Hybridization of single-stranded DNA targets to immobilized complementary DNA probes: comparison of hairpin versus linear capture probes

A microtiter-based assay system is described in which DNA hairpin probes with dangling ends and single-stranded, linear DNA probes were immobilized and compared based on their ability to capture single-strand target DNA. Hairpin probes consisted of a 16 bp duplex stem, linked by a T2-biotin·dT-T2 loop. The third base was a biotinylated uracil (UB) necessary for coupling to avidin coated microtiter wells. The capture region of the hairpin was a 3′ dangling end composed of either 16 or 32 bases. Fundamental parameters of the system, such as probe density and avidin adsorption capacity of the plates were characterized. The target DNA consisted of 65 bases whose 3′ end was complementary to the dangling end of the hairpin or to the linear probe sequence. The assay system was employed to measure the time dependence and thermodynamic stability of target hybridization with hairpin and linear probes. Target molecules were labeled with either a 5′-FITC, or radiolabeled with [γ-33P]ATP and captured by either linear or hairpin probes affixed to the solid support. Over the range of target concentrations from 10 to 640 pmol hybridization rates increased with increasing target concentration, but varied for the different probes examined. Hairpin probes displayed higher rates of hybridization and larger equilibrium amounts of captured targets than linear probes. At 25 and 45°C, rates of hybridization were better than twice as great for the hairpin compared with the linear capture probes. Hairpin–target complexes were also more thermodynamically stable. Binding free energies were evaluated from the observed equilibrium constants for complex formation. Results showed the order of stability of the probes to be: hairpins with 32 base dangling ends > hairpin probes with l6 base dangling ends > 16 base linear probes > 32 base linear probes. The physical characteristics of hairpins could offer substantial advantages as nucleic acid capture moieties in solid support based hybridization systems.

Comparison of stress induced by manual restraint and immobilisation in the estuarine crocodile, Crocodylus porosus

This study compared the stress induced in captive estuarine crocodiles, Crocodylus porosus, by two different handling methods: manual restraint (noosing with ropes) and immobilization by electro-stunning. To stun, a short charge (approx. 6 s) at 110 V was delivered to the back of the necks of C. porosus using a custom-built device, which immobilized the animals for 5-10 min. Immobilized and restrained animals were measured and sexed, and the condition of the skin assessed. Blood samples were taken from some animals immediately after restraint or immobilization. Other animals were returned to their pens to recover for periods of 30 min, 1, 4, 12, 24 or 48 hours after which they were stunned and blood samples taken. Individual animals (mean body length 1.96 m, N=99) were bled only once. Haematocrit and haemoglobin concentrations were measured and plasma samples were analysed for corticosterone, glucose and lactate levels. Following restraint, there were significant increases in haematocrit, haemoglobin, glucose, lactate and corticosterone concentrations in C. porosus. For restrained animals, recovery to baseline levels occurred after approximately 8 hours. The stress response of stunned animals was significantly reduced compared to manually captured and restrained crocodiles. Both groups showed a significant increase in haematocrit, haemoglobin concentration and lactate levels, however the magnitude of change was significantly reduced, and recovery was faster in stunned animals. No increase in either glucose or corticosterone levels occurred with immobilisation. The results imply that immobilization by electro-stunning is much less stressful. (C) 2003 Wiley-Liss, Inc.

