Characterization of dynamic solid phase DNA extraction from blood with magnetically controlled silica beads

A novel solid phase extraction technique is described where DNA is bound and eluted from magnetic silica beads in a manner where efficiency is dependent on the magnetic manipulation of the beads and not on the flow of solution through a packed bed. The utility of this technique in the isolation of reasonably pure, PCR-amplifiable DNA from complex samples is shown by isolating DNA from whole human blood, and subsequently amplifying a fragment of the beta-globin gene. By effectively controlling the movement of the solid phase in the presence of a static sample, the issues associated with reproducibly packing a solid phase in a microchannel and maintaining consistent flow rates are eliminated. The technique described here is rapid, simple, and efficient, allowing for recovery of more than 60% of DNA from 0.6 mu L of blood at a concentration which is suitable for PCR amplification. In addition, the technique presented here requires inexpensive, common laboratory equipment, making it easily adopted for both clinical point-of-care applications and on-site forensic sample analysis.

Projecto dum laboratório remoto para automação de processos industriais

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Mecânica

Collaborative learning in a qeb-accessible workbench

Web-based course management and delivery is regarded by many institutions as a key factor in an increasingly competitive education and training world, but the systems currently available are largely unsatisfactory in terms of supporting collaborative work and access to practical science facilities. These limitations are less important in areas where “pen-and-paper” courseware is the mainstream, but become unacceptably restrictive when student assignments require real-time teamwork and access to laboratory equipment. This paper presents a web-accessible workbench for electronics design and test, which was developed in the scope of an European IST project entitled PEARL, with the aim of supporting two main features: full web access and collaborative learning facilities.

Infecção por Treponema pallidum: análise serológica e pesquisa de DNA

RESUMO: A sífilis é uma infecção causada por T. pallidum que pode ser transmitida por via vertical, por contacto sexual ou por sangue, e cujo diagnóstico se baseia na associação entre manifestações clinicas e testes serológicos. Neste estudo utilizaram-se os testes serológicos RPR, TPHA, FTA-Abs, um teste rápido não comercializado (Signal-Spirolipin) que pesquisa anticorpos treponémicos (CDC-T) e não treponémicos (CDC-2) em simultâneo no mesmo dispositivo e uma técnica de PCR-multiplex para a pesquisa de ADN de T. pallidum. Da comparação das técnicas serológicas constatou-se que a sensibilidade dos testes RPR e TPHA foi de 84,5% e 98% respectivamente. A especificidade foi de 77,3% para o teste RPR e de 87,5% para o teste TPHA. Na avaliação do teste rápido a comparação do teste CDC-2 com o teste RPR resultou numa taxa de concordância de 93,1% enquanto que, a do teste CDC-T com o teste TPHA foi de 94,8%. A sensibilidade e especificidade obtidas pelos testes CDC-2 e CDC-T foram de 88,7% e 65% e de 94,9% e 91,3% respectivamente. Considerando o diagnóstico de sífilis activa com base na reactividade simultânea dos testes RPR e TPHA, avaliou-se a sensibilidade do teste rápido utilizando esse mesmo critério. A sensibilidade obtida foi de 98,4% para o teste rápido e de 97,2% para a associação dos testes RPR/TPHA. A técnica de PCR-multiplex apresentou fraca sensibilidade já que em apenas 33% dos casos de sífilis foi identificado ADN de T. pallidum. O teste rápido avaliado apresentou um comportamento idêntico aos testes geralmente utilizados na rotina laboratorial tais como os utilizados neste estudo. Apresenta a vantagem de pesquisar anticorpos treponémicos e não treponémicos, ao contrário dos testes rápidos comercializados que pesquisam apenas anticorpos treponémicos. Não sendo necessário para a sua execução equipamento laboratorial especializado poderá ser de grande utilidade para o clinico a exercer em locais sem laboratório.------------- ABSTRACT: Syphilis is an infection caused by T. pallidum. Transmission may be vertical, through sexual contact or blood. The diagnosis is based in both serology and clinical manifestations. In this study, we used the serological tests RPR, TPHA, FTA-Abs and a non -commercialized rapid test (Signal-Spirolipin) to detect both treponemal (CDC-T) and non – treponemal antibodies (CDC-2) in the same device. T. pallidum DNA was identified with a multiplex PCR technique. In this study, the RPR and TPHA tests sensitivity was 84,5% and 98%, respectively, and the specificity 77,3% for the RPR test and 87,5% for TPHA test, respectively. The concordance rate was 93,1% in the comparison between the RPR and the CDC2 tests and 94,8% between the CDC-T with the TPHA tests. Sensitivity and specificity of the CDC-2 and CDC-T tests were 88,7% and 65% and 94,9% e 91,3%, respectively. Taking into account that the diagnosis of active syphilis is made when both the RPR and TPHA tests are reactive, we evaluated the sensitivity of the rapid test (CDC2 and CDCT) in the diagnosis of active syphilis, using the above described criteria. The sensitivity was 98,4 % for the rapid test and 97,2 % for the association of reactivity in both RPA and TPHA tests. The multiplex PCR technique presented a low sensitivity, with T. pallidum DNA being identified in only 33% of the syphilis cases. The rapid test evaluated in this study presented identical results to the tests generally used in the routine laboratory diagnosis, such as those used here. However, it does have the advantage of detecting both treponemal and non – treponemal antibodies what is not the case of the commercialized rapid test. Furthermore, there is no need of specialized laboratory equipment, which makes it of great utility in regions where such conditions do not exist, as in developing countries.

