1,046 research outputs found
Optimizing a RF Coil for Prostate Imaging at 7 Tesla MRI
No full textUltra-high ?eld prostate MR imaging (?7T) becomes increasingly difficult due to insufficient radio frequency ?eld excitation penetration. RF coils used at ultra-high ?elds are adapted from lower ?eld strengths but their performance is suboptimal. These coils are designed as near-?eld antennas; however, better signal penetration can be obtained using far-?eld concept, speci?cally in the case of prostate which is located deep in the body. In this project the optimization of an RF coil for prostate imaging at 7T Magnetic Resonance system is investigated. This RF coil was designed following far-?eld-based concept recently proposed by Raaijmakers et al., who has demonstrated that higher transmit B1+ at depth can be obtained; thus increasing the transmit performance necessary to acquire good images. The RF coil consists of a fractionated dipole antenna mounted on an acrylic substrate, and it is used as part of a surface array. The optimization is evaluated in terms of safety (local SAR), transmit performance (B1+), and coupling measurements. A parameters study was performed to improve the performance of the RF coil. Numerical simulations were used to evaluate new designs obtained from the parameters study. From the simulated results, three designs were constructed for validation purposes. Two different measurements were performed to validate the simulations: B1 measurements in the 7 Tesla MR scanner and coupling measurements with a network analyzer; these measurements were performed on a phantom with tissue electrical properties. Finally, an in vivo measurement using two identical sinusoidal-shaped snake antennas (s20) aligned on the pelvis was performed to image a healthy prostate. Both, simulations and measurements in the snake antennas demonstrated that despite the improvement gained in safety with lower levels of SAR, the radiation ?eld penetration pattern is less homogeneous affecting the imaging process. Therefore, these antennas might show more efficiency imaging regions of interest where safety has to be ensured such as the heart, but for prostate imaging the fractionated dipole is preferable.Biomedical EngineeringBiomedical EngineeringMechanical, Maritime and Materials Engineerin
Effect of plant domestication on the rhizosphere microbiome of common bean (Phaseolus vulgaris) .
No full textPlant domestication was a pivotal achievement for human civilization and subsequent plant improvement increased crop productivity and quality. However, domestication also caused a strong reduction in the genetic diversity of modern cultivars compared to their wild relatives. It is known that plants rely, in part, on the rhizosphere microbial community for wreowth, development and tolerance to (a)biotic stresses. Hence, plant domestication events may have adversely affected the bacterial diversity of the rhizosphere of two wild relatives, three landraces and three modern cultivars of common bean (Phaseolus vulgaris). These different lines belong to the Mesoamerican bean gene pool of Colombia and were selected amongst more than 37,000 accessions kept in the Genetic Resources Program of the International Centre for Tropical Agriculture (CIAT, Colombia). The eight accessions were grown in both native and in agricultural soils collected in the province of Antioquia (Colombia). At different plant growth stages, DNA was extracted from rhizospheric soil and bacterial taxonomic diversity was analysed by metagenomic sequencing of the V3-V4 region of the 16S rRNA. Our Approach of going ?back to the roots? using native soils togheter with wild relatives provides new fundamental insights in host genotype-mediated recruitment of beneficial microbes and in the functional and metabolic potential of the rhizosphere microbiome of native soils and wild relatives of modern crop cultivars
The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms
No full textThe rhizosphere is a hot spot of microbial interactions as exudates released by plant roots are a main food source for microorganisms and a driving force of their population density and activities. The rhizosphere harbors many organisms that have a neutral effect on the plant, but also attracts organisms that exert deleterious or beneficial effects on the plant. Microorganisms that adversely affect plant growth and health are the pathogenic fungi, oomycetes, bacteria and nematodes. Most of the soilborne pathogens are adapted to grow and survive in the bulk soil, but the rhizosphere is the playground and infection court where the pathogen establishes a parasitic relationship with the plant. The rhizosphere is also a battlefield where the complex rhizosphere community, both microflora and microfauna, interact with pathogens and influence the outcome of pathogen infection. A wide range of microorganisms are beneficial to the plant and include nitrogen-fixing bacteria, endo- and ectomycorrhizal fungi, and plant growth-promoting bacteria and fungi. This review focuses on the population dynamics and activity of soilborne pathogens and beneficial microorganisms. Specific attention is given to mechanisms involved in the tripartite interactions between beneficial microorganisms, pathogens and the plant. We also discuss how agricultural practices affect pathogen and antagonist populations and how these practices can be adopted to promote plant growth and health
Impact of soil heat treatment on bacterial community reassembly in the rhizosphere.