Improving diagnosis and oral vaccination strategies against bovine tuberculosis

In this work peptide antigens [ESAT-6,p45 in water (1ml, 1mg/ml)] have been adsorbed onto 10mg inorganic substrates (hydroxyapatite (MHA P201;P120, CHA), polystyrene, calcium carbonate and glass microspheres) and in vitro release characteristics were determined. The aim of formulation was to enhance the interaction of peptides with antigen presenting cells and to achieve rapid peptide release from the carrier compartment system in a mildly acidic environment. Hydroxyapatite microparticle P201 has a greater surface area and thus has the largest peptide adsorption compared to the P120. CHA gave a further higher adsorption due to larger surface area than that available on microparticles. These particles were incorporated into the BOVIGAMTM assay to determine if they improve the sensitivity. After overnight incubation the blood plasma was removed and the amount of IFN-g in each plasma sample was estimated. CHA and MHA P201 gave a significantly higher immune response at low peptide concentration compared to the free peptide, thus indicating that these systems can be used to evaluate Tuberculosis (TB) amongst cattle using the BOVIGAMTM assay. Badgers are a source of TB and pass infection to cattle. At the moment vaccination against TB in badgers is via the parenteral route and requires a trained veterinary surgeon as well as catching the badgers. This process is expensive and time consuming; consequently an oral delivery system for delivery of BCG vaccines is easier and cheaper. The initial stage involved addition of various surfactants and suspending agents to disperse BCG and the second stage involved testing for BCG viability. Various copolymers of Eudragit were used as enteric coating systems to protect BCG against the acidic environment of the stomach (SGF, 0.1M HCl pH 1.2 at 37oC) while dissolving completely in the alkaline environment of the small intestine (SIF, IM PBS solution pH 7.4 at 37oC). Eudragit L100 dispersed in 2ml PBS solution and 0.9ml Tween 80 (0.1%w/v) gave the best results remaining intact in SGF loosing only approximately 10-15% of the initial weight and dissolving completely within 3 hours. BCG was incorporated within the matrix formulation adjusted to pH 7 at the initial formulation stage containing PBS solution and Tween 80. It gave viability of x106 cfu/ml at initial formulation stage, freezing and freeze-drying stages. After this stage the matrix was compressed at 4 tons for 3 mins and placed in SGF for 2 hours and then in SIF until dissolved. The BCG viability dropped to x106 cfu/ml. There is potential to develop it further for oral delivery of BCG vaccine.

Relentless patterns the immersive interior

What happens when patterns become all pervasive? When pattern contagiously corrupts and saturates adjacent objects, artefacts and surfaces; blurring internal and external environment and dissolving any single point of perspective or static conception of space. Mark Taylor ruminates on the possibilities of relentless patterning in interior space in both a historic and a contemporary context.

Designing spatial story-telling software

What does it mean when we design for accessibility, inclusivity and "dissolving boundaries" -- particularly those boundaries between the design philosophy, the software/interface actuality and the stated goals? This paper is about the principles underlying a research project called 'The Little Grey Cat engine' or greyCat. GreyCat has grown out of our experience in using commercial game engines as production environments for the transmission of culture and experience through the telling of individual stories. The key to this endeavour is the potential of the greyCat software to visualize worlds and the manner in which non-formal stories are intertwined with place. The apparently simple dictum of "show, don't tell" and the use of 3D game engines as a medium disguise an interesting nexus of problematic issues and questions, particularly in the ramifications for cultural dimensions and participatory interaction design. The engine is currently in alpha and the following paper is its background story. In this paper we discuss the problematic, thrown into sharp relief by a particular project, and we continue to unpack concepts and early designs behind the greyCat itself.

Recovery of Yeast Saccharomyces cerevisiae after Thermal Insult

All organisms have evolved mechanisms to acquire thermotolerance. A moderately high temperature activates heat shock genes and triggers thermotolerance towards otherwise lethal high temperature. The focus of this work is the recovery mechanisms ensuring survival of Saccharomyces cerevisiae yeast cells after thermal insult. Yeast cells, first preconditioned at 37˚C, can survive a short thermal insult at 48-50˚C and are able to refold heat-denatured proteins when allowed to recover at physiological temperature 24˚C. The cytoplasmic chaperone Hsp104 is required for the acquisition of thermotolerance and dissolving protein aggregates in the cytosol with the assistance of disaccharide trehalose. In the present study, Hsp104 and trehalose were shown to be required for conformational repair of heat-denatured secretory proteins in the endoplasmic reticulum. A reporter protein was first accumulated in the lumen of endoplasmic reticulum and heat-denatured by thermal insult, and then failed to be repaired to enzymatically active and secretion-competent conformation in the absence of Hsp104 or trehalose. The efficient transport of a glycoprotein CPY, accumulated in the endoplasmic reticulum, to the vacuole after thermal insult also needed the presence of Hsp104 and trehalose. However, proteins synthesized after thermal insult at physiological temperature were secreted with similar kinetics both in the absence and in the presence of Hsp104 or trehalose, demonstrating that the secretion machinery itself was functional. As both Hsp104 and trehalose are cytosolic, a cross-talk between cytosolic and luminal chaperone machineries across the endoplasmic reticulum membrane appears to take place. Global expression profiles, obtained with the DNA microarray technique, revealed that the gene expression was shut down during thermal insult and the majority of transcripts were destroyed. However, the transcripts of small cytosolic chaperones Hsp12 and Hsp26 survived. The first genes induced during recovery were related to refolding of denatured proteins and resumption of de novo protein synthesis. Transcription factors Spt3p and Med3p appeared to be essential for acquisition of full thermotolerance. The transcription factor Hac1p was found to be subject to delayed up-regulation at mRNA level and this up-regulation was diminished or delayed in the absence of Spt3p or Med3p. Consequently, production of the chaperone BiP/Kar2p, a target gene of Hac1p, was diminished and delayed in Δspt3 and Δmed3 deletion strains. The refolding of heat-denatured secretory protein CPY to a transport-competent conformation was retarded, and a heat-denatured reporter enzyme failed to be effectively reactivated in the cytoplasm of the deletion strains.

