Biomedical subjects

A Gabrielian

Publications and source records attributed to A Gabrielian.

7 recordsLinked to original sources

PubMed2000

Comparative genomics of the eukaryotes.

A comparative analysis of the genomes of Drosophila melanogaster, Caenorhabditis elegans, and Saccharomyces cerevisiae-and the proteins they are predicted to encode-was undertaken in the context of cellular, developmental, and evolutionary processes. The nonredundant protein sets of flies and worms are similar in size and are only twice that of yeast, but different gene families are expanded in each genome, and the multidomain proteins and signaling pathways of the fly and worm are far more complex than those of yeast. The fly has orthologs to 177 of the 289 human disease genes examined and provides the foundation for rapid analysis of some of the basic processes involved in human disease.

Animals↗

PubMed1999

Sequence complexity and DNA curvature.

A linguistic complexity measure was applied to the complete genomes of HIV-1, Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium, and to long human and yeast genomic fragments. Complexity values averaged over entire genomic sequences were compared, as were predicted average values of intrinsic DNA curvature. We found that both the most curved and the least complex fragments are located preferentially in non-coding parts of the genome. Analysis of location of the most curved and the simplest regions in bacteria showed that the low-complexity segments are preferentially located in close proximity to the highly curved sequences, which are, in turn, placed from 100 to 200 bases upstream to the start of the nearest coding sequence. We conclude that the parallel analysis of sequence complexity and DNA curvature might provide important information about sequence-structure-function relationship in genomes.

Bacillus subtilis↗

PubMed1999

Identification of the transcription initiation site of the asexually expressed rRNA genes of the malaria parasite Plasmodium berghei.

The start site of the A-type ribosomal RNA transcription units of the rodent malaria parasite, Plasmodium berghei, has been identified. The two A-type units cannot be distinguished within the transcription unit, yet exist as single copies on different chromosomes. Gene transcription initiates 820 bp upstream of the A-type small subunit (SSU) ribosomal gene and two major processing sites were mapped 610 and 611 nucleotides upstream of the SSU in the external transcribed spacer region. Surprisingly the nucleotide sequence of the DNA region containing the putative ribosomal promoter lacked repetitive DNA sequences typical of ribosomal promoters. This region was further analysed by computer using programs designed to reveal sequence-dependent structural features. Comparison of DNA curvature, duplex stability and pattern of twist angle variation revealed a striking degree of conservation between the ribosomal promoters from Plasmodium and other eukaryotes.

Animals↗

PubMed1997

Distribution of sequence-dependent curvature in genomic DNA sequences.

The distribution of inherent, sequence-dependent curvature was calculated for a number of prokaryotic (M. genitalium, H. influenzae, M. jannaschii), viral (adenovirus 2, equine herpes virus 1), phage (M13, lambda), eukaryotic (S. cerevisiae) and mitochondrial genomes as well as E. coli and human genomic fragments. The genomic averages are in the range of 6-8 degrees/helical turn and only about 20% of DNA is curved less than 3 degrees/helical turn. The prokaryotes and phages appear to have a consistently higher frequency of curved DNA in their genomes than the other genomes tested. Long, highly curved segments, similar to artificially designed curved DNA, are apparently absent from the genomes. Short, curved segments, differing in G+C content may provide environmentally modulated conformational signals for gene regulation. A WWW-server was constructed for the prediction of curved sites from DNA sequences (http://icgeb.trieste.it/dna/curve_it.html/)..

Animals↗

PubMed1996

Distribution of bending propensity in DNA sequences.

Local bending propensity and curvature of DNA can be characterized using a vector description of DNA bendability, based on a set of parameters derived from deoxyribonuclease I (DNase I) cleavage experiments. Two characteristics-arithmetic and vector averages of bendability-were successfully used to predict experimentally known bendable, rigid and curved segments in DNA. A characteristic distribution of bendability is conserved in evolutionarily related kinetoplast sequences. An analysis of the M. genitalium and H. influenzae genomes as well as fragments of human and yeast genomes shows, on the other hand, that highly curved segments--similar to artificially designed curved oligonucleotides--are extremely rare in natural DNA.

Animals↗

PubMed1996

Correlation of intrinsic DNA curvature with DNA property periodicity.

Twelve di- and trinucleotide parameter sets representing various structural, thermodynamic or bendability-related properties of DNA were tested in the prediction of DNA curvature applying Fourier analysis on curved and straight, A/T-type or G/C-type DNA sequence motifs. The best predictions were obtained with a new consensus bendability scale created by combining a nucleosome-based and a deoxyribonuclease I-based parameter set. Geometry calculations on the same sequences showed that the helical parameters derived from NMR structures can correctly predict curvature, as distinct from the parameters derived from X-ray crystallographic analysis.

Crystallography, X-Ray↗

PubMed1996

The SBASE protein domain library, Release 4.0: a collection of annotated protein sequence segments.

SBASE 4.0 is the fourth release of SBASE, a collection of annotated protein domain sequences that represent various structural, functional, ligand binding and topogenic segments of proteins. SBASE was designed to facilitate the detection of functional homologies and can be searched with standard database search tools, such as FASTA and BLAST3. The present release contains 61 137 entries provided with standardized names and cross-referenced to all major protein, nucleic acid and sequence pattern collections. The entries are clustered into 13 155 groups in order to facilitate detection of distant similarities. SBASE 4.0 is freely available by anonymous ftp file transfer from ftp.icgeb.trieste.it. Individual records can be retrieved with the gopher server at icgeb.trieste.it and with a World Wide Web server at http://www.icgeb.trieste.it. Automated searching of SBASE with BLAST can be carried out with the electronic mail server sbase@icgeb.trieste.it, which now also provides a graphic representation of the homologies. A related mail server, domain@hubi.abc.hu, assigns SBASE domain homologies on the basis of SWISS-PROT searches.

Amino Acid Sequence↗