Influence of end-capping on the self-assembly of model amyloid peptide fragments

The influence of charge and aromatic stacking interactions on the self-assembly of a series of four model amyloid peptides has been examined. The four model peptides are based on the KLVFF motif from the amyloid Beta peptide, ABeta(16-20) extended at the N terminus with two Beta-alanine residues. We have studied NH2-BetaABetaAKLVFF-COOH (FF), NH2-BetaABetaAKLVFCOOH (F), CH3CONH-BetaABetaAKLVFF-CONH2 (CapF), and CH3CONH-BetaABetaAKLVFFCONH2 (CapFF). The former two are uncapped (net charge plus 2) and differ by one hydrophobic phenylalanine residue; the latter two are the analogous capped peptides (net charge plus 1). The self-assembly characteristics of these peptides are remarkably different and strongly dependent on concentration. NMR shows a shift from carboxylate to carboxylic acid forms upon increasing concentration. Saturation transfer measurements of solvent molecules indicate selective involvement of phenylalanine residues in driving the self-assembly process of CapFF due presumably to the effect of aromatic stacking interactions. FTIR spectroscopy reveals beta-sheet features for the two peptides containing two phenylalanine residues but not the single phenylalanine residue, pointing again to the driving force for self-assembly. Circular dichroism (CD) in dilute solution reveals the polyproline II conformation, except for F which is disordered. We discuss the relationship of this observation to the significant pH shift observed for this peptide when compared the calculated value. Atomic force microscopy and cryogenic-TEM reveals the formation of twisted fibrils for CapFF, as previously also observed for FF. The influence of salt on the self-assembly of the model beta-sheet forming capped peptide CapFF was investigated by FTIR. Cryo-TEM reveals that the extent of twisting decreases with increased salt concentration, leading to the formation of flat ribbon structures. These results highlight the important role of aggregation-induced pKa shifts in the self-assembly of model beta-sheet peptides.

The interaction of Arp2/3 complex with actin: Nucleation, high affinity pointed end capping, and formation of branching networks of filaments

The Arp2/3 complex is a stable assembly of seven protein subunits including two actin-related proteins (Arp2 and Arp3) and five novel proteins. Previous work showed that this complex binds to the sides of actin filaments and is concentrated at the leading edges of motile cells. Here, we show that Arp2/3 complex purified from Acanthamoeba caps the pointed ends of actin filaments with high affinity. Arp2/3 complex inhibits both monomer addition and dissociation at the pointed ends of actin filaments with apparent nanomolar affinity and increases the critical concentration for polymerization at the pointed end from 0.6 to 1.0 μM. The high affinity of Arp2/3 complex for pointed ends and its abundance in amoebae suggest that in vivo all actin filament pointed ends are capped by Arp2/3 complex. Arp2/3 complex also nucleates formation of actin filaments that elongate only from their barbed ends. From kinetic analysis, the nucleation mechanism appears to involve stabilization of polymerization intermediates (probably actin dimers). In electron micrographs of quick-frozen, deep-etched samples, we see Arp2/3 bound to sides and pointed ends of actin filaments and examples of Arp2/3 complex attaching pointed ends of filaments to sides of other filaments. In these cases, the angle of attachment is a remarkably constant 70 ± 7°. From these in vitro biochemical properties, we propose a model for how Arp2/3 complex controls the assembly of a branching network of actin filaments at the leading edge of motile cells.

Development of 2-oxazoline-based hydrogels and porous polyester microparticles in scCO2

Thesis submitted to Faculdade de Ciências e Tecnologia from Universidade Nova de Lisboa in partial fulfillment of the requirements for the obtention of the degree of Master of Science in Biotechnology

