International Journal of Molecular Sciences

206 KiB

Open AccessArticle

Antimicrobial, Cytotoxic and Antioxidant Activities and Determination of the Total Tannin Content of Bark Extracts Endopleura uchi

by Flávio A. S. Politi, João C. P. de Mello, Ketylin F. Migliato, Andréa L. A. Nepomuceno, Raquel R. D. Moreira and Rosemeire C. L. R. Pietro

Int. J. Mol. Sci. 2011, 12(4), 2757-2768; https://doi.org/10.3390/ijms12042757 - 21 Apr 2011

Cited by 32 | Viewed by 12026

Abstract

Endopleura uchi is a typical Amazonian tree and its bark is popularly employed in the preparation of teas against myomas, arthritis, influenza, diarrhea and cancer. In this study, the antioxidant activity, cytotoxicity and antimicrobial activity of five different extracts of the bark, selected [...] Read more.

Endopleura uchi is a typical Amazonian tree and its bark is popularly employed in the preparation of teas against myomas, arthritis, influenza, diarrhea and cancer. In this study, the antioxidant activity, cytotoxicity and antimicrobial activity of five different extracts of the bark, selected by their total tannin content, were assessed. The potential antioxidant activity of the extracts was determined by 2.2-diphenyl-1-picrylhydrazyl radical scavenging assay and the values found were very similar among the extracts and to the standards antioxidants used in the tests. Cytotoxicity analysis in mammalian cells indicated that all the tested extracts exhibited IC₅₀ values higher than the highest concentration used, showing that they do not present a risk when consumed under these conditions. Extract tested against five bacterial strains and one yeast strain did not show satisfactory growth inhibitory activity, and even the extracts that showed some antimicrobial activity were not effective at any dilution to determine the minimum inhibitory concentration. The results may serve as a reference for subsequent works, since such reference values described in the literature for the bark of E. uchi. Full article

(This article belongs to the Section Biochemistry)

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168 KiB

Open AccessArticle

Antimicrobial Activities of Hexane Extract and Decussatin from Stembark Extract of Ficus congensis

by Chinwendum Stephenie Alaribe, Francis Shode, Herbert A. B. Coker, Gloria Ayoola, Adesegun Sunday, Nisha Singh and Silva Iwuanyanwu

Int. J. Mol. Sci. 2011, 12(4), 2750-2756; https://doi.org/10.3390/ijms12042750 - 21 Apr 2011

Cited by 8 | Viewed by 7728

Abstract

Ficus congensis (Moraceae) is used traditionally in the treatment of various diseases including infectious diseases, infertility, and gastrointestinal disorders. Investigation of hexane extract of the stem bark using chromatographic techniques led to isolation of a xanthone, 1-hydroxy-3,7,8-trimethoxyxanthone (Decussatin). The compound was elucidated based [...] Read more.

Ficus congensis (Moraceae) is used traditionally in the treatment of various diseases including infectious diseases, infertility, and gastrointestinal disorders. Investigation of hexane extract of the stem bark using chromatographic techniques led to isolation of a xanthone, 1-hydroxy-3,7,8-trimethoxyxanthone (Decussatin). The compound was elucidated based on spectroscopic methods such as nuclear magnetic resonance (NMR), UV, IR, and mass spectrometry (MS). Decussatin and the hexane extract were screened in vitro for antibacterial and antifungal activities using broth microdilution (MHB) and disc Agar diffusion (DAD) techniques against Escheichia coli, Bacilus substilis, Klebsiela pneumonia, Staphylococcus aureus, Aspergillus fumigatus, Trichophyton mentagrophytes, Trichophyton rubrum and Candida albicans. Hexane extracts showed potent antibacterial activity against E. coli and B. subtilis with minimum inhibitory concentrations (MIC) of 8 mg/mL and 5 mg/mL, respectively, while Decussatin of the highest concentration (8 mg/mL) used in this study showed no appreciable antimicrobial activity. Only hexane extract was active against C. albicans with a MIC of 1 mg/mL. Full article

(This article belongs to the Section Biochemistry)

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832 KiB

Open AccessReview

Database Survey of Anti-Inflammatory Plants in South America: A Review

by Gedson Rodrigues de Morais Lima, Camila de Albuquerque Montenegro, Cynthia Layse Ferreira de Almeida, Petrônio Filgueiras de Athayde-Filho, José Maria Barbosa-Filho and Leônia Maria Batista

Int. J. Mol. Sci. 2011, 12(4), 2692-2749; https://doi.org/10.3390/ijms12042692 - 21 Apr 2011

Cited by 31 | Viewed by 12028

Abstract

Inflammation is a complex event linked to tissue damage whether by bacteria, physical trauma, chemical, heat or any other phenomenon. This physiological response is coordinated largely by a variety of chemical mediators that are released from the epithelium, the immunocytes and nerves of [...] Read more.

Inflammation is a complex event linked to tissue damage whether by bacteria, physical trauma, chemical, heat or any other phenomenon. This physiological response is coordinated largely by a variety of chemical mediators that are released from the epithelium, the immunocytes and nerves of the lamina propria. However, if the factor that triggers the inflammation persists, the inflammation can become relentless, leading to an intensification of the lesion. The present work is a literature survey of plant extracts from the South American continent that have been reported to show anti-inflammatory activity. This review refers to 63 bacterial families of which the following stood out: Asteraceae, Fabaceae, Euphorbiaceae, Apocynaceae and Celastraceae, with their countries, parts used, types of extract used, model bioassays, organisms tested and their activity. Full article

(This article belongs to the Section Biochemistry)

759 KiB

Open AccessArticle

Preparation and Physicochemical Properties of 10-Hydroxycamptothecin (HCPT) Nanoparticles by Supercritical Antisolvent (SAS) Process

by Xiuhua Zhao, Yuangang Zu, Ru Jiang, Ying Wang, Yong Li, Qingyong Li, Dongmei Zhao, Baishi Zu, Baoyou Zhang, Zhiqiang Sun and Xiaonan Zhang

Int. J. Mol. Sci. 2011, 12(4), 2678-2691; https://doi.org/10.3390/ijms12042678 - 20 Apr 2011

Cited by 22 | Viewed by 9611

Abstract

The goal of the present work was to study the feasibility of 10-hydroxycamptothecin (HCPT) nanoparticle preparation using supercritical antisolvent (SAS) precipitation. The influences of various experimental factors on the mean particle size (MPS) of HCPT nanoparticles were investigated. The optimum micronization conditions are [...] Read more.

