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PubMed1991

[STAPHYOGRAM, a new rapid identification kit for the aerobic, gram-positive, catalase-positive cocci--application of fluorometric microplate hybridization for the pre-identification of 386 isolates used].

A new simplified test kit, STAPHYOGRAM plate, was developed for 4-hr identification of aerobic, Gram-positive and catalase-positive cocci. The plate has 18 wells, in which different dehydrated substrates and nutrients are fixed. An 18-hr agar-culture suspension of a test strain with a turbidity of McFarland No. 4 was distributed into all wells in 50-microliters quantities. After 4-hr incubation at 37C, the profile number was obtained by summarizing positive reactions. The ability of the plate to differentiate the type strains of the 30 species of the three genera in the family Micrococcaceae was confirmed. These three genera are Staphylococcus, Micrococcus and Stomatococcus. The applicability of the fluorometric microplate hybridization technique to identification of aerobic, Gram-positive and catalase-positive cocci was confirmed by homologous hybridization among the type strains of the 30 species. Thus, 386 isolates of human and animal origin were pre-identified by microplate hybridization and used for evaluating the STAPHYOGRAM plate. Of the 236 profile numbers thus obtained with the 386 isolates, 218 (92.4%) were species-proper each and all for the 15 species of Staphylococcus and Stomatococcus mucilaginosus. A total of 342 (88.6%) of the 386 isolates were given such profile numbers, and were identified without any additional test. Among the 15 species identified primarily by the results of STAPHYOGRAM plate culture, S. caprae, S. lugdunensis, S. gallinarum and S. delphini were validly published after Approved Lists of Bacterial Names. The identified strains of S. caprae (48), S. haemolyticus (46), S. capitis (35) numbered between those of S. epidermidis (67) and S. saprophyticus (31). Profile numbers common to two species were seven (27 strains) and that to four species was one (17 strains). These 44 strains were identified with one to three additional tests. From these results, we were convinced that the STAPHYOGRAM test plate is useful for the rapid identification of members of family Micrococcaceae. By compiling STAPHYOGRAM plate data on genetically identified strains, an exclusive list of profile numbers will soon be prepared for perfection of the kit.

Animals↗
PubMed2001

Miniaturization technologies for molecular diagnostics.

BACKGROUND: Molecular diagnostics devices are becoming smaller. With the advancement of miniaturization technologies, microchip-based systems will soon be available for genetic testing. The purpose of this review is to highlight the underlying principles in miniaturization, the strategies being developed for bioanalysis, and the potential impact on the practice of this rapidly growing medical discipline. APPROACH: The author discusses DNA microchips and their practical importation into the clinical laboratory, based on his background in medical device and microchip design and development. His discussion is supported by a body of literature covering both biomedical and electrical engineering and more recent publications in the field of molecular genetics and pathology. CONTENT: This review is descriptive and intended to outline the technologic and methodologic approaches to the creation of an integrated genetic analysis instrument based on miniature components. The review draws on published scientific evaluations of these devices without regard to the companies involved in their development. SUMMARY: The intent of this review is that the reader will better understand the variety of technical approaches toward the miniaturization of molecular genetic testing for the clinical laboratory. With insight into the principles underlying the operation of these chips and the integrated systems, the end user can better evaluate the value to the field in terms of making molecular genetics testing simpler, faster, and less expensive.

Biosensing Techniques↗
PubMed1997

Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms.

Combination of the targeted amplification of nuclear introns and the analysis of single-stranded conformational polymorphisms has the potential to provide an inexpensive, rapid, versatile and sensitive genetic assay for evolutionary studies and conservation. We are developing primers and protocols to analyse nuclear introns in vertebrates, and are testing them in a population genetic study of marbled murrelets Brachyramphus marmoratus. Here we present protocols and results for introns for aldolase B, alpha-enolase, glyceraldehyde-3-phosphate dehydrogenase and lamin A. Results suggest that this approach presents a potentially powerful method for detecting genetic variation within and among local populations and species of animals: (i) a variety of genes can be surveyed, including genes of special interest such as those involved in disease resistance; (ii) assays are rapid and relatively inexpensive; (iii) large numbers of genes can be assayed, enabling accurate estimation of variation in the total genome; (iv) almost any mutation can be detected in the genes amplified; (v) the exact nature of variation can be investigated by sequence analysis if desired; (vi) statistical methods previously developed for proteins and/or sequence data can be used; (vii) protocols can be easily transferred to other species and other laboratories; and (viii) assays can be performed on old or degraded samples, blood or museum skins, so that animals need not be killed. Results of analyses for murrelets support earlier evidence that North American and Asiatic subspecies represent reproductively isolated species, and that genetic differences exist among murrelets from different sites within North America.