Gestão de infra-estruturas e avaliação de equipamentos laboratoriais

RESUMO: A confiabilidade e qualidade dos resultados clínicos de um laboratório, estão dependentes da qualidade do equipamento onde estes são processados. A qualidade de um equipamento consiste em apresentar resultados com uma confiabilidade metrológica de acordo com os processos de medição realizados. Desta forma, os equipamentos de medição devem conter características metrológicas de acordo com os requisitos dos processos que estão inseridos, tais como: erro máximo, incerteza, resolução… Todos os equipamentos por muito bons que sejam, apresentam perdas das suas características metrológicas ao longo do tempo, o que se torna importante a determinação periódica das suas calibrações, manutenções e o seu respectivo ajuste. A periodicidade das calibrações, devem ser baseadas, em critérios bem estabelecidos de modo a evitar a ocorrência da não conformidade, devido às medições com os equipamentos fora das suas especificações, garantindo-se assim, a confiabilidade metrológica e o aumento da produtividade devido ao controlo dos processos, evitando-se desta forma qualquer tipo de avaria por parte destes. Os normativos de Qualidade e Certificação estabelecem como requisito a calibração dos equipamentos de medição em intervalos adequados, mas não definem claramente qual o intervalo adequado. O importante é gerir as etapas de calibração e manutenção de acordo com os equipamentos de modo a garantir que os resultados emitidos por estes sejam mantidos em condições confiáveis, dentro do período entre calibrações e manutenções, de modo a que nãoocorra uma condição de falha, e por conseguinte, medições com grande quantidade de erros.------------ ABSTRACT: The reliability and quality of the results of a clinical laboratory, are dependent on the quality of the equipment where they are processed. The quality of a product is to present results with a metrological reliability according to the measuring processes carried out. Thus, measuring equipment must contain metrological characteristics according to the requirements of the processes that are included, such as: maximum error, uncertainty, resolution ... All equipment for very good they are, show losses of its metrological characteristics over time, it becomes important to determine its periodic calibrations, maintenance and its adjustment. The frequency of calibrations should be based on well-established criteria in order to avoid the occurrence of non-compliance due to the measurements with the equipment beyond its specifications, thus ensuring the metrological reliability and increased productivity due to the control of processes, thus avoiding any kind of damage on the part thereof. The normative and Quality Certification as a requirement to establish calibration of measuring equipment at appropriate intervals, but not clearly stipulate the proper range. It is important to manage the steps of calibration and maintenance equipment according to ensure that the results emitted by these conditions are maintained in trusted within the period between calibrations and maintenance, sothat there occurs a fault condition, and therefore, large amount of measurements with errors.

