A molecular dynamics study of the influence of chain branching on the properties of polymer systems

Die vorliegende Arbeit beschäftigt sich mit dem Einfluß von Kettenverzweigungen unterschiedlicher Topologien auf die statischen Eigenschaften von Polymeren. Diese Untersuchungen werden mit Hilfe von Monte-Carlo- und Molekular-Dynamik-Simulationen durchgeführt.Zunächst werden einige theoretische Konzepte und Modelle eingeführt, welche die Beschreibung von Polymerketten auf mesoskopischen Längenskalen gestatten. Es werden wichtige Bestimmungsgrößen eingeführt und erläutert, welche zur quantitativen Charakterisierung von Verzweigungsstrukturen bei Polymeren geeignet sind. Es wird ebenso auf die verwendeten Optimierungstechniken eingegangen, die bei der Implementierung des Computerprogrammes Verwendung fanden. Untersucht werden neben linearen Polymerketten unterschiedliche Topolgien -Sternpolymere mit variabler Armzahl, Übergang von Sternpolymeren zu linearen Polymeren, Ketten mit variabler Zahl von Seitenketten, reguläre Dendrimere und hyperverzweigte Strukturen - in Abhängigkeit von der Lösungsmittelqualität. Es wird zunächst eine gründliche Analyse des verwendeten Simulationsmodells an sehr langen linearen Einzelketten vorgenommen. Die Skalierungseigenschaften der linearen Ketten werden untersucht in dem gesamten Lösungsmittelbereich vom guten Lösungsmittel bis hin zu weitgehend kollabierten Ketten im schlechten Lösungsmittel. Ein wichtiges Ergebnis dieser Arbeit ist die Bestätigung der Korrekturen zum Skalenverhalten des hydrodynamischen Radius Rh. Dieses Ergebnis war möglich aufgrund der großen gewählten Kettenlängen und der hohen Qualität der erhaltenen Daten in dieser Arbeit, insbesondere bei den linearen ketten, und es steht im Widerspruch zu vielen bisherigen Simulations-Studien und experimentellen Arbeiten. Diese Korrekturen zum Skalenverhalten wurden nicht nur für die linearen Ketten, sondern auch für Sternpolymere mit unterchiedlicher Armzahl gezeigt. Für lineare Ketten wird der Einfluß von Polydispersität untersucht.Es wird gezeigt, daß eine eindeutige Abbildung von Längenskalen zwischen Simulationsmodell und Experiment nicht möglich ist, da die zu diesem Zweck verwendete dimensionslose Größe eine zu schwache Abhängigkeit von der Polymerisation der Ketten besitzt. Ein Vergleich von Simulationsdaten mit industriellem Low-Density-Polyäthylen(LDPE) zeigt, daß LDPE in Form von stark verzweigten Ketten vorliegt.Für reguläre Dendrimere konnte ein hochgradiges Zurückfalten der Arme in die innere Kernregion nachgewiesen werden.

Regulation of product chain length by isoprenyl diphosphate synthases

An analysis of the x-ray structure of homodimeric avian farnesyl diphosphate synthase (geranyltransferase, EC 2.5.1.10) coupled with information about conserved amino acids obtained from a sequence alignment of 35 isoprenyl diphosphate synthases that synthesize farnesyl (C15), geranylgeranyl (C20), and higher chain length isoprenoid diphosphates suggested that the side chains of residues corresponding to F112 and F113 in the avian enzyme were important for determining the ultimate length of the hydrocarbon chains. This hypothesis was supported by site-directed mutagenesis to transform wild-type avian farnesyl diphosphate synthase (FPS) into synthases capable of producing geranylgeranyl diphosphate (F112A), geranylfarnesyl (C25) diphosphate (F113S), and longer chain prenyl diphosphates (F112A/F113S). An x-ray analysis of the structure of the F112A/F113S mutant in the apo state and with allylic substrates bound produced the strongest evidence that these mutations caused the observed change in product specificity by directly altering the size of the binding pocket for the growing isoprenoid chain in the active site of the enzyme. The proposed binding pocket in the apo mutant structure was increased in depth by 5.8 Å as compared with that for the wild-type enzyme. Allylic diphosphates were observed in the holo structures, bound through magnesium ions to the aspartates of the first of two conserved aspartate-rich sequences (D117–D121), with the hydrocarbon tails of all the ligands growing down the hydrophobic pocket toward the mutation site. A model was constructed to show how the growth of a long chain prenyl product may proceed by creation of a hydrophobic passageway from the FPS active site to the outside surface of the enzyme.

