Analysis, Modelling and Mitigation of Cross-Rate Interference in Enhanced Loran

Katedra radioelektronik

Models of Routing Protocols for Network Simulation and Analyze

Práce se zabývá způsobem implementace směrovacího protokolu RIP do simulátoru sítí ns-2Thesis describes the way of implementation of new routing protocol for network simulator ns-2

Contemplation on wheat vernalization

Vernalization is a period of low non-freezing temperatures, which provides the competence to flower. This mechanism ensures that plants sown before winter develop reproductive organs in more favourable conditions during spring. Such an evolutionary mechanism has evolved in both monocot and eudicot plants. Studies in monocots, represented by temperate cereals like wheat and barley, have identified and proposed the VERNALIZATION1 (VRN1) gene as a key player in the vernalization response. VRN1 belongs to MADS-box transcription factors and is expressed in the leaves and the apical meristem, where it subsequently promotes flowering. Despite substantial research advancement in the last two decades, there are still gaps in our understanding of the vernalization mechanism. Here we summarise the present knowledge of wheat vernalization. We discuss VRN1 allelic variation, review vernalization models, talk VRN1 copy number variation and devernalization phenomenon. Finally, we suggest possible future directions of the vernalization research in wheat

A novel resource for genomics of Triticeae: BAC library specific for the short arm of rye (Secale cereale L.) chromosome 1R (1RS)

<p>Abstract</p> <p>Background</p> <p>Genomics of rye (<it>Secale cereale </it>L.) is impeded by its large nuclear genome (1C~7,900 Mbp) with prevalence of DNA repeats (> 90%). An attractive possibility is to dissect the genome to small parts after flow sorting particular chromosomes and chromosome arms. To test this approach, we have chosen 1RS chromosome arm, which represents only 5.6% of the total rye genome. The 1RS arm is an attractive target as it carries many important genes and because it became part of the wheat gene pool as the 1BL.1RS translocation.</p> <p>Results</p> <p>We demonstrate that it is possible to sort 1RS arm from wheat-rye ditelosomic addition line. Using this approach, we isolated over 10 million of 1RS arms using flow sorting and used their DNA to construct a 1RS-specific BAC library, which comprises 103,680 clones with average insert size of 73 kb. The library comprises two sublibraries constructed using <it>Hin</it>dIII and <it>Eco</it>RI and provides a deep coverage of about 14-fold of the 1RS arm (442 Mbp). We present preliminary results obtained during positional cloning of the stem rust resistance gene <it>SrR</it>, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning.</p> <p>Conclusion</p> <p>We present a strategy that enables sorting short arms of several chromosomes of rye. Using flow-sorted chromosomes, we have constructed a deep coverage BAC library specific for the short arm of chromosome 1R (1RS). This is the first subgenomic BAC library available for rye and we demonstrate its potential for positional gene cloning. We expect that the library will facilitate development of a physical contig map of 1RS and comparative genomics of the homoeologous chromosome group 1 of wheat, barley and rye.</p

A first survey of the rye (Secale cereale) genome composition through BAC end sequencing of the short arm of chromosome 1R

<p>Abstract</p> <p>Background</p> <p>Rye (<it>Secale cereale </it>L.) belongs to tribe Triticeae and is an important temperate cereal. It is one of the parents of man-made species Triticale and has been used as a source of agronomically important genes for wheat improvement. The short arm of rye chromosome 1 (1RS), in particular is rich in useful genes, and as it may increase yield, protein content and resistance to biotic and abiotic stress, it has been introgressed into wheat as the 1BL.1RS translocation. A better knowledge of the rye genome could facilitate rye improvement and increase the efficiency of utilizing rye genes in wheat breeding.</p> <p>Results</p> <p>Here, we report on BAC end sequencing of 1,536 clones from two 1RS-specific BAC libraries. We obtained 2,778 (90.4%) useful sequences with a cumulative length of 2,032,538 bp and an average read length of 732 bp. These sequences represent 0.5% of 1RS arm. The GC content of the sequenced fraction of 1RS is 45.9%, and at least 84% of the 1RS arm consists of repetitive DNA. We identified transposable element junctions in BESs and developed insertion site based polymorphism markers (ISBP). Out of the 64 primer pairs tested, 17 (26.6%) were specific for 1RS. We also identified BESs carrying microsatellites suitable for development of 1RS-specific SSR markers.</p> <p>Conclusion</p> <p>This work demonstrates the utility of chromosome arm-specific BAC libraries for targeted analysis of large Triticeae genomes and provides new sequence data from the rye genome and molecular markers for the short arm of rye chromosome 1.</p

