Bioorthogonal chemistry provides one of the possibilities to modify various biomolecules in their native environment. The combination of Click chemistry with the BONCAT method (bioorthogonal non-canonical amino acid tagging) is widely used for tagging and analysis of newly synthesized proteins, which are clearly distinguishable from the pre-existing protein pool. However, the commonly used procedure results in low quality 2D electrophoretic profiles. We put a lot of effort into obtaining clear results using a standard Click protocol, with a negligible effect. Here we describe a Click-on-membrane approach which we successfully used not only to monitor de novo protein synthesis but also to detect newly synthesized RNA.
Ellagic acid, a natural substance found in various fruits and nuts, was previously shown to exhibit beneficial effects towards metabolic syndrome. In this study, using a genetic rat model of metabolic syndrome, we aimed to further specify metabolic and transcriptomic responses to ellagic acid treatment. Adult male rats of the SHR-Zbtb16Lx/k.o. strain were fed a high-fat diet accompanied by daily intragastric gavage of ellagic acid (50 mg/kg body weight; high-fat diet-ellagic acid (HFD-EA) rats) or vehicle only (high-fat diet-control (HFD-CTL) rats). Morphometric and metabolic parameters, along with transcriptomic profile of liver and brown and epididymal adipose tissues, were assessed. HFD-EA rats showed higher relative weight of brown adipose tissue (BAT) and decreased weight of epididymal adipose tissue, although no change in total body weight was observed. Glucose area under the curve, serum insulin, and cholesterol levels, as well as the level of oxidative stress, were significantly lower in HFD-EA rats. The most differentially expressed transcripts reflecting the shift induced by ellagic acid were detected in BAT, showing downregulation of BAT activation markers Dio2 and Nr4a1 and upregulation of insulin-sensitizing gene Pla2g2a. Ellagic acid may provide a useful nutritional supplement to ameliorate features of metabolic syndrome, possibly by suppressing oxidative stress and its effects on brown adipose tissue.
- MeSH
- biologické markery analýza MeSH
- dieta s vysokým obsahem tuků MeSH
- epididymis MeSH
- hnědá tuková tkáň chemie MeSH
- játra chemie MeSH
- krevní glukóza analýza MeSH
- krysa rodu rattus MeSH
- kyselina ellagová aplikace a dávkování MeSH
- messenger RNA analýza MeSH
- metabolický syndrom genetika metabolismus prevence a kontrola MeSH
- oxidační stres účinky léků MeSH
- potkani inbrední SHR MeSH
- RNA analýza MeSH
- transkriptom účinky léků MeSH
- tuková tkáň chemie MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Saliva, as a non-invasive and easily accessible biofluid, has been shown to contain RNA biomarkers for prediction and diagnosis of several diseases. However, systematic analysis done by our group identified two problematic issues not coherently described before: (1) most of the isolated RNA originates from the oral microbiome and (2) the amount of isolated human RNA is comparatively low. The degree of bacterial contamination showed ratios up to 1:900,000, so that only about one out of 900,000 RNA copies was of human origin, but the RNA quality (average RIN 6.7 + /- 0.8) allowed for qRT-PCR. Using 12 saliva samples from healthy donors, we modified the methodology to (1) select only human RNA during cDNA synthesis by aiming at the poly(A)+-tail and (2) introduced a pre-amplification of human RNA before qRT-PCR. Further, the manufacturer's criteria for successful pre-amplification (Ct values ≤ 35 for unamplified cDNA) had to be replaced by (3) proofing linear pre-amplification for each gene, thus, increasing the number of evaluable samples up to 70.6%. When considering theses three modifications unbiased gene expression analysis on human salivary RNA can be performed.
- MeSH
- bakteriální RNA genetika MeSH
- dospělí MeSH
- exprese genu * MeSH
- komplementární DNA genetika MeSH
- kvantitativní polymerázová řetězová reakce metody MeSH
- lidé MeSH
- RNA ribozomální 18S genetika MeSH
- RNA analýza MeSH
- sliny chemie metabolismus MeSH
- stanovení celkové genové exprese metody MeSH
- transkriptom MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
The distinction between lipoma and atypical lipomatous tumor can be challenging in some cases. While detection of MDM2 gene amplification via fluorescence in situ hybridization (FISH) has been well established as a diagnostic tool to distinguish atypical lipomatous tumor and well-differentiated liposarcoma from benign mimics, MDM2 RNA in situ hybridization (RNA-ISH) has recently been proposed as an alternative diagnostic assay. During clinical workup for lipomatous tumors using MDM2 RNA-ISH, we noticed several dysplastic lipomas that were positive for MDM2 RNA-ISH but negative for MDM2 amplification by FISH. In this study, we examined a series of 11 dysplastic lipomas, all confirmed to be negative for MDM2 amplification by FISH. Positive MDM2 RNA-ISH was noted in 10 (91%) dysplastic lipomas. Single-nucleotide polymorphism array on one dysplastic lipoma identified the presence of homozygous deletion of 13q, including the RB1 gene locus with no evidence of MDM2 copy number gain. Our findings on the discordance between MDM2 FISH and MDM2 RNA-ISH highlight the potential utility and pitfalls of using MDM2 RNA-ISH in the distinction of atypical lipomatous tumor and related liposarcomas from dysplastic lipoma.
