Current optical microscope objectives of low magnification have low numerical aperture and therefore have too little depth resolution and discrimination to perform well in confocal and nonlinear microscopy. This is a serious limitation in... more
Current optical microscope objectives of low magnification have low numerical aperture and therefore have too little depth resolution and discrimination to perform well in confocal and nonlinear microscopy. This is a serious limitation in important areas, including the phenotypic screening of human genes in transgenic mice by study of embryos undergoing advanced organogenesis. We have built an optical lens system for 3D imaging of objects up to 6 mm wide and 3 mm thick with depth resolution of only a few microns instead of the tens of microns currently attained, allowing sub-cellular detail to be resolved throughout the volume. We present this lens, called the Mesolens, with performance data and images from biological specimens including confocal images of whole fixed and intact fluorescently-stained 12.5-day old mouse embryos.
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We use regression models to investigate the effects of inbreeding in 119 zoo populations, encompassing 88 species of mammals, birds, reptiles and amphibians. Meta-analyses show that inbreeding depression for neonatal survival was... more
We use regression models to investigate the effects of inbreeding in 119 zoo populations, encompassing 88 species of mammals, birds, reptiles and amphibians. Meta-analyses show that inbreeding depression for neonatal survival was significant across the 119 populations although the severity of inbreeding depression appears to vary among taxa. However, few predictors of a population's response to inbreeding are found reliable. The models are most likely to detect inbreeding depression in large populations, that is, in populations in which their statistical power is maximised. Purging was found to be significant in 14 populations and a significant trend of purging was found across populations. The change in inbreeding depression due to purging averaged across the 119 populations is <1%, however, suggesting that the fitness benefits of purging are rarely appreciable. The study re-emphasises the necessity to avoid inbreeding in captive breeding programmes and shows that purging cannot be relied upon to remove deleterious alleles from zoo populations.
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We describe a Markov Chain Monte Carlo analysis of five human Y- chromosome microsatellite polymorphisms based on samples from five diverse populations. Our analysis provides strong evidence for mutational bias favoring increase in length... more
We describe a Markov Chain Monte Carlo analysis of five human Y- chromosome microsatellite polymorphisms based on samples from five diverse populations. Our analysis provides strong evidence for mutational bias favoring increase in length at all loci. Estimates of population coalescent times and population size from our two largest samples, one African and one European, suggest that the African population is older but smaller and that the English East Anglian population has undergone significant expansion, being larger but younger. We conclude that Markov Chain Monte Carlo analysis of microsatellite haplotypes can uncover information not apparent when the microsatellites are considered independently. Incorporation of population size as a variable should allow us to estimate the timing and magnitude of major historical population trends.
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... Profound geological changes have the potential to alter the distribution of ani-mals on a large scale, potentially splitting or reuniting populations (Brown et al., 2000; Macey et al., 2000; Matthee & Flemming, 2002; Oliverio et... more
... Profound geological changes have the potential to alter the distribution of ani-mals on a large scale, potentially splitting or reuniting populations (Brown et al., 2000; Macey et al., 2000; Matthee & Flemming, 2002; Oliverio et ... Almog, A., Bonen, H., Herman, K. & Werner, YL (2005 ...
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Microsatellites are now used ubiquitously as genetic markers. One important application is to the assessment of population subdivision and phylogenetic relatedness. Such applications require a method of estimation of genetic distance.... more
Microsatellites are now used ubiquitously as genetic markers. One important application is to the assessment of population subdivision and phylogenetic relatedness. Such applications require a method of estimation of genetic distance. Here we examine the most widely used measure of microsatellite genetic distance, Goldstein et al.'s delta-mu squared ([Δμ]2), with respect to a large data set of 213 markers typed across samples from four diverse human populations. We find that (Δμ)2 yields plausible interpopulation distances. For the first time, we report significant interpopulation differences in mean microsatellite length, although the effect of these differences on (Δμ)2 is negligible. However, we also show that the method is extremely sensitive to one or two loci that contribute extreme values, even when a sample size of >200 loci is used. Some of these extreme loci can be removed on the grounds that some alleles carry large indels, but for others there is no clear justification for exclusion a priori. Our data suggest a rather recent African/non-African split, with an upper limit of some 70,000–80,000 years ago.
