International Journal of Molecular Sciences

141 KiB

Open AccessCorrection

Correction: Vatani, A., et al. Prediction of Standard Enthalpy of Formation by a QSPR Model. Int. J. Mol. Sci. 2007, 8, 407-432.

by Ali Vatani, Mehdi Mehrpooya and Farhad Gharagheizi

Int. J. Mol. Sci. 2009, 10(2), 723; https://doi.org/10.3390/ijms10020723 - 24 Feb 2009

Cited by 1 | Viewed by 9476

Abstract

We found an error in our paper published in the Int. J. Mol. Sci. recently [1]: on page 409, the Equation (2) should be printed as: [...] Full article

190 KiB

Open AccessReview

A Systems Biology Approach to Investigating Apoptotic Stimuli as Effectors of Cell Metabolism: Practical Application of Top-Down Control Analysis to Attached Neurons

by Mika B. Jekabsons

Int. J. Mol. Sci. 2009, 10(2), 702-722; https://doi.org/10.3390/ijms10020702 - 23 Feb 2009

Cited by 3 | Viewed by 10444

Abstract

Reduced glycolytic and mitochondrial respiration rates are common features of apoptosis that may reflect key events contributing to cell death. However, it is unclear to what extent the rate changes can be explained by direct alterations in the kinetics of the participating reactions, [...] Read more.

Reduced glycolytic and mitochondrial respiration rates are common features of apoptosis that may reflect key events contributing to cell death. However, it is unclear to what extent the rate changes can be explained by direct alterations in the kinetics of the participating reactions, as changes in the concentrations of intermediates also affect reaction rates. Direct kinetic changes can be identified, ranked, and compared to the indirect effects mediated by the intermediates using top-down control analysis. Flux changes that are explained primarily by direct effects are likely to be prime targets of the pathways that signal death, and thus important contributors to apoptosis. Control analysis concepts relevant to identifying such effects are reviewed. Metabolic flux measurements are essential for this approach, but can be technically difficult, particularly when using adherent cells such as neurons. A simple method is described that renders such measurements feasible. Full article

(This article belongs to the Special Issue Molecular System Bioenergetics)

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179 KiB

Open AccessReview

Mitochondrial DNA Instability and Metabolic Shift in Human Cancers

by Hsin-Chen Lee and Yau-Huei Wei

Int. J. Mol. Sci. 2009, 10(2), 674-701; https://doi.org/10.3390/ijms10020674 - 23 Feb 2009

Cited by 110 | Viewed by 15570

Abstract

A shift in glucose metabolism from oxidative phosphorylation to glycolysis is one of the biochemical hallmarks of tumor cells. Mitochondrial defects have been proposed to play an important role in the initiation and/or progression of various types of cancer. In the past decade, [...] Read more.

A shift in glucose metabolism from oxidative phosphorylation to glycolysis is one of the biochemical hallmarks of tumor cells. Mitochondrial defects have been proposed to play an important role in the initiation and/or progression of various types of cancer. In the past decade, a wide spectrum of mutations and depletion of mtDNA have been identified in human cancers. Moreover, it has been demonstrated that activation of oncogenes or mutation of tumor suppressor genes, such as p53, can lead to the upregulation of glycolytic enzymes or inhibition of the biogenesis or assembly of respiratory enzyme complexes such as cytochrome c oxidase. These findings may explain, at least in part, the well documented phenomena of elevated glucose uptake and mitochondrial defects in cancers. In this article, we review the somatic mtDNA alterations with clinicopathological correlations in human cancers, and their potential roles in tumorigenesis, cancer progression, and metastasis. The signaling pathways involved in the shift from aerobic metabolism to glycolysis in human cancers are also discussed. Full article

(This article belongs to the Special Issue Molecular System Bioenergetics)

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Open AccessReview

Quantum Dots — Characterization, Preparation and Usage in Biological Systems

by Jana Drbohlavova, Vojtech Adam, Rene Kizek and Jaromir Hubalek

Int. J. Mol. Sci. 2009, 10(2), 656-673; https://doi.org/10.3390/ijms10020656 - 20 Feb 2009

Cited by 263 | Viewed by 24665

Abstract

The use of fluorescent nanoparticles as probes for bioanalytical applications is a highly promising technique because fluorescence-based techniques are very sensitive. Quantum dots (QDs) seem to show the greatest promise as labels for tagging and imaging in biological systems owing to their impressive [...] Read more.

