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1.
  • Wolniewicz, Peter, 1978-, et al. (författare)
  • Reactivity changes in lead-cooled fast reactors due to bubbles in the coolant
  • 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)
  • The Signal Recognition Particle of the diplomonad Giardia lacks the Alu domain responsible for translational arrest
  • 2008
  • Ingår i: RNA Society Meeting 2008.
  • 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)
  • Experimental challenge of Atlantic salmon (Salmo salar) with the diplomonad parasite Spironucleus salmonicida to characterize the infection cycle
  • 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)
  • A genomic survey of the fish parasite Spironucleus salmonicida indicates genomic plasticity among diplomonads and significant lateral gene transfer in eukaryote genome evolution
  • 2007
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 8, s. 51-
  • 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)
  • The genome of Giardia and other diplomonads
  • 2010
  • Ingår i: Anaerobic Parasitic Protozoa: Genomics and Molecular Biology. - : Caister Academic Press. - 9781904455615 ; , s. 23-44
  • Bokkapitel (övrigt vetenskapligt/konstnärligt)
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6.
  • Andersson, Peter, 1981-, et al. (författare)
  • Correction for dynamic bias error in transmission measurements of void fraction
  • 2012
  • Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 83:12, s. 125110-
  • 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)
  • Design and initial 1D radiography tests of the FANTOM mobile fast-neutron radiography and tomography system
  • 2014
  • Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 756, s. 82-93
  • 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)
  • Effects of proton escape on detection efficiency in thin scintillator elements and its consequences for optimization of fast-neutron imaging
  • 2011
  • Ingår i: Nuclear Instruments and Methods in Physics Research Section A. - : Elsevier BV. - 0168-9002 .- 1872-9576. ; 651:1, s. 110-116
  • 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)
  • Fast-Neutron Tomography using a Mobile Neutron Generator for Assessment of Steam-Water Distributions in Two-Phase Flows
  • 2014
  • 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)
  • Neutron tomography for void distribution measurements
  • 2010
  • Ingår i: ENC 2010 Transactions. - 9789295064096 ; , s. 40-45
  • 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)
  • Neutron tomography of axially symmetric objects using 14 MeV neutrons from a portable neutron generator
  • 2014
  • Ingår i: Review of Scientific Instruments. - : AIP Publishing. - 0034-6748 .- 1089-7623. ; 85:8, s. 085109-
  • 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)
  • Optimization of Equipment for Tomographic Measurements of Void Distributions using Fast Neutrons
  • 2011
  • 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)
  • A novel high-resolution multilocus sequence typing of Giardia intestinalis Assemblage A isolates reveals zoonotic transmission, clonal outbreaks and recombination
  • 2018
  • Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 60, s. 7-16
  • 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)
  • Allelic sequence heterozygosity in single Giardia parasites
  • 2012
  • Ingår i: BMC Microbiology. - : Springer Science and Business Media LLC. - 1471-2180. ; 12
  • 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)
  • Behind the smile : cell biology and disease mechanisms of Giardia species
  • 2010
  • Ingår i: Nature Reviews Microbiology. - : Springer Science and Business Media LLC. - 1740-1526 .- 1740-1534. ; 8:6, s. 413-422
  • 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)
  • Common Coinfections of Giardia intestinalis and Helicobacter pylori in Non-Symptomatic Ugandan Children
  • 2012
  • Ingår i: PLOS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2735. ; 6:8, s. e1780-
  • 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)
  • Comparative genomic analyses of freshly isolated Giardia intestinalis assemblage A isolates
  • 2015
  • Ingår i: BMC Genomics. - : Springer Science and Business Media LLC. - 1471-2164. ; 16
  • 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)
  • Inter and Intra-Assemblage Characterizations of Giardia intestinalis: from clinic to genome
  • 2012
  • 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)
  • Divergent Transcriptional Responses to Physiological and Xenobiotic Stress in Giardia duodenalis
  • 2016
  • Ingår i: Antimicrobial Agents and Chemotherapy. - 0066-4804 .- 1098-6596. ; 60:10, s. 6034-6045
  • 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)
  • Drug resistance in Giardia duodenalis
  • 2015
  • Ingår i: Biotechnology Advances. - : Elsevier BV. - 0734-9750 .- 1873-1899. ; 33:6, s. 888-901
  • 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)
  • Time-Dependent Transcriptional Changes in Axenic Giardia duodenalis Trophozoites
  • 2015
  • Ingår i: PLoS Neglected Tropical Diseases. - : Public Library of Science (PLoS). - 1935-2727 .- 1935-2735. ; 9:12
  • 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)
  • Transcriptomics Indicates Active and Passive Metronidazole Resistance Mechanisms in Three Seminal Giardia Lines
  • 2017
  • Ingår i: Frontiers in Microbiology. - : Frontiers Media SA. - 1664-302X. ; 8
  • 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)
  • Pathogenesis and Cell Biology of the Salmon Parasite Spironucleus salmonicida
  • 2019
  • 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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26.
