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Biomedical subjects

R A Nichols

Publications and source records attributed to R A Nichols.

At least 19 recordsLinked to original sources
PubMed2006

Genome-wide characterisation of hepatitis B mutations involved in clinical outcome.

Infection with the hepatitis B virus (HBV) leads to different disease outcomes, which can be broadly divided into three categories: acute mild infection, 'fulminant' and chronic hepatitis (long-term persistent form of the infection). The factors that influence the development of these different disease states are poorly understood and may include viral polymorphisms. To investigate this possibility, we analysed 116 published complete HBV genomes for which we knew disease outcome and had access to associated information on patients (age, sex and geographic origin). Our best statistical model correctly classified 72% of the cases and retained age and sex of the patient, as well as 29 candidate mutations. With the exception of one mutation in the X gene, all were located in the viral polymerase, suggesting this gene plays a critical role in clinical outcome. Our results highlight the importance of the genetics of HBV strains in the evolution of the disease and demonstrate that disease outcome can be predicted to a surprisingly large extent with a limited number of host and viral factors.

Age Distribution↗
PubMed2004

The origin and evolution of geminivirus-related DNA sequences in Nicotiana.

A horizontal transmission of a geminiviral DNA sequence, into the germ line of an ancestral Nicotiana, gave rise to multiple repeats of geminivirus-related DNA, GRD, in the genome. We follow GRD evolution in Nicotiana tabacum (tobacco), an allotetraploid, and its diploid relatives, and show GRDs are derived from begomoviruses. GRDs occur in two families: the GRD5 family's ancestor integrated into the common ancestor of three diploid species, Nicotiana kawakamii, Nicotiana tomentosa and Nicotiana tomentosiformis, on homeologous group 4 chromosomes. The GRD3 family was acquired more recently on chromosome 2 in a lineage of N. tomentosiformis, the paternal ancestor of tobacco. Both GRD families include individual members that are methylated and diverged. Using relative rates of synonymous and nonsynonymous nucleotide substitutions, we tested for evidence of selection on GRD units and found none within the GRD3 and GRD5 families. However, the substitutions between GRD3 and GRD5 do show a significant excess of synonymous changes, suggesting purifying selection and hence a period of autonomous evolution between GRD3 and GRD5 integration. We observe in the GRD3 family, features of Helitrons, a major new class of putative rolling-circle replicating eukaryotic transposon, not found in the GRD5 family or geminiviruses. We speculate that the second integration event, resulting in the GRD3 family, involved a free-living geminivirus, a Helitron and perhaps also GRD5. Thus our data point towards recurrent dynamic interplay between geminivirus and plant DNA in evolution.

Base Sequence↗
PubMed2004

Using molecular markers with high mutation rates to obtain estimates of relative population size and to distinguish the effects of gene flow and mutation: a demonstration using data from endemic Mauritian skinks.

We propose a method of analysing genetic data to obtain separate estimates of the size (N(p)) and migration rate (m(p)) for the sampled populations, without precise prior knowledge of mutation rates at each locus ( micro(L)). The effects of migration and mutation can be distinguished because high migration has the effect of reducing genetic differentiation across all loci, whereas a high mutation rate will only affect the locus in question. The method also takes account of any differences between the spectra of immigrant alleles and of new mutant alleles. If the genetic data come from a range of population sizes, and the loci have a range of mutation rates, it is possible to estimate the relative sizes of the different N(p) values, and likewise the m(p) and the micro(L). Microsatellite loci may also be particularly appropriate because loci with a high mutation rate can reach mutation-drift-migration equilibrium more quickly, and because the spectra of mutants arriving in a population can be particularly distinct from the immigrants. We demonstrate this principle using a microsatellite data set from Mauritian skinks. The method identifies low gene flow between a putative new species and populations of its sister species, whereas the differentiation of two other populations is attributed to small population size. These distinct interpretations were not readily apparent from conventional measures of genetic differentiation and gene diversity. When the method is evaluated using simulated data sets, it correctly distinguishes low gene flow from small population size. Loci that are not at mutation-migration-drift equilibrium can distort the parameter estimates slightly. We discuss strategies for detecting and overcoming this effect.

Animals↗
PubMed2003

An analysis of consanguinity and social structure within the UK Asian population using microsatellite data.