Amino Acid Sequence↗
PubMed1993

Providers and consumers of prenatal genetic testing services: what do the national data tell us?

Prenatal genetic services are currently available in all but a few states. The Council of Regional Networks for Genetic Services (CORN) has developed and implemented a data collection project to collect a minimum data set (MDS) on genetic services, including prenatal services, throughout the US. More than 400 reporting units were solicited for data in 1989, and approximately 240 (60%) responded. The CORN MDS Report for 1989 shows that more than 124,000 prenatal patients received services in the reporting centers. These individuals received almost 303,000 individual prenatal clinical services and accounted for more than 481,000 laboratory tests. Advanced maternal age was the primary indication for service in the vast majority of patients (62%). Based on data from the two major proficiency testing programs for laboratories performing screening tests for maternal serum alpha-fetoprotein (MSAFP), it is estimated that 50% of the pregnancies in the US are screened for MSAFP. The CORN database provides the only data available for the rapidly expanding area of genetic services. Therefore, it provides a unique resource for evaluating progress toward the Healthy People 2000 objectives regarding genetic services.

Adult↗
PubMed1974

Simple genetic transformation assay for rapid diagnosis of Moraxella osloensis.

A genetic transformation assay for unequivocal identification of strains of Moraxella osloensis is described. In this assay a stable tryptophan auxotroph is transformed to prototrophy by deoxyribonucleic acid (DNA) samples from other strains of M. osloensis but not by DNA samples from unrelated bacteria. The test is simple to perform and definitive results can be obtained in less than 24 h. The procedure, which is suitable for routine diagnosis in a clinical laboratory, involves a rapid method for preparation of crude transforming DNA from small quantities of bacterial cells and permits simultaneous examination of large numbers of isolated cultures. The assay was shown to correctly identify 27 strains previously classified as M. osloensis. Forty-five other gram-negative, oxidase-positive, nonmotile coccobacilli, which might be confused with M. osloensis unless subject to more extensive testing, were shown to be unrelated genetically to M. osloensis. The transformation assay clearly distinguishes M. osloensis from Acinetobacter. Although most strains of M. osloensis are nonfastidious, being able to grow in a mineral medium supplemented with a single organic carbon source, one of the strains tested was only able to grow on fairly complex media and could not be transformed to grow on simple media. Inability to alkalize Simmons citrate agar was shown not to be characteristic of all strains of M. osloensis.

Acinetobacter↗
PubMed2000

Development of conventional and real-time PCR assays for the rapid detection of group B streptococci.

BACKGROUND: Group B streptococci (GBS), or Streptococcus agalactiae, are the leading bacterial cause of meningitis and bacterial sepsis in newborns. Currently available rapid methods to detect GBS from clinical specimens are unsuitable for replacement of culture methods, mainly because of their lack of sensitivity. METHODS: We have developed a PCR-based assay for the rapid detection of GBS. The cfb gene encoding the Christie-Atkins-Munch-Petersen (CAMP) factor was selected as the genetic target for the assay. The PCR primers were initially tested by a conventional PCR method followed by gel electrophoresis. The assay was then adapted for use with the LightCycler(TM). For this purpose, two fluorogenic adjacent hybridization probes complementary to the GBS-specific amplicon were designed and tested. In addition, a rapid sample-processing protocol was evaluated by colony-forming unit counting and PCR. A total of 15 vaginal samples were tested by both standard culture method and the two PCR assays. RESULTS: The conventional PCR assay was specific because it amplified only GBS DNA among 125 bacterial and fungal species tested, and was able to detect all 162 GBS isolates from various geographical areas. This PCR assay allowed detection of as few as one genome copy of GBS. The real-time PCR assay was comparable to conventional PCR assay in terms of sensitivity and specificity, but it was more rapid, requiring only approximately 30 min for amplification and computer-based data analysis. The presence of vaginal specimens had no detrimental effect on the sensitivity of the PCR with the sample preparation protocol used. All four GBS-positive samples identified by the standard culture method were detected by the two PCR assays. CONCLUSION: These assays provide promising tools for the rapid detection and identification of GBS.

