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Genomics and proteomics: the next generation of health care.

Biotechnology research will dramatically impact health care, and the pharmaceutical industry in particular, in the coming decade. Health outcomes may be improved in a cost-effective manner through the ability to selectively prescribe medications; safer, more effective treatment may reduce long-term health care costs. As genetic testing becomes the standard of care, new challenges will surface around how genetic information will be used or misused, and how and where health care dollars are spent.

Delivery of Health Care↗

[The single cell microgelelectrophoresis technique in ecogenotoxicology].

BACKGROUND: The development of carcinoma in the upper aerodigestive tract is often associated with exposure to xenobiotics. Therefore, the identification of such tumor initiating substances is relevant. Most genotoxicity test systems require mammalian cells, human lymphocytes or cell cultures to detect genotoxicity caused by carcinogens. The single cell microgelelectrophoresis technique (Comet assay) is presented, being a sensitive method, identifying DNA strand breaks, alkali labile sites and DNA repair in human epithelial cells of the upper aerodigestive tract. It is compared to other common techniques for the identification of genotoxic damage. Future applications and contributions of the method are introduced. GENOTOXICITY TEST SYSTEMS: Using the alkaline microgel electrophoresis assay, freshly isolated single epithelial cells are incubated with xenobiotics causing DNA strand breaks and alkali labile sites. Data are examined using a digital computer analysis. The method is described for the application of epithelial cells of the upper aerodigestive tract and compared to other procedures for the monitoring of genotoxicity. These are the Ames test identifying mutagenicity in bacteria, the sister chromatid exchange and the micronucleus test demonstrating genomic instability in lymphocytes and cultured mammalian cells. CONCLUSIONS: The microgel electrophoresis technique is a sensitive method to detect genotoxic effects and DNA repair in human epithelia of the upper aerodigestive tract. The assay offers considerable advantages to other common genotoxicity tests. However, combining of the Comet assay with mini organ cultures allows to use repetitive incubations with xenobiotics. Furthermore, signalling selected chromosomal material by the combination of the assay with the fluorescence in situ hybridisation, DNA-damage and -repair mechanisms within comets can be identified.

Biopsy↗

Microevolutionary changes in Candida albicans identified by the complex Ca3 fingerprinting probe involve insertions and deletions of the full-length repetitive sequence RPS at specific genomic sites.

The 11 kb complex DNA fingerprinting probe Ca3 is effective both in cluster analyses of Candida albicans isolates and in identifying microevolutionary changes in the size of hypervariable genomic fragments. A 2.6 kb EcoRI fragment of Ca3, the C fragment, retains the capacity to identify these microevolutionary changes, and when the C fragment is cleaved with SacI, the capacity is retained exclusively by a 1 kb subfragment, C1, which contains a partial RPS repeat element. The microevolutionary changes identified by Ca3, therefore, may involve reorganization of RPS elements dispersed throughout the genome. To test this possibility, hypervariable fragments from several strains of C. albicans were sequenced and compared. The results demonstrate that the microevolutionary changes identified by Ca3 are due to the insertion and deletion of full-length tandem RPS elements at specific genomic sites dispersed throughout the C. albicans genome. The RPS elements at these dispersed sites are bordered by the same upstream and downstream sequences. The frequency of recombination was estimated to be one recombination per 1000 cell divisions by following RPS reorganization in vitro. The results are inconsistent with unequal recombination between homologous or heterologous chromosomes, but consistent with intrachromosomal recombination. Two alternative models of intrachromosomal recombination are proposed: unequal sister-chromatid exchange and slipped misalignment at the replication fork.

3' Untranslated Regions↗

Detection of hepatitis G virus RNA in patients with hepatitis B, hepatitis C, and non-A-E hepatitis by RT-PCR using multiple primer sets.

Hepatitis G virus(HGV)/GB virus C(GBV-C) is a newly identified virus associated with human hepatitis. The preliminary prevalence studies of HGV infection in Japan were entirely based on the detection of HGV RNA by RT-PCR. However, the selection of the different primer sets in such assay may influence sensitivity of the test because of the extensive genetic heterogeneity of HGV, and influence the estimation of the prevalence of HGV. To address this potential problem, we designed two primer sets from well conserved domains in the 5'NC and NS5 regions of HGV genome, and tested them together with the NS3-derived primer set in RT-PCR for their ability to detect HGV RNA in serial dilution of synthetic viral RNA templates. Subsequently, we used these three primer sets to detect HGV RNA in the sera of 371 Japanese patients with hepatitis B, hepatitis C, and non-A-E hepatitis. The results indicated that the primer set derived from the 5'NC region appeared to be most effective in detecting HGV RNA. The results also showed that only two out of the 126 patients (1.6%) with non-A-E hepatitis were positive for HGV RNA although the RNA were detected more frequently in patients with hepatitis B (2/38; 5.3%) and hepatitis C (17/207; 8.2%), suggesting that HGV is not a common causative agent for non-A-E hepatitis in Japan.

Base Sequence↗

Replication signals in the genome of vesicular stomatitis virus and its defective interfering particles: identification of a sequence element that enhances DI RNA replication.

We have analyzed the role of terminal sequences of a defective interfering (DI) particle RNA of vesicular stomatitis virus (VSV) in replication. A series of internal deletion mutants of DI cDNA was generated to obtain DI genomic RNAs that differed from one another by the presence of different lengths of 3'-terminal and/or 5'-terminal sequences. Analyses of the mutant. RNAs for their ability to replicate in cells transfected with the corresponding plasmids suggested that distinct regions at the termini of DI RNA are important for RNA replication. Region I, encompassing nucleotides 1-24, is absolutely required for replication since DI RNA genomes lacking any part of this region failed to replicate. Region II, spanning nucleotides 25-45, is not essential for replication but it functions as an enhancer of replication in that the presence of these specific sequences confers high efficiency of replication to the template. Deleting these specific sequences from both termini of DI RNA but maintaining the length of terminal complementarity as seen in wild-type DI RNA resulted in a template that replicated poorly (about 20-fold less efficiently). Furthermore, insertion or substitution of these sequences into the 3'-terminus of a VSV minigenome resulted in a template that replicated more efficiently (at least 4-fold to as high as 15-fold) than the parental minigenome. These results strongly support the conclusion that the presence of specific sequences rather than the extent of complementarity at the termini of DI RNA is a major determinant of the efficiency of replication. The presence of the specific sequences at the 3'-terminus of both genomic and antigenomic DI RNAs may explain in part the replicative dominance of DI RNA over the full-length VSV genome which contains these sequences only at the 3'-terminus of the antigenome.

Animals↗

Growing evidence for diabetes susceptibility genes from genome scan data.

Genome-wide scans for linkage have provided one of the dominant approaches adopted by researchers in their efforts to identify genes responsible for the inherited component of type 2 diabetes susceptibility. Around 20 genome scans have now been completed, in a wide variety of populations. Integration of data from these diverse scans has proven far from trivial, but the contours of genome-wide linkage topography are steadily emerging from the fog of data. Identification of the calpain-10 gene as the probable basis for the chromosome 2q linkage seen in Mexican Americans has provided validation of this positional cloning approach. This report provides an update on recent type 2 diabetes genome scan data, focusing on several chromosomal regions where the evidence for linkage has considerably strengthened in the past year. The current and future value of genome-wide linkage information in the search for type 2 diabetes susceptibility effects is also discussed.

Diabetes Mellitus, Type 2↗

Cowdria ruminantium DNA is unstable in a SuperCos1 library.

A Cowdria ruminantium genomic library was constructed in a cosmid vector to serve as a source of easily accessible and pure C. ruminantium DNA for molecular genetic studies. The cosmid library contained 846 clones which were arrayed into microtitre plates. Restriction enzyme digestion patterns indicated that these clones had an average insert size of 35 kb. Probing of the arrays did not detect any bovine clones and only one of the known C. ruminantium genes, pCS20, was detected. Due to the high AT content and the fact that C. ruminantium genes are active in the Escherichia coli host, the C. ruminantium clones were unstable in the SuperCos1 vector and most clones did not grow reproducibly. The library was contaminated with E. coli clones and these clones were maintained with greater fidelity than the C. ruminantium clones, resulting in a skewed representation over time. We have isolated seven C. ruminantium clones which we were able to serially culture reproducibly; two of these clones overlap. These clones constitute the first large regions of C. ruminantium DNA to be cloned and represent almost 10% of the C. ruminantium genome.