We analysed microsatellite genotypes sampled from the Pakistani and Indian communities in Nottingham, UK, to investigate the genetic consequences of substructuring mediated by traditional marriage customs. The application of a recently developed likelihood approach identified significant levels of population substructure within the Pakistani community as a whole, as well as within the finer divisions of castes and biradheri. In addition, high levels of cryptic or unacknowledged consanguinity were detected within subgroups of this community, including biradheri. The Indian sample showed no significant evidence of either substructure or consanguinity. We demonstrate that estimates of disease gene frequencies can be inaccurate unless they are made jointly with estimates of population substructure and consanguinity ((theta congruent to FST) and C). The magnitude of these estimates also highlights the importance of accounting for the finer scale of social structuring when making decisions regarding the risk of recessive disorders in offspring.

Analysis of Variance↗
PubMed2002

The effect of reproductive compensation on recessive disorders within consanguineous human populations.

We investigate the effects of consanguinity and population substructure on genetic health using the UK Asian population as an example. We review and expand upon previous treatments dealing with the deleterious effects of consanguinity on recessive disorders and consider how other factors, such as population substructure, may be of equal importance. For illustration, we quantify the relative risks of recessive lethal disorders by presenting some simple calculations that demonstrate the effect 'reproductive compensation' has on the maintenance of recessive alleles. The results show how reproductive compensation can effectively counteract the purging of deleterious alleles within consanguineous populations. Whereas inbreeding does not elevate the equilibrium frequency of affected individuals, reproductive compensation does. We suggest this effect must be built into interpretations of the incidence of genetic disease within populations such as the UK Asians. Information of this nature will benefit health care workers who inform such communities.

Alleles↗
PubMed2001

The persistence of Pliocene populations through the Pleistocene climatic cycles: evidence from the phylogeography of an Iberian lizard.

Ancient climatic fluctuations have caused changes in the demography and distribution of many species. The genetic differentiation between populations of the same species and of sister species is often attributed largely to the more recent Pleistocene fluctuations. Recent interpretations, which implicate earlier episodes, have proved controversial. We address the timing of genetic divergence in the Iberian lizard Lacerta schreiberi by studying the phylogeography of the cytochrome b sequence. The species has a remarkable morphological uniformity, yet our evidence suggests that earlier events in the Pliocene initiated the main divergence between populations. This interpretation implies that the different populations survived through the Pleistocene in separate localities. This conclusion is robust to different molecular clock calibrations. The persistence of earlier differentiation through the Pleistocene has wide implications for our understanding of Pleistocene refugia in this species and, by extension, to the biogeography of the whole region.

Animals↗
PubMed2001

Postsynaptic target regulates functional responses induced by 5-HT3 serotonin receptors on axonal varicosities of NG108-15 hybrid neuroblastoma cells.

Rat brain presynaptic 5-HT3 serotonin receptors, members of the ligand-gated ion channel superfamily, induce changes in nerve terminal [Ca2+]i in a manner distinct from that found for somatic 5-HT3 receptors. Here, we assessed the role of postsynaptic target in regulating the nature of presynaptic receptor-induced responses, using the hybrid neuroblastoma cell line NG108-15 as a model neuronal system that expresses 5-HT3 receptors. Using immunocytochemistry, 5-HT3 receptors were found to be present on the presynaptic-like varicosities of differentiated NG108-15 cells, indicating that these receptors possess an inherent ability to localize to potential presynaptic sites. In the absence of postsynaptic target, 5-HT3 receptors localized to the varicosities induce rapid but transient changes in [Ca2+]i that were initiated by voltage-gated Ca2+ channels, as assessed using Ca2+ channel blockers, these properties being typical of those found for somatic 5-HT3 receptors. In co-cultures containing rat myotubes, with which NG108-15 cells form functional cholinergic synapses, the 5-HT3 receptor-induced changes in [Ca2+]i in the axonal varicosities shifted over time (three to 10 days) to that found for brain nerve endings: sustained responses that were insensitive to blockade by antagonists of voltage-gated Ca2+ channels. The effect of co-culturing myotubes with the NG108-15 cells was mimicked by conditioned media from myotube cultures. These results indicate that regulatory molecules from the target postsynaptic cell dictate the functional responses elicited by presynaptic 5-HT3 receptors. Because the target-induced changes required several days before they were evident, we hypothesize that changes in protein expression, perhaps the consequence of altered gene regulation, underlie the changes in the responses to 5-HT3 receptor activation in the axonal varicosities of this neuronal cell line.

Animals↗
PubMed2001

Effects of bottlenecks on quantitative genetic variation in the butterfly Bicyclus anynana.

