Using of Linux Containers in Test Fixture

Táto práca sa zaoberá štúdiom Linuxových kontajnerov a ich aplikáciou na vytvorenie stabilného prostredia pre testovanie softvéru. Programové riešenie problém delí na niekoľko častí. Najprv sa podľa požiadavok používateľa vytvorí konfigurácia, následne sa podľa nej vytvorí kontajner a nakoniec sa tento kontajner spustí spolu s dodanými testami za použitia platformy Docker. Program sám o sebe naplňuje počiatočné požiadavky, avšak jeho funkcionalita nie je zaručená vzhľadom na využitie softvéru tretej strany ako napríklad správcovia balíkov, čo môže spôsobiť neočakávané chyby za behu programu. Hlavným prínosom práce je zaobalenie platformy Docker tak, aby od užívateľa vyžadovala minimálnu, alebo žiadnu znalosť platformy Docker a umožňovala vytvárať kontajnery zjednodušenou formou.The main focus of this thesis is the study of Linux containers and their application in creation of software test fixtures. The program solution divides the problem into several segments. At first, a configurationisset upin accordance with the user’s specification, next a container is created according to given configuration, and in the end,the created container is launched alongside supplied tests while using the Docker platform. The program itself meets initial requirements although its functionality is not guaranteed as a result of usage of third-party software such as package managers, which may cause unexpected runtime errors. Primary asset of the thesis is the wrapping of the Docker platform to the degree, that its user needs minimal, or no knowledge of the platform, and allows them to create containers in a simplified way

<i>w</i>AlbB induces a strong resistance to DENV-2 in mosquito cells.

<p><i>w</i>AlbB is a native infection in <i>Ae. albopictus</i> Aa23 cells (<b>A</b>) while Aa23T cells were initially generated by tetracycline treatment of Aa23 cell to remove <i>Wolbachia</i> infection. There is no <i>Wolbachia</i> in <i>Ae. aegypti</i> Aag2 cells (<b>B</b>). <i>w</i>-Aag2 was generated from Aag2 cells by introducing <i>w</i>AlbB from Aa23 using a shell-vial technique. Five days after inoculated with DENV-2, the cells were tested for dengue infection by plaque assay. Error bars are standard errors of the mean of at least three biological replicates. **, P<0.01; ***, P<0.001in Student's t-Test.</p

Localization of <i>Wolbachia</i> and DENV-2 in Aa23 cells.

<p>Double immunofluorescence staining of cells showing the localization of dengue virus (green) and <i>Wolbachia</i> (red). Cells were probed simultaneously with polyclonal anti-wsp antibody (<i>Wolbachia</i>) and monoclonal anti-DENV-2 antibody, followed by Alexa 594 (red) and Alexa 488 (green) conjugated antibodies, respectively. DNA (blue) is stained with DAPI. In panels (A, B, and C), the red, green and blue channels are merged. A and B show Aa23 cells with mock treatment and treatment with 5 µg/ml of rifampicin for 5 hr, respectively, followed by dengue infection. C is Aa23T cells without dengue infection (negative control). D to F or G to I is the same sample with different channel merged: D and G show only red and blue channel merged, E and H show only green and blue channel merged, F and I show all the red, green and blue merged. Aa23 cells treated with 5 µg/ml of rifampicin for 10 hr (D to F) and 40 hr (G to I), followed by dengue infection, are shown.</p

<i>Wolbachia</i> density in somatic tissues of <i>Ae. albopictus</i> is too low to induce resistance to DENV.

