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[en] A report on the Fifth Annual Nanostructural Genomics meeting, Bar Harbor, USA, 7-10 September 2005. It is a rare meeting where one can hear the latest developments in comparative genome analysis, relate these findings to advances in understanding both the linear and three-dimensional organization of the eukaryotic genome, and see it all beginning to fit into the context of the structure and function of the nucleus, visualized using state-of-the art labeling and microscopic techniques. These cross-disciplinary areas of research have been presented by a diverse group of scientists for the past five years at the Nanostructural Genomics meeting at the Jackson Laboratory in Bar Harbor, and the 2005 meeting again gave attendees much food for thought. In summary, the meeting provided a delightfully unique perspective on the application of exciting experimental breakthroughs at the interface of genomics, cell biology and optical physics.
[en] The human body contains approximately 1014 cells, wherein each one is a nucleus. The nucleus contains 2x23 chromosomes, or two complete sets of the human genome, one set coming from the mother and the other from the father. In principle each set includes 30.000-40.000 genes. If the genome was a book, it would be twenty-three chapters, called chromosomes,each chapter with several thousand stories, called genes. Each story made up of paragraphs, called exons and introns. Each paragraph made up of 3 letter words, called codons. Each word is written with letters called bases (AGCT). But the whole is written in a single very long sentence, which is the DNA molecule or deoxy nucleic acid. The usual state of DNA is two complementary strands intertwined forming a double helix. In the cell, DNA is duplicated during each cell division to ensure the transmission of the genome to the daughter cells. For expression, the DNA is transcribed to messenger RNA. The RNA is edited and finally translated to a protein, each three bases coding for one amino acid. When the whole message is translated, the chain of amino acids folds itself up into a distinctive shape that depends on its sequence. Proteins are the effectors of the genes, and are responsible for all metabolic, hormonal and enzymatic reactions in the cells. The expressed RNA determines the amount of proteins to be produced and subsequently the desired effect (strong or weak) in the cell. The microarray technology aims at quantifying the amount of RNA present in the cell from each expressed gene, and at evaluating the changes of these amounts after exposure of the cell to toxic chemicals, ionising radiation or other stress components. The global picture of expressed genes helps to understand the affected genetic pathways in the cell at the molecular level. The microarray technology is used in the Radiobiology and Microbiology topics to study the effect of ionising radiation on human cells and mouse tissue, as well as the effect of harsh environment and space conditions on micro-organisms
[en] The incidence of non melanoma skin cancer has permanently increasing tendency in populations of European origin. The similar situation is in Slovakia too. It is the most frequent cancer in Caucasian. The UVR is considered as the most important factor for development of such diseases. UV exposure leads to the generation of alterations in nuclear genes such as the p53 tumour suppressor gene as well as in the other genome in the cell - namely mitochondrial DNA (mtDNA). Except traditional surgical treatment, noninvasive treatment modalities are increasingly used, namely for superficial lesions.Together with them, also markant development of new noninvasive diagnostic technologies was observed in the last decade.The shift from the older age groups to the younger ones, forced us to give increased attention to this problem. (author)
[en] The purpose of this project is development of world-class headspring techniques of biological science for application of plant genomes/epigenomes through study on radiation- responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: practical application of ChIP in GR-treated Arabidopsis using anti-histone antibodies: mapping of DNA methylomes associated with GR-responsive transcriptomes: setup of methylated DNA quantification using HPLC: elucidation of aberrations in epigenetic regulation induced by low-dose GR using gamma phytotron: comparison of gene expression of histone-modifying enzymes after treatment of GR: elucidation of transcriptomes and physiological alterations associated with delayed senescence of drd1-6 mutant: comparison of gene expression of DNA methylation-related enzymes in GR-treated rice callus and Arabidopsis: investigation of germination capacity, low-temperature, salinity and drought stress-resistance in drd1-6 epigenetic mutant: investigation of aberrations in DNA methylation depending on dose rates of gamma radiation
[en] Sequence filtering is an essential step regardless of the type of technology applied for sequencing a genome, in which low-quality readings or a portion are eliminated. In an assembly, the construction of a genome is carried out from the union of short reads in contigs. Some assemblers measure the relationship between sequences of a fixed length (k-mer) that can be affected by the presence of low-quality sequences. A common approach to evaluating assemblies is based on the analysis of the number of contigs, the length of the longest contig, and the value of N50 defined as the length of the contig representing 50 % of the length of the assembly. In this context, the objective of this study was to evaluate the effect of the use of crude and filtered reads on the values of the quality parameters obtained from the genome assembly of Bacillus altituidinis 19RS3 isolated from Ilex paraguariensis. The quality analysis of both starting files was performed with the FastqC software and the readings were filtered with the Trimmomatic software. The SPAdes software was used for the assembly and the QUAST tool for its evaluation. The best assembly for B. altitudinis 19RS3 was obtained from the filtered readings with the value of k-mer 79, which generated 16 contigs greater than 500 bp with a N50 of 931 914 bp and the longest contig of 966 271 bp.