Animals↗

Identification of a plant-derived mollicute as a strain of an avian pathogen, Mycoplasma iowae, and its implications for mollicute taxonomy.

Strain PPAV, a filamentous but nonhelical mollicute, was isolated from aborted apple seeds in France in late 1979. This organism grew well in SP-4 broth, fermented glucose, and required sterol for growth, and most of its properties suggested that it belonged to the genus Mycoplasma. However, it was serologically distinct; in addition, unlike other Mycoplasma species, genome measurements consistently yielded values of about 1,000 MDa (ca. 1,500 kbp), and the organism had a growth temperature optimum of 43 degrees C. A comparison of strain PPAV 16S rRNA sequences with those of other mollicutes revealed a high degree of sequence similarity to a strain of Mycoplasma iowae, which is commonly encountered in poultry. This relationship was confirmed by performing a restriction endonuclease pattern analysis and DNA-DNA hybridization tests. The genome size of type strain 695 of M. iowae was determined to be about 1,000 MDa (1,500 kbp) by renaturation kinetics, a value which is much higher than any other value known in the genus. Additional measurements by pulsed-field gel electrophoresis yielded values of 1,300 kbp for both strain PPAV and M. iowae. Subsequent phenotypic comparisons supported this relationship. Serologic tests with strain PPAV and other strains of M. iowae confirmed the findings of other investigators that this species is serologically heterogeneous. The high optimum temperature for growth of strain PPAV was also shared by a number of M. iowae isolates. Genome size is an inappropriate character for taxonomic assignment to the family Mycoplasmataceae because strain PPAV and other established species in this family are now known to have genomes ranging in size from 1,000 to 1,400 kbp.

Animals↗

From genetics to genomics: using gene-based medicine to prevent disease and promote health in children.

The remarkable achievements of the Human Genome Project promise great opportunities for disease prediction, treatment, and prevention. In this paper, we discuss the continuum of genetic variation as medical practice begins to shift focus from the study of single genes (genetics) to the study of the entire genome (genomics). Pediatricians should anticipate an influx of genetic information and will need to become as facile in interpreting this type of predictive information as they are with other types of medical data, while recognizing the unique ethical, legal, and social implications of genetic testing in children. We discuss an approach to assist pediatricians in decision-making that emphasizes the need for knowledge about the analytic performance of genetic tests, their validity in predicting health outcomes, and the utility of the genetic information in improving health and preventing disease.

Adolescent↗

Functional characterization of IScs605, an insertion element carried by tetracycline-resistant Chlamydia suis.

Stable tetracycline resistance in Chlamydia suis is mediated by a family of genomic islands [the tet(C) islands] that are integrated into the chlamydial chromosome. The tet(C) islands contain several plasmid-specific genes, the tet(C) resistance gene and, in most cases, a novel insertion element (IScs605) encoding two predicted transposases. The hypothesis that IScs605 mediated the integration of the tet(C) resistance islands into the C. suis genome was tested using a plasmid-based transposition system in Escherichia coli. Both high- and medium-copy-number plasmids were used as carriers of IScs605 in these experiments. IScs605 integrated into a target plasmid (pOX38) when delivered by either donor plasmid, and integration of the entire donor plasmid was common. IScs605-mediated integration occurred at many positions within pOX38, with 36 of 38 events adjacent to a 5'-TTCAA-3' sequence. Deletions in each of the candidate transposase genes within IScs605 demonstrated that only one of the two ORFs was necessary for the observed transposition activity and target specificity. Analysis of progeny from the mating assays also indicated that IScs605 can excise following integration into a target DNA, and, in each tested case, the sequence 5'-AATTCAA-3' remained at the site of excision. Collectively, these results are consistent with the nucleotide sequence data collected for the tet(C) islands, and strongly suggest that a transposase within IScs605 is responsible for integration of these genomic islands into the C. suis chromosome.

Chlamydia↗

Three distinct regions of the murine gammaherpesvirus 68 genome are transcriptionally active in latently infected mice.

The program(s) of gene expression operating during murine gammaherpesvirus 68 (gammaHV68) latency is undefined, as is the relationship between gammaHV68 latency and latency of primate gammaherpesviruses. We used a nested reverse transcriptase PCR strategy (sensitive to approximately one copy of gammaHV68 genome for each genomic region tested) to screen for the presence of viral transcripts in latently infected mice. Based on the positions of known latency-associated genes in other gammaherpesviruses, we screened for the presence of transcripts corresponding to 11 open reading frames (ORFs) in the gammaHV68 genome in RNA from spleens and peritoneal cells of latently infected B-cell-deficient (MuMT) mice which have been shown contain high levels of reactivable latent gammaHV68 (K. E. Weck, M. L. Barkon, L. I. Yoo, S. H. Speck, and H. W. Virgin, J. Virol. 70:6775-6780, 1996). To control for the possible presence of viral lytic activity, we determined that RNA from latently infected peritoneal and spleen cells contained few or no detectable transcripts corresponding to seven ORFs known to encode viral gene products associated with lytic replication. However, we did detect low-level expression of transcripts arising from the region of gene 50 (encoding the putative homolog of the Epstein-Barr virus BRLF1 transactivator) in peritoneal but not spleen cells. Latently infected peritoneal cells consistently scored for expression of RNA derived from 4 of the 11 candidate latency-associated ORFs examined, including the regions of ORF M2, ORF M11 (encoding v-bcl-2), gene 73 (a homolog of the Kaposi's sarcoma-associated herpesvirus [human herpesvirus 8] gene encoding latency-associated nuclear antigen), and gene 74 (encoding a G-protein coupled receptor homolog, v-GCR). Latently infected spleen cells consistently scored positive for RNA derived from 3 of the 11 candidate latency-associated ORFs examined, including ORF M2, ORF M3, and ORF M9. To further characterize transcription of these candidate latency-associated ORFs, we examined their transcription in lytically infected fibroblasts by Northern analysis. We detected abundant transcription from regions of the genome containing ORF M3 and ORF M9, as well as the known lytic-cycle genes. However, transcription of ORF M2, ORF M11, gene 73, and gene 74 was barely detectable in lytically infected fibroblasts, consistent with a role of these viral genes during latent infection. We conclude that (i) we have identified several candidate latency genes of murine gammaHV68, (ii) expression of genes during latency may be different in different organs, consistent with multiple latency programs and/or multiple cellular sites of latency, and (iii) regions of the viral genome (v-bcl-2 gene, v-GCR gene, and gene 73) are transcribed during latency with both gammaHV68 and primate gammaherpesviruses. The implications of these findings for replacing previous operational definitions of gammaHV68 latency with a molecular definition are discussed.

Animals↗

Meta-analysis of linkage studies.

Lander and Kruglyak [1995] gave guidelines for interpreting linkage results based on estimating how often a particular threshold for significance would be exceeded by chance in a single genome scan. What is unknown is how often two or more genome scans would exceed a particular threshold within the same region. We develop theoretical estimates of these values and compare these with the empirical estimates derived from the GAW11 data. For single-point analysis, the theoretical estimates predict the empirical estimates. For multipoint analysis, the theoretical values overestimate what is observed. For both single point and multipoint, modest p-values within a single genome scan may give highly significant results when replicated in the same region in other scans.

Genetic Linkage↗

Transformation system for a wastewater treatment yeast, Hansenula fabianii J640: isolation of the orotidine-5'-phosphate decarboxylase gene (URA3) and uracil auxotrophic mutants.

