Among the most common endoparasites who infected small crustacean Daphnia pulex include microsporidia. These intracellular parasites appear to look like a simple single- celled organisms, but their cell structure and lifecycle prove the opposite. Microsporidia are species-specific. Although they infected most organisms of the animal kingdom, they are not yet sufficiently understood. This theses is inderectly followed up to the studies of waterflea Daphnia longispina and microsporidia Berwaldia schaefernai from the dam reservoirs The aim was to analyze closer microsporidian infection on host Daphnia pulex in a forest pool with simple enviroment, which included monitoring time dynamics of Daphnia population and identification infection caused by microsporidia Berwaldia singularis and yet unknown microsporidia labor-marked "HVH". Laboratory work included determination of zooplankton and parasites, calculation of prevalence, laboratory experiments with transmission of microsporidian infection between healthy and infected flea culture or by isolated spores. Genetic analysis of aquatic invertebrates from the forest pool, especially larvae of mite and mosquitos, helped make closer microsporidian life cycle and hypothesis about secondary hosts, for the presence of pathogen DNA using specific DNA...

Waterborne or foodborne diseases are caused by consuming contaminated fluids or foods. The presence of pathogenic microorganisms can contaminate food or drinking water. These microorganisms can cause sickness even if they are present in minimal concentrations. The World Health Organization (WHO) has defined the standards for clean drinking water as the absence of E. coli in a 100 mL collected volume. Contaminated water or food can cause many diseases, and diarrhea is one of a prominent disease. Early detection of contamination in food or drinking water is critical. Conventional culture-based methods are time-consuming, labour intensive, and not suitable for on-site testing. Nucleic acid-based tests are sensitive and can rapidly detect pathogens. Microfluidic technology can play a significant role to develop low-cost, rapid, integrated, and portable nucleic acid-based detection devices. Microfluidic systems for isothermal amplification assays can be classified into two groups such as droplet-based and chamber-based systems. In this thesis, both droplet-based and chamber-based approaches were used to build the microfluidic methods for isothermal amplification assays. First, a simple electromechanical probe (tweezers) was developed that can manipulate a small aqueous droplet in a bi-layer oil phase. The tweezer consisted of two needles positioned close to each other and used polarization of the aqueous droplet in an applied electrical field to confine the droplet between the needles with minimal solid contact. AC electric potential was applied to the two metal electrodes. Droplet acquired a charge from the high voltage electrode and consequently performed an oscillatory motion with the same electrode. This droplet motion was controlled using two parameters of electric potential and frequency of the applied signal. Initially, electrically actuated droplet (0.3 µL) motion was investigated for a range of applied potential (400-960 Volts) and frequencies (0.1-1000 Hz). The droplet motion with high voltage electrode was characterized into three modes such as detachment, oscillation, and attachment. Mechanical motion of tweezer was used to transport droplet to various positions. Consequently, operations such as transportation, extraction, and merging were demonstrated. First, droplet (5 µL) transportation was characterized under the applied potential of 2000 Volts at various frequencies (5 to 1000 Hz). The droplet was successfully transported to the speed of 15 mm/s at higher frequencies (100 or 1000 Hz). Droplets of various volumes (12-80 µL) were extracted by increasing applied electric potential, from 0 to 6000 Volts at 5 Hz. Then, the operation of droplets merging was demonstrated using operational conditions for electrical tweezer. Finally, electrical tweezer was used to prepare samples for isothermal amplification assays. Two droplets consisted of various reagents of isothermal amplification assays, were transported and merged using the electrical tweezer. Then, a merged droplet (25 µL) was transported and immobilized in the amplification zone. The temperature of the amplification zone (~65°C) was maintained using an in-situ heater. DNA amplification was verified by measuring the off-chip end-point fluorescence intensity of isothermal assays. Second, an integrated microfluidic device has been developed to prepare a sample for isothermal amplification assays. And in-situ real-time amplification assays were