| 1. |
- Wolniewicz, Peter, 1978-, et al.
(författare)
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Reactivity changes in lead-cooled fast reactors due to bubbles in the coolant
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The formation of bubbles in the coolant of a Lead-Cooled Fast Reactor (LFR) may originate from a leaking heat-exchanger and is a potential safety hazard. Small bubbles can travel with the coolant without escaping to the cover gas, causing an increasing effective voiding of the coolant in a homogeneous manner. If the small bubbles coalesce into a larger bubble located at a stagnation zone, the reactor core may eventually be exposed to a transient bubble travelling axially through the core with a resulting change in the reactivity of the system. This study is focused on the reactivity changes caused by bubbles of various sizes and for different vertical positions as the bubble rises through the core. Three different sizes of LFR’s; 50 MWth, 300 MWth and 1200 MWth,respectively were user for the study. The 300 MWth reactor design is based on the Advanced LFR European Demonstrator (ALFRED) and the two other reactors are scaled up and scaled down versions of it and these were simulated in order study the sensitivity to void as a function of reactor size. We show that LFR’s may have a positive reactivity response to transient bubbles and that the sensitivity to changes in reactivity is larger the smaller the reactor. For sufficiently large bubbles all reactors may reach prompt criticality.
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| 2. |
- Alm Rosenblad, Magnus, 1957, et al.
(författare)
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The Signal Recognition Particle of the diplomonad Giardia lacks the Alu domain responsible for translational arrest
- 2008
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Ingår i: RNA Society Meeting 2008.
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- One of the most conserved cellular processes is the co-translational targeting of secretory and membrane proteins to the Sec translocon by the Signal Recognition Particle (SRP). This ribonucleoprotein particle consists in most eukaryotes of one RNA molecule and six proteins, and may be divided into two domains with distinct functions: the "S domain", which is most conserved, binds to the nascent peptide chain as it emerges from the exit tunnel of the ribosome, and the "Alu domain" which has a translation-regulatory function and causes an elongation arrest of the peptide chain. Of the six proteins only two is part of the Alu domain: SRP9/14.
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| 3. |
- Anders, Alfjorden, et al.
(författare)
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Experimental challenge of Atlantic salmon (Salmo salar) with the diplomonad parasite Spironucleus salmonicida to characterize the infection cycle
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Experimental infections were performed of Atlantic salmon (Salmo salar) from the Baltic Sea region with the Diplomonad fish parasite Spironucleus salmonicida in order to define the infection cycle, specifically the time-line and putative routes of transmission. An oral infection protocol using axenic parasites was developed, as were new diagnostic tools using PCR and specific antibodies. We also produced firefly luciferase expressing S. salmonicida parasites that could be identified in the infected fish using in vivo and ex vivo imaging. The new tools made it possible to follow the S. salmonicida infection cycle in detail. Three different stages of the infection were identified: one initial intestinal stage, followed by a blood stage and a final tissue stage. Parasites intubated into the intestine attached to the intestinal surface and were identified in the blood after 1-3 weeks. Skin lesions and infections of the muscles, internal organs and eyes were seen 4-10 weeks after initiation of infection. Several morphologically different forms of S. salmonicida cells were detected in ex vivo cell-cultures of biopsies from skin lesions. By this infection trial we have been able to show that S. salmonicida may use several alternative routes of transmission. One alternative is the fecal-oral route, similar to other Diplomonad parasites but the parasites can also be excreted directly into the surrounding water from the mucous layer of the skin or from an ulcerated skin lesion. This information can be used to prevent the transmission of the parasite in fish farms.
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| 4. |
- Andersson, Jan O., et al.
(författare)
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A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
- 2007
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8, s. 51-
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Forskningsöversikt (refereegranskat)abstract
- Background: Comparative genomic studies of the mitochondrion-lacking protist group Diplomonadida (diplomonads) has been lacking, although Giardia lamblia has been intensively studied. We have performed a sequence survey project resulting in 2341 expressed sequence tags (EST) corresponding to 853 unique clones, 5275 genome survey sequences (GSS), and eleven finished contigs from the diplomonad fish parasite Spironucleus salmonicida (previously described as S. barkhanus). Results: The analyses revealed a compact genome with few, if any, introns and very short 3′ untranslated regions. Strikingly different patterns of codon usage were observed in genes corresponding to frequently sampled ESTs versus genes poorly sampled, indicating that translational selection is influencing the codon usage of highly expressed genes. Rigorous phylogenomic analyses identified 84 genes - mostly encoding metabolic proteins - that have been acquired by diplomonads or their relatively close ancestors via lateral gene transfer (LGT). Although most acquisitions were from prokaryotes, more than a dozen represent likely transfers of genes between eukaryotic lineages. Many genes that provide novel insights into the genetic basis of the biology and pathogenicity of this parasitic protist were identified including 149 that putatively encode variant-surface cysteine-rich proteins which are candidate virulence factors. A number of genomic properties that distinguish S. salmonicida from its human parasitic relative G. lamblia were identified such as nineteen putative lineage-specific gene acquisitions, distinct mutational biases and codon usage and distinct polyadenylation signals. Conclusion: Our results highlight the power of comparative genomic studies to yield insights into the biology of parasitic protists and the evolution of their genomes, and suggest that genetic exchange between distantly-related protist lineages may be occurring at an appreciable rate in eukaryote genome evolution.