The use of fluorescent nanoparticles as probes for bioanalytical applications is a highly promising technique because fluorescence-based techniques are very sensitive. Quantum dots (QDs) seem to show the greatest promise as labels for tagging and imaging in biological systems owing to their impressive photostability, which allow long-term observations of biomolecules. The usage of QDs in practical applications has started only recently, therefore, the research on QDs is extremely important in order to provide safe and effective biosensing materials for medicine. This review reports on the recent methods for the preparation of quantum dots, their physical and chemical properties, surface modification as well as on some interesting examples of their experimental use. Full article

(This article belongs to the Special Issue Quantum Dots: From Synthesis to Applications in Biomedicine and Life Sciences)

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161 KiB

Open AccessReview

Effect of Nanoparticles on Protein Folding and Fibrillogenesis

by Li Fei and Sarah Perrett

Int. J. Mol. Sci. 2009, 10(2), 646-655; https://doi.org/10.3390/ijms10020646 - 20 Feb 2009

Cited by 166 | Viewed by 17231

Abstract

The large surface area and small size of nanoparticles provide properties and applications that are distinct from those of bulk materials. The ability of nanoparticles to influence protein folding and aggregation is interesting, not only because of the potential beneficial applications, but also [...] Read more.

The large surface area and small size of nanoparticles provide properties and applications that are distinct from those of bulk materials. The ability of nanoparticles to influence protein folding and aggregation is interesting, not only because of the potential beneficial applications, but also the potential risks to human health and the environment. This makes it essential that we understand the effect of nanoparticles on fundamental biological process, like protein folding. Here, we review studies that have examined the effect of nanoparticles on protein folding and aggregation, providing insight both into the mechanisms of these processes and how they may be controlled. Full article

(This article belongs to the Special Issue Protein Folding 2009)

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374 KiB

Open AccessArticle

Genetic Exchange of Multidrug Efflux Pumps among Two Enterobacterial Species with Distinctive Ecological Niches

by Nehaya Al-Karablieh, Helge Weingart and Matthias S. Ullrich

Int. J. Mol. Sci. 2009, 10(2), 629-645; https://doi.org/10.3390/ijms10020629 - 19 Feb 2009

Cited by 12 | Viewed by 11021

Abstract

AcrAB-TolC is the major multidrug efflux system in Enterobacteriaceae recognizing structurally unrelated molecules including antibiotics, dyes, and detergents. Additionally, in Escherichia coli it mediates resistance to bile salts. In the plant pathogen Erwinia amylovora AcrAB-TolC is required for virulence and phytoalexin resistance. Exchange [...] Read more.

AcrAB-TolC is the major multidrug efflux system in Enterobacteriaceae recognizing structurally unrelated molecules including antibiotics, dyes, and detergents. Additionally, in Escherichia coli it mediates resistance to bile salts. In the plant pathogen Erwinia amylovora AcrAB-TolC is required for virulence and phytoalexin resistance. Exchange analysis of AcrAB-TolC was conducted by complementing mutants of both species defective in acrB or tolC with alleles from either species. The acrB and tolC mutants exhibited increased susceptibility profiles for 24 different antibiotics. All mutants were complemented with acrAB or tolC, respectively, regardless of the taxonomic origin of the alleles. Importantly, complementation of E. amylovora mutants with respective E. coli genes restored virulence on apple plants. It was concluded that AcrAB and TolC of both species could interact and that these interactions did not yield in altered functions despite the divergent ecological niches, to which E. coli and E. amylovora have adopted. Full article

(This article belongs to the Special Issue Antimicrobial Agents)

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288 KiB

Open AccessArticle

A New Approach for Characterizing the Intermediate Feature of α-Chymotrypsin Refolding by Hydrophobic Interaction Chromatography

by Congyu Ke, Jianjun Li, Zhenling Liu and Xindu Geng

Int. J. Mol. Sci. 2009, 10(2), 616-628; https://doi.org/10.3390/ijms10020616 - 18 Feb 2009

Cited by 5 | Viewed by 11596

Abstract

A new approach for characterizing the intermediate of urea-denatured α-chymotrypsin (α-Chy) by hydrophobic interaction chromatography (HIC) is presented. The contact surface region (Z, S), affinity (logI), and the character of interaction force (j) of the α-Chy to [...] Read more.

