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Int. J. Mol. Sci., Volume 10, Issue 3 (March 2009), Pages 724-1418

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Open AccessArticle AFM and Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) Studies on Formation of Air-Stable Supported Lipid Bilayers
Int. J. Mol. Sci. 2009, 10(3), 1407-1418; https://doi.org/10.3390/ijms10031407
Received: 31 January 2009 / Revised: 11 March 2009 / Accepted: 19 March 2009 / Published: 26 March 2009
Cited by 3 | PDF Full-text (402 KB) | HTML Full-text | XML Full-text
Abstract
Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the silicon
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Supported lipid bilayers (SLBs) were prepared by deposition of unilamellar vesicles on a silicon substrate. Atomic force microscopy (AFM) and a new Multiple Transmission-Reflection Infrared Spectroscopy (MTR-IR) developed by us were used to trace the dynamic formation of lipid bilayers on the silicon surfaces. The evolution from deformation of vesicles to formation of bilayers can be distinguished clearly by AFM imaging. MTR-IR provided high quality infrared spectra of ultrathin lipid bilayers with high sensitivity and high signal to noise ratio (SNR). The structural and orientational changes during vesicle’s fusion were monitored with MTR-IR. MTR-IR shows superiority over other infrared approaches for ultrathin films on standard silicon wafers in view of its economy and high sensitivity. Both MTR-IR and AFM results were consistent with each other and they provided more information for understanding the self-assembling procedure of SLBs. Full article
(This article belongs to the Special Issue Molecular Self-Assembly)
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Open AccessReview Molecular Pathogenesis of Alzheimer’s Disease: Reductionist versus Expansionist Approaches
Int. J. Mol. Sci. 2009, 10(3), 1386-1406; https://doi.org/10.3390/ijms10031386
Received: 27 February 2009 / Revised: 20 March 2009 / Accepted: 23 March 2009 / Published: 26 March 2009
Cited by 25 | PDF Full-text (239 KB) | HTML Full-text | XML Full-text
Abstract
Alzheimer’s disease (AD) is characterized clinically by dementia and pathologically by two hallmark lesions, senile plaques and neurofibrillary tangles. About a quarter century ago these hallmark lesions were purified and their protein constituents identified, precipitating an avalanche of molecular studies as well as
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Alzheimer’s disease (AD) is characterized clinically by dementia and pathologically by two hallmark lesions, senile plaques and neurofibrillary tangles. About a quarter century ago these hallmark lesions were purified and their protein constituents identified, precipitating an avalanche of molecular studies as well as substantial optimism about successful therapeutic intervention. In 2009, we now have copious knowledge on the biochemical cascades that produce these proteins, the different modifications and forms in which these proteins exist, and the ability to selectively target these proteins for therapeutic intervention on an experimental basis. At the same time, there has been no discernible alteration in the natural course of AD in humans. While it may be that the complexity of AD will exceed our capacity to make significant treatment progress for decades or more, a paradigm shift from the reductionism that defines amyloid-β and tau hypotheses, to one that more accurately reflects the meaning of neuropathological changes, may be warranted. We and others have demonstrated that AD pathology is a manifestation of cellular adaptation, specifically as a defense against oxidative injury. As such, AD pathology is therefore a host response rather than a manifestation of cytotoxic protein injury, and is unlikely to be a fruitful target for therapeutic intervention. An “expansionist” view of the disease, we believe, with oxidative stress as a pleiotropic and upstream process, more aptly describes the relationship between various and numerous molecular alterations and clinical disease. Full article
(This article belongs to the Special Issue Advances in Molecular Neuropathology)
Open AccessReview Slow Unfolding of Monomeric Proteins from Hyperthermophiles with Reversible Unfolding
Int. J. Mol. Sci. 2009, 10(3), 1369-1385; https://doi.org/10.3390/ijms10031369
Received: 28 January 2009 / Revised: 19 March 2009 / Accepted: 23 March 2009 / Published: 24 March 2009
Cited by 13 | PDF Full-text (250 KB) | HTML Full-text | XML Full-text
Abstract
Based on the differences in their optimal growth temperatures microorganisms can be classified into psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Proteins from hyperthermophiles generally exhibit greater stability than those from other organisms. In this review, we collect data about the stability and folding of