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| 5. |
- Andersson, Jan O., et al.
(författare)
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The genome of Giardia and other diplomonads
- 2010
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Ingår i: Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. - : Caister Academic Press. - 9781904455615 ; , s. 23-44
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 6. |
- Andersson, Peter, 1981-, et al.
(författare)
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Correction for dynamic bias error in transmission measurements of void fraction
- 2012
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 83:12, s. 125110-
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Tidskriftsartikel (refereegranskat)abstract
- Dynamic bias errors occur in transmission measurements, such as X-ray, gamma, or neutron radiography or tomography. This is observed when the properties of the object are not stationary in time and its average properties are assessed. The nonlinear measurement response to changes in transmission within the time scale of the measurement implies a bias, which can be difficult to correct for. A typical example is the tomographic or radiographic mapping of void content in dynamic two-phase flow systems. In this work, the dynamic bias error is described and a method to make a first-order correction is derived. A prerequisite for this method is variance estimates of the system dynamics, which can be obtained using high-speed, time-resolved data acquisition. However, in the absence of such acquisition, a priori knowledge might be used to substitute the time resolved data. Using synthetic data, a void fraction measurement case study has been simulated to demonstrate the performance of the suggested method. The transmission length of the radiation in the object under study and the type of fluctuation of the void fraction have been varied. Significant decreases in the dynamic bias error were achieved to the expense of marginal decreases in precision.
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| 7. |
- Andersson, Peter, 1981-, et al.
(författare)
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Design and initial 1D radiography tests of the FANTOM mobile fast-neutron radiography and tomography system
- 2014
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 756, s. 82-93
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Tidskriftsartikel (refereegranskat)abstract
- The FANTOM system is a tabletop sized fast-neutron radiography and tomography system newly developed at the Applied Nuclear Physics Division of Uppsala University. The main purpose of the system is to provide time-averaged steam-and-water distribution measurement capability inside the metallic structures of two-phase test loops for Light Water Reactor thermal-hydraulic studies using a portable fusion neutron generator. The FANTOM system provides a set of 1D neutron transmission data, which may be inserted into tomographic reconstruction algorithms to achieve a 2D mapping of the steam-and-water distribution. In this paper, the selected design of FANTOM is described and motivated. The detector concept is based on plastic scintillator elements, separated for spatial resolution. Analysis of pulse heights on an event-to-event basis is used for energy discrimination. Although the concept allows for close stacking of a large number of detector elements, this demonstrator is equipped with only three elements in the detector and one additional element for monitoring the yield from the neutron generator. The first measured projections on test objects of known configurations are presented. These were collected using a Sodern Genie 16 neutron generator with an isotropic yield of about 1E8 neutrons per second, and allowed for characterization of the instrument’s capabilities. At an energy threshold of 10 MeV, the detector offered a count rate of about 500 cps per detector element. The performance in terms of spatial resolution was validated by fitting a Gaussian Line Spread Function to the experimental data, a procedure that revealed a spatial unsharpness in good agreement with the predicted FWHM of 0.5 mm.
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| 8. |
- Andersson, Peter, 1981-, et al.
(författare)
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Effects of proton escape on detection efficiency in thin scintillator elements and its consequences for optimization of fast-neutron imaging
- 2011
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Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 651:1, s. 110-116
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Tidskriftsartikel (refereegranskat)abstract
- Plastic scintillators are commonly used for neutron detection in the MeV energy range, based on n–p scattering and the subsequent deposition of recoil proton's kinetic energy in the detector material. This detection procedure gives a quasi-rectangular energy deposition distribution for mono-energetic neutrons, extending from zero to the neutron energy. However, if the detector sensitive element (DSE) is small, the energy deposition may be incomplete due to the recoil proton escape.In the application of neutron imaging, here exemplified by fast-neutron tomography, two conflicting requirements have been identified: (1) thin DSEs are required to obtain high spatial resolution and (2) energy discrimination may be required to reduce the influence of neutrons being scattered into the DSEs, which generally occurs at lower energies. However, at small DSE widths, the reduction of energy deposition due to recoil proton escape may cause a significant decrease in detection efficiency when energy discrimination is applied.In this work, energy deposition distributions in small-size DSEs have been simulated for Deuterium–Deuterium (DD; 2.5 MeV) and Deuterium–Tritium (DT; 14.1 MeV) fusion neutrons. The intrinsic efficiency has been analyzed as a function of energy discrimination level for various detector widths. The investigations show that proton recoil escape causes a significant drop in intrinsic detection efficiency for thin DSEs. For DT neutrons, the drop is 10% at a width of 3.2 mm and 50% at a width of 0.6 mm, assuming an energy threshold at half the incident neutron energy. The corresponding widths for a DD detector are 0.17 and 0.03 mm, respectively.Finally, implications of the proton escape effect on the design of a fast-neutron tomography device for void distribution measurements at Uppsala University are presented. It is shown that the selection of DSE width strongly affects the instrument design when optimizing for image unsharpness.
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| 9. |
- Andersson, Peter, 1981-
(författare)
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Fast-Neutron Tomography using a Mobile Neutron Generator for Assessment of Steam-Water Distributions in Two-Phase Flows
- 2014
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This thesis describes the measurement technique of fast-neutron tomography for assessing spatial distributions of steam and water in two-phase flows. This so-called void distribution is of importance both for safe operation and for efficient use of the fuel in light water reactors, which compose the majority of the world’s commercial nuclear reactors. The technique is aimed for usage at thermal-hydraulic test loops, where heated two-phase flows are being investigated under reactor-relevant conditions.By deploying portable neutron generators in transmission tomography, the technique becomes applicable to stationary objects, such as thermal-hydraulic test loops. Fast neutrons have the advantage of high transmission through metallic structures while simultaneously being relatively sensitive to the water/void content. However, there are also challenges, such as the relatively low yield of commercially available fast-neutron generators, the tendency of fast neutrons to scatter in the interactions with materials and the relatively low efficiency encountered in fast-neutron detection.The thesis describes the design of a prototype instrument, FANTOM, which has been assembled and demonstrated. The main design parameters have been optimized to achieve maximal signal count rate in the detector elements, while simultaneously reaching an image unsharpness of ≤0.5 mm. Radiographic projections recorded with the assembled instrument are presented, and the performance parameters of FANTOM are deduced.Furthermore, tomographic reconstruction methods for axially symmetric objects, which is relevant for some test loops, have been developed and demonstrated on measured data from three test objects. The attenuation distribution was reconstructed with a radial resolution of 0.5 mm and an RMS error of 0.02 cm-1, based on data recorded using an effective measurement time of 3.5 hours per object. For a thermal-hydraulic test loop, this can give a useful indication of the flow mode, but further development is desired to improve the precision of the measurements.Instrument upgrades are foreseen by introducing a more powerful neutron generator and by adding detector elements, speeding up the data collection by several orders of magnitude and allowing for higher precision data. The requirements and performance of an instrument for assessment of arbitrary non-symmetric test loops is discussed, based on simulations.
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| 10. |
- Andersson, Peter, 1981-, et al.
(författare)
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Neutron tomography for void distribution measurements
- 2010
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Ingår i: ENC 2010 Transactions. - 9789295064096 ; , s. 40-45
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Neutron tomography has previously been performed using large, stationary neutron sources such as reactors and spallation sources for applications where the object under study can be transported to the source. This paper accounts for the challenges met when applying neutron tomography using a portable accelerator driven neutron generator, which is required when studying non-transportable objects. In general, portable sources offer significantly lower neutron yields than stationary sources, implying the need for either longer measurement times or highly efficient measurement and/or analysis procedures.The particular application investigated here is the mapping of steam distributions in water (void distribution), which is of high importance for the performance of nuclear fuel assemblies in boiling water reactors (BWR). The void distribution cannot be measured directly in a reactor core, so instead various electrically-heated thermal-hydraulic test loops are used. In these loops, void correlations can be determined in full-size fuel-assembly models, such as FRIGG in Sweden and DESIRE in Holland, but measurements are also performed in smaller, less complicated geometries. Previously, gamma tomography has been used to measure the void distribution in the FRIGG loop. However, improved capabilities to map the void distribution can be expected using neutrons because of their higher sensitivity to water relative to metal structures, as compared to gamma rays. At the same time, neutrons as probe also give rise to some challenges, such as high background from scattering.This paper investigates the possibility to use neutron tomography at axially symmetric objects such as the HWAT test loop in Sweden, where an annular two-phase flow of water/void is confined and heated by a steel cylinder. Monte Carlo simulations of the HWAT geometry and a suggested measurement setup have been carried out, using the particle transport code MCNPX. A reconstruction technique which exploits the symmetries in the test loop has been developed, making it possible to reconstruct the internal void distribution from one single projection. A reconstruction is presented, which is based on simulated data corresponding to a 13-min measurement using a DT source emitting 2∙109 neutrons/s. The reconstruction offers a radial view of the local void fraction in 10 annular sections of HWAT, with uncertainties between 2 and 5 void percent units.
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| 11. |
- Andersson, Peter, 1981-, et al.