Animals↗
PubMed1994

Viability criterion of muscle bundles used in the in vitro contracture test in patients with neuromuscular diseases.

We have compared the viability criteria of muscle bundles used in the in vitro contracture test for susceptibility to malignant hyperthermia (MH) in a group of 28 patients with various neuromuscular diseases (NMD) and 93 MH-related family patients. In the patients with NMD, this standard test gave one positive, six equivocal and 21 negative results. Compared with MH-related family patients, muscle bundles used had significantly smaller resting membrane potentials and smaller predrug twitch tension amplitudes. Some results from the group with NMD were obtained with muscles which were damaged, more rapidly deteriorating, non-standard or both, and should not be taken to indicate that the patients have the genetic trait for MH. The in vitro contracture test is not always relevant for myopathic muscle (especially dystrophic muscle) and this could explain the lack of specificity for MH.

Caffeine↗
PubMedDate not supplied

Genetic structure of human populations in the British Isles.

Spatial patterns were studied for 36 allele frequencies representing 14 genetic systems (blood antigens, enzymes and serum proteins) in the United Kingdom and Irish Republic. The total number of data points over all systems and localities is 331. Patterns of genetic variation in space are graphically represented by one-dimensional and directional correlograms, and by interpolated allele-frequency surfaces. The data surfaces were examined by the various techniques of spatial autocorrelation analysis. Zones of rapid change across allele surfaces were discovered by the wombling method. Six allele frequency surfaces from four genetic systems exhibit significant spatial patterns. Only one pattern (IO; in the ABO system) may be described as purely clinal in an east-west direction; another (IB; in ABO) approximates a cline or at least north-south differentiation. A method was developed for testing the direction of maximal genetic autocorrelation. Two previously unrecorded patterns for the British Isles, north-south gradients for Rhesus and P, were detected. Twelve zones of rapid genetic change were discovered; some of these seem to reflect maritime and montane physical barriers as well as long-held cultural and linguistic differences, particularly between early Germanic and Celtic speakers. Moreover, some appear to reflect past historic events such as the invasions of Anglo-Saxons and Anglo-Normans.

ABO Blood-Group System↗
PubMed1999

Dominantly inherited ataxias.

Molecular genetic studies in the past decade have demonstrated the enormous genetic heterogeneity among the dominantly inherited ataxias. Mutations at several distinct loci give rise to the progressive dominant ataxias and at least 2 different mutations cause episodic ataxias with dominant inheritance. The well-established genotypes for progressive dominant ataxias have all involved expansions of repeated CAG sequences. Clinically these patients present with progressive cerebellar deficits as well as signs relating to pathology in other neural systems in a variable fashion. Some of these other signs serve as diagnostic clues to the underlying genotype, but the identification of the genotype from the clinical phenotype alone is usually difficult. The CAG expansions involved usually are unstable with intergenerational expansions as well as contractions of the repeat size. Phenotypic features such as age of onset and to a lesser extent disease progression rate and the presence of specific clinical signs depend on the CAG repeat size. Identification of the mutations has allowed precise genotypic diagnosis in several families allowing more accurate genetic counseling, including predictive testing of at risk individuals when sought. Also, increasing information about the gene products and their abnormal distributions in disease brain is rapidly giving rise to rational ideas about the pathogenesis of neuronal degeneration in these diseases and raising hope for meaningful treatment strategies.

Ataxia↗
PubMed2005

Genotype-phenotype correlation of mouse pde6b mutations.

PURPOSE: To identify the underlying molecular defects causing retinal degeneration in seven N-ethyl-N-nitrosourea (ENU) induced mutant alleles of the Pde6b gene and to analyze the timescale of retinal degeneration in these new models of retinitis pigmentosa. METHODS: Conformation sensitive capillary electrophoresis and DNA sequencing were used to identify the mutations in the Pde6b gene. Visual acuity testing was performed with a visual-tracking drum at ages ranging from postnatal day 25 to week 10. Retinal examination was performed with an indirect ophthalmoscope. Animals were killed and eyes were prepared for histologic analysis. RESULTS: Point mutations in the seven new alleles of Pde6b were identified: Three generated premature stop codons, two were missense mutations, and two were splice mutations. The three stop codon mutants and one of the splice mutants had phenotypes indistinguishable from the Pde6b(rd1) mouse in rapidity of onset of retinal degeneration, suggesting that they are null alleles. However, the remaining alleles showed slower onset of retinal degeneration, as determined by visual acuity testing, fundus examination, and histology, indicating that they are hypomorphic alleles. CONCLUSIONS: These data demonstrate a correlation between genotype and phenotype. Four of the mutants with severe genetic lesions have rapid onset of retinal degeneration, as determined by fundus examination. These mice were indistinguishable from Pde6b(rd1) mice, which are effectively blind by 3 weeks of age. In contrast, the milder genetic lesions show a slower progression of the disease and provide the community with models that more closely mimic human retinitis pigmentosa.

Alkylating Agents↗
PubMed1993

Radish, a Drosophila mutant deficient in consolidated memory.

We have characterized the behavior and genetics of the Drosophila mutant radish (rsh gene). Initial learning of radish flies in two olfactory discrimination tests is high, but subsequent memory decays rapidly at both early and late times after training. Anesthesia-resistant memory (consolidated memory) is undetectable in radish flies 3 hr after training. The mutant shows normal locomotor activity and normal sensitivity to the odor cues and electric-shock reinforcement used in the learning tests. The radish gene maps within a 180-kb interval in the 11D-E region of the X chromosome.

Animals↗
PubMed2000

Survival of Escherichia coli in freshwater: beta-D-glucuronidase activity measurements and characterization of cellular states.

A rapid enzyme assay measuring beta-D-glucuronidase activity of Escherichia coli was tested in survival experiments after discharge of E. coli in river water. Enzyme activity was compared with several analyses performed to characterize cellular states under stressful conditions. Enzyme activity remained stable under starvation and light stress conditions despite losses of culturability, respiratory activity, and cytoplasmic membrane integrity. beta-D-Glucuronidase activity followed the pattern of genetic and morphologic cell integrity. The tested enzyme assay seems well adapted to study the fate of fecal coliforms in survival experiments, and appears to be a rapid and efficient way to estimate the microbiological quality of surface waters.

Bacteriological Techniques↗
PubMed2003

Genomics and proteomics in cancer.

Cancer development is driven by the accumulation of DNA changes in the approximately 40000 chromosomal genes. In solid tumours, chromosomal numerical/structural aberrations are common. DNA repair defects may lead to genome-wide genetic instability, which can drive further cancer progression. The genes code the actual players in the cellular processes, the 100000-10 million proteins, which in (pre)malignant cells can also be altered in a variety of ways. Over the past decade, our knowledge of the human genome and Genomics (the study of the human genome) in (pre)malignancies has increased enormously and Proteomics (the analysis of the protein complement of the genome) has taken off as well. Both will play an increasingly important role. In this article, a short description of the essential molecular biological cell processes is given. Important genomic and proteomic research methods are described and illustrated. Applications are still limited, but the evidence so far is exciting. Will genomics replace classical diagnostic or prognostic procedures? In breast cancers, the gene expression array is stronger than classical criteria, but in endometrial hyperplasia, quantitative morphological features are more cost-effective than genetic testing. It is still too early to make strong statements, the more so because it is expected that genomics and proteomics will expand rapidly. However, it is likely that they will take a central place in the understanding, diagnosis, monitoring and treatment of (pre)cancers of many different sites.