A new approach for characterizing the intermediate of urea-denatured α-chymotrypsin (α-Chy) by hydrophobic interaction chromatography (HIC) is presented. The contact surface region (Z, S), affinity (logI), and the character of interaction force (j) of the α-Chy to the stationary phase of HIC (STHIC) between the intermediate (M) and native (N) states were found to be quite different as urea concentration (C_urea) changes. With the changes in C_urea, a linear relationship between logI and Z was found to exist only for its N state, not for M state, indicating the interaction force between α-Chy in N state to the STHIC to be non-selective, but selective one for its M state. Also, the measured magnitude of both logI and Z in M state is only a fifth of that in N state. All three parameters were employed to distinguish protein in the N state from that in the M state. It would be expected that this result could be employed to distinguish any kind of non-functional protein having correct three-, or four-dimensional molecular structure from their stable M state of any kinds of proteins, and/or other proteins in proteome investigation, separation process of protein, and intensively understanding the intrinsic rule of protein folding in molecular biology. Full article

(This article belongs to the Special Issue Protein Folding 2009)

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285 KiB

Open AccessReview

Biodegradable Polydepsipeptides

by Yakai Feng and Jintang Guo

Int. J. Mol. Sci. 2009, 10(2), 589-615; https://doi.org/10.3390/ijms10020589 - 13 Feb 2009

Cited by 91 | Viewed by 13248

Abstract

This paper reviews the synthesis, characterization, biodegradation and usage of bioresorbable polymers based on polydepsipeptides. The ring-opening polymerization of morpholine-2,5-dione derivatives using organic Sn and enzyme lipase is discussed. The dependence of the macroscopic properties of the block copolymers on their structure is [...] Read more.

This paper reviews the synthesis, characterization, biodegradation and usage of bioresorbable polymers based on polydepsipeptides. The ring-opening polymerization of morpholine-2,5-dione derivatives using organic Sn and enzyme lipase is discussed. The dependence of the macroscopic properties of the block copolymers on their structure is also presented. Bioresorbable polymers based on polydepsipeptides could be used as biomaterials in drug controlled release, tissue engineering scaffolding and shape-memory materials. Full article

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

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686 KiB

Open AccessReview

Folding, Stability and Shape of Proteins in Crowded Environments: Experimental and Computational Approaches

by Antonios Samiotakis, Pernilla Wittung-Stafshede and Margaret S. Cheung

Int. J. Mol. Sci. 2009, 10(2), 572-588; https://doi.org/10.3390/ijms10020572 - 13 Feb 2009

Cited by 63 | Viewed by 13683

Abstract

How the crowded environment inside cells affects folding, stability and structures of proteins is a vital question, since most proteins are made and function inside cells. Here we describe how crowded conditions can be created in vitro and in silico and how we [...] Read more.

How the crowded environment inside cells affects folding, stability and structures of proteins is a vital question, since most proteins are made and function inside cells. Here we describe how crowded conditions can be created in vitro and in silico and how we have used this to probe effects on protein properties. We have found that folded forms of proteins become more compact in the presence of macromolecular crowding agents; if the protein is aspherical, the shape also changes (extent dictated by native-state stability and chemical conditions). It was also discovered that the shape of the macromolecular crowding agent modulates the folding mechanism of a protein; in addition, the extent of asphericity of the protein itself is an important factor in defining its folding speed. Full article

(This article belongs to the Special Issue Protein Folding 2009)

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239 KiB

Open AccessArticle

Evaluation of Various Metallic Coatings on Steel to Mitigate Biofilm Formation

by Hideyuki Kanematsu, Hajime Ikigai and Michiko Yoshitake

Int. J. Mol. Sci. 2009, 10(2), 559-571; https://doi.org/10.3390/ijms10020559 - 12 Feb 2009

Cited by 43 | Viewed by 11750

Abstract

In marine environments and water systems, it is easy for many structures to form biofilms on their surfaces and to be deteriorated due to the corrosion caused by biofilm formation by bacteria. The authors have investigated the antibacterial effects of metallic elements in [...] Read more.

