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PubMed1999

Toward functional genomics in bacteria: analysis of gene expression in Escherichia coli from a bacterial artificial chromosome library of Bacillus cereus.

As the study of microbes moves into the era of functional genomics, there is an increasing need for molecular tools for analysis of a wide diversity of microorganisms. Currently, biological study of many prokaryotes of agricultural, medical, and fundamental scientific interest is limited by the lack of adequate genetic tools. We report the application of the bacterial artificial chromosome (BAC) vector to prokaryotic biology as a powerful approach to address this need. We constructed a BAC library in Escherichia coli from genomic DNA of the Gram-positive bacterium Bacillus cereus. This library provides 5.75-fold coverage of the B. cereus genome, with an average insert size of 98 kb. To determine the extent of heterologous expression of B. cereus genes in the library, we screened it for expression of several B. cereus activities in the E. coli host. Clones expressing 6 of 10 activities tested were identified in the library, namely, ampicillin resistance, zwittermicin A resistance, esculin hydrolysis, hemolysis, orange pigment production, and lecithinase activity. We analyzed selected BAC clones genetically to identify rapidly specific B. cereus loci. These results suggest that BAC libraries will provide a powerful approach for studying gene expression from diverse prokaryotes.

Bacillus cereus↗
PubMedDate not supplied

Signal, noise, and reliability in molecular phylogenetic analyses.

DNA sequences and other molecular data compared among organisms may contain phylogenetic signal, or they may be randomized with respect to phylogenetic history. Some method is needed to distinguish phylogenetic signal from random noise to avoid analysis of data that have been randomized with respect to the historical relationships of the taxa being compared. We analyzed 8,000 random data matrices consisting of 10-500 binary or four-state characters and 5-25 taxa to study several options for detecting signal in systematic data bases. Analysis of random data often yields a single most-parsimonious tree, especially if the number of characters examined is large and the number of taxa examined is small (both often true in molecular studies). The most-parsimonious tree inferred from random data may also be considerably shorter than the second-best alternative. The distribution of tree lengths of all tree topologies (or a random sample thereof) provides a sensitive measure of phylogenetic signal: data matrices with phylogenetic signal produce tree-length distributions that are strongly skewed to the left, whereas those composed of random noise are closer to symmetrical. In simulations of phylogeny with varying rates of mutation (up to levels that produce random variation among taxa), the skewness of tree-length distributions is closely related to the success of parsimony in finding the true phylogeny. Tables of critical values of a skewness test statistic, g1, are provided for binary and four-state characters for 10-500 characters and 5-25 taxa. These tables can be used in a rapid and efficient test for significant structure in data matrices for phylogenetic analysis.

Animals↗
PubMed1992

Non-radioisotopic methods for DNA probes.

We have recently developed a new colorimetric method, DNA enzyme immunoassay (DEIA), for detecting specific hybrids of complementary nucleic acids. This technology is based on an antibody that selectively recognizes double, but not single-stranded DNA. The molecule does not react with a specific probe immobilized on microwells through an avidin-biotin bridge, nor with non-specific amplified sequences, since they are removed by washing. The antibody reveals the hybridization event, independently of the DNA sequences and, for this reason, the method is broadly applicable and extremely versatile. Although we chose a format based on the immobilization of the probe through an avidin-biotin interaction, DEIA assay can also be applied to other analytical schemes that do not require any modification of the probe. Most importantly, the test has an ELISA format and is rapid and convenient for processing large numbers of samples. This technology has been applied, in our laboratory, to different areas, including virology, genetic and basic immunology. The DEIA assay has been successfully used to detect the presence of hepatitis B (HBV), hepatitis C (HCV) and hepatitis delta virus (HDV) sequences in serum of patients, to discriminate different HLA alleles, to identify mutations in the Cystic Fibrosis gene, and to investigate the role of the T cell receptor in some immunological diseases. The results obtained in all our experiments demonstrated that the advantages offered by the assay do not penalize its analytical performance as compared to conventional Southern blot.

