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Results for “Copy Number Variations”

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PubMed2006

CCR5 expression and duration of high risk sexual activity among HIV-seronegative men who have sex with men.

OBJECTIVES: To test the hypothesis that in comparison with those with shorter risk duration, individuals with longer HIV risk duration would have reduced susceptibility to HIV-1 infection as measured by CCR5 expression, and to evaluate whether variation in CCR5 expression could be explained by known genetic polymorphisms. DESIGN AND METHODS: A cross-sectional study of HIV-1 exposed but uninfected men who have sex with men. The risk duration was estimated from self-reported years since first receptive anal intercourse. CCR5 expression on peripheral blood CD4+ monocytes and T cells was determined by flow cytometry. The CCR5-Delta32 mutation and polymorphisms in the CCR5 promoter and CCR2 as well as the copy number of CCL3L1 were analyzed by polymerase chain reaction. Plasma levels of MIP-1alpha (CCL3), MIP-1beta (CCL4) and RANTES (CCL5) were also measured. As risk duration varied with age, analyses were restricted to 67 individuals aged 30-49 years. RESULTS: Multiple linear regression analyses, adjusted for age and race, showed a significant negative association between HIV risk duration and CCR5 expression on monocytes (P = 0.01), and in a separate model, a similar negative association with CCR5 expression on T cells (P = 0.03). Low CCR5 expression was attributable mainly to CCR5-Delta32 heterozygosity and the CCR5-59029G allele. CONCLUSIONS: We confirmed a role for reduced CCR5 expression in HIV-1 resistance. CCR5-Delta32 heterozygosity and the CCR5-59029G allele were significant predictors of low CCR5 expression. Individuals with high CCR5 expression who resisted infection despite long HIV risk duration form an interesting group within which to search for additional mechanisms of resistance to HIV infection.

Adult↗

PubMed1994

Characterization of infectious molecular clones of equine infectious anaemia virus.

We have recovered five infectious molecular clones of the lentivirus equine infectious anaemia virus (EIAV). The clones were recovered from fetal equine kidney (FEK) cells infected with a virulent, cell culture-adapted virus stock (designated PV) and have been characterized at a molecular level. Each clone has unique envelope and long terminal repeat (LTR) sequences. We further investigated LTR sequence variation in the PV stock using PCR amplification to obtain additional LTR clones from infected FEK cells and from peripheral blood mononuclear cells (PBMCs) from animals experimentally infected with PV. Sequence analysis of resulting clones indicates a selection for different LTR populations in pony PBMCs compared to FEK cells. Finally, we observed that the cloned EIAV proviruses did not remain infectious when maintained in a derivative of pBR322. However, two proviruses have been stably maintained in a low copy number vector (pLG338-SPORT).

Amino Acid Sequence↗

PubMed1979

SV40 T-antigen expression in cultured fibroblasts from patients with Down syndrome and their parents.

Expression of simian papovavirus 40 (SV40) T-antigen following in vitro infection was studied in skin fibroblasts from patients with Down syndrome (DS) and their parents to determine whether the increased susceptibility to SV40 infection reflected the cytogenetic defect or the leukemia risk associated with this syndrome. As a group, fibroblasts from patients with DS showed elevated T-antigen expression 72 hrs after infection compared to that of a healthy control population. However, among 24 patients tested, the cell lines of only 11 showed statistically significant increases in T-antigen expression. A cell line from a patient with concurrent DS and acute myelogenous leukemia had a normal value. T-antigen expression did not correlate with the percentage of cells trisomic for chromosome 21 in 18 cell lines examined or with the number of copies of this chromosome in disomic and trisomic cell strains cloned from three mosaic patients.Collectively, cell lines from parents of trisomy 21 patients also showed increased susceptibility to SV40 infection; however, in five families tested, a consistent pattern of genetic transmission of elevated T-antigen expression from parent to offspring was not observed. Q-banding of cell lines in one family showed that elevated T-antigen expression is not a marker of parental nondisjunction. Variation in susceptibility to human interferon, an antiviral agent, did not account for variation in T-antigen levels among these cell lines. Thus, the abnormalities of T-antigen expression in DS appear independent of the hyperdiploid state and are not a sensitive indicator of cancer risk.

Antigens, Viral↗

PubMed1996

The Phytophthora sojae genome contains tandem repeat sequences which vary from strain to strain.

The oömycete Phytophthora sojae causes root and stem rot of soybean. In P. sojae, 37 cultivarspecific physiological races have been reported with different reactions against 13 single dominant resistance genes in soybean. Recent genetic studies have demonstrated that the P. sojae-soybean interaction follows Flor's gene-for-gene model. Genomic subtraction was carried out to isolate race-specific DNA sequences possibly including avirulence genes. DNA from a race 1 isolate was subtraction-enriched with the DNAs from race 19 and race 22 isolates. The enriched DNAs were used to differentially screen a P. sojae genomic library. Characterization of the clones obtained identified repetitive sequences with variable copy numbers among isolates. Five of these repetitive sequences were tandemly repeated and were localized on single chromosomes. The sixth corresponded to the ribosomal RNA genes. These observations suggest that gene amplification could contribute to the generation of genetic diversity in P. sojae. Enriched sequences corresponding to avirulence genes were not detected.

Base Sequence↗

PubMed2006

Use of 16S rRNA and rpoB genes as molecular markers for microbial ecology studies.

Several characteristics of the 16S rRNA gene, such as its essential function, ubiquity, and evolutionary properties, have allowed it to become the most commonly used molecular marker in microbial ecology. However, one fact that has been overlooked is that multiple copies of this gene are often present in a given bacterium. These intragenomic copies can differ in sequence, leading to identification of multiple ribotypes for a single organism. To evaluate the impact of such intragenomic heterogeneity on the performance of the 16S rRNA gene as a molecular marker, we compared its phylogenetic and evolutionary characteristics to those of the single-copy gene rpoB. Full-length gene sequences and gene fragments commonly used for denaturing gradient gel electrophoresis were compared at various taxonomic levels. Heterogeneity found between intragenomic 16S rRNA gene copies was concentrated in specific regions of rRNA secondary structure. Such "heterogeneity hot spots" occurred within all gene fragments commonly used in molecular microbial ecology. This intragenomic heterogeneity influenced 16S rRNA gene tree topology, phylogenetic resolution, and operational taxonomic unit estimates at the species level or below. rpoB provided comparable phylogenetic resolution to that of the 16S rRNA gene at all taxonomic levels, except between closely related organisms (species and subspecies levels), for which it provided better resolution. This is particularly relevant in the context of a growing number of studies focusing on subspecies diversity, in which single-copy protein-encoding genes such as rpoB could complement the information provided by the 16S rRNA gene.

Bacteria↗

PubMed1984

Copy number and the stability of 2-micron circle-based artificial plasmids of Saccharomyces cerevisiae.

The copy number and stability of artificial 2-micron circle-based plasmids have been accurately measured in [Cir+] and [Cir0] strains of Saccharomyces cerevisiae. We conclude that (i) instability and copy number vary greatly from plasmid to plasmid; (ii) instability and copy number are negatively correlated--that is, high copy number is associated with low instability; (iii) it is difficult to reconcile this variability with a strict and direct system of copy number control; (iv) instabilities are much higher than expected from random partition and the observed copy numbers: this may imply partition which is less efficient than random. Even so, (v) the partitioning of 2-micron circle-like plasmids is more efficient than that of ARS-based plasmids, which hints at the existence of a system for the (inefficient) distribution of 2-micron circles.

Chimera↗

PubMed2001

Evolution and function of tandem repeats in the major surface protein 1a of the ehrlichial pathogen Anaplasma marginale.

The major surface protein (MSP) 1a of the ehrlichial cattle pathogen Anaplasma marginale, encoded by the single-copy gene msp1alpha, has been shown to have a neutralization-sensitive epitope and to be an adhesin for bovine erythrocytes and tick cells. msp1alpha has been found to be a stable genetic marker for the identification of geographic isolates of A. marginale throughout development in acutely and persistently infected cattle and in ticks. The molecular weight of MSP1a varies among geographic isolates of A. marginale because of a varying number of tandemly repeated peptides of 28-29 amino acids. Variation in the sequence of the tandem repeats occurs within and among isolates, and may have resulted from evolutionary pressures exerted by ligand-receptor and host-parasite interactions. These repeated sequences include markers for tick transmissibility that may be important in the identification of ehrlichial pathogens because they may influence control strategies and the design of subunit vaccines.

Amino Acid Sequence↗

PubMed2001

[Genetic instability in cancer tissues analyzed by RAPD PCR].

In five kinds of tumors, total 128 specimens were analyzed by RAPD (random amplified polymorphic DNA) PCR with nine 10-base arbitrary primers for detecting instabilities of DNA and chromosome and screening new molecular markers coupled to putative or unknown oncogenes and/or tumor suppressor genes. Bands representing instabilities have been recovered and purified from agarose and cloned into pCAPs vector, and further labeled by DIG as probes for analysis of Southern blot, Northern blot and Sequencing. Results revealed that sample 5 and 3 of the gastric cancers showed the highest genomic changes and the average detectability in five sorts of cancers was up to at least 40% (42.2%-49.4%), and that there were significant differences in the ability of each primer to detect genomic instability, which ranged from 27% to 68%. Despite the highest detectability of genetic instability (68%) in tumor tissues, primer 2 could produce stable profiles of DNA bands in normal tissue genome with good reproducibility. On the contrary, primer 8 was of the lowest one (27%). Band B of single copy found to be allelic losses in gastric and colon cancers according to RFLP analysis was of a novel sequence and registered by Gen-Bank (Accession Number AF151005). Therefore the genetic instabilities often concentrated on some special locuses of chromosome e.g. repetitive sequences etc. and coupled to carcinogenesis. It was impossible or difficult to get great achievements for cancer treatments with the procedure of gene therapy only to one oncogene or one tumor suppressor gene because the extensive DNA variations occurred during the progression of tumor. RAPD assay connected with other techniques was a good tool for the detection of genomic instabilities and direct screening of some new molecular markers related to tumor suppressor genes or oncogenes.

Base Sequence↗

PubMed1998

Unusual and strongly structured sequence variation in a complex satellite DNA family from the nematode Meloidogyne chitwoodi.

An AluI satellite DNA family has been isolated in the genome of the root-knot nematode Meloidogyne chitwoodi. This repeated sequence was shown to be present at approximately 11,400 copies per haploid genome, and represents about 3.5% of the total genomic DNA. Nineteen monomers were cloned and sequenced. Their length ranged from 142 to 180 bp, and their A + T content was high (from 65.7 to 79.1%), with frequent runs of As and Ts. An unexpected heterogeneity in primary structure was observed between monomers, and multiple alignment analysis showed that the 19 repeats could be unambiguously clustered in six subfamilies. A consensus sequence has been deduced for each subfamily, within which the number of positions conserved is very high, ranging from 86.7% to 98.6%. Even though blocks of conserved regions could be observed, multiple alignment of the six consensus sequences did not enable the establishment of a general unambiguous consensus sequence. Screening of the six consensus sequences for evidence of internal repeated subunits revealed a 6-bp motif (AAATTT), present in both direct and inverted orientation. This motif was found up to nine times in the consensus sequences, also with the occurrence of degenerated subrepeats. Along with the meiotic parthenogenetic mode of reproduction of this nematode, such structural features may argue for the evolution of this satellite DNA family either (1) from a common ancestral sequence by amplification followed by mechanisms of sequence divergence, or (2) through independent mutations of the ancestral sequence in isolated amphimictic nematode populations and subsequent hybridization events. Overall, our results suggest the ancient origin of this satellite DNA family, and may reflect for M. chitwoodi a phylogenetic position close to the ancestral amphimictic forms of root-knot nematodes.

Animals↗

PubMed1990

The effect of T-DNA copy number, position and methylation on reporter gene expression in tobacco transformants.

Inter-transformant variability in the expression of introduced genes was studied in the R1 and R2 generations of 10 tobacco transformants, produced by Agrobacterium-mediated transformation. In replicated and physiologically equivalent material, tranformants showed considerable variability in the expression of the reporter gene uidA as shown by transcript levels and beta-glucuronidase (GUS) activity. However, homozygous R2 material could be investigated for seven of the transformants and among these, and in one line in which two inserts could segregate independently, this inter-transformant variability was reduced to simple bimodal expression. The two levels of expression for GUS activity in leaves were high or low (approximately 2.5 or 0.3 nmol cm-2 min-1 respectively), with no continuous variation. Transformants in the high group had single T-DNA insertions, while those in the low group had multiple T-DNA insertions, at the same or different loci. Within each group, although T-DNA was apparently integrated at different sites in the plant genome, there was no evidence of position effects. GUS activity levels of the transformants were very similar in the field and in environmentally controlled conditions under high or low light. Plants with multiple insertions and low expression also tended to have increased methylation of the integrated T-DNA.

Bacterial Proteins↗

PubMed1998

Origins of individual swimming behavior in bacteria.

Cells in a cloned population of coliform bacteria exhibit a wide range of swimming behaviors--a form of non-genetic individuality. We used computer models to examine the proposition that these variations are due to differences in the number of chemotaxis signaling molecules from one cell to the next. Simulations were run in which the concentrations of seven gene products in the chemotaxis pathway were changed either deterministically or stochastically, with the changes derived from independent normal distributions. Computer models with two adaptation mechanisms were compared with experimental results from observations on individuals drawn from genetically identical populations. The range of swimming behavior predicted for cells with a standard deviation of protein copy number per cell of 10% of the mean was found to match closely the experimental range of the wild-type population. We also make predictions for the swimming behaviors of mutant strains lacking the adaptational mechanism that can be tested experimentally.

Bacteria↗

PubMed2006

Independent occurrences of multiple repeats in the control region of mitochondrial DNA of white-tailed deer.

Deer in the genera Mazama and Odocoileus generally have two copies of a 75-base-pair (bp) repeat in the left domain of the control region of the mitochondrial DNA (mtDNA). Phylogenetic analyses further suggest an ancient origin for the duplication supporting a previously stated contention that this event occurred before the separation of Mazama and Odocoileus. However, white-tailed deer (Odocoileus virginianus) had three or four copies of a 75-bp repeat in the control region of their mtDNA in 7.8% of the individuals analyzed, and all of these animals were from the coastal plain of the southeastern United States. When copy 3 is present, it is very similar in sequence to copy 2, but variation suggests that copy 3 probably evolved multiple times from copy 2. The pattern of phylogenetic clustering of the haplotypes from across the coastal plain also suggests that phenotypes with three or four copies of the repeat have originated multiple times. The 44 observed haplotypes showed strong spatial subdivision across the area with subpopulations frequently showing complete shifts in haplotype frequencies from others taken from nearby areas. Many of the subpopulations right along the coast or on adjacent barrier islands have a limited number of haplotypes as would occur in populations undergoing drift because of small numbers of breeding females and limited female dispersal.

Animals↗

PubMed1988

Population dynamics of movable genetic elements in Japanese natural populations of Drosophila melanogaster. I. Microevolution of male recombination determinants in experimental populations.

Five natural populations of D. melanogaster in Japan were surveyed for male recombination frequency in terms of the quantities of the mean and variance after crossing with cn bw females. The experimental condition enabled P-M system hybrid dysgenesis to take place. The means were not so different from one another, but there was a vast variation in the variances between them. Using one of these populations, two additional experimental populations were started, and the male recombination frequencies were monitored for 30 generations. Both the means and variances decreased in value at 25 degrees C. The regression line was Y = -0.000030X + 0.001706 on generation for the mean values, and was Y = -0.000098X + 0.005068 for the standard deviations in the cage population. There was no correlation between the means or the standard deviations and the copy numbers of the members of P element family as a whole. The experimental results indicate that the complete P transposable elements still retained in population were decreased in frequency and replaced by its degenerative nonautonomous forms.

Analysis of Variance↗

PubMed2003

Problematic variation in local institutional review of a multicenter genetic epidemiology study.

CONTEXT: Sequencing of the human genome provides an immense resource for studies correlating DNA variation and epidemiology. However, appropriately powered genetic epidemiology studies often require recruitment from multiple sites. OBJECTIVES: To document the burden imposed by review of multicenter studies and to determine the variability among local institutional review boards (IRBs) in the approval of a multicenter genetic epidemiology study. DESIGN: A PubMed search was performed to determine the frequency of citations of multicenter studies by 5-year intervals from 1974 through 2002. A 7-question survey was sent to all participating study centers to obtain information on frequency of IRB meetings, dates for submission and approval, use/nonuse of a specific consent form, type of review performed, types of consent forms required, preparation time, and number of changes requested by the IRB at each center. Centers also provided a copy of all consent forms they generated and IRB correspondence regarding the study. SETTING AND PARTICIPANTS: Thirty-one of 42 cystic fibrosis care centers in this single US multicenter genetic epidemiology study of cystic fibrosis replied, yielding a 74% response rate. MAIN OUTCOME MEASURES: Frequency of published research studies and consistency among IRBs. RESULTS: The number of all published single-center studies has increased 1.3-fold since 1985, while the number of published epidemiology and genetic epidemiology multicenter studies increased by 8- and 9-fold, respectively, during this same period. Evaluation of the risk of the same genetic epidemiology study by 31 IRBs ranged from minimal to high, resulting in 7 expedited reviews (23%) and 24 full reviews (77%). The number of consents required by the IRBs ranged from 1 to 4; 15 IRBs (48%) required 2 or more consents, while 10 (32%) did not require assent for children. The most common concern (52%) of IRBs pertained to the genetic aspects of the study. CONCLUSIONS: Review of a protocol for a multicenter genetic epidemiology study by local IRBs was highly variable. Lack of uniformity in the review process creates uneven human subjects protection and incurs considerable inefficiency. The need for reform, such as the proposed centralized review, is underscored by the ever increasing rate of genetic discoveries facilitated by the Human Genome Project and the unprecedented opportunity to assess the relevance of genetic variation to public health.

Cystic Fibrosis↗

PubMed1987

Mutations altering the structure of epidermal growth factor-like coding sequences at the Drosophila Notch locus.

The Drosophila neurogenic protein Notch is largely composed of tandemly repeated copies of an epidermal growth factor-like sequence. Notch protein contains 36 EGF-like elements, but no two are identical. In the present study, eight mutations are correlated with single amino acid substitutions in EGF-homologous elements of this protein. Genetic analyses of the mutations and comparisons of DNA from mutant and wild-type flies indicate that differentiation of function exists among the tandemly repeated EGF-like sequences and that the total number of repeats and minor variations from the consensus repeat sequence are important for wild-type Notch protein function. One group of EGF-like repeats may be involved in the formation of functional Notch dimers or multimeric proteins. EGF-like elements in a second region of the Notch protein appear to govern its interaction with the product of Enhancer of split, another neurogenic locus of D. melanogaster.

Alleles↗

PubMed1998

A novel repetitive sequence of sugar cane, SCEN family, locating on centromeric regions.

Tandem repetitive sequences consisting of 140-bp repetitive units were cloned from sugar cane genomic DNA and designated the SCEN family. In situ hybridization revealed that they were located on the centromeric region of almost all of the chromosomes of sugar cane. The 140-bp sequence included three CENP-B box-like sequences. Phylogenetic analysis of the members of the SCEN family revealed that the sequences had 75% homology with each other, on average, and that the sequences could not be further classified into smaller subfamilies. The copy number of the sequence was estimated to be 2.6 x 10(5) per haploid sugar cane genome and, therefore, 4.6 x 10(3) or 630 kb per chromosome on average.

Autoantigens↗

PubMed1992

Isolation, characterization, and sequencing of Candida albicans repetitive element 2.

A 1059-bp Sau3A fragment, designated Candida albicans repetitive element 2 (CARE-2), was isolated from the genome of the pathogenic yeast, C. albicans. CARE-2 DNA was detected on several C. albicans chromosomes separated by transverse alternating-field electrophoresis. A high degree of interstrain variation in the pattern of hybridizing bands were observed by Southern blot analysis, with a minimum of 10-14 copies of CARE-2 per strain. A low frequency of new CARE-2 polymorphisms was observed over time for three strains grown at 25 degrees C or 37 degrees C. No new CARE-2 polymorphisms were observed from two naturally occurring switch phenotypes. To localize repeated DNA, oligodeoxyribonucleotide probes, each representing a different region of CARE-2, were hybridized to genomic blots. A lower number of copies were observed 5' and 3' to a 600-bp region of CARE-2. Nucleotide (nt) sequence analysis of CARE-2 DNA shows the element is characterized by six perfect direct repeats 6 bp in length and shows no significant DNA similarity with any known nt sequence.

Base Sequence↗

PubMed1990

Active mariner transposable elements are widespread in natural populations of Drosophila simulans.

The occurrence of active, or autonomous, mariner elements was investigated by crossing white-peach mutant Drosophila simulans females with wild-type males from various geographic origins. From a total of 194 experimental crosses only 17 failed to produce progeny with eye mosaicism (MOS, i.e. pigmented spots in otherwise white-peach eyes). Therefore, active mariner elements inducing somatic excision of the copy inserted at the white locus are abundant in all populations sampled. In the experimental crosses the frequency of mosaic offspring ranged from 0 to 100%, showing that the phenotypic expression is highly variable. The MOS phenotype, measured by the number of spots on the eyes, is quite variable within the progeny of single crosses. Although a difference was observed in the average MOS score (percentage of mosaic flies) between northern and southern populations of France, there was no indication of long range variation between geographic populations. Neither was there a systematic difference between recently collected populations and samples kept several years as isofemale lines.

Animals↗