  • Astvaldsson, Asgeir, 1981-, et al. (författare)
  • Proximity Staining using Enzymatic Protein Tagging in Diplomonads
  • 2019
  • Ingår i: mSphere. - 2379-5042. ; 4:2
  • Tidskriftsartikel (refereegranskat)abstract
    • The diplomonads are a group of understudied eukaryotic flagellates whose most prominent member is the human pathogen Giardia intestinalis. Methods commonly used in other eukaryotic model systems often require special optimization in diplomonads due to the highly derived character of their cell biology. We have optimized a proximity labeling protocol using pea ascorbate peroxidase (APEX) as a reporter for transmission electron microscopy (TEM), to enable study of ultrastructural cellular details in diplomonads. Currently available TEM-compatible tags requires light-induced activation (1, 2) or are inactive in many cellular compartments (3) while ascorbate peroxidase has not been shown to have those limitations. Here we have optimized the in vivo activity of two versions of pea ascorbate peroxidase (APXW41F and APEX) using the diplomonad fish parasite Spironucleus salmonicida, a relative of G. intestinalis. We exploited the well-known peroxidase substrates, Amplex UltraRed and 3,3’-diaminobenzidine (DAB), to validate the activity of the two tags and argue that APEX is the most stable version to use in Spironucleus salmonicida. Next, we fused APEX to proteins with established localization to evaluate the activity of APEX in different cellular compartments of the diplomonad cell and used Amplex UltraRed as well as antibodies along with super-resolution microscopy to confirm the protein-APEX localization. The ultrastructural details of protein-APEX fusions were determined by TEM and we observed marker activity in all cellular compartments tested when using the DAB substrate. Finally, we show that the optimized conditions established for S. salmonicida can be used in the related diplomonad G. intestinalis.
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27.
  • Balan, Balu, et al. (författare)
  • Multimodal regulation of encystation in Giardia duodenalis revealed by deep proteomics
  • 2021
  • Ingår i: International Journal of Parasitology. - : Elsevier. - 0020-7519 .- 1879-0135. ; 51:10, s. 809-824
  • Tidskriftsartikel (refereegranskat)abstract
    • Cyst formation in the parasitic protist Giardia duodenalis is critical to its transmission. Existing proteomic data quantifies only 17% of coding genes transcribed during encystation and does not cover the complete process from trophozoite to mature cyst. Using high-resolution mass spectrometry, we have quantified proteomic changes across encystation and compared this with published transcriptomic data. We reproducibly identified 3863 (64.5% of Giardia proteins) and quantified 3382 proteins (56.5% of Giardia proteins) over standard trophozoite growth (TY), during low-bile encystation priming (LB), 16 h into encystation (EC), and at cyst maturation (C). This work provides the first known expanded observation of encystation at the proteomic level and triples the coverage of previous encystation proteomes. Onethird (1169 proteins) of the quantified proteome is differentially expressed in the mature cyst relative to the trophozoite, including proteasomal machinery, metabolic pathways, and secretory proteins. Changes in lipid metabolism indicated a shift in lipid species dependency during encystation. Consistent with this, we identified the first, putative lipid transporters in this species, representing the steroidogenic acute regulatory protein-related lipid transfer (StARkin), oxysterol binding protein related protein (ORP/Osh) and glycosphingolipid transfer protein (GLTP) families, and follow their differential expression over cyst formation. Lastly, we undertook correlation analyses of the transcriptome and proteome of trophozoites and cysts, and found evidence of post-transcriptional regulation of key protein classes (RNA binding proteins) and stage-specific genes (encystation markers) implicating translationrepression in encystation. We provide the most extensive proteomic analysis of encystation in Giardia to date and the first known exploration across its complete duration. This work identifies encystation as highly coordinated, involving major changes in proteostasis, metabolism and membrane dynamics, and indicates a potential role for post-transcriptional regulation, mediated through RNA-binding proteins. Together our work provides a valuable resource for Giardia research and the development of transmission-blocking anti-giardials. (c) 2021 The Author(s). Published by Elsevier Ltd on behalf of Australian Society for Parasitology.
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28.
  • Birkeland, Shanda R., et al. (författare)
  • Transcriptome analyses of the Giardia lamblia life cycle
  • 2010
  • Ingår i: Molecular and biochemical parasitology (Print). - : Elsevier BV. - 0166-6851 .- 1872-9428. ; 174:1, s. 62-65
  • Tidskriftsartikel (refereegranskat)abstract
    • We quantified mRNA abundance from 10 stages in the Giardia lamblia life cycle in vitro using Serial Analysis of Gene Expression (SAGE). 163 abundant transcripts were expressed constitutively. 71 transcripts were upregulated specifically during excystation and 42 during encystation. Nonetheless, the transcriptomes of cysts and trophozoites showed major differences. SAGE detected co-expressed clusters of 284 transcripts differentially expressed in cysts and excyzoites and 287 transcripts in vegetative trophozoites and encysting cells. All clusters included known genes and pathways as well as proteins unique to Giardia or diplomonads. SAGE analysis of the Giardia life cycle identified a number of kinases, phosphatases, and DNA replication proteins involved in excystation and encystation, which could be important for examining the roles of cell signaling in giardial differentiation. Overall, these data pave the way for directed gene discovery and a better understanding of the biology of G. lamblia.
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29.
  • Branger, Erik, 1988-, et al. (författare)
  • Experimental evaluation of models for predicting Cherenkov light intensities from short-cooled nuclear fuel assemblies
  • 2018
  • Ingår i: Journal of Instrumentation. - 1748-0221. ; 13
  • Tidskriftsartikel (refereegranskat)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is a tool used by nuclear safeguards inspectors to verify irradiated nuclear fuel assemblies in wet storage based on the recording of Cherenkov light produced by the assemblies. One type of verification involves comparing the measured light intensity from an assembly with a predicted intensity, based on assembly declarations. Crucial for such analyses is the performance of the prediction model used, and recently new modelling methods have been introduced to allow for enhanced prediction capabilities by taking the irradiation history into account, and by including the cross-talk radiation from neighbouring assemblies in the predictions.In this work, the performance of three models for Cherenkov-light intensity prediction is evaluated by applying them to a set of short-cooled PWR 17x17 assemblies for which experimental DCVD measurements and operator-declared irradiation data was available; (1) a two-parameter model, based on total burnup and cooling time, previously used by the safeguards inspectors, (2) a newly introduced gamma-spectrum-based model, which incorporates cycle-wise burnup histories, and (3) the latter gamma-spectrum-based model with the addition to account for contributions from neighbouring assemblies.The results show that the two gamma-spectrum-based models provide significantly higher precision for the measured inventory compared to the two-parameter model, lowering the standard deviation between relative measured and predicted intensities from 15.2% to 8.1% respectively 7.8%.The results show some systematic differences between assemblies of different designs (produced by different manufacturers) in spite of their similar PWR 17x17 geometries, and possible ways are discussed to address such differences, which may allow for even higher prediction capabilities. Still, it is concluded that the gamma-spectrum-based models enable confident verification of the fuel assembly inventory at the currently used detection limit for partial defects, being a 30% discrepancy between measured and predicted intensities, while some false detection occurs with the two-parameter model. The results also indicate that the gamma-spectrum-based prediction methods are accurate enough that the 30% discrepancy limit could potentially be lowered.