The goal of the present work was to study the feasibility of 10-hydroxycamptothecin (HCPT) nanoparticle preparation using supercritical antisolvent (SAS) precipitation. The influences of various experimental factors on the mean particle size (MPS) of HCPT nanoparticles were investigated. The optimum micronization conditions are determined as follows: HCPT solution concentration 0.5 mg/mL, the flow rate ratio of CO₂ and HCPT solution 19.55, precipitation temperature 35 °C and precipitation pressure 20 MPa. Under the optimum conditions, HCPT nanoparticles with a MPS of 180 ± 20.3 nm were obtained. Moreover, the HCPT nanoparticles obtained were characterized by Scanning electron microscopy, Dynamic light scattering, Fourier-transform infrared spectroscopy, High performance liquid chromatography-mass spectrometry, X-ray diffraction and Differential scanning calorimetry analyses. The physicochemical characterization results showed that the SAS process had not induced degradation of HCPT. Finally, the dissolution rates of HCPT nanoparticles were investigated and the results proved that there is a significant increase in dissolution rate compared to unprocessed HCPT. Full article

(This article belongs to the Section Materials Science)

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338 KiB

Open AccessArticle

Genetic Variation in Safflower (Carthamus tinctorious L.) for Seed Quality-Related Traits and Inter-Simple Sequence Repeat (ISSR) Markers

by Pooran Golkar, Ahmad Arzani and Abdolmajid M. Rezaei

Int. J. Mol. Sci. 2011, 12(4), 2664-2677; https://doi.org/10.3390/ijms12042664 - 19 Apr 2011

Cited by 69 | Viewed by 9271

Abstract

Safflower (Carthamus tinctorious L.) is an oilseed crop that is valued as a source of high quality vegetable oil. The genetic diversity of 16 safflower genotypes originated from different geographical regions of Iran and some with exotic origin were evaluated. Eight [...] Read more.

Safflower (Carthamus tinctorious L.) is an oilseed crop that is valued as a source of high quality vegetable oil. The genetic diversity of 16 safflower genotypes originated from different geographical regions of Iran and some with exotic origin were evaluated. Eight different seed quality-related traits including fatty acid composition of seed oil (stearic acid, palmitic acid, oleic acid and linoleic acid), the contents of, oil, protein, fiber and ash in its seeds, as well as 20 inter-simple sequence repeat (ISSR) polymorphic primers were used in this study. Analysis of variance showed significant variation in genotypes for the seed quality-related traits. Based on ISSR markers, a total of 204 bands were amplified and 149 bands (about 70%) of these were polymorphic. Cluster analysis based on either biochemical or molecular markers classified the genotypes into four groups, showing some similarities between molecular and biochemical markers for evaluated genotypes. A logical similarity between the genotype clusters based on molecular data with their geographical origins was observed. Full article

(This article belongs to the Section Biochemistry)

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346 KiB

Open AccessArticle

In Vivo Anti-Tumor Activity of Polypeptide HM-3 Modified by Different Polyethylene Glycols (PEG)

by Zhendong Liu, Yinling Ren, Li Pan and Han-Mei Xu

Int. J. Mol. Sci. 2011, 12(4), 2650-2663; https://doi.org/10.3390/ijms12042650 - 19 Apr 2011

Cited by 21 | Viewed by 9596

Abstract

HM-3, designed by our laboratory, is a polypeptide composed of 18 amino acids. Pharmacodynamic studies in vivo and in vitro indicated that HM-3 could inhibit endothelial cell migration and angiogenesis, thereby inhibiting tumor growth. However, the half-life of HM-3 is short. In this [...] Read more.

HM-3, designed by our laboratory, is a polypeptide composed of 18 amino acids. Pharmacodynamic studies in vivo and in vitro indicated that HM-3 could inhibit endothelial cell migration and angiogenesis, thereby inhibiting tumor growth. However, the half-life of HM-3 is short. In this study, we modified HM-3 with different polyethylene glycols (PEG) in order to reduce the plasma clearance rate, extend the half-life in the body, maintain a high concentration of HM-3 in the blood and increase the therapeutic efficiency. HM-3 was modified with four different types of PEG with different molecular weights (ALD-mPEG₅_k, ALD-mPEG₁₀_k, SC-mPEG₁₀_k and SC-mPEG₂₀_k), resulting in four modified products (ALD-mPEG₅_k-HM-3, ALD-mPEG₁₀_k-HM-3, SC-mPEG₁₀_k-HM-3 and SC-mPEG₂₀_k-HM-3, respectively). Anti-tumor activity of these four modified HM-3 was determined in BALB/c mice with Taxol as a positive control and normal saline as a negative control. Tumor weight inhibition rates of mice treated with Taxol, HM-3, ALD-mPEG₅_k-HM-3, ALD-mPEG₁₀_k-HM-3, SC-mPEG₁₀_k-HM-3 and SC-mPEG₂₀_k-HM-3 were 44.50%, 43.92%, 37.95%, 31.64%, 20.27% and 50.23%, respectively. Tumor inhibition rates in the Taxol, HM-3 and SC-mPEG₂₀_k-HM-3 groups were significantly higher than that in the negative control group. The efficiency of tumor inhibition in the SC-mPEG₂₀_k-HM-3 group (drug treatment frequency: once per two days) was better than that in the HM-3 group (drug treatment frequency: twice per day). In addition, tumor inhibition rate in the SC-mPEG₂₀_k-HM-3 group was higher than that in the taxol group. We conclude that SC-mPEG₂₀_k-HM-3 had a low plasma clearance rate and long half-life, resulting in high anti-tumor therapeutic efficacy in vivo. Therefore, SC-mPEG₂₀_k-HM-3 could be potentially developed as new anti-tumor drugs. Full article

(This article belongs to the Special Issue Conjugated Polymers)

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170 KiB

Open AccessArticle

Infrared Assisted Production of 3,4-Dihydro-2(1H)-pyridones in Solvent-Free Conditions

by M. Olivia Noguez, Vanessa Marcelino, Hortensia Rodríguez, Osnieski Martín, Joel O. Martínez, Gabriel A. Arroyo, Francisco J. Pérez, Margarita Suárez and René Miranda

Int. J. Mol. Sci. 2011, 12(4), 2641-2649; https://doi.org/10.3390/ijms12042641 - 18 Apr 2011

Cited by 26 | Viewed by 10088

Abstract

A green approach for the synthesis of a set of ten 4-aryl substituted-5-alcoxy carbonyl-6-methyl-3,4-dihydro-2(1H)-pyridones using Meldrum’s acid has been devised, the absence of solvent and the activation with infrared irradiation in addition to a multicomponent protocol are the main reaction conditions. [...] Read more.

