MOTIVATION: Satellite DNA makes up significant portion of many eukaryotic genomes, yet it is relatively poorly characterized even in extensively sequenced species. This is, in part, due to methodological limitations of traditional methods of satellite repeat analysis, which are based on multiple alignments of monomer sequences. Therefore, we employed an alternative, alignment-free, approach utilizing k-mer frequency statistics, which is in principle more suitable for analyzing large sets of satellite repeat data, including sequence reads from next generation sequencing technologies. RESULTS: k-mer frequency spectra were determined for two sets of rice centromeric satellite CentO sequences, including 454 reads from ChIP-sequencing of CENH3-bound DNA (7.6 Mb) and the whole genome Sanger sequencing reads (5.8 Mb). k-mer frequencies were used to identify the most conserved sequence regions and to reconstruct consensus sequences of complete monomers. Reconstructed consensus sequences as well as the assessment of overall divergence of k-mer spectra revealed high similarity of the two datasets, suggesting that CentO sequences associated with functional centromeres (CENH3-bound) do not significantly differ from the total population of CentO, which includes both centromeric and pericentromeric repeat arrays. On the other hand, considerable differences were revealed when these methods were used for comparison of CentO populations between individual chromosomes of the rice genome assembly, demonstrating preferential sequence homogenization of the clusters within the same chromosome. k-mer frequencies were also successfully used to identify and characterize smRNAs derived from CentO repeats.

• MeSH
• centromera genetika   MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• molekulární sekvence - údaje MeSH
• rýže (rod) genetika   MeSH
• satelitní DNA genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH

Cyanobacteria are physiologically and morphologically diverse photosynthetic microbes that play major roles in the carbon and nitrogen cycles of the biosphere. Recently, they have gained attention as potential platforms for the production of biofuels and other renewable chemicals. Many cyanobacteria were characterized morphologically prior to the advent of genome sequencing. Here, we catalog cyanobacterial ultrastructure within the context of genomic sequence information, including high-magnification transmission electron micrographs that represent the diversity in cyanobacterial morphology. We place the image data in the context of tabulated protein domains-which are the structural, functional, and evolutionary units of proteins-from the 126 cyanobacterial genomes comprising the CyanoGEBA dataset. In particular, we identify the correspondence between ultrastructure and the occurrence of genes encoding protein domains related to the formation of cyanobacterial inclusions. This compilation of images and genome-level domain occurrence will prove useful for a variety of analyses of cyanobacterial sequence data and provides a guidebook to morphological features.

• MeSH
• bakteriální proteiny klasifikace   genetika   metabolismus   MeSH
• fylogeneze MeSH
• genom bakteriální genetika   MeSH
• genomika * MeSH
• proteinové domény MeSH
• sekvenční analýza DNA MeSH
• sinice * genetika   ultrastruktura   MeSH
• transmisní elektronová mikroskopie MeSH
• výpočetní biologie MeSH
• Publikační typ
• časopisecké články MeSH
• přehledy MeSH
• srovnávací studie MeSH

A nanopore-based devices are extremely sensitive analytical techniques, which uses the electrophoretic translocation of molecules in solution through a nano-scale pores. The nanopores, which mimic the functions of natural ion channels, seems to be the promissing tool for future fast and low-cost DNA sequencing. However, some difficulties in generating usable sequence data have to be solved. In this article the nanopores were reviewed. In the first part the development of nanopore technique was described and the ubiquitous presence of nanopores in living cells was highlighted. Next, the most important part of the principles of nanopore analysis was described, and the knowledges about biological and solid-state nanopores were summarized. Also the pros and cons of both kinds of nanopores and different approaches designed to circumvent the issues were mentioned.

• Klíčová slova
• biopóry, solid-state nanopóry,
• MeSH
• hemolyziny MeSH
• nanopóry * MeSH
• sekvenční analýza DNA * metody   přístrojové vybavení   MeSH
• Publikační typ
• práce podpořená grantem MeSH
• přehledy MeSH

