Immunoglobulin light chain amyloidosis (ALA) is a plasma cell dyscrasia characterized by deposition of amyloid fibrils in various organs and tissues. The current paper is devoted to clarify if ALA has a unique gene expression profile and to its pathogenetic argumentation. The meta-analysis of ALA patients vs. healthy donors, monoclonal gammopathy of undetermined significance, smoldering and multiple myeloma patients' cohorts have revealed molecular signature of ALA consists of 256 genes representing mostly ribosomal proteins and immunoglobulin regions. This signature appears pathogenetically supported and elucidates for the first time the role of ribosome dysfunction in ALA. In summary of our findings with literature overview, we hypothesize that ALA development is associated not only with changes in genes, coding amyloidogenic protein itself, but with post-transcriptional disbalance as well. Based on our data analysis in ALA, ribosome machinery is impaired and the affected link mainly involves translational initiation, elongation and co-translational protein folding.

• Klíčová slova
• AL amyloidosis, Gene expression profile, Meta-analysis, Monoclonal gammapaties, Ribosome,
• MeSH
• amyloidóza genetika   MeSH
• geny pro lehké řetězce imunoglobulinů * MeSH
• lidé MeSH
• paraproteinemie genetika   MeSH
• stanovení celkové genové exprese MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• dopisy MeSH
• metaanalýza MeSH
• přehledy MeSH

Hazelnut (Corylus), which has high commercial and nutritional benefits, is an important tree for producing nuts and nut oil consumed as ingredient especially in chocolate. While Corylus avellana L. (Euro-pean hazelnut, Betulaceae) and Corylus colurna L. (Turkish hazelnut, Betulaceae) are the two common hazelnut species in Europe, C. avellana L. (Tombul hazelnut) is grown as the most widespread hazelnut species in Turkey, and C. colurna L., which is the most important genetic resource for hazelnut breeding, exists naturally in Anatolia. We generated the transcriptome data of these two Corylus species and used these data for gene discovery and gene expression profiling. Total RNA from young leaves, flowers (male and female), buds, and husk shoots of C. avellana and C. colurna were used for two different libraries and were sequenced using Illumina HiSeq4000 with 100 bp paired-end reads. The transcriptome data 10.48 and 10.30 Gb of C. avellana and C. colurna, respectively, were assembled into 70,265 and 88,343 unigenes, respectively. These unigenes were functionally annotated using the TRAPID platform. We identified 25,312 and 27,051 simple sequen-ce repeats (SSRs) for C. avellana and C. colurna, respectively. TL1, GMPM1, N, 2MMP, At1g29670, CHIB1 unigenes were selected for validation with qPCR. The first de novo transcriptome data of C. co-lurna were used to compare data of C. avellana of commercial importance. These data constitute a valuable extension of the publicly available transcriptomic resource aimed at breeding, medicinal, and industrial research studies.

• Klíčová slova
• Corylus spp., RNA-seq, de novo, hazelnut, transcriptome,
• MeSH
• líska * genetika   metabolismus   MeSH
• ořechy MeSH
• stanovení celkové genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• Geografické názvy
• Turecko MeSH

Understanding the control of gene expression is critical for our understanding of the relationship between genotype and phenotype. The need for reliable assessment of transcript abundance in biological samples has driven scientists to develop novel technologies such as DNA microarray and RNA-Seq to meet this demand. This review focuses on comparing the two most useful methods for whole transcriptome gene expression profiling. Microarrays are reliable and more cost effective than RNA-Seq for gene expression profiling in model organisms. RNA-Seq will eventually be used more routinely than microarray, but right now the techniques can be complementary to each other. Microarrays will not become obsolete but might be relegated to only a few uses. RNA-Seq clearly has a bright future in bioinformatic data collection.

• MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů metody   MeSH
• sekvenční analýza RNA metody   MeSH
• stanovení celkové genové exprese metody   MeSH
• výpočetní biologie * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• srovnávací studie MeSH

Recent advances in molecular biology and technology have made it possible to monitor the expression levels of virtually all genes simultaneously. As the tools for gene expression profiling have become more widely available, the number of investigators applying this technology in hypertension research, as in other fields of biomedical research, has grown rapidly. At the same time, numerous articles have been published that discuss the technical aspects of gene profiling and its promise for advancing research on the pathogenesis and treatment of multiple clinical disorders. However, much of the research carried out with gene expression profiling has been of a correlational or descriptive nature, and the true value of this technology is unclear. Despite the initial wave of enthusiasm for gene expression profiling, its actual utility for studying multifactorial disorders like hypertension remains to be established. In this review, we offer a critical perspective on the use of gene expression profiling in hypertension research and discuss some emerging strategies for taking this technology beyond the limits of correlational and descriptive studies.