(författare)
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Neutron tomography of axially symmetric objects using 14 MeV neutrons from a portable neutron generator
- 2014
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Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 85:8, s. 085109-
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Tidskriftsartikel (refereegranskat)abstract
- In nuclear boiling water reactor cores, the distribution of water and steam (void) is essential for both safety and efficiency reasons. In order to enhance predictive capabilities, void distribution assessment is performed in two-phase test-loops under reactor-relevant conditions. This article proposes the novel technique of fast-neutron tomography using a portable deuterium-tritium neutron generator to determine the void distribution in these loops.Fast neutrons have the advantage of high transmission through the metallic structures and pipes typically concealing a thermal-hydraulic test loop, while still being fairly sensitive to the water/void content. However, commercially available fast-neutron generators also have the disadvantage of a relatively low yield and fast-neutron detection also suffers from relatively low detection efficiency. Fortunately, some loops are axially symmetric, a property which can be exploited to reduce the amount of data needed for tomographic measurement, thus limiting the interrogation time needed.In this article, three axially-symmetric test objects depicting a thermal-hydraulic test loop have been examined; steel pipes with outer diameter 24 mm, thickness 1.5 mm and with three different distributions of the plastic material POM inside the pipes. Data recorded with the FANTOM fast-neutron tomography instrument have been used to perform tomographic reconstructions to assess their radial material distribution. Here, a dedicated tomographic algorithm that exploits the symmetry of these objects has been applied, which is described in the paper.Results are demonstrated in 20 rixel (radial pixel) reconstructions of the interior constitution and 2D visualization of the pipe interior is demonstrated. The local POM attenuation coefficients in the rixels were measured with errors (RMS) of 0.025, 0.020 and 0.022 cm-1, solid POM attenuation coefficient. The accuracy and precision is high enough to provide a useful indication on the flow mode, and a visualization of the radial material distribution can be obtained. A benefit of this system is its potential to be mounted at any axial height of a two-phase test section without requirements for pre-fabricated entrances or windows. This could mean a significant increase in flexibility of the void distribution assessment capability at many existing two-phase test loops.
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| 12. |
- Andersson, Peter, 1981-
(författare)
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Optimization of Equipment for Tomographic Measurements of Void Distributions using Fast Neutrons
- 2011
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Licentiatavhandling (övrigt vetenskapligt/konstnärligt)abstract
- This licentiate thesis describes a novel nondestructive measuring technique for determiningspatial distributions of two-phase water flows. In Boiling Water Reactors, which compose themajority of the world's commercial nuclear reactors, this so called void distribution is of importance for safe operation.The presented measurement technique relies on fast neutron transmission tomography using portable neutron generators. Varying hardware options for such an instrument based on this technique and a prototype instrument, which is under construction, are described. The main design parameters are detailed and motivated from a performance point of view. A Paretomultiple objective optimization of the count rate and image unsharpness is presented. The resulting instrument design comprises an array of plastic scintillators for neutron detection. Such detector elements allow for spectroscopic data acquisition and subsequent reduction of background events at low energy by means of introducing an energy threshold in the analysis.The thesis includes two papers: In paper I, the recoil proton energy deposition distribution resulting from the interaction of the incoming neutrons is investigated for thin plastic scintillator elements. It is shown that the recoil proton losses have a large effect on the pulse height distribution and the intrinsic neutron detection efficiency is calculated for varying energy thresholds.In paper II the performance of the planned FANTOM device is investigated using the particle transport code MCNP5. An axially symmetric phantom void distribution is modeled and there construction is compared with the correct solution. According to the solutions, the phantom model can be reconstructed with 10 equal size ring-shaped picture elements, with a precision of better than 5 void percent units using a deuterium-tritium neutron generator with a yield of 3 · 107 neutrons per second and a measurement time of 13 h. However, it should be noted that commercial neutron generators with a factor of 103 higher yields exist and that the measurement time could decrease to less than a minute if such a neutron generator would beutilized.
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| 13. |
- Ankarklev, Johan, et al.
(författare)
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A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination
- 2018
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Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 60, s. 7-16
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Tidskriftsartikel (refereegranskat)abstract
- Molecular epidemiology and genotyping studies of the parasitic protozoan Giardia intestinalis have proven difficult due to multiple factors, such as low discriminatory power in the commonly used genotyping loci, which has hampered molecular analyses of outbreak sources, zoonotic transmission and virulence types. Here we have focused on assemblage A Giardia and developed a high-resolution assemblage-specific multilocus sequence typing (MLST) method. Analyses of sequenced G. intestinalis assemblage A genomes from different sub-assemblages identified a set of six genetic loci with high genetic variability. DNA samples from both humans (n = 44) and animals (n = 18) that harbored Giardia assemblage A infections, were PCR amplified (557-700 bp products) and sequenced at the six novel genetic loci. Bioinformatic analyses showed five to ten-fold higher levels of polymorphic sites than what was previously found among assemblage A samples using the classic genotyping loci. Phylogenetically, a division of two major clusters in assemblage A became apparent, separating samples of human and animal origin. A subset of human samples (n = 9) from a documented Giardia outbreak in a Swedish day-care center, showed full complementarity at nine genetic loci (the six new and the standard BG, TPI and GDH loci), strongly suggesting one source of infection. Furthermore, three samples of human origin displayed MLST profiles that were phylogenetically more closely related to MLST profiles from animal derived samples, suggesting zoonotic transmission. These new genotyping loci enabled us to detect events of recombination between different assemblage A isolates but also between assemblage A and E isolates. In summary, we present a novel and expanded MLST strategy with significantly improved sensitivity for molecular analyses of virulence types, zoonotic potential and source tracking for assemblage A Giardia.
