High direct estimate of the mutation rate in the mitochondrial genome of Caenorhabditis elegans

Mutations in the mitochondrial genome have been implicated in numerous human genetic disorders and offer important data for phylogenetic, forensic, and population genetic studies. Using a long-term series of Caenorhabditis elegans mutation accumulation lines, we performed a wide-scale screen for mutations in the mitochondrial genome that revealed a mutation rate that is two orders of magnitude higher than previous indirect estimates, a highly biased mutational spectrum, multiple mutations affecting coding function, as well as mutational hotspots at homopolymeric nucleotide stretches.

Consequences of epilepsy in the developing brain: implications for surgical management

The developing brain is highly susceptible to seizures, as demonstrated by both human and animal studies. Until recently, the brain has been considered to be relatively resistant to damage induced by seizures early in life. Accumulating evidence in animal models now suggests that early seizures can cause structural and physiologic changes in developing neural circuits that result in permanent alterations in the balance between neuronal excitation and inhibition, deficits in cognitive function, and increased susceptibility to additional seizures. The disruption of normal neuronal activity by seizures can affect multiple developmental processes, resulting in these long-lasting changes. These data should be considered in the clinical approach to children with intractable epilepsy and suggest that early intervention may avoid some of these long-term neurologic deficits.

Molecular characterization of rotavirus in Ireland: detection of novel strains circulating in the population

A collection of three hundred thirty rotavirus-positive stool samples from children with diarrhea in the southern and eastern regions of Ireland between 1997 and 1999 were submitted to the Molecular Diagnostics Unit of the Cork Institute of Technology, Cork, Ireland, for investigation. These strains were characterized by several methods, including polyacrylamide gel electropherotyping and G and P genotyping. A subset of the G types was confirmed by nucleic acid sequencing. The most prevalent types found in this collection included G1P[8] (n = 106; 32.1%), G2P[4] (n = 94; 28.5%), and G4P[8] (n = 37; 11.2%). Novel strains were also detected, including G1P[4] (n = 19; 5.8%), and G4P[4] (n = 2; 0.6%). Interestingly, mixed infections accounted for 18.8% (n = 62) of the total collection, with only 3% (n = 10) which were not G and/or P typeable. Significantly, six G8 and five G9 strains were identified as part of mixed infections. These strains have not previously been identified in Irish children, suggesting a greater diversity in rotavirus strains currently circulating in Ireland.

The fitness effects of spontaneous mutations in Caenorhabditis elegans

Spontaneous mutation to mildly deleterious alleles has emerged as a potentially unifying component of a variety of observations in evolutionary genetics and molecular evolution. However, the biological significance of hypotheses based on mildly deleterious mutation depends critically on the rate at which new mutations arise and on their average effects. A long-term mutation-accumulation experiment with replicate lines of the nematode Caenorhabditis elegans maintained by single-progeny descent indicates that recurrent spontaneous mutation causes approximately 0.1% decline in fitness per generation, which is about an order of magnitude less than that suggested by previous studies with Drosophila. Two rather different approaches, Bateman-Mukai and maximum likelihood, suggest that this observation, along with the observed rate of increase in the variance of fitness among lines, is consistent with a genomic deleterious mutation rate for fitness of approximately 0.03 per generation and with an average homozygous effect of approximately 12%. The distribution of mutational effects for fitness appears to have a relatively low coefficient of variation, being no more extreme than expected for a negative exponential, and for one composite fitness measure (total progeny production) approaches constancy of effects. These results are derived from assays in a benign environment. At stressful temperatures, estimates of the genomic deleterious mutation rate (for genes expressed at such temperatures) is sixfold lower, whereas those for the average homozygous effect is approximately eightfold higher. Our results are reasonably compatible with existing estimates for flies, when one considers the differences between these species in the number of germ-line cell divisions per generation and the magnitude of transposable element activity.

Expression and role of superoxide dismutases (SOD) in pathogenic bacteria

This review will be limited to the expression and roles of the family of metalloenzymes superoxide dismutases in pathogenic bacteria. Only animal pathogens will be described, with particular emphasis on those causing disease in man.