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30.
  • Branger, Erik, 1988-, et al. (författare)
  • Experimental study of background subtraction in Digital Cherenkov Viewing Device measurements
  • 2018
  • Ingår i: Journal of Instrumentation. - 1748-0221. ; 13:8
  • Tidskriftsartikel (refereegranskat)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is an imaging tool used by authority inspectors for partial defect verification of nuclear fuel assemblies in wet storage, i.e. to verify that part of an assembly has not been diverted. One of the currently adopted verification procedures is based on quantitative measurements of the assembly's Cherenkov light emissions, and comparisons to an expected intensity, calculated based on operator declarations. A background subtraction of the intensity data in the recorded images is necessary for accurate quantitative measurements. The currently used background subtraction is aimed at removing an electronics-induced image-wide offset, but it is argued here that the currently adopted procedure may be insufficient.It is recommended that a standard dark-frame subtraction should be used, to remove systematic pixel-wise background due to the electronics, replacing the currently used offset procedure. Experimental analyses show that a dark-frame subtraction would further enhance the accuracy and reliability of DCVD measurements. Furthermore, should ageing of the CCD chip result in larger systematic pixel-wise deviations over time, a dark-frame subtraction can ensure reliable measurements regardless of the age of the CCD chip. It can also help in eliminating any adverse effects of malfunctioning pixels. In addition to the background from electronic noise, ways to compensate for background from neighbouring fuel assemblies and ambient light are also discussed.
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31.
  • Branger, Erik, 1988-, et al. (författare)
  • Image analysis as a tool for improved use of the Digital Cherenkov Viewing Device for inspection of irradiated PWR fuel assemblies.
  • 2014
  • Rapport (övrigt vetenskapligt/konstnärligt)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is a tool used to measure the Cherenkov light emitted from irradiated nuclear fuel assemblies stored in water pools. It has been approved by the IAEA for attended gross defect verification, as well as for partial defect verification, where a fraction of the fuel material has been diverted. In this report, we have investigated the current procedures for recording images with the DCVD, and have looked into ways to improve these procedures. Using three different image sets of PWR fuel assemblies, we have analysed what information and results can be obtained using image analysis techniques. We have investigated several error sources that distort the images, and have shown how these errors affect the images. We have also described some of the errors mathematically, and have discussed how these error sources may be compensated for, if the character and magnitude of the errors are known. Resulting from our investigations are a few suggestions on how to improve the procedures and consequently the quality of the images recorded with the DCVD as well as suggestions on how to improve the analysis of collected images. Specifically, a few improvements that should be looked into in the short term are:• Images should be recorded with the fuel assembly perfectly centered in the image, and preferably without any tilt of the DCVD relative to the fuel in order to obtain accurate measurements of the light intensity. Image analysis procedures that may aid the alignment are presented.• To compensate for the distorting effect of the water surface and possible turbulence in the water, several images with short exposure time should be captured rather than one image with long exposure time. Using image analysis procedures, it is possible to sum the images resulting in a final image with less distortions and improved quality.• A reference image should be used to estimate device-related distortions, so that these distortions are compensated for. Ideally, this procedure can also be used to calibrate individual pixels.• The background should be carefully taken into account in order to separate the background level from diffuse signal components, allowing for the background to be subtracted. Accordingly, each measurement campaign should be accompanied by at least one background measurement, recorded from a section in the storage pool where no fuel assemblies are present. Furthermore, the background level should be determined from a larger region in the image and not from one individual pixel, as is currently done.• A database of measurements should be set up, containing DCVD images, information about the applied DCVD settings and the conditions that the DCVD was used in. Any partial defect verification procedure at any time could then be tested against as much data as possible. Accordingly, a database can aid in evaluating and improving partial defect verification methods using DCVD image analysis.Based on the findings and discussions in this report, some long-term improvements are also suggested.
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32.
  • Branger, Erik, 1988-, et al. (författare)
  • Improved DCVD assessments of irradiated nuclear fuel using image analysis techniques
  • 2014
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is a tool for measuring the Cherenkov light intensity emitted from irradiated nuclear fuel in wet storage. It is currently used in nuclear facilities where authority inspectors perform attended gross defect verification to ensure the presence of irradiated fuel material, as well as partial defect verification to ensure that a fraction of the fuel material has not been diverted. In 2013, Uppsala University (UU), supported by the Swedish Radiation Safety Authority, initiated a PhD project aimed at gaining a better understanding of the underlying physics process of the Cherenkov light emission and its detection, in order to improve and enhance the capabilities of the DCVD. The scope of this research is broad and includes modelling, simulations and experiments. As a first step, expertise on image analysis was brought into the project with the purpose to identify image analysis related opportunities and challenges relevant to the DCVD. The investigations performed so far cover general aspects of image analysis as well as aspects specific for verification of PWR fuels, where the fuel geometry may be extra challenging. Resulting from the investigation are suggestions on how to improve the measurement procedure and consequently the image quality obtained with the DCVD. This presentation describes these results and expected outcomes of their implementation.
