The complete mitochondrial genome of the recently discovered beetle family Iberobaeniidae is described and compared with known coleopteran mitogenomes. The mitochondrial sequence was obtained by shotgun metagenomic sequencing using the Illumina Miseq technology and resulted in an average coverage of 130 × and a minimum coverage of 35×. The mitochondrial genome of Iberobaeniidae includes 13 protein-coding genes, 2 rRNAs, 22 tRNAs genes, and 1 putative control region, and showed a unique rearrangement of protein-coding genes. This is the first rearrangement affecting the relative position of protein-coding and ribosomal genes reported for the order Coleoptera.
- MeSH
- Coleoptera genetics MeSH
- Phylogeny * MeSH
- Genome, Insect MeSH
- Genome, Mitochondrial * MeSH
- Genomics MeSH
- DNA, Mitochondrial MeSH
- Genes, Mitochondrial * MeSH
- Gene Order MeSH
- Sequence Analysis, DNA * MeSH
- Animals MeSH
- Check Tag
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
The product of the retinoblastoma susceptibility gene, pRb, is a negative regulator of cell growth. It functions by regulating the activity of transcription factors. Rb represses some genes by sequestering or inactivating the positive transcription factor E2F and seems to activate some others by interacting with factors like Sp1 or ATF-2. However, there are only a few examples of genes which are positively regulated by pRb. In order to find out if there are common mechanisms for promoter regulation by pRb, we were interested to identify more genes which are either stimulated or repressed by pRb. Using the method of differential display (DDRT-PCR) in combination with nuclear run-on analyses we were able to detect a number of genes which are upregulated by ectopic expression of the Rb gene in Rb-deficient mammary carcinoma cells. We could demonstrate not only stimulation of the endogenous mutant Rb gene but also positive regulation of genes coding for diverse classes of proteins, including the endothelial growth regulator endothelin-1 and the proteoglycans versican and PG40. As a second approach, we investigated gene expression in cell lines established from Rb deficient heterozygous and homozygous knockout mouse embryos and normal mice. We have identified several genes the expression of which correlates positively or negatively with the presence of Rb. These data provide further evidence for pRb being a master regulator of a complex network of gene activities defining the difference between dividing and resting or differentiated cells.
- MeSH
- Endothelins biosynthesis genetics MeSH
- Genes, Retinoblastoma physiology MeSH
- Humans MeSH
- Molecular Sequence Data MeSH
- Mice, Knockout MeSH
- Mice MeSH
- Tumor Cells, Cultured MeSH
- Polymerase Chain Reaction methods MeSH
- Proteoglycans biosynthesis genetics MeSH
- Gene Expression Regulation * MeSH
- Retinoblastoma Protein genetics physiology MeSH
- Base Sequence MeSH
- Transfection MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Mice MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
Cíl práce: U izolátů S. aureus z klinického materiálu zjistit přítomnost genů kódujících důležitý faktor virulence, Pantonův-Valentinův leukocidin. Materiál a metodiky: Kmeny S. aureus, zaslané v období 2004–2006 z mikrobiologických laboratoří ČR z klinického materiálů pacientů, především s kožním onemocněním. Kmeny byly diagnostikovány konvenčními metodami fenotypizace i molekulárně-biologickými postupy, především metodou polymerázové řetězové reakce. Výsledky: V souboru 1336 kmenů S. aureus bylo zjištěno 108 kmenů (tj. 8,1 %), které měly v DNA geny kódující Pantonův-Valentinův leukocidin. Pouze 11 z nich byly kmeny MRSA. Závěr: Kmeny S. aureus s produkcí Pantonova-Valentinova leukocidinu hrají podstatnou roli v závažných, především kožních infekcích. V NRL pro stafylokoky SZÚ-CEM jsme schopni zjistit produkci tohoto toxinu v optimálních podmínkách do dvou dnů.
Study objectives: To detect the genes encoding an important virulence factor, Panton-Valentine leukocidin, in S. aureus isolates from clinical specimens. Material and Methods: S. aureus strains from clinical specimens, mainly from patients with skin diseases, referred by microbiological laboratories of the Czech Republic. The strains were identified by both conventional phenotyping methods and molecular biological procedures, in particular polymerase chain reaction. Results: Altogether 108 (8.1 %) of 1336 S. aureus strains had the genes encoding Panton-Valentine leukocidin in DNA. Only 11 of these strains were MRSA. Conclusions: S. aureus strains producing Panton-Valentine leukocidin play an important role in serious infections, particularly of the skin. NRL for Staphylococci, National Institute of Public Health, Centre of Epidemiology and Microbiology, is able to detect the production of this toxin, under optimal conditions, within two days.
