Ortsbezogene Informationen in Internet-Datenbanken - das Beispiel "Baltic SeaWeb"

Whoever in future will need information about a location or an area, either literature, measurement data, photos or administrative information, might only click on that spot on a screen map in the internet. A search programme started thereby will offer all available information in databanks. A step forward to such a solution, to the retrieval of location related literature and measurement data from different kinds of databanks, is presented by the project “Baltic Sea Web” (http://www.baltic.vtt.fi/ demonstrator/index.html). The basic idea was to make the available information about a certain location accessible via a link of their geographical coordinates, longitude and latitude, to a map in a web browser

Developing peptide based capture agents for diagnostics and therapeutics

Iterative in situ click chemistry (IISCC) is a robust general technology for development of high throughput, inexpensive protein detection agents. In IISCC, the target protein acts as a template and catalyst, and assembles its own ligand from modular blocks of peptides. This process of ligand discovery is iterated to add peptide arms to develop a multivalent ligand with increased affinity and selectivity. The peptide based protein capture agents (PCC) should ideally have the same degree of selectivity and specificity as a monoclonal antibody, along with improved chemical stability. We had previously reported developing a PCC agent against bovine carbonic anhydrase II (bCAII) that could replace a polyclonal antibody. To further enhance the affinity or specificity of the PCC agent, I explore branching the peptide arms to develop branched PCC agents against bCAII. The developed branched capture agents have two to three fold higher affinities for the target protein. In the second part of my thesis, I describe the epitope targeting strategy, a strategy for directing the development of a peptide ligand against specific region or fragment of the protein. The strategy is successfully demonstrated by developing PCC agents with low nanomolar binding affinities that target the C-terminal hydrophobic motif of Akt2 kinase. One of the developed triligands inhibits the kinase activity of Akt. This suggests that, if targeted against the right epitope, the PCC agents can also influence the functional properties of the protein. The exquisite control of the epitope targeting strategy is further demonstrated by developing a cyclic ligand against Akt2. The cyclic ligand acts as an inhibitor by itself, without any iteration of the ligand discovery process. The epitope targeting strategy is a cornerstone of the IISCC technology and opens up new opportunities, leading to the development of protein detection agents and of modulators of protein functions.

A cocktail of thermally stable, chemically synthesized capture agents for the efficient detection of anti-gp41 antibodies from human sera and techniques

This thesis reports on a method to improve in vitro diagnostic assays that detect immune response, with specific application to HIV-1. The inherent polyclonal diversity of the humoral immune response was addressed by using sequential in situ click chemistry to develop a cocktail of peptide-based capture agents, the components of which were raised against different, representative anti-HIV antibodies that bind to a conserved epitope of the HIV-1 envelope protein gp41. The cocktail was used to detect anti-HIV-1 antibodies from a panel of sera collected from HIV-positive patients, with improved signal-to-noise ratio relative to the gold standard commercial recombinant protein antigen. The capture agents were stable when stored as a powder for two months at temperatures close to 60°C.

Development of protein-catalyzed capture (PCC) agents with application to the specific targeting of the E17K Point mutation of Akt1

This thesis describes the expansion and improvement of the iterative in situ click chemistry OBOC peptide library screening technology. Previous work provided a proof-of-concept demonstration that this technique was advantageous for the production of protein-catalyzed capture (PCC) agents that could be used as drop-in replacements for antibodies in a variety of applications. Chapter 2 describes the technology development that was undertaken to optimize this screening process and make it readily available for a wide variety of targets. This optimization is what has allowed for the explosive growth of the PCC agent project over the past few years.

These technology improvements were applied to the discovery of PCC agents specific for single amino acid point mutations in proteins, which have many applications in cancer detection and treatment. Chapter 3 describes the use of a general all-chemical epitope-targeting strategy that can focus PCC agent development directly to a site of interest on a protein surface. This technique utilizes a chemically-synthesized chunk of the protein, called an epitope, substituted with a click handle in combination with the OBOC in situ click chemistry libraries in order to focus ligand development at a site of interest. Specifically, Chapter 3 discusses the use of this technique in developing a PCC agent specific for the E17K mutation of Akt1. Chapter 4 details the expansion of this ligand into a mutation-specific inhibitor, with applications in therapeutics.

