Thèses sur le sujet « PCR-free »

Prenatal assessment of fetal health is routinely offered throughout pregnancy to ensure that the most effective management can be provided to maintain fetal and maternal well-being. Currently, invasive testing is used for definitive diagnosis of fetal aneuploidy, which is associated with a 1% risk of iatrogenic fetal loss. Developing non-invasive prenatal testing (NIPT) is a key area of research and methods to increase the level of cell-free fetal DNA (cffDNA) within the maternal circulation have been discussed to improve accuracy of such tests. In this study, three strategies; co-amplification at lower denaturation temperature polymerase chain reaction (COLD-PCR), inverse-PCR and Pippin Prep™ gel electrophoresis, were analysed to identify a novel approach to selectively enrich shorter cffDNA fragments from larger maternal cell-free DNA (cfDNA). The sensitivity of droplet digital PCR (ddPCR) against real-time PCR (qPCR) was compared for fetal sex and RHD genotyping. In addition RHD zygosity testing was carried out for non-maternal samples. Consequently, Pippin Prep™ gel electrophoresis was combined with ddPCR analysis for the NIPD of Down Syndrome (DS) in pseudo-maternal samples. The results revealed that the Pippin Prep™ gel electrophoresis enrichment approach successfully demonstrated 2-fold to 5-fold increases in the cffDNA fraction. However, further optimisation assays of COLD-PCR and inverse-PCR using actual maternal samples were required. The spike experiments for DS detection revealed that with the present assay IV overrepresentation of the chromosome 21 target could be significantly detected for samples with ≥15% ‘cffDNA fraction’. In conjunction with the Pippin Prep™ enrichment method, this would have enabled assessment of all 10 maternal samples. Alternatively, fetal sex and RHD genotyping results determined that ddPCR provides a more sensitive platform compared to qPCR approaches, particularly for samples that express low cffDNA fractions (<2%). The ddPCR platform also proved to be a rapid and accurate system for the determination of RHD zygosity. This study highlights that ddPCR could be used as opposed to qPCR for accurate determination of fetal sex and RHD status. While sequencing approaches currently provide the most sensitive platforms for NIPT of fetal aneuploidy, high costs (>£400) prevent universal application. The combination of cffDNA enrichment with ddPCR analysis could provide a cheaper and more widely available platform for NIPD. However, further large scale validation studies using actual maternal samples are required.

Non-invasive prenatal diagnosis (NIPD) is a promising approach that is currently being developed. The principle is that fetal material can be detected in maternal plasma and potentially enable women to pursue reliable and timely prenatal diagnosis, whilst eliminating the risk of miscarriage associated with chorionic villus sampling or amniocentesis. However NIPD research has been restricted up until now for the diagnosis of Down syndrome due to the low concentration of free fetal DNA (ffDNA) in maternal plasma. Various methods have been developed in an attempt to increase the concentration of ffDNA. This study uses COLD-PCR (co-amplification at lower denaturation temperature PCR) to analyse potential enrichment of ffDNA over maternal DNA through optimization of the critical denaturation temperature (Td), using Real Time-PCR in an attempt to selectively enrich smaller fetal DNA fragments. Fake fetal DNA was created in two different spike experiments to imitate the natural environment of viable ffDNA. One spike experiment used 5% of fake fetal DNA in a 95% maternal background to represent levels of ffDNA during early pregnancy. The other spike experiment utilized 10% of fake fetal DNA in 90% maternal background to denote late pregnancy. Before running COLD-PCR, various adjustments took place to find the critical Td at which one could run the spike experiment by COLD-PCR. Products of spike experiment were analysed on a genetic analyser for fragment analysis. Melt curve analysis was also performed for the spike experiment to identify the specificity of each sample at each denaturation temperatures. A critical Td (80°C) was identified for the D21S1890 region of chromosome 21 by COLD-PCR. This temperature does allow enrichment of fetal DNA, as fake maternal DNA was undetermined by RT-PCR compared to fake fetal DNA. The spike experiments clearly showed amplification of fake fetal DNA from the mixture of fake fetal and fake maternal DNA at the critical Td of 80°C. Running same samples of spike experiment on genetic analyser identified peaks from all samples at a Td of 95°C, while at a critical Td of 80°C the result showed decreased numbers of maternal peaks, regardless of stutter peaks formation. Melt curve analysis results clearly identified heteroduplex formation in the samples at the critical Td of 80°C. The results represent a good indication for using COLD-PCR in enriching ffDNA for detection by RT-PCR. However, as each individual has only two alleles, the observed results of multiple peaks for fragment analysis were not expected. Further research needs to focus on both eliminating heteroduplex formation and stutter peaks. COLD-PCR has the potential to open a new gateway in NIPD for aneuploidy detection. This method could be particularly useful in the detection of genetic abnormalities in the fetus, in particular Down syndrome and other aneuploidies.

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FAPEMIG - Fundação de Amparo à Pesquisa do Estado de Minas Gerais
A suplementação do ácido linoléico conjugado trans-10, cis-10 no meio de cultivo, representa uma importante alternativa para aumento da sobrevivência dos embriões após a criopreservação. No entanto este isômero de CLA no cultivo in vitro sem antioxidante pode aumentar a taxa apoptótica. O objetivo do presente estudo foi avaliar o efeito da adição CLA trans-10, cis-12 no cultivo in vitro de embriões sem antioxidante. Zigotos bovinos (n = 1.694) foram divididos em dois tratamentos: (T1) grupo controle, zigotos cultivados no meio CR2aa suplementado com soro fetal (n = 815); (T2) zigotos cultivados no meio CR2aa suplementado com soro fetal mais 100 µM CLA trans-10, cis-12. Os embriões foram avaliados quanto a desenvolvimento, quantidade de lípides e criotolerância. Transcritos dos RNA mensageiros (RNAm) dos genes selecionados foram mensurados pelo Real Time PCR. Suplementação de CLA trans-10, cis-12 não afeta significativamente a taxa de blastocisto (31,8% e 34,1% T1 e T2, respectivamente, p = 0,20) e nível dos RNAm dos genes relacionados com stress celular, apoptose e síntese de novo de ácido graxo. Quantidade de lípides e transcritos do RNAm do gene 1-acilglicerol-3-fosfato oaciltransferase 1 enzima relacionado a síntese de triglicérides foram significativamente reduzidos nos embriões cultivados na presença de CLA trans-10, cis-12 em comparação com o grupo controle. Teve aumento significativo na taxa de re-expansão dos blastocistos cultivados na presença de CLA trans-10, cis-12, após o descongelamento (34.4 e 56.3% para T1 e T2, respectivamente p = 0,002). Essa diferença não persistiu na taxa de eclosão (14,0% e 16,5% para T1 e T2, respectivamente, P = 0,62). Esses resultados mostram que o CLA trans-10, cis-12 reduz o acúmulo de lípides nos embriões pela redução nos níveis dos transcritos do gene 1-acilglicerol-3-fosfato o-aciltransferase 1 sem afetar a qualidade do embrião. Adicionalmente, este ácido graxo aumenta a taxa de re-expansão, no entanto, não melhora a taxa de eclosão.
Supplementation of conjugated linoleic acid trans-10, cis-10 in the culture medium, represents an important alternative to increasing the survival of embryos after cryopreservation. However the addition of culture media with CLA trans-10, cis-12 without antioxidant may increase the apoptotic rate. The aim of this study was to evaluate the effect of adding CLA trans-10, cis-12 in vitro culture of embryos without antioxidant. Bovine zygotes (n = 1,694) were divided into two treatments: (T1) control group, zygotes cultured in CR2aa medium supplemented with fetal calf serum (n = 815), (T2) zygotes cultured in CR2aa medium supplemented with fetal calf serum plus 100 µM CLA trans-10, cis-12. Embryos were evaluated for development, amount of lipids and cryotolerance. Transcripts of messenger RNA (mRNA) of selected genes were measured by real time PCR. Supplementation of CLA trans-10, cis-12 did not significantly affect the blastocyst rate (31.8% and 34.1% T1 and T2, respectively, p = 0,20) and the mRNA level of genes related to cell stress, apoptosis and de novo synthesis of fatty acid . Lipids and transcripts of the mRNA of the gene 1-acilglicerol-3-phosphate o-acyltransferase 1 enzyme related to the synthesis of triglycerides were significantly reduced in embryos cultured in the presence of CLA trans-10, cis-12 in comparison the control group. Had increased rate re-expansion of blastocysts cultured in the presence of CLA trans-10, cis-12, after thawing (34.4 and 56.3% for T1 and T2, respectively p = 0,002). This difference did not persist in the hatching rate (14.0 and 16.5% for T1 and T2, respectively, P = 0,62). These results show that the CLA trans-10, cis-12 reduces the accumulation of lipids in the embryos by reducing the levels of gene transcripts acilglicerol-1-3-phosphate oacyltransferase 1 without affecting the quality of the embryo. Additionally, this fatty acid increases the rate re-expansion, but does not improve the hatching rate.

Advances in DNA micro and macroarray technologies made these high-throughput systems good candidates for the development of cheaper, faster and easier qualitative and quantitative detection methods. In this study, a simple and cost effective sandwich hybridization-based method has been developed for the rapid and sensitive detection of various unmodified recombinant elements in transgenic plants. Attention was first focused on the optimization of conditions such as time, concentration and temperature using commercial ssDNA, which in turn could be used for real sample detection. In this sandwich-type DNA chip platform, capture probes complementary to the first half of recombinant element (target adapter) were immobilized onto poly-L-lysine covered conventional microscope slides. PCR-amplified un-purified target adapter and biotin labeled detection probe, which is complementary to the second half of target adapter, were hybridized in solution-phase to complementary capture probes to create a sandwiched tripartite complex. Later, hybridization signal was visualized by the attachment of streptavidin conjugated Quantum Dot to the sandwiched complex under UV illumination. Sandwich based array system that has been developed in this study allows multiplex screening of GMO events on a single DNA chip platform. 35S promoter, NOS terminator, CRY1Ab and BAR target sequences were successfully detected on the same DNA chip platform. The platform was able to detect unlabeled PCR amplified DNA fragments of CaMV 35S promoter sequence and NOS terminator and BAR transgene sequences from transgenic potato plants and NK603 Certified GMO Reference material, respectively. The DNA-chip platform developed in this study will allow multiple detection of label-free PCR-amplified transgenic elements from real GMO samples on a single slide via a cost effective, fast, reliable and sensitive sandwich hybridization assay.

Recombinant DNA technology has been commonly used in a number of fields to synthesize new products or generate products with a new pathway. Conventional cloning methods are expensive and require significant time and labor; λ-PCR, a new cloning method developed in the Senger lab, has a number of advantages compared to other cloning processes due to its employment of relatively inexpensive and widely available materials and time-efficiency. While the amount of lab work required for the cloning process is minimal, the importance of accurate primer design cannot be overstated. The target of this study was to create an effective procedure for λ-PCR primer design that ensures accurate cloning reactions. Additionally, synthetic ribosome binding sites (RBS) were included in the primer designs to test heterologous protein expression of the cyan fluorescent reporter with different RBS strengths. These RBS sequences were designed with an online tool, the RBS Calculator. A chimeric primer design procedure for λ-PCR was developed and shown to effectively create primers used for accurate cloning with λ-PCR; this method was used to design primers for CFP cloning in addition to two enzymes cloned in the Senger lab. A total of five strains of BL21(DE3) with pET28a + CFP were constructed, each with the same cyan fluorescent protein (CFP) reporter but different RBS sequences located directly upstream of the start codon of the CFP gene. Expression of the protein was measured using both whole-cell and cell-free systems to determine which system yields higher protein concentrations. A number of other factors were tested to optimize conditions for high protein expression, including: induction time, IPTG concentration, temperature, and media (for the cell-free experiments only). Additionally, expression for each synthetic RBS sequence was investigated to determine an accurate method for predicting protein translation. NUPACK and the Salis Lab RBS Calculator were both used to evaluate the effects of these different synthetic RBS sequences. The results of the plate reader experiments with the 5 CFP strains revealed a number of factors to be statistically significant when predicting protein expression, including: IPTG concentration, induction time, and in the cell-free experiments, type of media. The whole-cell system consistently produced higher amounts of protein than the cell-free system. Lastly, contrasts between the CFP strains showed each strain's performance did not match the predictions from the RBS Calculator. Consequently, a new method for improving protein expression with synthetic RBS sequences was developed using relationships between Gibbs free energy of the RBS-rRNA complex and expression levels obtained through experimentation. Additionally, secondary structure present at the RBS in the mRNA transcript was modeled with strain expression since these structures cause deviations in the relationship between Gibbs free energy of the mRNA-rRNA complex and CFP expression.
Master of Science
Recombinant DNA technology has been used to genetically enhance organisms to produce greater amounts of a product already made by the organism or to make an organism synthesize a new product. Genes are commonly modified in organisms using cloning practices which typically involves inserting a target gene into a plasmid and transforming the plasmid into the organism of interest. A new cloning process developed in the Senger lab, λ-PCR, improves the cloning process compared to other methods due to its use of relatively inexpensive materials and high efficiency. A primary goal of this study was to develop a procedure for λ-PCR primer design that allows for accurate use of the cloning method. Additionally, this study investigated the use of synthetic ribosome binding sites to control and improve expression of proteins cloned into an organism. Ribosome binding sites are sequences located upstream of the gene that increase the molecule’s affinity for the rRNA sequence on the ribosome, bind to the ribosome just upstream of the beginning of the gene, and initiate expression of the gene. Tools have been developed that create synthetic ribosome binding sites designed to produce specific amounts of protein. For example, the tools can increase or decrease expression of a gene depending on the application. These tools, the Salis Lab RBS Calculator and NUPACK, were used to design and evaluate the effects of the synthetic ribosome binding sites. Additionally, a new method was created to design synthetic ribosome binding sites since the methods used during the design process yielded inaccuracies. Each strain of E. coli contained the same gene, a cyan fluorescent protein (CFP), but had different RBS sequences located upstream of the gene. Expression of CFP was controlled via induction, meaning the addition of a particular molecule, IPTG in this system, triggered expression of CFP. Each of the CFP strains were tested with a variety of v conditions in order to find the conditions most suitable for protein expression; the variables tested include: induction time, IPTG (inducer) concentration, and temperature. Media was also tested for the cell-free systems, meaning the strains were grown overnight for 18 hours and lysed, a process where the cell membrane is broken in order to utilize the cell’s components for protein expression; the cell lysate was resuspended in new media for the experiments. ANOVA and multiple linear regression revealed IPTG concentration, induction time, and media to be significant factors impacting protein expression. This analysis also showed each CFP strain did not perform as the RBS Calculator predicted. Modeling each strain’s CFP expression using the RBS-rRNA binding strengths and secondary structures present in the RBS allowed for the creation of a new model for predicting and designing RBS sequences.