Cíl studie : Stanovit trendy a potencionální prognostický význam změn hladin apoptotické (aDNA) a genomické DNA (gDNA) u pacientů, u nichž inzult různého charakteru vedl k selhávání vitálních funkcí. Typ studie: Prospektivní otevřená studie. Název a sídlo pracoviště:Klinika anesteziologie a resuscitace a Chirurgická klinika 3. LF UK a FNKV, Praha; Ústav farmakologie 3. LF UK, Praha. Materiál a metody:Do studie byla zařazeno 94 kriticky nemocných. Vzorky krve k analýze byly odebírány v den přijetí a potom 3. a 5. den hospitalizace. U každého pacienta byla sledována základní diagnóza, věk a pohlaví, pří- jmové APACHE II skóre a orgánová dysfunkce; 3. a 5. den byla hodnocena metodikou SOFA délka hospitalizace ve dnech, přežití či úmrtí, z ukazatelů zánětu C-reaktivní protein a počet leukocytů. Analýza byla provedena na sekvenátoru (ABI Prism 377) s užitím originální fenolové extrakční metody. Získané hodnoty plazmy pacientů byly porovnávány s normou získanou z plazmy 86 zdravých dobrovolníků (norma aDNA a gDNA = 100%). Výsledky:Hladina volné aDNA po zátěži ovlivňuje celkovou hladinu volné DNA zásadním způsobem. Její navýše- ní v hodnotě mediánu je 16,3násobně vyšší než u gDNA. V trendu dalších 4 dnů vykazovala v celé hodnocené skupině snížení hladin, gDNA naopak zvýšení. Rozdíl v průběhu trendů i obě kvality DNA hodnocené proti normě byly na hladině statistické významnosti p < 0,001. Byly zjištěny statisticky významná korelace mezi hladinou aDNA v době přijetí a mortalitou nemocných. Závěr:U kriticky nemocných dochází bezprostředně po inzultu k výraznému zvýšení volné aDNA v plazmě, která je v dalším průběhu i ukazatelem přežití nemocných (p < 0,05).

Objective: To establish the trends and prognostic value of plasma levels of the free apoptotic (aDNA) and geno- mic DNA (gDNA) in patients with failure of vital functions. Type of study: Prospective observational study. Setting: University Dept. of Anaesthesiology/CCM and Dept. of Surgery, Charles University, 3rd School of Medici- ne, Prague. Material and Methods : 94 critically ill patientts were evaluated. The blood samples for DNA analysis were taken on the day of admission, the third and fifth day of hospital stay. The following data were collected: ICU admission diagnosis, age and gender, APACHE II, SOFA, ICU stay in days, ICU survival, CRP and WBC count. The analy- sis was done on a sequencer (ABI PRISM 377) using of the original phenol extraction method. The results were correlated to the plasma free DNA levels of 86 healthy volunteers (normal value = 100%). Results:The contribution of aDNA to the total plasma DNA in the critically ill was ~16fold greater than the contri- bution of gDNA. Apoptotic DNA levels were highest on the day of admission and declined thereafter (P < 0.001), whilst the opposite was true for gDNA (P < 0.001) The difference in trends and the aDNA and gDNA levels in cor- relation to normal levels was found statistically significant (P < 0.001). Apoptotic DNA on the day of admission sig- nificantly differs in survivors and non-survivors (P < 0.05). Conclusion:The free apoptotic DNA plasma level on admission could be a predictor of mortality in critical illness.

• MeSH
• apoptóza MeSH
• biochemická analýza krve metody   přístrojové vybavení   statistika a číselné údaje   MeSH
• C-reaktivní protein MeSH
• DNA MeSH
• finanční podpora výzkumu jako téma MeSH
• genom MeSH
• kritický stav ošetřování   terapie   MeSH
• leukocyty MeSH
• péče o pacienty v kritickém stavu metody   MeSH
• přehledová literatura jako téma MeSH
• prognóza MeSH
• Publikační typ
• srovnávací studie MeSH

Freshwater fauna of ancient lakes frequently contain endemic taxa thought to have originated during the long existence of these lakes, yet uncertainties remain as to whether they represent distinct genetic lineages with respect to more widespread relatives and to the relative roles of isolation and dispersal in their evolution. Phylogenetic analyses of sequence variation at nuclear and mitochondrial genes were used to examine these issues for the freshwater fish genus Barbus in two European ancient lake systems on the Balkan Peninsula. The nuclear and mitochondrial data yielded concordant phylogeographic patterns though incomplete sorting of nuclear haplotypes between some mitochondrial clades was detected. The distributions of two currently recognized species investigated here do not match the distributions of evolutionary lineages revealed by phylogenetic analyses. The Prespa barbel, Barbus prespensis, is not endemic to the lakes Prespa as previously thought but is instead found to be widespread in the south-eastern Adriatic Sea basin, with a distribution largely corresponding to the basin of the now extinct Lake Maliq historically connected with Lake Prespa. On the other hand, a cryptic phylogenetic subdivision in a widespread species, B. rebeli, was discovered to be more distant from B. rebeli than from other Barbus species and to be endemic to the system of connected lakes Ohrid and Shkodra. The division coincides with the hydrogeographical boundary delimiting distributions of other freshwater fishes, and we suggest that this newly discovered evolutionary lineage represents a distinct species. These findings support the emerging pattern that endemic taxa have evolved not through isolation of individual lakes, but in systems of currently and historically interconnected lakes and their wider basins.