Enzymatic degradation of polycaprolactone-gelatin blend

Blends of polycaprolactone (PCL), a synthetic polymer and gelatin, natural polymer offer a optimal combination of strength, water wettability and cytocompatibility for use as a resorbable biomaterial. The enzymatic degradation of PCL, gelatin and PCL-gelatin blended films was studied in the presence of lipase (Novozym 435, immobilized) and lysozyme. Novozym 435 degraded the PCL films whereas lysozyme degraded the gelatin. Though Novozym 435 and lysozyme individually could degrade PCL-gelatin blended films, the combination of these enzymes showed the highest degradation of these blended films. Moreover, the enzymatic degradation was much faster when fresh enzymes were added at regular intervals. The changes in physico-chemical properties of polymer films due to degradation were studied by scanning electron microscopy, Fourier transform infrared spectroscopy and differential scanning calorimetry. These results have important implications for designing resorbable biomedical implants.

Enzymatic degradation of polycaprolactone-gelatin blend

Blends of polycaprolactone (PCL), a synthetic polymer and gelatin, natural polymer offer a optimal combination of strength, water wettability and cytocompatibility for use as a resorbable biomaterial. The enzymatic degradation of PCL, gelatin and PCL-gelatin blended films was studied in the presence of lipase (Novozym 435, immobilized) and lysozyme. Novozym 435 degraded the PCL films whereas lysozyme degraded the gelatin. Though Novozym 435 and lysozyme individually could degrade PCL-gelatin blended films, the combination of these enzymes showed the highest degradation of these blended films. Moreover, the enzymatic degradation was much faster when fresh enzymes were added at regular intervals. The changes in physico-chemical properties of polymer films due to degradation were studied by scanning electron microscopy, Fourier transform infrared spectroscopy and differential scanning calorimetry. These results have important implications for designing resorbable biomedical implants.

The convection during NaClO3 crystal growth observed by the phase shift interferometer

An optical diagnostic system consisting of the Mach-Zehnder interferometer with the phase shift device and an image processor has been developed for the study of the kinetics of the crystal growing process. The dissolution and crystallization process of NaClO3 crystal has been investigated. The concentration distributions around a growing and dissolving crystal have been obtained by using phase-shift of four-steps theory for the interpretation of the interferograms. The convection (a plume flow) has been visualized and analyzed in the process of the crystal growth. The experiment demonstrates that the buoyancy convection dominates the growth rate of the crystal growing face on the ground-based experiment.

Interações do lantânio com células livres e imobilizadas em alginato em regimes de batelada e contínuo