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Research Interests: Evolutionary Biology, Animal Behavior, Migration, Family, Ecology, and 22 moreEvolution, Social Behaviour, Genetic Diversity, Molecular Ecology, Kinship, Biological Sciences, Social Structure, Relatedness, Mitochondrial DNA, Patterns, Whales, Microsatellites, Female, Animals, Male, Animal migration, Association, Genotype, Humpback whale, Movements, Megaptera Novaeangliae, and Bay
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Research Interests: Microbiology, Zoology, Gene Flow, Population Genetics, mtDNA, and 17 moreMitochondrial DNA, Sheep, Haplotypes, Parasite, Animals, Male, Host-parasite interactions, Effective Population Size, SHEEP DISEASES, For, Genetic variation, Veterinary Sciences, Base Sequence, Genetic Variability, Mutation Rate, Molecular Sequence Data, and Host
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Colonially breeding gray seals are polygynous. Males are larger than females, compete with each other for position among aggregated females, and contribute no parental care. Genetic analysis of pups born on the island of North Rona,... more
Colonially breeding gray seals are polygynous. Males are larger than females, compete with each other for position among aggregated females, and contribute no parental care. Genetic analysis of pups born on the island of North Rona, Scotland, reveals large numbers of full siblings, although dominant males father disproportionately few of these. This result cannot be explained by mating patterns based solely on male dominance and the spatio-temporal organization of the breeding colony. Instead, many full siblings must result from choices favoring previous parental combinations. Thus, polygyny and partner fidelity appear to operate simultaneously in this breeding colony.
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LENGTH polymorphisms within simple-sequence loci occur ubiquitously in non-coding eukaryotic DNA and can be highly informative in the analysis of natural populations1-4. Simple-sequence length polymorphisms (SSLP) in the long-finned pilot... more
LENGTH polymorphisms within simple-sequence loci occur ubiquitously in non-coding eukaryotic DNA and can be highly informative in the analysis of natural populations1-4. Simple-sequence length polymorphisms (SSLP) in the long-finned pilot whale Globicephala melas (Delphinidae) have provided useful information on the mating system as well as on the genetic structure of populations5. We have therefore tested whether the polymerase chain reaction primers designed for Globicephala could also be used to uncover variability in other whale species. Homologous loci could indeed be amplified from a divers range of whales, including all toothed (Odontoceti) and baleen whales (Mysticeti) tested. Cloning and sequencing these loci from 11 different species revealed an unusually high conservation of sequences flanking the simple-sequence stretches, averaging 3.2% difference over 35-40 Myr. This represents the lowest divergence rate for neutral nucleotide positions found for any species group so far and raises the possible need for a re-evaluation of the age of the modern whales. On the other hand, the high conservation of non-coding sequences in whales simplifies the application of SSLP DNA fingerprinting in cetacean species, as primers designed for one species will often uncover variability in other species.
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Research Interests: Genetics, Geography, Polymorphism, Conservation Genetics, Population Genetics, and 19 moreGenetic Diversity, Molecular Ecology, Biological Sciences, Molecular, Phylogeny, Population structure, Mitochondrial DNA, Animals, Cluster Analysis, Population Size, Population Density, Genetic variation, Demographic History, Marine Mammal, Geographic Range, Bayes Theorem, Genetic Markers, Sea Lions, and Genotypic diversity
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We demonstrate fluorescence imaging by two-photon excitation without scanning in biological specimens as previously described by Hwang and co-workers, but with an increased field size and with framing rates of up to 100 Hz. During... more
We demonstrate fluorescence imaging by two-photon excitation without scanning in biological specimens as previously described by Hwang and co-workers, but with an increased field size and with framing rates of up to 100 Hz. During recordings of synaptically-driven Ca2+ events in primary rat hippocampal neurone cultures loaded with the fluorescent Ca2+ indicator Fluo-4 AM, we have observed greatly reduced photo-bleaching in comparison with single-photon excitation. This method, which requires no costly additions to the microscope, promises to be useful for work where high time-resolution is required.
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Myotonic dystrophy (DM) is associated with abnormal expansions of the CTG repeats in the 3' untranslated region of its gene. Previous studies in individuals of European origin demonstrated strong linkage disequilibrium... more
Myotonic dystrophy (DM) is associated with abnormal expansions of the CTG repeats in the 3' untranslated region of its gene. Previous studies in individuals of European origin demonstrated strong linkage disequilibrium between different CTG repeat length alleles and an Alu element insertion/deletion polymorphism in intron 8 of the DM gene: CTG11-13 chromosomes were almost exclusively associated with the deletion allele, while chromosomes with five or 19-30 repeats or disease chromosomes were only found on the insertion allele. One of the models suggested by these results proposed that the triplet repeats on insertion-associated chromosomes were particularly prone to mutation. Studies of other triplet repeat disorders have suggested that arrays of perfect repeats are more prone to instability than those that are interrupted. We have examined the evolution of this locus by typing a variety of primates and samples drawn from several different human populations for both CTG repeat length and the insertion/deletion polymorphism. DM gene sequences from different primates revealed inter- and intraspecies variability in the number of CTG repeats. Human chromosomes with five repeats or 11-13 repeats (the two major modes of the human CTG repeat distributions) showed no evidence of preferential stabilization of these repeat sizes by imperfect sequences. The insertion and deletion allele frequencies showed large interpopulation variation and the degree of association between these alleles and various CTG repeat lengths is not nearly as complete as was previously supposed. We have found deletion alleles carrying long normal (> 19) CTG repeats and insertion alleles associated with CTG11 - 13 in two african populations.(ABSTRACT TRUNCATED AT 250 WORDS)
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Research Interests: Genetics, Polymorphism, Reproduction, Sexual Selection, Genetic Diversity, and 18 moreTerritoriality, Biological Sciences, Social behavior, Seasonality, Madagascar, Male-Male Competition, Birds, Animals, Male, Regression Analysis, Cooperative Breeding, Reproductive Success, Social System, Sex Factors, Genetic variation, Social Behavior, Seasons, and Female Choice
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... 2 Page 8. 18 WBAmos and George Salt: Development of ichneumon eggs for bright field observation. ... Can. J. Zool. 37 : 655-88. BRONSKILL JF 1964. Embryogenesis of Mesoleius tenthredinis Morl. (Hymenoptera : Ichneu-monidae). Can. J.... more
... 2 Page 8. 18 WBAmos and George Salt: Development of ichneumon eggs for bright field observation. ... Can. J. Zool. 37 : 655-88. BRONSKILL JF 1964. Embryogenesis of Mesoleius tenthredinis Morl. (Hymenoptera : Ichneu-monidae). Can. J. Zool. 42 : 439-53. ...
