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At least 415 records · Page 23Linked to original sources
PubMed2003

Remarkable sequence signatures in archaeal genomes.

Complete archaeal genomes were probed for the presence of long (> or = 25 bp) oligonucleotide repeats (words). We detected the presence of many words distributed in tandem with narrow ranges of periodicity (i.e., spacer length between repeats). Similar words were not identified in genomes of non-archaeal species, namely Escherichia coli, Bacillus subtilis, Haemophilus influenzae, Mycoplasma genitalium and Mycoplasma pneumoniae. BLAST similarity searches against the GenBank nucleotide sequence database revealed that these words were archaeal species-specific, indicating that they are of a signature character. Sequence analysis and genome viewing tools showed these repeats to be restricted to non-coding regions. Thus, archaea appear to possess a non-coding genomic signature that is absent in bacterial species. The identification of a species-specific genomic signature would be of great value to archaeal genome mapping, evolutionary studies and analyses of genome complexity.

Base Sequence↗
PubMed1998

The expression of histone genes during Drosophila melanogaster oogenesis.

A genomic fragment was cloned from a DNA library constructed from a Drosophila enhancer trap line in which reporter gene expression was observed at the anterior-most tip of the ovaries and testes. This genomic clone was identified as the L-repeat of the Drosophila melanogaster histone gene cluster. Northern blotting and in situ hybridisation to RNA in tissues with individual cDNAs and PCR-generated probes for each histone confirmed that gene expression was greatest at the anterior portion of each ovariole, in the germarium, and was also elevated in a few individual nurse cells and somatic follicle cells within the egg chamber during early developmental stages. Histone H1 and each of the core histones had a similar expression pattern which was correlated to cell division. Maternal stores of histone transcripts were also transported to the mature oocyte from the nurse cells at a later stage of oogenesis (stage 10), when virtually all the nurse cells contained high levels of histone transcripts. The results are consistent with expression of the somatic histone gene cluster during oogenesis as a co-ordinate unit. There does not seem to be a reduced level of somatic type H1 in the germ-line, as is observed in some other species. The relationship between the P[lacZ] expression pattern in the germarium and the overall expression of the histone cluster suggests there are specific regulatory elements for germ-line expression.

Animals↗
PubMed1992

A phage T4 in vitro packaging system for cloning long DNA molecules.

Recombinant plasmid DNAs containing long DNA inserts that can be propagated in Escherichia coli would be useful in the analysis of complex genomes. We tested a bacteriophage T4 in vitro DNA packaging system that has the capacity to package about 170 kb of DNA into its capsid for cloning long DNA fragments. We first asked whether the T4 in vitro system can package foreign DNA such as concatemerized lambda imm434 DNA and phage P1-pBR322 hybrid DNA. The data suggest that the T4 system can package foreign DNA as efficiently as the mature phage T4 DNA. We then tested the system for its ability to clone foreign DNA fragments using the P1-pBR322 hybrid vectors constructed by Sternberg [Proc. Natl. Acad. Sci. USA 87 (1990) 103-107]. E. coli genomic DNA fragments were ligated with the P1 vectors containing two directly oriented loxP sites, and the ligated DNA was packaged by the T4 in vitro system. The packaged DNA was then transduced into E. coli expressing the phage P1 cyclization recombination protein recombinase to circularize the DNA by recombination between the loxP sites situated at the ends of the transduced DNA molecule. Clones with long DNA inserts were obtained by using this approach, and these were maintained as single-copy plasmids under the control of the P1 plasmid replicon. Clones with up to about 122-kb size inserts were recovered using this approach.

Bacteriophage lambda↗
PubMed1988

Infectious in vitro transcripts from cowpea chlorotic mottle virus cDNA clones and exchange of individual RNA components with brome mosaic virus.

Complete cDNA copies of genomic RNA1, RNA2, and RNA3 of cowpea chlorotic mottle virus (CCMV) were cloned 1 base downstream from a T7 RNA polymerase promoter. The mixture of capped in vitro transcripts from all three clones produced normal CCMV infections in barley protoplasts and cowpea plants. By using transcripts from these clones and from a similar set of biologically active clones of the related brome mosaic virus (BMV), all possible single component exchanges between the BMV and CCMV tripartite genomes were tested. Viral RNA replication was not observed with any heterologous combination of RNA1 and RNA2, which encode trans-acting viral RNA replication factors. However, substitution of the heterologous RNA3 into either genome produced viable hybrid viruses, both of which replicated in barley protoplasts and produced lesions on Chenopodium hybridum, a local lesion host for both parent viruses. In hybrid infections, BMV and CCMV coat proteins each readily packaged RNAs from the heterologous virus, but BMV RNAs were replicated to a higher level than CCMV RNAs, even when trans-acting RNA replication factors were provided by CCMV genes. Neither hybrid systemically infected the natural host of either parent virus, suggesting that host specificity determinants in BMV and CCMV are encoded by RNA3 and at least one other genomic RNA.