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Based on the differences in their optimal growth temperatures microorganisms can be classified into psychrophiles, mesophiles, thermophiles, and hyperthermophiles. Proteins from hyperthermophiles generally exhibit greater stability than those from other organisms. In this review, we collect data about the stability and folding of monomeric proteins from hyperthermophilies with reversible unfolding, from the equilibrium and kinetic aspects. The results indicate that slow unfolding is a general strategy by which proteins from hyperthermophiles adapt to higher temperatures. Hydrophobic interaction is one of the factors in the molecular mechanism of the slow unfolding of proteins from hyperthermophiles. Full article
(This article belongs to the Special Issue Protein Folding 2009)
Open AccessEditorial Protein Dynamics: From Molecules, to Interactions, to Biology
Int. J. Mol. Sci. 2009, 10(3), 1360-1368; https://doi.org/10.3390/ijms10031360
Received: 19 February 2009 / Revised: 13 March 2009 / Accepted: 17 March 2009 / Published: 20 March 2009
PDF Full-text (164 KB) | HTML Full-text | XML Full-text
Abstract
Proteins have a remarkably rich diversity of dynamical behaviors, and the articles in this issue of the International Journal of Molecular Sciences are a testament to that fact. From the picosecond motions of single sidechains probed by NMR or fluorescence spectroscopy, to aggregation
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Proteins have a remarkably rich diversity of dynamical behaviors, and the articles in this issue of the International Journal of Molecular Sciences are a testament to that fact. From the picosecond motions of single sidechains probed by NMR or fluorescence spectroscopy, to aggregation processes at interfaces that take months, all time scales play a role. Proteins are functional molecules, so by their nature they always interact with their environment. This environment includes water, other biomolecules, or larger cellular structures. In a sense, it also includes the protein molecule itself: proteins are large enough to fold and interact with themselves. These interactions have been honed by evolution to produce behaviors completely different from those of random polymers. Full article
(This article belongs to the Special Issue Protein Folding 2009)
Open AccessReview Participation of Low Molecular Weight Electron Carriers in Oxidative Protein Folding
Int. J. Mol. Sci. 2009, 10(3), 1346-1359; https://doi.org/10.3390/ijms10031346
Received: 3 February 2009 / Revised: 8 March 2009 / Accepted: 17 March 2009 / Published: 20 March 2009
Cited by 6 | PDF Full-text (249 KB) | HTML Full-text | XML Full-text
Abstract
Oxidative protein folding is mediated by a proteinaceous electron relay system, in which the concerted action of protein disulfide isomerase and Ero1 delivers the electrons from thiol groups to the final acceptor. Oxygen appears to be the final oxidant in aerobic living organisms,
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Oxidative protein folding is mediated by a proteinaceous electron relay system, in which the concerted action of protein disulfide isomerase and Ero1 delivers the electrons from thiol groups to the final acceptor. Oxygen appears to be the final oxidant in aerobic living organisms, although the existence of alternative electron acceptors, e.g. fumarate or nitrate, cannot be excluded. Whilst the protein components of the system are well-known, less attention has been turned to the role of low molecular weight electron carriers in the process. The function of ascorbate, tocopherol and vitamin K has been raised recently. In vitro and in vivo evidence suggests that these redox-active compounds can contribute to the functioning of oxidative folding. This review focuses on the participation of small molecular weight redox compounds in oxidative protein folding. Full article
(This article belongs to the Special Issue Protein Folding 2009)
Open AccessReview Mechanism of Suppression of Protein Aggregation by α-Crystallin
Int. J. Mol. Sci. 2009, 10(3), 1314-1345; https://doi.org/10.3390/ijms10031314
Received: 30 January 2009 / Revised: 13 March 2009 / Accepted: 18 March 2009 / Published: 19 March 2009
Cited by 41 | PDF Full-text (474 KB) | HTML Full-text | XML Full-text
Abstract
This review summarizes experimental data illuminating the mechanism of suppression of heat-induced protein aggregation by a-crystallin, one of the small heat shock proteins. The dynamic light scattering data show that the initial stage of thermal aggregation of proteins is the formation of the
