HyBeacon probes for rapid DNA sequence detection and allele discrimination

HyBeacon probes are single-stranded oligonucleotides with one or more internal base(s) labeled with a fluorescent dye. When a probe forms a duplex with its target sequence, the level of fluorescence emission increases considerably. HyBeacons have been developed as new tools for rapid sequence detection and discrimination and have been employed in a wide variety of applications including infectious diagnostics and analysis of human polymorphisms. Single-labeled (FVG1) and dual-labeled (FVG11) probes were designed to analyze the factor V Leiden (R506Q) polymorphism which causes an increased risk of deep vein thrombosis and pulmonary embolism. Detection and identification of factor V alleles is performed by melting curve analysis and determination of probe melting temperature (T(m)). HyBeacon hybridization to the glutamine allele (Q) causes the formation of mismatched DNA duplexes that are detected through decreases in T(m). HyBeacon probes are included in homogeneous PCR assays to genotype samples with respect to the factor V polymorphism within 20 min, using purified DNAs and unpurified saliva/blood samples. This paper describes the preparation of homogeneous PCR assays, LightCycler target amplification, and subsequent melting curve analysis. This chapter also describes the use of homologous oligonucleotides and melting curve analysis as a method for probe evaluation.

The use of genetic markers for personal identification and the analysis of family relationships

In 1984 a family of hypervariable sequences was discovered in human DNA which when used as DNA probes provided a sufficiently informative sampling of an individual's DNA as to uniquely identify each person (except for genetically identical twins). Termed a DNA 'fingerprint', the DNA pattern revealed by the probes said nothing about characteristics of age, sex, height, or colour but immediately met a long-unanswered need for certain definition in the establishment of identity and family relationships. DNA tests are now a key tool in forensic investigations and are rapidly gaining acceptance in courts around the world. DNA tests are also replacing conventional serology for the resolution of paternity disputes. The definition provided by the DNA tests was possibly most urgently sought by immigration families in the UK who were separated by an inability to prove their family ties. The interest from the public has been overwhelming and Cellmark Diagnostics have already completed tests on over 15,000 individuals in the UK since opening in June 1987. Media coverage has been extensive, and continues to view DNA tests as beneficial; this, coupled with its commercial potential, suggests that DNA technology is here to stay.

Genetics of epilepsy: epilepsy research foundation workshop report

The Sixth Epilepsy Research Foundation workshop, held in Oxford in March 2006, brought together basic scientists, geneticists, epidemiologists, statisticians, pharmacologists and clinicians to consider progress, issues and strategies for harnessing genetics to improve the understanding and treatment of the epilepsies. General principles were considered, including the fundamental importance of clear study design, adequate patient numbers, defi ned phenotypes, robust statistical data handling, and follow-up of genetic discoveries. Topics where some progress had been made were considered including chromosomal abnormalities, neurodevelopment, hippocampal sclerosis, juvenile myoclonic epilepsy, focal cortical dysplasia and pharmacogenetics. The ethical aspects of epilepsy genetics were reviewed. Principles and limitations of collaboration were discussed. Presentations and their matched discussions are produced here. There was optimism that further genetic research in epilepsy was not only feasible, but might lead to improvements in the lives of people with epilepsy.

Imagery rehearsal in the treatment of posttraumatic nightmares in Australian veterans with chronic combat-related PTSD: 12-month follow-up data

Nightmares are often a distressing symptom for veterans with chronic combat-related posttraumatic stress disorder (PTSD). A psychological treatment that has recently shown considerable promise is Imagery Rehearsal Therapy (IRT). In a pilot study by the current authors, IRT was demonstrated to be effective in the treatment of posttraumatic nightmares in a group of combat veterans up to 3-month posttreatment. This study reports the 12-month follow-up data of the pilot study, examining the longer term outcome of the IRT treatment. Twelve Australian Vietnam veterans with chronic combat-related PTSD were treated with 6 once weekly sessions of imagery rehearsal and assessed using standardised measures of nightmare frequency and intensity, PTSD, depression, anxiety and broader symptomatology at intake, posttreatment, and 3-and 12-month follow-up. Significant improvements in targeted nightmare frequency and intensity were evident to 12-month posttreatment. Similarly, improvements in overall PTSD, depression, anxiety, and broader based symptomatology were also maintained to 12 months. This study provides preliminary evidence that the positive treatment effects of IRT on posttraumatic nightmares, PTSD, and broader symptomatology in males with chronic combat-related PTSD are maintained in the longer term.

MMPI-2 as a predictor of change in PTSD symptom clusters: a further analysis of the Forbes et al. (2002) data set

In this study, we reanalyzed the Forbes et al. (2002) data set to examine the Minnesota Multiphasic Personality Inventory (MMPI-2; Butcher, Dahlstrom, Graham, Tellegen, & Kaemmer, 1989) as a differential predictor of change across posttraumatic stress disorder symptom clusters following treatment in 141 Vietnam veterans. A series of partial correlation and linear multivariate regression analyses, controlling for initial symptom severity, identified several scales predictive of symptom change. None of the MMPI-2 scales, however, emerged as predictors of change in reexperiencing symptoms. Social alienation and marital distress were the most potent predictors for avoidance symptoms. Anger, alcohol use, and hypomania were the most potent predictors for the hyperarousal symptoms. Of the personality disorders, borderline personality was the strongest predictor of change in the avoidance and hyperarousal clusters. Further replication of the findings of this article and those reported by Forbes et al. (2002) is required.

MMPI-2 based subgroups of veterans with combat-related PTSD: differential patterns of symptom change after treatment

Considerable research has focused on the use of the MMPI to assess posttraumatic stress disorder (PTSD) through identification of mean profile configurations and the development of PTSD subscales. Little work, however, has addressed the heterogeneity of profiles evident in PTSD populations. This study investigated the MMPI-2 profiles of 158 Australian treatment-seeking Vietnam veterans with combat-related PTSD to identify distinct subgroups. Three robust subgroups were identified on the basis of their MMPI-2 profile and compared on PTSD and associated symptomatology. These subgroups consisted of a mild PTSD group with subclinical personality pathology, and two severe PTSD groups that differed in levels of personality disturbance and general psychopathology. Most notably, differences between these latter two groups occurred in the areas of externalization, alienation, and propensity for acting out. These groups were labeled as subclinical, trauma profile, and global. The groups demonstrated significant differences in the patterns of recovery after treatment. The subclinical group demonstrated little change after treatment. In contrast, the trauma profile and global groups both improved, although the trauma profile group demonstrated greater PTSD symptom reduction than the global group.

The MMPI-2 as a predictor of symptom change following treatment for posttraumatic stress disorder

This study sought to examine the impact of personality factors on symptom change following treatment for 141 Vietnam veterans with chronic combat-related posttraumatic stress disorder (PTSD) using the Minnesota Multiphasic Personality Inventory-2 (Butcher, Dahlstrom, Graham, Tellegen, & Kaemmer, 1989). A series of partial correlation and linear multivariate regression analyses identified social alienation, associated with anger and substance use, as the most potent negative predictor of symptom change. Of the scales assessing personality disorder, Borderline Personality was identified as the strongest negative predictor of outcome. Regression analyses examining the most salient scales identified 5 items that contributed 14% of the variance in the prediction of change scores independently of the 21% accounted for by pretreatment PTSD severity.

Evaluation of sequence variation and selection in the bindin locus of the red sea urchin, Strongylocentrotus franciscanus

Recent evidence suggests that gamete recognition proteins may be subjected to directed evolutionary pressure that enhances sequence variability. We evaluated whether diversity enhancing selection is operating on a marine invertebrate fertilization protein by examining the intraspecific DNA sequence variation of a 273-base pair region located at the 5' end of the sperm bindin locus in 134 adult red sea urchins (Strongylocentrotus franciscanus). Bindin is a sperm recognition protein that mediates species-specific gamete interactions in sea urchins. The region of the bindin locus examined was found to be polymorphic with 14 alleles. Mean pairwise comparison of the 14 alleles indicates moderate sequence diversity (p-distance = 1.06). No evidence of diversity enhancing selection was found. It was not possible to reject the null hypothesis that the sequence variation observed in S. franciscanus bindin is a result of neutral evolution. Statistical evaluation of expected proportions of replacement and silent nucleotide substitutions, observed versus expected proportions of radical replacement substitutions, and conformance to the McDonald and Kreitman test of neutral evolution all indicate that random mutation followed by genetic drift created the polymorphisms observed in bindin. Observed frequencies were also highly similar to results expected for a neutrally evolving locus, suggesting that the polymorphism observed in the 5' region of S. franciscanus bindin is a result of neutral evolution.

