GABAA receptor β3 subunit gene and psychiatric morbidity in a post-traumatic stress disorder population

GABAergic systems have been implicated in the pathogenesis of anxiety, depression and insomnia. These symptoms are part of the core and comorbid psychiatric disturbances in post-traumatic stress disorder (PTSD) In a sample of Caucasian male PTSD patients, dinucleotide repeat polymorphisms of the GABAA receptor beta3 subunit gene were compared to scores on the General Health Questionnaire-28 (GHQ). As the major allele at this gene locus (GABRB3) was GI, the alleles were divided into GI and non-GI groups. On the total score of the GHQ, which comprises the somatic symptoms, anxiety/insomnia, social dysfunction and depression subscales, patients with the GI non-GI genotype had a significantly higher score when compared to either the G1G1 genotype (alpha = 0.01) or the non-GI non-GI genotype (alpha = 0.05). No significant difference was found between the G1G1 and non-Gl non-G1 genotypes. When the GI non-G1 heterozygotes were compared to the combined G1G1 and non-GI non-GI homozygotes, a significantly higher total GHQ score was found in the heterozygotes (P = 0.002). These observations suggest a heterosis effect. Further analysis of GHQ subscale scores showed that heterozygotes compared to the combined homozygotes had higher scores on the somatic symptoms (P = 0.006), anxiety/insomnia (P = 0.003), social dysfunction (P = 0.054) and depression (P = 0.004) subscales. In conclusion, the present study indicates that in a population of PTSD patients, heterozygosity of the GABRB3 major (GI) allele confers higher levels of somatic symptoms, anxiety/insomnia, social dysfunction and depression than found in homozygosity. (C) 2001 Elsevier Science Ireland Ltd. All rights reserved.

Energy cost of physical activity in cystic fibrosis

Objective: The purpose of this study was to compare the energy cost of standardized physical activity (ECA) between patients with cystic fibrosis (CF) and healthy control subjects. Design: Cross-sectional study using patients with CF and volunteers from the community. Setting: University laboratory. Subjects: Fifteen patients (age 24.6 +/- 4.6 y) recruited with consent from their treating physician and 16 healthy control subjects (age 25.3 +/- 3.2) recruited via local advertisement. Interventions. Patients and controls walked on a computerised treadmill at 1.5 km/h for 60 min followed by a 60 min recovery period and, on a second occasion, cycled at 0.5 kp (kilopond), 30 rpm followed by a 60 min recovery. The ECA was measured via indirect calorimetry. Resting energy expenditure (REE), nutritional status, pulmonary function and genotype were determined. Results: The REE in patients was significantly greater than the REE measured in controls (P = 0.03) and was not related to the severity of lung disease or genotype. There was a significant difference between groups when comparing the ECA for walking kg root FFM (P = 0.001) and cycling kg root FFM (P = 0.04). The ECA for each activity was adjusted (ECA(adj)) for the contribution of REE (ECA kJ kg root FFM 120 min(-1) - REE kJ kg root FFM 120 min(-1)). ECA(adj) revealed a significant difference between groups for the walking protocol (P = 0.001) but no difference for the cycling protocol (P = 0.45). This finding may be related to the fact that the work rate during walking was more highly regulated than during cycling. Conclusions ECA in CF is increased and is likely to be explained by an additional energy-requiring component related to the exercise itself and not an increased REE. Sponsorship. The Prince Charles Hospital Foundation; MLR was in receipt of a QUTPRA Scholarship.

Biometrical Genetics

Biometrical genetics is the science concerned with the inheritance of quantitative traits. In this review we discuss how the analytical methods of biometrical genetics are based upon simple Mendelian principles. We demonstrate how the phenotypic covariance between related individuals provides information on the relative importance of genetic and environmental factors influencing that trait, and how factors such as assortative mating, gene-environment correlation and genotype-environment interaction complicate such interpretations. Twin and adoption studies are discussed as well as their assumptions and limitations. Structural equation modeling (SEM) is introduced and we illustrate how this approach may be applied to genetic problems. In particular, we show how SEM can be used to address complicated issues such as analyzing the causes of correlation between traits or determining the direction of causation (DOC) between variables. (C) 2002 Elsevier Science B.V. All rights reserved.

