Functionality
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Bordetella pertussis, the causative agent of human whooping cough (pertussis) produces a complex array of virulence factors in order to establish efficient infection in the host. The RNA chaperone Hfq and small regulatory RNAs are key players in posttranscriptional regulation in bacteria and have been shown to play an essential role in virulence of a broad spectrum of bacterial pathogens. This study represents the first attempt to characterize the Hfq regulon of the human pathogen B. pertussis under laboratory conditions as well as upon passage in the host and indicates that loss of Hfq has a profound effect on gene expression in B. pertussis. Comparative transcriptional profiling revealed that Hfq is required for expression of several virulence factors in B. pertussis cells including the Type III secretion system (T3SS). In striking contrast to the wt strain, T3SS did not become operational in the hfq mutant passaged either through mice or macrophages thereby proving that Hfq is required for the functionality of the B. pertussis T3SS. Likewise, expression of virulence factors vag8 and tcfA encoding autotransporter and tracheal colonization factor, respectively, was strongly reduced in the hfq mutant. Importantly, for the first time we demonstrate that B. pertussis T3SS can be activated upon contact with macrophage cells in vitro.
- MeSH
- bakteriální proteiny genetika metabolismus MeSH
- bakteriální RNA genetika metabolismus MeSH
- Bordetella pertussis genetika metabolismus patogenita MeSH
- buněčné linie MeSH
- faktory virulence rodu Bordetella genetika metabolismus MeSH
- infekce bakteriemi rodu Bordetella mikrobiologie MeSH
- interakce hostitele a patogenu MeSH
- makrofágy metabolismus mikrobiologie MeSH
- myši MeSH
- protein hostitelského faktoru 1 nedostatek genetika MeSH
- regulace genové exprese u bakterií * MeSH
- regulon MeSH
- sekreční systém typu III genetika metabolismus MeSH
- sekreční systém typu V genetika metabolismus MeSH
- stanovení celkové genové exprese MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Antiphospholipid syndrome (APS) is associated with recurrent pregnancy morbidity, yet the underlying mechanisms remain elusive. We performed multifaceted characterization of the biological and transcriptomic signatures of mouse placenta and uterine natural killer (uNK) cells in APS. Histological analysis of APS placentas unveiled placental abnormalities, including disturbed angiogenesis, occasional necrotic areas, fibrin deposition, and nucleated red blood cell enrichment. Analyses of APS placentas showed a reduced cell proliferation, lower protein content and thinning of endothelial cells. Disturbances in APS trophoblast cells were linked to a cell cycle shift in cytotrophoblast cells, and a reduced number of spiral artery-associated trophoblast giant cells (SpA-TGC). Transcriptomic profiling of placental tissue highlighted disruptions in cell cycle regulation with notable downregulation of genes involved in developmental or signaling processes. Cellular senescence, metabolic and p53-related pathways were also enriched, suggesting potential mechanisms underlying placental dysfunction in APS. Thrombotic events, though occasionally detected, appeared to have no significant impact on the overall pathological changes. The increased number of dysfunctional uNK cells was not associated with enhanced cytotoxic capabilities. Transcriptomic data corroborated these findings, showing prominent suppression of NK cell secretory capacity and cytokine signaling pathways. Our study highlights the multifactorial nature of APS-associated placental pathologies, which involve disrupted angiogenesis, cell cycle regulation, and NK cell functionality.