Improved polymeric medical devices for active substances delivery

The work presented in this thesis was developed in collaboration with a Portuguese company, BeyonDevices, devoted to pharmaceutical packaging, medical technology and device industry. Specifically, the composition impact and surface modification of two polymeric medical devices from the company were studied: inhalers and vaginal applicators. The polyethylene-based vaginal applicator was modified using supercritical fluid technology to acquire self-cleaning properties and prevent the transport of bacteria and yeasts to vaginal flora. For that, in-situ polymerization of 2-substituted oxazolines was performed within the polyethylene matrix using supercritical carbon dioxide. The cationic ring-opening polymerization process was followed by end-capping with N,N-dimethyldodecylamine. Furthermore, for the same propose, the polyethylene matrix was impregnated with lavender oil in supercritical medium. The obtained materials were characterized physical and morphologically and the antimicrobial activity against bacteria and yeasts was accessed. Materials modified using 2-substituted oxazolines showed an effective killing ability for all the tested microorganisms, while the materials modified with lavender oil did not show antimicrobial activity. Only materials modified with oligo(2-ethyl-2-oxazoline) maintain the activity during the long term stability. Furthermore, the cytotoxicity of the materials was tested, confirming their biocompatibilty. Regarding the inhaler, its surface was modified in order to improve powder flowability and consequently, to reduce powder retention in the inhaler´s nozzle. New dry powder inhalers (DPIs), with different needle’s diameters, were evaluated in terms of internal resistance and uniformity of the emitted dose. It was observed that they present a mean resistance of 0.06 cmH2O0.5/(L/min) and the maximum emitted dose obtained was 68.9% for the inhaler with higher needle´s diameter (2 mm). Thus, this inhaler was used as a test and modified by the coating with a commonly-used force control agent, magnesium stearate, dried with supercritical carbon dioxide (scCO2) and the uniformity of delivered dose tests were repeated. The modified inhaler showed an increase in emitted dose from 68.9% to 71.3% for lactose and from 30.0% to 33.7% for Foradil.

Green synthesis of 2-Oxazoline-based polymers with antimicrobial activity using scCO2

Using a green methodology, 17 different poly(2-oxazolines) were synthesized starting from four different oxazoline monomers. The polymerization reactions were conducted in supercritical carbon dioxide under a cationic ring-opening polymerization (CROP) mechanism using boron trifluoride diethyl etherate as the catalyst. The obtained living polymers were then end-capped with different types of amines, in order to confer them antimicrobial activity. For comparison, four polyoxazolines were end-capped with water, and by their hydrolysis the linear poly(ethyleneimine) (LPEI) was also produced. After functionalization the obtained polymers were isolated, purified and characterized by standard techniques (FT-IR, NMR, MALDI-TOF and GPC). The synthesized poly(2-oxazolines) revealed an unusual intrinsic blue photoluminescence. High concentration of carbonyl groups in the polymer backbone is appointed as a key structural factor for the presence of fluorescence and enlarges polyoxazolines’ potential applications. Microbiological assays were also performed in order to evaluate their antimicrobial profile against gram-positive Staphylococcus aureus NCTC8325-4 and gram-negative Escherichia coli AB1157 strains, two well known and difficult to control pathogens. The minimum inhibitory concentrations (MIC)s and killing rates of three synthesized polymers against both strains were determined. The end-capping with N,N-dimethyldodecylamine of living poly(2- methyl-2-oxazoline) and poly(bisoxazoline) led to materials with higher MIC values but fast killing rates (less than 5 minutes to achieve 100% killing for both bacterial species) than LPEI, a polymer which had a lower MIC value, but took a longer time to kill both E.coli and S.aureus cells. LPEI achieved 100% killing after 45 minutes in contact with E. coli and after 4 hours in contact with S.aureus. Such huge differences in the biocidal behavior of the different polymers can possibly underlie different mechanisms of action. In the future, studies to elucidate the obtained data will be performed to better understand the killing mechanisms of the polymers through the use of microbial cell biology techniques.