Desenvolvimento e otimização do projeto mecatrónico de um tribómetro rotativo (FRICTORQ)

Dissertação de mestrado integrado em Engenharia Mecânica

A simple method for human peripheral blood monocyte Isolation

We describe a simple method using percoll gradient for isolation of highly enriched human monocytes. High numbers of fully functional cells are obtained from whole blood or buffy coat cells. The use of simple laboratory equipment and a relatively cheap reagent makes the described method a convenient approach to obtaining human monocytes.

Characterization of Fly Ash for Use in Concrete, HR-225, 1983

Recent construction of new generation power plants burning western coal within Iowa has resulted in fly Ash production on the order of 760,000 tons annually. Although fly ash has long been accepted as a valuable replacement for portland cement in concrete, most experience has been with fly ash generated from eastern bituminous coals. A few years ago, fly ash in Iowa was not a significant factor because production was small and economics dictated disposal as the better alternative than construction use. Today, the economic climate, coupled with abundance of the material, makes constructive use in concrete feasible. The problem is, however, fly ash produced from new power plants is different than that for which information was available. It seems fly ash types have outgrown existing standards. The objective of this study was to develop fundamental information about fly ashes available to construction in Iowa such that its advantages and limitations as replacement to portland cement can be defined. Evaluative techniques used in this work involve sophisticated laboratory equipment, not readily available to potential fly ash users, so a second goal was preliminary development of rapid diagnostic tests founded on fundamental information. Lastly, Iowa Department of Transportation research indicated an interesting interdependency among coarse aggregate type, fly ash and concrete's resistance to freeze-thaw action. Thus a third charge of this research project was to verify and determine the cause for the phenomena. One objective of this project was to determine properties of Iowa fly ashes and evaluate their relevance to use of the material as an admixture of PCC. This phase of the research involved two approaches. The first involved the development of a rapid method for determining quantitative elemental composition while the second was aimed at both qualitative and quantitative determination of compounds. X-ray fluorescence techniques were adapted for rapid determination of elemental composition of fly ash. The analysis was performed using a Siemens SR-200 sequential x-ray spectrometer controlled by a PDP-11-03 microcomputer. The spectrometer was equipped with a ten sample specimen chamber and four interchangeable analyzing crystals. Unfiltered excitation radiation was generated using a chromium tube at 50 KV and 48 ma. Programs for the spectrometer were developed by the Siemens Corporation.

Química orgânica experimental: integração de teoria, experimento e análise

A new approach for teaching in basic experimental organic chemistry is presented. Experimental work goes on parallel to theoretical lectures leading to an immediate application of theoretical concepts transmitted therein. One day/week is dedicated exclusively to the organic laboratory. Reactions are proposed as problems to be solved; the student has to deduce the structure of the product on the basis of his observations, the analytical data and his mechanistical knowledge. 70 different experiments, divided in 7 thematical chapters, are presented. All experiments require the analysis and discussion of 1H and 13C NMR, IR and UV spectra. Additional questions about each reaction have to be answered by the student in his written report. Laboratory safety is garanteed by the exclusion or substitution of hazardous and toxic reagents. Microscale preparations are adopted in most cases to lower the cost of materials and the amount of waste. Recycling of many reaction products as starting materials in other experiments reduces the need for commercial reagents and allows the execution of longer reaction sequences. Only unexpensive standard laboratory equipment and simple glassware are required. All experiments include instructions for the save treatment or disposal of chemical waste.

New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

New methods for the concentration of viruses from urban sewage using quantitative PCR.