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This review summarizes experimental data illuminating the mechanism of suppression of heat-induced protein aggregation by a-crystallin, one of the small heat shock proteins. The dynamic light scattering data show that the initial stage of thermal aggregation of proteins is the formation of the initial aggregates involving hundreds of molecules of the denatured protein. Further sticking of the starting aggregates proceeds in a regime of diffusion-limited cluster-cluster aggregation. The protective effect of a-crystallin is due to transition of the aggregation process to the regime of reaction-limited cluster-cluster aggregation, wherein the sticking probability for the colliding particles becomes lower than unity. Full article
(This article belongs to the Special Issue Protein Folding 2009)
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Open AccessReview In Vitro Models in Biocompatibility Assessment for Biomedical-Grade Chitosan Derivatives in Wound Management
Int. J. Mol. Sci. 2009, 10(3), 1300-1313; https://doi.org/10.3390/ijms10031300
Received: 5 February 2009 / Revised: 12 March 2009 / Accepted: 16 March 2009 / Published: 18 March 2009
Cited by 57 | PDF Full-text (132 KB) | HTML Full-text | XML Full-text
Abstract
One of the ultimate goals of wound healing research is to find effective healing techniques that utilize the regeneration of similar tissues. This involves the modification of various wound dressing biomaterials for proper wound management. The biopolymer chitosan (b-1,4-D-glucosamine) has natural biocompatibility and
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One of the ultimate goals of wound healing research is to find effective healing techniques that utilize the regeneration of similar tissues. This involves the modification of various wound dressing biomaterials for proper wound management. The biopolymer chitosan (b-1,4-D-glucosamine) has natural biocompatibility and biodegradability that render it suitable for wound management. By definition, a biocompatible biomaterial does not have toxic or injurious effects on biological systems. Chemical and physical modifications of chitosan influence its biocompatibility and biodegradability to an uncertain degree. Hence, the modified biomedical-grade of chitosan derivatives should be pre-examined in vitro in order to produce high-quality, biocompatible dressings. In vitro toxicity examinations are more favorable than those performed in vivo, as the results are more reproducible and predictive. In this paper, basic in vitro tools were used to evaluate cellular and molecular responses with regard to the biocompatibility of biomedical-grade chitosan. Three paramount experimental parameters of biocompatibility in vitro namely cytocompatibility, genotoxicity and skin pro-inflammatory cytokine expression, were generally reviewed for biomedical-grade chitosan as wound dressing. Full article
(This article belongs to the Special Issue Biocompatibility of Materials)
Open AccessArticle Origin of Homochirality in Biosystems
Int. J. Mol. Sci. 2009, 10(3), 1290-1299; https://doi.org/10.3390/ijms10031290
Received: 12 January 2009 / Revised: 12 March 2009 / Accepted: 18 March 2009 / Published: 18 March 2009
Cited by 17 | PDF Full-text (187 KB) | HTML Full-text | XML Full-text
Abstract
Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous
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Experimental data for a series of central and simple molecules in biosystems show that some amino acids and a simple sugar molecule have a chiral discrimination in favor of homochirality. Models for segregation of racemic mixtures of chiral amphiphiles and lipophiles in aqueous solutions show that the amphiphiles with an active isomerization kinetics can perform a spontaneous break of symmetry during the segregation and self-assembly to homochiral matter. Based on this observation it is argued that biomolecules with a sufficiently strong chiral discrimination could be the origin of homochirality in biological systems. Full article
(This article belongs to the Special Issue Origin of Life)
Open AccessArticle Explaining Ionic Liquid Water Solubility in Terms of Cation and Anion Hydrophobicity
Int. J. Mol. Sci. 2009, 10(3), 1271-1289; https://doi.org/10.3390/ijms10031271
Received: 12 February 2009 / Revised: 11 March 2009 / Accepted: 16 March 2009 / Published: 18 March 2009
Cited by 68 | PDF Full-text (314 KB) | HTML Full-text | XML Full-text
Abstract
The water solubility of salts is ordinarily dictated by lattice energy and ion solvation. However, in the case of low melting salts also known as ionic liquids, lattice energy is immaterial and differences in hydrophobicity largely account for differences in their water solubility.