Thermo-responsive microphase separated supramolecular polyurethanes

The ability to generate very stable assemblies via non-covalent interactions has enabled materials to be constructed that were not feasible via traditional covalent bond formation processes. A series of low molecular mass bisurethane and bisurea polymers have been developed that form stable self-assembled networks through hydrogen bonding interactions. Thermo-responsive polymers were generated by end-capping poly(ethylene-co-butylene) or polybutadiene chains with the bisurethane or bisurea motif. Microphase separation is observed via TEM and small-angle X-ray scattering (SAXS) for the modified pseudo polymers and significant differences in the temperature dependence of microphase separation are analysed via SAXS. The importance of the polarity of the end groups is manifested in distinct temperature-dependent microphase separation behaviour. Information on the local hydrogen bonding structure is provided by wide-angle X-ray scattering and variable temperature FTI

Direct assembly of a metallodendrimer encompassing seven triruthenium clusters units

A general strategy for the assembly of dendrimeric metallo-cluster species based on tritopic trinuclear ruthenium acetate complexes is demonstrated. First, a central core consisting of a [Ru3O(CH3COO)(6)(TPEB)(3)]PF6 complex (G0), where TPEB is the tripodal 1,3,5-tri-4-pyridyl-1,2-ethenylbenzene ligand, was synthesized and then reacted with the end-capping complex [Ru3O(CH3COO)(6)(py)(2)(MeOH)]PF6, thus composing the first generation shell of a dendrimer encompassing twenty-one ruthenium ions (G1). The core and dendrimeric complexes were characterized by elemental analysis, UV-Vis, H-1 NMR, ESI-MS spectrometry and Differential pulse voltammetry. All results were consistent with the structure of that multinuclear cationic dendrimeric species. The isotopologic profile of daughter fragments and the strength of the metal-ligand bonds were carefully investigated providing the fragmentation pathway for the metallo-dendrimer upon ESI-MS dissociation conditions. (C) 2012 Elsevier B.V. All rights reserved.

From anionic polymerization in continuous flow to macromolecular architectures and stimuli-responsive surfaces

The thesis can be divided in four parts and summarized as follows:(i) The investigation and development of a continuous flow synthesis procedure affording end-functional polymers by anionic polymerization and subsequent termination in one reaction step and on a multigram scale was carried out. Furthermore, the implementation of not only a single hydroxyl but multiple orthogonal functionalities at the chain terminus was achieved by utilizing individually designed, functional epoxide-based end-capping reagents.(ii) In an additional step, the respective polymers were used as macroinitiators to prepare in-chain functionalized block copolymers and star polymers bearing intriguing novel structural and material properties. Thus, the second part of this thesis presents the utilization of end-functional polymers as precursors for the synthesis of amphiphilic complex and in some cases unprecedented macromolecular architectures, such as miktoarm star polymers based on poly(vinyl pyridine), poly(vinyl ferrocene) and PEO.(iii) Based on these structures, the third part of this thesis represents a detailed investigation of the preparation of stimuli-responsive ultrathin polymer films, using amphiphilic junction point-reactive block copolymers. The single functionality at the block interface can be employed as anchor group for the covalent attachment on surfaces. Furthermore, the change of surface properties was studied by applying different external stimuli.(iv) An additional topic related to the oxyanionic polymerizations carried out in the context of this thesis was the investigation of viscoelastic properties of different hyperbranched polyethers, inspired by the recent and intense research activities in the field of biomedical applications of multi-functional hyperbranched materials.

DNA double-strand break repair proteins are required to cap the ends of mammalian chromosomes

Recent findings intriguingly place DNA double-strand break repair proteins at chromosome ends in yeast, where they help maintain normal telomere length and structure. In the present study, an essential telomere function, the ability to cap and thereby protect chromosomes from end-to-end fusions, was assessed in repair-deficient mouse cell lines. By using fluorescence in situ hybridization with a probe to telomeric DNA, spontaneously occurring chromosome aberrations were examined for telomere signal at the points of fusion, a clear indication of impaired end-capping. Telomeric fusions were not observed in any of the repair-proficient controls and occurred only rarely in a p53 null mutant. In striking contrast, chromosomal end fusions that retained telomeric sequence were observed in nontransformed DNA-PKcs-deficient cells, where they were a major source of chromosomal instability. Metacentric chromosomes created by telomeric fusion became even more abundant in these cells after spontaneous immortalization. Restoration of repair proficiency through transfection with a functional cDNA copy of the human DNA-PKcs gene reduced the number of fusions compared with a negative transfection control. Virally transformed cells derived from Ku70 and Ku80 knockout mice also displayed end-to-end fusions. These studies demonstrate that DNA double-strand break repair genes play a dual role in maintaining chromosomal stability in mammalian cells, the known role in repairing incidental DNA damage, as well as a new protective role in telomeric end-capping.