Viruses are among the most important pathogens present in water contaminated with feces or urine and represent a serious risk to human health. Four procedures for concentrating viruses from sewage have been compared in this work, three of which were developed in the present study. Viruses were quantified using PCR techniques. According to statistical analysis and the sensitivity to detect human adenoviruses (HAdV), JC polyomaviruses (JCPyV) and noroviruses genogroup II (NoV GGII): (i) a new procedure (elution and skimmed-milk flocculation procedure (ESMP)) based on the elution of the viruses with glycine-alkaline buffer followed by organic flocculation with skimmed-milk was found to be the most efficient method when compared to (ii) ultrafiltration and glycine-alkaline elution, (iii) a lyophilization-based method and (iv) ultracentrifugation and glycine-alkaline elution. Through the analysis of replicate sewage samples, ESMP showed reproducible results with a coefficient of variation (CV) of 16% for HAdV, 12% for JCPyV and 17% for NoV GGII. Using spiked samples, the viral recoveries were estimated at 30-95% for HAdV, 55-90% for JCPyV and 45-50% for NoV GGII. ESMP was validated in a field study using twelve 24-h composite sewage samples collected in an urban sewage treatment plant in the North of Spain that reported 100% positive samples with mean values of HAdV, JCPyV and NoV GGII similar to those observed in other studies. Although all of the methods compared in this work yield consistently high values of virus detection and recovery in urban sewage, some require expensive laboratory equipment. ESMP is an effective low-cost procedure which allows a large number of samples to be processed simultaneously and is easily standardizable for its performance in a routine laboratory working in water monitoring. Moreover, in the present study, a CV was applied and proposed as a parameter to evaluate and compare the methods for detecting viruses in sewage samples.

DNA extraction and quantification from touch and scrape preparations obtained from autopsy liver cells

The objective of the present study was to develop a simplified low cost method for the collection and fixation of pediatric autopsy cells and to determine the quantitative and qualitative adequacy of extracted DNA. Touch and scrape preparations of pediatric liver cells were obtained from 15 cadavers at autopsy and fixed in 95% ethanol or 3:1 methanol:acetic acid. Material prepared by each fixation procedure was submitted to DNA extraction with the Wizard® genomic DNA purification kit for DNA quantification and five of the preparations were amplified by multiplex PCR (azoospermia factor genes). The amount of DNA extracted varied from 20 to 8,640 µg, with significant differences between fixation methods. Scrape preparation fixed in 95% ethanol provided larger amount of extracted DNA. However, the mean for all groups was higher than the quantity needed for PCR (50 ng) or Southern blot (500 ng). There were no qualitative differences among the different material and fixatives. The same results were also obtained for glass slides stored at room temperature for 6, 12, 18 and 24 months. We conclude that touch and scrape preparations fixed in 95% ethanol are a good source of DNA and present fewer limitations than cell culture, tissue paraffin embedding or freezing that require sterile material, culture medium, laboratory equipment and trained technicians. In addition, they are more practical and less labor intensive and can be obtained and stored for a long time at low cost.

Power efficiency estimation and simulation of different control methods for the rotary screw compressor

Nowadays the energy efficiency has become one of the most concerned topics. Compressors are the equipment, which is very common in industry. Moreover, they tend to operate during long cycles and therefore even small decrease in power consumption can significantly reduce electricity costs during the year. And therefore it is important to investigate ways of increasing the energy efficiency of the compressors. In the thesis rotary screw compressor alongside with different control approaches is described. Simulation models for various control types of rotary screw compressor are developed. Analysis of laboratory equipment is conducted and results are compared with simulation. Suggestions of the real laboratory equipment improvement are given.

A detailed study of the lithiation of iron phosphate as well as the development of a novel synthesis of lithium iron silicate as cathode material for lithium-ion batteries

Dans cette thèse nous démontrons le travail fait sur deux matériaux de cathodes pour les piles lithium-ion. Dans la première partie, nous avons préparé du phosphate de fer lithié (LiFePO4) par deux méthodes de lithiation présentées dans la littérature qui utilisent du phosphate de fer (FePO4) amorphe comme précurseur. Pour les deux méthodes, le produit obtenu à chaque étape de la synthèse a été analysé par la spectroscopie Mössbauer ainsi que par diffraction des rayons X (DRX) pour mieux comprendre le mécanisme de la réaction. Les résultats de ces analyses ont été publiés dans Journal of Power Sources. Le deuxième matériau de cathode qui a été étudié est le silicate de fer lithié (Li2FeSiO4). Une nouvelle méthode de synthèse a été développée pour obtenir le silicate de fer lithié en utilisant des produits chimiques peu couteux ainsi que de l’équipement de laboratoire de base. Le matériau a été obtenu par une synthèse à l’état solide. Les performances électrochimiques ont été obtenues après une étape de broyage et un dépôt d’une couche de carbone. Un essai a été fait pour synthétiser une version substituée du silicate de fer lithié dans le but d’augmenter les performances électrochimiques de ce matériau.