Cell Transformation, Neoplastic↗
PubMed2004

Evaluation of different methods to detect methicillin resistance in small-colony variants of Staphylococcus aureus.

To evaluate different methods for their abilities to detect methicillin resistance in small-colony variants (SCVs) of Staphylococcus aureus, 11 different methicillin-resistant S. aureus (MRSA) clones with the SCV phenotype were used in this study. The slow growth of SCVs often makes testing by disk diffusion or by automated methods invalid. Only detection of the mecA gene by PCR and the MRSA-Screen latex agglutination test using a higher colony number were shown to be reliable methods to rapidly detect methicillin resistance in these variants.

Genetic Variation↗
PubMed1989

Correlated responses in lines of Drosophila melanogaster selected for different oviposition behaviors.

D. melanogaster was subjected to selection for two different traits of oviposition behaviour in relation to oocyte retention in ovaries, i.e. the aptitude to stop laying in response to an unsuitable substrate, and the occurrence of a dusk peak in the circadian oviposition rhythm. Selection for high and low lines was rapidly successful for both characters. Each selected line was also tested for the non-selected trait. Results showed a genetic correlation between the two behaviours, suggesting a common mechanism for the control of oviposition, independently of the origin and the duration of oocyte retention.

Animals↗
PubMed1995

Microsatellite evolution--evidence for directionality and variation in rate between species.

Microsatellite DNA sequences are rapidly becoming the dominant source of nuclear genetic markers for a wide range of applications, from genome mapping to forensic testing to population studies. If misinterpretation is to be avoided, it is vital that we understand fully the way in which microsatellite sequences evolve. We have therefore compared allele length distributions for 42 microsatellites in humans with their homologues in a range of related primates. We find a highly significant trend for the loci to be longer in humans, showing that microsatellites can evolve directionally and at different rates in closely related species.

Alleles↗
PubMed2006

Genetic knowledge and moral responsibility: ambiguity at the interface of genetic research and clinical practice.

Despite a rapidly expanding literature on the issue of duty to warn at-risk relatives in the context of clinical genetic testing, little has been written on parallel issues with regard to the management of genetic research results. Some might view this lack as an indication that there is little to discuss in this regard. That is, standard practice is that data obtained through medical research should not be treated as though they are clinically relevant, and this standard should hold for genetic research as well. This paper challenges this conclusion and its underlying assumptions. We argue that the line between genetic research and clinical practice is often ambiguous. In some cases, research data gathered from a very small number of subjects could have immediate clinical implications. Hence, it is unethical for genetic researchers to absolve themselves of clinical responsibilities for research subjects and/or their families, on the grounds that the data were obtained for research purposes. Indeed, we argue that it could well be unethical to embark on some forms of genetic research unless advance arrangements have been made for genetic counseling and clinical follow-up. Furthermore, in some cases, it might be unethical to enroll subjects in studies if the subjects are unwilling to receive their individual results.

Arrhythmogenic Right Ventricular Dysplasia↗
PubMed1993

Gene therapy, concepts, current trials and future directions.

Since the initial human clinical trials of retroviral-mediated gene transfer in the USA in 1989, numerous additional protocols are in process or have been proposed. In the first therapeutic protocol, to treat the genetic disease ADA deficiency, encouraging signs of clinical benefit have been observed in the first two patients. Gene-marking properties are being extensively used in many protocols, particularly in the area of autologous bone marrow transplantation for various cancers. The drug delivery potential of gene therapy is initially being evaluated through delivery of various lymphokines and cytokines in cancer therapy protocols. Testing has also begun for other genetic diseases, Familial Hypercholesterolemia and Hemophilia B. Vector systems and retroviral vectors are developing rapidly, and a clinical trial using a liposome-based delivery has started. The pace of technical development and clinical application has intensified. Although significant clinical therapies are expected from these initial studies, the full potential of gene therapy for wide applications still requires innovative research programs, directed towards true in vivo vectors.

Animals↗