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| 14. |
- Ankarklev, Johan, 1980-, et al.
(författare)
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Allelic sequence heterozygosity in single Giardia parasites
- 2012
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Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 12
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genetic heterogeneity has become a major inconvenience in the genotyping and molecular epidemiology of the intestinal protozoan parasite Giardia intestinalis, in particular for the major human infecting genotype, assemblage B. Sequence-based genotyping of assemblage B Giardia from patient fecal samples, where one or several of the commonly used genotyping loci (beta-giardin, triosephosphate isomerase and glutamate dehydrogenase) are implemented, is often hampered due to the presence of sequence heterogeneity in the sequencing chromatograms. This can be due to allelic sequence heterozygosity (ASH) and /or co-infections with parasites of different assemblage B sub-genotypes. Thus, two important questions have arisen; i) does ASH occur at the single cell level, and/or ii) do multiple sub-genotype infections commonly occur in patients infected with assemblage B, G. intestinalis isolates? Results: We used micromanipulation in order to isolate single Giardia intestinalis, assemblage B trophozoites (GS isolate) and cysts from human patients. Molecular analysis at the tpi loci of trophozoites from the GS lineage indicated that ASH is present at the single cell level. Analyses of assemblage B Giardia cysts from clinical samples at the bg and tpi loci also indicated ASH at the single cell level. Additionally, alignment of sequence data from several different cysts that originated from the same patient yielded different sequence patterns, thus suggesting the presence of multiple sub-assemblage infections in congruence with ASH within the same patient. Conclusions: Our results conclusively show that ASH does occur at the single cell level in assemblage B Giardia. Furthermore, sequence heterogeneity generated during sequence-based genotyping of assemblage B isolates may possess the complexity of single cell ASH in concurrence with co-infections of different assemblage B sub-genotypes. These findings explain the high abundance of sequence heterogeneity commonly found when performing sequence based genotyping of assemblage B Giardia, and illuminates the necessity of developing new G. intestinalis genotyping tools.
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| 15. |
- Ankarklev, Johan, et al.
(författare)
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Behind the smile : cell biology and disease mechanisms of Giardia species
- 2010
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Ingår i: Nature Reviews Microbiology. - : Springer Science and Business Media LLC. - 1740-1526 .- 1740-1534. ; 8:6, s. 413-422
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Forskningsöversikt (refereegranskat)abstract
- The eukaryotic intestinal parasite Giardia intestinalis was first described in 1681, when Antonie van Leeuwenhoek undertook a microscopic examination of his own diarrhoeal stool. Nowadays, although G. intestinalis is recognized as a major worldwide contributor to diarrhoeal disease in humans and other mammals, the disease mechanisms are still poorly understood. Owing to its reduced complexity and proposed early evolutionary divergence, G. intestinalis is used as a model eukaryotic system for studying many basic cellular processes. In this Review we discuss recent discoveries in the molecular cell biology and pathogenesis of G. intestinalis.
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| 16. |
- Ankarklev, Johan, et al.
(författare)
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Common Coinfections of Giardia intestinalis and Helicobacter pylori in Non-Symptomatic Ugandan Children
- 2012
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Ingår i: PLOS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2735. ; 6:8, s. e1780-
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Tidskriftsartikel (refereegranskat)abstract
- Background: The protozoan parasite Giardia intestinalis and the pathogenic bacterium Helicobacter pylori are well known for their high prevalences in human hosts worldwide. The prevalence of both organisms is known to peak in densely populated, low resource settings and children are infected early in life. Different Giardia genotypes/assemblages have been associated with different symptoms and H. pylori with induction of cancer. Despite this, not much data are available from sub-Saharan Africa with regards to the prevalence of different G. intestinalis assemblages and their potential association with H. pylori infections.Methodology/Principal Findings: Fecal samples from 427 apparently healthy children, 0-12 years of age, living in urban Kampala, Uganda were analyzed for the presence of H. pylori and G. intestinalis. G. intestinalis was found in 86 (20.1%) out of the children and children age 1<5 years had the highest rates of colonization. H. pylori was found in 189 (44.3%) out of the 427 children and there was a 3-fold higher risk of concomitant G. intestinalis and H. pylori infections compared to non-concomitant G. intestinalis infection, OR = 2.9 (1.7-4.8). No significant association was found in the studied population with regard to the presence of Giardia and gender, type of toilet, source of drinking water or type of housing. A panel of 45 G. intestinalis positive samples was further analyzed using multi-locus genotyping (MLG) on three loci, combined with assemblage-specific analyses. Giardia MLG analysis yielded a total of five assemblage AII, 25 assemblage B, and four mixed assemblage infections. The assemblage B isolates were highly genetically variable but no significant association was found between Giardia assemblage type and H. pylori infection.Conclusions/Significance: This study shows that Giardia assemblage B dominates in children in Kampala, Uganda and that the presence of H. pylori is an associated risk factor for G. intestinalis infection.
