Publications

optimization of control strategies for epidemics in heterogeneous populations with symmetric and asymmetric transmission.	there is growing interest in incorporating economic factors into epidemiological models in order to identify optimal strategies for disease control when resources are limited. in this paper we consider how to optimize the control of a pathogen that is capable of infecting multiple hosts with different rates of transmission within and between species. our objective is to find control strategies that maximize the discounted number of healthy individuals. we consider two classes of host-pathogen sy ...	2010	19900466
incidence of endornaviruses in phytophthora taxon douglasfir and phytophthora ramorum.	in this investigation, we show that four phytophthora taxon douglasfir isolates from the usa, irrespective of their geographical location or host plant, and 20% of a representative cohort of phytophthora ramorum isolates contain endornavirus dsrnas. three endornavirus-specific rt-pcr amplicons were generated by rt-pcr using dsrna isolated from the four phytophthora taxon douglasfir isolates and one representative phytophthora ramorum isolate as template with oligonucleotide primers designed from ...	2010	19915969
clonal expansion of the belgian phytophthora ramorum populations based on new microsatellite markers.	co-existence of both mating types a1 and a2 within the eu1 lineage of phytophthora ramorum has only been observed in belgium, which begs the question whether sexual reproduction is occurring. a collection of 411 belgian p. ramorum isolates was established during a 7-year survey. our main objectives were genetic characterization of this population to test for sexual reproduction, determination of population structure, evolution and spread, and evaluation of the effectiveness and impact of control ...	2010	20002581
rapid detection of phytophthora ramorum and p. kernoviae by two-minute dna extraction followed by isothermal amplification and amplicon detection by generic lateral flow device.	abstract a method for nucleic-acid-based detection of pathogens in plant material has been developed which comprises a simple and rapid method for extracting dna on the nitrocellulose membranes of lateral-flow devices, loop-mediated isothermal amplification (lamp) of target dna using labeled primers, and detection of the generically labeled amplification products by a sandwich immunoassay in a lateral-flow-device format. each of these steps can be performed without specialist equipment and is su ...	2010	20055648
a five-minute dna extraction method for expedited detection of phytophthora ramorum following prescreening using phytophthora spp. lateral flow devices.	in a direct comparison with established methods for phytophthora ramorum detection (isolation followed by morphological identification, or conventional dna extraction followed by taqman real-time pcr) a rapid, simplified detection method in which membranes of lateral flow devices (lfds) are added directly to taqman real-time pcr reactions was used to test 202 plant samples collected by plant health inspectors in the field. p. ramorum prevalence within the 202 samples was approximately 40% accord ...	2010	20171248
myosin diversity in the diatom phaeodactylum tricornutum.	this report describes the domain architecture of ten myosins cloned from the pennate diatom phaeodactylum tricornutum. several of the p. tricornutum myosins show similarity to myosins from the centric diatom thalassiosira pseudonana as well as to one myosin from the oomycete phytophthora ramorum. the p. tricornutum myosins, ranging in size from 126 kda to over 250 kda, all possess the canonical head, neck and tail domains common to most myosins, though variations in each of these domains is evid ...	2010	20217677
apparent competition in canopy trees determined by pathogen transmission rather than susceptibility.	epidemiological theory predicts that asymmetric transmission, susceptibility, and mortality within a community will drive pathogen and disease dynamics. these epidemiological asymmetries can result in apparent competition, where a highly infectious host reduces the abundance of less infectious or more susceptible members in a community via a shared pathogen. we show that the exotic pathogen phytophthora ramorum and resulting disease, sudden oak death, cause apparent competition among canopy tree ...	2010	20391996
predicting the economic costs and property value losses attributed to sudden oak death damage in california (2010-2020).	phytophthora ramorum, cause of sudden oak death, is a quarantined, non-native, invasive forest pathogen resulting in substantial mortality in coastal live oak (quercus agrifolia) and several other related tree species on the pacific coast of the united states. we estimate the discounted cost of oak treatment, removal, and replacement on developed land in california communities using simulations of p. ramorum spread and infection risk over the next decade (2010-2020). an estimated 734 thousand oa ...	2011	21224033
aberrant genome size and instability of phytophthora ramorum oospore progenies.	the functionality of the sexual cycle in the heterothallic pathogen phytophthora ramorum, causal agent of sudden oak death, has recently been demonstrated. sexual reproduction could create genotypic variation and increase the pathogen's ability to adapt to other host plants or changing environments. genetic characterization using co-dominant microsatellite markers and flow cytometry of single-oospore progeny of crosses between a european a1 isolate and north american or european a2 isolates reve ...	2011	21272658
forest type influences transmission of phytophthora ramorum in california oak woodlands.	the transmission ecology of phytophthora ramorum from bay laurel (umbellularia californica) leaves was compared between mixed-evergreen and redwood forest types throughout winter and summer disease cycles in central, coastal california. in a preliminary multisite study, we found that abscission rates of infected leaves were higher at mixed-evergreen sites. in addition, final infection counts were slightly higher at mixed-evergreen sites or not significantly different than at redwood sites, in pa ...	2011	21391827
genetic characterization of phytophthora nicotianae by the analysis of polymorphic regions of the mitochondrial dna.	a new method based on the analysis of mitochondrial intergenic regions characterized by intraspecific variation in dna sequences was developed and applied to the study of the plant pathogen phytophthora nicotianae. two regions flanked by genes trny and rns and trnw and cox2 were identified by comparing the whole mitochondrial genomes of phytophthora infestans, phytophthora ramorum, and phytophthora sojae and amplified using primers designed from the flanking conserved genes. these regions were s ...	2011	21530925
