinogenicity as continuous values (logTD₅₀). These descriptors can be calculated using correlation weights of SMILES attributes calculated by the Monte Carlo method. A [...] Read more.

Optimal descriptors calculated with the simplified molecular input line entry system (SMILES) have been utilized in modeling of carcinogenicity as continuous values (logTD₅₀). These descriptors can be calculated using correlation weights of SMILES attributes calculated by the Monte Carlo method. A considerable subset of these attributes includes rare attributes. The use of these rare attributes can lead to overtraining. One can avoid the influence of the rare attributes if their correlation weights are fixed to zero. A function, limS, has been defined to identify rare attributes. The limS defines the minimum number of occurrences in the set of structures of the training (subtraining) set, to accept attributes as usable. If an attribute is present less than limS, it is considered “rare”, and thus not used. Two systems of building up models were examined: 1. classic training-test system; 2. balance of correlations for the subtraining and calibration sets (together, they are the original training set: the function of the calibration set is imitation of a preliminary test set). Three random splits into subtraining, calibration, and test sets were analysed. Comparison of abovementioned systems has shown that balance of correlations gives more robust prediction of the carcinogenicity for all three splits (split 1: r_test²=0.7514, s_test=0.684; split 2: r_test²=0.7998, s_test=0.600; split 3: r_test²=0.7192, s_test=0.728). Full article

(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)

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247 KiB

Open AccessReview

Bacterial Stressors in Minimally Processed Food

by Vittorio Capozzi, Daniela Fiocco, Maria Luisa Amodio, Anna Gallone and Giuseppe Spano

Int. J. Mol. Sci. 2009, 10(7), 3076-3105; https://doi.org/10.3390/ijms10073076 - 8 Jul 2009

Cited by 85 | Viewed by 17827

Abstract

Stress responses are of particular importance to microorganisms, because their habitats are subjected to continual changes in temperature, osmotic pressure, and nutrients availability. Stressors (and stress factors), may be of chemical, physical, or biological nature. While stress to microorganisms is frequently caused by [...] Read more.

Stress responses are of particular importance to microorganisms, because their habitats are subjected to continual changes in temperature, osmotic pressure, and nutrients availability. Stressors (and stress factors), may be of chemical, physical, or biological nature. While stress to microorganisms is frequently caused by the surrounding environment, the growth of microbial cells on its own may also result in induction of some kinds of stress such as starvation and acidity. During production of fresh-cut produce, cumulative mild processing steps are employed, to control the growth of microorganisms. Pathogens on plant surfaces are already stressed and stress may be increased during the multiple mild processing steps, potentially leading to very hardy bacteria geared towards enhanced survival. Cross-protection can occur because the overlapping stress responses enable bacteria exposed to one stress to become resistant to another stress. A number of stresses have been shown to induce cross protection, including heat, cold, acid and osmotic stress. Among other factors, adaptation to heat stress appears to provide bacterial cells with more pronounced cross protection against several other stresses. Understanding how pathogens sense and respond to mild stresses is essential in order to design safe and effective minimal processing regimes. Full article

(This article belongs to the Special Issue Biotic and Abiotic Stress)

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199 KiB

Open AccessArticle

Effect of Seven Newly Synthesized and Currently Available Oxime Cholinesterase Reactivators on Cyclosarin-Intoxicated Rats

by Jana Zdarova Karasova, Jiri Kassa, Kamil Musilek, Miroslav Pohanka, Ladislav Novotny and Kamil Kuca

Int. J. Mol. Sci. 2009, 10(7), 3065-3075; https://doi.org/10.3390/ijms10073065 - 7 Jul 2009

Cited by 13 | Viewed by 9959

Abstract

Seven new oxime-based acetylcholinesterase reactivators were compared with three currently available ones (obidoxime, trimedoxime, HI-6) for their ability to lessen cholinesterase inhibition in blood and brain of cyclosarin-treated rats. Oximes were given at doses of 5% their LD₅₀ along with 21 mg/kg [...] Read more.

Seven new oxime-based acetylcholinesterase reactivators were compared with three currently available ones (obidoxime, trimedoxime, HI-6) for their ability to lessen cholinesterase inhibition in blood and brain of cyclosarin-treated rats. Oximes were given at doses of 5% their LD₅₀ along with 21 mg/kg atropine five min before the LD₅₀ of cyclosarin (120 ug/kg) was administered. Blood and brain samples were collected 30 minutes later. The greatest difference between acetylcholinesterase inhibition in blood of cyclosarin-treated rats was found after administration of HI-6 (40%), compared to 22% for trimedoxime and 6% for obidoxime. Only two of the seven newly synthesized oximes had any effect (K203 at 7%, K156 at 5%). Effective oximes against cyclosarin-inhibited plasma butyrylcholinesterase were HI-6 (42%), trimedoxime (11%), and K156 (4%). The oximes were less effective in brain than in blood, with reactivation values for HI-6 30% against acetylcholinesterase and 10% against butyrylcholinesterase. Values for newly synthesized oximes were less than 10% for K206, K269 and K203. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Chirality Emergence in Thin Solid Films of Amino Acids by Polarized Light from Synchrotron Radiation and Free Electron Laser

by Jun-ichi Takahashi, Hiroyuki Shinojima, Michiko Seyama, Yuko Ueno, Takeo Kaneko, Kensei Kobayashi, Hajime Mita, Mashahiro Adachi, Masahito Hosaka and Masahiro Katoh

Int. J. Mol. Sci. 2009, 10(7), 3044-3064; https://doi.org/10.3390/ijms10073044 - 7 Jul 2009

Cited by 43 | Viewed by 12798

Abstract

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior [...] Read more.

One of the most attractive hypothesis for the origin of homochirality in terrestrial bioorganic compounds is that a kind of “chiral impulse” as an asymmetric excitation source induced asymmetric reactions on the surfaces of such materials such as meteorites or interstellar dusts prior to the existence of terrestrial life (Cosmic Scenario). To experimentally introduce chiral structure into racemic films of amino acids (alanine, phenylalanine, isovaline, etc.), we irradiated them with linearly polarized light (LPL) from synchrotron radiation and circularly polarized light (CPL) from a free electron laser. After the irradiation, we evaluated optical anisotropy by measuring the circular dichroism (CD) spectra and verified that new Cotton peaks appeared at almost the same peak position as those of the corresponding non-racemic amino acid films. With LPL irradiation, two-dimensional anisotropic structure expressed as linear dichroism and/or linear birefringence was introduced into the racemic films. With CPL irradiation, the signs of the Cotton peaks exhibit symmetrical structure corresponding to the direction of CPL rotation. This indicates that some kinds of chiral structure were introduced into the racemic film. The CD spectra after CPL irradiation suggest the chiral structure should be derived from not only preferential photolysis but also from photolysis-induced molecular structural change. These results suggest that circularly polarized light sources in space could be associated with the origin of terrestrial homochirality; that is, they would be effective asymmetric exciting sources introducing chiral structures into bio-organic molecules or complex organic compounds. Full article

(This article belongs to the Special Issue Origin of Life)

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Open AccessArticle

Hedgehog Signaling Regulates the Survival of Gastric Cancer Cells by Regulating the Expression of Bcl-2

by Myoung-Eun Han, Young-Suk Lee, Sun-Yong Baek, Bong-Seon Kim, Jae-Bong Kim and Sae-Ock Oh

Int. J. Mol. Sci. 2009, 10(7), 3033-3043; https://doi.org/10.3390/ijms10073033 - 6 Jul 2009

Cited by 43 | Viewed by 10992

Abstract

Gastric cancer is the second most common cause of cancer deaths worldwide. The underlying molecular mechanisms of its carcinogenesis are relatively poorly characterized. Hedgehog (Hh) signaling, which is critical for development of various organs including the gastrointestinal tract, has been associated with gastric [...] Read more.

