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Susceptibility genes : an additional source for improved resistance
Sun, Kaile - \ 2017
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Evert Jacobsen; Yuling Bai. - Wageningen : Wageningen University - ISBN 9789463431415 - 174
solanum tuberosum - potatoes - solanum lycopersicum - tomatoes - genes - susceptibility - plant pathogenic fungi - phytophthora infestans - disease resistance - plant breeding - aardappelen - tomaten - genen - vatbaarheid - plantenziekteverwekkende schimmels - ziekteresistentie - plantenveredeling

Potato is affected by several diseases. Although, resistance can be obtained by introgression of major resistance genes from wild species, this has rarely been durable. Hence, other sources of resistance are highly needed. New research with a focus on loss of function mutations has led to the identification of disease susceptibility (S) genes in plants. The research in this thesis was aimed at the identification and characterization of potato S genes involved in the interaction with Phytophthora infestans and Botrytis cinerea. We selected 11 Arabidopsis thaliana S genes and silenced their potato orthologs by RNAi in the potato cultivar Desiree. The silencing of six genes resulted in resistance to P. infestans. Moreover, silencing of StDND1 reduced the infection of B. cinerea. Microscopic analysis showed that spore attachment and/or germination of P. infestans and B. cinerea was hampered on the leaf surface of StDND1-silenced potato plants. On StDMR1- and StDMR6-silenced potato plants, hyphal growth of P. infestans was arrested by the hypersensitive response-like cell death. Our results demonstrate that impairment of plant S genes may open a new way for breeding potatoes with resistance to pathogens like P. infestans and B. cinerea.

Susceptibility pays off: insights into the mlo-based powdery mildew resistance
Appiano, Michela - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Yuling Bai; Anne-Marie Wolters. - Wageningen : Wageningen University - ISBN 9789462579484 - 265
solanum lycopersicum - tomatoes - disease resistance - susceptibility - oidium neolycopersici - genes - gene expression - genomics - molecular breeding - plant breeding - tomaten - ziekteresistentie - vatbaarheid - genen - genexpressie - genomica - moleculaire veredeling - plantenveredeling

Powdery mildew (PM) is a worldwide-occurring plant disease caused by ascomycete fungi of the order Erysiphales. A conspicuous number of plant species are susceptible to this disease, the occurrence of which is increasing due to the influence of climate change. Symptoms are easy to recognize by the powdery whitish fungal structures growing on the surface of plant organs. Severe infections cause significant losses in crops, such as tomato, cucumber and wheat, as well as in ornamentals, like rose and petunia. Accordingly, breeding crops with a robust immunity to this disease is of great economic importance.

A significant step in this direction was the discovery of mlo (mildew locus o) mutant alleles of the barley HvMlo gene, which are responsible for the non-race specific resistance to the barley PM pathogen, Blumeria graminis f.sp. hordei (Bgh). During the years, this recessively inherited resistance was observed to be durable, contrary to the short life-span of resistances conferred by dominant resistance (R-) genes used in barley breeding programs. Studies on the histological mechanisms of the mlo-based resistance showed that the PM pathogen was stopped during penetration of the cell wall by the formation of a papilla. This structure prevents the formation of the feeding structure of the pathogen, called a haustorium.

After sequencing many plant genomes, we are discovering that MLO genes are not only typical of this cereal, but are ubiquitously present in higher plant species in multiple copies per species, forming a gene family. The impairment of some members of a number of ever increasing plant species lead to broad-spectrum resistance towards their adapted PM pathogens. For example, in tomato the ol-2 gene, naturally harbored by the cherry tomato Solanum lycopersicum var. cerasiforme, represents the loss-of-function allele of the SlMLO1 gene, conferring resistance to the PM pathogen Oidium neolycopersici (On). Consequently, the use of mlo mutants represents a suitable alternative to the classical use of R-genes in breeding programs.

In Chapter 2, we describe the in silico identification of the complete tomato SlMLO gene family using the available information in the SOL genomic network database. In total, 16 tomato SlMLO members were cloned from leaf, root, flower and fruit of the susceptible tomato cv. Moneymaker to confirm the sequences retrieved from the database and to verify their actual expression in these tissues. We observed the presence of various types of splicing variants, although their possible functional meaning has not been investigated. Motif analyses of each of the translated protein sequences and phylogenetic studies highlighted, on one hand, amino acid stretches that characterize the whole MLO family, and, on the other hand, stretches conserved in MLO homologs that are phylogenetically related. Following a gene expression study upon On inoculation, we identified members of the SlMLO family that are upregulated few hours after pathogen challenge. Except SlMLO1, none of the three newly identified homologs in clade V, thus phylogenetically close to SlMLO1, are induced. Interestingly, two homologs, each found in different clades, are upregulated similarly to SlMLO1. Using an RNAi approach, we silenced the additional clade V-SlMLO homologs, namely SlMLO3, SlMLO5 and SlMLO8, to investigate their possible role in PM resistance. We observed that none of these homologs if individually silenced, leads to PM resistance. However, if SlMLO5 and SlMLO8 are silenced together with SlMLO1, a significantly higher level of resistance is achieved compared to plants carrying the ol-2 allele. The role of SlMLO3 could not be verified. We, therefore, concluded that there are three SlMLO genes in tomato unevenly contributing to the PM disease, of which SlMLO1 has a major role.