interacting disturbances: wildfire severity affected by stage of forest disease invasion.	sudden oak death (sod) is an emerging forest disease causing extensive tree mortality in coastal california forests. recent california wildfires provided an opportunity to test a major assumption underlying discussions of sod and land management: sod mortality will increase fire severity. we examined prefire fuels from host species in a forest monitoring plot network in big sur, california (usa), to understand the interactions between disease-caused mortality and wildfire severity during the 200 ...	2011	21563563
networks in plant epidemiology: from genes to landscapes, countries, and continents.	there is increasing use of networks in ecology and epidemiology, but still relatively little application in phytopathology. networks are sets of elements (nodes) connected in various ways by links (edges). network analysis aims to understand system dynamics and outcomes in relation to network characteristics. many existing natural, social, and technological networks have been shown to have small-world (local connectivity with short-cuts) and scale-free (presence of super-connected nodes) propert ...	2011	21062110
phytophthora ramorum in canada: evidence for migration within north america and from europe.	phytophthora ramorum, the cause of sudden oak death on oak and ramorum blight on woody ornamentals, has been reported in ornamental nurseries on the west coast of north america from british columbia to california. long-distance migration of p. ramorum has occurred via the nursery trade, and shipments of host plants are known to have crossed the u.s.-canadian border. we investigated the genotypic diversity of p. ramorum in canadian nurseries and compared the canadian population with u.s. and euro ...	2011	20879846
learning from history, predicting the future: the uk dutch elm disease outbreak in relation to contemporary tree disease threats.	expanding international trade and increased transportation are heavily implicated in the growing threat posed by invasive pathogens to biodiversity and landscapes. with trees and woodland in the uk now facing threats from a number of disease systems, this paper looks to historical experience with the dutch elm disease (ded) epidemic of the 1970s to see what can be learned about an outbreak and attempts to prevent, manage and control it. the paper draws on an interdisciplinary investigation into ...	2011	21624917
identification of new polymorphic microsatellite markers in the na1 and na2 lineages of phytophthora ramorum.	phytophthora ramorum is a recently introduced pathogen in europe and north america consisting of three clonal lineages. due to the very limited intra-lineage genetic variation, only a few polymorphic markers are available for use in studies involving the epidemiology and evolution of p. ramorum. a total of 159 primer pairs for candidate polymorphic ssr loci were tested with universal labeling. four polymorphic microsatellite loci were identified within the na1 lineage and one within the na2 line ...	2011	21642345
a test system to quantify inoculum in runoff from phytophthora ramorum-infected plant roots.	foliar hosts of phytophthora ramorum are often susceptible to root infection, but the epidemiological significance of such infections is unknown. a standardized test system was developed to quantify inoculum in runoff from root-infected viburnum tinus 'spring bouquet' or rhododendron 'cunningham's white' cuttings. cuttings of both species gave off a maximum amount of inoculum 1 to 3 weeks after inoculation. the greatest amount of inoculum was recovered from viburnum roots that were 48 to 70 days ...	2011	21830955
Horizontal gene transfer facilitated the evolution of plant parasitic mechanisms in the oomycetes.	Horizontal gene transfer (HGT) can radically alter the genomes of microorganisms, providing the capacity to adapt to new lifestyles, environments, and hosts. However, the extent of HGT between eukaryotes is unclear. Using whole-genome, gene-by-gene phylogenetic analysis we demonstrate an extensive pattern of cross-kingdom HGT between fungi and oomycetes. Comparative genomics, including the de novo genome sequence of Hyphochytrium catenoides, a free-living sister of the oomycetes, shows that thes ...	2011	21878562
forest species diversity reduces disease risk in a generalist plant pathogen invasion.	empirical evidence suggests that biodiversity loss can increase disease transmission, yet our understanding of the 'diversity-disease hypothesis' for generalist pathogens in natural ecosystems is limited. we used a landscape epidemiological approach to examine two scenarios regarding diversity effects on the emerging plant pathogen phytophthora ramorum across a broad, heterogeneous ecoregion: (1) an amplification effect exists where disease risk is greater in areas with higher plant diversity du ...	2011	21884563
the inclusion of downy mildews in a multi-locus-dataset and its reanalysis reveals a high degree of paraphyly in phytophthora.	pathogens belonging to the oomycota, a group of heterokont, fungal-like organisms, are amongst the most notorious pathogens in agriculture. in particular, the obligate biotrophic downy mildews and the hemibiotrophic members of the genus phytophthora are responsible for a huge variety of destructive diseases, including sudden oak death caused by p. ramorum, potato late blight caused by p. infestans, cucurbit downy mildew caused by pseudoperonospora cubensis, and grape downy mildew caused by plasm ...	2011	22679601
genome-wide identification of laccase gene family in three phytophthora species.	phytophthora spp. is a primary pathogen in oomycete, causing economically and environmentally devastating epidemics of plants. laccases have been found in all domains of life but have not been reported in oomycte. in this paper, laccase genes of phytophthora spp. were identified in three genomes (phytophthora capsici, phytophthora sojae and phytophthora ramorum). 18 laccase genes were identified in total, including four in p. capsici genome, six in p. sojae genome and eight in p. ramorum genome. ...	2012	23283515
landscape epidemiology and control of pathogens with cryptic and long-distance dispersal: sudden oak death in northern californian forests.	exotic pathogens and pests threaten ecosystem service, biodiversity, and crop security globally. if an invasive agent can disperse asymptomatically over long distances, multiple spatial and temporal scales interplay, making identification of effective strategies to regulate, monitor, and control disease extremely difficult. the management of outbreaks is also challenged by limited data on the actual area infested and the dynamics of spatial spread, due to financial, technological, or social cons ...	2012	22241973