Biomedical subjects

D Slavov

Publications and source records attributed to D Slavov.

8 recordsLinked to original sources

PubMed2002

Phylogenetic comparison of the pre-mRNA adenosine deaminase ADAR2 genes and transcripts: conservation and diversity in editing site sequence and alternative splicing patterns.

Adenosine deaminase that acts on RNA -2 (ADAR2) is a member of a family of vertebrate genes that encode adenosine (A)-to-inosine (I) RNA deaminases, enzymes that deaminate specific A residues in specific pre-mRNAs to produce I. Known substrates of ADAR2 include sites within the coding regions of pre-mRNAs of the ionotropic glutamate receptors, GluR2-6, and the serotonin receptor, 5HT2C. Mammalian ADAR2 expression is itself regulated by A-to-I editing and by several alternative splicing events. Because the biological consequences of ADAR2 function are significant, we have undertaken a phylogenetic comparison of these features. Here we report a comparison of cDNA sequences, genomic organization, editing site sequences and patterns of alternative splicing of ADAR2 genes from human, mouse, chicken, pufferfish and zebrafish. Coding sequences and intron/exon organization are highly conserved. All ADAR2 genes show evidence of transcript editing with required sequences and predicted secondary structures very highly conserved. Patterns and levels of editing and alternative splicing vary among organisms, and include novel N-terminal exons and splicing events.

Adenosine Deaminase↗

PubMed2001

Evolutionary breakpoints on human chromosome 21.

Segments of the long arm of human chromosome 21 are conserved, centromere to telomere, in mouse chromosomes 16, 17, and 10. There have been 28 genes identified in human chromosome 21 between TMPRSS2, whose orthologue is the most distal gene mapped to mouse chromosome 16, and PDXK, whose orthologue is the most proximal gene mapped to mouse chromosome 10. Only 6 of these 28 genes have been mapped in mouse, and all are located on chromosome 17. To better define the chromosome 17 segment and the 16 to 17 transition, we used a combination of mouse radiation hybrid panel mapping and physical mapping by mouse: human genomic sequence comparison. We have determined the mouse chromosomal location of an additional 12 genes, predicted the location of 7 more,and defined the endpoints of the mouse chromosome 17 region. The mouse chromosome 16/chromosome 17 evolutionary breakpoint is between human genes ZNF295 and UMODL1, showing there are seven genes in the chromosome 16 segment distal to Tmprss2. The chromosome 17/chromosome 10 breakpoint seems to have involved a duplication of the gene PDXK, which on chromosome 21 lies immediately distal to the KIAA0179 gene. These data suggest that there may be as few as 21 functional genes in the mouse chromosome 17 segment. This information is important for defining existing and constructing more complete mouse models of Down syndrome.

Animals↗

PubMed2000

Comparative analysis of the RED1 and RED2 A-to-I RNA editing genes from mammals, pufferfish and zebrafish.

One type of RNA editing involves the deamination of adenosine (A) residues to inosines (I) at specific sites in specific pre-mRNAs. These inosines are subsequently read as guanosines by the ribosome, with potentially significant consequences for protein sequence. In mammals, two such A-to-I RNA editases are RED1, which edits some serotonin and glutamate receptors, and RED2, with unidentified substrates. To study the evolutionary conservation among these editases, we have isolated homologous genes from the Japanese pufferfish, Fugu rubripes. Fugu has two genes homologous to Red1 that are similar in size and organization and that show a fivefold compaction relative to the human gene; they differ, however, in their base compositional features. The Fugu gene for RED2 is unusually large, spanning more than 50kb; within the largest intron, there is evidence for a novel gene on the opposite strand. Because of these unusual features, the partial genomic structure was determined for the mouse RED2 gene. A partial cDNA for RED1 was also isolated from zebrafish. Comparisons between fish and between fish and mammals of the protein sequences show that the catalytic domains are highly conserved for each gene, while the RNA-binding domains vary within a single protein in their levels of conservation. Different levels of conservation among domains of different functional roles may reflect differences in editase substrate specificity and/or substrate sequence conservation.

Adenosine Deaminase↗

PubMed2000

Comparative analysis of the DRADA A-to-I RNA editing gene from mammals, pufferfish and zebrafish.

The DRADA gene in mammals encodes an A-to-I RNA editase, an adenosine deaminase that acts on pre-mRNAs to produce site specific inosines. DRADA has been shown to deaminate specific adenosine residues in a subset of glutamate and serotonin receptors, and this editing results in proteins of altered sequences and functional properties. DRADA thus plays a role in creating protein diversity. To study the evolutionary significance of this gene, we have characterized the genomic structure of DRADA from Fugu rubripes, and compared the protein sequences of DRADA from mammals, pufferfish and zebrafish. The DRADA gene from Fugu is three-fold compacted with respect to the human gene, and contains a novel intron within the large second coding exon. DRADA cDNAs were isolated from zebrafish and a second pufferfish, Tetraodon fluviatilis. Comparisons among fish, and between fish and mammals, of the protein sequences show that the catalytic domains are highly conserved for each gene, while the RNA binding domains vary within a single protein in their levels of conservation. Conservation within the Z DNA binding domain has also been assessed. Different levels of conservation among domains of different functional roles may reflect differences in editase substrate specificity and/or substrate sequence conservation.

Adenosine Deaminase↗

PubMed2000

Criteria for gene identification and features of genome organization: analysis of 6.5 Mb of DNA sequence from human chromosome 21.

