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PubMed2002

A new case of dup(3q) syndrome due to a pure duplication of 3qter.

The characteristic clinical features of the dup(3q) syndrome include typical facial features, mental and growth retardation, and (often) congenital heart anomalies. However, pure duplication of 3qter is rare because most of the reported cases are patients who carry an unbalanced translocation and, in addition to the duplication for 3qter, have a deletion for another chromosomal segment. A new case with a pure duplication of 3q detected in a 2-month-old boy is presented here. Extensive cytogenetic analysis revealed an inverted duplication of the distal part of 3q (chromosomal band 3q26.3 up to the telomere), with no (detectable) loss of the original telomeric sequences. Clinical evaluation revealed several phenotypic hallmarks characteristic for the dup(3q) syndrome. By comparing the duplicated region of this patient with the duplicated regions of the other patients with a pure duplication of 3q, we were able to localize the critical region for the dup(3q) phenotype to band 3q26.3. Alongside this new case with a pure duplication of 3q, an overview of six previous cases is given.

Chromosome Aberrations↗
PubMed1997

Molecular evidence for an ancient duplication of the entire yeast genome.

Gene duplication is an important source of evolutionary novelty. Most duplications are of just a single gene, but Ohno proposed that whole-genome duplication (polyploidy) is an important evolutionary mechanism. Many duplicate genes have been found in Saccharomyces cerevisiae, and these often seem to be phenotypically redundant. Here we show that the arrangement of duplicated genes in the S. cerevisiae genome is consistent with Ohno's hypothesis. We propose a model in which this species is a degenerate tetraploid resulting from a whole-genome duplication that occurred after the divergence of Saccharomyces from Kluyveromyces. Only a small fraction of the genes were subsequently retained in duplicate (most were deleted), and gene order was rearranged by many reciprocal translocations between chromosomes. Protein pairs derived from this duplication event make up 13% of all yeast proteins, and include pairs of transcription factors, protein kinases, myosins, cyclins and pheromones. Tetraploidy may have facilitated the evolution of anaerobic fermentation in Saccharomyces.

Chromosomes, Fungal↗
PubMed2000

Duplicated popliteal and superficial femoral veins: incidence and potential significance.

BACKGROUND: Duplication of the popliteal and superficial femoral veins (PV, SFV) is a normal variant previously reported in up to 25% of limbs. Little clinical significance, however, has been attributed to this apparently common anomaly. The present study was designed to determine the incidence of duplications in individuals presenting for venous incompetence studies, and whether their presence could, in theory, act as a predisposing factor to deep venous thrombosis (DVT) formation. METHODS: Duplex ultrasound examinations were performed in which venous duplications were actively searched for and recorded. The diameters of both limbs of any duplicated system and the single vessel immediately distal to it were recorded. Using these measurements, the changes in total cross-sectional area (CSA) associated with these anomalies were calculated. In addition, with the knowledge that the volume flow rate must remain constant, the velocity changes associated with such systems were calculated. RESULTS: A total of 248 limbs from 177 patients was scanned. Duplications were found in 39 (15.7%) of these limbs. Of these, 30 limbs (77%) involved only the SFV, seven (18%) involved both the SFV and PV, and two (5%) involved only the PV. Short-segment SFV duplications were used to calculate the percentage change in total CSA and therefore blood flow velocities. Of the 13 (33%) suitable for such calculations, and calculating for each individual duplicated system, a mean increase in the vessel's total CSA of 42%, which corresponded to a theoretical decrease in blood flow velocity of 36%, was found. CONCLUSION: The present study confirms the significantly high incidence of duplications of the PV and SFV and raises the possibility of the potential for DVT formation secondary to changes in flow velocities.

Adolescent↗
PubMed1998

Segmental duplication of the fetal anterior cerebral artery.

Segmental duplications (also termed 'fenestrations') of the fetal anterior cerebral artery are a relatively rare anomaly. Their occurrence was studied in 200 fetuses at 20-40 wk gestational age. Duplications were found in 21 of the 200 fetuses, i.e. 10.5%. In 2 fetuses, i.e. 1%, the duplications were bilateral. In 1 case, i.e. 0.5%, 2 duplications were found on the left anterior cerebral artery. There were 15 segmental duplications on the left anterior cerebral artery, i.e. 62.5% of all duplications, and 9 on the right, i.e. 37.5%. The duplications were located in the distal part of the A1 segment in 45.7%, at the level of the anterior communicating artery (A1-A2) in 37.7%, and in the initial part of the A2 segment in 16.6%. The duplications had 4 different forms namely oviform, fissured, triangular and punctate.

Cerebral Arteries↗
PubMed1986

Duodenal duplication--a case with special features.

A duodenal duplication almost as large as the stomach proper was found along the greater curvature of the stomach in a 6-month-old Caucasian girl. There was a wide communication with the proximal part of the duodenum, from which the duplication blood supply originated. The duplication and the stomach shared the serosal lining, but had individual, full thickness walls. The duplication was removed in toto, and the communication with the duodenum was closed by transverse suture. The luminal lining of the duplication consisted of corpus type of gastric mucosa. There was a 1 X 1 cm mucosal ulceration in the region of which respiratory tract elements were found. The condition is interpreted as a duodenal duplication with ectopic gastric mucosa and respiratory tract elements. To our knowledge, the occurrence of respiratory tract elements in an intestinal duplication BELOW the diaphragm is being reported for the first time. It offers a challenging explanation for the ulceration found within this duplication.

Barium Sulfate↗
PubMed1981

Spontaneous tandem genetic duplications in Salmonella typhimurium arise by unequal recombination between rRNA (rrn) cistrons.

A method is described to detect and measure the frequency of spontaneous tandem genetic duplications located throughout the Salmonella genome. The method is based on the ability of duplication-containing strains to inherit two selectable alleles of a single gene during generalized transductional crosses. One allele of the gene carries an insertion of the translocatable tetracycline-resistance element Tn10; the other allele is a wild-type copy of that gene. Using this technique, we have measured the frequency of tandem duplications at 38 chromosomal sites and the amount of material included in 199 independent duplications. These results suggest that, in one region of the chromosome, tandem duplications are particularly frequent events. Such duplications have end points within rRNA (rrn) cistrons and probably arise by unequal cross-over between these dispersed repeated sequences. Spontaneously duplications of this type are harbored by as much as 3% of the bacterial population. Preliminary evidence suggests that such duplications may play a significant regulatory role under conditions of rapid growth. Our analysis has suggested the position on the genome of an additional rRNA cistron.

Base Sequence↗
PubMed1998

Extent of genomic rearrangement after genome duplication in yeast.

Whole-genome duplication approximately 10(8) years ago was proposed as an explanation for the many duplicated chromosomal regions in Saccharomyces cerevisiae. Here we have used computer simulations and analytic methods to estimate some parameters describing the evolution of the yeast genome after this duplication event. Computer simulation of a model in which 8% of the original genes were retained in duplicate after genome duplication, and 70-100 reciprocal translocations occurred between chromosomes, produced arrangements of duplicated chromosomal regions very similar to the map of real duplications in yeast. An analytical method produced an independent estimate of 84 map disruptions. These results imply that many smaller duplicated chromosomal regions exist in the yeast genome in addition to the 55 originally reported. We also examined the possibility of determining the original order of chromosomal blocks in the ancestral unduplicated genome, but this cannot be done without information from one or more additional species. If the genome sequence of one other species (such as Kluyveromyces lactis) were known it should be possible to identify 150-200 paired regions covering the whole yeast genome and to reconstruct approximately two-thirds of the original order of blocks of genes in yeast. Rates of interchromosome translocation in yeast and mammals appear similar despite their very different rates of homologous recombination per kilobase.

Chromosome Mapping↗
PubMed1960

Asynchronous duplication of chromosomes in cultured cells of Chinese hamster.

Chromosome duplication (DNA synthesis) was studied in cultured cells of Chinese hamsters by means of autoradiography following thymidine-H(3) incorporation. The technique used was to expose an asynchronously dividing population of rapidly growing cells for a 10 minute interval to a medium with thymidine-H(3). Cells were then transferred to a medium with excess unlabeled thymidine. The population was sampled at intervals thereafter and studies made of the frequency of labeled interphases and division figures, and the patterns of labeling of specific chromosomes. The average generation time during these experiments was about 14 hours. DNA synthesis occurred during an interval of about 6 hours and stopped 2 to 3 hours before metaphase. After metaphase the chromosomes usually begin duplication again within 5 to 6 hours. Grain counting, to estimate the amount of tritium incorporated after a short contact with thymidine-H(3) and at intervals after transfer to a medium with excess unlabeled thymidine, indicated that the intracellular pool of labeled precursors was diluted within less than a minute so that further labeling would not be detected. The chromosomes labeled during the contact period retained their precise pattern of labeling through another duplication cycle and no turnover of DNA or loss of tritium was detectable. Five or 6 chromosomes of the complement have segments typically late in duplication. Two of these are the X and Y chromosomes. The long arm of the X chromosome and the whole Y chromosome are duplicated in the last half of the interval of DNA synthesis. The short arm of the X chromosome in a male strain is duplicated in the first half of the interval. In another strain (female), one X chromosome had the same timing, but the other one was all duplicated in the last half of the period of DNA synthesis. The DNA in the short arms of 2 medium sized chromosomes, as well as most of the DNA in 1 or 2 of the smallest chromosomes of the complement was replicated late. The study has led to the hypothesis that various chromosomes or parts of chromosomes have a genetically controlled sequence in duplication which may have some functional significance.

Animals↗
PubMed2005

Gag-p6 Tsg101 binding site duplications in maternal-infant HIV infection.

Prevalence and patterns of HIV p6 duplications in HIV-1 mother-to-baby transmission are examined. Resistance genotyping was performed in a multisite U.S. study of antiretroviral resistance in vertical transmission. Sequence data were used in secondary analyses of HIV genetic variation. Two hundred sixty HIV viral RNA samples from HIV-infected pregnant women and their infants were analyzed with a commercial resistance genotyping kit. Chromatograms were examined for variability in the 3' region of gag. From 103 mother-baby sets, 190 samples gave readable p6 sequence. Of 103 mother-baby sets, 20 (19%) showed duplication of between 3 and 12 codons ending at the PTAPP motif of p6. When maternal p6 duplication was present and the p6 sequence was available from both maternal and infant isolates, all (seven of seven) infants had p6 duplications, but two cases showed discordancies between maternal and infant sequences. The prevalence of p6 duplication varied among geographical sites, ranging from 4 of 43 families (9%, Puerto Rico and New York sites) to 16 of 60 families (27%, Massachusetts, Texas, and Illinois). The presence of p6 duplication was not associated with differences in transmission, viral load, or disease progression in the infants, but showed a trend toward association with lower maternal CD4 count. Substantial p6 variation data are generated by resistance genotyping. PTAP duplication is prevalent in this group of HIV-infected women and infants. The duplication is efficiently transmitted from mother to infant, is present at variable prevalence at different geographic sites, and shows no clear association with vertical transmission risks.

Base Sequence↗
PubMed1985

Meiotic recombination between duplicated genetic elements in Saccharomyces cerevisiae.

We have studied the meiotic recombination behavior of strains carrying two types of duplications of an 18.6-kilobase HIS4 Bam HI fragment. The first type is a direct duplication of the HIS4 Bam HI fragment in which the repeated sequences are separated by Escherichia coli plasmid sequences. The second type, a tandem duplication, has no sequences intervening between the repeated yeast DNA. The HIS4 genes in each region were marked genetically so that recombination events between the duplicated segments could be identified. Meiotic progeny of the strains carrying the duplication were analyzed genetically and biochemically to determine the types of recombination events that had occurred. Analysis of the direct vs. tandem duplication suggests that the E. coli plasmid sequences are recombinogenic in yeast when homozygous. In both types of duplications recombination between the duplicated HIS4 regions occurs at high frequency and involves predominantly interchromosomal reciprocal exchanges (equal and unequal crossovers). The striking observation is that intrachromosomal reciprocal recombination is very rare in comparison with interchromosomal reciprocal recombination. However, intrachromosomal gene conversion occurs at about the same frequency as interchromosomal gene conversion. Reciprocal recombination events between regions on the same chromatid are the most infrequent exchanges. These data suggest that intrachromosomal reciprocal exchanges are suppressed.

Chromosomes↗
PubMed1994

Sequences with the potential to form stem-and-loop structures are associated with coding-region duplications in animal mitochondrial DNA.

Tandem duplications of gene-encoding regions occur in the mitochondrial DNA (mt DNA) of some individuals belonging to several species of whiptail lizards (genus Cnemidophorus). All or part of the duplicated regions of the mtDNAs from five different species were sequenced. In all, the duplication endpoints were within or immediately adjacent to sequences in tRNA, rRNA or protein genes that are capable of forming energetically stable stem-and-loop structures. In two of these mtDNAs, the duplication endpoints were also associated with a direct sequence repeat of 13 bp. The consistent association of stem-and-loop structures with duplication endpoints suggests that these structures may play a role in the duplication process. These data, combined with the absence of direct or palindromic repeats at three of the pairs of duplication endpoints, also suggest the existence of a mechanism for generating de novo duplications that is qualitatively different from those previously modeled.

Animals↗
PubMed1975

The use of duplication-generating rearrangements for studying heterokaryon incompatibility genes in Neurospora.

Heterokaryon (vegetative) incompatibility, governing the fusion of somatic hyphal filaments to form stable heterokaryons, is of interest because of its widespread occurrence in fungi and its bearing on cellular recognition. Conventional investigations of the genetic basis of heterokaryon incompatibility in N. crassa are difficult because in commonly used stocks differences are present at several het loci, all with similar incompatibility phenotypes. This difficulty is overcome by using duplications (partial diploids) that are unlikely to contain more than one het locus. A phenotypically expressed incompatibility reaction occurs when unlike het alleles are present within the same somatic nucleus, and this parallels the heterokaryon incompatibility reaction that occurs when unlike alleles in different haploid nuclei are introduced into the same somatic hypha by mycelial fusion. - Nontandem duplications were used to confirm that the incompatibility reactions in heterokaryons and in duplications are alternate expressions of the same genes. This was demonstrated for three loci which had previously been established by conventional heterokaryon test-het-e, het-c and mt. These were each obtained in duplications as recombinant chromosome rearrangements. The particular method of producing the duplications is irrelevant so long as the incompatibility alleles are heterozygous. - The duplication technique has made it possible to determine easily the het-e and het-c genotypes of numerous laboratory and wild strains of unknown constitution. In laboratory strains both loci are represented simply by two alleles. Analysis of het-c is more complicated in some wide strains, where differences have been demonstrated at one or more additional het loci within the duplication used and multiple allelism is also possible. - The results how that the duplication method can be used to identify and map additional vegetative incompatibility loci, without the necessity of heterokaryon tests.

Alleles↗
PubMed1993

An intraspecific gene duplication polymorphism of the urate oxidase gene of Drosophila virilis: a genetic and molecular analysis.

Nineteen strains of Drosophila virilis from diverse geographic locations were examined by genetic and molecular analyses, revealing (a) 12 strains with a single copy of the urate oxidase (UO) gene per haploid genome and (b) 7 strains with a tandem duplication of the UO locus. The D. virilis strains with the UO duplication appear to have identical restriction maps of this region, implying either a single origin for the duplication or several similar events occurring at a hot spot. On the basis of the location of the duplication breakpoints and the restriction sites flanking these breakpoints, this duplication probably arose through nonhomologous recombination involving either a breakage and rejoining event or replication slippage. because documented cases of intraspecific gene duplication polymorphism are rare, the D. virilis UO duplication will be useful in identifying the molecular event giving rise to a gene duplication.

Animals↗
PubMed1989

Surgical management of alimentary tract duplications.

Alimentary tract duplications are unusual anomalies that may require surgical intervention in the neonate, infant, and occasionally in the older child. The clinical presentation of patients with alimentary tract duplications includes bleeding, abdominal pain, intussusception, and respiratory distress, or it may be an incidental finding on either abdominal examination or chest x-ray. A review of 96 patients with 101 duplications seen over the last 37 years is reported herein. Twenty-one duplications were confined to the thorax; three were thoracoabdominal, and 77 were abdominal. Seventy-four patients presented as infants less than 2 years of age, and 22 patients were older. Ectopic gastric mucosa was found in 21 duplications, and pancreatic tissue was found in five. Seventy-five duplications were cystic and 26 were tubular. Ultrasonography, computed tomography (CT), and myelography are helpful diagnostic tools. Ninety-four of the 96 patients underwent surgical management for their duplications. One duplication was found at necropsy, and one patient was asymptomatic and did not undergo operation. A single death occurred in a 2-day-old infant who had intrauterine volvulus and meconium peritonitis. Management was based on the age and condition of the patient, the location of the lesion, whether it was cystic or tubular and communicating with the true intestinal lumen, and whether it involved one or more anatomic locations. Generally, total excision was preferred, but staged approaches were sometimes necessary.

Adolescent↗
PubMed1991

A detailed analysis of duplications appearing during early, high multiplicity infections with polyoma virus.

Serial undiluted passage of polyoma virus derived from transfection of mouse fibroblasts with well defined wild-type genomes results in the appearance of a very heterogeneous population of defective virus particles. Many of these variants show duplications which not only contain the cis-acting region minimally required for efficient replication, but also other regions. A detailed analysis of the duplication patterns appearing in high multiplicity infections is presented. We performed heteroduplex analyses of duplicated fragments using mung bean nuclease and demonstrated that the pattern of duplication junctions is conserved qualitatively and quantitatively. However, the distribution of fragment sizes varied in a number of independently derived virus stocks. Amplification of viral nucleotide sequences is an early event in virus replication, occurring at least as early as 3 days post-transfection. The pattern of duplication did not change significantly in successive early passages at high multiplicity. Although duplication was accompanied by deletion of various parts of the viral genome, a sequence bordering the duplications at the late side of the origin of replication was retained as a single copy in all defective viruses. The relevance of these findings to the mechanism that creates the duplications and the biological activity of defective virus is discussed.

Animals↗
PubMed2003

Some asymptotic properties of duplication graphs.

Duplication graphs are graphs that grow by duplication of existing vertices, and are important models of biological networks, including protein-protein interaction networks and gene regulatory networks. Three models of graph growth are studied: pure duplication growth, and two two-parameter models in which duplication forms one element of the growth dynamics. A power-law degree distribution is found to emerge in all three models. However, the parameter space of the latter two models is characterized by a range of parameter values for which duplication is the predominant mechanism of graph growth. For parameter values that lie in this "duplication-dominated" regime, it is shown that the degree distribution either approaches zero asymptotically, or approaches a nonzero power-law degree distribution very slowly. In either case, the approach to the true asymptotic degree distribution is characterized by a dependence of the scaling exponent on properties of the initial degree distribution. It is therefore conjectured that duplication-dominated, scale-free networks may contain identifiable remnants of their early structure. This feature is inherited from the idealized model of pure duplication growth, for which the exact finite-size degree distribution is found and its asymptotic properties studied.

Models, Statistical↗
PubMed1979

Duplications of the lower urinary tract in children.

Seven cases of bladder duplication are described, and compared with 27 cases of urethral duplication. Bladder duplication was collateral while urethral duplication was usually in the sagittal plane. The conditions may coexist when the duplication of the bladder extends caudally to produce a collateral urethral duplication, but in one boy bladder duplication was associated with 4 urethrae in the sagittal plane. In 5 cases the bladders were united; in 2 cases, one bladder was excised. The results were satisfactory in 6 and in one the bladder failed to empty. The basic defects that lead to duplication are unknown. Several features of the conditons suggest that there are different aetiologies in each type. There are similarities with the exstrophy epispadias complex. Even when there are major abnormalities in other systems the general and urological prognosis is good.

Abnormalities, Multiple↗
PubMed2003

Effect of duplicate isolates of methicillin-susceptible and methicillin-resistant Staphylococcus aureus on antibiogram data.

Duplicate Staphylococcus aureus isolates were analyzed to determine the impact of multiple isolates from the same patient on annual antibiogram data. During a 6-year period (1996 to 2001), 3,227 patients with 4,844 S. aureus isolates were evaluated. A total of 39% of patients with methicillin-resistant S. aureus (MRSA) (n = 860) and 23% of patients with methicillin-susceptible S. aureus (MSSA) (n = 2,367) infections had duplicate isolates. Cumulative data show that 91% of the patients during this 6-year period with duplicate isolates (2 to 13 duplicates/year) did not switch between MSSA and MRSA but retained the original S. aureus strain whether it was MSSA or MRSA. Rates of MRSA were calculated for each year by using all isolates and then eliminating duplicates. The impact of duplicate MRSA and MSSA isolates was evaluated by using the ratio of isolates per patient such that ratios of >1.0 indicate >1 isolate per patient. The 6-year ratio for MRSA was 1.90 isolates/patient, and the ratio for MSSA was 1.35. A significant difference (P < 0.05) was noted in the MRSA rates in 4 of 6 years when duplicate isolates were removed. Common phenotypic antibiogram patterns were compared for all MRSA isolates during the 6-year period, and 64% were of a single antibiogram phenotype. Eighty-eight percent of patients with duplicate MRSA isolates had phenotypically identical multiple isolates. The rate of MRSA differs when duplicate isolates are removed from the antibiogram data.

Anti-Bacterial Agents↗