Molecular networking has become a key method to visualize and annotate the chemical space in non-targeted mass spectrometry data. We present feature-based molecular networking (FBMN) as an analysis method in the Global Natural Products Social Molecular Networking (GNPS) infrastructure that builds on chromatographic feature detection and alignment tools. FBMN enables quantitative analysis and resolution of isomers, including from ion mobility spectrometry.

• MeSH
• biologické přípravky chemie   MeSH
• databáze faktografické MeSH
• hmotnostní spektrometrie * MeSH
• metabolomika metody   MeSH
• software MeSH
• výpočetní biologie metody   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Research Support, N.I.H., Extramural MeSH
• Research Support, U.S. Gov't, Non-P.H.S. MeSH
• Názvy látek
• biologické přípravky MeSH

In patients with hematological malignancies one of the most substantial findings is the karyotype of bone marrow cells at the time of diagnosis. The detection of clonal chromosome aberrations in diagnostic samples not only confirms a neoplastic or premalignant process but also provides important diagnostic and prognostic information essential for precise disease classification and choice of suitable therapy. Karyotype analysis during the disease course also allows monitoring of the treatment success reflected as well in the revised WHO classification where patients are often classified into the different diagnostic subtypes based on the finding of specific chromosome and/or genetic changes. Recently, also increases the number of advanced treatment approaches that directly or indirectly target the genetic aberrations present in tumor cells. Despite the large development of new sequencing technologies in recent years, cytogenetic analysis supplemented by the molecular cytogenetic methods still remains a very important part of diagnostics of hematological malignancies.

• Klíčová slova
• chromosome aberrations, clonal heterogeneity, conventional cytogenetic analysis, hematological malignancies, karyotype, molecular cytogenetic analysis,
• MeSH
• chromozomální aberace * MeSH
• cytogenetické vyšetření * MeSH
• hematologické nádory * diagnóza   genetika   MeSH
• karyotypizace MeSH
• lidé MeSH
• prognóza MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH

16S-23S rDNA internal transcribed spacer regions (ITS) similarities were determined in 8 Acetobacter and 1 Gluconacetobacter strains. ITS-PCR amplification of the 16S-23S spacers showed 2 products of similar size in 7 strains; only 1 product of similar size was found in the 2 remaining strains. Analysis of the PCR products using restriction endonucleases HaeIII, HpaII and AluI revealed 3 different restriction groups of A. pasteurianus for AluI and HaeIII, and 4 restriction groups for HpaII. ITS nucleotide sequences of all studied strains exhibited a 52-98% similarity.

• MeSH
• Acetobacter klasifikace   genetika   MeSH
• DNA bakterií analýza   MeSH
• Gluconacetobacter klasifikace   genetika   MeSH
• mezerníky ribozomální DNA analýza   MeSH
• molekulární sekvence - údaje MeSH
• polymerázová řetězová reakce metody   MeSH
• restrikční mapování MeSH
• RNA ribozomální 16S genetika   MeSH
• RNA ribozomální 23S genetika   MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Názvy látek
• DNA bakterií MeSH
• mezerníky ribozomální DNA MeSH
• RNA ribozomální 16S MeSH
• RNA ribozomální 23S MeSH

The complete genomes of three Czech isolates VIRUBRA 1/045, VIRUBRA 1/046, and VIRUBRA 1/047 of Potato leafroll virus (PLRV) were sequenced and compared with 13 complete sequences of PLRV isolates available in GenBank. Among the Czech isolates, VIRUBRA 1/046 and 1/047 showed the highest nucleotide (nt) identity (98.7%). PLRV was the most conserved virus in both open reading frames (ORFs) 3 and 4. The most variable regions were ORFs 0 and Rap1. Interestingly, isolate VIRUBRA 1/045 significantly differed from the other two Czech isolates in ORFs 0 and 1. Moreover, we identified mutations in the amino acid (aa) sequences, which were specific for the Czech isolates. Phylogenetic analysis based on ORF0 showed that the Czech isolates could be classified in two of the three groupings of the phylogenetic tree obtained. This is the first report on sequence analysis of the genome sequences of PLRV isolates from the Czech Republic.

• MeSH
• fylogeneze MeSH
• genom virový * MeSH
• Luteoviridae klasifikace   genetika   izolace a purifikace   MeSH
• molekulární sekvence - údaje MeSH
• sekvenční analýza DNA * MeSH
• sekvenční homologie MeSH
• shluková analýza MeSH
• Solanum tuberosum virologie   MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Geografické názvy
• Česká republika MeSH

Molecular dynamics simulations help to understand the complex behavior of molecules. The output of such a simulation describes the trajectories of individual atoms as snapshots of atom positions in time. Many compression schemes were developed to reduce the amount of data needed for storing long trajectories. This is achieved by limiting the precision of coordinates, encoding differences instead of absolute values, dimensionality reduction by principal component analysis, or by using polynomials approximating vertex trajectories. However, compression schemes using actual bonds between atoms have not been utilized to their full potential. Therefore, we developed a lossy compression method that captures the local, mostly rotational movement of atoms with respect to their bonded neighbors and predicts their positions in each frame. This allows full control over the data distortion. In our experiments, the method achieves data rates which are substantially better than the rates achieved by competing methods at the same error level.

• Klíčová slova
• 2010 MSC: 92C40, 68P30, Compression, Encoding, Graph traversal, Molecular dynamics, Molecular simulations, Trajectory,
• MeSH
• algoritmy * MeSH
• analýza hlavních komponent MeSH
• simulace molekulární dynamiky * MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH

Satellite DNA sequences consist of tandemly arranged repetitive units up to thousands nucleotides long in head-to-tail orientation. The evolutionary processes by which satellites arise and evolve include unequal crossing over, gene conversion, transposition and extra chromosomal circular DNA formation. Large blocks of satellite DNA are often observed in heterochromatic regions of chromosomes and are a typical component of centromeric and telomeric regions. Satellite-rich loci may show specific banding patterns and facilitate chromosome identification and analysis of structural chromosome changes. Unlike many other genomes, nuclear genomes of banana (Musa spp.) are poor in satellite DNA and the information on this class of DNA remains limited. The banana cultivars are seed sterile clones originating mostly from natural intra-specific crosses within M. acuminata (A genome) and inter-specific crosses between M. acuminata and M. balbisiana (B genome). Previous studies revealed the closely related nature of the A and B genomes, including similarities in repetitive DNA. In this study we focused on two main banana DNA satellites, which were previously identified in silico. Their genomic organization and molecular diversity was analyzed in a set of nineteen Musa accessions, including representatives of A, B and S (M. schizocarpa) genomes and their inter-specific hybrids. The two DNA satellites showed a high level of sequence conservation within, and a high homology between Musa species. FISH with probes for the satellite DNA sequences, rRNA genes and a single-copy BAC clone 2G17 resulted in characteristic chromosome banding patterns in M. acuminata and M. balbisiana which may aid in determining genomic constitution in interspecific hybrids. In addition to improving the knowledge on Musa satellite DNA, our study increases the number of cytogenetic markers and the number of individual chromosomes, which can be identified in Musa.

• MeSH
• banánovník genetika   MeSH
• chromozomy rostlin MeSH
• diploidie MeSH
• fylogeneze MeSH
• genetická variace MeSH
• genom rostlinný * MeSH
• mapování chromozomů MeSH
• molekulární sekvence - údaje MeSH
• rostlinné geny MeSH
• satelitní DNA * MeSH
• sekvence nukleotidů MeSH
• sekvenční analýza DNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• satelitní DNA * MeSH

A molecular analysis has three major roles in modern oncopathology--as an aid in the differential diagnosis, in molecular monitoring of diseases, and in estimation of the potential prognosis. In this report we review the application of the molecular analysis in a group of patients with mantle cell lymphoma (MCL). We demonstrate that detection of the cyclin D1 mRNA level is a molecular marker in 98% of patients with MCL. Cyclin D1 quantitative monitoring is specific and sensitive for the differential diagnosis and for the molecular monitoring of the disease in the bone marrow. Moreover, the dynamics of cyclin D1 in bone marrow reflects the disease development and it predicts the clinical course. We employed the molecular analysis for a precise quantitative detection of proliferation markers, Ki-67, topoisomerase IIalpha, and TPX2, that are described as effective prognostic factors. Using the molecular approach it is possible to measure the proliferation rate in a reproducible, standard way which is an essential prerequisite for using the proliferation activity as a routine clinical tool. Comparing with immunophenotyping we may conclude that the quantitative PCR-based analysis is a useful, reliable, rapid, reproducible, sensitive and specific method broadening our diagnostic tools in hematopathology. In comparison to interphase FISH in paraffin sections quantitative PCR is less technically demanding and less time-consuming and furthermore it is more sensitive in detecting small changes in the mRNA level. Moreover, quantitative PCR is the only technology which provides precise and reproducible quantitative information about the expression level. Therefore it may be used to demonstrate the decrease or increase of a tumor-specific marker in bone marrow in comparison with a previously aspirated specimen. Thus, it has a powerful potential to monitor the course of the disease in correlation with clinical data.

• MeSH
• cyklin D1 analýza   MeSH
• diagnostické techniky molekulární * MeSH
• diferenciální diagnóza MeSH
• lidé MeSH
• lymfom z plášťových buněk diagnóza   genetika   patologie   MeSH
• messenger RNA analýza   MeSH
• nádorové biomarkery analýza   MeSH
• polymerázová řetězová reakce MeSH
• prognóza MeSH
• reziduální nádor diagnóza   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• přehledy MeSH
• Názvy látek
• cyklin D1 MeSH
• messenger RNA MeSH
• nádorové biomarkery MeSH

The purpose of the paper is to demonstrate the usefulness of techniques of molecular similarity as an alternative method for estimation of both acute toxicity of chemicals and their partition coefficients. The technique of atom pairs was chosen. A series of aliphatic alcohols was treated. Acute toxicity was determined by the express laboratory method as the EC50 (inhibition of movement of the worms Tubifex tubifex). Partition coefficients were determined between oil and gas. The calculated results were sufficiently close to both experimental results and the estimates calculated by a technique of QSAR analysis.

• MeSH
• akutní nemoc MeSH
• alkoholy chemie   toxicita   MeSH
• chemické modely MeSH
• chromatografie plynová metody   normy   MeSH
• lidé MeSH
• molekulární struktura * MeSH
• otrava alkoholem etiologie   MeSH
• počítačová simulace MeSH
• prediktivní hodnota testů MeSH
• regresní analýza MeSH
• reprodukovatelnost výsledků MeSH
• toxikologie metody   normy   MeSH
• Check Tag
• lidé MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• alkoholy MeSH

The diversity of ZYMV isolates was analysed by the biological and molecular characterisation of 11 isolates sampled from cucumber, squash and zucchini between 2001 and 2006 in various localities of Slovakia and Czech Republic. Analysis of the molecular variability targeting three separate genomic regions of the ZYMV genome [P1, P3 and (Cter)NIb-(Nter)CP] revealed a remarkable low level of nucleotide variability between isolates, despite their temporal and spatial distinction. Phylogenetic analysis based on the 5'-terminal part of the CP gene highlighted the close relatedness of Slovak, Czech and other central European isolates. Low level of genetic diversity within central European ZYMV isolates is in contrast to the diversity observed for isolates from other geographical regions, in particular Asia. No evidence of recombination in the ZYMV genome was detected. Sequence comparison between aggressive and moderate ZYMV isolates revealed one amino acid difference in the N-terminal part of the P3 protein, potentially involved in the tolerance breaking.

• MeSH
• Cucurbita virologie   MeSH
• genetická variace * MeSH
• molekulární sekvence - údaje MeSH
• Potyvirus klasifikace   genetika   izolace a purifikace   MeSH
• sekvence aminokyselin MeSH
• sekvenční analýza RNA MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• srovnávací studie MeSH
• Geografické názvy
• Česká republika MeSH
• Slovenská republika MeSH

The optimized molecular structure, vibrational frequencies, corresponding vibrational assignments of 2-[(E)-2-(2-bromophenyl)ethenyl]quinoline-6-carboxylic acid have been investigated experimentally and theoretically using Gaussian09 software package. Potential energy distribution of the normal modes of vibrations was done using GAR2PED program. (1)H NMR chemical shifts calculations were carried out by using B3LYP functional with SDD basis set. The HOMO and LUMO analysis is used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. MEP was performed by the DFT method and the predicted infrared intensities and Raman activities have also been reported. The calculated geometrical parameters are in agreement with that of similar derivatives. The title compound forms a stable complex with PknB as is evident from the binding affinity values and the molecular docking results suggest that the compound might exhibit inhibitory activity against PknB and this may result in development of new anti-tuberculostic agents.

• Klíčová slova
• DFT, FT-IR, FT-Raman, MEP, Molecular docking, Quinoline,
• MeSH
• chinoliny chemie   MeSH
• kvantová teorie * MeSH
• kyseliny karboxylové chemie   MeSH
• molekulární modely MeSH
• molekulární struktura MeSH
• Ramanova spektroskopie metody   MeSH
• simulace molekulového dockingu MeSH
• spektrofotometrie ultrafialová MeSH
• spektroskopie infračervená s Fourierovou transformací metody   MeSH
• statická elektřina MeSH
• Publikační typ
• časopisecké články MeSH
• práce podpořená grantem MeSH
• Názvy látek
• 2-((E)-2-(2-bromophenyl)ethenyl)quinoline-6-carboxylic acid MeSH Prohlížeč
• chinoliny MeSH
• kyseliny karboxylové MeSH