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D E Riley

Publications and source records attributed to D E Riley.

At least 55 records · Page 3Linked to original sources
PubMed1991

Nucleotide sequence of the 3' nuclease-sensitive region of the human phosphoglycerate kinase 1 (PGK1) gene.

Many genes are known to have nuclease-sensitive sites and/or control sequences in their 3' flanking regions, but for very few genes has this region been sequenced. Previously, we mapped specific, gene activity-dependent DNAase I- and MspI-sensitive sites at the 3' end of the human X-linked housekeeping gene phosphoglycerate kinase (PGK1). Sequence information presented here shows that the 3' nuclease-sensitive site maps precisely to an Alu sequence and near a "BKM" repeat. This is the first report of an Alu sequence that has alternative chromatin configurations depending on gene activity.

Base Sequence↗
PubMed1991

Cognitive processes in idiopathic dystonia treated with high-dose anticholinergic therapy: implications for treatment strategies.

Studies utilizing single doses of scopolamine have suggested a role for the cholinergic system in memory. Results are consistent in identifying a selective effect on the early encoding stage of information processing. In terms of long-term administration of anticholinergics, patients with Parkinson's disease often display memory deficits. However, underlying pathology within the forebrain cholinergic system complicates the study of treatment effects in this disorder. We therefore assessed multiple memory routines in 20 cognitively intact patients with dystonia where no such pathology has been identified. Patients were tested before and after 2-4 months of 15-74 mg of trihexyphenidyl daily. Twelve tolerated this regime. Compared to control subjects, matched for age and I.Q., only tests with a single presentation of the material to be remembered were affected at follow-up. The speed of information processing was also significantly reduced. Age was strongly related to memory performance in the patient group alone and interacted with dose and duration of treatment. Results suggest that drug-induced slowing of mentation was responsible for impaired encoding, particularly in older patients. These findings affect treatment strategies, especially now that injections of botulinum toxin have proved to be highly effective for certain forms of focal dystonia.

Adult↗
PubMed1991

Detection of variable DNA repeats in diverse eukaryotic microorganisms by a single set of polymerase chain reaction primers.

We cloned and sequenced a variable DNA repeat from Trichomonas vaginalis, a flagellated protozoan parasite. Targeting of this repeat in the polymerase chain reaction resulted in complex and intense product patterns for a wide variety of eukaryotic microorganisms, including the pathogenic protozoan parasites T. vaginalis, Giardia lamblia, Leishmania donovani, three species of Trypanosoma, and four species of Acanthamoeba; the nonpathogenic protozoans, Paramecium tetraurelia and Tetrahymena thermophilia; and a yeast, Saccharomyces cerevisiae. Each microorganism exhibited a distinctive pattern of repeats. For example, a characteristic pattern was exhibited by six clinical T. vaginalis isolates. Eight G. lamblia isolates exhibited either one of two characteristic pattern types. There was no reaction with human DNA or DNA from the prokaryotes Ureaplasma urealyticum and Mycoplasma hominis. This approach may facilitate detection of a wide variety of eukaryotic microorganisms by use of a single primer set and holds promise for the development of typing schemes for both T. vaginalis and G. lamblia.

Acanthamoeba↗
PubMed1990

CQA 206-291 in Parkinson's disease: an acute single escalating dosage study.

CQA 206-291, a new ergot derivative with a "biphasic" dopaminergic profile, was studied in 6 patients with longstanding Parkinson's disease suffering from pronounced fluctuations in hourly mobility. On alternate days, up to seven single doses, escalating from 0.2 to 20 mg, were given as replacement for the usual first morning dose of levodopa. At the most effective dosage, four of the six patients obtained as good a peak response to CQA (8-20 mg) as to L-dopa. Side effects were common and similar to other ergot derivatives, suggesting that the initial weak dopamine antagonist properties of the parent compound, documented in animals, may be of little clinical significance. However, comparative studies will be needed to confirm this suspicion. The addition of domperidone successfully reduced the incidence and severity of side effects. CQA 206-291 has potent anti-parkinsonian properties; further longer-term treatment trials are indicated.

Aged↗
PubMed1990

A family of homologous X chromosomal sequences with some members showing evidence of enhancer activity.

Little is known about either the frequency of occurrence of enhancers or the interrelationships of various enhancers in mammalian genomes. Previous reports described a potent, transcriptional enhancer within the sequence termed "Xrep," a human X chromosomal genomic clone (Riley et al., 1986; Riley, 1989a). Additional Xrep-related sequences reside on the human X chromosome. A probe for the Xrep enhancer hybridized with multiple restriction fragments located on the X chromosome. Two of the fragments cross-hybridizing with the enhancer had identical enhancer-like sequences but dissimilar flanking sequences. However, both of the sequenced enhancers were flanked by poly(GT) repeats strongly implicated in the generation of polymorphisms. A third sequence cross-hybridizing to the enhancer probe was found, in chromatin form, to be extremely DNase I hypersensitive.