Gene-Environment Interaction Effects on Behavioral Variation and Risk of Complex Disorders: The Example of Alcoholism and Other Psychiatric Disorders

There have been few replicated examples of genotype x environment interaction effects on behavioral variation or risk of psychiatric disorder. We review some of the factors that have made detection of genotype x environment interaction effects difficult, and show how genotype x shared environment interaction (GxSE) effects are commonly confounded with genetic parameters in data from twin pairs reared together. Historic data on twin pairs reared apart can in principle be used to estimate such GxSE effects, but have rarely been used for this purpose. We illustrate this using previously published data from the Swedish Adoption Twin Study of Aging (SATSA), which suggest that GxSE effects could account for as much as 25% of the total variance in risk of becoming a regular smoker. Since few separated twin pairs will be available for study in the future, we also consider methods for modifying variance components linkage analysis to allow for environmental interactions with linked loci.

A genomewide search for type 2 diabetes-susceptibility genes in indigenous Australians

The prevalence of type 2 diabetes among Australian residents is 7.5%; however, prevalence rates up to six times higher have been reported for indigenous Australian communities. Epidemiological evidence implicates genetic factors in the susceptibility of indigenous Australians to type 2 diabetes and supports the hypothesis of the thrifty genotype, but, to date, the nature of the genetic predisposition is unknown. We have ascertained clinical details from a community of indigenous Australian descent in North Stradbroke Island, Queensland. In this population, the phenotype is characterized by severe insulin resistance. We have conducted a genomewide scan, at an average resolution of 10 cM, for type 2 diabetes-susceptibility genes in a large multigeneration pedigree from this community. Parametric linkage analysis undertaken using FASTLINK version 4.1p yielded a maximum two-point LOD score of +2.97 at marker D2S2345. Multipoint analysis yielded a peak LOD score of +3.9

Development of a mungbean (Vigna radiata) RFLP linkage map and its comparison with lablab (Lablab purpureus) revelas a high level of colinearity between the two genomes

A genetic linkage map of mungbean (Vigna radiata, 2n = 2x = 22) consisting of 255 RFLP loci was developed using a recombinant inbred population of 80 individuals. The population was derived from an intersubspecific cross between the cultivated mungbean variety 'Berken' and a wild mungbean genotype 'ACC 41' (V radiata subsp. sublobata). The total length of the map, which comprised 13 linkage groups, spanned 737.9 cM with an average distance between markers of 3.0 cM and a maximum distance between linked markers of 15.4 cM. The mungbean map was compared to a previously published map of lablab (Lablab purpureus, 2n = 2x = 24) using a common set of 65 RFLP probes. In contrast to some other comparative mapping studies among members of the Fabaceae, where a high level of chromosomal rearrangement has been observed, marker order between mungbean and lablab was found to be highly conserved. However, the two genomes have apparently accumulated a large number of duplications/deletions after they diverged.

The effects of temperature on the growth, survival and biomass of different families of juvenile Penaeus japonicus Bate