No full textThe rhizosphere microbiome offers a range of ecosystem services to the plant. Including nutrient acquisition, tolerance to abiotic stress and protection against diseases. Here we studied how heat treatment of soil disturbs the reassembly of the bacterial community in the rhizosphere and how this affects tolerance to pathogen infection. Using PhyloChip-based community profiling, we assessed the impact of 1-hour heat treatments of 50ºC or 80ºC on the bacterial community composition in the rhizosphere of sugar beet seedlings grown in a soil that is naturally suppressive to the soil-borne fungus Rhizoctonia solani. The heat disturbance caused significant increase of alpha diversity and led to a partial (50ºC) or complete (80ºC) loss of protection against fungal infection. The bacterial families Bacillaceae, Comamonadaceae, Paenibacillaceae and Alcaligenaceae showed a significant increase in relative abundance with increasing temperatures. The Pseudomonadaceae and Burkholderiaceae showed higher abundance only when the soil was heat-treated at 80ºC. Conversely, the bacterial families Streptomycetaceae, Micrococcaceae, Solibacteraceae and Mycobacteriaceae showed a reduction in relative abundance when the soil was heat-treated at 80ºC. Based on these results, we propose a reassembly model where bacterial groups that are most heat-tolerant and with high growth rates increase in relative abundance after heat disturbance, while temperature-sensitive and slow growing bacteria have a disadvantage. The results also point to a potential role of slow growing bacterial families from Actinobacteria and Acidobacteria phyla in protection of plants against fungal infection. With this study we showed that heat disturbance in soil results in a rearranged rhizosphere bacterial community, which in turn leads to changes in the ecosystem services of the soil
Biosynthesis and regulation of cyclic lipopeptides in Pseudomonas fluorescens
No full textCyclic lipopeptides (CLPs) are surfactant and antibiotic metabolites produced by a variety of bacterial genera. For the genus Pseudomonas, many structurally different CLPs have been identified. CLPs play an important role in surface motility of Pseudomonas strains, but also in virulence and attachment/detachment to and from surfaces. In this Ph.D. thesis project, two new CLP biosynthesis clusters were identified in Pseudomonas fluorescens and fully sequenced. In P. fluorescens strain SBW25, the viscosin biosynthesis cluster was identified by bioinformatic analyses of the genome followed by genetic and chemical analyses. For P. fluorescens strain SS101, the genes for massetolide biosynthesis were identified via random mutagenesis followed by cloning, sequencing and chemical analyses. Biosynthesis of viscosin and massetolide is governed by three nonribosomal peptide synthetase (NRPS) genes, designated viscABC and massABC, respectively. The viscosin and massetolide biosynthesis gene clusters are very similar, but different from CLP gene clusters described for other Pseudomonas as the viscA and massA genes are physically disconnected from viscBC and massBC, respectively. Viscosin differs from massetolide A only at position number four in the peptide moiety, which is a valine in viscosin and an isoleucine in massetolide A. Because of the modular structure of the NRPSs and the co-linearity of the assembly process, transfer of the mass genes of strain SS101 into strain SBW25 resulted in the production of both massetolide A and viscosin, demonstrating that the assembly line for CLP biosynthesis in Pseudomonas can be altered leading to the production of non-native products. Compared to the understanding of CLP biosynthesis, not so much is known about the regulation. This thesis shows that the GacA/GacS two-component system regulates massetolide and viscosin biosynthesis in strains SS101 and SBW25, respectively. No indications were found that massetolide or viscosin biosynthesis is regulated by quorum sensing via N-acylhomoserine lactones. Site-directed mutagenesis of the LuxR-type regulator genes luxR-vA and luxR-vBC flanking the viscosin biosynthesis cluster resulted in a loss of viscosin production, indicating that both LuxR-type transcriptional regulators are important for viscosin biosynthesis in strain SBW25. Phylogenetic analyses further suggested that these LuxR-type transcriptional regulators do not contain the autoinducerbinding domain found for the quorum sensing-associated LuxR regulator in Vibrio