DNA-Mediated Charge Transport Devices for Protein Detection

Detection of biologically relevant targets, including small molecules, proteins, DNA, and RNA, is vital for fundamental research as well as clinical diagnostics. Sensors with biological elements provide a natural foundation for such devices because of the inherent recognition capabilities of biomolecules. Electrochemical DNA platforms are simple, sensitive, and do not require complex target labeling or expensive instrumentation. Sensitivity and specificity are added to DNA electrochemical platforms when the physical properties of DNA are harnessed. The inherent structure of DNA, with its stacked core of aromatic bases, enables DNA to act as a wire via DNA-mediated charge transport (DNA CT). DNA CT is not only robust over long molecular distances of at least 34 nm, but is also especially sensitive to anything that perturbs proper base stacking, including DNA mismatches, lesions, or DNA-binding proteins that distort the π-stack. Electrochemical sensors based on DNA CT have previously been used for single-nucleotide polymorphism detection, hybridization assays, and DNA-binding protein detection. Here, improvements to (i) the structure of DNA monolayers and (ii) the signal amplification with DNA CT platforms for improved sensitivity and detection are described.

First, improvements to the control over DNA monolayer formation are reported through the incorporation of copper-free click chemistry into DNA monolayer assembly. As opposed to conventional film formation involving the self-assembly of thiolated DNA, copper-free click chemistry enables DNA to be tethered to a pre-formed mixed alkylthiol monolayer. The total amount of DNA in the final film is directly related to the amount of azide in the underlying alkylthiol monolayer. DNA monolayers formed with this technique are significantly more homogeneous and lower density, with a larger amount of individual helices exposed to the analyte solution. With these improved monolayers, significantly more sensitive detection of the transcription factor TATA binding protein (TBP) is achieved.

Using low-density DNA monolayers, two-electrode DNA arrays were designed and fabricated to enable the placement of multiple DNA sequences onto a single underlying electrode. To pattern DNA onto the primary electrode surface of these arrays, a copper precatalyst for click chemistry was electrochemically activated at the secondary electrode. The location of the secondary electrode relative to the primary electrode enabled the patterning of up to four sequences of DNA onto a single electrode surface. As opposed to conventional electrochemical readout from the primary, DNA-modified electrode, a secondary microelectrode, coupled with electrocatalytic signal amplification, enables more sensitive detection with spatial resolution on the DNA array electrode surface. Using this two-electrode platform, arrays have been formed that facilitate differentiation between well-matched and mismatched sequences, detection of transcription factors, and sequence-selective DNA hybridization, all with the incorporation of internal controls.

For effective clinical detection, the two working electrode platform was multiplexed to contain two complementary arrays, each with fifteen electrodes. This platform, coupled with low density DNA monolayers and electrocatalysis with readout from a secondary electrode, enabled even more sensitive detection from especially small volumes (4 μL per well). This multiplexed platform has enabled the simultaneous detection of two transcription factors, TBP and CopG, with surface dissociation constants comparable to their solution dissociation constants.

With the sensitivity and selectivity obtained from the multiplexed, two working electrode array, an electrochemical signal-on assay for activity of the human methyltransferase DNMT1 was incorporated. DNMT1 is the most abundant human methyltransferase, and its aberrant methylation has been linked to the development of cancer. However, current methods to monitor methyltransferase activity are either ineffective with crude samples or are impractical to develop for clinical applications due to a reliance on radioactivity. Electrochemical detection of methyltransferase activity, in contrast, circumvents these issues. The signal-on detection assay translates methylation events into electrochemical signals via a methylation-specific restriction enzyme. Using the two working electrode platform combined with this assay, DNMT1 activity from tumor and healthy adjacent tissue lysate were evaluated. Our electrochemical measurements revealed significant differences in methyltransferase activity between tumor tissue and healthy adjacent tissue.