A transformation system for Hansenula fabianii J640, a commonly used wastewater treatment yeast, was constructed. As a host cell, a uracil auxotrophic mutant designated as H. fabianii J640 u-1, which was confirmed to have a mutation at the locus of the gene for orotidine-5'-phosphate (OMP) decarboxylase (URA3), was obtained by positive selection using 5-fluoroorotic acid. A plasmid named pHFura3, which includes a 795-bp open-reading frame of the OMP decarboxylase H. fabianii, was obtained by complementation of the Escherichia coli pyrF mutant, pHFura3 could transform H. fabianii J640 u-1 by a non-homologous and frequently multicopy integration into the host genomic DNA.

Amino Acid Sequence↗

Complementation hypothesis: the necessity of a monoallelic gene expression mechanism in mammalian development.

Gene expression from both parental alleles (biallelic expression) is beneficial in minimizing the occurrence of recessive genetic disorders in diploid organisms. However, imprinted genes in mammals display parent of origin-specific monoallelic expression. As some imprinted genes play essential roles in mammalian development, the reason why mammals adopted the genomic imprinting mechanism has been a mystery since its discovery. In this review, based on the recent studies on imprinted gene regulation we discuss several advantageous features of a monoallelic expression mechanism and the necessity of genomic imprinting in the current mammalian developmental system. We further speculate how the present genomic imprinting system has been established during mammalian evolution by the mechanism of complementation between paternal and maternal genomes under evolutionary pressure predicted by the genetic conflict hypothesis.

Animals↗

EspFU is a translocated EHEC effector that interacts with Tir and N-WASP and promotes Nck-independent actin assembly.

Several microbial pathogens including enteropathogenic E. coli (EPEC) exploit mammalian tyrosine-kinase signaling cascades to recruit Nck adaptor proteins and activate N-WASP-Arp2/3-mediated actin assembly. To promote localized actin "pedestal formation," EPEC translocates the bacterial effector protein Tir into the plasma membrane, where it is tyrosine-phosphorylated and binds Nck. Enterohemorrhagic E. coli (EHEC) also generates Tir-dependent pedestals, but in the absence of phosphotyrosines and Nck recruitment. To identify additional EHEC effectors that stimulate phosphotyrosine-independent actin assembly, we systematically generated EHEC mutants containing specific deletions in putative pathogenicity-islands. Among 0.33 Mb of deleted sequences, only one ORF was critical for pedestal formation. It lies within prophage-U, and encodes a protein similar to the known effector EspF. This proline-rich protein, EspFU, is the only EHEC effector of actin assembly absent from EPEC. Whereas EHEC Tir cannot efficiently recruit N-WASP or trigger actin polymerization, EspFU associates with Tir, binds N-WASP, and potently stimulates Nck-independent actin assembly.

Actins↗

The large GTPase dynamin is required for hepatitis B virus protein secretion from hepatocytes.

BACKGROUND/AIMS: The hepatocellular transport pathways and cellular proteins utilized during the packaging and secretion of hepatitis B virus are poorly understood. In this study, we tested if the large GTPase dynamin, a protein involved in vesicle formation and secretion at the trans-Golgi network in hepatocytes, is also used by hepatitis B virus (HBV) in secreting viral proteins. METHODS: Using HepG2.2.15 cells expressing the full-length HBV genome, we tested the effects of wild-type and mutant dynamin on the localization and secretion of two hepatitis B antigens, hepatitis B surface antigen (HBsAg) and hepatitis B e antigen (HBeAg). Distribution of these two antigens was analyzed morphologically in cells transiently transfected with wild-type or mutant dynamin constructs, whereas secretion of the antigens was measured by testing for antigen levels in the media of transfected cells. RESULTS: Mutant dynamin was found to induce a striking redistribution of HBsAg and HBeAg to a perinuclear compartment, as well as a decrease in the levels of HBsAg and HBeAg present in cell culture media indicating a reduction in viral protein secretion. At the electron microscopy level, cells expressing the mutant dynamin showed a marked accumulation of viral particles in dilated cisternae of an uncharacterized cellular compartment. CONCLUSIONS: Intact dynamin function is required for secretion of HBV proteins from hepatocytes through an uncharacterized cellular compartment.

Biological Transport↗