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Int. J. Mol. Sci., Volume 13, Issue 10 (October 2012), Pages 12153-13763

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Open AccessArticle Effects of Intramolecular Distance between Amyloidogenic Domains on Amyloid Aggregation
Int. J. Mol. Sci. 2012, 13(10), 12169-12181; doi:10.3390/ijms131012169
Received: 10 August 2012 / Revised: 13 September 2012 / Accepted: 13 September 2012 / Published: 25 September 2012
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Abstract
Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical
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Peptide/protein aggregation is implicated in many amyloid diseases. Some amyloidogenic peptides/proteins, such as those implicated in Alzheimer’s and Parkinson’s diseases, contain multiple amyloidogenic domains connected by “linker” sequences displaying high propensities to form turn structures. Recent studies have demonstrated the importance of physicochemical properties of each amino acid contained in the polypeptide sequences in amyloid aggregation. However, effects on aggregation related to the intramolecular distance between amyloidogenic domains, which may be determined by a linker length, have yet to be examined. In the study presented here, we created peptides containing two copies of KFFE, a simple four-residue amyloidogenic domain, connected by GS-rich linker sequences with different lengths yet similar physicochemical properties. Our experimental results indicate that aggregation occurred most rapidly when KFFE domains were connected by a linker of an intermediate length. Our experimental findings were consistent with estimated entropic contribution of a linker length toward formation of (partially) structured intermediates on the aggregation pathway. Moreover, inclusion of a relatively short linker was found to inhibit formation of aggregates with mature fibril morphology. When the results are assimilated, our study demonstrates that intramolecular distance between amyloidogenic domains is an important yet overlooked factor affecting amyloid aggregation. Full article
(This article belongs to the Special Issue Molecular Self-Assembly 2012)
Open AccessArticle SIG1, a Sigma Factor for the Chloroplast RNA Polymerase, Differently Associates with Multiple DNA Regions in the Chloroplast Chromosomes in Vivo
Int. J. Mol. Sci. 2012, 13(10), 12182-12194; doi:10.3390/ijms131012182
Received: 1 June 2012 / Revised: 5 September 2012 / Accepted: 11 September 2012 / Published: 25 September 2012
Cited by 8 | PDF Full-text (1332 KB) | HTML Full-text | XML Full-text
Abstract
Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts,
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Chloroplasts have their own DNA and gene expression systems. Transcription in chloroplasts is regulated by two types of RNA polymerase, nuclear-encoded plastid RNA polymerase (NEP) and plastid-encoded plastid RNA polymerase (PEP), and multiple sigma factors for PEP. To study transcriptional regulation in chloroplasts, a molecular genetic approach has extensively been used. However, this method may include indirect effects, and it cannot be applied to the analysis of factors essential to survival. These limitations make understanding specific regulation by transcription factors difficult. Chromatin immunoprecipitation (ChIP) is a powerful and useful tool for obtaining information on transcription-factor binding sites; it can directly detect dynamic changes in their interaction patterns in vivo. To further understand transcriptional regulation in chloroplasts, we here established a ChIP-based method in Arabidopsis thaliana and analyzed the binding pattern of a chloroplast sigma factor, SIG1. We found that SIG1 specifically binds to newly identified target promoters as well as to a set of promoters of genes whose mRNA expression is dependent on OsSIG1 in rice and that this binding changed in response to high-light stress. These results suggested that the ChIP-based approach is very useful in understanding transcriptional regulation of chloroplast genes and can overcome several problems posed by conventional methods. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Four Novel Cellulose Synthase (CESA) Genes from Birch (Betula platyphylla Suk.) Involved in Primary and Secondary Cell Wall Biosynthesis
Int. J. Mol. Sci. 2012, 13(10), 12195-12212; doi:10.3390/ijms131012195
Received: 6 June 2012 / Revised: 7 September 2012 / Accepted: 11 September 2012 / Published: 25 September 2012
Cited by 8 | PDF Full-text (369 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cellulose synthase (CESA), which is an essential catalyst for the generation of plant cell wall biomass, is mainly encoded by the CesA gene family that contains ten or more members. In this study; four full-length cDNAs encoding CESA were isolated from Betula
[...] Read more.
Cellulose synthase (CESA), which is an essential catalyst for the generation of plant cell wall biomass, is mainly encoded by the CesA gene family that contains ten or more members. In this study; four full-length cDNAs encoding CESA were isolated from Betula platyphylla Suk., which is an important timber species, using RT-PCR combined with the RACE method and were named as BplCesA3, −4, −7 and −8. These deduced CESAs contained the same typical domains and regions as their Arabidopsis homologs. The cDNA lengths differed among these four genes, as did the locations of the various protein domains inferred from the deduced amino acid sequences, which shared amino acid sequence identities ranging from only 63.8% to 70.5%. Real-time RT-PCR showed that all four BplCesAs were expressed at different levels in diverse tissues. Results indicated that BplCESA8 might be involved in secondary cell wall biosynthesis and floral development. BplCESA3 appeared in a unique expression pattern and was possibly involved in primary cell wall biosynthesis and seed development; it might also be related to the homogalacturonan synthesis. BplCESA7 and BplCESA4 may be related to the formation of a cellulose synthase complex and participate mainly in secondary cell wall biosynthesis. The extremely low expression abundance of the four BplCESAs in mature pollen suggested very little involvement of them in mature pollen formation in Betula. The distinct expression pattern of the four BplCesAs suggested they might participate in developments of various tissues and that they are possibly controlled by distinct mechanisms in Betula. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Interferon-β1b Increases Th2 Response in Neuromyelitis Optica
Int. J. Mol. Sci. 2012, 13(10), 12213-12223; doi:10.3390/ijms131012213
Received: 6 August 2012 / Revised: 12 September 2012 / Accepted: 20 September 2012 / Published: 25 September 2012
Cited by 2 | PDF Full-text (348 KB) | HTML Full-text | XML Full-text
Abstract
A Japanese randomized controlled study showed that Interferon â (IFN-â1b) therapy is clinically effective in decreasing the frequency of attacks in multiple sclerosis (MS), even in optico-spinal MS (OSMS). However, recent studies have shown that IFN-â (IFN-â1a/IFN-â1b) treatment was not effective in neuromyelitis
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A Japanese randomized controlled study showed that Interferon â (IFN-â1b) therapy is clinically effective in decreasing the frequency of attacks in multiple sclerosis (MS), even in optico-spinal MS (OSMS). However, recent studies have shown that IFN-â (IFN-â1a/IFN-â1b) treatment was not effective in neuromyelitis optica (NMO) patients and that the diminished benefit of IFN-â treatment in NMO may be due to different immune responses to IFN-â. We determined longitudinally the expression of CCR5, CXCR3 and CCR4 on CD4+ T and CD8+ T cells in the blood from patients with NMO and MS treated with IFN-â1b. During a 12-month period of IFN-â1b therapy, the annualized relapse rate decreased in MS patients but not in NMO patients. There was no significant difference in the expression of the chemokine receptors between NMO and MS at baseline. The percentages of CD4+CCR5+ and CD4+CXCR3+ T cells, representative of the Th1 response, were decreased in both NMO and MS after treatment. The percentage of CD4+CCR4+ T cells, representative of the Th2 response, was decreased in MS, but those for NMO was significantly increased compared with the pretreatment levels. Our results indicate that IFN-â1b-induced up-modulation of the Th2 response in NMO patients may be the source of differences in the therapeutic response to IFN-â1b therapy. In the present study, Th2 predominance is involved in the pathogenesis of NMO. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessArticle The Effect of Postoperative Hyperbaric Oxygen Treatment on Intra-Abdominal Adhesions in Rats
Int. J. Mol. Sci. 2012, 13(10), 12224-12231; doi:10.3390/ijms131012224
Received: 13 August 2012 / Revised: 3 September 2012 / Accepted: 17 September 2012 / Published: 25 September 2012
Cited by 4 | PDF Full-text (750 KB) | HTML Full-text | XML Full-text
Abstract
Abdominal adhesions, whether caused by peritoneal trauma, radiation, infection, or a congenital condition, are associated with a wide range of complications. These complications include chronic abdominal or pelvic pain, infertility, and adhesive small bowel obstruction. Such adhesions render re-operation difficult, with attendant risks
[...] Read more.
Abdominal adhesions, whether caused by peritoneal trauma, radiation, infection, or a congenital condition, are associated with a wide range of complications. These complications include chronic abdominal or pelvic pain, infertility, and adhesive small bowel obstruction. Such adhesions render re-operation difficult, with attendant risks of inadvertent enterostomy and increased operation time. The purpose of this study was to investigate the potential of hyperbaric oxygen (HBO) therapy in the prevention of abdominal adhesions in an experimental animal study. A laparotomy was performed on Wistar rats to induce the formation of adhesions on the cecum and the intra-abdominal area (1 ´ 2 cm). A superficial layer of the underlying muscle from the right abdominal wall was also shaved and prepared for aseptic surgery. The rats were divided into four groups according to the duration of HBO therapy; five additional groups were designated according to the conditions of HBO therapy. When the rats were evaluated according to adhesion area and grade, a statistically significant difference was observed between the control and HBO treatment groups (p < 0.005). Results from this study suggest that HBO treatment could reduce adhesion formation; and further suggest that HBO therapy may have therapeutic potential in the treatment of postoperative peritoneal adhesion. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Biocatalytic Synthesis of Poly(δ-Valerolactone) Using a Thermophilic Esterase from Archaeoglobus fulgidus as Catalyst
Int. J. Mol. Sci. 2012, 13(10), 12232-12241; doi:10.3390/ijms131012232
Received: 26 July 2012 / Revised: 24 August 2012 / Accepted: 7 September 2012 / Published: 25 September 2012
Cited by 11 | PDF Full-text (218 KB) | HTML Full-text | XML Full-text
Abstract
The ring-opening polymerization of δ-valerolactone catalyzed by a thermophilic esterase from the archaeon Archaeoglobus fulgidus was successfully conducted in organic solvents. The effects of enzyme concentration, temperature, reaction time and reaction medium on monomer conversion and product molecular weight were systematically evaluated. Through
[...] Read more.
The ring-opening polymerization of δ-valerolactone catalyzed by a thermophilic esterase from the archaeon Archaeoglobus fulgidus was successfully conducted in organic solvents. The effects of enzyme concentration, temperature, reaction time and reaction medium on monomer conversion and product molecular weight were systematically evaluated. Through the optimization of reaction conditions, poly(δ-valerolactone) was produced in 97% monomer conversion, with a number-average molecular weight of 2225 g/mol, in toluene at 70 °C for 72 h. This paper has produced a new biocatalyst for the synthesis of poly(δ-valerolactone), and also deeper insight has been gained into the mechanism of thermophilic esterase-catalyzed ring-opening polymerization. Full article
(This article belongs to the Special Issue Enzyme Optimization and Immobilization)
Open AccessArticle Visible Light-Induced Degradation of Methylene Blue in the Presence of Photocatalytic ZnS and CdS Nanoparticles
Int. J. Mol. Sci. 2012, 13(10), 12242-12258; doi:10.3390/ijms131012242
Received: 4 July 2012 / Revised: 27 August 2012 / Accepted: 4 September 2012 / Published: 25 September 2012
Cited by 43 | PDF Full-text (4214 KB) | HTML Full-text | XML Full-text
Abstract
ZnS and CdS nanoparticles were prepared by a simple microwave irradiation method under mild conditions. The obtained nanoparticles were characterized by XRD, TEM and EDX. The results indicated that high purity of nanosized ZnS and CdS was successfully obtained with cubic and hexagonal
[...] Read more.
ZnS and CdS nanoparticles were prepared by a simple microwave irradiation method under mild conditions. The obtained nanoparticles were characterized by XRD, TEM and EDX. The results indicated that high purity of nanosized ZnS and CdS was successfully obtained with cubic and hexagonal crystalline structures, respectively. The band gap energies of ZnS and CdS nanoparticles were estimated using UV-visible absorption spectra to be about 4.22 and 2.64 eV, respectively. Photocatalytic degradation of methylene blue was carried out using physical mixtures of ZnS and CdS nanoparticles under a 500-W halogen lamp of visible light irradiation. The residual concentration of methylene blue solution was monitored using UV-visible absorption spectrometry. From the study of the variation in composition of ZnS:CdS, a composition of 1:4 (by weight) was found to be very efficient for degradation of methylene blue. In this case the degradation efficiency of the photocatalyst nanoparticles after 6 h irradiation time was about 73% with a reaction rate of 3.61 × 103 min−1. Higher degradation efficiency and reaction rate were achieved by increasing the amount of photocatalyst and initial pH of the solution. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Development of 22 Polymorphic Microsatellite Loci for the Critically Endangered Morato’s Digger Toad, Proceratophrys moratoi
Int. J. Mol. Sci. 2012, 13(10), 12259-12267; doi:10.3390/ijms131012259
Received: 22 August 2012 / Revised: 29 August 2012 / Accepted: 3 September 2012 / Published: 25 September 2012
Cited by 1 | PDF Full-text (188 KB) | HTML Full-text | XML Full-text
Abstract
The Morato’s digger toad (Proceratophrys moratoi) inhabits Brazilian moist savannas and is critically endangered due to its very limited geographic distribution, reduced number of isolated populations, and evidence of population decline and local extinctions. With the objective of providing tools for
[...] Read more.
The Morato’s digger toad (Proceratophrys moratoi) inhabits Brazilian moist savannas and is critically endangered due to its very limited geographic distribution, reduced number of isolated populations, and evidence of population decline and local extinctions. With the objective of providing tools for the genetic study of the species, 22 polymorphic microsatellite loci were isolated and screened using DNA extracted from samples of oral mucosa cells obtained from 113 individuals representing five remnant P. moratoi populations in the Brazilian state of São Paulo. These markers presented 2–18 alleles per locus, polymorphism information content (PIC) of 0.02–0.87, observed heterozygosity of 0.02–0.96 and expected heterozygosity of 0.02–0.87. Three of the loci deviated significantly from Hardy–Weinberg equilibrium in one of the populations, possibly due to the presence of null alleles. Significant linkage disequilibrium was also detected between three pairs of loci. The molecular markers developed in this study were able to discriminate each of the individuals sampled (identity analysis). This means that they will be extremely useful for future genetic studies applied to the conservation of P. moratoi, providing a baseline for estimating the levels of genetic diversity, pedigrees, inbreeding, and population structure, which will be essential for the development of effective genetic management programs. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Cytotoxicity of Phenol Red in Toxicity Assays for Carbon Nanoparticles
Int. J. Mol. Sci. 2012, 13(10), 12336-12348; doi:10.3390/ijms131012336
Received: 16 August 2012 / Revised: 18 September 2012 / Accepted: 19 September 2012 / Published: 26 September 2012
Cited by 21 | PDF Full-text (852 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
To explore the novel properties of carbon nanoparticles (CNPs) in nanotoxicity assays, the adsorption of phenol red (a pH indicator for culture medium) by multi-walled carbon nanotubes (MWNTs) and three kinds of carbon blacks (CBs) with nanosize, and its effects on cytotoxicity were
[...] Read more.
To explore the novel properties of carbon nanoparticles (CNPs) in nanotoxicity assays, the adsorption of phenol red (a pH indicator for culture medium) by multi-walled carbon nanotubes (MWNTs) and three kinds of carbon blacks (CBs) with nanosize, and its effects on cytotoxicity were studied. Results indicated that the phenol red adsorbed and delivered into cells by CBs was responsible for the toxicity to Hela cells in the medium without serum. The cellular uptake of phenol red was verified using 125I-labeling techniques. The size-dependent cytotoxicity of CBs was found to closely correlate to adsorption of phenol red, cellular uptake of phenol red-CB complexes and the amount of phenol red delivered into the cells by CBs. Although the CBs were either nontoxic or slightly toxic, as vehicles of phenol red, they played an essential role in the cytotoxicity induced by phenol red. However, MWNTs showed an intrinsic cytotoxicity independent of phenol red. The implications associated with these findings are discussed. Full article
(This article belongs to the Special Issue Bioactive Nanoparticles 2012)
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Open AccessArticle Mercuric Compounds Induce Pancreatic Islets Dysfunction and Apoptosis in Vivo
Int. J. Mol. Sci. 2012, 13(10), 12349-12366; doi:10.3390/ijms131012349
Received: 2 July 2012 / Revised: 2 September 2012 / Accepted: 17 September 2012 / Published: 26 September 2012
Cited by 6 | PDF Full-text (851 KB) | HTML Full-text | XML Full-text
Abstract
Mercury is a toxic heavy metal that is an environmental and industrial pollutant throughout the world. Mercury exposure leads to many physiopathological injuries in mammals. However, the precise toxicological effects of mercury on pancreatic islets in vivo are still unclear. Here, we investigated
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Mercury is a toxic heavy metal that is an environmental and industrial pollutant throughout the world. Mercury exposure leads to many physiopathological injuries in mammals. However, the precise toxicological effects of mercury on pancreatic islets in vivo are still unclear. Here, we investigated whether mercuric compounds can induce dysfunction and damage in the pancreatic islets of mice, as well as the possible mechanisms involved in this process. Mice were treated with methyl mercuric chloride (MeHgCl, 2 mg/kg) and mercuric chloride (HgCl2, 5 mg/kg) for more than 2 consecutive weeks. Our results showed that the blood glucose levels increased and plasma insulin secretions decreased in the mice as a consequence of their exposure. A significant number of TUNEL-positive cells were revealed in the islets of mice that were treated with mercury for 2 consecutive weeks, which was accompanied by changes in the expression of the mRNA of anti-apoptotic (Bcl-2, Mcl-1, and Mdm-2) and apoptotic (p53, caspase-3, and caspase-7) genes. Moreover, plasma malondialdehyde (MDA) levels increased significantly in the mice after treatment with mercuric compounds for 2 consecutive weeks, and the generation of reactive oxygen species (ROS) in the pancreatic islets also markedly increased. In addition, the mRNA expression of genes related to antioxidation, including Nrf2, GPx, and NQO1, were also significantly reduced in these islets. These results indicate that oxidative stress injuries that are induced by mercuric compounds can cause pancreatic islets dysfunction and apoptosis in vivo. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessArticle Proposal of a New Method for Measuring Förster Resonance Energy Transfer (FRET) Rapidly, Quantitatively and Non-Destructively
Int. J. Mol. Sci. 2012, 13(10), 12367-12382; doi:10.3390/ijms131012367
Received: 30 July 2012 / Revised: 11 September 2012 / Accepted: 17 September 2012 / Published: 26 September 2012
PDF Full-text (225 KB) | HTML Full-text | XML Full-text
Abstract
The process of radiationless energy transfer from a chromophore in an excited electronic state (the “donor”) to another chromophore (an “acceptor”), in which the energy released by the donor effects an electronic transition, is known as “Förster Resonance Energy Transfer” (FRET). The rate
[...] Read more.