Gastric cancer is the second most common cause of cancer deaths worldwide. The underlying molecular mechanisms of its carcinogenesis are relatively poorly characterized. Hedgehog (Hh) signaling, which is critical for development of various organs including the gastrointestinal tract, has been associated with gastric cancer. The present study was undertaken to reveal the underlying mechanism by which Hh signaling controls gastric cancer cell proliferation. Treatment of gastric cancer cells with cyclopamine, a specific inhibitor of Hh signaling pathway, reduced proliferation and induced apoptosis of gastric cancer cells. Cyclopamine treatment induced cytochrome c release from mitochondria and cleavage of caspase 9. Moreover, Bcl-2 expression was significantly reduced by cyclopamine treatment. These results suggest that Hh signaling regulates the survival of gastric cancer cells by regulating the expression of Bcl-2. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Protein and Metabolite Analysis Reveals Permanent Induction of Stress Defense and Cell Regeneration Processes in a Tobacco Cell Suspension Culture

by Rico Lippmann, Stephanie Kaspar, Twan Rutten, Michael Melzer, Jochen Kumlehn, Andrea Matros and Hans-Peter Mock

Int. J. Mol. Sci. 2009, 10(7), 3012-3032; https://doi.org/10.3390/ijms10073012 - 6 Jul 2009

Cited by 27 | Viewed by 12722

Abstract

The secretome of a tobacco cell suspension culture was investigated by a combined proteomic and metabolomic approach. Protein analysis from 2-DE gels led to identification of 32 out of 60 spots from culture medium. Identified proteins were mainly involved in stress defence and [...] Read more.

The secretome of a tobacco cell suspension culture was investigated by a combined proteomic and metabolomic approach. Protein analysis from 2-DE gels led to identification of 32 out of 60 spots from culture medium. Identified proteins were mainly involved in stress defence and cell regeneration processes. Among them three putative new isoforms, e.g. for chitinase, peroxidase and β-1,4-xylosidase were identified, not yet present in available protein databases for the genus Nicotiana. GC-MS analysis of time course experiments revealed significant changes for metabolites involved in energy transport, signalling and cell development. Among them, the most significant increase was found for putrescine in the medium of cultures entering the exponential phase. Results showed strong abundance of stress associated proteins and metabolites in the absence of elicitors or additional stress treatments. Full article

(This article belongs to the Special Issue Biotic and Abiotic Stress)

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Open AccessArticle

Molecular Characterization of Tb, a New Approach for an Ancient Brucellaphage

by Cai-Zhong Zhu, Hong-Yan Xiong, Jing Han, Bu-Yun Cui, Dong-Ri Piao, Ya-Fei Li, Hai Jiang, Qian Ren, Xiang-Yu Ma, Ya-Ming Chai, Xia Huang, Hong-Yan Zhao and Lan-Yu Li

Int. J. Mol. Sci. 2009, 10(7), 2999-3011; https://doi.org/10.3390/ijms10072999 - 3 Jul 2009

Cited by 9 | Viewed by 13693

Abstract

Tb (Tbilisi), the reference Brucellaphage strain, was classified as a member of the Podoviridae family with icosahedral capsids (57 ± 2 nm diameter) and short tails (32 ± 3 nm long). Brucellaphage DNA was double stranded and unmethylated; its molecular size was 34.5 [...] Read more.

Tb (Tbilisi), the reference Brucellaphage strain, was classified as a member of the Podoviridae family with icosahedral capsids (57 ± 2 nm diameter) and short tails (32 ± 3 nm long). Brucellaphage DNA was double stranded and unmethylated; its molecular size was 34.5 kilobase pairs. Some sequences were found through RAPD analysis, TA cloning technology, and structural proteins were observed by using SDS-PAGE. Thus, the results have laid the foundation for the wider use of Brucellaphage’s basic mechanisms and practical applications. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Organic Analysis of Peridotite Rocks from the Ashadze and Logatchev Hydrothermal Sites

by Marie-Paule Bassez, Yoshinori Takano and Naohiko Ohkouchi

Int. J. Mol. Sci. 2009, 10(7), 2986-2998; https://doi.org/10.3390/ijms10072986 - 3 Jul 2009

Cited by 16 | Viewed by 11933

Abstract

This article presents an experimental analysis of the organic content of two serpentinized peridotite rocks of the terrestrial upper mantle. The samples have been dredged on the floor of the Ashadze and Logatchev hydrothermal sites on the Mid-Atlantic Ridge. In this preliminary analysis, [...] Read more.

