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P Deininger

Publications and source records attributed to P Deininger.

17 recordsLinked to original sources
PubMed2005

Tandem insertions of Alu elements.

Alu elements are non-autonomous, non-LTR retroposons that represent the most abundant mobile elements in the human genome (1.1 x 10(6) copies/genome). They preferentially insert adjacent to existing Alu elements. It has been proposed that Alu elements utilize LINE-1 machinery for their retroposition. The LINE-1 endonuclease cleaves at a loose consensus sequence. We have utilized a bioinformatics approach to show the order of insertion of pairs of young (Y) and old (S or J) Alu subfamily members. Our data suggest that the consensus LINE-1 endonuclease cleavage site used for insertion of the old Alu elements can be reused for integration of the younger ones inserting adjacent to them. However, there is also a preference at the 3' end of Alu into a non-ideal cleavage site that may represent unique properties of the A-tail for integration. Alu elements inserting adjacent to one another may suggest the saturation of the optimal integration sites with existing Alu elements, rather than any innate preference for Alu elements to integrate adjacent to other Alus.

Alu Elements↗
PubMed2000

AluY insertion (IVS4-52ins316alu) in the glycerol kinase gene from an individual with benign glycerol kinase deficiency.

Glycerol kinase deficiency has three distinct forms: an isolated form which may be benign or symptomatic, and a complex form which is symptomatic and part of an Xp21 contiguous gene syndrome. Here we report the case of a male with benign isolated glycerol kinase deficiency who was incidentally identified after observation of pseudohypertriglyceridemia. DNA sequencing of this subject's glycerol kinase gene showed the insertion of an AluY sequence in intron 4 of the glycerol kinase gene. Although Alu insertions have been implicated in other diseases, and a closely related AluY element is found as an insert in the C1 inhibitor gene in patients with hereditary angioedema, this is the first case of glycerol kinase deficiency caused by an Alu insertion.

Adult↗
PubMed2000

Functional expression of three P2X(2) receptor splice variants from guinea pig cochlea.

ATP has been suggested to act as a neurotransmitter or a neuromodulator in the cochlea. The responses to ATP in different cell types of the cochlea vary in terms of the rate of desensitization and magnitude, suggesting that there may be different subtypes of P2X receptors distributed in the cochlea. Recently three ionotropic P2X(2) receptor splice variants, P2X(2-1), P2X(2-2), and P2X(2-3,) were isolated and sequenced from a guinea pig cochlear cDNA library. To test the hypothesis that these different splice variants could be expressed as functional homomeric receptors, the three P2X(2) receptor variants were individually and transiently expressed in human embryonic kidney cells (HEK293). The biophysical and pharmacological properties of these receptors were characterized using the whole cell patch-clamp technique. Extracellular application of ATP induced an inward current in HEK293 cells containing each of the three splice variants in a dose-dependent manner indicating the expression of homomeric receptors. Current-voltage (I-V) relationships for the ATP-gated current show that the three subtypes of the P2X(2) receptor had a similar reversal potential and an inward rectification index (I(50 mV)/I(-50 mV)). However, the ATP-induced currents in cells expressing P2X(2-1) and P2X(2-2) variants were large and desensitized rapidly whereas the current in those cells expressing the P2X(2-3) variant was much smaller and desensitized slower. The order of potency to ATP agonists was 2-MeSATP > ATP > alpha,beta -MeATP for all three expressed splice variants. The ATP receptor antagonists suramin and PPADS reduced the effects of ATP on all three variants. Results demonstrate that three P2X(2) splice variants from guinea pig cochlea, P2X(2-1), P2X(2-2), and P2X(2-3), can individually form nonselective cation receptor channels when these subunits are expressed in HEK293 cells. The distinct properties of these P2X(2) receptor splice variants may contribute to the differences in the response to ATP observed in native cochlear cells.

Adenosine Triphosphate↗
PubMed1994

Rodent BC1 RNA gene as a master gene for ID element amplification.