Chapter 3 focuses on the components of the tomato mlo-based resistance. In Arabidopsis, it is known that four members of the SNARE protein family, involved in membrane fusion, are involved in mlo-based resistance. In this chapter, we focused on the identification of tomato homologs of the Arabidopsis syntaxin PEN1 (AtSYP121). Among the group of syntaxins identified in tomato, two were closely related to each other and also to AtPEN1, denominated SlPEN1a and SlPEN1b. Another Arabidopsis syntaxin that shows a high level of homology with PEN1, called SYP122, was also found to group together with the newly identified SlPEN1 genes. However, the role of SYP122 in plant immunity was not shown in literature. After obtaining individual silencing RNAi constructs, we transformed the resistant ol-2 line, and we challenged the obtained transformants with the adapted PM On, and the non-adapted Bgh. Interestingly, we observed a significant On growth and an enhanced Bgh cell entry only in SlPEN1a silenced plants but not in SlPEN1b silenced ones. We performed a protein alignment of tomato and Arabidopsis functional and non-functional PEN sequences. The presence of three differently conserved non-synonymous amino-acid substitutions is hypothesised to be responsible for the specialization in plant immune function.

In Chapter 4 and Chapter 5, we build up a body of evidence pointing to the fact that the function of the MLO susceptibility genes is highly conserved between monocot and dicot plant species.

In Chapter 4 we started by identifying and functionally characterizing two new MLO genes of Solanaceous crops affected by the PM disease, tobacco (Nicotiana tabacum) and eggplant (Solanum melongena). We named them NtMLO1 and SmMLO1 in the respective species, as they are the closest homologs to tomato SlMLO1. By overexpressing these genes in the resistant ol-2 line, we obtained transgenic plants that were susceptible to the PM pathogen On. This finding demonstrates that both heterologous MLO proteins can rescue the function of the impaired ol-2 allele in tomato. In addition, we found in tobacco NtMLO1 an amino acid (Q198) of critical importance for the susceptibility function of this protein.

In Chapter 5, we used the same approach adopted in Chapter 4 to show that other MLO proteins of more distant dicot species, like pea PsMLO1, can rescue the loss-of-function of the tomato ol-2 allele. And finally, we stretched this concept also to monocot MLO proteins, using barley HvMlo. While performing these experiments, we could verify that the function of the monocot and dicot susceptibility MLO proteins does not rely on the presence of class-specific conservation. The latter can be the reason for the phylogenetic divergence, placing monocot MLO proteins in clade IV and dicot MLO proteins in clade V of the phylogenetic MLO tree. However, functional conservation might depend on crucial shared amino acids of clade IV and V MLO proteins. Therefore, we also conducted a codon-based evolutionary analysis that resulted in the identification of 130 codons under negative selection, thus strongly maintained during evolution.

In Chapter 6 we introduce the PM disease in cucumber caused by Podosphaera xanthii (Px). We cloned the candidate susceptibility gene for PM in cucumber, CsaMLO8, from susceptible and resistant genotypes. The latter was described as an advanced cucumber breeding line characterized by hypocotyl resistance. In this line, we found the presence of aberrant splicing variants of the CsaMLO8 mRNA due to the insertion in its corresponding genomic region of a Class LTR retrotransposon. Heterologous expression of the wild-type cucumber allele in the tomato ol-2 line restored its PM susceptibility, while the heterologous expression of the aberrant protein variant failed to do so. This finding confirms that the resistance of the advanced cucumber breeding line is due to the disruption of the coding region of this gene. We also showed that the expression of CsaMLO8 in the susceptible genotype is induced by Px in hypocotyl tissue, but not in cotyledon or leaf. Finally, by examination of the resequencing data of a collection of 115 cucumber accessions, we found the presence of the TE-containing allele in 31 of them among which a wild cucumber accession that might have been used in breeding programs to obtain resistance to the PM disease in cucumber.

In Chapter 7 a novel loss-of-function allele of the SlMLO1 gene is described, designated m200. This allele was found in a resistant plant (M200) from a mutagenized tomato Micro-Tom (MT) population obtained with the chemical mutagen ethyl methanesulfonate (EMS). The m200 mutation corresponds to a nucleotide transversion (T à A) which results in a premature stop codon. The length of the predicted SlMLO1 protein in the M200 plant is only 21 amino acids, thus much shorter than the predicted protein of the previously described ol-2 allele, consisting of 200 amino acids. Thanks to the development of a High-Resolution Melting (HRM) marker designed to detect the m200 mutation, we observed that this allele confers recessively inherited resistance in backcross populations of the resistant M200 plant with MT and Moneymaker. Histological study showed that the resistance of the m200 mutant is associated with papilla formation. Finally, we compared the rate of On penetration in epidermal cells of m200 plants with the one of plants carrying the ol-2 allele and the transgenic plants in which multiple SlMLO homologs were silenced, generated in Chapter 2.

Ultimately, in Chapter 8 the results of the previous chapters are discussed in the context of 1) practical applications in breeding programs aimed at introducing the mlo-based resistance in new crops, 2) possible research aimed at unraveling the function of the MLO protein and 3) the role of other SNARE proteins.

Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection
Anche, M.T. - \ 2016
Wageningen University. Promotor(en): Mart de Jong, co-promotor(en): Piter Bijma. - Wageningen : Wageningen University - ISBN 9789462577442 - 185 p.
livestock - hosts - genetic effects - susceptibility - infectivity - infectious diseases - breeding value - heritability - epidemics - vee - gastheren (dieren, mensen, planten) - genetische effecten - vatbaarheid - infectiviteit - infectieziekten - fokwaarde - epidemieën

Mahlet Teka Anche. (2016). Estimating host genetic effects on susceptibility and infectivity to infectious diseases and their contribution to response to selection. PhD thesis, Wageningen University, the Netherlands