The process of radiationless energy transfer from a chromophore in an excited electronic state (the “donor”) to another chromophore (an “acceptor”), in which the energy released by the donor effects an electronic transition, is known as “Förster Resonance Energy Transfer” (FRET). The rate of energy transfer is dependent on the sixth power of the distance between donor and acceptor. Determining FRET efficiencies is tantamount to measuring distances between molecules. A new method is proposed for determining FRET efficiencies rapidly, quantitatively, and non-destructively on ensembles containing donor acceptor pairs: at wavelengths suitable for mutually exclusive excitations of donors and acceptors, two laser beams are intensity-modulated in rectangular patterns at duty cycle ½ and frequencies ƒ1 and ƒ2 by electro-optic modulators. In an ensemble exposed to these laser beams, the donor excitation is modulated at ƒ1, and the acceptor excitation, and therefore the degree of saturation of the excited electronic state of the acceptors, is modulated at ƒ2. Since the ensemble contains donor acceptor pairs engaged in FRET, the released donor fluorescence is modulated not only at ƒ1 but also at the beat frequency Δƒ: = |ƒ1 − ƒ2|. The depth of the latter modulation, detectable via a lock-in amplifier, quantitatively indicates the FRET efficiency. Full article
(This article belongs to the Special Issue Förster Resonance Energy Transfer (FRET))
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Open AccessArticle Anti-Inflammatory and Analgesic Activities of a Novel Biflavonoid from Shells of Camellia oleifera
Int. J. Mol. Sci. 2012, 13(10), 12401-12411; doi:10.3390/ijms131012401
Received: 18 July 2012 / Revised: 2 September 2012 / Accepted: 13 September 2012 / Published: 27 September 2012
Cited by 15 | PDF Full-text (215 KB) | HTML Full-text | XML Full-text
Abstract
Shells are by-products of oil production from Camellia oleifera which have not been harnessed effectively. The purpose of this research is to isolate flavonoid from shells of Camellia oleifera and evaluate its anti-inflammatory and analgesic effects. The flavonoid was identified as bimolecular kaempferol
[...] Read more.
Shells are by-products of oil production from Camellia oleifera which have not been harnessed effectively. The purpose of this research is to isolate flavonoid from shells of Camellia oleifera and evaluate its anti-inflammatory and analgesic effects. The flavonoid was identified as bimolecular kaempferol structure by UV, MS, 1H NMR and 13C NMR spectra, which is a new biflavonoid and first found in Camellia oleifera. It showed dose-dependent anti-inflammatory activity by carrageenin-induced paw oedema in rats and croton oil induced ear inflammation in mice, and analgesic activity by hot plate test and acetic acid induced writhing. The mechanism of anti-inflammation of biflavonoid is related to both bradykinin and prostaglandins synthesis inhibition. The biflavonoid showed both central and peripheral analgesic effects different from aspirin, inhibition of the synthesis or action of prostaglandins may contribute to analgesic effect of biflavonoid. The biflavonoid significantly decreased malonaldehyde (MDA) and increased superoxidase dismutase (SOD) and Glutathione peroxidase (GSH-Px) activity in serum (p < 0.01), revealed strong free radical scavenging activity in vivo. It indicates the biflavonoid can control inflammation and pain by eliminating free radical so as to inhibit the mediators and decrease the prostaglandins. The biflavonoid can be used as a prospective medicine for inflammation and pain. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Influence of the Polyvinyl Pyrrolidone Concentration on Particle Size and Dispersion of ZnS Nanoparticles Synthesized by Microwave Irradiation
Int. J. Mol. Sci. 2012, 13(10), 12412-12427; doi:10.3390/ijms131012412
Received: 25 June 2012 / Revised: 25 August 2012 / Accepted: 10 September 2012 / Published: 27 September 2012
Cited by 31 | PDF Full-text (5677 KB) | HTML Full-text | XML Full-text
Abstract
Zinc sulfide semiconductor nanoparticles were synthesized in an aqueous solution of polyvinyl pyrrolidone via a simple microwave irradiation method. The effect of the polymer concentration and the type of sulfur source on the particle size and dispersion of the final ZnS nanoparticle product
[...] Read more.
Zinc sulfide semiconductor nanoparticles were synthesized in an aqueous solution of polyvinyl pyrrolidone via a simple microwave irradiation method. The effect of the polymer concentration and the type of sulfur source on the particle size and dispersion of the final ZnS nanoparticle product was carefully examined. Microwave heating generally occurs by two main mechanisms: dipolar polarization of water and ionic conduction of precursors. The introduction of the polymer affects the heating rate by restriction of the rotational motion of dipole molecules and immobilization of ions. Consequently, our results show that the presence of the polymer strongly affects the nucleation and growth rates of the ZnS nanoparticles and therefore determines the average particle size and the dispersion. Moreover, we found that PVP adsorbed on the surface of the ZnS nanoparticles by interaction of the C–N and C=O with the nanoparticle’s surface, thereby affording protection from agglomeration by steric hindrance. Generally, with increasing PVP concentration, mono-dispersed colloidal solutions were obtained and at the optimal PVP concentration (5%), sufficiently small size and narrow size distributions were obtained from both sodium sulfide and thioacetamide sulfur sources. Finally, the sulfur source directly influences the reaction mechanism and the final particle morphology, as well as the average size. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Effects of Genetically Engineered Stem Cells Expressing Cytosine Deaminase and Interferon-Beta or Carboxyl Esterase on the Growth of LNCaP Prostate Cancer Cells
Int. J. Mol. Sci. 2012, 13(10), 12519-12532; doi:10.3390/ijms131012519
Received: 26 July 2012 / Revised: 18 September 2012 / Accepted: 21 September 2012 / Published: 28 September 2012
Cited by 6 | PDF Full-text (966 KB) | HTML Full-text | XML Full-text
Abstract
The risk of prostate cancer has been increasing in men by degrees. To develop a new prostate cancer therapy, we used a stem cell-derived gene directed prodrug enzyme system using human neural stem cells (hNSCs) that have a tumor-tropic effect. These hNSCs were
[...] Read more.
The risk of prostate cancer has been increasing in men by degrees. To develop a new prostate cancer therapy, we used a stem cell-derived gene directed prodrug enzyme system using human neural stem cells (hNSCs) that have a tumor-tropic effect. These hNSCs were transduced with the therapeutic genes for bacterial cytosine deaminase (CD), alone or in combination with the one encoding human interferon-beta (IFN-β) or rabbit carboxyl esterase (CE) to generate HB1.F3.CD, HB1.F3.CD.IFN-β, and HB1.F3.CE cells, respectively. CD enzyme can convert the prodrug 5-fluorocytosine (5-FC) into the activated form 5-fluorouracil (5-FU). In addition, CE enzyme can convert the prodrug CPT-11 into a toxic agent, SN-38. In our study, the human stem cells were found to migrate toward LNCaP human prostate cancer cells rather than primary cells. This phenomenon may be due to interactions between chemoattractant ligands and receptors, such as VEGF/VEGFR2 and SCF/c-Kit, expressed as cancer and stem cells, respectively. The HB1.F3.CE, HB.F3.CD, or HB1.F3.CD.IFN-β cells significantly reduced the LNCaP cell viability in the presence of the prodrugs 5-FC or CPT-11. These results indicate that stem cells expressing therapeutic genes can be used to develop a new strategy for selectively treating human prostate cancer. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Microsatellite Mutation Rate during Allohexaploidization of Newly Resynthesized Wheat
Int. J. Mol. Sci. 2012, 13(10), 12533-12543; doi:10.3390/ijms131012533
Received: 30 July 2012 / Revised: 18 September 2012 / Accepted: 19 September 2012 / Published: 1 October 2012
Cited by 8 | PDF Full-text (839 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and
[...] Read more.
Simple sequence repeats (SSRs, also known as microsatellites) are known to be mutational hotspots in genomes. DNA rearrangements have also been reported to accompany allopolyploidization. A study of the effect of allopolyploidization on SSR mutation is therefore important for understanding the origin and evolutionary dynamics of SSRs in allopolyploids. Three synthesized double haploid (SynDH) populations were made from 241 interspecific F1 haploid hybrids between Triticum turgidum L. and Aegilops tauschii (Coss.) through spontaneous chromosome doubling via unreduced gametes. Mutation events were studied at 160 SSR loci in the S1 generation (the first generation after chromosome doubling) of the three SynDH populations. Of the 148260 SSR alleles investigated in S1 generation, only one mutation (changed number of repeats) was confirmed with a mutation rate of 6.74 × 10−6. This mutation most likely occurred in the respective F1 hybrid. In comparison with previously reported data, our results suggested that allohexaploidization of wheat did not increase SSR mutation rate. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Short Hairpin RNA (shRNA) Ether à go-go 1 (Eag1) Inhibition of Human Osteosarcoma Angiogenesis via VEGF/PI3K/AKT Signaling
Int. J. Mol. Sci. 2012, 13(10), 12573-12583; doi:10.3390/ijms131012573
Received: 13 August 2012 / Revised: 6 September 2012 / Accepted: 21 September 2012 / Published: 1 October 2012
Cited by 15 | PDF Full-text (1232 KB) | HTML Full-text | XML Full-text
Abstract
Ether à go-go 1 (Eag1) channel is overexpressed in a variety of cancers but the therapeutic potential of Eag1 in osteosarcoma remains elusive. In this study, we constructed an Ad5-Eag1-shRNA vector and evaluated its efficiency for Eag1 knockdown and its effects on osteosarcoma.
[...] Read more.
Ether à go-go 1 (Eag1) channel is overexpressed in a variety of cancers but the therapeutic potential of Eag1 in osteosarcoma remains elusive. In this study, we constructed an Ad5-Eag1-shRNA vector and evaluated its efficiency for Eag1 knockdown and its effects on osteosarcoma. Our results showed that Ad5-Eag1-shRNA had high interference efficiency of Eag1 expression and suppressed osteosarcoma growth both in vitro and in vivo. To explore the molecular mechanism underlying tumor growth inhibition induced by Eag1 silencing, the intratumoral microvessel density (MVD) was assessed by CD31 staining and the expression of vascular endothelial growth factor (VEGF) was detected by Western blot analysis. We found that Eag1 silencing led to decreased angiogenesis and VEGF expression in the xenograft model of osteosarcoma. Finally, we detected a time-dependent decrease in VEGF expression and considerably reduced phosphoinositide 3-kinase (PI3K) and protein kinase B (AKT) activation in osteosarcoma cells treated by Eag1 shRNA. Taken together, our results suggest that Eag1 silencing inhibits tumor growth and angiogenesis in osteosarcoma via the down regulation of VEGF/PI3K/AKT signaling. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Optimized Anti-pathogenic Agents Based on Core/Shell Nanostructures and 2-((4-Ethylphenoxy)ethyl)-N-(substituted-phenylcarbamothioyl)-benzamides
Int. J. Mol. Sci. 2012, 13(10), 12584-12597; doi:10.3390/ijms131012584
Received: 7 June 2012 / Revised: 29 August 2012 / Accepted: 11 September 2012 / Published: 1 October 2012
Cited by 13 | PDF Full-text (584 KB) | HTML Full-text | XML Full-text
Abstract
The purpose of this study was to design a new nanosystem for catheter surface functionalization with an improved resistance to Staphylococcus aureus ATCC 25923 and Pseudomonas aeruginosa ATCC 27853 colonization and subsequent biofilm development. New 2-((4 ethylphenoxy)methyl)-N-(substituted-phenylcarbamothioyl)-benzamides were synthesized and
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The purpose of this study was to design a new nanosystem for catheter surface functionalization with an improved resistance to Staphylococcus aureus ATCC 25923 and Pseudomonas aeruginosa ATCC 27853 colonization and subsequent biofilm development. New 2-((4 ethylphenoxy)methyl)-N-(substituted-phenylcarbamothioyl)-benzamides were synthesized and used for coating a core/shell nanostructure. Their chemical structures were elucidated by NMR, IR and elemental analysis, being in agreement with the proposed ones. Fe3O4/C12 of up to 5 nm size had been synthesized with lauric acid as a coating agent and characterized by XRD, FT-IR, TGA, TEM and biological assays. The catheter pieces were coated with the fabricated nanofluid in magnetic field. The microbial adherence ability was investigated in 6 multiwell plates by using culture based methods and Scanning Electron Microscopy (SEM). The nanoparticles coated with the obtained compounds 1ac inhibited the adherence and biofilm development ability of the S. aureus and P. aeruginosa tested strains on the catheter functionalized surface, as shown by the reduction of viable cell counts and SEM examination of the biofilm architecture. Using the novel core/shell/adsorption-shell to inhibit the microbial adherence could be of a great interest for the biomedical field, opening new directions for the design of film-coated surfaces with improved anti-biofilm properties. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Preparation and Physicochemical Properties of Vinblastine Microparticles by Supercritical Antisolvent Process
Int. J. Mol. Sci. 2012, 13(10), 12598-12607; doi:10.3390/ijms131012598
Received: 26 June 2012 / Revised: 12 September 2012 / Accepted: 18 September 2012 / Published: 3 October 2012
Cited by 1 | PDF Full-text (773 KB) | HTML Full-text | XML Full-text
Abstract
The objective of the study was to prepare vinblastine microparticles by supercritical antisolvent process using N-methyl-2-pyrrolidone as solvent and carbon dioxide as antisolvent and evaluate its physicochemical properties. The effects of four process variables, pressure, temperature, drug concentration and drug solution flow
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The objective of the study was to prepare vinblastine microparticles by supercritical antisolvent process using N-methyl-2-pyrrolidone as solvent and carbon dioxide as antisolvent and evaluate its physicochemical properties. The effects of four process variables, pressure, temperature, drug concentration and drug solution flow rate, on drug particle formation during the supercritical antisolvent process, were investigated. Particles with a mean particle size of 121 ± 5.3 nm were obtained under the optimized process conditions (precipitation temperature 60 °C, precipitation pressure 25 MPa, vinblastine concentration 2.50 mg/mL and vinblastine solution flow rate 6.7 mL/min). The vinblastine was characterized by scanning electron microscopy, X-ray diffraction, Fourier-transform infrared spectroscopy, mass spectrometry and dissolution test. It was concluded that physicochemical properties of crystalline vinblastine could be improved by physical modification, such as particle size reduction and generation of amorphous state using the supercritical antisolvent process. Furthermore, the supercritical antisolvent process was a powerful methodology for improving the physicochemical properties of vinblastine. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Genetic Diversity and Population Structure: Implications for Conservation of Wild Soybean (Glycine soja Sieb. et Zucc) Based on Nuclear and Chloroplast Microsatellite Variation
Int. J. Mol. Sci. 2012, 13(10), 12608-12628; doi:10.3390/ijms131012608
Received: 27 July 2012 / Revised: 24 August 2012 / Accepted: 12 September 2012 / Published: 3 October 2012
Cited by 9 | PDF Full-text (767 KB) | HTML Full-text | XML Full-text
Abstract
Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from
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Wild soybean (Glycine soja Sieb. et Zucc) is the most important germplasm resource for soybean breeding, and is currently subject to habitat loss, fragmentation and population decline. In order to develop successful conservation strategies, a total of 604 wild soybean accessions from 43 locations sampled across its range in China, Japan and Korea were analyzed using 20 nuclear (nSSRs) and five chloroplast microsatellite markers (cpSSRs) to reveal its genetic diversity and population structure. Relatively high nSSR diversity was found in wild soybean compared with other self-pollinated species, and the region of middle and lower reaches of Yangtze River (MDRY) was revealed to have the highest genetic diversity. However, cpSSRs suggested that Korea is a center of diversity. High genetic differentiation and low gene flow among populations were detected, which is consistent with the predominant self-pollination of wild soybean. Two main clusters were revealed by MCMC structure reconstruction and phylogenetic dendrogram, one formed by a group of populations from northwestern China (NWC) and north China (NC), and the other including northeastern China (NEC), Japan, Korea, MDRY, south China (SC) and southwestern China (SWC). Contrib analyses showed that southwestern China makes the greatest contribution to the total diversity and allelic richness, and is worthy of being given conservation priority. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
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Open AccessArticle Relation between Pro-inflammatory Cytokines and Acetylcholine Levels in Relapsing-Remitting Multiple Sclerosis Patients
Int. J. Mol. Sci. 2012, 13(10), 12656-12664; doi:10.3390/ijms131012656
Received: 1 August 2012 / Revised: 6 September 2012 / Accepted: 27 September 2012 / Published: 3 October 2012
Cited by 16 | PDF Full-text (171 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis (MS) is a chronic inflammatory, demyelinating and neurodegenerative disorder. Since acetylcholine (ACh) is known to participate in the inflammatory response, we investigated the possible relationship between pro-inflammatory cytokines and acetylcholine levels in relapsing-remitting multiple sclerosis (RR-MS) patients. Levels of ACh and
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Multiple sclerosis (MS) is a chronic inflammatory, demyelinating and neurodegenerative disorder. Since acetylcholine (ACh) is known to participate in the inflammatory response, we investigated the possible relationship between pro-inflammatory cytokines and acetylcholine levels in relapsing-remitting multiple sclerosis (RR-MS) patients. Levels of ACh and pro-inflammatory cytokines IL1-β and IL-17 were measured both in cerebrospinal fluid (CSF) and sera of 22 RR-MS patients in the relapsing phase and in 17 control subjects affected by other non-neurological diseases (OND). We observed higher levels of pro-inflammatory cytokines such as IL-1β and IL-17 in both CSF and serum of RR-MS patients compared to control subjects. Moreover, ACh levels were lower in CSF and serum of RR-MS patients compared to levels of control subjects. Although the relationship between high inflammatory cytokine levels and low ACh levels need to be further investigated in the future, our data suggest that IL-1β, and cytokines induced by it, such as IL-17 and ACh, may be involved in the pathogenesis of MS. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessArticle Preparation of a Cu(II)-PVA/PA6 Composite Nanofibrous Membrane for Enzyme Immobilization
Int. J. Mol. Sci. 2012, 13(10), 12734-12746; doi:10.3390/ijms131012734
