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PubMed2000

A novel interspersed type of organization of satellite DNAs in Tribolium madens heterochromatin.

Analysis of arrangement of satellite DNA sequences in Tribolium madens (Insecta, Coleoptera) by Southern analysis of pulsed-field blots and two colour FISH on extended chromosomes and DNA fibres revealed a novel type of heterochromatin organization. Two satellite DNAs, distributed over the whole pericentromeric heterochromatin of all chromosomes form clusters, ranging in size from 150 kb up to several Mb. Within the clusters, both satellites are in the form of highly interspersed, short homogeneous arrays which vary in size with a lowest length limit of only few kb. The longest arrays composed of a single satellite are relatively short, up to 70 kb for satellite I, and up to 45 kb for satellite II. Only a small fraction of about 15% of satellite II is organized in long tandem repeats, while the rest is in the form of only a few repeats intermingled with satellite I. The results indicate that large clusters composed of interspersed arrays of both satellites represent a major component of T. madens heterochromatin, which is mostly devoid of long regions of other sequences. The same organizational pattern probably also includes a region of the functional centromere. We propose that such an organizational pattern of DNA sequences in heterochromatin might be common in genomes characterized by a high rate of interchromosomal exchange. This pattern of organization is different from that in other animal as well as plant species analysed up to now, in which every satellite in heterochromatin is organized in a small number of large separate domains.

Animals↗

PubMed2003

Experimental infection of calves with bovine viral diarrhoea virus type-2 (BVDV-2) isolated from a contaminated vaccine.

A non-cytopathic strain of BVDV-2 was isolated from a batch of live infectious bovine rhinotracheitis (IBR) vaccine, and inoculated intranasally into four 3-month-old calves. Severe signs of disease developed by days 4 and 6 in three of the calves, free of BVDV and antibodies to BVDV, that had been exposed to the virus. These calves survived the acute phase of the infection and progressively recovered. BVDV was consistently isolated, or the respective viral RNA was detected, in the buffy coats from blood samples collected starting from days 2 or 4 up to days 11 or 14 after the experimental infection. Viral RNA was also detected in sera from these infected calves until the presence in the serum of virus neutralizing antibodies was demonstrated. By contrast, the only calf having pre-existing neutralizing antibodies to BVDV at the start of the study was protected from the disease. No virus was detected at any time after experimental inoculation of this calf. Genomic characterization of the BVDV-2 isolated in cell cultures, or detected in sera from the experimentally infected animals, revealed 100%, homology in the nucleotide sequence with the BVDV-2 detected as a contaminant of the live IBR virus vaccine. These findings provided evidence of the infective nature of the contaminant BVDV-2 and of its potential to generate disease outbreaks when inoculated into susceptible animals.

Animals↗

PubMed1980

Visualization of genetic recombination intermediates of human adenovirus type 2 DNA from infected HeLa cells.

The study of recombination in prokaryotes has been facilitated by the availability of recombinational mutants and simple genetic elements such as phages and plasmids. These small but defined molecules of DNA have been especially useful for electron microscopic analysis of structural detail of molecules undergoing recombination both in vivo and in vitro. A limitation in the structural analysis of plasmid recombination is the absolute number of recombining molecules which can be identified and analysed amidst a background of nonrecombining molecules. This limitation would be of even greater consequence in studies of genetic recombination in animal cells. We therefore chose virus-infected animal cells as a model system for the study of the molecular mechanism of genetic recombination in higher organisms. HeLa cells infected with adenovirus serotype 2 (Ad-2) offer several advantages for studying recombination: (1) the virus contains a small and well characterized genome of about 35 kilobases; (2) a large amount of Ad-2 DNA is accumulated during lytic infection and host DNA synthesis is suppressed; (3) Ad-2 recombines at a very high frequency; and (4) similar to phages, animal viruses and Ad-2 in particular are believed to use many of the host cell's enzymes in necessary metabolic processes, presumably including recombination. In this study we used electron microscopic techniques to visualize the structures of in vivo Ad-2 DNA recombination intermediates. Molecules were observed with structures at putative cross-over points which were consistent with the molecular mechanism of recombination proposed by Holliday. In addition, we observed Ad-2 DNA molecules engaged in recombination which were simultaneously serving as templates for replication and/or transcription. To the best of our knowledge, this is the first visualization of in vivo recombination intermediates of discrete DNA molecules isolated from eukaryotic cells.

