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PubMed1996

CTG triplet repeats from the myotonic dystrophy gene are expanded in Escherichia coli distal to the replication origin as a single large event.

The expansion and contraction of CTG and CGG trinucleotide repeat sequences have been associated with several heritable genetic diseases. We developed a system for investigating the expansion of triplet repeat sequences in Escherichia coli in order to elucidate molecular mechanisms. Analysis of expanded regions using the interrupting CTA triplet sequence as a location marker within the CTG tract revealed that the expansion of large CTG repeats is one event rather than an accumulation of multiple small expansions and that the expansions occur more frequently in the region distal from the replication origin. Also, we showed that a loss of interruptions increases the expansion frequency. Thus, the instability of large triplet repeats in hereditary diseases occurs by a mechanism different from the instability in microsatellite sequences caused by defects in mismatch repair systems for certain sporadic cancers and hereditary non-polyposis colorectal cancers.

Base Sequence↗
PubMed2000

Single amino acid substitutions at the acyl-CoA-binding domain interrupt 14[C]palmitoyl-CoA binding of ACBP2, an Arabidopsis acyl-CoA-binding protein with ankyrin repeats.

Cytosolic acyl-CoA-binding proteins (ACBPs) are small proteins (ca. 10 kDa) that bind long-chain acyl-CoAs and are involved in the storage and intracellular transport of acyl-CoAs. Previously, we have characterized an Arabidopsis thaliana cDNA encoding a novel membrane-associated ACBP, designated ACBP1, demonstrating the existence of a new form of ACBP in plants (M.-L. Chye, Plant Mol. Biol. 38 (1998) 827-838). ACBP1 likely participates in intermembrane lipid transport from the ER to the plasma membrane, where it could maintain a membrane-associated acyl pool (Chye et al., Plant J. 18 (1999) 205-214). Here we report the isolation of cDNAs encoding ACBP2 (Mr 38,479) that shows conservation in the acyl-CoA-binding domain to previously reported ACBPs, and contains ankyrin repeats at its carboxy terminus. These repeats, which likely mediate protein-protein interactions, could constitute a potential docking site in ACBP2 for an enzyme that uses acyl-CoAs as substrate, in vitro binding assays on recombinant (His)6-ACBP2 expressed in Escherichia coli show that it binds 14[C]palmitoyl-CoA preferentially to 14[C]oleoyl-CoA. Analysis of the acyl-CoA-binding domain in ACBP2 was carried out by in vitro mutagenesis. Mutant forms of recombinant (His)6-ACBP2 with single amino acid substitutions at conserved residues within the acyl-CoA-binding domain were less effective in binding 14[C]palmitoyl-CoA. Northern blot analysis showed that the 1.6 kb ACBP2 mRNA, like that of ACBP1, is expressed in all plant organs. Analysis of the ACBP2 promoter revealed that, like the ACBP1 promoter, it lacks a TATA box suggesting the possibility of a housekeeping function for ACBP2 in plant lipid metabolism.

Acyl Coenzyme A↗
PubMed1994

Myotonic dystrophy CTG repeats and the associated insertion/deletion polymorphism in human and primate populations.

Myotonic dystrophy (DM) is associated with abnormal expansions of the CTG repeats in the 3' untranslated region of its gene. Previous studies in individuals of European origin demonstrated strong linkage disequilibrium between different CTG repeat length alleles and an Alu element insertion/deletion polymorphism in intron 8 of the DM gene: CTG11-13 chromosomes were almost exclusively associated with the deletion allele, while chromosomes with five or 19-30 repeats or disease chromosomes were only found on the insertion allele. One of the models suggested by these results proposed that the triplet repeats on insertion-associated chromosomes were particularly prone to mutation. Studies of other triplet repeat disorders have suggested that arrays of perfect repeats are more prone to instability than those that are interrupted. We have examined the evolution of this locus by typing a variety of primates and samples drawn from several different human populations for both CTG repeat length and the insertion/deletion polymorphism. DM gene sequences from different primates revealed inter- and intraspecies variability in the number of CTG repeats. Human chromosomes with five repeats or 11-13 repeats (the two major modes of the human CTG repeat distributions) showed no evidence of preferential stabilization of these repeat sizes by imperfect sequences. The insertion and deletion allele frequencies showed large interpopulation variation and the degree of association between these alleles and various CTG repeat lengths is not nearly as complete as was previously supposed. We have found deletion alleles carrying long normal (> 19) CTG repeats and insertion alleles associated with CTG11 - 13 in two african populations.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1998

Structure of a polyubiquitin gene in Nicotiana tabacum.

Using a tobacco ubiquitin cDNA clone as a probe, a genomic clone in EMBL3 coding for a tobacco polyubiquitin protein was isolated. Southern blot hybridization of the genomic clone with the cDNA clone identified a BamHI/EcoRI fragment of 2.5 kb to contain the coding region of polyubiquitin, and thus the fragment was subcloned into a plasmid vector. Nucleotide sequence determination of the clone identified an open reading frame for the four head-to-tail repeats of ubiquitin monomer of 76 amino acids interrupted by an intron sequence of 55 nucleotides. The four ubiquitin units were completely conserved except for the extra glutamine at the carboxy terminus of the last ubiquitin monomer. At the 5'-region upstream of the open reading frame, a sequence of 630 nucleotides was determined. In this region, well-known regulatory sequences such as the CCAAT box, TATA box and heat-shock elements could not be located; instead, a region very rich in C and T and repeats of CA was noticed. In the 3'-downstream region of the open reading frame, a sequence of 474 nucleotides was determined which contained putative polyadenylation signals and a GU-rich region.

Amino Acid Sequence↗
PubMed2002

Premutation and intermediate-size FMR1 alleles in 10572 males from the general population: loss of an AGG interruption is a late event in the generation of fragile X syndrome alleles.

We previously reported a 1:259 prevalence of female carriers of FMR1 premutation-size alleles (greater than 54 triplet repeats) in the general population. We now have screened 10 572 independent males from the same population for similar alleles using high-throughput Southern blotting. We identified 13 male carriers of an allele with more than 54 repeats. This corresponds to a prevalence of 1:813 males (95% confidence interval 1:527 to 1:1781). Haplotype analysis of four markers flanking the triplet array revealed that the prevalence of the major fragile X mutation-associated haplotype was increased among FMR1 alleles of 40-54 repeats. Although sequencing of highly unstable premutation alleles from fragile X families revealed only pure CGG tracts, this was not the case for alleles of similar size that were identified in males from the general population. Forty-eight out of forty-nine alleles of 40 or more triplets had one or two AGG interruptions. This observation, combined with the observation of the enrichment of major fragile X syndrome haplotypes in all alleles of this size, is evidence that the loss of an AGG interruption in the triplet repeat array is not necessary for expansion of normal alleles of 29-30 triplets to intermediate size. The loss of AGG interruptions thus appears to be a late event that leads to greatly increased instability and may be related to the haplotype background of specific FMR1 alleles.

Fragile X Messenger Ribonucleoprotein 1↗
PubMed1995

Evaluation of the interrupter technique for measuring change in airway resistance in 5-year-old asthmatic children.

The interrupter technique is a noninvasive method for measuring airway resistance during quiet breathing which requires minimal subject cooperation. It, therefore, has enormous potential for use in young children unable to cooperate with conventional lung function tests. We evaluated the interrupter technique during bronchial challenge with methacholine administered by the tidal breathing method in 10 5-year-old asthmatic children. The mouth pressure/time [P mo(t)] curve obtained following brief airflow interruption during the expiratory phase of quiet breathing was analyzed to determine the interrupter resistance (Rint) using four different methods: RintC, a smooth curve fit with back-extrapolation; RintEO, calculated from the pressure change after the postinterruption oscillations had decayed (end-oscillation); RintL, two-point linear fit with back-extrapolation; and RintEI, calculated from the pressure change at the end of the period of interruption. The four Rint methods were compared for repeatability and sensitivity with the direct measurement of resistance by the forced oscillation technique (Rrs), and with an independent method of measuring the response to challenge, utilizing the change in transcutaneous oxygen tension (PtcO2). The sensitivity of the methods was defined by a sensitivity index (SI), the change after challenge expressed in multiples of the baseline standard deviation. The PtcO2 method had the lowest variability and was by far the most sensitive method (geometric mean SI 18.9), at least 1 doubling concentration more sensitive than the other techniques in every subject (P < 0.05). RintL was more sensitive than the other interrupter methods (geometric mean SI: RintL 4.2; RintC 1.0; RintEO 2.7; RintEI 3.1; P < 0.05) and similar in sensitivity to Rrs (geometric mean SI 4.6) in 7 out of 10 children in which this could be measured. We conclude that the interrupter method provides a simpler method than the oscillation technique for assessing airway obstruction in this age group.

Airway Resistance↗
PubMed1989

New tandem repeat region in the non-transcribed spacer of human ribosomal RNA gene.

A new repetitive DNA region was identified in the non-transcribed spacer of human rDNA, namely a long (4.6 kb) sequence motif (Xbal element) was present in two copies. The repeating unit composed of two parts. One of them consisted of unique nucleotide sequences, interrupted by some simple sequences. The other, about 3.1 kb long one assembled only from highly repeated simple sequences. The unique sequence region contained two, inverted copies of the human AluI type repetitive DNA family. The authors suggest that the XbaI elements may flank the tandem arrays of human rRNA genes as terminal repeats and they might function both as the origin of rDNA replication and/or site of homologous recombination.

Base Sequence↗
PubMed2002

Noninvasive measurement of bladder pressure by controlled inflation of a penile cuff.

PURPOSE: A noninvasive test providing reliable objective quantification of bladder pressure during the voiding cycle would make an important contribution to the management of lower urinary tract symptoms. We developed a new noninvasive test to measure bladder pressure in males based on controlled inflation of a penile cuff during voiding. We compared the new technique with simultaneous invasive bladder pressure measurement. MATERIALS AND METHODS: We evaluated 7 volunteers and 32 patients. A conventional pressure flow study was performed first. The bladder was refilled, a penile cuff was fitted and after voiding commenced the cuff was inflated in steps of 10 cm. water every 0.75 seconds until urine flow was interrupted. The cuff was rapidly deflated, allowing flow to resume, and the cycle was repeated until the end of voiding. The flow rate was graphed against cuff pressure for each interruption cycle to determine the pressure at which flow was interrupted. This pressure was compared with simultaneous invasive isovolumetric bladder pressure. RESULTS: Invasive and noninvasive pressure measurements agreed well. Average cuff pressure at interruption of flow exceeded mean simultaneous isovolumetric bladder pressure plus or minus standard deviation by 14.5 +/- 14.0 cm. water. CONCLUSIONS: The new method provides noninvasive quantitative information on voiding bladder pressure in males. Further study is required to assess whether the technique can contribute to the management of lower urinary tract symptoms.

Adult↗
PubMed1996

Physical mapping and genomic structure of the human TNFR2 gene.

The tumor necrosis factor receptor 2 (TNFR2) gene localizes to 1p36. 2, a genomic region characteristically deleted in neuroblastomas and other malignancies. In addition, TNFR2 is the principal mediator of the effects of TNF on cellular immunity, and it may cooperate with TNFR1 in the killing of nonlymphoid cells. Therefore, we undertook an analysis of the genomic structure and precise physical mapping of this gene. The TNFR2 gene is contained on 10 exons that span 26 kb. Most of the functional domains of TNFR2 are encoded by separate exons, and each of the repeats of the extracellular cysteine-rich domain is interrupted by an intron. The genomic structure reveals a close relationship to TNFR1, another member of the TNFR superfamily. Based on electrophoretic analysis of yeast artificial chromosomes, TNFR2 maps within 400 kb of the genetic marker D1S434. In addition, we have identified a new polymorphic dinucleotide repeat within intron 4 of TNFR2. The genetic sequence information and exon-intron boundaries we have determined will facilitate mutational analysis of this gene to determine its potential role in neuroblastoma, as well as in other cancers with characteristic deletions or rearrangements of 1p36.

Amino Acid Sequence↗
PubMed1993

The Drosophila ankyrin repeat protein cactus has a predominantly alpha-helical secondary structure.

The cactus protein is the Drosophila homologue of the mammalian I kappa B family of cytoplasmic anchor proteins. We have expressed in E. coli and purified a cactus fusion protein, CACT-Bgl. CACT-Bgl protein contains the six ankyrin repeat sequences which are necessary for specific binding to the Drosophila rel family transcription factor dorsal. We show that the purified CACT-Bgl protein can bind specifically to dorsal and, using circular dichroism spectroscopy, that the protein adopts a largely alpha-helical secondary structure. A further analysis of the ankyrin repeat domains of cactus, using an improved secondary structure prediction program indicates that the N-terminal of the repeat will form into a loop structure and the C-terminal section into an interrupted, amphipathic alpha-helix. On the basis of these findings we propose that the ankyrin repeats of cactus fold together into helical bundles interconnected by diverged loops.

Amino Acid Sequence↗
PubMedDate not supplied

Study of three intragenic polymorphisms in the Machado-Joseph disease gene (MJD1) in relation to genetic instability of the (CAG)n tract.

Intergenerational instability is one of the most important features of the disease-associated trinucleotide expansions, leading to variation in size of the repeat among and within families, which manifests as variable age at onset and severity, and is probably the basis for the occurrence of anticipation. Several factors are known to affect the degree of instability, namely the type of repeated sequence, its initial size, the presence or absence of interruptions in the repetitive tract and the gender of the transmitting parent. A recent study demonstrated the effect of an intragenic polymorphism (C987GG/G987GG) in the Machado-Joseph disease causative gene, immediately downstream of the CAG repeat, on the intergenerational instability of the expanded repeat. Surprisingly, there was an effect not only of the specific allele in cis to the disease chromosome, but also of the allele on the normal chromosome, suggesting the existence of an interaction between the normal and expanded alleles that affects the fidelity of replication of the (CAG)n tract. This effect could be a direct effect of the polymorphism studied or, alternatively, this polymorphism could be in disequilibrium with some other flanking sequence which affects the instability of the repetitive (CAG)n tract. In order to confirm the previous results in a different population and to distinguish between a direct and indirect effect of the CGG/GGG polymorphism, we typed 70 parent-progeny pairs for which the variation in the (CAG)n length in the MJD1 gene was known, for three intragenic polymorphisms: C987GG/G987GG and two additional, newly described ones, TAA1118/TAC1118 and A669TG/G669TG. We also typed a control population of 125 individuals for the A669TG/G669TG, C987GG/G987GG and TAA1118/TAC1118 polymorphisms, in an attempt to identify any association between haplotype and (CAG)n length in normal chromosomes, suggestive of an instability-predisposing effect of the repeat-flanking sequences, which could have led to the origin of the MJD mutation in the human population. We confirmed the effect of the C987GG/G987GG polymorphism on intergenerational instability when present in trans. Our results suggest that this effect is restricted to a small region of the gene, immediately downstream of the CAG repeat, which includes this particular nucleotide substitution and the stop codon of the MJD1 cDNA, and is not a more widespread chromosomal effect. The lack of a significant association of any specific intragenic haplotype with larger CAG repeats in normal chromosomes, together with the absence of an effect of the intragenic haplotype in cis on the intergenerational instability of the expanded (CAG)n in MJD families does not indicate the existence of an instability-predisposing haplotype.

Alleles↗
PubMed1993

Ischemia with intermittent reperfusion reduces functional and morphologic damage following renal ischemia in the rat.

Attempts to minimize ischemic injury by interrupting a given ischemic period might be compromised if repeated bouts of reperfusion injury occurred. To determine whether intermittent ischemia improved or worsened functional and morphologic outcome of renal ischemia, halothane-anesthetized rats underwent a right nephrectomy and placement of a snare about the left renal vascular pedicle at 37 degrees C. Eleven animals underwent 45 minutes of continuous renal ischemia (C-ISC), whereas 10 animals received 45 minutes of vessel occlusion interrupted (I-ISC) at 15 and 30 minutes by snare release and 5 minutes of reperfusion. A group of three sham rats underwent the above procedure but did not have the snare tightened. Blood samples were drawn preoperatively and 24, 48, and 72 hours postoperatively for creatinine analysis. At 72 hours the animals were sacrificed and their kidneys morphologically evaluated. The C-ISC group had a significantly higher mean postoperative plasma creatinine (p < 0.01) as well as significantly higher plasma creatinine levels at 24 (p < 0.005) and 48 hours (p < 0.05) than did the I-ISC group. The C-ISC group also demonstrated significantly greater histologic damage than the I-ISC group (p < 0.002) when assessed by a pathologist blinded to the intervention. Sham rats did not demonstrate functional or morphologic damage. These data demonstrate a significantly improved outcome when 45 minutes of renal ischemia is interrupted by periods of reperfusion. We are led to conclude that in this setting reperfusion injury did not overwhelm the salutary effects of interrupting the 45-minute ischemic event.

Animals↗
PubMed2001

Human intrachromosomal telomeric-like repeats: sequence organization and mechanisms of origin.

The intrachromosomal location of (T2AG3)n telomeric sequences has been reported in several species. It was proposed that interstitial telomeres (ITs) originated through telomeric fusion of ancestral chromosomes. However, the data so far obtained derive mainly from cytogenetic observations. Cloning and database searching of human IT sequences allowed us to identify three classes: (i) short ITs, composed of few, essentially exact T2AG3 units; (ii) subtelomeric ITs, composed of larger arrays (several hundred base pairs) including many degenerate units within subtelomeric domains; (iii) fusion ITs, in which two extended stretches of telomeric repeats are oriented head-to-head. The number of short ITs is over 50 and subtelomeric ITs are probably present at all chromosomal ends. Surprisingly, the telomeric sequence in 2q13 remains the only fusion IT so far characterized, and evidence presented here suggests that another member of this class may be present in 1q41. Different molecular mechanisms generated the three classes. In particular, several short ITs interrupt precisely repetitive elements or are flanked by direct repeats of 10-41 bp, and are conserved in gorilla and chimpanzee. These features strongly suggest that telomeric repeats were inserted at intrachromosomal sites through the repair of double-strand breaks that occurred in the germline during evolution.

Animals↗
PubMed1988

Molecular cloning and sequencing of a murine pgk-1 pseudogene family.

Seven genomic mouse DNA fragments carrying pgk-1-homologous regions have been cloned and sequenced. They have to be classified as processed genes because intervening sequences, present in their productive counterpart, are absent. Four pseudogenes (I-IV) represent nearly the complete sequence of pgk-1 cDNA. Two of these genes (I and II), although rather different from the published mouse pgk-1 cDNA in the 3'-untranslated region, represent the actual mouse pgk-1 cDNA sequence in the coding part except for substitutions in the third position of three codons. These genes can code for a functional PGK protein but, lacking as they do classical promoter structures, are probably not expressed. They show the typical characteristics of retroposons, being flanked by A-rich regions and direct repeats which are localized at the positions where the homology with the mouse pgk-1 cDNA is interrupted. Pseudogenes III and IV have numerous mutations. Gene III is also flanked by direct repeats, whereas gene IV is flanked by inverted repeats. The other three genes are flanked by direct repeats localized further inside the target sites. They are truncated and mutated extensively as usually observed with pseudogenes.

Animals↗
PubMed2003

Alpha-helical coiled-coil oligomerization domains are almost ubiquitous in the collagen superfamily.

Alpha-helical coiled-coils are widely occurring protein oligomerization motifs. Here we show that most members of the collagen superfamily contain short, repeating heptad sequences typical of coiled coils. Such sequences are found at the N-terminal ends of the C-propeptide domains in all fibrillar procollagens. When fused C-terminal to a reporter molecule containing a collagen-like sequence that does not spontaneously trimerize, the C-propeptide heptad repeats induced trimerization. C-terminal heptad repeats were also found in the oligomerization domains of the multiplexins (collagens XV and XVIII). N-terminal heptad repeats are known to drive trimerization in transmembrane collagens, whereas fibril-associated collagens with interrupted triple helices, as well as collagens VII, XIII, XXIII, and XXV, were found to contain heptad repeats between collagen domains. Finally, heptad repeats were found in the von Willebrand factor A domains known to be involved in trimerization of collagen VI, as well as in collagen VII. These observations suggest that coiled-coil oligomerization domains are widely used in the assembly of collagens and collagen-like proteins.

Amino Acid Sequence↗
PubMed2000

Removal of microsatellite interruptions by DNA replication slippage: phylogenetic evidence from Drosophila.

Microsatellites are tandem repetitions of short (1-6 bp) motifs. It is widely assumed that microsatellites degenerate through the accumulation of base substitutions in the repeat array. Using a phylogenetic framework, we studied the evolutionary dynamics of interruptions in three Drosophila microsatellite loci. For all three loci, we show that the interruptions in a microsatellite can be lost, resulting in a longer uninterrupted microsatellite stretch. These results indicate that mutations in the microsatellite array do not necessarily lead to decay but may represent only a transition state during the evolution of a microsatellite. Most likely, this purification of interrupted microsatellites is caused by DNA replication slippage.

Animals↗
PubMed2004

Hepatitis C virus incidence among injecting drug users on opioid replacement therapy.

OBJECTIVE: To determine hepatitis C virus (HCV) incidence among injecting drug users (IDUs) receiving opioid replacement therapy (ORT). METHODS: A retrospective cohort study was established in a primary care drug dependency treatment clinic. The cohort included all IDUs who commenced ORT after January 1996 with an initial anti-HCV antibody negative result and repeat testing prior to July 2003. HCV incidence was estimated for all subjects, with further comparison among those with continuous versus interrupted ORT. RESULTS: Fifty-four subjects were initially HCV antibody negative and had repeat testing. Five cases of HCV antibody seroconversion occurred during a total follow-up period of 131.1 person years (py), an incidence of 3.8/100 py (95% CI 1.2-8.9/ 100 py). Four seroconversions occurred in the subgroup with interrupted ORT (n=20), an incidence of 7.4/100 py (95% CI 2.0-18.9/100 py), compared with one seroconversion in the subgroup with continuous ORT (n=34), an incidence of 1.3/100 py (95% CI 0.03-7.3/100 py). CONCLUSIONS: HCV incidence among IDUs receiving ORT in our clinic was relatively low. Those IDUs without interruptions to their treatment appeared to be at particularly low risk of HCV infection. These findings support the role of ORT in HCV prevention for IDUs.

Adult↗
PubMed2002

Effects of inhaled gentamicin prophylaxis on acquisition of Pseudomonas aeruginosa in children with cystic fibrosis: a pilot study.

Inhaled antibiotics are an established treatment for chronic Pseudomonas aeruginosa (PA) infection in patients with cystic fibrosis (CF). However, inhaled antibiotics might also have prophylactic potential to delay acquisition of PA in early stages of the disease. From 1986-1999, all CF patients at this center who experienced defined risk situations for acquisition of PA (28 patients) received inhaled gentamicin (80 mg BID for those < 12 months; 120 mg BID for those > 12 months) for a minimum of 3 years. Twelve patients had repeated risk situations and continued this prophylaxis without interruption during the entire study period (group 1). In the remaining 16 patients, inhaled antibiotics were discontinued at various times for a variety of reasons (group 2). None of the patients in group 1, but 7 in group 2, became chronically infected with PA (P = 0.01). Lung function and chest X-ray scores were significantly worse in those 7 infected patients, when compared to the noninfected ones in both groups. This suggests that long-term-prophylaxis with inhaled gentamicin can effectively delay acquisition of PA and decrease disease progression in children with CF.

Anti-Bacterial Agents↗