This article presents an experimental analysis of the organic content of two serpentinized peridotite rocks of the terrestrial upper mantle. The samples have been dredged on the floor of the Ashadze and Logatchev hydrothermal sites on the Mid-Atlantic Ridge. In this preliminary analysis, amino acids and long chain n-alkanes are identified. They are most probably of biological/microbial origin. Some peaks remain unidentified. Full article

(This article belongs to the Special Issue Origin of Life)

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Open AccessReview

Hyaluronan Benzyl Ester as a Scaffold for Tissue Engineering

by Vincenzo Vindigni, Roberta Cortivo, Laura Iacobellis, Giovanni Abatangelo and Barbara Zavan

Int. J. Mol. Sci. 2009, 10(7), 2972-2985; https://doi.org/10.3390/ijms10072972 - 3 Jul 2009

Cited by 87 | Viewed by 14562

Abstract

Tissue engineering is a multidisciplinary field focused on in vitro reconstruction of mammalian tissues. In order to allow a similar three-dimensional organization of in vitro cultured cells, biocompatible scaffolds are needed. This need has provided immense momentum for research on “smart scaffolds” for [...] Read more.

Tissue engineering is a multidisciplinary field focused on in vitro reconstruction of mammalian tissues. In order to allow a similar three-dimensional organization of in vitro cultured cells, biocompatible scaffolds are needed. This need has provided immense momentum for research on “smart scaffolds” for use in cell culture. One of the most promising materials for tissue engineering and regenerative medicine is a hyaluronan derivative: a benzyl ester of hyaluronan (HYAFF®). HYAFF® can be processed to obtain several types of devices such as tubes, membranes, non-woven fabrics, gauzes, and sponges. All these scaffolds are highly biocompatible. In the human body they do not elicit any adverse reactions and are resorbed by the host tissues. Human hepatocytes, dermal fibroblasts and keratinocytes, chondrocytes, Schwann cells, bone marrow derived mesenchymal stem cells and adipose tissue derived mesenchymal stem cells have been successfully cultured in these meshes. The same scaffolds, in tube meshes, has been applied for vascular tissue engineering that has emerged as a promising technology for the design of an ideal, responsive, living conduit with properties similar to that of native tissue. Full article

(This article belongs to the Special Issue Biocompatibility of Materials)

380 KiB

Open AccessArticle

Characterization and Purification of Polydisperse Reconstituted Lipoproteins and Nanolipoprotein Particles

by Craig D. Blanchette, Brent W. Segelke, Nicholas Fischer, Michele H. Corzett, Edward A. Kuhn, Jenny A. Cappuccio, William Henry Benner, Matthew A. Coleman, Brett A. Chromy, Graham Bench, Paul D. Hoeprich and Todd A. Sulchek

Int. J. Mol. Sci. 2009, 10(7), 2958-2971; https://doi.org/10.3390/ijms10072958 - 2 Jul 2009

Cited by 19 | Viewed by 16326

Abstract

Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, important [...] Read more.

