Helena Skutkova

Content of Phenolic Compounds and Antioxidant Capacity in Fruits of Apricot Genotypes

Research on natural compounds is increasingly focused on their effects on human health. In this study, we were interested in the evaluation of nutritional value expressed as content of total phenolic compounds and antioxidant capacity of new apricot (Prunus armeniaca L.) genotypes resistant against Plum pox virus (PPV) cultivated on Department of Fruit Growing of Mendel University in Brno. Fruits of twenty one apricot genotypes were collected at the onset of consumption ripeness. Antioxidant capacities of the genotypes were determined spectrometrically using DPPH• (1,1-diphenyl-2-picryl-hydrazyl free radicals) scavenging test, TEAC (Trolox Equivalent Antioxidant Capacity), and FRAP (Ferric Reducing Antioxidant Power)methods. The highest antioxidant capacities were determined in the genotypes LE-3228 and LE-2527, the lowest ones in the LE-985 and LE-994 genotypes. Moreover, close correlation (r = 0.964) was determined between the TEAC and DPPH assays. Based on the antioxidant capacity and total polyphenols content, a clump analysis dendrogram of the monitored apricot genotypes was constructed. In addition, we optimized high performance liquid chromatography coupled with tandem electrochemical and spectrometric detection and determined phenolic profile consisting of the following fifteen phenolic compounds: gallic acid, 4-aminobenzoic acid, chlorogenic acid, ferulic acid, caffeic acid, procatechin, salicylic acid, p-coumaric acid, the flavonols quercetin and quercitrin, the flavonol glycoside rutin, resveratrol, vanillin, and the isomers epicatechin, (–)- and (+)- catechin.

Effect of five different stages of ripening on chemical compounds in medlar (Mespilus germanica L.).

The study of changes of nutritional value of fruit during the ripening process can help estimate the optimal date for fruit harvesting to achieve the best quality for direct consumption and further utilization. The aim of this study was to monitor the changes of chemical composition of medlar fruit (Mespilus germanica L.) measured at five various ripening stages including 134, 144, 154, 164 and 174 days after full bloom (DAFB). Fruits were analyzed and ascorbic acid (AA) and total phenolic compound content with respect to the total antioxidant activity were determined. In addition, selected micronutrients and macronutrients were monitored. The results of our experiments demonstrate that ascorbic acid, total phenolic compound content and total antioxidant activity decreased significantly with increasing time of ripeness. The decreasing tendency in potassium, calcium and magnesium contents during the ripening stages was also determined. During the ripening period, the content of all micronutrients as well as phosphorus and sodium was balanced, with no statistically significant differences between the monitored ripening stages, which can be considered as a positive fact with respect to ideal consumption quality of fruit.

Mathematical Evaluation of the Amino Acid and Polyphenol Content and Antioxidant Activities of Fruits from Different Apricot Cultivars

Functional foods are of interest because of their significant effects on human health, which can be connected with the presence of some biologically important compounds. In this study, we carried out complex analysis of 239 apricot cultivars (Prunus armeniaca L.) cultivated in Lednice (climatic area T4), South Moravia, Czech Republic. Almost all previously published studies have focused only on analysis of certain parameters. However, we focused on detection both primary and secondary metabolites in a selection of apricot cultivars with respect to their biological activity. The contents of thirteen biogenic alpha-L-amino acids (arginine, asparagine, isoleucine, lysine, serine, threonine, valine, leucine, phenylalanine, tryptophan, tyrosine, proline and alanine) were determined using ion exchange chromatography with UV-Vis spectrometry detection. Profile of polyphenols, measured as content of ten polyphenols with significant antioxidant properties (gallic acid, procatechinic acid, p-aminobenzoic acid, chlorogenic acid, caffeic acid, vanillin, p-coumaric acid, rutin, ferrulic acid and quercetrin), was determined by high performance liquid chromatography with spectrometric/electrochemical detection. Moreover, content of total phenolics was determined spectrophotometrically using the Folin-Ciocalteu method. Antioxidant activity was determined using five independent spectrophotometric methods: DPPH assay, DMPD method, ABTS method, FRAP and Free Radicals methods. Considering the complexity of the obtained data, they were processed and correlated using bioinformatics techniques (cluster analysis, principal component analysis). The studied apricot cultivars were clustered according to their common biochemical properties, which has not been done before. The observed similarities and differences were discussed.

Structural changes in metallothionein isoforms revealed by capillary electrophoresis and Brdicka reaction

Metallothionein (MT) as a potential cancer marker is at the center of interest and its properties, functions and behavior under various conditions is intensively studied. In the present study, two major mammalian MT isoforms (MT‐1 and MT‐2) were separated using capillary electrophoresis (CE) coupled with UV detector in order to describe their basic behavior. Under the optimized conditions, the separation of both isoforms was enabled as well as estimation of detection limits as subunits and units of ng per μL for MT‐2 and MT‐1, respectively. Further, the effects of thermal treatment and the presence of denaturing agent such as urea on MT‐1 and MT‐2 isoforms were studied by CE‐UV. Thermal treatment caused an increase in the signals of both isoforms. A new parameter called precipitation rate has been defined based on this finding. This parameter can be expressed as a slope of the linear regression of the time dependency curve recalculated on the MT concentration. The thermal precipitation rate for MT‐1 and MT‐2 was determined as 1.1 and 0.9 ng of MT/min, respectively. The chemical precipitation rate calculated from the linear regression for both isoforms provided the same value of 0.25 ng of MT/min. The results were confirmed by manual spectrometric measurements and by differential pulse voltammetry Brdicka reaction. Based on these results, a model of MT behavior under the conditions studied was suggested.

Complete genome sequence of Clostridium pasteurianum NRRL B-598, a non-type strain producing butanol.

The strain Clostridium pasteurianum NRRL B-598 is non-type, oxygen tolerant, spore-forming, mesophilic and heterofermentative strain with high hydrogen production and ability of acetone-butanol fermentation (ethanol production being negligible). Here, we present the annotated complete genome sequence of this bacterium, replacing the previous draft genome assembly. The genome consisting of a single circular 6,186,879 bp chromosome with no plasmid was determined using PacBio RSII and Roche 454 sequencing.

Classification of genomic signals using dynamic time warping

BackgroundClassification methods of DNA most commonly use comparison of the differences in DNA symbolic records, which requires the global multiple sequence alignment. This solution is often inappropriate, causing a number of imprecisions and requires additional user intervention for exact alignment of the similar segments. The similar segments in DNA represented as a signal are characterized by a similar shape of the curve. The DNA alignment in genomic signals may adjust whole sections not only individual symbols. The dynamic time warping (DTW) is suitable for this purpose and can replace the multiple alignment of symbolic sequences in applications, such as phylogenetic analysis.MethodsThe proposed method is composed of three main parts. The first part represent conversion of symbolic representation of DNA sequences in the form of a string of A,C,G,T symbols to signal representation in the form of cumulated phase of complex components defined for each symbol. Next part represents signals size adjustment realized by standard signal preprocessing methods: median filtration, detrendization and resampling. The final part necessary for genomic signals comparison is position and length alignment of genomic signals by dynamic time warping (DTW).ResultsThe application of the DTW on set of genomic signals was evaluated in dendrogram construction using cluster analysis. The resulting tree was compared with a classical phylogenetic tree reconstructed using multiple alignment. The classification of genomic signals using the DTW is evolutionary closer to phylogeny of organisms. This method is more resistant to errors in the sequences and less dependent on the number of input sequences.ConclusionsClassification of genomic signals using dynamic time warping is an adequate variant to phylogenetic analysis using the symbolic DNA sequences alignment; in addition, it is robust, quick and more precise technique.

Progressive alignment of genomic signals by multiple dynamic time warping

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.

Set of rules for genomic signal downsampling

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.

Evaluation of Antioxidant Activity, Polyphenolic Compounds, Amino Acids and Mineral Elements of Representative Genotypes of Lonicera edulis

The aim of this study was to evaluate the bioactive substances in 19 berry cultivars of edible honeysuckle (Lonicera edulis). A statistical evaluation was used to determine the relationship between the content of selected bioactive substances and individual cultivars. Regarding mineral elements, the content of sodium was measured using potentiometry and spectrophotometry. The content of selected polyphenolic compounds with high antioxidant activity was determined by a HPLC–UV/ED method. The total amount of polyphenols was determined by the Folin-Ciocalteu method. The antioxidant activity was determined using five methods (DPPH, FRAP, ABTS, FR and DMPD) that differ in their principles. The content of 13 amino acids was determined by ion-exchange chromatography. The experimental results obtained for the different cultivars were evaluated and compared by statistical and bioinformatic methods. A unique feature of this study lies in the exhaustive analysis of the chosen parameters (amino acids, mineral elements, polyphenolic compounds and antioxidant activity) during one growing season.

Bipartite Graphs for Visualization Analysis of Microbiome Data

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.