Feasibility of physical map construction from fingerprinted bacterial artificial chromosome libraries of polyploid plant species

<p>Abstract</p> <p>Background</p> <p>The presence of closely related genomes in polyploid species makes the assembly of total genomic sequence from shotgun sequence reads produced by the current sequencing platforms exceedingly difficult, if not impossible. Genomes of polyploid species could be sequenced following the ordered-clone sequencing approach employing contigs of bacterial artificial chromosome (BAC) clones and BAC-based physical maps. Although BAC contigs can currently be constructed for virtually any diploid organism with the SNaPshot high-information-content-fingerprinting (HICF) technology, it is currently unknown if this is also true for polyploid species. It is possible that BAC clones from orthologous regions of homoeologous chromosomes would share numerous restriction fragments and be therefore included into common contigs. Because of this and other concerns, physical mapping utilizing the SNaPshot HICF of BAC libraries of polyploid species has not been pursued and the possibility of doing so has not been assessed. The sole exception has been in common wheat, an allohexaploid in which it is possible to construct single-chromosome or single-chromosome-arm BAC libraries from DNA of flow-sorted chromosomes and bypass the obstacles created by polyploidy.</p> <p>Results</p> <p>The potential of the SNaPshot HICF technology for physical mapping of polyploid plants utilizing global BAC libraries was evaluated by assembling contigs of fingerprinted clones in an <it>in silico </it>merged BAC library composed of single-chromosome libraries of two wheat homoeologous chromosome arms, 3AS and 3DS, and complete chromosome 3B. Because the chromosome arm origin of each clone was known, it was possible to estimate the fidelity of contig assembly. On average 97.78% or more clones, depending on the library, were from a single chromosome arm. A large portion of the remaining clones was shown to be library contamination from other chromosomes, a feature that is unavoidable during the construction of single-chromosome BAC libraries.</p> <p>Conclusions</p> <p>The negligibly low level of incorporation of clones from homoeologous chromosome arms into a contig during contig assembly suggested that it is feasible to construct contigs and physical maps using global BAC libraries of wheat and almost certainly also of other plant polyploid species with genome sizes comparable to that of wheat. Because of the high purity of the resulting assembled contigs, they can be directly used for genome sequencing. It is currently unknown but possible that equally good BAC contigs can be also constructed for polyploid species containing smaller, more gene-rich genomes.</p