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33.
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34.
  • Branger, Erik, 1988-, et al. (författare)
  • On the inclusion of light transport in prediction tools for Cherenkov light intensity assessment of irradiated nuclear fuel assemblies
  • 2019
  • Ingår i: Journal of Instrumentation. - 1748-0221. ; 14
  • Tidskriftsartikel (refereegranskat)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is a tool used to verify irradiated nuclear fuel assemblies in wet storage by imaging the Cherenkov light produced by the radiation emitted from the assemblies. It is frequently used for partial defect verification, verifying that part of an assembly has not been removed and/or replaced. In one of the verification procedures used, the detected total Cherenkov light intensities from a set of assemblies are compared to predicted intensities, which are calculated using operator declarations for the assemblies.This work presents a new, time-efficient method to simulate DCVD images of fuel assemblies, allowing for estimations of the Cherenkov light production, transport and detection. Qualitatively, good agreement between simulated and measured images is demonstrated. Quantitatively, it is shown that relative intensity predictions based on simulated images are within 0.5% of corresponding predictions based solely on the production of Cherenkov light, neglecting light transport and detection. Consequently, in most cases it is sufficient to use predictions based on produced Cherenkov light, neglecting transport and detection, thus substantially reducing the time needed for simulations.In a verification campaign, assemblies are grouped according to their type, and the relative measured and predicted intensities are compared in a group. By determining transparency factors, describing the fraction of Cherenkov light that is blocked by the top plate of an assembly, it is possible to adjust predictions based on the production of Cherenkov light to take the effect of the top plate into account. This procedure allows assemblies of the same type bit with different top plates to be compared with increased accuracy. The effect of using predictions adjusted with transparency factors were assessed experimentally on a set of Pressurized Water Reactor 17x17 assemblies having five different top plate designs. As a result of the adjustment, the agreement between measured and predicted relative intensities for the whole data set was enhanced, resulting in a reduction of an RMSE from 14.1% to 10.7%. It is expected that further enhancements may be achieved by introducing more detailed top-plate and spacer descriptions.
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35.
  • Branger, Erik, 1988-, et al. (författare)
  • Towards unattended partial-defect verification of irradiated nuclear fuel assemblies using the DCVD
  • 2014
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • The Digital Cherenkov Viewing Device (DCVD) is a tool used by authority inspectors to verify irradiated nuclear fuel assemblies in wet storage by measuring the Cherenkov light emitted. The DCVD is approved by the IAEA for gross defect verification, and is one of the few inspection tools approved for partial defect verification.There is interest in adapting the DCVD to work in unattended mode, so that it can be used to verify large quantities of irradiated fuel assemblies prior to moving them to difficult-to-access storage locations. This work presents methods based on image analysis that can be used to reduce the effects of different types of distortions encountered when performing measurements with the DCVD. Implementing these methods will ensure that data of high quality is obtained. Verification prior to moving fuels to difficult-to-access storage may also require a dedicated measurement station to be built, and it is argued that by constructing these stations with the DCVD in mind, many distortions can be reduced or eliminated. Thus, by implementing safeguards-by-design, it is possible to ensure that the DCVD is used in near optimal conditions.
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36.
  • Buret, Andre G., et al. (författare)
  • Update on Giardia : Highlights from the seventh International Giardia and Cryptosporidium Conference
  • 2020
  • Ingår i: Parasite. - : EDP Sciences. - 1252-607X .- 1776-1042. ; 27
  • Forskningsöversikt (refereegranskat)abstract
    • Although Giardia duodenalis is recognized as one of the leading causes of parasitic human diarrhea in the world, knowledge of the mechanisms of infection is limited, as the pathophysiological consequences of infection remain incompletely elucidated. Similarly, the reason for and consequences of the very specific genome-organization in this parasite with 2 active nuclei is only partially known. Consistent with its tradition, the 7th International Giardia and Cryptosporidium Conference (IGCC 2019) was held from June 23 to 26, 2019, at the Faculty of Medicine and Pharmacy of the University of Rouen-Normandie, France, to discuss current research perspectives in the field. This renowned event brought together an international delegation of researchers to present and debate recent advances and identify the main research themes and knowledge gaps. The program for this interdisciplinary conference included all aspects of host-parasite relationships, from basic research to applications in human and veterinary medicine, as well as the environmental issues raised by water-borne parasites and their epidemiological consequences. With regard to Giardia and giardiasis, the main areas of research for which new findings and the most impressive communications were presented and discussed included: parasite ecology and epidemiology of giardiasis, Giardia-host interactions, and cell biology of Giardia, genomes and genomic evolution. The high-quality presentations discussed at the Conference noted breakthroughs and identified new opportunities that will inspire researchers and funding agencies to stimulate future research in a “one health” approach to improve basic knowledge and clinical and public health management of zoonotic giardiasis.
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37.