• MeSH
• buněčné jádro genetika   MeSH
• Cyprinidae klasifikace   genetika   MeSH
• fylogeneze MeSH
• genetická variace MeSH
• haplotypy MeSH
• mitochondriální DNA genetika   MeSH
• modely genetické MeSH
• molekulární evoluce MeSH
• populační genetika MeSH
• pravděpodobnostní funkce MeSH
• sekvenční analýza DNA MeSH
• sladká voda MeSH
• tok genů MeSH
• zeměpis MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Albánie MeSH

DNA cruciforms play an important role in the regulation of natural processes involving DNA. These structures are formed by inverted repeats, and their stability is enhanced by DNA supercoiling. Cruciform structures are fundamentally important for a wide range of biological processes, including replication, regulation of gene expression, nucleosome structure and recombination. They also have been implicated in the evolution and development of diseases including cancer, Werner's syndrome and others.Cruciform structures are targets for many architectural and regulatory proteins, such as histones H1 and H5, topoisomerase IIβ, HMG proteins, HU, p53, the proto-oncogene protein DEK and others. A number of DNA-binding proteins, such as the HMGB-box family members, Rad54, BRCA1 protein, as well as PARP-1 polymerase, possess weak sequence specific DNA binding yet bind preferentially to cruciform structures. Some of these proteins are, in fact, capable of inducing the formation of cruciform structures upon DNA binding. In this article, we review the protein families that are involved in interacting with and regulating cruciform structures, including (a) the junction-resolving enzymes, (b) DNA repair proteins and transcription factors, (c) proteins involved in replication and (d) chromatin-associated proteins. The prevalence of cruciform structures and their roles in protein interactions, epigenetic regulation and the maintenance of cell homeostasis are also discussed.

• MeSH
• DNA vazebné proteiny chemie   metabolismus   MeSH
• DNA chemie   metabolismus   ultrastruktura   MeSH
• konformace nukleové kyseliny MeSH
• konformace proteinů MeSH
• molekulární sekvence - údaje MeSH
• regulace genové exprese MeSH
• replikace DNA MeSH
• sekvence nukleotidů MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH

The sequences of 10 conservative regions (CR) of minicircles of 6 selected isolates of freshwater fish trypanosomes have typical organization of this region with high degree of sequence conservation. The comparison with CRs of other trypanosomatids showed that freshwater fish trypanosomes represent a compact separate group within the genus Trypanosoma. The alignment of all sequences obtained revealed, however, the existence of 2 types of CRs in sequenced minicircles, with the differences concentrated in a short region. Taxonomic consequences of these results are discussed.

• MeSH
• kinetoplastová DNA genetika   MeSH
• konzervovaná sekvence genetika   MeSH
• molekulární sekvence - údaje MeSH
• polymorfismus délky restrikčních fragmentů MeSH
• ryby parazitologie   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sladká voda MeSH
• Trypanosoma genetika   MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

In early studies of empirical structure-activity relationships, monodentate Pt(II) complexes were considered to be biologically inactive. Examples of such inactive monodentate Pt(II) compounds are [PtCl(dien)]+ (dien=diethylenetriamine) and [PtCl(NH3)3]+. DNA is considered the major biological target of platinum compounds. Thus, monodentate DNA binding of Pt(II) compounds was previously expected to display insignificant biological effects because it was assumed to affect DNA conformation and downstream cellular processes markedly less than the cross-links of bifunctional Pt(II) complexes. More recently it was shown that some monodentate Pt(II) complexes do exhibit biological effects; the active monodentate Pt(II) complexes commonly feature bulkier amine ligands than the hitherto used dien or NH(3) groups. We were therefore interested in determining whether a simple but marked enhancement of the bulkiness of the dien ligand in monodentate [Pt(NO3)(dien)]+ by multiple methylation of this ligand affects the early phases in which platinum compounds exert their biological activity. More specifically, the goals of this study, performed in cell-free media, were to determine how the modification of DNA duplexes by methylated analogues of [Pt(NO3)(dien)]+ affects their energetics and how the alterations of this biophysical parameter are reflected by the recognition of these duplexes by DNA polymerases and the DNA repair system. We have found that the impact of the methylation of [Pt(NO3)(dien)]+ on the biophysical properties of DNA (thermodynamic, thermal, and conformational properties) and its biochemical processes (DNA polymerization and the repair of DNA adducts) is remarkable. Hence, we conclude that monodentate DNA binding of Pt(II) compounds may considerably affect the biophysical properties of DNA and consequently downstream cellular processes as a result of a large increase in the bulkiness of the nonleaving ligands in this class of metal complex.