Heterogeneity is a fact that plagues the characterization and application of many self-assembled biological constructs. The importance of obtaining particle homogeneity in biological assemblies is a critical goal, as bulk analysis tools often require identical species for reliable interpretation of the results—indeed, important tools of analysis such as x-ray diffraction typically require over 90% purity for effectiveness. This issue bears particular importance in the case of lipoproteins. Lipid-binding proteins known as apolipoproteins can self assemble with liposomes to form reconstituted high density lipoproteins (rHDLs) or nanolipoprotein particles (NLPs) when used for biotechnology applications such as the solubilization of membrane proteins. Typically, the apolipoprotein and phospholipids reactants are self assembled and even with careful assembly protocols the product often contains heterogeneous particles. In fact, size polydispersity in rHDLs and NLPs published in the literature are frequently observed, which may confound the accurate use of analytical methods. In this article, we demonstrate a procedure for producing a pure, monodisperse NLP subpopulation from a polydisperse self-assembly using size exclusion chromatography (SEC) coupled with high resolution particle imaging by atomic force microscopy (AFM). In addition, NLPs have been shown to self assemble both in the presence and absence of detergents such as cholate, yet the effects of cholate on NLP polydispersity and separation has not been systematically examined. Therefore, we examined the separation properties of NLPs assembled in both the absence and presence of cholate using SEC and native gel electrophoresis. From this analysis, NLPs prepared with and without cholate showed particles with well defined diameters spanning a similar size range. However, cholate was shown to have a dramatic affect on NLP separation by SEC and native gel electrophoresis. Furthermore, under conditions where different sized NLPs were not sufficiently separated or purified by SEC, AFM was used to deconvolute the elution pattern of different sized NLPs. From this analysis we were able to purify an NLP subpopulation to 90% size homogeneity by taking extremely fine elutions from the SEC. With this purity, we generate high quality NLP crystals that were over 100 μm in size with little precipitate, which could not be obtained utilizing the traditional size exclusion techniques. This purification procedure and the methods for validation are broadly applicable to other lipoprotein particles. Full article

(This article belongs to the Special Issue Molecular Self-Assembly)

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251 KiB

Open AccessReview

Applications of Isothermal Titration Calorimetry in Biophysical Studies of G-quadruplexes

by Bruno Pagano, Carlo Andrea Mattia and Concetta Giancola

Int. J. Mol. Sci. 2009, 10(7), 2935-2957; https://doi.org/10.3390/ijms10072935 - 2 Jul 2009

Cited by 77 | Viewed by 14946

Abstract

G-quadruplexes are higher-order nucleic acids structures formed by G-rich sequences that are stabilized by tetrads of hydrogen-bonded guanine bases. Recently, there has been growing interest in the study of G-quadruplexes because of their possible involvement in many biological processes. Isothermal titration calorimetry (ITC) [...] Read more.

G-quadruplexes are higher-order nucleic acids structures formed by G-rich sequences that are stabilized by tetrads of hydrogen-bonded guanine bases. Recently, there has been growing interest in the study of G-quadruplexes because of their possible involvement in many biological processes. Isothermal titration calorimetry (ITC) has been proven to be a useful tool to study the energetic aspects of G-quadruplex interactions. Particularly, ITC has been applied many times to determine the thermodynamic properties of drug-quadruplex interactions to screening among various drugs and to address drug design. In the present review, we will focus on the ITC studies of G-quadruplex structures and their interaction with proteins and drugs and the most significant results will be discussed. Full article

(This article belongs to the Special Issue Isothermal Titration Calorimetry)

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248 KiB

Open AccessArticle

The Dimeric Proto-Ribosome: Structural Details and Possible Implications on the Origin of Life

by Ilana Agmon

Int. J. Mol. Sci. 2009, 10(7), 2921-2934; https://doi.org/10.3390/ijms10072921 - 30 Jun 2009

Cited by 60 | Viewed by 10517

Abstract

A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide [...] Read more.

A symmetric pocket-like entity, composed of two L-shaped RNA units, encircles the peptide synthesis site within the contemporary ribosome. This entity was suggested to be the vestige of a dimeric proto-ribosome, which could have formed spontaneously in the prebiotic world, catalyzing non-coded peptide bond formation and elongation. This structural element, beyond offering the initial step in the evolution of translation, is hypothesized here to be linked to the origin of life. By catalyzing the production of random peptide chains, the proto-ribosome could have enabled the formation of primary enzymes, launching a process of co-evolution of the translation apparatus and the proteins, thus presenting an alternative to the RNA world hypothesis. Full article

(This article belongs to the Special Issue Origin of Life)

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193 KiB

Open AccessArticle

Heats of Mixing Using an Isothermal Titration Calorimeter: Associated Thermal Effects

by Manuel Rodríguez de Rivera, Fabiola Socorro and José S. Matos

Int. J. Mol. Sci. 2009, 10(7), 2911-2920; https://doi.org/10.3390/ijms10072911 - 29 Jun 2009

Cited by 11 | Viewed by 11494

Abstract

The correct determination of the energy generated or absorbed in the sample cell of an Isothermal Titration Calorimeter (ITC) requires a thorough analysis of the calorimetric signal. This means the identification and quantification of any thermal effect inherent to the working method. In [...] Read more.

