• MeSH
• biologické vědy MeSH
• genetika MeSH

• Konspekt
• Obecná genetika. Obecná cytogenetika. Evoluce
• NLK Obory
• genetika, lékařská genetika

We proposed here a sequence-based approach predicting some microorganisms as possible sources of autoantigen-related molecular mimicry concerning Idiopathic Pulmonary Arterial Hypertension (IPAH) and related hypertension mostly accompanying autoimmune diseases and AIDS (APAH). This approach (SPECIES_VALENCE) processes the database occurrences of linear autoepitope-related short Dense Quasi-Pattern Sequences (DQPA) generated based on identities of important autoantigenic sequences. The corresponding enumeration comprises two types of statistical evaluations performed in each of eight proposed models. Based on this enumeration, we selected nine microorganisms, whereas revaluation of the obtained scoring values restricted Pseudomonas aeruginosa, Aspergillus fumigatus and the two co-infecting herpes viruses (Epstein Barr virus and cytomegalovirus) as most favourable. The results are discussed in terms of (a) the validity of increased DQPA occurrence in functionally correlated sequences, (b) the possible mechanisms leading to autoantibody response, (c) selected additional pathogenic effects of predicted microorganisms and (d) possible effects of cross-reactivities and immune tolerance.

• MeSH
• druhová specificita MeSH
• epitopy chemie   genetika   imunologie   MeSH
• familiární plicní arteriální hypertenze genetika   imunologie   mikrobiologie   MeSH
• konzervovaná sekvence MeSH
• lidé MeSH
• molekulární mimikry genetika   imunologie   MeSH
• molekulární sekvence - údaje MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza proteinů metody   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH

Here we introduce the Protein Cutter (http:// biochemie.upol.cz/software/proteincutter), a web application for the prediction of results of protein digestion by proteolytic enzymes, which is accessible over the Internet network. In the beginning, previous and current approaches for protein sequencing are summarized. This includes the use of dinitrofluorobenzene and substituted isothiocyanate reagents as well as mass-spectrometry-based strategies and translation of genomic sequences. The following text characterizes bioinformatics as a modern scientific discipline, which solves problems arising from the management and analysis of biological data. The most important nucleotide and amino acid sequence databases are described together with the databases of DNA and protein structures. The program Protein Cutter, which is described in detail with respect to its design and technology, allows predicting peptide sequences generated by proteolytic digestion of a protein (represented by a user-entered amino acid or coding nucleotide sequence). In addition to other comparable applications, Protein Cutter offers more complex information calculated from amino acid sequences (i.e. molecular mass, amino acid composition, isoelectric point, hydropathicity index etc.), it works with nucleotide sequences upon automatic translation, it is open and friendly for user-entered cutting rules and provides more options for the filtration and sorting of results.

• MeSH
• databáze proteinů * MeSH
• genomika MeSH
• hmotnostní spektrometrie * metody   přístrojové vybavení   využití   MeSH
• matematické výpočty počítačové MeSH
• molekulární sekvence - údaje * MeSH
• peptidové mapování * MeSH
• polymerázová řetězová reakce metody   využití   MeSH
• proteasy * MeSH
• proteomika MeSH
• sekvence aminokyselin * MeSH
• sekvenční analýza proteinů * MeSH
• software * MeSH
• systémy řízení databází * MeSH
• výpočetní biologie MeSH
• Publikační typ
• práce podpořená grantem MeSH

Experimental cDNA sequence determinations lag behind in silico gene structure predictions in some recently sequenced genomes. This may be due in part to low transcript abundance and/or the severely spatio-temporarily restricted expression pattern of some genes. Here we characterize the predicted repressed gene of Arabidopsis thaliana (At4g21130) that encodes a homologue of the Arabidopsis U3-55K-like protein (At4g05410) and of the U3-55K (RNU3IP2, Rrp9p) proteins from other eukaryotes. In man and yeast, U3-55K is involved in the processing of the pre-ribosomal RNA. Here we show that treatment with inhibitors of histone deacetylases (trichostatin A, sodium butyrate) or DNA methyltransferases (5-aza-2'-deoxycytidine) induces a low but distinct level of mRNA from the repressed Arabidopsis At4g21130 locus, which can be detected by RT-PCR amplification. Direct sequencing of PCR products reveals the open reading frame that differs, in part, from the hypothetical one and encodes a seven-WD-repeat protein highly conserved when compared to U3-55K proteins from various eukaryotic species. This suggests the conservation of its function. The described approach may help to determine the nucleotide sequences of transcripts from predicted genes with a low level of expression.