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| 17. |
- Ankarklev, Johan, et al.
(författare)
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Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates
- 2015
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Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
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Tidskriftsartikel (refereegranskat)abstract
- Background: The diarrhea-causing protozoan Giardia intestinalis makes up a species complex of eight different assemblages (A-H), where assemblage A and B infect humans. Comparative whole-genome analyses of three of these assemblages have shown that there is significant divergence at the inter-assemblage level, however little is currently known regarding variation at the intra-assemblage level. We have performed whole genome sequencing of two sub-assemblage AII isolates, recently axenized from symptomatic human patients, to study the biological and genetic diversity within assemblage A isolates. Results: Several biological differences between the new and earlier characterized assemblage A isolates were identified, including a difference in growth medium preference. The two AII isolates were of different sub-assemblage types (AII-1 [AS175] and AII-2 [AS98]) and showed size differences in the smallest chromosomes. The amount of genetic diversity was characterized in relation to the genome of the Giardia reference isolate WB, an assemblage AI isolate. Our analyses indicate that the divergence between AI and AII is approximately 1 %, represented by similar to 100,000 single nucleotide polymorphisms (SNP) distributed over the chromosomes with enrichment in variable genomic regions containing surface antigens. The level of allelic sequence heterozygosity (ASH) in the two AII isolates was found to be 0.25-0.35 %, which is 25-30 fold higher than in the WB isolate and 10 fold higher than the assemblage AII isolate DH (0.037 %). 35 protein-encoding genes, not found in the WB genome, were identified in the two AII genomes. The large gene families of variant-specific surface proteins (VSPs) and high cysteine membrane proteins (HCMPs) showed isolate-specific divergences of the gene repertoires. Certain genes, often in small gene families with 2 to 8 members, localize to the variable regions of the genomes and show high sequence diversity between the assemblage A isolates. One of the families, Bactericidal/ Permeability Increasing-like protein (BPIL), with eight members was characterized further and the proteins were shown to localize to the ER in trophozoites. Conclusions: Giardia genomes are modular with highly conserved core regions mixed up by variable regions containing high levels of ASH, SNPs and variable surface antigens. There are significant genomic variations in assemblage A isolates, in terms of chromosome size, gene content, surface protein repertoire and gene polymorphisms and these differences mainly localize to the variable regions of the genomes. The large genetic differences within one assemblage of G. intestinalis strengthen the argument that the assemblages represent different Giardia species.
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| 18. |
- Ankarklev, Johan, 1980-
(författare)
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Inter and Intra-Assemblage Characterizations of Giardia intestinalis: from clinic to genome
- 2012
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- The protozoan parasite Giardia intestinalis (syn. G. lamblia, G. duodenalis) is one of the most common causes of diarrheal disease throughout the world, where an estimated 500 million people are infected annually. Despite efforts in trying to elucidate factors associated with virulence in G. intestinalis little is currently known. The disease outcome is highly variable in Giardia infected individuals, ranging from asymptomatic carriers to severe disease. The reasons behind the differences in disease outcome are vaguely understood and studies trying to link infectivity to different Giardia assemblages or sub-assemblages have rendered conflicting results. Prior to this study, little was known about the prevalence and genetic diversity of different G. intestinalis assemblages across the world.In this thesis, molecular characterization of clinical G. intestinalis samples from Eastern Africa and Central America, has been performed, enabling a better understanding of the prevalence of different Giardia genotypes in endemic areas (Papers I and II). A correlation between Giardia colonization and the presence of Helicobacter pylori in the human host was established. We found that the currently available genotyping tools provide low resolution when used to characterize assemblage A Giardia. Also, genotyping of assemblage B isolates at these loci is troublesome due to the polymorphic substitutions frequently found in the sequencing chromatograms. This ambiguity was investigated by using micromanipulation to isolate single assemblage B Giardia cells (Paper III). Both cultured trophozoites and cysts from giardiasis patients were analyzed. The data showed that allelic sequence heterozygosity (ASH) does occur at the single cell level, but also that multiple sub-assemblage infections appear to be common in human giardiasis patients.Furthermore, genome-wide sequencing followed by comparative genomics was performed in order to better characterize differences between and within different Giardia assemblages. The genome of a non-human infecting, assemblage E isolate (Paper IV) was sequenced. The genomes of two freshly isolated human infecting assemblage AII isolates were also sequenced (Paper V). Subsequent, comparative analyses were performed and included the genomes of two human infecting isolates, WB (AI) and GS/M (B). Several important differences were found between assemblages A, B and E, but also within assemblage A; including unique gene repertoires for each isolate, observed differences in the variable gene families and an overall difference in ASH between the different isolates. Also, a new multi-locus genotyping (MLG) strategy for genotyping of assemblage A Giardia has been established and evaluated on clinical samples from human giardiasis patients.