Genetic approaches aiming to reduce the prevalence of an infection in a population usually focus on improving host susceptibility to an infection. The prevalence of an infection, however, is also affected by the infectivity of individuals. Studies reported that there exists among host (genetic/phenotypic) variation in susceptibility and infectivity to infectious diseases. The effect of host genetic variation in susceptibility and infectivity on the prevalence and risk of an infection is usually measured by the value of the basic reproduction ratio, R0. R0 is an important epidemiological parameter that determines the risk and prevalence of an infection. It has a threshold value of 1, where major disease outbreak can occur when R0 > 1 and the disease will die out when R0 < 1. Due to this threshold property, genetic improvements aiming to reduce the prevalence of an infection should focus on reducing R0 to a value below 1. The overall aim of this thesis was to develop methodologies that allow us to investigate the genetic effects of host susceptibility and infectivity on the prevalence of an infection, which is measured by the value of R0. Moreover, we also aim to investigating the effect of relatedness among groupmates on the utilization of among host genetic variation in susceptibility and infectivity so as to reduce the prevalence of infectious diseases. The theory of direct-indirect genetic effects and epidemiological concepts were combined to develop methodologies. In addition, a simulation study was performed to validate the methodologies developed and examine the effect of relatedness on the utilization of genetic variation in susceptibility and infectivity. It was shown that an individual’s genetic effect on its susceptibility and infectivity affect the prevalence of an infection and that an individual’s breeding value for R0 can be defined as a function of its own allele frequencies for susceptibility and infectivity and of population average susceptibility and infectivity. Moreover, simulation results show that, not only an individual’s infectivity but also an individual’s susceptibility represents an indirect genetic effect on the disease status of individuals and on the prevalence of an infection in a population. It was shown that having related groupmates allows breeders to utilize the genetic variation in susceptibility and infectivity, so as to reduce the prevalence of an infection.

Resistentieveredeling - Verdedigingsmechanisme : Kennisclip Bogo-project e-learning
Hop, M.E.C.M. - \ 2016
Groen Kennisnet
resistance breeding - susceptibility - resistance - tolerance - host pathogen interactions - plant protection - teaching materials - disease resistance - resistentieveredeling - vatbaarheid - weerstand - tolerantie - gastheer-pathogeen interacties - gewasbescherming - lesmaterialen - ziekteresistentie
Deze kennisclip maakt onderdeel uit van de lesmodule Resistentie Veredeling van het CIV T&U.
Role of MLO genes in susceptibility to powdery mildew in apple and grapevine
Pessina, Stefano - \ 2016
Wageningen University. Promotor(en): Richard Visser, co-promotor(en): Henk Schouten; M. Malnoy; Yuling Bai. - Wageningen : Wageningen University - ISBN 9789462576209 - 222 p.
malus domestica - apples - vitis vinifera - grapes - plant pathogenic fungi - podosphaera leucotricha - erysiphe necator - disease resistance - susceptibility - genes - gene expression - gene knock-out - resistance breeding - appels - druiven - plantenziekteverwekkende schimmels - ziekteresistentie - vatbaarheid - genen - genexpressie - inactivering van genen - resistentieveredeling

Powdery mildew (PM) is a major fungal disease that threatens thousands of plant species. PM is caused by Podosphaera leucotricha in apple and Erysiphe necator in grapevine. Powdery mildew is controlled by frequent applications of fungicides, having negative effects on the environment, and leading to additional costs for growers. To reduce the amount of chemicals required to control this pathogen, the development of resistant apple and grapevine varieties should become a priority.

PM pathogenesis is associated with up-regulation of specific MLO genes during early stages of infection, causing down-regulation of plant defense pathways. These up-regulated genes are responsible for PM susceptibility (S-genes) and their knock-out causes durable and broad-spectrum resistance. All MLO S-genes of dicots belong to the phylogenetic clade V. In grapevine, four genes belong to clade V. VvMLO7, 11 and 13 are up-regulated during PM infection, while VvMLO6 is not.

Chapter 2 reports the genome-wide characterization and sequence analysis of the MLO gene family in apple, peach and woodland strawberry, and the isolation of apricot MLO homologs. Twenty-one homologues were found in apple, 19 in peach and 17 in woodland strawberry. Evolutionary relationships between MLO homologs were studied and syntenic blocks constructed. Candidate genes for causing PM susceptibility were inferred by phylogenetic relationships with functionally characterized MLO genes and, in apple, by monitoring their expression following inoculation with the PM causal pathogen P. leucotricha. In apple, clade V genes MdMLO11 and 19 were up-regulated, whereas the two other members of clade V, MdMLO5 and 7, were not up-regulated. The clade VII gene MdMLO18 was also up-regulated upon P. leucotricha infection.

Chapter 3 reports the knock-down, through RNA interference, of MdMLO11 and 19, as well as complementation of the mutant phenotype by expression of the MdMLO18 gene in the Arabidopsis thaliana triple mlo mutant Atmlo2/6/12. The knock-down of MdMLO19 resulted in a reduction of PM disease severity up to 75%, whereas the knock-down of MdMLO11, alone or combined with MdMLO19, did not cause any reduction or additional reduction of susceptibility compared to MdMLO19 alone. Complementation by MdMLO18 did not restore susceptibility. Cell wall appositions (papillae), a response to PM infection, were found in both susceptible plants and PM resistant plants where MdMLO19 was knocked-down, but were larger in resistant lines. The expression analysis of 17 genes related to plant defense, and quantification of phenolic metabolites in resistant lines revealed line-specific changes compared to the control.

Chapter 4 evaluates the presence of non-functional alleles of the MdMLO19 S-gene in apple germplasm. The screening of the re-sequencing data of 63 apple genotypes led to the identification of 627 SNP in five MLO genes (MdMLO5, MdMLO7, MdMLO11, MdMLO18 and MdMLO19). Insertion T-1201 in MdMLO19 caused the formation of an early stop codon, resulting in a truncated protein lacking 185 amino-acids and the calmodulin-binding domain. The presence of the insertion was evaluated in a collection of 159 apple genotypes: it was homozygous in 53 genotypes, 45 of which were resistant or very resistant to PM, four partially susceptible and four not assessed. These results strongly suggest that this insertion is causative for the observed PM resistance. The absence of a clear fitness cost associated to the loss-of-function of MdMLO19, might have contributed to the high frequency of the mutation in breeding germplasm and cultivars. Among the genotypes containing the homozygous insertion, ‘McIntosh’ and ‘Fuji’ are commonly used in apple breeding. After barley and tomato, apple is the third species with a reported natural non-functional mlo allele in its germplasm, with the important difference that the allele is present in a relatively large number of apple genotypes, most of which not related to each other.

