Blending of political and media power: The case of Radek John and his programme Bez cenzury

This thesis considers the role of former politician and journalist Radek John in an investigative programme Bez cenzury on TV Barrandov. Even though John was a politician and leader of Czech political party Věci veřejné, he decided to return to journalism. He did so with no intention of resigning his chair in the Chamber of Deputies, part of the Parliament of the Czech Republic. With this in mind, this could be considered as a specific representation of political parallelism. This study describes specific cases where Radek John might have acted contrary to normative journalistic values and journalism ethics. Furthermore, the thesis analyses the possibility that Radek John's own political interests and opinions affected the television programme itself. The research is conducted using the method of a case study which combines qualitative and quantitative content analysis, qualitative interviews and other research methods. Consequently, the analysis found signs of biased reporting in the programme's introduction and some stories, which reflected Radek John's antipathy towards traditional political parties and their leaders. However, the research did not reveal any direct support of Věci veřejné or their representatives. Furthermore, the thesis also presents media, academic and political responses to..

Visualization 5: Integral imaging microscopy with enhanced depth-of-field using a spatial multiplexing

Visualization 5 Originally published in Optics Express on 08 February 2016 (oe-24-3-2072

Targeted Next-Generation Sequencing at Copy-Number Breakpoints for Personalized Analysis of Rearranged Ends in Solid Tumors

<div><p>Background</p><p>The concept of the utilization of rearranged ends for development of personalized biomarkers has attracted much attention owing to its clinical applicability. Although targeted next-generation sequencing (NGS) for recurrent rearrangements has been successful in hematologic malignancies, its application to solid tumors is problematic due to the paucity of recurrent translocations. However, copy-number breakpoints (CNBs), which are abundant in solid tumors, can be utilized for identification of rearranged ends.</p><p>Method</p><p>As a proof of concept, we performed targeted next-generation sequencing at copy-number breakpoints (TNGS-CNB) in nine colon cancer cases including seven primary cancers and two cell lines, COLO205 and SW620. For deduction of CNBs, we developed a novel competitive single-nucleotide polymorphism (cSNP) microarray method entailing CNB-region refinement by competitor DNA.</p><p>Result</p><p>Using TNGS-CNB, 19 specific rearrangements out of 91 CNBs (20.9%) were identified, and two polymerase chain reaction (PCR)-amplifiable rearrangements were obtained in six cases (66.7%). And significantly, TNGS-CNB, with its high positive identification rate (82.6%) of PCR-amplifiable rearrangements at candidate sites (19/23), just from filtering of aligned sequences, requires little effort for validation.</p><p>Conclusion</p><p>Our results indicate that TNGS-CNB, with its utility for identification of rearrangements in solid tumors, can be successfully applied in the clinical laboratory for cancer-relapse and therapy-response monitoring.</p></div

TNGS-CNB schematic.

<p>The copy-number statuses of seven primary colon cancer tissues and two colon cancer cell lines were analyzed by the cSNP microarray method, and 91 CNBs were deduced. After removing 3.8 Mb of repetitive sequences from the CNB regions, the area for targeted capture was 2.2 Mb. After paired-end NGS of the captured sequences, the reads were aligned to the NCBI human genome assembly (build 37, hg19), and 23 candidate rearranged sequences were deduced. After PCR confirmation of the candidate rearranged sequences, 19 PCR-amplifiable rearrangements were identified.</p

PCR-amplified rearrangements identified by TNGS-CNB.

<p>*Chromosome number.</p><p>**Two rearrangements were amplified also in normal samples, indicating that these are constitutive genomic rearrangements.</p><p>***Two candidate rearrangements were analyzed by next-generation sequencing in the same region as sample C6, but only one was amplified by PCR.</p><p>****Samples C7 and C8 are the COLO205 and SW620 cancer cell lines, respectively.</p><p>ID, identification number.</p

Copy-number status information by cSNP microarray.

<p>The allele B is the B allele, and the values for various parameters are the expected values.</p><p>N-H mixture or N-H mix, the mixture of normal and H-mole DNAs; C-H mixture or C-H mix, the mixture of cancer and H-mole DNAs; N-H mix ratio, the ratio of normal and H-mole DNA amounts in the N-H mixture; C-H mix ratio, the ratio of cancer and H-mole DNA amounts in the C-H mixture; Copy Number, the copy number in cancer; Cancer Genotype, the genotype in cancer-sample DNA; Normal genotype, the genotype in normal-sample DNA; N-H mix genotype, the genotype in the N-H mixture; C-H mix genotype, the genotype in the C-H mixture; BAF_NH, the ratio of B allele and total allele amounts (or B allele frequency) in the N-H mixture; AR_NH, the ratio of B allele and A allele amounts (or allelic ratio) in the N-H mixture; BAF_CH, the ratio of B allele and total allele amounts (or B allele frequency) in the C-H mixture; AR_CH, the ratio of B allele and A allele amounts (or allelic ratio) in the C-H mixture; ARR, the ratio of AR_CH and AR_NH, or the AR ratio; nARR, the ARR values that are divided by the median ARR value, or normalized ARR.</p><p>The median ARR value (underlined) was used for normalization.</p

Copy-number changes at CNBs according to nARR values or LRRs.

<p>The copy-number statuses at nine CNBs in four primary colon cancer samples are shown. The CNBs were apparent with the nARR values, but the LRRs showed no clear breakpoints at most sites. The arrows indicate the CNBs employed for capture probes; at all of the CNBs marked by an arrow, the PCR-amplifiable tumor-specific rearrangements were successfully identified by TNGS-CNB.</p

cSNP microarray for determination of copy-number breakpoints.

<p>A. Schematic procedure for cSNP microarray. For each sample, SNP microarray experiments were performed for 1) H-mole DNA, 2) normal-sample DNA, 3) the mixture of normal and H-mole DNAs (N-H mixture), and 4) the mixture of cancer and H-mole DNAs (C-H mixture). An SNP microarray experiment for cancer samples was performed for the purpose of comparison. Only alter homozygous alleles (box) were selected for the cSNP microarray analysis. B. Representative LRR, nAR_CH, and nARR results for colon cancer samples. The LRR was obtained by Genome Studio software; the nAR_CH was calculated by cSNP software for the cancer and H-mole DNAs; the nARR was calculated by the same cSNP software for DNAs from the cancer tissues, corresponding normal tissues, and H-mole.</p