As differential activity was observed between colorectal tumor tissue and healthy adjacent tissue, ten tumor sets were subsequently analyzed for DNMT1 activity both electrochemically and by tritium incorporation. These results were compared to expression levels of DNMT1, measured by qPCR, and total DNMT1 protein content, measured by Western blot. The only trend detected was that hyperactivity was observed in the tumor samples as compared to the healthy adjacent tissue when measured electrochemically. These advances in DNA CT-based platforms have propelled this class of sensors from the purely academic realm into the realm of clinically relevant detection.

Efficacy and safety of autologous platelet rich plasma for the treatment of vascular ulcers in primary care: Phase III study

Background: Vascular ulcers are commonly seen in daily practice at all levels of care and have great impact at personal, professional and social levels with a high cost in terms of human and material resources. Given that the application of autologous platelet rich plasma has been shown to decrease healing times in various different studies in the hospital setting, we considered that it would be interesting to assess the efficacy and feasibility of this treatment in primary care. The objectives of this study are to assess the potential efficacy and safety of autologous platelet rich plasma for the treatment of venous ulcers compared to the conventional treatment (moist wound care) in primary care patients with chronic venous insufficiency (C, clinical class, E, aetiology, A, anatomy and P, pathophysiology classification C6). Design: We will conduct a phase III, open-label, parallel-group, multicentre, randomized study. The subjects will be 150 patients aged between 40 and 100 years of age with an at least 2-month history of a vascular venous ulcer assigned to ten primary care centres. For the treatment with autologous platelet rich plasma, all the following tasks will be performed in the primary care setting: blood collection, centrifugation, separation of platelet rich plasma, activation of coagulation adding calcium chloride and application of the PRP topically after gelification. The control group will receive standard moist wound care. The outcome variables to be measured at baseline, and at weeks 5 and 9 later include: reduction in the ulcer area, Chronic Venous Insufficiency Quality of Life Questionnaire score, and percentage of patients who require wound care only once a week. Discussion: The results of this study will be useful to improve the protocol for using platelet rich plasma in chronic vascular ulcers and to favour wider use of this treatment in primary care.

El pintor navarro Juan Ochoa de Arín (1600-1652) y su producción en Gipuzkoa

Investigación realizada dentro del Programa de Formación y Perfeccionamiento de Personal Investigador del Gobierno Vasco (2010-2013).

Centro de gestión de contenido en RDF

La primera idea de la realización de este proyecto, fue concebida por la necesidad de tener un sistema por el cual se pudieran cambiar datos de una aplicación, en un sistema móvil, a través de una página web. Sin embargo al conocer la potencia que tiene RDF para ser muy escalable terminó siendo un sistema de gestión de contenido general en RDF. Este sistema de gestión se ha realizado para ser lo más simple posible para un usuario, de tal manera que con solo 2 click en la página web y rellenando un formulario simple, pudiera tener una base de datos sin muchos conocimientos sobre la gestión de las mismas. Aunque claramente no es un sistema potente como si fuera una base de datos en Oracle, por citar un ejemplo, sirve para poder agregar, modificar y eliminar datos con sencillez. Así este sistema de gestión da una posibilidad muy sencilla de realizar tus propias bases de datos. Además aunque tiene un motor SQL para la gestión interna de almacenamiento, la salida de los datos es en RDF/XML con lo que podría ser compatible con un sistema más amplio como Oracle Database Semantic Technologies. Este CMS también tendrá un sistema de seguridad basado en usuario y contraseña. Para que la edición del contenido sea accesible solo a usuarios con acceso, mientras que la exportación de los datos será pública, y podrá ser accesible por cualquier usuario mediante una URI.