Chapter 5 reports the knock-down through RNA interference of four grapevine MLO genes, all members of clade V. VvMLO7, 11 and 13 are up-regulated in early stages of infection, whereas VvMLO6 is not responsive to the pathogen. Knock-down of VvMLO6, 11 and 13, alone or combined, did not decrease PM severity, whereas the knock-down of VvMLO7, alone or in combination with VvMLO6 and VvMLO11, caused a reduction of severity of 77%. Cell wall appositions (papillae), a response to PM attack, were present in both resistant and susceptible lines, but were larger in resistant lines. Thirteen genes involved in defense were less up-regulated in resistant plants, highlighting the reduction of PM disease severity.

In Chapter 6 we discuss the results presented in this thesis. The pivotal role of MLO genes in the interaction of PM pathogens with apple and grapevine is described and further experiments aimed at addressing open questions are proposed. The results described in this thesis open interesting avenues in MLO genes research, particularly the finding that a natural mlo mutation in apple appeared to be more common than expected. This mutation is directly applicable in marker assisted breeding for durable PM resistance in apple.

Gut microbiota facilitates dietary heme-induced epithelial hyperproliferation by opening the mucus barrier in colon
IJssennagger, N. ; Belzer, C. ; Hooiveld, G.J.E.J. ; Dekker, J. ; Mil, S.W.C. ; Müller, M.R. ; Kleerebezem, M. ; Meer, R. van der - \ 2015
Proceedings of the National Academy of Sciences of the United States of America 112 (2015)32. - ISSN 0027-8424 - p. 10038 - 10043.
colorectal-cancer - red meat - mice - mucin - fat - susceptibility - cytotoxicity - expression - inhibitor - bacterial
Colorectal cancer risk is associated with diets high in red meat. Heme, the pigment of red meat, induces cytotoxicity of colonic contents and elicits epithelial damage and compensatory hyperproliferation, leading to hyperplasia. Here we explore the possible causal role of the gut microbiota in heme-induced hyperproliferation. To this end, mice were fed a purified control or heme diet (0.5 µmol/g heme) with or without broad-spectrum antibiotics for 14 d. Heme-induced hyperproliferation was shown to depend on the presence of the gut microbiota, because hyperproliferation was completely eliminated by antibiotics, although heme-induced luminal cytotoxicity was sustained in these mice. Colon mucosa transcriptomics revealed that antibiotics block heme-induced differential expression of oncogenes, tumor suppressors, and cell turnover genes, implying that antibiotic treatment prevented the heme-dependent cytotoxic micelles to reach the epithelium. Our results indicate that this occurs because antibiotics reinforce the mucus barrier by eliminating sulfide-producing bacteria and mucin-degrading bacteria (e.g., Akkermansia). Sulfide potently reduces disulfide bonds and can drive mucin denaturation and microbial access to the mucus layer. This reduction results in formation of trisulfides that can be detected in vitro and in vivo. Therefore, trisulfides can serve as a novel marker of colonic mucolysis and thus as a proxy for mucus barrier reduction. In feces, antibiotics drastically decreased trisulfides but increased mucin polymers that can be lysed by sulfide. We conclude that the gut microbiota is required for heme-induced epithelial hyperproliferation and hyperplasia because of the capacity to reduce mucus barrier function.
The potential effect of greenwater technology on water quality in the pond culture of Penaeus monodon Fabricius
Tendencia, E.A. ; Bosma, R.H. ; Verdegem, M.C.J. ; Verreth, J.A.J. - \ 2015
Aquaculture Research 46 (2015)1. - ISSN 1355-557X - p. 1 - 13.
white-spot-syndrome - syndrome virus - shrimp ponds - litopenaeus-vannamei - chlorella-vulgaris - vibrio-harveyi - salinity - temperature - susceptibility - mortalities
Whitespot syndrome virus (WSSV) has caused severe production drops in the shrimp industry. Numerous scientific manuscripts deal with WSSV epidemiology, but reports on minimizing disease outbreaks through ecological means are rare. Industry stakeholders resorted to various innovative techniques to recover from heavy economic losses. Some shrimp farmers in the Philippines claimed that 'greenwater' (GW) technology could prevent disease outbreaks due to WSSV. The efficiency of the GW technology was evaluated by comparing three ponds using the GW culture technique with three ponds not using it. WSSV was detected only in one of the GW ponds and not in the non-GW ponds. No WSSV disease outbreak occurred, and no conclusion could be reached. In GW ponds, available soil sulphur content was lower; and in water, the observed counts of luminous bacteria were lower and counts of Chlorophyceae were higher. Chlorophyceae, i.e. algae, enhanced nutrient uptake in effluent streams resulting in improved water quality in Penaeus monodon Fabricius culture ponds. This suggests that the use of the GW technique to culture P. monodon improved water quality.
Natural variation in virulence of the entomopathogenic fungus Beauveria bassiana against malaria mosquitoes
Valero Jimenez, C.A. ; Debets, A.J.M. ; Kan, J.A. van; Schoustra, S.E. ; Takken, W. ; Zwaan, B.J. ; Koenraadt, C.J.M. - \ 2014
Malaria Journal 13 (2014). - ISSN 1475-2875 - 8 p.
metarhizium-anisopliae - anopheles-gambiae - infection - agents - susceptibility - degradation - persistence - expression - resistance - behavior
Background Insecticide resistance is greatly hampering current efforts to control malaria and therefore alternative methods are needed. Entomopathogenic fungi have been proposed as an alternative with a special focus on the cosmopolitan species Beauveria bassiana. However, few studies have analysed the effects of natural variation within fungal isolates on mosquito survival, and the implications and possible exploitation for malaria control. Methods Laboratory bioassays were performed on adult female mosquitoes (Anopheles coluzzii) with spores from 29 isolates of B. bassiana, originating from different parts of the world. In addition, phenotypic characteristics of the fungal isolates such as sporulation, spore size and growth rate were studied to explore their relationship with virulence. Results All tested isolates of B. bassiana killed An. coluzzii mosquitoes, and the rate at which this happened differed significantly among the isolates. The risk of mosquitoes dying was around ten times higher when they were exposed to the most virulent as compared to the least virulent isolate. There was significant variation among isolates in spore size, growth rate and sporulation, but none of these morphological characteristics were correlated, and thus predictive, for the ability of the fungal isolate to kill malaria mosquitoes. Conclusions This study shows that there is a wide natural variation in virulence of isolates of B. bassiana, and that selecting an appropriate fungal isolate is highly relevant in killing and thus controlling malaria mosquitoes, particularly if used as part of an integrated vector management strategy. Also, the wide variation observed in virulence offers the opportunity to better understand the molecular and genetic mechanisms that drive this variation and thus to address the potential development of resistance against entomopathogenic fungi
Phytophthora infestans RXLR effector AVR1 and its host target Sec5
Du, Y. - \ 2014
Wageningen University. Promotor(en): Francine Govers, co-promotor(en): Klaas Bouwmeester. - Wageningen : Wageningen University - ISBN 9789462571310 - 188
phytophthora infestans - oömycota - plantenziekteverwekkende schimmels - virulentie - genen - plant-microbe interacties - ziekteresistentie - verdedigingsmechanismen - vatbaarheid - uitschakelen van genexpressie - oomycota - plant pathogenic fungi - virulence - genes - plant-microbe interactions - disease resistance - defence mechanisms - susceptibility - gene silencing