To establish criteria for and the limitations of novel gene identification, to identify novel genes of potential relevance to Down Syndrome and to investigate features of genome organization, 6. 550kb. In total, 41 novel gene models were predicted, and for a subset of these, RT-PCR experiments helped to verify and refine the models, and were used to assess expression in early development and in adult brain regions of potential relevance to Down syndrome. Results suggest generally low and/or restricted patterns of expression, and also reveal examples of complex alternative processing, especially in brain, that may have important implications for regulation of protein function. Analysis of complete gene structures of the known genes identified a number of very large introns, a number of very short intergenic distances, and at least one potentially bi-directional promoter. At least 3/4 of known genes and 1/2 of predicted genes are associated with CpG islands. For novel genes, three cases of overlapping genes are predicted. Results of these analyses illustrate some of the complexities inherent in mammalian genome organization and some of the limitations of current sequence analysis technologies. They also doubled the number of potential genes within the region.

Adult↗

PubMed2000

Alpha 2-b interferon and farmarubicin in the prophylaxis of recurrence of superficial transitional cell carcinoma of the urinary bladder.

OBJECTIVE: To ascertain the effect of intravesical instillation of Alpha 2-b Interferon (IFN a-2) 10 million I.U. in 50 ml physiological saline as a monotherapy and in combination with Farmarubicin (FRC) 50 mg dissolved together in 50 ml of physiological saline. These substances were administered four times during the first month after TUR-BT and then once monthly for one year either in the form of an IFN a-2 monotherapy or as an IFN a-2 and FRC combination in the therapy of recurrence of transitional cell carcinoma (TCC) of the urinary bladder after transurethral resection of the bladder tumor (TUR-BT). THEORETICAL CONSIDERATION: One of the causes of malignancy is an irreversible shift in the balance between protooncogens and tumor supressorgens. In the genetical process of the control of cell apoptosis, an important role is played by the tumor-supressorgen p 53. By the means of mutation of protooncogenes, cellular oncogenes(C-MYC) are formed, inducing the proliferation of cells of the tumor and via feedback induce also the p53 mutation. By the reduction of cellular oncogenes, IFN a-2 and FRC intervene by blocking the proliferation of tumor cells. PATIENTS AND METHODS: Authors have checked and treated 33 patients (pts) with recurrent TCC. The first group of 20 pts were after TUR-BT with BCG unsuccessful intravesical therapy, and 13 pts in the second group were with recurrence of TCC, but contraindicated for BCG treatment. These 33 pts (the first and second groups) were compared with 33 pts of the third group after TUR-BT but without intravesical instillation therapy. The pts of the third group did not suffer from any other significant ailment. IFN a-2 monotherapy (10 mill. I.U./or a combination of IFN a-2 + FRC (50 mg/50 ml solution were administered for 2 hours, 1 week after TUR-BT. During the first month, instillations were done weekly, from the second to the twelfth month only once monthly. The results were evaluated for 12 to 33 months (median: 24 months). RESULTS: Group I: From 20 pts after TUR-BT + unsuccessful BCG + IFN a-2 monotherapy recurrence was registered in 4 pts (20%). Group II: Out of 13 pts after TUR-BT + IFN a-2 + FRC, recurrence was registered in 3 pts (23%). Group I + II: Recurrence in both groups was observed in 7 pts (21.2%). Group III: Out of 33 pts after TUR-BT without immuno- et chemotherapy recurrence was registered in 18 pts (54.5%). After one year of treatment, patients were checked for 24 months. The transition into an invasive tumor was observed in 4 pts (12.1%). In the comparative group of 33 pts without instillation after TUR-BT, recurrence was detected after one year in 18 pts (54.5%) and the transition into an invasive tumor was observed in 7 pts (21.2%). CONCLUSION: Intravesical instillation of BCG used to be the most frequently applied therapy following TUR-BT. The toxicity of this vaccine as well as the contraindication of this treatment in some diseases, and also the primary or secondary resistance of TCC to BCG have challenged the search for alternative possibilities of the intravesical instillation treatment. IFN a-2 monotherapy and IFN a-2 in combination with FRC are new alternative approaches in the improvement of TCC treatment. This therapy is also supported by research of molecular genetics. (Ref.18.)

Administration, Intravesical↗

PubMed1999

Gene expression relevant to Down syndrome: problems and approaches.

The long arm of human chromosome 21 likely contains several hundred genes. To determine which of these are responsible for specific aspects of the Down Syndrome phenotype, protein functional analysis coupled to phenotypic analysis of transgenic mice will be required. Because such experiments are both time consuming and expensive, prioritizing 21q genes for further studies would be advantageous. Here, we discuss expression analysis, specifically the use of Northern analysis, cDNA array screening and RNA tissue in situ hybridization to assess place and time of expression of forty-two genes. For a subset of these, over expression in normal versus trisomy cell lines and mouse tissues is discussed. Lastly, several examples of alternative processing and their potential for generation of brain specific proteins are described. Together, these experiments give information on time, place and level of expression of a number of 21q genes and suggest some interesting candidates worth further investigation for relevance to Down Syndrome. These data also illustrate the complexities and ambiguities inherent in interpretation and use of expression information.

Adult↗

PubMedDate not supplied

[New forms of gene transcripts in human and mouse intersectin].

New human and mouse cDNAs which are homologous to human intersectin gene (ITSN) mapped on a q22.1-22.2 region of human chromosome 21 have been obtained. ITSN gene structure has been determined using nucleotide sequences of human chromosome 21 presented in nucleotide's data bases. The analysis of human and mouse ITSN gene transcripts revealed that their pre-mRNA splicing could occur in different ways. New form of ITSN gene transcripts with alternatively spliced SH3C domain (exon 25 and 26) was detected in different human and mouse tissues. The other splice form with absence of exons 6-14 that results in reading frame shift and stop-codon formation was identified in the mouse adult lung and kidney. In addition, we showed alternative splicing of exons 20, 25 and part of exon 6.

Adaptor Proteins, Vesicular Transport↗