Received: 25 July 2012 / Revised: 25 August 2012 / Accepted: 14 September 2012 / Published: 5 October 2012
Cited by 13 | PDF Full-text (508 KB) | HTML Full-text | XML Full-text
Abstract
PVA/PA6 composite nanofibers were formed by electrospinning. Cu(II)-PVA/PA6 metal chelated nanofibers, prepared by the reaction between PVA/PA6 composite nanofibers and Cu2+ solution, were used as the support for catalase immobilization. The result of the experiments showed that PVA/PA6 composite nanofibers had an
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PVA/PA6 composite nanofibers were formed by electrospinning. Cu(II)-PVA/PA6 metal chelated nanofibers, prepared by the reaction between PVA/PA6 composite nanofibers and Cu2+ solution, were used as the support for catalase immobilization. The result of the experiments showed that PVA/PA6 composite nanofibers had an excellent chelation capacity for Cu2+ ions, and the structures of nanofibers were stable during the reaction with Cu2+ solution. The adsorption of Cu(II) onto PVA/PA6 composite nanofibers was studied by the Langmuir isothermal adsorption model. The maximum amount of coordinated Cu(II) (qm) was 3.731 mmol/g (dry fiber), and the binding constant (Kl) was 0.0593 L/mmol. Kinetic parameters were analyzed for both immobilized and free catalases. The value of Vmax (3774 μmol/mg·min) for the immobilized catalases was smaller than that of the free catalases (4878 μmol/mg·min), while the Km for the immobilized catalases was larger. The immobilized catalases showed better resistance to pH and temperature than that of free form, and the storage stabilities, reusability of immobilized catalases were significantly improved. The half-lives of free and immobilized catalases were 8 days and 24 days, respectively. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Protective Effect of Tulbaghia violacea Harv. on Aortic Pathology, Tissue Antioxidant Enzymes and Liver Damage in Diet-Induced Atherosclerotic Rats
Int. J. Mol. Sci. 2012, 13(10), 12747-12760; doi:10.3390/ijms131012747
Received: 17 June 2012 / Revised: 26 September 2012 / Accepted: 28 September 2012 / Published: 8 October 2012
Cited by 7 | PDF Full-text (346 KB) | HTML Full-text | XML Full-text
Abstract
The protective effect Tulbaghia violacea rhizomes (TVR) against derangements in serum lipid profile, tissue antioxidant enzyme depletion, endothelium dysfunction and histopathological changes in the aorta and liver of rats fed with an atherosclerogenic (Ath) diet (4% cholesterol, 1% cholic acid and 0.5% thiouracil)
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The protective effect Tulbaghia violacea rhizomes (TVR) against derangements in serum lipid profile, tissue antioxidant enzyme depletion, endothelium dysfunction and histopathological changes in the aorta and liver of rats fed with an atherosclerogenic (Ath) diet (4% cholesterol, 1% cholic acid and 0.5% thiouracil) was investigated in this study. Co-treatment with the TVR extracts (250 and 500 mg/kg body weight for two weeks significantly (p < 0.05) protected against elevated serum triglyceride (TG), total cholesterol (TC), LDL-cholesterol, VLDL-cholesterol and decreased HDL-cholesterol in a dose-dependent manner when compared with the atherogenic control. The extracts also reduced (p < 0.05) elevated thiobabutric reacting substance (TBARS) and reversed endothelial dysfunction parameters (fibrinogen and total NO levels) and tissue antioxidant enzyme activities to near normal. The protective ability of the extract was confirmed by the significant (p < 0.05) reduction in the activities of serum markers of liver (LDH, AST, ALT, ALP, bilirubin) and kidney damage (creatinine and bilirubin) in extract-treated groups compared with the atherogenic control group. Also, histopathology evaluations of aorta sections revealed that the extracts protected against the development of fatty streak plaques (aorta) and fatty changes in hepatocytes. The observed activities of the extracts compared favorably with standard drug atorvastatin. Our study thus showed that the methanolic extract of TVR could protect against the early onset of atherosclerosis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessCommunication Proteins of Unknown Function in the Protein Data Bank (PDB): An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis
Int. J. Mol. Sci. 2012, 13(10), 12761-12772; doi:10.3390/ijms131012761
Received: 11 September 2012 / Revised: 21 September 2012 / Accepted: 21 September 2012 / Published: 8 October 2012
Cited by 10 | PDF Full-text (664 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files)
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Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under “unknown function” are true examples of proteins of unknown function at this point in time. The remainder 1465 entries also annotated as such appear to be able to have their annotations re-assessed, based on the availability of direct functional characterization experiments for the protein itself, or for homologous sequences or structures thus enabling computational function inference. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
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Open AccessArticle Substrate Temperature Dependent Surface Morphology and Photoluminescence of Germanium Quantum Dots Grown by Radio Frequency Magnetron Sputtering
Int. J. Mol. Sci. 2012, 13(10), 12880-12889; doi:10.3390/ijms131012880
Received: 16 August 2012 / Revised: 19 September 2012 / Accepted: 21 September 2012 / Published: 9 October 2012
PDF Full-text (1292 KB) | HTML Full-text | XML Full-text
Abstract
The visible luminescence from Ge nanoparticles and nanocrystallites has generated interest due to the feasibility of tuning band gap by controlling the sizes. Germanium (Ge) quantum dots (QDs) with average diameter ~16 to 8 nm are synthesized by radio frequency magnetron sputtering under
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The visible luminescence from Ge nanoparticles and nanocrystallites has generated interest due to the feasibility of tuning band gap by controlling the sizes. Germanium (Ge) quantum dots (QDs) with average diameter ~16 to 8 nm are synthesized by radio frequency magnetron sputtering under different growth conditions. These QDs with narrow size distribution and high density, characterized using atomic force microscopy (AFM) and field emission scanning electron microscopy (FESEM) are obtained under the optimal growth conditions of 400 °C substrate temperature, 100 W radio frequency powers and 10 Sccm Argon flow. The possibility of surface passivation and configuration of these dots are confirmed by elemental energy dispersive X-ray (EDX) analysis. The room temperature strong visible photoluminescence (PL) from such QDs suggests their potential application in optoelectronics. The sample grown at 400 °C in particular, shows three PL peaks at around ~2.95 eV, 3.34 eV and 4.36 eV attributed to the interaction between Ge, GeOx manifesting the possibility of the formation of core-shell structures. A red shift of ~0.11 eV in the PL peak is observed with decreasing substrate temperature. We assert that our easy and economic method is suitable for the large-scale production of Ge QDs useful in optoelectronic devices. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Erythropoietin Modulates Autophagy Signaling in the Developing Rat Brain in an In Vivo Model of Oxygen-Toxicity
Int. J. Mol. Sci. 2012, 13(10), 12939-12951; doi:10.3390/ijms131012939
Received: 19 July 2012 / Revised: 28 August 2012 / Accepted: 21 September 2012 / Published: 10 October 2012
Cited by 11 | PDF Full-text (836 KB) | HTML Full-text | XML Full-text
Abstract
Autophagy is a self-degradative process that involves turnover and recycling of cytoplasmic components in healthy and diseased tissue. Autophagy has been shown to be protective at the early stages of programmed cell death but it can also promote apoptosis under certain conditions. Earlier
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Autophagy is a self-degradative process that involves turnover and recycling of cytoplasmic components in healthy and diseased tissue. Autophagy has been shown to be protective at the early stages of programmed cell death but it can also promote apoptosis under certain conditions. Earlier we demonstrated that oxygen contributes to the pathogenesis of neonatal brain damage, which can be ameliorated by intervention with recombinant human erythropoietin (rhEpo). Extrinsic- and intrinsic apoptotic pathways are involved in oxygen induced neurotoxicity but the role of autophagy in this model is unclear. We analyzed the expression of autophagy activity markers in the immature rodent brain after exposure to elevated oxygen concentrations. We observed a hyperoxia-exposure dependent regulation of autophagy-related gene (Atg) proteins Atg3, 5, 12, Beclin-1, microtubule-associated protein 1 light chain 3 (LC3), LC3A-II, and LC3B-II which are all key autophagy activity proteins. Interestingly, a single injection with rhEpo at the onset of hyperoxia counteracted these oxygen-mediated effects. Our results indicate that rhEpo generates its protective effect by modifying the key autophagy activity proteins. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessArticle Effects of White Rice, Brown Rice and Germinated Brown Rice on Antioxidant Status of Type 2 Diabetic Rats
Int. J. Mol. Sci. 2012, 13(10), 12952-12969; doi:10.3390/ijms131012952
Received: 31 May 2012 / Revised: 13 September 2012 / Accepted: 18 September 2012 / Published: 10 October 2012
Cited by 15 | PDF Full-text (440 KB) | HTML Full-text | XML Full-text
Abstract
Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR). Though brown rice (BR) and germinated brown rice (GBR) have high antioxidant potentials as a result of their bioactive compounds, reports of their
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Oxidative stress is implicated in the pathogenesis of diabetic complications, and can be increased by diet like white rice (WR). Though brown rice (BR) and germinated brown rice (GBR) have high antioxidant potentials as a result of their bioactive compounds, reports of their effects on oxidative stress-related conditions such as type 2 diabetes are lacking. We hypothesized therefore that if BR and GBR were to improve antioxidant status, they would be better for rice consuming populations instead of the commonly consumed WR that is known to promote oxidative stress. This will then provide further reasons why less consumption of WR should be encouraged. We studied the effects of GBR on antioxidant status in type 2 diabetic rats, induced using a high-fat diet and streptozotocin injection, and also evaluated the effects of WR, BR and GBR on catalase and superoxide dismutase genes. As dietary components, BR and GBR improved glycemia and kidney hydroxyl radical scavenging activities, and prevented the deterioration of total antioxidant status in type 2 diabetic rats. Similarly, GBR preserved liver enzymes, as well as serum creatinine. There seem to be evidence that upregulation of superoxide dismutase gene may likely be an underlying mechanism for antioxidant effects of BR and GBR. Our results provide insight into the effects of different rice types on antioxidant status in type 2 diabetes. The results also suggest that WR consumption, contrary to BR and GBR, may worsen antioxidant status that may lead to more damage by free radicals. From the data so far, the antioxidant effects of BR and GBR are worth studying further especially on a long term to determine their effects on development of oxidative stress-related problems, which WR consumption predisposes to. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A Molecular Dynamics (MD) and Quantum Mechanics/Molecular Mechanics (QM/MM) Study on Ornithine Cyclodeaminase (OCD): A Tale of Two Iminiums
Int. J. Mol. Sci. 2012, 13(10), 12994-13011; doi:10.3390/ijms131012994
Received: 10 September 2012 / Revised: 27 September 2012 / Accepted: 27 September 2012 / Published: 11 October 2012
Cited by 7 | PDF Full-text (4638 KB) | HTML Full-text | XML Full-text
Abstract
Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM)
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Ornithine cyclodeaminase (OCD) is an NAD+-dependent deaminase that is found in bacterial species such as Pseudomonas putida. Importantly, it catalyzes the direct conversion of the amino acid L-ornithine to L-proline. Using molecular dynamics (MD) and a hybrid quantum mechanics/molecular mechanics (QM/MM) method in the ONIOM formalism, the catalytic mechanism of OCD has been examined. The rate limiting step is calculated to be the initial step in the overall mechanism: hydride transfer from the L-ornithine’s Cα–H group to the NAD+ cofactor with concomitant formation of a Cα=NH2+ Schiff base with a barrier of 90.6 kJ mol−1. Importantly, no water is observed within the active site during the MD simulations suitably positioned to hydrolyze the Cα=NH2+ intermediate to form the corresponding carbonyl. Instead, the reaction proceeds via a non-hydrolytic mechanism involving direct nucleophilic attack of the δ-amine at the Cα-position. This is then followed by cleavage and loss of the α-NH2 group to give the Δ1-pyrroline-2-carboxylate that is subsequently reduced to L-proline. Full article
(This article belongs to the Special Issue Enzyme Optimization and Immobilization)
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Open AccessArticle Transcriptomic Analysis of Phenotypic Changes in Birch (Betula platyphylla) Autotetraploids
Int. J. Mol. Sci. 2012, 13(10), 13012-13029; doi:10.3390/ijms131013012
Received: 19 August 2012 / Revised: 30 September 2012 / Accepted: 30 September 2012 / Published: 11 October 2012
Cited by 11 | PDF Full-text (1725 KB) | HTML Full-text | XML Full-text
Abstract
Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and
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Plant breeders have focused much attention on polyploid trees because of their importance to forestry. To evaluate the impact of intraspecies genome duplication on the transcriptome, a series of Betula platyphylla autotetraploids and diploids were generated from four full-sib families. The phenotypes and transcriptomes of these autotetraploid individuals were compared with those of diploid trees. Autotetraploids were generally superior in breast-height diameter, volume, leaf, fruit and stoma and were generally inferior in height compared to diploids. Transcriptome data revealed numerous changes in gene expression attributable to autotetraploidization, which resulted in the upregulation of 7052 unigenes and the downregulation of 3658 unigenes. Pathway analysis revealed that the biosynthesis and signal transduction of indoleacetate (IAA) and ethylene were altered after genome duplication, which may have contributed to phenotypic changes. These results shed light on variations in birch autotetraploidization and help identify important genes for the genetic engineering of birch trees. Full article
(This article belongs to the Special Issue Advances in Molecular Plant Biology)
Open AccessArticle Binding of the Phage Display Derived Peptide CaIX-P1 on Human Colorectal Carcinoma Cells Correlates with the Expression of Carbonic Anhydrase IX
Int. J. Mol. Sci. 2012, 13(10), 13030-13048; doi:10.3390/ijms131013030
Received: 27 July 2012 / Revised: 8 September 2012 / Accepted: 21 September 2012 / Published: 11 October 2012
Cited by 4 | PDF Full-text (1905 KB) | HTML Full-text | XML Full-text
Abstract
Phage display represents an attractive screening strategy for the identification of novel, specific binding ligands that could be used for tumor targeting. Recently, a new peptide (CaIX-P1) with affinity for human carbonic anhydrase IX (CAIX) was identified and evaluated. The aim of the
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Phage display represents an attractive screening strategy for the identification of novel, specific binding ligands that could be used for tumor targeting. Recently, a new peptide (CaIX-P1) with affinity for human carbonic anhydrase IX (CAIX) was identified and evaluated. The aim of the present study is to characterize the properties of CaIX-P1 for targeting human colorectal carcinoma and investigate the correlation of peptide binding with the expression of carbonic anhydrase IX. Human colorectal carcinoma HCT116 and HT29 cells were investigated for CAIX expression using Western Blot analysis. Binding and competition studies of 125I-radiolabeled CaIX-P1 were performed on HCT116 cells in vitro. FACS analysis and fluorescence microscopy studies were carried out after cell incubation with fluorescein-labeled CaIX-P1 and rhodamine-labeled anti-human CAIX-mAb. Our studies revealed an enhanced in vitro expression of carbonic anhydrase IX in HCT116 and HT29 cells with increasing cell density. Binding of 125I-labeled-CaIX-P1 on HCT116 cells increased with increasing cell density and correlated to the CAIX expression. FACS analysis demonstrated a correlation of cell labeling between FITC-CaIX-P1 and rhodamine-labeled anti-CAIX-mAb in both HCT116 and HT29 cells. The results of our study indicate that the phage display identified peptide CaIX-P1 might be an attractive candidate for the development of a ligand targeting CAIX in colorectal cancer. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Formulation Optimization of a Palm-Based Nanoemulsion System Containing Levodopa
Int. J. Mol. Sci. 2012, 13(10), 13049-13064; doi:10.3390/ijms131013049
Received: 2 August 2012 / Revised: 26 August 2012 / Accepted: 9 October 2012 / Published: 11 October 2012
Cited by 11 | PDF Full-text (271 KB) | HTML Full-text | XML Full-text
Abstract
Response surface methodology (RSM) was utilized to investigate the influence of the main emulsion composition; mixture of palm and medium-chain triglyceride (MCT) oil (6%–12% w/w), lecithin (1%–3% w/w), and Cremophor EL (0.5%–1.5% w/w) as
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Response surface methodology (RSM) was utilized to investigate the influence of the main emulsion composition; mixture of palm and medium-chain triglyceride (MCT) oil (6%–12% w/w), lecithin (1%–3% w/w), and Cremophor EL (0.5%–1.5% w/w) as well as the preparation method; addition rate (2–20 mL/min), on the physicochemical properties of palm-based nanoemulsions. The response variables were the three main emulsion properties; particle size, zeta potential and polydispersity index. Optimization of the four independent variables was carried out to obtain an optimum level palm-based nanoemulsion with desirable characteristics. The response surface analysis showed that the variation in the three responses could be depicted as a quadratic function of the main composition of the emulsion and the preparation method. The experimental data could be fitted sufficiently well into a second-order polynomial model. The optimized formulation was stable for six months at 4 °C. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Supercritical Carbon Dioxide Extraction of Flavonoids from Pomelo (Citrus grandis (L.) Osbeck) Peel and Their Antioxidant Activity
Int. J. Mol. Sci. 2012, 13(10), 13065-13078; doi:10.3390/ijms131013065
Received: 17 July 2012 / Revised: 11 September 2012 / Accepted: 25 September 2012 / Published: 12 October 2012
Cited by 9 | PDF Full-text (888 KB) | HTML Full-text | XML Full-text
Abstract
Supercritical carbon dioxide (SC-CO2) extraction of flavonoids from pomelo (Citrus grandis (L.) Osbeck) peel and their antioxidant activity were investigated. Box-Behnken design combined with response surface methodology was employed to maximize the extraction yield of flavonoids. Correlation analysis of the
[...] Read more.