Late blight, caused by the oomycete Phytophthora infestans, is one of the most devastating potato diseases worldwide. To successfully colonize its host, P. infestans secretes a plethora of RXLR effectors that translocate into host cells to modulate plant defense. The RXLR effectors form the largest and most diverse effector family in oomycete plant pathogens, and include several that were demonstrated to trigger host resistance mediated by intracellular host immune receptors. Chapter 1 is a summary focussing on the molecular mechanisms underlying host–pathogen interactions. It introduces the multi-layered innate immune system of plants, as well as the strategies that pathogens exploit to circumvent and suppress host defense. Furthermore, it highlights the importance of vesicle-trafficking during plant defense.

The central subject of this thesis is AVR1, one of the race-specific avirulence (AVR) factors of P. infestans. AVR1 triggers plant resistance mediated by its corresponding potato Nucleotide-binding Leucine-rich repeat (NLR) resistance protein R1. P. infestans isolates that are avirulent on R1-containing potato cultivars always contain AVR1, while virulent isolates lack AVR1 but contain a related gene that we baptized as AVR1-like. AVR1 has all hallmarks of a typical RXLR effector; it contains a signal peptide, an RXLR domain and a C-terminal effector domain that contains two W motifs and one Y motif. In addition, it has, at the very end a stretch of 38 amino acids in length that we named the Tail (T)-region. AVR1-like, or in short A-L, shares high sequence similarity with AVR1. However, due to a premature stop codon the 38 amino acid T-region is missing.

Chapter 2 explores the conserved motifs and regions in the C-terminal effector domain of AVR1 that are required to trigger R1-mediated hypersensitive response (HR). Various truncated and chimeric constructs of AVR1 and A-L were generated and assayed for their ability to elicit R1-mediated HR. Results show that the T-region of AVR1 plays an important role in HR activation. Furthermore, we revealed that R1 recognizes two epitopes in AVR1, one located in the C-terminal region containing the conserved W and Y motifs, and one comprised by the T region.

In Chapter 3 the subcellular localization of AVR1 and R1 was investigated. Both were demonstrated to be nucleocytoplasmic proteins. We artificially modified the nucleocytoplasmic partitioning of AVR1 and R1 using nuclear localization and export signals (NLS/NES), and studied the effect on R1-AVR1 recognition. This revealed that nuclear localization of both AVR1 and R1 is important to induce R1-mediated immunity. In addition, we showed that AVR1-mediated suppression of CRN2-induced cell death is dependent on cytosolic localization of AVR1.

In Chapter 4, we investigated how AVR1 modulates host defense. In a yeast two-hybrid screening we identified the exocyst subunit Sec5 as a host target for AVR1. Interaction between AVR1 and Sec5 was confirmed in planta by co-immunoprecipitation and bimolecular fluorescent complementation. Although A-L shares high sequence similarity with AVR1, we found that it is not able to interact with Sec5. Sec5 was shown to be required for proper plant defense against P. infestans. The role of Sec5 in plant response upon pathogen attack was further supported by its role in callose deposition and in secretion of the pathogenesis-related protein PR-1, which indicates that Sec5 plays a crucial role in vesicle trafficking during host defense. AVR1 is able to suppress callose deposition while A-L is not, which suggests that P. infestans manipulates host vesicle trafficking by secretion of AVR1 to target Sec5. Overall, our findings unravelled a novel strategy that oomycete pathogens exploit in order to modulate host defense.