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| 19. |
- Ansell, Brendan R. E., et al.
(författare)
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Divergent Transcriptional Responses to Physiological and Xenobiotic Stress in Giardia duodenalis
- 2016
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Ingår i: Antimicrobial Agents and Chemotherapy. - 0066-4804 .- 1098-6596. ; 60:10, s. 6034-6045
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Tidskriftsartikel (refereegranskat)abstract
- Understanding how parasites respond to stress can help to identify essential biological processes. Giardia duodenalis is a parasitic protist that infects the human gastrointestinal tract and causes 200 to 300 million cases of diarrhea annually. Metronidazole, a major antigiardial drug, is thought to cause oxidative damage within the infective trophozoite form. However, treatment efficacy is suboptimal, due partly to metronidazole-resistant infections. To elucidate conserved and stress-specific responses, we calibrated sublethal metronidazole, hydrogen peroxide, and thermal stresses to exert approximately equal pressure on trophozoite growth and compared transcriptional responses after 24 h of exposure. We identified 252 genes that were differentially transcribed in response to all three stressors, including glycolytic and DNA repair enzymes, a mitogen-activated protein (MAP) kinase, high-cysteine membrane proteins, flavin adenine dinucleotide (FAD) synthetase, and histone modification enzymes. Transcriptional responses appeared to diverge according to physiological or xenobiotic stress. Downregulation of the antioxidant system and alpha-giardins was observed only under metronidazole-induced stress, whereas upregulation of GARP-like transcription factors and their subordinate genes was observed in response to hydrogen peroxide and thermal stressors. Limited evidence was found in support of stress-specific response elements upstream of differentially transcribed genes; however, antisense derepression and differential regulation of RNA interference machinery suggest multiple epigenetic mechanisms of transcriptional control.
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| 20. |
- Ansell, Brendan R. E., et al.
(författare)
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Drug resistance in Giardia duodenalis
- 2015
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Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33:6, s. 888-901
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Forskningsöversikt (refereegranskat)abstract
- Giardia duodenalis is a microaerophilic parasite of the human gastrointestinal tract and a major contributor to diarrheal and post-infectious chronic gastrointestinal disease world-wide. Treatment of G. duodenalis infection currently relies on a small number of drug classes. Nitroheterocyclics, in particular metronidazole, have represented the front line treatment for the last 40 years. Nitroheterocyclic-resistant G. duodenalis have been isolated from patients and created in vitro, prompting considerable research into the biomolecular mechanisms of resistance. These compounds are redox-active and are believed to damage proteins and DNA after being activated by oxidoreductase enzymes in metabolically active cells. In this review, we explore the molecular phenotypes of nitroheterocyclic-resistant G. duodenalis described to date in the context of the protisfs unusual glycolytic and antioxidant systems. We propose that resistance mechanisms are likely to extend well beyond currently described resistance-associated enzymes (i.e., pyruvate ferredoxin oxidoreductases and nitroreductases), to include NAD(P)H- and flavin-generating pathways, and possibly redox-sensitive epigenetic regulation. Mechanisms that allow G. duodenalis to tolerate oxidative stress may lead to resistance against both oxygen and nitroheterocyclics, with implications for clinical control. The present review highlights the potential for systems biology tools and advanced bioinformatics to further investigate the multifaceted mechanisms of nitroheterocyclic resistance in this important pathogen.
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| 21. |
- Ansell, Brendan R. E., et al.
(författare)
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Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites
- 2015
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Ingår i: PLoS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2727 .- 1935-2735. ; 9:12
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Tidskriftsartikel (refereegranskat)abstract
- Giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. Although G. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. The present study employed RNA sequencing to characterize the mRNA transcriptome of G. duodenalis trophozoites in axenic culture, at log (48 h of growth), stationary (60 h), and declining (96 h) growth phases. Using similar to 400-times coverage of the transcriptome, we identified 754 differentially transcribed genes (DTGs), mainly representing two large DTG groups: 438 that were down-regulated in the declining phase relative to log and stationary phases, and 281 that were up-regulated. Differential transcription of prominent antioxidant and glycolytic enzymes implicated oxygen tension as a key factor influencing the transcriptional program of axenic trophozoites. Systematic bioinformatic characterization of numerous DTGs encoding hypothetical proteins of unknown function was achieved using structural homology searching. This powerful approach greatly informed the differential transcription analysis and revealed putative novel antioxidant-coding genes, and the presence of a nearcomplete two-component-like signaling system that may link cytosolic redox or metabolite sensing to the observed transcriptional changes. Motif searching applied to promoter regions of the two large DTG groups identified different putative transcription factor-binding motifs that may underpin global transcriptional regulation. This study provides new insights into the drivers and potential mediators of transcriptional variation in axenic G. duodenalis and provides context for static transcriptional studies.