Supercritical carbon dioxide (SC-CO2) extraction of flavonoids from pomelo (Citrus grandis (L.) Osbeck) peel and their antioxidant activity were investigated. Box-Behnken design combined with response surface methodology was employed to maximize the extraction yield of flavonoids. Correlation analysis of the mathematical-regression model indicated that a quadratic polynomial model could be used to optimize the SC-CO2 extraction of flavonoids. The optimal conditions for obtaining the highest extraction yield of flavonoids from pomelo peel were a temperature of 80 °C, a pressure of 39 MPa and a static extraction time of 49 min in the presence of 85% ethanol as modifier. Under these conditions, the experimental yield was 2.37%, which matched positively with the value predicted by the model. Furthermore, flavonoids obtained by SC-CO2 extraction showed a higher scavenging activity on hydroxyl, 1,1-diphenyl-2-picrylhydrazyl (DPPH) and 2,2'-azino-bis(3-ethylbenzthiazoline-6-sulphonic acid) (ABTS) radicals than those obtained by conventional solvent extraction (CSE). Therefore, SC-CO2 extraction can be considered as a suitable technique for the obtainment of flavonoids from pomelo peel. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Pyrosequencing-Based Transcriptome Analysis of the Asian Rice Gall Midge Reveals Differential Response during Compatible and Incompatible Interaction
Int. J. Mol. Sci. 2012, 13(10), 13079-13103; doi:10.3390/ijms131013079
Received: 13 August 2012 / Revised: 14 September 2012 / Accepted: 27 September 2012 / Published: 12 October 2012
Cited by 6 | PDF Full-text (3497 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of
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The Asian rice gall midge (Orseolia oryzae) is a major pest responsible for immense loss in rice productivity. Currently, very little knowledge exists with regard to this insect at the molecular level. The present study was initiated with the aim of developing molecular resources as well as identifying alterations at the transcriptome level in the gall midge maggots that are in a compatible (SH) or in an incompatible interaction (RH) with their rice host. Roche 454 pyrosequencing strategy was used to develop both transcriptomics and genomics resources that led to the identification of 79,028 and 85,395 EST sequences from gall midge biotype 4 (GMB4) maggots feeding on a susceptible and resistant rice variety, TN1 (SH) and Suraksha (RH), respectively. Comparative transcriptome analysis of the maggots in SH and RH revealed over-representation of transcripts from proteolysis and protein phosphorylation in maggots from RH. In contrast, over-representation of transcripts for translation, regulation of transcription and transcripts involved in electron transport chain were observed in maggots from SH. This investigation, besides unveiling various mechanisms underlying insect-plant interactions, will also lead to a better understanding of strategies adopted by insects in general, and the Asian rice gall midge in particular, to overcome host defense. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Inhibition of Enzyme Activity of Rhipicephalus (Boophilus) microplus Triosephosphate Isomerase and BME26 Cell Growth by Monoclonal Antibodies
Int. J. Mol. Sci. 2012, 13(10), 13118-13133; doi:10.3390/ijms131013118
Received: 5 July 2012 / Revised: 1 October 2012 / Accepted: 6 October 2012 / Published: 12 October 2012
Cited by 2 | PDF Full-text (357 KB) | HTML Full-text | XML Full-text
Abstract
In the present work, we produced two monoclonal antibodies (BrBm37 and BrBm38) and tested their action against the triosephosphate isomerase of Rhipicephalus (Boophilus) microplus (RmTIM). These antibodies recognize epitopes on both the native and recombinant forms of the protein. rRmTIM inhibition 
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In the present work, we produced two monoclonal antibodies (BrBm37 and BrBm38) and tested their action against the triosephosphate isomerase of Rhipicephalus (Boophilus) microplus (RmTIM). These antibodies recognize epitopes on both the native and recombinant forms of the protein. rRmTIM inhibition  by BrBm37 was up to 85% whereas that of BrBrm38 was 98%, depending on the antibody-enzyme ratio. RmTIM activity was lower in ovarian, gut, and fat body tissue extracts treated with BrBm37 or BrBm38 mAbs. The proliferation of the embryonic tick cell line (BME26) was inhibited by BrBm37 and BrBm38 mAbs. In summary, the results reveal that it is possible to interfere with the RmTIM function using antibodies, even in intact cells. Full article
(This article belongs to the Special Issue Advances in Molecular Immunology)
Open AccessCommunication A Tumor Surveillance Model: A Non-Coding RNA Senses Neoplastic Cells and Its Protein Partner Signals Cell Death
Int. J. Mol. Sci. 2012, 13(10), 13134-13139; doi:10.3390/ijms131013134
Received: 31 July 2012 / Revised: 22 September 2012 / Accepted: 26 September 2012 / Published: 12 October 2012
Cited by 5 | PDF Full-text (363 KB) | HTML Full-text | XML Full-text
Abstract
nc886 (= pre-miR-886 or vtRNA2-1) is a non-coding RNA that has been recently identified as a natural repressor for the activity of PKR (Protein Kinase R). The suppression of nc886 activates PKR and thereby provokes a cell death pathway. When combined with the
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nc886 (= pre-miR-886 or vtRNA2-1) is a non-coding RNA that has been recently identified as a natural repressor for the activity of PKR (Protein Kinase R). The suppression of nc886 activates PKR and thereby provokes a cell death pathway. When combined with the fact that nc886 is suppressed in a wide range of cancer cells, the nc886-PKR relationship suggests a tumor surveillance model. When neoplastic cells develop and nc886 decreases therein, PKR is released from nc886 and becomes the active phosphorylated form, which initiates an apoptotic cascade to eliminate those cells. The nc886-PKR pathway is distinct from conventional mechanisms, such as the immune surveillance hypothesis or intrinsic mechanisms that check/proofread the genomic integrity, and thus represents a novel example of tumor surveillance. Full article
(This article belongs to the Special Issue Non-Coding RNAs 2012)
Open AccessArticle Optimization of Lipase-Mediated Synthesis of 1-Nonene Oxide Using Phenylacetic Acid and Hydrogen Peroxide
Int. J. Mol. Sci. 2012, 13(10), 13140-13149; doi:10.3390/ijms131013140
Received: 27 July 2012 / Revised: 1 September 2012 / Accepted: 21 September 2012 / Published: 12 October 2012
Cited by 5 | PDF Full-text (441 KB) | HTML Full-text | XML Full-text
Abstract
Herein, an efficient epoxidation of 1-nonene is described. In a simple epoxidation system, commercially available Novozym 435, an immobilized Candida antarctica lipase B, and hydrogen peroxide (H2O2) were utilized to facilitate the in situ oxidation of phenylacetic acid to
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Herein, an efficient epoxidation of 1-nonene is described. In a simple epoxidation system, commercially available Novozym 435, an immobilized Candida antarctica lipase B, and hydrogen peroxide (H2O2) were utilized to facilitate the in situ oxidation of phenylacetic acid to the corresponding peroxy acid which then reacted with 1-nonene to give 1-nonene oxide with high yield and selectivity. The aliphatic terminal alkene was epoxidised efficiently in chloroform to give an excellent yield (97%–99%) under the optimum reaction conditions, including temperature (35 °C), initial H2O2 concentration (30%), H2O2 amount (4.4 mmol), H2O2 addition rate (one step), acid amount (8.8 mmol), and stirring speed (250 rpm). Interestingly, the enzyme was stable under the single-step addition of H2O2 with a catalytic activity of 190.0 Ug−1. The entire epoxidation process was carried out within 12 h using a conventional water bath shaker. Full article
(This article belongs to the Special Issue Organic Synthesis Using Biocatalyst)
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Open AccessArticle Construction and Evaluation of Normalized cDNA Libraries Enriched with Full-Length Sequences for Rapid Discovery of New Genes from Sisal (Agave sisalana Perr.) Different Developmental Stages
Int. J. Mol. Sci. 2012, 13(10), 13150-13168; doi:10.3390/ijms131013150
Received: 4 July 2012 / Revised: 25 September 2012 / Accepted: 26 September 2012 / Published: 12 October 2012
Cited by 8 | PDF Full-text (3628 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to
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To provide a resource of sisal-specific expressed sequence data and facilitate this powerful approach in new gene research, the preparation of normalized cDNA libraries enriched with full-length sequences is necessary. Four libraries were produced with RNA pooled from Agave sisalana multiple tissues to increase efficiency of normalization and maximize the number of independent genes by SMART™ method and the duplex-specific nuclease (DSN). This procedure kept the proportion of full-length cDNAs in the subtracted/normalized libraries and dramatically enhanced the discovery of new genes. Sequencing of 3875 cDNA clones of libraries revealed 3320 unigenes with an average insert length about 1.2 kb, indicating that the non-redundancy of libraries was about 85.7%. These unigene functions were predicted by comparing their sequences to functional domain databases and extensively annotated with Gene Ontology (GO) terms. Comparative analysis of sisal unigenes and other plant genomes revealed that four putative MADS-box genes and knotted-like homeobox (knox) gene were obtained from a total of 1162 full-length transcripts. Furthermore, real-time PCR showed that the characteristics of their transcripts mainly depended on the tight expression regulation of a number of genes during the leaf and flower development. Analysis of individual library sequence data indicated that the pooled-tissue approach was highly effective in discovering new genes and preparing libraries for efficient deep sequencing. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Lower Salinomycin Concentration Increases Apoptotic Detachment in High-Density Cancer Cells
Int. J. Mol. Sci. 2012, 13(10), 13169-13182; doi:10.3390/ijms131013169
Received: 7 September 2012 / Revised: 28 September 2012 / Accepted: 9 October 2012 / Published: 12 October 2012
Cited by 9 | PDF Full-text (717 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The present study identified a novel salinomycin (Sal) sensitization mechanism in cancer. We tested whether Sal reduced proliferation in a high-density population by counting attached cell numbers after Sal treatment. Sal reduced proliferation in high-density cell populations. Longer exposure to Sal further reduced
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The present study identified a novel salinomycin (Sal) sensitization mechanism in cancer. We tested whether Sal reduced proliferation in a high-density population by counting attached cell numbers after Sal treatment. Sal reduced proliferation in high-density cell populations. Longer exposure to Sal further reduced proliferation. Sal concentrations of 0.1 and 5 μM had similar sensitization effects, suggesting that Sal toxicity was minimal with longer exposure to a high-density cell population. The results suggest that Sal can be applied at a relatively low concentration for a longer time to overcome drug-resistant solid tumors. The 0.5 μM Sal treatment resulted in fewer attached cells than that of the 5 μM Sal treatment with a longer exposure. The lower Sal concentration mainly increased the number of easily detachable cells on the surface. In particular, 0.5 μM Sal increased cellular detachment of newly produced daughter cells. The easily-detachable cells were undergoing apoptosis. It seems that the 0.5 μM Sal treatment also increased cellular toxicity. These novel findings may contribute to the development of Sal-based therapy for patients with drug-resistant cancer or a high-density solid tumor. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessArticle Altered DNA Binding and Amplification of Human Breast Cancer Suppressor Gene BRCA1 Induced by a Novel Antitumor Compound, [Ru(η6-p-phenylethacrynate)Cl2(pta)]
Int. J. Mol. Sci. 2012, 13(10), 13183-13202; doi:10.3390/ijms131013183
Received: 15 June 2012 / Revised: 25 August 2012 / Accepted: 8 October 2012 / Published: 15 October 2012
Cited by 6 | PDF Full-text (1320 KB) | HTML Full-text | XML Full-text
Abstract
The ruthenium-based complex [Ru(η6-p-phenylethacrynate)Cl2(pta)] (pta = 1,3,5-triaza-7-phosphatricyclo-[3.3.1.1]decane), termed ethaRAPTA, is an interesting antitumor compound. The elucidation of the molecular mechanism of drug activity is central to the drug development program. To this end, we have characterized the
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The ruthenium-based complex [Ru(η6-p-phenylethacrynate)Cl2(pta)] (pta = 1,3,5-triaza-7-phosphatricyclo-[3.3.1.1]decane), termed ethaRAPTA, is an interesting antitumor compound. The elucidation of the molecular mechanism of drug activity is central to the drug development program. To this end, we have characterized the ethaRAPTA interaction with DNA, including probing the sequence specific modified DNA structural stability and DNA amplification using the breast cancer suppressor gene 1 (BRCA1) of human breast and colon adenocarcinoma cell lines as models. The preference of ethaRAPTA base binding is in the order A > G > T > C. Once modified, the ethaRAPTA-induced BRCA1 structure has higher thermal stability than the modified equivalents of its related compound, RAPTA-C. EthaRAPTA exhibits a higher efficiency than RAPTA-C in inhibiting BRCA1 amplification. With respect to both compounds, the inhibition of BRCA1 amplification is more effective in an isolated system than in cell lines. These data provide evidence that will help to understand the process of elucidating the pathways involved in the response induced by ethaRAPTA. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessArticle Lower Temperature Cultures Enlarge the Effects of Vitreoscilla Hemoglobin Expression on Recombinant Pichia pastoris
Int. J. Mol. Sci. 2012, 13(10), 13212-13226; doi:10.3390/ijms131013212
Received: 2 August 2012 / Revised: 19 September 2012 / Accepted: 8 October 2012 / Published: 15 October 2012
Cited by 9 | PDF Full-text (1630 KB) | HTML Full-text | XML Full-text
Abstract
An heterologous expression of Vitreoscilla hemoglobin (VHb) for improving cell growth and recombinant protein production has been successfully demonstrated in various hosts, including Pichia pastoris. Lower temperature cultures can enhance target protein production in some studies of P. pastoris. In this
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An heterologous expression of Vitreoscilla hemoglobin (VHb) for improving cell growth and recombinant protein production has been successfully demonstrated in various hosts, including Pichia pastoris. Lower temperature cultures can enhance target protein production in some studies of P. pastoris. In this study, the strategy of combining heterologous VHb expression and lower temperature cultures in P. pastoris showed that final cell density and viability of VHb+ strain at 23 °C were higher than that at 30 °C. In addition, the effects of VHb expression on recombinant β-galactosidase production and oxygen uptake rate were also higher at 23 °C than at 30 °C. Consequently, lower temperature cultures can enlarge VHb effectiveness on cell performance of P. pastoris. This is because VHb activity obtained at 23 °C cultures was twofold higher than that at 30 °C cultures, due to a different heme production. This strategy makes P. pastoris an excellent expression host particularly suitable for increasing the yields of the low-stability and aggregation-prone recombinant proteins. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Over-Expression of Semaphorin4D, Hypoxia-Inducible Factor-1α and Vascular Endothelial Growth Factor Is Related to Poor Prognosis in Ovarian Epithelial Cancer
Int. J. Mol. Sci. 2012, 13(10), 13264-13274; doi:10.3390/ijms131013264
Received: 20 August 2012 / Revised: 12 September 2012 / Accepted: 7 October 2012 / Published: 16 October 2012
Cited by 14 | PDF Full-text (2865 KB) | HTML Full-text | XML Full-text
Abstract
Semaphorin4D (SEMA4D) has been regarded as an important protein in tumor angiogenesis, though originally identified in neurodevelopment. SEMA4D is extensively expressed in several malignant solid tumors. Nevertheless, the function and expression of SEMA4D in epithelial ovarian cancer (EOC) is as yet not well
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Semaphorin4D (SEMA4D) has been regarded as an important protein in tumor angiogenesis, though originally identified in neurodevelopment. SEMA4D is extensively expressed in several malignant solid tumors. Nevertheless, the function and expression of SEMA4D in epithelial ovarian cancer (EOC) is as yet not well understood. The aim of this study was to investigate SEMA4D expression in EOC and evaluate its clinical–pathological and prognostic significance. Immunohistochemistry was used to analyze SEMA4D expression and tumor angiogenesis-related proteins (HIF-1α and VEGF) in tissues from 40 patients with normal ovarian epithelia and 124 EOC patients. SEMA4D was found to be expressed in 61.3% of the 124 EOC tissues, which was significantly higher than in the normal ovarian epithelia (p < 0.001). SEMA4D expression correlated with HIF-1α and VEGF closely (ρ = 0.349 and 0.263, p < 0.001). Positive SEMA4D staining was significantly higher in tissues from patients with low histological grade, FIGO stage III-IV, lymph node metastasis and residual disease ≥1 cm (p < 0.05). In the Cox proportional hazard mode, SEMA4D expression and histologic grade were independent indicators of overall survival (OS) and progress-free survival (PFS) for EOC patients. These findings suggest that the cooperation of SEMA4D, HIF-1α, and VEGF may indicate poor prognosis for patients with EOC, thereby demonstrating that SEMA4D and its role in angiogenesis in EOC warrants further study. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle The Effect of Sodium Dodecyl Sulfate (SDS) and Cetyltrimethylammonium Bromide (CTAB) on the Properties of ZnO Synthesized by Hydrothermal Method
Int. J. Mol. Sci. 2012, 13(10), 13275-13293; doi:10.3390/ijms131013275
Received: 23 July 2012 / Revised: 16 September 2012 / Accepted: 17 September 2012 / Published: 16 October 2012
Cited by 46 | PDF Full-text (2055 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
ZnO nanostructures were synthesized by hydrothermal method using different molar ratios of cetyltrimethylammonium bromide (CTAB) and Sodium dodecyl sulfate (SDS) as structure directing agents. The effect of surfactants on the morphology of the ZnO crystals was investigated by field emission scanning electron microscopy
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ZnO nanostructures were synthesized by hydrothermal method using different molar ratios of cetyltrimethylammonium bromide (CTAB) and Sodium dodecyl sulfate (SDS) as structure directing agents. The effect of surfactants on the morphology of the ZnO crystals was investigated by field emission scanning electron microscopy (FESEM) and transmission electron microscopy (TEM) techniques. The results indicate that the mixture of cationic-anionic surfactants can significantly modify the shape and size of ZnO particles. Various structures such as flakes, sheets, rods, spheres, flowers and triangular-like particles sized from micro to nano were obtained. In order to examine the possible changes in other properties of ZnO, characterizations like powder X-ray diffraction (PXRD), thermogravimetric and differential thermogravimetric analysis (TGA-DTG), FTIR, surface area and porosity and UV-visible spectroscopy analysis were also studied and discussed. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Improved Production of Cyclodextrins by Alkalophilic Bacilli Immobilized on Synthetic or Loofa Sponges
Int. J. Mol. Sci. 2012, 13(10), 13294-13307; doi:10.3390/ijms131013294
Received: 16 September 2012 / Revised: 4 October 2012 / Accepted: 8 October 2012 / Published: 17 October 2012
Cited by 3 | PDF Full-text (305 KB) | HTML Full-text | XML Full-text
Abstract
This study aimed to improve the production of β-cyclodextrin (β-CD) by microbial cells immobilized on synthetic or loofa sponges both with and without the use of alginate or chitosan. The most suitable matrix for the immobilization of Bacillus firmus strain 7B was synthetic
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This study aimed to improve the production of β-cyclodextrin (β-CD) by microbial cells immobilized on synthetic or loofa sponges both with and without the use of alginate or chitosan. The most suitable matrix for the immobilization of Bacillus firmus strain 7B was synthetic sponge and for Bacillus sphaericus strain 41 was loofa sponge. After 330 days of storage, the β-CD production by Bacillus firmus and Bacillus sphaericus remained at around 41% and 49%, respectively, of initial levels. After 24 days of immobilization on loofa sponge, Bacillus sphaericus strain 41 achieved an improved operational stability, reaching 86.6 mM β-CD after 20 days of production, compared to only 32.8 mM of β-CD produced by free Bacillus sphaericus strain 41 cells. The expected increase in β-CD production by immobilized cells of Bacillus firmus strain 7B on synthetic sponge for 4 days was not statistically different to that for cells immobilized for 24 days. The application of this process on an industrial scale using loofa sponge, an inexpensive and renewable matrix, will allow the stable production of β-CD. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
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Open AccessArticle ABO Blood Group System and Gastric Cancer: A Case-Control Study and Meta-Analysis
Int. J. Mol. Sci. 2012, 13(10), 13308-13321; doi:10.3390/ijms131013308
Received: 24 July 2012 / Revised: 3 September 2012 / Accepted: 8 October 2012 / Published: 17 October 2012
Cited by 29 | PDF Full-text (1687 KB) | HTML Full-text | XML Full-text
Abstract
This study focuses on the association between the ABO blood group system and the risk of gastric cancer or Helicobacter pylori infection. The data for the ABO blood group was collected from 1045 cases of gastric cancer, whereby the patient underwent a gastrectomy
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This study focuses on the association between the ABO blood group system and the risk of gastric cancer or Helicobacter pylori infection. The data for the ABO blood group was collected from 1045 cases of gastric cancer, whereby the patient underwent a gastrectomy in Ruijin Hospital, Shanghai. The information on the ABO blood group from 53,026 healthy blood donors was enrolled as control. We searched the Pubmed database on the relationship between ABO blood groups and gastric cancer risk for meta-analysis. In our case-control study, the risk of gastric cancer in blood group A was significantly higher than that in non-A groups (O, B and AB) (odd ratio, OR1.34; 95% confidential interval, CI 1.25–1.44). Compared with non-O groups (A, B and AB), individuals with blood group O demonstrated a reduced risk of gastric cancer (OR = 0.80; 95% CI 0.72–0.88). The proportion of H. pylori infection in blood group A individuals was significantly higher than that in non-A blood groups (OR = 1.42; 95% CI 1.05–1.93). We further combined our data with the published data of others, and crossreferenced the risk of gastric cancer with the blood type, finding consistent evidence that gastric cancer risk in the blood A group was higher than that in the non-A groups (OR = 1.11; 95% CI 1.07–1.15), and that blood type O individuals were consistently shown gastric cancer risk reduction (OR = 0.91; 95% CI 0.89–0.94). Our study concluded that there was a slightly increased risk of gastric cancer in blood group A individuals, and people with blood type A are more prone to be infected by H. pylori than other ABO blood type individuals, whereas, a slightly decreased risk of gastric cancer was identified in blood type O individuals. Full article
(This article belongs to the Section Molecular Diagnostics)
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Open AccessArticle Ischemic Postconditioning Alleviates Neuronal Injury Caused by Relief of Carotid Stenosis in a Rat Model of Cerebral Hypoperfusion
Int. J. Mol. Sci. 2012, 13(10), 13338-13351; doi:10.3390/ijms131013338
Received: 27 August 2012 / Revised: 11 September 2012 / Accepted: 10 October 2012 / Published: 18 October 2012
Cited by 5 | PDF Full-text (1932 KB) | HTML Full-text | XML Full-text
Abstract
The effects of early relief of heavy bilateral carotid stenosis and ischemic postconditioning on hippocampus CA1 neurons are still unclear. In this study, we used a rat model to imitate severe bilateral carotid stenosis in humans. The rats were divided into sham group,
