• MeSH
• diagnostické techniky molekulární MeSH
• nádory * diagnóza   genetika   MeSH
• stanovení celkové genové exprese MeSH

• Konspekt
• Biochemie. Molekulární biologie. Biofyzika
• NLK Obory
• molekulární biologie, molekulární medicína
• onkologie
• NLK Publikační typ
• kolektivní monografie

Bordetella pertussis, a strictly human re-emerging pathogen and the causative agent of whooping cough, exploits a broad variety of virulence factors to establish efficient infection. Here, we used RNA sequencing to analyse the changes in gene expression profiles of human THP-1 macrophages resulting from B. pertussis infection. In parallel, we attempted to determine the changes in intracellular B. pertussis-specific transcriptomic profiles resulting from interaction with macrophages. Our analysis revealed that global gene expression profiles in THP-1 macrophages are extensively rewired 6 h post-infection. Among the highly expressed genes, we identified those encoding cytokines, chemokines, and transcription regulators involved in the induction of the M1 and M2 macrophage polarization programmes. Notably, several host genes involved in the control of apoptosis and inflammation which are known to be hijacked by intracellular bacterial pathogens were overexpressed upon infection. Furthermore, in silico analyses identified large temporal changes in expression of specific gene subsets involved in signalling and metabolic pathways. Despite limited numbers of the bacterial reads, we observed reduced expression of majority of virulence factors and upregulation of several transcriptional regulators during infection suggesting that intracellular B. pertussis cells switch from virulent to avirulent phase and actively adapt to intracellular environment, respectively.

• MeSH
• Bordetella pertussis fyziologie   MeSH
• buněčné linie MeSH
• genová ontologie MeSH
• genové regulační sítě MeSH
• interakce hostitele a patogenu genetika   imunologie   MeSH
• kultivované buňky MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• lidé MeSH
• makrofágy imunologie   metabolismus   mikrobiologie   MeSH
• pertuse genetika   imunologie   virologie   MeSH
• regulace genové exprese MeSH
• reprodukovatelnost výsledků MeSH
• stanovení celkové genové exprese * metody   MeSH
• transkriptom * MeSH
• výpočetní biologie metody   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Osteoblastic differentiation is a multistep process characterized by osteogenic induction of mesenchymal stem cells, which then differentiate into proliferative pre-osteoblasts that produce copious amounts of extracellular matrix, followed by stiffening of the extracellular matrix, and matrix mineralization by hydroxylapatite deposition. Although these processes have been well characterized biologically, a detailed transcriptional analysis of murine primary calvaria osteoblast differentiation based on RNA sequencing (RNA-seq) analyses has not previously been reported. Here, we used RNA-seq to obtain expression values of 29,148 genes at four time points as murine primary calvaria osteoblasts differentiate in vitro until onset of mineralization was clearly detectable by microscopic inspection. Expression of marker genes confirmed osteogenic differentiation. We explored differential expression of 1386 protein-coding genes using unsupervised clustering and GO analyses. 100 differentially expressed lncRNAs were investigated by co-expression with protein-coding genes that are localized within the same topologically associated domain. Additionally, we monitored expression of 237 genes that are silent or active at distinct time points and compared differential exon usage. Our data represent an in-depth profiling of murine primary calvaria osteoblast differentiation by RNA-seq and contribute to our understanding of genetic regulation of this key process in osteoblast biology.

• MeSH
• alternativní sestřih MeSH
• buněčná diferenciace genetika   MeSH
• kultivované buňky MeSH
• lebka fyziologie   MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• osteoblasty fyziologie   MeSH
• osteogeneze genetika   MeSH
• RNA analýza   MeSH
• stanovení celkové genové exprese MeSH
• transkriptom genetika   MeSH
• zvířata MeSH
• Check Tag
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Intratumor heterogeneity is a primary feature of high-grade gliomas, complicating their therapy. As accumulating evidence suggests that intratumor heterogeneity is a consequence of cellular subsets with different cycling frequencies, we developed a method for transcriptional profiling of gliomas, using a novel technique to dissect the tumors into two fundamental cellular subsets, namely, the proliferating and non-proliferating cell fractions. The tumor fractions were sorted whilst maintaining their molecular integrity, by incorporating the thymidine analog 5-ethynyl-2'-deoxyuridine into actively dividing cells. We sorted the actively dividing versus non-dividing cells from cultured glioma cells, and parental and clonally derived orthotopic tumors, and analyzed them for a number of transcripts. While there was no significant difference in the transcriptional profiles between the two cellular subsets in cultured glioma cells, we demonstrate ∼2-6 fold increase in transcripts of cancer and neuronal stem cell and tumor cell migration/invasion markers, and ∼2-fold decrease in transcripts of markers of hypoxia and their target genes, in the dividing tumor cells of the orthotopic glioma when compared to their non-proliferative counterparts. This suggests the influence of the brain microenvironment in transcriptional regulation and, thereby, the physiology of glioma cells in vivo. When clonal glioma cells were derived from a parental glioma and the resultant orthotopic tumors were compared, their transcriptional profiles were closely correlated to tumor aggression and consequently, survival of the experimental animals. This study demonstrates the resolution of intratumor heterogeneity for profiling studies based on cell proliferation, a defining feature of cancers, with implications for treatment design.