The effects of a single population bottleneck of differing severity on heritability and additive genetic variance was investigated experimentally using a butterfly. An outbred laboratory stock was used to found replicate lines with one pair, three pairs and 10 pairs of adults, as well as control lines with approximately 75 effective pairs. Heritability and additive genetic variance of eight wing pattern characters and wing size were estimated using parent-offspring covariances in the base population and in all daughter lines. Individual morphological characters and principal components of the nine characters showed a consistent pattern of treatment effects in which average heritability and additive genetic variance was lower in one pair and three pair lines than in 10 pair and control lines. Observed losses in heritability and additive genetic variance were significantly greater than predicted by the neutral additive model when calculated with coefficients of inbreeding estimated from demographic parameters alone. However, use of molecular markers revealed substantially more inbreeding, generated by increased variance in family size and background selection. Conservative interpretation of a statistical analysis incorporating this previously undetected inbreeding led to the conclusion that the response to inbreeding of the morphological traits studied showed no significant departure from the neutral additive model. This result is consistent with the evidence for minimal directional dominance for these traits. In contrast, egg hatching rate in the same experimental lines showed strong inbreeding depression, increased phenotypic variance and rapid response to selection, highly indicative of an increase in additive genetic variance due to dominance variance conversion.

Analysis of Variance↗
PubMed2001

Genetic differentiation of a European caddisfly: past and present gene flow among fragmented larval habitats.

We describe the genetic structure of a freshwater insect species and interpret it in terms of present-day population dynamics and possible postglacial colonization history. The sampling regime represented a large area of the species range in northwest Europe, particularly focusing on Britain, a region relatively neglected in molecular population genetic studies. Plectrocnemia conspersa generally showed low levels of genetic variation across the sampled populations (Nei's D = 0.0138) and subdivision was unrelated to the pattern of the drainage network. However, the results do suggest that populations across the region are not at equilibrium and that British populations still show effects of the recolonization of the species following the last glacial maximum. Levels of genetic diversity were lower in Britain than in mainland Europe. Two-dimensional scaling showed genetic differentiation between major regions and the pattern of genetic diversity indicates a more recent origin of populations in the north and west of the area compared with the south and east. We argue that, despite the highly fragmented larval habitat, dispersal over tens of kilometres is frequent. Over longer distances, however, P. conspersa does still show evidence of founder effects and postglacial range expansion into Britain.

Animals↗
PubMed2001

Sustaining genetic variation in a small population: evidence from the Mauritius kestrel.

We obtained measures of genetic diversity in 10 kestrel species at a suite of 12 microsatellite loci. We estimated the relative effective size (Ne) of the species using a Markov chain Monte Carlo (MCMC) approach, which jointly estimated the locus specific mutation rates as nuisance parameters. There was surprisingly high genetic diversity found in museum specimens of the Mauritius kestrel. Being an endemic species on a small island, it is known to have a long history of small population size. Conversely, kestrels with a continental distribution had Ne estimates that were only one order of magnitude larger and similar to each other, despite having current population sizes that were between one and three orders of magnitude larger than the Mauritius kestrel. We show how many of the theoretical results describing the effective size of a subdivided population can be captured in terms of three rates which describe the branching pattern of the gene genealogy, and that they are useful in estimating the time to migration-drift and mutation-drift equilibrium. We use this approach to argue that population subdivision has helped retain genetic diversity in the Mauritius kestrel, and that the continental species' genetic diversity has yet to reach equilibrium after the range changes following the last ice age. We draw parallels with Hewitt's observation that genetic variation seems to survive species' range compression and is rather vulnerable to range expansion.

Animals↗
PubMed2001

Mating patterns, relatedness and the basis of natal philopatry in the brown long-eared bat, Plecotus auritus.

The brown long-eared bat, Plecotus auritus, is unusual among temperate zone bats in that summer maternity colonies are composed of adult males and females, with both sexes displaying natal philopatry and long-term association with a colony. Here, we describe the use of microsatellite analysis to investigate colony relatedness and mating patterns, with the aim of identifying the evolutionary determinants of social organization in P. auritus. Mean colony relatedness was found to be low (R=0.033 +/- 0.002), with pairwise estimates of R within colonies ranging from -0.4 to 0.9. The proportion of young fathered by males in their own colony was investigated using a Bayesian approach, incorporating parameters detailing the number of untyped individuals. This analysis revealed that most offspring were fathered by males originating from a different colony to their own. In addition, we determined that the number of paternal half-sibs among cohorts of young was low, inferring little or no skew in male reproductive success. The results of this study suggest that kin selection cannot account for colony stability and natal philopatry in P. auritus, which may instead be explained by advantages accrued through the use of familiar and successful roost sites, and through long-term associations with conspecifics. Moreover, because the underlying causes of male natal dispersal in mammals, such as risk of inbreeding or competition for mates, appear to be avoided via extra-colony copulation and low male reproductive skew, both P. auritus males and females are able to benefit from long-term association with the natal colony.

