| 1. |
- Borgmästars, Emmy, et al.
(author)
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Comparison of Skimmed Milk and Lanthanum Flocculation for Concentration of Pathogenic Viruses in Water
- 2021
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In: Food and Environmnetal Virology. - : Springer. - 1867-0334 .- 1867-0342. ; 13:3, s. 380-389
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Journal article (peer-reviewed)abstract
- Concentration of viruses in water is necessary for detection and quantification of the viruses present, in order to evaluate microbiological barriers in water treatment plants and detect pathogenic viruses during waterborne outbreaks, but there is currently no standardised procedure. In this study, we implemented a previously described fast and simple lanthanum-based protocol for concentration of norovirus genogroup I (GI), genogroup II (GII) and hepatitis A virus (HAV) in drinking and surface water. We compared the results with those of a widely used skimmed milk flocculation method, followed by nucleic acid extraction and RT-qPCR detection. Three seeding levels, with intended concentrations 5 × 103, 5 × 104 and 5 × 105 genome copies/10 L, were added to drinking water or surface water. All seed levels were detected with both flocculation methods. Samples extracted with skimmed milk flocculation had on average 1.82, 1.86 and 1.38 times higher measured concentration of norovirus GI, GII and HAV, respectively, than those extracted with lanthanum flocculation, across all seeding levels and water types tested. Mengovirus was used as a positive process control. Mengovirus recovery was higher for skimmed milk (40.7% in drinking water, 26.0% in surface water) than for lanthanum flocculation (24.4% in drinking water, 9.7% in surface water). Together, this indicates that skimmed milk flocculation provides higher viral recovery than lanthanum flocculation. However, lanthanum-based flocculation can be performed much faster than skimmed milk flocculation (1.5 h versus 16 h flocculation time) and thus could be a good alternative for rapid monitoring of viruses in water.
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| 2. |
- Borgmästars, Emmy, et al.
(author)
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Improved Detection of Norovirus and Hepatitis A Virus in Surface Water by Applying Pre-PCR Processing
- 2017
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In: Food and Environmental Virology. - : Springer Science and Business Media LLC. - 1867-0334 .- 1867-0342. ; 9:4, s. 395-405
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Journal article (peer-reviewed)abstract
- Quantitative reverse transcriptase polymerase chain reaction (RT-qPCR) detection of waterborne RNA viruses generally requires concentration of large water volumes due to low virus levels. A common approach is to use dead-end ultrafiltration followed by precipitation with polyethylene glycol. However, this procedure often leads to the co-concentration of PCR inhibitors that impairs the limit of detection and causes false-negative results. Here, we applied the concept of pre-PCR processing to optimize RT-qPCR detection of norovirus genogroup I (GI), genogroup II (GII), and hepatitis A virus (HAV) in challenging water matrices. The RT-qPCR assay was improved by screening for an inhibitor-tolerant master mix and modifying the primers with twisted intercalating nucleic acid molecules. Additionally, a modified protocol based on chaotropic lysis buffer and magnetic silica bead nucleic acid extraction was developed for complex water matrices. A validation of the modified extraction protocol on surface and drinking waters was performed. At least a 26-fold improvement was seen in the most complex surface water studied. The modified protocol resulted in average recoveries of 33, 13, 8, and 4% for mengovirus, norovirus GI, GII, and HAV, respectively. The modified protocol also improved the limit of detection for norovirus GI and HAV. RT-qPCR inhibition with Cq shifts of 1.6, 2.8, and 3.5 for norovirus GI, GII, and HAV, respectively, obtained for the standard nucleic acid extraction were completely eliminated by the modified protocol. The standard nucleic acid extraction method worked well on drinking water with no RT-qPCR inhibition observed and average recoveries of 80, 124, 89, and 32% for mengovirus, norovirus GI, GII, and HAV, respectively.
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| 3. |
- Buckel, Alexander, et al.
