Detection of chromosome aberrations in metaphase and interphase tumor cells by in situ hybridization using chromosome-specific library probes

Chromosome aberrations in two glioma cell lines were analyzed using biotinylated DNA library probes that specifically decorate chromosomes 1, 4, 7, 18 and 22 from pter to qter. Numerical changes, deletions and rearrangements of these chromosomes were radily visualized in metaphase spreads, as well as in early prophase and interphase nuclei. Complete chromosomes, deleted chromosomes and segments of translocated chromosomes were rapidly delineated in very complex karyotypes. Simultaneous hybridizations with additional subregional probes were used to further define aberrant chromosomes. Digital image analysis was used to quantitate the total complement of specific chromosomal DNAs in individual metaphase and interphase cells of each cell line. In spite of the fact that both glioma lines have been passaged in vitro for many years, an under-representation of chromosome 22 and an over-representation of chromosome 7 (specifically 7p) were observed. These observations agree with previous studies on gliomas. In addition, sequences of chromosome 4 were also found to be under-represented, especially in TC 593. These analyses indicate the power of these methods for pinpointing chromosome segments that are altered in specific types of tumors

Training models employing physico-chemical properties of DNA for protein binding site detection

Transcription Factors (TFs) are one of the most important agents acting on gene expression regulation, fundamentally determining the organized functional operation of cellular machinery. At a molecular level, this effect is achieved by the sequence specific physical binding of TF proteins to particular parts of the DNA. Transcription Factors regulate gene expression in complex ways and the detection of their binding sites is an important part of many experiments. Predicting Transcription Factor Binding Sites (TFBS) from DNA sequence data has been a challenging task in the field of bioinformatics. The abundance of available DNA sequences strongly encourages the use of machine learning for this problem. Until now most of these efforts were primarily based on the traditional nucleotide-based representation of DNA. To elaborate a more detailed description of this macromolecule, we have worked out a new Physico-Chemical Descriptor (PCD) based DNA representation and used it as input for training neural networks to predict TFBSs. We show that the PCD representation is a viable format for deep learning models, and our feature selection investigation highlights the importance of proper PCD subset choices. The distinct prediction efficiencies detected upon the usage of arbitrarily selected feature subsets indicates that the different DNA features affect the DNA binding process of TFs to various extent

Wavelet analysis of DNA sequences

Using wavelet transform as a core signal processing technique, this thesis work provides a new insight into understanding the DNA sequences, specifically genes with variable protein coding capabilities. The GC-rich region of gene tends to show a universal pattern when analyzed using three different kinds of wavelet transforms and to verify this approach, various model organisms and genes with different biological importance are chosen for analysis. Two different types of input signal were created from DNA sequence using Voss representation and Z-curve. The three existing variants of wavelet transform applied are discrete, complex and wavelet packets. Thus, a total of six plots were obtained from DNA sequence (genes) of each model species. The discrete and complex wavelet techniques were also applied to longer versions of DNA sequence (chromosomes and isochores). The uniformity of results for these techniques in all chosen species confirms and validates the research idea

Novel simple sequence repeats (SSRs) detected by ND-FISH in heterochromatin of Drosophila melanogaster

<p>Abstract</p> <p>Background</p> <p>In recent years, substantial progress has been made in understanding the organization of sequences in heterochromatin regions containing single-copy genes and transposable elements. However, the sequence and organization of tandem repeat DNA sequences, which are by far the majority fraction of <it>D. melanogaster </it>heterochromatin, are little understood.</p> <p>Results</p> <p>This paper reports that the heterochromatin, as well as containing long tandem arrays of pentanucleotide satellites (AAGAG, AAGAC, AATAT, AATAC and AACAC), is also enriched in other simple sequence repeats (SSRs) such as A, AC, AG, AAG, ACT, GATA and GACA. Non-denaturing FISH (ND-FISH) showed these SSRs to localize to the chromocentre of polytene chromosomes, and was used to map them on mitotic chromosomes. Different distributions were detected ranging from single heterochromatic clusters to complex combinations on different chromosomes. ND-FISH performed on extended DNA fibres, along with Southern blotting, showed the complex organization of these heterochromatin sequences in long tracts, and revealed subclusters of SSRs (several kilobase in length) flanked by other DNA sequences. The chromosomal characterization of C, AAC, AGG, AAT, CCG, ACG, AGC, ATC and ACC provided further detailed information on the SSR content of <it>D. melanogaster </it>at the whole genome level.</p> <p>Conclusion</p> <p>These data clearly show the variation in the abundance of different SSR motifs and reveal their non-random distribution within and between chromosomes. The greater representation of certain SSRs in <it>D. melanogaster </it>heterochromatin suggests that its complexity may be greater than previously thought.</p

Targeted identification of genomic regions using TAGdb

Background: The introduction of second generation sequencing technology has enabled the cost effective sequencing of genomes and the identification of large numbers of genes and gene promoters. However, the assembly of DNA sequences to create a representation of the complete genome sequence remains costly, especially for the larger and more complex plant genomes. Results: We have developed an online database, TAGdb, that enables researchers to identify paired read sequences that share identity with a submitted query sequence. These tags can be used to design oligonucleotide primers for the PCR amplification of the region in the target genome. Conclusions: The ability to produce large numbers of paired read genome tags using second generation sequencing provides a cost effective method for the identification of genes and promoters in large, complex or orphan species without the need for whole genome assembly