• MeSH
• genetická vazba MeSH
• geneticky modifikovaná zvířata MeSH
• genomika MeSH
• hypertenze genetika   metabolismus   MeSH
• inbrední kmeny zvířat MeSH
• kardiovaskulární nemoci genetika   MeSH
• kinetika MeSH
• krysa rodu Rattus MeSH
• lidé MeSH
• myši MeSH
• stanovení celkové genové exprese * MeSH
• výzkum MeSH
• zvířata MeSH
• Check Tag
• krysa rodu Rattus MeSH
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Research Support, U.S. Gov't, P.H.S. MeSH

In this review, we present an overview of transcriptomic responses to chemical exposures in a variety of fish species. We have discussed the use of several molecular approaches such as northern blotting, differential display reverse transcription-polymerase chain reaction (DDRT-PCR), suppression subtractive hybridization (SSH), real time quantitative PCR (RT-qPCR), microarrays, and next-generation sequencing (NGS) for measuring gene expression. These techniques have been mainly used to measure the toxic effects of single compounds or simple mixtures in laboratory conditions. In addition, only few studies have been conducted to examine the biological significance of differentially expressed gene sets following chemical exposure. Therefore, future studies should focus more under field conditions using a multidisciplinary approach (genomics, proteomics and metabolomics) to understand the synergetic effects of multiple environmental stressors and to determine the functional significance of differentially expressed genes. Nevertheless, recent developments in NGS technologies and decreasing costs of sequencing holds the promise to uncover the complexity of anthropogenic impacts and biological effects in wild fish populations.

• Klíčová slova
• Aquatic toxicology, Ecotoxicology, Environmental monitoring, Pollution, Toxicants, Toxicogenomics,
• MeSH
• chemické látky znečišťující vodu toxicita   MeSH
• kvantitativní polymerázová řetězová reakce MeSH
• ryby genetika   MeSH
• stanovení celkové genové exprese * MeSH
• subtraktivní hybridizace MeSH
• toxikologie metody   MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• Názvy látek
• chemické látky znečišťující vodu MeSH

Cardiovascular defects are one of the most common congenital defects associated with maternal diabetes. Based on whole embryo gene expression microarray analysis, 11 genes were chosen for temporal expression analysis of diabetes-exposed hearts. The majority of the selected genes were deregulated in diabetes-exposed hearts compared to our controls at E13.5, E14.5, and E18.5. We showed increased hypoxia and HIF-1α protein levels in diabetes-exposed hearts at E10.5, which is a critical time point for the induction of developmental defects associated with diabetic embryopathy. Additionally, we found increased cardiac Vegfa levels that might trigger developmental abnormalities associated with diabetic embryopathy. Our results show that maternal diabetes affects the temporal expression pattern of gene encoding molecules involved in heart development and tissue remodelling and that these molecules might affect heart maturation processes and thus, the final outcome of diabetic pregnancies.

• Klíčová slova
• Cardiovascular defects, Diabetic embryopathy, Gene expression, Vascular endothelial growth factor A (VEGF-A),
• MeSH
• embryo savčí MeSH
• experimentální diabetes mellitus genetika   metabolismus   MeSH
• faktor 1 indukovatelný hypoxií - podjednotka alfa metabolismus   MeSH
• hypoxie genetika   metabolismus   MeSH
• inbrední kmeny myší MeSH
• messenger RNA metabolismus   MeSH
• myokard metabolismus   MeSH
• srdce embryologie   MeSH
• stanovení celkové genové exprese MeSH
• těhotenství při diabetu genetika   metabolismus   MeSH
• těhotenství MeSH
• vaskulární endoteliální růstový faktor A genetika   MeSH
• vývojová regulace genové exprese * MeSH
• zvířata MeSH
• Check Tag
• těhotenství MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• faktor 1 indukovatelný hypoxií - podjednotka alfa MeSH
• Hif1a protein, mouse MeSH Prohlížeč
• messenger RNA MeSH
• vascular endothelial growth factor A, mouse MeSH Prohlížeč
• vaskulární endoteliální růstový faktor A MeSH