fischeri. Instead, the LuxR-type regulator genes flanking the massetolide and viscosin biosynthesis genes are closely related to the LuxR-type regulators identified for syringomycin/ syringopeptin biosynthesis and appear to belong to a separate LuxR-type regulator subfamily, different from the autonomous effector domain protein GerE. Via random mutagenesis and subsequent screening for massetolide-deficient mutants, also other regulator genes were identified including clpP. ClpP is a serine protease that plays a crucial role in intracellular refolding and degradation of proteins, which is an essential process for the viability of cells. ClpP was shown to affect transcription of luxR-mA, thereby regulating transcription of the massetolide biosynthesis genes. Results further suggested that, at the transcriptional level, ClpPmediated regulation of massetolide biosynthesis operates independently from regulation by the GacA/GacS two-component system. In conclusion, the results of this thesis led to the identification of several genes and previously unknown pathways involved in regulation of CLP biosynthesis and highlighted the complexity of the signaling cascades underlying CLP biosynthesis in Pseudomonas. CLPs have diverse functions for the producing bacterial strains, including a role in motility, biofilm formation, antimicrobial activity and virulence. Also in establishment and persistence in plant environments, CLPs were shown to confer a competitive advantage. A new function of CLPs, identified in a collaboration with Mark Mazzola (USDA) and presented in this thesis, is their protective effects against predation by protozoa. In vitro assays showed that both massetolide and viscosin can lyse the trophozoites of Naeglaria americana and that wild type strains SS101 and SBW25 were substantially less sensitive to protozoan grazing than their CLP-deficient mutants. Also in soil containing N. americana, population densities of wild type strains SS101 and SBW25 were significantly higher compared to the massetolide and viscosin-deficient mutants, showing that CLP production confers a competitive advantage in survival in complex environments. Moreover, transcription of the CLP-biosynthesis genes increased significantly upon protozoan grazing, indicating that the Pseudomonas strains sense the protozoa and react by producing CLPs as defense compounds. Which signal triggers the induction of the CLP biosynthesis genes is not known yet and currently under investigation. Based on these results, we postulate that CLPs are an important component of the preingestional defense mechanisms of bacteria against protozoan predation, not only due to their lytic effects on protozoa, but also because CLPs contribute to evasion of protozoan grazing via altered cell surface properties, swimming and swarming, and microcolony and biofilm formation. <br/
The storage of newly learned information in semantic memory
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mmubn000001_184347718.pdf (Publisher’s version ) (Open Access)Promotores : J. Raaijmakers en E. Roskam169 p
Impact of plant domestication on rhizosphere microbiome assembly and functions.
No full textAbstract: The rhizosphere microbiome is pivotal for plant health and growth, providing defence against pests and diseases, facilitating nutrient acquisition and helping plants to withstand abiotic stresses. Plants can actively recruit members of the soil microbial community for positive feedbacks, but the underlying mechanisms and plant traits that drive microbiome assembly and functions are largely unknown. Domestication of plant species has substantially contributed to human civilization, but also caused a strong decrease in the genetic diversity of modern crop cultivars that may have affected the ability of plants to establish beneficial associations with rhizosphere microbes. Here, we review how plants shape the rhizosphere microbiome and how domestication may have impacted rhizosphere microbiome assembly and functions via habitat expansion and via changes in crop management practices, root exudation, root architecture, and plant litter quality. We also propose a ?back to the roots? framework that comprises the exploration of the microbiome of indigenous plants and their native habitats for the identification of plant and microbial traits with the ultimate goal to reinstate beneficial associations that may have been undermined during plant domestication
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