(author)
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Importance of First Cycle Conditions on the Electrochemical Performance of Hard Carbon and Prussian White Based Sodium-Ion Batteries Using Fire Resistant, Fluorine-Free Electrolyte
- 2024
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In: Batteries & Supercaps. - : John Wiley & Sons. - 2566-6223. ; 7:2
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Journal article (peer-reviewed)abstract
- Electrolytes based on sodium bis(oxolato)borate (NaBOB) in organophosphates (trimethyl phosphate and triethyl phosphate (TEP)) have shown promise in sodium-ion batteries when compared to conventional electrolytes in that they are fire resistant, fluorine-free and are of lower toxicity. However, these electrolytes tend to exhibit low initial Coulombic efficiency and high overpotentials. We have here demonstrated that NaBOB in TEP can be used in cells with near-commercial capacity loadings. Furthermore, we have shown that formation cycle conditions have a significant positive effect on the cell performance in these higher mass loading cells, and that modification of the formation cycle conditions can be used to increase the capacity retention, lower the overpotentials, and as such increase the rate capability. The viability of optimized formation protocols was also demonstrated in scaled up prototype cells. Formation cycling: In this article we present a solution to the poor cyclability of non-flammable sodium bis(oxolato)borate (NaBOB) in triethyl phosphate (TEP) electrolyte. By developing a formation cycle specific to this NaBOB in TEP electrolyte, we are able to cycle a 4.5 Ah full cell with high mass loading electrodes to beyond 900 cycles before reaching 80 % state of health.image
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| 4. |
- Enkirch, Theresa, et al.
(author)
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Hepatitis A outbreak linked to imported frozen strawberries by sequencing, Sweden and Austria, June to September 2018
- 2018
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In: Eurosurveillance. - : European Centre for Disease Prevention and Control. - 1025-496X .- 1560-7917. ; 23:41
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Journal article (peer-reviewed)abstract
- Between June-September 2018, 20 hepatitis A cases were notified in six counties in Sweden. Combined epidemiological and microbiological investigations identified imported frozen strawberries produced in Poland as the source of the outbreak. Sequence analysis confirmed the outbreak strain IB in the strawberries with 100 % identity and the respective batch was withdrawn. Sharing the sequence information internationally led to the identification of 14 additional cases in Austria, linked to strawberries from the same producer.
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| 5. |
- Eriksson, Ronnie, et al.
(author)
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Multiplex and quantifiable detection of nucleic acid from pathogenic fungi using padlock probes, generic real time PCR and specific suspension array readout
- 2009
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In: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012 .- 1872-8359. ; 78:2, s. 195-202
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Journal article (peer-reviewed)abstract
- A new concept for multiplex detection and quantification of microbes is here demonstrated on a range of infectious fungal species. Padlock probe methodology in conjunction with qPCR and Luminex technology was used for simultaneous detection of ten fungal species in one single experiment. By combining the multiplexing properties of padlock probes and Luminex detection with the well established quantitative characteristics of qPCR, quantitative microbe detection was done in 10-plex mode. A padlock probe is an oligonucleotide that via a ligation reaction forms circular DNA when hybridizing to specific target DNA. The region of the padlock probe that does not participate in target DNA hybridization contains generic primer sequences for amplification and a tag sequence for Luminex detection. This was the fundament for well performing multiplexing. Circularized padlock probes were initially amplified by rolling circle amplification (RCA), followed by a SybrGreen real time PCR which allowed an additive quantitative assessment of target DNA in the sample. Detection and quantification of amplified padlock probes were then done on color coded Luminex microspheres carrying anti-tag sequences. A novel technique, using labeled oligonucleotides to prevent reannealing of amplimers by covering the flanks of the address sequence, improved the signal to noise ratio in the detection step considerably. The method correctly detected fungi in a variety of clinical samples and offered quantitative information on fungal nucleic acid.
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| 6. |
- Horak, Josef, et al.
(author)
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Recombinant Spider Silk as Mediator for One-Step, Chemical-Free Surface Biofunctionalization
- 2018
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In: Advanced Functional Materials. - : Wiley. - 1616-301X .- 1616-3028. ; 28:21
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Journal article (peer-reviewed)abstract
- A unique strategy for effective, versatile, and facile surface biofunctionalization employing a recombinant spider silk protein genetically functionalized with the antibody-binding Z domain (Z-4RepCT) is reported. It is demonstrated that Z-silk can be applied to a variety of materials and platform designs as a truly one-step and chemical-free surface modification that site specifically captures antibodies while simultaneously reducing nonspecific adsorption. As a model surface, SiO2 is used to optimize and characterize Z-silk performance compared to the Z domain immobilized by a standard silanization method. First, Z-silk adsorption is investigated and verified its biofunctionality in a long-term stability experiment. To assess the binding capacity and protein-protein interaction stability of Z-silk, the coating is used to capture human antibodies in various assay formats. An eightfold higher binding capacity and 40-fold lower detection limit are obtained in the immunofluorescence assay, and the complex stability of captured antibodies is shown to be improved by a factor of 20. Applicability of Z-silk to functionalize microfluidic devices is demonstrated by antibody detection in an electrokinetic microcapillary biosensor. To test Z-silk for biomarker applications, real-time detection and quantification of human immunoglobulin G are performed in a plasma sample and C1q capture from human serum using an anti-C1q antibody.