- MeSH
- antifosfolipidový syndrom * imunologie patologie MeSH
- buňky NK * imunologie metabolismus MeSH
- modely nemocí na zvířatech * MeSH
- myši MeSH
- placenta * metabolismus patologie MeSH
- proliferace buněk MeSH
- stanovení celkové genové exprese MeSH
- těhotenství MeSH
- transkriptom MeSH
- trofoblasty metabolismus patologie imunologie MeSH
- uterus * patologie metabolismus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
Gene expression profiling was made more cost-effective by the NIH LINCS program that profiles only ∼1, 000 selected landmark genes and uses them to reconstruct the whole profile. The D-GEX method employs neural networks to infer the entire profile. However, the original D-GEX can be significantly improved. We propose a novel transformative adaptive activation function that improves the gene expression inference even further and which generalizes several existing adaptive activation functions. Our improved neural network achieves an average mean absolute error of 0.1340, which is a significant improvement over our reimplementation of the original D-GEX, which achieves an average mean absolute error of 0.1637. The proposed transformative adaptive function enables a significantly more accurate reconstruction of the full gene expression profiles with only a small increase in the complexity of the model and its training procedure compared to other methods.
Malfunction of the circadian timing system may result in cardiovascular and metabolic diseases, and conversely, these diseases can impair the circadian system. The aim of this study was to reveal whether the functional state of the circadian system of spontaneously hypertensive rats (SHR) differs from that of control Wistar rat. This study is the first to analyze the function of the circadian system of SHR in its complexity, i.e., of the central clock in the suprachiasmatic nuclei (SCN) as well as of the peripheral clocks. The functional properties of the SCN clock were estimated by behavioral output rhythm in locomotor activity and daily profiles of clock gene expression in the SCN determined by in situ hybridization. The function of the peripheral clocks was assessed by daily profiles of clock gene expression in the liver and colon by RT-PCR and in vitro using real time recording of Bmal1-dLuc reporter. The potential impact of the SHR phenotype on circadian control of the metabolic pathways was estimated by daily profiles of metabolism-relevant gene expression in the liver and colon. The results revealed that SHR exhibited an early chronotype, because the central SCN clock was phase advanced relative to light/dark cycle and the SCN driven output rhythm ran faster compared to Wistar rats. Moreover, the output rhythm was dampened. The SHR peripheral clock reacted to the dampened SCN output with tissue-specific consequences. In the colon of SHR the clock function was severely altered, whereas the differences are only marginal in the liver. These changes may likely result in a mutual desynchrony of circadian oscillators within the circadian system of SHR, thereby potentially contributing to metabolic pathology of the strain. The SHR may thus serve as a valuable model of human circadian disorders originating in poor synchrony of the circadian system with external light/dark regime.
- MeSH
- časové faktory MeSH
- cirkadiánní hodiny * MeSH
- druhová specificita MeSH
- fenotyp MeSH
- fibroblasty metabolismus MeSH
- játra metabolismus patofyziologie MeSH
- kolon metabolismus patofyziologie MeSH
- krysa rodu rattus MeSH
- metabolické sítě a dráhy fyziologie MeSH
- nucleus suprachiasmaticus metabolismus patofyziologie MeSH
- orgánová specificita MeSH
- pohybová aktivita fyziologie MeSH
- potkani inbrední SHR MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Bacterial pathogens sense specific cues associated with different host niches and integrate these signals to appropriately adjust the global gene expression. Bordetella pertussis is a Gram-negative, strictly human pathogen of the respiratory tract and the etiological agent of whooping cough (pertussis). Though B. pertussis does not cause invasive infections, previous results indicated that this reemerging pathogen responds to blood exposure. Here, omics RNA-seq and LC-MS/MS techniques were applied to determine the blood-responsive regulon of B. pertussis. These analyses revealed that direct contact with blood rewired global gene expression profiles in B. pertussis as the expression of almost 20% of all genes was significantly modulated. However, upon loss of contact with blood, the majority of blood-specific effects vanished, with the exception of several genes encoding the T3SS-secreted substrates. For the first time, the T3SS regulator BtrA was identified in culture supernatants of B. pertussis. Furthermore, proteomic analysis identified BP2259 protein as a novel secreted T3SS substrate, which is required for T3SS functionality. Collectively, presented data indicate that contact with blood represents an important cue for B. pertussis cells.