Long-term consequences of early postnatal seizures on hippocampal learning and plasticity

Neural activity influences the patterning of synaptic connections and functional organization of developing sensory and motor systems, but the long-term consequences of intense neural activity such as seizures in the developing hippocampus are not adequately understood. To evaluate the possibility that abnormal neural activity during early development may have long-term functional effects in hippocampal circuitry that plays a role in learning, memory and epilepsy, functional properties of hippocampal circuitry were assessed in adult rats that had experienced seizures induced by kainic acid on specific days during early postnatal development. Although previous studies have suggested that the immature hippocampus is relatively resistant to seizure-induced alterations compared with adults, independent behavioural and physiological experiments demonstrated that seizures evoked by kainic acid during early postnatal development induced a long-term loss of hippocampal plasticity manifesting as reduced capacity for long-term potentiation, reduced susceptibility to kindling, and impaired spatial learning, which was associated with enhanced paired-pulse inhibition in the dentate gyrus. The enhancement of inhibition and loss of plasticity were maximal when the seizures occurred on the first day of life, but were also observed when seizures were induced as late as postnatal day 14, which delimited a period of postnatal susceptibility in the developing rat hippocampus when disruption of normal neural activity by seizures produced consistent effects on a hippocampal-dependent behaviour and several forms of hippocampal plasticity implicated in learning, memory and the development of epilepsy in adulthood.

Organellar genes: why do they end up in the nucleus?

Many mitochondrial and plastid proteins are derived from their bacterial endosymbiotic ancestors, but their genes now reside on nuclear chromosomes instead of remaining within the organelle. To become an active nuclear gene and return to the organelle as a functional protein, an organellar gene must first be assimilated into the nuclear genome. The gene must then be transcribed and acquire a transit sequence for targeting the protein back to the organelle. On reaching the organelle, the protein must be properly folded and modified, and in many cases assembled in an orderly manner into a larger protein complex. Finally, the nuclear copy must be properly regulated to achieve a fitness level comparable with the organellar gene. Given the complexity in establishing a nuclear copy, why do organellar genes end up in the nucleus? Recent data suggest that these genes are worse off than their nuclear and free-living counterparts because of a reduction in the efficiency of natural selection, but do these population-genetic processes drive the movement of genes to the nucleus? We are now at a stage where we can begin to discriminate between competing hypotheses using a combination of experimental, natural population, bioinformatic and theoretical approaches.

A comparison of telemedicine with face-to-face consultations for trauma management

We compared the accuracy of teleconsultations for minor injuries with face-to-face consultations. Two hundred patients were studied. Colour change, swelling, decreased movement, tenderness, instability, radiological examination, severity of illness, treatment and diagnosis were recorded for both telemedicine and face-to-face consultations. Colour change showed an accuracy of 97%, presence of swelling or deformity of 98%, diminution of joint movement of 95%, presence of tenderness of 97%, weight bearing and gait of 99%, and radiological diagnosis of 98%. The severity of illness or injury was overestimated in one case and underestimated in five cases. Treatment was over-prescribed in one case and under-prescribed in three cases. The final diagnosis was correct in all but the two cases in which mistakes were made in the teleradiology. Overall, there was good accuracy using teleconsultations.

Discrimination and instructional comprehension: guided discretion, racial bias, and the death penalty

This study links two previously unrelated lines of research: the lack of comprehension of capital penalty-phase jury instructions and discriminatory death sentencing. Jury-eligible subjects were randomly assigned to view one of four versions of a simulated capital penalty trial in which the race of defendant (Black or White) and the race of victim (Black or White) were varied orthogonally. Dependent measures included a sentencing verdict (life without the possibility of parole or the death penalty), ratings of penalty phase evidence, and a test of instructional comprehension. Results indicated that instructional comprehension was poor overall and that, although Black defendants were treated only slightly more punitively than White defendants in general, discriminatory effects were concentrated among participants whose comprehension was poorest. In addition, the use of penalty phase evidence differed as a function of race of defendant and whether the participant sentenced the defendant to life or death. The study suggest that racially biased and capricious death sentencing may be in part caused or exacerbated by the inability to comprehend penalty phase instructions.

