The occurrence of GC clusters in Saccharomyces spp. and related yeasts was examined to clarify their association with the stability of intact mitochondrial genome. Abundance of nonspecific or specific GC clusters in these species decreases with phylogenetic distance from S. cerevisiae. Their number but not the number of replication origins correlates with the ability to form respiration-deficient mutants induced by ethidium bromide. This effect is not associated with the nuclear background since the cybrids having identical nuclei and mitochondria from different species gave similar results. In contrast to grand genomes, the presence of GC clusters in rho- mutants does not play any role in ethidium bromide induced mtDNA loss. The most plausible explanation for mitotically lost petite mtDNA seems to be dilution during the distribution.

• MeSH
• DNA fungální chemie   účinky léků   MeSH
• ethidium farmakologie   MeSH
• GC bohatá sekvence * účinky léků   MeSH
• genotyp MeSH
• mitochondriální DNA chemie   MeSH
• mutace MeSH
• restrikční mapování MeSH
• Saccharomyces cerevisiae účinky léků   genetika   MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA fungální MeSH
• ethidium MeSH
• mitochondriální DNA MeSH

The study of fish cytogenetics has been impeded by the inability to produce G-bands that could assign chromosomes to their homologous pairs. Thus, the majority of karyotypes published have been estimated based on morphological similarities of chromosomes. The reason why chromosome G-banding does not work in fish remains elusive. However, the recent increase in the number of fish genomes assembled to the chromosome level provides a way to analyse this issue. We have developed a Python tool to visualize and quantify GC percentage (GC%) of both repeats and unique DNA along chromosomes using a non-overlapping sliding window approach. Our tool profiles GC% and simultaneously plots the proportion of repeats (rep%) in a color scale (or vice versa). Hence, it is possible to assess the contribution of repeats to the total GC%. The main differences are the GC% of repeats homogenizing the overall GC% along fish chromosomes and a greater range of GC% scattered along fish chromosomes. This may explain the inability to produce G-banding in fish. We also show an occasional banding pattern along the chromosomes in some fish that probably cannot be detected with traditional qualitative cytogenetic methods.

• Klíčová slova
• AT/GC heterogeneity, GC-profile, chromosome banding, fish cytogenetics, repeats organization,
• MeSH
• genom * MeSH
• Gorilla gorilla klasifikace   genetika   MeSH
• karyotypizace metody   MeSH
• kočky MeSH
• mapování chromozomů metody   statistika a číselné údaje   MeSH
• pruhování chromozomů MeSH
• ryby klasifikace   genetika   MeSH
• software * MeSH
• tandemové repetitivní sekvence MeSH
• zastoupení bazí * MeSH
• zvířata MeSH
• Check Tag
• kočky MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

BACKGROUND AND AIMS: Studies in the carnivorous family Lentibulariaceae in the last years resulted in the discovery of the smallest plant genomes and an unusual pattern of genomic GC content evolution. However, scarcity of genomic data in other carnivorous clades still prevents a generalization of the observed patterns. Here the aim was to fill this gap by mapping genome evolution in the second largest carnivorous family, Droseraceae, where this evolution may be affected by chromosomal holokinetism in Drosera METHODS: The genome size and genomic GC content of 71 Droseraceae species were measured by flow cytometry. A dated phylogeny was constructed, and the evolution of both genomic parameters and their relationship to species climatic niches were tested using phylogeny-based statistics. KEY RESULTS: The 2C genome size of Droseraceae varied between 488 and 10 927 Mbp, and the GC content ranged between 37·1 and 44·7 %. The genome sizes and genomic GC content of carnivorous and holocentric species did not differ from those of their non-carnivorous and monocentric relatives. The genomic GC content positively correlated with genome size and annual temperature fluctuations. The genome size and chromosome numbers were inversely correlated in the Australian clade of Drosera CONCLUSIONS: Our results indicate that neither carnivory (nutrient scarcity) nor the holokinetism have a prominent effect on size and DNA base composition of Droseraceae genomes. However, the holokinetic drive seems to affect karyotype evolution in one of the major clades of Drosera Our survey confirmed that the evolution of GC content is tightly connected with the evolution of genome size and also with environmental conditions.