Adenoviruses, Human↗

PubMed1996

A high efficiency technique for the generation of transgenic sugar beets from stomatal guard cells.

An optimized protocol has been developed for the efficient and rapid genetic modification of sugar beet (Beta vulgaris L.). A polyethylene glycol-mediated DNA transformation technique could be applied to protoplast populations enriched specifically for a single totipotent cell type derived from stomatal guard cells, to achieve high transformation frequencies. Bialaphos resistance, conferred by the pat gene, produced a highly efficient selection system. The majority of plants were obtained within 8 to 9 weeks and were appropriate for plant breeding purposes. All were resistant to glufosinate-ammonium-based herbicides. Detailed genomic characterization has verified transgene integration, and progeny analysis showed Mendelian inheritance.

Biotechnology↗

PubMed2001

Efficient metaphase II transgenesis with different transgene archetypes.

Mammalian genome characterization and biotechnology each require the mobilization of large DNA segments to produce transgenic animals. We recently showed that mouse metaphase II (mII) oocytes could efficiently promote transgenesis (mII transgenesis) when coinjected with sperm and small (<5 kilobases) ubiquitously expressed transgenes (tgs). We have extended this work and now report that mII transgenesis can readily be applied to a range of larger tgs (11.9-170 kilobases), including bacterial and mammalian artificial chromosome (BAC and MAC) constructs. The efficiency of large-construct mII transgenesis was at least as high as that with small constructs; 11-47% of offspring carried the large tgs. More than 95% of these transgenic founders transmitted the tg to offspring. These data demonstrate the ability of mII transgenesis to deliver large tgs efficiently.

Animals↗

PubMed2005

The natural history of small renal masses.

The incidence of renal cell carcinoma is increasing, in part due to the growing use of cross-sectional imaging. Most renal tumors are now incidentally detected as small masses in asymptomatic patients. A minority of small renal masses, presumed to be renal cell carcinoma, grow significantly over time if managed conservatively, but the growth rate of the majority is slow or undetectable. In the absence of other prognostic factors, measurement of tumor growth rate can be helpful for initial conservative management of selected patients with small renal tumors. To date, there have been no reports of progression to metastatic disease occurring during active surveillance, but longer follow-up is needed to confirm this observation. The standard of care for small localized renal neoplasms is partial or radical nephrectomy. At the present time, active surveillance of small renal masses, with delayed therapy for patients whose disease progresses, is an experimental approach that can be considered for the elderly or patients with significant comorbidity. Renal core biopsy and fine-needle aspiration can provide essential information for treatment decision-making and should therefore be considered in the diagnostic work-up of all small renal masses. In future, the identification of prognostic indicators, with the use of new techniques including functional imaging and molecular or genomic characterization of tissue from needle biopsies, are expected to help clinicians differentiate between indolent and potentially aggressive small renal tumors.

Carcinoma, Renal Cell↗

PubMed2006

Recombineering in Mycobacterium tuberculosis.

Genetic dissection of M. tuberculosis is complicated by its slow growth and its high rate of illegitimate recombination relative to homologous DNA exchange. We report here the development of a facile allelic exchange system by identification and expression of mycobacteriophage-encoded recombination proteins, adapting a strategy developed previously for recombineering in Escherichia coli. Identifiable recombination proteins are rare in mycobacteriophages, and only 1 of 30 genomically characterized mycobacteriophages (Che9c) encodes homologs of both RecE and RecT. Expression and biochemical characterization show that Che9c gp60 and gp61 encode exonuclease and DNA-binding activities, respectively, and expression of these proteins substantially elevates recombination facilitating allelic exchange in both M. smegmatis and M. tuberculosis. Mycobacterial recombineering thus provides a simple approach for the construction of gene replacement mutants in both slow- and fast-growing mycobacteria.