Prospecção química e avaliação biológica de Banisteriopsis laevifolia (Malpighiaceae)

The Banisteriopsis genus is widespread in traditional medicine. This work aims to contribute with information about the chemical composition and on the evaluation of the biological activity of the essential oil, the ethanol extract of the leaves and partitions of the Banisteriopsis laevifolia. The phytochemical screeningtest of ethanol extract and partitions of leaves indicated the presence of flavonoids, terpenoids, saponins, phenols and steroids compounds. Nitrogenous compounds, characteristic of some species of this family, were not detected. Flavonoids were the predominant metabolite, with the highest concentrations on the partitions ethyl acetate and n-butanol. The antibacterial activity, antifungal and cytotoxicity of the essetial oil, ethanol extract and partitions were assyed by microdilution broth method (MBM), where the minimum inhibitory concentrations (MIC) were calculated. The ethanol extract and partitions did not inhibit growth against to Gram positive bacteria tested, with MIC less than 400 mg L-1. For the Gram negative bacteria tested, the hexane and hydroethanol partitios were more effective against F. nucleatum bacteria (MIC 100 ug mL-1). The ethanol extract showed antifungal activity with MIC of 31.2 mg L-1. Ethyl acetate and n-butanol partitions showed MIC 187.5 mg L-1 and 93.7 mg L-1, respectively, arousing interest for isolation studies. The antioxidant activity was evaluated by the DPPH free radical method. The ethanolic extract, ethyl acetate and n-butanol partitions were active, since they showed EC50 values (4.53 ug mL-1, 4.07 and 8.39 ug mL-1, respectively), values equivalent to the BHT (7.3 mg L-1). The analysis by HPLC-MS/MS of the most active fractions (ethyl acetate and n-butanol) identified phenolic compounds (flavonols and phenolic acids) which exert recognized biological activity. The GC-MS analysis of the essential oils from leaves collected in two periods studied (dry and wet), showed a small variation in the number of compounds. The major classes identified for the oil collected in the dry period were aliphatic alcohols (23,4%), terpenoids (18.7%), sterols (10.4%) and long-chain alkanes (9.2%) compounds. Terpenoids (26.8%) were the major class for the rain season. The major compounds (3Z) -hexenol, phytol and untriacontano are present in the two seasons but in different amounts (19.4%, 9.8% and 7.5% during the dry season, and 17.0 %, 14.9% and 15.3% in the rainy season, respectively). The essential oil from rainy season was not effective against to the oral bacteria Gram positive and Gram negative tested. However, showed significant antifungal activity with MIC 1000 mg L-1 against Candidas. Thus, the promising results with respect to biological assays of ethanolic extract and partitions from B. laevifolia contributed to the chemical and biological knowledge of the species B. laevifolia.

Two novel COLVI long chains in zebrafish that are essential for muscle development

Collagen VI (COLVI), a protein ubiquitously expressed in connective tissues, is crucial for structural integrity, cellular adhesion, migration and survival. Six different genes are recognized in mammalians, encoding six COLVI-chains that assemble as two ‘short’ (α1, α2) and one ‘long’ chain (theoretically any one of α3–6). In humans, defects in the most widely expressed heterotrimer (α123), due to mutations in the COL6A1-3 genes, cause a heterogeneous group of neuromuscular disorders, collectively termed COLVI-related muscle disorders. Little is known about the function(s) of the recently described α4-6 chains and no mutations have been detected yet. In this study, we characterized two novel COLVI long chains in zebrafish that are most homologous to the mammalian α4 chain; therefore, we named the corresponding genes col6a4a and col6a4b. These orthologues represent ancestors of the mammalian Col6a4-6 genes. By in situ hybridization and RT-qPCR, we unveiled a distinctive expression kinetics for col6a4b, compared with the other col6a genes. Using morpholino antisense oligonucleotides targeting col6a4a, col6a4b and col6a2, we modelled partial and complete COLVI deficiency, respectively. All morphant embryos presented altered muscle structure and impaired motility. While apoptosis was not drastically increased, autophagy induction was defective in all morphants. Furthermore, motoneuron axon growth was abnormal in these morphants. Importantly, some phenotypical differences emerged between col6a4a and col6a4b morphants, suggesting only partial functional redundancy. Overall, our results further confirm the importance of COLVI in zebrafish muscle development and may provide important clues for potential human phenotypes associated with deficiency of the recently described COLVI-chains.