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Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may... more
Although the grey seal Halichoerus grypus is one of the most familiar and intensively studied of all pinniped species, its global population structure remains to be elucidated. Little is also known about how the species as a whole may have historically responded to climate-driven changes in habitat availability and anthropogenic exploitation. We therefore analysed samples from over 1500 individuals collected from 22 colonies spanning the Western and Eastern Atlantic and the Baltic Sea regions, represented by 350 bp of the mitochondrial hypervariable region and up to nine microsatellites. Strong population structure was observed at both types of marker, and highly asymmetrical patterns of gene flow were also inferred, with the Orkney Islands being identified as a source of emigrants to other areas in the Eastern Atlantic. The Baltic and Eastern Atlantic regions were estimated to have diverged a little over 10 000 years ago, consistent with the last proposed isolation of the Baltic Se...
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Levels of parental relatedness can affect offspring survival and susceptibility to disease. We investigated parental relatedness of live and dead Halichoerus grypus pups between and within island populations and between possible causes of... more
Levels of parental relatedness can affect offspring survival and susceptibility to disease. We investigated parental relatedness of live and dead Halichoerus grypus pups between and within island populations and between possible causes of mortality. Nine microsatellites were used to calculate internal relatedness (IR) and standardized mean d2. We find that pups with higher than average levels of IR have significantly lower survival and that this varied between island populations and that certain loci contributed to the effect more than others. Although, there were no significant differences between causes of mortality, peritonitis, infection and stillborn had the highest levels of IR. These results provide evidence that parental relatedness is an important determinant of pre-weaning pup survival in the grey seal and that this may vary with cause of mortality given a larger sample size.
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Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species... more
Seals and commercial fisheries are potential competitors for fish and cephalopods. Research into the diet of British seal species has been based on conventional dietary analyses, but these methods often do not allow assignment of species identity to scat samples. We present a protocol for obtaining DNA from seal scat (faecal) samples which can be used in polymerase chain reactions to amplify both nuclear and mitochondrial DNA. This can provide a method of identifying the species, sex and individual identity of the seal, from a particular scat sample. Combined with conventional dietary analyses these techniques will allow us to assess sources of variation in seal diet composition. Scat samples have been collected from intertidal haul-out sites around the inner Moray Firth, north-east Scotland. We have assessed methods to extract and purify faecal DNA, a combination of DNA from the individual seal, prey items, and gut bacteria, for use in PCR. Controls using faecal and blood samples f...
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Research Interests: Genetics, Geography, Population Genetics, Population Dynamics, Parameter estimation, and 13 moreMolecular Ecology, Biological Sciences, Colonization, Molecular, Markov chains, Computer Simulation, Animals, Bayesian methods, Bayes Theorem, Likelihood Functions, Environment, Monte Carlo Method, and Founder Effect
Standing-wave excitation of fluorescence is highly desirable in optical microscopy because it improves the axial resolution. We demonstrate here that multiplanar excitation of fluorescence by a standing wave can be produced in a... more
Standing-wave excitation of fluorescence is highly desirable in optical microscopy because it improves the axial resolution. We demonstrate here that multiplanar excitation of fluorescence by a standing wave can be produced in a single-spot laser scanning microscope by placing a plane reflector close to the specimen. We report here a variation in the intensity of fluorescence of successive planes related to the Stokes shift of the dye. We show by the use of dyes specific for the cell membrane how standing-wave excitation can be exploited to generate precise contour maps of the surface membrane of red blood cells, with an axial resolution of ≈90 nm. The method, which requires only the addition of a plane mirror to an existing confocal laser scanning microscope, may well prove useful in studying diseases which involve the red cell membrane, such as malaria.