Colorimetry↗
PubMed1989

[Current trends in the development of salmonella detection methods].

The cultural methods require 4 to 7 days for presumptive evidence of Salmonella in foodstuffs. Attempts in time shortening have resulted in combination of pre-enrichment or selective enrichment with time saving genetical or immunological tests. Proceedings of enzyme immunoassays for applications in Salmonella screening are important. Involving monoclonal antibodies, fluorescent or chemiluminescent substrates, there are some commercial Salmonella test kits. Especially rapid EIA methods, here advantages and disadvantages are discussed.

Animals↗
PubMed1985

The attitudes of religious, environmental, and science policy leaders toward biotechnology.

Biotechnology is an increasingly visible and important item on the national science policy agenda. With growing corporate and governmental funding, basic research in recombinant DNA and related technologies is expanding rapidly. In a parallel and related process, new agricultural, medical, and other applications are being developed and a growing list of genetically-engineered products is ready for field testing and market distribution. In the months and years ahead, the flow of genetically-engineered products into the marketplace and the media coverage related to those new products will increase the public's awareness of biotechnology. In addition, it is possible that some public policy debate will occur over the issue of field testing new genetically-engineered materials. Media coverage of this type of controversy will also heighten awareness and influence the aggregate level of public awareness of biotechnology. The prospect of a public debate or controversy over any biotechnology issue illustrates a fundamental problem in the formulation of science policy within a democratic political system. The processes and techniques involved in genetic engineering and complex and require some level of scientific background knowledge. A 1979 study found that only seven per cent of American adults met a minimal definition of scientific literacy. It is clear that the current levels of public awareness and knowledge about biotechnology will not allow a public policy debate similar to those associated with controversies involving Social Security or gasoline prices. How, then, does a democratic society establish public policies on advanced technical issues like biotechnology? This report will outline a model of policy formulation for specialized issues and describe the results of a national study of relevant policy leaders concerning biotechnology. To understand the formulation of public policy toward biotechnology, it is necessary to focus on the role of the policy leaders in a stratified model. In general, when there is agreement on a given policy between the decision-makers and the policy leaders, the policy is implemented and there is no wider involvement in the policy formulation process. A large number of science and technology policy issues have been handled in this manner in the decades since the Second World War and it is likely that most science policy matters will continue to be resolved directly between policy leaders and decision-makers. Looking at the general science policy formulation process, it is clear that policy leaders are an important component.(ABSTRACT TRUNCATED AT 400 WORDS)

Attitude↗
PubMedDate not supplied

The International Collaborative Group on HNPCC.

The international collaborative group on HNPCC (ICG-HNPCC) was established in 1989. The original aims of the group were: (1) to develop minimal criteria for the identification of HNPCC, to provide a basis for uniformity in collaborative studies; (2) to improve patient and physician education about HNPCC; (3) to establish international collaborative studies, and (4) to promote the establishment of national (or regional) HNPCC registries. The administrative base of the group is attached to the Netherlands Foundation for the Detection of Hereditary Tumours at Leiden. The Netherlands. An International Informational Center on HNPCC was established at Creighton University in Omaha. The Hereditary Colon Cancer Newsletter (previously the Polyposis Newsletter) serves as a medium for communication about activities of the Group. At present, the Group has about 70 members from 23 countries, and its meetings are held annually. After a period of five years, it can be concluded that the objectives of the ICG-HNPCC have been successfully accomplished. The existence of the ICG-HNPCC has contributed to an increase in awareness of HNPCC among specialists throughout the world. Due to the rapid developments in molecular genetics in HNPCC, it seems very likely that HNPCC will be the first common hereditary cancer syndrome, which can be identified by simple blood DNA tests. The value of the ICG-HNPCC will be extremely important in finding a uniform answer to the question how to utilize DNA technology for the benefit of the human race.

Colorectal Neoplasms, Hereditary Nonpolyposis↗
PubMed1997

[Clinical genetics in The Netherlands. II. Genetic counseling and prenatal diagnosis].

The main feature of clinical genetics is the involvement of close relatives in the diagnostics of a hereditary disorder, and the possible consequences of the findings for future generations. Complex genetic counseling is required in cases with different, possibly hereditary disorders or congenital anomalies in the family or by a syndrome with variable risks of recurrence, depending on the exact nature of the disorder; also the difficult, often emotionally charged choices with which counselees are faced demands the expertise of a clinical genetic centre. Results of follow-up studies after genetic counseling show that experience with a handicap or disease in the own environment and the presence of healthy issue are the main determinants for the decision about reproduction of persons with an enhanced genetic risk who request counseling. Because of the great variety in perception of risks and of the severity of a disorder, and because of the marked clinical heterogeneity, rigid legislation should be avoided in the field of prenatal diagnosis. In the future, the training of the clinical geneticist has to be adapted to the rapid progress in human genetics. Increasingly, the clinical geneticist will function in collaboration with other disciplines such as oncology, obstetrics and gynaecology, paediatrics and neurology; in connection with family testing and counseling, there will also be more collaboration with primary health care.

Adult↗
PubMed2006

A modified Vibrio harveyi mutagenicity assay based on bioluminescence induction.

AIMS: Mutagenic pollution of natural environment is currently one of the most serious ecological problems. Therefore, rapid detection of the presence of mutagens is a very important issue. Although many mutagenicity assays have already been described, only a few are suitable for testing samples from natural environment. One of such assays is a microbiological mutagenicity test based on genetically modified Vibrio harveyi strains. The aim of this work was to modify and improve the V. harveyi assay. METHODS AND RESULTS: A series of V. harveyi dark and dim mutants were tested for reversion of their phenotype towards efficient light emission in response to incubation with known mutagens. Luminescence of the A16 strain (luxE mutant) increased significantly after a few hours of such a treatment with various mutagenic agents, revealing a dose-response correlation. Sensitivity of the assay has been determined for different mutagens. CONCLUSIONS: The luminescence-based V. harveyi mutagenicity assay is rapid, sensitive and reveals a dose-response correlation for various mutagens. SIGNIFICANCE AND IMPACT OF THE STUDY: The assay developed in this study is a potentially useful tool in studies on mutagenic pollution of environment, especially marine water.

Aminacrine↗
PubMed2005

Rapid prenatal diagnostic testing for Down syndrome only or longer wait for full karyotype: the views of pregnant women.

OBJECTIVES: Prenatal diagnosis by karyotype analysis determines the copy number and structure of each chromosome and is considered to be the 'gold standard' in detection of chromosome abnormality. This method is, however, time consuming and women may have to wait up to 21 days for the results. With improving molecular genetic techniques, the most commonly occurring chromosome abnormalities can be diagnosed within 2 days from amniotic fluid. This study investigates the value pregnant women place on these alternative prenatal diagnostic tests. METHODS: A structured self-completion discrete choice experiment questionnaire was designed. The subjects were 40 pregnant women, of unknown risk, attending for their 11-week booking scan and 10 elevated-risk women attending for amniocentesis at the Aberdeen Maternity Hospital, Scotland. RESULTS: Women value 'comprehensive' information of a full karyotype analysis at pounds 791, and 'simple' information of a rapid diagnostic test at pounds 690. Willingness to pay for a day's reduction in waiting time for results is pounds 18. Women prefer a prenatal service providing simple over comprehensive information as long as they receive results 6 days sooner than the comprehensive results would be provided. CONCLUSIONS: While women prefer comprehensive information, the bulk of the value is placed on knowing whether the fetus has Down syndrome. Given the longer wait times for comprehensive information, simple information is preferred as long as results are received 6 days sooner than would be the case for comprehensive information. These results have implications for the resources dedicated to providing a rapid prenatal diagnostic service.