Fatty Acid Synthase Inhibitors Induce Apoptosis In Non-tumorigenic Melan-a Cells Associated With Inhibition Of Mitochondrial Respiration.

The metabolic enzyme fatty acid synthase (FASN) is responsible for the endogenous synthesis of palmitate, a saturated long-chain fatty acid. In contrast to most normal tissues, a variety of human cancers overexpress FASN. One such cancer is cutaneous melanoma, in which the level of FASN expression is associated with tumor invasion and poor prognosis. We previously reported that two FASN inhibitors, cerulenin and orlistat, induce apoptosis in B16-F10 mouse melanoma cells via the intrinsic apoptosis pathway. Here, we investigated the effects of these inhibitors on non-tumorigenic melan-a cells. Cerulenin and orlistat treatments were found to induce apoptosis and decrease cell proliferation, in addition to inducing the release of mitochondrial cytochrome c and activating caspases-9 and -3. Transfection with FASN siRNA did not result in apoptosis. Mass spectrometry analysis demonstrated that treatment with the FASN inhibitors did not alter either the mitochondrial free fatty acid content or composition. This result suggests that cerulenin- and orlistat-induced apoptosis events are independent of FASN inhibition. Analysis of the energy-linked functions of melan-a mitochondria demonstrated the inhibition of respiration, followed by a significant decrease in mitochondrial membrane potential (ΔΨm) and the stimulation of superoxide anion generation. The inhibition of NADH-linked substrate oxidation was approximately 40% and 61% for cerulenin and orlistat treatments, respectively, and the inhibition of succinate oxidation was approximately 46% and 52%, respectively. In contrast, no significant inhibition occurred when respiration was supported by the complex IV substrate N,N,N',N'-tetramethyl-p-phenylenediamine (TMPD). The protection conferred by the free radical scavenger N-acetyl-cysteine indicates that the FASN inhibitors induced apoptosis through an oxidative stress-associated mechanism. In combination, the present results demonstrate that cerulenin and orlistat induce apoptosis in non-tumorigenic cells via mitochondrial dysfunction, independent of FASN inhibition.

Otimização das condições de produção de ésteres etílicos a partir de óleo de peixe com elevado teor de ácidos graxos ômega-3

The production of ethyl esters by alcoholysis is an alternative for splitting triacylglycerols due to the possibility of using low temperatures, which results in oxidative protection of the polyunsaturated fatty acids. Ethyl esters produced under mild conditions of temperature could be used as substrate for obtaining structured lipids. The reaction parameters of production of ethyl esters from fish oil with high content of omega-3 fatty acids by alcoholysis were optimized using response surface methodology. An experimental design (2³) (with levels +1 and -1, six axial points with levels -alpha and +alpha and three central points) was applied. The variables investigated were concentration of catalyst, amount of ethyl alcohol and temperature. Ethyl ester conversion was monitored by high performance size exclusion chromatography (HPSEC) and the best result obtained was 95% conversion rate. The optimal conditions were 40 °C, 1% of NaOH and 36% of ethanol.

Fracionamento de polifosfato de sódio e caracterização por RMN de 31P: um experimento para aulas de físico-química

This text describes an experiment on fractional precipitation of a polymer together with determination of average degree of polymerization by NMR. Commercial sodium polyphosphate was fractionated by precipitation from aqueous solution by adding increasing amounts of acetone. The polydisperse salt and nine fractions obtained from it were analyzed by 31P Nuclear Magnetic Resonance and the degree of polymerization of the salts and of the fractions were calculated. Long-chain sodium polyphosphate was also synthesized and analyzed. This experiment was tested in a PChem lab course but it can be used also to illustrate topics of inorganic polymers and analytical chemistry.

