- MeSH
- bcr-abl fúzové proteiny genetika MeSH
- blastická krize * genetika farmakoterapie patologie MeSH
- chronická myeloidní leukemie * farmakoterapie genetika patologie MeSH
- imidazoly * terapeutické užití aplikace a dávkování MeSH
- inhibitory proteinkinas terapeutické užití farmakologie MeSH
- lidé MeSH
- mutace * MeSH
- myši MeSH
- niacinamid analogy a deriváty MeSH
- protokoly antitumorózní kombinované chemoterapie terapeutické užití MeSH
- pyrazoly MeSH
- pyridaziny * terapeutické užití aplikace a dávkování MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- dopisy MeSH
- MeSH
- bcr-abl fúzové proteiny genetika MeSH
- chemorezistence genetika MeSH
- chronická myeloidní leukemie * genetika MeSH
- chronická nemoc MeSH
- inhibitory proteinkinas farmakologie MeSH
- lidé MeSH
- mutace MeSH
- myeloidní leukemie * MeSH
- vysoce účinné nukleotidové sekvenování MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- dopisy MeSH
SugarSketcher is an intuitive and fast JavaScript interface module for online drawing of glycan structures in the popular Symbol Nomenclature for Glycans (SNFG) notation and exporting them to various commonly used formats encoding carbohydrate sequences (e.g., GlycoCT) or quality images (e.g., svg). It does not require a backend server or any specific browser plugins and can be integrated in any web glycoinformatics project. SugarSketcher allows drawing glycans both for glycobiologists and non-expert users. The "quick mode" allows a newcomer to build up a glycan structure having only a limited knowledge in carbohydrate chemistry. The "normal mode" integrates advanced options which enable glycobiologists to tailor complex carbohydrate structures. The source code is freely available on GitHub and glycoinformaticians are encouraged to participate in the development process while users are invited to test a prototype available on the ExPASY web-site and send feedback.
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
Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.
- MeSH
- chromozomy rostlin genetika MeSH
- Cicer genetika MeSH
- cytogenetika metody MeSH
- DNA rostlinná genetika MeSH
- genetická vazba MeSH
- genetické markery MeSH
- genom rostlinný MeSH
- hybridizace in situ fluorescenční MeSH
- mapování chromozomů metody MeSH
- polymerázová řetězová reakce MeSH
- průtoková cytometrie MeSH
- umělé bakteriální chromozomy MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Positional cloning in bread wheat is a tedious task due to its huge genome size and hexaploid character. BAC libraries represent an essential tool for positional cloning. However, wheat BAC libraries comprise more than million clones, which makes their screening very laborious. Here, we present a targeted approach based on chromosome-specific BAC libraries. Such libraries were constructed from flow-sorted arms of wheat chromosome 7D. A library from the short arm (7DS) consisting of 49,152 clones with 113 kb insert size represented 12.1 arm equivalents whereas a library from the long arm (7DL) comprised 50,304 clones of 116 kb providing 14.9x arm coverage. The 7DS library was PCR screened with markers linked to Russian wheat aphid resistance gene DnCI2401, the 7DL library was screened by hybridization with a probe linked to greenbug resistance gene Gb3. The small number of clones combined with high coverage made the screening highly efficient and cost effective.
- MeSH
- chromozomy rostlin genetika MeSH
- fluorescence MeSH
- hybridizace nukleových kyselin genetika MeSH
- karyotypizace MeSH
- klonování DNA metody MeSH
- mikrosatelitní repetice genetika MeSH
- mšice fyziologie MeSH
- nemoci rostlin genetika imunologie parazitologie MeSH
- polymerázová řetězová reakce MeSH
- přirozená imunita genetika MeSH
- pšenice genetika imunologie parazitologie MeSH
- rostlinné geny genetika MeSH
- umělé bakteriální chromozomy genetika MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Chromosome analysis and sorting using flow cytometry (flow cytogenetics) is an attractive tool for fractionating plant genomes to small parts. The reduction of complexity greatly simplifies genetics and genomics in plant species with large genomes. However, as flow cytometry requires liquid suspensions of particles, the lack of suitable protocols for preparation of solutions of intact chromosomes delayed the application of flow cytogenetics in plants. This chapter outlines a high-yielding procedure for preparation of solutions of intact mitotic chromosomes from root tips of young seedlings and for their analysis using flow cytometry and sorting. Root tips accumulated at metaphase are mildly fixed with formaldehyde, and solutions of intact chromosomes are prepared by mechanical homogenization. The advantages of the present approach include the use of seedlings, which are easy to handle, and the karyological stability of root meristems, which can be induced to high degree of metaphase synchrony. Chromosomes isolated according to this protocol have well-preserved morphology, withstand shearing forces during sorting, and their DNA is intact and suitable for a range of applications.
- MeSH
- buněčný cyklus MeSH
- chromozomy rostlin MeSH
- cytogenetika MeSH
- DNA rostlinná genetika MeSH
- hybridizace in situ fluorescenční metody MeSH
- karyotypizace MeSH
- meristém cytologie MeSH
- průtoková cytometrie metody MeSH
- rostlinné buňky MeSH
- rostliny genetika MeSH
- semena rostlinná růst a vývoj MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
BACKGROUND: Genomics of rye (Secale cereale L.) is impeded by its large nuclear genome (1C approximately 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. RESULTS: 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 HindIII and EcoRI 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 SrR, which confirm a potential of the library to speed up isolation of agronomically important genes by map-based cloning. CONCLUSION: 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.
- MeSH
- chromozomy rostlin genetika MeSH
- DNA rostlinná genetika izolace a purifikace MeSH
- financování organizované MeSH
- genom rostlinný MeSH
- genomová knihovna MeSH
- hybridizace in situ fluorescenční MeSH
- karyotypizace MeSH
- nemoci rostlin genetika MeSH
- průtoková cytometrie MeSH
- pšenice genetika MeSH
- translokace genetická MeSH
- umělé bakteriální chromozomy genetika MeSH
- žito genetika MeSH