Base Sequence↗
PubMed1997

Incorporation of covariates into genome scanning using sib-pair analysis in bipolar affective disorder.

Assessing heterogeneity in affected relative pair linkage analysis can help control type I error or identify important subgroups. We develop a method to incorporate covariates into sib-pair analysis, and hence are able to test for covariate effects on allele sharing in sib pairs. We propose a way of combining the five bipolar data sets to do a joint analysis of chromosome 18 data using this new method. Our results from a limited set of analyses do not show significant heterogeneity, and do not confirm the linkage previously identified on chromosome 18.

Algorithms↗
PubMed1997

Comparative genomic hybridization is a powerful tool, complementary to cytogenetics, to identify chromosomal abnormalities in childhood acute lymphoblastic leukaemia.

Cytogenetics has a strong prognostic value in childhood acute lymphoblastic leukaemia (ALL), but results are often incomplete because of the poor chromosome morphology. To improve this analysis, we tested comparative genomic hybridization (CGH) for the detection of chromosomal imbalances. 72 children were retrospectively analysed using CGH. Only 53% of the patients had been fully banded by standard methods. With CGH, 36 patients retained a normal chromosomal profile and 36 had unbalanced abnormalities. No amplification was detected. Fluorescence in situ hybridization (FISH) with centromeric and unique sequence probes was used in those cases with discrepancies or unsuccessful karyotype to validate CGH results. CGH enabled clear identification of unbalanced chromosomal abnormalities, even in some cases which had a normal karyotype. In view of the strong prognostic value of hyperdiploidy in childhood ALL, CGH appears to be a powerful technique, complementary to conventional cytogenetics.

Adolescent↗
PubMed1981

New genes in the left arm of the bacteriophage phi 80 chromosome.

We describe the isolation and partial genetic characterization of 247 amber (suppressor-sensitive) mutants of temperate bacteriophage phi 80 of Escherichia coli. Of these 247 mutants, the mutations of 201 mapped to the left arm of the phi 809 chromosome and the mutations of 39 mapped to the right arm of the genome. Complementation tests among these and previously described left arm mutants defined five additional genes in the left arm of the chromosome. The positions of these genes are consistent with the hypothesis that four of them represent functions essential for phi 80 tail assembly and one represents a capsid assembly function, probably the major coat protein. The identification of these genes brings the phi 80 genome into closer correspondence with the organization of the phage lambda genome. Two- and three-factor crosses performed between mutants with defects in each of the previously identified genes and mutants with defects in the five new genes allowed us to construct a consistent, roughly additive recombination map of the left arm of the bacteriophage phi 80 genome.

Alleles↗
PubMed1993

[Analysis of cell specific transcription of the human cone transducin alpha subunit gene].

Cone transducin alpha subunit (Tc alpha), together with the two other components; beta and gamma subunits, composes a heterotrimeric G protein and transmits visual signals in the optic system. Genomic Tc alpha gene was cloned from human placental library using a cDNA probe isolated from a human T-cell cell line, Jurkat. The 5' region of Tc alpha was sequenced and the mechanism of Tc alpha expression was analysed by primer extension and CAT assay. Furthermore DNase 1 hypersensitivity test and genomic sequencing were performed. Primer extension revealed two transcription initiation sites. A TATA box and an inverted CCAAT box were identified just upstream of the transcription initiation sites, which constituted a typical promoter structure. In further upstream region, an octamer sequence (ATGCAAAT) and an inverted GGCCCC were found. The latter sequence is frequently present upstream of the genes expressed exclusively in retinal cells. No specific DNA element enhancing the expression of Tc alpha in Y79 cells (a Tc alpha expressing cell line) was found by CAT assay. However, DNaseI hypersensitivity test revealed the region to be in an active chromatin structure in Y79 as opposed to HeLa (a Tc alpha non-expressing cell line). By further study utilizing genomic sequencing, HeLa DNA was methylated in contrast to Y79, suggesting methylation as one of the transcription-regulating factors of this region.

Base Sequence↗
PubMed1997

Factors influencing the identification of major genes in a complex disease genome scan.

A two-stage linkage strategy was employed to identify major genes for a simulated complex disease via a genome scan. The importance of several approaches for improving the ability to locate major genes has been illustrated. These approaches are: adjusting for covariates, ascertaining through multiple affected family members, increasing the sample size, and using multipoint linkage analysis.

Chromosome Mapping↗
PubMed1976

The capacity of Drosophila for detecting relevant genetic damage.

For the detection and study of mutagenic agents, Drosophila offers many advantages. It is a higher organism with a short generation time that is cheap and easy to breed in large numbers. The simple genetic testing methods provide unequivocal answers about the whole spectrum of relevant genetic damage. A comparison of the detection capacity of assays sampling different kinds of genetic damage revealed that various substances are highly effective in inducing mutations, but do not produce chromosome breakage effects at all, or only at much higher concentrations than those required for mutation induction. Of the different assay systems available, the classical sex-linked recessive lethal test thus deserves priority, in view of its superior capacity to detect mutagens. Of practical importance is also its high sensitivity, because a large number of loci in one-fifth of the genome is tested for newly induced forward mutations, including small deletions. Drosophila is capable of carrying out the same metabolic activation reactions as the mammalian liver. An additional advantage, in this respect, is the capacity of Drosophila for detecting short-lived activation products, because intracellular activation occurs within the spermatids ans spermatocytes. These properties make the test for recessive sex-linked lethals a useful tool for verifying results obtained in the pre-screening of potential mutagens with fast microbial assay systems. In studies on non-disjunction, detailed genetic analysis of the induced changes is possible, and these may shed light on the mechanisms involved. A new adaptation of the bithorax transvection method by Mendelson permits the recovery of high yields of chromosome aberrations in a fast one-generation test.

Animals↗
PubMed2004

Expression profiling and comparative genomics identify a conserved regulatory region controlling midline expression in the zebrafish embryo.

Differential gene transcription is a fundamental regulatory mechanism of biological systems during development, body homeostasis, and disease. Comparative genomics is believed to be a rapid means for the identification of regulatory sequences in genomes. We tested this approach to identify regulatory sequences that control expression in the midline of the zebrafish embryo. We first isolated a set of genes that are coexpressed in the midline of the zebrafish embryo during somitogenesis stages by gene array analysis and subsequent rescreens by in situ hybridization. We subjected 45 of these genes to Compare and DotPlot analysis to detect conserved sequences in noncoding regions of orthologous loci in the zebrafish and Takifugu genomes. The regions of homology that were scored in nonconserved regions were inserted into expression vectors and tested for their regulatory activity by transient transgenesis in the zebrafish embryo. We identified one conserved region from the connective tissue growth factor gene (ctgf), which was able to drive expression in the midline of the embryo. This region shares sequence similarity with other floor plate/notochord-specific regulatory regions. Our results demonstrate that an unbiased comparative approach is a relevant method for the identification of tissue-specific cis-regulatory sequences in the zebrafish embryo.

Animals↗
PubMed1997

The performance of MIM in comparison with MAPMAKER/SIBS to detect QTLs.

This paper summarizes the results of searching for evidence of loci contributing to simulated quantitative traits which are associated with a common genetic disease using two multipoint identity by descent (IBD) sharing methods: MIM and MAPMAKER/SIBS. In brief, by varying the lod-score threshold from 1 to 3, we found that MIM and MAPMAKER/SIBS have similar power to detect linkage, but MAPMAKER/SIBS consistently produces a higher number of false positives.

Chromosome Mapping↗
PubMed1999

Hunting genetic diseases: exploring a multistage approach to identifying disease loci.

Genomic screen data for a hypothetical disease was used in a two-stage analysis to search for disease loci. We performed both trait-model-dependent and trait-model-free analyses to test their relative power. Results of our first-stage screen in 200 families suggested 13 regions for further analysis. Second-stage follow-up in another 200 families confirmed a single region on chromosome 3 near marker D3G045 with a combined lod score across all 400 families of 6.24 and a sib-pair maximum lod score (MLS) of 4.79. The MLS were highly correlated with both the autosomal dominant and autosomal recessive lod scores in all data sets, suggesting that both trait-model-dependent and trait-model-free methods can be useful for identifying candidate regions for complex disease loci. Reanalysis of the data using alternative sampling schemes suggested that sampling variation has a significant effect on locus detection.

Genetic Markers↗
PubMed2005

[More hereditary intestinal cancer can be detected if patients with colorectal carcinoma that are selected by the pathologist are examined for microsatellite instability].

OBJECTIVE: To determine whether an investigation of microsatellite instability (MSI) in patients with colorectal carcinoma that have been selected by the pathologist could increase the number of detected families with hereditary non-polyposis colorectal carcinoma (HNPCC). DESIGN: Prospective inventory. METHOD: Pathologists selected patients with a newly diagnosed colorectal carcinoma for MSI analysis of their tumour tissue if they met one of the following four criteria: (a) colorectal carcinoma diagnosed below 50 years of age; (b) a second colorectal carcinoma; (c) a combination of colorectal carcinoma and another HNPCC-related cancer; (d) colorectal adenoma with high-grade dysplasia diagnosed below 40 years of age. Patients with a positive MSI-test were referred to a clinical geneticist. The new strategy was introduced and explored in 5 hospitals for a period of to months. RESULTS: The new strategy was adopted and implemented successfully by pathologists and surgeons and accepted with satisfaction by the patients. Of the 55 patients included, 10 had a positive MSI-test. In 8/10 patients, DNA-mutation analysis was started by the clinical geneticist and 3 germline mutations in the MSH2-gene were detected. In 2 of 3 families with a pathogenic mutation, the family history alone did not fulfil the clinical criteria for HNPCC. CONCLUSION: Selection by the pathologist for MSI investigation was feasible in daily practice and identified more HNPCC patients than selection based on family history alone.

Adult↗