[en] Genomic DNA from the genotypes Khyber-87, Saleem 2000, Suleman-96, Pir Sabak-2004, Pir Sabak-2005, NRL-0320, NRL-0517, RAS-II, Tatara, RAS-I, Bathoor, Fakhare Sarhad, Bakhtawar-94, Inqilab-91, Haider-2002, Noshera-96, and Auqab-2000 was amplified using RAPD primers. Loci of 100-1400 bp sizes were amplified and on average 3.51 loci per genotype were amplified. Average genetic diversity using the twelve RAPD primers ranged from 30-90%. Phylogenetic relationship among the wheat genotypes was carried out using dendrogram analysis. The seventeen genotypes were clustered in five groups. It was found that the genotypes Pirsabak 2004 and Ras 1 were most distantly related to Khyber-87. It is suggested that these two genotypes be crossed with Khyber 87 for creating maximum genetic variations. (author)
[en] The individual variability in response to radiation was examined in a group of 77 healthy individuals, 35-45 years aged, employing Cytochalasin-blocking micronucleus test. Blood samples were irradiated by the most explored therapeutical gamma dose of 2 Gy (60 Co) in vitro. The results of our examination demonstrated statistically significant difference in the yield of spontaneously occurring micronuclei between genders of the same age group, while in the yields of induced micronuclei no statistical significance was observed. Out of 77 persons, 4% showed extreme radiosensitivity, while 2% showed extreme radioresistance. Since both extremes are genetically controlled, such genomes could easily be recognized employing CB micronuclei test. It would be useful to perform this type of analysis instead of 'null control' chromosomal aberration analysis for all professionals working in ionizing radiation zone. Persons with such genetic predisposition should be advised to work out of ionizing radiation zone. (author)
[en] RAPDs were quite efficient in bringing out the diversity at DNA level among non-edible legumes viz., Acacia nilotica, Adenanthera pavonina, Prosopis juliflora, Pithecolobium dulce, Clitoria ternatea and Pongamia pinnata. The RAPD primer index reveals the information content of the RAPD primer per se. Of the 82 primers tested, OPE 8, OPI 6, OPL 2, OPL 16, OPI 18, OPI 13, OPI 14, OPP 1, OPE 20 and OPI 4 with comparatively higher primer index were more informative and can be used for further DNA finger printing and population studies in tree legumes. CTAB protocol was found to be superior in isolating genomic DNA of good quality. The 260/280 ratios varied between 1.70 and 2.09. Though the genomic DNA isolated by potassium acetate method was found to be intact in 0.8% agarose gel, the yield was significantly lower than the modified CTAB method. (author)
[en] The purpose of this project is development of world-class head spring techniques of biological science for application of plant genomes/epigenomes through study on radiation-responsive epigenomes and improvement of the national competitiveness in the field of fundamental technology for biological science and industry. Research scope includes 1) Investigation of radiation-responsive epigenomes and elucidation of their relation with phenotypes, 2) Elucidation of interaction and transcription control of epigenomes and epigenetic regulators using IR, 3) Investigation of epigenome-mediated traits in plant development, differentiation and antioxidant defense using IR, and 4) Development of application techniques of radiation-responsive epigenomes for eco-monitoring and molecular breeding. Main results are as follow: investigation of the expression level of histone-modifying enzymes by IR; elucidation of the structural and functional changes of chaperone protein by IR; development of transgenic plant (DRD1-6); investigation of transcription control of epigenetic regulators by IR; investigation of relevance between DNA methylation and miRNA; comparison of gene expression in wild type and cmt mutant from Arabidopsis using gene chip; investigation control of epigenetic regulators in drd1-6 mutant by drought stress; development of transgenic plant using epigenetic regulators
[en] MPF2-like genes belonging to STMADS11 clade of MADS-box transcription factors are mostly involved in calyx inflation, floral reversion and fertility. However their role in fertility remained enigmatic. In this study we transformed WSA206 gene paralog - originated through genome duplication in a Solanaceous plant Withaniasomnifera - ectopically in a heterologous host Arabidopsis thaliana. Interesting phenotypes in floral organs and fruits were observed. Overexpression of WSA206 leads to arrest in silique development. The siliques were compressed and size was drastically reduced from 34mm to 3mm. Along with siliques, the seed development was also suppressed as revealed by shriveling of seeds and reduction in seed number. In extreme cases the siliques were devoid of any seeds. In cases where seeds developed, these were impaired in viability. Besides, the transgenic Arabidopsis also exhibited exorbitant growth of calyx to an extent that it resembled inflated calyx in Solanaceae. The calyx remained persistent and encapsulated the under-developed siliques containing non-viable seeds inside. Thus, fertility and sepal development are tightly coupled traits that are controlled by WSA206 paralog in heterologous system. (author)