The subdominant hand increases in the efficacy of voluntary alterations in bimanual coordination

Subjects performed a bimanual circle-tracing task in time with an auditory metronome while restricted to moving with either proximal or distal musculature of the upper limb. Patterns were made in symmetric or asymmetric directions with respect to the midline. Symmetric patterns were more stable than asymmetric patterns. In response to a visual stimulus, subjects reversed the direction of one limb. Unwanted disruptions (momentary or lasting reversals) in the limb contralateral to the reversing limb were observed in 48% of trials. Incidence of disruption was equivalent between postures, but occurred more frequently when the dominant hand reversed direction. This result is consistent with anisotropy in coupling between hands and reveals a unifying constraint between spontaneous and intentional dynamics in bimanual coordination.

Safety and acceptability of a baggy latex condom

A total of 104 couples participated in a randomized crossover trial to compare a new baggy condom with a straight-shaft condom produced by the same manufacturer. Participants completed a coital log after using each condom. All couples used five condoms of each type. Among 102 couples who did not report major deviations from the protocol, the breakage rate was eight of 510 (1.6%) for the baggy condom, and six of 510 (1.2%) for the standard condom (rate difference, RD = 0. 4%, 95% confidence interval of the RD, CI = -1.0%; +1.8%). Slippage was reported in 50 baggy condom logs and in 58 standard condom logs; the slippage rate was 50 of 510 (9.8%) for the baggy condom, and 58 of 510 (11.4%) for the standard condom (RD = -1.6%, 95% CI = -5.4%; +2.2%). Slippage was most often partial (<1 inch) and may not indicate condom failure. Severe slippage rates were 11 of 510 (2.2%) for the baggy condom, and 18 of 510 (3.5%) for the standard condom (RD = -1.4%, 95% CI = -3.4%; +0.7%). The findings support the conclusion that the two condoms are equivalent with respect to breakage and slippage. The participants appeared to prefer the baggy condom, suggesting that the new product may be more acceptable to the public than the traditional straight-shaft condoms, and may be easier to use consistently over long time periods.

Financial incentives and primary care provision in Britain: do general practitioners maximise their income?

The system of remunerating general practitioners (GPs) in Britain underwent significant changes in April 1990 with the implementation of a new contract between individual GPs and health authorities. The changes were a precursor to a wide-ranging programme of reforms of the British National Health Service. This paper investigates the relationship between financial incentives and the provision of primary health care services in Britain. A comprehensive anonymized data set was used, comprising information on 208 general practices in Scotland which serve just under one million people. An econometric model was tested to identify the determinants of cross-practice variation in the magnitude of the changes in GPs' remuneration levels between the two contracts. A linear programming model was used to examine the GPs' response to the financial incentives built into the new contract. The results of the econometric model indicated that the main beneficiaries of the 1990 contract were the practices which had expanded over the 1989-92 period, re-structured the GPs' partnership and made use of managerial skills by employing a practice manager; those practices also had larger lists in 1992 and relatively more patients attracting deprivation payments. The linear programming model showed that only a small minority of the practices (4.8%) maximised the remuneration from the new contract. Optimal solutions concerning income maximization strategies identified financial disincentives in the fee structure of the remuneration system associated with the provision of selected services and the care of particular groups of patients. The successful adoption of these strategies would involve cream skimming and selective service provision. However, there is no conclusive evidence of British GPs engaging in such activities.

Recurrent excitatory connectivity in the dentate gyrus of kindled and kainic acid-treated rats

Repeated seizures induce mossy fiber axon sprouting, which reorganizes synaptic connectivity in the dentate gyrus. To examine the possibility that sprouted mossy fiber axons may form recurrent excitatory circuits, connectivity between granule cells in the dentate gyrus was examined in transverse hippocampal slices from normal rats and epileptic rats that experienced seizures induced by kindling and kainic acid. The experiments were designed to functionally assess seizure-induced development of recurrent circuitry by exploiting information available about the time course of seizure-induced synaptic reorganization in the kindling model and detailed anatomic characterization of sprouted fibers in the kainic acid model. When recurrent inhibitory circuits were blocked by the GABA(A) receptor antagonist bicuculline, focal application of glutamate microdrops at locations in the granule cell layer remote from the recorded granule cell evoked trains of excitatory postsynaptic potentials (EPSPs) and population burst discharges in epileptic rats, which were never observed in slices from normal rats. The EPSPs and burst discharges were blocked by bath application of 1 microM tetrodotoxin and were therefore dependent on network-driven synaptic events. Excitatory connections were detected between blades of the dentate gyrus in hippocampal slices from rats that experienced kainic acid-induced status epilepticus. Trains of EPSPs and burst discharges were also evoked in granule cells from kindled rats obtained after > or = 1 wk of kindled seizures, but were not evoked in slices examined 24 h after a single afterdischarge, before the development of sprouting. Excitatory connectivity between blades of the dentate gyrus was also assessed in slices deafferented by transection of the perforant path, and bathed in artificial cerebrospinal fluid (ACSF) containing bicuculline to block GABA(A) receptor-dependent recurrent inhibitory circuits and 10 mM [Ca(2+)](o) to suppress polysynaptic activity. Low-intensity electrical stimulation of the infrapyramidal blade under these conditions failed to evoke a response in suprapyramidal granule cells from normal rats (n = 15), but in slices from epileptic rats evoked an EPSP at a short latency (2.59 +/- 0.36 ms) in 5 of 18 suprapyramidal granule cells. The results are consistent with formation of monosynaptic excitatory connections between blades of the dentate gyrus. Recurrent excitatory circuits developed in the dentate gyrus of epileptic rats in a time course that corresponded to the development of mossy fiber sprouting and demonstrated patterns of functional connectivity corresponding to anatomic features of the sprouted mossy fiber pathway.

The probability of duplicate gene preservation by subfunctionalization

It has often been argued that gene-duplication events are most commonly followed by a mutational event that silences one member of the pair, while on rare occasions both members of the pair are preserved as one acquires a mutation with a beneficial function and the other retains the original function. However, empirical evidence from genome duplication events suggests that gene duplicates are preserved in genomes far more commonly and for periods far in excess of the expectations under this model, and whereas some gene duplicates clearly evolve new functions, there is little evidence that this is the most common mechanism of duplicate-gene preservation. An alternative hypothesis is that gene duplicates are frequently preserved by subfunctionalization, whereby both members of a pair experience degenerative mutations that reduce their joint levels and patterns of activity to that of the single ancestral gene. We consider the ways in which the probability of duplicate-gene preservation by such complementary mutations is modified by aspects of gene structure, degree of linkage, mutation rates and effects, and population size. Even if most mutations cause complete loss-of-subfunction, the probability of duplicate-gene preservation can be appreciable if the long-term effective population size is on the order of 10(5) or smaller, especially if there are more than two independently mutable subfunctions per locus. Even a moderate incidence of partial loss-of-function mutations greatly elevates the probability of preservation. The model proposed herein leads to quantitative predictions that are consistent with observations on the frequency of long-term duplicate gene preservation and with observations that indicate that a common fate of the members of duplicate-gene pairs is the partitioning of tissue-specific patterns of expression of the ancestral gene.

Characteristics of effective village treatment assistants: the Kongwa Trachoma Project

PURPOSE

Mass treatment of entire communities with tetracycline eye ointment is one method for treatment of hyperendemic trachoma. Village Treatment Assistants (VTAs) are often recruited to implement mass treatment in their neighborhoods. We determined characteristics of these volunteers that were associated with effective treatment outcomes.

METHODS

Three villages received mass treatment with tetracycline ointment daily for four weeks as part of a clinical trial. Community members selected VTAs to administer the ointment. Trachoma status was assessed by grading photographs of the tarsal conjunctiva in a sample of children randomly selected from households in each village. Change in trachoma status was determined from baseline to one month post treatment. VTA performance outcome was "good" if there was improvement in the majority of the children treated by the VTA, "poor" if the majority worsened, and "neutral" if there was neither improvement nor worsening on average. Trained interviewers administered a questionnaire measuring socioeconomic and demographic variables to 82% of all VTAs.