A green approach for the synthesis of a set of ten 4-aryl substituted-5-alcoxy carbonyl-6-methyl-3,4-dihydro-2(1H)-pyridones using Meldrum’s acid has been devised, the absence of solvent and the activation with infrared irradiation in addition to a multicomponent protocol are the main reaction conditions. The transformations proceeded with moderated yields (50–75%) with a reasonable reaction rate (3 h). It is worth noting that two novel molecules of the new class of the bis-3,4-dihydropyridones were also obtained. In addition, a comparison without the use of infrared irradiation was performed. Full article

(This article belongs to the Section Green Chemistry)

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Graphical abstract

218 KiB

Open AccessArticle

Assessment of Acetylcholinesterase Activity Using Indoxylacetate and Comparison with the Standard Ellman’s Method

by Miroslav Pohanka, Martina Hrabinova, Kamil Kuca and Jean-Pierre Simonato

Int. J. Mol. Sci. 2011, 12(4), 2631-2640; https://doi.org/10.3390/ijms12042631 - 18 Apr 2011

Cited by 134 | Viewed by 16711

Abstract

Assay of acetylcholinesterase (AChE) activity plays an important role in diagnostic, detection of pesticides and nerve agents, in vitro characterization of toxins and drugs including potential treatments for Alzheimer’s disease. These experiments were done in order to determine whether indoxylacetate could be an [...] Read more.

Assay of acetylcholinesterase (AChE) activity plays an important role in diagnostic, detection of pesticides and nerve agents, in vitro characterization of toxins and drugs including potential treatments for Alzheimer’s disease. These experiments were done in order to determine whether indoxylacetate could be an adequate chromogenic reactant for AChE assay evaluation. Moreover, the results were compared to the standard Ellman’s method. We calculated Michaelis constant Km (2.06 × 10⁻⁴ mol/L for acetylthiocholine and 3.21 × 10⁻³ mol/L for indoxylacetate) maximum reaction velocity V_max (4.97 × 10⁻⁷ kat for acetylcholine and 7.71 × 10⁻⁸ kat for indoxylacetate) for electric eel AChE. In a second part, inhibition values were plotted for paraoxon, and reactivation efficacy was measured for some standard oxime reactivators: obidoxime, pralidoxime (2-PAM) and HI-6. Though indoxylacetate is split with lower turnover rate, this compound appears as a very attractive reactant since it does not show any chemical reactivity with oxime antidots and thiol used for the Ellman’s method. Thus it can be advantageously used for accurate measurement of AChE activity. Suitability of assay for butyrylcholinesterase activity assessment is also discussed. Full article

(This article belongs to the Section Biochemistry)

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588 KiB

Open AccessArticle

Antioxidant Effects of the Ethanol Extract from Flower of Camellia japonica via Scavenging of Reactive Oxygen Species and Induction of Antioxidant Enzymes

by Mei Jing Piao, Eun Sook Yoo, Young Sang Koh, Hee Kyoung Kang, Junoh Kim, Yong Jin Kim, Hak Hee Kang and Jin Won Hyun

Int. J. Mol. Sci. 2011, 12(4), 2618-2630; https://doi.org/10.3390/ijms12042618 - 18 Apr 2011

Cited by 52 | Viewed by 12244

Abstract

The aim of this study was to investigate the antioxidant properties of the ethanol extract of the flower of Camellia japonica (Camellia extract). Camellia extract exhibited 1,1-diphenyl-2-picrylhydrazyl radical and intracellular reactive oxygen species (ROS) scavenging activity in human HaCaT keratinocytes. In addition, [...] Read more.

The aim of this study was to investigate the antioxidant properties of the ethanol extract of the flower of Camellia japonica (Camellia extract). Camellia extract exhibited 1,1-diphenyl-2-picrylhydrazyl radical and intracellular reactive oxygen species (ROS) scavenging activity in human HaCaT keratinocytes. In addition, Camellia extract scavenged superoxide anion generated by xanthine/xanthine oxidase and hydroxyl radical generated by the Fenton reaction (FeSO₄ + H₂O₂) in a cell-free system, which was detected by electron spin resonance spectrometry. Furthermore, Camellia extract increased the protein expressions and activity of cellular antioxidant enzymes, such as superoxide dismutase, catalase and glutathione peroxidase. These results suggest that Camellia extract exhibits antioxidant properties by scavenging ROS and enhancing antioxidant enzymes. Camellia extract contained quercetin, quercetin-3-O-glucoside, quercitrin and kaempferol, which are antioxidant compounds. Full article

(This article belongs to the Section Biochemistry)

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916 KiB

Open AccessArticle

Effect of Temperature on the Physico-Chemical Properties of a Room Temperature Ionic Liquid (1-Methyl-3-pentylimidazolium Hexafluorophosphate) with Polyethylene Glycol Oligomer

by Tzi-Yi Wu, Bor-Kuan Chen, Lin Hao, Yu-Chun Peng and I-Wen Sun

Int. J. Mol. Sci. 2011, 12(4), 2598-2617; https://doi.org/10.3390/ijms12042598 - 18 Apr 2011

Cited by 31 | Viewed by 10285

Abstract

A systematic study of the effect of composition on the thermo-physical properties of the binary mixtures of 1-methyl-3-pentyl imidazolium hexafluorophosphate [MPI][PF₆] with poly(ethylene glycol) (PEG) [M_w = 400] is presented. The excess molar volume, refractive index deviation, viscosity deviation, and [...] Read more.

A systematic study of the effect of composition on the thermo-physical properties of the binary mixtures of 1-methyl-3-pentyl imidazolium hexafluorophosphate [MPI][PF₆] with poly(ethylene glycol) (PEG) [M_w = 400] is presented. The excess molar volume, refractive index deviation, viscosity deviation, and surface tension deviation values were calculated from these experimental density, ρ, refractive index, n, viscosity, η, and surface tension, γ, over the whole concentration range, respectively. The excess molar volumes are negative and continue to become increasingly negative with increasing temperature; whereas the viscosity and surface tension deviation are negative and become less negative with increasing temperature. The surface thermodynamic functions, such as surface entropy, enthalpy, as well as standard molar entropy, Parachor, and molar enthalpy of vaporization for pure ionic liquid, have been derived from the temperature dependence of the surface tension values. Full article

(This article belongs to the Section Materials Science)

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839 KiB

Open AccessReview

Droplets Formation and Merging in Two-Phase Flow Microfluidics

by Hao Gu, Michel H. G. Duits and Frieder Mugele

Int. J. Mol. Sci. 2011, 12(4), 2572-2597; https://doi.org/10.3390/ijms12042572 - 15 Apr 2011

Cited by 249 | Viewed by 29372

Abstract

Two-phase flow microfluidics is emerging as a popular technology for a wide range of applications involving high throughput such as encapsulation, chemical synthesis and biochemical assays. Within this platform, the formation and merging of droplets inside an immiscible carrier fluid are two key [...] Read more.