In Chapter 5 we further analysed the potential virulence activities of AVR1 and A-L. Both AVR1 and A-L were able to promote P. infestans colonization, indicating that both are genuine P. infestans virulence factors. Moreover, AVR1 was found to suppress not only callose deposition, but also Sec5-dependent cell death induced by the P. infestans elicitors INF1 and CRN2. In contrast, A-L was neither able to suppress Sec5-dependent nor Sec5-independent cell death. The conserved C-terminal motifs and regions required for virulence activity of AVR1 were investigated using AVR1 truncated constructs. In addition, the conserved C-terminal motifs and regions of AVR1 required for Sec5 interaction were studied by Y2H assays. Although the T-region of AVR1 was found to be sufficient to facilitate P. infestans colonization and suppression of CRN2-induced cell death, it could not fully accommodate the interaction of AVR1 with Sec5. Instead, both the Y motif and the T-region of AVR1 appear to be required for Sec5 targeting.

Next to Sec5, the role of other exocyst subunits in Phytophthora resistance was studied (Chapter 6). The evolutionary relationships of exocyst subunits from three Solanaceous plants, i.e. Nicotiana benthamiana, tomato and potato, were investigated in comparison to their Arabidopsis orthologs. Virus-induced gene silencing in N. benthamiana of the majority of the exocyst subunit genes (exo84s were not yet included) showed that, except for some Exo70 members, all other tested exocyst subunits are required for plant defense against P. infestans and callose deposition. In addition, all of the analysed exocyst subunit gene-silenced tomato plants showed gain of susceptibility to both P. infestans and Phytophthora capsici.

In Chapter 7, our findings obtained in this thesis on the mechanisms of AVR1-triggered host immunity and susceptibility are discussed in a broader perspective with emphasis on the current developments in the field of effector biology.