In marine environments and water systems, it is easy for many structures to form biofilms on their surfaces and to be deteriorated due to the corrosion caused by biofilm formation by bacteria. The authors have investigated the antibacterial effects of metallic elements in practical steels so far to solve food-related problems, using Escherichia coli and Staphylococcus aureus. However, from the viewpoint of material deterioration caused by bacteria and their antifouling measures, we should consider the biofilm behavior as aggregate rather than individual bacterium. Therefore, we picked up Pseudomonas aeruginosa and Pseudoalteromonas carageenovara in this study, since they easily form biofilms in estuarine and marine environments. We investigated what kind of metallic elements could inhibit the biofilm formation at first and then discussed how the thin films of those inhibitory elements on steels could affect biofilm formation. The information would lead to the establishment of effective antifouling measures against corrosion in estuarine and marine environments. Full article

(This article belongs to the Special Issue Green Antifouling)

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1176 KiB

Open AccessArticle

Selective Binding, Self-Assembly and Nanopatterning of the Creutz-Taube Ion on Surfaces

by Yuliang Wang, Marya Lieberman, Qingling Hang and Gary Bernstein

Int. J. Mol. Sci. 2009, 10(2), 533-558; https://doi.org/10.3390/ijms10020533 - 12 Feb 2009

Cited by 4 | Viewed by 12310

Abstract

The surface attachment properties of the Creutz-Taube ion, i.e., [(NH₃)₅Ru(pyrazine)Ru(NH₃)₅]⁵⁺, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS). The results indicated that the Creutz-Taube ions only [...] Read more.

The surface attachment properties of the Creutz-Taube ion, i.e., [(NH₃)₅Ru(pyrazine)Ru(NH₃)₅]⁵⁺, on both hydrophilic and hydrophobic types of surfaces were investigated using X-ray photoelectron spectroscopy (XPS). The results indicated that the Creutz-Taube ions only bound to hydrophilic surfaces, such as SiO₂ and –OH terminated organic SAMs on gold substrates. No attachment of the ions on hydrophobic surfaces such as –CH₃ terminated organic SAMs and poly(methylmethacrylate) (PMMA) thin films covered gold or SiO₂ substrates was observed. Further ellipsometric, atomic force microscopy (AFM) and time-dependent XPS studies suggested that the attached cations could form an inorganic analog of the self-assembled monolayer on SiO₂ substrate with a “lying-down” orientation. The strong electrostatic interaction between the highly charged cations and the anionic SiO₂ surface was believed to account for these observations. Based on its selective binding property, patterning of wide (~200 nm) and narrow (~35 nm) lines of the Creutz-Taube ions on SiO₂ surface were demonstrated through PMMA electron resist masks written by electron beam lithography (EBL). Full article

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

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Graphical abstract

381 KiB

Open AccessArticle

Biomass Production Potential of a Wastewater Alga Chlorella vulgaris ARC 1 under Elevated Levels of CO₂ and Temperature

by Senthil Chinnasamy, Balasubramanian Ramakrishnan, Ashish Bhatnagar and Keshav C. Das

Int. J. Mol. Sci. 2009, 10(2), 518-532; https://doi.org/10.3390/ijms10020518 - 05 Feb 2009

Cited by 209 | Viewed by 16526

Abstract

The growth response of Chlorella vulgaris was studied under varying concentrations of carbon dioxide (ranging from 0.036 to 20%) and temperature (30, 40 and 50^oC). The highest chlorophyll concentration (11 µg mL^-1) and biomass (210 µg mL^-1), [...] Read more.