• MeSH
• Arabidopsis genetika   metabolismus   MeSH
• financování organizované MeSH
• histondeacetylasy metabolismus   MeSH
• inhibitory enzymů farmakologie   MeSH
• inhibitory histondeacetylas MeSH
• klonování DNA MeSH
• komplementární DNA genetika   MeSH
• lokus kvantitativního znaku genetika   MeSH
• molekulární sekvence - údaje MeSH
• posttranskripční úpravy RNA genetika   MeSH
• proteiny huseníčku genetika   metabolismus   MeSH
• regulace genové exprese u rostlin fyziologie   účinky léků   MeSH
• ribonukleoproteiny malé jadérkové genetika   metabolismus   MeSH
• RNA ribozomální metabolismus   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza DNA metody   MeSH
• sekvenční analýza proteinů metody   MeSH
• sekvenční homologie aminokyselin MeSH

BACKGROUND: The first systematic study of small non-coding RNAs (sRNA, ncRNA) in Streptomyces is presented. Except for a few exceptions, the Streptomyces sRNAs, as well as the sRNAs in other genera of the Actinomyces group, have remained unstudied. This study was based on sequence conservation in intergenic regions of Streptomyces, localization of transcription termination factors, and genomic arrangement of genes flanking the predicted sRNAs. RESULTS: Thirty-two potential sRNAs in Streptomyces were predicted. Of these, expression of 20 was detected by microarrays and RT-PCR. The prediction was validated by a structure based computational approach. Two predicted sRNAs were found to be terminated by transcription termination factors different from the Rho-independent terminators. One predicted sRNA was identified computationally with high probability as a Streptomyces 6S RNA. Out of the 32 predicted sRNAs, 24 were found to be structurally dissimilar from known sRNAs. CONCLUSION: Streptomyces is the largest genus of Actinomyces, whose sRNAs have not been studied. The Actinomyces is a group of bacterial species with unique genomes and phenotypes. Therefore, in Actinomyces, new unique bacterial sRNAs may be identified. The sequence and structural dissimilarity of the predicted Streptomyces sRNAs demonstrated by this study serve as the first evidence of the uniqueness of Actinomyces sRNAs.

• MeSH
• algoritmy MeSH
• bakteriální RNA genetika   chemie   MeSH
• druhová specificita MeSH
• financování organizované MeSH
• genom bakteriální MeSH
• intergenová DNA MeSH
• konformace nukleové kyseliny MeSH
• molekulární modely MeSH
• nekódující RNA genetika   chemie   MeSH
• polymerázová řetězová reakce s reverzní transkripcí MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza hybridizací s uspořádaným souborem oligonukleotidů MeSH
• Streptomyces coelicolor genetika   MeSH
• Streptomyces genetika   MeSH
• terminátorové oblasti (genetika) MeSH
• výpočetní biologie MeSH

The complete nucleotide sequence (1448 nucleotides) of RNA 2 of a Czechoslovakian isolate TpM-34 of red clover necrotic mosaic virus (RCNMV-TpM-34) has been determined. The sequence contained one major open reading frame (ORF) with the potential to encode a protein of 326 amino acids (Mr 35755), designated P2. The nucleotide sequence of RNA 2 of RCNMV-TpM-34 and the previously published sequence of RNA 2 of an Australian isolate of the virus (RCNMV-Aus) were 83% identical and there was 80% amino acid sequence identity between the P2 proteins of these isolates. However the N-terminal two-thirds of the P2 proteins shared a higher degree of similarity than the C-terminal regions which were predicted to have a more flexible structure. An ORF in the 3' portion of RNA 2 of RCNMV-Aus, which could encode a protein of Mr 5000, was not present in RNA 2 of RCNMV-TpM-34. RNAs 1 and 2 of RCNMV-TpM-34 and RCNMV-Aus are bilaterally compatible.

• MeSH
• konformace proteinů MeSH
• molekulární sekvence - údaje MeSH
• otevřené čtecí rámce MeSH
• RNA virová genetika   MeSH
• sekvence aminokyselin MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• virové proteiny genetika   MeSH
• viry mozaiky genetika   izolace a purifikace   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Československo MeSH

Mutations in the first nucleotide of exons (E(+1)) mostly affect pre-mRNA splicing when found in AG-dependent 3' splice sites, whereas AG-independent splice sites are more resistant. The AG-dependency, however, may be difficult to assess just from primary sequence data as it depends on the quality of the polypyrimidine tract. For this reason, in silico prediction tools are commonly used to score 3' splice sites. In this study, we have assessed the ability of sequence features and in silico prediction tools to discriminate between the splicing-affecting and non-affecting E(+1) variants. For this purpose, we newly tested 16 substitutions in vitro and derived other variants from literature. Surprisingly, we found that in the presence of the substituting nucleotide, the quality of the polypyrimidine tract alone was not conclusive about its splicing fate. Rather, it was the identity of the substituting nucleotide that markedly influenced it. Among the computational tools tested, the best performance was achieved using the Maximum Entropy Model and Position-Specific Scoring Matrix. As a result of this study, we have now established preliminary discriminative cut-off values showing sensitivity up to 95% and specificity up to 90%. This is expected to improve our ability to detect splicing-affecting variants in a clinical genetic setting.