Two-phase flow microfluidics is emerging as a popular technology for a wide range of applications involving high throughput such as encapsulation, chemical synthesis and biochemical assays. Within this platform, the formation and merging of droplets inside an immiscible carrier fluid are two key procedures: (i) the emulsification step should lead to a very well controlled drop size (distribution); and (ii) the use of droplet as micro-reactors requires a reliable merging. A novel trend within this field is the use of additional active means of control besides the commonly used hydrodynamic manipulation. Electric fields are especially suitable for this, due to quantitative control over the amplitude and time dependence of the signals, and the flexibility in designing micro-electrode geometries. With this, the formation and merging of droplets can be achieved on-demand and with high precision. In this review on two-phase flow microfluidics, particular emphasis is given on these aspects. Also recent innovations in microfabrication technologies used for this purpose will be discussed. Full article

(This article belongs to the Special Issue Microfluidics)

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631 KiB

Open AccessArticle

Simultaneous Structural Identification of Natural Products in Fractions of Crude Extract of the Rare Endangered Plant Anoectochilus roxburghii Using ¹H NMR/RRLC-MS Parallel Dynamic Spectroscopy

by Xiao-Xue Wang, Jiu-Ming He, Chun-Lan Wang, Rui-Ping Zhang, Wen-Yi He, Shun-Xing Guo, Rui-Xiang Sun and Zeper Abliz

Int. J. Mol. Sci. 2011, 12(4), 2556-2571; https://doi.org/10.3390/ijms12042556 - 15 Apr 2011

Cited by 16 | Viewed by 11376

Abstract

Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to ¹H NMR and rapid resolution liquid chromatography-mass [...] Read more.

Nuclear magnetic resonance/liquid chromatography-mass spectroscopy parallel dynamic spectroscopy (NMR/LC-MS PDS) is a method aimed at the simultaneous structural identification of natural products in complex mixtures. In this study, the method is illustrated with respect to ¹H NMR and rapid resolution liquid chromatography-mass spectroscopy (RRLC-MS) data, acquired from the crude extract of Anoectochilus roxburghii, which was separated into a series of fractions with the concentration of constituent dynamic variation using reversed-phase preparative chromatography. Through fraction ranges and intensity changing profiles in ¹H NMR/RRLC–MS PDS spectrum, ¹H NMR and the extracted ion chromatogram (XIC) signals deriving from the same individual constituent, were correlated due to the signal amplitude co-variation resulting from the concentration variation of constituents in a series of incompletely separated fractions. ¹H NMR/RRLC-MS PDS was then successfully used to identify three types of natural products, including eight flavonoids, four organic acids and p-hydroxybenzaldehyde, five of which have not previously been reported in Anoectochilus roxburghii. In addition, two groups of co-eluted compounds were successfully identified. The results prove that this approach should be of benefit in the unequivocal structural determination of a variety of classes of compounds from extremely complex mixtures, such as herbs and biological samples, which will lead to improved efficiency in the identification of new potential lead compounds. Full article

(This article belongs to the Section Biochemistry)

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412 KiB

Open AccessArticle

An Oligodeoxynucleotide with Promising Modulation Activity for the Proliferation and Activation of Osteoblast

by Zhiyuan Feng, Yuqin Shen, Liying Wang, Lin Cheng, Jing Wang, Quanshun Li, Wei Shi and Xinhua Sun

Int. J. Mol. Sci. 2011, 12(4), 2543-2555; https://doi.org/10.3390/ijms12042543 - 15 Apr 2011

Cited by 15 | Viewed by 8482

Abstract

The paper explored the regulatory role of oligodeoxynucleotides (ODNs) with specific sequences in the proliferation and activation of osteoblast, using human osteoblast-like cell line MG 63 as the model. Through the administration of ODNs to MG 63 cells at a concentration of 1.0 [...] Read more.

The paper explored the regulatory role of oligodeoxynucleotides (ODNs) with specific sequences in the proliferation and activation of osteoblast, using human osteoblast-like cell line MG 63 as the model. Through the administration of ODNs to MG 63 cells at a concentration of 1.0 µg/mL, ODN MT01 with positive effects on proliferation and activation of osteoblast was selected from 11 different ODNs by methyl thiazolyl tetrazolium (MTT) assay and alkaline phosphatase (ALP) activity measurement. To get a deeper insight into the molecular mechanism, effects of ODN MT01 treatment on the expression level of Sp7, runx-2, collagen-I, osteoprotegerin (OPG) and RANK ligand (RANKL) were determined using quantitative real time PCR and Western blotting. Remarkably, the mRNA and protein expression levels of Sp7, runx-2, collagen-I and OPG were improved after ODN MT01 treatment. Meanwhile, the protein expression level of RANKL was dramatically decreased. These results suggested that ODN MT01 had a significant impact in facilitating osteogenic proliferation and activation, and provided a direct evidence for the notion that single strand ODN could regulate the balance of bone formation and resorption, and thus was of great potential in the rebuilding of alveolar bone. Full article

(This article belongs to the Section Biochemistry)

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634 KiB

Open AccessReview

Functioning Nanomachines Seen in Real-Time in Living Bacteria Using Single-Molecule and Super-Resolution Fluorescence Imaging

by Sheng-Wen Chiu and Mark C. Leake

Int. J. Mol. Sci. 2011, 12(4), 2518-2542; https://doi.org/10.3390/ijms12042518 - 15 Apr 2011

Cited by 40 | Viewed by 12802

Abstract

Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the [...] Read more.

Molecular machines are examples of “pre-established” nanotechnology, driving the basic biochemistry of living cells. They encompass an enormous range of function, including fuel generation for chemical processes, transport of molecular components within the cell, cellular mobility, signal transduction and the replication of the genetic code, amongst many others. Much of our understanding of such nanometer length scale machines has come from in vitro studies performed in isolated, artificial conditions. Researchers are now tackling the challenges of studying nanomachines in their native environments. In this review, we outline recent in vivo investigations on nanomachines in model bacterial systems using state-of-the-art genetics technology combined with cutting-edge single-molecule and super-resolution fluorescence microscopy. We conclude that single-molecule and super-resolution fluorescence imaging provide powerful tools for the biochemical, structural and functional characterization of biological nanomachines. The integrative spatial, temporal, and single-molecule data obtained simultaneously from fluorescence imaging open an avenue for systems-level single-molecule cellular biophysics and in vivo biochemistry. Full article

(This article belongs to the Special Issue Molecular Machines and Nanomachines)

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Graphical abstract

291 KiB

Open AccessArticle

Global Transcriptomic Profiling Using Small Volumes of Whole Blood: A Cost-Effective Method for Translational Genomic Biomarker Identification in Small Animals

by Meagan M. Fricano, Amy C. Ditewig, Paul M. Jung, Michael J. Liguori, Eric A. G. Blomme and Yi Yang

Int. J. Mol. Sci. 2011, 12(4), 2502-2517; https://doi.org/10.3390/ijms12042502 - 13 Apr 2011

Cited by 9 | Viewed by 10583

Abstract

Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin [...] Read more.