Adolescent↗
PubMed2007

A versatile denaturing HPLC approach for human beta-globin gene mutation screening.

Hemoglobinopathies represent the most common genetic disorder worldwide, with a higher prevalence among populations with a history of malaria endemicity. More than 690 mutations in the human beta-globin gene are usually the cause of beta-type hemoglobinopathies. Here, we report a rapid and highly sensitive beta-globin gene mutation screening approach based on denaturing high-performance liquid chromatography (DHPLC), which contrary to the previously described ones can be used in every HPLC apparatus. The sensitivity and specificity of the method were tested in 120 healthy Greek subjects and 25 beta-thalassemia heterozygotes and homozygotes, in which 11 different beta-globin sequence variations had been previously characterized by denaturing gradient gel electrophoresis. Using this method, we were able to rapidly identify the commonest beta-globin gene mutations, accounting for more than 90% of the mutant beta-globin alleles reported for the Hellenic population. Compared to classical mutation screening approaches, our DHPLC approach provides the means for rapid, highly sensitive, cost-effective, and semi-automated simultaneous mutational scanning of a large number of samples.

Chromatography, High Pressure Liquid↗
PubMed1992

Lysine biosynthesis in selected pathogenic fungi: characterization of lysine auxotrophs and the cloned LYS1 gene of Candida albicans.

The alpha-aminoadipate pathway for the biosynthesis of lysine is present only in fungi and euglena. Until now, this unique metabolic pathway has never been investigated in the opportunistic fungal pathogens Candida albicans, Cryptococcus neoformans, and Aspergillus fumigatus. Five of the eight enzymes (homocitrate synthase, homoisocitrate dehydrogenase, alpha-aminoadipate reductase, saccharopine reductase, and saccharopine dehydrogenase) of the alpha-aminoadipate pathway and glucose-6-phosphate dehydrogenase, a glycolytic enzyme used as a control, were demonstrated in wild-type cells of these organisms. All enzymes were present in Saccharomyces cerevisiae and the pathogenic organisms except C. neoformans 32608 serotype C, which exhibited no saccharopine reductase activity. The levels of enzyme activity varied considerably from strain to strain. Variation among organisms was also observed for the control enzyme. Among the pathogens, C. albicans exhibited much higher homocitrate synthase, homoisocitrate dehydrogenase, and alpha-aminoadipate reductase activities. Seven lysine auxotrophs of C. albicans and one of Candida tropicalis were characterized biochemically to determine the biochemical blocks and gene-enzyme relationships. Growth responses to alpha-aminoadipate- and lysine-supplemented media, accumulation of alpha-aminoadipate semialdehyde, and the lack of enzyme activity revealed that five of the mutants (WA104, WA153, WC7-1-3, WD1-31-2, and A5155) were blocked at the alpha-aminoadipate reductase step, two (STN57 and WD1-3-6) were blocked at the saccharopine dehydrogenase step, and the C. tropicalis mutant (X-16) was blocked at the saccharopine reductase step. The cloned LYS1 gene of C. albicans in the recombinant plasmid YpB1078 complemented saccharopine dehydrogenase (lys1) mutants of S. cerevisiae and C. albicans. The Lys1+ transformed strains exhibited significant saccharopine dehydrogenase activity in comparison with untransformed mutants. The cloned LYS1 gene has been localized on a 1.8-kb HindIII DNA insert of the recombinant plasmid YpB1041RG1. These results established the gene-enzyme relationship in the second half of the alpha-aminoadipate pathway. The presence of this unique pathway in the pathogenic fungi could be useful for their rapid detection and control.

Candida albicans↗
PubMedDate not supplied

Computer assisted small-scale Tay-Sachs carrier screening.

Fluorescence data from serum beta-hexosaminidase assays for Tay-Sachs heterozygote screening is processed by a program in BASIC for a Wang 2200 desk-top computer. An estimation of overall error in the results gives a measure of reliability. A preliminary classification is made on the clinical status of the unknown samples as a normal, heterozygous, homozygous, or inconclusive carrier/normal condition. This program allows a small-scale screening center convenient and rapid data processing and analysis.

Clinical Enzyme Tests↗
PubMed1998

[Screening mutations in phenylketonuria by means of nonradioactive reverse dot blot hybridization].

OBJECTIVE: To establish a simple, accurate and rapid method for screening of the mutant genes in phenylketonuria (PKU). METHODS: Four exons harboring the mutations, Y204C (exon6, E6), R243Q(E7), Y356X(E11) and R413P(E12), were amplified by polymerase chain reaction (PCR) with incorporation of biotinylated deoxynucleotide(biotinylated-11-dUTP or biotinylated-14-dCTP). Hybridization between immobilized allele-specific oligonucleotide probes and biotin-labelled amplified DNA was performed and nonradioactively detected by a colorimetric reaction using streptavidin-alkaline phosphatase. RESULTS: The methods of non-radioactive reverse dot blot hybridization were established to screen the mutations. We detected the genotypes of five PKU patients and found that three of them carried R243Q mutation and one of the three also carried Y356X mutation. These results were confirmed by PCR-single strand conformation polymorphism. CONCLUSION: This method is suitable for rapid screening for common mutations in Chinese PKU patients.

Genetic Testing↗
PubMed2002

Haemophagocytic lymphohistiocytosis: proposal of a diagnostic algorithm based on perforin expression.

Haemophagocytic lymphohistiocytosis (HLH) is a rare, fatal disorder of early infancy. Mutations of the PRF1 gene have been identified in a subset of patients. However, the distinction between the different genetically determined and environmental subtypes of the disease remains a major issue to be solved. This may result in delayed or inappropriate application of bone marrow transplantation (BMT). We propose an algorithm that uses a combination of three rapid laboratory tests, i.e. perforin expression by peripheral lymphocytes, assessment of the behaviour of the 2B4 lymphocyte receptor and natural killer (NK) cell activity, to identify the different subgroups of HLH. In 19 patients diagnosed according to current criteria, we tested perforin expression, 2B4 receptor function and NK cell activity. PRF1 mutations were found in all seven patients showing absent perforin expression. In one male with abnormal behaviour of the 2B4 receptor, SH2D1A mutation confirmed the diagnosis of X-linked lymphoproliferative disease. Four patients with normal NK cell activity had evidence of associated infections. Of the seven with impaired NK cell activity, two had a probable genetically determined subtype of HLH and five appeared as sporadic, infection-associated cases. Improving the diagnostic approach may restrict the use of BMT, the only recognized curative treatment, to HLH patients with a documented poor prognosis while patients with milder disorders may be treated less intensively. Our flow chart could also lead to better selection of patients for specific gene analysis.

Algorithms↗
PubMed2006

Calcium entry mediated by GLR3.3, an Arabidopsis glutamate receptor with a broad agonist profile.