Hepatocellular carcinoma (HCC) remains a highly prevalent and deadly disease, being among the top causes of cancer-related deaths worldwide. Despite the fact that the liver is the major site of biotransformation, studies on drug metabolizing enzymes in HCC are scarce. It is known that malignant transformation of hepatocytes leads to a significant alteration of their metabolic functions and overall deregulation of gene expression. Advanced stages of the disease are thus frequently associated with liver failure, and severe alteration of drug metabolism. However, the impact of dysregulation of metabolic enzymes on therapeutic efficacy and toxicity in HCC patients is largely unknown. Here we demonstrate a significant down-regulation in European Caucasian patients of cytochromes P450 (CYPs), the major xenobiotic-metabolizing enzymes, in HCC tumour samples as compared to their surrounding non-cancerous (reference) tissue. Moreover, we report for the first time the association of the unique CYP profiles with specific transcriptome changes, and interesting correlations with expression levels of nuclear receptors and with the histological grade of the tumours. Integrated analysis has suggested certain co-expression profiles of CYPs with lncRNAs that need to be further characterized. Patients with large tumours with down-regulated CYPs could be more vulnerable to drug toxicity; on the other hand, such tumours would eliminate drugs more slowly and should be more sensitive to pharmacotherapy (except in the case of pro-drugs where activation is necessary).

• Klíčová slova
• CYP, Cytochrome P450, Drug metabolism, Gene expression, Hepatocellular carcinoma, Non-coding RNA,
• MeSH
• dospělí MeSH
• hepatocelulární karcinom enzymologie   patologie   MeSH
• hepatocyty metabolismus   MeSH
• játra metabolismus   MeSH
• kohortové studie MeSH
• lidé středního věku MeSH
• lidé MeSH
• metabolická inaktivace genetika   MeSH
• nádory jater enzymologie   patologie   MeSH
• receptory cytoplazmatické a nukleární genetika   metabolismus   MeSH
• regulace genové exprese enzymů * MeSH
• senioři MeSH
• stanovení celkové genové exprese MeSH
• stupeň nádoru MeSH
• systém (enzymů) cytochromů P-450 genetika   MeSH
• transkriptom * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• senioři MeSH
• ženské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• receptory cytoplazmatické a nukleární MeSH
• systém (enzymů) cytochromů P-450 MeSH

BACKGROUND: Yeast infections are often connected with formation of biofilms that are extremely difficult to eradicate. An excellent model system for deciphering multifactorial determinants of yeast biofilm development is the colony biofilm, composed of surface ("aerial") and invasive ("root") cells. While surface cells have been partially analyzed before, we know little about invasive root cells. In particular, information on the metabolic, chemical and morphogenetic properties of invasive versus surface cells is lacking. In this study, we used a new strategy to isolate invasive cells from agar and extracellular matrix, and employed it to perform genome wide expression profiling and biochemical analyses of surface and invasive cells. RESULTS: RNA sequencing revealed expression differences in 1245 genes with high statistical significance, indicating large genetically regulated metabolic differences between surface and invasive cells. Functional annotation analyses implicated genes involved in stress defense, peroxisomal fatty acid β-oxidation, autophagy, protein degradation, storage compound metabolism and meiosis as being important in surface cells. In contrast, numerous genes with functions in nutrient transport and diverse synthetic metabolic reactions, including genes involved in ribosome biogenesis, biosynthesis and translation, were found to be important in invasive cells. Variation in gene expression correlated significantly with cell-type specific processes such as autophagy and storage compound accumulation as identified by microscopic and biochemical analyses. Expression profiling also provided indications of cell-specific regulations. Subsequent knockout strain analyses identified Gip2p, a regulatory subunit of type 1 protein phosphatase Glc7p, to be essential for glycogen accumulation in surface cells. CONCLUSIONS: This is the first study reporting genome wide differences between surface and invasive cells of yeast colony biofilms. New findings show that surface and invasive cells display very different physiology, adapting to different conditions in different colony areas and contributing to development and survival of the colony biofilm as a whole. Notably, surface and invasive cells of colony biofilms differ significantly from upper and lower cells of smooth colonies adapted to plentiful laboratory conditions.

