Communication between noncontacting macromolecules

We present a quantitative experimental demonstration of solvent-mediated communication between noncontacting biopolymers. We show that changes in the activity of a solvent component brought about by a conformational change in one biopolymer can result in changes in the physical properties of a second noncontacting biopolymer present in solution. Specifically, we show that the release of protons on denaturation of a donor polymer (in this case, a four-stranded DNA tetraplex, iDNA) modulates the melting temperature of a noncontacting, acceptor polymer [in this case poly(A)]. In addition to such proton-mediated cross talk, we also demonstrate counterion-mediated cross talk between noncontacting biopolymers. Specifically, we show that counterion association/release on denaturation of native salmon sperm DNA (the donor polymer) can modulate the melting temperature of poly(dA)⋅poly(dT) (the acceptor polymer). Taken together, these two examples demonstrate how poly(A) and poly(dA)⋅poly(dT) can serve as molecular probes that report the pH and free salt concentrations in solution, respectively. Further, we demonstrate how such through-solvent dialogue between biopolymers that do not directly interact can be used to evaluate (in a model-free manner) association/dissociation reactions of solvent components (e.g., protons, sodium cations) with one of the two biopolymers. We propose that such through-solution dialogue is a general property of all biopolymers. As a result, such solvent-mediated cross talk should be considered when assessing reactions of multicomponent systems such as those that exist in essentially all biological processes.

Estudo da microestrutura e dinâmica molecular do Poly(3-(2\'-ethylhexyl)thiophene)(P3EHT) via ressonância magnética nuclear

O estudo da microestrutura e dinâmica molecular de polímeros conjugados é de grande importância para o entendimento das propriedades físicas desta classe de materiais. No presente trabalho utilizou-se técnicas de ressonância magnética nuclear em baixo e alto campo para elucidar os processos de dinâmica molecular e cristalização do polímero Poly(3-(2’-ethylhexyl)thiophene) - P3EHT. O P3EHT é um polímero modelo para tal estudo, pois apresenta temperatura de fusão bem inferior a sua temperatura de degradação. Esta característica permite acompanhar os processos de cristalização in situ utilizando RMN. Além disso, sua similaridade ao já popular P3HT o torna um importante candidato a camada ativa em dispositivos eletrônicos orgânicos. O completo assinalamento do espectro de 13C para o P3EHT foi realizado utilizando as técnicas de defasamento dipolar e HETCOR. Os processos de dinâmica molecular, por sua vez, foram sondados utilizando DIPSHIFT. Observou-se um gradiente de mobilidade na cadeia lateral do polímero. Além disso, os baixos valores de parametros de ordem obtidos em comparação a experimentos similares realizados no P3HT na literatura indicam um aparente aumento no volume livre entre cadeias consecutivas na fase cristalina. Isso indica que a presença do grupo etil adicional no P3EHT causa um completo rearranjo das moléculas e dificulta seu empacotamento. Constatou-se ainda pouca variação das curvas de DIPSHIFT para os carbonos da cadeia lateral como função do método de excitação utilizado, o que aponta para um polímero que apresenta cadeia lateral móvel mesmo em sua fase cristalina. Os dados de dinâmica molecular foram corroborados por medidas de T1, T1ρ e TCH. Utilizando filtros dipolares em baixo campo observou-se três temperaturas de transição para o P3EHT: 250 K, 325 K e 350 K. A cristalização desse material é um processo lento. Verificou-se que o mesmo pode se estender por até até 24h a temperatura ambiente. Mudanças no espectro de 13C utilizando CPMAS em alto campo indicam um ordenamento dos anéis tiofeno (empacotamento π – π) como o principal processo de cristalização para o P3EHT.

Thermophysical properties of solid materials

"Materials Central, Contract No. AF 33(616)-5212, Project No. 7381."

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA Microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design microarray probes with high specificities and sensitivities. Highly specific probes correspond to probes having unique DNA sequences; whereas highly sensitive probes correspond to those with melting temperature within a desired range and having no secondary structure. The selection of these probes from a set of functional DNA sequences (exons) constitutes a computationally expensive discrete non-linear search problem. We delegate the search task to a simple yet effective Evolution Strategy algorithm. The computational efficiency is also greatly improved by making use of an available bioinformatics tool.