Metabolic engineering has enabled studying microorganisms by the modification of their genetic material and analysis of their metabolism for the isolation of microbial strains capable of producing high yields of high value chemicals and biofuels. In this research, novel tools were developed to improve genetic engineering of microbial cells. In this matter, λ-PCR (lambda-PCR) was developed enabling the construction of plasmid DNA. This technique allows DNA assembly and manipulation (insertion, substitution and/or deletion) at any location of a vector. λ-PCR addresses the need for an easy, highly-efficient, rapid and inexpensive tool for genetic engineering and overcoming limitations encountered with traditional techniques. Then, novel synthetic small RNA (sRNA) regulators were designed in a cell-free-system (in vitro) in order to modulate protein expression in biosynthetic pathways. The ability of the sRNAs to regulate mRNA expression with statistical significance was demonstrated. Up to 70% decrease in protein expression level was achieved by targeting specific secondary structures of the mRNA with antisense binding regions of the sRNA. Most importantly, a sRNA was identified capable of protein overexpression by up to 65%. An understanding of its mechanism showed that its mRNA target region(s) likely lead to occlusion of RNase E binding. This mechanism was translated for expression of a diaphorase enzyme, which has relevance to synthetic biology and metabolic engineering in in vitro systems. Results were successful, showing a greater than 75% increase in diaphorase expression in a cell-free protein synthesis reaction. Next, Raman spectroscopy was employed as a near real-time method for microbial phenotyping. Here, Raman spectroscopy was used in combination with chemometric analysis methods through RametrixTM Toolboxes to study the effects of environmental conditions (i.e. illumination, glucose, nitrate deprivation, acetate, sodium chloride and magnesium sulfate) on the phenotypic response of the cyanobacterium Synechocystis sp. PCC6803. The RametrixTM LITE Toolbox for MATLAB® enabled processing of Raman spectra and application of principal component analysis (PCA) and discriminant analysis of principal components (DAPC). Two studies were performed. PCA and DAPC produces distinct clustering of Raman spectra, representing multiple Synechocystis phenotypes, based on the (i) presence of glucose in the growth medium, (ii) illumination, (iii) nitrate limitation, and (iv) throughout a circadian rhythm growth cycle, in the first study. The second study focused on the phenotypic response based on (i) growth in presence of acetate, (ii) presence of high concentrations of sodium chloride and (iii) magnesium sulfate starvation. RametrixTM PRO was applied for the validation of the DAPC models through leave-one-out method that allowed calculation of prediction accuracy, sensitivity and selectivity for an unkown Raman spectrum. Statistical tests (ANOVA and pairwise comparison) were performed on Raman spectra to identify statistically relevant changes in Synechocystis phenotypes. Next, comparison between Raman data and standardized analytical methods (GF-FID, UPLC, spectrometric assays) was established. Overall, good correlation were obtained (R > 0.7). Finally, genomic DNA libraries were enriched to isolate a deoxynivalenol detoxifying enzyme. To do this, library fragments from microorganisms was generated through oligonucleotide primed polymerase chain reaction (DOP-PCR) and transformed in a DON-sensitive yeast strain. Rounds of subculture were performed in the presence of DON and ferulic acid in order to isolate a strain capable of enzymatic degradation of DON.
Doctor of Philosophy

Droplet microfluidics is an emerging technology for analysis of single cells and biomolecules at high throughput. The controlled encapsulation of particles along with the surrounding microenvironment in discrete droplets, which acts as miniaturized reaction vessels, allows millions of particles to be screened in parallel. By utilizing the unit operations developed to generate, manipulate and analyze droplets, this technology platform has been used to miniaturize a wide range of complex biological assays including, but not limited to, directed evolution, rare cell detection, single cell transcriptomics, rare mutation detection and drug screening. The aim of this thesis is to develop droplet microfluidics based methods for analysis of single cells and nucleic acids. In Paper I, a method for time-series analysis of mammalian cells, using automated fluorescence microscopy and image analysis technique is presented. The cell-containing droplets were trapped on-chip and imaged continuously to assess the viability of hundreds of isolated individual cells over time. This method can be used for studying the dynamic behavior of cells. In Paper II, the influence of droplet size on cell division and viability of mammalian cell factories during cultivation in droplets is presented. The ability to achieve continuous cell division in droplets will enable development of mammalian cell factory screening assays in droplets. In Paper III, a workflow for detecting the outcome of droplet PCR assay using fluorescently color-coded beads is presented. This workflow was used to detect the presence of DNA biomarkers associated with poultry pathogens in a sample. The use of color-coded detection beads will help to improve the scalability of the detection panel, to detect multiple targets in a sample. In Paper IV, a novel unit operation for label-free enrichment of particles in droplets using acoustophoresis is presented. This technique will be useful for developing droplet-based assays that require label-free enrichment of cells/particles and removal of droplet content. In general, droplet microfluidics has proven to be a versatile tool for biological analysis. In the years to come, droplet microfluidics could potentially be used to improve clinical diagnostics and bio-based production processes.

QC 20160926

Aufgrund ihres sehr hohen Metastasierungsrisikos weisen Patienten mit klarzelligem Nierenzellkarzinom (kzNZK) eine sehr hohe Sterblichkeit auf. Mit den zurzeit zur Verfügung stehenden klinischen Parametern kann der Krankheitsverlauf der Patienten nach der operativen Entfernung des Primärtumors nur unzureichend vorhergesagt werden. Um das Nachsorge- und Therapieregime der Patienten zu optimieren, muss die Vorhersagegenauigkeit der bestehenden Prognosemodelle durch molekulare Marker erhöht werden. Um geeignete Gene für eine Abschätzung von Metastasierungsrisiko und krankheitsfreiem Überleben (DFS) zu identifizieren, wurden genomweite Expressionsanalysen sowohl an Lungenmetastasen (n = 24) als auch an Primärtumoren (n = 24) des kzNZK vorgenommen. Durch Vergleich von Metastasensubgruppen, die sich nach unterschiedlich langen DFS entwickelt hatten bzw. Primärtumoren, die nach unterschiedlich langen DFS Metastasen bedingten, wurden tumorintrinsische DFS-assoziierte Expressionsmuster identifiziert. Weiterhin wurden Gene identifiziert, deren Expression sich zwischen Primärtumoren unterschied, die im Krankheitsverlauf manifeste Metastasen bedingten und solchen, die dies nicht taten. Die differenzielle Expression funktionell interessanter, teilweise auch in anderen publizierten Microarraystudien an kzNZK bestätigter Gene wurde im Folgenden mittels quantitativer Polymerasekettenreaktion (qPCR) validiert. Anschließend wurde die Assoziation ausgewählter Gene mit klinischen Parametern und dem Überleben der Patienten untersucht. Ein von klinischen Parametern unabhängiger Einfluss auf den Krankheitsverlauf der Patienten wurde dabei für EDNRB und PECAM1 auf Expressionsebene (qPCR; n = 86) sowie für TSPAN7 auf Proteinebene (Immunhistochemie an „Tissue Microarrays“; n = 106) belegt. EDNRB und PECAM1 waren signifikant höher exprimiert in Primärtumoren mit günstigen klinischen Parametern (TNMI/II, G1/2, V0, N0/M0). TSPAN7 war vorwiegend in den Gefäßen der primären kzNZK nachweisbar; eine signifikant höhere Zahl TSPAN7-positiver Gefäße war ebenfalls in Tumoren mit günstigen klinischen Parametern zu verzeichnen (pT1/2, TNMI/II, N0). Überlebensanalysen zeigten ein signifikant längeres DFS für Patienten mit einer hohen im Vergleich zu solchen mit einer geringen EDNRB-Expression und für Patienten, die in beiden untersuchten Gewebestanzen der „Tissue Microarrays“ TSPAN7-positive Gefäße aufwiesen im Vergleich zu Patienten mit nur einer oder keiner TSPAN7-gefäßpositiven Stanze. Für Patienten mit einer hohen im Vergleich zu solchen mit einer geringen EDNRB- bzw. PECAM1-Expression oder mit zwei im Vergleich zu keiner oder einer TSPAN7-gefäßpositiven Gewebestanze war zudem ein signifikant längeres tumorspezifisches Überleben (TSS) zu verzeichnen. Mit Hilfe multivariater Cox-Regressionsanalysen wurde eine unabhängige günstige prognostische Relevanz für EDNRB auf das DFS sowie für EDNRB, PECAM1 und TSPAN7 auf das TSS nachgewiesen. Somit sind diese molekularen Faktoren geeignet, um die Genauigkeit der bestehenden und ausschließlich auf klinischen Parametern basierenden Prognosemodelle zu erhöhen. Für eine Abschätzung von DFS und Metastasierungsrisiko erscheint dabei insbesondere EDNRB geeignet
Patients with clear cell renal cell carcinoma (ccRCC) have an extremely poor prognosis due to their high risk of metastases. Currently used clinico-patological parameters are insufficient for reliable prediction of metastatic risk and disease free survival (DFS) after surgical resection of the primary tumor. Molecular markers are strongly needed to improve outcome prediction, and thus to optimize the follow up and treatment schedule for patients with ccRCC. To identify genes which are suitable for the prediction of metastatic risk and DFS, genome-wide expression analyses were performed on pulmonary metastases (n = 24) and primary tumors (n = 24) obtained from patients with ccRCC. Tumor-intrinsic DFS-associated expression patterns were observed by comparing subgroups of metastases, which had developed within different DFS as well as primary tumors, which had caused metastases after different DFS. Furthermore, genes differentially expressed in primary tumors, which caused macroscopic metastases and tumors, which did not were identified. The differential expression of genes with a potential function in metastatic spread, which has in part been identified in independent published microarray studies as well, were validated by quantitative polymerase chain reaction (qPCR). Moreover, an independent prognostic impact on the survival of ccRCC patients was observed for the EDNRB und the PECAM1 gene expression (qPCR; n = 86) as well as for the TSPAN7 protein level (immunohistochemistry on tissue microarrays; n = 106). Primary tumors of patients with favourable clinico-pathological parameters (TNMI/II, G1/2, V0, N0/M0) showed a significantly higher EDNRB und PECAM1 gene expression than those with unfavorable parameters. TSPAN7 was predominantly detected in blood vessels of ccRCC tissues. In patients with favourable clinico-pathological parameters (pT1/2, TNMI/II, N0) a significantly higher number of TSPAN7-positive vessels was observed. Using survival analyses, a significantly longer DFS was observed for patients with a high compared to those with a low EDNRB expression as well as for patients with TSPAN7-positive vessels in both cores compared to no or one of the both cores investigated on tissue microarrays. A significantly longer TSS was observed for patients with a high EDNRB or PECAM1 expression as well as for patients with TSPAN7-positive vessles in both tissue cores investigated. Furthermore, EDNRB was an independent prognostic factor for the DFS of the patients; EDNRB, PECAM and TSPAN7 had an independent prognostic impact on the TSS. Therefore, these molecular markers are suitable to improve the accuracy of outcome prediction based on clinico-pathological parameters in ccRCC. For the prediction of DFS and metastatic risk EDNRB is particularly interesting