• Klíčová slova
• Cell differentiation, Colony biofilms, Invasive cell subpopulation, Regulation of glycogen metabolism, Saccharomyces cerevisiae, Transcriptomics,
• MeSH
• biofilmy * MeSH
• metabolické sítě a dráhy MeSH
• regulace genové exprese u hub * MeSH
• Saccharomyces cerevisiae - proteiny genetika   metabolismus   MeSH
• Saccharomyces cerevisiae genetika   fyziologie   MeSH
• stanovení celkové genové exprese MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• Saccharomyces cerevisiae - proteiny MeSH

BACKGROUND: Optimization of the immunoglobulin (Ig) yield in bovine milk used as therapeutic immune milk or whey for the prevention of Clostridium difficile-associated diarrhea in humans is of great importance to improve the economic efficiency of production. Individual dairy cows have diverse immune responses upon vaccination, resulting in a variable Ig yield in blood and milk. Therefore, it is advisable to pre-select cows with the best ability to produce and secrete high yields of specific Igs. RESULTS: The gene expression profile of pbMEC (primary bovine mammary epithelial cells), challenged with the gram-positive, non-mastitis, pathogen Clostridium difficile showed distinct and significant differences in the gene expression of effector molecules of the innate immune system. A number of genes were identified that could possibly serve as molecular biomarkers to differentiate high responder cows from low responder cows. These identified genes play key roles in the promotion of innate immunity. CONCLUSION: Using a gene expression profiling approach, we showed that upon others, especially the gene expression of the pro-inflammatory cytokines was altered between the high and low responder cows. Those genes are indicated as potential molecular biomarkers in the pre-selection of cows that are able to secrete high immunoglobulin yields in milk.

• Klíčová slova
• Clostridium difficile-associated diarrhea, Innate immunity, Microfluidic gene expression profiling, Molecular biomarkers, Primary bovine mammary epithelial cells,
• MeSH
• biologické markery * MeSH
• Clostridioides difficile imunologie   MeSH
• cytokiny metabolismus   MeSH
• epitelové buňky imunologie   MeSH
• imunoglobuliny genetika   metabolismus   MeSH
• mléčné žlázy zvířat imunologie   MeSH
• mléko imunologie   MeSH
• přirozená imunita MeSH
• skot genetika   imunologie   MeSH
• stanovení celkové genové exprese veterinární   MeSH
• zvířata MeSH
• Check Tag
• skot genetika   imunologie   MeSH
• ženské pohlaví MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• Názvy látek
• biologické markery * MeSH
• cytokiny MeSH
• imunoglobuliny MeSH

Using array technology that allows the simultaneous detection of gene expression of hundreds of genes, four patients with chronic myeloid leukemia (CML) were investigated at diagnosis and after starting administration of hydroxyurea. To detect the gene expression of peripheral blood mononuclears and granulocytes Human Cancer cDNA Array (CLONTECH) with 588 gene probes was used. Gene expression mononuclear and granulocyte profiles of patients at diagnosis were compared with the control profiles. The significant expression changes observed in most patients seemed to be important. Increased expression of c-jun N-terminal kinase 2 (JNK2), integrin alpha E, MMP-8, MMP-9 was detected in both fractions of most patients. In some samples PCNA, HDGF, MAPK p38, CD59 increased expressions were found. Significant down-regulation of expression in patients was detected in genes CDK4 inhibitor A, PURA, notch1 in mononuclears; STAT2, STAT5, RAR-alpha, MCL-1, junB, caspase 4 in granulocytes; CDK6, GADD153, ERBB-3, cadherin 5 in both fractions. Expression profiles detected in patients at diagnosis did not differ markedly from those after one-week treatment with hydroxyurea. Only in a few genes were significant changes after hydroxyurea administration observed and inter-individual expression differences were rather common.

• MeSH
• chronická myeloidní leukemie farmakoterapie   genetika   MeSH
• chronická nemoc MeSH
• dospělí MeSH
• genetická variace MeSH
• hydroxymočovina farmakologie   terapeutické užití   MeSH
• lidé středního věku MeSH
• lidé MeSH
• nádorové proteiny biosyntéza   genetika   MeSH
• protinádorové antimetabolity farmakologie   terapeutické užití   MeSH
• regulace genové exprese u nádorů účinky léků   MeSH
• reprodukovatelnost výsledků MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů * MeSH
• stanovení celkové genové exprese * MeSH
• Check Tag
• dospělí MeSH
• lidé středního věku MeSH
• lidé MeSH
• mužské pohlaví MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• hydroxymočovina MeSH
• nádorové proteiny MeSH
• protinádorové antimetabolity MeSH