Formation and mechanical properties of Mg65Cu25Er10 and Mg65Cu15Ag10Er10 bulk amorphous alloys

Mg65Cu25Er10 and Mg65Cu15Ag10Er10 bulk amorphous alloys were produced by a copper mould casting method. The alloys have high glass-forming ability and good thermal stability. The maximum diameter of glass formation (D-c), glass transition temperature (T-g), crystallization onset temperature (T-x), temperature interval of the supercooled region (Delta T-x), melting temperature (T-m), liquidus temperature (T-1) as well as heats of crystallization (Delta H-x) and melting (Delta H-m) are reported for these alloys. Both alloys exhibit high hardness and high strength at room temperature. (c) 2005 Elsevier B.V. All rights reserved.

Stirring in 3-d spherical models of convection in the Earth's mantle

On a global scale basalts from mid-ocean ridges are strikingly more homogeneous than basalts from intraplate volcanism. The observed geochemical heterogeneity argues strongly for the existence of distinct reservoirs in the Earth's mantle. It is an unresolved problem of Geodynamics as to how these findings can be reconciled with large-scale convection. We review observational constraints, and investigate stirring properties of numerical models of mantle convection. Conditions in the early Earth may have supported layered convection with rapid stirring in the upper layers. Material that has been altered near the surface is transported downwards by small-scale convection. Thereby a layer of homogeneous depleted material develops above pristine mantle. As the mantle cools over Earth history, the effects leading to layering become reduced and models show the large-scale convection favoured for the Earth today. Laterally averaged, the upper mantle below the lithosphere is least affected by material that has experienced near-surface differentiation. The geochemical signature obtained during the previous episode of small-scale convection may be preserved there for the longest time. Additionally, stirring is less effective in the high viscosity layer of the central lower mantle [1, 2], supporting the survival of medium-scale heterogeneities there. These models are the first, using 3-d spherical geometry and mostly Earth-like parameters, to address the suggested change of convective style. Although the models are still far from reproducing our planet, we find that proposal might be helpful towards reconciling geochemical and geophysical constraints.

Searching oligo sets of human chromosome 12 using evolutionary strategies

DNA microarray is a powerful tool to measure the level of a mixed population of nucleic acids at one time, which has great impact in many aspects of life sciences research. In order to distinguish nucleic acids with very similar composition by hybridization, it is necessary to design probes with high specificities, i.e. uniqueness, and also sensitivities, i.e., suitable melting temperature and no secondary structure. We make use of available biology tools to gain necessary sequence information of human chromosome 12, and combined with evolutionary strategy (ES) to find unique subsequences representing all predicted exons. The results are presented and discussed.

The application of reduced-size short tandem repeat primer sets in the analysis of human DNA from degraded and compromised samples

The purpose of this research was to demonstrate the applicability of reduced-size STR (Miniplex) primer sets to challenging samples and to provide the forensic community with new information regarding the analysis of degraded and inhibited DNA. The Miniplex primer sets were validated in accordance with guidelines set forth by the Scientific Working Group on DNA Analysis Methods (SWGDAM) in order to demonstrate the scientific validity of the kits. The Miniplex sets were also used in the analysis of DNA extracted from human skeletal remains and telogen hair. In addition, a method for evaluating the mechanism of PCR inhibition was developed using qPCR. The Miniplexes were demonstrated to be a robust and sensitive tool for the analysis of DNA with as low as 100 pg of template DNA. They also proved to be better than commercial kits in the analysis of DNA from human skeletal remains, with 64% of samples tested producing full profiles, compared to 16% for a commercial kit. The Miniplexes also produced amplification of nuclear DNA from human telogen hairs, with partial profiles obtained from as low as 60 pg of template DNA. These data suggest smaller PCR amplicons may provide a useful alternative to mitochondrial DNA for forensic analysis of degraded DNA from human skeletal remains, telogen hairs, and other challenging samples. In the evaluation of inhibition by qPCR, the effect of amplicon length and primer melting temperature was evaluated in order to determine the binding mechanisms of different PCR inhibitors. Several mechanisms were indicated by the inhibitors tested, including binding of the polymerase, binding to the DNA, and effects on the processivity of the polymerase during primer extension. The data obtained from qPCR illustrated a method by which the type of inhibitor could be inferred in forensic samples, and some methods of reducing inhibition for specific inhibitors were demonstrated. An understanding of the mechanism of the inhibitors found in forensic samples will allow analysts to select the proper methods for inhibition removal or the type of analysis that can be performed, and will increase the information that can be obtained from inhibited samples.