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| 7. |
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| 8. |
- Håkansson, Peter, 1979-
(author)
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The United Nations Reformed : Responsibility, Protection and the Standing of States
- 2011
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Doctoral thesis (other academic/artistic)abstract
- This study is about reform of the United Nations. The study does not address reform proposals that set out to change the organizational structure of the UN, but focuses on initiatives that affect the normative basis of the international society that the United Nations and the UN Charter enable and sustain. Empirically, the study focuses on the international principle responsibility 10 prolecl, which prescribes that states have an individual and collective responsibility to protect against human rights violations. It is argued that the responsibility to protect and the Security Council's increased attention to protection of civilians in armed conflicts are politically and legally significant developments that challenge the pluralist international order that was instituted through the establishment of the UN in 1945. Both the responsibility to proteet and the protection of civilians are based on an understanding of statehood and international society that in the study is referred to as anti-pluralist. The results of the study show that the contemporary notion of protection once again brings into international political discourse the idea that states and political communities, in order to enjoy legal autonomy and a right to non-intervention, must abide by universally applicable standards of state hood. The results also show that the idea of protection is based on a progressivist philosophy that leads to a differentiation of states.
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| 9. |
- Jansson, Linda, et al.
(author)
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Evaluation and modification of lanthanum-based flocculation for isolation of bacteria from water samples
- 2018
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In: Biotechnology Reports. - : Elsevier BV. - 2215-017X. ; 19
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Journal article (peer-reviewed)abstract
- Molecular detection of pathogenic microorganisms in drinking and natural water is often challenged by low concentrations of the sought-after agents. Convenient methods to concentrate bacteria from water samples ranging from 1-10 L are highly warranted. Here we account for the evaluation of a lanthanum-based flocculation method to concentrate bacteria from water samples, applying four different bacterial species in tap water as well as river water. Our results show that the success of lanthanum-based flocculation is determined by both the bacterial species and the nature of the water sample. For tap water, satisfying flocculation efficiencies (above 60 %) were only reached for autoclaved water samples. However, the performance of the lanthanum-based flocculation method for non-autoclaved water was markedly improved by the addition of 20 mM bicarbonate to increase alkalinity. Our modified flocculation protocol may be applied as an alternative concentration method for bacteria in water samples of one liter or more.
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| 10. |
- Jansson, Linda, et al.
(author)
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Impact of swab material on microbial surface sampling
- 2020
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In: Journal of Microbiological Methods. - : Elsevier BV. - 0167-7012. ; 176
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Journal article (peer-reviewed)abstract
- Efficient microbial sampling from surfaces for subsequent detection and quantification is crucial in fields such as food safety and hygiene monitoring. Cotton swabs are traditionally used for sample collection, but today there are numerous swabs of alternative material and different sizes available. Recovery efficiencies of swabs for different applications have been compared in several studies. However, the results are often contradictory. We have compared 15 different swabs made of cotton (n = 5), flocked nylon (n = 3) and foam (n = 7), for sampling of Listeria monocytogenes and mengovirus on small (4 cm2) and large (100 cm2) areas of window glass, ridged plastic and absorbing wood. Molecular quantification methods (qPCR and RT-qPCR) were applied, and all sampling and sample processing were standardized. Specific swabs gave higher DNA/RNA yields than others, depending on both the surface characteristics and the collected target. The highest DNA yields were achieved by applying Selefa or Puritan cotton swabs for Listeria sampling on 4 cm2 areas of window glass and ridged plastic. Certain foam swabs (Critical swab with medium head and Macrofoam) gave the highest yields when sampling Listeria on 4 cm2 areas of wood and on 100 cm2 areas of ridged plastic and wood. Most foam swabs, and especially Sigma Virocult, were advantageous for virus sampling, regardless of surface. Nylon-flocked swabs showed poor recovery regardless of surface characteristics. The recovery varied substantially between swabs made of the same material, suggesting that a single swab may not be representative for a certain swab material.