• Klíčová slova
• DNA base composition, DNA content, Droseraceae, GC content, carnivorous plants, flow cytometry, genome size evolution, holocentric chromosomes, holokinetic chromosomes,
• MeSH
• biologická evoluce * MeSH
• chromozomy rostlin genetika   MeSH
• Droseraceae genetika   MeSH
• fylogeneze MeSH
• genetická variace genetika   MeSH
• genom rostlinný genetika   MeSH
• masožravci MeSH
• zastoupení bazí genetika   MeSH
• Publikační typ
• časopisecké články MeSH

• MeSH
• alfa-globuliny analýza   genetika   MeSH
• fenotyp MeSH
• lidé MeSH
• protein vázající vitamin D MeSH
• rodokmen MeSH
• transportní proteiny analýza   genetika   MeSH
• vitamin D analýza   genetika   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• anglický abstrakt MeSH
• časopisecké články MeSH
• Názvy látek
• alfa-globuliny MeSH
• protein vázající vitamin D MeSH
• transportní proteiny MeSH
• vitamin D MeSH

Liquid transportation fuels in the middle distillate range contain thousands of hydrocarbons making the predictions and calculations of properties from composition a challenging process. We present a new approach of hydrogen content determination by comprehensive two-dimensional gas chromatography with flame ionization detector (GC×GC-FID) using a weighted average method. GC×GC-FID hydrogen determination precision was excellent (0.005 wt% repeatability). The method accuracy was evaluated by high-resolution nuclear magnetic resonance (NMR) technique, which is non-biased, measures the H signal directly and was independently validated by controls in the current study. The hydrogen content (in the range of 12.72-15.54 wt%) in 28 fuel samples were determined using GC×GC-FID. Results were within ± 2% of those obtained via NMR. Owing to the fact that NMR is accepted as an accurate technique for hydrogen content determination, the GC×GC method proposed in this study can be considered precise and accurate.

• Klíčová slova
• Aviation jet fuel, Diesel, GC×GC, Hydrogen content, NMR,
• Publikační typ
• časopisecké články MeSH

Genome sequencing now permits direct visual representation, at any scale, of GC heterogeneity along the chromosomes of several higher eukaryotes. Plots can be easily obtained from the chromosomal sequences, yet sequence releases of mammalian or plant chromosomes still tend to use small scales or window sizes that obscure important large-scale compositional features. To faithfully reveal, at one glance, the compositional variation at a given scale, we have devised a simple scheme that combines line plots with color-coded shading of the regions underneath the plots. The scheme can be applied to different eukaryotic genomes to facilitate their comparison, as illustrated here for a sample of chromosomes chosen from seven selected species. As a complement to a previously published compact view of isochores in the human genome sequence, we include here an analogous map for the recently sequenced mouse genome, and discuss the contribution of repetitive DNA to the GC variation along the plots. Supplementary information, including a database of color-coded GC profiles for all recently sequenced eukaryotes and the program draw_chromosomes_gc.pl used to obtain them, are available at.

• MeSH
• Anopheles genetika   MeSH
• Arabidopsis genetika   MeSH
• Caenorhabditis elegans genetika   MeSH
• chromozomy genetika   MeSH
• DNA genetika   MeSH
• Drosophila melanogaster genetika   MeSH
• eukaryotické buňky metabolismus   MeSH
• genom MeSH
• isochory genetika   MeSH
• lidé MeSH
• myši MeSH
• repetitivní sekvence nukleových kyselin genetika   MeSH
• Saccharomyces cerevisiae genetika   MeSH
• software MeSH
• zastoupení bazí genetika   MeSH
• zvířata MeSH
• Check Tag
• lidé MeSH
• myši MeSH
• zvířata MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• DNA MeSH
• isochory MeSH

Genomic DNA base composition (GC content) is predicted to significantly affect genome functioning and species ecology. Although several hypotheses have been put forward to address the biological impact of GC content variation in microbial and vertebrate organisms, the biological significance of GC content diversity in plants remains unclear because of a lack of sufficiently robust genomic data. Using flow cytometry, we report genomic GC contents for 239 species representing 70 of 78 monocot families and compare them with genomic characters, a suite of life history traits and climatic niche data using phylogeny-based statistics. GC content of monocots varied between 33.6% and 48.9%, with several groups exceeding the GC content known for any other vascular plant group, highlighting their unusual genome architecture and organization. GC content showed a quadratic relationship with genome size, with the decreases in GC content in larger genomes possibly being a consequence of the higher biochemical costs of GC base synthesis. Dramatic decreases in GC content were observed in species with holocentric chromosomes, whereas increased GC content was documented in species able to grow in seasonally cold and/or dry climates, possibly indicating an advantage of GC-rich DNA during cell freezing and desiccation. We also show that genomic adaptations associated with changing GC content might have played a significant role in the evolution of the Earth's contemporary biota, such as the rise of grass-dominated biomes during the mid-Tertiary. One of the major selective advantages of GC-rich DNA is hypothesized to be facilitating more complex gene regulation.