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| 22. |
- Ansell, Brendan R. E., et al.
(författare)
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Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines
- 2017
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Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Giardia duodenalis is an intestinal parasite that causes 200-300 million episodes of diarrhoea annually. Metronidazole (Mtz) is a front-line anti-giardial, but treatment failure is common and clinical resistance has been demonstrated. Mtz is thought to be activated within the parasite by oxidoreductase enzymes, and to kill by causing oxidative damage. In G. duodenalis, Mtz resistance involves active and passive mechanisms. Relatively low activity of iron-sulfur binding proteins, namely pyruvate: ferredoxin oxidoreductase (PFOR), ferredoxins, and nitroreductase-1, enable resistant cells to passively avoid Mtz activation. Additionally, low expression of oxygen-detoxification enzymes can allow passive (non-enzymatic) Mtz detoxification via futile redox cycling. In contrast, active resistance mechanisms include complete enzymatic detoxification of the pro-drug by nitroreductase-2 and enhanced repair of oxidized biomolecules via thioredoxin-dependent antioxidant enzymes. Molecular resistance mechanisms may be largely founded on reversible transcriptional changes, as some resistant lines revert to drug sensitivity during drug-free culture in vitro, or passage through the life cycle. To comprehensively characterize these changes, we undertook strand-specific RNA sequencing of three laboratory-derived Mtz-resistant lines, 106-2ID(10), 713-M3, and WB-M3, and compared transcription relative to their susceptible parents. Common up-regulated genes encoded variant-specific surface proteins (VSPs), a high cysteine membrane protein, calcium and zinc channels, a Mad-2 cell cycle regulator and a putative fatty acid a alpha-oxidase. Down-regulated genes included nitroreductase-1, putative chromate and quinone reductases, and numerous genes that act proximal to PFOR. Transcriptional changes in 106-2ID(10) diverged from those in 713-r and WB-r (r <= 0.2), which were more similar to each other (r = 0.47). In 106-2ID(10), a nonsense mutation in nitroreductase-1 transcripts could enhance passive resistance whereas increased transcription of nitroreductase-2, and a MATE transmembrane pump system, suggest active drug detoxification and efflux, respectively. By contrast, transcriptional changes in 713-M3 and WB-M3 indicated a higher oxidative stress load, attributed to Mtz- and oxygen-derived radicals, respectively. Quantitative comparisons of orthologous gene transcription between Mtz-resistant G. duodenalis and Trichomonas vaginalis, a closely related parasite, revealed changes in transcripts encoding peroxidases, heat shock proteins, and FMN-binding oxidoreductases, as prominent correlates of resistance. This work provides deep insight into Mtz-resistant G. duodenalis, and illuminates resistance-associated features across parasitic species.
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| 23. |
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| 24. |
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| 25. |
- Ástvaldsson, Ásgeir, 1981-
(författare)
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Pathogenesis and Cell Biology of the Salmon Parasite Spironucleus salmonicida
- 2019
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Spironucleus species are classified as diplomonad organisms, diverse eukaryotic flagellates found in oxygen-deprived environments. Members of Spironucleus are parasitic and can infect a variety of hosts, such as mice and birds, while the majority are found to infect fish. Massive outbreaks of severe systemic infection caused by a Spironucleus member, Spironucleus salmonicida (salmonicida = salmon killer), have been reported in farmed salmonids resulting in large economic impacts for aquaculture.In this thesis, the S. salmonicida genome was sequenced and compared to the genome of its diplomonad relative, the mammalian pathogen G. intestinalis (Paper I). Our analyses revealed large genomic differences between the two parasites that collectively suggests that S. salmonicida is more capable of adapting to different environments. As S. salmonicida can infiltrate different host tissues, we provide molecular evidence for how the parasite can tolerate oxygenated environments and suggest oxygen as a potential regulator of virulence factors (Paper III). To further investigate the molecular responses of the parasite and in addition, its host, during infection we set up an interaction system of S. salmonicida and ASK (Atlantic salmon kidney) cells (Paper VI).To study the cell biology in S. salmonicida we optimized an enzymatic proximity labeling method using ascorbate peroxidase (APEX) as a reporter for transmission electron microscopy (TEM) (Paper IV). As the system is robust and versatile, we showed the localization and performed ultrastructural characterization of numerous proteins in S. salmonicida and G. intestinalis. We furthermore utilized the APEX system to study the annexin protein family in S. salmonicida (Paper II). Super resolution microscopy and TEM were applied to show that the annexins are mostly associated with cytoskeletal and membranous structures. In addition, we performed phylogenetic analyses concluding that the annexin gene family is expanded in diplomonads.We performed experimental infection in Atlantic salmon and derived a potential model for the route of infection (Paper V). The results suggested multiple routes of transmission between hosts for the parasite.To conclude, the comprehensive work in this thesis has provided valuable insights into the pathogenesis and cell biology of the highly adaptable diplomonad parasite S. salmonicida.
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