- MeSH
- amplifikace genu MeSH
- diferenciální diagnóza MeSH
- dospělí MeSH
- hybridizace in situ metody MeSH
- lidé středního věku MeSH
- lidé MeSH
- lipom diagnóza genetika MeSH
- liposarkom diagnóza genetika MeSH
- mladý dospělý MeSH
- nádorové biomarkery analýza MeSH
- protoonkogenní proteiny c-mdm2 analýza genetika MeSH
- RNA analýza MeSH
- senioři MeSH
- Check Tag
- dospělí MeSH
- lidé středního věku MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- senioři MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
In human cells, the intergenic spacers (IGS), which separate ribosomal genes, are complex approximately 30 kb-long loci. Recent studies indicate that all, or almost all, parts of IGS may be transcribed, and that at least some of them are involved in the regulation of the ribosomal DNA (rDNA) transcription, maintenance of the nucleolar architecture, and response of the cell nucleus to stress. However, since each cell contains hundreds not quite identical copies of IGS, the structure and functions of this locus remain poorly understood, and the dynamics of its products has not been specially studied. In this work, we used quantitative PCR to measure the expression levels of various rDNA regions at different times after inhibition of the transcription by Actinomycin D applied in high doses. This approach allowed us to measure real or extrapolated half-life times of some IGS loci. Our study reveals characteristic dynamic patterns suggestive of various pathways of RNA utilization and decay.
- MeSH
- HeLa buňky MeSH
- lidé MeSH
- mezerníky ribozomální DNA chemie genetika metabolismus MeSH
- RNA analýza biosyntéza genetika izolace a purifikace MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články 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
- MeSH
- DNA analýza MeSH
- falešně pozitivní reakce MeSH
- imunofenotypizace MeSH
- imunologické techniky * MeSH
- lidé MeSH
- proliferace buněk MeSH
- průtoková cytometrie MeSH
- řízení kvality MeSH
- RNA analýza MeSH
- separace buněk MeSH
- směrnice jako téma * MeSH
- software MeSH
- T-lymfocyty cytologie MeSH
- výzkumný projekt MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- MeSH
- algoritmy MeSH
- databáze genetické MeSH
- lidé MeSH
- melanom chemie genetika mortalita MeSH
- myši MeSH
- receptory antigenů T-buněk chemie genetika MeSH
- receptory antigenů * analýza genetika metabolismus MeSH
- RNA analýza genetika MeSH
- sekvenční analýza RNA metody MeSH
- stanovení celkové genové exprese metody MeSH
- výpočetní biologie metody MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: High-throughput sequencing (HTS) has revolutionized the way in which epigenetic research is conducted. When coupled with fully-sequenced genomes, millions of small RNA (sRNA) reads are mapped to regions of interest and the results scrutinized for clues about epigenetic mechanisms. However, this approach requires careful consideration in regards to experimental design, especially when one investigates repetitive parts of genomes such as transposable elements (TEs), or when such genomes are large, as is often the case in plants. RESULTS: Here, in an attempt to shed light on complications of mapping sRNAs to TEs, we focus on the 2,300 Mb maize genome, 85% of which is derived from TEs, and scrutinize methodological strategies that are commonly employed in TE studies. These include choices for the reference dataset, the normalization of multiply mapping sRNAs, and the selection among sRNA metrics. We further examine how these choices influence the relationship between sRNAs and the critical feature of TE age, and contrast their effect on low copy genomic regions and other popular HTS data. CONCLUSIONS: Based on our analyses, we share a series of take-home messages that may help with the design, implementation, and interpretation of high-throughput TE epigenetic studies specifically, but our conclusions may also apply to any work that involves analysis of HTS data.
Závěrečná zpráva o řešení grantu Interní grantové agentury MZ ČR
1 svazek : ilustrace, tabulky ; 30 cm
The aim of the project is to detect circulating tumor cells (CTC) in peripheral blood of patients with metastatic prostate cancer before and during the cytotoxic therapy. Detection will be performed by the method of immunomagnetic separation and RNA isolation from this fraction. Then we will perform the cultivation of the detected cells including the cultivation in milieu of cytotoxic agents. In the next stage the genetic profile of the detected cells will be assessed (a panel of 24 genes) and a similar profile will be evaluated also in histological specimen of a primary tumor. Analysis results will be correlated to the clinical course of disease and the prognostic factors of treatment effect on CTC count decline and patients‘ survival will be determined.
Cílem projektu je detekovat cirkulující nádorové buňky (CTC) v periferní krvi u pacientů s metastatickým karcinomem prostaty před cytotoxickou léčbou a v jejím průběhu. Detekce bude provedena metodou imunomagnetické separace buněk a izolací RNA z této frakce. Dále proběhne kultivace části detekovaných buněk včetně kultivace v prostředí cytotoxických látek. V další fázi bude hodnocen genetický profil zjištěných buněk (stanovení panelu 24 genů) a obdobný profil také u histologického preparátu primárního tumoru. Výsledky analýz budou vztaženy na klinický průběh onemocnění a budou stanoveny prognostické faktory účinku léčby na pokles CTC a přežití pacientů.
- MeSH
- analýza přežití MeSH
- diagnostické techniky molekulární MeSH
- exprese genu MeSH
- imunomagnetická separace MeSH
- individualizovaná medicína MeSH
- nádorové buněčné linie cytologie MeSH
- nádorové cirkulující buňky MeSH
- nádory prostaty rezistentní na kastraci diagnóza MeSH
- prognóza MeSH
- prostatický specifický antigen analýza MeSH
- RNA analýza MeSH
- Konspekt
- Biochemie. Molekulární biologie. Biofyzika
- NLK Obory
- biologie
- andrologie
- onkologie
- NLK Publikační typ
- závěrečné zprávy o řešení grantu IGA MZ ČR