  • Caccio, Simone M., et al. (författare)
  • Host specificity in the Giardia duodenalis species complex
  • 2018
  • Ingår i: Infection, Genetics and Evolution. - : Elsevier BV. - 1567-1348 .- 1567-7257. ; 66, s. 335-345
  • Forskningsöversikt (refereegranskat)abstract
    • Giardia duodenalis is a unicellular flagellated parasite that infects the gastrointestinal tract of a wide range of mammalian species, including humans. Investigations of protein and DNA polymorphisms revealed that G. duodenalis should be considered as a species complex, whose members, despite being morphologically indistinguishable, can be classified into eight groups, or Assemblages, separated by large genetic distances. Assemblages display various degree of host specificity, with Assemblages A and B occurring in humans and many other hosts, Assemblage C and D in canids, Assemblage E in hoofed animals, Assemblage F in cats, Assemblage G in rodents, and Assemblage H in pinnipeds. The factors determining host specificity are only partially understood, and clearly involve both the host and the parasite. Here, we review the results of in vitro and in vivo experiments, and clinical observations to highlight relevant biological and genetic differences between Assemblages, with a focus on human infection.
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38.
  • Carolina Touz, Maria, et al. (författare)
  • Arginine deiminase has multiple regulatory roles in the biology of Giardia lamblia
  • 2008
  • Ingår i: Journal of Cell Science. - : The Company of Biologists. - 0021-9533 .- 1477-9137. ; 121:17, s. 2930-2938
  • Tidskriftsartikel (refereegranskat)abstract
    • The protozoan parasite Giardia lamblia uses arginine deiminase (ADI) to produce energy from free L-arginine under anaerobic conditions. In this work, we demonstrate that, in addition to its known role as a metabolic enzyme, it also functions as a peptidylarginine deiminase, converting protein-bound arginine into citrulline. G. lamblia ADI specifically binds to and citrullinates the arginine in the conserved CRGKA tail of variant-specific surface proteins (VSPs), affecting both antigenic switching and antibody-mediated cell death. During encystation, ADI translocates from the cytoplasm to the nuclei and appears to play a regulatory role in the expression of encystation-specific genes. ADI is also sumoylated, which might modulate its activity. Our findings reveal a dual role played by ADI and define novel regulatory pathways used by Giardia for survival.
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39.
  • Carranza, Pedro G., et al. (författare)
  • Specific histone modifications play critical roles in the control of encystation and antigenic variation in the early-branching eukaryote Giardia lamblia
  • 2016
  • Ingår i: International Journal of Biochemistry and Cell Biology. - : Elsevier BV. - 1357-2725 .- 1878-5875. ; 81, s. 32-43
  • Tidskriftsartikel (refereegranskat)abstract
    • During evolution, parasitic microorganisms have faced the challenges of adapting to different environments to colonize a variety of hosts. Giardia lamblia, a common cause of intestinal disease, has developed fascinating strategies to adapt both outside and inside its host's intestine, such as trophozoite differentiation into cyst and the switching of its major surface antigens. How gene expression is regulated during these adaptive processes remains undefined. Giardia lacks some typical eukaryotic features, like canonical transcription factors, linker histone H1, and complex promoter regions; suggesting that post transcriptional and translational control of gene expression is essential for parasite survival. However, epigenetic factors may also play critical roles at the transcriptional level. Here, we describe the most common post -translational histone modifications; characterize enzymes involved in these reactions, and analyze their association with the Giardia's differentiation processes. We present evidence that NAD(+)-dependent and NAD(+)-independent histone deacetylases regulate encystation; however, a unique NAD(+)-independent histone deacetylase modulate antigenic switching. The rates of acetylation of H4K8 and H4K16 are critical for encystation, whereas a decrease in acetylation of H4K8 and methylation of H3K9 occur preferentially during antigenic variation. These results show the complexity of the mechanisms regulating gene expression in this minimalistic protozoan parasite.
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40.
  •  
41.
  • Davids, Barbara J., et al. (författare)
  • Identification of Conserved Candidate Vaccine Antigens in the Surface Proteome of Giardia lamblia
  • 2019
  • Ingår i: Infection and Immunity. - : AMER SOC MICROBIOLOGY. - 0019-9567 .- 1098-5522. ; 87:6
  • Tidskriftsartikel (refereegranskat)abstract
    • Giardia lamblia, one of the most common protozoal infections of the human intestine, is an important worldwide cause of diarrheal disease, malabsorption, malnutrition, delayed cognitive development in children, and protracted postinfectious syndromes. Despite its medical importance, no human vaccine is available against giardiasis. A crude veterinary vaccine has been developed, and experimental vaccines based on expression of multiple variant-specific surface proteins have been reported, but poorly defined vaccine components and excessive antigen variability are problematic for pharmaceutical vaccine production. To expand the repertoire of antigen candidates for vaccines, we reasoned that surface proteins may provide an enriched source of such antigens since key host effectors, such as secretory IgA, can directly bind to such antigens in the intestinal lumen and interfere with epithelial attachment. Here, we have applied a proteomics approach to identify 23 novel surface antigens of G. lamblia that show >90% amino acid sequence identity between the two human-pathogenic genetic assemblages (A and B) of the parasite. Surface localization of a representative subset of these proteins was confirmed by immunostaining. Four selected proteins, uridine phosphorylase-like protein-1, protein 21.1 (GL50803_ 27925), alpha 1-giardin, and alpha 11-giardin, were subsequently produced in recombinant form and shown to be immunogenic in mice and G. lamblia-infected humans and confer protection against G. lamblia infection upon intranasal immunization in rodent models of giardiasis. These results demonstrate that identification of conserved surface antigens provides a powerful approach for overcoming a key rate-limiting step in the design and construction of an effective vaccine against giardiasis.
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42.