The growth response of Chlorella vulgaris was studied under varying concentrations of carbon dioxide (ranging from 0.036 to 20%) and temperature (30, 40 and 50^oC). The highest chlorophyll concentration (11 µg mL^-1) and biomass (210 µg mL^-1), which were 60 and 20 times more than that of C. vulgaris at ambient CO₂ (0.036%), were recorded at 6% CO₂ level. At 16% CO₂ level, the concentrations of chlorophyll and biomass values were comparable to those at ambient CO₂ but further increases in the CO₂ level decreased both of them. Results showed that the optimum temperature for biomass production was 30^oC under elevated CO₂ (6%). Although increases in temperature above 30^oC resulted in concomitant decrease in growth response, their adverse effects were significantly subdued at elevated CO₂. There were also differential responses of the alga, assessed in terms of NaH¹⁴CO₃ uptake and carbonic anhydrase activity, to increases in temperature at elevated CO₂. The results indicated that Chlorella vulgaris grew better at elevated CO₂ level at 30^oC, albeit with lesser efficiencies at higher temperatures. Full article

(This article belongs to the Section Green Chemistry)

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309 KiB

Open AccessCommunication

Anomalously Strong Effect of the Ion Sign on the Thermochemistry of Hydrogen Bonded Aqueous Clusters of Identical Chemical Composition

by Alexey B. Nadykto, Fangqun Yu and Anas Al Natsheh

Int. J. Mol. Sci. 2009, 10(2), 507-517; https://doi.org/10.3390/ijms10020507 - 05 Feb 2009

Cited by 8 | Viewed by 13490

Abstract

The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H₂O)_i (n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large [...] Read more.

The sign preference of hydrogen bonded aqueous ionic clusters Χ±(H₂O)_i (n =1-5, Χ = F; Cl; Br) has been investigated using the Density Functional Theory and ab initio MP2 method. The present study indicates the anomalously large difference in formation free energies between cations and anions of identical chemical composition. The effect of vibrational anharmonicity on stepwise Gibbs free energy changes has been investigated, and possible uncertainties associated with the harmonic treatment of vibrational spectra have been discussed. Full article

(This article belongs to the Special Issue The Chemical Bond and Bonding)

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858 KiB

Open AccessArticle

Expression of Mipu1 in Response to Myocardial Infarction in Rats

by Guiliang Wang, Xiaoxia Zuo, Junwen Liu, Lei Jiang, Ying Liu, Yazhu Zheng, Bin Zhang and Xianzhong Xiao

Int. J. Mol. Sci. 2009, 10(2), 492-506; https://doi.org/10.3390/ijms10020492 - 03 Feb 2009

Cited by 10 | Viewed by 11197

Abstract

Myocardial ischemic preconditioning up-regulated protein 1 (Mipu1) was cloned in our laboratory. Male Wistar rats were subjected to left anterior coronary artery ligation and sham-operation and sacrificed at 1 h, 3 h, 6 h, 12 h, 24 h, 3 d or 5 d [...] Read more.

Myocardial ischemic preconditioning up-regulated protein 1 (Mipu1) was cloned in our laboratory. Male Wistar rats were subjected to left anterior coronary artery ligation and sham-operation and sacrificed at 1 h, 3 h, 6 h, 12 h, 24 h, 3 d or 5 d after ligation. Expression of Mipu1 mRNA and protein were assessed by Northern blotting, real-time quantitative RT-PCR, In Situ hybridization and Western blotting. Expression of Mipu1 was up-regulated at 3 h and lasted to 12 h with a peak at 6 h. Mipu1 mRNA and protein signals express in the endothelium and myocardium in normal and infarcted heart, mainly in infarcted zone. Fluorescent immunocytochemistry showed that Mipu1 protein was localized to the nuclei of H9c2 myogenic cells and was upregulated after the cells being exposed to H₂O₂. These observations indicates that Mipu1 may play a role in maintaining vascular homeostasis and protecting the myogenic cells from being injured by ischemia-reperfusion or oxidation stress. Full article

(This article belongs to the Section Biochemistry)

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Open AccessReview

Quantum Dots for Live Cell and In Vivo Imaging

by Maureen A. Walling, Jennifer A. Novak and Jason R. E. Shepard

Int. J. Mol. Sci. 2009, 10(2), 441-491; https://doi.org/10.3390/ijms10020441 - 03 Feb 2009

Cited by 425 | Viewed by 38024

Abstract

In the past few decades, technology has made immeasurable strides to enable visualization, identification, and quantitation in biological systems. Many of these technological advancements are occurring on the nanometer scale, where multiple scientific disciplines are combining to create new materials with enhanced properties. [...] Read more.

