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Search Results: 1 - 10 of 173486 matches for " Sybren de Hoog "
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Low effective dispersal of asexual genotypes in heterogeneous landscapes by the endemic pathogen Penicillium marneffei.
Fisher Matthew C,Hanage William P,de Hoog Sybren,Johnson Elizabeth
PLOS Pathogens , 2005,
Abstract: Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such "ubiquitous dispersal" has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological "species" will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.
Low Effective Dispersal of Asexual Genotypes in Heterogeneous Landscapes by the Endemic Pathogen Penicillium marneffei
Matthew C Fisher ,William P Hanage,Sybren de Hoog,Elizabeth Johnson,Michael D Smith,Nicholas J White,Nongnuch Vanittanakom
PLOS Pathogens , 2005, DOI: 10.1371/journal.ppat.0010020
Abstract: Long-distance dispersal in microbial eukaryotes has been shown to result in the establishment of populations on continental and global scales. Such “ubiquitous dispersal” has been claimed to be a general feature of microbial eukaryotes, homogenising populations over large scales. However, the unprecedented sampling of opportunistic infectious pathogens created by the global AIDS pandemic has revealed that a number of important species exhibit geographic endemicity despite long-distance migration via aerially dispersed spores. One mechanism that might tend to drive such endemicity in the face of aerial dispersal is the evolution of niche-adapted genotypes when sexual reproduction is rare. Dispersal of such asexual physiological “species” will be restricted when natural habitats are heterogeneous, as a consequence of reduced adaptive variation. Using the HIV-associated endemic fungus Penicillium marneffei as our model, we measured the distribution of genetic variation over a variety of spatial scales in two host species, humans and bamboo rats. Our results show that, despite widespread aerial dispersal, isolates of P. marneffei show extensive spatial genetic structure in both host species at local and country-wide scales. We show that the evolution of the P. marneffei genome is overwhelmingly clonal, and that this is perhaps the most asexual fungus yet found. We show that clusters of genotypes are specific to discrete ecological zones and argue that asexuality has led to the evolution of niche-adapted genotypes, and is driving endemicity, by reducing this pathogen's potential to diversify in nature.
Madurella mycetomatis Is Highly Susceptible to Ravuconazole
Sarah Abdalla Ahmed ,Wendy Kloezen,Frederick Duncanson,Ed E. Zijlstra,G. Sybren de Hoog,Ahmed H. Fahal,Wendy W. J. van de Sande
PLOS Neglected Tropical Diseases , 2014, DOI: 10.1371/journal.pntd.0002942
Abstract: The current treatment of eumycetoma utilizing ketoconazole is unsatisfactory because of high recurrence rates, which often leads to complications and unnecessary amputations, and its comparatively high cost in endemic areas. Hence, an effective and affordable drug is required to improve therapeutic outcome. E1224 is a potent orally available, broad-spectrum triazole currently being developed for the treatment of Chagas disease. E1224 is a prodrug that is rapidly converted to ravuconazole. Plasma levels of E1224 are low and transient, and its therapeutically active moiety, ravuconazole is therapeutically active. In the present study, the in vitro activity of ravuconazole against Madurella mycetomatis, the most common etiologic agent of eumycetoma, was evaluated and compared to that of ketoconazole and itraconazole. Ravuconazole showed excellent activity with MICs ranging between ≤0.002 and 0.031 μg/ml, which were significantly lower than the MICs reported for ketoconazole and itraconazole. On the basis of our findings, E1224 with its resultant active moiety, ravuconazole, could be an effective and affordable therapeutic option for the treatment of eumycetoma.
Lichtheimia Species Exhibit Differences in Virulence Potential
Volker U. Schwartze, Kerstin Hoffmann, Ildikó Nyilasi, Tamás Papp, Csaba Vágv?lgyi, Sybren de Hoog, Kerstin Voigt, Ilse D. Jacobsen
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0040908
Abstract: Although the number of mucormycosis cases has increased during the last decades, little is known about the pathogenic potential of most mucoralean fungi. Lichtheimia species represent the second and third most common cause of mucormycosis in Europe and worldwide, respectively. To date only three of the five species of the genus have been found to be involved in mucormycosis, namely L. corymbifera, L. ramosa and L. ornata. However, it is not clear whether the clinical situation reflects differences in virulence between the species of Lichtheimia or whether other factors are responsible. In this study the virulence of 46 strains of all five species of Lichtheimia was investigated in chicken embryos. Additionally, strains of the closest-related genus Dichotomocladium were tested. Full virulence was restricted to the clinically relevant species while all strains of L. hyalospora, L. sphaerocystis and Dichotomocladium species were attenuated. Although virulence differences were present in the clinically relevant species, no connection between origin (environmental vs clinical) or phylogenetic position within the species was observed. Physiological studies revealed no clear connection of stress resistance and carbon source utilization with the virulence of the strains. Slower growth at 37°C might explain low virulence of L. hyalospora, L. spaherocystis and Dichotomocladium; however, similarly slow growing strains of L. ornata were fully virulent. Thus, additional factors or a complex interplay of factors determines the virulence of strains. Our data suggest that the clinical situation in fact reflects different virulence potentials in the Lichtheimiaceae.
Phylogenetic Analysis Reveals a High Prevalence of Sporothrix brasiliensis in Feline Sporotrichosis Outbreaks
Anderson Messias Rodrigues,Marcus de Melo Teixeira,G. Sybren de Hoog,Tania Maria Pacheco Schubach,Sandro Antonio Pereira,Geisa Ferreira Fernandes,Leila Maria Lopes Bezerra,Maria Sueli Felipe,Zoilo Pires de Camargo
PLOS Neglected Tropical Diseases , 2013, DOI: 10.1371/journal.pntd.0002281
Abstract: Sporothrix schenckii, previously assumed to be the sole agent of human and animal sporotrichosis, is in fact a species complex. Recently recognized taxa include S. brasiliensis, S. globosa, S. mexicana, and S. luriei, in addition to S. schenckii sensu stricto. Over the last decades, large epidemics of sporotrichosis occurred in Brazil due to zoonotic transmission, and cats were pointed out as key susceptible hosts. In order to understand the eco-epidemiology of feline sporotrichosis and its role in human sporotrichosis a survey was conducted among symptomatic cats. Prevalence and phylogenetic relationships among feline Sporothrix species were investigated by reconstructing their phylogenetic origin using the calmodulin (CAL) and the translation elongation factor-1 alpha (EF1α) loci in strains originated from Rio de Janeiro (RJ, n = 15), Rio Grande do Sul (RS, n = 10), Paraná (PR, n = 4), S?o Paulo (SP, n = 3) and Minas Gerais (MG, n = 1). Our results showed that S. brasiliensis is highly prevalent among cats (96.9%) with sporotrichosis, while S. schenckii was identified only once. The genotype of Sporothrix from cats was found identical to S. brasiliensis from human sources confirming that the disease is transmitted by cats. Sporothrix brasiliensis presented low genetic diversity compared to its sister taxon S. schenckii. No evidence of recombination in S. brasiliensis was found by split decomposition or PHI-test analysis, suggesting that S. brasiliensis is a clonal species. Strains recovered in states SP, MG and PR share the genotype of the RJ outbreak, different from the RS clone. The occurrence of separate genotypes among strains indicated that the Brazilian S. brasiliensis epidemic has at least two distinct sources. We suggest that cats represent a major host and the main source of cat and human S. brasiliensis infections in Brazil.
Phylogenetic Findings Suggest Possible New Habitat and Routes of Infection of Human Eumyctoma
G. Sybren de Hoog,Sarah A. Ahmed ,Mohammad J. Najafzadeh,Deanna A. Sutton,Maryam Saradeghi Keisari,Ahmed H. Fahal,Ursala Eberhardt,Gerard J. Verkleij,Lian Xin,Benjamin Stielow,Wendy W. J. van de Sande
PLOS Neglected Tropical Diseases , 2013, DOI: 10.1371/journal.pntd.0002229
Abstract: Eumycetoma is a traumatic fungal infection in tropical and subtropical areas that may lead to severe disability. Madurella mycetomatis is one of the prevalent etiologic agents in arid Northeastern Africa. The source of infection has not been clarified. Subcutaneous inoculation from plant thorns has been hypothesized, but attempts to detect the fungus in relevant material have remained unsuccessful. The present study aims to find clues to reveal the natural habitat of Madurella species using a phylogenetic approach, i.e. by comparison of neighboring taxa with known ecology. Four species of Madurella were included in a large data set of species of Chaetomium, Chaetomidium, Thielavia, and Papulaspora (n = 128) using sequences of the universal fungal barcode gene rDNA ITS and the partial LSU gene sequence. Our study demonstrates that Madurella species are nested within the Chaetomiaceae, a family of fungi that mainly inhabit animal dung, enriched soil, and indoor environments. We hypothesize that cattle dung, ubiquitously present in rural East Africa, plays a significant role in the ecology of Madurella. If cow dung is an essential factor in inoculation by Madurella, preventative measures may involve the use of appropriate footwear in addition to restructuring of villages to reduce the frequency of contact with etiologic agents of mycetoma. On the other hand, the Chaetomiaceae possess a hidden clinical potential which needs to be explored.