Animals↗
PubMed2001

Ca(2+) changes induced by different presynaptic nicotinic receptors in separate populations of individual striatal nerve terminals.

Presynaptic nicotinic acetylcholine receptors likely play a modulatory role in the nerve terminal. Using laser-scanning confocal microscopy, we have characterized physiological responses obtained on activation of presynaptic nicotinic receptors by measuring calcium changes in individual nerve terminals (synaptosomes) isolated from the rat corpus striatum. Nicotine (500 nM) induced Ca(2+) changes in a subset (10-25%) of synaptosomes. The Ca(2+) responses were dependent on extracellular Ca(2+) and desensitized very slowly (several minutes) on prolonged exposure to agonist. The nicotine-induced Ca(2+) responses were dose-dependent and were completely blocked by dihydro-beta-erythroidine (5 microM), differentially affected by mecamylamine (10 microM) and alpha-conotoxin MII (100 nM), and not affected by alpha-bungarotoxin (500 nM). Immunocytochemical studies using well-characterized monoclonal antibodies revealed the presence of the alpha4 and alpha3/alpha5 nicotinic subunits. The nicotine-induced responses were unaffected by prior depolarization or by a mixture of Ca(2+) channel toxins including omega-conotoxin MVIIC (500 nM), omega-conotoxin GVIA (500 nM) and agatoxin TK (200 nM). Our results indicate that nicotinic receptors present on striatal nerve terminals induce Ca(2+) entry largely without involving voltage-gated Ca(2+) channels, most likely by direct permeation via the receptor channel itself. In addition, at least two subpopulations of presynaptic nicotinic receptors reside on separate terminals in the striatum, suggesting distinct modulatory roles.

Animals↗
PubMed2001

A method for distinguishing consanguinity and population substructure using multilocus genotype data.

We use the patterns of homozygosity at multiple loci to distinguish between excess homozygosity caused by consanguineous mating and that due to undetected population subdivision (the Wahlund effect). Clarification of the underlying causes of excess homozygosity is of practical importance in explaining the occurrence of recessive genetic disorders and in forensic match probability calculations. We calculated a likelihood surface for two parameters: C, the proportion of the population practicing consanguinity, and theta, the genetic correlation due population subdivision. To illustrate the method, we applied it to multilocus genotypic data of two U.K. Asian populations, one practicing a high frequency of cousin marriage, and another in which caste endogamy was suspected. The method was able to successfully distinguish the different patterns of relatedness. The method also returned accurate estimates of C and theta using simulated data sets. We show how our method can be extended to allow for degrees of inbreeding closer than cousin unions, including selfing. With closer inbreeding, the relatedness of recent ancestors beyond the parents becomes an issue.

Algorithms↗
PubMed2000

Functional IP3- and ryanodine-sensitive calcium stores in presynaptic varicosities of NG108-15 (rodent neuroblastoma x glioma hybrid) cells.

Presynaptic varicosities of the model neuronal cell line NG108-15, a cholinergic neuroblastoma cell x glioma cell hybrid capable of innervating striated myotubes, were examined for the presence of inositol 1,4,5-trisphosphate (IP3)-sensitive and Ca2+-activated (ryanodine-sensitive) Ca2+ stores using confocal microscopic imaging of Ca2+-sensitive fluorescent dye loaded into the cells. Initial demonstration of the presence of IP3 receptors and ryanodine receptors in the NG108-15 varicosities was obtained using immunocytochemistry. Treatment of NG108-15 cells with bradykinin (0.1 microM), whose receptor is linked to IP3 generation, and separately, caffeine (10 mM), an activator of endoplasmic reticulum ryanodine receptors, resulted in substantial increases in [Ca2+]i in the varicosities. K+-evoked changes in [Ca2+]i in the varicosities were reduced (52 %) after emptying the ryanodine-sensitive Ca2+ store using caffeine (10 mM), but were not affected by prior depletion of the IP3-sensitive Ca2+ store using thapsigargin (1 microM). Bradykinin-induced changes in [Ca2+]i were abolished following depletion of the IP3-sensitive Ca2+ store using thapsigargin (1 microM) and were reduced (72 %) by prior emptying of the ryanodine-sensitive Ca2+ store with caffeine (10 mM). The same results were obtained when the varicosities of the NG108-15 cells had formed synaptic junctions with co-cultured rat hindlimb myotubes. Taken together, the results suggest that, in the varicosities, activation of the IP3 pathway evoked the release of Ca2+ from the IP3-sensitive store, which, in turn, secondarily induced the release of Ca2+ from the ryanodine-sensitive store via Ca2+-induced Ca2+ release, and that depolarization-induced Ca2+ entry evoked Ca2+-induced Ca2+ release only from the ryanodine-sensitive store. Thus, functional internal Ca2+ stores are inherent components of presynaptic varicosities in this neural cell line.