Phenotypic variability in a family with x-linked adrenoleukodystrophy caused by the p.Trp132Ter mutation

X-linked adrenoleukodystrophy (X-ALD) is an inherited disease with clinical heterogeneity varying from presymptomatic individuals to rapidly progressive cerebral ALD forms. This disease is characterized by increased concentration of very long chain fatty acids (VLCFAs) in plasma and in adrenal, testicular and nervous tissues. Affected individuals can be classified in different clinical settings, according to phenotypic expression and age at onset of initial symptoms. Molecular defects in X-ALD individuals usually result from ABCD1 gene mutations. In the present report we describe clinical data and the ABCD1 gene study in two boys affected with the childhood cerebral form that presented with different symptomatic manifestations at diagnosis. In addition, their maternal grandfather had been diagnosed with Addison's disease indicating phenotypic variation for X-ALD within this family. The mutation p.Trp132Ter was identified in both male patients; additionally, three females, out of eleven family members, were found to be heterozygous after screening for this mutation. In the present report, the molecular analysis was especially important since one of the heterozygous females was in first stages of pregnancy. Therefore, depending on the fetus outcome, if male and p.Trp132Ter carrier, storage of the umbilical cord blood should be recommended as hematopoietic stem cell transplantation could be considered as an option for treatment in the future.

Influência do treinamento físico aeróbio no transporte mitocondrial de ácidos graxos de cadeia longa no músculo esquelético: papel do complexo carnitina palmitoil transferase

O ácido graxo (AG) é uma importante fonte de energia para o músculo esquelético. Durante o exercício sua mobilização é aumentada para suprir as necessidades da musculatura ativa. Acredita-se que diversos pontos de regulação atuem no controle da oxidação dos AG, sendo o principal a atividade do complexo carnitina palmitoil transferase (CPT), entre os quais três componentes estão envolvidos: a CPT I, a CPT II e carnitina acilcarnitina translocase. A função da CPT I durante o exercício físico é controlar a entrada de AG para o interior da mitocôndria, para posterior oxidação do AG e produção de energia. Em resposta ao treinamento físico há um aumento na atividade e expressão da CPT I no músculo esquelético. Devido sua grande importância no metabolismo de lipídios, os mecanismos que controlam sua atividade e sua expressão gênica são revisados no presente estudo. Reguladores da expressão gênica de proteínas envolvidas no metabolismo de lipídios no músculo esquelético, os receptores ativados por proliferadores de peroxissomas (PPAR) alfa e beta, são discutidos com um enfoque na resposta ao treinamento físico.

Bioassay guided purification of the antimicrobial fraction of a Brazilian propolis from Bahia state

Background: Brazilian propolis type 6 (Atlantic forest, Bahia) is distinct from the other types of propolis especially due to absence of flavonoids and presence of other non-polar, long chain compounds, but presenting good in vitro and in vivo antimicrobial activity. Several authors have suggested that fatty acids found in this propolis might be responsible for its antimicrobial activity; however, so far no evidence concerning this finding has been reported in the literature. The goals of this study were to evaluate the antibacterial activity of the main pure fatty acids in the ethanolic extract and fractions and elucidate the chemical nature of the bioactive compounds isolated from Brazilian propolis type 6. Methods: Brazilian propolis type 6 ethanolic extract (EEP), hexane fraction (H-Fr), major fatty acids, and isolated sub-fractions were analyzed using high performance liquid chromatography (HPLC), high resolution gas chromatography with flame ionization detection (HRGC-FID), and gas chromatography-mass spectrometry (GC-MS). Three sub-fractions of H-Fr were obtained through preparative HPLC. Antimicrobial activity of EEP, H-Fr, sub-fractions, and fatty acids were tested against Staphyloccus aureus ATCC 25923 and Streptococcus mutans Ingbritt 1600 using minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC). Results: EEP and H-Fr inhibited the growth of the microorganisms tested; nevertheless, no antimicrobial activity was found for the major fatty acids. The three sub-fractions (1, 2, and 3) were isolated from H-Fr by preparative HPLC and only sub-fraction 1 showed antimicrobial activity. Conclusion: a) The major fatty acids tested were not responsible for the antimicrobial activity of propolis type 6; b) Sub-fraction 1, belonging to the benzophenone class, was responsible for the antimicrobial activity observed in the present study. The identification of the bioactive compound will improve the development of more efficient uses of this natural product.