ID elements are short interspersed repetitive DNA elements (SINEs) which have amplified in rodent genomes via retroposition, a process involving an RNA intermediate. BC1, an abundant ID-related transcript, is transcribed from a conserved, single-copy gene in rodents. The gene encoding BC1 RNA represents one of the earliest and possibly the first ID-containing sequence. Comparison of consensus sequences of each rodent ID with its corresponding BC1 RNA gene showed that the variations of BC1 RNA within rodents corresponded to specific changes within the ID consensus sequence for each rodent species. This supports the hypothesis that the BC1 gene is a master gene responsible for the amplification and evolution of ID elements. The rat ID family consists of at least four subfamilies, with the oldest subfamily having been derived from the BC1 RNA. The other three subfamilies appear to have been derived from a new master gene(s), which has been responsible for the large increase in ID element copy number within the rat genome. We have found that the guinea pig genome contains two copies of the BC1 gene, apparently the result of a DNA-mediated duplication event. Both of these guinea pig BC1 genes have a conserved TATA-like element in the 5' flanking region and have contributed to guinea pig ID amplifications.

Animals↗
PubMed1993

cDNA equalization for reverse transcription-polymerase chain reaction quantitation.

Reverse transcription coupled with the polymerase chain reaction has been increasingly utilized to study gene expression. However, most previously published quantitative techniques are limited by accurate initial RNA quantitation and do not account well for the relative efficiency of reverse transcription. We have developed a technique of labeling and quantitating the random-primed cDNA product of a reverse transcription reaction. Using the polymerase chain reaction in conjunction with template dilutions or with an internal competitive template, we show that by normalizing the cDNA input into the polymerase chain reaction, we get accurate quantitation of gene expression. We call this procedure cDNA equalization of reverse transcriptase-polymerase chain reaction. This method is ideal for small clinical samples where accurate quantitation of input RNA is difficult.

Animals↗
PubMed1991

Posttranslational modifications of rat proenkephalin overexpressed in Chinese hamster ovary cells.

Rat proenkephalin was overexpressed in Chinese hamster ovary cells using the dihydrofolate reductase-coupled genetic amplification method. About 2 mg purified protein could be obtained from 250 ml conditioned medium; multiple successive harvests could be obtained from the same roller bottle. Degradation of proenkephalin released into the conditioned medium was reduced significantly in the presence of 2% fetal bovine serum. Forty-eight percent of recombinant proenkephalin was glycosylated; glycosylation could be entirely prevented by the addition of tunicamycin. Two-dimensional isoelectric focusing experiments showed that recombinant proenkephalin exhibited considerable charge heterogeneity, with two major unglycosylated isoelectric forms and six or seven glycosylated isoelectric forms. The estimated isoelectric points of the major unglycosylated proenkephalins were 6.0 and 6.1, while glycosylated proenkephalins ranged in pI from 5.7-6.1. Some of this isoelectric heterogeneity is due to phosphorylation; [32P] orthophosphate was readily incorporated into serine residues within newly synthesized proenkephalin.

Animals↗
PubMed1991

Hybridization selections, using immobilized driver DNA, to enrich for clones unique to a library.

We have developed a technique which allowed us to isolate sex-specific repeats of chickens (Gallus g. domesticus) from a genomic library originally containing one sex-specific repeat clone per 300 clones. Using this plus/minus selection method, we were able to enrich a sub-library in which the sex-specific repetitive clones made up over half of the population (170-fold increase in representation). This enrichment technique used hybridization kinetics to collect clones which are bound (plus selection) or not bound (minus selection) to their respective driver DNAs immobilized on nitrocellulose paper. Plus selections enriched for repetitive sequences and removed from the library most unique sequences as well as vectors containing no inserted sequences. These plus-selected sub-libraries were enriched for repetitive clones, yet still contained sequences representing as little as 10(-4) of the genome. Minus selection removed repetitive sequences shared between the driver and the library. When a plus-selected sub-library was minus selected, the doubly selected sub-library was enriched in repetitive sequences present in the library but not the minus driver.

Animals↗
PubMed1987

Clustering and subfamily relationships of the Alu family in the human genome.