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| 11. |
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| 12. |
- Lassinantti, Lena, 1993-
(author)
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Exploring the mechanistic details of Gram-positive Type 4 Secretion Systems
- 2022
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Doctoral thesis (other academic/artistic)abstract
- Hospital acquired (i.e. nosocomial) infections and antibiotic resistance are large issues in the world today, with about 1.3 million people estimated to have died from antibiotic resistant infections in 2019 alone, and these problems are on the rise. Type 4 Secretion Systems (T4SSs) are complex nanomachineries commonly found on conjugative plasmids. T4SSs are a major route for the translocation of genes encoding for antibiotic resistance and other virulence factors. These systems have primarily been studied in Gram-negative (G-) bacteria even though Gram-positive (G+) bacteria stand for about half of the nosocomial infections. To develop ways to limit the spread of both antibiotic resistance and virulence factors, we need to gain fundamental knowledge of T4SSs in G+ bacteria.Our work has focused on the conjugative plasmid pCF10 from the G+ bacteria Enterococcus faecalis where all the genes needed for the T4SS are under the regulation of one promoter named PQ. Most G+ T4SSs consist of three groups of proteins, namely the DNA transfer and replication (Dtr) proteins, the channel proteins and the adhesin proteins. In my work, I have focused my attention specifically on i) the regulatory protein PrgU, ii) the Dtr protein PcfF, and iii) the adhesin protein PrgB. These three proteins provide insights into three different parts of the T4SS. PrgU is part of the regulatory process of T4SS expression and has been shown to inhibit cell-toxicity mitigated by PrgB. The Dtr protein PcfF is needed for the formation of the relaxosome complex critical for conjugative transfer of the plasmid, and PrgB is involved in cellular aggregation events and is also a known virulence factor. Interestingly, increased levels of PrgB have been shown to be toxic to the cells. To inhibit PrgB induced cell toxicity, its production needs to be tightly regulated.The aims of my PhD thesis were to examine conjugation complexes belonging to Type 4 Secretion Systems in Gram-positive bacteria and to determine their function, molecular structures, and regulation. By using a combination of in vivo and in vitro methods we have; i) showed that PrgU binds to the IGR located downstream of the PQ promoter, and that the deletion of prgU in pCF10 containing cells produces increased mRNA levels of the full prgQ transcript, ii) solved the crystal structure of PcfF and identified residues that are important for the interaction with the relaxase and the origin of transfer (oriT) DNA in vitro, and confirmed this by biochemical assays and, iii) solved the entire structure of PrgB using a combination of X-ray crystallography and cryo-EM and performed in vivo assays to confirm its functions.
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| 13. |
- Marklund, Matti, et al.
(author)
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Fatty Acid Proportions in Plasma Cholesterol Esters and Phospholipids Are Positively Correlated in Various Swedish Populations
- 2017
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In: Journal of Nutrition. - : Elsevier BV. - 0022-3166 .- 1541-6100. ; 147:11, s. 2118-2125
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Journal article (peer-reviewed)abstract
- Background: Fatty acid (FA) proportions in cholesterol esters (CEs) and plasma phospholipids are widely used as dietary biomarkers. Information on how proportions in these fractions correlate could have implications for interpretation and use of FA biomarkers in observational and interventional studies. Objective: We investigated correlations between FA proportions in CEs and phospholipids in free-living individuals and assessed how diet-induced alterations of FA proportions correlate between fractions. Methods: Spearman's rank correlation coefficients (rs) between FA proportions (percentage of total FAs) in circulating CEs and phospholipids were calculated separately in 8 individual study populations including Swedish females and males (N = 2052; age range: 11-84 y), and pooled by inverse-variance weighted meta-analysis. In addition, study populations were stratified by age, sex, body mass index (BMI; in kg/m(2)), and diabetes status, and strata-specific rs were pooled by meta-analysis. In 2 randomized trials (N = 79) in which dietary saturated FAs were isocalorically replaced with unsaturated FAs, treatment-wise calculations of rs were conducted between FA changes in CEs and phospholipids. Results: Overall, FA proportions in CEs and phospholipids correlated well and especially strongly for polyunsaturated FAs (PUFAs), with pooled rs (95% CIs) ranging from 0.74 (0.72, 0.76) for a-linolenic acid to 0.92 (0.91, 0.93) for eicosapentaenoic acid. Weak correlations (pooled rs <0.4) were observed only for palmitic acid and stearic acid, with pooled rs (95% CIs): 0.29 (0.24, 0.33) and 0.30 (0.25, 0.34), respectively. Overall, correlations were not affected by age, sex, BMI, or diabetes status. Strong correlations (r(s) >= 0.6) between diet-induced FA changes in CEs and phospholipids were observed for most PUFAs. Conclusions: Proportions of most FAs in CEs and phospholipids ranked individuals similarly, suggesting that FA proportions in these fractions can be used interchangeably in populations of diverse age, sex, body composition, and diabetes status. Caution is advised, however, when comparing results from studies assessing palmitic acid or stearic acid in different lipid fractions.