  • Davids, Barbara J., et al. (författare)
  • Polymeric immunoglobulin receptor in intestinal immune defense against the lumen-dwelling protozoan parasite Giardia
  • 2006
  • Ingår i: Journal of Immunology. - 0022-1767 .- 1550-6606. ; 177:9, s. 6281-6290
  • Tidskriftsartikel (refereegranskat)abstract
    • The polymeric Ig receptor (pIgR) is conserved in mammals and has an avian homologue, suggesting evolutionarily important functions in vertebrates. It transports multimeric IgA and IgM across polarized epithelia and is highly expressed in the intestine, yet little direct evidence exists for its importance in defense against common enteric pathogens. In this study, we demonstrate that pIgR can play a critical role in intestinal defense against the lumen-dwelling protozoan parasite Giardia, a leading cause of diarrheal disease. The receptor was essential for the eradication of Giardia when high luminal IgA levels were required. Clearance of Giardia muris, in which IgA plays a dominant role, was severely compromised in pIgR-deficient mice despite significant fecal IgA output at 10% of normal levels. In contrast, eradication of the human strain Giardia lamblia GS/M, for which adaptive immunity is less IgA dependent in mice, was unaffected by pIgR deficiency, indicating that pIgR had no physiologic role when lower luminal IgA levels were sufficient for parasite elimination. Immune IgA was greatly increased in the serum of pIgR-deficient mice, conferred passive protection against Giardia, and recognized several conserved giardial Ags, including ornithine carbamoyltransferase, arginine deiminase, alpha-enolase, and alpha- and beta-giardins, that are also detected in human giardiasis. Corroborative observations were made in mice lacking the J chain, which is required for pIgR-dependent transepithelial IgA transport. These results, together with prior data on pIgR-mediated immune neutralization of luminal cholera toxin, suggest that pIgR is essential in intestinal defense against pathogenic microbes with high-level and persistent luminal presence.
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43.
  • Davour, Anna, et al. (författare)
  • Applying image analysis techniques to tomographic images of irradiated nuclear fuel assemblies
  • 2016
  • Ingår i: Annals of Nuclear Energy. - : Elsevier BV. - 0306-4549 .- 1873-2100. ; 96, s. 223-229
  • Tidskriftsartikel (refereegranskat)abstract
    • In this paper we present a set of image analysis techniques used for extraction of information from cross-sectional images of nuclear fuel assemblies, achieved from gamma emission tomography measurements. These techniques are based on template matching, an established method for identifying objects with known properties in images.We demonstrate a rod template matching algorithm for identification and counting of the fuel rods present in the image. This technique may be applicable in nuclear safeguards inspections, because of the potential of verifying the presence of all fuel rods, or potentially discovering any that are missing.We also demonstrate the accurate determination of the position of a fuel assembly, or parts of the assembly, within the imaged area. Accurate knowledge of the assembly position enables detailed modelling of the gamma transport through the fuel, which in turn is needed to make tomographic reconstructions quantifying the activity in each fuel rod with high precision.Using the full gamma energy spectrum, details about the location of different gamma-emitting isotopes within the fuel assembly can be extracted. We also demonstrate the capability to determine the position of supporting parts of the nuclear fuel assembly through their attenuating effect on the gamma rays emitted from the fuel. Altogether this enhances the capabilities of non-destructive nuclear fuel characterization.
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44.
  • Davour, Anna, 1975-, et al. (författare)
  • Image analysis methods for partial defect detection using tomographic images on nuclear fuel assemblies
  • 2015
  • Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
    • A promising non-destructive assay method for verification of irradiated nuclear fuel is gammatomography, i.e. the use of measurements of the gamma radiation field around a nuclear fuel assembly to reconstruct detailed information about the internal source distribution.Typically, tomographic reconstructions result in two-dimensional images of cross sections of the fuel. We demonstrate how such images can be searched for fuel rods using a template matching technique, which is a method commonly used in the field of image analysis. In this case, a template or mask corresponding to the size and shape of a fuel rod is translated across the image in order to find the region with the highest reconstructed activity, which is assumed to correspond to the location of a fuel rod in the image. This is done iteratively, allowing no overlap of the rods. By defining the threshold between background and fuel rod objects in the image, we can identify and count the fuel rods using no other assumptions than the rod radius.Thus the rod identification procedure provides a possible means to verify whether all fuel rods arepresent, and it may also be implemented to identify the fuel type of the measured assembly. Theprocedure is robust in cases of irregularities, such as assembly bow or torsion, or the dislocation ofindividual fuel rods in the measured cross section.Here we demonstrate fuel rod identification procedure, using authentic images collected with a tomographic measurement device on commercial fuel assemblies. The results show that image analysis can support tomographic partial defect verification of irradiated nuclear fuel assemblies, even on the single fuel rod level.
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45.
  • Dube, Faruk, et al. (författare)
  • Gene co-expression network analysis reveal core responsive genes in Parascaris univalens tissues following ivermectin exposure
  • 2024
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 19:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Anthelmintic resistance in equine parasite Parascaris univalens, compromises ivermectin (IVM) effectiveness and necessitates an in-depth understanding of its resistance mechanisms. Most research, primarily focused on holistic gene expression analyses, may overlook vital tissue-specific responses and often limit the scope of novel genes. This study leveraged gene co-expression network analysis to elucidate tissue-specific transcriptional responses and to identify core genes implicated in the IVM response in P. univalens. Adult worms (n = 28) were exposed to 10−11 M and 10−9 M IVM in vitro for 24 hours. RNA-sequencing examined transcriptional changes in the anterior end and intestine. Differential expression analysis revealed pronounced tissue differences, with the intestine exhibiting substantially more IVM-induced transcriptional activity. Gene co-expression network analysis identified seven modules significantly associated with the response to IVM. Within these, 219 core genes were detected, largely expressed in the intestinal tissue and spanning diverse biological processes with unspecific patterns. After 10−11 M IVM, intestinal tissue core genes showed transcriptional suppression, cell cycle inhibition, and ribosomal alterations. Interestingly, genes PgR028_g047 (sorb-1), PgB01_g200 (gmap-1) and PgR046_g017 (col-37 & col-102) switched from downregulation at 10−11 M to upregulation at 10−9 M IVM. The 10−9 M concentration induced expression of cuticle and membrane integrity core genes in the intestinal tissue. No clear core gene patterns were visible in the anterior end after 10−11 M IVM. However, after 10−9 M IVM, the anterior end mostly displayed downregulation, indicating disrupted transcriptional regulation. One interesting finding was the non-modular calcium-signaling gene, PgR047_g066 (gegf-1), which uniquely connected 71 genes across four modules. These genes were enriched for transmembrane signaling activity, suggesting that PgR047_g066 (gegf-1) could have a key signaling role. By unveiling tissue-specific expression patterns and highlighting biological processes through unbiased core gene detection, this study reveals intricate IVM responses in P. univalens. These findings suggest alternative drug uptake of IVM and can guide functional validations to further IVM resistance mechanism understanding.