• MeSH
• agamaglobulinemie genetika   MeSH
• bodová mutace * MeSH
• exony MeSH
• genetické nemoci vázané na chromozom X genetika   MeSH
• HeLa buňky MeSH
• lidé MeSH
• místa sestřihu RNA * MeSH
• modely genetické MeSH
• molekulární sekvence - údaje MeSH
• počítačová simulace MeSH
• sekvenční analýza DNA MeSH
• sestřih RNA MeSH
• software * MeSH
• tyrosinkinasy genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• hodnotící studie MeSH
• práce podpořená grantem MeSH

The complete nucleotide sequences of RNA1 and RNA2 of the Holandský červený strain of currant latent virus (CuLV) were determined using next-generation sequencing. The RNA1 is predicted to encode a polyprotein 2124 amino acid long with RdRp motifs. The RNA2 is predicted to encode a polyprotein 957 amino acid long with homology to the capsid protein of apple latent spherical virus and cherry rasp leaf virus. Phylogenetic analysis confirms that CuLV is a new distinct member of the genus Cheravirus.

• MeSH
• fylogeneze MeSH
• genom virový * MeSH
• molekulární sekvence - údaje MeSH
• Ribes virologie   MeSH
• RNA virová genetika   MeSH
• RNA-viry genetika   izolace a purifikace   MeSH
• rostlinné viry genetika   izolace a purifikace   MeSH
• sekvenční analýza DNA MeSH
• sekvenční homologie MeSH
• shluková analýza MeSH
• vysoce účinné nukleotidové sekvenování MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

SUMMARY: We present the cpPredictor webserver that implements a novel template-based method for prediction of secondary structure of RNA. The method outperforms available prediction methods as it uses RNA structures of related molecules, either predicted or experimentally identified, as structural templates. The server aims at three major tasks: i) prediction of RNA secondary structures that are difficult to predict by available methods, ii) characterization of uncharacterized RNAs as compatible or incompatible with a chosen template structure and iii) an identification of the most relevant structure among different candidate structures of a single RNA ambiguously predicted by available methods. The web server is accompanied with a comprehensive documentation. AVAILABILITY AND IMPLEMENTATION: The web server is freely available at http://cppredictor.elixir-czech.cz/. The source code of the cpPredictor algorithm is freely available from the webserver under the Apache License, Version 2.0.

• MeSH
• algoritmy MeSH
• internet MeSH
• konformace nukleové kyseliny * MeSH
• RNA MeSH
• sekundární struktura proteinů MeSH
• sekvenční analýza RNA MeSH
• software * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Genome predictions based on selected genes would be a very welcome approach for taxonomic studies. We analyzed three genes, recN, flaA, and ftsY, for determining if these genes are useful tools for systematic analyses in the genus Anoxybacillus. The genes encoding a DNA repair and genetic recombination protein (recN), the flagellin protein (flaA), and GTPase signal docking protein (ftsY) were sequenced for ten Anoxybacillus species. The sequence comparisons revealed that recN sequence similarities range between 61% and 99% in the genus Anoxybacillus. Comparisons to other bacterial recN genes indicated that levels of similarity did not differ from the levels within genus Anoxybacillus. These data showed that recN is not a useful marker for the genus Anoxybacillus. A 550-600-bp region of the flagellin gene was amplified for all Anoxybacillus strains except for Anoxybacillus contaminans. The sequence similarity of flaA gene varies between 61% and 76%. Comparisons to other bacterial flagellin genes obtained from GenBank (Bacillus, Pectinatus, Proteus, and Vibrio) indicated that the levels of similarity were lower (3-42%). Based on these data, we concluded that the variability in this single gene makes it a particularly useful marker. Another housekeeping gene ftsY suggested to reflect the G+C (mol/mol) content of whole genome was analyzed for Anoxybacillus strains. A mean difference of 1.4% was observed between the G+C content of the gene ftsY and the G+C content of the whole genome. These results showed that the gene ftsY can be used to represent whole G+C content of the Anoxybacillus species.

• MeSH
• Anoxybacillus chemie   klasifikace   genetika   izolace a purifikace   MeSH
• bakteriální proteiny chemie   genetika   MeSH
• flagelin chemie   genetika   MeSH
• fylogeneze MeSH
• molekulární sekvence - údaje MeSH
• receptory cytoplazmatické a nukleární chemie   genetika   MeSH
• restrikční enzymy chemie   genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční homologie nukleových kyselin MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH