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Search Results: 1 - 10 of 238210 matches for " Andrew R Leitch "
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Genome Size Dynamics and Evolution in Monocots
Ilia J. Leitch,Jeremy M. Beaulieu,Mark W. Chase,Andrew R. Leitch,Michael F. Fay
Journal of Botany , 2010, DOI: 10.1155/2010/862516
Abstract: Monocot genomic diversity includes striking variation at many levels. This paper compares various genomic characters (e.g., range of chromosome numbers and ploidy levels, occurrence of endopolyploidy, GC content, chromosome packaging and organization, genome size) between monocots and the remaining angiosperms to discern just how distinctive monocot genomes are. One of the most notable features of monocots is their wide range and diversity of genome sizes, including the species with the largest genome so far reported in plants. This genomic character is analysed in greater detail, within a phylogenetic context. By surveying available genome size and chromosome data it is apparent that different monocot orders follow distinctive modes of genome size and chromosome evolution. Further insights into genome size-evolution and dynamics were obtained using statistical modelling approaches to reconstruct the ancestral genome size at key nodes across the monocot phylogenetic tree. Such approaches reveal that while the ancestral genome size of all monocots was small ( ?pg), there have been several major increases and decreases during monocot evolution. In addition, notable increases in the rates of genome size-evolution were found in Asparagales and Poales compared with other monocot lineages. 1. Introduction: How Distinctive Are MonocotGenomes? Monocotyledons (monocots) comprise c. 25% of all angiosperms and are a remarkably variable group with species found growing on all continents and in all habitats. They were first distinguished from other angiosperms by the presence of a single cotyledon [1] and they have since been shown to be strongly supported as sister to the eudicots + Ceratophyllum clade ([2] plus others). At the genomic level, monocots are remarkably diverse, with striking variation at many levels ranging from gene sequences through to the number of chromosomes per genome, the number of genomes (ploidy), and the amount of DNA per genome (genome size). Yet how different are monocot genomes from other angiosperms? In this post-genomics era of large-scale sequencing and comparative analysis, the availability of large amounts of sequence information together with increasing amounts of more traditional cytological data provides new insights into this question. This paper reviews available data to highlight some of the similarities and differences between monocots and the remaining angiosperms that have been revealed. One of the most striking features of monocots is their wide range of genome sizes, and this genomic character is analysed in greater detail
Review of the Application of Modern Cytogenetic Methods (FISH/GISH) to the Study of Reticulation (Polyploidy/Hybridisation)
Michael Chester,Andrew R. Leitch,Pamela S. Soltis,Douglas E. Soltis
Genes , 2010, DOI: 10.3390/genes1020166
Abstract: The convergence of distinct lineages upon interspecific hybridisation, including when accompanied by increases in ploidy (allopolyploidy), is a driving force in the origin of many plant species. In plant breeding too, both interspecific hybridisation and allopolyploidy are important because they facilitate introgression of alien DNA into breeding lines enabling the introduction of novel characters. Here we review how fluorescence in situ hybridisation (FISH) and genomic in situ hybridisation (GISH) have been applied to: 1) studies of interspecific hybridisation and polyploidy in nature, 2) analyses of phylogenetic relationships between species, 3) genetic mapping and 4) analysis of plant breeding materials. We also review how FISH is poised to take advantage of nextgeneration sequencing (NGS) technologies, helping the rapid characterisation of the repetitive fractions of a genome in natural populations and agricultural plants.