<p>(A). The density of <i>w</i>AlbA is significantly lower than <i>w</i>AlbB in midgut, fatbody, salivary gland and ovary of <i>Ae. albopictus</i>. The copy number of the <i>Wolbachia</i> wsp was normalized by <i>Ae. albopictus</i> actin; (B). <i>Wolbachia</i> density in somatic tissues is significantly lower in the <i>Ae. albopictus</i> HOU strain than in the transinfected <i>Ae. aegypti</i> WB1 strain. The copy number of the <i>Wolbachia</i> wsp was normalized by one conserved RPS6 in both <i>Ae. albopictus</i> and <i>Ae. aegypti</i>. In all the assays, midguts, salivary glands, fatbodies and ovaries of 7-day-old non blood fed females were dissected and used for extraction of total genomic DNA. ***, P<0.001; **, P<0.01 in Student's t-Test. Error bars are standard errors of the mean of ten biological replicates.</p

The native <i>Wolbachia</i> does not inhibit dissemination of DENV-2 to mosquito heads in <i>Ae. albopictus</i>.

<p>The HOU strain of <i>Ae. albopictus</i> and its aposymbiotic strain HT1 were infected with the blood containing DENV-2 at titers of 10⁶, 10⁵, and 10⁴ PFU/ml. At Day 14 post infection, heads of ten mosquitoes were collected and used for diagnosis of DENV-2 by RT-PCR. Data from two experiments were pooled together.</p

Generation of Aa23 cells with different <i>Wolbachia</i> density.

<p>Cells were treated using sub-lethal doses of rifampicin for a different time periods. Three dosages (0.05 µg/ml, 0.5 µg/ml and 5 µg/ml) and four time periods (4 h, 10 h, 40 h and 70 h) were used. The genome copies of wsp were measure by q-PCR, normalized by host gene actin. Error bars are standard errors of the mean of at least three biological replicates. Statistical significance is represented by letters above each column, with different letters signifying distinct statistical groups. Student's t test: a vs. b, P<0.001; b vs. c, P<0.001; d vs. a, P<0.05.</p

Distribution of the relative expression of 6,769 genes in the infected S2versus uninfected S2cell lines

<p><b>Copyright information:</b></p><p>Taken from "Genome-wide analysis of the interaction between the endosymbiotic bacterium and its host"</p><p>http://www.biomedcentral.com/1471-2164/9/1</p><p>BMC Genomics 2008;9():1-1.</p><p>Published online 2 Jan 2008</p><p>PMCID:PMC2253531.</p><p></p> Genes with differential expression are defined as those with P < 0.05 and a ± 1.2 fold change

Resistance of MTB mosquitoes to DENV-2 is associated with a high density of <i>Wolbachia</i> in mosquito somatic tissues.

<p>The fold change in genome copy of the <i>Wolbachia</i> surface protein (WSP) gene in MTB mosquitoes is compared to APM mosquitoes. The copy number of the <i>Wolbachia</i> wsp was normalized by <i>Ae. polynesiensis</i> RPS6. In all the assays, the midguts, salivary glands, fat bodies, and ovaries of 7-day-old non-blood-fed females were dissected and used for extraction of total genomic DNA. Error bars are standard errors of the mean of twelve biological replicates.</p

Inhibition of dengue infection in the whole bodies of MTB mosquitoes.

<p>At 14 dpi (days post infection) through a blood meal or intrathoracic injection, the whole bodies of MTB and APM mosquitoes were collected, and the number of genome copies of the DENV genome was determined by qRT-PCR using primers for the NS5 gene; the results were normalized to the <i>Ae. polynesiensis</i> ribosomal protein S6 (RPS6). Lines indicate the median of the ten biological replicates. Significance was determined using a Mann-Whitney U test.</p

The expression of DEFD was induced by <i>Wolbachia</i> in density-dependent manner in Aa23 cell lines.

<p>Seven days after rifampicin treatment, cells were collected to measure <i>Wolbachia</i> densities and DEFD expression. Because treatment with 5 µg/ml of rifampicin for 70 h resulted in both <i>Wolbachia</i> infection and DEFD expression at lowest level, it serves as a reference for all the other treatments to calculate a fold increase in both <i>Wolbachia</i> density and DEFD expression. Each point is the mean of at least three biological replicates.</p