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| 14. |
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| 15. |
- Persson, Sofia, et al.
(author)
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Comparison between RT droplet digital PCR and RT real-time PCR for quantification of noroviruses in oysters.
- 2018
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In: International Journal of Food Microbiology. - : Elsevier BV. - 0168-1605 .- 1879-3460. ; 284, s. 73-83
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Journal article (peer-reviewed)abstract
- Oysters are frequently associated with norovirus outbreaks, but the presence of norovirus RNA in oysters does not necessarily imply a health risk to humans. There is a close link between human illness and consumption of oysters with high levels of norovirus RNA, but oysters with low levels of norovirus RNA are more unlikely to be associated with illness. Reliable and precise quantification methods are therefore important for outbreak investigations and risk assessments. This study optimised and validated RT droplet digital PCR (RT-ddPCR) assays for quantification of norovirus genogroups I and II in artificially contaminated oysters, and compared them with the standard method, RT real-time PCR (RT-qPCR). The two methods had comparable 95% limits of detection, but RT-ddPCR generally showed greater precision in quantification. Differences between fluorometric measurements and quantification with RT-ddPCR were determined on in vitro transcribed RNA with targets for norovirus genogroups I and II. Quantification by RT-ddPCR was on average 100 times lower than the fluorometric value for norovirus GI and 15.8 times lower than the fluorometric value for norovirus GII. The large inter-assay difference observed highlights the need for monitoring the RT efficiency in RT-ddPCR, especially when results from different assays are compared. Overall, this study suggests that RT-ddPCR can be a suitable method for precise quantification of norovirus genogroups I and II in oysters.
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| 16. |
- Persson, Sofia, et al.
(author)
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Missing the Match Might Not Cost You the Game : Primer-Template Mismatches Studied in Different Hepatitis A Virus Variants
- 2019
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In: Food and Environmnetal Virology. - : Springer Science and Business Media LLC. - 1867-0334 .- 1867-0342. ; 11:3, s. 297-308
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Journal article (peer-reviewed)abstract
- Mismatches between template sequences and reverse transcription (RT) or polymerase chain reaction (PCR) primers can lead to underestimation or false negative results during detection and quantification of sequence-diverse viruses. We performed an in silico inclusivity analysis of a widely used RT-PCR assay for detection of hepatitis A virus (HAV) in food, described in ISO 15216-1. One of the most common mismatches found was a single G (primer) to U (template) mismatch located at the terminal 3 '-end of the reverse primer region. This mismatch was present in all genotype III sequences available in GenBank. Partial HAV genomes with common or potentially severe mismatches were produced by in vitro transcription and analysed using RT-ddPCR and RT-qPCR. When using standard conditions for RT-qPCR, the mismatch identified resulted in underestimation of the template concentration by a factor of 1.7-1.8 and an increase in 95% limit of detection from 8.6 to 19 copies/reaction. The effect of this mismatch was verified using full-length viral genomes. Here, the same mismatch resulted in underestimation of the template concentration by a factor of 2.8. For the partial genomes, the presence of additional mismatches resulted in underestimation of the template concentration by up to a factor of 232. Quantification by RT-ddPCR and RT-qPCR was equally affected during analysis of RNA templates with mismatches within the reverse primer region. However, on analysing DNA templates with the same mismatches, we found that ddPCR quantification was less affected by mismatches than qPCR due to the end-point detection technique.