The correct determination of the energy generated or absorbed in the sample cell of an Isothermal Titration Calorimeter (ITC) requires a thorough analysis of the calorimetric signal. This means the identification and quantification of any thermal effect inherent to the working method. In this work, it is carried out a review on several thermal effects, studied by us in previous work, and which appear when an ITC is used for measuring the heats of mixing of liquids in a continuous mode. These effects are due to: (i) the difference between the temperature of the injected liquid and the temperature of the mixture during the mixing process, (ii) the increase of the liquid volume located in the mixing cell and (iii) the stirring velocity. Besides, methods for the identification and quantification of the mentioned effects are suggested. Full article

(This article belongs to the Special Issue Isothermal Titration Calorimetry)

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417 KiB

Open AccessArticle

Co-localization of Carbonic Anhydrase and Phosphoenol-pyruvate Carboxylase and Localization of Pyruvate Kinase in Roots and Hypocotyls of Etiolated Glycine max Seedlings

by Maria Dimou, Anca Paunescu, Georgios Aivalakis, Emmanouil Flemetakis and Panagiotis Katinakis

Int. J. Mol. Sci. 2009, 10(7), 2896-2910; https://doi.org/10.3390/ijms10072896 - 29 Jun 2009

Cited by 11 | Viewed by 11156

Abstract

We investigated the presence of carbonic anhydrase in root and hypocotyl of etiolated soybean using enzymatic, histochemical, immunohistochemical and in situ hybridization approaches. In parallel, we used in situ hybridization and immunolocaliza-tion to determine the expression pattern and localization of phosphoenolpyruvate [...] Read more.

We investigated the presence of carbonic anhydrase in root and hypocotyl of etiolated soybean using enzymatic, histochemical, immunohistochemical and in situ hybridization approaches. In parallel, we used in situ hybridization and immunolocaliza-tion to determine the expression pattern and localization of phosphoenolpyruvate carboxylase. Their co-localization in the root tip as well as in the central cylinder, suggests that a large fraction of the CO₂ may be re-introduced into C4 compounds. GmPK3 expression, coding for a cytoplasmic isoform of pyruvate kinase, was detected in all different root cell types, suggesting that both phosphoenolpyruvate-utilizing enzymes are involved in phosphoenolpyruvate metabolism in etiolated soybean roots; a case indicative of the necessary flexibility plant metabolism has to adopt in order to compensate various physiological conditions. Full article

(This article belongs to the Section Biochemistry)

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288 KiB

Open AccessReview

Thermodynamics of Surfactants, Block Copolymers and Their Mixtures in Water: The Role of the Isothermal Calorimetry

by Rosario De Lisi, Stefania Milioto and Nicola Muratore

Int. J. Mol. Sci. 2009, 10(7), 2873-2895; https://doi.org/10.3390/ijms10072873 - 29 Jun 2009

Cited by 14 | Viewed by 14140

Abstract

The thermodynamics of conventional surfactants, block copolymers and their mixtures in water was described to the light of the enthalpy function. The two methodologies, i.e. the van’t Hoff approach and the isothermal calorimetry, used to determine the enthalpy of micellization of pure surfactants [...] Read more.

The thermodynamics of conventional surfactants, block copolymers and their mixtures in water was described to the light of the enthalpy function. The two methodologies, i.e. the van’t Hoff approach and the isothermal calorimetry, used to determine the enthalpy of micellization of pure surfactants and block copolymers were described. The van’t Hoff method was critically discussed. The aqueous copolymer+surfactant mixtures were analyzed by means of the isothermal titration calorimetry and the enthalpy of transfer of the copolymer from the water to the aqueous surfactant solutions. Thermodynamic models were presented to show the procedure to extract straightforward molecular insights from the bulk properties. Full article

(This article belongs to the Special Issue Isothermal Titration Calorimetry)

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Int. J. Mol. Sci., Volume 10, Issue 7 (July 2009) – 25 articles , Pages 2873-3268

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