• Klíčová slova
• Poaceae, genome size evolution, geographical stratification, phylogenetic regression, plant genome,
• MeSH
• aklimatizace genetika   MeSH
• chromozomy rostlin genetika   MeSH
• DNA rostlinná chemie   genetika   MeSH
• ekosystém MeSH
• fylogeneze MeSH
• genetická variace MeSH
• genom rostlinný MeSH
• lipnicovité chemie   klasifikace   genetika   MeSH
• Magnoliopsida chemie   klasifikace   genetika   MeSH
• molekulární evoluce * MeSH
• zastoupení bazí MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

• Knowledge of the phylogenetic pattern and biological relevance of the base composition of large eukaryotic genomes (including those of plants) is poor. With the use of flow cytometry (FCM), the amount of available data on the guanine + cytosine (GC) content of plants has nearly doubled in the last decade. However, skepticism exists concerning the reliability of the method because of uncertainty in some input parameters. • Here, we tested the reliability of FCM for estimating GC content by comparison with the biochemical method of DNA temperature melting analysis (TMA). We conducted measurements in 14 plant species with a maximum currently known GC content range (33.6-47.5% as measured by FCM). We also compared the estimations of the GC content by FCM with genomic sequences in 11 Oryza species. • FCM and TMA data exhibited a high degree of correspondence which remained stable over the relatively wide range of binding lengths (3.39-4.09) assumed for the base-specific dye used. A high correlation was also observed between FCM results and the sequence data in Oryza, although the latter GC contents were consistently lower. • Reliable estimates of the genomic base composition in plants by FCM are comparable with estimates obtained using other methods, and so wider application of FCM in future plant genomic research, although it would pose a challenge, would be supported by these findings.

• MeSH
• Bacteria genetika   MeSH
• denaturace nukleových kyselin MeSH
• DNA rostlinná genetika   MeSH
• druhová specificita MeSH
• genom rostlinný genetika   MeSH
• průtoková cytometrie metody   MeSH
• reprodukovatelnost výsledků MeSH
• sekvence nukleotidů MeSH
• teplota MeSH
• zastoupení bazí genetika   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

• Klíčová slova
• GC content, Lentibulariaceae, carnivorous plants, flow cytometry, genome miniaturization, genome size evolution, genomic DNA base composition, genomic models,
• MeSH
• délka genomu * MeSH
• DNA rostlinná genetika   MeSH
• genom rostlinný * MeSH
• Magnoliopsida klasifikace   genetika   MeSH
• molekulární evoluce * MeSH
• zastoupení bazí MeSH
• Publikační typ
• dopisy MeSH
• práce podpořená grantem MeSH
• Názvy látek
• DNA rostlinná MeSH

Comprehensive two-dimensional gas chromatography coupled with mass spectrometry (GC × GC-MS) has great potential for analyses of complicated mixtures and sample matrices, due to its separation power and possible high resolution. The second component of the measurement results, the mass spectra, is reproducible. However, the reproducibility of two-dimensional chromatography is affected by many factors and makes the evaluation of long-term experiments or cross-laboratory collaborations complicated. This paper presents a new open-source data alignment tool to tackle the problem of retention time shifts - with 5 different algorithms implemented: BiPACE 2D, DISCO, MSort, PAM, and TNT-DA, along with Pearson's correlation and dot product as optional methods for mass spectra comparison. The implemented data alignment algorithms and their variations were tested on real samples to demonstrate the functionality of the presented tool. The suitability of each implemented algorithm for significantly/non-significantly shifted data was discussed on the basis of the results obtained. For the evaluation of the "goodness" of the alignment, Kolmogorov-Smirnov test values were calculated, and comparison graphs were generated. The DA_2DChrom is available online with its documentation, fully open-sourced, and the user can use the tool without the need of uploading their data to external third-party servers.

• Klíčová slova
• Data alignment algorithm, Data alignment automation, GC × GC–TOF real samples, Human scent,
• Publikační typ
• časopisecké články MeSH