• MeSH
• genetická transkripce * MeSH
• gliom patologie   MeSH
• heterografty MeSH
• lidé MeSH
• myši inbrední NOD MeSH
• myši SCID MeSH
• myši MeSH
• nádorové buněčné linie MeSH
• nádory mozku patologie   MeSH
• proliferace buněk * MeSH
• stanovení celkové genové exprese * MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

• MeSH
• časná diagnóza MeSH
• diagnostické techniky molekulární MeSH
• exprese genu MeSH
• genom lidský MeSH
• lidé MeSH
• messenger RNA analýza   MeSH
• mikro RNA analýza   MeSH
• polymerázová řetězová reakce MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• stanovení celkové genové exprese MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• recenze MeSH

BACKGROUND: Thinning supplies of natural resources increase attention to sustainable microbial production of bio-based fuels. The strain Clostridium beijerinckii NRRL B-598 is a relatively well-described butanol producer regarding its genotype and phenotype under various conditions. However, a link between these two levels, lying in the description of the gene regulation mechanisms, is missing for this strain, due to the lack of transcriptomic data. RESULTS: In this paper, we present a transcription profile of the strain over the whole fermentation using an RNA-Seq dataset covering six time-points with the current highest dynamic range among solventogenic clostridia. We investigated the accuracy of the genome sequence and particular genome elements, including pseudogenes and prophages. While some pseudogenes were highly expressed, all three identified prophages remained silent. Furthermore, we identified major changes in the transcriptional activity of genes using differential expression analysis between adjacent time-points. We identified functional groups of these significantly regulated genes and together with fermentation and cultivation kinetics captured using liquid chromatography and flow cytometry, we identified basic changes in the metabolism of the strain during fermentation. Interestingly, C. beijerinckii NRRL B-598 demonstrated different behavior in comparison with the closely related strain C. beijerinckii NCIMB 8052 in the latter phases of cultivation. CONCLUSIONS: We provided a complex analysis of the C. beijerinckii NRRL B-598 fermentation profile using several technologies, including RNA-Seq. We described the changes in the global metabolism of the strain and confirmed the uniqueness of its behavior. The whole experiment demonstrated a good reproducibility. Therefore, we will be able to repeat the experiment under selected conditions in order to investigate particular metabolic changes and signaling pathways suitable for following targeted engineering.

• MeSH
• bakteriofágy genetika   MeSH
• butanoly metabolismus   MeSH
• Clostridium beijerinckii genetika   metabolismus   virologie   MeSH
• DNA virů genetika   MeSH
• fermentace MeSH
• genetická transkripce MeSH
• kinetika MeSH
• pseudogeny genetika   MeSH
• sekvenční analýza RNA * MeSH
• stanovení celkové genové exprese * MeSH
• Publikační typ
• časopisecké články MeSH

BACKGROUND: The hop plant (Humulus lupulus L.) is a valuable source of several secondary metabolites, such as flavonoids, bitter acids, and essential oils. These compounds are widely implicated in the beer brewing industry and are having potential biomedical applications. Several independent breeding programs around the world have been initiated to develop new cultivars with enriched lupulin and secondary metabolite contents but met with limited success due to several constraints. In the present work, a pioneering attempt has been made to overexpress master regulator binary transcription factor complex formed by HlWRKY1 and HlWDR1 using a plant expression vector to enhance the level of prenylflavonoid and bitter acid content in the hop. Subsequently, we performed transcriptional profiling using high-throughput RNA-Seq technology in leaves of resultant transformants and wild-type hop to gain in-depth information about the genome-wide functional changes induced by HlWRKY1 and HlWDR1 overexpression. RESULTS: The transgenic WW-lines exhibited an elevated expression of structural and regulatory genes involved in prenylflavonoid and bitter acid biosynthesis pathways. In addition, the comparative transcriptome analysis revealed a total of 522 transcripts involved in 30 pathways, including lipids and amino acids biosynthesis, primary carbon metabolism, phytohormone signaling and stress responses were differentially expressed in WW-transformants. It was apparent from the whole transcriptome sequencing that modulation of primary carbon metabolism and other pathways by HlWRKY1 and HlWDR1 overexpression resulted in enhanced substrate flux towards secondary metabolites pathway. The detailed analyses suggested that none of the pathways or genes, which have a detrimental effect on physiology, growth and development processes, were induced on a genome-wide scale in WW-transgenic lines. CONCLUSIONS: Taken together, our results suggest that HlWRKY1 and HlWDR1 simultaneous overexpression positively regulates the prenylflavonoid and bitter acid biosynthesis pathways in the hop and thus these transgenes are presented as prospective candidates for achieving enhanced secondary metabolite content in the hop.