Animals↗
PubMed1990

Cortical-basal ganglionic degeneration.

We report our experience with 15 patients believed to have cortical-basal ganglionic degeneration. The clinical picture is distinctive, comprising features referable to both cortical and basal ganglionic dysfunction. Characteristic manifestations include cortical sensory loss, focal reflex myoclonus, "alien limb" phenomena, apraxia, rigidity and akinesia, a postural-action tremor, limb dystonia, hyperreflexia, and postural instability. The asymmetry of symptoms and signs is often striking. Brain imaging may demonstrate greater abnormalities contralateral to the more affected side. Postmortem studies in 2 patients revealed the characteristic pathologic features of swollen, poorly staining (achromatic) neurons and degeneration of cerebral cortex and substantia nigra. Biochemical analysis of 1 brain showed a severe, diffuse loss of dopamine in the striatum. This condition is more frequent than previously believed, and the diagnosis can be predicted during life on the basis of clinical findings. However, as with other "degenerative" diseases of the nervous system, a definitive diagnosis of cortical-basal ganglionic degeneration requires confirmation by autopsy.

Aged↗
PubMed1989

Very rapid nucleotide sequence analysis of improved, double-stranded minipreps.

Recently, the combination of double-stranded sequencing and Sequenase has been used to accomplish rapid, high-performance sequencing. This combination is relatively resistant to the usual compression effects of palindromes seen with sequencing enzymes such as Klenow fragment of DNA polymerase I or reverse transcriptase. However, for optimal results the method has still relied on plasmids purified by centrifugation through CsCl gradients. The preparation of large-scale cultures, CsCl gradients, and subsequent dialysis are time-consuming processes. The present report describes an improved, miniprep procedure which eliminates the need for CsCl gradients or single-stranded vectors. The effectiveness of the procedure is due to increased ampicillin concentration which amplifies the plasmids, destruction of contaminating enzymes by diethylpyrocarbonate treatment, and vortexing to facilitate rapid sample handling. Sequences of the resulting minipreps are equal in resolution and quality to sequences of CsCl-gradient-purified plasmids.

Base Sequence↗
PubMed1989

Pain in Gilles de la Tourette syndrome and related tic disorders.

Although pain is not generally recognized as a symptom of tic disorders, we have seen a number of patients in whom this was a prominent feature, at times even the symptom of greatest concern. The commonest pain complaints are those arising from the actual performance of a tic. Most often this follows directly from the discomfort produced by sudden or repeated extreme exertion. Here the origin of the pain is usually musculoskeletal, though rare examples of neuropathic pain may occur. Pain also may arise from striking or being struck by a moving body part involved in large amplitude tics. Other related painful acts include deliberate self-injury and pain inflicted upon others. A second major category is represented by a smaller number of patients who complain of pain during voluntary efforts to suppress their tics. Finally, there are patients who obtain relief from tics while experiencing pain, to such an extent that they will deliberately provoke pain to obtain its benefit. We feel that pain should be recognized as a common complaint, and occasionally a source of significant disability, in patients with tics.

Adolescent↗
PubMed1986

Xrep, a plasmid-stimulating X chromosomal sequence bearing similarities to the BK virus replication origin and viral enhancers.

The human X chromosome-linked fragment, "Xrep," was sequenced because it exerts a positive effect on plasmid growth in both E. coli and Saccharomyces cerevisiae. The sequence revealed three features similar to the human BK virus replication origin: Xrep has a true palindrome, CCTCC(T)3CCTCC, which is similar to "true" palindrome-like sequences found at the replication origins of polyoma [CCTC(T/C)10CTCC], BK [CCTC(A/G)8CCTCC] and SV40 [CCTCC(A)6GCCTCC] viruses. Twenty nucleotides away from the true palindrome, Xrep has the sequence GAATCCTATTCACTTTT while BK virus, the human analogue of SV40, has GAAATCCCTATTCTTTT in exactly the same position relative to the true palindrome. These two 17-mers differ only in the positions of two nucleotides comparing Xrep and BK virus. Also similar to the replication origins of DNA viruses, Xrep appears to have a cluster of enhancers adjacent to the origin-like sequences. Potent enhancer-like activity was detected in pSV1 X CAT/Xrep constructs. Xrep may originate from an endogenous virus, or from an X chromosomal replication origin.

Acetyltransferases↗
PubMed1986

Chromatin structure of active and inactive human X-linked phosphoglycerate kinase gene.