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The effects of early relief of heavy bilateral carotid stenosis and ischemic postconditioning on hippocampus CA1 neurons are still unclear. In this study, we used a rat model to imitate severe bilateral carotid stenosis in humans. The rats were divided into sham group, carotid stenosis group, stenosis relief group and ischemic postconditioning group. Ischemic postconditioning consisted of three cycles of 30 s ischemia and 30 s reperfusion. The cerebral blood flow was measured with a laser Doppler flowmeter. Neuronal death in the CA1 region was observed by hematoxylin-eosin staining, and the number of live neurons was assessed by cell counting under a light microscope. The levels of oxidative products MDA and 8-iso-PGF2α, inflammatory factors IL-1β and TNF-α, and the activities of anti-oxidative enzymes SOD and CAT were assayed by specific enzyme-linked immunosorbent assay (ELISA) kits, respectively. We found that relief of carotid stenosis and ischemic postconditioning could increase cerebral blood flow. When stenosis was relieved, the percentage of live neurons was 66.6% ± 6.2% on day 3 and 62.3% ± 9.8% on day 27, which was significantly higher than 55.5% ± 4.8% in stenosis group. Ischemic postconditioning markedly improved the live neurons to 92.5% ± 6.7% on day 3 and 88.6% ± 9.1% on day 27. Further study showed that, neuronal death caused by relief of stenosis is associated with increased oxidative stress and enhanced inflammatory response, and the protection of ischemic postconditioning is related to inhibition of oxidative stress and suppression of inflammatory response. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle NotI Microarrays: Novel Epigenetic Markers for Early Detection and Prognosis of High Grade Serous Ovarian Cancer
Int. J. Mol. Sci. 2012, 13(10), 13352-13377; doi:10.3390/ijms131013352
Received: 10 August 2012 / Revised: 12 September 2012 / Accepted: 12 September 2012 / Published: 18 October 2012
Cited by 13 | PDF Full-text (938 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Chromosome 3-specific NotI microarray (NMA) containing 180 clones with 188 genes was used in the study to analyze 18 high grade serous ovarian cancer (HGSOC) samples and 7 benign ovarian tumors. We aimed to find novel methylation-dependent biomarkers for early detection and
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Chromosome 3-specific NotI microarray (NMA) containing 180 clones with 188 genes was used in the study to analyze 18 high grade serous ovarian cancer (HGSOC) samples and 7 benign ovarian tumors. We aimed to find novel methylation-dependent biomarkers for early detection and prognosis of HGSOC. Thirty five NotI markers showed frequency of methylation/deletion more or equal to 17%. To check the results of NMA hybridizations several samples for four genes (LRRC3B, THRB, ITGA9 and RBSP3 (CTDSPL)) were bisulfite sequenced and confirmed the results of NMA hybridization. A set of eight biomarkers: NKIRAS1/RPL15, THRB, RBPS3 (CTDSPL), IQSEC1, NBEAL2, ZIC4, LOC285205 and FOXP1, was identified as the most prominent set capable to detect both early and late stages of ovarian cancer. Sensitivity of this set is equal to (72 ± 11)% and specificity (94 ± 5)%. Early stages represented the most complicated cases for detection. To distinguish between Stages I + II and Stages III + IV of ovarian cancer the most perspective set of biomarkers would include LOC285205, CGGBP1, EPHB1 and NKIRAS1/RPL15. The sensitivity of the set is equal to (80 ± 13)% and the specificity is (88 ± 12)%. Using this technique we plan to validate this panel with new epithelial ovarian cancer samples and add markers from other chromosomes. Full article
(This article belongs to the Special Issue Cancer Molecules in Ovarian Cancer 2012)
Open AccessArticle Proteomic Analysis of Albumins and Globulins from Wheat Variety Chinese Spring and Its Fine Deletion Line 3BS-8
Int. J. Mol. Sci. 2012, 13(10), 13398-13413; doi:10.3390/ijms131013398
Received: 31 August 2012 / Revised: 8 October 2012 / Accepted: 9 October 2012 / Published: 18 October 2012
Cited by 2 | PDF Full-text (2252 KB) | HTML Full-text | XML Full-text
Abstract
The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance
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The relationship between chromosome deletion in wheat and protein expression were investigated using Chinese Spring and fine deletion line 3BS-8. Through 2-DE (2-D electrophoresis) analysis, no differentially expressed proteins (DEPs) were found in leaf samples; however, 47 DEPs showed at least two-fold abundance variation (p < 0.05) in matured wheat grains and 21 spots were identified by tandem MALDI-TOF/TOF-MS. Among the identified spots, four were cultivar-specific, including three (spots B15, B16, and B21) in Chinese Spring and one in 3BS-8 (spot B10). Among variety-different DEPs between Chinese Spring and 3BS-8, most spots showed a higher express profile in CS; only four spots showed up-regulated expression tendency in 3BS-8. An interesting observation was that more than half of the identified protein spots were involved in storage proteins, of which 11 spots were identified as globulins. According to these results, we can presume that the encoded genes of protein spots B15, B16, and B21 were located on the chromosome segment deleted in 3BS-8. Full article
(This article belongs to the collection Advances in Proteomic Research)
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Open AccessArticle Effect of High-Dose Vitamin D3 Intake on Ambulation, Muscular Pain and Bone Mineral Density in a Woman with Multiple Sclerosis: A 10-Year Longitudinal Case Report
Int. J. Mol. Sci. 2012, 13(10), 13461-13483; doi:10.3390/ijms131013461
Received: 20 July 2012 / Revised: 28 August 2012 / Accepted: 18 September 2012 / Published: 19 October 2012
Cited by 2 | PDF Full-text (1041 KB) | HTML Full-text | XML Full-text
Abstract
Mounting evidence correlate vitamin D3 (cholecalciferol) supplementation or higher serum levels of vitamin D (25(OH)D) with a lower risk of developing multiple sclerosis (MS), reduced relapse rate, slower progression or fewer new brain lesions. We present here the case of a woman who
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Mounting evidence correlate vitamin D3 (cholecalciferol) supplementation or higher serum levels of vitamin D (25(OH)D) with a lower risk of developing multiple sclerosis (MS), reduced relapse rate, slower progression or fewer new brain lesions. We present here the case of a woman who was diagnosed with MS in 1990. From 1980 to 2000, her ability to walk decreased from ~20 to 1 km per day. Since January 2001, a vitamin D3 supplement was ingested daily. The starting dose was 20 mcg (800 IU)/day and escalated to 100 mcg (4000 IU)/day in September 2004 and then to 150 mcg (6000 IU)/day in December 2005. Vitamin D3 intake reduced muscular pain and improved ambulation from 1 (February 2000) to 14 km/day (February 2008). Vitamin D intake over 10 years caused no adverse effects: no hypercalcaemia, nephrolithiasis or hypercalciuria were observed. Bowel problems in MS may need to be addressed as they can cause malabsorption including calcium, which may increase serum PTH and 1,25(OH)2D levels, as well as bone loss. We suggest that periodic assessment of vitamin D3, calcium and magnesium intake, bowel problems and the measurement of serum 25(OH)D, PTH, Ca levels, UCa/Cr and bone health become part of the integral management of persons with MS. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessArticle Injury-Induced Accumulation of Glial Cell Line-Derived Neurotrophic Factor in the Rostral Part of the Injured Rat Spinal Cord
Int. J. Mol. Sci. 2012, 13(10), 13484-13500; doi:10.3390/ijms131013484
Received: 29 August 2012 / Revised: 2 October 2012 / Accepted: 8 October 2012 / Published: 19 October 2012
Cited by 5 | PDF Full-text (747 KB) | HTML Full-text | XML Full-text
Abstract
The spinal cord of a 7-week-old female Wistar rat was hemi-transected at thoracic position 10 with a razor blade, and changes in glial cell line-derived neurotrophic factor (GDNF) protein and mRNA expression levels in the spinal cord were examined. GDNF protein and mRNA
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The spinal cord of a 7-week-old female Wistar rat was hemi-transected at thoracic position 10 with a razor blade, and changes in glial cell line-derived neurotrophic factor (GDNF) protein and mRNA expression levels in the spinal cord were examined. GDNF protein and mRNA expression levels were evaluated by enzyme immunoassay and reverse transcription polymerase chain reaction, respectively. Although GDNF is distributed in the healthy spinal cord from 150 to 400 pg/g tissue in a regionally dependent manner, hemi-transection (left side) of the spinal cord caused a rapid increase in GDNF content in the ipsilateral rostral but not in the caudal part of the spinal cord. On the other hand, injury-induced GDNF mRNA was distributed limitedly in both rostral and caudal stumps. These observations suggest the possibility that increased GDNF in the rostral part is responsible for the accumulation of GDNF that may be constitutively transported from the rostral to caudal side within the spinal cord. Although such local increase of endogenous GDNF protein may not be sufficient for nerve regeneration and locomotor improvement, it may play a physiological role in supporting spinal neurons including motoneurons. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle A Systems Biology Approach to Understanding the Mechanisms of Action of Chinese Herbs for Treatment of Cardiovascular Disease
Int. J. Mol. Sci. 2012, 13(10), 13501-13520; doi:10.3390/ijms131013501
Received: 5 September 2012 / Revised: 11 October 2012 / Accepted: 15 October 2012 / Published: 19 October 2012
Cited by 27 | PDF Full-text (3576 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Traditional Chinese Medicine (TCM) involves a broad range of empirical testing and refinement and plays an important role in the health maintenance for people all over the world. However, due to the complexity of Chinese herbs, a full understanding of TCM’s action mechanisms
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Traditional Chinese Medicine (TCM) involves a broad range of empirical testing and refinement and plays an important role in the health maintenance for people all over the world. However, due to the complexity of Chinese herbs, a full understanding of TCM’s action mechanisms is still unavailable despite plenty of successful applications of TCM in the treatment of various diseases, including especially cardiovascular diseases (CVD), one of the leading causes of death. Thus in the present work, by incorporating the chemical predictors, target predictors and network construction approaches, an integrated system of TCM has been constructed to systematically uncover the underlying action mechanisms of TCM. From three representative Chinese herbs, i.e., Ligusticum chuanxiong Hort., Dalbergia odorifera T. Chen and Corydalis yanhusuo WT Wang which have been widely used in CVD treatment, by combinational use of drug absorption, distribution, metabolism and excretion (ADME) screening and network pharmacology techniques, we have generated 64 bioactive ingredients and identified 54 protein targets closely associated with CVD, of which 29 are common targets (52.7%) of the three herbs. The result provides new information on the efficiency of the Chinese herbs for the treatment of CVD and also explains one of the basic theories of TCM, i.e., “multiple herbal drugs can treat one disease”. The predicted potential targets were then mapped to target-disease and target-signal pathway connections, which revealed the relationships of the active ingredients with their potential targets, diseases and signal systems. This means that for the first time, the action mechanism of these three important Chinese herbs for the treatment of CVD is uncovered, by generating and identifying both their active ingredients and novel targets specifically related to CVD, which clarifies some of the common conceptions in TCM, and thus provides clues to modernize such specific herbal medicines. Full article
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Open AccessArticle A Simple Bioconjugate Attachment Protocol for Use in Single Molecule Force Spectroscopy Experiments Based on Mixed Self-Assembled Monolayers
Int. J. Mol. Sci. 2012, 13(10), 13521-13541; doi:10.3390/ijms131013521
Received: 22 August 2012 / Revised: 9 September 2012 / Accepted: 29 September 2012 / Published: 19 October 2012
Cited by 3 | PDF Full-text (4127 KB) | HTML Full-text | XML Full-text
Abstract
Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of
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Single molecule force spectroscopy is a technique that can be used to probe the interaction force between individual biomolecular species. We focus our attention on the tip and sample coupling chemistry, which is crucial to these experiments. We utilised a novel approach of mixed self-assembled monolayers of alkanethiols in conjunction with a heterobifunctional crosslinker. The effectiveness of the protocol is demonstrated by probing the biotin-avidin interaction. We measured unbinding forces comparable to previously reported values measured at similar loading rates. Specificity tests also demonstrated a significant decrease in recognition after blocking with free avidin. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessArticle Production of (R)-3-Quinuclidinol by E. coli Biocatalysts Possessing NADH-Dependent 3-Quinuclidinone Reductase (QNR or bacC) from Microbacterium luteolum and Leifsonia Alcohol Dehydrogenase (LSADH)
Int. J. Mol. Sci. 2012, 13(10), 13542-13553; doi:10.3390/ijms131013542
Received: 30 August 2012 / Revised: 27 September 2012 / Accepted: 11 October 2012 / Published: 19 October 2012
Cited by 6 | PDF Full-text (320 KB) | HTML Full-text | XML Full-text
Abstract
We found two NADH-dependent reductases (QNR and bacC) in Microbacterium luteolum JCM 9174 (M. luteolum JCM 9174) that can reduce 3-quinuclidinone to optically pure (R)-(−)-3-quinuclidinol. Alcohol dehydrogenase from Leifsonia sp. (LSADH) was combined with these reductases to regenerate NAD+
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We found two NADH-dependent reductases (QNR and bacC) in Microbacterium luteolum JCM 9174 (M. luteolum JCM 9174) that can reduce 3-quinuclidinone to optically pure (R)-(−)-3-quinuclidinol. Alcohol dehydrogenase from Leifsonia sp. (LSADH) was combined with these reductases to regenerate NAD+ to NADH in situ in the presence of 2-propanol as a hydrogen donor. The reductase and LSADH genes were efficiently expressed in E. coli cells. A number of constructed E. coli biocatalysts (intact or immobilized) were applied to the resting cell reaction and optimized. Under the optimized conditions, (R)-(−)-3-quinuclidinol was synthesized from 3-quinuclidinone (15% w/v, 939 mM) giving a conversion yield of 100% for immobilized QNR. The optical purity of the (R)-(−)-3-quinuclidinol produced by the enzymatic reactions was >99.9%. Thus, E. coli biocatalysis should be useful for the practical production of the pharmaceutically important intermediate, (R)-(−)-3-quinuclidinol. Full article
(This article belongs to the Special Issue Organic Synthesis Using Biocatalyst)
Open AccessArticle The Properties of Sintered Calcium Phosphate with [Ca]/[P] = 1.50
Int. J. Mol. Sci. 2012, 13(10), 13569-13586; doi:10.3390/ijms131013569
Received: 18 August 2012 / Revised: 10 October 2012 / Accepted: 15 October 2012 / Published: 22 October 2012
Cited by 8 | PDF Full-text (696 KB) | HTML Full-text | XML Full-text
Abstract
In order to obtain the properties of the sintered as-dried calcium phosphate with [Ca]/[P] = 1.50, the characteristics of sintered pellets have been investigated using X-ray diffraction (XRD), inductively coupled plasma-mass spectrometry (ICP-MS), Fourier-transform infrared (FT-IR) spectra, Vickers hardness indentation and scanning electron
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In order to obtain the properties of the sintered as-dried calcium phosphate with [Ca]/[P] = 1.50, the characteristics of sintered pellets have been investigated using X-ray diffraction (XRD), inductively coupled plasma-mass spectrometry (ICP-MS), Fourier-transform infrared (FT-IR) spectra, Vickers hardness indentation and scanning electron microscopy (SEM). When the pellet samples were sintered between 700 °C and 1200 °C for 4 h, the hydroxyapatite (Ca10(PO4)6(OH)2, HA) still maintained the major phase, accompanied with the rhenanite (NaCaPO4) as the secondary phase and β-tricalcium phosphate (β-Ca3(PO4)2, β-TCP) as the minor phases. In addition, the HA partially transformed to α-tricalcium phosphate (α-Ca3(PO4)2, α-TCP) and tetracalcium phosphate (Ca4(PO4)2O, TTCP), when the pellet samples were sintered at 1300 °C and 1400 °C, respectively, for 4 h. The maximum density and Vickers Hardness (HV) of sintered pellet samples were 2.85 g/cm3 (90.18% theoretical density (T.D.)) and 407, which appeared at 1200 °C and 900 °C, respectively. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle A Bead-Based Multiplexed Immunoassay to Evaluate Breast Cancer Biomarkers for Early Detection in Pre-Diagnostic Serum
Int. J. Mol. Sci. 2012, 13(10), 13587-13604; doi:10.3390/ijms131013587
Received: 30 August 2012 / Revised: 20 September 2012 / Accepted: 25 September 2012 / Published: 22 October 2012
Cited by 11 | PDF Full-text (476 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF))
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This study investigates whether a set of ten potential breast cancer serum biomarkers and cancer antigens (osteopontin (OPN), haptoglobin, cancer antigen 15-3 (CA15-3), carcinoembryonic antigen (CEA), cancer antigen 125 (CA-125), prolactin, cancer antigen 19-9 (CA19-9), α-fetoprotein (AFP), leptin and migration inhibitory factor (MIF)) can predict early stage breast cancer in samples collected before clinical diagnosis (phase III samples). We performed a nested case-control study within the Prospect-EPIC (European Prospective Investigation into Cancer and nutrition) cohort. We examined to what extent the biomarker panel could discriminate between 68 women diagnosed with breast cancer up to three years after enrollment and 68 matched healthy controls (all 56-64 years at baseline). Using a quantitative bead-based multiplexed assay, we determined protein concentrations in serum samples collected at enrollment. Principal Component Analysis (PCA) and Random Forest (RF) analysis revealed that on the basis of all ten proteins, early cases could not be separated from controls. When we combined serum protein concentrations and subject characteristics related to breast cancer risk in the RF analysis, this did not result in classification accuracy scores that could correctly classify the samples (sensitivity: 50%, specificity: 50%). Our findings indicate that this panel of selected tumor markers cannot be used for diagnosis of early breast cancer. Full article
(This article belongs to the collection Advances in Proteomic Research)
Open AccessArticle Enhancement of Tendon–Bone Healing for Anterior Cruciate Ligament (ACL) Reconstruction Using Bone Marrow-Derived Mesenchymal Stem Cells Infected with BMP-2
Int. J. Mol. Sci. 2012, 13(10), 13605-13620; doi:10.3390/ijms131013605
Received: 12 July 2012 / Revised: 13 September 2012 / Accepted: 8 October 2012 / Published: 22 October 2012
Cited by 18 | PDF Full-text (1120 KB) | HTML Full-text | XML Full-text
Abstract
At present, due to the growing attention focused on the issue of tendon–bone healing, we carried out an animal study of the use of genetic intervention combined with cell transplantation for the promotion of this process. Here, the efficacy of bone marrow stromal
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At present, due to the growing attention focused on the issue of tendon–bone healing, we carried out an animal study of the use of genetic intervention combined with cell transplantation for the promotion of this process. Here, the efficacy of bone marrow stromal cells infected with bone morphogenetic protein-2 (BMP-2) on tendon–bone healing was determined. A eukaryotic expression vector containing the BMP-2 gene was constructed and bone marrow-derived mesenchymal stem cells (bMSCs) were infected with a lentivirus. Next, we examined the viability of the infected cells and the mRNA and protein levels of BMP-2-infected bMSCs. Gastrocnemius tendons, gastrocnemius tendons wrapped by bMSCs infected with the control virus (bMSCs+Lv-Control), and gastrocnemius tendons wrapped by bMSCs infected with the recombinant BMP-2 virus (bMSCs+Lv-BMP-2) were used to reconstruct the anterior cruciate ligament (ACL) in New Zealand white rabbits. Specimens from each group were harvested four and eight weeks postoperatively and evaluated using biomechanical and histological methods. The bMSCs were infected with the lentivirus at an efficiency close to 100%. The BMP-2 mRNA and protein levels in bMSCs were significantly increased after lentiviral infection. The bMSCs and BMP-2-infected bMSCs on the gastrocnemius tendon improved the biomechanical properties of the graft in the bone tunnel; specifically, bMSCs infected with BMP-2 had a positive effect on tendon–bone healing. In the four-week and eight-week groups, bMSCs+Lv-BMP-2 group exhibited significantly higher maximum loads of 29.3 ± 7.4 N and 45.5 ± 11.9 N, respectively, compared with the control group (19.9 ± 6.4 N and 21.9 ± 4.9 N) (P = 0.041 and P = 0.001, respectively). In the eight-week groups, the stiffness of the bMSCs+Lv-BMP-2 group (32.5 ± 7.3) was significantly higher than that of the bMSCs+Lv-Control group (22.8 ± 7.4) or control groups (12.4 ± 6.0) (p = 0.036 and 0.001, respectively). Based on the histological findings, there was an increased amount of perpendicular collagen fibers formed between the tendon and bone in the bMSCs+Lv-Control and bMSCs+Lv-BMP-2 group, compared with the gastrocnemius tendons. The proliferation of cartilage-like cells and the formation of fibrocartilage-like tissue were highest within the bone tunnels in the bMSCs+Lv-BMP-2 group. These results suggest that this lentivirus can be used to efficiently infect bMSCs with BMP-2. Furthermore, tendons wrapped by bMSCs+Lv-BMP-2 improved tendon–bone healing. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessArticle Interleukin-6 Gene Promoter-572 C Allele May Play a Role in Rate of Disease Progression in Multiple Sclerosis
Int. J. Mol. Sci. 2012, 13(10), 13667-13679; doi:10.3390/ijms131013667
Received: 2 August 2012 / Revised: 20 September 2012 / Accepted: 27 September 2012 / Published: 22 October 2012
Cited by 6 | PDF Full-text (676 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis (MS) is an inflammatory demyelinating disease affecting the central nervous system. Although the exact pathogenesis of MS is unknown, it is generally considered to be an autoimmune disease, with numerous genetic and environmental factors determining disease susceptibility and severity. One important
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Multiple sclerosis (MS) is an inflammatory demyelinating disease affecting the central nervous system. Although the exact pathogenesis of MS is unknown, it is generally considered to be an autoimmune disease, with numerous genetic and environmental factors determining disease susceptibility and severity. One important mediator of immune responses and inflammation is interleukin-6 (IL-6). Previously, elevated levels of IL-6 in mononuclear cells in blood and in brain tissue from MS patients have been reported. Various polymorphisms in the promoter region of the IL6 gene have also been linked with IL-6 protein levels. In MS, several small studies have investigated whether two IL6 promoter polymorphisms (−597 G>A and −174 G>C) correlate with MS susceptibility, but with varying results. In the present study, we analyzed these polymorphisms, together with an additional polymorphism (−572 G>C) in 279 healthy controls and 509 patients with MS. We found no significant differences between MS patients and healthy controls for the different −597 or −174 IL6 promoter alleles or genotypes. There was a slight reduction in the percentage of individuals with MS who carried a C allele at position −572, although this was not significant after correction for multiple comparisons. Interestingly, however, the −572 C allele showed a significant correlation with the MS severity score, suggesting a possible role in disease progression. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessArticle Lack of Association of Estrogen Receptor Alpha Gene Polymorphisms with Cardiorespiratory and Metabolic Variables in Young Women
Int. J. Mol. Sci. 2012, 13(10), 13691-13703; doi:10.3390/ijms131013691
Received: 27 August 2012 / Revised: 25 September 2012 / Accepted: 10 October 2012 / Published: 22 October 2012
Cited by 3 | PDF Full-text (234 KB) | HTML Full-text | XML Full-text
Abstract
This study examined the association of estrogen receptor alpha gene (ESR1) polymorphisms with cardiorespiratory and metabolic parameters in young women. In total, 354 healthy women were selected for cardiopulmonary exercise testing and short-term heart rate (HR) variability (HRV) evaluation. The HRV