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The water solubility of salts is ordinarily dictated by lattice energy and ion solvation. However, in the case of low melting salts also known as ionic liquids, lattice energy is immaterial and differences in hydrophobicity largely account for differences in their water solubility. In this contribution, the activity coefficients of ionic liquids in water are split into cation and anion contributions by regression against cation hydrophobicity parameters that are experimentally determined by reversed phase liquid chromatography. In this way, anion hydrophobicity parameters are derived, as well as an equation to estimate water solubilities for cation-anion combinations for which the water solubility has not been measured. Thus, a new pathway to the quantification of aqueous ion solvation is shown, making use of the relative weakness of interactions between ionic liquid ions as compared to their hydrophobicities. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
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Open AccessArticle Dielectric Properties of Binary Solvent Mixtures of Dimethyl Sulfoxide with Water
Int. J. Mol. Sci. 2009, 10(3), 1261-1270; https://doi.org/10.3390/ijms10031261
Received: 6 February 2009 / Revised: 8 March 2009 / Accepted: 11 March 2009 / Published: 17 March 2009
Cited by 34 | PDF Full-text (275 KB) | HTML Full-text | XML Full-text
Abstract
In this paper, the dielectric properties of water-dimethylsulfoxide (DMSO) mixtures with different mole ratios have been investigated in the range of 1 GHz to 40 GHz at 298 K by using a molecular dynamics (MD) simulation. Only one dielectric loss peak was observed
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In this paper, the dielectric properties of water-dimethylsulfoxide (DMSO) mixtures with different mole ratios have been investigated in the range of 1 GHz to 40 GHz at 298 K by using a molecular dynamics (MD) simulation. Only one dielectric loss peak was observed in the frequency range and the relaxation in these mixtures can be described by a single relaxation time of the Davidson-Cole. It was observed that within experimental error the dielectric relaxation can be described by the Debye-like model (β ≈ 1, S.M. Puranik, et al. J. Chem. Soc. Faraday Trans.1992, 88, 433 - 435). In general, the results are very consistent with the experimental measurements. Full article
(This article belongs to the Section Physical Chemistry, Theoretical and Computational Chemistry)
Open AccessReview Physiological and Pathological Role of Alpha-synuclein in Parkinson’s Disease Through Iron Mediated Oxidative Stress; The Role of a Putative Iron-responsive Element
Int. J. Mol. Sci. 2009, 10(3), 1226-1260; https://doi.org/10.3390/ijms10031226
Received: 31 December 2008 / Revised: 3 March 2009 / Accepted: 11 March 2009 / Published: 17 March 2009
Cited by 47 | PDF Full-text (307 KB) | HTML Full-text | XML Full-text
Abstract
Parkinson’s disease (PD) is the second most common progressive neurodegenerative disorder after Alzheimer's disease (AD) and represents a large health burden to society. Genetic and oxidative risk factors have been proposed as possible causes, but their relative contribution remains unclear. Dysfunction of alpha-synuclein
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Parkinson’s disease (PD) is the second most common progressive neurodegenerative disorder after Alzheimer's disease (AD) and represents a large health burden to society. Genetic and oxidative risk factors have been proposed as possible causes, but their relative contribution remains unclear. Dysfunction of alpha-synuclein (α-syn) has been associated with PD due to its increased presence, together with iron, in Lewy bodies. Brain oxidative damage caused by iron may be partly mediated by α-syn oligomerization during PD pathology. Also, α-syn gene dosage can cause familial PD and inhibition of its gene expression by blocking translation via a newly identified Iron Responsive Element-like RNA sequence in its 5’-untranslated region may provide a new PD drug target. Full article
