Biomedical subjects

Genomics

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PubMed1979

14q+ marker chromosome in an EBV-genome-negative lymph node without signs of malignancy in a patient with EBV-genome-positive nasopharyngeal carcinoma.

In a patient with an EBV-genome-positive nasopharyngeal carcinoma, an EBV-genome-negative inguinal lymph node without histological evidence of malignant lymphoma or metastatic carcinoma growth was found to contain a 14q+ marker chromosome, identified as an 8;14 translocation, in all cells analyzed. This observation indicates that chromosome aberrations may precede histological signs of malignancy. The possible implication of this finding in relation to the postulated role of the 14q+ marker and lymphoma development is discussed.

Adult↗

PubMed1995

Acquisition of a fourth genomic segment in bacteriophage phi 6, a bacteriophage with a genome of three segments of dsRNA.

Bacteriophage phi 6 has a genome of three segments of double-stranded RNA enclosed in a polyhedral procapsid. Packaging of individual segments is dependent upon unique packaging sequences near the 5' ends of the segments. We have prepared deletions in segments L and M that decrease their size by half. Phages with these deletions can be propagated on host strains carrying plasmids with complementing genes. The deletion segments are present in two copies per virion. Phage carrying a deletion segment can acquire the transcript of the complementing plasmid if the latter has a packaging sequence. If the packaging sequence is homologous to that of the deletion segment, acquisition occurs at high frequency. If it is heterologous, then recombination exchanges the heterologous packaging sequence for a homologous one or it attaches the transcript to one of the other genomic segments.

Bacteriophages↗

PubMed1993

Proposed classification of the bipartite-genomed raspberry bushy dwarf idaeovirus, with tripartite-genomed viruses in the family Bromoviridae.

Raspberry bushy dwarf virus (RBDV) has an unusual combination of properties and has been classified as the sole member of a new plant virus genus, for which the name idaeovirus has been proposed. Particles of RBDV resemble those of ilarviruses (family Bromoviridae) in appearance and in being transmitted in association with pollen. RBDV has two genomic RNA species, RNA-1 (5,449 nt) and RNA-2 (2,231 nt). The particles also contain RNA-3 (946 nt), a subgenomic monocistronic coat protein mRNA which is derived from the 3' end of the bicistronic RNA-2. The single 190 K protein encoded by RNA-1 contains methyltransferase, helicase and polymerase domains. Evolutionary distance data obtained from multiple alignments of the amino acid sequence of the RBDV 190 K protein and corresponding proteins with replicative function from other plant viruses suggest that the closest affinities of RBDV are with the tripartite genomed viruses in the family Bromoviridae. We propose that the genus idaeovirus be included in the family Bromoviridae.

Cluster Analysis↗

PubMed1997

Olfactory neuroblastoma: detection of genomic imbalances by comparative genomic hybridization.

Olfactory neuroblastoma (esthesioneuroblastoma) is a very rare tumour of the olfactory mucosa. Morphological features and cytogenetic studies strongly suggest a neuro-ectodermal origin. Up to now, cytogenetic studies are inconsistent. Some of them have proposed that the tumour belongs to the pPNET family. In the present study we describe genomic imbalances in olfactory neuroblastoma in a 46-year-old woman by using the molecular cytogenetic technique--comparative genomic hybridization (CGH)--in order to define the spectrum of genetic abnormalities in the tumour. The anatomical location and morphological findings were the basis for the diagnosis of esthesionearoblastoma. Immunohistochemical reactions for NSE, synaptophysin, chromogranin A, HNK-1/Leu-7 and S-100 revealed a characteristic immunophenotype. The CGH analysis showed multiple changes including DNA overrepresentations of chromosomes 4, 8, 11 and 14, partial DNA gains of the long arms of chromosomes 1 and 17, deletions of the entire chromosomes 16, 18, 19 and X, and partial losses of chromosomes 5q and 17p. This study represents an early utilisation of the CGH technique in olfactory neuroblastoma and demonstrates that the tumour carries complex chromosomal aberrations.

Biomarkers, Tumor↗

PubMed1984

Influenza B virus genome: complete nucleotide sequence of the influenza B/lee/40 virus genome RNA segment 5 encoding the nucleoprotein and comparison with the B/Singapore/222/79 nucleoprotein.

The complete nucleotide sequence of a cloned full-length DNA copy of genome RNA segment 5 of influenza B/Lee/40 virus has been determined. The genome segment is 1841 nucleotides in length and is capable of coding for a nucleoprotein (NP) of 560 amino acids. Comparison with the only other known sequence of an influenza B virus nucleoprotein gene (B/Singapore/222/79) indicates striking homology. Only 113 nucleotide substitutions are present between the two strains in their protein coding region and these lead to only 22 amino acid substitutions between nucleoproteins of identical polypeptide chain length. Assuming a common lineage, this reflects a calculated rate of amino acid sequence divergence of 0.1% per year. Like its influenza A virus counterpart, the influenza B/Lee/40 nucleoprotein is a basic protein with a relatively even distribution of its charged residues. The remarkable conservation of nucleoprotein primary structure over a 39-year period probably reflects both selection for performance of specific functions and protection from antigenic selection by the host immune system.

Amino Acid Sequence↗

PubMed1991

Non-genomic and genomic effects of steroids on neural activity.

Steroid hormones are recognized as producing their major long-term effects on cell structure and function via intracellular receptors acting on the expression of genes. There is now increasing evidence that steroids also affect the surface of cells and alter ion permeability, as well as release of neurohormones and neurotransmitters. Progesterone appears to be one of the most active of the steroids, and its naturally produced metabolites and some synthetic analogs show activities that are different from the parent steroid. Other steroids, such as estrogens and adrenal steroids and their naturally produced and synthetic analogs, also show membrane effects. Bruce McEwen reviews evidence that synergistic interactions occur between non-genomic and genomic actions of steroids.

Animals↗

PubMed1997

Comparative genomic hybridization detects genomic abnormalities in 80% of follicular lymphomas.

Comparative genomic hybridization (CGH) was used to analyse 34 follicular lymphoma (FL) samples. 27 samples showed DNA sequence copy number changes of at least one genomic region (26 samples with at least one gain and nine with at least one loss). Some chromosomes or chromosomal regions were preferentially involved. The most frequently gained regions were chromosome 18q (29% of samples), chromosome X (21%), chromosome 7 (18%), chromosomes 2, 6p and 8q (12%). Two regions were preferentially lost: 6q (12%) and 17p (9%). All these gained and lost regions have been previously reported in cytogenetic studies, confirming the accuracy of CGH in detecting genetic abnormalities in FL. 21% of samples displayed normal profiles, probably reflecting the absence of unbalanced abnormality, which is also in agreement with the cytogenetic data. In conclusion, we showed that CGH is an accurate, reliable and rapid method and we propose the inclusion of CGH in the evaluation of FL at diagnosis.

Chromosome Aberrations↗

PubMed1981

Tandemly repeated C-C-C-C-A-A hexanucleotide of Tetrahymena rDNA is present elsewhere in the genome and may be related to the alteration of the somatic genome.

The ribosomal RNA genes of the Tetrahymena macronucleus exist as extrachromosomal, linear molecules. The termini of these molecules have been shown to contain the tandemly repeated hexanucleotide (C-C-C-C-A-A)n. In this study the same or related sequences were found in other locations of the genome. Using the depurination method, we showed that macronuclear DNA contained this sequence even after rDNA had been removed. The sequence was found mainly in the repetitive fraction of the DNA. The presence of this sequence in both the macronucleus and the micronucleus was also shown by Southern hybridization using C-C-C-C-A-A repeat as a probe. Comparison between the hybridization patterns of macronuclei and micronuclei reveals interesting differences. Whereas the two nuclei share the same genetic origin, the majority of the restriction enzyme digestion sites flanking the C-C-C-C-A-A repeat appear to be different. Such a difference was found to be specific for this sequence, because it was not detected when other sequences were used for hybridization. These results suggest that some kind of alteration has occurred in the genome during the formation of the macronucleus, and that the C-C-C-C-A-A repeat may be related to this process.

Animals↗

PubMed1990

Amplification of genomic sequences flanking transposable elements in host and heterologous plants: a tool for transposon tagging and genome characterization.

The isolation of sequences flanking integrated transposable elements is an important step in gene tagging strategies. We have demonstrated that sequences flanking transposons integrated into complex genomes can be simply and rapidly obtained using the polymerase chain reaction. Amplification of such sequences was established in a model system, a transgenic tobacco plant carrying a single Ac element, and successfully applied to the cloning of a specific Spm element from a maize line carrying multiple Spm hybridizing sequences. The described utilization of methylation sensitive restriction enzymes (including those with degenerate recognition sequences) in the generation of templates for amplification will simplify the cloning and mapping of genomic sequences adjacent to transposable elements.

Base Sequence↗

PubMed1996

The Genome Sequence DataBase (GSDB): meeting the challenge of genomic sequencing.

The genome sequence database (GSDB) is a complete, publicly available relational database of DNA sequences and annotation maintained by the National Center for Genome Resources (NCGR) under a Cooperative Agreement with the US Department of Energy (DOE). GSDB provides direct, client- server access to the database for data contributions, community annotation and SQL queries. The GSDB Annotator, a multi-platform graphic user interface, is freely available. Automatically updated relational replicates of GSDB are also freely available.

Amino Acid Sequence↗

PubMed1984

Nucleotide sequence of the tobacco mosaic virus (tomato strain) genome and comparison with the common strain genome.

The sequence of about 4,500 nucleotides of the internal part of tobacco mosaic virus (TMV)-tomato strain (L) RNA has been newly determined using cloned cDNAs. Together with the previously determined partial sequences at both ends, the entire sequence of the 6,384 nucleotide genome has been completed. The 130K (1,115 amino acids), 180K (1,615 amino acids), 30K (263 amino acids) and coat protein (158 amino acids) cistrons are located at residues 72-3442, 72-4922, 4906-5700, and 5703-6182 on the genome, respectively. Sequence polymorphism was not observed except for heterogeneity in the length of the A cluster near the 3' end. The homology of the nucleotide sequences of TMV-L and TMV-vulgare, a common strain, is about 80% on average. Remarkable differences between them were found in a part of the N-terminal portion of the 130K/180K protein and the C-terminal portion of the 30K protein. A new method for cDNA cloning was developed by which the cDNA of the 5'-terminus of viral RNA can be cloned efficiently.

Base Sequence↗

PubMed1979

Comparison of the genomes of simian, bovine, and human rotaviruses by gel electrophoresis and detection of genomic variation among bovine isolates.

By co-electrophoresis in polyacrylamide gels, the segmented double-standed RNA genome of the simian rotavirus, SA 11, was compared with those of human and bovine rotaviruses. A comparison between SA 11 virus and the Northern Ireland cell culture adapted bovine virus showed that the electrophoretic mobilities of each of the 11 corresponding segments differed. In other comparisons, four to seven segment variations were more common. When the genomes of various bovine rotaviruses were compared, eight different electropherotypes were detected. Four of these electropherotypes were obtained from one property during a single outbreak of disease. In view of such genetic diversity, a scheme for the systematic designation of different rotavirus samples is proposed. The significance of the variations in relation to the molecular epidemiology of bovine rotavirus infections is discussed.

Animals↗

PubMed1980

Baboon endogenous virus genome. I. Restriction enzyme map of the unintegrated DNA genome of a primate retrovirus.

A detailed restriction map was deduced for the genome of an endogenous retrovirus of a higher primate, that of baboon. The cleavage sites for 12 restriction enzymes were mapped. The unintegrated linear viral DNA intermediate that is produced by infection of permissive cells with baboon endogenous virus was isolated. Hybridization with a strong-stop complementary DNA probe demonstrated presence of a terminal repetition in the linear viral DNA. The positions of restriction sites for two particular enzymes, SmaI and XhoI, near each end were consistent with this result and indicated that the length of the repetition is 0.55 +/- 0.01 kilobase. The linear viral DNA had a unique restriction map indicating that it is not a set of random circular permutations of the RNA genome. From hybridization with a 3'-specific probe, the DNA restriction map was aligned relative to the 5'-to-3' orientation of the viral RNA. We observed a minor heterogeneity in a BamHI recognition site 1.95 kilobases from the right end of the linear map.

Animals↗

PubMed1986

Molecular cloning and sequence determination of the genomic regions encoding protease and genome-linked protein of three picornaviruses.

To investigate the degree of similarity between picornavirus proteases, we cloned the genomic cDNAs of an enterovirus, echovirus 9 (strain Barty), and two rhinoviruses, serotypes 1A and 14LP, and determined the nucleotide sequence of the region which, by analogy to poliovirus, encodes the protease. The nucleotide sequence of the region encoding the genome-linked protein VPg, immediately adjacent to the protease, was also determined. Comparison of nucleotide and deduced amino acid sequences with other available picornavirus sequences showed remarkable homology in proteases and among VPgs. Three highly conserved peptide regions were identified in the protease; one of these is specific for human picornaviruses and has no obvious counterpart in encephalomyocarditis virus, foot-and-mouth disease virus, or cowpea mosaic virus proteases. Within the other two peptide regions two conserved amino acids, Cys 147 and His 161, could be the reactive residues of the active site. We used a statistical method to predict certain features of the secondary structures, such as alpha helices, beta sheets, and turns, and found many of these conformations to be conserved. The hydropathy profiles of the compared proteases were also strikingly similar. Thus, the proteases of human picornaviruses very probably have a similar three-dimensional structure.

Amino Acid Sequence↗

PubMed1994

Isolation of human nm23 genomes and analysis of loss of heterozygosity in primary colorectal carcinomas using a specific genomic probe.

Genomic clones of nm23-H1 and -H2 were isolated. The nm23-H1 and -H2 genes were located in a tandem array 4 kilobases apart. Each genome contained 5 exons and most of the splicing sites in the exon-intron junctions of two isotypes were essentially identical. A probe derived from intron 4 of nm23-H1 was used to examine the loss of heterozygosity (LOH) in primary colorectal carcinomas. Twenty-nine of 42 samples were informative and LOH was found in 3 of these 29. In all three samples with LOH, cancer tissues expressed lower levels of nm23-H1 mRNA when compared with those without LOH.

Amino Acid Sequence↗

PubMed1995

The use of restriction landmark genomic scanning to scan the mouse genome for endogenous loci with imprinted patterns of methylation.

Restriction landmark genomic scanning (RLGS) has been used to screen endogenous loci for imprinted patterns of methylation. The screening method is based upon the identification of genetic variation in RLGS profiles between different strains and determining whether specific variant landmarks are transmitted equally to the progeny of reciprocal F1 matings. The RLGS profiles of C57BL/6 (B6) and DBA/2 (D2) and their reciprocal hybrids were produced with two enzyme combinations that used NotI as the landmark enzyme and two combinations that used BssHII. An estimated 13% of the spots are either B5- or D2-specific in these tests, giving a total of nearly 1000 variant loci that were examined for imprinted methylation. Three candidate loci for imprinted regulation were identified in these analyses. We also used crosses of more genetically diverse parents to increase the number of variant loci screened. Interspecific crosses of B6 with the M. musculus strain PWK and intrasubspecific crosses between B6 and the M. molossinus strain MSM expanded the levels of variation between the parental strains in the cross to an estimated 31% and 26%, respectively. The RLGS patterns for one NotI combination and one BssHII profile were examined for each of these crosses, giving approximately 2000 additional loci that were screened for imprinted patterns of methylation. Eight loci with imprinted patterns of transmission were observed out of 3040 loci tested. The chromosomal locations for the three B6 and D2 specific loci, Irlgs 1-3, were identified using BXD recombinant inbred strain analysis. Irlgs 1 and 3 are B6- and D2-specific loci that had the same strain distribution pattern which mapped to the central region of chromosome 9.(ABSTRACT TRUNCATED AT 250 WORDS)

Alleles↗

PubMed2025

Genome-wide identification of potassium transporters and channels in Malus domestica genome.

Potassium (K+) is an essential nutrient for plants. It contributes to most physiological and biochemical pathways for plant metabolism, growth, and development. It is the most available plant nutrient, comprising 10–15% of plant weight. Plants have a sophisticated system of K+ transporters and channels for distribution in plant body. Apple is one of the most consumed fruits in the world. Its fruit quality and yield are positively affected by K+. However, limited information is available about K+ transport systems in Apple. In this study, 47 candidate genes (26 K+ transporters and 21 K+ channels) have been identified in Apple (Malus domestica) genome. The phylogenetic comparisons with other plants (Glycine max, Arabidopsis thaliana, and Oryza sativa) indicated that the K+ transport system is much conserved among different plants. The analysis of Gene structure showed the presence of specific introns and exon patterns for these gene families. Transcriptomic data analysis and RT-qPCR demonstrated significant variations in the transcript abundance of these genes in response to abiotic stresses. The current project represents the first report about the K+ transport system in Apple. Therefore, it may act as a starting point for further functional characterizations.

Malus↗

PubMed1996

Very fast identification of RNA motifs in genomic DNA. Application to tRNA search in the yeast genome.

A common strategy characterises the various methods independently defined to identify almost unambiguously different types of RNA molecules in DNA fragments. So far, the good quality of detection of RNA motif has been the prior motivation and effectively delayed the optimisation of programs. As an illustration of possible improvements, a modified version of tRNAscan is described. The previous algorithm was altered to run 500 times faster and to lower both rates of false positives and false negatives. The newly sequenced genome of Saccharomyces cerevisiae is scanned both ways in less than three minutes and results match annotations found in databanks with three exceptions, two of which being arguably not real tRNAs.

Algorithms↗