This thesis reports the viability of E. coli cell extracts prepared using equipment that is both common to biotechnology laboratories and able to process small volume samples and expression of proteins containing unnatural amino acids (UAAs) at higher level using PCR amplified linear DNA templates (LETs) in cell-free protein synthesis (CFPS) system. E. coli-based cell extracts are a vital component of inexpensive and high-yielding CFPS reactions. However, effective preparation of E. coli cell extract is limited to high-pressure homogenizers (French press style or impinge-style) or bead mill homogenizers, which all require a significant capital investment. This work specifically assessed the following capital cost lysis techniques: (1) sonication, (2) bead vortex mixing, (3) freeze-thaw cycling, and (4) lysozyme incubation to prepare E. coli cell extract for CFPS. In this work, simple shake flask fermentation with a commercially available E. coli strain was used. Additionally, the RNA polymerase was over expressed in the E. coli cells prior to lysis which eliminated the need to add independently purified RNA polymerase to the CFPS reaction. As a result, high yielding E. coli-based cell extract was prepared using equipment requiring reduced capital investment and common to biotechnology laboratories. To our knowledge, this is the first successful prokaryote-based CFPS reaction to be carried out with extract prepared by sonication or bead vortex mixing. LETs are an attractive alternative to plasmids for site-specific incorporation of unnatural amino acids in proteins in the CFPS system because of their short preparation time and ease of production. However, major limitations associated with LETs are: (1) their degradation by RecBCD enzyme present in the cell-extract used for CFPS and (2) high CFPS energy costs. In this work, we report the optimization of LET-based CFPS for improved protein yield by inhibiting the RecBCD enzyme with small inhibitor molecules resulting in three fold increment in yield of protein containing UAA. We also assessed alternative energy sources such as glucose, fructose-1,6-bisphospate, creatine phosphate/creatine kinase, and high glutamate salt for cost reduction. This work could be important for high-throughput applications based on linear expression templates. This work demonstrates simple E. coli extract preparation and improved yield with linear expression templates for further advancements of cell-free protein synthesis system.

This thesis describes the implementation of different types of genosensors for microRNA (miRNA) electrochemical detection. miRNAs are intensely studied as candidates for diagnostic and prognostic biomarkers. Herein, miRNA 221 and miRNA-222 detection was studied since it is well known that these two sequences are involved into different type of lung, liver and brain cancers. Both electrochemical and photoelectrochemical transduction method was adopted. The analytical approaches were based on a recognition event through the hybridization of miRNAs to a specific capture probe. Several modifications of the sensor surface were studied in order to obtain the optimal analytical performances.