Variation in the growth, survival and change in total biomass (termed biomass increase) of different families of juvenile Penaeus japonicus was investigated over a range of temperatures in controlled laboratory experiments. In the first experiment, the effects of temperature on six families of juveniles were examined over a broad range of temperatures (24 to 30 degreesC). In the second experiment, the effects of temperature on six more families of juveniles were examined over a narrower range of temperatures (27.5 to 31.2 degreesC). Over the broad temperature range, mean growth and biomass increase were highest at 27 degreesC and mean survival was highest at 24 degreesC. Mean growth was lowest at 24 degreesC, whilst survival and biomass increase were lowest at 30 degreesC. However, there was a significant interaction between family and temperature, with some families tolerating a broader range of temperatures than others. As a result, the ranking of families in relation to growth, survival and biomass increase changed at each temperature. This effect was more pronounced for survival than for growth. Over the narrower range, temperature significantly affected growth, survival and biomass increase, but there was no significant interaction between family and temperature. Growth, survival and biomass increase were significantly lower at 31.2 than at 27.5 and 29.2 degreesC. These results suggest that if grow-out conditions for P. japonicus vary by more than a few degrees, interactions between family and temperature could affect the efficiency of selection. The results also suggest that the family x temperature interaction may have a more pronounced effect on survival than on growth. Crown Copyright (C) 2002 Published by Elsevier Science B.V. All rights reserved.

Detection and stability of Japanese encephalitis virus RNA and virus viability in dead infected mosquitoes under different storage conditions

A semi-nested polymerase chain reaction (PCR) was evaluated for detection of Japanese encephalitis (JE) virus in infected mosquitoes stored under simulated northern Australian summer conditions. The effect of silica gel, thymol, and a combination of the two on RNA stability and virus viability in dead mosquitoes were also examined. While JE virus RNA was relatively stable in mosquitoes held for up to 14 days after death, viable virus was not detected after day 1. Thymol vapor inhibited fungal contamination. Detection of single mosquitoes infected with JE virus in large pools of mosquitoes was also investigated. Single laboratory-infected mosquitoes were detected in pools of less than or equal to200 mosquitoes and in pools diluted to 0.2/100 and 0.1/100 mosquitoes, using the semi-nested PCR. However, the ability to detect live virus decreased as pool size increased. The semi-nested PCR proved more expensive than virus isolation for pools of 100 mosquitoes. However, the semi-nested PCR was faster and more economical using larger pools. Results indicate that surveillance of JE virus in mosquitoes using the semi-nested PCR is an alternative to monitoring seroconversions in sentinel pigs.

Shoot control of hypernodulation and aberrant root formation in the har1-1 mutant of Lotus japonicus

The har1-1 mutant of Lotus japonicus B-129-S9 Gifu is characterized by two phenotypes: greater than normal nodulation (hypernodulation) and significantly inhibited root growth in the presence of its microsymbiont Mesorhizobium loti strain NZP2235. We demonstrate that the two traits co-segregate, suggesting a single genetic alteration involving developmental pleiotropy. A cross between the mutant and genotype Funakura (with wild-type root and nodule morphology) demonstrated Mendelian recessive segregation of both phenotypes (root and nodule) in 216 F2 individuals. Using DNA-amplification fingerprinting polymorphisms in Gifu har1-1 and Funakura, the mutant locus was positioned between two markers at about 7 and 13 cM distance. Reciprocal hypocotyl grafting of shoots and roots showed that the hypernodulation and reduced root phenotypes are both predominantly controlled by the shoot.

Germline BRCA1 promoter deletions in UK and Australian familial breast cancer patients: Identification of a novel deletion consistent with BRCA1 :psi VBRCA1 recombination

Inherited susceptibility to breast cancer results from germline mutations in one of a number of genes including BRCA1. A significant number of BRCA1-linked familial breast cancer patients, however, have no detectable BRCA1 mutation. This could be due in part to the inability of commonly used mutation-detection techniques to identify mutations outside the BRCA1 coding region. This paper addresses the hypothesis that non coding region mutations, specifically in the BRCA1 promoter, account for some of these cases. We describe a new and detailed restriction map of the 5' region of the BRCA1 gene including the nearby NBR2, psiBRCA1, and NBR1 genes and the isolation of a number of new informative hybridization probes suitable for Southern analysis. Using this information we screened DNA from lymphoblastoid cell-lines made from 114 UK familial breast cancer patients and detected one large deletion in the 5' region of BRCA1. We show that the breakpoints for this deletion are in BRCA1 intron 2 and between NBR2 and exon 2 of psiBRCA1, raising the possibility that this deletion arose via a novel mechanism involving BRCA1:psiBRCA1 recombination. We have also screened 60 familial breast cancer patients from the Australian population, using an amplification refractory mutation system (ARMS) technique described previously by our group, and found one patient with a genotype consistent with a BRCA1 promoter deletion. These findings indicate that germline BRCA1 promoter deletions are a rare and yet significant mutation event and that they could arise via a novel genetic mechanism. Hum Mutat 19:435-442, 2002. (C) 2002 Wiley-Liss, Inc.

Alterations in Plasmodium falciparum genotypes during sequential infections suggest the presence of strain specific immunity

Many of the asexual stage Plasmodium falciparum proteins that are the targets of host protective responses are markedly polymorphic. The full repertoire of diversity is not defined for any antigen. Most studies have focused on the genes encoding merozoite surface proteins 1 and 2 (MSP1, MSP2). We explored the extent of diversity of some of the less studied merozoite surface antigens and analyzed the degree of complexity of malaria field isolates by deriving nucleotide sequences of several antigens. We have determined the genotype of apical membrane antigen 1 (AMA1) in a group of 30 field samples, collected over 29 months, from individuals living in an area of intense malaria transmission in Irian Jaya, identifying 14 different alleles. AMA1 genotyping was combined with previously determined MSP2 typing. AMA1 had the greatest power in distinguishing between isolates but methodological problems, especially when mixed infections are present, suggest it is not an ideal typing target. MSP1, MSP3, and glutamate-rich protein genotypes were also determined from a smaller group of samples, and all results were combined to derive an extended antigenic haplotype. Within this subset of 10 patients, nine different genotypes could be discerned; however, five patients were all infected with the same strain. This strain was present in individuals from two separate villages and was still present 12 months later. This strain was predominant at the first time point but had disappeared at the fourth time point. This significant change in malaria genotypes could be due to strain-specific immunity developing in this population.

Spatial structure and habitat variation in a grasshopper hybrid zone

A hybrid zone between the grasshoppers Chorthippus brunneus and C. jacobsi (Orthoptera: Acrididae) in northern Spain has been analyzed for variation in morphology and ecology. These species are readily distinguished by the number of stridulatory pegs on the hind femur. Both sexes are fully winged and inhabit disturbed habitats throughout the study area. We develop a maximum-likelihood approach to fitting a two-dimensional cline to geographical variation in quantitative traits and for estimating associations of population mean with local habitat. This method reveals a cline in peg number approximately 30 km south of the Picos de Europa Mountains that shows substantial deviations in population mean compared with the expectations of simple tension zone models. The inclusion of variation in local vegetation in the model explains a significant proportion of the residual variation in peg number, indicating that habitat-genotype associations contribute to the observed spatial pattern. However, this association is weak, and a number of populations continue to show strong deviations in mean even after habitat is included in the final model. These outliers may be the result of long-distance colonization of sites distant from the cline center or may be due to a patchy pattern of initial contact during postglacial expansion. As well as contrasting with the smooth hybrid zones described for Chorthippus parallelus, this situation also contrasts with the mosaic hybrid zones observed in Gryllus crickets and in parts of the hybrid zone between Bombina toad species, where habitat-genotype associations account for substantial amounts of among-site variation.

Simulating growth, development, and yield of tillering pearl millet. III. Biomass accumulation and partitioning