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| 17. |
- Persson, Sofia, et al.
(author)
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Optimisation and evaluation of an automated system for extraction of viral RNA from oysters
- 2020
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In: International Journal of Food Microbiology. - : ELSEVIER. - 0168-1605 .- 1879-3460. ; 315
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Journal article (peer-reviewed)abstract
- The NucliSENS MiniMAG (Minimag) system from bioMerieux is widely used for extraction of viral RNA from oysters and is included as informative material in the ISO method for quantification of hepatitis A virus (HAV) and norovirus genogroups I and II (GI and GII) in food (ISO 15216-1:2017). However, the system is no longer on sale within the EU and alternative methods are therefore needed. We optimised and evaluated an automated benchtop system for extraction of viral RNA from oysters artificially contaminated with HAV, norovirus GI, norovirus GII and mengovirus, using the same reagents and a similar protocol as with the Minimag method. Using the automated system instead of Minimag increased measured viral concentration by on average 1.3 times, suggesting that the automated system extracts viral RNA more efficiently than Minimag. A drawback with the automated system was that it displayed higher variability in measured concentration for mengovirus. The median viral recovery was 17%, 37%, 44% and 41% for samples extracted with the automated system and 15%, 27%, 34% and 23% for samples extracted with Minimag for HAV, norovirus GI, norovirus GII and mengovirus, respectively. All samples displayed < 75% inhibition in RT-qPCR when extracted with the automated system or Minimag. Together, these results suggest that the automated system can be a suitable alternative to Minimag in analysis of HAV, norovirus GI and norovirus GII in oysters. However, verification using naturally contaminated oysters is needed before it can be used for food safety control purposes.
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| 18. |
- Persson, Sofia, et al.
(author)
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Validation of an optimised method for quantitative detection of hepatitis E virus in pork sausage
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Other publication (other academic/artistic)abstract
- Hepatitis E virus (HEV) is an emerging zoonosis that can be transmitted to humans through the consumption of raw or undercooked pork meat products. Several methods for detecting the virus in food have been described, but there are still few robust data on qualitative and quantitative performance characteristics. In this study, we developed an optimised workflow for quantitative detection of HEV in pork sausage based on a combination of previously existing protocols. The protocol uses sample disruption and phase separation with tri-reagent and 1-bromo-3-chloropropane, followed by RNA concentration with isopropanol precipitation. We validated the protocol for use on reverse transcription quantitative real-time PCR (RT-qPCR) and reverse transcription droplet digital (RT-ddPCR). The 95% limit of detection and limit of quantification was 200 copies/g for both RT-qPCR and RT-ddPCR. The RT-ddPCR technology has previously shown promise as a more precise alternative to RT-qPCR. However, we found no evidence for improved performance using RT-ddPCR instead of RT-qPCR in this method. Furthermore, we also evaluated different combinations of RNA concentration methods and PCR detection strategies. This showed that isopropanol precipitation of viral RNA was more than twice as efficient as magnetic silica bead-based extraction when an inhibitor tolerant RT-PCR detection strategy was used. In conclusion, we present an efficient and well-characterised method for quantitative detection of HEV in pork sausage. Such methods are valuable to provide high quality data for risk assessments and food monitoring.
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| 19. |
- Sharma, Sumit, 1978-, et al.