We have carried out a comparative analysis of DNase I sensitivity of the active and inactive X-linked phosphoglycerate kinase (Pgk) genes in human lymphoblast and fibroblast cultured cells. Three DNase I-sensitive regions were detected: a 5' hypersensitive site, a sensitive region in the interior of the gene and a 3' slightly sensitive site which we previously reported and have now mapped with some precision. A comparison of these sensitive sites in single and multiple X cell lines indicates that the sensitive sites are unique to the active X chromosome. A similar study of an X-linked Pgk pseudogene shows no difference in DNase I sensitivity between the pseudogenes on the active and inactive X chromosomes. These latter results imply that sex chromatin does not confer a unique level of DNase I resistance to DNA on the inactive X chromosome. The exact role of sex chromatin in differential DNase I sensitivity of genes on the inactive and active X chromosomes is discussed.

Cells, Cultured↗
PubMed1986

Mapping of human autosomal phosphoglycerate kinase sequence to chromosome 19.

In order to map human PGK sequences, DNA was prepared from 55 human-mouse somatic cell lines. The DNA was digested to completion with HindIII and Southern filters prepared. These filters were hybridized at high stringency conditions to a human PGK cDNA. Mouse and human X-linked and autosomal bands were distinguished and, in addition to known X-linked sequences, two autosomal PGK sequences were mapped: a 1-kb band to chromosome 19 and a 5-kb band to chromosome 6. The PGK cDNA probe was also hybridized to flow-sorted chromosomes confirming the presence of PGK sequences on the X chromosome and chromosomes 6 and 19.

Animals↗
PubMed1986

The utilization of the human phosphoglycerate kinase gene in the investigation of X-chromosome inactivation.

The X-linked human Pgk gene has been cloned and partially characterized, and some preliminary results have been obtained regarding active vs. inactive gene comparisons of chromatin structure and methylation patterns. As yet we can say nothing definitive about what role, if any, these differences may play in X inactivation. The studies showing that DNA from the inactive X chromosome in mature somatic cells does not function in transformation of the Hprt gene strongly imply modification of the inactive X chromosome at the DNA level. However, methylation studies with the Hprt, Gd Pgk genes have revealed a complexity of methylation patterns including hypermethylation of parts of the active X gene. Resolution of just what difference is critical in expression, differentiating between cause and effect, and extrapolating to the spreading and initiation aspects of X inactivation are still, unfortunately, long-range goals. The Pgk system may be of special value in unraveling some of these difficult questions. A unique autosomal Pgk locus exists and should allow an informative comparison between an X-linked housekeeping gene and an autosomal, tissue-specific gene encoding proteins of identical enzymatic function. The proximity of Pgk to the X-inactivation control center may be useful in identifying the starting point of this very important event in early mammalian development.

Base Sequence↗
PubMed1985

Comparison of the thin layer chromatography/flame ionization detection system with other methods for the quantitative analysis of liver lipid contents in alcohol-fed rats and controls.

In this study, we have examined the feasibility of using the Thin Layer Chromatography/Flame Ionization Detection (TLC/FID) system to evaluate the lipid content of alcohol-induced fatty liver by comparing the results with those from other methods. Various amounts of standards (tripalmitin, phosphatidylcholine and cholesterol) were spotted on Chromarods and scanned either with or without development in a solvent system. The detector responses were significantly greater when the spots were not developed. From the results with developed rods, conversion factors (amount/area) were calculated. These were used for the quantitative analysis of the liver lipids from rats fed a Lieber-DeCarli ethanol diet or a control diet for four weeks. The triglyceride (TG), phospholipid (PL), cholesterol (CH) and cholesterol ester (CE) contents (65.9, 25.4, 2.9 and 6.8 mg/g, respectively) obtained by the TLC/FID system were similar to those observed by other methods (67.9, 27.6, 3.0 and 8.3 mg/g, respectively). The liver lipid content in control rats also was similar to that obtained by other methods (TG, 19.0 vs 20.6; PL, 24.2 vs 21.8, CH, 2.1 vs 2.1 and CE, 1.8 vs 2.6 mg/g). Thus, the magnitude of changes in liver lipid levels due to chronic alcohol ingestion obtained by alternate methods also was found with TLC/FID. The TLC/FID system provides a convenient method for rapid analysis of the extent of fatty liver in alcohol-fed animals.

Animals↗
PubMed1985

A human histone H4 gene exhibits cell cycle-dependent changes in chromatin structure that correlate with its expression.

By use of synchronized human HeLa S3 cells, a site sensitive to both DNase I and nuclease S1 was identified 50-150 base pairs upstream of the ATG codon of a cell cycle-dependent histone H4 gene. This site expanded to include a broad region of approximately equal to 300 base pairs sensitive to DNase I throughout S phase and then narrowed again to the original site after the completion of DNA replication. The level of nuclease S1 sensitivity was greatest during early S phase, when the gene is replicated and its transcription rate is maximal. The chromatin structure of the human beta-globin gene, which is not expressed in HeLa cells, was also analyzed throughout the cell cycle, and in no case was a sub-band seen as a result of DNase I or nuclease S1 digestion, nor were there any changes in nuclease sensitivity correlated with its replication. Thus the cell cycle-dependent chromatin alterations in this histone H4 gene appear to be due to the coupled replication and expression of this gene rather than simply its replication. These results suggest that histone genes, as compared with developmentally regulated genes, exhibit an "intermediate" level of regulation whereby the gene is never in a completely inactive conformation, but changes in chromatin structure occur as a function of the cell cycle and expression.