Evaluation of two mineral trioxide aggregate compounds as pulp-capping agents in human teeth

The present randomized, controlled prospective study evaluated the histomorphological response of human dental pulps capped with two grey mineral trioxide aggregate (MTA) compounds. Pulp exposures were performed on the occlusal floor of 40 human permanent pre-molars. The pulp was capped either with ProRoot (Dentsply) or MTA-Angelus (Angelus) and restored with zinc oxide eugenol cement. After 30 and 60 days, teeth were extracted and processed for histological examination and the effects on the pulp were scored. The data were subjected to Kruskal-Wallis and Conover tests (alpha = 0.05). In five out of the 40 teeth bacteria were present in pulp tissue. No significant difference was observed between the two materials (P > 0.05) in terms of overall histological features (hard tissue bridge, inflammatory response, giant cells and particles of capping materials). Overall, 94% and 88% of the specimens capped with MTA-Angelus and ProRoot, respectively, showed either total or partial hard tissue bridge formation (P > 0.05). Both commercial materials ProRoot (Dentsply) and MTA-Angelus (Angelus) produced similar responses in the pulp when used for pulp capping in intact, caries-free teeth.

Pulp capping materials exert an effect on the secretion of IL-1β and IL-8 by migrating human neutrophils

Pulp repair is a complex process whose mechanisms are not yet fully understood. The first immune cells to reach the damaged pulp are neutrophils that play an important role in releasing cytokines and in phagocytosis. The objective of this study was to analyze the effect of different pulp-capping materials on the secretion of interleukin-1 beta (IL-1β) and interleukin-8 (IL-8) by migrating human neutrophils. Neutrophils were obtained from the blood of three healthy donors. The experimental groups were calcium hydroxide [Ca(OH)2], an adhesive system (Single Bond), and mineral trioxide aggregate (MTA). Untreated cells were used as control. Transwell chambers were used in performing the assays to mimic an in vivo situation of neutrophil chemotaxis. The pulp-capping materials were placed in the lower chamber and the human neutrophils, in the upper chamber. The cells were counted and the culture medium was assayed using ELISA kits for detecting and quantifying IL-1β and IL8. The data were compared by ANOVA followed by Tukey's test (p < 0.05). The secretion of IL-8 was significantly higher in all groups in comparison to the control group (p < 0.05). The adhesive system group showed higher IL-8 than the MTA group (p < 0.05). The secretion of IL-1β was significantly greater only in the MTA group (p < 0.001). It was concluded that only MTA is able to improve the secretion of IL-1β, and all materials tested increased IL-8 secretion. These results combined with all the other biological advantages of MTA indicate that it could be considered the material of choice for dental pulp capping.

Endothelial Nitric Oxide Genotypes and Haplotypes Are Not Associated with End-Stage Renal Disease

The identification of genetic markers associated with chronic kidney disease (CKD) may help to predict its development. Because reduced nitric oxide (NO) bioavailability and endothelial dysfunction are involved in CKD, genetic polymorphisms in the gene encoding the enzyme involved in NO synthesis (endothelial NO synthase [eNos]) may affect the susceptibility to CKD and the development of end-stage renal disease (ESRD). We compared genotype and haplotype distributions of three relevant eNOS polymorphisms (T(-786) C in the promoter region, Glu298Asp in exon 7, and 4b/4a in intron 4) in 110 healthy control subjects and 127 ESRD patients. Genotypes for the T(-786) C and Glu298Asp polymorphisms were determined by TaqMan (R) Allele Discrimination assay and real-time polymerase chain reaction. Genotypes for the intron 4 polymorphism were determined by polymerase chain reaction and fragment separation by electrophoresis. The software program PHASE 2.1 was used to estimate the haplotypes frequencies. We considered significant a probability value of p < 0.05/number of haplotypes (p < 0.05/8 = 0.0063). We found no significant differences between groups with respect to age, ethnicity, and gender. CKD patients had higher blood pressure, total cholesterol, and creatinine levels than healthy control subjects (all p < 0.05). Genotype and allele distributions for the three eNOS polymorphisms were similar in both groups (p > 0.05). We found no significant differences in haplotype distribution between groups (p > 0.05). The lack of significant associations between eNOS polymorphisms and ESRD suggests that eNOS polymorphisms may not be relevant to the genetic component of CKD that leads to ESRD.