Blood is an ideal tissue for the identification of novel genomic biomarkers for toxicity or efficacy. However, using blood for transcriptomic profiling presents significant technical challenges due to the transcriptomic changes induced by ex vivo handling and the interference of highly abundant globin mRNA. Most whole blood RNA stabilization and isolation methods also require significant volumes of blood, limiting their effective use in small animal species, such as rodents. To overcome these challenges, a QIAzol-based RNA stabilization and isolation method (QSI) was developed to isolate sufficient amounts of high quality total RNA from 25 to 500 μL of rat whole blood. The method was compared to the standard PAXgene Blood RNA System using blood collected from rats exposed to saline or lipopolysaccharide (LPS). The QSI method yielded an average of 54 ng total RNA per μL of rat whole blood with an average RNA Integrity Number (RIN) of 9, a performance comparable with the standard PAXgene method. Total RNA samples were further processed using the NuGEN Ovation Whole Blood Solution system and cDNA was hybridized to Affymetrix Rat Genome 230 2.0 Arrays. The microarray QC parameters using RNA isolated with the QSI method were within the acceptable range for microarray analysis. The transcriptomic profiles were highly correlated with those using RNA isolated with the PAXgene method and were consistent with expected LPS-induced inflammatory responses. The present study demonstrated that the QSI method coupled with NuGEN Ovation Whole Blood Solution system is cost-effective and particularly suitable for transcriptomic profiling of minimal volumes of whole blood, typical of those obtained with small animal species. Full article

(This article belongs to the Special Issue Toxicogenomics)

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Open AccessArticle

Enhancement of Salinity Tolerance during Rice Seed Germination by Presoaking with Hemoglobin

by Sheng Xu, Bing Hu, Ziyi He, Fei Ma, Jianfei Feng, Wenbiao Shen and Jie Yang

Int. J. Mol. Sci. 2011, 12(4), 2488-2501; https://doi.org/10.3390/ijms12042488 - 12 Apr 2011

Cited by 55 | Viewed by 10645

Abstract

Salinity stress is an important environmental constraint limiting the productivity of many crops worldwide. In this report, experiments were conducted to investigate the effects of seed presoaking by bovine hemoglobin, an inducer of heme oxygenase-1 (HO-1), on salinity tolerance in rice (Oryza [...] Read more.

Salinity stress is an important environmental constraint limiting the productivity of many crops worldwide. In this report, experiments were conducted to investigate the effects of seed presoaking by bovine hemoglobin, an inducer of heme oxygenase-1 (HO-1), on salinity tolerance in rice (Oryza sativa) plants. The results showed that different concentrations of the hemoglobin (0.01, 0.05, 0.2, 1.0, and 5.0 g/L) differentially alleviated the inhibition of rice seed germination and thereafter seedling shoot growth caused by 100 mM NaCl stress, and the responses of 1.0 g/L hemoglobin was the most obvious. Further analyses showed that application of hemoglobin not only increased the HO-1 gene expression, but also differentially induced catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD) activities or transcripts, thus decreasing the lipid peroxidation in germinating rice seeds subjected to salt stress. Compared with non-hemoglobin treatment, hemoglobin presoaking also increased the potassium (K) to sodium (Na) ratio both in the root and shoot parts after salinity stress. The effect is specific for HO-1 since the potent HO-1 inhibitor zinc protoporphyrin IX (ZnPPIX) blocked the positive actions of hemoglobin on seed germination and seedling shoot growth. Overall, these results suggested that hemoglobin performs an advantageous role in enhancement of salinity tolerance during rice seed germination. Full article

(This article belongs to the Section Biochemistry)

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378 KiB

Open AccessArticle

YueF Overexpression Inhibits Cell Proliferation Partly through p21^WAF1/Cip1 Upregulation in Renal Cell Carcinoma

by Hsuan-Wei Huang, Jian-Ping Peng and Jie Zhang

Int. J. Mol. Sci. 2011, 12(4), 2477-2487; https://doi.org/10.3390/ijms12042477 - 11 Apr 2011

Cited by 5 | Viewed by 8054

Abstract

YueF is a novel putative tumor suppressor gene that can inhibit proliferation and induce apoptosis in hepatoma cells, but its role in renal cell carcinoma (RCC) remains unclear. Here, we examined the expression of the YueF gene in RCC tissues and the effect [...] Read more.

YueF is a novel putative tumor suppressor gene that can inhibit proliferation and induce apoptosis in hepatoma cells, but its role in renal cell carcinoma (RCC) remains unclear. Here, we examined the expression of the YueF gene in RCC tissues and the effect of YueF on cell proliferation in RCC 786-0 cells. The results showed that YueF was expressed at high levels in normal kidney tissues and cell lines but was reduced or absent in RCC tissues and 786-0 cells. Lentivirus-mediated YueF overexpression in RCC 786-0 cells caused cell-cycle arrest in the G1 phase and dramatically reduced proliferation in culture. YueF overexpression resulted in increased protein levels of p53 and p21^WAF1/Cip1, whereas the protein levels of cyclin D1 and pRb were decreased. The proliferation defects caused by YueF overexpression could be partially rescued by the expression of p21 siRNA. These findings suggest a critical role for p21 in the YueF-induced growth inhibition of 786-0 cells and provide novel insights into the mechanism underlying the tumor-suppressive action of YueF. Full article

(This article belongs to the Section Biochemistry)

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Open AccessArticle

Economic Optimized Medium for Tensio-Active Agent Production by Candida sphaerica UCP0995 and Application in the Removal of Hydrophobic Contaminant from Sand

by Juliana M. Luna, Raquel D. Rufino, Clarissa D.C. Albuquerque, Leonie A. Sarubbo and Galba M. Campos-Takaki

Int. J. Mol. Sci. 2011, 12(4), 2463-2476; https://doi.org/10.3390/ijms12042463 - 8 Apr 2011

Cited by 43 | Viewed by 8796

Abstract

Statistical experimental designs and response surface methodology were employed to optimize the concentrations of agroindustrial residues as soybean oil (SORR) from refinery, and corn steep liquor (CSL) from corn industry, for tensio-active agent produced by Candida sphaerica UCP 0995. Three 2²full [...] Read more.

Statistical experimental designs and response surface methodology were employed to optimize the concentrations of agroindustrial residues as soybean oil (SORR) from refinery, and corn steep liquor (CSL) from corn industry, for tensio-active agent produced by Candida sphaerica UCP 0995. Three 2²full factorial design were applied sequentially to investigate the effects of the concentrations and interactions of soybean oil refinery residue and corn steep liquor on the surface tension of free-cell culture broth for 144 h. Two 2² central composite designs and response surface methodology were adopted to derive a statistical model to measure the effect of SORR and CSL on the surface tension of the free-cell culture broth for 144 h. The regression equation obtained from the experimental data using a central composite design was solved, and by analyzing the response surface contour plots, the optimal concentrations of the constituents of the medium were determined: 8.63% v/v (≈9% v/v) of SORR and 8.80% v/v (≈9% v/v) CSL. The minimum surface tension predicted and experimentally confirmed was 25.25 mN/m. The new biosurfactant, denominated Lunasan, recovered 95% of motor oil adsorbed in a sand sample, thus showing great potential for use in bioremediation processes, especially in the petroleum industry. Full article

(This article belongs to the Special Issue Biosurfactants)

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438 KiB

Open AccessArticle

A Quantitative Structure-Property Relationship (QSPR) Study of Aliphatic Alcohols by the Method of Dividing the Molecular Structure into Substructure

by Fengping Liu, Chenzhong Cao and Bin Cheng

Int. J. Mol. Sci. 2011, 12(4), 2448-2462; https://doi.org/10.3390/ijms12042448 - 7 Apr 2011

Cited by 17 | Viewed by 8743

Abstract

A quantitative structure–property relationship (QSPR) analysis of aliphatic alcohols is presented. Four physicochemical properties were studied: boiling point (BP), n-octanol–water partition coefficient (lg P_OW), water solubility (lg W) and the chromatographic retention indices (RI) on different polar stationary phases. [...] Read more.