DNA-Binding Proteins↗

PubMed1996

Characterization of the rat glutathione S-transferase Yc2 subunit gene, GSTA5: identification of a putative antioxidant-responsive element in the 5'-flanking region of rat GSTA5 that may mediate chemoprotection against aflatoxin B1.

We have isolated and characterized genomic DNA encoding the rat glutathione S-transferase Yc2 subunit. This protein is now referred to as rGSTA5 and is noteworthy because of its high activity towards aflatoxin B1-8,9-epoxide, its marked inducibility by chemoprotectors, its sex-specific regulation, and its over-expression in hepatoma and preneoplastic nodules. The rGSTA5 gene, which was isolated on two overlapping bacteriophage lambda clones, is approx. 12 kb in length and, unlike other class Alpha genes described to date, it comprises six exons. The transcription start site has been identified 228 bp upstream from the ATG translational initiation codon, and is situated 51 bp downstream from a consensus TATA-box. Deletion analysis, using luciferase reporter constructs, has shown that the region between -177 bp and +65 bp from the transcriptional start site contains a functional promoter. Computer-assisted analysis of the upstream sequence has indicated the presence of an antioxidant-responsive element (ARE), and several elements thought to be required for tissue-specific expression of the enzyme. In addition, several putative oestrogen-responsive half sites were observed in both upstream and intronic sequences.

Aflatoxin B1↗

PubMed2001

Lack of evidence of a specific role for C4A gene deficiency in determining disease susceptibility among C4-deficient patients with systemic lupus erythematosus (SLE).

The aim of the present study was to investigate the prevalence of C4 and C2 deficiencies and to characterize genomic alterations in C4 genes in a large cohort of 125 unselected patients with SLE. We determined the protein concentration and functional activity of C2 and C4, as well as the C4 phenotype. C4 genotyping included Taq 1 restricted fragment lengh polymorphism (RFLP) analysis and polymerase chain reaction using sequence-specific primers (SSP-PCR). Type I C2 deficiency was diagnosed by PCR. Overall, 79.2% of the patients exhibited abnormalities of the C4 genes including deletion, non-expression, gene conversion and duplication. Among C4-deficient patients (n = 66, 52.8% prevalence), 41.0% of the patients exhibited a C4A deficiency and 59.0% a C4B deficiency. Half of the C4 deficiencies were due to a gene deletion. There was a strong association between C4A and C4B gene deletion and the presence of the DRB1*03 allele. Among the silent C4A genes, only two cases were related to a 2-bp insertion in exon 29 of the C4A gene. A gene conversion was demonstrated in eight patients (6.4%). One patient had a homozygous C4A deficiency. Three (2.4%) patients presented with a heterozygous type I C2 deficiency and none with homozygous deficiency. Our results argue against a specific role for C4A gene deficiency in determining disease susceptibility among patients with SLE that are C4-deficient.

Adolescent↗

PubMed1998

Regional expression and regulation of alternative forms of mRNAs derived from two distinct transcription initiation sites of the rat mGluR5 gene.

Metabotropic glutamate receptor (mGluR) subtype 5 is expressed in both neuronal and glial cells and is thought to play an important role in neuronal plasticity. This expression is up-regulated during the early postnatal period and is induced in cultured astrocytes by specific growth factors. To investigate the mechanism underlying the regulation of mGluR5 expression, we isolated and characterized genomic clones containing the 5'-upstream exons and their flanking regions of the mGluR5 gene. On the basis of the mGluR5 genomic structure, cDNA recloning of the 5'-extreme region of mGluR5 as well as primer extension analysis indicated that mGluR5 mRNA is generated from two alternative first exons, termed exon 1A and exon 1B, which are separated by 1,949 bp and then connected to the common exon 2. Northern blot and in situ hybridization analyses indicated that two distinct transcription initiation sites are commonly used in the expression of mGluR5 mRNA in various, but specialized, brain regions and that these two alternative forms of mGluR5 mRNA are similarly up-regulated or down-regulated during the early postnatal period, depending on the brain regions. The two mRNAs are also expressed in cultured astrocytes but respond differently to growth factor-mediated induction. This study provides the genetic basis indicating the diverse mechanisms involved in the regulation of mGluR5 expression.