Growth and capping of InAs/GaAs quantum dots investigated by x-ray Bragg-surface diffraction

An x-ray diffraction method, based on the excitation of a surface diffracted wave, is described to investigate the capping process of InAs/GaAs (001) quantum dots (QDs). It is sensitive to the tiny misorientation of (111) planes at the surface of the buffer layer on samples with exposed QDs. After capping, the misorientation occurs in the cap-layer lattice faceting the QDs and its magnitude can be as large as 10 degrees depending on the QDs growth rates, probably due to changes in the size and shape of the QDs. A slow strain release process taking place at room temperature has also been observed by monitoring the misorientation angle of the (111) planes.

Runoff sources and land cover change in the Amazon: an end-member mixing analysis from small watersheds

The flowpaths by which water moves from watersheds to streams has important consequences for the runoff dynamics and biogeochemistry of surface waters in the Amazon Basin. The clearing of Amazon forest to cattle pasture has the potential to change runoff sources to streams by shifting runoff to more surficial flow pathways. We applied end-member mixing analysis (EMMA) to 10 small watersheds throughout the Amazon in which solute composition of streamwater and groundwater, overland flow, soil solution, throughfall and rainwater were measured, largely as part of the Large-Scale Biosphere-Atmosphere Experiment in Amazonia. We found a range in the extent to which streamwater samples fell within the mixing space determined by potential flowpath end-members, suggesting that some water sources to streams were not sampled. The contribution of overland flow as a source of stream flow was greater in pasture watersheds than in forest watersheds of comparable size. Increases in overland flow contribution to pasture streams ranged in some cases from 0% in forest to 27-28% in pasture and were broadly consistent with results from hydrometric sampling of Amazon forest and pasture watersheds that indicate 17- to 18-fold increase in the overland flow contribution to stream flow in pastures. In forest, overland flow was an important contribution to stream flow (45-57%) in ephemeral streams where flows were dominated by stormflow. Overland flow contribution to stream flow decreased in importance with increasing watershed area, from 21 to 57% in forest and 60-89% in pasture watersheds of less than 10 ha to 0% in forest and 27-28% in pastures in watersheds greater than 100 ha. Soil solution contributions to stream flow were similar across watershed area and groundwater inputs generally increased in proportion to decreases in overland flow. Application of EMMA across multiple watersheds indicated patterns across gradients of stream size and land cover that were consistent with patterns determined by detailed hydrometric sampling.

Integrating technology roadmapping and portfolio management at the front-end of new product development

Many authors point out that the front-end of new product development (NPD) is a critical success factor in the NPD process and that numerous companies face difficulties in carrying it out appropriately. Therefore, it is important to develop new theories and proposals that support the effective implementation of this earliest phase of NPD. This paper presents a new method to support the development of front-end activities based on integrating technology roadmapping (TRM) and project portfolio management (PPM). This new method, called the ITP Method, was implemented at a small Brazilian high-tech company in the nanotechnology industry to explore the integration proposal. The case study demonstrated that the ITP Method provides a systematic procedure for the fuzzy front-end and integrates innovation perspectives into a single roadmap, which allows for a better alignment of business efforts and communication of product innovation goals. Furthermore, the results indicated that the method may also improve quality, functional integration and strategy alignment. (C) 2010 Elsevier Inc. All rights reserved.