Salmonella subtypes with increased MICs for Azithromycin in travelers returned to the Netherlands.
Hassing, R.J. ; Goessens, W.H. ; Pelt, W. van; Mevius, D.J. ; Stricker, B.H. ; Molhoek, W.M.L. ; Verbon, A. ; Genderen, P.J. - \ 2014
Emerging Infectious Diseases 20 (2014)4. - ISSN 1080-6040 - p. 705 - 708.
uncomplicated typhoid-fever - in-vitro activity - enteric fever - multidrug-resistant - ciprofloxacin - trial - susceptibility - ofloxacin - paratyphi - india
Antimicrobial susceptibility was analyzed for 354 typhoidal Salmonella isolates collected during 1999-2012 in the Netherlands. In 16.1% of all isolates and in 23.8% of all isolates that showed increased MICs for ciprofloxacin, the MIC for azithromycin was increased. This resistance may complicate empirical treatment of enteric fever.
Bloedingsziekte in paardenkastanje werkgroep Aesculaap
Os, Gera van - \ 2014
aesculus - hippocastanaceae - plant pathogenic bacteria - infection - epidemiology - susceptibility - varietal susceptibility - site factors - tree care - disease control
The role of genes in talking about overweight: An analysis of discourse on genetics, overweight and health risks in relation to nutrigenomics
Komduur, R.H. ; Molder, H. te - \ 2014
Public Understanding of Science 23 (2014)8. - ISSN 0963-6625 - p. 886 - 902.
technology-assessment - quit smoking - life-style - obesity - susceptibility - understandings - information - motivation - disease - smokers
This study examines whether the assumptions embedded in nutrigenomics, especially the alleged relation between information about personal health risks and healthy behaviour, match how people account for the relation between food, health and genes in everyday life. We draw on discourse analysis to study accounts of overweight in six group interviews with people who are and who are not overweight. The results show potentially contradictory normative orientations towards behavioural explanations of (over)weight. Overt gene accounts are interactionally problematic (in contrast to more indirect accounts such as ‘build’), indicating that participants treat ‘behaviour’ as the normatively appropriate explanation for overweight. At the same time, however, healthy behaviour is an accountable matter, i.e. it is dealt with in interaction as behaviour that is not self-evidently right but requires an explanation. It is discussed how bringing these interactional concerns to the surface is essential for understanding future users’ response to nutrigenomics and emergent technologies more in general
Multilocus Sequence Typing for Characterization of Staphylococcus pseudintermedius
Solyman, S.M. ; Black, C.C. ; Duim, B. ; Perreten, V. ; Duijkeren, E. van; Wagenaar, J.A. ; Eberlein, L.C. ; Sadeghi, L.N. ; Videla, R. ; Bemis, D.A. ; Kania, S.A. - \ 2013
Journal of Clinical Microbiology 51 (2013)1. - ISSN 0095-1137 - p. 306 - 310.
methicillin-resistant - antibiotic-resistance - north-america - dogs - intermedius - meca - clones - aureus - susceptibility - emergence
Staphylococcus pseudintermedius is an opportunistic pathogen in dogs. Four housekeeping genes with allelic polymorphisms were identified and used to develop an expanded multilocus sequence typing (MLST) scheme. The new seven-locus technique shows S. pseudintermedius to have greater genetic diversity than previous methods and discriminates more isolates based upon host origin.
Haptoglobin phenotype prevalence and cytokine profiles during plasmodium falciparum infection in Dogon and Fulani ethnic groups living in Mali
Perdijk, O. ; Arama, C. ; Giusti, P. ; Maiga, B. ; Troye-Blomberg, M. ; Dolo, A. ; Doumbo, O. ; Persson, J.O. ; Bostrom, S. - \ 2013
Malaria Journal 12 (2013). - ISSN 1475-2875
hemoglobin scavenger receptor - severe malaria - soluble cd163 - west-africa - children - susceptibility - polymorphism - association - genotypes - ahaptoglobinemia
Background The Fulani are known to have a lower parasitaemia and less clinical episodes of malaria as compared to the Dogon sympatric ethnic group, living in Mali. Higher circulating malaria-specific antibody titers and increased pro-inflammatory cytokine levels have been shown in Fulani individuals. Several studies have tried to link haptoglobin (Hp) phenotypes with susceptibility to malaria, but without consensus. This study investigated the role of Hp phenotypes and cytokine levels in Dogon and Fulani during asymptomatic Plasmodium falciparum infection. Methods Two different cohorts were combined in this study: a 2008 cohort with 77 children aged between two and ten years and a 2001 cohort, with 82 children and adults, aged between 11 and 68 years. Hp phenotypes in plasma were measured by Western Blot. Circulating levels of sCD163, IL-6, IL-10, IFN-¿ and TNF were measured by ELISA. Multiple regression analysis was performed to associate Hp phenotypes with cytokine profiles. In addition, in vitro stimulation of peripheral blood mononuclear cells (PBMCs) with Hp:Hb complexes was performed and cytokine release in corresponding supernatants were measured using cytometric bead array. Results The results revealed a higher Hp2-2 phenotype prevalence in the Fulani. The Hp2-2 phenotype was associated with a higher susceptibility to P. falciparum infection in Dogon, but not in Fulani. In concordance with previous studies, Fulani showed increased inflammatory mediators (IL-6, IFN-¿) and additionally also increased sCD163 levels compared to Dogon, irrespective of infection. Furthermore, infected individuals showed elevated sCD163 levels compared to uninfected individuals, in both Fulani and Dogon. Multiple regression analysis revealed that the Hp1-1 phenotype was associated with higher levels of TNF and IFN-¿, as compared to the Hp2-2 phenotype. In vitro stimulation of PBMCs with Hb:Hp1-1 complexes resulted in a pro-inflammatory cytokine profile, whilst stimulation with Hb:Hp2-2 complexes showed a more balanced profile. Conclusions Ethnicity might be an important confounder on the Hp phenotype-dependent susceptibility to malaria and future studies could consider taking this into account when designing new immunological studies. Although, the relatively small sample size used in this study warrens for precautions in the interpretation of the data and these findings should ideally be validated in a bigger cohort.
Human intestinal metagenomics: state of the art and future
Blottière, H.M. ; Vos, W.M. de; Ehrlich, S.D. ; Doré, J. - \ 2013
Current Opinion in Microbiology 16 (2013)3. - ISSN 1369-5274 - p. 232 - 239.
irritable-bowel-syndrome - human gut microbiome - early-life - gastrointestinal microbiota - dietary fiber - disease - diversity - health - mice - susceptibility
Over the last few years our understanding of human biology has undergone profound transformation. The key role of the 'world inside us', namely the gut microbiota, once considered a forgotten organ, has been revealed, with strong impact on our health and well-being. The present review highlights the most important recent findings on the role of gut microbiota and its impact on the host and raises crucial questions to be considered in future studies
Induced plant responses to microbes and insects
Pieterse, C.M.J. ; Poelman, E.H. ; Wees, S.C.M. van; Dicke, M. - \ 2013
Frontiers in Plant Science 4 (2013). - ISSN 1664-462X - 3 p.
induced resistance - arabidopsis - volatiles - susceptibility - pathways - immunity - defense - stress - growth - acid
Plants are members of complex communities and interact both with antagonists and beneficial organisms. An important question in plant defense-signaling research is how plants integrate signals induced by pathogens, insect herbivores and beneficial microbes into the most appropriate adaptive response. Molecular and genomic tools are now being used to uncover the complexity of the induced defense signaling networks that have evolved during the arms races between plants and the other organisms with which they intimately interact. To understand the functioning of the complex defense signaling network in nature, molecular biologists and ecologists have joined forces to place molecular mechanisms of induced plant defenses in an ecological perspective. In this Research Topic, we aim to provide an on-line, open-access snapshot of the current state of the art of the field of induced plant responses to microbes and insects, with a special focus on the translation of molecular mechanisms to ecology and vice versa. We will collect Original Research and Review papers on the topic, but also other article types, such as Methods and Opinions are welcome.