Genetic structure of populations of the red sea urchin, Strongylocentrotus franciscanus

Population subdivision was evaluated in the red sea urchin, Strongylocentrotus franciscanus, using DNA sequence data from 134 adult individuals collected in 1995 and 1996. On average 22 individuals were sequenced from six geographic locations between Alaska and Baja California (N=134), nearly the full extent of the species range. DNA sequence data was obtained from direct sequencing of a 273 base pair region of the bindin gene, which encodes a sperm fertilization protein. Results indicate that bindin is sufficiently polymorphic to serve as a genetic marker. We identified 14 unique alleles present in the entire range sampled with a maximum of eight alleles at a specific site. Mean pairwise comparison of the 14 unique alleles indicates moderate sequence diversity (p-distance=1.06). Although there is conflicting evidence to suggest that Alaska populations may deviate from the Hardy-Weinberg expectations, analysis of bindin genotype frequencies indicate that it is not possible to reject the null hypothesis of random mating throughout the species range. The results of a chi-square test with pooling conform to Hardy-Weinberg expectations for all populations (P>0.05) except for the Alaska population (P=0.037). Inbreeding coefficients are consistent with this result and suggest that for the bindin locus, there is high gene flow. These results are compared with previously published results of genetic substructuring in sea urchins to examine relationships among population structure, dispersal potential and biogeography.

The efficiency of multilocus DNA fingerprint probes for individualization and establishment of family relationships, determined from extensive casework

The properties of human DNA fingerprints detected by multilocus minisatellite probes 33.6 and 33.15 have been investigated in 36 large sibships and in 1,702 Caucasian paternity cases involving the analysis of over 180,000 DNA fingerprint bands. The degree of overlap of minisatellite loci detected by these two probes is shown to be negligible (approximately 1%), and the resulting DNA fingerprints are therefore derived from independent sets of hypervariable loci. The level of allelism and linkage between different hypervariable DNA fragments scored with these probes is also low, implying substantial statistical independence of DNA fragments. Variation between the DNA fingerprints of different individuals indicates that the probability of chance identity is very low (much less than 10(-7) per probe). Empirical observations and theoretical considerations both indicate that genetic heterogeneity between subpopulations is unlikely to affect substantially the statistical evaluation of DNA fingerprints, at least among Caucasians. In paternity analysis, the proportion of nonmaternal DNA fragments in a child which cannot be attributed to the alleged father is shown to be an efficient statistic for distinguishing fathers from nonfathers, even in the presence of minisatellite mutation. Band-sharing estimates between a claimed parent and a child can also distinguish paternity from nonpaternity, though with less efficiency than comparison of a trio of mother, child, and alleged father.

Fertility in a male with trisomy 21

We review the published reports on reproduction in cases of non-mosaic trisomy 21 (Down's syndrome) and present the first fully documented case of a non-mosaic male with Down's syndrome fathering a pregnancy, a fact which has important implications in the light of caring for these people in the community.

The influence of ribonucleoside triphosphates, and other factors, on the formation of very-salt-stable RNA-polymerase . su+III-tRNA(tRNATyr)-promoter complexes

The formation of a stable RNA-polymerase . su+III-tRNA-promoter complex was found to require sigma factor and the incorporation of ribonucleoside triphosphates which match the 5' sequence of the su+III tRNA transcript. This complex, stable to at least 2 M KCl, can be retained on a Millipore filter. Its formation closely parallels the extent of transcription obtained from the su+III tRNA promoter in response both to increasing ionic strength and to temperature during incubation of RNA polymerase with the DNA. The RNA-polymerase . DNA complex retained during this assay therefore appears to relate directly to that formed during promoter-directed transcription. The formation of RNA-polymerase . su+III-tRNA-promoter complexes is sensitive to the presence of ppGpp.

Selective inhibition of tRNATyr transcription by guanosine 3'-diphosphate 5'-diphosphate

Guanosine 3'-diphosphate 5'-diphosphate (ppGpp) selectively reduces the synthesis of su+III tRNA from omega 80 psu+III DNA relative to the synthesis of omega 80 RNA in a system in vitro containing DNA and Escherichia coli RNA polymerase holoenzyme as the sole macromolecular components. The response of su+III tRNA synthesis to increasing salt and to temperature in the presence of ppGpp suggests that the nucleotide may reduce the affinity of the enzyme for su+III promoters. The Ki for the selective inhibition of tRNA synthesis by ppGpp is 4 muM in contrast to the value of 150 muM for the inhibition of rRNA synthesis.