• MeSH
• DNA-dependentní DNA-polymerasy chemie   MeSH
• DNA chemie   MeSH
• kalorimetrie MeSH
• konformace nukleové kyseliny MeSH
• lidé MeSH
• metylace MeSH
• molekulární sekvence - údaje MeSH
• molekulární struktura MeSH
• oprava DNA genetika   MeSH
• organoplatinové sloučeniny chemická syntéza   chemie   MeSH
• sekvence nukleotidů MeSH
• vazebná místa MeSH
• vztahy mezi strukturou a aktivitou MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• práce podpořená grantem MeSH

Satellite DNAs (satDNA) are tandemly arrayed repeated sequences largely present in eukaryotic genomes, which play important roles in genome evolution and function, and therefore, their analysis is vital. Here, we describe the isolation of a novel satellite DNA family (PMSat) from the rodent Peromyscus eremicus (Cricetidae, Rodentia), which is located in pericentromeric regions and exhibits a typical satellite DNA genome organization. Orthologous PMSat sequences were isolated and characterized from three species belonging to Cricetidae: Cricetus cricetus, Phodopus sungorus and Microtus arvalis. In these species, PMSat is highly conserved, with the absence of fixed species-specific mutations. Strikingly, different numbers of copies of this sequence were found among the species, suggesting evolution by copy number fluctuation. Repeat units of PMSat were also found in the Peromyscus maniculatus bairdii BioProject, but our results suggest that these repeat units are from genome regions outside the pericentromere. The remarkably high evolutionary sequence conservation along with the preservation of a few numbers of copies of this sequence in the analyzed genomes may suggest functional significance but a different sequence nature/organization. Our data highlight that repeats are difficult to analyze due to the limited tools available to dissect genomes and the fact that assemblies do not cover regions of constitutive heterochromatin.

• MeSH
• druhová specificita MeSH
• fylogeneze MeSH
• fyzikální mapování chromozomů MeSH
• genom * MeSH
• genová dávka * MeSH
• křeček rodu Peromyscus genetika   MeSH
• molekulární evoluce * MeSH
• molekulární sekvence - údaje MeSH
• počítačová simulace MeSH
• restrikční mapování MeSH
• satelitní DNA genetika   izolace a purifikace   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• sekvenční seřazení MeSH
• Southernův blotting MeSH
• zvířata MeSH
• Check Tag
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

DNA containing a sequence that generates a local curvature exhibits a pronounced retardation in electrophoretic mobility. Various theoretical models have been proposed to explain relationship between DNA structural features and migration anomaly. Here, we studied the capacity of 15 static wedge-bending models to predict electrophoretic behavior of 69 satellite monomers derived from four divergent families. All monomers exhibited retarded mobility in PAGE corresponding to retardation factors ranging 1.02-1.54. The curvature varied both within and across the groups and correlated with the number, position, and lengths of A-tracts. Two dinucleotide models provided strong correlation between gel mobility and curvature prediction; two trinucleotide models were satisfactory while remaining dinucleotide models provided intermediate results with reliable prediction for subsets of sequences only. In some cases, similarly shaped molecules exhibited relatively large differences in mobility and vice versa. Generally less accurate predictions were obtained in groups containing less homogeneous sequences possessing distinct structural features. In conclusion, relatively universal theoretical models were identified suitable for the analysis of natural sequences known to harbor relatively moderate curvature. These models could be potentially applied to genome wide studies. However, in silico predictions should be viewed in context of experimental measurement of intrinsic DNA curvature.

• MeSH
• chemické modely MeSH
• DNA rostlinná chemie   MeSH
• molekulární sekvence - údaje MeSH
• nativní elektroforéza na polyakrylamidovém gelu metody   normy   MeSH
• počítačová simulace MeSH
• reprodukovatelnost výsledků MeSH
• retardační test metody   normy   MeSH
• satelitní DNA chemie   MeSH
• sekvence nukleotidů MeSH
• sekvenční seřazení MeSH
• tabák chemie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH