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Cucumber (Cucumis sativus) has one of the largest mitochondrial genomes known among all eukaryotes, due in part to the accumulation of short 20 to 60 by repetitive DNA motifs. Recombination among these repetitive DNAs produces rearrangements affecting organization and expression of mitochondrial genes. To more efficiently identify rearrangements in the cucumber mitochondrial DNA, we built two nonoverlapping 800 and 220 kb BAC contigs and assigned major mitochondrial genes to these BACs. Polymorphism carried on the largest BAC contig was used to confirm paternal transmission. Mitochondrial genes were distributed across BACs and physically distant, although occasional clustering was observed. Introns in the nad1, nad4, and nad7 genes were larger than those reported in other plants, due in part to accumulation of short repetitive DNAs and indicating that increased intron sizes contributed to mitochondrial genome expansion in cucumber. Mitochondrial genes atp6 and atp9 are physically close to each other and cotranscribed. These physical contigs will be useful for eventual sequencing of the cucumber mitochondrial DNA, which can be exploited to more efficiently screen for unique rearrangements affecting mitochondrial gene expression. Key words: Cucumis sativus, bacterial artificial chromosome, FPC, organellar genome. Le concombre (Cucumis sativus) possede fun des plus grands genomms mitochondriaux chez les eucaryotes en raison, en partie, dune accumulation de courts motifs repetitifs d'ADN de 20 a 60 pb. La recombinaison entre ces sequences repetees produit des rearrangements qui affectent l'organisation et (expression des genes mitochondriaux. Afin d'identifier plus efficacement les rearrangements au sein de l'ADN mitochondrial du concombre, les auteurs ont assemble deux contigs totalisant 800 et 220 kb de clones BAC sans chevauchements et ont assigne les principaux genes mitochondriaux a ces BAC. Le polymorphisme present sur le plus grand contig BAC a ete employe pour en confirmer la transmission paternelle. Les genes mitochondriaux etaient distrbbues sur les BAC et separes dune grande distance physique, bien que quelques groupements aient ete observes. Les Introns dens les genes nad1, nad4 et nad7 etaient plus grands que leurs homologues chez d'autres plantes en raison, en partie, de l'accumulation de courts motifs repetes d'ADN, ce qui indique que des Introns de taille accrue ont contribue a l'expansion du genome mitochondrial chez le concombre. Les genes mitochondriaux atp6 et atp9 sont physiquement proches l'un de l'autre et co-transcrits. Ces contigs physiques seront utiles en vue du sequencage de l'ADN mitochondrial du concombre qu'il serait possible d'exploiter pour identifier efficacement des rearrangements uniques affectent (expression de genes mitochondriaux. Mots-cles : Cucumis sativus, chromosome bacterien artifcial, FBC, genome d'organite. [Traduit par la Redaction], Introduction Plant mitochondrial genomes are larger than those of most other eukaryotes, even though the numbers of mitochondrially encoded genes are similar (Unseld et al. 1997; Kubo et al. 2000; [...]

The development of modern clinical medicine and the truthful medical diagnosis require hard physicochemical data. Furthermore, the social demands for more accurate and collected data, which refer to human health in real conditions and in real time, force the quest for techniques which would be possible to be applied in a broadly understood clinical field. In this article two techniques are described. A high vacuum technique which is an X-ray photoelectron spectroscopy (XPS), and a functional near infrared spectroscopy (fNIRS), which might be applied in vivo condition. For the both techniques, the results pointing their applicability in the clinical and modern biochemical research are described. [ABSTRACT FROM AUTHOR]

Abstract Background Sequence analysis of organelle genomes has revealed important aspects of plant cell evolution. The scope of this study was to develop an approach for de novo assembly of the carrot mitochondrial genome using next generation sequence data from total genomic DNA. Results Sequencing data from a carrot 454 whole genome library were used to develop a de novo assembly of the mitochondrial genome. Development of a new bioinformatic tool allowed visualizing contig connections and elucidation of the de novo assembly. Southern hybridization demonstrated recombination across two large repeats. Genome annotation allowed identification of 44 protein coding genes, three rRNA and 17 tRNA. Identification of the plastid genome sequence allowed organelle genome comparison. Mitochondrial intergenic sequence analysis allowed detection of a fragment of DNA specific to the carrot plastid genome. PCR amplification and sequence analysis across different Apiaceae species revealed consistent conservation of this fragment in the mitochondrial genomes and an insertion in Daucus plastid genomes, giving evidence of a mitochondrial to plastid transfer of DNA. Sequence similarity with a retrotransposon element suggests a possibility that a transposon-like event transferred this sequence into the plastid genome. Conclusions This study confirmed that whole genome sequencing is a practical approach for de novo assembly of higher plant mitochondrial genomes. In addition, a new aspect of intercompartmental genome interaction was reported providing the first evidence for DNA transfer into an angiosperm plastid genome. The approach used here could be used more broadly to sequence and assemble mitochondrial genomes of diverse species. This information will allow us to better understand intercompartmental interactions and cell evolution.

Next-generation sequencing (NGS) is a powerful tool for massive detection of DNA sequence variants such as single nucleotide polymorphisms (SNPs), multi-nucleotide polymorphisms (MNPs) and insertions/deletions (indels). For routine screening of numerous samples, these variants are often converted into cleaved amplified polymorphic sequence (CAPS) markers which are based on the presence versus absence of restriction sites within PCR products. Current computational tools for SNP to CAPS conversion are limited and usually infeasible to use for large datasets as those generated with NGS. Moreover, there is no available tool for massive conversion of MNPs and indels into CAPS markers. Here, we present VCF2CAPS–a new software for identification of restriction endonucleases that recognize SNP/MNP/indel-containing sequences from NGS experiments. Additionally, the program contains filtration utilities not available in other SNP to CAPS converters–selection of markers with a single polymorphic cut site within a user-specified sequence length, and selection of markers that differentiate up to three user-defined groups of individuals from the analyzed population. Performance of VCF2CAPS was tested on a thoroughly analyzed dataset from a genotyping-by-sequencing (GBS) experiment. A selection of CAPS markers picked by the program was subjected to experimental verification. CAPS markers, also referred to as PCR-RFLPs, belong to basic tools exploited in plant, animal and human genetics. Our new software–VCF2CAPS–fills the gap in the current inventory of genetic software by high-throughput CAPS marker design from next-generation sequencing (NGS) data. The program should be of interest to geneticists involved in molecular diagnostics. In this paper we show a successful exemplary application of VCF2CAPS and we believe that its usefulness is guaranteed by the growing availability of NGS services. [ABSTRACT FROM AUTHOR]

Electrodeposited SiO electrodes were shown to be photoactive and exhibit n- and p-type effects for electrodes placed in aqueous and organic solutions, respectively. As seen by Fourier transform infrared (FTIR) spectroscopy and X-ray photoelectron (XPS) spectroscopy, the mechanism of the electrodeposition included reactions with the used electrolyte as well as with traces of water as sources of oxygen and hydrogen. The lowest band gap energy ( E ) of the films of approximately 1.6 eV was observed for the film electrodeposited at −2.5 V in comparison to 1.9 eV for the films obtained at −2.25 and −2.75 V. The depth profiles of Si and O in the films were registered by XPS, secondary ion mass spectrometry (SIMS), and glow discharge optical emission spectroscopy (GD-OES), which showed that Si and O were relatively uniformly distributed across the entire layer of the film. The n-type photoactivity was associated with the evolution of oxygen from the aqueous solution, and the p-type was attributed to the reductive deterioration of the amorphous SiO deposit and simultaneous photodecomposition of the electrolyte. Graphical Abstract: [ABSTRACT FROM AUTHOR]

Several parasitic plants are known to have acquired mitochondrial genes via a horizontal transfer from their hosts. However, mitochondrial gene transfer in this direction has not yet been found in the parasite-rich family Orobanchaceae. Based on a phylogenetic analysis of the mitochondrial atp6 gene in selected species of Orobanche s.l., we provide evidence of a host-to-parasite transfer of this gene in O. coerulescens, which is a Eurasiatic species that parasitises Artemisia (Asteraceae). We did not find the original Orobanche atp6 gene in this species, which suggests that it has been replaced by a gene that was acquired from Asteraceae. In addition, our data suggest the occurrence of a second HGT event in the atp6 sequence - from Asteraceae to Phelipanche. Our results support the view that the transfer of genetic material from hosts to parasites influences the mitochondrial genome evolution in the latter. [ABSTRACT FROM AUTHOR]

Objective: The inadequate efficiency of existing therapeutic anti-cancer regiments and the increase in the multidrug resistance of cancer cells underscore the need to investigate novel anticancer strategies. The induction of apoptosis in tumors by cytotoxic agents produced by pathogenic microorganisms is an example of such an approach. Nevertheless, even the most effective drug should be delivered directly to targeted sites to reduce any negative impact on other cells. Accordingly, the stabilized nanosystem (SNS) for active agent delivery to cancer cells was designed for further application in local anti-tumor therapy. A product of genetically modified Escherichia coli, listeriolysin O (LLO), was immobilized within the polyelectrolyte membrane (poly(ethylenimine)|hyaluronic acid) shells of ‘LLO nanocarriers’ coupled with the stabilizing element of natural origin. Methods and results: The impact of LLO was evaluated in human leukemia cell lines in vitro. Correspondingly, the influence of the SNS and its elements was assessed in vitro. The viability of targeted cells was evaluated by flow cytometry. Visualization of the system structure was performed using confocal microscopy. The membrane shell applied to the nanocarriers was analyzed using atomic force microscopy and Fourier transform infrared spectroscopy techniques. Furthermore, the presence of a polyelectrolyte layer on the nanocarrier surface and/or in the cell was confirmed by flow cytometry. Finally, the structural integrity of the SNS and the corresponding release of the fluorescent solute listeriolysin were investigated. Conclusion: The construction of a stabilized system offers LLO release with a lethal impact on model eukaryotic cells. The applied platform design may be recommended for local anti-tumor treatment purposes. [ABSTRACT FROM AUTHOR]

Key message: Petaloid cytoplasmic male-sterile carrots exhibit overexpression of the mitochondrial atp9 genes which is associated with specific features in organization and expression of these sequences. Abstract: In carrots, the S-cytoplasm causes transformation of stamens into petal-like organs, while plants carrying normal N-cytoplasm exhibit normal flower morphology. Our work was aimed at characterization of distinct features both cytoplasms display with respect to organization and expression of the mitochondrial atp9 genes. We show that two carrot atp9 genes, previously reported as cytoplasm-specific, in fact occur in heteroplasmic condition. In the S-cytoplasm the atp9- 1 version dominates over atp9- 3, while in N-cytoplasmic plants this proportion is reversed. Herein, we also indicate the presence and recombination activity of a 130-/172-bp sequence repeat which likely shaped the present organization of carrot atp9 loci. Furthermore, cDNA sequence examination revealed that the atp9 open reading frames (ORFs) were C to U edited in 4 nucleotide positions. One of the editing events turns a glutamine triplet into the stop codon, thereby equalizing ORFs of atp9- 1 and atp9- 3. A certain fraction of partially edited molecules was identified-they all represented the atp9- 3 sequence. In either S- or N-cytoplasmic plants multiple 5′ transcript termini were observed. Of these, the ones mapping more distantly from the atp9 ORF were more pronounced in case of petaloid accessions. It was also shown that despite comparable copy number of the genomic atp9 sequences, the level of the respective mRNAs was approximately 3 times higher in case of petaloid carrots. The latter fact corresponded to the elevated content of the ATP9 protein in plants carrying S-cytoplasm. The semi-fertile phenotype of such plants is associated with a drop in ATP9 accumulation. [ABSTRACT FROM AUTHOR]

Tomato (Solanum lycopersicum L.) is a vegetable frequently exposed to hypoxia stress induced either by being submerged, flooded or provided with limited oxygen in hydroponic cultivation systems. The purpose of the study was to establish the metabolic mechanisms responsible for overcoming hypoxia in two tomato accessions with different tolerance to this stress, selected based on morphological and physiological parameters. For this purpose, 3-week-old plants (plants at the juvenile stage) of waterlogging-tolerant (WL-T), i.e., POL 7/15, and waterlogging-sensitive (WL-S), i.e., PZ 215, accessions were exposed to hypoxia stress (waterlogging) for 7 days, then the plants were allowed to recover for 14 days, after which another 7 days of hypoxia treatment was applied. Root samples were collected at the end of each time-point and 2D-DIGE with MALDI TOF/TOF, and expression analyses of gene and protein-encoded alcohol dehydrogenase (ADH2) and immunolabelling of ADH were conducted. After collating the obtained results, the different responses to hypoxia stress in the selected tomato accessions were observed. Both the WL-S and WL-T tomato accessions revealed a high amount of ADH2, which indicates an intensive alcohol fermentation pathway during the first exposure to hypoxia. In comparison to the tolerant one, the expression of the adh2 gene was about two times higher for the sensitive tomato. Immunohistochemical analysis confirmed the presence of ADH in the parenchyma cells of the cortex and vascular tissue. During the second hypoxia stress, the sensitive accession showed a decreased accumulation of ADH protein and similar expression of the adh2 gene in comparison to the tolerant accession. Additionally, the proteome showed a greater protein abundance of glyceraldehyde-3-phosphate dehydrogenase in primed WL-S tomato. This could suggest that the sensitive tomato overcomes the oxygen limitation and adapts by reducing alcohol fermentation, which is toxic to plants because of the production of ethanol, and by enhancing glycolysis. Proteins detected in abundance in the sensitive accession are proposed as crucial factors for hypoxia stress priming and their function in hypoxia tolerance is discussed. [ABSTRACT FROM AUTHOR]

Transfer of DNA between different compartments of the plant cell, i.e., plastid, mitochondrion and nucleus, is a well-known phenomenon in plant evolution. Six directions of inter-compartmental DNA migration are possible in theory, however only four of them have been previously reported. These include frequent cases of mitochondrion and plastid to nucleus transfer, plastid to mitochondrion transfer, and rare nucleus to mitochondrion migrations. The connection between the plastid and mitochondrial genomes in flowering plants has been viewed as a one way road. Contrary to these observations we found that a sequence widespread in the carrot mitochondrial genome, designated as DcMP, was transferred to the plastid genome of a carrot ancestor. Interestingly, DcMP was integrated into a tRNA promoter of the plastid trnV gene, replacing the original promoter sequence. The rearrangement of the plastid genome is specific for carrot and closely related species belonging Scandiceae clade. The structure of the sequence and the presence of a 6 nt target site duplication led us to speculate that the transfer was a result of a transposition event of a non-LTR retrotransposon. These findings open interesting questions about the evolution of organellar genomes and mobile genetic elements and provide a useful plastid marker to phylogenetically delineate species relationships within the Scandiceae clade. [ABSTRACT FROM AUTHOR]

The aim of this work was to improve plating efficiency of sugar beet mesophyll protoplast cultures. Preliminary experiments showed that cultures of good quality, viable protoplasts were obtained in rich media based on the Kao and Michayluk formulation and with the calcium alginate as an embedding matrix. Nevertheless, in these cultures cell divisions were either not observed or very seldom confirming earlier reported recalcitrance of sugar beet protoplasts. The recalcitrant status of these cultures was reversed upon application of exogenous phytosulfokine (PSK)-a peptidyl plant growth factor. The highest effectiveness of PSK was observed at 100 nM concentration. Plating efficiencies obtained in the presence of PSK reached approximately 20% of the total cultured cells. The stimulatory effect of phytosulfokine was observed for all tested breeding stocks of sugar beet. Our data indicate that PSK is a powerful agent able to overcome recalcitrance of plant protoplast cultures. [ABSTRACT FROM AUTHOR]

High- and low-stringency FISH and base-specific fluorescence were performed on the permanent translocation heterozygote Rhoeo spathacea (2n = 12). Our results indicate that 45S rDNA arrays, rDNA-related sequences and other GC-rich DNA fraction(s) are located within the pericentromeric regions of all twelve chromosomes, usually colocalizing with the chromomycin A-positive bands. Homogenization of the pericentromeric regions appears to result from the concerted spread of GC-rich sequences, with differential amplification likely. We found new 5S rDNA patterns, which suggest a variability in the breakpoints and in the consequent chromosome reorganizations. It was found that the large 5S rDNA locus residing on each of the 8E and 9E arms consisted of two smaller loci. On each of the two chromosome arms 3b and 4b, in addition to the major subtelomeric 5S rDNA locus, a new minor locus was found interstitially about 40% along the arm length. The arrangement of cytotogenetic landmarks and chromosome arm measurements are discussed with regard to genome repatterning in Rhoeo. [ABSTRACT FROM AUTHOR]

Abstract: Polyaniline and its derivatives have gained a unique interest because of their chemical stability and stimulating physical properties which strongly depend on their preparation procedure. The determination of a monomer transport from the bulk of the solution to the electrode surface is one of the key factors to understand the initiation process of the polymerization. In this paper the results of the study on diffusion coefficient (D) for aniline (ANI), o-methoxyaniline (OMA) and o-ethoxyaniline (OEA) are described by means of the rotating disc electrode (RDE) technique. The calculated values of D are 2.4×10−6 cm2 s−1, 3.9×10−6 cm2 s−1 and 4.7×10−6 cm2 s−1 for ANI, OMA and OEA, respectively. D value increases with the length of the alkoxy substituents, which indicates a faster molecular movement with the increase in molecular dimensions. The proposed explanation for this dependence is based on the real Stokes radius of a diffusing monomer, which depends on the number of water molecules forming a water shell around monomer molecule which decreases with the length of alkoxy substituents. The increasing diffusion coefficient values with the length of the alkoxy substituents correspond well with the increase in the determined rate constants, showing the diffusive control of the oxidation of the monomers to a radical cation under studied experimental conditions. [Copyright &y& Elsevier]