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Search Results: 1 - 10 of 17488 matches for " Andrew Paterson "
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A cornucopia of genomes
Andrew H Paterson
Genome Biology , 2006, DOI: 10.1186/gb-2006-7-3-311
Abstract: The 14th annual Plant and Animal Genome conference held recently in San Diego highlighted the challenges facing researchers who attempt to annotate and interpret the burgeoning numbers of plant and animal genome sequences. These include the genomes of the world's leading crops and provide valuable models for the study of genetics, evolution and development. More than 80 workshops addressed emerging results and opportunities, as well as technological developments, in a host of plant, animal and microbial genomes. Two recurring themes of the meeting were the continuing 'siliconization' of plant and animal biology and the rapid progress being made in understanding the mechanisms of epigenetics and its biological roles.Progress in sequencing plant genomes was highlighted by Aristotle Patrinos (US Department of Energy (DOE), Washington DC, USA) who announced that the Joint Genome Institute will be sequencing the soybean (Glycine max) genome, to add to its current whole-genome sequencing projects for sorghum (Sorghum bicolor), Arabidopsis lyrata and Capsella rubella (close relatives of the model plant Arabidopsis thaliana), and Mimulus guttatus (monkey flower), and its participation in the maize (Zea mays) genome project. Patrinos briefly outlined DOE systems biology approaches to its missions, in particular a 10-15-year goal of its 'Genomes To Life' program to generate a microbial sequence, produce all proteins and molecular tags, identify multiprotein complexes, generate regulatory networks, identify metabolic capabilities and engineer control strategies - "all in a few days".Patrinos's description of the informatics challenge as a "tsunami looming over genome projects" was further elaborated on by Kimmen Sjolander (University of California, Berkeley, USA), who noted that only 3% of gene annotations have empirical support. In addition to mechanical and/or technical errors, domain shuffling and gene duplication play an important role in generating annotation errors. Sjol
Genomics of Sorghum
Andrew H. Paterson
International Journal of Plant Genomics , 2008, DOI: 10.1155/2008/362451
Abstract: Sorghum (Sorghum bicolor (L.) Moench) is a subject of plant genomics research based on its importance as one of the world's leading cereal crops, a biofuels crop of high and growing importance, a progenitor of one of the world's most noxious weeds, and a botanical model for many tropical grasses with complex genomes. A rich history of genome analysis, culminating in the recent complete sequencing of the genome of a leading inbred, provides a foundation for invigorating progress toward relating sorghum genes to their functions. Further characterization of the genomes other than Saccharinae cereals may shed light on mechanisms, levels, and patterns of evolution of genome size and structure, laying the foundation for further study of sugarcane and other economically important members of the group.
Predicting the Impact of Long-Term Temperature Changes on the Epidemiology and Control of Schistosomiasis: A Mechanistic Model
Tara D. Mangal, Steve Paterson, Andrew Fenton
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001438
Abstract: Background Many parasites of medical and veterinary importance are transmitted by cold-blooded intermediate hosts or vectors, the abundance of which will vary with ambient temperatures, potentially altering disease prevalence. In particular, if global climate change will increase mean ambient temperature in a region endemic with a human pathogen then it is possible that the incidence of disease will similarly increase. Here we examine this possibility by using a mathematical model to explore the effects of increasing long-term mean ambient temperature on the prevalence and abundance of the parasite Schistosoma mansoni, the causative agent of schistosomiasis in humans. Principal Findings The model showed that the impact of temperature on disease prevalence and abundance is not straightforward; the mean infection burden in humans increases up to 30°C, but then crashes at 35°C, primarily due to increased mortalities of the snail intermediate host. In addition, increased temperatures changed the dynamics of disease from stable, endemic infection to unstable, epidemic cycles at 35°C. However, the prevalence of infection was largely unchanged by increasing temperatures. Temperature increases also affected the response of the model to changes in each parameter, indicating certain control strategies may become less effective with local temperature changes. At lower temperatures, the most effective single control strategy is to target the adult parasites through chemotherapy. However, as temperatures increase, targeting the snail intermediate hosts, for example through molluscicide use, becomes more effective. Conclusions These results show that S. mansoni will not respond to increased temperatures in a linear fashion, and the optimal control strategy is likely to change as temperatures change. It is only through a mechanistic approach, incorporating the combined effects of temperature on all stages of the life-cycle, that we can begin to predict the consequences of climate change on the incidence and severity of such diseases.
Gene Conversion in Angiosperm Genomes with an Emphasis on Genes Duplicated by Polyploidization
Xi-Yin Wang,Andrew H. Paterson
Genes , 2011, DOI: 10.3390/genes2010001
Abstract: Angiosperm genomes differ from those of mammals by extensive and recursive polyploidizations. The resulting gene duplication provides opportunities both for genetic innovation, and for concerted evolution. Though most genes may escape conversion by their homologs, concerted evolution of duplicated genes can last for millions of years or longer after their origin. Indeed, paralogous genes on two rice chromosomes duplicated an estimated 60–70 million years ago have experienced gene conversion in the past 400,000 years. Gene conversion preserves similarity of paralogous genes, but appears to accelerate their divergence from orthologous genes in other species. The mutagenic nature of recombination coupled with the buffering effect provided by gene redundancy, may facilitate the evolution of novel alleles that confer functional innovations while insulating biological fitness of affected plants. A mixed evolutionary model, characterized by a primary birth-and-death process and occasional homoeologous recombination and gene conversion, may best explain the evolution of multigene families.
A new set of qualitative reliability criteria to aid inferences on palaeomagnetic dipole moment variations through geological time
Andrew J. Biggin,Greig A. Paterson
Frontiers in Earth Science , 2014, DOI: 10.3389/feart.2014.00024
Abstract: Records of reversal frequency support forcing of the geodynamo over geological timescales but obtaining these for earlier times (e.g., the Precambrian) is a major challenge. Changes in the measured virtual (axial) dipole moment of the Earth, averaged over several millions of years or longer, also have the potential to constrain core and mantle evolution through deep time. There have been a wealth of recent innovations in palaeointensity methods, but there is, as yet, no comprehensive means for assessing the reliability of new and existing dipole moment data. Here we present a new set of largely qualitative reliability criteria for palaeointensity results at the site mean level, which we term QPI in reference to the long-standing Q criteria used for assessing palaeomagnetic poles. These represent the first attempt to capture the range of biasing agents applicable to palaeointensity measurements and to recognize the various approaches employed to obviate them. A total of 8 criteria are proposed and applied to 312 dipole moment estimates recently incorporated into the PINT global database. The number of these criteria fulfilled by a single dipole moment estimate (the QPI value) varies between 1 and 6 in the examined dataset and has a median of 3. Success rates for each of the criteria are highly variable, but each criterion was met by at least a few results. The new criteria will be useful for future studies as a means of gauging the reliability of new and published dipole moment estimates.
Host-Pathogen Wars: New Weapons from Biotechnology and Genomics  [PDF]
Mychele B. da Silva, Richard F. Davis, Andrew H. Paterson, Nelson Dias Suassuna, Shavannor M. Smith, Peng W. Chee
American Journal of Plant Sciences (AJPS) , 2019, DOI: 10.4236/ajps.2019.103029
Abstract: Pathogens are imminent threats to crop production. Among the management tools available to protect crops from diseases, the use of host-plant resistance had been hindered by a lack of tools and resources to identify resistance genes (R-genes). Genomic technologies have empowered acquisition of a new level and quality of information on plant-pathogen interactions. Next generation sequencing, differential transcriptome analysis, gene editing, and use of bioinformatics have greatly expanded the numbers of R-genes identified, enriched understanding of R-avirulence gene interactions, and disease diagnosis. In this review, we highlight the application of genomic technologies to identification of pathogen machinery for future improvement of host plant resistance.
A novel joint location-scale testing framework for improved detection of variants with main or interaction effects
David Soave,Andrew Paterson,Lisa Strug,Lei Sun
Statistics , 2014,
Abstract: We propose a novel and easy-to-implement joint location-scale association testing procedure that can account for complex genetic architecture without explicitly modeling interaction effects, and is suitable for large-scale whole-genome scans and meta-analyses. We focus on Fisher's method and use it to combine evidence from the standard location test and the more recent scale test, and we describe its use for single-variant, gene-set and pathway association analyses.
The Application of Restriction Landmark Genome Scanning Method for Surveillance of Non-Mendelian Inheritance in Hybrids
Tomoko Takamiya,Saeko Hosobuchi,Tomotsugu Noguchi,Andrew H. Paterson,Hiroshi Iijima,Yasufumi Murakami,Hisato Okuizumi
Comparative and Functional Genomics , 2009, DOI: 10.1155/2009/245927
Abstract: We analyzed inheritance of DNA methylation in reciprocal F1 hybrids (subsp. japonica cv. Nipponbare × subsp. indica cv. Kasalath) of rice (Oryza sativa L.) using restriction landmark genome scanning (RLGS), and detected differing RLGS spots between the parents and reciprocal F1 hybrids. MspI/HpaII restriction sites in the DNA from these different spots were suspected to be heterozygously methylated in the Nipponbare parent. These spots segregated in F1 plants, but did not segregate in selfed progeny of Nipponbare, showing non-Mendelian inheritance of the methylation status. As a result of RT-PCR and sequencing, a specific allele of the gene nearest to the methylated sites was expressed in reciprocal F1 plants, showing evidence of biased allelic expression. These results show the applicability of RLGS for scanning of non-Mendelian inheritance of DNA methylation and biased allelic expression.
Genetic Diversity in Cytokines Associated with Immune Variation and Resistance to Multiple Pathogens in a Natural Rodent Population
Andrew K. Turner ,Mike Begon,Joseph A. Jackson,Janette E. Bradley,Steve Paterson
PLOS Genetics , 2011, DOI: 10.1371/journal.pgen.1002343
Abstract: Pathogens are believed to drive genetic diversity at host loci involved in immunity to infectious disease. To date, studies exploring the genetic basis of pathogen resistance in the wild have focussed almost exclusively on genes of the Major Histocompatibility Complex (MHC); the role of genetic variation elsewhere in the genome as a basis for variation in pathogen resistance has rarely been explored in natural populations. Cytokines are signalling molecules with a role in many immunological and physiological processes. Here we use a natural population of field voles (Microtus agrestis) to examine how genetic diversity at a suite of cytokine and other immune loci impacts the immune response phenotype and resistance to several endemic pathogen species. By using linear models to first control for a range of non-genetic factors, we demonstrate strong effects of genetic variation at cytokine loci both on host immunological parameters and on resistance to multiple pathogens. These effects were primarily localized to three cytokine genes (Interleukin 1 beta (Il1b), Il2, and Il12b), rather than to other cytokines tested, or to membrane-bound, non-cytokine immune loci. The observed genetic effects were as great as for other intrinsic factors such as sex and body weight. Our results demonstrate that genetic diversity at cytokine loci is a novel and important source of individual variation in immune function and pathogen resistance in natural populations. The products of these loci are therefore likely to affect interactions between pathogens and help determine survival and reproductive success in natural populations. Our study also highlights the utility of wild rodents as a model of ecological immunology, to better understand the causes and consequences of variation in immune function in natural populations including humans.
Comparative genomic analysis of C4 photosynthetic pathway evolution in grasses
Xiyin Wang, Udo Gowik, Haibao Tang, John E Bowers, Peter Westhoff, Andrew H Paterson
Genome Biology , 2009, DOI: 10.1186/gb-2009-10-6-r68
Abstract: We show that both whole-genome and individual gene duplication have contributed to the evolution of C4 photosynthesis. The C4 gene isoforms show differential duplicability, with some C4 genes being recruited from whole genome duplication duplicates by multiple modes of functional innovation. The sorghum and maize carbonic anhydrase genes display a novel mode of new gene formation, with recursive tandem duplication and gene fusion accompanied by adaptive evolution to produce C4 genes with one to three functional units. Other C4 enzymes in sorghum and maize also show evidence of adaptive evolution, though differing in level and mode. Intriguingly, a phosphoenolpyruvate carboxylase gene in the C3 plant rice has also been evolving rapidly and shows evidence of adaptive evolution, although lacking key mutations that are characteristic of C4 metabolism. We also found evidence that both gene redundancy and alternative splicing may have sheltered the evolution of new function.Gene duplication followed by functional innovation is common to evolution of most but not all C4 genes. The apparently long time-lag between the availability of duplicates for recruitment into C4 and the appearance of C4 grasses, together with the heterogeneity of origins of C4 genes, suggests that there may have been a long transition process before the establishment of C4 photosynthesis.Many of the most productive crops in agriculture use the C4 photosynthetic pathway. Despite their multiple origins, they are all characterized by high rates of photosynthesis and efficient use of water and nitrogen. As a morphological and biochemical innovation [1], the C4 photosynthetic pathway is proposed to have been an adaptation to hot, dry environments or CO2 deficiency [2-5]. The C4 pathway independently appeared at least 50 times during angiosperm evolution [6,7]. Multiple origins of the C4 pathway within some angiosperm families [8,9] imply that its evolution may not be complex, perhaps suggesting that there
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