Este trabalho teve como objetivo descrever o potencial de biossorção de lantânio pelas microalgas Ankistrodesmus sp. e Golenkinia sp. livres e pellets de alginato de cálcio, com e sem as microalgas imobilizadas, a partir de soluções aquosas. Para isso foram realizados estudos em regime batelada e em coluna de leito fixo. Modelos cinéticos de pseudo-primeira ordem e de segunda ordem e isotermas de equilíbrio de Langmuir e de Freundlich foram utilizados para a descrição quantitativa e a previsão do comportamento de adsorção do metal pelas biomassas livres e imobilizadas no sistema descontínuo. Os dados foram mais bem ajustados pelo modelo cinético de segunda ordem, com coeficientes de determinação (r2) maiores que 0,98. Foram obtidos tempos de equilibrio muito curtos, na faixa de 1-30 minutos. A isoterma de Langmuir foi a que melhor se ajustou aos dados experimentais, com valores de r2 maiores que 0,94. Foram observados valores de qmáx, isto é, a quantidade máxima de metal captado pelo biossorvente, entre 0,96 e 10,43 mmol/g. As células livres mostraram-se mais eficientes do que os pellets caracterizados com e sem os micro-organismos. Os pellets mostraram melhor potencial quando contendo microalgas imobilizadas, em comparação com eles puros. No estudo dinâmico, 12 L de solução contendo uma concentração de La (III) de 150 mmol/L ascenderam pela coluna contendo Ankistrodesmus sp. e Golenkinia sp. imobilizadas e pellets de alginato de cálcio puros durante 8 horas. No último minuto, os três biossorventes ainda apresentaram cerca de 80% de eficiência de remoção. Desta forma, o ponto de satuação não foi atingido. A rápida e alta capacidade de adsorção das microalgas revelou que sua aplicação em escala superior é possível em ambos os processos estudados, uma vez que a imobilização desses biomateriais não mudou a sua capacidade de sorção e nem o rápido contato entre o adsorvente e o soluto no processo de biossorção de lantânio

Site-selective self-assembly of MPA-bridged CuHCF multilayers on APTMS-supported gold colloid electrodes

(3-Aminopropyl)trimethoxysilane (APTMS)-supported gold colloid electrode was constructed by virtue of a recently developed solution-based self-assembly strategy. The preparing procedure of 3-mercaptopropionic acid (MPA)-bridged copper hexacyanoferrate (CuHCF) multilayers on a planar macroelectrode (Bharathi et al. Langmuir 2001, 17, 7468) was copied to the as-prepared colloid electrode. The optical spectra, atomic force microscopy, and electrochemistry demonstrate successful copy of the multilayer system on a macroelectrode to the as-prepared colloid electrode. Remarkably, it was found that multilayer growth is highly selective to the nanoscale sites where gold nanoparticles are immobilized, and multilayer growth does not take place on the sites without nanoparticles. Interestingly, a preliminary electrochemical investigation indicates that electrochemical properties of multilayers systems on the colloid electrode are different from their counterparts on a planar macroelectrode, which might be due to high curvature effects of the gold nanoparticles. This indicates a different motif of multilayers on the colloid electrode from that on a planar macroelectrode.

Self-assembled gold nanoparticles on functionalized gold (111) studied by scanning tunneling microscopy

Nanogold colloidal solutions are prepared by the reduction of HAuClO4 with sodium citrate and sodium borohydride. 4-Aminothiophenol (ATP) self-assembled monolayers (SAMs) are formed on gold(lll) surface, on which gold nanoparticles are immobilized and a sub-monolayer of the particles appears. This sub-monolayer of gold nanoparticles is characterized with scanning tunneling microscopy (STM), and a dual energy barrier tunneling model is proposed to explain the imageability of the gold nanoparticles by STM. This model can also be used to construct multiple energy barrier structure on solid/liquid interface and to evaluate the electron transport ability of some organic monolayers with the aid of electrochemical method.