Modificação química do poli(cloreto de vinila) com nucleófilos nitrogenados assistida por micro-ondas

Nesse trabalho foram realizadas reações de substituição nucleofílica (SN2), utilizando aquecimento térmico convencional e por irradiação de micro-ondas (MO), de alguns átomos cloro em amostras comerciais de poli(cloreto de vinila) (PVC), por grupos nitrila e também por grupos azida. Os grupos nitrila e azida foram substituidos na matriz em diferentes teores (10% e 20%). As reações do PVC com azida foram eficazes, apresentado percentuais de derivatização muito próximos dos valores desejados. Já no estudo com a nitrila não foi obtido o resultado esperado. Os copolímeros PVC azido substituídos foram modificados com propargilato de etila, sob catálise de iodeto de cuproso (CuI), para a obtenção de heterocíclicos do tipo triazólicos. Todos os copolímeros obtidos foram caracterizados por espectroscopia na região do infravermelho (FTIR) e os teores de nitrogênio incorporado foram determinados por análise elementar (AE). Através da análise dos dados obtidos, foi comprovado que a utilização da irradiação micro-ondas, quando comparada ao aquecimento convencional, é um processo mais seletivo e diminui, significativamente, os tempos de reação

Efficient Synthesis of Single-Chain Polymer Nanoparticles via Amide Formation

Single-chain technology (SCT) allows the transformation of individual polymer chains to folded/collapsed unimolecular soft nanoparticles. In this work we contribute to the enlargement of the SCT toolbox by demonstrating the efficient synthesis of single-chain polymer nanoparticles (SCNPs) via intrachain amide formation. In particular, we exploit cross-linking between active methylene groups and isocyanate moieties as powerful "click" chemistry driving force for SCNP construction. By employing poly(methyl methacrylate)- (PMMA-) based copolymers bearing beta-ketoester units distributed randomly along the copolymer chains and bifunctional isocyanate cross-linkers, SCNPs were successfully synthesized at r.t. under appropriate reaction conditions. Characterization of the resulting SCNPs was carried out by means of a combination of techniques including size exclusion chromatography (SEC), infrared (IR) spectroscopy, proton nuclear magnetic resonance (H-1 NMR) spectroscopy, dynamic light scattering (DLS), and elemental analysis (EA).

Estudo da reação de modificação do poli(cloreto de vinila) com nucleófilos nitrogenados e das aplicações como suporte em reações de acoplamento

Neste trabalho foi realizada a modificação química do poli(cloreto de vinila) (PVC) pela sua reação com azida de sódio, onde alguns dos seus átomos de cloro foram substituídos por azidas. Em seguida o grupo incorporado foi transformado em triazóis por uma reação de cicloadição 1,3 entre o polímero modificado e propiolato de etila, sendo a reação catalisada por iodeto de cobre. Essas reações foram conduzidas sob aquecimento convencional e empregando irradiação de micro-ondas. Inicialmente, a reação incorporou 20% de triazol no PVC, sendo avaliadas as condições reacionais ideais. Essas condições foram usadas para a formação de novos copolímeros com diferentes teores de triazóis incorporados. Os produtos obtidos foram usados para o suporte de paládio que é utilizado como catalisador na reação de Suzuki-Miyaura. Todos os copolímeros foram caracterizados por espectroscopia na região do infravermelho com transformada de Fourier (FTIR)

Preparação e Avaliação da Atividade Catalítica de Polímeros de Condensação de Metilpiridinas e Tereftalaldeído em Reações de Nitroaldol e Cicloadição Heterodipolar [3+2]

Nesse estudo, foram preparadas bases poliméricas derivadas de 2,6-dimetilpiridinas e tereftaladeído utilizando a 2,4,6-trimetilpiridina como agente de reticulação. As resinas foram sintetizadas sob aquecimento convencional e purificadas por precipitação em metanol, apresentando rendimentos variando de 59 a 95%. Os copolímeros produzidos foram caracterizados por análise termogravimétrica (TGA), ressonância nuclear magnética de núcleo de hidrogênio (RMN-1H) e espectroscopia na região do infravermelho com técnica de ATR (FTIR - ATR), além de sua atividade básica. A capacidade catalítica do material produzido foi avaliada em reações nitroaldólicas, do tipo Henry, tanto em aquecimento convencional quanto com o uso de reator de micro-ondas. Não sendo observada atividade catalítica significativa para as resinas testadas, nestas reações. O material polimérico produzido também foi testado como suporte para cobre na catálise de reações de cicloadição heterodipolar do tipo [3+2] com benzilazida e propiolato de etila, para a formação de triazóis, processadas em reator de micro-ondas e sob aquecimento convencional. A reação mostrou-se regiosseletiva e processos de reciclo do catalisador se mostrou eficiente em reações consecutivas