(This article belongs to the Special Issue Advances in Molecular Neuropathology)
Open AccessArticle Ultra Low-Dose Radiation: Stress Responses and Impacts Using Rice as a Grass Model
Int. J. Mol. Sci. 2009, 10(3), 1215-1225; https://doi.org/10.3390/ijms10031215
Received: 5 February 2009 / Revised: 11 March 2009 / Accepted: 13 March 2009 / Published: 16 March 2009
Cited by 13 | PDF Full-text (358 KB) | HTML Full-text | XML Full-text
Abstract
We report molecular changes in leaves of rice plants (Oryza sativa L. - reference crop plant and grass model) exposed to ultra low-dose ionizing radiation, first using contaminated soil from the exclusion zone around Chernobyl reactor site. Results revealed induction of stress-related
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We report molecular changes in leaves of rice plants (Oryza sativa L. - reference crop plant and grass model) exposed to ultra low-dose ionizing radiation, first using contaminated soil from the exclusion zone around Chernobyl reactor site. Results revealed induction of stress-related marker genes (Northern blot) and secondary metabolites (LC-MS/MS) in irradiated leaf segments over appropriate control. Second, employing the same in vitro model system, we replicated results of the first experiment using in-house fabricated sources of ultra low-dose gamma (g) rays and selected marker genes by RT-PCR. Results suggest the usefulness of the rice model in studying ultra low-dose radiation response/s. Full article
(This article belongs to the Special Issue Biotic and Abiotic Stress)
Open AccessArticle Quantum-SAR Extension of the Spectral-SAR Algorithm. Application to Polyphenolic Anticancer Bioactivity
Int. J. Mol. Sci. 2009, 10(3), 1193-1214; https://doi.org/10.3390/ijms10031193
Received: 18 January 2009 / Revised: 9 March 2009 / Accepted: 11 March 2009 / Published: 16 March 2009
Cited by 33 | PDF Full-text (295 KB) | HTML Full-text | XML Full-text
Abstract
Aiming to assess the role of individual molecular structures in the molecular mechanism of ligand-receptor interaction correlation analysis, the recent Spectral-SAR approach is employed to introduce the Quantum-SAR (QuaSAR) “wave” and “conversion factor” in terms of difference between inter-endpoint inter-molecular activities for a
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Aiming to assess the role of individual molecular structures in the molecular mechanism of ligand-receptor interaction correlation analysis, the recent Spectral-SAR approach is employed to introduce the Quantum-SAR (QuaSAR) “wave” and “conversion factor” in terms of difference between inter-endpoint inter-molecular activities for a given set of compounds; this may account for inter-conversion (metabolization) of molecular (concentration) effects while indicating the structural (quantum) based influential/detrimental role on bio-/eco- effect in a causal manner rather than by simple inspection of measured values; the introduced QuaSAR method is then illustrated for a study of the activity of a series of flavonoids on breast cancer resistance protein. Full article
(This article belongs to the Special Issue Recent Advances in QSAR/QSPR Theory)
Open AccessReview Philosophical Basis and Some Historical Aspects of Systems Biology: From Hegel to Noble - Applications for Bioenergetic Research
Int. J. Mol. Sci. 2009, 10(3), 1161-1192; https://doi.org/10.3390/ijms10031161
Received: 3 February 2009 / Revised: 7 March 2009 / Accepted: 12 March 2009 / Published: 13 March 2009
Cited by 28 | PDF Full-text (1541 KB) | HTML Full-text | XML Full-text
Abstract
We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems
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We live in times of paradigmatic changes for the biological sciences. Reductionism, that for the last six decades has been the philosophical basis of biochemistry and molecular biology, is being displaced by Systems Biology, which favors the study of integrated systems. Historically, Systems Biology - defined as the higher level analysis of complex biological systems - was pioneered by Claude Bernard in physiology, Norbert Wiener with the development of cybernetics, and Erwin Schrödinger in his thermodynamic approach to the living. Systems Biology applies methods inspired by cybernetics, network analysis, and non-equilibrium dynamics of open systems. These developments follow very precisely the dialectical principles of development from thesis to antithesis to synthesis discovered by Hegel. Systems Biology opens new perspectives for studies of the integrated processes of energy metabolism in different cells. These integrated systems acquire new, system-level properties due to interaction of cellular components, such as metabolic compartmentation, channeling and functional coupling mechanisms, which are central for regulation of the energy fluxes. State of the art of these studies in the new area of Molecular System Bioenergetics is analyzed. Full article
(This article belongs to the Special Issue Molecular System Bioenergetics)
Open AccessArticle Changes in Metallothionein Level in Rat Hepatic Tissue after Administration of Natural Mouldy Wheat
Int. J. Mol. Sci. 2009, 10(3), 1138-1160; https://doi.org/10.3390/ijms10031138
Received: 3 January 2009 / Revised: 28 February 2009 / Accepted: 9 March 2009 / Published: 12 March 2009
Cited by 16 | PDF Full-text (644 KB) | HTML Full-text | XML Full-text
Abstract
Mycotoxins are secondary metabolites produced by microfungi that are capable of causing disease and death in humans and other animals. This work was aimed at investigation of influence of mouldy wheat contaminated by pathogenic fungi producing mycotoxins on metallothionein levels in hepatic tissue
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Mycotoxins are secondary metabolites produced by microfungi that are capable of causing disease and death in humans and other animals. This work was aimed at investigation of influence of mouldy wheat contaminated by pathogenic fungi producing mycotoxins on metallothionein levels in hepatic tissue of rats. The rats were administrating feed mixtures with different contents of vitamins or naturally mouldy wheat for 28 days. It was found that the wheat contained deoxynivalenol (80 ± 5 µg per kg of mouldy wheat), zearalenone (56 ± 3 µg/kg), T2-toxin (20 ± 2 µg/kg) and aflatoxins as a sum of B1, B2, G1 and G2 (3.9 ± 0.2 µg/kg). Rats were fed diets containing 0, 33, 66 and 100% naturally moulded wheat. Control group 0, 33, 66 and 100% contained vitamins according to Nutrient Requirements of Rats (NRC). Other four groups (control group with vitamins, vit33, vit66 and vit100%) were fed on the same levels of mouldy wheat, also vitamins at levels 100% higher than the previous mixtures. We determined weight, feed conversion and performed dissection to observe pathological processes. Changes between control group and experimental groups exposed to influence of mouldy wheat and experimental groups supplemented by higher concentration of vitamins and mouldy wheat were not observed. Livers were sampled and did not demonstrate significant changes in morphology compared to control either. In the following experiments the levels of metallothionein as a marker of oxidative stress was determined. We observed a quite surprising trend in metallothionein levels in animals supplemented with increased concentration of vitamins. Its level enhanced with increasing content of mouldy wheat. It was possible to determine a statistically significant decline (p<0.05) between control group and groups of animals fed with 33, 66 and 100% mouldy wheat. It is likely that some mycotoxins presented in mouldy wheat are able to block the mechanism of metallothionein synthesis. Full article
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