- MeSH
- Drug Resistance, Bacterial genetics immunology MeSH
- Bacterial Proteins genetics immunology isolation & purification MeSH
- Phenotype MeSH
- Genetic Code genetics MeSH
- Clinical Laboratory Techniques utilization MeSH
- Humans MeSH
- Polymerase Chain Reaction methods utilization MeSH
- Staphylococcus aureus genetics immunology MeSH
- Check Tag
- Humans MeSH
... Outline -- Part 1 Genes Part 5 The Nucleus -- 1 Genes are DNA 1 1 9 Chromosomes 545 -- 2 The interrupted ... ... gene 33 20 Nucleosomes 571 -- 3 The content of the genome 51 21 Promoters and enhancers 597 -- 4 Clusters ... ... and repeats 85 22 Activating transcription 631 -- Part 2 Proteins 23 Controlling chromatin structure ... ... 135 26 Immune diversity 751 -- 7 Using the genetic code 8 Protein localization 167 195 Part 6 Cells ... ... -- Part 3 Gene expression 27 Protein trafficking 28 Signal transduction 787 811 -- 9 Transcription 241 ...
xxi, 1027 stran : ilustrace, tabulky ; 28 cm
Peroxizómy predstavujú subcelulárne štruktúry kategórie mikroteliesok, prítomné tak u jednobunkových eukryo- tov, ako aj u väčšiny živočíšnych a rastlinných buniek. Peroxizómy obsahujú približne 50 enzýmov s vysokou variabilitou v ich spektre a množstve, v závislosti od nutričných podmienok a vplyvu xenobiotík tzv. peroxizómo- vých proliferátorov. Nové peroxizómy vznikajú delením existujúcich štruktúr po importe proteínov alebo formova- ním de novo. K biogenéze peroxizómov sú potrebné cytosólové bielkoviny, membránové importné proteíny a typické zoskupenie aminokyselín v polypeptidových reťazcoch, ktoré má charakter topogénneho signálu - PTS (peroxisomal targeting signal). Funkciu PTS zabezpečuje C-koncový tripeptid zložený spravidla z aminokyselín serínu, lyzínu a leucínu (SKL tripeptid - PTS1) alebo N-koncový PTS2 charakterizovaný konsenzom sekvencie AMK Arg-Leu/Ile- -XXXXX-Gln/His-Leu (X-ľubovoľná AMK). Pre biogenézu peroxizómov sú nevyhnutné membránové proteíny – peroxíny kódované PEX génmi. Tieto proteíny fungujú vo forme homo a heterodimérov, patria medzi ATP transportéry a podmieňujú funkčnosť peroxizómovej biogenézy. Expresia jadrových génov je regulovaná jadrovými receptormi, ktoré sú aktivované peroxizómovými proliferátormi (PPAR – peroxisome proliferations activated receptors). C-doména týchto receptorov sa viaže na špecifickú oblasť promótorov peroxizómových génov (PPREs – peroxisomal proliferation response elements) obsahujúcu najčastejšie tandemové usporiadanie sekvencie TGACCT. Polynenasýtené mastné kyseliny sú účinnými prirodzenými regulátormi peroxizómovej génovej expresie.
Peroxisomes represent cell organelles present in both unicellular eukaryotes and most of the animal and plant cells. Peroxisomes contain about 50 enzymes with high variability in spectrum and quantity, depending on nutritional conditions and presence of some xenobiotics (peroxisome proliferations). New peroxisomes are formed after the protein intake by splitting of the existing peroxisomes or de novo. Biogenesis of peroxisomes requires cytosolic proteins, membrane transporting proteins, and the typical groups of amino acids in polypeptide chains, which have the character of topogenic signal - PTS (peroxisomal targeting signal). PTS signal is based on the terminal tripeptide, formed usually by amino acids serine, lysine and leucine (SKL tripeptide – PTS1) or by the N-terminal PTS2 with amino acid sequence Arg-Leu/Ile-XXXXX-Gln/His-Leu (X is any amino acid). Biogenesis of peroxisomes requires also special membrane proteins – peroxins, which are coded by PEX genes. These proteins act as homo- or heterodimes, they belong to ATP transports, and determine efficacy of the peroxisome biogenesis. Nuclear gene expression is regulated by nuclear receptors activated by peroxisome proliferators (PPAR– proxisome proliferators activated receptors). C-domain of the receptor binds to the specific region of the promotors of peroxisome genes (PPREs-Peroxisomal proliferator response elements), often with tandem arrangement of sequences TGACCT. Polyunsaturated fatty acids represent the effective natural regulator of the peroxisomal gene expression.
Nonsense mutations turn a coding (sense) codon into an in-frame stop codon that is assumed to result in a truncated protein product. Thus, nonsense substitutions are the hallmark of pseudogenes and are used to identify them. Here we show that in-frame stop codons within bacterial protein-coding genes are widespread. Their evolutionary conservation suggests that many of them are not pseudogenes, since they maintain dN/dS values (ratios of substitution rates at non-synonymous and synonymous sites) significantly lower than 1 (this is a signature of purifying selection in protein-coding regions). We also found that double substitutions in codons-where an intermediate step is a nonsense substitution-show a higher rate of evolution compared to null models, indicating that a stop codon was introduced and then changed back to sense via positive selection. This further supports the notion that nonsense substitutions in bacteria are relatively common and do not necessarily cause pseudogenization. In-frame stop codons may be an important mechanism of regulation: Such codons are likely to cause a substantial decrease of protein expression levels.