performed to detect bacteria. The device consisted of two chambers (lysis and amplification) connected through a microchannel. A low-cost fabrication method was introduced to embed two resistive wire heaters around both chambers. Initially, bacteria cells were thermally lysed in the lysis chamber at 92°C for 5 min. Then, DNA was electrophoretically transported from lysis to the amplification chamber. The electric potential of 10 Volts was applied for 10 min for DNA transportation. Next, transported DNA was amplified at 65°C and DNA amplification was detected by measuring in-situ fluorescence intensity in the real-time format. The operation of the integrated microfluidic device was demonstrated in three steps. 1) Operation of individual components. 2) Operation of two components in a coupled format. 3) Integrated operation of three components with measurement of fluorescent intensity in a real-time format. The bacteria samples with the concentration of 100 CFU/mL were detected in less than one hour. / Thesis / Doctor of Philosophy (PhD)

O uso da microfluídica na área de análises genéticas possibilita não apenas a diminuição de custos, mas também menor manipulação de amostras e reagentes e ainda maior portabilidade das análises. Com isso aumenta a possibilidade da sua utilização em locais remotos, sem a infraestrutura de um laboratório bem equipado. Dispositivos capazes de usar apenas a força centrifuga para movimentação de fluidos juntamente com a utilização de válvulas passivas para controle dos fluidos pode potencializar a sua utilização nos diagnósticos Point-of-Care. Este trabalho teve como objetivo o desenvolvimento de um microdispositivo descartável de poliéster para análises genéticas, visando a extração e amplificação do DNA alvo, de forma rápida, barata, integrada e automatizada. Os resultados confirmam a viabilidade dos dispositivos poliéster-toner (PeT) e poliéster-fita dupla face (PeDF) automatizados de extração, obtendo por meio da extração dinâmica em fase sólida de amostras complexas, DNA com qualidade compatível à técnica da reação em cadeia de polimerase (PCR). Esses resultados foram confirmados por meio da amplificação por PCR dos genes β-globina nas amostras de sangue e urina, e o gene malB nas amostras de Escherichia coli. Também foi confirmado a compatibilidade dos dispositivos de PeT para amplificação por PCR mediado por infravermelho (IV-PCR) do gene malB presente no DNA genômico de bactéria E. coli. Por fim, os dispositivos de extração e amplificação foram interligados para obtenção de um dispositivo integrado e automatizado formado pela combinação de dispositivos fabricados com diferentes filmes e métodos, PeT e PeDF. O controle de todas as soluções no interior dos dispositivos foi realizado por meio da força centrífuga combinada a válvulas passivas, sem qualquer necessidade de equipamento adicional. Portanto, podemos concluir que o dispositivo integrado PeDF - PeT possui grande potencial para aplicações em análises genéticas de forma mais barata, portátil e com menor manipulação das amostras pelo analista. / The development of microfluidics for genetic analysis allows not only cost reduction but also reduces sample and reagents handling, and increases the chances of a portable analysis. With this, increasing the possibility to use the techniques on remote places without the infrastructure of an equipped laboratory. Microdevices capable of using the centrifugal force in combination with passive valves to fluidic control can promote Point-of-Care analysis. The primary goal of this thesis was to associate these tools for the development of a disposable microdevice for genetic analysis, aiming faster, inexpensive, integrated and automated DNA extraction and amplification. The results confirmed the viability of PeT and PeDF automated microdevices, for DNA dynamic solid phase extraction, in providing high-quality DNA compatible to PCR analysis using complex samples. These results were confirmed by the β-globin PCR amplification using blood and urine samples, and the malB gene amplification in Escherichia coli samples. We have also verified the compatibility of the PeT microdevices with IV-PCR for malB gene amplification in genomic E. coli DNA. The extraction and amplification modules were interconnected to obtain an integrated and automated microdevice by the combination of devices made with different films and microfabrication methods, PeT and PeDF. The fluidic control in the devices was made using the centrifugal force combined to passive valves, with no requirement of any extra equipment. Therefore, we can conclude that the integrated PeDF - PeT microdevice has a great potential for cheaper and portable genetic analysis application, with less operator manipulation.