RESULTS

A total of 280 VTAs (229 with questionnaire) were evaluated: 36.8% had good outcomes and 12.5% had poor outcomes. Those VTAs with poor outcomes tended to be unmarried females (OR = 11.73) and those who used a bicycle to carry out treatment activities (OR = 4.16). Formal education or prior experience as a health worker were not predictors of performance.

CONCLUSION

Community selection and effective, non-formal, training are key components for the use of VTAs in mass treatment campaigns. Prior education or health training does not play a major role in effectiveness. The possible effects of gender roles in the community need to be considered in program design.

Incidence of trichiasis in a cohort of women with and without scarring

BACKGROUND

Blindness from trachoma is a significant problem for many underdeveloped countries. While active trachoma is common in children, trichiasis, the potentially blinding sequella, develops in adulthood and affects mainly women. Little is known about factors associated with the development of trichiasis.

METHODS

The 7-year incidence of trichiasis and its association with ocular chlamydia infection was examined in a cohort of women from a hyperendemic area. A total of 4,932 women 18 years and older, living in 11 villages in Central Tanzania, were examined in 1989. A follow-up examination in 1996 was performed on all women with scars living in six of the 11 villages and on a random sample of women without scars from the same villages. Trachoma was graded clinically, chlamydia infection was ascertained at follow-up using polymerase chain reaction-enzyme immunoassay (PCR-EIA).

RESULTS

A total 523 of the women with scars and 503 of the women without scars were re-examined. Forty-eight of the women with scars (incidence, 9.2%) and three of the women without scars (0.6%) developed trichiasis in the 7-year period. Prevalence of chlamydia infection was significantly higher in the group with scars (11.7% versus 7.1%). Trichiasis cases were more likely to be older, and to have chlamydia infection at follow-up odds ratio (95% confidence interval) 2.5 (1.1-5.7).

CONCLUSION

The 7-year incidence rate in the population with scars was high, over 1% per year. Ocular chlamydia infection was more common in the group with scars at baseline and was also associated with being a trichiasis case, suggesting the importance of potentially long-term chlamydia infection in the progression to trichiasis. Antibiotic distribution programmes for trachoma control should include women with scars.

Nitric oxide synthetase and Helicobacter pylori in patients undergoing appendicectomy

BACKGROUND: This study was designed to determine whether Helicobacter pylori forms part of the normal microenvironment of the appendix, whether it plays a role in the pathogenesis of acute appendicitis, and whether it is associated with increased expression of inducible nitric oxide synthetase (iNOS) in appendicular macrophages. METHODS: Serology for H. pylori was performed on 51 consecutive patients undergoing emergency appendicectomy. Appendix samples were tested for urease activity, cultured and stained for H. pylori, graded according to the degree of inflammatory infiltrate, and probed immunohistochemically for iNOS expression. RESULTS: The mean age of the patients was 21 (range 7-51) years. Seventeen patients (33 per cent) were seropositive for H. pylori but no evidence of H. pylori was found in any appendix specimen. However, an enhanced inflammatory cell infiltration was observed in seropositive patients (P < 0.04) and the expression of macrophage iNOS in the mucosa of normal and inflamed appendix specimens was increased (P < 0.01). CONCLUSION: H. pylori does not colonize the appendix and is unlikely to be a pathogenic stimulus for appendicitis. Priming effects on mucosal immunology downstream from the foregut may occur after infection with H. pylori.

Estimating genetic correlations in natural populations

Information on the genetic correlation between traits provides fundamental insight into the constraints on the evolutionary process. Estimates of such correlations are conventionally obtained by raising individuals of known relatedness in artificial environments. However, many species are not readily amenable to controlled breeding programmes, and considerable uncertainty exists over the extent to which estimates derived under benign laboratory conditions reflect the properties of populations in natural settings. Here, non-invasive methods that allow the estimation of genetic correlations from phenotypic measurements derived from individuals of unknown relatedness are introduced. Like the conventional approach, these methods demand large sample sizes in order to yield reasonably precise estimates, and special precautions need to be taken to eliminate bias from shared environmental effects. Provided the sample consists of at least 20% or so relatives, informative estimates of the genetic correlation are obtainable with sample sizes of several hundred individuals, particularly if supplemental information on relatedness is available from polymorphic molecular markers.

The EGF/TGFalpha response element within the TGFalpha promoter consists of a multi-complex regulatory element

Autocrine TGFalpha is an important growth effector in the transformed phenotype. Growth stimulation of some colon cancer cells as well as other types of cancer cells is effected by activation of the epidermal growth factor receptor. Importantly, this receptor activation leads to further stimulation of TGFalpha transcription and increased peptide synthesis. However, the molecular mechanism by which TGFalpha transcription is activated is poorly understood. In this paper, we describe the localization of a cis-sequence within the TGFalpha promoter which mediates this stimulation. This region contains parallel cis-acting elements which interact to regulate both basal and EGF-induced TGFalpha expression. The well differentiated colon carcinoma cell line designated FET was employed in these studies. It produces autocrine TGFalpha but requires exogenous EGF in the medium for optimal growth. Addition of EGF to FET cells maintained in the absence of EGF resulted in a 2 - 3-fold increase of both TGF promoter activity and endogenous TGFalpha mRNA at 4 h. This addition of EGF also stimulated protein synthesis. The use of deletion constructs of the TGFalpha promoter in chimeras with chloramphenicol acetyl transferase localized EGF-responsiveness to between -247 and -201 within the TGFalpha promoter. A 25 bp sequence within this region conferred EGF-responsiveness to heterologous promoter constructs. Further use of deletion/mutation chimeric constructs revealed the presence of at least two interacting cis-elements, one binding a repressor activity and the other, an activator. Gel shift studies indicate the presence of distinct complexes representing activator and repressor binding, which are positively modulated by EGF. The type and amount of complexes formed by these proteins interact to regulate both the basal activity and EGF-responsiveness of the TGFalpha promoter. The interaction of an activator protein with an EGF-responsive repressor may serve to regulate the level of this progression-associated, transforming protein within tight limits.

Spontaneous deleterious mutation in Arabidopsis thaliana

The frequency and selective impact of deleterious mutations are fundamental parameters in evolutionary theory, yet they have not been directly measured in a plant species. To estimate these quantities, we allowed spontaneous mutations to accumulate for 10 generations in 1,000 inbred lines of the annual, self-fertilizing plant Arabidopsis thaliana and assayed fitness differences between generations 0 and 10 in a common garden. Germination rate, fruit set, and number of seeds per fruit each declined by less than 1% per generation in the mutation lines, and total fitness declined by 0.9% per generation. Among-line variances increased in the mutation lines for all traits. Application of an equal-effects model suggests a downwardly biased genomic deleterious mutation rate of 0.1 and a upwardly biased effect of individual mutations on total fitness of 20%. This genomic deleterious mutation rate is consistent with estimates of nucleotide substitution rates in flowering plants, the genome size of Arabidopsis, and the equilibrium inbreeding depression observed in this highly selfing plant species.

Estimation of pairwise relatedness with molecular markers

Applications of quantitative genetics and conservation genetics often require measures of pairwise relationships between individuals, which, in the absence of known pedigree structure, can be estimated only by use of molecular markers. Here we introduce methods for the joint estimation of the two-gene and four-gene coefficients of relationship from data on codominant molecular markers in randomly mating populations. In a comparison with other published estimators of pairwise relatedness, we find these new "regression" estimators to be computationally simpler and to yield similar or lower sampling variances, particularly when many loci are used or when loci are hypervariable. Two examples are given in which the new estimators are applied to natural populations, one that reveals isolation-by-distance in an annual plant and the other that suggests a genetic basis for a coat color polymorphism in bears.