(author)
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Secretor Status is Associated with Susceptibility to Disease in a Large GII.6 Norovirus Foodborne Outbreak
- 2020
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In: Food and Environmnetal Virology. - : Springer. - 1867-0334 .- 1867-0342. ; 12, s. 28-34
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Journal article (peer-reviewed)abstract
- Norovirus is commonly associated with food and waterborne outbreaks. Genetic susceptibility to norovirus is largely dependent on presence of histo-blood group antigens (HBGA), specifically ABO, secretor, and Lewis phenotypes. The aim of the study was to determine the association between HBGAs to norovirus susceptibility during a large norovirus foodborne outbreak linked to genotype GII.6 in an office-based company in Stockholm, Sweden, 2015. A two-episode outbreak with symptoms of diarrhea and vomiting occurred in 2015. An online questionnaire was sent to all 1109 employees that had worked during the first outbreak episode. Food and water samples were collected from in-house restaurant and tested for bacterial and viral pathogens. In addition, fecal samples were collected from 8 employees that had diarrhea. To investigate genetic susceptibility during the outbreak, 98 saliva samples were analyzed for ABO, secretor, and Lewis phenotypes using ELISA. A total of 542 of 1109 (49%) employees reported gastrointestinal symptoms. All 8 fecal samples tested positive for GII norovirus, which was also detected in coleslaw collected from the in-house restaurant. Eating at the in-house restaurant was significantly associated with risk of symptom development. Nucleotide sequencing was successful for 5/8 fecal samples and all belonged to the GII.6 genotype. HBGA characterization showed a strong secretor association to norovirus-related symptoms (P = 0.014). No association between norovirus disease and ABO phenotypes was observed. The result of this study shows that non-secretors were significantly less likely to report symptoms in a large foodborne outbreak linked to the emerging GII.6 norovirus strain.
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| 20. |
- Verma, Apoorv, et al.
(author)
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Insights into the evolution of enzymatic specificity and catalysis : from Asgard archaea to human adenylate kinases
- 2022
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In: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 8:44
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Journal article (peer-reviewed)abstract
- Enzymatic catalysis is critically dependent on selectivity, active site architecture, and dynamics. To contribute insights into the interplay of these properties, we established an approach with NMR, crystallography, and MD simulations focused on the ubiquitous phosphotransferase adenylate kinase (AK) isolated from Odinarchaeota (OdinAK). Odinarchaeota belongs to the Asgard archaeal phylum that is believed to be the closest known ancestor to eukaryotes. We show that OdinAK is a hyperthermophilic trimer that, contrary to other AK family members, can use all NTPs for its phosphorylation reaction. Crystallographic structures of OdinAK-NTP complexes revealed a universal NTP-binding motif, while 19F NMR experiments uncovered a conserved and rate-limiting dynamic signature. As a consequence of trimerization, the active site of OdinAK was found to be lacking a critical catalytic residue and is therefore considered to be "atypical." On the basis of discovered relationships with human monomeric homologs, our findings are discussed in terms of evolution of enzymatic substrate specificity and cold adaptation.
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| 21. |
- Welch, Jonas, et al.
(author)
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Optimization of Sodium Bis(oxalato)borate (NaBOB) in Triethyl Phosphate (TEP) by Electrolyte Additives
- 2022
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In: Journal of the Electrochemical Society. - : Institute of Physics (IOP). - 0013-4651 .- 1945-7111. ; 169:12
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Journal article (peer-reviewed)abstract
- The electrolyte solution of NaBOB in TEP is a low-cost, fluorine-free and flame-retardant electrolyte with ionic conductivity of 5 mS cm(-1), recently discovered to show promises for sodium-ion batteries. Here, the abilities of this electrolyte to effectively form a solid electrolyte interphase (SEI) was augmented with five common electrolyte additives of fluoroethylene carbonate (FEC), vinylene carbonate (VC), prop-1-ene-1,3-sultone (PES), 1,3,2-dioxathiolane 2,2-dioxide (DTD) and tris(trimethylsilyl)phosphite (TTSPi). Full-cells with electrodes of Prussian white and hard carbon and industrial mass loadings of >10 mg cm(-2) and electrolyte volumes of <5 ml g(-1) were used. X-ray photoelectron spectroscopy (XPS) and pressure analysis were also deployed to investigate parasitic reactions. Cells using electrolyte additives of PES, PES+DTD and PES+TTSPi (3 wt%) showed significantly increased performance in terms of capacity retention and initial Coulombic efficiency as compared to additive-free NaBOB-TEP. The best cell retained 80% discharge capacity (89 mAh g(-1)) after 450 cycles, which is also significantly better than reference cells using 1 M NaPF6 in EC:DEC electrolyte. This study sheds light on opportunities to optimize the NaBOB-TEP electrolyte for full-cell sodium-ion batteries in order to move from low-mass-loading lab-scale electrodes to high mass loading electrodes aiming for commercialization of sodium-ion batteries.
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| 22. |
- Xia, Hongyan, et al.
