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At least 37 records · Page 2Linked to original sources
PubMed1979

DNA of Epstein-Barr virus. V. Direct repeats of the ends of Epstein-Barr virus DNA.

Previous data indicated that Epstein-Barr virus DNA is terminated at both ends by direct or inverted repeats of from 1 to 12 copies of a 3 X 10(5)-dalton sequence. Thus, restriction endonuclease fragments which include either terminus vary in size by 3 X 10(5)-dalton increments (D. Given and E. Kieff, J. Virol. 28:524--542, 1978; S. D. Hayward and E. Kieff, J. Virol. 23:421--429, 1977). Furthermore, defined fragments containing either terminus hybridize to each other (Given and Kieff, J. Virol. 28:524--542, 1978). The 5' ends of the DNA are susceptible to lambda exonuclease digestion (Hayward and Kieff, J. Virol. 23:421--429, 1977). To determine whether the terminal DNA is a direct or inverted repeat, the structures formed after denaturation and reannealing of the DNA from one terminus and after annealing of lambda exonuclease-treated DNA were examined in the electron microscope. The data were as follows. (i) No inverted repeats were detected within the SalI D or EcoRI D terminal fragments of Epstein-Barr virus DNA. The absence of "hairpin- or pan-handle-like" structures in denatured and partially reannealed preparations of the SalI D or EcoRI D fragment and the absence of repetitive hairpin- or pan-handle-like structures in the free 5' tails of DNA treated with lambda exonuclease indicate that there is no inverted repeat within the 3 X 10(5)-dalton terminal reiteration. (ii) Denatured SalI D or EcoRI D fragments reanneal to form circles ranging in size from 3 X 10(5) to 2.5 X 1O(6) daltons, indicating the presence of multiple direct repeats within this terminus. (iii) Lambda exonuclease treatment of the DNA extracted from virus that had accumulated in the extracellular fluid resulted in asynchronous digestion of ends and extensive internal digestion, probably a consequence of nicks and gaps in the DNA. Most full-length molecules, after 5 min of lambda exonuclease digestion, annealed to form circles, indicating that there exists a direct repeat at both ends of the DNA. (iv) The finding of several circularized molecules with small, largely double-strand circles at the juncture of the ends indicates that the direct repeat at both ends is directly repeated within each end. Hybridization between the direct repeats at the termini is likely to be the mechanism by which Epstein-Barr virus DNA circularizes within infected cells (T. Lindahl, A. Adams, G. Bjursell, G. W. Bornkamm, C. Kaschka-Dierich, and U. Jehn, J. Mol. Biol. 102:511-530, 1976).

Animals↗
PubMed2026

The Spatial and Temporal Repeatability of Genomic Responses to Natural Selection as Demonstrated in Stickleback Populations Experiencing Highly Dynamic Environments.

The evolution of genotypic parallelism under shared environmental conditions provides strong evidence for the role of natural selection. However, analyses typically examine genomic signatures of selection long after the putative selection event and only assess the repeatability of responses across spatial population replicates. This impedes our ability to attribute a particular response to a given selection pressure and to distinguish non-parallel responses caused by stochastic processes from those caused by local selection. As such, the consistency of natural selection over space and time is unknown, and the role of persistent local selection pressures is unclear. Here, we leveraged the natural bar-built estuary system of Santa Cruz, California, to examine the repeatability of seasonal genomic change in threespine stickleback (Gasterosteus aculeatus) over space and time. By comparing allele-frequency shifts that are shared across locations (spatial repeatability) with those that are shared across years within locations (temporal repeatability), we identified both spatially shared and local components of putative selection. We found that repeated seasonal outlier responses occurred more often than expected under a neutral null model. Although repeatability declined as the number of estuaries sharing an outlier increased, enrichment above neutral expectations increased with broader spatial sharing, particularly for outliers repeated across both years. While the precise outlier SNPs varied across years, estuary-specific patterns of responses were broadly consistent, suggesting an important role for local conditions. Together, our findings show that temporal sampling can reveal components of putative selection that would be missed from spatial comparisons alone. More broadly, they highlight the importance of examining repeatability over both space and time to understand the parallel and non-parallel components of adaptive genomic change.

Animals↗
PubMed1976

Repeat lymphography in children with Hodgkin's disease.

Repeat lymphography was performed in 37 children less than 16 years old with histologically proven Hodgkin's disease. The repeat studies had the same lymphatic cannulation success rates as the first lymphogram; one patient had a bilaterally unsuccessful repeat study, which left 36 for analysis. Both first and repeat lymphograms were negative in 33% of children, whereas a negative lymphogram became positive for tumor in 39%. The remaining 28% had a positive first lymphogram, with an equal incidence of positive and negative repeat studies. Reactive hyperplasia was seen in 16.7%, and post-therapeutic lymph node alteration in 22%, of all cases. Of the 22 children studied for routine opacification or because of suspected but unproved relapse, 10 (45%) had positve repeat studies. The repeat lymphogram in these patients was of utmost importance in initiating therapy. Nine of 14 patients studied for documented clinical relapse had positive repeat studies.

Adolescent↗
PubMed1976

Isolation of inverted repeat sequences, including IS1, IS2, and IS3, in Escherichia coli plasmids.

A method is described for isolation of inverted repeat DNA sequences that occur in E. coli plasmids. The procedures of the isolation involved: (a) denaturation of intact plasmid DNA, (b) a rapid, 30 sec, renaturation of inverted-repeat sequences in the genome, (c) digestion of the single-stranded portion by S1 nuclease to recover duplex DNA, and (d) detection and purification of the duplexes using 1.4% agarose gel electrophoresis. If a plasmid DNA carried inverted repeats of either one type or two different types of special DNA sequences, these procedures enabled us to observe either one or two characteristic DNA bands, respectively, in the agarose gels. If a plasmid DNA did not carry any inverted repeats, or if the plasmid DNA only carried direct repeat sequences, no characteristic DNA bands were recovered. Cleavage of the spacer DNA between inverted repeat sequences generated no gel bands. This indicated that the inverted repeat sequences must be in the same strand. Using this method, we isolated and purified several repeated sequences, including IS1, IS2, and IS3, from derivatives of F and R plasmids.

Base Sequence↗
PubMed1976

Interspersion of different repeated sequences in the wheat genome revealed by interspecies DNA/DNA hybridisation.

The repeated sequences in oats DNA have been used to study chromosomal repeated sequence organisation in wheat. Approximately 75% of the wheat genome consists of repeated sequences but only approximately 20% will form heteroduplexes with repeated sequences from oats DNA at 60 degrees C in 0.18 M Na+. The proportion of wheat DNA that forms heteroduplexes with oats DNA is shown to be independent of the wheat DNA fragment length. However, the proportion of wheat DNA that is retained with the heteroduplexes when fractionated on hydroxyapatite is very dependent upon the wheat fragment length up to 3500 nucleotides. This is because more non-renatured wheat DNA is attached to the heteroduplexes with longer fragments. The results indicate that the repeated sequences in the wheat genome homologous to repeated sequences in oats are not clustered in the chromosomes but distributed amongst other repeated and possible non-repeated sequences.

Base Sequence↗
PubMed1978

Characterization of inverted repeated sequences in wheat nuclear DNA.

The properties of inverted repeated sequences in wheat nuclear DNA have been studied by HAP(1) chromatography, nuclease S1 digestion and electron microscopy. Inverted repeated sequences comprise 1.7% of wheat genome. The HAP studies show that the amount of "foldback HAP bound DNA" depends on DNA length. Inverted repeats appear to be clustered with an average intercluster distance of 25 kb. It is estimated that there are approximately 3 x 10(6) inverted repeats per haploid wheat genome. The sequences around inverted repeats involve all families of repetition frequencies. Inverted repeats are observed as hairpins in electron microscopy. 20% of hairpins are terminated by a single-stranded spacer ranging from 0.3 to 1.5 kb in length. Duplex regions of the inverted repeats range from 0.1 to 0.45 kb with number average values of 0.24 kb and 0.18 kb for unlooped and looped hairpin respectively. Thermal denaturations and nuclease S1 digestions have revealed a length of about 100 bases for duplex regions. The methods used to study inverted repeated sequences are compared and discussed.

Base Sequence↗
PubMed1979

Repeat abortions: blaming the victims.

A study of 1,505 women obtaining abortions in a freestanding abortion clinic in Western New York state revealed that women having repeat abortions were more likely to be using contraception at the time of conception than women having first abortions. However, nearly one-half the non-contracepting repeaters were not contracepting at the time of the repeat pregnancy. Repeaters who were not contracepting at the time of the repeat pregnancy listed medical contraindications or lack of supplies as the major reasons for not contracepting at the time of the present conception--indicating that they had tried one or more methods since their first abortion. Repeaters were sexually more active than first timers, thus increasing their statistical risk of unwanted pregnancy even as they contracepted more than first timers. The data indicate that both first timers and repeaters overwhelmingly reject the premise that abortion is a primary or even a back-up birth control method. The essential difficulty for repeaters appears to be that they are victims of technological, organizational, and logistical inadequacies as well as statistical probabilities rather than being motivationally deficient or indifferent to the dangers of unprotected sexual intercourse.

Abortion, Legal↗
PubMed1977

[Content of 5-methylcytosine in various families of repeating sequences of DNA in some higher plants].

Three families of repeating DNA sequences from 6 higher plants species are isolated. It is found that DNAs of plants examined at the same developmental stages differ considerably in the content of fractions with different repetition frequency of nucleotide sequences. The content of non-repeating sequences in the genome of the plants varies from 23.8 to 41.4%, the differences in the content of highly repeating fractions are less expressed (from 20.3 to 29.4% of the genome). The ratio of fractions changes considerably during ontogenesis: DNA of seeds contains more highly repeating sequences than DNA of seedlings. Fractions of nucleotide sequences with different repetition frequency, isolated from the same DNA, are little distinguished in the GC-pair content, and are characterized by a relatively high content of 5-methylcytosine: the methylation degree of cytosine is at least 17%. However, the degree of cytosine methylation is increased in fractions with high content of copies per genome in seedlings and leaves DNA of all the plants studied. The content of 5-methylcytosine in highly repeating fractions is 12% higher than in non-repeating sequences. Seed DNAs have some other distribution of 5-methylcytosine in different fractions: the degree of cytosine methylation in non-repeating and highly repeating sequences is practically the same.

Base Sequence↗
PubMed2025

First clinical diagnosis of FAME3 via commercial Long-Read sequencing reveals mosaic repeat expansion in MARCHF6 gene.

Familial Adult Myoclonic Epilepsy type 3 (FAME3) is a rare autosomal dominant disorder characterized by cortical tremor and epilepsy, caused by a noncoding pentanucleotide repeat expansion (TTTTA/TTTCA)n in the MARCHF6 gene. Conventional genetic testing often fails to detect this expansion due to its repetitive structure and intronic location. We evaluated a 61-year-old woman with refractory myoclonic and generalized tonic-clonic seizures, whose prior genetic testing-including exome and genome sequencing-was non-diagnostic. Using PacBio HiFi long-read whole-genome sequencing and the tandem repeat genotyping tool TRGT, we identified a pathogenic MARCHF6 intronic expansion. The proband harbored one allele with 15 TTTTA repeats and a second allele with a compound expansion of 661 TTTTA and 12 TTTCA repeats. Three affected relatives shared similarly expanded alleles, but with increasing repeat size in the latter generations. Importantly, analysis using TRGT-instability revealed repeat mosaicism in all affected individuals, reflected by variability in motif counts across individual sequencing reads. This somatic heterogeneity may contribute to the phenotypic penetrance, variable expressivity and pleiotropism seen in FAME3 disease expression. To our knowledge, this is the first clinical diagnosis of FAME3 using a commercially available long-read sequencing platform, underscoring its diagnostic utility in resolving complex repeat expansion disorders and uncovering biologically relevant mosaicism.

Humans↗
PubMed2026

AniAnn's: alignment-free annotation of tandem repeat arrays using fast average nucleotide identity estimates.

MOTIVATION: Satellite DNA has long posed challenges for genome assembly and analysis due to its low sequence complexity and poor mappability. These large heterochromatic arrays of tandem repeats are ubiquitous across eukaryotic genomes, yet remain understudied. Current methods for annotating satellite regions, and other classes of tandem repeat arrays, are limited in their ability to annotate divergent or novel sequences. RESULTS: In this work, we introduce AniAnn's, an algorithm for annotating large blocks of tandemly repeating DNAs. AniAnn's exploits the high Average Nucleotide Identity (ANI) shared between repeat units of the same array to quickly and accurately infer the boundaries of such arrays. We show that AniAnn's improves the annotation of satellites and other tandem repeats within a variety of plant and animal genomes, while requiring only a fraction of the runtime compared to previous approaches. We conclude by exploring several use cases of AniAnn's as a lightweight method for masking repeats prior to whole-genome alignment as well as the de novo annotation and classification of satellite repeats. AVAILABILITY: AniAnn's is open source software and available at github.com/marbl/anianns.

Algorithms↗
PubMed2025

The CGG triplet repeat binding protein 1 counteracts R-loop induced transcription-replication stress.

The CGG triplet repeat binding protein 1 (CGGBP1) binds to CGG repeats and has several important cellular functions, but how this DNA sequence-specific binding factor affects transcription and replication processes is an open question. Here, we show that CGGBP1 binds human gene promoters containing short (<&#x2009;5) CGG-repeat tracts prone to R-loop formation. Loss of CGGBP1 leads to deregulated transcription, transcription-replication-conflicts (TRCs) and accumulation of Serine-5 phosphorylated RNA polymerase II (RNAPII), indicative of promoter-proximal stalling and a defect in transcription elongation. Consistently, an episomal CGG-repeat-containing model locus as well as endogenous genes show deregulated transcription, R-loop accumulation and increased RNAPII chromatin occupancy in CGGBP1-depleted cells. We identify the DEAD-box RNA:DNA helicases DDX41 and DHX15 as interaction partners specifically recruited by CGGBP1. Co-depletion experiments show that DDX41 and CGGBP1 work in the same pathway to unwind R-loops and avoid TRCs. Together, our work shows that short trinucleotide repeats are a source of genome-destabilizing secondary structures, and cells rely on specific DNA-binding factors to maintain proper transcription and replication coordination at short CGG repeats.

Humans↗
PubMed2025

tidk: a toolkit to rapidly identify telomeric repeats from genomic datasets.

SUMMARY: "tidk" (short for telomere identification toolkit) uses a simple, fast algorithm to scan long DNA reads for the presence of short tandemly repeated DNA in runs, and to aggregate them based on canonical DNA string representation. These are telomeric repeat candidates. Our algorithm is shown to be accurate in genomes for which the telomeric repeat unit is known and is tested across a wide variety of newly assembled genomes to uncover new telomeric repeat units. Tools are provided to identify telomeric repeats de novo, scan genomes for known telomeric repeats, and to visualize telomeric repeats on the assembly. "tidk" is implemented in Rust and is available as a command line tool which can be compiled using the Rust toolchain or downloaded as a binary from bioconda. AVAILABILITY AND IMPLEMENTATION: The "tidk" Rust crate is freely available under the MIT license (https://crates.io/crates/tidk), and the source code is available at https://github.com/tolkit/telomeric-identifier.

Telomere↗
PubMed1978

Effects of repeated assessment on standardized test performance by infants.

Infant-intervention programs that evaluate their effectiveness by repeatedly testing infants with standardized tests may confound intervention effects with repeated-testing effects. Further, maternal participation in testing may increase infants' test scores, either directly by giving infants practice with test-like items at home between test administrations or indirectly by helping infants adapt to the test setting. Thirty-five infants were tested at 3-month intervals between 4 and 28 months of age with the Bayley Scales of Infant Development and at 31 months of age with the Stanford-Binet; 25 infants were tested with the Bayley at 4 months and the Stanford-Binet at 31 months. Mothers of some infants in each group participated in the testing process. Between-subjects analysis on the Stanford-Binet revealed no effects for repeated testing or maternal participation. Within-subjects analyses for repeatedly tested groups demonstrated that maternal presence during testing, but not repeated testing, was associated with significantly higher Bayley scores. It was concluded that maternal presence is a potent influence on Bayley performance, that repeated experience with the Bayley biased neither performance on another standardized test of development nor subsequent Bayley performance, and that infant intervention programs are not likely to confound their evaluation designs by testing infants repeatedly.

Age Factors↗
PubMed1976

Actions of repeated injections of LSD and apomorphine on the copulatory response of female rats.

LSD, a serotonin receptor stimulating agent, inhibits copulatory behavior (lordosis response) in the ovariectomized and estrogen + progesterone treated female rat. The same effect is obtained by apomorphine, a dopamine receptor stimulating compounds. The lordosis has been shown to be dependent on serotonin, but also dopamine has been implicated in its mediation. Tolerance develops to certain responses after repeated injections of LSD and in the present study the influence of apomorphine and LSD was compared, when given in repeated doses. Possible cross-tolerance between the two compounds was also tested on the frequency of lordosis responding in ovariectomized and hormone treated female rats. Tolerance to LSD develops over seven days, while the suppressing influence of apomorphine on lordosis in seven repeated doses is not significantly altered from that of a single dose. No cross-tolerance was observed on the lordosis response with either order of treatments. Repeated doses of LSD did not influence locomotor activity differently from a single dose, while repeated doses of apomorphine enhanced this response in comparison with the effect of an acute dose. These results indicate differential sensitivity to the repeated treatments and further support an interpretation of the LSD effects on lordosis responding to be primarily on serotonergic rather than dopaminergic receptors.

Animals↗
PubMed1976

Repeating units of Xenopus laevis oocyte-type 5S DNA are heterogeneous in length.

The restriction enzymes Hind III and Hae III cleave Xenopus laevis 5S DNA at one and three sites, respectively, in each repeating unit of approximately 700 base pairs. The cleavage sites for both enzymes have been located within the repeating unit by denaturation mapping of the restriction fragments. The Hind III products and one of the Hae III fragments are variable in length, indicating heterogeneity in the length of the repeating unit in 5S DNA. This length heterogeneity is confined to the major A + T-rich spacer region. Repeating units differ from each other by discrete quanta of approximately 15 base pairs. The A + T-rich spacer has been shown to consist largely of tandem subrepeats of just this size (Brownlee, Cartwright, and Brown, 1974). We suggest that the repeat-length heterogeneity is due to variable numbers of these subrepeats in the spacer regions of the major repeating units.

Adenine↗
PubMed2026

Parallel Analysis of Repeat Expansions: An Updated Clinical Nanopore Cas9-Targeted Sequencing Workflow for Nanopore R10 Flow Cells.

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. An updated Clinical Nanopore Cas9-Targeted Sequencing workflow is presented for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the Oxford Nanopore Technologies wf-human-variation Epi2Me workflow, including the Straglr tool to analyze base-called reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 and introduces new gene panels for ataxia, myopathy, neurodegeneration, and amyotrophic lateral sclerosis/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches. In this work, the use of multiplexing, Flongle flow cells, and single-gene targeting were explored as alternatives to panel-based approaches in the Clinical Nanopore Cas9-Targeted Sequencing workflow, finding that only single-gene targeting provides compatibility and reliable performance.

Journal Article↗
PubMed2026

Financial incentives and social messaging for repeat SARS-CoV-2 antibody testing among the underserved: A randomized trial.

Financial incentives may influence health behavior beyond their expected monetary value, and their effectiveness may depend on how the behavior is framed. Behavioral theories of decision making suggest that individuals may value protection against small-stakes losses more than expected utility predicts, while theories of family-centered health behavior suggest that messages emphasizing benefits to family members may strengthen participation in preventive health activities. We tested these ideas in a 2&#xd7;2 factorial randomized trial involving 625 households recruited from a Federally Qualified Health Center serving low-income Latino/Hispanic communities. Participants completed repeat SARS-CoV-2 antibody testing. The trial crossed two messaging strategies (Family vs. Personal) with two incentive structures (Loss Protection vs. Lottery) that offered equivalent expected monetary value. Family Messaging emphasized protecting one's family from COVID-19, whereas Personal Messaging emphasized protecting oneself. Loss Protection allowed participants to secure an at-risk reward through repeat testing, whereas the Lottery condition offered a chance of a large reward. Repeat testing was approximately 8 percentage points higher under Family Messaging and 7 percentage points higher under Loss Protection. Baseline trust in medical providers, financial barriers to vaccination, and risk aversion were associated with initial testing, whereas household characteristics were not associated with repeat testing. Incentive design may matter beyond expected monetary value and that framing health behaviors in terms of family welfare may increase participation in repeated healthy activities. Broadly, the results support behavioral theories emphasizing loss aversion, anticipated regret, and family-centered motivations, and suggest practical approaches for improving engagement in repeat health behaviors. CLINICALTRIALS.GOV REGISTRATION NUMBER:: NCT01901624.

Adult↗
PubMed1977

Cutaneous microflora of patients with repeated skin infections.

The microflora of normal skin in 16 patients with repeated staphylococcal and streptococcal skin infections was examined to determine whether abnormalities existed which would indicate a protective role for the indigenous flora against colonization by pathogens. Five sites-hands, feet, axilla, groin and back-were examined quantitatively and qualitatively and compared with a control group. Total populations of indigenous flora were significantly higher from patients with repeated skin infections of the back, axillae and feet. The frequency of isolation of different species from normal skin was comparable between the control and experimental groups, with the exception of the incidence of Staphylococcus aureus and Proteus species which were isolated only from patients with repeated skin infections. Gram-negative bacteria were isolated with comparable frequency between the two groups, but patients with repeated skin infections tended to carry gram-negative bacteria on multiple sites. It was concluded from the high population of indigenous flora and the types of microogranisms present that the microflora of normal skin did not appear to protect patients with repeated skin infections against colonization by pathogens. The presence of high populations of Staphylococcus aureus on the normal skin of patients with repeated skin infections would appear to be the most important contributing factor.

Bacteria↗