Remoção de corantes utilizando tensoativos: extração por ponto de nuvem e floculação iônica

The textile sector is one of the main contributors to the generation of industrial wastewaters due to the use of large volumes of water, which has a high organic load content. In these, it is observed to the presence of dyes, surfactants, starch, alcohols, acetic acid and other constituents, from the various processing steps of the textiles. Hence, the treatment of textile wastewater becomes fundamental before releasing it into water bodies, where they can cause disastrous physical-chemical changes for the environment. Surfactants are substances widely used in separation processes and their use for treating textile wastewaters was evaluated in this research by applying the cloud point extraction and the ionic flocculation. In the cloud point extraction was used as surfactant nonylphenol with 9.5 ethoxylation degree to remove reactive dye. The process evaluation was performed in terms of temperature, surfactant and dye concentrations. The dye removal reached 91%. The ionic flocculation occurs due to the presence of calcium, which reacts with anionic surfactant to form insoluble surfactants capable of attracting the organic matter by adsorption. In this work the ionic flocculation using base soap was applied to the treatment of synthetic wastewater containing dyes belonging to three classes: direct, reactive, and disperse. It was evaluated by the influence of the following parameters: surfactant and electrolyte concentrations, stirring speed, equilibrium time, temperature, and pH. The flocculation of the surfactant was carried out in two ways: forming the floc in the effluent itself and forming the floc before mixing it to the effluent. Removal of reactive and direct dye, when the floc is formed into textile effluent was 97% and 87%, respectively. In the case where the floc is formed prior to adding it to the effluent, the removal to direct and disperse dye reached 92% and 87%, respectively. These results show the efficience of the evaluated processes for dye removal from textile wastewaters.

Incomplete DJH rearrangements as a novel tumor target for minimal residual disease quantitation in multiple myeloma using real-time PCR.

The hypervariable regions of immunoglobulin heavy-chain (IgH) rearrangements provide a specific tumor marker in multiple myeloma (MM). Recently, real-time PCR assays have been developed in order to quantify the number of tumor cells after treatment. However, these strategies are hampered by the presence of somatic hypermutation (SH) in VDJH rearrangements from multiple myeloma (MM) patients, which causes mismatches between primers and/or probes and the target, leading to a nonaccurate quantification of tumor cells. Our group has recently described a 60% incidence of incomplete DJH rearrangements in MM patients, with no or very low rates of SH. In this study, we compare the efficiency of a real-time PCR approach for the analysis of both complete and incomplete IgH rearrangements in eight MM patients using only three JH consensus probes. We were able to design an allele-specific oligonucleotide for both the complete and incomplete rearrangement in all patients. DJH rearrangements fulfilled the criteria of effectiveness for real-time PCR in all samples (ie no unspecific amplification, detection of less than 10 tumor cells within 10(5) polyclonal background and correlation coefficients of standard curves higher than 0.98). By contrast, only three out of eight VDJH rearrangements fulfilled these criteria. Further analyses showed that the remaining five VDJH rearrangements carried three or more somatic mutations in the probe and primer sites, leading to a dramatic decrease in the melting temperature. These results support the use of incomplete DJH rearrangements instead of complete somatically mutated VDJH rearrangements for investigation of minimal residual disease in multiple myeloma.

Internal cooling in rotational molding-A review

Rotational molding suffers from a relatively long cycle time, which hampers more widespread growth of the process. During each cycle, both the polymer and mold must be heated from room temperature to above polymer melting temperature and subsequently cooled to room temperature. The cooling time in this process is relatively long due to the poor thermal conductivity of plastics. Although rapid external cooling is possible, internal cooling rates are the major limitation. This causes the process to be uneconomical for large production runs of small parts. Various researchers have strived to minimize cycle times by applying various internal cooling procedures. This article presents a review of these methods, including computer simulations and practical investigations published to date. The effects of cooling rate on the morphology, shrinkage, warpage, and impact properties of rotationally molded polyolefins are also highlighted. In general, rapid and symmetrical cooling across the mold results in smaller spherulite size, increased mechanical properties and less potential warpage or distortion in moldings. POLYM. ENG. SCI., 2011. ©2011 Society of Plastics Engineers.

Investigating wetting characteristics on microstructured surfaces for superhydrophobicity and metal microcasting