Age Factors↗

PubMed1988

Chromosomal organization of the cytochrome P450-2C gene family in the mouse: a locus associated with constitutive aryl hydrocarbon hydroxylase.

Cytochromes P-450 represent a superfamily of enzymes with a central role in the metabolism of drugs, chemical toxins, and carcinogens. We have used genetic analysis to establish the complexity and catalytic function of a recently identified constitutively expressed murine hepatic cytochrome P-450 encoded by P450-2C. Southern blotting analysis shows that there are at least seven or eight genes within this family in the mouse and rat and that DNA restriction fragment length variants between different mouse inbred strains are observed. Analysis of recombinant inbred strains derived from these parent strains shows (i) these genes are clustered within 1 centimorgan, (ii) this gene family does not correspond to any of the known cytochrome P-450 loci or map near any well-characterized genomic markers, and (iii) this gene family segregates to within 1-2 centimorgans of a locus controlling constitutive aryl hydrocarbon hydroxylase activity in mice. With use of Chinese hamster/mouse somatic cell hybrids, the P450-2C locus was assigned to a region of mouse chromosome 19 that appears to be syntenic with the previously mapped human P450C2C locus on human chromosome 10. By in situ hybridization to mitotic mouse chromosomes, we have localized this region to the tip of chromosome 19. These results are discussed in relation to the physiological roles of this P-450 family in foreign compound metabolism and steroid oxidations.

Animals↗

PubMed1995

Optical melting of 128 octamer DNA duplexes. Effects of base pair location and nearest neighbors on thermal stability.

The use of short oligonucleotide probes is finding increased application in DNA sequencing and genome characterization techniques, but a lack of knowledge of the hybridization properties of short duplexes hinders their use. Melting data were acquired on 128 DNA duplexes based on the length proposed in sequencing by hybridization procedures and formed from the general sequences 5'-XYZTGGAC-3',5'-GTCCAXYZ-3',5'-GCXYZGAC-3', and 5'-GTCXYZGC-3' where X, Y, and Z are either A, T, G, or C. These molecules were designed to elucidate the effects of location and nearest-neighbor stacking on the stability of base pairing in short DNA duplexes. The type of base pairs present had a major effect on stability, but was insufficient to predict stability without the inclusion of nearest-neighbor terms. Furthermore, the addition of information on position, or distance from the end, of the nearest-neighbor doublets led to statistically better fitting of the melting data. However, the positionally dependent stabilization differences are small compared with the contributions of base pairing and stacking.

Base Composition↗

PubMed2006

Frequent occurrence of uniparental disomy in colorectal cancer.

We used SNP arrays to identify and characterize genomic alterations associated with colorectal cancer (CRC). Laser microdissected cancer cells from 15 adenocarinomas were investigated by Affymetrix Mapping 10K SNP arrays. Analysis of the data extracted from the SNP arrays revealed multiple regions with copy number alterations and loss of heterozygosity (LOH). Novel LOH areas were identified at chromosomes 13, 14 and 15. Combined analysis of the LOH and copy number data revealed genomic structures that could not have been identified analyzing either data type alone. Half of the identified LOH regions showed no evidence of a reduced copy number, indicating the presence of uniparental structures. The distribution of these structures was non-random, primarily involving 8q, 13q and 20q. This finding was supported by analysis of an independent set of array-based transcriptional profiles, consisting of 17 normal mucosa and 66 adenocarcinoma samples. The transcriptional analysis revealed an unchanged expression level in areas with intact copy number, including regions with uniparental disomy, and a reduced expression level in the LOH regions representing factual losses (including 5q, 8p and 17p). The analysis also showed that genes in regions with increased copy number (including 7p and 20q) were predominantly upregulated. Further analyses of the SNP data revealed a subset of the identified alterations to be specifically associated with TP53 inactivation (including 8q gain and 17p loss) and lymph node metastasis status (gain of 7q and 13q). Another subset of the identified alterations was shown to represent intratumor heterogeneity. In conclusion, we demonstrate that uniparental disomy is frequent in CRC, and identify genomic alterations associated with TP53 inactivation and lymph node status.

Adenocarcinoma↗

PubMed2026

Evaluation of sequential phage-antibiotic therapy reveals enhanced biofilm control with meropenem and colistin in clinical MDR hypervirulent Klebsiella pneumoniae strain.

AIMS: The convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae (MDR-HvKp) has narrowed treatment options. Despite growing interest in phage-antibiotic synergy, this study evaluates the underexplored combinatorial effects of phage and antibiotics, including drug-specific interactions and sequence dependency, against the biofilm-forming MDR-HvKp clinical strain. METHODS AND RESULTS: A T5-like Klebsiella bacteriophage, Round, within the genus Webervirus, was therapeutically and genomically characterized. A biofilm-forming clinical strain, Kleb_134, was used to evaluate in vitro phage-antibiotic interactions with meropenem, colistin, and tigecycline in planktonic and biofilm models.In planktonic assays, phage combinations with meropenem and colistin resulted in a multi-log CFU reduction compared to monotherapies, whereas reduced efficacy was observed with tigecycline. In biofilm assays, pre-phage treatment followed by antibiotic exposure demonstrated the strongest biofilm reduction. Drug-specific and sequence-dependent effects were evident. Meropenem-phage combinations reduced biofilm biomass by 2.85-fold (high phage titre) and 3.8-fold (low phage titre), while colistin-phage combinations achieved reductions of 8.4-fold (high phage titre) and 2.8-fold (low phage titre). CONCLUSIONS: Sequential phage-antibiotic treatment was effective against MDR-HvKp biofilms, with pre-phage exposure enhancing antibiotic access through biofilm disruption. The bacteriostatic nature of tigecycline reduced efficacy by affecting phage replication. These findings highlight the importance of treatment sequence and antibiotic selection, and extend existing knowledge in optimizing therapeutic outcomes in MDR-HvKp infections.

Biofilms↗

PubMed2003

PCP gene family in Symbiodinium from Hippopus hippopus: low levels of concerted evolution, isoform diversity, and spectral tuning of chromophores.

Photosynthetic dinoflagellates have evolved unique water-soluble light harvesting complexes known as peridinin-chlorophyll a-binding proteins (PCPs). Most species of dinoflagellates express either 14 to 17 kDa or 32 to 35 kDa mature PCP apoproteins and do so in stable combinations of isoforms that differ in isoelectric point (pI). The source (posttranslational modification, protein degradation, or genetic) and functional significance of PCP isoform variation have remained unclear. PCPs are encoded by multigene families. However, previous reports conflict over the diversity of PCP genes within gene arrays. We present the first genomic characterization of the PCP gene family from a symbiotic dinoflagellate. Symbiodinium from the Pacific bivalve Hippopus hippopus (203) contains genes for 33 kDa PCP apoproteins that are organized in tandem arrays like those of free-living dinoflagellates Amphidinium carterae, Lingulodinium (Gonyaulax) polyedra, and Heterocapsa pygmaea. The Symbiodinium 203 PCP cassette consists of 1,098-bp coding regions separated by approximately 900-bp spacers. The spacers contain a conserved upstream sequence similar to the promoter in L. polyedra. Surprisingly, sequences of cloned coding regions are not identical, and can differ at up to 2.2% of the nucleotide sites. Sequence variation is found at both silent and nonsilent sites, and analysis of cDNA clones indicate that the variation is present in the mRNA pool. We propose that this variation represents nucleotide diversity among PCP gene copies that are evolving under low-level concerted evolution. Interestingly, the predicted proteins have pIs that are within the range of those published for other species of Symbiodinium. Thus, posttranslational modifications are not necessary to explain the multiple PCP isoforms. We have also identified several polymorphic sites that may influence spectral absorption tuning of chromophores.