  •  
46.
  • Dube, Faruk, et al. (författare)
  • Ivermectin-induced gene expression changes in adult Parascaris univalens and Caenorhabditis elegans : a comparative approach to study anthelminthic metabolism and resistance in vitro
  • 2022
  • Ingår i: Parasites & Vectors. - : Springer Nature. - 1756-3305. ; 15:1
  • Tidskriftsartikel (refereegranskat)abstract
    • Background: The nematode Parascaris univalens is one of the most prevalent parasitic pathogens infecting horses but anthelmintic resistance undermines treatment approaches. The molecular mechanisms underlying drug activity and resistance remain poorly understood in this parasite since experimental in vitro models are lacking. The aim of this study was to evaluate the use of Caenorhabditis elegans as a model for P. univalens drug metabolism/resistance studies by a comparative gene expression approach after in vitro exposure to the anthelmintic drug ivermectin (IVM).Methods: Twelve adult P. univalens worms in groups of three were exposed to ivermectin (IVM, 10(-13) M, 10(-11) M, 10(-9 )M) or left unexposed for 24 h at 37 degrees C, and total RNA, extracted from the anterior end of the worms, was sequenced using Illumina NovaSeq. Differentially expressed genes (DEGs) involved in metabolism, transportation, or gene expression with annotated Caemorhabditis elegans orthologues were identified as candidate genes to be involved in IVM metabolism/resistance. Similarly, groups of 300 adult C. elegans worms were exposed to IVM (10(-9) M, 10(-8) M and 10(-7) M) or left unexposed for 4 h at 20 degrees C. Quantitative RT-PCR of RNA extracted from the C. elegans worm pools was used to compare against the expression of selected P. univalens candidate genes after drug treatment.Results: After IVM exposure, 1085 DEGs were found in adult P. univalens worms but the relative gene expression changes were small and large variabilities were found between different worms. Fifteen of the DEGs were chosen for further characterization in C. elegans after comparative bioinformatics analyses. Candidate genes, including the putative drug target Igc-37, responded to IVM in P. univalens, but marginal to no responses were observed in C. elegans despite dose-dependent behavioral effects observed in C. elegans after IVM exposure. Thus, the overlap in IVM-induced gene expression in this small set of genes was minor in adult worms of the two nematode species.Conclusion: This is the first time to our knowledge that a comparative gene expression approach has evaluated C. elegans as a model to understand IVM metabolism/resistance in P. univalens. Genes in P. univalens adults that responded to IVM treatment were identified. However, identifying conserved genes in P. univalens and C. elegans involved in IVM metabolism/resistance by comparing gene expression of candidate genes proved challenging. The approach appears promising but was limited by the number of genes studied (n = 15). Future studies comparing a larger number of genes between the two species may result in identification of additional candidate genes involved in drug metabolism and/or resistance.
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47.
  • Dube, Faruk, et al. (författare)
  • Transcriptomics of ivermectin response in Caenorhabditis elegans : Integrating abamectin quantitative trait loci and comparison to the Ivermectin-exposed DA1316 strain
  • 2023
  • Ingår i: PLOS ONE. - : Public Library of Science (PLoS). - 1932-6203. ; 18:5
  • Tidskriftsartikel (refereegranskat)abstract
    • Parasitic nematodes pose a significant threat to human and animal health, as well as cause economic losses in the agricultural sector. The use of anthelmintic drugs, such as Ivermectin (IVM), to control these parasites has led to widespread drug resistance. Identifying genetic markers of resistance in parasitic nematodes can be challenging, but the free-living nematode Caenorhabditis elegans provides a suitable model. In this study, we aimed to analyze the transcriptomes of adult C. elegans worms of the N2 strain exposed to the anthelmintic drug Ivermectin (IVM), and compare them to those of the resistant strain DA1316 and the recently identified Abamectin Quantitative Trait Loci (QTL) on chromosome V. We exposed pools of 300 adult N2 worms to IVM (10(-7) and 10(-8) M) for 4 hours at 20 degrees C, extracted total RNA and sequenced it on the Illumina NovaSeq6000 platform. Differentially expressed genes (DEGs) were determined using an in-house pipeline. The DEGs were compared to genes from a previous microarray study on IVM-resistant C. elegans and Abamectin-QTL. Our results revealed 615 DEGs (183 up-regulated and 432 down-regulated genes) from diverse gene families in the N2 C. elegans strain. Of these DEGs, 31 overlapped with genes from IVM-exposed adult worms of the DA1316 strain. We identified 19 genes, including the folate transporter (folt-2) and the transmembrane transporter (T22F3.11), which exhibited an opposite expression in N2 and the DA1316 strain and were deemed potential candidates. Additionally, we compiled a list of potential candidates for further research including T-type calcium channel (cca-1), potassium chloride cotransporter (kcc-2), as well as other genes such as glutamate-gated channel (glc-1) that mapped to the Abamectin-QTL.
