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PubMed2024

Critically unwell infants and children with mitochondrial disorders diagnosed by ultrarapid genomic sequencing.

PURPOSE: To characterize the diagnostic and clinical outcomes of a cohort of critically ill infants and children with suspected mitochondrial disorders (MD) undergoing ultrarapid genomic testing as part of a national program. METHODS: Ultrarapid genomic sequencing was performed in 454 families (genome sequencing: n = 290, exome sequencing +/- mitochondrial DNA sequencing: n = 164). In 91 individuals, MD was considered, prompting analysis using an MD virtual gene panel. These individuals were reviewed retrospectively and scored according to modified Nijmegen Mitochondrial Disease Criteria. RESULTS: A diagnosis was achieved in 47% (43/91) of individuals, 40% (17/43) of whom had an MD. Seven additional individuals in whom an MD was not suspected were diagnosed with an MD after broader analysis. Gene-agnostic analysis led to the discovery of 2 novel disease genes, with pathogenicity validated through targeted functional studies (CRLS1 and MRPL39). Functional studies enabled diagnosis in another 4 individuals. Of the 24 individuals ultimately diagnosed with an MD, 79% had a change in management, which included 53% whose care was redirected to palliation. CONCLUSION: Ultrarapid genetic diagnosis of MD in acutely unwell infants and children is critical for guiding decisions about the need for additional investigations and clinical management.

Humans↗
PubMed2002

Rational identification of new antibacterial drug targets that are essential for viability using a genomics-based approach.

In the last two decades, the search for completely novel antibacterial agents has acquired a new sense of urgency due to the remarkable rise of antibiotic resistance among key bacterial pathogens. More recently, the advent of bacterial genomics has provided investigators with the data and bioinformatic tools to rationally identify novel antibacterial targets and the genome-scaled methodologies to validate them. Only 6 years have elapsed since the publication of the first complete bacterial genome sequence, but more than 50 complete microbial genome sequences are now available. This review will discuss the advantages and limitations of the existing bacterial genome dataset for the rational identification of novel antibacterial targets. Since the ability to rapidly identify essential genes where loss of function is coincident with loss of viability is the most important task of genomics-based target validation, essentiality testing methodologies (in which molecular genetic techniques are used to determine whether or not a gene product is required for viability of the parent cell) will be surveyed and their amenability to genome-scaled analysis assessed. Finally, we will discuss the impact of bacterial genomics to date on the development of novel and effective antibiotics.

Anti-Infective Agents↗
PubMed1999

Antiviral drug resistance in human cytomegalovirus.

Drug-resistant cytomegalovirus (CMV) should be considered when viral shedding persists after several weeks of therapy. The problem is most likely to arise in the setting of a severely immunosuppressed host with continuing or relapsing disease. Not all treatment failure can be attributed to drug resistance. The testing of CMV isolates for drug resistance in cell culture is time-consuming and labor-intensive, but recent advances in understanding of the genetics of resistance have resulted in rapid genotypic assays for specific mutations in the viral UL97 phosphotransferase or UL54 DNA polymerase genes that can predict resistance and cross-resistance to specific drugs. This information may help in the selection of alternative therapy.

Antiviral Agents↗
PubMed1996

Molecular genetic analysis of volatile-anesthetic action.

The mechanism(s) and site(s) of action of volatile inhaled anesthetics are unknown in spite of the clinical use of these agents for more than 150 years. In the present study, the model eukaryote Saccharomyces cerevisiae was used to investigate the action of anesthetic agents because of its powerful molecular genetics. It was found that growth of yeast cells is inhibited by the five common volatile anesthetics tested (isoflurane, halothane, enflurane, sevoflurane, and methoxyflurane). Growth inhibition by the agents is relatively rapid and reversible. The potency of these compounds as yeast growth inhibitors directly correlates with their lipophilicity as is predicted by the Meyer-Overton relationship, which directly correlates anesthetic potency of agents and their lipophilicity. The effects of isoflurane on yeast cells were characterized in the most detail. Yeast cells survive at least 48 h in a concentration of isoflurane that inhibits colony formation. Mutants resistant to the growth-inhibitory effects of isoflurane are readily selected. The gene identified by one of these mutations, zzz4-1, has been cloned and characterized. The predicted ZZZ4 gene product has extensive homology to phospholipase A2-activating protein, a GO effector protein of mice. Both zzz4-1 and a deletion of ZZZ4 confer resistance to all five of the agents tested, suggesting that signal transduction may be involved in the response of these cells to volatile anesthetics.

Adaptor Proteins, Signal Transducing↗
PubMed2007

The cancer worry chart: a single-item screening measure of worry about developing breast cancer.

BACKGROUND: Brief pictograph measures of health functioning have clinical value to office-based practice. Many women with a close family history of breast cancer will experience worry about their risk of developing breast cancer that influences decision-making and can interfere with health-related functioning. PURPOSE: To develop a clinically - useful triage measure of breast cancer worry for the field setting of office based practice. METHODS DESIGN: qualitative pilot testing followed by mailed survey. SURVEY SAMPLE: women registered with the Cancer Genetics Network who have a first or second-degree family history of breast cancer and no personal history of any cancer. Novel measure: single pictograph item modeled upon the Dartmouth COOP Charts. Comparison gold-standard measure: four-item Cancer Worry Scale (CWS). RESULTS: Pilot testing: participants found the item to be easily understood, rapidly completed and unobtrusive. Quantitative: 469 women responded (78% response rate); the Cancer Worry Chart demonstrated strong correlation to the CWS (Pearson correlation coefficient: 0.66, P < 0.001); Receiver operator curve identified favorable characteristics (AUC = 0.86) of the Cancer Worry Chart for identifying cancer worry-related mood or social role dysfunction. CONCLUSIONS: The new Cancer Worry Chart is a valid triage measure for breast cancer worry.

Adult↗
PubMed2004

Inherited cancer in children: practical/ethical problems and challenges.

Over recent years significant molecular advances have led to a better understanding of the genetics of both syndromic and non-syndromic paediatric cancers. In addition many hereditary cancer predisposition syndromes are now recognised, some of which have implications for children in affected families. Improvements in gene mutation screening will increase the sensitivity, accuracy and therefore the applicability of genetic testing in these conditions. This review will deal with four main areas pertaining to paediatric cancer genetics (i) genetic aspects of some non-syndromic paediatric cancers (ii) paediatric cancer predisposition syndromes, (iii) the management of children in families with predominantly adult- onset cancer predisposition syndromes and (iv) special ethical, legal, social and psychological considerations in the management of children, with actual or possible genetic cancer predisposition. Current concepts and controversies in the rapidly changing field of paediatric cancer genetics will be examined in detail and the application of existing guidelines and their limitations will be discussed.

Child↗
PubMed1999

Intra-specific diversity of Aureobasidium pullulans strains isolated from rocks and other habitats assessed by physiological methods and by random amplified polymorphic DNA (RAPD).

Intra-specific diversity of Aureobasidium pullulans strains isolated from environmental sources and from stones was studied by assessment of morphological, biochemical and physiological characters as well as random amplified polymorphic DNA (RAPD) using microsatellite or minisatellite DNA primers (GTG)5, (GACA)4, M13. The results showed that both classical and molecular techniques evidenced a phenotypic and genetic diversity of analysed A. pullulans strains. A different behaviour was observed in reference to the growth responses with D-glucosamine, citrate, galactitol and with different salt concentrations and range of growth temperature. Molecular analysis partially confirmed the data obtained with biochemical and physiological tests, additionally showing common fragments in all strains, to be used for a possible application as 'in situ' probes and for a rapid identification of A. pullulans strains.

Ascomycota↗
PubMed1991

The structure of human mitochondrial DNA variation.

Restriction analysis of mitochondrial DNA (mtDNA) of 3065 humans from 62 geographic samples identified 149 haplotypes and 81 polymorphic sites. These data were used to test several aspects of the evolutionary past of the human species. A dendrogram depicting the genetic relatedness of all haplotypes shows that the native African populations have the greatest diversity and, consistent with evidence from a variety of sources, suggests an African origin for our species. The data also indicate that two individuals drawn at random from the entire sample will differ at approximately 0.4% of their mtDNA nucleotide sites, which is somewhat higher than previous estimates. Human mtDNA also exhibits more interpopulation heterogeneity (GST = 0.351 +/- 0.025) than does nuclear DNA (GST = 0.12). Moreover, the virtual absence of intermediate levels of linkage disequilibrium between pairs of sites is consistent with the absence of genetic recombination and places constraints on the rate of mutation. Tests of the selective neutrality of mtDNA variation, including the Ewens-Watterson and Tajima tests, indicate a departure in the direction consistent with purifying selection, but this departure is more likely due to the rapid growth of the human population and the geographic heterogeneity of the variation. The lack of a good fit to neutrality poses problems for the estimation of times of coalescence from human mtDNA data.