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This study examined the association of estrogen receptor alpha gene (ESR1) polymorphisms with cardiorespiratory and metabolic parameters in young women. In total, 354 healthy women were selected for cardiopulmonary exercise testing and short-term heart rate (HR) variability (HRV) evaluation. The HRV analysis was determined by the temporal indices rMSSD (square root of the mean squared differences of successive R–R intervals (RRi) divided by the number of RRi minus one), SDNN (root mean square of differences from mean RRi, divided by the number of RRi) and power spectrum components by low frequency (LF), high frequency (HF) and LF/HF ratio. Blood samples were obtained for serum lipids, estradiol and DNA extraction. ESR1 rs2234693 and rs9340799 polymorphisms were analyzed by PCR and fragment restriction analysis. HR and oxygen uptake (VO2) values did not differ between the ESR1 polymorphisms with respect to autonomic modulation. We not find a relationship between ESR1 T–A, T–G, C–A and C–G haplotypes and cardiorespiratory and metabolic variables. Multiple linear regression analysis demonstrated that VO2, total cholesterol and triglycerides influence HRV (p < 0.05). The results suggest that ESR1 variants have no effect on cardiorespiratory and metabolic variables, while HRV indices are influenced by aerobic capacity and lipids in healthy women. Full article
Open AccessArticle Detection of Ricin Intoxication in Mice Using Serum Peptide Profiling by MALDI-TOF/MS
Int. J. Mol. Sci. 2012, 13(10), 13704-13712; doi:10.3390/ijms131013704
Received: 4 September 2012 / Revised: 20 September 2012 / Accepted: 11 October 2012 / Published: 22 October 2012
Cited by 6 | PDF Full-text (468 KB) | HTML Full-text | XML Full-text
Abstract
Ricin toxin has been regarded as one of the most potent poisons in the plant kingdom, and there is no effective therapeutic countermeasure or licensed vaccine against it. Consequently, early detection of ricin intoxication is necessary. In this study, we took mice as
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Ricin toxin has been regarded as one of the most potent poisons in the plant kingdom, and there is no effective therapeutic countermeasure or licensed vaccine against it. Consequently, early detection of ricin intoxication is necessary. In this study, we took mice as test subjects, and used the technique of Matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF/MS) and ClinProt™ microparticle beads to set up an effective detection model with an accuracy of almost 100%. Eighty-two peaks in the mass range 1000–10,000 m/z were detected by ClinProTools software, and five different peaks with m/z of 4982.49, 1333.25, 1537.86, 4285.05 and 2738.88 had the greatest contribution to the accuracy and sensitivity of this model. They may therefore provide biomarkers for ricin intoxication. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessArticle Synthesis and Characterization of Mesoporous Silica Functionalized with Calix[4]arene Derivatives
Int. J. Mol. Sci. 2012, 13(10), 13726-13736; doi:10.3390/ijms131013726
Received: 20 July 2012 / Revised: 12 October 2012 / Accepted: 12 October 2012 / Published: 23 October 2012
Cited by 6 | PDF Full-text (412 KB) | HTML Full-text | XML Full-text
Abstract
This work reports a new method to covalently attach calix[4]arene derivatives onto MCM-41, using a diisocyanate as a linker. The modified mesoporous silicates were characterized by fourier transform infrared spectroscopy (FTIR), thermal analysis (TGA) and elemental analysis. The FTIR spectra and TGA analysis
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This work reports a new method to covalently attach calix[4]arene derivatives onto MCM-41, using a diisocyanate as a linker. The modified mesoporous silicates were characterized by fourier transform infrared spectroscopy (FTIR), thermal analysis (TGA) and elemental analysis. The FTIR spectra and TGA analysis verified that the calix[4]arene derivates are covalently attached to the mesoporous silica. The preservation of the MCM-41 channel system was checked by X-ray diffraction and nitrogen adsorption analysis. Full article
(This article belongs to the Section Material Sciences and Nanotechnology)
Open AccessArticle Transcriptome Analysis Reveals Putative Genes Involved in Iridoid Biosynthesis in Rehmannia glutinosa
Int. J. Mol. Sci. 2012, 13(10), 13748-13763; doi:10.3390/ijms131013748
Received: 6 August 2012 / Revised: 16 October 2012 / Accepted: 17 October 2012 / Published: 23 October 2012
Cited by 12 | PDF Full-text (461 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R
[...] Read more.
Rehmannia glutinosa, one of the most widely used herbal medicines in the Orient, is rich in biologically active iridoids. Despite their medicinal importance, no molecular information about the iridoid biosynthesis in this plant is presently available. To explore the transcriptome of R. glutinosa and investigate genes involved in iridoid biosynthesis, we used massively parallel pyrosequencing on the 454 GS FLX Titanium platform to generate a substantial EST dataset. Based on sequence similarity searches against the public sequence databases, the sequences were first annotated and then subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) based analysis. Bioinformatic analysis indicated that the 454 assembly contained a set of genes putatively involved in iridoid biosynthesis. Significantly, homologues of the secoiridoid pathway genes that were only identified in terpenoid indole alkaloid producing plants were also identified, whose presence implied that route II iridoids and route I iridoids share common enzyme steps in the early stage of biosynthesis. The gene expression patterns of four prenyltransferase transcripts were analyzed using qRT-PCR, which shed light on their putative functions in tissues of R. glutinosa. The data explored in this study will provide valuable information for further studies concerning iridoid biosynthesis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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Open AccessReview Prognostic and Predictive Roles of KRAS Mutation in Colorectal Cancer
Int. J. Mol. Sci. 2012, 13(10), 12153-12168; doi:10.3390/ijms131012153
Received: 26 July 2012 / Revised: 6 September 2012 / Accepted: 6 September 2012 / Published: 25 September 2012
Cited by 46 | PDF Full-text (1127 KB) | HTML Full-text | XML Full-text
Abstract
The RAS gene family is among the most studied and best characterized of the known cancer-related genes. Of the three human ras isoforms, KRAS is the most frequently altered gene, with mutations occurring in 17%–25% of all cancers. In particular, approximately 30%–40% of
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The RAS gene family is among the most studied and best characterized of the known cancer-related genes. Of the three human ras isoforms, KRAS is the most frequently altered gene, with mutations occurring in 17%–25% of all cancers. In particular, approximately 30%–40% of colon cancers harbor a KRAS mutation. KRAS mutations in colon cancers have been associated with poorer survival and increased tumor aggressiveness. Additionally, KRAS mutations in colorectal cancer lead to resistance to select treatment strategies. In this review we examine the history of KRAS, its prognostic value in patients with colorectal cancer, and evidence supporting its predictive value in determining appropriate therapies for patients with colorectal cancer. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Molecular Mechanisms of Cardiotoxicity Induced by ErbB Receptor Inhibitor Cancer Therapeutics
Int. J. Mol. Sci. 2012, 13(10), 12268-12286; doi:10.3390/ijms131012268
Received: 20 June 2012 / Revised: 20 August 2012 / Accepted: 17 September 2012 / Published: 26 September 2012
Cited by 11 | PDF Full-text (632 KB) | HTML Full-text | XML Full-text
Abstract
The introduction of the so-called “targeted therapies”, particularly those drugs that inhibit the activity of tyrosine kinases, has represented a remarkable progress in the treatment of cancer. Although these drugs improve survival rates in cancer, significant cardiotoxicity, manifesting as left vertricular dysfunction and/or
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The introduction of the so-called “targeted therapies”, particularly those drugs that inhibit the activity of tyrosine kinases, has represented a remarkable progress in the treatment of cancer. Although these drugs improve survival rates in cancer, significant cardiotoxicity, manifesting as left vertricular dysfunction and/or heart failure, has emerged. The ErbB receptor tyrosine kinases are being pursued as therapeutic targets because of their important roles in normal physiology and in cancer. Besides the fact that the ErbB receptors are indispensable during development and in normal adult physiology, epidermal growth factor (EGFR) and ErbB2 in particular have been implicated in the development of many human cancers. This review focuses on the rationale for targeting members of ErbB receptor family and numerous agents that are in use for inhibiting the pathway. We summarize the current knowledge on the physiological role of ErbB signaling in the ventricle and on structural aspects of ErbB receptor activation in cancer and cardiac cells. We examine the underlying mechanisms that result in on-target or off-target cardiotoxicities of ErbB inhibitors, which can influence the design of future anticancer therapies. Full article
(This article belongs to the Special Issue Molecular Mechanisms of Organ-Specific Toxicity)
Open AccessReview Phosphoproteomics and Lung Cancer Research
Int. J. Mol. Sci. 2012, 13(10), 12287-12314; doi:10.3390/ijms131012287
Received: 8 August 2012 / Revised: 14 September 2012 / Accepted: 19 September 2012 / Published: 26 September 2012
Cited by 8 | PDF Full-text (314 KB) | HTML Full-text | XML Full-text
Abstract
Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide
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Massive evidence suggests that genetic abnormalities contribute to the development of lung cancer. These molecular abnormalities may serve as diagnostic, prognostic and predictive biomarkers for this deadly disease. It is imperative to search these biomarkers in different tumorigenesis pathways so as to provide the most appropriate therapy for each individual patient with lung malignancy. Phosphoproteomics is a promising technology for the identification of biomarkers and novel therapeutic targets for cancer. Thousands of proteins interact via physical and chemical association. Moreover, some proteins can covalently modify other proteins post-translationally. These post-translational modifications ultimately give rise to the emergent functions of cells in sequence, space and time. Phosphoproteomics clinical researches imply the comprehensive analysis of the proteins that are expressed in cells or tissues and can be employed at different stages. In addition, understanding the functions of phosphorylated proteins requires the study of proteomes as linked systems rather than collections of individual protein molecules. In fact, proteomics approaches coupled with affinity chromatography strategies followed by mass spectrometry have been used to elucidate relevant biological questions. This article will discuss the relevant clues of post-translational modifications, phosphorylated proteins, and useful proteomics approaches to identify molecular cancer signatures. The recent progress in phosphoproteomics research in lung cancer will be also discussed. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Asymmetric Dimethylarginine as a Surrogate Marker of Endothelial Dysfunction and Cardiovascular Risk in Patients with Systemic Rheumatic Diseases
Int. J. Mol. Sci. 2012, 13(10), 12315-12335; doi:10.3390/ijms131012315
Received: 20 August 2012 / Revised: 15 September 2012 / Accepted: 19 September 2012 / Published: 26 September 2012
Cited by 23 | PDF Full-text (364 KB) | HTML Full-text | XML Full-text
Abstract
The last few decades have witnessed an increased life expectancy of patients suffering with systemic rheumatic diseases, mainly due to improved management, advanced therapies and preventative measures. However, autoimmune disorders are associated with significantly enhanced cardiovascular morbidity and mortality not fully explained by
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The last few decades have witnessed an increased life expectancy of patients suffering with systemic rheumatic diseases, mainly due to improved management, advanced therapies and preventative measures. However, autoimmune disorders are associated with significantly enhanced cardiovascular morbidity and mortality not fully explained by traditional cardiovascular disease (CVD) risk factors. It has been suggested that interactions between high-grade systemic inflammation and the vasculature lead to endothelial dysfunction and atherosclerosis, which may account for the excess risk for CVD events in this population. Diminished nitric oxide synthesis—due to down regulation of endothelial nitric oxide synthase—appears to play a prominent role in the imbalance between vasoactive factors, the consequent impairment of the endothelial hemostasis and the early development of atherosclerosis. Asymmetric dimethylarginine (ADMA) is one of the most potent endogenous inhibitors of the three isoforms of nitric oxide synthase and it is a newly discovered risk factor in the setting of diseases associated with endothelial dysfunction and adverse cardiovascular events. In the context of systemic inflammatory disorders there is increasing evidence that ADMA contributes to the vascular changes and to endothelial cell abnormalities, as several studies have revealed derangement of nitric oxide/ADMA pathway in different disease subsets. In this article we discuss the role of endothelial dysfunction in patients with rheumatic diseases, with a specific focus on the nitric oxide/ADMA system and we provide an overview on the literature pertaining to ADMA as a surrogate marker of subclinical vascular disease. Full article
(This article belongs to the Special Issue ADMA and Nitrergic System)
Open AccessReview Protein Arginine Methyltransferases (PRMTs): Promising Targets for the Treatment of Pulmonary Disorders
Int. J. Mol. Sci. 2012, 13(10), 12383-12400; doi:10.3390/ijms131012383
Received: 3 September 2012 / Revised: 19 September 2012 / Accepted: 19 September 2012 / Published: 27 September 2012
Cited by 12 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
Protein arginine methylation is a novel posttranslational modification that plays a pivotal role in a variety of intracellular events, such as signal transduction, protein-protein interaction and transcriptional regulation, either by the direct regulation of protein function or by metabolic products originating from protein
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Protein arginine methylation is a novel posttranslational modification that plays a pivotal role in a variety of intracellular events, such as signal transduction, protein-protein interaction and transcriptional regulation, either by the direct regulation of protein function or by metabolic products originating from protein arginine methylation that influence nitric oxide (NO)-dependent processes. A growing body of evidence suggests that both mechanisms are implicated in cardiovascular and pulmonary diseases. This review will present and discuss recent research on PRMTs and the methylation of non-histone proteins and its consequences for the pathogenesis of various lung disorders, including lung cancer, pulmonary fibrosis, pulmonary hypertension, chronic obstructive pulmonary disease and asthma. This article will also highlight novel directions for possible future investigations to evaluate the functional contribution of arginine methylation in lung homeostasis and disease. Full article
(This article belongs to the Special Issue ADMA and Nitrergic System)
Open AccessReview Computational Protein Engineering: Bridging the Gap between Rational Design and Laboratory Evolution
Int. J. Mol. Sci. 2012, 13(10), 12428-12460; doi:10.3390/ijms131012428
Received: 20 August 2012 / Revised: 16 September 2012 / Accepted: 17 September 2012 / Published: 28 September 2012
Cited by 17 | PDF Full-text (2055 KB) | HTML Full-text | XML Full-text
Abstract
Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary
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Enzymes are tremendously proficient catalysts, which can be used as extracellular catalysts for a whole host of processes, from chemical synthesis to the generation of novel biofuels. For them to be more amenable to the needs of biotechnology, however, it is often necessary to be able to manipulate their physico-chemical properties in an efficient and streamlined manner, and, ideally, to be able to train them to catalyze completely new reactions. Recent years have seen an explosion of interest in different approaches to achieve this, both in the laboratory, and in silico. There remains, however, a gap between current approaches to computational enzyme design, which have primarily focused on the early stages of the design process, and laboratory evolution, which is an extremely powerful tool for enzyme redesign, but will always be limited by the vastness of sequence space combined with the low frequency for desirable mutations. This review discusses different approaches towards computational enzyme design and demonstrates how combining newly developed screening approaches that can rapidly predict potential mutation “hotspots” with approaches that can quantitatively and reliably dissect the catalytic step can bridge the gap that currently exists between computational enzyme design and laboratory evolution studies. Full article
(This article belongs to the Special Issue Enzyme Optimization and Immobilization)
Open AccessReview Implication of Posttranslational Histone Modifications in Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(10), 12461-12486; doi:10.3390/ijms131012461
Received: 21 August 2012 / Revised: 17 September 2012 / Accepted: 20 September 2012 / Published: 28 September 2012
Cited by 7 | PDF Full-text (1085 KB) | HTML Full-text | XML Full-text
Abstract
Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of
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Histones are highly alkaline proteins that package and order the DNA into chromatin in eukaryotic cells. Nucleotide excision repair (NER) is a conserved multistep reaction that removes a wide range of generally bulky and/or helix-distorting DNA lesions. Although the core biochemical mechanism of NER is relatively well known, how cells detect and repair lesions in diverse chromatin environments is still under intensive research. As with all DNA-related processes, the NER machinery must deal with the presence of organized chromatin and the physical obstacles it presents. A huge catalogue of posttranslational histone modifications has been documented. Although a comprehensive understanding of most of these modifications is still lacking, they are believed to be important regulatory elements for many biological processes, including DNA replication and repair, transcription and cell cycle control. Some of these modifications, including acetylation, methylation, phosphorylation and ubiquitination on the four core histones (H2A, H2B, H3 and H4) or the histone H2A variant H2AX, have been found to be implicated in different stages of the NER process. This review will summarize our recent understanding in this area. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview Photoluminescence Intermittency from Single Quantum Dots to Organic Molecules: Emerging Themes
Int. J. Mol. Sci. 2012, 13(10), 12487-12518; doi:10.3390/ijms131012487
Received: 1 August 2012 / Revised: 11 September 2012 / Accepted: 17 September 2012 / Published: 28 September 2012
Cited by 17 | PDF Full-text (2058 KB) | HTML Full-text | XML Full-text
Abstract
Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to
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Recent experimental and theoretical studies of photoluminescence intermittency (PI) or “blinking” exhibited by single core/shell quantum dots and single organic luminophores are reviewed. For quantum dots, a discussion of early models describing the origin of PI in these materials and recent challenges to these models are presented. For organic luminophores the role of electron transfer, proton transfer and other photophysical processes in PI are discussed. Finally, new experimental and data analysis methods are outlined that promise to be instrumental in future discoveries regarding the origin(s) of PI exhibited by single emitters. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Figures

Open AccessReview MicroRNAs as Diagnostic Biomarkers in Gastric Cancer
Int. J. Mol. Sci. 2012, 13(10), 12544-12555; doi:10.3390/ijms131012544
Received: 24 July 2012 / Revised: 31 August 2012 / Accepted: 5 September 2012 / Published: 1 October 2012
Cited by 18 | PDF Full-text (183 KB) | HTML Full-text | XML Full-text
Abstract
Considering the high mortality rates and the unfavorable prognosis of gastric cancer (GC) as well as the lack of a clinical predictive marker, which is sufficiently sensitive to GC, it is of great significance to investigate new sensitive and specific markers for GC
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Considering the high mortality rates and the unfavorable prognosis of gastric cancer (GC) as well as the lack of a clinical predictive marker, which is sufficiently sensitive to GC, it is of great significance to investigate new sensitive and specific markers for GC diagnosis. MicroRNAs (miRNAs) could be a practical form of potential biomarkers in the diagnosis of human disease, and they are confirmed to be closely associated with GC. In this review, we discuss the recent research results that indicate the feasibility and clinical applications of miRNAs in GC. Although several challenges remain to be addressed, miRNAs have the potential to be applied in the diagnosis of GC. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview The Complexities of Epidemiology and Prevention of Gastrointestinal Cancers
Int. J. Mol. Sci. 2012, 13(10), 12556-12572; doi:10.3390/ijms131012556
Received: 1 August 2012 / Revised: 27 August 2012 / Accepted: 27 August 2012 / Published: 1 October 2012
Cited by 9 | PDF Full-text (204 KB) | HTML Full-text | XML Full-text
Abstract
Cancer epidemiology and prevention is one of the most well studied fields today. The more we can understand about the incidence and pathogenesis of this disease, the better we will be able to prevent it. Effective prevention strategies can decrease the mortality rate
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Cancer epidemiology and prevention is one of the most well studied fields today. The more we can understand about the incidence and pathogenesis of this disease, the better we will be able to prevent it. Effective prevention strategies can decrease the mortality rate of cancer significantly; this is why it is important to delineate the underlying causes. It has been well recognized that genetic mutations, sporadic or hereditary, may lead to increased chance of tumorigenesis. Detecting genetic mutations can lead to the identification of high-risk individuals with hereditary cancer syndromes, which may assist in devising prevention strategies. Further, environmental factors are known to play important roles in epidemiology and suggest prevention tools that could be implemented to reduce cancer incidence and subsequent cancer-associated morbidity and mortality. Chemoprevention has been tried in colon cancer and is finding new advancements in other carcinomas as well. Out of many environmental cancer preventive agents, the most notable developments are the identification of the role of vitamins E, vitamin D and folic acid. Increased consumption of these vitamins has shown to be inversely correlated with cancer risk. This review will highlight important aspects of cancer epidemiology in the most aggressive carcinomas of the gastrointestinal system focusing on colorectal adenocarcinoma and pancreatic adenocarcinoma. Additionally, some of the well-known and evolving aspects of epidemiology of colorectal and pancreatic cancer along with current and new prevention strategies will also be reviewed. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview The Role of Glucose Transporters in Brain Disease: Diabetes and Alzheimer’s Disease
Int. J. Mol. Sci. 2012, 13(10), 12629-12655; doi:10.3390/ijms131012629
Received: 1 August 2012 / Revised: 19 September 2012 / Accepted: 24 September 2012 / Published: 3 October 2012
Cited by 39 | PDF Full-text (632 KB) | HTML Full-text | XML Full-text
Abstract
The occurrence of altered brain glucose metabolism has long been suggested in both diabetes and Alzheimer’s diseases. However, the preceding mechanism to altered glucose metabolism has not been well understood. Glucose enters the brain via glucose transporters primarily present at the blood-brain barrier.