Insight into PMD Regimes: An Analysis on Buried Optical Fibres
Winston T. Ireeta,Vitalis Musara,Lorinda Wu,Andrew W. R. Leitch
International Journal of Optics , 2013, DOI: 10.1155/2013/367967
Abstract: Polarization mode dispersion (PMD) field measurements on deployed buried fibres showed that the PMD variation over the 1520 to 1570 nm wavelength was stochastic. The PMD variation over the 98-hour period for each wavelength was directional and limited; they are due to the presence of random mode coupling along the fibre length and limited influence from extrinsic perturbations over time, respectively. PMD variation in the wavelength domain showed that the mean first-order PMD (FO-PMD) value is independent of whether the FO-PMD statistics of a fibre link approaches the Maxwellian theoretical distribution; the key factor is sufficient random mode coupling. The accompanying second-order PMD (SO-PMD) statistics, with FO-PMD statistics approaching Maxwellian, followed the PDF given by Foschini et al. (1999). The FO- and SO-PMD statistics at a given wavelength gave nonstochastic PMD distributions with time. 1. Introduction The polarization mode dispersion (PMD) in deployed fibres is known to evolve in a stochastic pattern due to unpredictable extrinsic perturbations (i.e., environmental changes, vibrations, and human interactions) with time and nonuniform intrinsic perturbations (i.e., core asymmetry and internal stress) experienced along the fibre length. The unpredictable variation of extrinsic and intrinsic perturbations with time and fibre length makes PMD statistics stochastic about some average value, either with wavelength or with time. This means that the PMD of optical systems with time and wavelength is unpredictable; therefore, one must resort to statistical analysis. The statistical property of PMD that attracted the initial interest was the mean first-order PMD (FO-PMD) [1, 2]. Thus, all PMD measurement techniques currently in use in the telecommunication industry require an averaging procedure in order to determine the overall PMD of a fibre link [2, 3]. Most, if not all, of thework done has been focused mainly on FO- and second-order PMD (SO-PMD) statistics, which is likely due to the FO- and SO-PMD vectors being known to be statistically dependent on each other [4, 5]. However, Phua and Haus [6] concluded that FO-PMD can be more accurately characterised than SO-PMD. Understanding the nature and characteristics of PMD is a key step towards the construction of effective PMD emulators and compensation techniques. The statistical characterisation of PMD includes the probability densities of FO- and SO-PMD, the scaling of the PMD phenomena with changes in the mean FO-PMD, various correlation functions, and characteristics associated with the
Independent, Rapid and Targeted Loss of Highly Repetitive DNA in Natural and Synthetic Allopolyploids of Nicotiana tabacum
Simon Renny-Byfield, Ales Kova?ík, Michael Chester, Richard A. Nichols, Jiri Macas, Petr Novák, Andrew R. Leitch
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0036963
Abstract: Allopolyploidy (interspecific hybridisation and polyploidy) has played a significant role in the evolutionary history of angiosperms and can result in genomic, epigenetic and transcriptomic perturbations. We examine the immediate effects of allopolyploidy on repetitive DNA by comparing the genomes of synthetic and natural Nicotiana tabacum with diploid progenitors N. tomentosiformis (paternal progenitor) and N. sylvestris (maternal progenitor). Using next generation sequencing, a recently developed graph-based repeat identification pipeline, Southern blot and fluorescence in situ hybridisation (FISH) we characterise two highly repetitive DNA sequences (NicCL3 and NicCL7/30). Analysis of two independent high-throughput DNA sequencing datasets indicates NicCL3 forms 1.6–1.9% of the genome in N. tomentosiformis, sequences that occur in multiple, discontinuous tandem arrays scattered over several chromosomes. Abundance estimates, based on sequencing depth, indicate NicCL3 is almost absent in N. sylvestris and has been dramatically reduced in copy number in the allopolyploid N. tabacum. Surprisingly elimination of NicCL3 is repeated in some synthetic lines of N. tabacum in their forth generation. The retroelement NicCL7/30, which occurs interspersed with NicCL3, is also under-represented but to a much lesser degree, revealing targeted elimination of the latter. Analysis of paired-end sequencing data indicates the tandem component of NicCL3 has been preferentially removed in natural N. tabacum, increasing the proportion of the dispersed component. This occurs across multiple blocks of discontinuous repeats and based on the distribution of nucleotide similarity among NicCL3 units, was concurrent with rounds of sequence homogenisation.
Similar patterns of rDNA evolution in synthetic and recently formed natural populations of Tragopogon (Asteraceae) allotetraploids
Hana Malinska, Jennifer A Tate, Roman Matyasek, Andrew R Leitch, Douglas E Soltis, Pamela S Soltis, Ales Kovarik
BMC Evolutionary Biology , 2010, DOI: 10.1186/1471-2148-10-291
Abstract: Using Southern blot hybridization and fluorescent in situ hybridization (FISH), we analyzed copy numbers and distribution of these highly reiterated genes in seven lines of synthetic T. mirus (110 individuals) and four lines of synthetic T. miscellus (71 individuals). Variation among diploid parents accounted for most of the observed gene imbalances detected in F1 hybrids but cannot explain frequent deviations from repeat additivity seen in the allotetraploid lines. Polyploid lineages involving the same diploid parents differed in rDNA genotype, indicating that conditions immediately following genome doubling are crucial for rDNA changes. About 19% of the resynthesized allotetraploid individuals had equal rDNA contributions from the diploid parents, 74% were skewed towards either T. porrifolius or T. pratensis-type units, and only 7% had more rDNA copies of T. dubius-origin compared to the other two parents. Similar genotype frequencies were observed among natural populations. Despite directional reduction of units, the additivity of 35S rDNA locus number is maintained in 82% of the synthetic lines and in all natural allotetraploids.Uniparental reductions of homeologous rRNA gene copies occurred in both synthetic and natural populations of Tragopogon allopolyploids. The extent of these rDNA changes was generally higher in natural populations than in the synthetic lines. We hypothesize that locus-specific and chromosomal changes in early generations of allopolyploids may influence patterns of rDNA evolution in later generations.Chromosome counts suggest that between 30 and 100% of angiosperm species are polyploids [1], and Wood et al. [2] propose that 15% of angiosperm speciation events are associated with polyploidy whereas recent genomic studies of selected model and crop species have revealed that all plant genomes sequenced to date have signatures of one or more whole-genome duplications in their evolutionary history [3,4]. The success of newly formed angiosperm
Differential Dynamics of Transposable Elements during Long-Term Diploidization of Nicotiana Section Repandae (Solanaceae) Allopolyploid Genomes
Christian Parisod, Corinne Mhiri, K. Yoong Lim, James J. Clarkson, Mark W. Chase, Andrew R. Leitch, Marie-Angèle Grandbastien
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050352
Abstract: Evidence accumulated over the last decade has shown that allopolyploid genomes may undergo drastic reorganization. However, timing and mechanisms of structural diploidization over evolutionary timescales are still poorly known. As transposable elements (TEs) represent major and labile components of plant genomes, they likely play a pivotal role in fuelling genome changes leading to long-term diploidization. Here, we exploit the 4.5 MY old allopolyploid Nicotiana section Repandae to investigate the impact of TEs on the evolutionary dynamics of genomes. Sequence-specific amplified polymorphisms (SSAP) on seven TEs with expected contrasted dynamics were used to survey genome-wide TE insertion polymorphisms. Comparisons of TE insertions in the four allopolyploid species and descendents of the diploid species most closely related to their actual progenitors revealed that the polyploids showed considerable departure from predicted additivity of the diploids. Large numbers of new SSAP bands were observed in polyploids for two TEs, but restructuring for most TE families involved substantial loss of fragments relative to the genome of the diploid representing the paternal progenitor, which could be due to changes in allopolyploids, diploid progenitor lineages or both. The majority of non-additive bands were shared by all polyploid species, suggesting that significant restructuring occurred early after the allopolyploid event that gave rise to their common ancestor. Furthermore, several gains and losses of SSAP fragments were restricted to N. repanda, suggesting a unique evolutionary trajectory. This pattern of diploidization in TE genome fractions supports the hypothesis that TEs are central to long-term genome turnover and depends on both TE and the polyploid lineage considered.
Rapid Chromosome Evolution in Recently Formed Polyploids in Tragopogon (Asteraceae)
K. Yoong Lim, Douglas E. Soltis, Pamela S. Soltis, Jennifer Tate, Roman Matyasek, Hana Srubarova, Ales Kovarik, J. Chris Pires, Zhiyong Xiong, Andrew R. Leitch
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003353
Abstract: Background Polyploidy, frequently termed “whole genome duplication”, is a major force in the evolution of many eukaryotes. Indeed, most angiosperm species have undergone at least one round of polyploidy in their evolutionary history. Despite enormous progress in our understanding of many aspects of polyploidy, we essentially have no information about the role of chromosome divergence in the establishment of young polyploid populations. Here we investigate synthetic lines and natural populations of two recently and recurrently formed allotetraploids Tragopogon mirus and T. miscellus (formed within the past 80 years) to assess the role of aberrant meiosis in generating chromosomal/genomic diversity. That diversity is likely important in the formation, establishment and survival of polyploid populations and species. Methodology/Principal Findings Applications of fluorescence in situ hybridisation (FISH) to natural populations of T. mirus and T. miscellus suggest that chromosomal rearrangements and other chromosomal changes are common in both allotetraploids. We detected extensive chromosomal polymorphism between individuals and populations, including (i) plants monosomic and trisomic for particular chromosomes (perhaps indicating compensatory trisomy), (ii) intergenomic translocations and (iii) variable sizes and expression patterns of individual ribosomal DNA (rDNA) loci. We even observed karyotypic variation among sibling plants. Significantly, translocations, chromosome loss, and meiotic irregularities, including quadrivalent formation, were observed in synthetic (S0 and S1 generations) polyploid lines. Our results not only provide a mechanism for chromosomal variation in natural populations, but also indicate that chromosomal changes occur rapidly following polyploidisation. Conclusions/Significance These data shed new light on previous analyses of genome and transcriptome structures in de novo and establishing polyploid species. Crucially our results highlight the necessity of studying karyotypes in young (<150 years old) polyploid species and synthetic polyploids that resemble natural species. The data also provide insight into the mechanisms that perturb inheritance patterns of genetic markers in synthetic polyploids and populations of young natural polyploid species.
The Discovery of Anomalous Microwave Emission
Erik M. Leitch,A. C. R. Readhead
Advances in Astronomy , 2013, DOI: 10.1155/2013/352407
Abstract:
The Discovery of Anomalous Microwave Emission
Erik M. Leitch,A. C. R. Readhead
Advances in Astronomy , 2013, DOI: 10.1155/2013/352407
Abstract: We discuss the first detection of anomalous microwave emission, in the Owens Valley RING5M experiment, and its interpretation in the context of the ground-based cosmic microwave background (CMB) experiments of the early 1990s. The RING5M experiment was one of the first attempts to constrain the anisotropy power on sub-horizon scales, by observing a set of -size fields around the North Celestial Pole (NCP). Fields were selected close to the NCP to allow continuous integration from the Owens Valley site. The experiment detected significant emission at both 14.5?GHz and 30?GHz, consistent with a mixture of CMB and a flat-spectrum foreground component, which we termed anomalous, as it could be explained neither by thermal dust emission, nor by standard models for synchrotron or free-free emission. A significant spatial correlation was found between the extracted foreground component and structure in the IRAS 100?μm maps. While microwave emission from spinning dust may be the most natural explanation for this correlation, spinning dust is unlikely to account for all of the anomalous emission seen in the RING5M data. 1. Introduction From the perspective of the 21st century cosmology, it can be hard to imagine how primitive the state of our knowledge was a short twenty years ago and how rapidly the landscape was changing at the time. Today, ground-based experiments like the South Pole Telescope (SPT) and the Atacama Cosmology Telescope (ACT) have measured the high- power spectrum with enough resolution to detect the first nine Doppler peaks (SPT [1, 2], ACT [3]) and enough sensitivity to detect the background of SZ power from unresolved galaxy clusters [4]. The combination of ground, balloon-borne, and space-based missions have already determined fundamental cosmological parameters to uncertainties of a few percent (c.f. DASI [5], ACBAR [6], Boomerang [7], WMAP [8]), and new data from Planck are poised to refine these further. The E-mode polarization of the CMB, whose detection was unthinkable twenty years ago, is now routinely measured by ground-based experiments (first detected by DASI [9, 10], with progressive improvements in resolution and sensitivity by CBI [11], QUaD [12], BICEPI [13], and QUIET [14]), while ever more sensitive limits on the B-mode power spectrum are beginning to place interesting constraints on the tensor-to-scalar ratio [13] (with the next generation cameras like SPTpol, BICEPII, the Keck Array, PolarBear, and ACTpol already in operation). By contrast, the early 1990s had just witnessed the first ever detection of CMB anisotropy on
The Status of the “Biopsychosocial” Model in Health Psychology: Towards an Integrated Approach and a Critique of Cultural Conceptions  [PDF]
Andrew R. Hatala
Open Journal of Medical Psychology (OJMP) , 2012, DOI: 10.4236/ojmp.2012.14009
Abstract: The current status of the “Biopsychosocial” Model in health psychology is contested and arguably exists in a stage of infancy. Despite original goals, medical researchers have developed theoretical and empirical integrations across bio-psycho-social domains only to a limited extent. This review article addresses this issue by making connections across research findings in health psychology and related medical fields in order to strengthen the associations across bio-psycho-social domains. In particular, research in sociosomatics, neuroplasticity and psychosocial genomics are introduced and explored. The role of “culture” as conceived of within the Biopsychosocial Model is also ambiguous and somewhat problematic. Arthur Klienman’s conceptions of culture as what is at stake for individuals in their local social and moral worlds is adopted to offer a critique of previous perspectives of culture and question its role amidst bio-psycho-social domains. Overall, a multilevel integrative or ‘holistic’ perspective is advanced to strengthen the Biopsychosocial Model for use within health psychology and biomedical research. In the end, some clinical implications are discussed.
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