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Results for “Genome Components”

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PubMed2004

Genome size of human oral Treponema species by pulsed-field gel electrophoresis.

The genome sizes of seven strains of oral treponemes were determined using pulsed-field gel electrophoresis (PFGE). These strains represent members from six of the currently known cultivable oral treponeme groups. The PFGE fragments were digitally recorded and then quantitated using GIMP v 1.2, an image manipulation program. The results show that the six oral treponeme genomes are comparable in size, ranging from approximately 2.2 to 2.5 Mbp. The genome sizes of these strains are 20-25% smaller than Treponema denticola strains, which have genome sizes of approximately 2.8-3.0 Mbp.

DNA, Bacterial↗

PubMedDate not supplied

A genetic screen for vegetative gene expression in the micronucleus of Tetrahymena thermophila.

The presence of a micronucleus with at least a small portion of the micronuclear genome appears to be indispensable for vegetative viability in the ciliate Tetrahymena thermophila. A genetic screen was devised to detect evidence of expression of essential genes in the vegetative micronucleus by identification of thermosensitive-lethal mutations expressed in the absence of nuclear reorganization. Although control experiments demonstrated the efficacy of the method for induction and recovery of thermosensitive lethal mutations in micronuclear genes, no expressed mutations were recovered in the absence of nuclear reorganization. This finding complements the existing lack of convincing biochemical evidence for gene expression in the vegetative micronucleus and suggests that the essential function may involve genomic DNA sequences for which thermosensitive mutant alleles are not recoverable, or perhaps a non-genomic component of the organelle.

Animals↗

PubMed1997

cis elements that contribute to geminivirus transcriptional regulation and the efficiency of DNA replication.

The A genomic component of the geminivirus tomato golden mosaic virus (TGMV) contains a 5' intergenic sequence that includes the overlapping AL61 promoter and positive-strand origin of DNA replication. The TGMV AL1 protein negatively regulates its own transcription and mediates origin recognition by binding to a repeated motif shared by the AL61 promoter and the viral origin. We examined a series of truncated or mutated 5' intergenic regions in transient expression and replication assay to identify other DNA sequences that contribute to TGMV promoter and origin function. These experiments revealed that negative regulation of the AL61 promoter is complex, involving multiple cis-acting sequences and the AL1 and AL4 proteins, which acted through different DNA elements. We also found that mutation of the TATA box motif in the AL61 promoter reduced overall transcriptional activity and AL1-mediated repression, confirming the importance of this sequence in promoter function. Mutation of a G-box consensus sequence was highly detrimental to AL61 transcription and abolished AL1 sensitivity, suggesting that AL1 interferes with transcriptional activation. Cotransfection experiments showed that the TATA box and G-box motif mutations also impaired viral DNA replication in the presence of a wild-type origin but had no effect in its absence, demonstrating that these transcriptional motifs also function as replication efficiency elements.

Base Sequence↗

PubMed2003

Muscle fibrillin deficiency in Marfan's syndrome myopathy.

OBJECTIVE: To report a family with Marfan's syndrome in whom a myopathy was associated with respiratory failure; muscle biopsies from affected individuals were examined to determine whether there were abnormalities in fibrillin. METHODS: 21 family members underwent detailed clinical examination, including neurological and pulmonary assessment. Muscle biopsies in the most severely affected cases were immunostained using monoclonal antibodies to specific fibrillin components. Genomic DNA from all 21 members was analysed for mutations in the fibrillin gene, FBN1, on 15q21. RESULTS: 13 individuals had a C4621T base change in exon 37 of the FBN1 gene, which in four cases segregated with muscle weakness or evidence of respiratory muscle dysfunction or both. Their muscle biopsies revealed an abnormality in fibrillin immunoreactivity. CONCLUSIONS: Abnormalities in fibrillin can be detected in muscle biopsies from patients with Marfan's syndrome who have myopathy. This pedigree, with a point mutation in FBN1, also draws attention to the potential for respiratory failure associated with myopathy.

Adolescent↗

PubMed2004

Comparative genomic structure of prokaryotes.

Recent advances in DNA-sequencing technologies have made available an enormous resource of data for the study of bacterial genomes. The broad sample of complete genomes currently available allows us to look at variation in the gross features and characteristics of genomes while the detail of the sequences reveal some of the mechanisms by which these genomes evolve. This review aims to describe bacterial genome structures according to current knowledge and proposed hypotheses. We also describe examples where mechanisms of genome evolution have acted in the adaptation of bacterial species to particular niches.

Bacteria↗

PubMed2024

Molecular Analysis of Persistent and Recurrent Barrett's Esophagus in the Setting of Endoscopic Therapy.

INTRODUCTION: Early neoplastic progression of Barrett's esophagus (BE) is often treated with endoscopic therapy. Although effective, some patients are refractory to therapy or recur after apparent eradication of the BE. The goal of this study was to determine whether genomic alterations within the treated BE may be associated with persistent or recurrent disease. METHODS: We performed DNA sequencing on pre-treatment esophageal samples from 45 patients who were successfully treated by endoscopic therapy and did not recur as well as pre-treatment and post-treatment samples from 40 patients who had persistent neoplasia and 21 patients who had recurrent neoplasia. The genomic alterations were compared between groups. RESULTS: The genomic landscape was similar between all groups. Patients with persistent disease were more likely to have pre-treatment alterations involving the receptor tyrosine kinase pathway ( P = 0.01), amplifications of oncogenes ( P = 0.01), and deletions of tumor suppressor genes ( P = 0.02). These associations were no longer significant after adjusting for patient age and BE length. More than half of patients with persistent (52.5%) or recurrent (57.2%) disease showed pre-treatment and post-treatment samples that shared at least 50% of their driver mutations. DISCUSSION: Pre-treatment samples were genomically similar between those who responded to endoscopic therapy and those who had persistent or recurrent disease, suggesting there is not a strong genomic component to treatment response. Although it was expected to find shared driver mutations in pre-treatment and post-treatment samples in patients with persistent disease, the finding that an equal number of patients with recurrent disease also showed this relation suggests that many recurrences represent undetected minimal residual disease.

Humans↗

PubMed2005

Comparative genomics of microsporidia.

Microsporidia have been known for some time to possess among the smallest genomes of any eukaryote. There is now a completely sequenced microsporidian genome, as well as several other large-scale sequencing efforts, so the nature of these genomes is becoming apparent. This paper reviews some of the characteristics of microsporidian genomes in general, and some of the recent discoveries made through comparative genomic analyses. In general, microsporidian genomes are both reduced and compacted. Reduction takes place through gene loss, which is understandable in obligate intracellular parasites that rely on their host for many metabolites. Compaction is a more complex process, and is as yet not fully understood. It is clear from genomes surveyed thus far that the remaining genes are tightly packed and that there is little non-coding sequence, resulting in some extraordinary arrangements, including overlapping genes. Compaction also seems to affect certain aspects of genome evolution, like the frequency of rearrangements. The force behind this compaction is not known, and is especially interesting in light of the fact that surveys of genomes that are significantly different in size yield similar complements of protein-coding genes. There are some interesting exceptions, including catalase, photolyase and some mitochondrial proteins, but the rarity of these raises an interesting question as to what accounts for the significant differences seen in the genome sizes among microsporidia.

Animals↗

PubMed1996

Deletion of the Herpes simplex 1 internal repeat sequences affects pathogenicity in the mouse.

We have isolated three different herpes simplex virus 1 (HSV-1) recombinant viruses, each frozen in either the P (prototype), IS (inversion of S component), or ILS (inversion of both components) genome arrangement. Common to all three recombinant viruses is the deletion of approximately 14 kilobases (kb) of viral DNA sequences representing greater than 95% of the internal repeat sequences and the insertion of a 9.6 kb mini-Mu genome containing a functional thymidine kinase gene. No unique DNA sequences were deleted from the viral genomes. Analyses of growth curves of the wild-type and recombinant viruses in cell culture has revealed that the recombinants grow somewhat more slowly, producing final titers within 1.5 logs of wild-type HSV-1(F). There is no discernible difference in plaque size or plaque morphology between the recombinant and wild type strains. Analysis of the recombinant viruses in mice reveals the following: I), the recombinant viruses are essentially avirulent, exhibiting drastically increased LD50 values as compared to the wild-type strain by intracerebral injection; ii), the recombinant viruses are not neuroinvasive in that they do not spread from the cornea to sensory ganglion; iii), the recombinant viruses exhibit minimal local replication both in the corneas of infected mice and in the brains of mice inoculated by intracerebral injection; and iv), the recombinant viruses do not establish a reactivable latent infection in the trigeminal ganglion following either intracerebral inoculation or inoculation of scarified corneas. These properties suggest a unique pattern of pathogenesis for HSV mutants in the mouse model.

Animals↗

PubMed2000

Identification of genomic variations among geographic isolates of white spot syndrome virus using restriction analysis and Southern blot hybridization.

White spot syndrome virus (WSSV) is widely distributed in most of the Asian countries where penaeid shrimp are cultured, as well as in some regions of the USA. Six geographic isolates of WSSV-1 each from penaeid shrimp from China, India, Thailand, and the US states of Texas and South Carolina, and 1 isolated from crayfish at the National Zoological Park in Washington, DC-were compared by combining the methods of restriction analysis and Southern blot hybridization. DNA was extracted from purified viruses and then digested with selected endonucleases: AccI, BglII, ClaI, BamHI, EcoRI, HindII, HaeI, SacI and XhoI. The blots were detected with digoxigenin-11-dUTP-labeled WSSV genomic probes: LN4, C42 and A6. No distinctive differences among the 5 WSSV isolates from penaeid shrimp were detected; however, differences in the WSSV isolate from crayfish were observed. A 2.8 kb DNA fragment originating from the crayfish isolate and encompassing the LN4 region was subcloned into pBluescript and sequenced for comparison with the LN4 fragment from the Thailand WSSV isolate. The results indicate that some genomic components of WSSV from different geographic regions share a high degree of homology. This method can be used to distinguish between the WSSV isolate from crayfish and the WSSV isolates from penaeid shrimp.

Animals↗

PubMed1999

Detection and nucleotide analysis of RNA5 of beet necrotic yellow vein virus isolated in China.

Using the RT-PCR method, five isolates of beet necrotic yellow vein virus from China were used for the RNA5 genomic component detection and sequence analysis. The result showed that RNA5 was only found in the isolates from Baotou and Hohhot, but not in those of Xingjiang, Helongjiang, and Wulate of Inner Mongolia. The RNA5 components had 1338 nucleotides and 1358 nucleotides in the length of Baotou and Hohhot isolates, respectively, in which the single open reading frame (ORF) encoding for a proteins of 26kD were contained. Compared with the published sequences of F72 and D5 isolates, these RNA5 components shared the identity of 93.7% approximately 98.5% in nucleotide acids and 91.8%-98.2% in deduced amino acids.

Base Sequence↗

PubMed2000

Alphavirus DNA and particle replicons for vaccines and gene therapy.

Alphaviruses have several features that make them attractive as gene delivery platforms, and vectors derived principally from Sindbis virus (SIN), Semliki Forest virus (SFV), and Venezuelan equine encephalitis virus (VEE), are currently being developed as prophylactic and therapeutic vaccines for infectious diseases and cancer. Alphavirus vectors, termed "replicons", retain the nonstructural protein genes encoding the viral replicase, that in turn programme high level cytoplasmic amplification of the vector RNA. We have developed plasmid DNA and recombinant vector particle delivery systems derived from the prototype alphavirus, SIN. Each system uses RNA polymerase II-based expression of alphavirus genome components and both vector formats are highly efficacious towards inducing robust antigen-specific immune responses in vaccinated animals. To increase the potency of SIN vector particles, which are not known to be lymphotropic, the tropism was re-directed for efficient infection of dendritic cells, both in vitro and in vivo.

Alphavirus↗

PubMedDate not supplied

[Primary structure of RNA 3 of barley stripe mosaic virus and its variability].

The complete nucleotide sequence was determined for three variants of the third genomic component of BSMV strain Argentina mild. The common variant, RNA 3 (2797 nucleotide), contains two open reading frames (ORFs) coding for two proteins with Mr of 74,229 (putative BSMV RNA polymerase) and Mr of 16,994. The second ORF is expressed from a subgenomic RNA. The extended variant RNA 3 differs from the common one only by the presence of a direct tandem repeat 351-363 nucleotides in length (with some variability) encompassing part of the leader sequence and the beginning of the first ORF. The resulting protein has a Mr of about 86,000. The defective variant, RNA 4, carries a deletion of 185 nucleotides in the 3'-end proximal part of the first ORF, which shortens the product to a Mr of 60,344.

Amino Acid Sequence↗

PubMedDate not supplied

[Free radical damage of the nuclear genetic apparatus of cells].

Data which prove the important role of the lipid (as well as chromatin-bound lipids) peroxidation free radical reactions in the mechanisms of nuclear genome components damages are presented. Free radical nature of chromatin damages is proved in case of effects of ionising radiation and heavy metals ions. The role of lipid peroxidation reactions in the effects of the natural aging process, chlor- and phosphororganic chemicals intoxications is less investigated. The importance of the research of this scientific problem is discussed because of the unfavorable chemical and radiation situations.

Animals↗

PubMed1996

Facts and paradoxes in current notions of nuclear organization and function.

Invisible compartments, identified rather by their activities than by their morphology, seem to operate in the nucleus. These compartments interrelate somehow, including mediation by the nuclear matrix. As our knowledge about the nucleus increases, more paradoxes become evident. We here consider some of them: 1) the well-known C-paradox of Cavalier-Smith, concerning the disproportionate amount of nuclear DNA content in comparison with the amount of DNA potentially able to transcribe; 2) the DNA folding in the chromatin fibre and its superorganization within the nucleus, which seems to be in opposition with the transcribing and self-replicating activities; 3) the elusive role of the DNA sequences with different degrees of repetitivity; and 4) the compartmentalization in the nucleus and how it relates to transcription, processing and transport of transcripts, and to DNA reduplication. We conclude by introducing the concept of species specific, minimal, but essential genome components, i.e. the elusive few thousand DNA bases that, in our hypothesis, act as a functional bridge between the nuclear matrix and chromatin.

Animals↗

PubMed1987

A new human cytomegalovirus isolate has an invertible subsegment within its L component producing eight genome isomers.

A HindIII cleavage map of the genome DNA of a new isolate of human cytomegalovirus (HCMV), strain Tanaka, was constructed by cosmid cloning and Southern blot hybridization of virion DNA. The genome was found to be unique in that its long (L) component was composed of two subsegments, L1 and L2, and subsegment L2 underwent inversion relative to L1 at high frequency. In addition to the normal inversions of the L and short (S) components, this produced eight genome isomers. The novel invertible subsegment was flanked by an inverted sequence distinct from the inversion-specific a sequence present in the terminal and junction regions of the genome.

Cell Line↗

PubMed1984

Simple sequences are ubiquitous repetitive components of eukaryotic genomes.

Simple sequences are stretches of DNA which consist of only one, or a few tandemly repeated nucleotides, for example poly (dA) X poly (dT) or poly (dG-dT) X poly (dC-dA). These two types of simple sequence have been shown to be repetitive and interspersed in many eukaryotic genomes. Several other types have been found by sequencing eukaryotic DNA. In this report we have undertaken a systematical survey for simple sequences. We hybridized synthetical simple sequence DNA to genome blots of phylogenetically different organisms. We found that many, probably even all possible types of simple sequence are repetitive components of eukaryotic genomes. We propose therefore that they arise by common mechanisms namely slippage replication and unequal crossover and that they might have no general function with regards to gene expression. This latter inference is supported by the fact that we have detected simple sequences only in the metabolically inactive micronucleus of the protozoan Stylonychia, but not in the metabolically active macronucleus which is derived from the micronucleus by chromosome diminution.

Animals↗

PubMed1997

Comparison of sib-pair and variance-components methods for genomic screening.

The statistical properties of sib-pair and variance-components linkage methods were compared using the nuclear family data from Problem 2. Overall, the power to detect linkage was not high for either method. The variance-components method had better power for detection of linkage, particularly when covariates were included in the model. Type I error rates were similar to nominal error rates for both methods.

Analysis of Variance↗

PubMed1989

Nucleotide sequences at recombinational junctions present in pseudorabies virus variants with an invertible L component.

The genome of pseudorabies virus (PrV) consists of two components--a noninvertible long (L) and an invertible short (S) component. The S component is bracketed by inverted repeats. In some variant strains of PrV (which have a selective growth advantage in certain cell lines), a sequence normally present at the left end of the L component has been translocated to the right end of the L component next to the inverted repeat. Consequently, these strains have acquired a genome with an L component that is bracketed by inverted repeats and that also inverts. We have determined the restriction maps and have analyzed the nucleotide sequences of those parts of the genome of three strains with invertible L components that contain the translocated segment of DNA. The results were as follows. The translocated fragments were derived in all cases from the extreme left end of the L component only. The sizes of the translocated fragments were similar, ranging from 1.3 to 1.4 kilobase pairs. The junction between the L and S components in these strains was the same as that in standard viral concatemeric DNA. The translocation of sequences from the left end of the genome next to the inverted repeats was always accompanied by a deletion of sequences from the right end of the L component. The sizes of the deleted fragments varied considerably, ranging from 0.8 to 2.3 kilobase pairs. Sequence homology at the points of recombination, i.e., at the junction between the right end and the left end of the L component, existed sometimes but not always. A model depicting how a virus with a class 2 genome (such as PrV) may acquire a genome with characteristics of a class 3 genome (such as herpes simplex virus) is presented.

Animals↗