New Coherence and RIP Analysis for Weak Orthogonal Matching Pursuit
Mingrui Yang,Frank de Hoog
Mathematics , 2014,
Abstract: In this paper we define a new coherence index, named the global 2-coherence, of a given dictionary and study its relationship with the traditional mutual coherence and the restricted isometry constant. By exploring this relationship, we obtain more general results on sparse signal reconstruction using greedy algorithms in the compressive sensing (CS) framework. In particular, we obtain an improved bound over the best known results on the restricted isometry constant for successful recovery of sparse signals using orthogonal matching pursuit (OMP).
Orthogonal Matching Pursuit with Thresholding and its Application in Compressive Sensing
Mingrui Yang,Frank de Hoog
Computer Science , 2013,
Abstract: Greed is good. However, the tighter you squeeze, the less you have. In this paper, a less greedy algorithm for sparse signal reconstruction in compressive sensing, named orthogonal matching pursuit with thresholding is studied. Using the global 2-coherence , which provides a "bridge" between the well known mutual coherence and the restricted isometry constant, the performance of orthogonal matching pursuit with thresholding is analyzed and more general results for sparse signal reconstruction are obtained. It is also shown that given the same assumption on the coherence index and the restricted isometry constant as required for orthogonal matching pursuit, the thresholding variation gives exactly the same reconstruction performance with significantly less complexity.
Hyperspectral Image Recovery from Incomplete and Imperfect Measurements via Hybrid Regularization
Reza Arablouei,Frank de Hoog
Computer Science , 2015,
Abstract: Natural images tend to mostly consist of smooth regions with individual pixels having highly correlated spectra. This information can be exploited to recover hyperspectral images of natural scenes from their incomplete and noisy measurements. To perform the recovery while taking full advantage of the prior knowledge, we formulate a composite cost function containing a square-error data-fitting term and two distinct regularization terms pertaining to spatial and spectral domains. The regularization for the spatial domain is the sum of total-variation of the image frames corresponding to all spectral bands. The regularization for the spectral domain is the l_1-norm of the coefficient matrix obtained by applying a suitable sparsifying transform to the spectra of the pixels. We use an accelerated proximal-subgradient method to minimize the formulated cost function. We analyse the performance of the proposed algorithm and prove its convergence. Numerical simulations using real hyperspectral images exhibit that the proposed algorithm offers an excellent recovery performance with a number of measurements that is only a small fraction of the hyperspectral image data size. Simulation results also show that the proposed algorithm significantly outperforms an accelerated proximal-gradient algorithm that solves the classical basis-pursuit denoising problem to recover the hyperspectral image.
Parascedosporium and its relatives: phylogeny and ecological trends
M. Lackner,G.S. de Hoog
IMA Fungus , 2011,
Abstract: The genus Seedosporiurn and its relatives comprising microascalean anamorphs with slimy conidia were studied. Graphiurn and Paraseedosporiurn also belong to this complex, while teleomorphs are found in Pseudalleseheria, Petriella, Petriellopsis, and Lophotriehus. Species complexes were clearly resolved by rDNA ITS sequencing. Significantly different ecological trends were observed between resolved species aggregates. The Pseudalleseheria and Seedosporiurn pro/ifieans clades were the only lineages with a marked opportunistic potential to mammals, while Petriella species were associated primarily with soil enriched by, e.g.dung. A consistent association with bark beetles was observed in the Graphiurn clade. The ex-type strain of Rhinoe/adiurn /esnei, CBS 108.10 was incorrectly implicated by Vuillemin (1910) in a case of human mycetoma; its sequence was identical to that of the ex-type strain of Paraseedosporiurn teetonae, CBS 127.84.
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