A quantitative structure–property relationship (QSPR) analysis of aliphatic alcohols is presented. Four physicochemical properties were studied: boiling point (BP), n-octanol–water partition coefficient (lg P_OW), water solubility (lg W) and the chromatographic retention indices (RI) on different polar stationary phases. In order to investigate the quantitative structure–property relationship of aliphatic alcohols, the molecular structure ROH is divided into two parts, R and OH to generate structural parameter. It was proposed that the property is affected by three main factors for aliphatic alcohols, alkyl group R, substituted group OH, and interaction between R and OH. On the basis of the polarizability effect index (PEI), previously developed by Cao, the novel molecular polarizability effect index (MPEI) combined with odd-even index (OEI), the sum eigenvalues of bond-connecting matrix (SX_1CH) previously developed in our team, were used to predict the property of aliphatic alcohols. The sets of molecular descriptors were derived directly from the structure of the compounds based on graph theory. QSPR models were generated using only calculated descriptors and multiple linear regression techniques. These QSPR models showed high values of multiple correlation coefficient (R > 0.99) and Fisher-ratio statistics. The leave-one-out cross-validation demonstrated the final models to be statistically significant and reliable. Full article

(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)

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Open AccessArticle

Reactive Oxygen Species Released from Hypoxic Hepatocytes Regulates MMP-2 Expression in Hepatic Stellate Cells

by Jing Li, Renhua Fan, Susu Zhao, Leilei Liu, Shanshan Guo, Nan Wu, Wandong Zhang and Pingsheng Chen

Int. J. Mol. Sci. 2011, 12(4), 2434-2447; https://doi.org/10.3390/ijms12042434 - 7 Apr 2011

Cited by 46 | Viewed by 10128

Abstract

Hypoxia is a common environmental stress factor and is associated with fibrogenesis. Matrix metalloproteinase-2 (MMP-2), produced by hepatic stellate cells (HSCs), plays an important role in liver fibrogenesis. However, inconsistent results have been reported on the impact of hypoxia on MMP-2 expression and [...] Read more.

Hypoxia is a common environmental stress factor and is associated with fibrogenesis. Matrix metalloproteinase-2 (MMP-2), produced by hepatic stellate cells (HSCs), plays an important role in liver fibrogenesis. However, inconsistent results have been reported on the impact of hypoxia on MMP-2 expression and activity in HSCs. We speculated that cell–cell interaction is involved in the regulation of MMP-2 expression and activity at low oxygen level in vivo. Therefore, in this report we investigated the mechanism by which hypoxic hepatocytes regulates MMP-2 expression in HSCs. Our results showed that the conditioned medium from hypoxia-treated rat hepatocytes strongly induced the expression of MMP-2 mRNA and protein in rat HSC-T6 cells. Reduced glutathione neutralized ROS released from hypoxic hepatocytes, leading to reduced MMP-2 expression in HSC-T6 cells. In addition, phospho-IκB-α protein level was increased in HSC-T6 cells treated with hypoxia conditioned medium, and NF-κB signaling inhibitor inhibited MMP-2 expression in HSC-T6 cells. Taken together, our data suggest that ROS is an important factor released by hypoxic hepatocytes to regulate MMP-2 expression in HSCs, and NF-κB signaling is crucially involved in ROS-induced MMP-2 expression in HSCs. Our findings suggest that strategies aimed at antagonizing the generation of ROS in hypoxic hepatocytes and inhibiting NF-κB signaling in HSCs may represent novel therapeutic options for liver fibrosis. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Nutritional Deficiencies and Phospholipid Metabolism

by María S. Gimenez, Liliana B. Oliveros and Nidia N. Gomez

Int. J. Mol. Sci. 2011, 12(4), 2408-2433; https://doi.org/10.3390/ijms12042408 - 6 Apr 2011

Cited by 42 | Viewed by 12465

Abstract

Phospholipids are important components of the cell membranes of all living species. They contribute to the physicochemical properties of the membrane and thus influence the conformation and function of membrane-bound proteins, such as receptors, ion channels, and transporters and also influence cell function [...] Read more.

Phospholipids are important components of the cell membranes of all living species. They contribute to the physicochemical properties of the membrane and thus influence the conformation and function of membrane-bound proteins, such as receptors, ion channels, and transporters and also influence cell function by serving as precursors for prostaglandins and other signaling molecules and modulating gene expression through the transcription activation. The components of the diet are determinant for cell functionality. In this review, the effects of macro and micronutrients deficiency on the quality, quantity and metabolism of different phospholipids and their distribution in cells of different organs is presented. Alterations in the amount of both saturated and polyunsaturated fatty acids, vitamins A, E and folate, and other micronutrients, such as zinc and magnesium, are discussed. In all cases we observe alterations in the pattern of phospholipids, the more affected ones being phosphatidylcholine, phosphatidylethanolamine and sphingomyelin. The deficiency of certain nutrients, such as essential fatty acids, fat-soluble vitamins and some metals may contribute to a variety of diseases that can be irreversible even after replacement with normal amount of the nutrients. Usually, the sequelae are more important when the deficiency is present at an early age. Full article

(This article belongs to the Special Issue Phospholipids: Molecular Sciences)

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Open AccessArticle

Optimization of Antibacterial Activity of Perilla frutescens var. acuta Leaf against Staphylococcus aureus Using Evolutionary Operation Factorial Design Technique

by Dae-Hyun Kim, Young-Chan Kim and Ung-Kyu Choi

Int. J. Mol. Sci. 2011, 12(4), 2395-2407; https://doi.org/10.3390/ijms12042395 - 6 Apr 2011

Cited by 36 | Viewed by 9347

Abstract

This study was undertaken to optimize extraction using evolutionary operation-factorial (EVOP) design technique to elicit the antibacterial activity of Perilla frutescens var. acuta leaf against Staphylococcus aureus ATCC6538. Higher antibacterial activity was achieved at higher extraction temperature and over a longer extraction time. [...] Read more.