Thirteen and 10 sequences of the Alu family of repeated DNA elements found within the human thymidine kinase and beta-tubulin genes, respectively, were compared. These genes have approximately five times the expected density of Alu family members. The consensus sequence that could be drawn from these 23 Alu family members would differ slightly from others drawn from random Alu family sequences but only at very heterogeneous positions. The different Alu family members do show different pairwise percentage identities, with approximately 15% (7 of 48 Alu family members analyzed) of them clearly representing a separate subfamily of sequences. This analysis also confirms the species-specific differences between human and the prosimian Galago crassicaudatus Alu family members. These data are consistent with both the origin of these sequences in primates less than 65-70 Myr ago and amplification since that time to their present 500,000 copies. The data do not show any special relationships among densely clustered Alu family members.

Animals↗
PubMed1985

Repeat arrays in cellular DNA related to the Epstein-Barr virus IR3 repeat.

We isolated clones and determined the sequence of portions of mouse and human cellular DNA which cross-hybridize strongly with the IR3 repetitive region of Epstein-Barr virus. The sequences were found to be tandem arrays of a simple sequence based on the triplet GGA, very similar to the IR3 repeat. The cellular repeats have distinct differences from the viral repeat region, however, and their sequences do not appear capable of being translated into a purely glycine-plus-alanine protein domain like the portion of the Epstein-Barr nuclear antigen coded by IR3. Although the relationship between IR3 and the cellular repeats is left unclear, the cellular repeats have many interesting features. The tandem arrays are about 1 to several kilobases long, much shorter than satellite tandem repeats and larger than other interspersed, tandem repeats. Each of the repeats is a distinct variation, perhaps diverged from a common sequence, (GGA)n. This family is present in the genomes of all species tested and appears to be a ubiquitous feature of all higher eucaryotic genomes.

Animals↗
PubMed1983

Latent and lytic cycle promoters of Epstein-Barr virus.

Four RNA polymerase II promoters have been mapped in the DNA sequence of the EcoRI-H and -Dhet fragments of B95-8 Epstein-Barr virus. RNAs transcribed from three of these promoters are dramatically induced by treatment of B95-8 cells with 12-O-tetradecanoylphorbol-13-acetate (TPA). The other promoter is active with or without TPA treatment of the cells and is thus active in the latent virus cycle. Deletion mapping suggests that DNA sequence homologies between some of the promoters lie in the same region as essential upstream promoter elements.

Base Sequence↗
PubMed1979

Regions of the polyoma genome coding for T antigens.

The early region of the polyoma genome encodes three T antigens. We have analyzed the organization of the coding regions for the T antigens, using the nucleotide sequence of polyoma DNA and peptides derived from purified, radio-labeled T antigens, separated by two-dimensional electrophoresis and chromatography. We compared the peptides, predicted from the nucleotide sequence of the DNA, with those derived from the purified T antigens. We also compared chemically synthesized peptides, predicted from the DNA sequence, with observed peptides. The results show that the three polyoma T antigens are encoded in overlapping regions of the viral DNA, translated, in part, in two different reading frames.

Antigens, Viral↗
PubMedDate not supplied

Supported liquid membrane technique for selective sample workup of basic drugs in plasma prior to capillary zone electrophoresis.

The potential of using the supported liquid membrane (SLM) technique for pretreatment of plasma samples before analysis with capillary zone electrophoresis (CZE) has been investigated. A basic drug, bambuterol, was used as a model substance in a system, where either 6-undecanone or a mixture of di-n-hexyl ether (DHE) and tri-n-octyl phosphine oxide (TOPO) was used as membrane liquids. It was found that the electropherograms obtained after SLM enrichment of bambuterol in plasma samples were as clean as when aqueous samples containing the same substance were processed in the same way. The low ionic strength of the SLM treated blood plasma samples permitted subsequent sample stacking in the CZE step. The linearity of the detector signal for different concentrations of bambuterol in plasma was satisfactory from 50 to 1000 nmol/L with regression co-efficients of 0.997 using 6-undecanone as membrane liquid and 0.999 with the other liquid. In both systems, the confidence interval of the intercept included the origin. The detection limit was about 50 nmol/L. The long-term stability of the two membrane liquids proved adequate as a membrane lasted at least through the working day.

Electrophoresis, Capillary↗