碩士
國立中興大學
機械工程學系所
102
Chronic hepatitis B virus (HBV) infection is an important health burden because of its worldwide prevalence and potential adverse outcomes, including liver cirrhosis and hepatocellular carcinoma. Although the DNA level of HBV in the serum is an important biomarker associated with several important outcomes of HBV patients, it is not regularly monitored in clinical practice because of its high cost. So it is necessary to develop a highly sensitive and low-cost technique for effective detection of HBV concentration in blood. In this study, a PCR free technique for effective detection of HBV DNA obtained directly from clinical samples was presented. We use a sensitive nanostructured biosensor with a sensing electrode of gold nanoparticles (GNPs) uniformly deposited on a uniform nanohemisphere array. A specially designed single-strand gene fragment of the target genomic DNA of HBV based on the genome sequences of HBV was immobilized on the nanostructured electrode as the capture probe. Target HBV DNA obtained from clinical samples were hybridized to the sensing probes. Detection results illustrate two dynamic linear ranges, 10^2-10^3 and 10^3-10^5.1 copies/mL, having R^2 values of 0.801 and 0.996 could be obtained, respectively. The detection limit of the proposed sending scheme was measured to be 111 copies/mL. The total of 45 target samples, including 20 samples with HBV concentration being lower than 102 copies/mL and 25 samples with HBV concentration being in the range of 10^3-10^5.1 copies/mL. A detection limit of 186 copies/mL could be achieved. The concentration of these 45 HBV DNA samples was measured by the COBAS Ampliprep system. Comparing the measured results of the COBAS Ampliprep and our system, it was illustrated that the HBV DNA concentrations measured by the proposed method in this study had a high linear correlation with the COBAS Ampliprep, having R^2 values of 0.983 .The proposed sensing scheme is highly feasible for future clinical applications.

Bovine tuberculosis is a global cause for concern in livestock, free-ranging wildlife, zoological collections and the human population. Large amount of time, effort and resources are spent on its diagnosis and control methods. This study was aimed at determining the sensitivity and specificity of the IS6110 specific PCR test on formalin fixed, paraffin embedded (FFPE) tissue blocks, compared to that of the gold standard method culture and to differentiate M. bovis from other members of the M. tuberculosis complex using the RD4 region of difference specific PCR test. A total of 141 FFPE tissue blocks of wild animals from game reserves, the National Zoological Gardens and routine tuberculosis (TB) surveys in Kruger National Park were tested. Among the 50 known TB positive samples (35 M. bovis culture positive, twelve M. tuberculosis culture positive and three diagnosed tuberculosis positive on histopathology examination) the IS6110 PCR had an overall sensitivity of 22%. The positive predictive value of the IS6110 test (91.67%) was quite high implying that although sensitivity was low, one can be highly confident that a positive test result is a true reflection of the positive disease status. The overall sensitivity of the RD4 PCR was 20%. The positive predictive value of the RD4 test (41.67%) was low, implying that a positive test result may be unreliable. The sensitivities of the M. tuberculosis and M. bovis culture positive samples were compared and a significant difference was noted. Sensitivities of the IS6110 and RD4 assays in M. tuberculosis culture positive samples were 66.67% and 33.33%, respectively; sensitivities of the IS6110 and RD4 assays in M. bovis culture positive samples were 8.57% and 17.14%, respectively. Difference in bacterial load in tissues infected with the two mycobacterial species may account for this finding (i.e. M. bovis infections have a lower bacteria load). Of the 91 known TB negative samples, the specificity of the IS6110 (98.90%) and RD4 (84.62%) PCR tests were high, but the negative predictive values of 69.67% and 65.81%, respectively, suggest that the probability of negative test results being incorrect still exists. The resultant sensitivity was increased when parallel interpretation was applied to histopathology examination and the IS6110 or RD4 PCR tests and when applied to the IS6110 and RD4 PCR tests. Both histopathology examination and PCR tests produce rapid results and their combination can be used in routine diagnostics. The RD4 PCR assay was unable to distinguish M. bovis from other members of the MTB complex and based on the findings of this study the RD4 PCR cannot add value to the diagnosis of suspect tuberculosis samples at this stage, but successful troubleshooting relating to 1) extraction method, 2) DNA inhibitors, 3) contamination and 4) multisampling protocol, may enable its use in future.
Dissertation (MSc)--University of Pretoria, 2013.
gm2014
Veterinary Tropical Diseases
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In current days, examination of circulating tumor DNA (ctDNA) finds new use across different cancers. It is directed at tumor-derived short fragments of DNA present in peripheral blood of patiens (mainly in advanced stages). Due to its minimal invasivity, almost 100 % specificity and relatively high sensitivity in stage IV patients, this approch found its main potential clinical utility especially in early detection of disease relapse or progression after tumor resection (i.e. post-operative follow-up), prediction and monitoring of therapy response and estimation of prognosis. As a result of minute levels of ctDNA on a high background of other non-tumor DNA fragments present in plasma, a suitable method exhibiting highest sensitivity is the key for proper detection of this marker. The approach is predominantly based on initial identification of a mutation in tumor tissue and its subsequent detection in plasma. The present work is aimed at optimization of ctDNA isolation and method of its detection based on PCR amplification followed by heteroduplex analysis by denaturing capillary electrophoresis (DCE) to achieve highest sensitivity for detection of mutated fraction in plasma sample. I have applied the optimized protocol to examine ctDNA in three types of cancers, namely colorectal cancer (122...