水热条件下钾长石碱性分解反应机理的实验研究

It is well known that our country is short of water-soluble potassium, but rich in insoluble potassium ores. Based on the work of the formers, using the orthogonal and monofactor experiments, the author optimized the production technology of micro-porous potassium silicon calcium mineral fertilizer by non-stirring hydrothermal chemical reaction when the alkaline earth booster CaO was available. The influences of temperature、time、reactant ratio and water-solid ratio on the dissolution rate of production’s elements were studied by orthogonal experiments, and the production technology was further optimized by monofactor experiments. By XRD、SEM、EDS and dissolving experiments, it was systematically studied that the effects of the reactant ratio、reaction time and reaction temperature on the properties of the production obtained by the hydrothermal reaction between KAlSi3O8 and CaO. The results showed that：when changing of the reaction condition, the reaction productions included tobermorite、 hibschite、α-C2SH and K2Ca(CO3)2; among which, K2Ca(CO3)2 was not the first production containing potassium, but K2Ca(CO3)2 was synthesized by the reaction among KOH、Ca(OH)2 and CO2. Whether the phase was synthesized was related to not only the reaction condition, but also their physicochemical properties; when the reaction condition was changed, the changes of different phases were different. The results of XRD and dissolution rate experiments explained the dissolution characteristic of every element of hydrothermal productions very well, and the relation between the dissolution rate of element and the phase of productions poured a good illumination on the production technology. The results of SEM and EDS showed that: hydrogarnet looked like spherical, and its surface was covered by some productions including K phase and Ca、Si phase; but the morphology of tobermorite was platy or lamellar or needlelike, and parts of Si in the structure of tobermorite were substituted by Al，and some K+ cations were inserted into the Ca interlayer of tobermorite at the same time. It was the first time that the interface between KAlSi3O8 and Ca(OH)2 was observed directly by SEM and EDS after the hydrothermal reaction, and the mechanism of hydrothermal reaction of KAlSi3O8 and Ca(OH)2 was further discussed. These results indicated that: the Ca-KAlSi3O8 intermediate compound was formed at first, and some K was released into the solution and KOH was produced at the same time; the C-S-H phase appeared before hydrogarnet, and then hydrogarnet was synthesized when the chemical reaction was carried on; if the reaction was carried on furthermore, α-C2SH、tobermorite and other C-S-H phases of different atom ratio appeared. The author found that the structure of KAlSi3O8 would be more drastically destroyed if there were some reactants, such as Ca(OH)2 which reacted with KAlSi3O8 and new phases were formed after the hydrothermal reaction between KAlSi3O8 and alkaline solution of equal ionic strength was finished. With the combination of calcination and hydrothermal reaction methods, the dissolution rate of products were greatly improved when the hydrothermal reaction was carried out after KAlSi3O8 and CaCO3 were calcined. Furthermore, the author has tentatively explored how to evaluate the effects of the differences of the activity of lime on the dissolution properties of hydrothermal products.

Argilas aniónicas multifuncionais

O presente trabalho aborda a imobilização de vários complexos do tipo dioxomolibdénio(VI), dioxotungsténio(VI) e de cobre(II) em suportes do tipo hidróxidos duplos lamelares (LDHs). Numa primeira parte descrevem-se os suportes LDHs e a síntese e caracterização em solução e estado sólido de complexos catecolato cis-MoO2 e cis-WO2. Investigou-se depois a química de intercalação deste tipo de complexos, nomeadamente a influência dos LDHs percursores, temperatura de intercalação, excesso de anião e mudança de metal no complexo intercalado (M=Mo, W). De seguida foi estudada a imobilização de oxocomplexos de molibdénio(VI) num LDH com pilares de bipiridina dicarboxilato e procedeu-se à avaliação da sua aplicabilidade em reacções catalíticas de oxidação de álcoois e olefinas. Com o objectivo de desenvolver as aplicações dos LDHs com pilares foi estudada a imobilização de um complexo de cobre(II) neste material e avaliada a sua aplicação como catalizador na oxidação de substratos orgânicos.

Síntese e estudos estruturais de novos materiais luminescentes

A presente dissertação teve como objectivo a síntese, caracterização e estudo das propriedades luminescentes de complexos livres e/ou imobilizados no material mesoporoso MCM-41. Na primeira parte estudaram-se complexos do tipo, Eu(NTA)3L2, onde NTA corresponte ao β-dicetonato 1-(2-naftoil)-3,3,3-trifluoro-acetonato, e L2 aos ligandos bidentados de azoto derivados do pirazolilpiridina e L aos ligandos monodentados (etil-4-piridilacetato, água, piridina e metilfenilsulfóxido). Alguns destes ligandos foram imobilizados e/ou impregnados no MCM-41, tendo-se posteriormente complexado o fragmento Eu(NTA)3. Na segunda parte estudou-se o efeito do contra-ião no complexo C[Eu(NTA)4], usando os catiões (C): tetrabutilamónio [NBu4]+, 1-butil-3-metilimidazolilo [C4mim]+ e 1-butil-3-metilpiridínio [C4mpy]+. O anião [Eu(NTA)4]- foi imobilizado no MCM-41 derivatizado com grupos 1-propil-3-metilimidazolilo. Todos os complexos preparados foram caracterizados pelas técnicas de análise elementar, termogravimetria, espectroscopias vibracionais (Infravermelho e Raman) e de ressonância magnética nuclear, e os materiais preparados foram adicionalmente analisados por difracção de raios-X de pós e ressonância magnética nuclear de estado sólido. Foram também estudadas as propriedades fotoluminescentes dos compostos, e para facilitar a análise dos resultados, nalguns casos foram preparados e caracterizados os compostos análogos de gadolínio.