In the past few decades, technology has made immeasurable strides to enable visualization, identification, and quantitation in biological systems. Many of these technological advancements are occurring on the nanometer scale, where multiple scientific disciplines are combining to create new materials with enhanced properties. The integration of inorganic synthetic methods with a size reduction to the nano-scale has lead to the creation of a new class of optical reporters, called quantum dots. These semiconductor quantum dot nanocrystals have emerged as an alternative to organic dyes and fluorescent proteins, and are brighter and more stable against photobleaching than standard fluorescent indicators. Quantum dots have tunable optical properties that have proved useful in a wide range of applications from multiplexed analysis such as DNA detection and cell sorting and tracking, to most recently demonstrating promise for in vivo imaging and diagnostics. This review provides an in-depth discussion of past, present, and future trends in quantum dot use with an emphasis on in vivo imaging and its related applications. Full article

(This article belongs to the Special Issue Quantum Dots: From Synthesis to Applications in Biomedicine and Life Sciences)

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852 KiB

Open AccessReview

Drosophila melanogaster as a Model Organism of Brain Diseases

by Astrid Jeibmann and Werner Paulus

Int. J. Mol. Sci. 2009, 10(2), 407-440; https://doi.org/10.3390/ijms10020407 - 02 Feb 2009

Cited by 108 | Viewed by 32034

Abstract

Drosophila melanogaster has been utilized to model human brain diseases. In most of these invertebrate transgenic models, some aspects of human disease are reproduced. Although investigation of rodent models has been of significant impact, invertebrate models offer a wide variety of experimental tools [...] Read more.

Drosophila melanogaster has been utilized to model human brain diseases. In most of these invertebrate transgenic models, some aspects of human disease are reproduced. Although investigation of rodent models has been of significant impact, invertebrate models offer a wide variety of experimental tools that can potentially address some of the outstanding questions underlying neurological disease. This review considers what has been gleaned from invertebrate models of neurodegenerative diseases, including Alzheimer’s disease, Parkinson’s disease, metabolic diseases such as Leigh disease, Niemann-Pick disease and ceroid lipofuscinoses, tumor syndromes such as neurofibromatosis and tuberous sclerosis, epilepsy as well as CNS injury. It is to be expected that genetic tools in Drosophila will reveal new pathways and interactions, which hopefully will result in molecular based therapy approaches. Full article

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

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363 KiB

Open AccessArticle

Investigation on the Protective Effect of α-Mannan against the DNA Damage Induced by Aflatoxin B₁ in Mouse Hepatocytes

by Eduardo Madrigal-Santillán, José Antonio Morales-González, Manuel Sánchez-Gutiérrez, Alicia Reyes-Arellano and Eduardo Madrigal-Bujaidar

Int. J. Mol. Sci. 2009, 10(2), 395-406; https://doi.org/10.3390/ijms10020395 - 01 Feb 2009

Cited by 15 | Viewed by 12917

Abstract

Aflatoxin B₁ is a contaminant of agricultural and dairy products that can be related to mutagenic and carcinogenic effects. In this report we explore the capacity of α-mannan (Man) to reduce the DNA damage induced by AFB₁ in mouse hepatocytes. For [...] Read more.

Aflatoxin B₁ is a contaminant of agricultural and dairy products that can be related to mutagenic and carcinogenic effects. In this report we explore the capacity of α-mannan (Man) to reduce the DNA damage induced by AFB₁ in mouse hepatocytes. For this purpose we applied the comet assay to groups of animals which were first administered Man (100, 400 and 700 mg/kg, respectively) and 20 min later 1.0 mg/kg of AFB₁. Liver cells were obtained at 4, 10, and 16 h after the chemical administration and examined. The results showed no protection of the damage induced by AFB₁ with the low dose of the polysaccharide, but they did reveal antigenotoxic activity exerted by the two high doses. In addition, we induced a co-crystallization between both compounds, determined their fusion points and analyzed the molecules by UV spectroscopy. The obtained data suggested the formation of a supramolecular complex between AFB₁ and Man. Full article

(This article belongs to the Special Issue Mycotoxins: Mechanisms of Toxicological Activity - Treatment and Prevention)

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Int. J. Mol. Sci., Volume 10, Issue 2 (February 2009) – 17 articles , Pages 395-723

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