- MeSH
- anotace sekvence MeSH
- bakteriální proteiny metabolismus MeSH
- Bordetella pertussis fyziologie MeSH
- chromatografie kapalinová MeSH
- faktory virulence MeSH
- genomika * metody MeSH
- lidé MeSH
- proteomika * metody MeSH
- regulace genové exprese u bakterií MeSH
- sekreční systém typu III genetika metabolismus MeSH
- stanovení celkové genové exprese MeSH
- tandemová hmotnostní spektrometrie MeSH
- transkriptom MeSH
- virulence MeSH
- výpočetní biologie metody MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- MeSH
- kalretikulin genetika MeSH
- lidé MeSH
- myeloproliferativní poruchy genetika metabolismus MeSH
- myši MeSH
- nádorová transformace buněk genetika metabolismus MeSH
- receptory thrombopoetinu metabolismus MeSH
- transkriptom MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- dopisy MeSH
- práce podpořená grantem MeSH
Decades of liver regeneration studies still left the termination phase least elucidated. However regeneration ending mechanisms are clinicaly relevant. We aimed to analyse the timing and transcriptional control of the latest phase of liver regeneration, both controversial. Male Wistar rats were subjected to 2/3 partial hepatectomy with recovery lasting from 1 to 14 days. Time-series microarray data were assessed by innovative combination of hierarchical clustering and principal component analysis and validated by real-time RT-PCR. Hierarchical clustering and principal component analysis in agreement distinguished three temporal phases of liver regeneration. We found 359 genes specifically altered during late phase regeneration. Gene enrichment analysis and manual review of microarray data suggested five pathways worth further study: PPAR signalling pathway; lipid metabolism; complement, coagulation and fibrinolytic cascades; ECM remodelling and xenobiotic biotransformation. Microarray findings pertinent for termination phase were substantiated by real-time RT-PCR. In conclusion, transcriptional profiling mapped late phase of liver regeneration beyond 5th day of recovery and revealed 5 pathways specifically acting at this time. Inclusion of longer post-surgery intervals brought improved coverage of regeneration time dynamics and is advisable for further works. Investigation into the workings of suggested pathways
- MeSH
- genetická transkripce MeSH
- hepatektomie MeSH
- játra * metabolismus MeSH
- krysa rodu rattus MeSH
- metabolismus lipidů MeSH
- modely nemocí na zvířatech MeSH
- nemoci jater * genetika metabolismus veterinární MeSH
- potkani Wistar MeSH
- receptory aktivované proliferátory peroxizomů metabolismus MeSH
- regenerace jater * MeSH
- regulace genové exprese MeSH
- transkriptom * MeSH
- zvířata MeSH
- Check Tag
- krysa rodu rattus MeSH
- mužské pohlaví MeSH
- zvířata MeSH
Odhadovat směřování jakéhokoliv vědního oboru je sice tématem velice přitažlivým, nicméně riskantním, a v dnešním pojetí něčím na způsob adrenalinového sportu. Zvláště posouzení rychlosti, kterou se biologické vědy budou pohybovat, může být ošidné, protože se stává stále méně závislou na lidských pozorovacích schopnostech, paměti a zručnosti, tedy na lidských mírách. Stáváme se stále více závislými na technickém pokroku, na tom, v čem nás předčí přístroje. I v genetice můžeme díky nim sledovat neustálé zrychlování, s jakou přibývají naše poznatky. Množí se proto i způsoby pohledu a po dlouhém období klasické genetiky založené na pozorováních fenotypových znaků jsme postupně dospěli až do období nejrůznějších „omics“. Za vrchol a předěl současné genetiky považujeme dokončení stanovení sekvence nukleotidů celého lidského genomu potažmo roky 2000–2003. Dnes máme již k dispozici genomové sekvence celé řady dalších organismů a věnujeme svou pozornost modifikacím, které, aniž by měnily sekvenci samu, dokážou dočasně měnit funkční vlastnosti genetických informací – potlačovat, anebo aktivovat jejich uvolňování. Další intenzivně studovanou oblastí jsou „mezigenové vztahy“, jejich sítivo, a zdá se, že nezbytným směrem našeho dalšího postupu bude návrat k fenotypu, ovšem na úrovni vyplývající ze současných znalostí funkce genetického aparátu. Tuto historickou cestu lze schematicky vyjádřit jako fenom › genom › fenom.