(author)
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A microsphere-based immunoassay for rapid and sensitive detection of bovine viral diarrhoea virus antibodies
- 2010
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In: Journal of Virological Methods. - : Elsevier BV. - 0166-0934 .- 1879-0984. ; 168:1-2, s. 18-21
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Journal article (peer-reviewed)abstract
- This study describes a novel blocking microsphere-based immunoassay for highly sensitive and specific detection of antibodies against bovine viral diarrhoea virus (BVDV). The intra- and inter-assay variability are 4.9% and less than 7%, respectively, and variability of bead conjugations is less than 6.6%. The diagnostic performance of the assay was evaluated by testing a total of 509 serum samples. Based on a negative/positive cut-off value of 30.3%, the assay has a sensitivity of 99.4% and a specificity of 98.3% relative to ELISA. The new microsphere immunoassay provides an alternative to conventional ELISA systems and can be used for high-throughput screening in the BVD control programmes.
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| 23. |
- Öhrmalm, Christina, et al.
(author)
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Hybridization properties of long nucleic acid probes for detection of variable target sequences, and development of a hybridization prediction algorithm
- 2010
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In: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 38:21, s. e195-
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Journal article (peer-reviewed)abstract
- One of the main problems in nucleic acid-based techniques for detection of infectious agents, such as influenza viruses, is that of nucleic acid sequence variation. DNA probes, 70-nt long, some including the nucleotide analog deoxyribose-Inosine (dInosine), were analyzed for hybridization tolerance to different amounts and distributions of mismatching bases, e.g. synonymous mutations, in target DNA. Microsphere-linked 70-mer probes were hybridized in 3M TMAC buffer to biotinylated single-stranded (ss) DNA for subsequent analysis in a Luminex® system. When mismatches interrupted contiguous matching stretches of 6 nt or longer, it had a strong impact on hybridization. Contiguous matching stretches are more important than the same number of matching nucleotides separated by mismatches into several regions. dInosine, but not 5-nitroindole, substitutions at mismatching positions stabilized hybridization remarkably well, comparable to N (4-fold) wobbles in the same positions. In contrast to shorter probes, 70-nt probes with judiciously placed dInosine substitutions and/or wobble positions were remarkably mismatch tolerant, with preserved specificity. An algorithm, NucZip, was constructed to model the nucleation and zipping phases of hybridization, integrating both local and distant binding contributions. It predicted hybridization more exactly than previous algorithms, and has the potential to guide the design of variation-tolerant yet specific probes.
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| 24. |
- Öhrmalm, Christina, et al.
(author)
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Variation-tolerant capture and multiplex detection of nucleic acids : application to detection of microbes
- 2012
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In: Journal of Clinical Microbiology. - 0095-1137 .- 1098-660X. ; 50:10, s. 3208-3215
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Journal article (peer-reviewed)abstract
- In contrast to ordinary PCRs, which have a limited multiplex capacity and often return false-negative results due to target variation or inhibition, our new detection strategy, VOCMA (variation-tolerant capture multiplex assay), allows variation-tolerant, target-specific capture and detection of many nucleic acids in one test. Here we demonstrate the use of a single-tube, dual-step amplification strategy that overcomes the usual limitations of PCR multiplexing, allowing at least a 22-plex format with retained sensitivity. Variation tolerance was achieved using long primers and probes designed to withstand variation at known sites and a judicious mix of degeneration and universal bases. We tested VOCMA in situations where enrichment from a large sample volume with high sensitivity and multiplexity is important (sepsis; streptococci, enterococci, and staphylococci, several enterobacteria, candida, and the most important antibiotic resistance genes) and where variation tolerance and high multiplexity is important (gastroenteritis; astrovirus, adenovirus, rotavirus, norovirus genogroups I and II, and sapovirus, as well as enteroviruses, which are not associated with gastroenteritis). Detection sensitivities of 10 to 1,000 copies per reaction were achieved for many targets. VOCMA is a highly multiplex, variation-tolerant, general purpose nucleic acid detection concept. It is a specific and sensitive method for simultaneous detection of nucleic acids from viruses, bacteria, fungi, and protozoa, as well as host nucleic acid, in the same test. It can be run on an ordinary PCR and a Luminex machine and is suitable for both clinical diagnoses and microbial surveillance.
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