This study was undertaken to optimize extraction using evolutionary operation-factorial (EVOP) design technique to elicit the antibacterial activity of Perilla frutescens var. acuta leaf against Staphylococcus aureus ATCC6538. Higher antibacterial activity was achieved at higher extraction temperature and over a longer extraction time. Antibacterial activity was not affected by differentiation of the ethanol concentration in the extraction solvent. The maximum antibacterial activity of ethanolic extract of P. frutescens leaf against S. aureus was obtained at 75 °C (R= −0.7904^**) extraction temperature, 24 h (R= −0.7273^**) extraction time, and 45% (R = −0.0635) ethanol concentration. The population of S. aureus was decreased from 7.535 log CFU/mL in the initial set to 4.865 log CFU/mL in the third set by EVOP factorial design technique, as well as to 2.600 log CFU/mL by extraction with ethyl acetate. Further, the ethyl acetate extract revealed the highest phenolic contents (111.3 ± 8.6 mg% of dry sample) as compared to the other extracts. Also, the scanning electronic microscopic study of the ethanolic extract of P. frutescens revealed potential detrimental effect on the morphology of S. aureus. Full article

(This article belongs to the Section Biochemistry)

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436 KiB

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Effect of 2-Hydroxypropyl-β-cyclodextrin on Solubility of Sparingly Soluble Drug Derivatives of Anthranilic Acid

by Urszula Domańska, Aleksandra Pelczarska and Aneta Pobudkowska

Int. J. Mol. Sci. 2011, 12(4), 2383-2394; https://doi.org/10.3390/ijms12042383 - 6 Apr 2011

Cited by 31 | Viewed by 9346

Abstract

Guest-host complex formation of three drug derivatives of anthranilic acid, mefenamic acid, niflumic acid, and flufenamic acid with 2-hydroxypropyl-β-cyclodextrin (2HP-β-CD) in aqueous solutions was investigated using “Phase solubility study” with UV-vis spectrophotometry. Solubility of sparingly soluble drugs has been [...] Read more.

Guest-host complex formation of three drug derivatives of anthranilic acid, mefenamic acid, niflumic acid, and flufenamic acid with 2-hydroxypropyl-β-cyclodextrin (2HP-β-CD) in aqueous solutions was investigated using “Phase solubility study” with UV-vis spectrophotometry. Solubility of sparingly soluble drugs has been improved by addition of 2HP-β-CD at two temperatures 298.15 K and 310.15 K and two pH values 2 and 7. The influence of different 2HP-β-CD concentration on solubility of drugs at different pH and temperatures has been investigated. The 2HP-β-CD-drug complex stability constants (K_s), and dissociations constants (K_d), as well as the thermodynamic parameters of reaction, i.e., the free energy change (ΔG), the enthalpy change (ΔH) and the entropy change (ΔS), were determined. The experimental data indicated formation of 1:1 inclusion complexes, which were found effective binders increasing the solubility of drugs. Full article

(This article belongs to the Section Biochemistry)

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483 KiB

Open AccessReview

Individual Variations in Inorganic Arsenic Metabolism Associated with AS3MT Genetic Polymorphisms

by Tetsuro Agusa, Junko Fujihara, Haruo Takeshita and Hisato Iwata

Int. J. Mol. Sci. 2011, 12(4), 2351-2382; https://doi.org/10.3390/ijms12042351 - 4 Apr 2011

Cited by 88 | Viewed by 12615

Abstract

Individual variations in inorganic arsenic metabolism may influence the toxic effects. Arsenic (+3 oxidation state) methyltransferase (AS3MT) that can catalyze the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to trivalent arsenical, may play a role in arsenic metabolism in humans. Since [...] Read more.

Individual variations in inorganic arsenic metabolism may influence the toxic effects. Arsenic (+3 oxidation state) methyltransferase (AS3MT) that can catalyze the transfer of a methyl group from S-adenosyl-L-methionine (AdoMet) to trivalent arsenical, may play a role in arsenic metabolism in humans. Since the genetic polymorphisms of AS3MT gene may be associated with the susceptibility to inorganic arsenic toxicity, relationships of several single nucleotide polymorphisms (SNPs) in AS3MT with inorganic arsenic metabolism have been investigated. Here, we summarize our recent findings and other previous studies on the inorganic arsenic metabolism and AS3MT genetic polymorphisms in humans. Results of genotype dependent differences in arsenic metabolism for most of SNPs in AS3MT were Inconsistent throughout the studies. Nevertheless, two SNPs, AS3MT 12390 (rs3740393) and 14458 (rs11191439) were consistently related to arsenic methylation regardless of the populations examined for the analysis. Thus, these SNPs may be useful indicators to predict the arsenic metabolism via methylation pathways. Full article

(This article belongs to the Section Molecular Toxicology)

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Open AccessArticle

Lead, Cadmium and Cobalt (Pb, Cd, and Co) Leaching of Glass-Clay Containers by pH Effect of Food

by Carmen Valadez-Vega, Clara Zúñiga-Pérez, Samuel Quintanar-Gómez, José A. Morales-González, Eduardo Madrigal-Santillán, José Roberto Villagómez-Ibarra, María Teresa Sumaya-Martínez and Juan Diego García-Paredes

Int. J. Mol. Sci. 2011, 12(4), 2336-2350; https://doi.org/10.3390/ijms12042336 - 4 Apr 2011

Cited by 37 | Viewed by 13121

Abstract

Recent studies have shown that handcrafted glass-clay containers are a health risk because they can be contaminated by heavy metals, which can be transferred to food, thus reaching the human body to potentially cause illness. Therefore, in the present work, we evaluate the [...] Read more.

Recent studies have shown that handcrafted glass-clay containers are a health risk because they can be contaminated by heavy metals, which can be transferred to food, thus reaching the human body to potentially cause illness. Therefore, in the present work, we evaluate the leaching of lead, cadmium, and cobalt from glass-clay containers into two types of food: tomato sauce (salsa), and chickpea puree. The containers were obtained from four regions in the Mexican state of Hidalgo. Repetitive extractions from the containers were carried out to quantify the leaching of the heavy metals into the salsa, the chickpea puree, and acetic acid using the technique proposed by the USFDA. The results show that greater use of the containers leads to more leaching of heavy metals into both types of food and into the acetic acid, with the greatest metal extraction recorded for the Ixmiquilpan vessels. These results indicate that the metals present in the glass-clay containers leach into the food and that increased reuse increases the risk to the people who use them in food preparation. Full article

(This article belongs to the Section Biochemistry)

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0 pages, 769 KiB

Open AccessArticle

RETRACTED: Dextran Sulfate Sodium Inhibits Alanine Synthesis in Caco-2 Cells

by Zhong Ye, Darya O. Mishchuk, Natasha S. Stephens and Carolyn M. Slupsky

Int. J. Mol. Sci. 2011, 12(4), 2325-2335; https://doi.org/10.3390/ijms12042325 - 4 Apr 2011

Cited by 1 | Viewed by 10542 | Retraction

Abstract

To understand and characterize the pathogenic mechanisms of inflammatory bowel disease, dextran sulfate sodium (DSS) has been used to induce acute and chronic colitis in animal models by causing intestinal epithelium damage. The mechanism of action of DSS in producing this outcome is [...] Read more.

