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Helena Škutková

Brno University of Technology

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Ivo Provazník

Brno University of Technology

René Kizek

Research Institute of Inorganic Chemistry

Markéta Nykrýnová

Brno University of Technology

Karel Sedlář

Brno University of Technology

Martina Lengerová

University Hospital Brno

Matěj Bezdíček

University Hospital Brno

Martin Vítek

Brno University of Technology

Vojtěch Adam

Mendel University in Brno

Vojtěch Bartoň

Brno University of Technology

Petr Babula

Masaryk University

Cooperative Institutions

University of Zagreb

Brno University of Technology

Mendel University in Brno

Masaryk University

Central European Institute of Technology

Software (Spain)

University of Veterinary Sciences Brno

Algebra University College

Bavarian Research Institute for Digital Transformation

University Hospital Brno

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Progressive alignment of genomic signals by multiple dynamic time warping

Journal of Theoretical Biology (2015)

Helena Škutková Martin Vítek Karel Sedlář Ivo Provazník

This paper presents the utilization of progressive alignment principle for positional adjustment of a set of genomic signals with different lengths. The new method of multiple alignment of signals based on dynamic time warping is tested for the purpose of evaluating the similarity of different length genes in phylogenetic studies. Two sets of phylogenetic markers were used to demonstrate the effectiveness of the evaluation of intraspecies and interspecies genetic variability. The part of the proposed method is modification of pairwise alignment of two signals by dynamic time warping with using correlation in a sliding window. The correlation based dynamic time warping allows more accurate alignment dependent on local homologies in sequences without the need of scoring matrix or evolutionary models, because mutual similarities of residues are included in the numerical code of signals.

Dynamic Time Warping

Image warping

Multiple sequence alignment

Similarity (geometry)

Sliding window protocol

10.1016/j.jtbi.2015.08.007

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Citations (30)

Effect of fluoranthene on plant cell model: Tobacco BY-2 suspension culture

Environmental and Experimental Botany (2011)

Petr Babula Ondřej Vodička Vojtěch Adam Marie Kummerová Ladislav Havel

Suspension culture

Fluoranthene

Suspension

10.1016/j.envexpbot.2011.12.024

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Citations (24)

Entropy-Based Detection of Genetic Markers for Bacteria Genotyping

Lecture notes in computer science (2019)

Markéta Nykrýnová Denisa Maděránková Vojtěch Bartoň Matěj Bezdíček Martina Lengerová

Multilocus sequence typing

10.1007/978-3-030-17935-9_17

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Citations (1)

The identification of replication origin in bacterial genomes by cumulated phase signal

Denisa Maděránková Karel Sedlář Martin Vítek Helena Škutková

The origin of replication (oriC) plays an important role in the cell cycle as the place where DNA replication is initiated. In bacterial cells, a single replication origin can be found and its correct identification is necessary in the annotation process of newly sequenced genomes. Although the rearrangement of a whole genome sequence according to oriC should be a standard procedure, public databases still contain lots of genomes starting at a random place. This situation complicates the comparative analysis of whole bacterial genomes as only two genomes rearranged according to oriC can be reliably aligned. In this paper, we present a novel technique for oriC prediction based exclusively on utilization of cumulated phase signal which distinguishes our approach from current techniques combining application of genomic signal processing techniques with a standard character based comparison. Proposed technique is therefore fast and suitably complements the current pipeline for comparison of whole bacterial genomes by aligned downsampled signals.

Replication

Bacterial genome size

Identification

10.1109/cibcb.2017.8058561

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Citations (3)

Mammalian metallothioneins: properties and functions

Metallomics (2012)

Petr Babula Michal Masařík Vojtěch Adam Tomáš Eckschlager Marie Stiborová

Metallothioneins (MT) are a family of ubiquitous proteins, whose role is still discussed in numerous papers, but their affinity to some metal ions is undisputable. These cysteine-rich proteins are connected with antioxidant activity and protective effects on biomolecules against free radicals, especially reactive oxygen species. In this review, the connection between zinc(ii) ions, reactive oxygen species, heavy metal ions and metallothioneins is demonstrated with respect to effect of these proteins on cell proliferation and a possible negative role in resistance to heavy metal-based and non-heavy metal-based drugs.

Metallothionein

Biomolecule

10.1039/c2mt20081c

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Citations (235)

Rapid and Ultrasensitive Method for Determination of Phytochelatin2 using High Performance Liquid Chromatography with Electrochemical Detection

International Journal of Electrochemical Science (2011)

Ondřej Zítka Helena Škutková Olga Kryštofová Pavlína Šobrová Vojtěch Adam

Plants respond to heavy metal toxicity in a variety of different ways including synthesis of phytochelatins. The synthesis of phytochelatins is catalyzed by γ-Glu-Cys dipeptidyl transpeptidase named as phytochelatin synthase (PCS). The main aim of this study was to optimize high performance liquid chromatography coupled with electrochemical detector for determination of phytochelatin2. The optimized procedure was subsequently used for determination of the mentioned molecules with special attention aimed at the possibility to determine PC2 after activation of PCS in the tobacco BY-2 cells treated with different concentrations of cadmium(II) ions. The optimized conditions were as follows. Both the detector and the column were thermostated at 30 °C. Mobile phase consisted of A: trifluoroacetic acid (80 mM) and B: 100% methanol. Compounds were eluted by the following linear increasing gradient: 0-1 min (3 % of B), 1→12 min (20 % of B), 12→15 min (98 % of B), 15→20 min (98 % of B). Flow rate of the mobile phase was 1 ml min-1. Detection was carried out at applied potential 900 mV postponed on four electrodes. Time of one analysis was 15 minutes. The estimated detection limit for PC2 was 17 nM. In addition, the recoveries were from 93 to 98 %. Good precision was obtained with %C.V.s ranging from 5.3 to 7.5 % in the intra-assay. The inter-assay %C.V.s ranged from 8.9 to 10.2 %. Overall recoveries of were from 102 to 106 % (n = 30). Accuracy (%Bias) was about ±5 %. Further, the attention was aimed at determination of PC2 in BY-2 tobacco cells treated with cadmium(II) ions (0, 5, 10, 25, 50 and 100 µM). It clearly follow from the results obtained that the content of PC2 enhanced with increasing concentration of the substrate and with the applied concentration of cadmium(II) ions.

Trifluoroacetic acid

10.1016/s1452-3981(23)15080-2

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Citations (30)

Bioinformatic Tools for Genotyping of Klebsiella pneumoniae Isolates

Advances in intelligent systems and computing (2018)

Markéta Nykrýnová Denisa Maděránková Matěj Bezdíček Martina Lengerová Helena Škutková

Multilocus sequence typing

Identification

10.1007/978-3-319-91211-0_37

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Citations (4)

Set of rules for genomic signal downsampling

Computers in Biology and Medicine (2015)

Karel Sedlář Helena Škutková Martin Vítek Ivo Provazník

Comparison and classification of organisms based on molecular data is an important task of computational biology, since at least parts of DNA sequences for many organisms are available. Unfortunately, methods for comparison are computationally very demanding, suitable only for short sequences. In this paper, we focus on the redundancy of genetic information stored in DNA sequences. We proposed rules for downsampling of DNA signals of cumulated phase. According to the length of an original sequence, we are able to significantly reduce the amount of data with only slight loss of original information. Dyadic wavelet transform was chosen for fast downsampling with minimum influence on signal shape carrying the biological information. We proved the usability of such new short signals by measuring percentage deviation of pairs of original and downsampled signals while maintaining spectral power of signals. Minimal loss of biological information was proved by measuring the Robinson-Foulds distance between pairs of phylogenetic trees reconstructed from the original and downsampled signals. The preservation of inter-species and intra-species information makes these signals suitable for fast sequence identification as well as for more detailed phylogeny reconstruction.

Upsampling

Sequence (biology)

SIGNAL (programming language)

10.1016/j.compbiomed.2015.05.022

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Citations (13)

First Complete Genome of the Thermophilic Polyhydroxyalkanoates-Producing Bacterium Schlegelella thermodepolymerans DSM 15344

Genome Biology and Evolution (2021)

Jana Musilová Xenie Kouřilová Matěj Bezdíček Martina Lengerová Stanislav Obruča

Schlegelella thermodepolymerans is a moderately thermophilic bacterium capable of producing polyhydroxyalkanoates-biodegradable polymers representing an alternative to conventional plastics. Here, we present the first complete genome of the type strain S. thermodepolymerans DSM 15344 that was assembled by hybrid approach using both long (Oxford Nanopore) and short (Illumina) reads. The genome consists of a single 3,858,501-bp-long circular chromosome with GC content of 70.3%. Genome annotation identified 3,650 genes in total, whereas 3,598 open reading frames belonged to protein-coding genes. Functional annotation of the genome and division of genes into clusters of orthologous groups revealed a relatively high number of 1,013 genes with unknown function or unknown clusters of orthologous groups, which reflects the fact that only a little is known about thermophilic polyhydroxyalkanoates-producing bacteria on a genome level. On the other hand, 270 genes involved in energy conversion and production were detected. This group covers genes involved in catabolic processes, which suggests capability of S. thermodepolymerans DSM 15344 to utilize and biotechnologically convert various substrates such as lignocellulose-based saccharides, glycerol, or lipids. Based on the knowledge of its genome, it can be stated that S. thermodepolymerans DSM 15344 is a very interesting, metabolically versatile bacterium with great biotechnological potential.

GC-content

10.1093/gbe/evab007

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Citations (5)

Bipartite graphs for metagenomic data analysis and visualization

2021 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) (2015)

Karel Sedlář Helena Škutková Petra Vídeňská Ivan Rychlı́k Ivo Provazník

Metagenomics became very popular after expansion of next-generation sequencing techniques that allowed simple implementation of extensive studies. With a target gene sequencing approach, an identification of organisms in a metagenome is quite effortless since only a small reference database of the particular gene is needed. Moreover, by counting the copies of individual genes, also quantitative analysis can be applied. Unfortunately, current bioinformatics tools aim mainly on the analysis of a single metagenome. A cluster analysis, a heatmap of correlation coefficients, biclustering or other statistics techniques can only show relations inside the metagenome or the relation between the metagenome composition and other parameters. On the other hand, there is a lack of tools to provide a comparative analysis of two or more metagenomes. Suitable properties for this kind of analysis can be found in a bipartite graph. Here, we present a novel workflow for finding the suitable representation of metagenomic data to provide a comparative analysis of metagenomes. The resulting graph can take into account information about the actual composition of the metagenome as well as the environment it relates to. Thus, it can provide different view of the data to the naked eye that can complement other techniques such as principal coordinate analysis.

Identification

10.1109/bibm.2015.7359839

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Citations (1)