Structure and evolution of Apetala3, a sex-linked gene in Silene latifolia

<p>Abstract</p> <p>Background</p> <p>The evolution of sex chromosomes is often accompanied by gene or chromosome rearrangements. Recently, the gene <it>AP3 </it>was characterized in the dioecious plant species <it>Silene latifolia</it>. It was suggested that this gene had been transferred from an autosome to the Y chromosome.</p> <p>Results</p> <p>In the present study we provide evidence for the existence of an X linked copy of the <it>AP3 </it>gene. We further show that the Y copy is probably located in a chromosomal region where recombination restriction occurred during the first steps of sex chromosome evolution. A comparison of X and Y copies did not reveal any clear signs of degenerative processes in exon regions. Instead, both X and Y copies show evidence for relaxed selection compared to the autosomal orthologues in <it>S. vulgaris </it>and <it>S. conica</it>. We further found that promoter sequences differ significantly. Comparison of the genic region of <it>AP3 </it>between the X and Y alleles and the corresponding autosomal copies in the gynodioecious species <it>S. vulgaris </it>revealed a massive accumulation of retrotransposons within one intron of the Y copy of <it>AP3</it>. Analysis of the genomic distribution of these repetitive elements does not indicate that these elements played an important role in the size increase characteristic of the Y chromosome. However, <it>in silico </it>expression analysis shows biased expression of individual domains of the identified retroelements in male plants.</p> <p>Conclusions</p> <p>We characterized the structure and evolution of <it>AP3</it>, a sex linked gene with copies on the X and Y chromosomes in the dioecious plant <it>S. latifolia</it>. These copies showed complementary expression patterns and relaxed evolution at protein level compared to autosomal orthologues, which suggests subfunctionalization. One intron of the Y-linked allele was invaded by retrotransposons that display sex-specific expression patterns that are similar to the expression pattern of the corresponding allele, which suggests that these transposable elements may have influenced evolution of expression patterns of the Y copy. These data could help researchers decipher the role of transposable elements in degenerative processes during sex chromosome evolution.</p

Divide and Conquer: Chromosomal Approach to Cope with the Wheat Genome

Póster presentado en el Olomouc Biotech. Plant Biotechnology: green for good, celebrado en Olomouc (República Checa) del 19 al 21 de junio de 2011.Peer Reviewe

The use of UAV in cadastral mapping of the Czech Republic

The main challenge in the renewal and updating of the Cadastre of Real Estate of the Czech Republic is to achieve maximum efficiency but to retain the required accuracy of all points in the register. The paper discusses the possibility of using UAV photogrammetry and laser scanning for cadastral mapping in the Czech Republic. Point clouds from images and laser scans together with orthoimages were derived over twelve test areas. Control and check points were measured using geodetic methods (RTK-GNSS and total stations). The accuracy of the detailed survey based on UAV technologies was checked on hundreds of points, mainly building corners and fence foundations. The results show that the required accuracy of 0.14 m was achieved on more than 80% and 98% of points in the case of the image point clouds and orthoimages and the case of the LiDAR point cloud, respectively. Nevertheless, the methods lack completeness of the performed survey that must be supplied by geodetic measurements. The paper also provides a comparison of the costs connected to traditional and UAV-based cadastral mapping, and it addresses the necessary changes in the organisational and technological processes in order to utilise the UAV based technologies.Web of Science106art. no. 38

Physical mapping integrated with syntenic analysis to characterize the gene space of the long arm of wheat chromosome 1A

Background: Bread wheat (Triticum aestivum L.) is one of the most important crops worldwide and its production faces pressing challenges, the solution of which demands genome information. However, the large, highly repetitive hexaploid wheat genome has been considered intractable to standard sequencing approaches. Therefore the International Wheat Genome Sequencing Consortium (IWGSC) proposes to map and sequence the genome on a chromosome-by-chromosome basis. Methodology/Principal Findings: We have constructed a physical map of the long arm of bread wheat chromosome 1A using chromosome-specific BAC libraries by High Information Content Fingerprinting (HICF). Two alternative methods (FPC and LTC) were used to assemble the fingerprints into a high-resolution physical map of the chromosome arm. A total of 365 molecular markers were added to the map, in addition to 1122 putative unique transcripts that were identified by microarray hybridization. The final map consists of 1180 FPC based or 583 LTC based contigs. Conclusions/Significance: The physical map presented here marks an important step forward in mapping of hexaploid bread wheat. The map is orders of magnitude more detailed than previously available maps of this chromosome, and the assignment of over a thousand putative expressed gene sequences to specific map locations will greatly assist future functional studies. This map will be an essential tool for future sequencing of and positional cloning within chromosome 1A