• MeSH
• anotace sekvence MeSH
• exprese genu MeSH
• geneticky modifikované rostliny MeSH
• genomika * MeSH
• Humulus genetika   MeSH
• rostlinné proteiny genetika   MeSH
• stanovení celkové genové exprese * MeSH
• transkripční faktory genetika   MeSH
• Publikační typ
• časopisecké články MeSH

The aim of current study was to evaluate the effect of the most common anthocyanidins (cyanidin, delphinidin, malvidin, pelargonidin, and peonidin) on the transcriptional activity of steroid and nuclear receptors. The activities of steroid receptors - progesterone receptor (PR), estrogen receptor (ER), androgen receptor (AR), glucocorticoid receptor (GR), and nuclear receptors - vitamin D receptor (VDR), retinoid X receptor (RXR), retinoic acid receptor (RAR), pregnane X receptor (PXR), and thyroid receptor (TR) were assessed using either stable transfected luciferase gene reporter cell lines or transiently transfected cell lines. The cytotoxicity assays and gene reporter assays were performed after the 24-h treatment of cells with increasing range of concentrations (10 nM to 50 µM) of selected anthocyanidins. The results of experiments indicate that none of the examined anthocyanidins in all tested concentrations caused remarkable changes of transcriptional activity of studied steroid receptors, but their increasing concentrations slightly inhibited transcriptional activity of nuclear receptors induced by model agonists.

• MeSH
• anthokyaniny farmakologie   MeSH
• genetická transkripce účinky léků   MeSH
• lidé MeSH
• nádorové buňky kultivované MeSH
• receptory cytoplazmatické a nukleární genetika   MeSH
• steroidní receptory genetika   MeSH
• viabilita buněk účinky léků   MeSH
• vztah mezi dávkou a účinkem léčiva MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

A better understanding of the molecular basis of tumor progression and invasion is needed to improve therapy for malignant tumors. Recently, we established a mouse metastatic MK16 model by transduction of secondary kidney cells with human papillomavirus type 16 (HPV16) E6 and E7 oncogenes and human H-ras activated by G12V mutation. In this study, we extended the model to MK16 cell lines derived from lung metastases and compared the oncogenicity of seven cell lines successively isolated from primary tumors or metastases. By observing the formation and growth of subcutaneous tumors and generation of lung metastasis, we showed a gradual increase in oncogenicity of MK16 cell lines. Interestingly, we demonstrated metastatic potential of MK16/A cells with low oncogenic potential in primary tumor development. To detect changes in gene expression associated with increasing oncogenicity of MK16 cell lines, we performed transcriptional profiling with the Atlas Plastic Mouse 5K microarray. We found that a substantial proportion of up-regulated genes encoded ribosomal proteins. Among the down-regulated genes, the highest number (n=10) belonged to a group coding for transcription factors. Expression of two of these, Pou3f2 and Gtl3, was reduced both in cells derived from primary tumors and those isolated from metastases. Furthermore, microarray hybridization suggested that the down-regulation of cyclin-dependent kinase inhibitors p16(Ink4a) and p57(Kip2) and up-regulation of A6 and A10 members of the S100 protein family might play a role in the increase of MK16 oncogenicity.

• MeSH
• experimentální nádory genetika   patologie   MeSH
• financování organizované MeSH
• geny ras genetika   MeSH
• lidé MeSH
• myši inbrední C57BL MeSH
• myši MeSH
• nádorová transformace buněk genetika   MeSH
• nádorové buňky kultivované MeSH
• onkogenní proteiny virové genetika   MeSH
• polymerázová řetězová reakce s reverzní transkripcí metody   MeSH
• progrese nemoci MeSH
• represorové proteiny genetika   MeSH
• reprodukovatelnost výsledků MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody   MeSH
• stanovení celkové genové exprese MeSH
• transformované buněčné linie MeSH
• transplantace nádorů MeSH
• virová transformace buněk genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• ženské pohlaví MeSH
• zvířata MeSH

The Fulani ethnic group has relatively better protection from Plasmodium falciparum malaria, as reflected by fewer symptomatic cases of malaria, lower infection rates, and lower parasite densities compared to sympatric ethnic groups. However, the basis for this lower susceptibility to malaria by the Fulani is unknown. The incidence of classic malaria resistance genes are lower in the Fulani than in other sympatric ethnic populations, and targeted SNP analyses of other candidate genes involved in the immune response to malaria have not been able to account for the observed difference in the Fulani susceptibility to P.falciparum. Therefore, we have performed a pilot study to examine global transcription and DNA methylation patterns in specific immune cell populations in the Fulani to elucidate the mechanisms that confer the lower susceptibility to P.falciparum malaria. When we compared uninfected and infected Fulani individuals, in contrast to uninfected and infected individuals from the sympatric ethnic group Mossi, we observed a key difference: a strong transcriptional response was only detected in the monocyte fraction of the Fulani, where over 1000 genes were significantly differentially expressed upon P.falciparum infection.

• MeSH
• etnicita * MeSH
• genetická transkripce * MeSH
• kultivované buňky MeSH
• lidé MeSH
• metylace DNA MeSH
• monocyty imunologie   MeSH
• odolnost vůči nemocem * MeSH
• pilotní projekty MeSH
• stanovení celkové genové exprese MeSH
• tropická malárie genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH