Biomedical subjects

Genomics

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PubMed1998

PCR fingerprinting of whole genomes: the spacers between the 16S and 23S rRNA genes and of intergenic tRNA gene regions reveal a different intraspecific genomic variability of Bacillus cereus and Bacillus licheniformis [corrected].

Genomic diversity in 21 strains of Bacillus cereus and 10 strains of Bacillus licheniformis was investigated by random amplified polymorphic DNA (RAPD) analysis, which samples the whole genome, and by two PCR fingerprinting techniques sampling the hypervariable spacers between the conserved 16S and 23S rRNA genes of the rRNA gene operon (ITS-PCR) and regions between tRNA genes (tDNA-PCR). RAPD analysis showed a remarkable diversity among strains of B. cereus that was not observed with the rRNA and tRNA intergenic-spacer-targeted PCR, where all the strains showed practically identical fingerprints. A wide variability among the B. cereus strains was also observed in the plasmid profiles, suggesting that the genetic diversity within B. cereus species can arise from plasmid transfer. One contribution to the diversity detected by RAPD analysis was determined by the presence of large extrachromosomal elements that were amplified during RAPD analysis as shown by Southern hybridization experiments. In contrast to the strains of B. cereus, the 10 strains of B. licheniformis were grouped into two clusters which were the same with all the methods employed. The 16S rRNA genes were identical in all 10 strains when examined using single strand conformation polymorphism analysis after digestion with Alul and Rsal. From these data we hypothesize two different evolutionary schemes for the two species.

Bacillus cereus↗

PubMed1996

Toward the construction of integrated physical and genetic maps of the mouse genome using interspersed repetitive sequence PCR (IRS-PCR) genomics.

Using two recently developed techniques, IRS-PCR YAC walking and IRS-PCR genotyping, a framework-integrated physical and genetic map of the mouse genome was constructed. The map consists of 821 contigs, containing 7746 YAC clones originating from three different YAC libraries. Three hundred eighty of the contigs have been anchored to the genetic map. Approximately 16% of the physical length of the mouse genome is estimated to be represented.

Animals↗

PubMed1993

Analysis of the genome of the five Bifidobacterium breve strains: plasmid content, pulsed-field gel electrophoresis genome size estimation and rrn loci number.

The genomes of the five Bifidobacterium breve strains available from culture collections were compared by restriction endonuclease analysis. Electrophoretic migration of undigested DNA allowed us to detect a 5.6-kb circular plasmid in two of these strains. A restriction map of this plasmid was constructed using 10 enzymes. With DraI endonuclease, pulsed-field gel electrophoresis has allowed the determination of the five B. breve genome sizes to 2.1 Mb. This estimation was further confirmed for CIP 6469 (type strain) and ATCC 15698 using XbaI and SpeI enzymes. In addition, rRNA gene regions were used as probes for strain characterization and suggest that there are at least three rrn loci in B. breve.

Bifidobacterium↗

PubMed2026

Genomic introgressions from wild relatives in the wheat genome alter meiotic dynamics in inter-varietal hybrids.

The use of wild relatives to introduce original diversity in the genome of bread wheat (Triticum aestivum L.) is an interesting approach to face the challenges of sustainable agriculture and the impact of climate change on wheat production. However, the influence of these wild-species introgressions on meiosis in inter-varietal wheat hybrids remains poorly understood. We analyzed the French wheat variety Renan (Re) carrying Aegilops ventricosa (Aev)-derived 2AS/2NS and 7DL/7DvL introgressions, the reference cultivar Chinese Spring (CS), which lacks these introgressions, and their inter-varietal hybrid Chinese Spring × Renan (CSRe). This analysis combined cytogenetic approaches with the assessment of reproductive performance. Furthermore, we generated a cytological atlas of meiosis in wild tetraploid Aev, quantifying bivalent configurations and chiasma frequency. We observed a reduced pollen viability and a slight decrease in floret fertility in the hybrid CSRe. Exploration of the meiotic behavior showed that CSRe exhibited increased numbers of rod bivalents and univalents, leading to a reduced average chiasma number and frequent chromosome bridges and fragmentations, whereas the parental lines maintained stable chromosome pairing. These rearrangements indicate that homologous chromosome pairing and recombination are affected in CSRe. We applied introgression-specific oligo-Fluorescent In Situ Hybridization to localize alien segments in CSRe, providing a novel strategy to investigate the meiotic behavior of introgressed regions. The 2AS/2NS introgressed segments in CSRe were frequently located on rod bivalents or univalents, while 7DL/7DvL segments consistently formed ring bivalents. Our results provide a foundation for guiding alien gene introgression and for understanding the behavior of chromosomes with introgressions in the wheat genome.

Meiosis↗

PubMed1995

Intestinal calcium transport in mole-rats (Cryptomys damarensis and Heterocephalus glaber) is independent of both genomic and non-genomic vitamin D mediation.

The role of vitamin D in mineral uptake in the gastrointestinal tract (GIT) of mole-rats (Heterocephalus glaber and Cryptomys damarensis; family Bathyergidae), animals with a naturally impoverished vitamin D status, was investigated. We measured relative rates of passage of radioactive markers, mode of calcium (Ca) uptake, paracellular movement and the opening of voltage-sensitive Ca channels (VSCCs) along the GIT with and without oral vitamin D3 supplementation. The ratio of relative absorption of labelled 45Ca to [14C]polyethylene glycol ([14C]PEG) indicated that within 24 h more than 88% of the Ca in the diet had been absorbed. Most absorption occurred in the duodenum within 12 h. The contribution of the hindgut (caecum and proximal and distal colon) to total Ca absorption was small (approximately 11%). Only passive uptake occurred in the duodenum (serosal (S): mucosal (M) ratios approximately 1). Active uptake occurred in the hindgut (S:M > 2), although hindgut absorption appears to play a secondary role to passive uptake in the duodenum. Vitamin D3 supplementation had no effect on the mode of Ca uptake in either the small intestine or the hindgut. Although we found VSCCs in mole-rat intestinal epithelial cells, they occurred in very low concentrations. Calcium influx through VSCCs did not change following vitamin D stimulation. Furthermore, mole-rats pretreated with intraperitoneal (I.P.) 1,25(OH)2D3 showed no enhancement of VSCC Ca uptake, indicating that active uptake plays a minor role, if any, in GIT mineral absorption. Our data support the hypothesis that intestinal Ca transport in mole-rats is independent of both genomic and non-genomic vitamin D mediation.

Animals↗

PubMed1997

Versatile insertion plasmids for targeted genome manipulations in bacteria: isolation, deletion, and rescue of the pathogenicity island LEE of the Escherichia coli O157:H7 genome.

A system of versatile insertion plasmids was constructed that permits efficient delivery of the target sites of an ultra-rare-cutting endonuclease and the recombinase FLP into preselected sites of the bacterial genome. With the help of this system, the pathogenicity island LEE of the Escherichia coli O157:H7 genome was excised and isolated in vitro, deleted in vivo, rescued as a plasmid, and transferred into another strain.

Base Sequence↗

PubMed1989

The genomics of long tandem arrays of satellite DNA in the human genome.

At least 10% of DNA in the human genome consists of long arrays of repeated sequences, arranged in tandem head-to-tail arrays in a number of discrete, highly localized chromosomal regions. Different families of these so-called "satellite DNA" sequences have been defined, organized in diverged subsets on different chromosomes. The molecular, cytogenetic, and evolutionary analysis of the hierarchical organization of such sequences in the human and other complex genomes encompasses a variety of approaches, including chromosomal mapping, in situ hybridization, genetic linkage analysis, long-range restriction mapping, and DNA sequencing. Investigation of the organization of satellite arrays constitutes a necessary first step towards eventual elucidation of the origin, evolution, and maintenance of these sequences and their contribution to the structure and behavior of human chromosomes.

Chromosome Mapping↗

PubMed2026

Natural Selection Drives Codon Usage Bias in the Mitochondrial Genome of Ligula intestinalis (Linnaeus, 1758) Gmelin, 1790 (Cestoda: Diphyllobothriidea): Insights from Comparative Genomics and Optimal Codon Identification.

Codon usage bias (CUB) is a useful indicator of evolutionary forces shaping mitochondrial genomes. Codon usage bias in mitochondrial genomes of Diphyllobothriidae and especially in Ligula intestinalis was characterized. The roles of natural selection and mutation pressure in framing this bias were evaluated on the basis of 12 protein-coding genes in Diphyllobothriidae. The complete mitogenome (13,725 bp) of L. intestinalis comprises 12 protein-coding genes (PCGs), 22 tRNAs, and two rRNAs, all positioned on the heavy strand, and contains an overall AT content of 66.15%. The mean CAI (0.176), CBI (-0.105), and ENC (45.33) and an evident preference for U-ending codons observed in all examined genes indicate weak CUB. Neutrality, ENC, and PR2 plots consistently demonstrate that natural selection is the predominant force driving CUB and contributes approximately 56% in L. intestinalis and 83% in other Diphyllobothriidea species, with mutation pressure playing a secondary role. Phylogenetic reconstruction supported the monophyly of Diphyllobothriidea, confirmed the paraphyly of Diphyllobothrium as traditionally defined, and placed Ligula and Digramma as sister taxa. These findings clarify the evolutionary constraints governing codon usage in cestode mitogenomes and provide practical resources for codon optimization in heterologous gene expression and genetic studies of this economically important parasite.

Diphyllobothriidea↗

PubMedDate not supplied

[Study of the structure-function organization of the variola virus genome. IV. Sequencing and analysis of the nucleotide sequence of the right terminus of the India-1967 strain genome].

Sequencing and computer analysis of the variola major virus strain India-1967 (VAR-IND) genome segment (53,018 bp) from the right terminal region have been carried out. Fifty nine potential open reading frames (ORFs) of over 60 amino acid residues have been identified. Structure-function organization of VAR-IND DNA segment under study was compared with the previously reported sequences from the analogous genomic regions of vaccinia virus strains Copenhagen (VAC-COP) and Western Reserve (VAC-WR) and variola virus strain Harvey (VAR-HAR). Multiple distinctions in the genetic map of VAR-IND from VAC-COP and VAC-WR have been revealed along with the high similarity to the corresponding VAR-HAR segment. Possible functions of the predicted viral proteins and the effect of their differences on the features of orthopoxviruses are discussed.

Amino Acid Sequence↗

PubMed1995

[A full-size DNA copy of the tick-borne encephalitis virus genome. I. Analysis of the 5'- and 3'-terminal noncoding regions of the genome].

Using reverse transcription and the polymerase chain reaction, cDNA fragments of noncoding regions of the tick-borne encephalitis virus (TBEV) genome were obtained. These fragments were cloned into a pGEM3 vector, and their nucleotide sequences were determined. The heterogeneity of the 3'-terminal untranslated region of the TBEV RNA was revealed. To create a stable full-size DNA copy of the TBEV genome, four cDNA variants differing in length and structure of the 3'-terminal fragment of the viral RNA were cloned into a pBR322-derived vector.

Base Sequence↗

PubMedDate not supplied

[Structure-activity organization of the variola virus genome. III. Sequencing and analysis of the nucleotide sequence of the conserved region of HindIII-F, -N-, and -A-fragments of the India 1967 strain genome].

Computer analysis of variola major virus (VAR) genomic fragment bounded by open reading frames (ORFs) D1R and A33L which is 47,961 bp long revealed 46 potential ORFs. The VAR proteins were compared with the analogous proteins of vaccinia virus strain Copenhagen. The subunits of DNA-dependent RNA polymerase, as well as the transcription factors, mRNA capping enzymes, and proteins necessary for the virion morphogenesis proved to be highly conservative within orthopoxviruses. The most pronounced differences between the VAR genome fragment under study and the corresponding vaccinia virus fragment were revealed in the vicinity of the gene encoding the A-type inclusion body protein. The possible functions of the analyzed viral proteins are discussed.

Amino Acid Sequence↗

PubMed1997

[Comparison between HGV genome and HGBV-C genome].

New hepatitis viruses, hepatitis G virus(HGV) and hepatitis GB virus C(HGBV-C), were reported from two groups of researchers. Now these two are thought to be similar but HGV genome(U44402) and HGBV-C genome(U36380) do not have the same sequence. We compare these two sequences in both nucleotide and aminoacid analyses. Homology of nucleotide between HGV and HGBV-C is 83.8% in 5'NC region, 88.8% in core, 85.1% in E1, 85.7% in E2, 85.1% in NS2-3, 84.5% in NS4A, 86.8% in NS4B-5A, 88.6% in NS5B and 18.0% in 3'NC. The length of 3'NC is quite different between HGV and HGBV-C. Homology of aminoacid between these two viruses is 82.9% in core region, 87.3% in E1, 91.0% in E2, 97.4% in NS2-3, 93.8% in NS4A, 96.2% in NS4B-5A and 96.6% in NS5B. Especially helicase and replicase regions are highly conserved in 99.0% and 92.7% of aminoacid homology, respectively.

Amino Acid Sequence↗

PubMed1995

Comparative genomic hybridization analysis of human sarcomas: I. Occurrence of genomic imbalances and identification of a novel major amplicon at 1q21-q22 in soft tissue sarcomas.

Comparative genomic hybridization (CGH) was recently developed as a tool to survey entire genomes for variations in DNA sequence copy numbers. We have applied this technique to detect and map amplified regions in 54 soft tissue sarcomas. Aberrations were detected by visual analysis of hybridizations or contrast-enhanced digital images, followed by quantitative digital ratio imaging of the aberrant chromosomes. Several tumors showed increased DNA sequence copy number at 12q14, as expected. However, CGH analysis detected amplification of 12q14 also in some tumors where neither MDM2 nor CDK4 was amplified, suggesting that another as yet unknown gene(s) may drive amplification of this region in sarcomas. Furthermore, a novel recurring amplicon was detected at 1q21-q22. DNA amplifications coinciding with this segment were as frequent as those observed for 12q14, indicating that 1q21-q22-linked gene(s) may also play an important role in the development and/or progression of human soft tissue sarcomas.

Animals↗

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↗