Animals↗
PubMed2000

Nicotinic receptors co-localize with 5-HT(3) serotonin receptors on striatal nerve terminals.

Nicotinic acetylcholine receptors and 5-HT(3) serotonin receptors are present on presynaptic nerve terminals in the striatum, where they have been shown to be involved in the regulation of dopamine release. Here, we explored the possibility that both receptor systems function on the same individual nerve terminals in the striatum, as assessed by confocal imaging of synaptosomes. On performing sequential stimulation, nicotine (500 nM) induced changes in [Ca(2+)](i) in most of the synaptosomes ( approximately 80%) that had previously responded to stimulation with the 5-HT(3) receptor agonist m-chlorophenylbiguanide (mCPBG; 100 nM), whereas mCPBG induced [Ca(2+)](i) responses in approximately half of the synaptosomes that showed responses on nicotinic stimulation. The 5-HT(3) receptor-specific antagonist tropisetron blocked only the mCPBG-induced responses, but not the nicotinic responses on the same synaptosomes. Immunocytochemical staining revealed extensive co-localization of the 5-HT(3) receptor with the alpha4 nicotinic receptor subunit on the same synaptosomes, but not with the alpha3 and/or alpha5 subunits. Immunoprecipitation studies indicate that the 5-HT(3) receptor and the alpha4 nicotinic receptor subunit do not interact on the nerve terminals. The presence of nicotinic and 5-HT(3) receptors on the same presynaptic striatal nerve terminal indicates a convergence of cholinergic and serotonergic systems in the striatum.

Animals↗
PubMed1999

Antibodies against the extracellular domain of the 5-HT3 receptor label both native and recombinant receptors.

We have developed polyclonal antibodies (pAb120) against a peptide corresponding to a region within the extracellular domain of the 5-hydroxytryptamine3 (5-HT3) receptor subunit, thus permitting, for the first time, localization of 5-HT3 receptors at the cell surface in intact (non-permeabilized) systems. The antibodies are both specific and sensitive: pAb120 recognized as little as 63 ng of protein from HEK293 cells expressing recombinant 5-HT3 receptors, whilst Western blots of recombinant 5-HT3 receptors purified from Sf9 cells revealed two bands at 48 and 54 kDa, and native 5-HT3 receptors from N1E-115 cell membranes produced a broad band at 50-54 kDa with a smaller band at 35 kDa. These bands were also labelled by antibodies against the intracellular loop of the 5-HT3 receptor. Immunofluorescent labelling revealed a ring of intense fluorescence in the plasma membrane of non-permeabilized HEK293 cells expressing recombinant 5-HT3 receptors. Studies on native 5-HT3 receptors revealed that pAb120 could recognize 5-HT3 receptors on presynaptic terminals isolated from rat striatum, and immunohistochemical studies in rat brain sections revealed labelling of cell bodies, dendrites and varicose axons in hippocampus, cortex and lateral hypothalamus; all of these areas have been reported to express 5-HT3 receptors. We conclude that pAb120 is a highly specific and sensitive antiserum that will assist in clarifying fundamental questions about 5-HT3 receptor neurobiology.

Animals↗
PubMed1999

Minisatellite mutational processes reduce F(st) estimates.

We have used a new method for binning minisatellite alleles (semi-automated allele aggregation) and report the extent of population diversity detectable by eleven minisatellite loci in 2,689 individuals from 19 human populations distributed widely throughout the world. Whereas population relationships are consistent with those found in other studies, our estimate of genetic differentiation (F(st)) between populations is less than 8%, which is lower than comparative estimates of between 10%-15% obtained by using other sources of polymorphism data. We infer that mutational processes are involved in reducing F(st) estimates from minisatellite data because, first, the lowest F(st) estimates are found at loci showing autocorrelated frequencies among alleles of similar size and, second, F(st) declines with heterozygosity but by more than predicted assuming simple models of mutation. These conclusions are consistent with the view that minisatellites are subject to selective or mutational constraints in addition to those expected under simple step-wise mutation models.

Alleles↗