Alleles↗
PubMed1992

Detection of ABO blood group polymorphism by denaturing gradient gel electrophoresis.

We report the use of a polymerase chain reaction (PCR) format together with denaturing gradient gel electrophoresis (DGGE) which allows rapid identification of the 6 major genotypes (AA, AO, BB, BO, AB and OO) of the human ABO blood group polymorphism in a single amplification. The procedure also distinguishes hitherto undescribed polymorphisms associated with the O and B alleles. Thus in testing 95 unrelated European individuals 4 different O alleles, 2 B alleles and 1 A allele were identified by DGGE and the level of recognisable heterozygosity, and hence the information content of the locus as a genetic marker, was raised from 3/95 (3%) to 66/95 (70%). The procedure is robust, genotyping is rapid and clear-cut, and has immediate implications for the use of the ABO locus in linkage analysis on chromosome 9q, the investigation of disease associations and forensic identification.

ABO Blood-Group System↗
PubMed2007

Combination of immunosensor detection with viability testing and confirmation using the polymerase chain reaction and culture.

Rapid and accurate differential determination of viable versus nonviable microbes is critical for formulation of an appropriate response after pathogen detection. Sensors for rapid bacterial identification can be used for applications ranging from environmental monitoring and homeland defense to food process monitoring, but few provide viability information. This study combines the rapid screening capability of the array biosensor using an immunoassay format with methods for determination of viability. Additionally, cells captured by the immobilized antibodies can be cultured following fluorescence imaging to further confirm viability and for cell population expansion for further characterization, e.g., strain identification or antibiotic susceptibility testing. Finally, we demonstrate analysis of captured bacteria using the polymerase chain reaction (PCR). PCR results for waveguide-captured cells were 3 orders of magnitude more sensitive than the fluorescence immunoassay and can also provide additional genetic information on the captured microbes. These approaches can be used to rapidly detect and distinguish viable versus nonviable and pathogenic versus nonpathogenic captured organisms, provide culture materials for further analysis on a shorter time scale, and assess the efficacy of decontamination or sterilization procedures.

Bacillus subtilis↗
PubMed1993

Melanocyte culture lines from Tyr-SV40E transgenic mice: models for the molecular genetic evolution of malignant melanoma.

Transgenic Tyr-SV40E mice previously produced on the C57BL/6 inbred-strain background, with SV40 oncogenic sequences specifically expressed in pigment cells, are predisposed to melanoma [Bradl, M., Klein-Szanto, A., Porter, S. & Mintz, B. (1991). Proc. Natl. Acad. Sci. USA, 88, 164-168]. Separate lines of these animals differ genetically only in the number of copies and chromosomal site of integration of the transgene. Skin melanocytes from young mice with no apparent skin lesions were established in continuous culture from hemizygous donors with low, medium and high numbers of transgene copies, and from a homozygous offspring of the low-copy mouse line. The standard culture conditions enable C57BL/6 wild-type melanocytes to become stably immortalized without transformation. The transgenic cell lines all changed over time in an orderly progression. However, with greater numbers of transgene copies, the cells more rapidly displayed shorter doubling times, increased anchorage independence, reduced serum and growth factor requirements, decreased tyrosinase expression and melanin content, increased oncogene expression, and capacity to form malignant melanomas when tested by grafting. Melanocytes with the lowest number of transgene copies were of special interest. They grew more rapidly than the wild-type cells from the outset, but did not become tumorigenic until an apparently small number of still-unknown genetic changes had spontaneously occurred, or until the number of transgene copies was increased slightly by homozygosity. In contrast to the hemizygous low-copy cells, the homozygous counterparts underwent striking and rapid transformational changes and early conversion to malignancy. Thus such low-copy transgenic melanocyte lines afford an exceptional opportunity for molecular analysis of somatic genetic evolution toward malignant melanoma.

Animals↗
PubMed1992

Use of tRNA consensus primers to indicate subgroups of Pseudomonas solanacearum by polymerase chain reaction amplification.

Polymerase chain reaction amplification of DNA from 112 Pseudomonas solanacearum strains with the tRNA consensus primers T3A and T5A divided the species into three fingerprint groups. These groups correspond well with previous divisions made by restriction fragment length polymorphism analysis. This polymerase chain reaction test is a facile method for rapidly classifying P. solanacearum strains.

Base Sequence↗
PubMed1997

Rayleigh match ranges of red/green color-deficient observers: psychophysical and molecular studies.

Large-field Rayleigh match ranges were measured in 27 red/green color-deficient male observers, using bright, temporally alternating, 3-9 deg annular test fields. The observers' X-linked opsin gene arrays were characterized by molecular genetic techniques, and used to infer the absorption maxima of each observer's L and/or M cone photopigment(s). Measured match ranges decreased rapidly as the inferred separation in pigment absorption maxima increased from 0 to 2-3 nm, and varied irregularly thereafter. Following He & Shevell [(1995) Vision Research, 35, 2579-2588] predicted match ranges were calculated for various pigment separations and assumed values of pigment optical density. The predicted variations in match range encompassed the measured match ranges of most (but not all) of the color-deficient observers. The calculations also showed that differences in pigment optical density, in two cone types containing the same pigment, are sufficient to allow a moderate degree of chromatic discrimination. Such models thus provide a possible account of the fact that some color-deficient observers, with only a single X-linked opsin gene, can make red/green chromatic discriminations.

Adolescent↗
PubMed2001

Score tests for association between traits and haplotypes when linkage phase is ambiguous.

A key step toward the discovery of a gene related to a trait is the finding of an association between the trait and one or more haplotypes. Haplotype analyses can also provide critical information regarding the function of a gene; however, when unrelated subjects are sampled, haplotypes are often ambiguous because of unknown linkage phase of the measured sites along a chromosome. A popular method of accounting for this ambiguity in case-control studies uses a likelihood that depends on haplotype frequencies, so that the haplotype frequencies can be compared between the cases and controls; however, this traditional method is limited to a binary trait (case vs. control), and it does not provide a method of testing the statistical significance of specific haplotypes. To address these limitations, we developed new methods of testing the statistical association between haplotypes and a wide variety of traits, including binary, ordinal, and quantitative traits. Our methods allow adjustment for nongenetic covariates, which may be critical when analyzing genetically complex traits. Furthermore, our methods provide several different global tests for association, as well as haplotype-specific tests, which give a meaningful advantage in attempts to understand the roles of many different haplotypes. The statistics can be computed rapidly, making it feasible to evaluate the associations between many haplotypes and a trait. To illustrate the use of our new methods, they are applied to a study of the association of haplotypes (composed of genes from the human-leukocyte-antigen complex) with humoral immune response to measles vaccination. Limited simulations are also presented to demonstrate the validity of our methods, as well as to provide guidelines on how our methods could be used.

Algorithms↗
PubMed1976

Rapid test for assay of ozone sensitivity in Escherichia coli.

A rapid test devised for assay of ozone sensitivity in Escherichia coli is described. The detection of new mutants, either more resistant or more sensitive than wild type strain to ozone, and the genetic analysis of ozone recombinants are now possible. Results confirm that ozone resistance is probably involved with DNA repair mechanism; and show that ozone and ultraviolet light inhibit the cell division capacity of lon mutant in a similar way.

Bacteriological Techniques↗
PubMed2026

Development of a new recombineering system for Edwardsiella species.

Edwardsiella species are important aquaculture pathogens that also cause opportunistic infections in humans, necessitating efficient genome editing tools to study their pathogenesis and develop control strategies. In this study, we identified and characterized six endogenous recombinases pairs from Edwardsiella and its phages. Among these, the BAS_MS17 system exhibited the highest recombination efficiency in E. piscicida EIB202&#x394;p. Extending homology arms from 150 bp to 200 bp improved editing efficiency by 2-fold, while the addition of Redg or Plug further enhanced recombination by 3-fold and 2.5-fold, respectively, without compromising accuracy (100%). More importantly, when applied to E. piscicida sdu12S, Redg or Plug improved the editing efficiency by 8-fold and 7-fold, respectively. Deletion of the phage-derived single-strand binding protein (SSB) reduced efficiency to 25% of the BAS_MS17 level, whereas expression of the endogenous RecA-family SSB (rSSB) increased recombinant yield by 5-fold, highlighting functional conservation. Furthermore, SSB proteins from heterologous hosts failed to enhance recombination efficiency. Using the optimized system, we successfully knocked out ten distinct genes, including virulence-associated loci, with editing accuracy exceeding 85%. Phenotypic analysis revealed that luxR, but not the other tested genes, contributes to biofilm formation. Virulence evaluation results showed that aroA, fur, and hfq are critical virulence-associated factors. Collectively, this streamlined recombineering system provides a simple, rapid, and efficient genetic tool for Edwardsiella, supporting mechanistic studies of virulence and the development of live attenuated vaccine candidates.

Edwardsiella piscicida↗