Pearl millet landraces from Rajasthan, India, yield significantly less than improved cultivars under optimum growing conditions, but not under stressed conditions. To successfully develop a simulation model for pearl millet, capable of capturing such genotype x environment (G x E) interactions for grain yield, we need to understand the causes of the observed yield interaction. The aim of this paper is to quantify the key parameters that determine the accumulation and partitioning of biomass: the,light extinction coefficient, radiation use efficiency (RUE), pattern of dry matter allocation to the leaf blades, the determination of grain number, and the rate and duration of dry matter accumulation into individual grains. We used data on improved cultivars and landraces, obtained from both published and unpublished sources collected at ICRISAT, Patancheru, India. Where possible, the effects of cultivar and axis (main shoot vs. tillers) on these parameters were analysed, as previous research suggested that G x E interactions for grain yield are associated with differences in tillering habit. Our results indicated there were no cultivar differences in extinction coefficient, RUE, and biomass partitioning before anthesis, and differences between axes in biomass partitioning were negligible. This indicates there was no basis for cultivar differences in the potential grain yield. Landraces, however, produced consistently less grain yield for a given rate of dry matter accumulation at anthesis than did improved cultivars. This was caused by a combination of low grain number and small grain size. The latter was predominantly due to a lower grain growth rate, as genotypic differences in the duration of grain filling were relatively small. Main shoot and tillers also had a similar duration of grain filling. The low grain yield of the landraces was associated with profuse nodal tillering, supporting the hypothesis that grain yield was below the potential yield that could be supported by assimilate availability. We hypothesise this is a survival strategy, which enhances the prospects to escape the effects of stress around anthesis. (C) 2002 E.J. van Oosterom. Published by Elsevier Science B.V. All rights reserved.

Phase variation in meningococcal lipooligosaccharide biosynthesis genes

Neisseria meningitidis expresses a range of lipooligosaccharide (LOS) structures, comprising of at least 13 immunotypes (ITs). Meningococcal LOS is subject to phase variation of its terminal structures allowing switching between ITs, which is proposed to have functional significance in disease. The objectives of this study were to investigate the repertoire of structures that can be expressed in clinical isolates, and to examine the role of phase-variable expression of LOS genes during invasive disease. Southern blotting was used to detect the presence of LOS biosynthetic genes in two collections of meningococci, a global set of strains previously assigned to lineages of greater or lesser virulence, and a collection of local clinical isolates which included paired throat and blood isolates from individual patients. Where the phase-variable genes lgtA, lgtC or IgtG were identified, they were amplified by PCR and the homopolymeric tracts, responsible for their phase-variable expression, were sequenced. The results revealed great potential for variation between alternate LOS structures in the isolates studied, with most strains capable of expressing several alternative terminal structures. The structures predicted to be currently expressed by the genotype of the strains agreed well with conventional immunotyping. No correlation was observed between the structural repertoire and virulence of the isolate. Based on the potential for LOS phase variation in the clinical collection and observations with the paired patient isolates, our data suggest that phase variation of LOS structures is not required for translocation between distinct compartments in the host. (C) 2002 Published by Elsevier Science B.V. on behalf of the Federation of European Microbiological Societies.

The impact of genotyping error on haplotype reconstruction and frequency estimation

The choice of genotyping families vs unrelated individuals is a critical factor in any large-scale linkage disequilibrium (LD) study. The use of unrelated individuals for such studies is promising, but in contrast to family designs, unrelated samples do not facilitate detection of genotyping errors, which have been shown to be of great importance for LD and linkage studies and may be even more important in genotyping collaborations across laboratories. Here we employ some of the most commonly-used analysis methods to examine the relative accuracy of haplotype estimation using families vs unrelateds in the presence of genotyping error. The results suggest that even slight amounts of genotyping error can significantly decrease haplotype frequency and reconstruction accuracy, that the ability to detect such errors in large families is essential when the number/complexity of haplotypes is high (low LD/common alleles). In contrast, in situations of low haplotype complexity (high LD and/or many rare alleles) unrelated individuals offer such a high degree of accuracy that there is little reason for less efficient family designs. Moreover, parent-child trios, which comprise the most popular family design and the most efficient in terms of the number of founder chromosomes per genotype but which contain little information for error detection, offer little or no gain over unrelated samples in nearly all cases, and thus do not seem a useful sampling compromise between unrelated individuals and large families. The implications of these results are discussed in the context of large-scale LD mapping projects such as the proposed genome-wide haplotype map.