The dynamics of hippocampal sensory gating during the development of morphine dependence and withdrawal in rats

The effects of morphine on hippocampal sensory gating (N40) during the development of morphine dependence and withdrawal were investigated in the double click auditory evoked potential (EP) suppression paradigm. Rats were made dependent upon morphine hydrochloride by a series of injections (every 12h) over 6 days, followed by withdrawal after stopping morphine administration. Hippocampal gating was examined during the development of dependence and withdrawal. Moreover, the DA antagonist haloperidol was used to assess the contribution of dopamine to hippocampal gating induced by morphine. Our results showed that the morphine-treated rats exhibited significantly disrupted hippocampal gating during the development of morphine dependence and this disrupted gating was partially reversed by haloperidol pretreatment. In contrast, there was significantly enhanced hippocampal gating at the fifth and sixth days of withdrawal. The dynamics of hippocampal gating during the development of morphine dependence and withdrawal suggests the interaction between the hippocampus and opioids. (c) 2005 Elsevier Ireland Ltd. All rights reserved.

Influence of physical parameters of sound on the sensory gating effects of N40 in rats

Sensory gating is the ability of the brain to modulate its sensitivity to incoming stimuli. The N40 component of the auditory evoked potential, evaluated with the paired click paradigm, was used to probe the gating effect in rats. The physical characteris

Ageing, Adaption and Accessibility: Time for the Inclusive Revolution!

Information and Communication Technology (ICT) is becoming increasingly central to many people’s lives, making it possible to be connected in any place at any time, be unceasingly and instantly informed, and benefit from greater economic and educational opportunities. With all the benefits afforded by these new-found capabilities, however, come potential drawbacks. A plethora of new PCs, laptops, tablets, smartphones, Bluetooth, the internet, Wi-Fi (the list goes on) expect us to know or be able to guess, what, where and when to connect, click, double-click, tap, flick, scroll, in order to realise these benefits, and to have the physical and cognitive capability to do all these things. One of the groups most affected by this increase in high-demand technology is older people. They do not understand and use technology in the same way that younger generations do, because they grew up in the simpler electro-mechanical era and embedded that particular model of the world in their minds. Any consequential difficulty in familiarising themselves with modern ICT and effectively applying it to their needs can also be exacerbated by age-related changes in vision, motor control and cognitive functioning. Such challenges lead to digital exclusion. Much has been written about this topic over the years, usually by academics from the area of inclusive product design. The issue is complex and it is fair to say that no one researcher has the whole picture. It is difficult to understand and adequately address the issue of digital exclusion among the older generation without looking across disciplines and at industry’s and government’s understanding, motivation and efforts toward resolving this important problem. To do otherwise is to risk misunderstanding the true impact that ICT has and could have on people’s lives across all generations. In this European year of Active Ageing and Solidarity between Generations and as the British government is moving forward with its Digital by Default initiative as part of a wider objective to make ICT accessible to as many people as possible by 2015, the Engineering Design Centre (EDC) at the University of Cambridge collaborated with BT to produce a book of thought pieces to address, and where appropriate redress, these important and long-standing issues. “Ageing, Adaption and Accessibility: Time for the Inclusive Revolution!” brings together opinions and insights from twenty one prominent thought leaders from government, industry and academia regarding the problems, opportunities and strategies for combating digital exclusion among senior citizens. The contributing experts were selected as individuals, rather than representatives of organisations, to provide the broadest possible range of perspectives. They are renowned in their respective fields and their opinions are formed not only from their own work, but also from the contributions of others in their area. Their views were elicited through conversations conducted by the editors of this book who then drafted the thought pieces to be edited and approved by the experts. We hope that this unique collection of thought pieces will give you a broader perspective on ageing, people’s adaption to the ever changing world of technology and insights into better ways of designing digital devices and services for the older population.