Alternative treatments for indoor residual spraying for malaria control in a village with pyrethroid- and DDT-resistant vectors in The Gambia
Tangena, J.A.A. ; Adiamoh, M. ; Alessandro, U. D'; Jarju, L. ; Jawara, M. ; Jeffries, D. ; Malik, N. ; Nwakanma, D. ; Kaur, H. ; Takken, W. ; Lindsay, S.W. ; Pinder, M. - \ 2013
PLoS ONE 8 (2013)9. - ISSN 1932-6203
insecticide-treated nets - anopheles-gambiae - pirimiphos-methyl - molecular-forms - area - complex - susceptibility - identification - protection - mozambique
Background: Malaria vector control is threatened by resistance to pyrethroids, the only class of insecticides used for treating bed nets. The second major vector control method is indoor residual spraying with pyrethroids or the organochloride DDT. However, resistance to pyrethroids frequently confers resistance to DDT. Therefore, alternative insecticides are urgently needed. Methodology/Principal Findings: Insecticide resistance and the efficacy of indoor residual spraying with different insecticides was determined in a Gambian village. Resistance of local vectors to pyrethroids and DDT was high (31% and 46% mortality, respectively) while resistance to bendiocarb and pirimiphos methyl was low (88% and 100% mortality, respectively). The vectors were predominantly Anopheles gambiae s.s. with 94% of them having the putative resistant genotype kdr 1014F. Four groups of eight residential compounds were each sprayed with either (1) bendiocarb, a carbamate, (2) DDT, an organochlorine, (3) microencapsulated pirimiphos methyl, an organophosphate, or (4) left unsprayed. All insecticides tested showed high residual activity up to five months after application. Mosquito house entry, estimated by light traps, was similar in all houses with metal roofs, but was significantly less in IRS houses with thatched roofs (p=0.02). Residents participating in focus group discussions indicated that IRS was considered a necessary nuisance and also may decrease the use of long-lasting insecticidal nets. Conclusion/Significance: Bendiocarb and microencapsulated pirimiphos methyl are viable alternatives for indoor residual spraying where resistance to pyrethroids and DDT is high and may assist in the management of pyrethroid resistance.
Gene Expression Analysis of Peripheral Cells for Subclassification of Pediatric Inflammatory Bowel Disease in Remission
Lierop, P.P.E. van; Swagemakers, S.M. ; Bie, C.I. de; Middendorp, S.A. ; Baarlen, P. van; Samsom, J.N. ; Ijcken, W.F.J. van; Escher, J.C. ; Spek, P.J. van der; Nieuwenhuis, E.E.S. - \ 2013
PLoS ONE 8 (2013)11. - ISSN 1932-6203
crohns-disease - ulcerative-colitis - molecular classification - cytokine production - activity index - ibd - susceptibility - profiles - onset - risk
Objective: In current clinical practice, optimal treatment of inflammatory bowel disease (IBD) aims at the induction and maintenance of clinical remission. Clinical remission is apparent when laboratory markers of inflammation are normal and clinical symptoms are absent. However, sub-clinical inflammation can still be present. A detailed analysis of the immune status during this inactive state of disease may provide a useful tool to categorize patients with clinical remission into subsets with variable states of immune activation. Design: By using Affymetrix GeneChips, we analysed RNA gene expression profiles of peripheral blood leukocytes from pediatric IBD patients in clinical remission and controls. We performed (un)supervised clustering analysis of IBD-associated genes and applied Ingenuity (R) pathway software to identify specific molecular profiles between patients. Results: Pediatric IBD patients with disease in clinical remission display heterogeneously distributed gene expression profiles that are significantly distinct from controls. We identified three clusters of IBD patients, each displaying specific expression profiles of IBD-associated genes. Conclusion: The expression of immune-and IBD-associated genes in peripheral blood leukocytes from pediatric IBD patients in clinical remission was different from healthy controls, indicating that sub-clinical immune mechanisms are still active during remission. As such, RNA profiling of peripheral blood may allow for non-invasive patient subclassification and new perspectives in treatment regimes of IBD patients in the future.
A spatially explicit scenario-driven model of adaptive capacity to global change in Europe
Acosta, L. ; Klein, R.J.T. ; Reidsma, P. ; Metzger, M.J. ; Rounsevell, M.D.A. ; Leemans, R. - \ 2013
Global environmental change : human and policy dimensions 23 (2013)5. - ISSN 0959-3780 - p. 1211 - 1224.
klimaatverandering - scenario-analyse - modellen - klimaatadaptatie - europa - climatic change - scenario analysis - models - climate adaptation - europe - quantitative vulnerability assessment - fuzzy-set-theory - land-use change - climate-change - environmental-change - adaptation - indicators - growth - susceptibility - uncertainty
Traditional impact models combine exposure in the form of scenarios and sensitivity in the form of parameters, providing potential impacts of global change as model outputs. However, adaptive capacity is rarely addressed in these models. This paper presents the first spatially explicit scenario-driven model of adaptive capacity, which can be combined with impact models to support quantitative vulnerability assessment. The adaptive capacity model is based on twelve socio-economic indicators, each of which is projected into the future using four global environmental change scenarios, and then aggregated into an adaptive capacity index in a stepwise approach using fuzzy set theory
Glycoform-selective prion formation in sporadic and familial forms of prion disease
Xiao, X. ; Yuan, J. ; Haïk, S. ; Cali, I. ; Zhan, Y. ; Moudjou, M. ; Li, B. ; Laplanche, J.L. ; Laude, H. ; Langeveld, J.P.M. ; Gambetti, P. - \ 2013
PLoS ONE 8 (2013)3. - ISSN 1932-6203 - 9 p.
creutzfeldt-jakob-disease - prpsc formation - protein - scrapie - glycosylation - mutation - antibody - cells - susceptibility - conformers
The four glycoforms of the cellular prion protein (PrP(C)) variably glycosylated at the two N-linked glycosylation sites are converted into their pathological forms (PrP(Sc)) in most cases of sporadic prion diseases. However, a prominent molecular characteristic of PrP(Sc) in the recently identified variably protease-sensitive prionopathy (VPSPr) is the absence of a diglycosylated form, also notable in familial Creutzfeldt-Jakob disease (fCJD), which is linked to mutations in PrP either from Val to Ile at residue 180 (fCJD(V180I)) or from Thr to Ala at residue 183 (fCJD(T183A)). Here we report that fCJD(V180I), but not fCJD(T183A), exhibits a proteinase K (PK)-resistant PrP (PrP(res)) that is markedly similar to that observed in VPSPr, which exhibits a five-step ladder-like electrophoretic profile, a molecular hallmark of VPSPr. Remarkably, the absence of the diglycosylated PrP(res) species in both fCJD(V180I) and VPSPr is likewise attributable to the absence of PrP(res) glycosylated at the first N-linked glycosylation site at residue 181, as in fCJD(T183A). In contrast to fCJD(T183A), both VPSPr and fCJD(V180I) exhibit glycosylation at residue 181 on di- and monoglycosylated (mono181) PrP prior to PK-treatment. Furthermore, PrP(V180I) with a typical glycoform profile from cultured cells generates detectable PrP(res) that also contains the diglycosylated PrP in addition to mono- and unglycosylated forms upon PK-treatment. Taken together, our current in vivo and in vitro studies indicate that sporadic VPSPr and familial CJD(V180I) share a unique glycoform-selective prion formation pathway in which the conversion of diglycosylated and mono181 PrP(C) to PrP(Sc) is inhibited, probably by a dominant-negative effect, or by other co-factors.
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