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The occurrence of altered brain glucose metabolism has long been suggested in both diabetes and Alzheimer’s diseases. However, the preceding mechanism to altered glucose metabolism has not been well understood. Glucose enters the brain via glucose transporters primarily present at the blood-brain barrier. Any changes in glucose transporter function and expression dramatically affects brain glucose homeostasis and function. In the brains of both diabetic and Alzheimer’s disease patients, changes in glucose transporter function and expression have been observed, but a possible link between the altered glucose transporter function and disease progress is missing. Future recognition of the role of new glucose transporter isoforms in the brain may provide a better understanding of brain glucose metabolism in normal and disease states. Elucidation of clinical pathological mechanisms related to glucose transport and metabolism may provide common links to the etiology of these two diseases. Considering these facts, in this review we provide a current understanding of the vital roles of a variety of glucose transporters in the normal, diabetic and Alzheimer’s disease brain. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
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Open AccessReview What Do Effective Treatments for Multiple Sclerosis Tell Us about the Molecular Mechanisms Involved in Pathogenesis?
Int. J. Mol. Sci. 2012, 13(10), 12665-12709; doi:10.3390/ijms131012665
Received: 2 August 2012 / Revised: 8 September 2012 / Accepted: 12 September 2012 / Published: 4 October 2012
Cited by 13 | PDF Full-text (554 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis is a potentially debilitating disease of the central nervous system. A concerted program of research by many centers around the world has consistently demonstrated the importance of the immune system in its pathogenesis. This knowledge has led to the formal testing
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Multiple sclerosis is a potentially debilitating disease of the central nervous system. A concerted program of research by many centers around the world has consistently demonstrated the importance of the immune system in its pathogenesis. This knowledge has led to the formal testing of a number of therapeutic agents in both animal models and humans. These clinical trials have shed yet further light on the pathogenesis of MS through their sometimes unexpected effects and by their differential effects in terms of impact on relapses, progression of the disease, paraclinical parameters (MRI) and the adverse events that are experienced. Here we review the currently approved medications for the commonest form of multiple sclerosis (relapsing-remitting) and the emerging therapies for which preliminary results from phase II/III clinical trials are available. A detailed analysis of the molecular mechanisms responsible for the efficacy of these medications in multiple sclerosis indicates that blockade or modulation of both T- and B-cell activation and migration pathways in the periphery or CNS can lead to amelioration of the disease. It is hoped that further therapeutic trials will better delineate the pathogenesis of MS, ultimately leading to even better treatments with fewer adverse effects. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessReview Crossing Paths in Human Renal Cell Carcinoma (hRCC)
Int. J. Mol. Sci. 2012, 13(10), 12710-12733; doi:10.3390/ijms131012710
Received: 26 July 2012 / Revised: 11 September 2012 / Accepted: 26 September 2012 / Published: 5 October 2012
Cited by 1 | PDF Full-text (1100 KB) | HTML Full-text | XML Full-text
Abstract
Historically, cell-signaling pathways have been studied as the compilation of isolated elements into a unique cascade that transmits extracellular stimuli to the tumor cell nucleus. Today, growing evidence supports the fact that intracellular drivers of tumor progression do not flow in a single
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Historically, cell-signaling pathways have been studied as the compilation of isolated elements into a unique cascade that transmits extracellular stimuli to the tumor cell nucleus. Today, growing evidence supports the fact that intracellular drivers of tumor progression do not flow in a single linear pathway, but disseminate into multiple intracellular pathways. An improved understanding of the complexity of cancer depends on the elucidation of the underlying regulatory networks at the cellular and intercellular levels and in their temporal dimension. The high complexity of the intracellular cascades causes the complete inhibition of the growth of one tumor cell to be very unlikely, except in cases in which the so-called “oncogene addiction” is known to be a clear trigger for tumor catastrophe, such as in the case of gastrointestinal stromal tumors or chronic myeloid leukemia. In other words, the separation and isolation of the driver from the passengers is required to improve accuracy in cancer treatment. This review will summarize the signaling pathway crossroads that govern renal cell carcinoma proliferation and the emerging understanding of how these pathways facilitate tumor escape. We outline the available evidence supporting the putative links between different signaling pathways and how they may influence tumor proliferation, differentiation, apoptosis, angiogenesis, metabolism and invasiveness. The conclusion is that tumor cells may generate their own crossroads/crosstalk among signaling pathways, thereby reducing their dependence on stimulation of their physiologic pathways. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview Theoretical Models for Surface Forces and Adhesion and Their Measurement Using Atomic Force Microscopy
Int. J. Mol. Sci. 2012, 13(10), 12773-12856; doi:10.3390/ijms131012773
Received: 2 July 2012 / Revised: 7 September 2012 / Accepted: 17 September 2012 / Published: 8 October 2012
Cited by 35 | PDF Full-text (2323 KB) | HTML Full-text | XML Full-text
Abstract
The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems.
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The increasing importance of studies on soft matter and their impact on new technologies, including those associated with nanotechnology, has brought intermolecular and surface forces to the forefront of physics and materials science, for these are the prevailing forces in micro and nanosystems. With experimental methods such as the atomic force spectroscopy (AFS), it is now possible to measure these forces accurately, in addition to providing information on local material properties such as elasticity, hardness and adhesion. This review provides the theoretical and experimental background of afs, adhesion forces, intermolecular interactions and surface forces in air, vacuum and in solution. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessReview Fragment-Based Screening by Protein Crystallography: Successes and Pitfalls
Int. J. Mol. Sci. 2012, 13(10), 12857-12879; doi:10.3390/ijms131012857
Received: 4 July 2012 / Revised: 30 August 2012 / Accepted: 19 September 2012 / Published: 8 October 2012
Cited by 14 | PDF Full-text (802 KB) | HTML Full-text | XML Full-text
Abstract
Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper,
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Fragment-based drug discovery (FBDD) concerns the screening of low-molecular weight compounds against macromolecular targets of clinical relevance. These compounds act as starting points for the development of drugs. FBDD has evolved and grown in popularity over the past 15 years. In this paper, the rationale and technology behind the use of X-ray crystallography in fragment based screening (FBS) will be described, including fragment library design and use of synchrotron radiation and robotics for high-throughput X-ray data collection. Some recent uses of crystallography in FBS will be described in detail, including interrogation of the drug targets β-secretase, phenylethanolamine N-methyltransferase, phosphodiesterase 4A and Hsp90. These examples provide illustrations of projects where crystallography is straightforward or difficult, and where other screening methods can help overcome the limitations of crystallography necessitated by diffraction quality. Full article
(This article belongs to the Special Issue Protein Crystallography in Molecular Biology)
Open AccessReview Fluorescence Lifetime Correlation Spectroscopy (FLCS): Concepts, Applications and Outlook
Int. J. Mol. Sci. 2012, 13(10), 12890-12910; doi:10.3390/ijms131012890
Received: 15 August 2012 / Revised: 14 September 2012 / Accepted: 19 September 2012 / Published: 9 October 2012
Cited by 20 | PDF Full-text (400 KB) | HTML Full-text | XML Full-text
Abstract
Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data
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Fluorescence Lifetime Correlation Spectroscopy (FLCS) is a variant of fluorescence correlation spectroscopy (FCS), which uses differences in fluorescence intensity decays to separate contributions of different fluorophore populations to FCS signal. Besides which, FLCS is a powerful tool to improve quality of FCS data by removing noise and distortion caused by scattered excitation light, detector thermal noise and detector afterpulsing. We are providing an overview of, to our knowledge, all published applications of FLCS. Although these are not numerous so far, they illustrate possibilities for the technique and the research topics in which FLCS has the potential to become widespread. Furthermore, we are addressing some questions which may be asked by a beginner user of FLCS. The last part of the text reviews other techniques closely related to FLCS. The generalization of the idea of FLCS paves the way for further promising application of the principle of statistical filtering of signals. Specifically, the idea of fluorescence spectral correlation spectroscopy is here outlined. Full article
(This article belongs to the Special Issue Advances in Single Molecule Spectroscopy)
Open AccessReview Peripheral Nerve Injuries and Transplantation of Olfactory Ensheathing Cells for Axonal Regeneration and Remyelination: Fact or Fiction?
Int. J. Mol. Sci. 2012, 13(10), 12911-12924; doi:10.3390/ijms131012911
Received: 2 August 2012 / Revised: 7 September 2012 / Accepted: 7 September 2012 / Published: 10 October 2012
Cited by 5 | PDF Full-text (1270 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Successful nerve regeneration after nerve trauma is not only important for the restoration of motor and sensory functions, but also to reduce the potential for abnormal sensory impulse generation that can occur following neuroma formation. Satisfying functional results after severe lesions are difficult
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Successful nerve regeneration after nerve trauma is not only important for the restoration of motor and sensory functions, but also to reduce the potential for abnormal sensory impulse generation that can occur following neuroma formation. Satisfying functional results after severe lesions are difficult to achieve and the development of interventional methods to achieve optimal functional recovery after peripheral nerve injury is of increasing clinical interest. Olfactory ensheathing cells (OECs) have been used to improve axonal regeneration and functional outcome in a number of studies in spinal cord injury models. The rationale is that the OECs may provide trophic support and a permissive environment for axonal regeneration. The experimental transplantation of OECs to support and enhance peripheral nerve regeneration is much more limited. This chapter reviews studies using OECs as an experimental cell therapy to improve peripheral nerve regeneration. Full article
(This article belongs to the Special Issue Neuroprotective Strategies 2012)
Open AccessReview Hyaluronan Synthase and Hyaluronidase Expression in Serous Ovarian Carcinoma is Related to Anatomic Site and Chemotherapy Exposure
Int. J. Mol. Sci. 2012, 13(10), 12925-12938; doi:10.3390/ijms131012925
Received: 3 August 2012 / Revised: 19 September 2012 / Accepted: 29 September 2012 / Published: 10 October 2012
Cited by 5 | PDF Full-text (394 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The present study investigated the expression and clinical role of hyaluronan synthases (HAS1-3) and hyaluronidases (Hyal1-3) in serous ovarian carcinoma. HAS and HYAL mRNA expression was analyzed in 97 tumors (61 effusions, 27 primary carcinomas, 9 solid metastases) using PCR and further studied
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The present study investigated the expression and clinical role of hyaluronan synthases (HAS1-3) and hyaluronidases (Hyal1-3) in serous ovarian carcinoma. HAS and HYAL mRNA expression was analyzed in 97 tumors (61 effusions, 27 primary carcinomas, 9 solid metastases) using PCR and further studied for association with clinicopathologic parameters, including survival. HAS1 mRNA was overexpressed in effusions compared to primary carcinomas and solid metastases (p < 0.001), and an alternatively spliced HAS1 was expressed only in effusions. HAS2 mRNA was overexpressed in solid metastases and primary carcinomas compared to effusions (p = 0.043), and HAS3 mRNA was overexpressed in primary carcinomas and effusions compared to solid metastases (p = 0.008). HYAL1 mRNA was absent in all specimens, whereas HYAL2 was expressed as two splice variants, of which HYAL2-var2 was overexpressed in solid metastases compared to effusions and primary carcinomas (p < 0.001). HYAL3 mRNA was expressed as wild-type and variant 1-3 form, the latter more highly in primary carcinomas and effusions compared to solid metastases (p = 0.006). HAS1 mRNA was overexpressed in pre- compared to post-chemotherapy effusions (p < 0.001), with opposite finding for HYAL2-var1 and HYAL3-WT (p = 0.016 and p = 0.024, respectively). Higher HYAL2-var1 and HAS1 splice variant mRNA expression in effusions was associated with longer (p = 0.033) and shorter (p = 0.047) overall survival, respectively. These data are the first to document a role for HAS and Hyal members in tumor progression in ovarian carcinoma, as evidenced by their differential expression as function of anatomic site and chemotherapy exposure, with a possible prognostic role for patients with malignant effusions. Full article
(This article belongs to the Special Issue Cancer Molecules in Ovarian Cancer 2012)
Open AccessReview Molecular Pathogenesis of Neuromyelitis Optica
Int. J. Mol. Sci. 2012, 13(10), 12970-12993; doi:10.3390/ijms131012970
Received: 3 August 2012 / Revised: 8 September 2012 / Accepted: 13 September 2012 / Published: 11 October 2012
Cited by 12 | PDF Full-text (1843 KB) | HTML Full-text | XML Full-text
Abstract
Neuromyelitis optica (NMO) is a rare autoimmune disorder, distinct from multiple sclerosis, causing inflammatory lesions in the optic nerves and spinal cord. An autoantibody (NMO IgG) against aquaporin-4 (AQP4), a water channel expressed on astrocytes is thought to be causative. Peripheral production of
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Neuromyelitis optica (NMO) is a rare autoimmune disorder, distinct from multiple sclerosis, causing inflammatory lesions in the optic nerves and spinal cord. An autoantibody (NMO IgG) against aquaporin-4 (AQP4), a water channel expressed on astrocytes is thought to be causative. Peripheral production of the antibody is triggered by an unknown process in genetically susceptible individuals. Anti-AQP4 antibody enters the central nervous system (CNS) when the blood brain barrier is made permeable and has high affinity for orthogonal array particles of AQP4. Like other autoimmune diseases, Th17 cells and their effector cytokines (such as interleukin 6) have been implicated in pathogenesis. AQP4 expressing peripheral organs are not affected by NMO IgG, but the antibody causes extensive astrocytic loss in specific regions of the CNS through complement mediated cytotoxicity. Demyelination occurs during the inflammatory process and is probably secondary to oligodendrocyte apoptosis subsequent to loss of trophic support from astrocytes. Ultimately, extensive axonal injury leads to severe disability. Despite rapid advances in the understanding of NMO pathogenesis, unanswered questions remain, particularly with regards to disease mechanisms in NMO IgG seronegative cases. Increasing knowledge of the molecular pathology is leading to improved treatment strategies. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessReview Disease Progression Mediated by Egr-1 Associated Signaling in Response to Oxidative Stress
Int. J. Mol. Sci. 2012, 13(10), 13104-13117; doi:10.3390/ijms131013104
Received: 2 August 2012 / Revised: 4 October 2012 / Accepted: 9 October 2012 / Published: 12 October 2012
Cited by 19 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
When cellular reducing enzymes fail to shield the cell from increased amounts of reactive oxygen species (ROS), oxidative stress arises. The redox state is misbalanced, DNA and proteins are damaged and cellular transcription networks are activated. This condition can lead to the initiation
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When cellular reducing enzymes fail to shield the cell from increased amounts of reactive oxygen species (ROS), oxidative stress arises. The redox state is misbalanced, DNA and proteins are damaged and cellular transcription networks are activated. This condition can lead to the initiation and/or to the progression of atherosclerosis, tumors or pulmonary hypertension; diseases that are decisively furthered by the presence of oxidizing agents. Redox sensitive genes, like the zinc finger transcription factor early growth response 1 (Egr-1), play a pivotal role in the pathophysiology of these diseases. Apart from inducing apoptosis, signaling partners like the MEK/ERK pathway or the protein kinase C (PKC) can activate salvage programs such as cell proliferation that do not ameliorate, but rather worsen their outcome. Here, we review the currently available data on Egr-1 related signal transduction cascades in response to oxidative stress in the progression of epidemiologically significant diseases. Knowing the molecular pathways behind the pathology will greatly enhance our ability to identify possible targets for the development of new therapeutic strategies. Full article
(This article belongs to the Special Issue Redox Signaling in Biology and Patho-Biology)
Open AccessReview MicroRNAs as Active Players in the Pathogenesis of Multiple Sclerosis
Int. J. Mol. Sci. 2012, 13(10), 13227-13239; doi:10.3390/ijms131013227
Received: 13 August 2012 / Revised: 27 September 2012 / Accepted: 8 October 2012 / Published: 15 October 2012
Cited by 22 | PDF Full-text (253 KB) | HTML Full-text | XML Full-text
Abstract
MicroRNAs (miRNAs) are a recently discovered group of small noncoding RNAs that regulate gene expression post-transcriptionally. They are highly expressed in cells of the immune system, as well as in the central nervous system, and they are deregulated in various neurological disorders. Emerging
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MicroRNAs (miRNAs) are a recently discovered group of small noncoding RNAs that regulate gene expression post-transcriptionally. They are highly expressed in cells of the immune system, as well as in the central nervous system, and they are deregulated in various neurological disorders. Emerging evidence underlines an involvement of miRNAs in the pathogenesis of Multiple Sclerosis (MS). A number of miRNAs have been found to be dysregulated in blood cells from MS patients, in brain lesions, as well as in biological fluids such as serum and plasma. Despite miRNA altered expression likely showing a high tissue specificity, some profile similarities could be observed for certain miRNAs such as miR-326—such as upregulation in both active lesions and blood—though not for others such as miR-323, which demonstrated upregulation in whole blood, active brain lesions, and T-reg cells, but not in the serum of MS patients. In this review, the possible role of miRNAs in MS pathogenesis will be discussed according to all the available literature, with a particular emphasis on the possibility of considering extracellular miRNAs as a new source for both biomarker identification and therapeutic target discovery. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessReview The Behavior of Matrix Metalloproteinases and Their Inhibitors in Colorectal Cancer
Int. J. Mol. Sci. 2012, 13(10), 13240-13263; doi:10.3390/ijms131013240
Received: 28 August 2012 / Revised: 8 October 2012 / Accepted: 10 October 2012 / Published: 16 October 2012
Cited by 31 | PDF Full-text (233 KB) | HTML Full-text | XML Full-text
Abstract