Degradation of formaldehyde in anaerobic sequencing batch biofilm reactor (ASBBR)

The present study evaluated the degradation of formaldehyde in a bench-scale anaerobic sequencing batch reactor, which contained biomass immobilized in polyurethane foam matrices. The reactor was operated for 212 days at 35 C with 8 h sequential cycles, under different affluent formaldehyde concentrations ranging from 31.6 to 1104.4 mg/L (formaldehyde loading rates from 0.08 to 2.78 kg/m(3) day). The results indicate excellent reactor stability and over 99% efficiency in formaldehyde removal, with average effluent formaldehyde concentration of 3.6 + 1.7 mg/L. Formaldehyde degradation rates increased from 204.9 to 698.3 mg/L h as the initial concentration of formaldehyde was increased from around 100 to around 1100 mg/L. However, accumulation of organic matter was observed in the effluent (chemical oxygen demand (COD) values above 500 mg/L) due to the presence of non-degraded organic acids, especially acetic and propionic acids, This observation poses an important question regarding the anaerobic route of formaldehyde degradation, which might differ Substantially from that reported in the literature. The anaerobic degradation pathway can be associated with the formation of long-chain oligomers from formaldehyde. Such long- or short-chain polymers are probably the precursors of organic acid formation by means of acidogenic anaerobic microorganisms. (C) 2008 Elsevier B.V. All rights reserved.

Phase Equilibrium and Optimization Tools: Application for Enhanced Structured Lipids for Foods

Solid-liquid phase equilibrium modeling of triacylglycerol mixtures is essential for lipids design. Considering the alpha polymorphism and liquid phase as ideal, the Margules 2-suffix excess Gibbs energy model with predictive binary parameter correlations describes the non ideal beta and beta` solid polymorphs. Solving by direct optimization of the Gibbs free energy enables one to predict from a bulk mixture composition the phases composition at a given temperature and thus the SFC curve, the melting profile and the Differential Scanning Calorimetry (DSC) curve that are related to end-user lipid properties. Phase diagram, SFC and DSC curve experimental data are qualitatively and quantitatively well predicted for the binary mixture 1,3-dipalmitoyl-2-oleoyl-sn-glycerol (POP) and 1,2,3-tripalmitoyl-sn-glycerol (PPP), the ternary mixture 1,3-dimyristoyl-2-palmitoyl-sn-glycerol (MPM), 1,2-distearoyl-3-oleoyl-sn-glycerol (SSO) and 1,2,3-trioleoyl-sn-glycerol (OOO), for palm oil and cocoa butter. Then, addition to palm oil of Medium-Long-Medium type structured lipids is evaluated, using caprylic acid as medium chain and long chain fatty acids (EPA-eicosapentaenoic acid, DHA-docosahexaenoic acid, gamma-linolenic-octadecatrienoic acid and AA-arachidonic acid), as sn-2 substitutes. EPA, DHA and AA increase the melting range on both the fusion and crystallization side. gamma-linolenic shifts the melting range upwards. This predictive tool is useful for the pre-screening of lipids matching desired properties set a priori.

Visualizing inhibition of fatty acid synthase through mass spectrometric analysis of mitochondria from melanoma cells

Fatty acid synthase (FASN) is the metabolic enzyme responsible for the endogenous synthesis of the saturated long-chain fatty acid palmitate. In contrast to most normal cells, FASN is overexpressed in a variety of human cancers including cutaneous melanoma, in which its levels of expression are associated with a poor prognosis and depth of invasion. Recently, we have demonstrated the mitochondrial involvement in FASN inhibition-induced apoptosis in melanoma cells. Herein we compare, via electrospray ionization mass spectrometry (ESI-MS), free fatty acids (FFA) composition of mitochondria isolated from control (EtOH-treated cells) and Orlistat-treated B16-F10 mouse melanoma cells. Principal component analysis (PCA) was applied to the ESI-MS data and found to separate the two groups of samples. Mitochondria from control cells showed predominance of six ions, that is, those of m/z 157 (Pelargonic, 9:0), 255 (Palmitic, 16:0), 281 (Oleic, 18:1), 311 (Arachidic, 20:0), 327 (Docosahexaenoic, 22:6) and 339 (Behenic, 22:0). In contrast, FASN inhibition with Orlistat changes significantly mitochondrial FFA composition by reducing synthesis of palmitic acid, and its elongation and unsaturation products, such as arachidic and behenic acids, and oleic acid, respectively. ESI-MS of mitochondria isolated from Orlistat-treated cells presented therefore three major ions of m/z 157 (Pelargonic, 9:0), 193 (unknown) and 199 (Lauric, 12:0). These findings demonstrate therefore that FASN inhibition by Orlistat induces significant changes in the FFA composition of mitochondria. Copyright (C) 2011 John Wiley & Sons, Ltd.