To understand and characterize the pathogenic mechanisms of inflammatory bowel disease, dextran sulfate sodium (DSS) has been used to induce acute and chronic colitis in animal models by causing intestinal epithelium damage. The mechanism of action of DSS in producing this outcome is not well understood. In an effort to understand how DSS might impact epithelial cell metabolism, we studied the intestinal epithelial cell line Caco-2 incubated with 1% DSS over 56 hours using ¹H NMR spectroscopy. We observed no difference in cell viability as compared to control cultures, and an approximately 1.5-fold increase in IL-6 production upon incubation with 1% DSS. The effect on Caco-2 cell metabolism as measured through changes in the concentration of metabolites in the cell supernatant included a three-fold decrease in the concentration of alanine. Given that the concentrations of other amino acids in the cell culture supernatant were not different between treated and control cultures over 56 hours suggest that DSS inhibits alanine synthesis, specifically alanine aminotransferase, without affecting other key metabolic pathways. The importance of alanine aminotransferase in inflammatory bowel disease is discussed. Full article

(This article belongs to the Special Issue Advances in Molecular Toxicology)

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301 KiB

Open AccessArticle

Molecular Recognition of Arginine by Supramolecular Complexation with Calixarene Crown Ether Based on Surface Plasmon Resonance

by Hongxia Chen, Limin Gu, Yongmei Yin, Kwangnak Koh and Jaebeom Lee

Int. J. Mol. Sci. 2011, 12(4), 2315-2324; https://doi.org/10.3390/ijms12042315 - 4 Apr 2011

Cited by 31 | Viewed by 11365

Abstract

Arginine plays an important role in cell division and the functioning of the immune system. We describe a novel method by which arginine can be identified using an artificial monolayer based on surface plasmon resonance (SPR). The affinity of arginine binding its recognition [...] Read more.

Arginine plays an important role in cell division and the functioning of the immune system. We describe a novel method by which arginine can be identified using an artificial monolayer based on surface plasmon resonance (SPR). The affinity of arginine binding its recognition molecular was compared to that of lysine. In fabrication of an arginine sensing interface, a calix[4]crown ether monolayer was anchored onto a gold surface and then characterized by Fourier Transform infrared reflection absorption spectroscopy, atomic force microscopy, and cyclic voltammetry. The interaction between arginine and its host compound was investigated by SPR. The calix[4]crown ether was found to assemble as a monolayer on the gold surface. Recognition of calix[4]crown monolayer was assessed by the selective binding of arginine. Modification of the SPR chip with the calix[4]crown monolayer provides a reliable and simple experimental platform for investigation of arginine under aqueous conditions. Full article

(This article belongs to the Section Molecular Recognition)

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725 KiB

Open AccessArticle

Characterization of a Deswapped Triple Mutant Bovine Odorant Binding Protein

by Eugenia Polverini, Paolo Lardi, Alberto Mazzini, Robert T. Sorbi, Conti Virna, Roberto Ramoni and Roberto Favilla

Int. J. Mol. Sci. 2011, 12(4), 2294-2314; https://doi.org/10.3390/ijms12042294 - 4 Apr 2011

Cited by 4 | Viewed by 8325

Abstract

The stability and functionality of GCC-bOBP, a monomeric triple mutant of bovine odorant binding protein, was investigated, in the presence of denaturant and in acidic pH conditions, by both protein and 1-aminoanthracene ligand fluorescence measurements, and compared to that of both bovine and [...] Read more.

The stability and functionality of GCC-bOBP, a monomeric triple mutant of bovine odorant binding protein, was investigated, in the presence of denaturant and in acidic pH conditions, by both protein and 1-aminoanthracene ligand fluorescence measurements, and compared to that of both bovine and porcine wild type homologues. Complete reversibility of unfolding was observed, though refolding was characterized by hysteresis. Molecular dynamics simulations, performed to detect possible structural changes of the monomeric scaffold related to the presence of the ligand, pointed out the stability of the β-barrel lipocalin scaffold. Full article

(This article belongs to the Special Issue Protein Folding 2011)

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547 KiB

Open AccessReview

Glass Formation, Chemical Properties and Surface Analysis of Cu-Based Bulk Metallic Glasses

by Chunling Qin, Weimin Zhao and Akihisa Inoue

Int. J. Mol. Sci. 2011, 12(4), 2275-2293; https://doi.org/10.3390/ijms12042275 - 4 Apr 2011

Cited by 13 | Viewed by 9398

Abstract

This paper reviews the influence of alloying elements Mo, Nb, Ta and Ni on glass formation and corrosion resistance of Cu-based bulk metallic glasses (BMGs). In order to obtain basic knowledge for application to the industry, corrosion resistance of the Cu–Hf–Ti–(Mo, Nb, Ta, [...] Read more.

This paper reviews the influence of alloying elements Mo, Nb, Ta and Ni on glass formation and corrosion resistance of Cu-based bulk metallic glasses (BMGs). In order to obtain basic knowledge for application to the industry, corrosion resistance of the Cu–Hf–Ti–(Mo, Nb, Ta, Ni) and Cu–Zr–Ag–Al–(Nb) bulk glassy alloy systems in various solutions are reported in this work. Moreover, X-ray photoelectron spectroscopy (XPS) analysis is performed to clarify the surface-related chemical characteristics of the alloy before and after immersion in the solutions; this has lead to a better understanding of the correlation between the surface composition and the corrosion resistance. Full article

(This article belongs to the Special Issue Advances in Bulk Metallic Glasses)

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305 KiB

Open AccessReview

Multi-Step Usage of in Vivo Models During Rational Drug Design and Discovery

by Charles H. Williams and Charles C. Hong

Int. J. Mol. Sci. 2011, 12(4), 2262-2274; https://doi.org/10.3390/ijms12042262 - 1 Apr 2011

Cited by 41 | Viewed by 12251

Abstract

In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a [...] Read more.

In this article we propose a systematic development method for rational drug design while reviewing paradigms in industry, emerging techniques and technologies in the field. Although the process of drug development today has been accelerated by emergence of computational methodologies, it is a herculean challenge requiring exorbitant resources; and often fails to yield clinically viable results. The current paradigm of target based drug design is often misguided and tends to yield compounds that have poor absorption, distribution, metabolism, and excretion, toxicology (ADMET) properties. Therefore, an in vivo organism based approach allowing for a multidisciplinary inquiry into potent and selective molecules is an excellent place to begin rational drug design. We will review how organisms like the zebrafish and Caenorhabditis elegans can not only be starting points, but can be used at various steps of the drug development process from target identification to pre-clinical trial models. This systems biology based approach paired with the power of computational biology; genetics and developmental biology provide a methodological framework to avoid the pitfalls of traditional target based drug design. Full article

(This article belongs to the Special Issue A Systematic Development Method for Rational Drug Design)

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Int. J. Mol. Sci., Volume 12, Issue 4 (April 2011) – 42 articles , Pages 2088-2768

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