Base Sequence↗
PubMed1984

Chromatin structure of active and inactive human X chromosomes.

Nuclei from a variety of human cell lines and tissues were digested with gradually increasing levels of DNase I. The DNA was then purified, treated with restriction enzymes and subjected to Southern blot hybridization using a cloned cDNA probe to 3-phosphoglycerate kinase (PGK) a housekeeping enzyme. At relatively high levels of DNase I, a specific, slightly sensitive site in chromatin sequences encoding PGK was observed in all of the cell types examined. This slightly sensitive site resides on the active X-chromosome since cell lines with increased numbers of inactive X-chromosomes do not show an increase in the region of chromatin which is sensitive. Except for this restricted region of enhanced sensitivity on the active X-chromosome, the data suggest that, for PGK encoding sequences, chromatin configurations on the active and inactive X-chromosomes are similar.

Base Sequence↗
PubMed1984

Fatty liver caused by chronic alcohol ingestion is prevented by dietary supplementation with pyruvate or glycerol.

Earlier studies showed that the fatty liver, caused by feeding rats the Lieber-DeCarli alcohol diet for four weeks, was prevented if the diet was supplemented with dihydroxyacetone (22 g/l), pyruvate (22 g/l) and riboflavin (2.2 g/l). In the present study, we observed that fatty liver was prevented if the alcohol diet was supplemented with glycerol and lactate (22 g/l each) and riboflavin (2.2 g/l). Hence, the prevention of alcoholic fatty liver by the dietary supplementation with dihydroxyacetone and pyruvate may not be related to their capacity to serve as hydrogen acceptors and to oxidize NADH produced during ethanol metabolism. When rats were fed the alcohol diet supplemented with either glycerol or pyruvate, the hepatic triglyceride (TG) levels were similar to those in rats pair-fed a Lieber-DeCarli control diet in which alcohol was replaced with an isocaloric amount of dextrins. Therefore, the prevention of fatty liver does not require the simultaneous presence of several supplements. Dietary dihydroxyacetone or riboflavin did not reduce alcoholic fatty liver. Supplementation of the ethanol diet with isocaloric amounts of lactate or glucose, instead of pyruvate, did not abolish the development of fatty liver but caused a marked reduction in the hepatic TG levels. Animals fed the alcohol diet consumed only small amounts of carbohydrate for long periods of time. Since the inclusion of glucose or its metabolites in the alcohol diet fed to rats caused a marked decrease in the liver TG content, it is likely that the production or prevention of fatty liver is related to carbohydrate metabolism.

Animals↗
PubMed1980

Deoxyribonuclease I generates single-stranded gaps in chromatin deoxyribonucleic acid.

Production of 10-base multiple DNA ladder fragments during DNase I digestion of chromatin is explained by a model which does not involve site-specific nicking by the DNase I. This model was tested because it explains why 10-base (actually 10.4 base) multiple-related fragments are paradoxically generated by both endonucleolytic (DNase I) and exonucleolytic (exonuclease III) mechanisms. This new model also explains the phenomenon of substantial single-stranded DNA production during DNase I digestion of chromatin. The latter phenomenon has been widely observed but is not explained by previous models. The single-stranded gap model to be presented makes testable predictions. Primarily, these are that DNase I produces single-stranded gaps in chromatin DNA and that the termini of 10-base multiple ladder fragments are separated by single-stranded gaps. Single-stranded gap production by DNase I was confirmed by a number of methods. Sensitivity of ladder band components (from DNase I but not staphylococcal nuclease digests) to S1 nuclease suggested that the ladder fragments themselves may compose a significant portion of these gaps. Separation of ladder fragment termini by single-stranded gaps was verified by demonstrating both resistance to the nick-specific NAD+-dependent ligase and sensitivity to T4 ligase which can ligate across gaps. Many single-stranded gaps, occurring both individually and clusters, were observed by electron microscopy using either cytochrome c labeling (where the gaps) are thinner than duplex) or gene 32 protein labeling (gaps thicker than duplex). Gap sizes were estimated by protecting them with gene 32 protein and digesting away unprotected duplexes. By this method, gap sizes fall into a ladder distribution (from 10 or 20 bases up to 120 bases), which, at least in the region of the shorter sizes, clearly indicates the sizes of single-stranded gaps formed in chromatin by DNase I.

Animals↗