O uso da microfluídica na área de análises genéticas possibilita não apenas a diminuição de custos, mas também menor manipulação de amostras e reagentes e ainda maior portabilidade das análises. Com isso aumenta a possibilidade da sua utilização em locais remotos, sem a infraestrutura de um laboratório bem equipado. Dispositivos capazes de usar apenas a força centrifuga para movimentação de fluidos juntamente com a utilização de válvulas passivas para controle dos fluidos pode potencializar a sua utilização nos diagnósticos Point-of-Care. Este trabalho teve como objetivo o desenvolvimento de um microdispositivo descartável de poliéster para análises genéticas, visando a extração e amplificação do DNA alvo, de forma rápida, barata, integrada e automatizada. Os resultados confirmam a viabilidade dos dispositivos poliéster-toner (PeT) e poliéster-fita dupla face (PeDF) automatizados de extração, obtendo por meio da extração dinâmica em fase sólida de amostras complexas, DNA com qualidade compatível à técnica da reação em cadeia de polimerase (PCR). Esses resultados foram confirmados por meio da amplificação por PCR dos genes β-globina nas amostras de sangue e urina, e o gene malB nas amostras de Escherichia coli. Também foi confirmado a compatibilidade dos dispositivos de PeT para amplificação por PCR mediado por infravermelho (IV-PCR) do gene malB presente no DNA genômico de bactéria E. coli. Por fim, os dispositivos de extração e amplificação foram interligados para obtenção de um dispositivo integrado e automatizado formado pela combinação de dispositivos fabricados com diferentes filmes e métodos, PeT e PeDF. O controle de todas as soluções no interior dos dispositivos foi realizado por meio da força centrífuga combinada a válvulas passivas, sem qualquer necessidade de equipamento adicional. Portanto, podemos concluir que o dispositivo integrado PeDF - PeT possui grande potencial para aplicações em análises genéticas de forma mais barata, portátil e com menor manipulação das amostras pelo analista. / The development of microfluidics for genetic analysis allows not only cost reduction but also reduces sample and reagents handling, and increases the chances of a portable analysis. With this, increasing the possibility to use the techniques on remote places without the infrastructure of an equipped laboratory. Microdevices capable of using the centrifugal force in combination with passive valves to fluidic control can promote Point-of-Care analysis. The primary goal of this thesis was to associate these tools for the development of a disposable microdevice for genetic analysis, aiming faster, inexpensive, integrated and automated DNA extraction and amplification. The results confirmed the viability of PeT and PeDF automated microdevices, for DNA dynamic solid phase extraction, in providing high-quality DNA compatible to PCR analysis using complex samples. These results were confirmed by the β-globin PCR amplification using blood and urine samples, and the malB gene amplification in Escherichia coli samples. We have also verified the compatibility of the PeT microdevices with IV-PCR for malB gene amplification in genomic E. coli DNA. The extraction and amplification modules were interconnected to obtain an integrated and automated microdevice by the combination of devices made with different films and microfabrication methods, PeT and PeDF. The fluidic control in the devices was made using the centrifugal force combined to passive valves, with no requirement of any extra equipment. Therefore, we can conclude that the integrated PeDF - PeT microdevice has a great potential for cheaper and portable genetic analysis application, with less operator manipulation.

The alpaca is a small South American camelid (SAC) that is an important production animal in Peru, especially among the highly impoverished communities of the high Andes, and raised for its fiber and meat. Alpacas are highly reliant on the microbes within their digestive tracts to digest the plant material they consume; volatile fatty acids (VFAs) are released as a byproduct of this microbial fermentation and used as a major source of energy by the alpaca. To explore optimal parameters for alpaca microbiome analysis, performed 16S rRNA gene surveys on alpaca C1 and fecal samples that had been extracted using one of three different DNA extraction methods (PowerFecal® DNA Isolation Kit (MO BIO); ZR Fecal DNA MiniPrep™ (Zymo); and a non-commercial extraction method called salting out) and amplified using one of two different polymerase enzyme mixes (AccuPrime™ Pfx SuperMix and 5 PRIME HotMasterMix). We found that choice of polymerase enzyme had a profound effect on the recovered microbiome, with the majority of 5 PRIME-amplified fecal samples failing to amplify. Extraction method had an effect on the recovered microbiome of fecal samples (but not C1 samples), with samples extracted using the MO BIO kit and the salting out method recovering different communities. The Zymo extraction kit returned microbial communities comparable to each of the other extraction methods. These results suggested that the AccuPrime enzyme and either the MO BIO or Zymo kits were optimal for alpaca gut microbiome analysis. We also performed two 16S rRNA gene surveys, the first from alpacas fed either a grass hay (GH) or alfalfa hay (AH) diet, and the second a C1 survey of alpacas fed two-week periods of mixed grass hay plus one of four supplements. We discovered body site and diet effects on the microbiota of alpacas fed either the GH or AH diet, with samples grouping by general body site (C1, small intestine, and distal intestine) and diet. However, we found no significant effect on the C1 microbiome of alpacas administered grain supplements. To study how energy extraction related to the microbiome, we correlated OTUs from GH/AH-fed alpaca with C1 VFA abundances. We discovered no significant correlations, and a 16S survey of low body condition (LBC) and good body condition (GBC) alpacas showed no difference in C1 microbial communities. We concluded that the microbiota of the alpaca digestive tract follow trends seen in microbiome studies of ruminants, but found no evidence of a relationship between body condition, energy extraction, and the C1 microbiome in alpacas.