Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Duplication”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 325 records · Page 18Linked to original sources
PubMed2004

Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis.

In plants, duplication of individual genes, long chromosomal regions, and complete genomes provides a major source for evolutionary innovation. We investigated two different types of duplications, tandem and segmental duplications, in Arabidopsis for correlation, conservation, and differences of expression characteristics by making use of large genome-wide expression data as measured by the massively parallel signature sequencing method. Our analysis indicates that large fractions of duplicated gene pairs still share transcriptional characteristics. However, our results also indicate that expression divergence occurs frequently between duplicated gene pairs, a process which frequently might be employed for the retention of sequence redundant gene pairs. Preserved overall similarity between promoters of duplicated genes as well as preservation of individual cis-elements within the respective promoters indicates that the process of transcriptional neo- and subfunctionalization is restricted to only a fraction of cis-elements. We show that sequence similarities and shared regulatory properties within duplicated promoters provide a powerful means to undertake large-scale cis-regulatory element identification by applying an intragenomic phylogenetic footprinting approach. Our work lays a foundation for future comparative studies to elucidate the molecular manifestation of regulatory similarities and dissimilarities of duplicated genes.

Arabidopsis↗
PubMed2005

Asymmetric evolution of duplicate genes encoding the CCAAT-binding factor NF-Y in plant genomes.

NF-Y is a ubiquitous CCAAT-binding factor composed of NF-YA, NF-YB and NF-YC. Multiple genes encoding NF-Y subunits have been identified in plant genomes. It remains unclear whether the duplicate genes underwent different evolutionary patterns. Likelihood-ratio tests were used to examine whether the amino acid substitution rates are the same between duplicate genes. The influences of selection on evolution were evaluated by comparing the conservative and radical amino acid substitution rates, as well as maximum-likelihood analysis. Some NF-YB and NF-YC duplicates showed significant evidence of asymmetric evolution but not the NF-YA duplicates. Most amino acid replacements in the NF-YB and NF-YC duplicates result in changes in hydropathy, polar requirement and polarity. The physicochemical changes in the sequences of NF-YB seem to be coupled to asymmetric divergence in gene function. Plant NF-Y genes have evolved in different patterns. Relaxed selective constraints following gene duplication are most likely responsible for the unequal evolutionary rates and distinct divergence patterns of duplicate NF-Y genes. Positive selection may have promoted amino acid hydropathy changes in the NF-YC duplicates.

Amino Acid Substitution↗
PubMed2005

Duplication and DNA segmental loss in the rice genome: implications for diploidization.

* Large-scale duplication events have been recently uncovered in the rice genome, but different interpretations were proposed regarding the extent of the duplications. * Through analysing the 370 Mb genome sequences assembled into 12 chromosomes of Oryza sativa subspecies indica, we detected 10 duplicated blocks on all 12 chromosomes that contained 47% of the total predicted genes. Based on the phylogenetic analysis, we inferred that this was a result of a genome duplication that occurred c. 70 million years ago, supporting the polyploidy origin of the rice genome. In addition, a segmental duplication was also identified involving chromosomes 11 and 12, which occurred c. 5 million years ago. * Following the duplications, there have been large-scale chromosomal rearrangements and deletions. About 30-65% of duplicated genes were lost shortly after the duplications, leading to a rapid diploidization. * Together with other lines of evidence, we propose that polyploidization is still an ongoing process in grasses of polyploidy origins.

Biological Evolution↗
PubMed1995

Duplicate publication in the nursing literature.

The purpose of this study was to identify examples of duplicate publication in the nursing literature and determine what types of duplicate articles are published. From the sample of 642 articles published by 77 authors during a 5-year period, 181 articles were classified as duplicate. Forty-one authors published at least one form of duplicate article. Fifty-nine duplicate articles did not reference the primary article. Duplicate publication itself is not unethical, but duplicate publication without referencing duplicate work is unethical and may violate copyright law.

Authorship↗
PubMed2004

Genomic background predicts the fate of duplicated genes: evidence from the yeast genome.

Gene duplication with subsequent divergence plays a central role in the acquisition of genes with novel function and complexity during the course of evolution. With reduced functional constraints or through positive selection, these duplicated genes may experience accelerated evolution. Under the model of subfunctionalization, loss of subfunctions leads to complementary acceleration at sites with two copies, and the difference in average rate between the sequences may not be obvious. On the other hand, the classical model of neofunctionalization predicts that the evolutionary rate in one of the two duplicates is accelerated. However, the classical model does not tell which of the duplicates experiences the acceleration in evolutionary rate. Here, we present evidence from the Saccharomyces cerevisiae genome that a duplicate located in a genomic region with a low-recombination rate is likely to evolve faster than a duplicate in an area of high recombination. This observation is consistent with population genetics theory that predicts that purifying selection is less effective in genomic regions of low recombination (Hill-Robertson effect). Together with previous studies, our results suggest the genomic background (e.g., local recombination rate) as a potential force to drive the divergence between nontandemly duplicated genes. This implies the importance of structure and complexity of genomes in the diversification of organisms via gene duplications.

Evolution, Molecular↗
PubMed2006

Genome duplications of early vertebrates as a possible chronicle of the evolutionary history of the neural crest.

It is now accepted that ancestral vertebrates underwent two rounds of genome duplication. Here we test the possible utility of these genome duplication events as a reference time for the evolutionary history of vertebrates, by tracing the molecular evolutionary history of the genes involved in vertebrate neural crest development. For most transcription factors that are involved in neural crest specification, more than two paralogs are involved in that process. These were likely involved in the specification of the neural crest before the genome duplications occurred in ancestral vertebrates, although FoxD3 may have acquired that role after the genome duplications. By contrast, the epithelial-mesenchymal transition of neural crest cells is controlled by genes that evolved after the genome duplications, such as cadherin6, cadherin7, cadherin11, and rhoB. This suggests that primitive neural crest cells control their delamination by using a small or distinct set of cell adhesion molecules. Alternatively, these observations suggest that delamination of the neural crest evolved after the genome duplications. In that case, the neural crest might have evolved in sequential steps; the specification of the neural crest occurred before the genome duplications, and the neural crest acquired a new cell migration property after the genome duplications.

Animals↗
PubMed2001

New polymorphic short tandem repeats for PCR-based Charcot-Marie-Tooth disease type 1A duplication diagnosis.

BACKGROUND: Charcot-Marie-Tooth disease type 1A (CMT1A) accounts for 70-90% of cases of CMT1 and is most frequently caused by the tandem duplication of a 1.4-Mb genomic fragment on chromosome 17p12. Molecular diagnosis of CMT1A has been based primarily on pulsed-field electrophoresis, fluorescence in situ hybridization, polymorphic allele dosage analysis, and quantitative PCR. We sought to improve the fidelity and applicability of PCR-based diagnosis by developing a panel of novel, highly polymorphic short tandem repeats (STRs) from within the CMT1A duplicated region. METHODS: We used a recently available genomic sequence to identify potentially polymorphic simple repeats. We then amplified these sequences in a multiethnic cohort of unaffected individuals and assessed the heterozygosity and number of alleles for each STR. Highly informative markers were then tested in a set of previously diagnosed CMT1A duplication patients, and the ability to identify the genomic duplication through the presence of three bands was assessed. RESULTS: We identified 34 polymorphic markers, 15 of which were suitable for CMT1A diagnosis on the basis of high heterozygosity in different ethnic groups, peak uniformity, and a large number of alleles. On the basis of the fluorescent dye and allele range of each marker, we developed two panels, each of which could be analyzed concurrently. Panel 1, which comprised 10 markers, detected 37 of 39 duplications, whereas panel 2, which comprised the remaining 5 markers, identified 21 of 39 duplications. Through the combination of both panels, we identified 39 of 39 duplications in previously diagnosed CMT1A patients. CONCLUSIONS: The newly developed 15-marker set has the capability of detecting > 99% of duplications and thus is a powerful and versatile diagnostic tool.

Asian People↗
PubMed1998

Chromosomal duplication accompanies allelic loss in non-small cell lung carcinoma.

Hemizygous deletion in the short (p) arm of chromosome 3 is a common finding in non-small cell lung carcinoma (NSCLC) and is postulated to be a crucial early change in lung tumorigenesis. Yet one of the most frequent nuclear abnormalities in both NSCLC and premalignant bronchial epithelium is increase in chromosomal copy number. Deletion and duplication have not been assessed in the same tumor set by both molecular and cytogenetic methods to determine whether allelic loss correlates with chromosomal duplication in the same tumor cell populations. It is also not established what biological mechanisms might lead to allelic deletion and chromosomal duplication. We have investigated changes in the copy number of chromosome 3 in touch preparations of 38 NSCLCs (19 adenocarcinomas and 19 squamous cell carcinomas) using dual-target, dual-color fluorescence in situ hybridization (FISH) assays. Chromosome 3 centromere probe was matched with a 3p14.2 probe [intron 4 of the fragile histidine triad (FHIT) gene] and a 3p21.31 probe (HSemaIV gene). We then correlated FISH results with results of molecular analyses for allelic losses at loci in the regions to which the FISH probes mapped in 20 of these cases. Although various combinations of FISH abnormalities were sometimes detected within the same specimens, individual cases could be classified according to the predominant FISH pattern, usually with one abnormality present in >60% of tumor cells. Chromosomal duplication, indicated by the presence of more than two centromeric signals, was the most frequent abnormality observed by FISH and was accompanied by loss of specific sequences on 3p in approximately one-half of the specimens in which it was observed. The most frequent abnormality observed by molecular analysis was loss of heterozygosity (LOH) in both of the chromosomal regions tested and was demonstrated in 83% of cases with chromosomal duplication. We conclude that LOH may occur in the presence of chromosomal duplication, suggesting that the duplicated chromosome is homozygous. Our findings imply that LOH occurs before chromosomal duplication during lung carcinogenesis.

Acid Anhydride Hydrolases↗
PubMed1987

Base substitutions in transposable element IS1 cause DNA duplication of variable length at the target site for plasmid co-integration.

We demonstrate that base substitutions in the IS1 sequence affect the length of the nucleotide sequence which is duplicated during IS1-mediated co-integration. IS1K, an IS1 variant present in the Escherichia coli chromosome, has seven base substitutions in its sequence as compared with that of IS1R derived from the plasmid R100. All substitutions are located in the internal region of IS1K. We have constructed plasmids containing IS1R, IS1K and hybrids between them: one contains four base substitutions causing an amino acid substitution in the insA gene and the other has three substitutions producing an amino acid substitution in the insB gene. We have isolated co-integrate plasmids formed by each IS1 and analysed nucleotide sequences of the target sites duplicated at the co-integration junctions. The results show that IS1K generates duplications of 8 or 14 bp as well as 9 bp, while IS1R exclusively generates the 9-bp duplications. Both hybrid IS1s also create 8- or 7-bp target duplications in addition to 9-bp duplications. These results indicate that the base substitutions in either insA or insB are sufficient for the occurrence of unusual target duplications, suggesting that both genes are involved in the target duplication.

Base Sequence↗
PubMed1982

Facial duplication: case, review, and embryogenesis.

The craniofacial anatomy of an infant with facial duplication is described. There were four eyes, two noses, two maxillae, and one mandible. Anterior to the single pituitary the brain was duplicated and there was bilateral arhinencephaly. Portions of the brain were extruded into a large frontal encephalocele. Cases of symmetrical facial duplication reported in the literature range from two complete faces on a single head (diprosopus) to simple nasal duplication. The variety of patterns of duplication suggests that the doubling of facial components arises in several different ways: Forking of the notochord, duplication of the prosencephalon, duplication of the olfactory placodes, and duplication of maxillary and/or mandibular growth centers around the margins of the stomatodeal plate. Among reported cases, the female:male ratio is 2:1.

Eye Abnormalities↗
PubMed1979

Evolution of the differential regulation of duplicate genes after polyploidization.

In the 50 million years since the polyploidization event that gave rise to the catostomid family of fishes the duplicate genes encoding isozymes have undergone different fates. Ample opportunity has been available for regulatory evolution of these duplicate genes. Approximately half the duplicate genes have lost their expressions during this time. Of the duplicate genes remaining, the majority have diverged to different extents in their expression within and among adult tissues. The pattern of divergence of duplicate gene expression is consistent with the accumulation of mutations at regulatory genes. The absence of a correlation of extent of divergence of gene expression with the level of genetic variability for isozymes at these loci is consistent with the view that the rates of regulatory gene and structural gene evolution are uncoupled. The magnitude of divergence of duplicate gene expressions varies among tissues, enzymes, and species. Little correlation was found with the extent of divergence of duplicate gene expression within a species and its degree of morphological "conservatism", although species pairs which are increasingly taxonomically distant are less likely to share specific patterns of differential gene expression. Probable phylogenetic times of origin of several patterns of differential gene expression have been proposed. Some patterns of differential gene expression have evolved in recent evolutionary times and are specific to one or a few species, whereas at least one pattern of differential gene expression is present in nearly all species and probably arose soon after the polyploidization event. Multilocus isozymes, formed by polyploidization, provide a useful model system for studying the forces responsible for the maintenance of duplicate genes and the evolution of these once identical genes to new spatially and temporally specific patterns of regulation.

Animals↗
PubMed2000

Experience with gastro-intestinal duplications in childhood.

BACKGROUND: Intestinal duplications are rare congenital malformations. The different locations and sizes of these duplications require a specific diagnostic and surgical approach. This study reviews our paediatric patients with intestinal duplications in order to analyse the influence of prenatal sonography and laparoscopy on the clinical course. PATIENTS AND METHODS: Thirteen duplications of the alimentary tract in 12 patients have been treated over a 10-year period from 1989 to 1999. Six of our patients were diagnosed prenatally by ultrasound and were free of symptoms until surgery, except for one patient who had meconium-ileus owing to cystic fibrosis. In another five patients, the diagnosis was made on the basis of symptoms with signs of obstruction. In one child, the duplication was found incidentally during an operation for an anorectal malformation. The location of the 13 duplications was the stomach in three cases, the duodenum in one case, the jejunum in two cases, the ileum in six cases and the rectum in one case. Laparotomy was performed in ten patients. Two cases were treated by laparoscopic-assisted resection. CONCLUSION: Early diagnosis and treatment of uncomplicated intestinal duplications by means of prenatal sonographic screening and laparoscopic-assisted resection, respectively, are desirable in this congenital malformation. Resection of the duplication with or without minimal resection of the adjacent normal intestine should be mandatory.

Adolescent↗
PubMed1981

Evaluation of the quality of duplicated radiographs.

This experiment evaluated the image quality of duplicated radiographs made at different ultraviolet light exposures. Image quality was measured in terms of "residual" film fog, film density, mottle, image contrast, and resolution. The "residual" fog density of duplicates decreased with increases in ultraviolet exposures until it was less than the fog density of the original. The density of duplicates decreased with increases in ultraviolet exposures until it leveled off at a certain density, depending on the density of the original film. Mottle was less on lighter duplicates than on darker duplicates. Contrast of duplicates increased initially with increases in ultraviolet exposures and later decreased with further increases in ultraviolet exposures. Resolution of duplicates was nearly the same as the original as long as the duplicate had acceptable "residual" fog density.

Copying Processes↗
PubMed1990

Sensitometric comparison of unexpired and expired duplicating films used in dentistry.

This investigation compared the sensitometric properties of unexpired and expired duplicating films. The characteristic curve derived for a duplicating film is the negative slope of a solarization curve; that is, it is different in direction to that of a regular x-ray film. An expired duplicating film is slower than an unexpired duplicating film. Unlike a negative working film, which gains fog past its expiration date, a positive working film (for example, a duplicating film) gains contrast past its expiration date. An expired duplicating film has a narrower latitude than that of an unexpired duplicating film for a useful density range. Clinically, a duplicating film can be used years after its expiration date even though there is a change in its speed and contrast.

Copying Processes↗
PubMed2003

[Urethral duplication in boys: report of 4 cases].

Urethral duplication is a rare anomaly, affecting mainly boys. The clinical presentation varies because of the different anatomical patterns of this abnormality. We report 4 cases of urethral duplication in children. An epispadiac duplication was present in 1 case, hypospadiac duplication in 1 case, Y-duplication in 1 case and a congenital prepubic sinus in the last case. The pre-operative probe was based on urethrocystography and fistulography. The surgical management included excision of the duplicated urethra in 3 cases. Transurethral incision of the intra-urethral septum was performed in the case of hypospadiac duplication. The characteristics of male urethral duplication are reviewed.

Child↗
PubMed2002

Slip prevention: validation of duplicates reproducing industrial floor surface state microgeometry.

The present study falls within the scope of work on the prevention of slips occurring on industrial workplace floor surfaces. Floor microgeometry is a determining factor in anti-slip flooring. Industrial environment-based quantification of floor microgeometrical properties is more restricting than laboratory quantification. The aim of the present study was to develop a duplication technique allowing reproduction of in situ floor microgeometry so as to be able to quantify this microgeometry in the laboratory. Duplicates were produced from a sample of five industrial floors. Surface microgeometry was characterized for both industrial floors and associated duplicates in order to study their microgeometrical changes following the duplicating operation. The purpose of this process was to reach a conclusion on the "reliability" of the duplication technique, on which the use of such duplicates depends. Parameters established from digitalized surfaces reveal differences of less than 5% between duplicates and original floor and this enables us to conclude that these duplicates offer a high degree of reliability with respect to results dispersion.

Accidental Falls↗
PubMed2001

Effect of removal of duplicate isolates on cumulative susceptibility reports.

The objective of our study is to assess the impact of different methods of duplicate isolate removal on cumulative susceptibility reports. Over a 1-year period, we studied the effect of 3 methods of duplicate isolate removal on the cumulative percentage susceptibility of 9 Gram-negative bacilli to 15 antimicrobials. Raw data from which no duplicate isolates were removed (NR) were generated by the Sensititre breakpoint susceptibility testing system. D3 and D7 were methods of duplicate isolate removal defined as follows: same patient, bacterial species, irrespective of susceptibility within either three (D3) or seven (D7) calendar days of the date of the previous culture. The third method evaluated was an algorithm utilized by Cerner, a laboratory management program that defines duplicate isolates as follows: same patient, bacterial species, and NCCLS susceptibility category to an individual antimicrobial. Differences in percentage susceptibility between the three methods of duplicate isolate removal and NR were assessed. The number of isolates studied ranged from 80 (E. aerogenes) to 681 (P. aeruginosa). Of the methods of duplicate isolate removal, the highest percentage susceptibility occurred most frequently with Cerner followed by D7 and D3. Differences in percentage susceptibility between methods of removal and NR ranged from -11 to 25%, -5 to 8%, and -3 to 10%, with Cerner, D3, and D7, respectively. The percentage susceptibility was at least 5% higher than NR with a method of removal for 15 individual organism/antimicrobial combinations in which susceptibility was > or = 70% by at least one of the methods. These occurred most frequently with Enterobacter species and Cerner. Although there is no consensus on the ideal method of duplicate isolate removal, one should be cognizant that these manipulations may produce different cumulative susceptibility reports.

Algorithms↗
PubMed2002

[Gastrointestinal system duplications in children (19 cases)].

UNLABELLED: Digestive duplications are a rare condition in children, characterized by an important anatomoclinical polymorphism. Diagnosis suspected on clinics and evoked by radiology, require histological confirmation. PATIENTS AND METHODS: Nineteen children with duplications were managed in our department, from 1989 to 2001: their hospital chart was retrospectively studied. RESULTS: Ten of our patients were less than one year of age, ten were boys and nine were girls. Clinical signs consisted of pain and abdominal mass, with some transit disturbs, and these signs led to ultrasonography and tomodensitometry. In one case alimentary tract duplication was revealed by digestive hemorrhage, leading to scintigraphic study. The digestive duplications were localized on the stomach in one case, the duodenum in two cases, the jejuno-ileum in twelve cases, the colon in two cases, and the rectum in two cases. Five digestive duplications were tubular, with one communicating duplication. All cases benefited from surgical treatment, and resection procedure was chosen according to duplication type and site. Histological study showed eight cases of ectopic mucosa, six ectopic gastric mucosa and two pancreatic ectopic mucosa. CONCLUSION: Diagnosis and surgical precocious treatment of digestive duplications are the only way to warn complications of this benign pathology.

Biopsy↗