- MeSH
- Bacteria classification genetics MeSH
- Bacterial Proteins classification genetics MeSH
- Point Mutation MeSH
- Phylogeny MeSH
- Models, Genetic MeSH
- Evolution, Molecular MeSH
- Codon, Nonsense * MeSH
- Open Reading Frames genetics MeSH
- Prokaryotic Cells metabolism MeSH
- Pseudogenes genetics MeSH
- Base Sequence MeSH
- Sequence Homology, Nucleic Acid MeSH
- Selection, Genetic MeSH
- Codon, Terminator genetics MeSH
- Publication type
- Journal Article MeSH
Přestavba chromatinu je spojena se základními buněčnými funkcemi jako např. replikací DNA, rekombinací, opravami DNA a transkripce genů. Na přestavbě chromatinu se podffí chromatin remodelující komplexy závislé na ATP a proteinové komplexy, které kovalentně modi%kují histony. Vrozené mutace genů, jejichž produkty se účastní přestavby chromatinu, způsobují závažná vývojová onemocnění a mohou zvyšovat riziko vzniku nádorového onemocnění. Somatické mutace nebo translokace těchto genů jsou spojeny s vývojem některých nádorů. Mechanizmy přestavby chromatinu mohou být proto cílem nové strategie nádorové terapie.
Chromatin remodeling is engaged in basic cell functions as DNA replication, recombination, DNA repair and transcription of genes. Chromatin is remodeled by ATP-dependent chromatin remodeling complexes and protein complexes covalently modifying histones. Germ-line mutations of the genes coding fot proteins which participate in chromatin remodeling cause severe developmental diseases and they increase a risk of cancer development. Somatic mutations and translocations of such genes are associated with cancer development of certain tumors. Chromatin remodeling mechanisms can thus be targeted by special strategy of cancer therapy.
... Product of a Gene 33 -- Proteins Are Trans-acting, but Sites on DNA Are Os-acting 35 Summary 36 -- 3.2 ... ... of Sizes 43 -- Some DNA Sequences Code for More Than One Protein 45 -- How Did Interrupted Genes Evolve ... ... 53 Summary 53 -- Genes Code for Proteins 23 -- Introduction 24 -- A Gene Codes for a Single Polypeptide ... ... The Chloroplast Genome Codes for Many Proteins and RNAs 71 -- ??*? ... ... Code for Multifunction Proteins 716 -- ??? ...
xvii, 892 s. : il.
- MeSH
- DNA genetics MeSH
- Genetic Phenomena MeSH
- Genome MeSH
- Genes physiology MeSH
- Proteins genetics MeSH
- RNA genetics MeSH
- Publication type
- Monograph MeSH
- Conspectus
- Obecná genetika. Obecná cytogenetika. Evoluce
- NML Fields
- genetika, lékařská genetika
Two strains of an unidentified perithecial ascomycete with a dactylaria-like anamorph and another morphologically similar strain of a dactylaria-like fungus were collected on decaying wood submerged in freshwater. To study their phylogenetic relationships we (i) combined sequence data from the nuclear small and large subunits ribosomal DNA (nc18S and nc28S) and the second largest subunit of RNA polymerase II (RPB2) for a multigene phylogenetic analysis and (ii) used sequences of the internal transcribed spacer region (ITS) of the rRNA operon for a species-level analysis. The new genus Pleurotheciella is described for two new species, Pla. rivularia and Pla. centenaria, with nonstromatic perithecia, unitunicate asci, persistent paraphyses and hyaline, septate ascospores and dactylaria-like anamorphs characterized by holoblastic, denticulate conidiogenesis, subhyaline conidiophores and hyaline, septate conidia. Based on morphological and molecular data, Pleurotheciella is closely related to the genera Pleurothecium and Sterigmatobotrys. A key to the three genera and the known species is provided. In the three-gene inferred phylogeny, these genera grouped as a sister clade to the Savoryellales within a robust clade of uncertain higher rank affiliation. Phylogenetic study of the 12 strains that represent Pleurothecium recurvatum revealed four that grouped apart from the core of the species. Two of these strains, which form a monophyletic well supported clade in both phylogenies and share similar morphological characteristics, are described as a new species, Pleurothecium semifecundum.
- MeSH
- Ascomycota classification cytology genetics isolation & purification MeSH
- DNA, Fungal chemistry genetics MeSH
- Wood microbiology MeSH
- Fungal Proteins genetics MeSH
- Phylogeny * MeSH
- DNA, Ribosomal Spacer chemistry genetics MeSH
- Molecular Sequence Data MeSH
- Multilocus Sequence Typing MeSH
- Mycological Typing Techniques MeSH
- DNA, Ribosomal chemistry genetics MeSH
- RNA Polymerase II genetics MeSH
- Base Sequence MeSH
- Sequence Analysis, DNA MeSH
- Fresh Water MeSH
- Spores, Fungal classification cytology genetics isolation & purification MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