The amino acids glutamate (Glu) and glycine (Gly) trigger large, rapid rises in cytosolic Ca(2+) concentration and a concomitant rise in membrane potential (depolarization) in plants. The possibility that plant homologs of neuronal ionotropic glutamate receptors mediate these neuron-like ionic responses was tested in Arabidopsis (Arabidopsis thaliana) seedlings using a combination of Ca(2+) measurements, electrophysiology, and reverse genetics. The membrane depolarization triggered by Glu was greatly reduced or completely blocked in some conditions by mutations in GLR3.3, one of the 20 GLR genes in Arabidopsis. The same mutations completely blocked the associated rise in cytosolic Ca(2+). These results genetically demonstrate the participation of a glutamate receptor in the rapid ionic responses to an amino acid. The GLR3.3-independent component of the depolarization required Glu concentrations above 25 mum, did not display desensitization, and was strongly suppressed by increasing extracellular pH. It is suggested to result from H(+)-amino acid symport. Six amino acids commonly present in soils (Glu, Gly, alanine, serine, asparagine, and cysteine) as well as the tripeptide glutathione (gamma-glutamyl-cysteinyl-Gly) were found to be strong agonists of the GLR3.3-mediated responses. All other amino acids induced a small depolarization similar to the non-GLR, putative symporter component and in most cases evoked little or no Ca(2+) rise. From these results it may be concluded that sensing of six amino acids in the rhizosphere and perhaps extracellular peptides is coupled to Ca(2+) signaling through a GLR-dependent mechanism homologous to a fundamental component of neuronal signaling.

Amino Acids↗
PubMed2000

Testing of SHIRPA, a mouse phenotypic assessment protocol, on Dmd(mdx) and Dmd(mdx3cv) dystrophin-deficient mice.

The SHIRPA protocol was proposed as a rapid, comprehensive screening method for qualitatively abnormal phenotypes in the mouse (Rogers et al., Mamm Genome 8, 711, 1997). This screening technique is currently being used to identify mutants induced by N-ethylnitrosourea (ENU) mutagenesis (Brown and Nolan, Hum Mol Genet 7, 1627, 1998). SHIRPA can be used to identify mutants with neuromuscular abnormalities, but the sensitivity of the protocol is unknown. We tested two dystrophin-deficient mutants Dmd(mdx) and Dmd(mdx3cv), both of which are indistinguishable from wild-type by a simple visual assessment, at different ages, using the primary screen of the SHIRPA protocol. The most dramatic observation was that both Dmd(mdx) and Dmd(mdx3cv) mice showed extreme fatigue after testing, while mice from the same C57BL strains appeared unaffected. Each strain of dystrophin-deficient mice showed a different profile in locomotor activity and deficiencies in the wire maneuver, righting reflex, and negative geotaxis tests. Furthermore, the wire maneuver test indicated an earlier onset of muscular impairment in Dmd(mdx) than Dmd(mdx3cv) mice. These data suggest that the SHIRPA primary screen is effective not only in identifying subtle neuromuscular mutants, but also in distinguishing qualitative differences between mutants with neuromuscular abnormalities.

Animals↗
PubMed1999

Molecular cloning and tissue-specific expression of the mutator2 gene (mu2) in Drosophila melanogaster.

We present here the molecular cloning and characterization of the mutator2 (mu2) gene of Drosophila melanogaster together with further genetic analyses of its mutant phenotype. mu2 functions in oogenesis during meiotic recombination, during repair of radiation damage in mature oocytes, and in proliferating somatic cells, where mu2 mutations cause an increase in somatic recombination. Our data show that mu2 represents a novel component in the processing of double strand breaks (DSBs) in female meiosis. mu2 does not code for a DNA repair enzyme because mu2 mutants are not hypersensitive to DSB-inducing agents. We have mapped and cloned the mu2 gene and rescued the mu2 phenotype by germ-line transformation with genomic DNA fragments containing the mu2 gene. Sequencing its cDNA demonstrates that mu2 encodes a novel 139-kD protein, which is highly basic in the carboxy half and carries three nuclear localization signals and a helix-loop-helix domain. Consistent with the sex-specific mutant phenotype, the gene is expressed in ovaries but not in testes. During oogenesis its RNA is rapidly transported from the nurse cells into the oocyte where it accumulates specifically at the anterior margin. Expression is also prominent in diploid proliferating cells of larval somatic tissues. Our genetic and molecular data are consistent with the model that mu2 encodes a structural component of the oocyte nucleus. The MU2 protein may be involved in controlling chromatin structure and thus may influence the processing of DNA DSBs.

Amino Acid Sequence↗