  •  
48.
  • Einarsson, Elin, et al. (författare)
  • An up-date on Giardia and giardiasis
  • 2016
  • Ingår i: Current Opinion in Microbiology. - : Elsevier BV. - 1369-5274 .- 1879-0364. ; 34, s. 47-52
  • Forskningsöversikt (refereegranskat)abstract
    • Giardia intestinalis is a non-invasive protozoan parasite infecting the upper small intestine causing acute, watery diarrhea or giardiasis in 280 million people annually. Asymptomatic infections are equally common and recent data have suggested that infections even can be protective against other diarrhea! diseases. Most symptomatic infections resolve spontaneously but infections can lead to chronic disease and treatment failures are becoming more common world-wide. Giardia infections can also result in irritable bowel syndrome (IBS) and food allergies after resolution. Until recently not much was known about the mechanism of giardiasis or the cause of post-giardiasis syndromes and treatment failures, but here we will describe the recent progress in these areas.
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49.
  • Einarsson, Elin, et al. (författare)
  • Comparative cell biology and evolution of Annexins in Diplomonads
  • 2016
  • Ingår i: mSphere. - Uppsala. - 2379-5042. ; 1:2
  • Tidskriftsartikel (refereegranskat)abstract
    • Annexins are multifunctional, calcium-binding proteins found in organisms across all kingdoms. Most studies of annexins from single-celled eukaryotes have focused on the alpha-giardins, proteins assigned to the group E annexins, expressed by the diplomonad Giardia intestinalis. We have characterized the annexin gene family in another diplomonad parasite, Spironucleus salmonicida, by phylogenetic and experimental approaches. We constructed a comprehensive phylogeny of the diplomonad group E annexins and found that they are abundant across the group with frequent gene duplications and losses. The annexins of S. salmonicida were found to be related to alpha-giardins but with better-preserved type II Ca2+ coordination sites. Two annexins were confirmed to bind phospholipids in a Ca2+-dependent fashion but with different specificities. Superresolution and confocal microscopy of epitope-tagged S. salmonicida annexins revealed localization to distinct parts of the cytoskeleton and membrane. The ultrastructural details of the localization of several annexins were determined by proximity labeling and transmission electron microscopy. Two annexins localize to a novel cytoskeletal structure in the anterior of the cell. Our results show that the annexin gene family is expanded in diplomonads and that these group E annexins are associated mostly with cytoskeletal and membrane structures. IMPORTANCE Annexins are proteins that associate with phospholipids in a Ca2+-dependent fashion. These proteins have been intensely studied in animals and plants because of their importance in diverse cellular processes, yet very little is known about annexins in single-celled eukaryotes, which represent the largest diversity of organisms. The human intestinal parasite Giardia intestinalis is known to have more annexins than humans, and they contribute to its pathogenic potential. In this study, we investigated the annexin complement in the salmon pathogen Spironucleus salmonicida, a relative of G. intestinalis. We found that S. salmonicida has a large repertoire of annexins and that the gene family has expanded separately across diplomonads, with members showing sequence diversity similar to that seen across kingdom-level groups such as plants and animals. S. salmonicida annexins are prominent components of the cytoskeleton and membrane. Two annexins are associated with a previously unrecognized structure in the anterior of the cell.
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50.
  • Einarsson, Elin, 1986- (författare)
  • Comparative Cell Biology in Diplomonads
  • 2015
  • Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
    • The diplomonads are a diverse group of eukaryotic flagellates found in microaerophilic and anaerobic environments. The most studied diplomonad is the intestinal parasite Giardia intestinalis, which infects a variety of mammals and cause diarrheal disease. Less is known about Spironucleus salmonicida, a parasite of salmonid fish, known to cause systemic infections with high mortality.We created a transfection system for S. salmonicida to study cellular functions and virulence in detail (Paper I). The system was applied to explore the mitochondrion-related organelle (MRO) in S. salmonicida. We showed that S. salmonicida possesses a hydrogenosome (Paper II) with a higher metabolic capacity than the corresponding MRO of Giardia, the mitosome. Evolutionary analysis of key hydrogenosomal proteins showed ancient origin, indicating their presence in the ancestral diplomonad and subsequent loss in Giardia. Annexins are of evolutionary interest since these proteins are found across all kingdoms. Annexin-like proteins are intriguingly expanded into multigene families in Giardia and Spironucleus. The annexins of S. salmonicida were characterized (Paper III) with distinct localizations to various cellular structures, including a putative adhesion structure anterior in the cell.The disease-causing Giardia trophozoites differentiate into infectious cysts, a process essential for transmission and virulence of the parasite. Cysts are often spread via contaminated water and exposed to environmental stressors, such as UV irradiation. We studied the survival and transcriptional response to this stress factor (Paper IV) and results showed the importance of active DNA replication machinery for parasite survival after DNA damage. In addition, we studied transcriptional changes along the trajectory of encystation (Paper V), which revealed a coordinated cascade of gene regulation. This was observed for the entire transcriptome as well as putative regulators. Large transcriptional changes appeared late in the process with the majority of differentially regulated genes encoding hypothetical proteins. We studied the localizations of several of these to gain information of their possible function.To conclude, the diplomonads are complex eukaryotic microbes with cellular processes adjusted to match their life styles. The work in this thesis has provided insight of their adaptations, differences and similarities, but also new interesting leads for future studies of diplomonad biology and virulence. 
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