Meine Untersuchungen zeigen, dass es sich bei der zellfreien DNA (cfDNA, engl. cell-free DNA) des Spenderorgans (GcfDNA, engl. graft-derived cell-free DNA) um einen klinisch vielversprechenden Biomarker zur direkten Ermittlung der Organschädigung im Sinne einer „flüssigen Biopsie“ handelt. Alles was dafür notwendig ist, ist eine Blutprobe des Empfängerpatienten. Im Gegensatz zu konventionellen Markern wird die Organschädigung unmittelbar, direkt und hochspezifisch angezeigt. Durch neue Entwicklungen in der Labordiagnostik lässt sich dieser Marker im routinemäßigen Einsatz mittels digital droplet PCR (ddPCR) bestimmen. Die Analyseergebnisse können bei verhältnismäßig niedrigen Kosten innerhalb eines Arbeitstages erstellt werden. Unmittelbar nach Transplantation ist bei allen Patienten eine sehr hohe Konzentration der GcfDNA messbar. Innerhalb von wenigen Tagen fallen die Werte schnell ab und erreichen die Größenordnung stabiler Transplantatempfänger, die in der Lebertransplantation unter 10% liegen. Dabei besteht keine signifikante Korrelation der initialen GcfDNA-Freisetzung mit der Ischämieschädigung des Spenderorgans, ermittelt durch die Dauer der kalten Ischämiezeit (WIZ). Bei unzureichender Immunsuppression ist eine erhöhte GcfDNA-Freisetzung zu beobachten. Mithilfe der GcfDNA als Marker der Organintegrität lässt sich auch der gemeinsame Effekt verschiedener Immunsuppressiva ermitteln. Die GcfDNA verhält sich dabei umgekehrt proportional zur immunsuppressiven Therapie. Patienten mit akuten Abstoßungen haben im Mittel GcfDNA-Werte oberhalb von 50%. Die GcfDNA-Werte sind bereits mehrere Tage vor einer klinisch manifestierten akuten Abstoßung erhöht. Auch eine virusassoziierte Transplantatschädigung durch Hepatitis C manifestiert sich in vergleichsweise höheren GcfDNA-Werten. Cholestasen gehen hingegen nicht mit erhöhten GcfDNA-Werten einher. Die immunsuppressive Therapie könnte sich durch den routinemäßigen Einsatz der GcfDNA sicherer, einfacher, zuverlässiger und individueller gestalten lassen. Unter-Immunsuppressionen und daraus resultierende Abstoßungen würden sich bereits in der subklinischen Phase erkennen lassen und die Therapie von der bloßen Reaktion auf klinische Ereignisse hin zur Prävention verschieben. Um das Ziel einer personalisierten Medizin zu erreichen, könnte die Immunsuppression für jeden Patienten auf das absolut notwendige und damit gegenüber der bisherigen Praxis optimale Maß festgelegt werden. Geringere Nebenwirkungen und eine Reduktion der Kosten für das Gesundheitswesen wären die Konsequenz. Dieser Marker könnte dazu beitragen, das finale Ziel, nämlich eine Verbesserung des Langzeiterfolges nach Organtransplantationen, zu erreichen. Multizentrische Studien zur Validierung dieses Markers vor dem routinemäßigen Einsatz laufen bereits.

This work presents the results ofour research of cell-free nucleic acids (cfNA). The first part shows changes in methylation patterns of immune response genes promoters that are detectable in plasma during the hemodialysis sessions and also differences in methylation between patients and healthy subjects. Alterations include genes that play their role in the regulation of hematopoiesis and these changes are in close relation with the need of anemia therapy. In the other plasma cfNA study we detected miRNA signatures in patients with acute myeloid leukemia at diagnosis (6 highly abundant miRNAs found) and in remission achieved after standard chemotherapy (trend to n01malization, lower levels ofthese miRNAs). Another part of work presents data from the study of potential non-invasive biomarker of bladder cancer. The amounts of cfDNA in urine are higher in patients than in healthy subjects and there were found 5 down-regulated miRNAs. Simultaneously it was established set of 30 miRNAs that are constantly present in urine supematants independently on sex, age and healthy status of subjects. The last part presents analysis ofcell-free fetal DNA. We analyzed differences between a new quantification method - droplet digital PCR and real-time PCR which is used routinely nowadays. Slightly more precise was...