The engineering of liquid behavior on surfaces is important for infrastructure, transportation, manufacturing, and sensing. Surfaces can be rendered superhydrophobic by microstructuring, and superhydrophobic devices could lead to practical corrosion inhibition, self-cleaning, fluid flow control, and surface drag reduction. To more fully understand how liquid interacts with microstructured surfaces, this dissertation introduces a direct method for determining droplet solid-liquid-vapor interfacial geometry on microstructured surfaces. The technique performs metrology on molten metal droplets deposited onto microstructured surfaces and then frozen. Unlike other techniques, this visualization technique can be used on large areas of curved and opaque microstructured surfaces to determine contact line. This dissertation also presents measurements and models for how curvature and flexing of microstructured polymers affects hydrophobicity. Increasing curvature of microstructured surfaces leads to decreased slide angle for liquid droplets suspended on the surface asperities. For a surface with regularly spaced asperities, as curvature becomes more positive, droplets suspended on the tops of asperities are suspended on fewer asperities. Curvature affects superhydrophobicity because microscopic curvature changes solid-liquid interaction, pitch is altered, and curvature changes the shape of the three phase contact line. This dissertation presents a model of droplet interactions with curved microstructured surfaces that can be used to design microstructure geometries that maintain the suspension of a droplet when curved surfaces are covered with microstructured polymers. Controlling droplet dynamics could improve microfluidic devices and the shedding of liquids from expensive equipment, preventing corrosion and detrimental performance. This dissertation demonstrates redirection of dynamic droplet spray with anisotropic microstructures. Superhydrophobic microstructured surfaces can be economically fabricated using metal embossing masters, so this dissertation describes casting-based microfabrication of metal microstructures and nanostructures. Low melting temperature metal was cast into flexible silicone molds which were themselves cast from microfabricated silicon templates. The flexibility of the silicone mold permits casting of curved surfaces, which this dissertation demonstrates by fabricating a cylindrical metal roller with microstructures. The metal microstructures can be in turn used as a reusable molding tool. This dissertation also describes an industrial investment casting process to produce aluminum molds having integrated microstructures. Unlike conventional micromolding tools, the aluminum mold was large and had complex curved surfaces. The aluminum was cast into curved microstructured ceramic molds which were themselves cast from curved microstructured rubber. Many structures were successfully cast into the aluminum with excellent replication fidelity, including circular, square, and triangular holes. This dissertation demonstrates molding of large, curved surfaces having surface microstructures using the aluminum mold. This work contributes a more full understanding of the phenomenon of superhydrophobicity and techniques for the economic fabrication of superhydrophobic microstructures.

Desenvolvimento e caracterização de filmes a base de isolado protéico de resíduos de corvina (micropogonias furnieri) e óleo de palma

Nas últimas duas décadas, o descarte e o acúmulo de embalagens não biodegradáveis têm agravado os problemas ambientais. Uma das soluções encontradas, particularmente na área de embalagens de alimentos, é o desenvolvimento de filmes a partir de polímeros que possam substituir os materiais sintéticos. Fontes alternativas de proteína, como os resíduos de pescados, tornam-se importante, pois estes representam de 60 a 70% da matéria-prima e são descartados pelas indústrias de filetagem contribuindo com os danos ao meio ambiente. As propriedades funcionais dos filmes biodegradáveis são resultantes das características das macromoléculas utilizadas, das interações entre os constituintes envolvidos na formulação (macromolécula, solvente, plastificante e outros aditivos), dos parâmetros de fabricação (temperatura, tipo de solvente, pH, entre outras), do processo de dispersão da solução filmogênica (pulverização, espalhamento, etc.) e das condições de secagem. Um problema limitante no uso de filmes biodegradáveis a base de proteínas de pescado é a sua susceptibilidade à umidade, devido à hidrofilicidade dos aminoácidos das moléculas de proteína. O objetivo geral do trabalho foi desenvolver e caracterizar filmes a base de isolado proteico de resídeos de corvina (IPC) e óleo de palma (OP). O desenvolvimento dos filmes foi estudado em duas etapas. Neste estudo utilizou-se resíduos de corvina (Micropogonias furnieri) para a obtenção do isolado protéico, glicerol como plastificante e óleo de palma para conferir hidrofobicidade ao filme. Na primeira etapa, o objetivo foi investigar o efeito das concentrações de IPC, de glicerol e do pH sobre as propriedades dos filmes de proteína de resíduos de corvina (Micropogonias furnieri). Os filmes foram avaliados quanto aos parâmetros de cor, opacidade, propriedades mecânicas, espessura, solubilidade em água, permeabilidade de vapor de água (PVA) e propriedades morfológicas. Como resultado foi observado que a opacidade e a luminosidade dos filmes não foram afetados pelas variáveis do processo. Os filmes de IPC ficaram amarelados e opacos. Apresentaramse mais claros quando elaborados com baixas concentrações de IPC e altas concentrações de glicerol nas soluções filmogênicas. A menor solubilidade em água ocorreu nos filmes com pH baixo e menores concentrações de glicerol. Com relação as propriedades mecânicas, os filmes apresentaram alta elongação e sua resistência à tração aumentou quando utilizadas maiores concentrações de IPC, menores concentrações de glicerol e pHs mais baixos.Os filmes apresentaram superficies ásperas e irregulares. Na segunda etapa foram elaborados filmes biodegradáveis de IPC contendo diferentes concentrações de óleo de palma (OP) (10 e 20 g de OP /100g de IPC) e suas propriedades de barreira, mecânicas, físico-químicas, térmicas e morfológicas foram estudadas. A adição de OP aumentou as espessuras dos filmes com 2 e 4% de IPC, no entanto a solubilidade não foi afetada pela adição do OP. Os filmes com 3 e 4% de IPC ficaram menos permeáveis a água quando incorporado 20% de OP nos mesmos. A opacidade dos filmes aumentou com a adição do OP. A incorporação do OP nos filmes resultou em uma diminuição da resistência à tração e no aumento da elongação dos filmes. Nos filmes com 2% de IPC o aumento na elongação foi significativo apenas quando adicionado 20% de OP. O aparecimento de apenas uma temperatura de fusão nos filmes sugeriu uma homogeneidade dos mesmos. A decomposição térmica dos filmes iniciou em torno de 120 -173ºC. Os filmes apresentaram uma superfície descontínua.

