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University of Tampere, BioMediTech

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Abstract bachelor project 2017-2018: Mycobacterium marinum infection in Zebrafish: Production of knock out strains of Mycobacterium marinum

Tuberculosis is a bacterial infection that is caused by Mycobacterium tuberculosis and is often found in human lungs. For this research, it is more feasible to use Mycobacterium marinum, a zebrafish pathogen that is less contagious than M. tuberculosis. With this experiment we want to optimize the production of knockout strains of Mycobacterium marinum and the identification of true knockout strains among the colonies. Electroporation of a plasmid that is unable to replicate in mycobacteria is used to construct possible knockout strains of the mycobacteria via homologous recombination consisting of two subsequent cross-over events. As a result, the gene-of-interest will be replaced by a hygromycin resistance gene. The plasmid also contains other marker genes (LacZ and sucrose sensitivity), these genes can be used for colony PCR and sucrose test of potential single- and double-crossover strains. During the optimisation of the PCR protocol, we observed small facts to look at: the use of the correct positive control (pTEC27 versus maxiprep plasmid), time of the growth of the bacteria and the “age” of the culture or the colonies on the plate of the mycobacteria. Secondly, the sucrose test is a suitable way to test for the sensitivity of single crossover bacteria for sucrose. In addition to the optimization, possible knockouts were created (MMAR_0514 and MMAR_4524). The obtained results of the marker gene tests are looking very promising. Since the results of the sucrose test, we know that the chance is bigger that the strains (MMAR_0514 and MMAR_4524) are a single-crossover. Furthermore, the possible knockout strains to confirm the insertion site of the hygromycin resistance gene, in the bacteria. After this, the created knockouts could be tested for infectivity and ability to reactivate by injecting them into the zebrafish.

 
Abstract bachelorproef 2015-2016Changes in foxo gene expression after parasitoid wasp infection in Drosophila hemocytes

Wegens confidentialiteit kan de samenvatting niet gepubliceerd worden.
 
Samenvatting eindwerk 2014-2015: Integrated analysis of miRNA and mRNA microarray data in prostate cancer cells
The goal of this project is to get a better insight between ERG-subtyped prostate cancer by doing an integrated analysis on miRNA expression data as well as on gene expression data. The final result would be to find miRNA-mRNA interactions that behave differently between ERG negative (under expression of ERG) and ERG positive (over expression of ERG) prostate cancers, this is done in a dataset that was derived from xenograft samples. Thereafter these interactions need to be validated in a dataset derived from prostate cancer patients (Tampere pca).
Performing a first differential analysis on the xenograft dataset resulted in the finding of no miRNA-mRNA interactions. This was the cause of an overall bad result of the differential expression analysis performed on the miRNA data, only two miRNAs were found, these miRNAs contained no predicted target genes that were differential expressed in the gene expression data.
Thereafter a clustering analysis was performed on the miRNA expression data of both datasets this resulted in the discovery of two clusters, that had a big similarity to the ERG subtyped groups of the xenograft dataset. A clustering analysis was performed on the gene expression data but this resulted in an overall bad clustering of the data.
Another differential expression analysis was performed based on the found clusters. The analysis resulted in the finding of eight differential expressed miRNAs and five differential expressed genes. After using a linear model to check if there is a negative correlation between the miRNAs and their target genes, four miRNA-mRNA interactions were found.
These four interactions are:
hsa-miR-135a − RNF24
hsa-miR-125b − ELMO2
hsa-miR-200b − FECH
hsa-miR-200a – FECH
Three of these interactions were more or less validated in the CRPC samples of the ERG subtyped Tampere Pca dataset and 3 of them were more or less validated in the PC samples. 

Address

Biokatu 6
Tampere, Finland
+358 40 190 1664
Finland
Biokatu 6
Tampere, Finland
+358 40 190 1664
Finland

Contacts

Traineeship supervisor
Mika Rämet
Traineeship supervisor
Laura Vesala
Traineeship supervisor
Matti Nykter
Traineeship supervisor
Henna Myllymäki

Getuigenis internationale stage (Enia)

Finland het land van de sneeuw, de rendieren en een heel vooruitstrevend land op vlak van wetenschap. Dit laatste is dus zeker een pluspunt om in één van de Scandinavische landen een internationale stage te doen. Ik mocht twee weken toekijken en daarna begon mijn echte onderzoek "Analyzing mutant zebrafish lines in their resistance against Mycobacterium marinum". Internationalisering stond echt centraal op mijn stageplaats, Engels was dan ook de hoofdtaal voor alle vergaderingen. Een internationale stage is zeker de moeite waard. Je leert er zelfstandig worden, ik heb hier leren koken, uitstapjes plannen en mijn kleren wassen. Ook kun je oefenen op vlak van Engels en schaaf je jouw sociale vaardigheden bij. Mijn stage was een heel leerrijke ervaring, niet alleen op wetenschapsvlak maar je groeit er ook als persoon. ~ Enia Vande Vyvere

blog: http://enia-tampere.blogspot.fi/

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