Amino Acid Substitution↗

PubMed1986

Characterization of diverse forms of myosin heavy chain expressed in adult human skeletal muscle.

In an attempt to define myosin heavy chain (MHC) gene organization and expression in adult human skeletal muscle, we have isolated and characterized genomic sequences corresponding to different human sarcomeric MHC genes (1). In this report, we present the complete DNA sequence of two different adult human skeletal muscle MHC cDNA clones, one of which encodes the entire light meromyosin (LMM) segment of MHC and represents the longest described MHC cDNA sequence. Additionally, both clones provide new sequence data from a 228 amino acid segment of the MHC tail for which no protein or DNA sequence has been previously available. One clone encodes a "fast" form of skeletal muscle MHC while the other clone most closely resembles a MHC form described in rat cardiac ventricles. We show that the 3' untranslated region of skeletal MHC cDNAs are homologous from widely separated species as are cardiac MHC cDNAs. However, there is no homology between the 3' untranslated region of cardiac and skeletal muscle MHCs. Isotype-specific preservation of MHC 3' untranslated sequences during evolution suggests a functional role for these regions.

Adult↗

PubMed1998

Leptospira fainei sp. nov., isolated from pigs in Australia.

Pathogenic leptospires can be causative agents of reproductive problems in pigs. Cultures of uteri and kidneys from two pigs herds in New South Wales and Victoria (Australia) yielded five strains identified as Leptospira on morphological and cultural grounds. Phenotypic characteristics (growth at 13 and 30 degrees C, growth in the presence of 8-azaguanine) were intermediate between those of pathogenic and saprophytic leptospires. No cross-agglutination was observed with reference antisera representing the 24 pathogenic serogroups and the main saprophytic ones. Antiserum against one of the strains did not agglutinate reference stains representative of any serogroup. This provided evidence of a new serovar, designated hurstbridge. Genomic characterization of the five strains was achieved using five molecular approaches. Mapped restriction site polymorphisms in the rrs (16S rRNA) gene were not related to those of any reference strains. Arbitrarily primed PCR fingerprints suggested clonality of the five strains. The strains all showed an identical and unique PFGE profile. PCR, using primers specific for the rrs gene of pathologic leptospires, amplified corresponding sequences from the strains. DNA-DNA hybridization (and reciprocal experiments) using the S1 nucleas/TCA method was performed between one of the strains and the reference strains of Leptospira species. The homology ranged from 0 to 36% (the latter being was Leptospira inadai) thus satisfying the criterion of a new species, Leptospira fainei (type strain BUT 6T). Phylogenetic analysis of 16S rRNA sequence showed that L. fainei and L. inadai formed a clade separate from the previously recognized 'saprophyte' and 'pathogen' clades.

Animals↗

PubMed2004

Genotype C of hepatitis B virus can be classified into at least two subgroups.

A genomic characterization of hepatitis B virus (HBV) was done for 56 pre-S1/pre-S2 genes and 10 full-length HBV genotype C isolates from five Asian countries. Phylogenetic analysis of the pre-S1/pre-S2 genes revealed two major groups within genotype C: one for isolates from southeast Asia including Vietnam, Myanmar and Thailand (named HBV/C1) and the other for isolates from Far East Asia including Japan, Korea and China (named HBV/C2). This finding was confirmed by phylogenetic analysis based on the full-length sequence of 32 HBV genotype C isolates, including 22 from database entries. Two isolates from Okinawa, the island off the southern end of Japan, formed a different branch. Specific amino acid sequence changes were identified in the large S protein (amino acids 51, 54, 60, 62 and 73) and P protein (amino acids 231, 233, 236, 248, 252 and 304). Our results indicate that genotype C of HBV can be classified into at least two subgroups.

Asia↗