Production of bioplastics from hydrolysates of paper industry by Haloferax mediterranei

The biorefinery concept has attracted much attention over the last decade due to increasing concerns about the use of fossil resources. In this context emerged the use of bioplastics, namely polyhydroxyalkanoates (PHA). PHA are biocompatible and biodegradable plastics that can be obtained from renewable raw materials and can constitute an alternative solution to conventional plastics. In this work, hydrolysed cellulose pulp, coming from Eucalyptus globulus wood cooking, was used as substrate to the PHA-storing bacteria Haloferax mediterranei. The hydrolysed pulp is rich in simple sugars, mainly glucose (81.96 g.L-1) and xylose (20.90 g.L-1). Tests were made in defined medium with glucose and xylose and in hydrolysate supplemented with salts and yeast extract. Different concentrations of glucose were tested, namely 10, 15, 20, 30 and 40 g.L-1. The best accumulation results (27.1 % of PHA) were obtained in hydrolysate medium with 10 g.L-1. Using this concentration, assays were performed in fed-batch and sequencing batch reactor conditions in order to determine the best feeding strategy. The strategy that led to the best results was fed-batch assay with 24.7 % of PHA. An assay without sterile conditions was performed, in which was obtained the same growth than in sterilization test. Finally it was performed an assay in a bioreactor and a fast growth (0.14 h-1) with high glucose and xylose consumption rates (0.368 g.L-1.h-1 and 0.0947 g.L-1.h-1, respectively) were obtained. However 1.50 g.L-1 of PHA, corresponding to 16.1 % (92.52 % of 3HB and 3HV of 7.48 %) of % PHA were observed. The polymer was further characterized by DSC with a glass transition temperature of -6.07 °C, a melting temperature of 156.3 °C and a melting enthalpy of 63.07 J.g-1, values that are in accordance with the literature. This work recognizes for the first time the suitability of the pulp paper hydrolysate as a substrate for PHA production by H. mediterranei.

Diketonylpyridinium cations as a support of new ionic liquid crystals and ion-conductive materials: analysis of counter-ion effects

Ionic liquid crystals (ILCs) allow the combination of the high ionic conductivity of ionic liquids (ILs) with the supramolecular organization of liquid crystals (LCs). ILCs salts were obtained by the assembly of long-chained diketonylpyridinium cations of the type [HOO^(R(n)pyH)] + and BF_(4)^(-) , ReO_(4)^(-), NO_(3)^(-), CF_(3)SO_(3)^(-), CuCl_(4)^(2-) counter-ions. We have studied the thermal behavior of five series of compounds by differential scanning calorimetry (DSC) and hot stage polarized light optical microscopy (POM). All materials show thermotropic mesomorphism as well as crystalline polymorphism. X-ray diffraction of the [HOO^(R(12)pyH)][ReO_(4)] crystal reveals a layered structure with alternating polar and apolar sublayers. The mesophases also exhibit a lamellar arrangement detected by variable temperature powder X-ray diffraction. The CuCl_(4)^(2-) salts exhibit the best LC properties followed by the ReO_(4)^(-) ones due to low melting temperature and wide range of existence. The conductivity was probed for the mesophases in one species each from the ReO_(4)^(-) , and CuCl_(4)^(2-) families, and for the solid phase in one of the non-mesomorphic Cl^(-) salts. The highest ionic conductivity was found for the smectic mesophase of the ReO_(4)^(-) containing salt, whereas the solid phases of all salts were dominated by electronic contributions. The ionic conductivity may be favored by the mesophase lamellar structure.