Though we start to speak about postgenomic era, the genomic era has not been finished yet and the structure, function and variability of our genome is being still intensively studied and these studies bring us continually new scientific information – more than we are able to digest. The classical genetics utilized phenotype observation for discovering the function of genetic information and proceeded to the molecular basis represented by nucleic acids. Determination of the nucleotide sequence of the human genome is the top outcome of the effort. At present, the function, regulatory pathways and genome modifications have become principal targets of our research. If we compare variability, it increases in the direction from human genome to transcriptome and to proteom reaching the highest level in phenome. Differences concern not only quantity, but also quality with the exception of genome which is relatively stable and „we hand over to our children what we have inherited from our parents“ - all other levels undergo dynamic changes, and from this point of view are much less stable and under continuous influence of environment. To understand enviromental factors shaping our phenome, a long-term monitoring of our living functions will be necessary and an instrumental approach has to be looked for.
- Klíčová slova
- metylom, fenom, epigenetika, remodelace chromatinu,
- MeSH
- epigeneze genetická MeSH
- genom lidský MeSH
- genom MeSH
- genomika MeSH
- lidé MeSH
- metabolom MeSH
- proteom MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
BACKGROUND: Transcriptome-wide association studies have been successful in identifying candidate susceptibility genes for colorectal cancer (CRC). To strengthen susceptibility gene discovery, we conducted a large transcriptome-wide association study and an alternative splicing transcriptome-wide association study in CRC using improved genetic prediction models and performed in-depth functional investigations. METHODS: We analyzed RNA-sequencing data from normal colon tissues and genotype data from 423 European descendants to build genetic prediction models of gene expression and alternative splicing and evaluated model performance using independent RNA-sequencing data from normal colon tissues of the Genotype-Tissue Expression Project. We applied the verified models to genome-wide association studies (GWAS) summary statistics among 58 131 CRC cases and 67 347 controls of European ancestry to evaluate associations of genetically predicted gene expression and alternative splicing with CRC risk. We performed in vitro functional assays for 3 selected genes in multiple CRC cell lines. RESULTS: We identified 57 putative CRC susceptibility genes, which included the 48 genes from transcriptome-wide association studies and 15 genes from splicing transcriptome-wide association studies, at a Bonferroni-corrected P value less than .05. Of these, 16 genes were not previously implicated in CRC susceptibility, including a gene PDE7B (6q23.3) at locus previously not reported by CRC GWAS. Gene knockdown experiments confirmed the oncogenic roles for 2 unreported genes, TRPS1 and METRNL, and a recently reported gene, C14orf166. CONCLUSION: This study discovered new putative susceptibility genes of CRC and provided novel insights into the biological mechanisms underlying CRC development.
- MeSH
- celogenomová asociační studie MeSH
- genetická predispozice k nemoci MeSH
- jednonukleotidový polymorfismus MeSH
- kolorektální nádory * genetika MeSH
- lidé MeSH
- represorové proteiny genetika MeSH
- RNA MeSH
- transkriptom * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
Recent technological advances have made next-generation sequencing (NGS) a popular and financially accessible technique allowing a broad range of analyses to be done simultaneously. A huge amount of newly generated NGS data, however, require advanced software support to help both in analyzing the data and biologically interpreting the results. In this article, we describe SATrans (Software for Annotation of Transcriptome), a software package providing fast and robust functional annotation of novel sequences obtained from transcriptome sequencing. Moreover, it performs advanced gene ontology analysis of differentially expressed genes, thereby helping to interpret biologically-and in a user-friendly form-the quantitative changes in gene expression. The software is freely available and provides the possibility to work with thousands of sequences using a standard personal computer or notebook running on the Linux operating system.