Matrix metalloproteinases (MMPs) play an important role in the degradation of extracellular matrix components crucial for tumor growth, invasion and metastasis. MMPs are controlled by natural inhibitors called tissue inhibitors of metalloproteinases (TIMPs). We and others have demonstrated that MMPs and TIMPs are
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Matrix metalloproteinases (MMPs) play an important role in the degradation of extracellular matrix components crucial for tumor growth, invasion and metastasis. MMPs are controlled by natural inhibitors called tissue inhibitors of metalloproteinases (TIMPs). We and others have demonstrated that MMPs and TIMPs are especially important in the process of tumor invasion, progression and the metastasis of colorectal cancer (CRC). It has been proposed that MMPs and TIMPs might play a part not only in tumor invasion and initiation of metastasis but also in carcinogenesis from colorectal adenomas. Several recent studies demonstrated that high preoperative serum or plasma MMP-2, MMP-9 and TIMP-1 antigen levels are strong predictive factors for poor prognosis in patients with CRC and their determination might be useful for identification of patients with higher risk for cancer recurrence. MMP-9 and TIMP-1 have significant potential tumor marker impact in CRC. Their diagnostic sensitivity is consistently higher than those of conventional biomarkers. The pharmacological targeting of CRC by the development of a new generation of selective inhibitors of MMPs, that is highly specific for certain MMPs, is a promising and challenging area for the future. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Histone Displacement during Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(10), 13322-13337; doi:10.3390/ijms131013322
Received: 5 September 2012 / Revised: 29 September 2012 / Accepted: 9 October 2012 / Published: 17 October 2012
Cited by 3 | PDF Full-text (267 KB) | HTML Full-text | XML Full-text
Abstract
Nucleotide excision repair (NER) is an important DNA repair mechanism required for cellular resistance against UV light and toxic chemicals such as those found in tobacco smoke. In living cells, NER efficiently detects and removes DNA lesions within the large nuclear macromolecular complex
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Nucleotide excision repair (NER) is an important DNA repair mechanism required for cellular resistance against UV light and toxic chemicals such as those found in tobacco smoke. In living cells, NER efficiently detects and removes DNA lesions within the large nuclear macromolecular complex called chromatin. The condensed nature of chromatin inhibits many DNA metabolizing activities, including NER. In order to promote efficient repair, detection of a lesion not only has to activate the NER pathway but also chromatin remodeling. In general, such remodeling is thought on the one hand to precede NER, thus allowing repair proteins to efficiently access DNA. On the other hand, after completion of the repair, the chromatin must be returned to its previous undamaged state. Chromatin remodeling can refer to three separate but interconnected processes, histone post-translational modifications, insertion of histone variants and histone displacement (including nucleosome sliding). Here we review current knowledge, and speculate about current unknowns, regarding those chromatin remodeling activities that physically displace histones before, during and after NER. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
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Open AccessReview Genetic Variability in DNA Repair Proteins in Age-Related Macular Degeneration
Int. J. Mol. Sci. 2012, 13(10), 13378-13397; doi:10.3390/ijms131013378
Received: 8 August 2012 / Revised: 11 September 2012 / Accepted: 14 September 2012 / Published: 18 October 2012
Cited by 10 | PDF Full-text (205 KB) | HTML Full-text | XML Full-text
Abstract
The pathogenesis of age-related macular degeneration (AMD) is complex and involves interactions between environmental and genetic factors, with oxidative stress playing an important role inducing damage in biomolecules, including DNA. Therefore, genetic variability in the components of DNA repair systems may influence the
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The pathogenesis of age-related macular degeneration (AMD) is complex and involves interactions between environmental and genetic factors, with oxidative stress playing an important role inducing damage in biomolecules, including DNA. Therefore, genetic variability in the components of DNA repair systems may influence the ability of the cell to cope with oxidative stress and in this way contribute to the pathogenesis of AMD. However, few reports have been published on this subject so far. We demonstrated that the c.977C>G polymorphism (rs1052133) in the hOGG1 gene and the c.972G>C polymorphism (rs3219489) in the MUTYH gene, the products of which play important roles in the repair of oxidatively damaged DNA, might be associated with the risk of AMD. Oxidative stress may promote misincorporation of uracil into DNA, where it is targeted by several DNA glycosylases. We observed that the g.4235T>C (rs2337395) and c.−32A>G (rs3087404) polymorphisms in two genes encoding such glycosylases, UNG and SMUG1, respectively, could be associated with the occurrence of AMD. Polymorphisms in some other DNA repair genes, including XPD (ERCC2), XRCC1 and ERCC6 (CSB) have also been reported to be associated with AMD. These data confirm the importance of the cellular reaction to DNA damage, and this may be influenced by variability in DNA repair genes, in AMD pathogenesis. Full article
(This article belongs to the Special Issue DNA Damage and Repair in Degenerative Diseases)
Open AccessReview The Role of MicroRNAs in Breast Cancer Migration, Invasion and Metastasis
Int. J. Mol. Sci. 2012, 13(10), 13414-13437; doi:10.3390/ijms131013414
Received: 27 August 2012 / Revised: 19 September 2012 / Accepted: 9 October 2012 / Published: 18 October 2012
Cited by 58 | PDF Full-text (340 KB) | HTML Full-text | XML Full-text
Abstract
MicroRNAs (miRNAs) are a major class of small, noncoding RNA molecules that regulate gene expression by targeting mRNAs to trigger either translational repression or mRNA degradation. They have recently been more widely investigated due to their potential role as targets for cancer therapy.
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MicroRNAs (miRNAs) are a major class of small, noncoding RNA molecules that regulate gene expression by targeting mRNAs to trigger either translational repression or mRNA degradation. They have recently been more widely investigated due to their potential role as targets for cancer therapy. Many miRNAs have been implicated in several human cancers, including breast cancer. miRNAs are known to regulate cell cycle and development, and thus may serve as useful targets for exploration in anticancer therapeutics. The link between altered miRNA signatures and breast cancer development and metastasis can be observed either through the loss of tumor suppressor miRNAs, such as let-7s, miR-30a/31/34a/125s/200s/203/205/206/342 or the overexpression of oncogenic miRNAs, such as miR-10b/21/135a/155/221/222/224/373/520c in breast cancer cells. Some of these miRNAs have also been validated in tumor specimens of breast cancer patients, underscoring their potential roles in diagnostics, as well as targets for novel therapeutics for breast cancer. In this review article, we will provide an overview and update of our current understanding of the mode of action of several of these well characterized miRNAs in breast cancer models. Therefore, better understanding of the gene networks orchestrated by these miRNAs may help exploit the full potential of miRNAs in regards to cancer diagnosis, treatment, and therapeutics. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Multiple Sclerosis: The Role of Cytokines in Pathogenesis and in Therapies
Int. J. Mol. Sci. 2012, 13(10), 13438-13460; doi:10.3390/ijms131013438
Received: 2 August 2012 / Revised: 1 October 2012 / Accepted: 11 October 2012 / Published: 19 October 2012
Cited by 22 | PDF Full-text (962 KB) | HTML Full-text | XML Full-textRetraction
Abstract
Multiple sclerosis, the clinical features and pathological correlate for which were first described by Charcot, is a chronic neuroinflammatory disease with unknown etiology and variable clinical evolution. Although neuroinflammation is a descriptive denominator in multiple sclerosis based on histopathological observations, namely the penetration
[...] Read more.
Multiple sclerosis, the clinical features and pathological correlate for which were first described by Charcot, is a chronic neuroinflammatory disease with unknown etiology and variable clinical evolution. Although neuroinflammation is a descriptive denominator in multiple sclerosis based on histopathological observations, namely the penetration of leukocytes into the central nervous system, the clinical symptoms of relapses, remissions and progressive paralysis are the result of losses of myelin and neurons. In the absence of etiological factors as targets for prevention and therapy, the definition of molecular mechanisms that form the basis of inflammation, demyelination and toxicity for neurons have led to a number of treatments that slow down disease progression in specific patient cohorts, but that do not cure the disease. Current therapies are directed to block the immune processes, both innate and adaptive, that are associated with multiple sclerosis. In this review, we analyze the role of cytokines in the multiple sclerosis pathogenesis and current/future use of them in treatments of multiple sclerosis. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)
Open AccessReview E2F1 and p53 Transcription Factors as Accessory Factors for Nucleotide Excision Repair
Int. J. Mol. Sci. 2012, 13(10), 13554-13568; doi:10.3390/ijms131013554
Received: 17 August 2012 / Revised: 10 October 2012 / Accepted: 15 October 2012 / Published: 19 October 2012
Cited by 6 | PDF Full-text (551 KB) | HTML Full-text | XML Full-text
Abstract
Many of the biochemical details of nucleotide excision repair (NER) have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating mechanisms
[...] Read more.
Many of the biochemical details of nucleotide excision repair (NER) have been established using purified proteins and DNA substrates. In cells however, DNA is tightly packaged around histones and other chromatin-associated proteins, which can be an obstacle to efficient repair. Several cooperating mechanisms enhance the efficiency of NER by altering chromatin structure. Interestingly, many of the players involved in modifying chromatin at sites of DNA damage were originally identified as regulators of transcription. These include ATP-dependent chromatin remodelers, histone modifying enzymes and several transcription factors. The p53 and E2F1 transcription factors are well known for their abilities to regulate gene expression in response to DNA damage. This review will highlight the underappreciated, transcription-independent functions of p53 and E2F1 in modifying chromatin structure in response to DNA damage to promote global NER. Full article
(This article belongs to the Special Issue Excising DNA Damage from Chromosomes: Entry Visas and Exit Strategies)
Open AccessReview Tanshinones: Sources, Pharmacokinetics and Anti-Cancer Activities
Int. J. Mol. Sci. 2012, 13(10), 13621-13666; doi:10.3390/ijms131013621
Received: 5 September 2012 / Revised: 8 October 2012 / Accepted: 11 October 2012 / Published: 22 October 2012
Cited by 39 | PDF Full-text (1085 KB) | HTML Full-text | XML Full-text
Abstract
Tanshinones are a class of abietane diterpene compound isolated from Salvia miltiorrhiza (Danshen or Tanshen in Chinese), a well-known herb in Traditional Chinese Medicine (TCM). Since they were first identified in the 1930s, more than 40 lipophilic tanshinones and structurally related compounds have
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Tanshinones are a class of abietane diterpene compound isolated from Salvia miltiorrhiza (Danshen or Tanshen in Chinese), a well-known herb in Traditional Chinese Medicine (TCM). Since they were first identified in the 1930s, more than 40 lipophilic tanshinones and structurally related compounds have been isolated from Danshen. In recent decades, numerous studies have been conducted to investigate the isolation, identification, synthesis and pharmacology of tanshinones. In addition to the well-studied cardiovascular activities, tanshinones have been investigated more recently for their anti-cancer activities in vitro and in vivo. In this review, we update the herbal and alternative sources of tanshinones, and the pharmacokinetics of selected tanshinones. We discuss anti-cancer properties and identify critical issues for future research. Whereas previous studies have suggested anti-cancer potential of tanshinones affecting multiple cellular processes and molecular targets in cell culture models, data from in vivo potency assessment experiments in preclinical models vary greatly due to lack of uniformity of solvent vehicles and routes of administration. Chemical modifications and novel formulations had been made to address the poor oral bioavailability of tanshinones. So far, human clinical trials have been far from ideal in their design and execution for the purpose of supporting an anti-cancer indication of tanshinones. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))
Open AccessReview Involvement of Oxidative Stress in Suppression of Insulin Biosynthesis under Diabetic Conditions
Int. J. Mol. Sci. 2012, 13(10), 13680-13690; doi:10.3390/ijms131013680
Received: 11 September 2012 / Revised: 9 October 2012 / Accepted: 18 October 2012 / Published: 22 October 2012
Cited by 7 | PDF Full-text (216 KB) | HTML Full-text | XML Full-text
Abstract
Type 2 diabetes is characterized by pancreatic β-cell dysfunction and insulin resistance, and the number of patients has markedly increased worldwide. In the diabetic state, hyperglycemia per se and subsequent induction of oxidative stress decrease insulin biosynthesis and secretion, leading to the aggravation
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Type 2 diabetes is characterized by pancreatic β-cell dysfunction and insulin resistance, and the number of patients has markedly increased worldwide. In the diabetic state, hyperglycemia per se and subsequent induction of oxidative stress decrease insulin biosynthesis and secretion, leading to the aggravation of Type 2 diabetes. In addition, there is substantial reduction in expression and/or activities of several insulin gene transcription factors. This process is known as β-cell glucose toxicity, which is often observed under diabetic conditions. Taken together, it is likely that oxidative stress explains, at least in part, the molecular mechanism for β-cell glucose toxicity, which is often observed in Type 2 diabetes. Full article
(This article belongs to the Section Molecular Toxicology)
Open AccessReview The Role of Neurotrophins in Multiple Sclerosis—Pathological and Clinical Implications
Int. J. Mol. Sci. 2012, 13(10), 13713-13725; doi:10.3390/ijms131013713
Received: 14 August 2012 / Revised: 28 September 2012 / Accepted: 10 October 2012 / Published: 22 October 2012
Cited by 3 | PDF Full-text (397 KB) | HTML Full-text | XML Full-text
Abstract
Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS) with unknown etiology. It was recently suggested that autoimmunity, which had long been considered to be destructive in MS, might also play a protective role in
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Multiple sclerosis (MS) is a chronic inflammatory demyelinating and neurodegenerative disease of the central nervous system (CNS) with unknown etiology. It was recently suggested that autoimmunity, which had long been considered to be destructive in MS, might also play a protective role in the CNS of MS patients. Neurotrophins are polypeptides belonging to the neurotrophic factor family. While neurotrophins mediate cell survival and proliferation in the nervous system, they are also expressed within peripheral blood mononuclear cells fraction (PBMCs) of immunological system. In MS additional neurotrophic support from PBMCs might compensate relative neurotrophins deficiency in the damaged CNS tissue that needs to be repaired. Failure to produce the adequate neurotrophins concentrations might result in decreased protection of the CNS, consequently leading to increased atrophy, which is the main determinant of MS patients’ end-point disability. There are several lines of evidence, both from clinical research and animal models, suggesting that neurotrophins play a pivotal role in neuroprotective and neuroregenerative processes that are often defective in the course of MS. It seems that neuroprotective strategies might be used as potentially valuable add-on therapies, alongside traditional immunomodulatory treatment in multiple sclerosis. Full article
(This article belongs to the Special Issue Recent Advances in the Research of Multiple Sclerosis)
Open AccessReview The Criteria to Confirm the Role of Epstein-Barr Virus in Nasopharyngeal Carcinoma Initiation
Int. J. Mol. Sci. 2012, 13(10), 13737-13747; doi:10.3390/ijms131013737
Received: 5 September 2012 / Revised: 16 October 2012 / Accepted: 17 October 2012 / Published: 23 October 2012
Cited by 7 | PDF Full-text (165 KB) | HTML Full-text | XML Full-text
Abstract
Epstein-Barr virus (EBV) is associated with nasopharyngeal carcinoma (NPC), but it remains obscure whether EBV is a viral cause of, or only an accompaniment of, NPC. We will discuss the accumulated evidence pointing to the relationship between EBV infection and NPC initiation from
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Epstein-Barr virus (EBV) is associated with nasopharyngeal carcinoma (NPC), but it remains obscure whether EBV is a viral cause of, or only an accompaniment of, NPC. We will discuss the accumulated evidence pointing to the relationship between EBV infection and NPC initiation from epidemiologic, pathogenic, molecular oncogenic, and experimental animal studies. We believe that convincing evidence from these perspectives must be provided before we can ascertain the causal role of EBV infection in NPC. Specifically, (1) epidemiological studies should reveal EBV infection as a risk factor; (2) the introduction of EBV into an animal model should produce NPC; (3) in the animal model NPC, the main molecular event(s) or the involved signaling pathway(s) should be identical to that in human NPC; and (4) finally and most importantly, prevention of EBV infection or clearance of EBV from infected individuals must be able to reduce the incidence rate of NPC. Full article
(This article belongs to the Special Issue Advances in Molecular Oncology (special issue))

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Open AccessShort Note Isolation and Characterization of Novel Genomic and EST-SSR Markers in Coreoperca whiteheadi Boulenger and Cross-Species Amplification
Int. J. Mol. Sci. 2012, 13(10), 13203-13211; doi:10.3390/ijms131013203
Received: 23 August 2012 / Revised: 13 September 2012 / Accepted: 8 October 2012 / Published: 15 October 2012
Cited by 4 | PDF Full-text (190 KB) | HTML Full-text | XML Full-text
Abstract
We described and characterized 11 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and seven genomic (G)-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide
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We described and characterized 11 expressed sequence tag (EST)-derived simple sequence repeats (SSR) and seven genomic (G)-derived SSRs in Coreoperca whiteheadi Boulenger. The EST-SSRs comprised 62.2% di-nucleotide repeats, 32.2% tri-nucleotide repeats and 5.5% tetra-nucleotide repeats, whereas the majority of the G-SSRs were tri-nuleotide repeats (81.4%). The number of alleles for the 18 loci ranged from 3 to 6, with a mean of 3.8 alleles per locus. The observed (Ho) and expected heterozygosities (He) values ranged from 0.375 to 1.000, and 0.477 to 0.757, respectively. The polymorphic information content (PIC) values ranged from 0.466 to 0.706. The mean values number of alleles, Ho, He, and PIC of EST-SSRs were higher than those of the G-SSRs. Four microsatellite loci deviated significantly from Hardy-Weinberg equilibrium (HWE) after Bonferroni correction and no significant deviations in linkage disequilibrium (LD) were observed. These loci are the first to be characterized in C. whiteheadi and should be useful in the investigation of a genetic evaluation for conservation. Compared with 11 loci in C. whiteheadi, 37 potential polymorphic EST-SSRs were found in Siniperca chuatsi (Basilewsky), which will provide a valuable tool for mapping studies and molecular breeding programs in S. chuatsi. Full article
(This article belongs to the Section Biochemistry, Molecular Biology and Biophysics)

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